TRANSGENIC NON-HUMAN VERTEBRATE FOR THE IN VIVO PRODUCTION OF DUAL SPECIFICITY IMMUNOGLOBULINS OR HYPERMUTATED HEAVY CHAIN ONLY IMMUNOGLOBULINS
The invention relates, in one aspect, generally to novel concept of guided selection of antibody variable domains, combination and expression entirely in vivo. An application is to produce multivalent polypeptides. The present invention relates to multivalent (eg, multispecific) antibodies, antibody chains and polypeptides, as well as heavy chain-only antibodies (H2 antibodies) that are devoid of light chains. The invention further relates to the selection, maturation and production of these in vivo in non-human vertebrates and non-human vertebrate cells. To this end the invention also relates to such non-human vertebrates and cells. The invention also relates to the provision of means to produce and select heavy chain-only antibodies and heavy chains comprising variable domains that have undergone affinity maturation.
This application is a Divisional Application of U.S. application Ser. No. 14/543,359, filed Nov. 17, 2014, which is a Continuation Application of International Application No. PCT/GB2013/051280, filed May 17, 2013, which claims priority to GB 1208708.6, filed May 17, 2012, the contents of each of which are hereby incorporated by reference in their entirety.
SEQUENCE LISTINGThe attached sequence listing, titled “39080-17701-cc-seq-listing_from_parent.pdf” (of size 1003 kb), created on Feb. 2, 2015, is hereby incorporated by reference in its entirety.
The invention relates, in one aspect, generally to novel concept of guided selection of antibody variable domains, combination and expression entirely in vivo. An application is to produce multivalent polypeptides.
The present invention also relates to multivalent (eg, multispecific) antibodies, antibody chains and polypeptides, as well as heavy chain-only antibodies (H2 antibodies) that are devoid of light chains. The invention further relates to the selection, maturation and production of these in vivo in non-human vertebrates and non-human vertebrate cells. To this end the invention also relates to such non-human vertebrates and cells. The invention also relates to the provision of means to produce and select heavy chain-only antibodies and heavy chains comprising variable domains that have undergone affinity maturation.
BACKGROUNDThe state of the art provides methods for producing antibodies in vitro (eg, using phage, ribosome or yeast display) or in vivo (eg, using non-human vertebrates (eg, mice and rats) and cells comprising transgenic immunoglobulin loci). Such in vivo systems (eg, Xenomouse™) have used completely human transgenic heavy chain loci which comprise human variable regions (human VH, D and JH gene segments) upstream of human constant regions (eg, human mu upstream of human gamma constant gene segments). Subsequently, it has been discovered that the use of totally human transgenic loci in such in vivo systems is detrimental and B-cell development is hampered, leading to relatively small B-cell compartments and restricted utility for generating antibodies. Later-generation transgenic animals (eg, the Velocimouse™) have been created which have chimaeric heavy chain loci in which a human variable region is upstream of endogenous (eg, mouse or rat) constant regions (ie, mouse mu constant region upstream of gamma constant region, in germline configuration). This enables the harnessing of endogenous control mechanisms for B-cell and antibody development, and as such the extent of problems of totally human transgenic loci are not seen. Methods of constructing transgenic vertebrates and use of these to generate antibodies and nucleic acids thereof following antigen immunisation are known in the art, eg, see U.S. Pat. No. 7,501,552 (Medarex); U.S. Pat. Nos. 5,939,598 & 6,130,364 (Abgenix); WO02066630, WO2011163311 & WO2011163314 (Regeneron); WO2011004192 & WO2011158009 (Kymab Limited); WO2009076464, WO2009143472, EP1414858, WO2009013620A2, WO2010070263A1 & WO2010109165A2 (Harbour Antibodies); EP1399559 (Crescendo Biologics) and WO2010039900 (Ablexis), the disclosures of which are explicitly incorporated herein including, but not limited to, for the purpose of providing the skilled person with guidance of how to make non-human animals bearing transgenic immunoglobulin loci and to inactivate endogenous loci expression.
The art has recognised the desirability of producing artificial combinations of epitope or antigen binding sites and specificities. So, the art has proposed multivalent antigen-binding antibodies and polypeptides in which a plurality of binding sites are synthetically combined to provide for binding to multiple epitopes on the same or different targets. When the targets are different, multispecific constructs are possible that can target and bind to a plurality of different antigens providing the epitopes (eg, to neutralise the antigens). One technique involves the in vitro combination (fusion) of different hybridomas to produce quadromas in which pairings of heavy and light chains from different antibodies are obtained (Milstein & Cuello, Nature, 1983, 305(5934): pp 537-40). This technique disadvantageously leads to mis-match pairings and multiple different combinations of antibody chains, so that the yield of the desired combination of specificities is relatively low. Subsequent techniques have used in vitro antibody engineering in order to synthetically combine epitope binding moieties (eg, antibody variable domains, dAbs or scFvs) to produce multivalent, multispecific constructs. The Epitope binding moieties are individually selected (usually on the basis of epitope binding affinity) in in vitro techniques such as phage display, ribosome display and yeast display. Once desirable moieties have been identified, these are then combined in vitro by engineering and the performance and characteristics of the resultant multivalent constructs are assessed. While providing for multi-valency and multi-specificity, these techniques are hampered, however, because such engineering in vitro can downgrade the desirable characteristics of the resultant antibody. For example, antigen-binding affinity, antigen specificity, expressability (eg, in cell lines such as CHO or HEK293 cells), half-life and/or biophysical characteristics (eg, melting temperature, solution state, resistance to aggregation etc) can be downgraded, thereby hampering development of the antibody as drugs for human therapeutic or prophylactic use. It would be desirable to have means for producing, maturing and selecting multivalent and multispecific antibodies that addresses these shortcomings in the art. Multivalent and multispecific formats are disclosed, for example, in Trends Biotechnol. 2010 July; 28(7):355-62. Epub 2010 May 4; “Multivalent antibodies: when design surpasses evolution”; Cuesta A M et al.
Reference is made to the patent applications cited above from Harbour Antibodies and Crescendo Biologics; these relate to the production of heavy chain-only antibodies (H2 antibodies) which lack CH1 and are devoid of light chains. In Proc Natl Acad Sci USA. 2006 Oct. 10; 103(41):15130-5. Epub 2006 Oct. 2; “Generation of heavy-chain-only antibodies in mice”; Janssens et al transgenic mice (MGΔ mice) are disclosed which comprise an antibody heavy chain locus comprising llama VHH exons and a Cμ region upstream of Cγ2 and Cγ3 regions in which CH1 has been deleted. The mice have a μMT background and express light chains. The heavy chain MGΔ loci are introduced by injection of DNA into fertilized mouse eggs follow by random integration of one to five copies of the locus into the mouse genomes. The MGΔ loci did not rescue B-cell development. MGΔ mice contained very few B-cells expressing cell-surface chimaeric Ig; 30% of the bone marrow B220+ cells expressed intracellular IgM, but no IgG. Thus, there is a need for improved transgenic heavy chain loci as well as vertebrates and cells comprising these for the generation of H2 antibodies (eg, class-switched H2 antibodies such as gamma-type H2 antibodies).
SUMMARY OF THE INVENTIONThe present invention addresses the need for improved multivalent and multispecific antibodies, chains and polypeptides and means for producing and selecting these. In this respect, the invention provides a solution by providing for the production, maturation and selection of combinations of epitope binding specificities completely in vivo. In this way, the invention enables the skilled person to select antibody variable domains that have been produced, matured and expressed by in vivo systems in the context of one or more predetermined other binding sites or specificities.
Thus, using the present invention it is possible straightforwardly and rapidly to obtain multi-antigen-specific antibodies, chains and polypeptides that comprise an antigen-specific variable domain that has undergone junctional mutation and affinity maturation in vivo in the context of one or more predetermined other binding moieties. Such antibodies, chains and polypeptides are produced and selected totally in vivo in the combination to be used as a final product, and as such the present invention harnesses in vivo filtering for expressability (and provides possibly for aspects of affinity and biophysical characteristics to be factored into in vivo selection) in the context of the desired variable domain and predetermined epitope binding moiety pairings. This avoids problems of down-grading biophysical and affinity characteristics seen in the prior art when separately selecting and then combining epitope binding moieties in vitro. Thus, the present invention allows the skilled person to select multivalent and multispecific antibodies, chains and polypeptides directly in the format that they will be used for subsequent human therapeutic and prophylactic use.
The present invention also addresses the need for improved in vivo production of heavy chain-only antibodies. Using the present invention it is possible to produce and select heavy chain-only antibodies and heavy chains comprising variable domains that have undergone affinity maturation. The invention enables antibody and B-cell compartment development to pass through a favourable 4-chain endogenous IgM stage before proceeding to a subsequent (eg, gamma) stage which selects solely heavy chain-only (H2) antibodies from the good pool of heavy chain VDJ recombinations provided by the earlier 4-chain IgM stage, this subsequent stage essentially eliminating the possibility for 4-chain antibodies. This subsequent stage can incorporate additional epitope specificities in a predetermined way, so that the heavy chain-only antibodies and chains can optionally be multispecific. The invention is expected to provide one or more of the following advantages: good B-cell compartment development (eg, normal bone marrow and/or spleen or secondary lymphoid compartments at or approximating wild-type); normal B-cell ratios in bone marrow and/or splenic compartments; normal serum antibody levels; normal serum gamma-H2 antibody levels; good antigen binding affinities for H2 antibodies; production exclusively of isotype-switched H2 antibodies; and production exclusively of isotype-switched antibodies whose variable domains are antibody single variable domains (ie, dAbs).
Thus, in a first configuration, the invention provides
In a first aspect:
A non-human vertebrate (eg, a mouse or a rat), wherein the vertebrate comprises lymphocytic cells, each cell genome comprising
(i) an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region, a first switch, a mu constant region (eg, comprising a CH1 gene segment), a second switch and a non-mu (eg, gamma) constant region; wherein the heavy chain locus of each cell is capable of undergoing IgM to the non-mu (eg, IgG) isotype switching; and
wherein
(ii) the non-mu constant region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, wherein following isotype switching the vertebrate expresses multivalent polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the heavy chain locus, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes.
In a second aspect:
A non-human vertebrate cell (eg, a mouse cell or a rat cell, such as an ES cell or a B-cell), the cell genome comprising
(i) an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region, a first switch, a mu constant region (eg, comprising a CH1 gene segment), a second switch and a non-mu (eg, gamma) constant region; wherein the heavy chain locus of each cell is capable of undergoing IgM to a non-mu (eg, IgG) isotype switching; and
wherein
(ii) the non-mu constant region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, for expressing a multivalent polypeptide chain comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the heavy chain locus, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes.
In a second configuration, the invention provides
In a first aspect:
A non-human vertebrate (eg, a mouse or a rat), wherein the vertebrate comprises lymphocytic cells whose genomes comprise an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged variable region and a non-mu (eg, gamma) constant region;
wherein
the non-mu constant region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, wherein the vertebrate expresses multivalent polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the heavy chain locus, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes.
In a second aspect:
A non-human vertebrate cell (eg, a mouse cell or a rat cell) or a hybridoma, the cell genome comprising an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged variable region and a non-mu (eg, gamma) constant region;
wherein
the non-mu constant region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, wherein the cell expresses a multivalent polypeptide chain comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the heavy chain locus, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes.
In a third configuration, the invention provides
In a first aspect:
A non-human vertebrate (eg, a mouse or a rat), wherein the vertebrate comprises lymphocytic cells, the genome of each cell comprising an antibody light chain locus which comprises (in 5′ to 3′ direction) a rearranged or unrearranged variable region and a second region;
wherein
the second region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, wherein the vertebrate expresses polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the light chain locus, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes.
In a second aspect:
A non-human vertebrate cell (eg, a mouse cell or a rat cell) or a hybridoma, wherein the cell genome comprises an antibody light chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region and a second region;
wherein
the second region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, for expressing a polypeptide chain comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the light chain locus, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes.
In a fourth configuration, the invention provides
In a first aspect:
A method of producing multivalent polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes, the method comprising
(a) expressing in a non-human vertebrate (eg, a mouse or a rat) IgM antibodies in immature B-cells, wherein the antibodies comprise heavy and light chains expressed from heavy and light chain loci respectively, optionally the heavy chains comprising CH1 domains;
(b) immunising the vertebrate with a first predetermined antigen bearing the first epitope and obtaining isotype switching to expression from a non-mu (eg, gamma) constant region in at least some of the heavy chain loci and expression of variable regions that have undergone somatic hypermutation; and
(c) selecting one or more polypeptide chains from said immunised vertebrate by selection for variable regions that bind said first epitope, wherein each selected chain comprises a somatically hypermutated variable region that specifically binds the epitope; and
wherein the method further comprises
(d) providing the nucleotide sequence of the epitope binding moiety in the non-mu constant region of heavy chain loci in the genome of the vertebrate, wherein the polypeptide chains selected in step (c) bind the first and second epitopes.
In a second aspect:
A method of producing in a non-human vertebrate (eg, a mouse or a rat) multivalent polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes), the method comprising
(a) immunising the vertebrate with a first predetermined antigen bearing the first epitope, obtaining isotype switching to expression from a non-mu (eg, gamma) constant region in at least some of the heavy chain loci of the vertebrate and expression of variable regions that have undergone somatic hypermutation; and
(b) selecting one or more polypeptide chains from said immunised vertebrate by selection for variable regions that bind said first epitope, wherein each selected chain comprises a somatically hypermutated variable region that specifically binds the epitope; and
wherein the method further comprises
(d) providing the nucleotide sequence of the epitope binding moiety in the non-mu constant region of heavy chain loci in the genome of the vertebrate, wherein the polypeptide chains selected in step (b) bind the first and second epitopes.
In a fifth configuration, the invention provides
In a first aspect:
A multivalent (eg, multispecific or bispecific) polypeptide chain having (in N- to C-terminal direction) the structure V-X-L-E-L-C, where
(i) V is an antibody variable domain that specifically binds a first epitope,
(ii) X is absent, an antibody hinge region or an antibody constant region comprising a constant domain,
(iii) Each L is an optional linker,
(iv) E is an epitope binding moiety that specifically binds a second epitope, and
(v) C is absent or an antibody constant region comprising a constant domain (eg, C is a human gamma Fc),
wherein V is a rearranged antibody variable domain derived from the rearrangement of variable region gene segments in vivo in a non-human vertebrate with somatic hypermutation of the resulting variable region gene in a nucleotide sequence also encoding for the epitope binding moiety; and
wherein the rearranged antibody variable domain comprises endogenous AID-pattern somatic hypermutations.
In a second aspect:
A multivalent (eg, multispecific or bispecific) antibody comprising heavy chains associated with light chains, wherein
Each heavy chain is a polypeptide chain as recited in the first aspect of the fifth configuration, wherein E is an antibody variable domain;
Each light chain is a polypeptide chain having (in N- to C-terminal direction) the structure V′-L′-E′-L′-C′, where
(i) V′ is an antibody variable domain,
(ii) Each L′ is an optional linker,
(iv) E′ is an epitope binding moiety, and
(v) C′ is absent or an antibody constant region comprising a constant domain (eg, C′ is a human CL);
wherein
V′ is a rearranged antibody variable domain derived from the rearrangement of variable region gene segments in vivo in a non-human vertebrate with somatic hypermutation of the resulting variable region gene in a nucleotide sequence also encoding for E′; and
V′ comprises endogenous AID-pattern somatic hypermutations;
V and V′ form a first binding site that specifically binds a first epitope; and
Optionally E and E′ form a second binding site that specifically binds a second epitope when E′ is an antibody variable domain (eg, E is a VH and E′ is a VL; or E is a VL and E′ is a VH).
In a third aspect:
An antigen-binding polypeptide comprising a protein scaffold which is linked to one or more epitope binding moieties wherein the antigen-binding polypeptide comprises at least two epitope binding sites at least one of which is provided by an epitope binding moiety and at least one of which is provided by a first antibody variable domain paired with a second antibody variable domain, wherein each variable domain is a rearranged antibody variable domain derived from the rearrangement of variable region gene segments in vivo in a non-human vertebrate with somatic hypermutation of the resulting variable region gene in a nucleotide sequence also encoding for one or more of the epitope binding moiety(ies); and wherein in that the rearranged antibody variable domains comprise endogenous AID-pattern somatic hypermutations.
In a fourth aspect:
A multispecific antigen binding polypeptide, dimer or antibody according to the first, second or third aspect, which is capable of recruiting the activity of a human immune effector cell by specifically binding to an effector antigen (eg, human CD3) located on the human immune effector cell, a first of the epitope binding sites of the polypeptide, dimer or antibody being capable of specifically binding to said effector antigen, and a second of the epitope binding sites of the polypeptide, dimer or antibody being capable of specifically binding to a target antigen (eg, human EpCAM or human CD19) other than the effector antigen; optionally wherein said target antigen is located on a target cell other than said human immune effector cell.
In a sixth configuration, the invention provides
In a first aspect:
A non-human vertebrate (eg, a mouse or a rat), wherein
(a) the vertebrate expresses IgM antibodies comprising heavy and light chains encoded by antibody heavy and light chain loci respectively, optionally wherein each heavy chain comprises a CH1 domain;
(b) the vertebrate is capable of expressing non-mu (eg, IgG) antibodies, each non-mu antibody heavy chain lacking a functional CH1 domain; and
(c) the IgM antibodies are expressed by lymphocytic cells, each cell comprising a functional light chain locus for expressing light chains of IgM antibodies expressed by the cell; and
wherein
(d) the non-mu antibodies are expressed by lymphocytic cells, each cell lacking a functional light chain locus wherein non-mu antibodies are expressed by the cell in the absence of light chain expression.
In a second aspect:
A non-human vertebrate (eg, a mouse or a rat), wherein the vertebrate comprises lymphocytic cells whose genomes comprise
(i) an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region, a first switch, a mu constant region (eg, comprising a CH1 gene segment), a second switch and a non-mu (eg, gamma) constant region lacking a CH1 gene segment;
(ii) a functional antibody light chain locus for expressing light chains;
wherein the cells can express IgM antibodies comprising IgM-type heavy chains and light chains;
wherein the heavy chain locus of each cell is capable of undergoing isotype switching to produce non-mu (eg, IgG) antibodies comprising one or more non-mu-type (eg, IgG-type) heavy chains in the absence of light chains, each heavy chain lacking a CH1 domain; and
(iii) means for turning off light chain expression, wherein functional light chains are not expressed after isotype switching to said non-mu-type antibodies.
In a third aspect:
A non-human vertebrate cell (eg, a mouse cell or a rat cell), wherein the cell genome comprises
(i) a functional antibody light chain locus for expressing light chains;
(ii) an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region, a first switch, a mu constant region (eg, comprising a CH1 gene segment), a second switch and a non-mu (eg, gamma) constant region lacking a CH1 gene segment for expressing IgM antibodies comprising IgM-type heavy chains and light chains; and for IgM to non-mu (eg, IgG) isotype switching to produce non-mu (eg, IgG) antibodies comprising one or more non-mu-type heavy chains in the absence of light chains, each heavy chain lacking a CH1 domain; and
(iii) means for turning off light chain expression, wherein functional light chains are not expressed after isotype switching to said non-mu-type antibodies.
In a seventh configuration, the invention provides
A method of producing polypeptide chains comprising somatically hypermutated variable regions in a non-human vertebrate (eg, a mouse or a rat), the method comprising
(a) expressing in the vertebrate IgM antibodies in immature B-cells, wherein the antibodies comprise heavy and light chains expressed from heavy and light chain loci respectively;
(b) immunising the vertebrate with a predetermined epitope and obtaining isotype switching in at least some of the heavy chain loci and expression of non-mu (eg, IgG) antibodies that have undergone somatic hypermutation, wherein the antibodies comprise heavy chains that lack a CH1 domain and comprise variable regions that specifically bind the antigen; and
(c) selecting one or more polypeptide chains from said immunised vertebrate by selection for variable regions that bind said epitope, wherein each selected chain comprises a somatically hypermutated variable region that specifically binds the epitope; and
the method further comprising expressing the non-mu antibodies in step (b) in the absence of light chain expression.
In an eighth configuration, the invention provides
A non-human vertebrate (eg, a mouse or a rat) whose genome comprises an antibody heavy chain locus and an antibody light chain locus,
(a) the light chain locus comprising (in 5′ to 3′ direction) a light chain variable region and a constant region for expressing light chains in lymphocytic cells expressing IgM antibodies; and
(b) means for turning off light chain expression in lymphocytic cells expressing non-mu (eg, IgG) antibodies.
A non-human vertebrate cell (eg, a mouse cell or a rat cell) or hybridoma whose genome comprises an antibody heavy chain locus and an antibody light chain locus, the light chain locus comprising
(a) (in 5′ to 3′ direction) a light chain variable region and a constant region for expressing light chains in lymphocytic cells expressing IgM antibodies; and
(b) means for turning off light chain expression in lymphocytic cells expressing non-mu (eg, IgG) antibodies.
The invention also provides:
A non-human vertebrate (eg, a mouse or a rat) or cell (eg, a mouse cell or a rat cell), wherein an Ig heavy or light chain locus of the genome of the vertebrate or cell comprises (in 5′ to 3′ orientation) (i) an unrearranged human variable region for encoding a first variable domain, (ii) a sequence encoding an optional linker and (iii) a sequence encoding an epitope binding moiety.
A polypeptide comprising a binding site specific for a target epitope, the binding site having the structure V1-L-E, where V1 is an antibody variable domain, E is an epitope binding moiety and L is an optional peptide linker; and wherein V1 is derived from the rearrangement of human variable region gene segments in vivo in a non-human vertebrate with somatic hypermutation of the resulting variable region gene in a nucleotide sequence also encoding E, wherein V1 comprises endogenous AID-pattern somatic hypermutations and specifically binds the target epitope.
A non-human vertebrate (eg, a mouse or a rat), wherein the vertebrate comprises lymphocytic cells whose genomes comprise an antibody heavy or light chain locus comprising (in 5′ to 3′ direction) a rearranged variable region and a non-mu constant region;
wherein
the non-mu constant region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and the rearranged variable region which encodes a first variable domain, wherein following isotype switching the vertebrate expresses polypeptide chains comprising (in N- to C-terminal direction) an epitope binding site comprising second and first antibody variable domains derived respectively from a rearranged second variable domain nucleotide sequence and from the first variable domain nucleotide sequence, wherein the second nucleotide sequence has been rearranged in the vertebrate.
A non-human vertebrate cell (eg, a mouse cell or a rat cell) or a hybridoma, the cell genome comprising (in 5′ to 3′ direction) a rearranged variable region and a non-mu constant region;
wherein
the non-mu constant region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and the rearranged variable region which encodes a first variable domain, for expressing polypeptide chains comprising (in N- to C-terminal direction) an epitope binding site comprising second and first antibody variable domains derived respectively from a rearranged second variable domain nucleotide sequence and from the first variable domain nucleotide sequence, wherein the second nucleotide sequence has been rearranged in the cell.
A method of producing a vertebrate of a non-human species, the method comprising breeding two vertebrates of said species together, wherein both of the vertebrates are according to any aspect of the invention.
By turning off light chain expression, isotype switched heavy chains are expressed in the absence of light chain expression and thus there is no possibility for newly-expressed light chains to associate with heavy chains during B-cell proliferation and during somatic mutation and selection of heavy chains following antigen or epitope immunisation. Thus, heavy chain production is essentially exclusively the production of H2 antibody-type heavy chains, wherein the variable regions bind antigen in the absence of a light chain variable region partner. Such H2 antibodies can be a good source for antibody single variable domain sequences (eg, human VH single variable domains when the heavy chain loci comprise human variable regions). Thus, the in vivo antibody production machinery of the non-human vertebrate or cell of the invention can be dedicated to H2 antibody production without any significant 4-chain antibody (H2L2) production hampering the extent of H2 antibody response following immunisation and ultimately the desirable levels of H2 that are obtainable. This advantage enables this isotype-switched, antigen/epitope-specific in vivo response to develop from the desirable recombined VDJ repertoire and B-cell compartments arising from the retention of endogenous IgM stage as further discussed below.
By retaining an endogenous IgM stage, configurations and aspects of the invention retain the ability to harness the endogenous antibody and B-cell development control mechanisms of the non-human vertebrate or cell. This includes the ability to harness endogenous terminal deoxynucleotidyl transferase (TdT) activity and junctional mutation as well as proper B-cell development (including at early stages of development when IgM is expressed) to yield good size B-cell compartments and good size and quality repertoires of recombined VDJ diversity from which to subsequently select and mature isotype-switched heavy chains produced from the antibody heavy or light chain locus of the invention. Thus, for example, a vertebrate of the invention can be immunised with a predetermined therapeutic target antigen (eg, a human, viral or bacterial antigen) and antibodies (eg, gamma-type) or heavy chains (eg, gamma-type heavy chains) can be isolated that (i) have undergone junctional and somatic mutation, and thus affinity maturation in vivo in response to antigen challenge, (ii) have human variable domains, and (iii) have been selected by a totally in vivo system for expression and ability to bind antigen(s) or epitope(s). Thus, the invention employs in vivo systems to direct the skilled person to viable human antibodies (eg, H2 or 4-chain bispecific antibodies) and heavy chains that can be expressed well in vivo and which are specific for a predetermined antigen.
The multivalent configurations of the invention are simply produced by avoiding multi-step combinations of in vivo and in vitro production and engineering to produce multivalent formats as per the prior art methods.
Moreover, having undergone affinity maturation in the vertebrate or cell, the selected antibodies have had their antigen binding affinities tuned by nature—rather than by man. Thus, vertebrates and cells of the invention provide good sources for fully human antigen-specific antibodies and heavy chains with therapeutically-amenable affinities without the need to perform laborious in vitro affinity maturation (or risk downgrading desirable characteristics due to in vitro manipulation).
Additionally, the present invention enables the skilled person to design vertebrates and cells to produce multivalent antibodies, chains and polypeptides of a specific, desired isotype in a predictable way. For example, the skilled person is able to design the heavy chain loci in a vertebrate of the invention so that all gamma constant region gene segments comprise the multivalent design described above. In this way, the skilled person will know that all IgG-type antibodies or heavy chains selected from the vertebrate will be multivalent in their H chains and will have been subjected to endogenous antibody development (eg, affinity maturation) and in vivo expression and selection in the context of combinations of binding sites. Going a step further, the skilled person could design a vertebrate in which just the IgG1 isotype gene segments have the multivalent design. Thus, the skilled person will know from the outset that all IgG1 isotype antibodies will be multivalent (eg, bispecific) and matured, expressed and selected in vivo. This is useful for in vivo tailoring antibody sub-types, such as IgG1 or IgG4, to particular target epitope or antigen combinations in a predictable manner.
The following definitions apply to any configuration, aspect, provision, clause, attribute, example or embodiment of the invention.
“Derived from” is used in the ordinary sense of the term. Exemplary synonyms include “produced as”, “resulting from”, “received from”, “obtained from”, “a product of”, “consequence of”, and “modified from” For example, a human variable region of a heavy chain can be derived from recombination of human VH, D and JH gene segments and this reflects the in vivo recombination of these gene segments in, for example, a heavy chain locus according to the invention with any accompanying mutation (eg, junctional mutation).
Samples from which B-cells can be obtained include but are not limited to blood, serum, spleen, splenic tissue, bone marrow, lymph, lymph node, thymus, and appendix. Antibodies and immunoglobulin chains can be obtained from each of the previous-mentioned samples and also from the following non-limiting list of B-cells, ascites fluid, hybridomas, and cell cultures.
“Plurality” is used in the ordinary sense of the term and means “at least one” or “more than one”.
The term “germline configuration” refers to a germline genomic configuration. For example, human immunoglobulin gene segments of a transgenic immunoglobulin locus are in a germline configuration when the relative order of the gene segments is the same as the order of corresponding gene segments in a human germline genome. For example, when the transgenic locus is a heavy chain locus of the invention comprising hypothetical human immunoglobulin gene segments A, B and C, these would be provided in this order (5′ to 3′ in the locus) when the corresponding gene segments of a human germline genome comprises the arrangement 5′-A-B-C-3′. In an example, when elements of a human immunoglobulin locus (eg, gene segments, enhancers or other regulatory elements) are provided in a transgenic immunoglobulin locus according to the invention, the human Ig locus elements are in germline configuration when the relative order of the gene segments is the same as the order of corresponding gene segments in a human germline genome and human sequences between the elements are included, these corresponding to such sequences between corresponding elements in the human germline genome. Thus, in a hypothetical example the transgenic locus comprises human elements in the arrangement 5′-A-S1-B-S2-C-S3-3′, wherein A, B and C are human immunoglobulin gene segments and S1-S3 are human inter-gene segment sequences, wherein the corresponding arrangement 5′-A-S1-B-S2-C-S3-3′ is present in a human germline genome. For example, this can be achieved by providing in a transgenic immunoglobulin locus of the invention a DNA insert corresponding to the DNA sequence from A to C in a human germline genome (or the insert comprising the DNA sequence from A to C). The arrangements in human germline genomes and immunoglobulin loci are known in the art (eg, see the IMGT at the World Wide Web (see above), Kabat and other antibody resources referenced herein).
The term “antibody” includes monoclonal antibodies (including full length antibodies which have an immunoglobulin Fc region), antibody compositions with polyepitopic specificity, multispecific antibodies (e.g., bispecific antibodies, diabodies, and single-chain molecules, as well as antibody fragments (e.g., dAb, Fab, F(ab′)2, and Fv). The term “antibody” also includes H2 antibodies that comprise a dimer of a heavy chain (5′-VH-(optional Hinge)-CH2-CH3-3′) and are devoid of a light chain (akin to naturally-occurring H2 antibodies; see, eg, Nature. 1993 Jun. 3; 363(6428):446-8; Naturally occurring antibodies devoid of light chains; Hamers-Casterman C, Atarhouch T, Muyldermans S, Robinson G, Hamers C, Songa E B, Bendahman N, Hamers R). Thus, in an embodiment of the present invention, RNA produced from the transgenic heavy chain locus encodes for heavy chains that re devoid of a CH1 gene segment and comprise no functional antibody light chain. In an example, RNA produced from the transgenic heavy chain locus encodes for VH single variable domains (dAbs; domain antibodies). These can optionally comprise a constant region.
The term “immunoglobulin” (Ig) is used interchangeably with “antibody” herein.
Examples of antibodies are classic 4-chain antibodies comprising two heavy chains paired with two light chains (such as, a dimer of 5′-VH-CH1-Hinge-CH2-CH3-3′ paired with 5′-VL-CL-3′) or H2 antibodies that comprise a dimer of a heavy chain (5′-VH-(optional Hinge)-CH2-CH3-3′) and are devoid of a light chain Thus, in an embodiment of the present invention, the heavy chain sequence repertoire encodes for heavy chains that re devoid of a CH1 gene segment and comprise no functional antibody light chain. In an example, the heavy chain sequence repertoire produced by the vertebrate encodes a repertoire of VH single variable domains (dAbs; domain antibodies) with one or more human constant domains.
In an example of any configuration of the invention, a repertoire comprises a plurality of different members (thus, for example, a heavy chain repertoire comprises a plurality of different heavy chain sequences, such as sequences differing in their variable regions and/or human non-mu constant regions). In an example of any configuration of the invention, a repertoire comprises or consists of 2, 3, 4, 5, 6, 7, 8, 9, 10, at least 15, at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 103, at least 104, at least 105, at least 106, at least 107, at least 108, at least 109, at least 1010, at least 1011, at least 1012, at least 1013, or at least 1014 members. For example, a repertoire of antibody heavy chains or antibodies comprises or consists of at least 100, at least 103, at least 104, at least 105, at least 106, at least 107, at least 108, at least 109, at least 1010, at least 1011, at least 1012, at least 1013, or at least 1014 antibody chain sequences or antibodies respectively. For example, a repertoire comprises or consists of 2, 3, 4, 5, 6, 7, 8, 9, 10, at least 15, at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 103, at least 104, at least 109, at least 106, at least 107, at least 108, at least 109, at least 1010, at least 1011, at least 1012, at least 1013, or at least 1014 different members. For example, a repertoire of gene segments comprises or consists of 2, 3, 4, 5, 6, 7, 8, 9, 10, at least 15, at least 20, at least 30, at least 40, at least 50 gene segments.
An “isolated” antibody is one that has been identified, separated and/or recovered from a component of its production environment (eg, naturally or recombinantly). Preferably, the isolated polypeptide is free of association with all other components from its production environment, eg, so that the antibody has been isolated to an FDA-approvable or approved standard. Contaminant components of its production environment, such as that resulting from recombinant transfected cells, are materials that would typically interfere with research, diagnostic or therapeutic uses for the antibody, and may include enzymes, hormones, and other proteinaceous or non-proteinaceous solutes. In preferred embodiments, the polypeptide will be purified: (1) to greater than 95% by weight of antibody as determined by, for example, the Lowry method, and in some embodiments, to greater than 99% by weight; (2) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator, or (3) to homogeneity by SDS-PAGE under non-reducing or reducing conditions using Coomassie blue or, preferably, silver stain. Isolated antibody includes the antibody in situ within recombinant cells since at least one component of the antibody's natural environment will not be present. Ordinarily, however, an isolated polypeptide or antibody will be prepared by at least one purification step.
An “antibody fragment” comprises a portion of an intact antibody, preferably the antigen binding and/or the variable region of the intact antibody. Examples of antibody fragments include dAb, Fab, Fab′, F(ab′)2 and Fv fragments; diabodies; linear antibodies; single-chain antibody molecules and multispecific antibodies formed from antibody fragments.
An antibody that “specifically binds to” or is “specific for” a particular polypeptide, antigen, or epitope is one that binds to that particular polypeptide, antigen, or epitope without substantially binding to other polypeptides, antigens or epitopes. For example, binding to the antigen or epitope is specific when the antibody binds with a KD of 100 μM or less, 10 μM or less, 1 μM or less, 100 nM or less, eg, 10 nM or less, 1 nM or less, 500 pM or less, 100 pM or less, or 10 pM or less. The binding affinity (KD) can be determined using standard procedures as will be known by the skilled person, eg, binding in ELISA and/or affinity determination using surface plasmon resonance (eg, Biacore™, Proteon™ or KinExA™ solution phase affinity measurement which can detect down to fM affinities (Sapidyne Instruments, Idaho)).
In one embodiment, the surface plasmon resonance (SPR) is carried out at 25° C. In another embodiment, the SPR is carried out at 37° C.
In one embodiment, the SPR is carried out at physiological pH, such as about pH7 or at pH7.6 (eg, using Hepes buffered saline at pH7.6 (also referred to as HBS-EP)).
In one embodiment, the SPR is carried out at a physiological salt level, eg, 150 mM NaCl.
In one embodiment, the SPR is carried out at a detergent level of no greater than 0.05% by volume, eg, in the presence of P20 (polysorbate 20; eg, Tween-20™) at 0.05% and EDTA at 3 mM.
In one example, the SPR is carried out at 25° C. or 37° C. in a buffer at pH7.6, 150 mM NaCl, 0.05% detergent (eg, P20) and 3 mM EDTA. The buffer can contain 10 mM Hepes. In one example, the SPR is carried out at 25° C. or 37° C. in HBS-EP. HBS-EP is available from Teknova Inc (California; catalogue number H8022).
In an example, the affinity is determined using SPR by
1. Coupling anti-mouse (or other relevant non-human vertebrate) IgG (eg, Biacore BR-1008-38) to a biosensor chip (eg, GLM chip) such as by primary amine coupling;
2. Exposing the anti-mouse IgG (non-human vertebrate antibody) to a test IgG antibody or heavy chain to capture test antibody on the chip;
3. Passing the test antigen over the chip's capture surface at 1024 nM, 256 nM, 64 nM, 16 nM, 4 nM with a 0 nM (i.e. buffer alone); and
4. And determining the affinity of binding of test antibody/chain to test antigen using surface plasmon resonance, eg, under an SPR condition discussed above (eg, at 25° C. in physiological buffer). SPR can be carried out using any standard SPR apparatus, such as by Biacore™ or using the ProteOn XPR36™ (Bio-Rad®).
Regeneration of the capture surface can be carried out with 10 mM glycine at pH1.7. This removes the captured antibody and allows the surface to be used for another interaction. The binding data can be fitted to 1:1 model inherent using standard techniques, eg, using a model inherent to the ProteOn XPR36™ analysis software.
“Pharmaceutically acceptable” refers to approved or approvable by a regulatory agency of the USA Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, including humans. A “pharmaceutically acceptable carrier, excipient, or adjuvant” refers to an carrier, excipient, or adjuvant that can be administered to a subject, together with an agent, e.g., any antibody or antibody chain described herein, and which does not destroy the pharmacological activity thereof and is nontoxic when administered in doses sufficient to deliver a therapeutic amount of the agent.
The term “Fc” as used herein refer to the protein comprising (in N- to C-terminal direction) an immunoglobulin CH2 and CH3 domain. The CH2 and CH3 domains can form at least a part of the constant region of an antibody or heavy chain.
“Constant region” as used herein when referring to an antibody locus of the invention (eg, a heavy chain locus of a genome), is a reference to a stretch of DNA sequence comprising gene segments (constant region gene segments) that combine in vivo with recombined VDJ sequence in the locus. The VDJ yield (optionally following hypermutation), together with the constant region gene segments RNA transcripts in the vertebrate or cell from which can be produced antibody chains (eg, following splicing of RNA), each chain comprising an variable domain and one or more constant domains. When “constant region” is used with reference to an antibody or antibody heavy chain, this is referring to the region C-terminal to the variable domain and comprising one or more constant domains.
“Endogenous” as used herein indicates that the constant region etc is a type of constant region etc that is normally found in the vertebrate or cell (as opposed to an exogenous constant region whose sequence is not normally found in such a vertebrate or cell, eg a human sequence). For example, the endogenous constant region can be those encoded by the wild-type genome of the non-human vertebrate or cell. So, in an example wherein the vertebrate is a mouse, the endogenous constant region would be a mouse constant region. Going further, the endogenous regions are, in an example, strain-matched to the vertebrate or cell. So, in one embodiment, the vertebrate or cell is a mouse 129 ES cell, the endogenous constant region would be mouse 129 constant region. In another embodiment, the vertebrate or cell is a JM8 strain mouse or mouse cell, the endogenous constant region would be mouse JM8 constant region. In another embodiment, the vertebrate or cell is a Black 6 mouse or mouse cell, the endogenous constant region would be mouse Black 6 constant region.
Guided Selection In Vivo
Reference is made to Biotechnology, 1994 September; 12(9):899-903, “Guiding the selection of human antibodies from phage display repertoires to a single epitope of an antigen”; Jespers L S et al. This discloses a route to the guided selection of variable domain pairs in vitro in which a mouse antibody binding site (VH/VL pairing) can be converted into a human VH/VL pairing that retains antigen specificity. This technique does not assess whether or not the resultant product variable domain pairings are well suited to in vivo systems and expression. The following aspect of the invention addresses that problem by providing for in vivo guided selection to effect variable domain combination with another variable domain (or other epitope binding moiety), maturation and expression.
In aspects of the present invention, a non-human vertebrate or cell is provided wherein an Ig heavy or light chain locus of the genome of the vertebrate or cell comprises (in 5′ to 3′ orientation) (i) an unrearranged human variable region for encoding a first variable domain, (ii) a sequence encoding an optional linker and (iii) an epitope binding moiety (optionally a rearranged sequence of a second variable domain). The epitope binding moiety or second variable domain nucleotide sequence is a predetermined sequence, eg, the sequence encoding a VH or VL domain of the binding site of a known antibody, or a dummy (germline) VH or VL sequence. Sequences (i) and (iii) are close together in the Ig locus (eg, directly adjacent or only separated by a peptide linker-encoding sequence, eg, a linker of no more than 20, 15, 10 or 5 amino acids in the protein product) thereby enabling pairing for combination and selection in vivo. Thus, for example, in the protein product there is no protein domain between the products derived from (i) and (iii). Similarly, in the Ig locus there is, for example, no sequence encoding such a protein domain.
In an embodiment, for (iii) it is desirable to use the VH domain sequence of the binding site of a known antibody, since binding contribution by the VH in a VH/VL pairing is commonly most strong, thereby being useful to guide the selection of the partner variable domain encoded by (i) following rearrangement in vivo. In an example of this embodiment, (i) is an unrearranged human light chain variable region (kappa or lambda human variable region) for pairing with the VH domain derived from (iii). In another example, (i) is an unrearranged human heavy chain variable region or a variable region comprising heavy and light chain variable region gene segments (eg, as disclosed in WO2012018764).
The human variable region of (i) can rearrange in vivo and following immunisation of the vertebrate with a target antigen epitope, affinity maturation and selection occur. Variable regions that successfully rearrange, mature and express a variable domain that can combine with the product encoded by sequence (iii) to provide combinations of V-optional linker-E (eg, V-optional linker-V).
The skilled person is able to find antigen binding sites provided by such combinations that can specifically bind a desired antigen (eg, the target antigen or a related antigen). This is useful because this aspect of the invention enables the known sequence of (iii) and its product to guide the selection of suitable partner V domains encoded by the rearranged and matured sequence of (i). The vertebrate is used, therefore, to provide a repertoire of potential matured rearranged sequences whose selection in vivo has been guided by the adjacent epitope binding moiety (eg, V domain) derived from sequence (iii). Successful expression of combinations provides a further selection criterion for potentially useful drugs and drug candidates based on the pairing of the expressed V and E.
Use of a V domain sequence from a known antibody for (iii) is desirable for producing biobetter drugs that bind the same target as the known antibody, but that have modified antigen binding sites based on guided selection using the known V domain as a starting point. The product binding site may have one or more characteristics that are better than those displayed by the binding site of the known, original antibody. For example, the guided selection method can be used to find V pairings that have one or more of a higher affinity binding for the target antigen (eg, better on rate, off rate and/or KD as determined by surface plasmon resonance, eg, Biacore™), a new target specificity (eg, an additional specificity, thereby providing for bispecific binding sites), better pharmacokinetics, better pharmacodynamics, ability to specifically bind a novel epitope on the target antigen (ie, an epitope that is not specifically bound by the original binding site), better in vivo antibody clearance, better in vivo antibody distribution and lower toxicity to an organism (eg, a human patient or a mouse). By finding higher affinity binding sites, it is possible to clone the V domains of the pairing selected by the guided selection method and insert the V domain sequences into standard heavy and light chain vectors for the expression of antibody heavy and light chains that associate to form the binding site. In this way, it is possible to reconstitute biobetter antibodies that specifically bind the target antigen.
In one embodiment, the target antigen used for immunisation is different from the antigen to which the known antibody binding site binds. This provides the possibility of generating bispecific V-optional linker-V pairings using the invention in which the pairing is able to specifically bind the target antigen and the other antigen. In an embodiment, the two antigens are structurally related antigens (see, eg, WO 2002/002773).
In another embodiment, the sequence of (iii) is a germline human variable domain sequence which encodes a dummy V domain. In this case, the dummy may fulfill a scaffolding function, such that the variable domain encoded by rearranged sequence (i) following immunisation is an antibody single variable domain (dAb), ie, it is able to specifically bind the target antigen in the absence of another variable domain. This then provides a useful source of human antibody single variable domains (optionally joined to, and selected in the context of, an Fc or other constant region encoded by the Ig locus 3′ of sequence (iii)).
In examples described above, this aspect of the invention is provided in the context of an Ig locus for producing multispecific products based on a further epitope binding moiety (aka, binding module, eg, a known scFv that replaces CH1). In this way, the invention provides combinations of the N-terminal V-optional-linker-E (eg, V-optional linker-V) with the scFv or other binding module.
In other examples of the present aspect of the invention, no such additional epitope binding moiety sequence is provided in the Ig locus, so that the product of the locus is the N-terminal V-optional-linker-E (eg, V-optional linker-V) linked to a constant region (eg, Fc) or without a constant region (eg, where cleavage following the IgM stage is effected using locus construction as described elsewhere herein).
In embodiments, the non-human vertebrate or cell genome comprises sequences (ii) and (iii) 5′ of an Ig heavy chain constant region, eg a mouse or human constant region, eg, the heavy chain constant region endogenous to the vertebrate or cell. In an example, the constant region is a gamma (eg, gamma-1) constant region.
In an example, the genome comprises sequences (ii) and (iii) downstream of (3′ of) the S-mu, for example downstream of the mu constant region. The sequence (iii) is protected from the action of AID as described above. Thus, this is useful for providing the guided selection based on the known sequence (iii) product. In an example, genome comprises sequence (iii) in place of a gamma CH1 gene (eg, gamma-1 CH1). In this way, the constant region is devoid of a CH1 and heavy chain-only products can be produced. In another embodiment, the sequence (i)-(ii)-(iii) is provided upstream of (5′ of) the S-mu so that V-optional linker-E pairings are produced at the IgM stage and then class switching to a gamma (or other non-mu) isotype is obtained after immunisation. This allows for maturation of the WE pairings by AID, thereby providing a useful repertoire of matured binding sites that are in part related to the input sequence (iii).
In an example of any guided selection aspect of the invention herein, the second variable domain is a Vκ1-39/Jκ or Vκ3-20/Jκ VL domain. These promiscuously pair with VH domains and are thus useful pairing partners in the guided selection method for producing a repertoire of V-V pairings from which to select desired antigen-binding chains. By selecting for two or more VH domains that individually pair with a common VL such as one of these, it is possible to produce mixtures of VH/VL binding sites more simply by expressing the different VHs with a single VL. For example, once suitable VH domains have been selected for pairing with the common VL, it is possible to clone the VH and VL domains into standard heavy and light chain vectors containing heavy and light chains constant regions respectively (eg, heavy chain CH1 to CH3; or Cκ or Cλ respectively) for the production of two or more heavy chains that express different VH domains and for the production of a single light chain containing the VL domain. By mixing or co-expressing such chains together, it is possible to produce mixtures of antibodies all based on a common light chain. Thus, in one embodiment, the invention provides an antibody composition comprising a plurality of different antibodies, wherein the antibodies comprise heavy and light chains, the heavy chains each comprising a VH encoded by a VH-VL pair selected in any guided selection method of the invention, optionally wherein in the method the second variable domain is a Vκ1-39/Jκ or Vκ3-20/Jκ VL domain. In an example, each antibody of the composition comprises a single type of VH/VL pairing. This can be obtained by conventional purification techniques to resolve out the desired mixture. See, eg, EP1523496, WO2004061104, WO2008145133, WO2011097603 and WO2010151792.
In an embodiment, the product of the guided selection vertebrate, cell or method aspect of the invention is an expressed heavy chain comprising the V-optional linker-E (eg, V-optional linker-V) binding site and (3′ of that) a heavy chain constant region (eg, Fc, eg, CH2-CH3) devoid of a CH1 domain. In this embodiment, the heavy chains are capable of dimerising to produce H2 antibodies (heavy chain-only antibodies that are devoid of a light chain) that bear paired V-optional linker-V binding sites at their N termini. Thus, in an embodiment, the invention provides such a heavy chain and such a H2 antibody that comprises a V-optional linker-V binding site that specifically binds a target antigen. According to further embodiments of the invention, this aspect can be combined with turning off of light chain expression after isotype switching to non-mu isotype, as described further herein.
Applications of the guided selection aspect are described further below for use in producing multivalent products.
Multivalent Products
The present invention relates to multivalent (eg, multispecific) antibodies, antibody chains and polypeptides, as well as heavy chain-only antibodies (H2 antibodies) that re devoid of light chains. The invention further relates to the selection, maturation and production of these in vivo in non-human vertebrates and non-human vertebrate cells. To this end the invention also relates to such non-human vertebrates and cells.
Thus, the invention provides
A non-human vertebrate (eg, a mouse or a rat), wherein the vertebrate comprises lymphocytic cells, each cell genome comprising
(i) an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region, a first switch (eg, an S-mu, eg a human or endogenous S-mu), a mu constant region (eg, comprising a CH1 gene segment), a second switch (eg, an S-gamma, eg a human or endogenous S-gamma), and a non-mu (eg, gamma) constant region; wherein the heavy chain locus of each cell is capable of undergoing IgM to the non-mu (eg, IgG) isotype switching; and optionally the non-mu constant region lacks a CH1 gene segment and/or a hinge nucleotide sequence; and
wherein
(ii) the non-mu constant region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, wherein following isotype switching the vertebrate expresses multivalent polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the heavy chain locus, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes.
The variable domain is derived from the variable region of the heavy chain locus. Thus, when the variable region of the locus is a rearranged variable region, the variable domain is encoded by the sequence of the variable region (eg, a VHDJH or VLJL region) optionally with somatic hypermutation. When the variable region is an unrearranged variable region, this region comprises one or more V gene segments, one or more J gene segments and optionally one or more D gene segments (eg, wherein all of these segments are human). Following rearrangement of gene segments in the heavy chain locus, a rearranged VDJ or VJ is formed and this encodes the variable domain optionally following somatic hypermutation.
Optionally, the non-mu constant region comprises nucleotide sequences encoding a plurality of epitope binding moieties, eg, two or three epitope binding moieties joined by optional linkers.
Optionally, the non-mu constant region comprises nucleotide sequences encoding one or a plurality of epitope binding moieties (optionally joined by linkers) in place of a CH1 gene segment.
Advantageously, the skilled person is able, in view of the present invention, to choose a desirable, predetermined, epitope binding moiety and purposely include the corresponding nucleotide sequence into the locus for subsequent in vivo mixing-and-matching with a repertoire of variable domains produced by the vertebrate. Successful pairings are those that can be expressed and selected, for example following immunization with a target antigen or epitope. In this sense, selection is firstly performed by the vertebrate's in vivo system, since B-cells that express isotype-switched heavy chains (eg, as part of non-mu antibodies) and wherein the chains (or antibodies) can specifically recognize and bind to the target are selected for proliferation and B-cell expansion by the vertebrate's immune system as per a classic immune response. Thus, those products that are antigen-specific and which can be expressed in the multivalent format are naturally selected. Furthermore, a repertoire of paired binding specificities and valencies is provided, wherein one or more specificities and valencies is provided by a predetermined epitope binding moiety, and one or more other specificities or valencies is provided by a variable domain that has been in vivo selected and matured in the context of the epitope binding moiety(ies). In this way, there is natural selection for combinations that perform well (eg, are expressible to detectable levels and have in vivo-compatible biophysical characteristics, which is useful for subsequent use in drug development). A skilled person is able to perform selection of one or more multivalent heavy chains (or antibodies) from the repertoire (eg, from serum or spleen cells) according to a desirable antibody characteristic, such as affinity for target binding (eg, using surface plasmon resonance as is well known). Thus, the present invention uses a totally in vivo combinatorial process for selection and maturation of variable domains in the context of predetermined further valencies and specificities—and thus in the context of the final drug format for subsequent use in human or animal therapy or prophylaxis. This is a significant advancement over prior art techniques of producing multivalent products that rely on in vitro manipulation, selection and then the need for further in vitro affinity maturation.
Furthermore, the present inventors realized that it is advantageous to provide the known epitope binding moiety nucleotide sequence downstream of the S-mu or mu constant region. The inventors considered the desirability of minimizing mutation the epitope binding moiety sequence during the affinity maturation process following target antigen or epitope exposure. This would be useful for retaining the desired epitope-binding characteristics (eg, affinity) and possibly also desirable biophysical characteristics of the moiety. The inventors considered the typical pattern of activity of activation induced cytidine deaminase (AID), the enzyme responsible for introducing sequence mutations during somatic hypermutation. Reference is made to
Furthermore, advantageously, the inventors realised that they could selectively situate the coding sequence(s) for the predetermined epitope binding moiety(ies) in a way that enables the production, maturation and selection of isotype (class) switched products (eg, gamma-type antibodies or heavy chains) without compromising the proper functioning of the IgM stage that is so important during early B-cell compartment and primary variable region repertoire development. To this end, the inventors, in certain configurations, decided to provide the epitope binding moiety(ies) coding sequence(s) downstream of (3′ of) the mu constant region. Thus, according to an embodiment, the inventors provided these coding sequence(s) in one or more non-mu constant regions 3′ of the mu constant region. For example, one (eg, gamma-1) or all gamma constant regions can comprise one or more epitope binding moiety nucleotide sequences. In this way, all gamma heavy chains (and antibodies providing these) will bear a variable domain and one or more epitope binding moieties. Since the coding sequences for the moieties are in this position, the resultant moiety protein sequences will be unmutated (or substantially unmutated) and will be selected for combination and expression together with the upstream variable domain.
In an alternative embodiment, a nucleotide sequence encoding one or more epitope binding moieties is provided in a mu constant region. Thus, these sequences are downstream of the S-mu, which is the extent of the AID activity. In this embodiment, the vertebrate produces multivalent (eg, multispecific) heavy chains (eg, provided by antibodies, eg, H2 antibodies) of mu-isotype comprising one or more epitope binding moieties downstream of an N-terminal antibody variable domain. Following immunization, for example, the variable domain will be matured in the context of the epitope binding moiety(ies). Thus, the invention provides:
A non-human vertebrate (eg, a mouse or a rat), wherein the vertebrate comprises lymphocytic cells, each cell genome comprising an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region and a mu constant region comprising a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, wherein the vertebrate expresses multivalent polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the heavy chain locus, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes. Optionally the mu constant region lacks a CH1 gene segment; this example is useful for producing multivalent H2 antibodies that bind the first and second epitopes. In another example, the mu constant region comprises a CH1; this is useful for producing 4-chain (H2L2) multivalent antibodies that bind the first and second epitopes. Optionally, the mu constant region lacks a hinge nucleotide sequence.
B-cells are an example of lymphocytic cells. Samples from which B-cells can be obtained include but are not limited to blood, serum, spleen, splenic tissue, bone marrow, lymph, lymph node, thymus, and appendix. For example, the B-cells are immature B-cells and/or mature B-cells.
The non-mu constant region is, in one embodiment, a gamma constant region (eg, gamma-1). Alternatively, the non-mu constant region is a delta, alpha or epsilon constant region. In an embodiment, each non-mu constant region of the heavy chain locus (or all the heavy chain loci) of the genome is according to (ii) above. In an embodiment, each gamma constant region of the heavy chain locus (or all the heavy chain loci) of the genome is according to (ii) above. For example, the heavy chain locus (or loci) of the genome comprises gamma-1, gamma-2a, gamma-2b and optionally a gamma-4 constant regions, wherein each of these constant regions is according to (ii) above.
In an embodiment, the genome is homozygous for said heavy chain locus.
Optionally, in an alternative the mu constant region does not comprise a CH1 gene segment. By including a CH1 gene segment in the mu constant region, however, it is possible to express heavy chains during antibody repertoire and B-cell compartment development that are 4-chain (H2L2) IgM antibodies. Surface-expression of such constructs can be advantageous during early B-cell development to provide good spleen and bone marrow B-cell compartments. Thus, a useful primary antibody repertoire can be provided from which to subsequently select isotype-switched chains (with our without CH1) in response to antigen.
Omission of a CH1 gene segment in a non-mu constant region is useful for producing and selecting heavy chains without light chain pairing, eg, as seen when H2 antibodies are produced. In the absence of light chain pairing the variable domains of the non-mu-type heavy chains expressed by the locus recited above are selected and matured without a variable domain partner (eg, where the variable domains of the heavy chains are VH, these are produced, affinity matured and selected in the absence of a VH/VL pair, and thus the VH are antibody single variable domains (aka dAbs or domain antibodies). The utility and advantages of H2 antibodies and dAbs are well known in the art, as described, for example, in the Harbour Antibodies and Crescendo Biologics patent applications mentioned herein and as described in patent applications filed in the name of Domantis Limited and Ablynx. Optionally, light chain expression does not occur when the non-mu-type chains are expressed. This provides the advantages described above for the production of H2 antibodies and heavy chains.
The variable region can be unrearranged, ie, the variable region of the heavy chain locus comprises one or more VH gene segments, one or more D gene segments and one or more JH gene segments (eg, a plurality of human VH gene segments, one or more human D gene segments and one or more human JH gene segments). The gene segments are capable of rearranging to form a rearranged variable region (a VDJ, eg, a human VDJ) which can combine with a constant region sequence. Thus, following rearrangement of the variable region, the heavy chain can encode RNA comprising a nucleotide sequence encoding an antibody heavy chain variable domain and constant region.
Alternatively, the variable region of the heavy chain locus is rearranged (ie, a VDJ nucleotide sequence).
In order to obtain switching from the mu to non-mu isotype, the locus comprises a switch 5′ of the mu constant region (eg, the endogenous S-mu is retained) and a second switch 5′ of the (or each) non-mu constant region. The second switch can be the switch usually present with the constant region (eg, when the constant region is a gamma-1 constant region, the gamma-1 switch is retained). Switch sequences are known in the art, for example, see Nikaido et al, Nature 292: 845-848 (1981) and also WO2011004192, U.S. Pat. Nos. 7,501,552, 6,673,986, 6,130,364, WO2009/076464 and U.S. Pat. No. 6,586,251, eg, SEQ ID NOs: 9-24 disclosed in U.S. Pat. No. 7,501,552. Commercial human and mouse BAC libraries (eg, the RPC-11 and Caltech A, B, C and D libraries) are sources of suitable immunoglobulin locus sequences, eg, sequences of switches or constant regions. Alternatively, human DNA samples can be obtained de novo from consenting donors (eg, using cheek swabs) and DNA sequences obtained from the samples.
In any configuration of the invention, there is provided a multivalent antibody, antibody chain or polypeptide. By “multivalent” in the context of an antibody chain is meant that the chain comprises two or more valencies (ie, epitope or antigen binding sites). For example, a heavy chain according to the invention can comprise first and second epitope binding sites (an no other epitope binding sites), and as such the chain is bivalent. This contrasts with antibody chains produced in vivo in the state of the art, which are monovalent by virtue of an N-terminal variable domain (eg, which pairs with a V domain on a partner light chain to form a VH/VL epitope binding site). By “multivalent” in the context of an antibody is meant that the antibody comprises two or more valencies (ie, epitope or antigen binding sites) when the antibody is a H2 antibody, or three or more valencies when the antibody is a 4-chain (H2L2) antibody. Corresponding epitope-binding fragments of such antibodies (eg, a Fab) comprises more epitope binding sites than equivalent antibody fragments in the art. For example, a Fab-like structure according to the invention may have two epitope binding sites, whereas a conventional Fab would have one binding site (provided by a VH/VL pair). A polypeptide according to the invention is multivalent when it comprises two or more epitope or antigen binding sites.
In addition to being multivalent, the antibody, chain or polypeptide of the invention is optionally multispecific (eg, bispecific). This means that the antibody, chain or polypeptide specifically binds to two or more different epitopes or antigens (simultaneously or non-simultaneously). The epitopes can, for example, be provided by different antigens or the same antigenic species (which is advantageous for providing an avidity of binding to target antigen). Binding can be assessed using standard in vitro techniques, eg, competition surface plasmon resonance (eg, Biacore™ or Proteon) or competition ELISA. Binding to different epitopes in a patient administered with a drug (eg, an antibody, chain or polypeptide or derivative thereof of the invention) is useful for addressing many diseases or conditions in humans or animals.
Alternatively, the antibody, chain or polypeptide is multivalent and monospecific, ie comprises a plurality of epitope binding sites that specifically bind to the same epitopic species (eg, bind simultaneously to copies of the same epitope, eg on a single antigen, which may be useful of providing avidity of binding).
The antigen is, for example, any of the antigens disclosed in EP1697421 (Micromet AG), WO2007024715 (Abbott Laboratories) or WO2010136485 (Glaxo Group Limited), the disclosures of which are incorporated herein by reference. For example, the present invention can related to one or more antigens and antigen classes specifically discussed in WO2007024715 at page 6, line 14-page 8, line 23; page 16, line 15-page 18, line 26; page 24, lines 9-26; page 52, lines 5-22; and page 55, line 10-page 66, line 23, with or without use in one or more of the medical indications cited.
These examples of antigens are specifically incorporated herein as though specifically and explicitly disclosed herein as possible antigens with respect to the present invention and for possible inclusion in one or more claims herein. For example, the present invention can related to one or more antigens and antigen classes specifically discussed in WO2010136485, including but not limited to VEGF, TNFα, EGFR, VEGFR2, IL-13 and HER2, with or without use in one or more of the medical indications cited. These examples of antigens are specifically incorporated herein as though specifically and explicitly disclosed herein as possible antigens with respect to the present invention and for possible inclusion in one or more claims herein. Examples of suitable epitopes for use in the present invention are epitopes provided by one or more of these antigens.
For example in any configuration of the invention, the or each antigen is selected from the group consisting of ABCF1; ACVR1; ACVR1B; ACVR2; ACVR2B; ACVRL1; ADORA2A; Aggrecan; AGR2; AICDA; AWI; AIG1; AKAP1; AKAP2; AIYIH; AMHR2; ANGPT1; ANGPT2; ANGPTL3; ANGPTL4; ANPEP; APC; APOC1; AR; AZGP1 (zinc-a-glycoprotein); B7.1; B7.2; BAD; BAFF; BAG1; BAI1; BCL2; BCL6; BDNF; BLNK; BLR1 (MDR15); B1yS; BMP1; BMP2; BMP3B (GDF1O); BMP4; BMP6; BMP8; BMPR1A; BMPR1B; BMPR2; BPAG1 (plectin); BRCA1; Cl9orflO (IL27w); C3; C4A; C5; C5R1; CANT1; CASP1; CASP4; CAV1; CCBP2 (D6/JAB61); CCL1 (I-309); CCL11 (eotaxin); CCL13 (MCP-4); CCL15 (MIP-id); CCL16 (HCC-4); CCL17 (TARC); CCL18 (PARC); CCL19 (MIP-3b); CCL2 (MCP-1); MCAF; CCL2O (MIP-3a); CCL21 (MIP-2); SLC; exodus-2; CCL22 (MDC/STC-1); CCL23 (MPIF-1); CCL24 (MPIF-2 I eotaxin-2); CCL25 (TECK); CCL26 (eotaxin-3); CCL27 (CTACK/ILC); CCL28; CCL3 (MIP-1a); CCL4 (MIP-1b); CCL5 (RANTES); CCL7 (MCP-3); CCL8 (mcp-2); CCNA1; CCNA2; CCND1; CCNE1; CCNE2; CCR1 (CKR1/HM145); CCR2 (mcp-1RB/RA); CCR3 (CKR3/CMKBR3); CCR4; CCR5 (CMKBR5/ChemR13); CCR6 (CMKBR6/CKR-L3/STRL22/DRY6); CCR7 (CKR7/EBI1); CCR8 (CMKBR8/TER1/CKR-L1); CCR9 (GPR-9-6); CCRL1 (VSHK1); CCRL2 (L-CCR); CD164; CD19; CD1C; CD2O; CD200; CD-22; CD24; CD28; CD3; CD37; CD38; CD3E; CD3G; CD3Z; CD4; CD4O; CD4OL; CD44; CD45RB; CD52; CD69; CD72; CD74; CD79A; CD79B; CD8; CD80; CD81; CD83; CD86; CDH1 (E-cadherin); CDH10; CDH12; CDH13; CDH18; CDH19; CDH20; CDH5; CDH7; CDH8; CDH9; CDK2; CDK3; CDK4; CDK5; CDK6; CDK7; CDK9; CDKN1A (p2IWap1/Cip1); CDKN1B (p27Kip1); CDKNIC; CDKN2A (p16INK4a); CDKN2B; CDKN2C; CDKN3; CEBPB; CER1; CHGA; CHGB; Chitinase; CHST10; CKLFSF2; CKLFSF3; CKLFSF4; CKLFSF5; CKLFSF6; CKLFSF7; CKLFSF8; CLDN3; CLDN7 (claudin-7); CLN3; CLU (clusterin); CMKLR1; CMKOR1 (RDC1); CNR1; COL18A1; COL1A1; COL4A3; COL6A1; CR2; CRP; CSF1 (M-CSF); CSF2 (GM-CSF); CSF3 (GCSF); CTLA4; CTNNB1 (b-catenin); CTSB (cathepsin B); CX3CL1 (SCYDi); CX3CR1 (V28); CXCL1 (GRO1); CXCL1O (1P-10); CXCL11 (1-TAC/IP-9); CXCL12 (SDF1); CXCL13; CXCL14; CXCL16; CXCL2 (GRO2); CXCL3 (GRO3); CXCL5 (ENA-78 I LIX); CXCL6 (GCP-2); CXCL9 (MIG); CXCR3 (GPR9/CKR-L2); CXCR4; CXCR6 (TYMSTR ISTRL331Bonzo); CYB5; CYC1; CYSLTR1; DAB2IP; DES; DKFZp451J0118; DNCL1; DPP4; E2F1; ECGF1; EDG1; EFNAI; EFNA3; EFNB2; EGF; EGFR; ELAC2; ENG; ENO1; ENO2; ENO3; EPHB4; EPO; ERBB2 (Her-2); EREG; ERK8; ESR1; ESR2; F3 (TF); FADD; FasL; FASN; FCER1A; FCER2; FCGR3A; FGF; FGF1 (aFGF); FGF1O; FGF11; FGF12; FGF12B; FGF13; FGF14; FGF16; FGF17; FGF18; FGF19; FGF2 (bFGF); FGF2O; FGF21; FGF22; FGF23; FGF3 (int-2); FGF4 (HST); FGF5; FGF6 (HST-2); FGF7 (KGF); FGF8; FGF9; FGFR3; FIGF (VEGFD); FIL1 (EPSILON); FIL1 (ZETA); FLJ12584; FLJ25530; FLRT1 (fibronectin); FLT1; FOS; FOSL1 (FRA-I); FY (DARC); GABRP (GABAa); GAGEB1; GAGEC1; GALNAC4S-65T; GATA3; GDF5; GFI1; GGT1; GM-CSF; GNAS1; GNRH1; GPR2 (CCR1O); GPR31; GPR44; GPR81 (FKSG80); GRCC10 (C10); GRP; GSN (Gelsolin); GSTP1; HAVCR2; HDAC4; EDAC5; HDAC7A; HDAC9; HGF; HIF1A; HIP1; histamine and histamine receptors; HLA-A; HLA-DRA; HM74; HMOX1; HUMCYT2A; ICEBERG; ICOSL; 1D2; IFN-a; IFNA1; IFNA2; IFNA4; IFNA5; IFNA6; IFNA7; IFNB1; IFNgamma; TFNW1; IGBP1; IGF1; IGF1R; IGF2; IGFBP2; IGFBP3; IGFBP6; IL-1; IL10; IL10RA; IL10RB; IL11; IL11RA; IL-12; IL12A; IL12B; IL12RB1; IL12RB2; IL13; IL13RA1; IL13RA2; IL14; IL15; IL15RA; IL16; IL17; IL17B; IL17C; IL17R; IL18; IL18BP; IL18R1; IL18RAP; IL19; IL1A; IL1B; IL1F10; IL1F5; IL1F6; IL1F7; IL1F8; IL1F9; IL1HY1; IL1R1; IL1R2; IL1RAP; IL1RAPL1; IL1RAPL2; IL1RL1; IL1RL2 IL1RN; IL2; IL20; IL2ORA; IL21R; IL22; IL22R; IL22RA2; IL23; IL24; IL25; IL26; IL27; IL28A; IL28B; IL29; IL2RA; IL2RB; IL2RG; IL3; IL30; IL3RA; IL4; IL4R; IL5; IL5RA; IL6; IL6R; IL6ST (glycoprotein 130); IL7; TL7R; IL8; IL8RA; IL8RB; IL8RB; IL9; IL9R; ILK; INHA; INHBA; INSL3; INSL4; IRAK1; IRAK2; ITGA1; ITGA2; ITGA3; ITGA6 (a6 integrin); ITGAV; ITGB3; ITGB4 (b 4 integrin); JAG1; JAK1; JAK3; JUN; K6HF; KAI1; KDR; MTLG; KLF5 (GC Box BP); KLF6; KLK10; KLK12; KLK13; KLK14; KLK15; KLK3; KLK4; KLK5; KLK6; KLK9; KRT1; KRT19 (Keratin 19); KRT2A; KRTHB6 (hair-specific type II keratin); LAMA5; LEP (leptin); Lingo-p75; Lingo-Troy; LPS; LTA (TNF-b); LTB; LTB4R (GPR16); LTB4R2; LTBR; MACMARCKS; MAG or Omgp; MAP2K7 (c-Jun); MDK; MIB1; midkine; MIF; MIP-2; MK167 (Ki-67); MMP2; MMP9; MS4A1; MSMB; MT3 (metallothionectin-ifi); MTSS 1; MUC 1 (mucin); MYC; MYD88; NCK2; neurocan; NFKB 1; NFKB2; NGFB (NGF); NGFR; NgR-Lingo; NgR-Nogo66 (Nogo); NgR-p75; NgR-Troy; NME1 (NM23A); NOX5; NPPB; NROB1; NROB2; NR1D1; NR1D2; NR1H2; NR1H3; NR1H4; NR112; NR113; NR2C1; NR2C2; NR2E1; NR2E3; NR2F1; NR2F2; NR2F6; NR3C1; NR3C2; NR4A1; NR4A2; NR4A3; NR5A1; NR5A2; NR6A1; NRP1; NRP2; NT5E; NTN4; ODZ1; OPRD1; P2RX7; PAP; PART1; PATE; PAWR; PCA3; PCNA; PDGFA; PDGFB; PECAM1; PF4 (CXCL4); PGF; PGR; phosphacan; PIAS2; PIK3CG; PLAU (uPA); PLG; PLXDC1; PPBP (CXCL7); PPID; PR1; PRKCQ; PRKD1; PRL; PROC; PROK2; PSAP; PSCA; PTAFR; PTEN; PTGS2 (COX-2); PTN; RAC2 (p2IRac2); RARB; RGS1; RGS13; RGS3; RNF11O (ZNF144); ROBO2; S100A2; SCGB1D2 (lipophilin B); SCGB2A1 (mammaglobin 2); SCGB2A2 (mammaglobin 1); SCYE1 (endothelial Monocyte-activating cytokine); SDF2; SERPINA1; SERPINIA3; SERPINB5 (maspin); SERPINE1 (PAT-i); SERPINF1; SHBG; SLA2; SLC2A2; SLC33A1; SLC43A1; SLIT2; SPP1; SPRR1B (Spri); ST6GAL1; STAB1; STATE; STEAP; STEAP2; TB4R2; TBX21; TCP1O; TDGF1; TEK; TGFA; TGFB1; TGFB111; TGFB2; TGFB3; TGFBI; TGFBR1; TGFBR2; TGFBR3; TH1L; THBS1 (thrombospondin-1); THBS2; THBS4; THPO; TIE (Tie-i); T]MP3; tissue factor; TLR1O; TLR2; TLR3; TLR4; TLR5; TLR6; TLR7; TLR8; TLR9; TNF; TNF-a; TNFAIP2 (B94); TNFAIP3; TNFRSF11A; TNFRSF1A; TNFRSF1B; TNFRSF21; TNFRSF5; TNFRSF6 (Fas); TNFRSF7; TNFRSF8; TNFRSF9; TNFSF1O (TRAIL); TNFSF11 (TRANCE); TNFSF12 (APO3L); TNFSF13 (April); TNFSF13B; TNFSF14 (HVEM-L); TNFSF15 (VEGI); TNFSF18; TNFSF4 (0X40 ligand); TNFSF5 (CD4O ligand); TNFSF6 (FasL); TNFSF7 (CD27 ligand); TNFSF8 (CD3O ligand); TNFSF9 (4-1BB ligand); TOLLIP; Toll-like receptors; TOP2A (topoisomerase Iia); TP53; TPM1; TPM2; TRADD; TRAF1; TRAF2; TRAF3; TRAF4; TRAF5; TRAF6; TREM1; TREM2; TRPC6; TSLP; TWEAK; VEGF; VEGFB; VEGFC; versican; VHL C5; VLA-4; XCL1 (lymphotactin); XCL2 (SCM-1b); XCR1 (GPR5/CCXCR1); YY1; and ZFPM2. Examples of suitable epitopes for use in the present invention are epitopes provided by one or more of these antigens.
For example in any configuration of the invention, the first and second epitope or antigen are selected from the group consisting of EpCAM and CD3; CD19 and CD3; VEGF and VEGFR2; VEGF and EGFR; CD138 and CD2O; CD138 and CD4O; CD2O and CD3; CD38 and CD138; CD38 and CD2O; CD38 and CD4O; CD4O and CD2O; CD19 and CD2O; CD-8 and IL-6; PDL-1 and CTLA-4; CTLA-4 and BTNO2; CSPGs and RGM A; IGF1 and IGF2; IGF1 and/or 2 and Erb2B; IL-12 and IL-18; IL-12 and TWEAK; IL-13 and ADAM8; IL-13 and CL25; IL-13 and IL-1beta; IL-13 and IL-25; IL-13 and IL-4; IL-13 and IL-5; IL-13 and IL-9; IL-13 and LHR agonist; IL-13 and MDC; IL-13 and MIF; IL-13 and PED2; IL-13 and SPRR2a; IL-13 and SPRR2b; IL-13 and TARC; IL-13 and TGF-beta; IL-1 alpha and IL-1 beta; MAG and RGM A; NgR and RGM A; NogoA and RGM A; OMGp and RGM A; RGM A and RGM B; Te38 and TNF alpha; TNF alpha and IL-12; TNF alpha and IL-12p40; TNF alpha and IL-13; TNF alpha and IL-15; TNF alpha and IL-17; TNF alpha and IL-18; TNF alpha and IL-1 beta; TNF alpha and IL-23; TNF alpha and MIF; TNF alpha and PEG2; TNF alpha and PGE4; TNF alpha and VEGF; and VEGFR and EGFR; TNF alpha and RANK ligand; TNF alpha and Blys; TNF alpha and GP130; TNF alpha and CD-22; and TNF alpha and CTLA-4.
For example in any configuration of the invention, the first epitope or antigen is selected from the group consisting of CD3; CD16; CD32; CD64; and CD89; and the second epitope or antigen is selected from the group consisting of EGFR; VEGF; IGF-1R; Her2; c-Met (aka HGF); HER3; CEA; CD33; CD79a; CD19; PSA; EpCAM; CD66; CD30; HAS; PSMA; GD2; ANG2; IL-4; IL-13; VEGFR2; and VEGFR3.
It is contemplated that the use of an antibody, chain or polypeptide of the invention is any use disclosed in EP1697421 (Micromet AG), WO2007024715 (Abbott Laboratories) or WO2010136485 (Glaxo Group Limited), the disclosures of which are incorporated herein by reference. For example, the present invention can related to one or more uses specifically discussed in WO2007024715 at page 11, line 24-page 15, line 14; page 51, line 6-page 66, line 23; page 76, line 1-page 79, line 29; and page 84, line 1-page 90, line 2. These examples of uses are specifically incorporated herein as though specifically and explicitly disclosed herein as possible uses with respect to the present invention and for possible inclusion in one or more claims herein. For example, the present invention can related to one or more uses specifically discussed in WO2010136485, including but not limited to those uses disclosed at page 12, line 33-page 13, line 7; and page 15, lines 16-32. These examples of uses are specifically incorporated herein as though specifically and explicitly disclosed herein as possible antigens with respect to the present invention and for possible inclusion in one or more claims herein. For example, the present invention can related to one or more uses specifically discussed in EP1697421, including but not limited to those uses disclosed at page 6, lines 31-33. These examples of uses are specifically incorporated herein as though specifically and explicitly disclosed herein as possible antigens with respect to the present invention and for possible inclusion in one or more claims herein.
It is contemplated that the use of, or composition comprising, an antibody, chain or polypeptide of the invention is any use or composition in combination with a second agent as disclosed in EP1697421 (Micromet AG), WO2007024715 (Abbott Laboratories) or WO2010136485 (Glaxo Group Limited), the disclosures of which are incorporated herein by reference. For example, the present invention can related to an antibody, chain or polypeptide of the invention with one or more additional pharmaceutically-acceptable agents specifically discussed in WO2007024715 at page 11, lines 7-23; page 15, lines 15-32; and page 79, line 30-page 90, line 2. These examples of uses, combinations and compositions are specifically incorporated herein as though specifically and explicitly disclosed herein as possible uses, combinations and compositions with respect to the present invention and for possible inclusion in one or more claims herein, with the exception that an antibody, chain or polypeptide of the invention is used instead of an antibody, chain or polypeptide disclosed in these prior art disclosures.
It is contemplated that the composition comprising, an antibody, chain or polypeptide of the invention has the general mixture of ingredients of any composition disclosed in EP1697421 (Micromet AG), WO2007024715 (Abbott Laboratories) or WO2010136485 (Glaxo Group Limited), the disclosures of which are incorporated herein by reference, with the exception that an antibody, chain or polypeptide of the invention is used instead of an antibody, chain or polypeptide disclosed in these prior art documents. For example, the present invention can relate to an antibody, chain or polypeptide of the invention in a pharmaceutical composition specifically discussed in WO2007024715 at page 66, line 25-page 75, line 23; and page 90, lines 2-26. These examples of compositions are specifically incorporated herein as though specifically and explicitly disclosed herein as possible compositions with respect to the present invention and for possible inclusion in one or more claims herein, with the exception that an antibody, chain or polypeptide of the invention is used instead of an antibody, chain or polypeptide disclosed in these prior art disclosures.
It is contemplated that an composition, antibody, chain or polypeptide of the invention is administered or administrable as disclosed in EP1697421 (Micromet AG), WO2007024715 (Abbott Laboratories) or WO2010136485 (Glaxo Group Limited), the disclosures of which are incorporated herein by reference, with the exception that an antibody, chain or polypeptide of the invention is used instead of an antibody, chain or polypeptide disclosed in these prior art documents. For example, the present invention can related to the administration of an antibody, chain or polypeptide of the invention (or a pharmaceutical composition for this purpose) as per administration specifically discussed in WO2007024715 at page 69, line 29-page 75, line 23; and page 90, lines 3-33. These examples of compositions are specifically incorporated herein as though specifically and explicitly disclosed herein as possible compositions, and administration routes and regimes with respect to the present invention and for possible inclusion in one or more claims herein, with the exception that an antibody, chain or polypeptide of the invention is used instead of an antibody, chain or polypeptide disclosed in these prior art disclosures.
Each linker (when present) is an amino acid sequence in the antibody, chain or polypeptide of the invention. In the locus of the genome, the locus comprises a corresponding nucleotide sequence to encode each linker.
For use in the present invention, it is contemplated that one, more or each linker is as disclosed in EP1697421 (Micromet AG), WO2007024715 (Abbott Laboratories) or WO2010136485 (Glaxo Group Limited), the disclosures of which are incorporated herein by reference. For example, the present invention can use a linker as specifically discussed in WO2007024715 at page 4, line 25-page 6, line 13; page 24, line 27-page 25, line 2; page 44, line 11-page 45, line 3. These examples of linkers are specifically incorporated herein as though specifically and explicitly disclosed herein as possible linkers for use with respect to the present invention and for possible inclusion in one or more claims herein. For example, the present invention can use a linker as specifically discussed in WO2010136485 at page 10, line 27-page 12, line 28; and page 14, lines 6-14; or a linker set out in SEQ ID NO: 10-38 of WO2010136485. These examples of linkers are specifically incorporated herein as though specifically and explicitly disclosed herein as possible linkers for use with respect to the present invention and for possible inclusion in one or more claims herein.
For example in any configuration of the invention, one, more or each linker is a (GGGGS), linker, where n=1, 2, 3, 4, 5, 6, 7, 8, 9 or 10.
For example in any configuration of the invention, one, more or each linker is a linker selected from the group consisting of AKTTPKLEEGEFSEAR; AKTTPKLBEGEFSEARV; AKTTPKLGG; SAKTTPKLGG; AKTTPKLEEGEFSEARV; SAKTTP; SAKTTPKLGG; RADAAP; RADAAPTVS; RADAAAAGGPGS; RADAAAA(G4S)4; SAKTTP; SAKTTPKLGG; SAKTTPKLEBGEFSEARV; ADAAP; ADAAPTVSIFPP; TVAAP; TVAAPSVFIFPP; QPKAAP; QPKAAPSVTLFPP; AKTTPP; AKTTPPSVTPLAP; AKTTAP; AKTTAPSVYPLAP; ASTKGP; ASTKGPSVFPLAP; GGGGSGGGGSGGGGS; GBNKVEYAPALMALS; GPAKELTPLKEAKVS; and GHEAAAVMQVQYPAS.
For example in any configuration of the invention, one, more or each linker is an amino acid sequence from 1 amino acid to 150 amino acids in length, or from 1 amino acid to 140 amino acids, for example, from 1 amino acid to 130 amino acids, or from 1 to 120 amino acids, or from 1 to 80 amino acids, or from 1 to 50 amino acids, or from 1 to 20 amino acids, or from 1 to 10 amino acids, or from 5 to 18 amino acids. Such sequences may have their own tertiary structure, for example, a linker of the present invention may be or comprise a domain, eg, an antibody single variable domain. The size of a linker in one embodiment is equivalent to a single variable domain. Suitable linkers may be of a size from 1 to 20 angstroms, for example less than 15 angstroms, or less than 10 angstroms, or less than 5 angstroms.
In one embodiment of the present invention a linker comprises from 1 to 150 amino acids, for example 1 to 50 amino acids, for example 1 to 20 amino acids, for example 1 to 10 amino acids. Such linkers may be selected from any one of those set out in SEQ ID NO: 10-38 or SEQ ID NO: 42-44 as disclosed in WO2010136485 (which disclosure is explicitly incorporated herein by reference as though specifically and explicitly disclosed herein as possible linkers for use with respect to the present invention and for possible inclusion in one or more claims herein), or multiples of such linkers.
Linkers may comprise alone or in addition to other linkers, one or more sets of GS residues, for example GSTVAAPS or TVAAPSGS or GSTVAAPSGS.
An example of a linker is (PAS)n(GS)m. In another embodiment, a linker is (GGGGS)n(GS)m. In another embodiment a linker is (TVAAPS)n(GS)m. In another embodiment a linker is (GS)m(TVAAPSGS)n. In another embodiment a linker is (PAVPPP)n(GS)m. In another embodiment a linker is (TVSDVP)n(GS)m. In another embodiment a linker is (TGLDSP)n(GS)m. In all such embodiments, n=1, 2, 3, 4, 5, 6, 7, 8, 9 or 10, and m=0, 1, 2, 3 or 4.
Examples of such linkers include (PAS)n(GS)m, wherein n=1 and m=1, (PAS)n(GS)m, wherein n=2 and m=1, (PAS)n(GS)m, wherein n=3 and m=1, (PAS)n(GS)m wherein n=4 and m=1, (PAS)n(GS)m wherein n=2 and m=0, (PAS)n(GS)m wherein n=3 and m=0, (PAS)n(GS)m wherein n=4 and m=0.
Examples of such linkers include (GGGGS)n(GS)m wherein n=1 and m=1, (GGGGS)n(GS)m wherein n=2 and m=1, (GGGGS)n(GS)m wherein n=3 and m=1, (GGGGS)n(GS)m wherein n=4 and m=1, (GGGGS)n(GS)m wherein n=2 and m=0, (GGGGS)n(GS)m wherein n=3 and m=0, (GGGGS)n(GS)m wherein n=4 and m=0.
Examples of such linkers include (TVAAPS)n(GS)m wherein n=1 and m=1, (TVAAPS)n(GS)m wherein n=2 and m=1, (TVAAPS)n(GS)m wherein n=3 and m=1, (TVAAPS)n(GS)m wherein n=4 and m=1, (TVAAPS)n(GS)m wherein n=2 and m=0, (TVAAPS)n(GS)m wherein n=3 and m=0, (TVAAPS)n(GS)m wherein n=4 and m=0.
Examples of such linkers include (GS)m(TVAAPSGS)n wherein n=1 and m=1, (GS)m(TVAAPSGS)n wherein n=2 and m=1, (GS)m(TVAAPSGS)n wherein n=3 and m=1, (GS)m(TVAAPSGS)n wherein n=4 and m=1, (GS)m(TVAAPSGS)n wherein n=5 and m=1, (GS)m(TVAAPSGS)n wherein n=6 and m=1, (GS)m(TVAAPSGS)n wherein n=1 and m=0, (GS)m(TVAAPSGS)n wherein n=2 and m=10, (GS)m(TVAAPSGS)n wherein n=3 and m=0, or (GS)m wherein m=0, 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10.
Examples of such linkers include (PAVPPP)n(GS)m wherein n=1 and m=1, (PAVPPP)n(GS)m wherein n=2 and m=1, (PAVPPP)n(GS)m wherein n=3 and m=1, (PAVPPP)n(GS)m wherein n=4 and m=1, (PAVPPP)n(GS)m wherein n=2 and m=0, (PAVPPP)n(GS)m wherein n=3 and m=0, or (PAVPPP)n(GS)m wherein n=4 and m=0.
Examples of such linkers include (TVSDVP)n(GS)m wherein n=1 and m=1, (TVSDVP)n(GS)m wherein n=2 and m=1, (TVSDVP)n(GS)m wherein n=3 and m=1, (TVSDVP)n(GS)m wherein n=4 and m=1, (TVSDVP)n(GS)m wherein n=2 and m=0, (TVSDVP)n(GS)m wherein n=3 and m=0, (TVSDVP)n(GS)m wherein n=4 and m=0.
Examples of such linkers include (TGLDSP)n(GS)m wherein n=1 and m=1, (TGLDSP)n(GS)m wherein n=2 and m=1, (TGLDSP)n(GS)m wherein n=3 and m=1, (TGLDSP)n(GS)m wherein n=4 and m=1, (TGLDSP)n(GS)m wherein n=2 and m=0, (TGLDSP)n(GS)m wherein n=3 and m=0, or (TGLDSP)n(GS)m wherein n=4 and m=0.
In another embodiment there is no linker between the epitope binding moiety and the variable domain (and thus the locus does not comprise a corresponding linker-encoding nucleotide sequence). In another embodiment the epitope binding moiety is linked to the variable domain by the linker TVAAPS. In another embodiment the epitope binding moiety, is linked to the variable domain by the linker TVAAPSGS. In another embodiment the epitope binding moiety is linked to the variable domain by the linker GS. In another embodiment the epitope binding moiety is linked to the variable domain by the linker ASTKGPT.
In an embodiment, the vertebrate or cell of the invention comprises an antibody heavy chain locus that comprises (in 5′ to 3′ direction) a rearranged or unrearranged variable region, a first switch (eg, an S-mu switch, eg an endogenous S-mu), an endogenous mu constant region, a second switch (an S-gamma switch; eg, endogenous S-gamma) and a human constant region of said non-mu isotype; wherein the heavy chain locus is capable of undergoing switching from IgM to the non-mu isotype. Thus, for example, this can be provided by inserting one or more human non-mu constant region sequences downstream (3′) of an endogenous mu region in the genome of a non-human vertebrate or cell (eg, ES cell). In this way, the human sequences are provided within the location of the endogenous heavy chain locus and expression from the human sequence can be effectively controlled using endogenous antibody and B-cell mechanisms.
In the present invention, the variable region of the or each locus is optionally a human variable region. For example, the variable region is a human rearranged VDJ or VI For example, the variable region is unrearranged and comprises a plurality of human V gene segments, one or more human J gene segments and optionally one or more human D gene segments (eg, a plurality of human VH gene segments, one or more human JH gene segments and one or more human D gene segments). It is contemplated that the variable region can encode heavy or light chain variable domains (VH, VHH or VL). The variable region can be any variable region disclosed in any of the Kymab Limited, Regeneron, Harbour Antibodies, Crescendo Biologics or Ablexis patent applications cited herein, and the disclosures of the composition of these variable region (such as the repertoire of gene segments contained therein) is incorporated herein by reference as though explicitly written herein, and for possible inclusion in one or more claims herein.
In the present invention, the mu constant region of the or each locus is optionally a non-human vertebrate mu constant region, eg of the same species or strain as the vertebrate per se. For example, the mu constant region is a mouse constant region.
In the present invention, the mu constant region of the or each locus is optionally an endogenous host mu constant region. In this way, the constant region (and the IgM stage) is host-matched for good B-cell compartment and primary repertoire development.
In the present invention, the or each non-mu constant region of the or each locus is optionally a non-human vertebrate constant region, eg of the same species or strain as the vertebrate per se. For example, the or each non-mu constant region is a mouse constant region.
In the present invention, the or each non-mu constant region of the or each locus is optionally an endogenous host constant region. In this way, the constant region is host-matched for good B-cell compartment and antibody/chain development.
In an embodiment, the vertebrate species is selected from human, mouse, rat, rabbit, guinea pig, chicken, a fish, a bird, a reptile, a Camelid, bovine, chimpanzee, a non-human primate and a primate.
In an embodiment, the vertebrate is a mouse. In an embodiment, the vertebrate is a rat.
The invention also provides a non-human vertebrate cell (eg, a mouse cell or a rat cell), the cell genome comprising
(i) an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region, a first switch (eg, an S-mu switch, eg, an endogenous S-mu), a mu constant region (eg, comprising a CH1 gene segment), a second switch (eg, an S-gamma switch, eg, an endogenous S-gamma) and a non-mu (eg, gamma) constant region; wherein the heavy chain locus of each cell is capable of undergoing IgM to a non-mu (eg, IgG) isotype switching; and
wherein
(ii) the non-mu constant region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, for expressing a multivalent (eg, multispecific, eg, bispecific) polypeptide chain comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the heavy chain locus, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes (eg, wherein the epitopes are different).
Optionally the gamma constant region lacks a CH1 gene segment, as described above.
Optional features described herein with reference to a vertebrate are also applicable to cells of the invention.
In one example, the cell is a B-cell, hybridoma, ES cell or iPS cell. ES cells and iPS cells (induced pluripotent stem cells) can be used to develop corresponding non-human vertebrates (vertebrates of the invention).
In an embodiment of the vertebrate or cell of the invention, the genome comprises a functional antibody light chain locus for expressing light chains; wherein the cells can express IgM antibodies comprising IgM-type heavy chains and light chains, each heavy chain comprising a CH1 domain. Optionally, the light chain locus comprises a human rearranged or unrearranged variable region.
Optionally, the light chain locus comprises means for turning off light chain expression, wherein functional light chains are not expressed after IgM to non-mu isotype switching. Examples of suitable means are described below. Optionally, also the non-mu gamma constant region does not comprise a CH1 gene segment. Thus, non-mu heavy chains lacking a CH1 domain are expressible by the vertebrate or cell in the absence of light chains; this is useful for producing H2 multivalent antibodies.
In an embodiment, the vertebrate expresses polypeptide chains comprising (in N- to C-terminal direction) (a) an antibody variable domain derived from said variable region of the heavy chain locus (optionally following somatic hypermutation), an optional linker, an epitope binding moiety and a non-mu (eg, gamma) constant domain (eg, gamma Fc) or (b) an antibody variable domain derived from said variable region of the heavy chain locus (optionally following somatic hypermutation), a non-mu (eg, gamma) constant domain (eg, gamma Fc), an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind the respective first and second epitopes. In an example, the polypeptide chains have the structure V-L-E or V-L-E-L, where V is an antibody variable domain (VH, VHH or VL) derived from said variable region of the heavy chain locus, L is an optional linker and E is an epitope binding domain. Possible structures are V-L-E-Fc or V-L-E-L-Fc, where Fc is an antibody Fc region (eg a gamma Fc).
In an embodiment, the or each epitope binding moiety is an epitope binding domain.
In an embodiment of the vertebrate or cell of the invention, the non-mu constant region is a gamma constant region and the heavy chain locus is capable of undergoing isotype switching to produce IgG antibodies comprising one or more IgG heavy chains in the absence of light chains, each heavy chain lacking a CH1 domain.
In an embodiment of the vertebrate or cell of the invention, there is provided a non-human (eg, rat or mouse) vertebrate or cell that expresses multivalent heavy chains (or dimers thereof) comprising the structure V-L-E or V-L-E-L (eg, V-L-E-Fc or V-L-E-L-Fc), where V is an antibody variable domain (VH, VHH or VL), L is an optional linker and E is an epitope binding moiety, wherein V and E specifically bind respective first and second antigens, wherein the antigens are different.
Rearranged Non-Mu (eg, Gamma) Locus
The invention also relates to non-human vertebrates and cells that have a non-mu isotype, such as a gamma isotype constant region without a mu constant region—for production of non-mu heavy chains (optionally provided by non-mu antibodies). The invention also relates to non-human vertebrates and cells that have undergone isotype switching to a non-mu isotype, such as a gamma isotype for production of non-mu heavy chains (optionally provided by non-mu antibodies). To this end, the invention provides:
A non-human vertebrate (eg, a mouse or a rat), wherein the vertebrate comprises lymphocytic cells whose genomes comprise an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged variable region and a non-mu (eg, gamma) constant region;
wherein
the non-mu constant region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, wherein the vertebrate expresses multivalent (eg, bivalent, eg, bispecific) polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the heavy chain locus, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes (eg, wherein the epitopes are different).
Also, the invention provides a non-human vertebrate cell (eg, a mouse cell or a rat cell) or a hybridoma, the cell genome comprising an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged variable region and a non-mu (eg, gamma) constant region;
wherein
the non-mu constant region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, wherein the cell expresses a multivalent polypeptide chain comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the heavy chain locus, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes.
Optional features described above in the context of vertebrates and cells comprising mu constant regions are also applicable to these isotype-switched embodiments of vertebrates and cells.
In an embodiment of the vertebrate or cell, the heavy chain locus has undergone IgM to non-mu (eg, IgG) isotype switching.
In an embodiment of the vertebrate or cell, the linker and/or epitope binding moiety nucleotide sequence is provided in place of a CH1 domain gene segment in the non-mu (eg, gamma) constant region. Thus, the product comprises or consists of the structure V-L-E (eg, V-L-E-CH2-CH3, where the constant domains are gamma-type constant domains).
L Chain Locus for Multivalent Products
The invention similarly provides light chain loci for expression of multivalent (eg, multispecific, eg, bispecific) light chains. To this end, the invention provides:
A non-human vertebrate (eg, a mouse or a rat), wherein the vertebrate comprises lymphocytic cells, the genome of each cell comprising an antibody light chain locus (eg, a kappa or lambda locus) which comprises (in 5′ to 3′ direction) a rearranged or unrearranged variable region and a second region;
wherein
the second region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, wherein the vertebrate expresses polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the light chain locus (optionally following mutation, eg, somatic hypermutation), an optional linker and an epitope binding moiety , wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes (eg, wherein the epitopes are different).
The variable domain is derived from the variable region of the light chain locus. Thus, when the variable region of the locus is a rearranged variable region, the variable domain is encoded by the sequence of the variable region (eg, a VHDJH or VLJL region) optionally with somatic hypermutation. When the variable region is an unrearranged variable region, this region comprises one or more V gene segments, one or more J gene segments and optionally one or more D gene segments (eg, wherein all of these segments are human). Following rearrangement of gene segments in the light chain locus, a rearranged VDJ or VJ is formed and this encodes the variable domain optionally following somatic hypermutation.
Optionally, the second region comprises nucleotide sequences encoding a plurality of epitope binding moieties, eg, two or three epitope binding moieties joined by optional linkers.
Optionally, the second region comprises nucleotide sequences encoding one or a plurality of epitope binding moieties (optionally joined by linkers) in place of a CL gene segment or in addition thereto. For example, the second region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker, a predetermined epitope binding moiety and a CL; or CL, an optional linker and a predetermined epitope binding moiety; or an optional linker and a predetermined epitope binding moiety (in the absence of a CL).
For example, the polypeptide chains each comprise an antibody variable domain derived from said variable region of the light chain locus, an optional linker, an epitope binding moiety and a CL domain; or an antibody variable domain derived from said variable region of the light chain locus, a CL domain, an optional linker and an epitope binding moiety; or an antibody variable domain derived from said variable region of the light chain locus, an optional linker and an epitope binding moiety.
Features described herein that relate to a non-human vertebrate comprising the light chain locus of the invention also apply to a cell that comprises a light chain locus of the invention. The invention, thus also provides:
A non-human vertebrate cell (eg, a mouse cell or a rat cell) or a hybridoma, wherein the cell genome comprises an antibody light chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region and a second region;
wherein
the second region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, for expressing a polypeptide chain comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the light chain locus, an optional linker and an epitope binding moiety , wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes.
In an example, there is provided a non-human vertebrate or cell comprising a heavy chain and light chain of the invention as herein described. Thus, the vertebrate is capable of expressing multivalent heavy chains and multivalent light chains, eg, as provided by multivalent antibodies. For example, the antibodies can be bispecific, trispecific, tetraspecific, pentaspecific, hexaspecific or heptaspecific or have more than 7 specificities. For example, the antibodies can have 3, 4, 5, 6, 7, 8 or more valencies. Valencies and specificities refer to specific epitope or antigen binding.
In an example, there is provided a non-human vertebrate or cell comprising a heavy chain and light chain of the invention as described. Optionally, the vertebrate or cell genome comprises said heavy and light chain loci, wherein said polypeptide chain variable domains derived from the heavy chain locus form binding sites with the polypeptide chain variable domains derived from the light chain locus, wherein the binding sites specifically bind the first epitope. For example, the epitope binding moieties of the polypeptide chains derived from the heavy and light chain loci are antibody variable domains, wherein the epitope binding domains of the chains derived from the heavy chain locus associate with the epitope binding domains of the chains derived from the light chain locus to form binding sites that specifically bind the second epitope. In one embodiment, the epitope binding moieties in chains derived from the heavy chain locus are VH domains; and the epitope binding moieties in chains derived from the light chain locus are VL domains. In another embodiment, the epitope binding moieties in chains derived from the heavy chain locus are VL domains; and the epitope binding moieties in chains derived from the light chain locus are VH domains. The VH and VL domains between heavy and light chains optionally form VH/VL pairs, each VH/VL providing an epitope binding site. Chains are derived from a locus when, for example following rearrangement and somatic hypermutation the loci encode RNA, the RNA in turn encoding for the chains. This may take place, for example, following immunisation of the vertebrate to the first epitope (ie, the epitope that is specifically bound by the N-terminal variable domain in the product chain).
In an example, the vertebrate or cell of the invention is homozygous for a heavy chain as described herein and/or a light chain as described herein.
Methods
The invention also provides methods for the in vivo production, maturation and selection of multivalent antibodies, antibody chains and polypeptides that specifically bind first and second epitopes. To this end, the invention provides:
A method of producing multivalent (eg, bivalent, eg, bispecific) polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes (eg, wherein the epitopes are different or the same), the method comprising
(a) expressing in a non-human vertebrate (eg, a mouse or a rat) IgM antibodies in immature B-cells (eg, T1 and T2 B-cells, eg, splenic B-cells), wherein the antibodies comprise heavy and light chains expressed from heavy and light chain loci respectively;
(b) immunising the vertebrate with a first predetermined antigen bearing the first epitope and obtaining isotype switching to expression from a non-mu (eg, gamma) constant region in at least some of the heavy chain loci and expression of variable regions that have undergone somatic hypermutation (eg, variable regions provided by IgG antibody heavy chains); and
(c) selecting one or more polypeptide chains from said immunised vertebrate by selection for variable regions that bind said first epitope (eg, by selection of heavy chains of said non-mu isotype), wherein each selected chain comprises a somatically hypermutated variable region that specifically binds the epitope; and
wherein the method comprises
(d) providing the nucleotide sequence of the epitope binding moiety (or a predetermined parent thereof that specifically binds the second epitope) in the non-mu constant region of heavy chain loci in the genome of the vertebrate, wherein the polypeptide chains selected in step (c) bind the first and second epitopes.
Optionally in (a) the heavy chains comprise CH1 domains.
Optional features described herein with reference to vertebrates and cells also apply mutatis mutandis to methods of the invention.
For example in any method of the invention, the epitopes are provided by first and second antigens that are different, so the product is multispecific (eg, bispecific where the product is bivalent).
In spleen, B cells are characterized as immature (T1 and T2) and mature (M) based on the levels of cell surface markers, IgM and IgD. T1 cells have high IgM and low IgD. T2 cells have medium levels of both them. M cells have low IgM but high IgD (
For example, in step (c) selection of the chains is from serum, blood, spleen tissue, lymph node tissue, or secondary lymphoid organ tissue. For example, the chains are B-cell secreted chains.
Optionally in any method of the invention the polypeptide chains comprise one or more heavy chain constant domains and in this sense, the chains can be regarded as heavy chains. In another embodiment, the chains are chains comprising no constant domains, eg, wherein the chain consists of a V-L-E polypeptide as described herein.
Step (d) can be performed by any standard genome manipulation technology, as will be readily apparent to the skilled person. For example, using ES cell technology with subsequent generation of progeny organism(s).
In an example, each somatically mutated variable region in step (b) is provided by an non-mu-type (eg, IgG-type) heavy chain that lacks a CH1 domain. This is useful for producing heavy chain-only (H2) antibodies, particularly when light chain expression is inactive. Thus, for example, step (b) comprises expressing the somatically mutated variable regions in the absence of light chain expression.
The invention further provides a method of producing in a non-human vertebrate (eg, a mouse or a rat) multivalent (eg, bivalent, eg, bispecific) polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes (eg, wherein the epitopes are different or the same), the method comprising
(a) immunising the vertebrate with a first predetermined antigen bearing the first epitope, obtaining isotype switching to expression from a non-mu (eg, gamma) constant region in at least some of the heavy chain loci of the vertebrate and expression of variable regions (eg, as provided by IgG antibody heavy chains) that have undergone somatic hypermutation; and
(b) selecting one or more polypeptide chains from said immunised vertebrate by selection for variable regions that bind said first epitope, wherein each selected chain comprises a somatically hypermutated variable region that specifically binds the epitope; and
wherein
(d) providing the nucleotide sequence of the epitope binding moiety (or a predetermined parent thereof that specifically binds the second epitope) in the non-mu constant region of heavy chain loci in the genome of the vertebrate (eg, done using ES cell technology), wherein the polypeptide chains selected in step(b) bind the first and second epitopes.
In an example, each somatically mutated variable region in step (a) is provided by a non-mu-type (eg, IgG-type) heavy chain that lacks a CH1 domain. Optionally, step (a) comprises expressing the somatically mutated variable regions in the absence of light chain expression.
Optionally in any method of the invention, the vertebrate is according to any configuration, aspect, embodiment or example of the invention herein.
Optionally a method of the invention further comprises isolating or synthesizing a nucleic acid comprising a nucleotide sequence encoding a polypeptide chain selected in the method; and optionally humanising the sequence (eg, replacing non-human antibody constant domains with one or more (or corresponding) human antibody constant domains).
The invention also provides a multivalent (eg, multispecific, eg, bispecific) polypeptide chain obtained by the method of the invention or a derivative thereof that specifically binds the first and second epitopes. Examples of derivatives (eg, conjugates or crystals or glycosylated forms) are disclosed at page 9, line 22 to page 10, line 4; page 10, line 25 to page 11, line 6; and page 47, line 26 to page 50, line 23 of WO2007024715. These examples are specifically incorporated herein as though specifically and explicitly disclosed herein as possible derivatives with respect to the present invention and for possible inclusion in one or more claims herein, with the exception that an antibody, chain or polypeptide of the invention is used instead of an antibody, chain or polypeptide disclosed in these prior art disclosures.
Products
The invention provides multivalent products as follows:
A multivalent (eg, multispecific, eg, bispecific) polypeptide chain having or consisting of (in N- to C-terminal direction) the structure V-X-L-E-L-C, where
(i) V is an antibody variable domain that specifically binds a first epitope,
(ii) X is absent, an antibody hinge region or an antibody constant region comprising a constant domain (eg, gamma-type CH1, a human gamma constant domain, an antibody hinge region-CH domain; or a CH domain-antibody hinge region),
(iii) Each L is an optional linker,
(iv) E is an epitope binding moiety that specifically binds a second epitope, and
(v) C is absent or an antibody constant region comprising one or more (eg, 1, 2, 3 or 4) constant domains (eg, C is a human gamma Fc or gamma CH1-hinge-CH2-CH3),
wherein V is a rearranged antibody variable domain derived from the rearrangement of variable region gene segments in vivo in a non-human vertebrate with somatic hypermutation of the resulting variable region gene in a nucleotide sequence also encoding for the epitope binding moiety (or a parent thereof sharing the same epitope binding specificity); and
wherein the rearranged antibody variable domain comprises endogenous AID-pattern somatic hypermutations.
This means that the B-cell has carried out somatic hypermutation and selection of the rearranged variable domain in the context of the predetermined epitope binding domain. This is superior to current methods in which binding moieties are separately selected (eg, in separate phage display experiments in vitro) and then combined to form a bispecific polypeptide. In this prior art case, consideration is given to bispecificity, but not to construction for well-behaved polypeptides that have good biophysical characteristics and expression compatible with in vivo animal systems.
Thus, where a variable domain was produced in a mouse, each rearranged variable domain will comprise somatic hypermutations caused by mouse AID. Mutation hotspots for AID are known (see Mauel, R. W. & Gearhart, P. J.; “AID and somatic hypermutation” Advances in Immunology 2010. 105: 159-191”), and thus the skilled person will readily be able to identify one or more mutations that are at such hotspots for the endogenous AID (eg, by comparing against the predicted amino acid sequence that would be produced in the absence of any mutation).
In an example, V is a rearranged antibody variable domain derived from the rearrangement of human VH with a DH and JH. In another example, V is a VL domain derived from the rearrangement of human VL and a JL (eg, Vκ and a Jκ or a Vλ and a Jλ).
In one embodiment, in addition to E, a plurality (eg, 1, 2 or 3) further epitope binding moieties is provided between V and C, each further moiety having binding specificity for a respective epitope. In an example, the epitope binding moieties have different epitope specificities. In another example, they share specificity for the second epitope. For example, the chain has or consists of the structure (in N- to C-terminal direction) the structure V-X-L-E-L-E″L-C, where E″ is a further epitope binding domain, eg, having binding specificity for a third epitope that is different from the first and second epitopes.
The antibody hinge can be from any species, eg, a mouse hinge, a rat hinge, a human hinge or a Camelid hinge.
Examples of polypeptides according to the invention are the following N- to C-terminally:
-
- (i) V-dAb-human Fc (optionally as a dimer), wherein V is a VH, VHH or VL and the dAb is a VH, VHH or VL;
- (ii) V-dAb (optionally as a dimer), wherein V is a VH, VHH or VL and the dAb is a VH, VHH or VL;
- (iii) V-scFv-human Fc (optionally as a dimer), wherein V is a VH, VHH or VL
- (iv) V-scFv (optionally as a dimer), wherein V is a VH, VHH or VL and the dAb is a VH, VHH or VL;
- (v) mAb-dAb (ie, a mAb covalently attached to or comprising one or more dAbs, eg in the heavy chains of the mAb), wherein the heavy chain variable domains of the mAb are V domains as recited, wherein V represents a VH, VHH or VL;
- (vi) Fab-dAb (ie, a Fab covalently attached to or comprising one or more dAbs, eg in the heavy chains of the Fab), wherein the heavy chain variable domain of the Fab is V as recited, wherein V represents a VH, VHH or VL;
- (vii) Fab2-dAb (ie, a Fab2 covalently attached to or comprising one or more dAbs, eg in the heavy chains of the Fab2), wherein the heavy chain variable domains of the Fabs are V domains as recited, wherein V represents a VH, VHH or VL.
VHH denotes a Camelid heavy chain single variable domain or a camelised human VH single variable domain, as is known in the art.
There is provided a method of producing a polypeptide chain of the invention, the method comprising immunising a non-human vertebrate (eg, a mouse or a rat) with the first epitope and causing somatic hypermutation of a variable region gene in a nucleotide sequence also encoding for the epitope binding moiety (E), the variable region gene encoding V; and isolating said polypeptide chain comprising V and E. The method optionally further comprises producing a derivative polypeptide chain (eg, a humanised version thereof) which retains specificity for the first and second epitopes.
According to an embodiment of the method of polypeptide chain, the epitope binding moiety lacks endogenous AID-pattern somatic hypermutations. Thus, when a mouse according to the invention is used to generate the chain, the epitope binding moiety of the chain does not comprise endogenous (mouse) AID mutations and neither does its nucleotide sequence. Advantageously, this may result from positioning of the moiety nucleotide sequence downstream of S-mu or the mu constant region in a heavy chain locus of the invention. Thus, the desired characteristics (eg, binding characteristics) of the epitope binding moiety are not down-graded by AID mutations.
In an alternative, the epitope binding moiety comprises endogenous AID-pattern somatic hypermutations. This may be useful for providing in vivo-selected variants of the predetermined epitope binding domain, which variants can be combined with the repertoire of N-terminal variable domains and which can be expressed by in vivo systems in this format. Variants can be selected (in this multivalent product format) for one or more desirable characteristics, such as an improvement in epitope binding affinity versus the parent epitope binding moiety.
There is further provided a dimer of polypeptides according to the invention, wherein the dimer lacks antibody light chains. Thus, for example, when the polypeptides are heavy chains lacking CH1 domains, the dimer may provide a multivalent (eg, multispecific) heavy chain-only (H2) antibody that is produced, matured and selected in vivo in this format.
There is further provided a polypeptide, dimer or method according to the invention, wherein the polypeptide has (in N- to C-terminal direction) the structure V-N-E; V-CH1-M-CH2-CH3-L-E; or V-M-CH2-CH3-L-E, wherein N is L together with an optional antibody hinge region; and M is an optional antibody hinge region. Optionally the constant domains are human gamma constant domains. Thus, M can be L alone; hinge-L; L-hinge; or hinge.
There is further provided a polypeptide, dimer or method according to the invention, wherein V is peptide bonded to a second antibody variable domain (V2) to form a binding site comprising first and second variable domains that specifically binds the first epitope; optionally wherein V and V2 are provided as an scFv. For example, V is a VH (eg, human VH) selected as a multivalent polypeptide chain from a heavy chain locus of the invention, wherein the VH pairs with a VL to form a binding site for the first epitope (eg, wherein the VL is a human VL encoded by a light chain locus of the vertebrate or cell). Following selection of the heavy chain or a nucleotide encoding this, using recombinant DNA technology or protein engineering the VL or a nucleotide sequence encoding this can be combined with the VL (or VL nucleotide sequence) to produce a heavy chain comprising an N-terminal scFv and also an epitope binding moiety. The scFv provides a binding site for the first epitope and the epitope binding moiety provides a binding site for the second epitope.
In one embodiment of the polypeptide, dimer or method of the invention, the polypeptide lacks a CH1 domain.
In one embodiment of the polypeptide, dimer or method of the invention, the polypeptide comprises a CH1 domain and the polypeptide is present in first and second copies in antibody, the first polypeptide being associated with a first antibody light chain, and the second copy being associated with a second antibody light chain. Optionally, the light chains are identical. Thus, the product can have a 4-chain mAb-like structure.
The invention provides an antibody comprising the dimer, polypeptide chain or a humanised version thereof as recited herein.
The invention provides a bivalent (eg, bispecific) antibody comprising or consisting of a dimer of a heavy chain, wherein each heavy chain is a polypeptide as recited herein and has in N- to C-terminal direction) the structure
V-CH1-M-CH2-CH3-L-E,
V-M-CH2-CH3-L-E,
V-L-E-L-CH1-M-CH2-CH3,
V-L-E-L-M-CH2-CH3,
V-CH1-N-E,
V-L-E-N-CH1, or
V-N-E-L-CH1,
wherein N is L together with an optional antibody hinge region; M is an optional antibody hinge region (thus, M can be L alone; hinge-L; L-hinge; or hinge);
optionally wherein the constant domains are human constant domains (eg, human gamma constant domains).
Optionally the human and constant regions of the antibody or polypeptide of the invention are human.
Somatically Hypermutated VH/VL Pairs with Fixed Epitope Binding Domain(s)
Optionally, the antibody comprises two copies of a light chain, each heavy chain being associated with a respective light chain, wherein V in each heavy chain forms an antigen binding site with the variable domain of its respective light chain and the variable domain of each light chain comprises endogenous AID-pattern somatic hypermutations. Thus, the variable domain of each heavy chain can be selected as a V pair (eg, VH/VL) with a V from a light chain partner, the V pair being affinity matured and selected in vivo following immunisation with target antigen. For example, the antibody is a mAb-dAb (ie, a mAb structure comprising one or more dAbs on the heavy chains, eg at the C-termini thereof).
Optionally the human and constant regions of the antibody of the invention are human.
The invention provides a multivalent (eg, multispecific, eg, bispecific) antibody comprising heavy chains associated with light chains, wherein
Each heavy chain is a polypeptide chain as recited above having or consisting of the structure V-X-L-E-L-C, wherein E is an antibody variable domain;
Each light chain is a polypeptide chain having or consisting of (in N- to C-terminal direction) the structure V′-L′-E′-L′-C′, where
(i) V′ is an antibody variable domain,
(ii) Each L′ is an optional linker,
(iv) E′ is an epitope binding moiety, and
(v) C′ is absent or an antibody constant region comprising a constant domain (eg, one, two, three or four constant domains, eg, C′ is a human CL);
wherein
V′ is a rearranged antibody variable domain derived from the rearrangement of variable region gene segments in vivo in a non-human vertebrate with somatic hypermutation of the resulting variable region gene in a nucleotide sequence also encoding for E′ (or a parent thereof that specifically binds the epitope that is specifically bound by E′); and
V′ comprises endogenous AID-pattern somatic hypermutations;
V and V′ form a first binding site that specifically binds a first epitope; and
Optionally E and E′ form a second binding site that specifically binds a second epitope when E′ is an antibody variable domain (eg, E is a VH and E′ is a VL).
In an example, V′ is derived from the rearrangement of human VH with a DH and JH. In another example, V′ is a VL domain derived from the rearrangement of human VL and a JL (eg, Vκ and a Jκ or a Vλ and a Jλ).
The invention also provides an antigen-binding polypeptide comprising a protein scaffold which is linked to one or more epitope binding moieties wherein the antigen-binding polypeptide comprises at least two epitope binding sites at least one of which is provided by an epitope binding moiety and at least one of which is provided by a first antibody variable domain paired with a second antibody variable domain, wherein each variable domain is a rearranged antibody variable domain derived from the rearrangement of variable region gene segments in vivo in a non-human vertebrate with somatic hypermutation of the resulting variable region gene in a nucleotide sequence also encoding for one or more of the epitope binding moiety(ies) (or a respective parent thereof having the same epitope binding specificity); and wherein the rearranged antibody variable domains comprise endogenous AID-pattern somatic hypermutations.
Thus, where the variable domain was produced in a mouse, each rearranged variable domain will comprise somatic hypermutations caused by mouse AID. Mutation hotspots for AID are known (see Mauel, R. W. & Gearhart, P. J.; “AID and somatic hypermutation” Advances in Immunology 2010. 105: 159-191”), and thus the skilled person will readily be able to identify one or more mutations that are at such hotspots for the endogenous AID (eg, by comparing against the predicted amino acid sequence that would be produced in the absence of any mutation).
The invention also provides an antigen-binding polypeptide that is a copy of the antigen binding polypeptide comprising the protein scaffold. Thus, the variable domain(s) of the copies need not themselves have been produced in a vertebrate, but could for example be expressed in vitro from a vector comprising nucleotide sequence encoding the polypeptide.
In an example, each variable domain is a rearranged antibody variable domain derived from the rearrangement of human VH with a DH and JH. In another example, each variable domain is a VL domain derived from the rearrangement of human VL and a JL (eg, Vκ and a Jκ or a Vλ and a Jλ).
In an example, the protein scaffold is an antibody scaffold, ie, a scaffold comprising a heavy chain (or dimer thereof, eg, H2 antibody); a heavy chain and a paired light chain (or a dimer thereof, eg, a H2L2 antibody).
In an example, the protein scaffold is an Ig scaffold, eg, an IgG scaffold. For example, the IgG scaffold is selected from IgG1, IgG2, IgG3 and IgG4. For example, an epitope binding domain is attached to the Ig scaffold at the N-terminus of the light chain thereof. For example, an epitope binding domain is attached to the Ig scaffold at the N-terminus of the heavy chain. For example, an epitope binding domain is attached to the Ig scaffold at the C-terminus of the light chain. For example, an epitope binding domain is attached to the Ig scaffold at the C-terminus of the heavy chain.
In an example, the protein scaffold comprises or consists of a monovalent or bivalent antibody (eg, bivalent monospecific antibody).
In an example, at least one of said epitope binding moieties linked to the protein scaffold by a peptide linker which comprises at least 10 amino acids (eg, between 10 and 50 amino acids). In one example, a (or each) epitope binding moiety (eg, domain) is linked to the protein scaffold by a linker selected from those set out in SEQ ID NO: 53 to 60, SEQ ID NO:62-72, SEQ ID NO:74, SEQ ID NO:76-78 and SEQ ID NO:112-114 and combinations or multiples of such linkers (wherein the sequences are those disclosed in WO2010136483, the disclosure of which is incorporated herein by reference for use with the present invention and for possible inclusion in claims herein). In an example, the linker is selected from (PAS)n(GS)m, (GGGGS)p(GS)m, (TVAAPS)p(GS)m, (GS)m(TVAAPSGS)p, (PAVPPP)n(GS)m, (TVSDVP)n(GS)m, and (TGLDSP)n(GS)m, wherein n=an integer from 1-10, and m=0 or a integer from 1-4, and p=an integer from 2-10.
In an example, the linker is selected from (PAS)n(GS)m wherein n=an integer from 1-10, and m=0 or an integer from 1-4.
In an example, the linker is selected from (TVAAPS)p(GS)m and (GS)m wherein m=0 or an integer from 1-10, and p=or an integer from 2-10.
The invention provides a polynucleotide sequence encoding a heavy chain of an antigen binding polypeptide recited above. The invention provides a polynucleotide sequence encoding a light chain of an antigen binding polypeptide recited above.
The invention also relates to multispecific polypeptides that are useful for recruiting immune effector cells in patients. Thus, the invention provides a multispecific antigen binding polypeptide, dimer or antibody according to the description above, which is capable of recruiting the activity of a human immune effector cell by specifically binding to an effector antigen (eg, human CD3) located on a human immune effector cell, a first of the epitope binding sites of the polypeptide, dimer or antibody being capable of specifically binding to said effector antigen, and a second of the epitope binding sites of the polypeptide, dimer or antibody being capable of specifically binding to a target antigen (eg, human EpCAM or human CD19) other than the effector antigen; optionally wherein said target antigen is located on a target cell other than said human immune effector cell.
For example, the effector antigen is selected from the group consisting of CD3, CD16, CD32, CD64 and CD89.
For example, the target antigen is selected from the group consisting of EGFR; VEGF; IGF-1R; Her2; c-Met (aka HGF); HER3; CEA; CD33; CD79a; CD19; PSA; EpCAM; CD66; CD30; HAS; PSMA; GD2; ANG2; IL-4; IL-13; VEGFR2; and VEGFR3.
In an embodiment, there is provided the vertebrate, cell polypeptide, dimer or antibody of the invention, wherein the second epitope is provided by human immune effector cell antigen (eg, human CD3).
In an embodiment, there is provided the vertebrate, cell polypeptide, dimer or antibody of the invention, wherein the first epitope is provided by a target antigen (eg, human EpCAM or human CD19) other than the effector antigen; optionally wherein said target antigen is an antigen of a target cell other than said human immune effector cell.
The invention also provides light chains and light chain dimers. To this end, the invention provides a multivalent (eg, multispecific) light chain having (in N- to C-terminal direction) the structure V-X-L-E-L-C, where
(i) V is an antibody variable domain (eg, a VL) that specifically binds a first epitope,
(ii) X is absent, or an antibody constant region comprising a constant domain (eg, a CL),
(iii) Each L is an optional linker,
(iv) E is an epitope binding moiety that specifically binds a second epitope, and
(v) C is absent or an antibody constant region comprising a constant domain (eg, C is a CL),
wherein V is a rearranged antibody variable domain derived from the rearrangement of variable region gene segments in vivo in a non-human vertebrate with somatic hypermutation of the resulting variable region gene in a nucleotide sequence also encoding for the epitope binding moiety; and
wherein the rearranged antibody variable domain comprises endogenous AID-pattern somatic hypermutations.
The invention also provides a dimer of such a light chain.
A corresponding vertebrate is provided which comprises a light chain locus for producing such a construct. To this end, the invention provides
A non-human vertebrate (eg, a mouse or a rat), wherein the vertebrate comprises lymphocytic cells, each cell genome comprising
(i) an antibody light chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region, a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, and a CL gene segment, wherein the vertebrate expresses multivalent light chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the light chain locus, an optional linker, an epitope binding moiety and a CL domain, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes (which can be any epitopes as defined herein); or
(ii) an antibody light chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region, a CL gene segment, a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, wherein the vertebrate expresses multivalent light chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the light chain locus, a CL domain, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes (which can be any epitopes as defined herein).
A non-human vertebrate cell (eg, a mouse cell or a rat cell), the cell genome comprising
(i) an antibody light chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region, a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, and a CL gene segment, wherein the cell expresses multivalent light chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the light chain locus, an optional linker, an epitope binding moiety and a CL domain, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes (which can be any epitopes as defined herein); or
(ii) an antibody light chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region, a CL gene segment, a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, wherein the cell expresses multivalent light chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the light chain locus, a CL domain, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes (which can be any epitopes as defined herein).
Examples of Epitope Binding Domains
In an example, the or each epitope binding moiety or domain is selected from the group consisting of an antibody variable domain (eg, a VL or a VH, an antibody single variable domain (domain antibody or dAb), a camelid VHH antibody single variable domain, a shark immunoglobulin single variable domain (NARV), a Nanobody™ or a camelised VH single variable domain); a T-cell receptor binding domain; an immunoglobulin superfamily domain; an agnathan variable lymphocyte receptor (J Immunol; 2010 Aug. 1; 185(3):1367-74; “Alternative adaptive immunity in jawless vertebrates; Herrin B R & Cooper M D.); a fibronectin domain (eg, an Adnectin™); an antibody constant domain (eg, a CH3 domain, eg, a CH2 and/or CH3 of an Fcab™) wherein the constant domain is not a functional CH1 domain (defined as a CH1 domain that can associate with a light chain); an scFv; an (scFv)2; an sc-diabody; an scFab; a centyrin and an epitope binding domain derived from a scaffold selected from CTLA-4 (Evibody™); a lipocalin domain; Protein A such as Z-domain of Protein A (eg, an Affibody™ or SpA); an A-domain (eg, an Avimer™ or Maxibody™); a heat shock protein (such as and epitope binding domain derived from GroEI and GroES); a transferrin domain (eg, a trans-body); ankyrin repeat protein (eg, a DARPin™); peptide aptamer; C-type lectin domain (eg, Tetranectin™); human γ-crystallin or human ubiquitin (an affilin); a PDZ domain; scorpion toxin; and a kunitz type domain of a human protease inhibitor.
Further sources of epitope binding moieties are variable domains and VH/VL pairs of antibodies disclosed in WO2007024715 at page 40, line 23 to page 43, line 23. This specific disclosure is incorporated herein by reference as though explicitly written herein to provide basis for epitope binding moieties for use in the present invention and for possible inclusion in claims herein.
A “domain” is a folded protein structure which has tertiary structure independent of the rest of the protein. Generally, domains are responsible for discrete functional properties of proteins and in many cases may be added, removed or transferred to other proteins without loss of function of the remainder of the protein and/or of the domain. A “single antibody variable domain” is a folded polypeptide domain comprising sequences characteristic of antibody variable domains. It therefore includes complete antibody variable domains and modified variable domains, for example, in which one or more loops have been replaced by sequences which are not characteristic of antibody variable domains, or antibody variable domains which have been truncated or comprise N- or C-terminal extensions, as well as folded fragments of variable domains which retain at least the binding activity and specificity of the full-length domain.
The phrase “immunoglobulin single variable domain” refers to an antibody variable domain (VH, VHH, VL) that specifically binds an antigen or epitope independently of a different V region or domain. An immunoglobulin single variable domain can be present in a format (e.g., homo- or hetero-multimer) with other, different variable regions or variable domains where the other regions or domains are not required for antigen binding by the single immunoglobulin variable domain (i.e., where the immunoglobulin single variable domain binds antigen independently of the additional variable domains). A “domain antibody” or “dAb” is the same as an “immunoglobulin single variable domain” which is capable of binding to an antigen as the term is used herein. An immunoglobulin single variable domain may be a human antibody variable domain, but also includes single antibody variable domains from other species such as rodent (for example, as disclosed in WO 00/29004), nurse shark and Camelid VHH immunoglobulin single variable domains. Camelid VHH sre immunoglobulin single variable domain polypeptides that are derived from species including camel, llama, alpaca, dromedary, and guanaco, which produce heavy chain antibodies naturally devoid of light chains. Such VHH domains may be humanised according to standard techniques available in the art, and such domains are still considered to be “domain antibodies” according to the invention. As used herein “VH includes camelid VHH domains. NARV are another type of immunoglobulin single variable domain which were identified in cartilaginous fish including the nurse shark. These domains are also known as Novel Antigen Receptor variable region (commonly abbreviated to V(NAR) or NARV). For further details see Mol. Immunol. 44, 656-665 (2006) and US20050043519A.
CTLA-4 (Cytotoxic T Lymphocyte-associated Antigen 4) is a CD28-family receptor expressed on mainly CD4+ T-cells. Its extracellular domain has a variable domain-like Ig fold. Loops corresponding to CDRs of antibodies can be substituted with heterologous sequence to confer different binding properties. CTLA-4 molecules engineered to have different binding specificities are also known as Evibodies. For further details see Journal of Immunological Methods 248 (1-2), 31-45 (2001)
Lipocalins are a family of extracellular proteins which transport small hydrophobic molecules such as steroids, bilins, retinoids and lipids. They have a rigid β-sheet secondary structure with a number of loops at the open end of the conical structure which can be engineered to bind to different target antigens. Anticalins are between 160-180 amino acids in size, and are derived from lipocalins. For further details see Biochim Biophys Acta 1482: 337-350 (2000), U.S. Pat. No. 7,250,297B1 and US20070224633 An affibody is a scaffold derived from Protein A of Staphylococcus aureus which can be engineered to bind to antigen. The domain consists of a three-helical bundle of approximately 58 amino acids. Libraries have been generated by randomisation of surface residues. For further details see Protein Eng. Des. Sel. 17, 455-462 (2004) and EP1641818A1.
Avimers™ are multidomain proteins derived from the A-domain scaffold family. The native domains of approximately 35 amino acids adopt a defined disulphide bonded structure. Diversity is generated by shuffling of the natural variation exhibited by the family of A-domains. For further details see Nature Biotechnology 23(12), 1556-1561 (2005) and Expert Opinion on Investigational Drugs 16(6), 909-917 (June 2007).
A transferrin is a monomeric serum transport glycoprotein. Transferrins can be engineered to bind different target antigens by insertion of peptide sequences in a permissive surface loop. Examples of engineered transferrin scaffolds include the Trans-body. For further details see J. Biol. Chem 274, 24066-24073 (1999).
Designed Ankyrin Repeat Proteins (DARPins™) are derived from ankyrin which is a family of proteins that mediate attachment of integral membrane proteins to the cytoskeleton. A single ankyrin repeat is a 33 residue motif consisting of two α-helices and a β-turn. They can be engineered to bind different target antigens by randomising residues in the first α-helix and a β-turn of each repeat. Their binding interface can be increased by increasing the number of modules (a method of affinity maturation). For further details see J. Mol. Biol. 332, 489-503 (2003), PNAS 100(4), 1700-1705 (2003) and J. Mol. Biol. 369, 1015-1028 (2007) and US20040132028A1.
Fibronectin is a scaffold which can be engineered to bind to antigen. Adnectins™ consist of a backbone of the natural amino acid sequence of the 10th domain of the 15 repeating units of human fibronectin type III (FN3). Three loops at one end of the β-sandwich can be engineered to enable an Adnectin to specifically recognize a therapeutic target of interest. For further details see Protein Eng. Des. Sel. 18, 435-444 (2005), US20080139791, WO2005056764 and U.S. Pat. No. 6,818,418B1.
Peptide aptamers are combinatorial recognition molecules that consist of a constant scaffold protein, typically thioredoxin (TrxA) which contains a constrained variable peptide loop inserted at the active site. For further details see Expert Opin. Biol. Ther. 5, 783-797 (2005).
Microbodies are derived from naturally occurring microproteins of 25-50 amino acids in length which contain 3-4 cysteine bridges—examples of microproteins include KalataBI and conotoxin and knottins. The microproteins have a loop which can be engineered to include upto 25 amino acids without affecting the overall fold of the microprotein. For further details of engineered knottin domains, see WO2008098796.
Other epitope binding moieties and domains include proteins which have been used as a scaffold to engineer different target antigen binding properties include human γ-crystallin and human ubiquitin (affilins), kunitz type domains of human protease inhibitors, PDZ-domains of the Ras-binding protein AF-6, scorpion toxins (charybdotoxin), C-type lectin domain (tetranectins) are reviewed in Chapter 7—Non-Antibody Scaffolds from Handbook of Therapeutic Antibodies (2007, edited by Stefan Dubel) and Protein Science 15:14-27 (2006). Epitope binding moieties and domains of the present invention could be derived from any of these alternative protein domains.
In one embodiment of the invention a or each Epitope binding moiety, domain or antigen-binding site binds to antigen or second epitope with a KD of 1 mM, for example a KD of 10 nM, 1 nM, 500 pM, 200 pM, 100 pM or 10 pM or less (ie, better affinity) to each antigen as measured by Biacore™ or Proteon™, such as the Biacore™ method as described in method 4 or 5 of WO2010136485 or as described elsewhere herein.
In one embodiment of the invention a or each variable domain, variable domain pair or antigen-binding site at the N-terminus of a polypeptide, chain or antibody of the invention binds to antigen or first epitope with a KD of 1 mM, for example a KD of 10 nM, 1 nM, 500 pM, 200 pM, 100 pM or 10 pM or less (ie, better affinity) to each antigen as measured by Biacore™ or Proteon™, such as the Biacore™ method as described in method 4 or 5 of WO2010136485 or as described elsewhere herein.
In an example of the vertebrate, cell polypeptide, dimer or antibody of the present invention, the or each N-terminal variable domain or 5′-terminal variable region is a human variable domain or region.
In an example of the vertebrate, cell polypeptide, dimer or antibody of the invention, each constant region or domain is an endogenous non-human vertebrate constant region or domain.
The invention provides a non-human vertebrate (eg, a mouse or a rat), wherein the vertebrate comprises lymphocytic cells, each cell genome comprising an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region and a mu constant region comprising a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, wherein the vertebrate expresses multivalent polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the heavy chain locus, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes. This is useful for producing mu-type multivalent (eg, multispecific, eg, bispecific) heavy chains and antibodies.
The invention provides a non-human vertebrate cell (eg, a mouse cell or a rat cell), wherein the cell genome comprises an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region and a mu constant region comprising a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, wherein the cell expresses multivalent polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the heavy chain locus, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes. This is useful for producing mu-type multivalent (eg, multispecific, eg, bispecific) heavy chains and antibodies.
The invention provides a non-human (eg, rat or mouse) vertebrate or cell that expresses multivalent, multispecific heavy chains (or dimers thereof) comprising the structure V-L-E or V-L-E-L (eg, V-L-E-Fc or V-L-E-L-Fc), where V is an N-terminal antibody variable domain, L is an optional linker and E is an epitope binding moiety, wherein V and E specifically bind respective first and second antigens, wherein the antigens are different. Optionally, V is a human variable domain.
Heavy Chain-Only Antibodies & Loci
As explained above and as exemplified below, the invention relates also to the improved production of heavy chain antibodies (H2 antibodies) in vivo.
Thus, the invention provides a non-human vertebrate (eg, a mouse or a rat), wherein
(a) the vertebrate expresses IgM antibodies comprising heavy and light chains encoded by antibody heavy and light chain loci respectively;
(b) the vertebrate is capable of expressing non-mu (eg, IgG) antibodies, each non-mu antibody heavy chain lacking a functional CH1 domain; and
(c) the IgM antibodies are expressed by lymphocytic cells (eg, immature B-cells), each cell comprising a functional light chain locus for expressing light chains of IgM antibodies expressed by the cell; and
wherein
(d) the non-mu antibodies are expressed by lymphocytic cells (eg, mature B-cells, plasmablasts or plasma cells), each cell lacking a functional light chain locus wherein non-mu antibodies are expressed by the cell substantially in the absence of light chain expression.
Optionally in (a) each heavy chain comprises a CH1 domain.
In an example, in (b) expression of the non-mu antibodies is following immunisation with a predetermined antigen and isotype switching.
The invention also provides a non-human vertebrate (eg, a mouse or a rat), eg, a vertebrate according to the embodiment immediately above, wherein the vertebrate comprises lymphocytic cells whose genomes comprise
(i) an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region, a first switch (eg, a S-mu, eg, an endogenous S-mu), a mu constant region (eg, comprising a CH1 gene segment), a second switch (eg, a S-gamma, eg, an endogenous S-gamma) and a non-mu (eg, gamma) constant region lacking a CH1 gene segment;
(ii) a functional antibody light chain locus for expressing light chains (following V.I rearrangement);
wherein the cells can express IgM antibodies comprising IgM-type heavy chains and light chains, (optionally each heavy chain comprising a CH1 domain);
wherein the heavy chain locus of each cell is capable of undergoing isotype switching to produce non-mu (eg, IgG) antibodies comprising one or more non-mu-type (eg, IgG-type) heavy chains in the absence of light chains, each heavy chain lacking a CH1 domain; and
(iii) means for turning off light chain expression, wherein functional light chains are not expressed after isotype switching to said non-mu-type antibodies.
Similarly, the invention relates to cells. Thus, there is provided a non-human vertebrate cell (eg, a mouse cell or a rat cell, eg, a lymphocytic cell or other cell defined herein), wherein the cell genome comprises
(i) a functional antibody light chain locus for expressing light chains;
(ii) an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region, a first switch (eg, a S-mu, eg, an endogenous S-mu), a mu constant region (eg, comprising a CH1 gene segment), a second switch (eg, a S-gamma, eg, an endogenous S-gamma) and a non-mu (eg, gamma) constant region lacking a CH1 gene segment for expressing IgM antibodies comprising IgM-type heavy chains and light chains, (optionally each heavy chain comprising a CH1 domain); and for IgM to non-mu (eg, IgG) isotype switching to produce non-mu (eg, IgG) antibodies comprising one or more non-mu-type heavy chains in the absence of light chains, each heavy chain lacking a CH1 domain; and
(iii) means for turning off light chain expression, wherein functional light chains are not expressed after isotype switching to said non-mu-type antibodies.
In an example, of the vertebrate or cell, the means for turning off light chain expression comprises a nucleotide sequence (eg, a light chain variable region, J region and/or a CL region of the light chain locus) that is essential for functional light chain expression from said light chain locus, wherein the nucleotide sequence is functional in immature B-cells expressing IgM, but the nucleotide sequence is absent or substantially non-functional in mature B-cells expressing said non-mu-type antibodies.
For example, all or substantially all of each light chain locus is deleted in the vertebrate. For example, the kappa (or kappa and lambda) light chain loci are rendered non-functional by deleting the light chain constant gene segments and/or the J region of each locus. Deletion can be performed using stage-specific recombinase, for example, as described in the examples below. For example, the kappa (or kappa and lambda) light chain loci are rendered non-functional by deleting the light chain variable region (rearranged or unrearranged V-J) gene segments. In another example, the kappa (or kappa and lambda) light chain loci are rendered non-functional by insertion of an interfering sequence such as a neomycin resistance nucleotide sequence into the or each said light chain locus or by recombinase or transposase-mediated inversion of light chain loci gene segments (eg, constant region and/or J region segments). Inversion can inactivate loci, as discussed further in the Kymab Limited PCT application mentioned herein.
In one example, the nucleotide sequence is the light chain locus or a portion thereof, the sequence being flanked by first and second site-specific recombination elements (SSRE) and wherein the genome comprises one or more gene(s) that encodes a corresponding site-specific recombinase(s), wherein the gene is inactive in immature B-cells expressing IgM, but active to cut at the first and second SSREs and delete the light chain locus or portion from the genome or inactivate the locus in mature B-cells expressing said IgG-type antibodies.
Required genetic manipulations can be made in an ES cell, so that conditional light chain inactivation can be effected in subsequent differentiation states of progeny B-cells and corresponding vertebrates as exemplified below.
In an embodiment, kappa chain expression is turned off using this means. In an embodiment, lambda chain expression is turned off using this means. In an embodiment, kappa and lambda chain expression is turned off using this means. Where a mouse system is used, lambda chain expression is normally low (around 5%), so it may not be necessary to turn off lambda chain expression as long as kappa chain expression is turned off when isotype-switched chains are being expressed.
In an embodiment of the vertebrate or cell the means for turning off light chain expression comprises a nucleotide sequence comprising a regulatory element (eg, a promoter) for driving light chain expression from said light chain locus in immature B-cells expressing IgM, and wherein the regulatory element is substantially inactive or absent in mature B-cells expressing said non-mu-type antibodies.
In an embodiment of the vertebrate or cell the nucleotide sequence or regulatory element is flanked by (eg, 5′ and 3′ immediately upstream and downstream) first and second combination elements (eg, site-specific recombination elements or transposase elements, such as piggyBac LTRs) and wherein the genome comprises a gene(s) that encodes a corresponding recombinase(s) or transposase(s), wherein the gene is inactive in immature B-cells expressing IgM, but active to cut at the first and second recombination elements and inactivate the nucleotide sequence or regulatory element in mature B-cells expressing said non-mu-type antibodies. The cutting can lead to deletion, translocation and/or inversion of the nucleotide sequence or regulatory element to inactivate it.
Examples of site-specific recombination elements and recombinases are frt/flp, dre/rox and cre/lox or combinations of these. The first and second recombination elements can be different.
In an embodiment of the vertebrate or cell the regulatory element is induced in immature B-cells expressing IgM and/or repressed in mature B-cells expressing said non-mu-type antibodies.
In an embodiment of the vertebrate or cell the means for turning off light chain expression is another locus in the genome for expressing a polypeptide chain comprising a rearranged light chain variable domain, eg, a predetermined VL of known epitope binding specificity. This uses light chain allelic exclusion to switch off light chain expression. Similarly, in an alternative example, said another locus is a heavy chain locus as defined above, wherein following said isotype switching the heavy chain locus encodes an antibody chain comprising said rearranged light chain variable domain. Optionally, the antibody chain further comprises a second antibody variable domain; optionally wherein the light chain variable domain and said second antibody variable domain specifically bind respective first and second epitopes that are different.
In an embodiment of the vertebrate or cell the rearranged light chain variable domain is derived from said unrearranged variable region of the heavy chain locus as defined above (eg, a VL-Fc is produced), wherein the unrearranged variable region of the heavy chain locus comprises one or more light chain V gene segments 5′ of one or more light chain J gene segments.
In an embodiment of the vertebrate or cell the antibody chain comprises (in 5′ to 3′ direction) a variable domain derived from said variable region of the heavy chain locus as defined above (eg, a VL-Fc is produced), an optional linker (eg, any linker defined herein) and said rearranged light chain variable domain.
In an embodiment of the vertebrate or cell the non-mu constant region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety (or a plurality of epitope binding domains, eg, two or three with optional linkers; eg, in place of a CH1 domain), wherein following isotype switching the vertebrate expresses multivalent (eg, bivalent, eg, bispecific) polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the heavy chain locus, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes (eg, wherein the epitopes are different or the same).
For example, the polypeptide chains have the structure V-L-E, where V is antibody variable domain derived from said rearranged variable region of the heavy chain locus, L is the optional linker and E is the epitope binding domain), such as defined above.
In an embodiment of the vertebrate, the non-mu constant region comprises one or more non-mu constant region gene segments (eg, CH2 and CH3 gene segments) 3′ of said epitope binding moiety, wherein following isotype switching the vertebrate expresses multivalent polypeptide chains each comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the heavy chain locus, an optional linker, an epitope binding moiety and said one or more non-mu constant region gene segments.
In an embodiment of the vertebrate or cell, a poly(A) site is 3′ (eg, immediately 3′) of the nucleotide sequence encoding the epitope binding moiety, wherein following isotype switching the vertebrate expresses multivalent polypeptide chains having or consisting of (in N- to C-terminal direction) the structure V-X-L-E, where V is an antibody variable domain derived from said variable region of the heavy chain locus, X is absent an antibody hinge region or a polypeptide encoded by the gamma constant region, L is the optional linker and E is the epitope binding moiety; optionally wherein the vertebrate expresses V-X-L-E or V-L-E dimers.
For example, the poly(A) site is provided together with a stop codon to terminate transcription.
For example, the non-mu constant region is a gamma-type CH2-CH3. Thus, in one example a bispecific chain is expressed having the structure V-CH2-CH3-L-E, and this may for example be produced as a dimer (in this case, the mutual affinity of the CH2-CH3 of the chains may aid dimerisation). Dimers provide multiple binding sites for each epitope specificity, which is useful for providing avidity of binding. The provision of gamma CH2 and CH3 in embodiments of the invention also is useful for providing Fc activity, such as half-life extension, recirculation, ADCC or cell killing activity, in vivo. ADCC and cell killing may be useful for treating indications in the cancer, inflammatory disease, autoimmune disease and infectious disease fields.
“Antibody-dependent cell-mediated cytotoxicity” or ADCC” refers to a form of cytotoxicity in which secreted Ig bound onto Fc receptors (FcRs) present on certain cytotoxic cells (e.g., Natural Killer (NK) cells, neutrophils, and macrophages) that enables these cytotoxic effector cells to bind specifically to an antigen-bearing target cell and subsequently kill the target cell with cytotoxins. Ligand specific high-affinity IgG antibodies directed to the surface of target cells stimulate the cytotoxic cells and are required for such killing. Lysis of the target cell is extracellular, requires direct cell-to-cell contact, and does not involve complement.
The ability of any particular antibody to mediate lysis of the target cell by ADCC can be assayed. To assess ADCC activity, an antibody of interest is added to target cells displaying the target ligand in combination with immune effector cells, which may be activated by the antigen antibody complexes resulting in cytolysis of the target cell. Cytolysis is generally detected by the release of label (e.g., radioactive substrates, fluorescent dyes or natural intracellular proteins) from the lysed cells. Useful effector cells for such assays include peripheral blood mononuclear cells (PBMC) and Natural Killer (NK) cells. Specific examples of in vitro ADCC assays are described in Wisecarver et al, 1985, 19:21 1; Bruggemann et al, 1987, J Exp Med 166: 1351; Wilkinson et al, 2001, J Immunol Methods 258: 183; Patel et al, 1995 J Immunol Methods 184:29 (each of which is incorporated by reference). Alternatively, or additionally, ADCC activity of the antibody of interest may be assessed in vivo, e.g., in an animal model, such as that disclosed in Clynes et al, 1998, PNAS USA 95:652, the contents of which are incorporated by reference in its entirety.
“Complement-directed cytotoxicity” or CDC refers to the form of cytotoxicity in which the complement cascade is activated by the complement component C1q binding to antibody Fc.
The term “Fc” as used herein refer to the protein comprising (in N- to C-terminal direction) an immunoglobulin CH2 and CH3 domain. The CH2 and CH3 domains can form at least a part of the constant region of an antibody or heavy chain.
In an example, a poly(A) site is 3′ of the nucleotide sequence encoding the one or more non-mu constant region gene segments, wherein following isotype switching the vertebrate expresses multivalent polypeptide chains having or consisting of (in N- to C-terminal direction) the structure V-X-L-E-L-C, where V is an antibody variable domain derived from said variable region of the heavy chain locus, X is absent an antibody hinge region or a polypeptide encoded by the non-mu constant region, L is the optional linker, E is the epitope binding moiety and C, is the one or more non-mu constant region gene segments (eg, gamma Fc); optionally wherein the vertebrate expresses V-X-L-E-L-C or V-L-E-L-C dimers.
In an example, the non-mu constant region is a gamma-type CH2, CH3 or CH2-CH3. Thus, in one example a bispecific chain is expressed having the structure V-CH2-L-E-CH3, and this may for example be produced as a dimer (in this case, the mutual affinity of the CH2 and CH3 between the chains may aid dimerisation). Dimers provide multiple binding sites for each antigen specificity, which is useful for providing avidity of binding.
In an example of the vertebrate or cell, the or each epitope binding moiety is any such moiety disclosed herein, for example it is selected from the group consisting of an antibody variable domain (eg, a VL or a VH, an antibody single variable domain (domain antibody or dAb), a camelid VHH antibody single variable domain, a shark immunoglobulin single variable domain (NARV), a Nanobody™ or a camelised VH single variable domain); a T-cell receptor binding domain; an immunoglobulin superfamily domain; an agnathan variable lymphocyte receptor; a fibronectin domain (eg, an Adnectin™); an antibody constant domain (eg, a CH3 domain, eg, a CH2 and/or CH3 of an Fcab™) wherein the constant domain is not a functional CH1 domain; an scFv; an (scFv)2; an sc-diabody; an scFab; a centyrin and an epitope binding domain derived from a scaffold selected from CTLA-4 (Evibody™); a lipocalin domain; Protein A such as Z-domain of Protein A (eg, an Affibody™ or SpA); an A-domain (eg, an Avimer™ or Maxibody™); a heat shock protein (such as and epitope binding domain derived from GroEI and GroES); a transferrin domain (eg, a trans-body); ankyrin repeat protein (eg, a DARPin™); peptide aptamer; C-type lectin domain (eg, Tetranectin™); human γ-crystallin or human ubiquitin (an affilin); a PDZ domain; scorpion toxin; and a kunitz type domain of a human protease inhibitor.
In an example of the vertebrate or cell, the vertebrate comprises lymphocytic cells that have undergone isotype switching to produce said non-mu-type (eg, IgG-type) antibodies; or the cell has undergone isotype switching to produce said non-mu-type (eg, IgG-type) antibodies.
In an example of the vertebrate or cell, the vertebrate has been immunised with a predetermined antigen, the vertebrate expressing non-mu-type (eg, IgG-type) antibodies lacking a CH1 domain and comprising a variable domain that specifically binds the predetermined antigen; or the cell is isolated from such a vertebrate.
In an example of the vertebrate or cell, the or each N-terminal variable domain or 5′-terminal variable region is a human variable domain or region. Human variable domains are variable domains that are encoded by RNA that is derived from a rearranged variable region DNA sequence, wherein the rearrangement is a rearrangement of a human V gene segment with a human J gene segment (and also optionally with a human D gene segment if the rearranged variable region is a VH region). Thus, for example, the RNA is derived from a rearranged variable region DNA sequence when it is encoded by such a DNA sequence, optionally with mutation naturally seen in vivo during antibody production.
In an example of the vertebrate or cell, the or each N-terminal variable domain or 5′-terminal variable region is a Camelid, camelised human; mouse; rat; rodent; rabbit; chicken; or bovine variable domain or region.
In an example of the polypeptide, chain, antibody, vertebrate or cell, each constant region or domain is an endogenous non-human vertebrate constant region or domain. In an example of the polypeptide, chain, antibody, vertebrate or cell, each non-mu constant region or domain is a human non-human vertebrate constant region or domain.
In an example of the vertebrate or cell, the lymphocytic cells comprise B-cells expressing said non-mu antibodies or bivalent polypeptide chains, wherein the non-mu antibodies or multivalent chains are specific for an antigen that is foreign to said non-human vertebrate (eg, a human antigen or an antigen of an infectious disease pathogen); or wherein said non-human vertebrate cell is such a B-cell.
The invention also provides B-cells, hybridomas and products as follows.
An immortalised B-cell or hybridoma produced from a B-cell recited above.
A non-mu-type (eg, IgG-type) antibody or multivalent chain isolated from a B-cell or hybridoma recited above; or a humanised version thereof wherein non-human constant domains have been replaced with human constant domains. For example, all of the non-human constant domains have been deleted and optionally replaced with one or more human constant domains (eg, corresponding to the deleted non-human domains). Thus, in one embodiment, a non-human (eg, mouse) Fc is replaced with a human Fc.
Methods
The invention provides improved methods for the in vivo production of isotype-switched non-mu H2 antibodies and heavy chains as follows.
Thus, the invention provides a method of producing polypeptide chains comprising somatically hypermutated variable regions in a non-human vertebrate (eg, a mouse or a rat), the method comprising
(a) expressing in the vertebrate IgM antibodies in immature B-cells, wherein the antibodies comprise heavy and light chains expressed from heavy and light chain loci respectively, (optionally the heavy chains comprising CH1 domains);
(b) immunising the vertebrate with a predetermined epitope and obtaining isotype switching in at least some of the heavy chain loci and expression of non-mu (eg, IgG) antibodies that have undergone somatic hypermutation, wherein the antibodies comprise heavy chains that lack a CH1 domain and comprise variable regions that specifically bind the antigen; and
(c) selecting one or more polypeptide chains from said immunised vertebrate by selection for variable regions that bind said epitope, wherein each selected chain comprises a somatically hypermutated variable region that specifically binds the epitope; and
the method further comprising expressing the non-mu antibodies in step (b) in the absence of light chain expression.
For example, in step (c) the chains are selected from serum, blood, spleen cells or tissue, lymph node cells or tissue or secondary lymphoid organ cells or tissue.
Optionally the polypeptide chains comprise one or more heavy chain constant domains and in this sense, the chains can be regarded as heavy chains. In another embodiment, the chains are chains comprising no constant domains, eg, wherein the chain is a V-L-E polypeptide as described herein.
The method optionally comprises isolating from the immunised vertebrate a B-cell that expresses a polypeptide chain comprising a somatically hypermutated variable region that binds the epitope; and optionally immortalising the cell or producing a hybridoma therefrom.
The method optionally comprises obtaining a nucleotide sequence that encodes a selected polypeptide chain comprising a somatically hypermutated variable region that binds the epitope, and introducing the nucleotide sequence into a expression vector for expression of the polypeptide chain or a humanised version thereof; optionally wherein vector is in a host cell (eg, an E. coli, yeast, Picchia, Saccharomyces, CHO or HEK293 cell).
In an embodiment of the method, the vertebrate is according to any aspect of the invention herein.
The invention provides a multispecific polypeptide chain obtained by the method or a derivative thereof that specifically binds the epitope.
Stage-Switchable Light Chain Locus
As explained herein and in the examples below, it is desirable to provide conditional, or stage-specific, light chain expression in the vertebrates and cells of the invention. This is useful, for example, when expressing non-mu heavy chains or antibodies that specifically bind a predetermined epitope or antigen.
Thus, the invention provides a non-human vertebrate (eg, a mouse or a rat), optionally according to any other aspect of the invention, whose genome comprises an antibody heavy chain locus and an antibody light chain locus,
(a) the light chain locus comprising (in 5′ to 3′ direction) a light chain variable region and a constant region (eg, a Cκ or Cλ) for expressing light chains in lymphocytic cells expressing IgM antibodies (eg, in immature B-cells); and
(b) means for turning off light chain expression in lymphocytic cells expressing non-mu (eg, IgG) antibodies.
For example, the light chain variable region comprises one or more human Vκ gene segments and one or more human Jκ gene segments; or one or more human Vλ gene segments and one or more human Jλ gene segments.
A non-human vertebrate cell (eg, a mouse cell or a rat cell) or hybridoma, optionally according to any other aspect of the invention, whose genome comprises an antibody heavy chain locus and an antibody light chain locus, the light chain locus comprising
(a) (in 5′ to 3′ direction) a light chain variable region and a constant region (eg, a Cκ or Cλ) for expressing light chains in lymphocytic cells expressing IgM antibodies (eg, in immature B-cells); and
(b) means for turning off light chain expression in lymphocytic cells expressing non-mu (eg, IgG) antibodies.
For example, the light chain variable region comprises one or more human Vκ gene segments and one or more human Jκ gene segments; or one or more human Vλ gene segments and one or more human Jλ gene segments.
Examples of means for turning off light chain expression are provided above and in the examples.
Each heavy and light chain locus is, in a preferred embodiment, a heavy chain or light chain locus of the endogenous non-human vertebrate genome, ie, it is in the germline location of a heavy or light chain locus of said type of vertebrate or cell. In this example, therefore, a locus of the invention can be constructed by inserting exogenous DNA into the endogenous (ie, non-human vertebrate) heavy or light chain locus. In another embodiment, a locus of the invention is synthetically constructed elsewhere in the genome (ie, not in the endogenous heavy chain locus location) and may be on a different chromosome to that chromosome harbouring the heavy chain locus in a wild-type vertebrate or cell. For example, the locus of the invention is constructed at the Rosa26 locus.
Stretches of human DNA can be inserted in one piece or in serial insertions into the genome of a non-human vertebrate or cell (eg, ES cell) genome. For example, a plurality of bacterial artificial chromosomes (BACs) can be constructed using standard recombineering techniques which between them comprise the entire sequence of human constant region DNA to be inserted, each BAC containing a portion of that stretch of DNA. By using serial insertions from serial BACs (eg, using standard homologous recombination (eg, see the Regeneron and Ablexis PCTs disclosed herein) or serial recombinase mediated cassette exchange—sRMCE—(eg, see the Kymab Limited PCTs disclosed herein) the skilled person can build up transgenic loci in the genome. When an ES cell is manipulated in this way, the ES cell can be used, as is standard, to implant in a donor blastocyst, which is then implanted into a foster mother. With germline transmission and any necessary subsequent breeding and crossing (again as is conventional), the skilled person can arrive at progeny vertebrates and cells bearing a gene locus of the invention. The gene locus may be present in a homozygous state (eg, a gene locus of the invention at each heavy chain allele) or heterozygous state (eg, with the second allele being an inactivated endogenous heavy chain so that only heavy chain expression from the first allele—bearing the gene locus of the invention—provides expression of heavy chains). In an alternative, different gene loci of the invention are provided at the first and second alleles of the heavy chain locus in the genome, so that different combinations of human isotype switched heavy chains can be expressed by the combination of loci.
In an embodiment, the genome also comprises transgenic light chain loci that express human light chain variable regions and endogenous light chain expression is substantially inactive; also endogenous heavy chain expression is substantially inactive. This embodiment advantageously provides a genome for predictable expression of only fully human heavy chain and light chain N-terminal variable regions, from which pool of antibodies the skilled person can select (eg, after immunisation with target antigen) non-mu type antibodies (eg, gamma type) that have undergone mutation and maturation and selection by the in vivo machinery of the vertebrate or cell.
By accommodating VH, D and JH recombination and initial expression in the context of an endogenous IgM, this advantageously enables endogenous RAG-1 and RAG-2 to be efficiently employed, as well as harnessing endogenous control, mutation and signaling involved in antibody and B-cell development. The invention subsequently enables switching to a human non-mu C region, which enables one to produce product heavy chains which have been affinity matured by somatic hypermutation effected by endogenous activation induced cytidine deaminase (AID). Those rearranged variable regions that still work well (eg, good expression, affinity, biophysical characteristics) (eg, in the context of the epitope binding moiety) are selected in vivo by the mouse and amplified following immunisation with a predetermined antigen. This retains the advantage of harnessing endogenous antibody and B-cell production and control, together with affinity maturation and in vivo amplification of selected B-cells expressing desirable antibodies/heavy chains in a way that harnesses the mouse (or other non-vertebrate) system to select for good, fully-human antibodies and heavy chains. This is superior to the prior art method of engineering in vitro, where selection for good biophysical characteristics, expression, affinity etc is not factored in (thus often resulting in a down-grading of these in the prior art) and which adds multi-step procedures following initial production in vivo.
In one embodiment, the vertebrate or cell of the invention does not express endogenous antibody heavy chains of said non-mu isotype. For example, this is effected using standard methods to delete or inactivate endogenous heavy chain variable regions. Thus, the skilled person will know that heavy chains (and antibodies comprising these) of the predetermined human non-mu isotype (eg, IgG antibodies) produced by the vertebrate or cell will always comprise human variable regions when human V, D and J gene segments (or a human rearranged VDJ) are included in the heavy chain locus.
In one embodiment, in the vertebrate or cell of the invention the human non-mu constant region is a gamma constant region (eg, gamma-1, -2, 3 or -4). Instead of a gamma constant region, the constant region can be a delta, alpha (eg, alpha-1 or -2) or epsilon constant region. Thus, the invention allows the skilled person to tailor the genome of the vertebrate or cell according to desired constant region functionality of resultant antibodies and heavy chains.
In one embodiment, in the vertebrate or cell of the invention the gamma constant region comprises CH2 and CH3 gene segments for encoding an antibody Fc region. In an example, the constant region also comprises a CH1 gene segment. This is useful for producing heavy chains that are to form part of 4-chain antibodies (classic H2L2 antibodies). In another example, the constant region lacks a CH1 gene segment. This is useful for producing heavy chains that are to form part of heavy-chain only antibodies (H2 antibodies) which are devoid of light chains.
In one embodiment, in the vertebrate or cell of the invention the genome comprises a light chain locus comprising human VL and JL gene segments upstream of a constant region for expression of light chains comprising human variable regions; optionally wherein the constant region is a human light chain constant region. For example, the genome comprises a light chain locus comprising human Vκ and Jκ gene segments upstream of an endogenous or human kappa constant region in the endogenous kappa locus for expression of kappa light chains comprising human variable regions. In this example, where the vertebrate is a mouse, it may not be necessary to humanise the lambda locus, since lambda chain expression in mice is relatively low. Optionally, the lambda locus is inactive and/or comprises human Vλ and Jλ upstream of an endogenous or human lambda constant region. Optionally, endogenous kappa chain expression is inactive.
For example, the vertebrate or cell does not substantially express endogenous light chains following isotype switching.
Inactivation of endogenous antibody, antibody chain or gene segment usage is, for example, substantially complete inactivation or prevention (substantially 100%, ie, essentially none (eg, less than 10, 5, 4, 3, 2, 1 or 0.5%) of the endogenous antibody chain etc (eg, no endogenous heavy chains etc) is expressed). This can be determined, for example, at the antibody chain (protein) level by assessing the antibody repertoire produced by the non-human vertebrate or cell or at the nucleotide level by assessing mRNA transcripts of antibody gene loci, eg, using RACE . In an embodiment, inactivation is more than 50% (ie, 50% or less of the antibodies or transcripts are of an endogenous antibody chain), 60%, 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99%. For example, in an embodiment, endogenous heavy chain expression is substantially inactivated such that no more than 85%, 90%, 95%, 96%, 97%, 98% or 99% of the heavy chain repertoire of the vertebrate is provided by endogenous heavy chains. For example, endogenous heavy chain expression is substantially inactivated such that substantially none of the heavy chain repertoire of the vertebrate is provided by endogenous heavy chains. For example, in an embodiment, endogenous kappa chain expression is substantially inactivated such that no more than 85%, 90%, 95%, 96%, 97%, 98% or 99% of the kappa chain repertoire of the vertebrate is provided by endogenous kappa chains. For example, endogenous kappa chain expression is substantially inactivated such that substantially none of the kappa chain repertoire of the vertebrate is provided by endogenous kappa chains. For example, in an embodiment, endogenous lambda chain expression is substantially inactivated such that no more than 85%, 90%, 95%, 96%, 97%, 98% or 99% of the lambda chain repertoire of the vertebrate is provided by endogenous lambda chains. For example, endogenous lambda chain expression is substantially inactivated such that substantially none of the lambda chain repertoire of the vertebrate is provided by endogenous lambda chains.
In one embodiment, in the vertebrate or cell of the invention the gamma constant region does not comprise a CH1 gene segment. In this embodiment, in an example, light chain expression is inactive when the non-mu heavy chains are expressed. This is useful for producing heavy-chain only antibodies of the non-mu isotype.
In an example, the variable region and/or mu constant region are in human and endogenous germline configurations respectively. The term “germline configuration” refers to a germline genomic configuration. For example, human immunoglobulin gene segments present in the gene locus of the invention are in a germline configuration when the relative order of the human gene segments is the same as the order of corresponding gene segments in a human germline genome. For example, when the gene locus of the invention comprises hypothetical human immunoglobulin constant region gene segments A, B and C, these would be provided in this order (5′ to 3′ in the locus) when the corresponding gene segments of a human germline genome comprises the arrangement 5′-A-B-C-3′; and optionally the inter-gene segments too are in germline configuration (ie, the nucleotide sequence from A to C corresponds to a stretch of contiguous nucleotide sequence from A to C in a human germline genome). Available databases and sources of human germline sequence are discussed below. Thus, in an example, when elements of a human immunoglobulin locus (eg, gene segments, enhancers or other regulatory elements) are provided in a gene locus according to the invention, the human Ig locus elements are in germline configuration when the relative order of the elements is the same as the order of corresponding elements in a human germline genome and human sequences between the elements are included, these corresponding to such sequences between corresponding elements in the human germline genome. Thus, in a hypothetical example the transgenic locus comprises human elements in the arrangement 5′-A-S1-B-S2-C-S3-3′, wherein A, B and C are human immunoglobulin gene segments and S1-S3 are human inter-gene segment sequences, wherein the corresponding arrangement 5′-A-S1-B-S2-C-S3-3′ is present in a human germline genome. For example, this can be achieved by providing in a transgenic immunoglobulin locus of the invention a DNA insert corresponding to the DNA sequence from A to C in a human germline genome (or the insert comprising the DNA sequence from A to C). The arrangements in human germline genomes and immunoglobulin loci are known in the art (eg, see the IMGT, Kabat and other antibody resources).
In an embodiment, VH gene segment repertoire of the heavy chain locus (or each heavy chain locus) is a substantially complete repertoire of functional human VH gene segments; optionally providing at least 6 different human JH gene segments, 27 different human D segments and at least 40 different human VH gene segments.
In an embodiment, VH gene segment repertoire of the heavy chain locus (or each heavy chain locus) is at least 20, 25, 30, 35 or 40 different human VH gene segments.
In an embodiment, the method of the invention comprises the step of selecting one or more heavy chains or antibodies on the basis of a desired antibody or heavy chain characteristic (eg, binding affinity for target antigen), wherein the selected antibodies comprise non-mu heavy chains, or the selected heavy chains are non-mu chains.
Methods of Antibody/Chain Selection
An aspect provides a method of isolating an antibody, heavy chain or nucleotide sequence encoding said antibody, the method comprising
(a) immunising (see e.g. Harlow, E. & Lane, D. 1998, 5th edition, Antibodies: A Laboratory Manual, Cold Spring Harbor Lab. Press, Plainview, N.Y.; and Pasqualini and Arap, Proceedings of the National Academy of Sciences (2004) 101:257-259) a vertebrate according to the invention with an antigen such that the vertebrate produces antibodies; and
(b) isolating from the immunised vertebrate an antibody or heavy chain that specifically binds to said antigen and/or a nucleotide sequence encoding at least the heavy chain variable region of said antibody.
Suitably an immunogenic amount of the antigen is delivered in the method of the invention. The invention also relates to a method for detecting a target antigen comprising detecting an antibody or heavy chain produced as above or a derivative thereof with a secondary detection agent which recognises a portion of that antibody/chain.
Isolation of the antibody in step (b) can be carried out using conventional antibody selection techniques, eg, panning for antibodies against antigen that has been immobilised on a solid support, optionally with iterative rounds at increasing stringency, as will be readily apparent to the skilled person.
As a further optional step, after step (b) the amino acid sequence of the heavy chain variable region is mutated to improve affinity for binding to said antigen. Mutation can be generated by conventional techniques as will be readily apparent to the skilled person, eg, by error-prone PCR. Affinity can be determined by conventional techniques as will be readily apparent to the skilled person, eg, by surface plasmon resonance, eg, using Biacore™ or Proteon™.
Additionally or alternatively, as a further optional step, after step (b) the amino acid sequence of the heavy chain variable region is mutated to further improve one or more biophysical characteristics of the antibody, eg, one or more of melting temperature, solution state (monomer or dimer), stability and expression (eg, in CHO or E coli).
An aspect provides an antibody, chain or polypeptide of the invention, optionally for use in human medicine, eg, for treating and/or preventing a medical condition or disease in a human patient.
The invention provides a pharmaceutical composition comprising an antibody, chain or polypeptide of the invention or a copy or derivative thereof.
Optionally, the method comprises the step of isolating a B-cell from said immunised vertebrate, wherein the B-cell expresses said isolated antibody or heavy chain; and optionally immortalising the B-cell.
Optionally, the method comprises the step of isolating a nucleotide sequence from said immunised vertebrate or B-cell, wherein the nucleotide sequence encodes said isolated antibody or a heavy chain thereof.
The method provides a vector (optionally in a host cell) comprising the nucleotide sequence of the invention or a copy thereof, or a derivative thereof; optionally comprising up to 15, 10, 9,8,7,6,5,4,3, or 1 mutations. The derivative specifically binds target antigen.
The method provides a method of treating or preventing a medical condition or disease in a human associated or caused by one or more of said antigens epitopes, the method comprising administering to the human the antigen-specific antibody or heavy chain obtained in the method or isolated from a vertebrate or cell of the invention.
The method provides the antigen-specific antibody or heavy chain obtained in the method or isolated from a vertebrate or cell of the invention for use in the treatment or prophylaxis of a medical condition or disease in a human associated or caused by said antigen.
The method provides the use of the antigen-specific antibody or heavy chain obtained in the method or isolated from a vertebrate or cell of the invention in the manufacture of a medicament for use in the treatment or prophylaxis of a medical condition or disease in a human associated or caused by said antigen.
As will be readily apparent to the skilled person, the operable connection of a human gene segment (eg, a V or J gene segment) upstream of a constant region in an Ig locus in any configuration of the invention enables the gene segment to be recombined and expressed in an immunoglobulin chain comprising sequence encoded by the constant region of the locus.
In one embodiment in any configuration of the invention, each vertebrate is a non-human mammal. In one embodiment in any configuration of the invention, the vertebrate is a mouse, rat, rabbit, Camelid (eg, a llama, alpaca or camel), chicken, lamprey or shark. For example, all vertebrates are of the same vertebrate species, eg, all mice or all rats.
In any configuration of the invention, the human gene regions or segments may be derived from the same individual or different individuals, or be synthetic (synthetically mutated human gene segments) or represent human consensus sequences.
Techniques for constructing non-human vertebrates and vertebrate cells whose genomes comprise a human immunoglobulin gene segments are well known in the art. For example, reference is made to WO2011004192, U.S. Pat. Nos. 7,501,552, 6,673,986, 6,130,364, WO2009076464 and U.S. Pat. No. 6,586,251, the disclosures of which are incorporated herein by reference in their entirety.
In one example, a non-human vertebrate of any configuration of the invention is able to generate a diversity of at least 1×106 different functional non-mu immunoglobulin sequence combinations.
Human variable regions are suitably inserted upstream of a non-human vertebrate mu constant region, the latter together with downstream human constant region(s) comprising all of the DNA required to encode the full constant region or a sufficient portion of the constant region to allow the formation of an effective non-mu antibody/heavy chain capable of specifically recognising a target antigen.
The endogenous mu non-human vertebrate constant region herein is optionally the endogenous host wild-type constant region located at the wild type locus, as appropriate for the heavy chain.
In one optional aspect where the vertebrate is a mouse, the insertion of human variable region DNA (V, D and J gene segments) is targeted to the region between the J4 exon and the endogenous Sμ locus in the mouse genome IgH locus, and in one aspect is inserted between coordinates 114,667,090 and 114,665,190, suitably at coordinate 114,667,091, after 114,667,090.
All nucleotide co-ordinates for the mouse are those corresponding to NCBI m37 for the mouse C57BL/6J strain, e.g. April 2007 ENSEMBL Release 55.37h, e.g. NCBI37 July 2007 (NCBI build 37) (e.g. UCSC version mm9 see www.genome.ucsc.edu and http://genome.ucsc.edu/FAQ/FAQreleases.html) unless otherwise specified. Human nucleotides coordinates are those corresponding to GRCh37 (e.g. UCSC version hg 19, http://genome.ucsc.edu/FAQ/FAQreleases.html), February 2009 ENSEMBL Release 55 or are those corresponding to NCBI36, Ensemble release 54 unless otherwise specified. Rat nucleotides are those corresponding to RGSC 3.4 December 2004 ENSEMBL release 55.34w, or Baylor College of Medicine HGSC v3.4 November 2004(e.g., UCSC rn4, see www.genome.ucsc.edu and http://genome.ucsc.edu/FAQ/FAQreleases.html) unless otherwise specified.
Reference to location of a human variable region, constant region or a gene segment upstream or downstream of an endogenous mu constant region means that there is a suitable relative location of the antibody nucleotide elements to enable formation of mu and then non-mu heavy chains in vivo in the vertebrate. Thus, the inserted human DNA and endogenous constant region and any other endogenous sequences are in operable connection with one another for antibody or antibody chain production.
As a source of human and non-human antibody gene segment sequences, the skilled person will also be aware of the following available databases and resources (including updates thereof) the contents of which are incorporated herein by reference:
The Kabat Database (G. Johnson and T. T. Wu, 2002; World Wide Web (www) kabatdatabase.com). Created by E. A. Kabat and T. T. Wu in 1966, the Kabat database publishes aligned sequences of antibodies, T-cell receptors, major histocompatibility complex (MHC) class I and II molecules, and other proteins of immunological interest. A searchable interface is provided by the SeqhuntII tool, and a range of utilities is available for sequence alignment, sequence subgroup classification, and the generation of variability plots. See also Kabat, E. A.,Wu, T. T., Perry, H., Gottesman, K., and Foeller, C. (1991) Sequences of Proteins of Immunological Interest, 5th ed., NIH Publication No. 91-3242, Bethesda, Md., which is incorporated herein by reference, in particular with reference to human gene segments for use in the present invention.
KabatMan (A. C. R. Martin, 2002; World Wide Web (www) bioinf.org.uk/abs/simkab.html). This is a web interface to make simple queries to the Kabat sequence database.
IMGT (the International ImMunoGeneTics Information System®; M.-P. Lefranc, 2002; World Wide Web (www) imgt.cines.fr). IMGT is an integrated information system that specializes in antibodies, T cell receptors, and MHC molecules of all vertebrate species. It provides a common portal to standardized data that include nucleotide and protein sequences, oligonucleotide primers, gene maps, genetic polymorphisms, specificities, and two-dimensional (2D) and three-dimensional (3D) structures. IMGT includes three sequence databases (IMGT/LIGM-DB, IMGT/MHC-DB, IMGT/PRIMERDB), one genome database (IMGT/GENE-DB), one 3D structure database (IMGT/3Dstructure-DB), and a range of web resources (“IMGT Marie-Paule page”) and interactive tools.
V-BASE (I. M. Tomlinson, 2002; World Wide Web (www) mrc-cpe.cam.ac.uk/vbase). V-BASE is a comprehensive directory of all human antibody germline variable region sequences compiled from more than one thousand published sequences. It includes a version of the alignment software DNAPLOT (developed by Hans-Helmar Althaus and Werner Müller) that allows the assignment of rearranged antibody V genes to their closest germline gene segments.
Antibodies—Structure and Sequence (A. C. R. Martin, 2002; World Wide Web (www) bioinf.org.uk/abs). This page summarizes useful information on antibody structure and sequence. It provides a query interface to the Kabat antibody sequence data, general information on antibodies, crystal structures, and links to other antibody-related information. It also distributes an automated summary of all antibody structures deposited in the Protein Databank (PDB). Of particular interest is a thorough description and comparison of the various numbering schemes for antibody variable regions.
AAAAA (A Ho's Amazing Atlas of Antibody Anatomy; A. Honegger, 2001; World Wide Web (www) unizh.ch/˜antibody). This resource includes tools for structural analysis, modeling, and engineering. It adopts a unifying scheme for comprehensive structural alignment of antibody and T-cell-receptor sequences, and includes Excel macros for antibody analysis and graphical representation.
WAM (Web Antibody Modeling; N. Whitelegg and A. R. Rees, 2001; World Wide Web (www) antibody.bath.ac.uk). Hosted by the Centre for Protein Analysis and Design at the University of Bath, United Kingdom. Based on the AbM package (formerly marketed by Oxford Molecular) to construct 3D models of antibody Fv sequences using a combination of established theoretical methods, this site also includes the latest antibody structural information.
Mike's Immunoglobulin Structure/Function Page (M. R. Clark, 2001; World Wide Web (www) path.cam.ac.uk/˜mrc7/mikeimages.html) These pages provide educational materials on immunoglobulin structure and function, and are illustrated by many colour images, models, and animations. Additional information is available on antibody humanization and Mike Clark's Therapeutic Antibody Human Homology Project, which aims to correlate clinical efficacy and anti-immunoglobulin responses with variable region sequences of therapeutic antibodies.
The Antibody Resource Page (The Antibody Resource Page, 2000; World Wide Web (www) antibodyresource.com). This site describes itself as the “complete guide to antibody research and suppliers.” Links to amino acid sequencing tools, nucleotide antibody sequencing tools, and hybridoma/cell-culture databases are provided.
Humanization bY Design (J. Saldanha, 2000; World Wide Web (www) people.cryst.bbk.ac.uk/˜ubcg07s). This resource provides an overview on antibody humanization technology. The most useful feature is a searchable database (by sequence and text) of more than 40 published humanized antibodies including information on design issues, framework choice, framework back-mutations, and binding affinity of the humanized constructs.
See also Antibody Engineering Methods and Protocols, Ed. Benny K C Lo, Methods in Molecular Biology™, Human Press. Also at World Wide Web (www) blogsua.com/pdf/antibody-engineering-methods-and-protocolsantibody-engineering-methods-and-protocols.pdf
Samples from which B-cells can be obtained include but are not limited to blood, serum, spleen, splenic tissue, bone marrow, lymph, lymph node, thymus, and appendix. Antibodies and immunoglobulin chains can be obtained from each of the previous-mentioned samples and also from the following non-limiting list of B-cells, ascites fluid, hybridomas, and cell cultures.
In one embodiment in any configuration of the invention, the genome of the vertebrate or cell has been modified to prevent or reduce the expression of fully-endogenous antibody or heavy chains. Examples of suitable techniques for doing this can be found in WO2011004192, U.S. Pat. Nos. 7,501,552, 6,673,986, 6,130,364, WO2009/076464, EP1399559 and U.S. Pat. No. 6,586,251, the disclosures of which are incorporated herein by reference. In one embodiment, the non-human vertebrate VDJ region of the endogenous heavy chain immunoglobulin locus, and optionally VJ region of the endogenous light chain immunoglobulin loci (lambda and/or kappa loci), have been inactivated. For example, all or part of the non-human vertebrate VDJ region is inactivated by inversion in the endogenous heavy chain immunoglobulin locus of the mammal, optionally with the inverted region being moved upstream or downstream of the endogenous Ig locus. For example, all or part of the non-human vertebrate VJ region is inactivated by inversion in the endogenous kappa chain immunoglobulin locus of the mammal, optionally with the inverted region being moved upstream or downstream of the endogenous Ig locus. For example, all or part of the non-human vertebrate VJ region is inactivated by inversion in the endogenous lambda chain immunoglobulin locus of the mammal, optionally with the inverted region being moved upstream or downstream of the endogenous Ig locus. In one embodiment the endogenous heavy chain locus is inactivated in this way as is one or both of the endogenous kappa and lambda loci.
Additionally or alternatively, the vertebrate has been generated in a genetic background which prevents the production of mature host B and T lymphocytes, optionally a RAG-1-deficient and/or RAG-2 deficient background. See U.S. Pat. No. 5,859,301 for techniques of generating RAG-1 deficient animals.
In one embodiment of any configuration of the vertebrate or cell of the invention the genome comprises an antibody light chain locus which comprises all or part of the human Igλ locus including at least one human Jλ region and at least one human Cλ region, optionally Cλ6 and/or Cλ7. Optionally, the light chain locus comprises a plurality of human Jλ regions, optionally two or more of Jλ1, Jλ2, Jλ6 and Jλ7, optionally all of Jλ1, Jλ2, Jλ6 and Jλ7. The human lambda immunoglobulin locus comprises a unique gene architecture composed of serial J-C clusters. In order to take advantage of this feature, the invention in optional aspects employs one or more such human J-C clusters. Thus, optionally the light chain locus comprises at least one human Jλ-Cλ cluster, optionally at least Jλ7-Cλ7.
The construction of such transgenes is facilitated by being able to use all or part of the human lambda locus such that the transgene comprises one or more J-C clusters in germline configuration, advantageously also including intervening sequences between clusters and/or between adjacent J and C regions in the human locus. This preserves any regulatory elements within the intervening sequences which may be involved in VJ and/or JC recombination and which may be recognised by endogenous AID (activation-induced deaminase).
An aspect provides a nucleotide sequence encoding the polypeptide, antibody, chain or derivative of the invention, optionally wherein the nucleotide sequence is part of a vector. Suitable vectors will be readily apparent to the skilled person, eg, a conventional antibody expression vector comprising the nucleotide sequence together in operable linkage with one or more expression control elements.
An aspect provides a pharmaceutical composition comprising the polypeptide, antibody, chain or derivative of the invention and a diluent, excipient or carrier, optionally wherein the composition is contained in an IV container (eg, and IV bag) or a container connected to an IV syringe.
An aspect provides the use of the polypeptide, antibody, chain or derivative of the invention in the manufacture of a medicament for the treatment and/or prophylaxis of a disease or condition in a human patient.
The skilled person will generally be familiar with standard cloning techniques and recombinant DNA technology—see e.g. Sambrook, J and Russell, D. (2001, 3'd edition) Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Lab. Press, Plainview, N.Y.).
In a further aspect the invention relates to humanised antibodies and antibody heavy chains produced according to the present invention, and use of said antibodies in human medicine. The invention also relates to a pharmaceutical composition comprising such an antibody or heavy chain and a pharmaceutically acceptable carrier or other excipient.
Methods for the generation of both monoclonal and polyclonal antibodies are well known in the art, and the present invention relates to both polyclonal and monoclonal antibodies of fully humanised antibodies and heavy chains produced in response to antigen challenge in a vertebrate or cel according to the present invention.
In a further aspect, the invention relates to use of a non-human vertebrate of the present invention in the analysis of the likely effects of drugs and vaccines in the context of an antibody chain repertoire.
The invention also relates to a method for identification or validation of a drug or vaccine, the method comprising delivering the vaccine or drug to a vertebrate of the invention and monitoring one or more of: the immune response, the safety profile; the effect on disease.
The invention also relates to a kit comprising an antibody, polypeptide, chain or derivative as disclosed herein and either instructions for use of such optionally with a suitable laboratory reagent, such as a buffer, antibody detection reagent.
The invention also relates to a method for making an antibody, or part thereof, the method comprising providing:
(i) a nucleic acid encoding an polypeptide, antibody or chain, obtained using the vertebrate or cell of the present invention; or
(ii) sequence information from which a nucleic acid encoding an antibody, polypeptide or chain, obtained using the vertebrate or cell of the present invention can be expressed to allow an antibody, chain or polypeptide to be produced.
In an embodiment, each vertebrate is a non-human vertebrate, mouse or rat, whose genome comprises
(a) a heavy chain locus as defined above; and
(b) an antibody kappa light chain locus and/or an antibody lambda chain locus;
wherein all of the V, D and J in said loci are human V, D and J;
wherein endogenous antibody heavy and light chain expression has been inactivated; and optionally wherein said genome is homozygous for said heavy and light chain loci. This is useful for generating, predictably, only human N-terminal variable domains in antibodies and chains in the vertebrate.
In an embodiment, each kappa chain locus comprises a substantially complete human functional Vκ and Jκ repertoire; and each lambda chain locus comprises a substantially complete human functional Vλ and Jλ repertoire. “Functional” here acknowledges that Ig gene segment pseudogenes and non-functional human Ig gene segments can be excluded.
In one example the gene locus of the invention is a heavy chain locus which comprises a S-mu switch (eg, endogenous S-mu) as said first switch and a S-gamma switch (eg, endogenous S-gamma) as said second switch. For example, the C-mu region and switches are mouse 129 C-mu region and switches; or the C-mu region and switches are mouse Black 6 C-mu region and switches. In another embodiment (where the non-human vertebrate species is mouse or rat), S-mu is a rat Smu and the C-mu region is mouse and optionally there is a mouse S-gamma 3′ of the non-mu C region.
In one aspect each vertebrate is a mouse whose genetic background is selected from mouse strains C57BL/6, M129 such as 129/SV, BALB/c, and any hybrid of C57BL/6, M129 such as 129/SV, or BALB/c.
In an embodiment, the J segments of each gene locus of the invention are human JH gene segments; optionally wherein each heavy chain locus comprises a substantially complete functional repertoire of human JH gene segments.
In an embodiment, each gene locus of the invention comprises at least 2, 3, 4, 5 or 6 different human JH gene segments.
In an embodiment, the D segments of each gene locus of the invention are human D gene segments; optionally wherein each heavy chain locus comprises a substantially complete functional repertoire of human D gene segments.
In an embodiment, each gene locus of the invention comprises at least 5, 10, 15, 20, 25, 26 or 27 different human D gene segments.
In an embodiment, each heavy chain locus comprises at least two human JH gene segments selected from the group consisting of .11, J2, J3, J4, J5 and J6; optionally all of the gene segments of the group.
In an embodiment, each heavy chain locus comprises human VH gene segments selected from the group consisting of V6-1, V1-2, V1-3, V4-4, V7-41, V2-5, V3-7, V1-8, V3-9, V3-11, V3-15, V1-18, V3-20, V3-21, V3-23, V1-24, V2-26, V4-28, V3-30, V4-31, V3-33, V4-34, V4-39, V3-43, V1-45, V1-46, V3-48, V3-49, V5-51, V3-53, V1-58, V4-59, V4-61, V3-64, V3-66, V1-69, V2-70, V3-72, V3-73 and V3-74; wherein the VH gene repertoire comprises a substantially complete human functional VH gene repertoire.
In an embodiment, endogenous antibody heavy chain expression has been inactivated in the vertebrate or cell of the invention. For example, less than 10, 5, 4, 3, 2, 1 or 0.5% (or 0) of heavy chains are provided by endogenous heavy chains (ie, heavy chains whose variable regions are derived from recombination of non-human vertebrate V, D and J gene segments).
The VL gene segments of a repertoire can, in one embodiment, be recombined VL, ie, provided as part of a variable region sequence derived from the recombination of human VL with JL (eg, where the VL and JL are human).
In an embodiment, the J segments of each light chain locus are human JL gene segments; optionally wherein each light chain locus comprises a substantially complete functional repertoire of human Jκ or Jλ gene segments (eg, each locus comprises human Vλ gene segments and Jλ gene segments, optionally a substantially complete functional repertoire of human Jλ gene segments; or each locus comprises human Vκ gene segments and Jκ gene segments, optionally a substantially complete functional repertoire of human Jκ gene segments).
In an embodiment, the kappa chain repertoire of the vertebrate or cell genome comprises a substantially complete repertoire of functional human Vκ gene segments; optionally providing at least 5 different human Jκ gene segments and at least at least 40 different human Vκ gene segments.
In an embodiment, the kappa chain repertoire comprises at least 20, 25, 30, 35 or 40 different human Vκ gene segments.
In an embodiment, the lambda chain repertoire of the vertebrate or cell genome comprises a substantially complete repertoire of functional human Vλ gene segments; optionally providing at least 5 different human Jλ gene segments and at least 40 different human Vλ gene segments.
In an embodiment, the lambda chain repertoire comprises at least 20, 25, 30, 35 or 40 different human Vλ gene segments.
In an embodiment, each light chain locus of the vertebrate or cell comprises at least 2, 3, 4, 5 or 6 different human Jκ or Jλ gene segments.
In an embodiment, endogenous antibody kappa and/or lambda light chain expression has been inactivated in the vertebrate or cell.
For selection of antibodies, chains or polypeptides in the methods of the invention, examples of a desirable antibody/chain/polypeptide characteristic are affinity for binding a predetermined antigen or epitope (eg, as determined by surface plasmon resonance), completion with a known antibody for binding to a predetermined antigen or epitope, epitopic specificity (eg, as determined by X-ray crystallography, competition with a known antibody for antigen binding wherein the known antibody specifically binds to the antigen (eg, as determined by surface plasmon resonance, eg, Biacore™ or Proteon™), performance in ELISA or another immunoassay, a desirable biophysical characteristic (eg, melting temperature, pI, solution state, degree of aggregation, storage profile etc). In an embodiment, affinity is determined by surface plasmon resonance.
Methods of immunisation for use in the invention are well known to the skilled person and may involve a classic prime-boost regime, RIMMS or any other protocol. An adjuvant may be administered with the antigen, as is known in the art.
Examples of derivative antibodies/chains/polypeptides (according to any aspect herein) are antibodies/chains/polypeptides that have one or more mutations compared to the isolated antibody or chain or polypeptide (eg, to improve antigen-binding affinity and/or to enhance or inactivate Fc function). Such mutants specifically bind the antigen. Mutation or adaptation to produce a derivative includes, eg, mutation to produce Fc enhancement or inactivation. A derivative can be an a antibody or chain or polypeptide following conjugation to a toxic payload or reporter or label or other active moiety.
In an embodiment, the vertebrate is naïve (ie, not immunised with a predetermined antigen, as the term is understood in the art; for example, such a vertebrate that has been kept in a relatively sterile environment as provided by an animal house used for R&D). In another example, the vertebrate has been immunised with a predetermined antigen, eg, an antigen bearing a human epitope.
In an embodiment, the method comprises comprising selecting one or more antibody heavy chains (eg, as part of an antibodies) from said population or repertoire according to a desired characteristic (eg, affinity for biding an antigen).
It is expected for example that, by using the present invention, this does not substantially change the ratio of B-cells in the splenic compartment and/or bone marrow B progenitor compartment and the immunoglobulin levels in serum are normal and the correct Ig subtypes are expressed. This would demonstrate that loci according to the invention (eg, heavy chain loci comprising an insertion of at least human VH gene segments VH2-5, 7-4-1, 4-4, 1-3, 1-2, 6-1, and all the human D and JH gene segments D1-1, 2-2, 3-3, 4-4, 5-5, 6-6, 1-7, 2-8, 3-9, 5-12, 6-13, 2-15, 3-16, 4-17, 6-19, 1-20, 2-21, 3-22, 6-25, 1-26 and 7-27; and J1, J2, J3, J4, J5 and J6) are fully functional for VDJ gene segment rearrangement from the transgenic heavy chain locus, B-cell receptor (BCR) signaling and proper B-cell maturation
Thus, in one aspect it is expected that mice according to the invention can for example express a normal relative proportion of serum IgG1, IgG2a, IgG2b and IgM antibodies.
By “normal” is meant comparable to expression in a mouse (eg, a naïve mouse) expressing only mouse antibody chains, eg, a mouse whose genome comprises only wild-type functional Ig heavy and light chain loci, eg, a wild-type mouse.
Thus, in one aspect it is expected that mice according to the invention can for example express
(i) serum IgG1 at a concentration of about 25-350 μg/ml;
(ii) serum IgG2a at a concentration of about 0-200 μg/ml;
(iii) serum IgG2b at a concentration of about 30-800 μg/ml; and
(iv) serum IgM at a concentration of about 50-300 μg/ml;
or
(i) serum IgG1 at a concentration of about 10-600 μg/ml;
(ii) serum IgG2a at a concentration of about 0-500 μg/ml;
(iii) serum IgG2b at a concentration of about 20-700 μg/ml; and
(iv) serum IgM at a concentration of about 50-700 μg/ml;
as determined by Ig capture on a plate followed by incubation (eg, for one hour at RT, eg, for one hour at 20° C.) with anti-mouse isotype-specific labeled antibodies and quantification of Ig using the label (eg, using anti-mouse Ig isotype specific antibodies each conjugated to horseradish peroxidase conjugated at a ratio of 1/10000 in PBS with 0.1% Tween™, followed by development of the label with tetramethylbenzidine substrate (TMB) for 4-5 minutes in the dark at room temperature (eg, 20° C.), adding sulfuric acid to stop development of the label and reading of the label at 450 nm).
Thus, in one aspect it is expected that mice according to the invention can for example express
(i) serum IgG1 at a concentration of about 25-150 μg/ml;
(ii) serum IgG2a at a concentration of about 0-200 μg/ml;
(iii) serum IgG2b at a concentration of about 30-300 μg/ml; and
(iv) serum IgM at a concentration of about 50-200 μg/ml;
or
(i) serum IgG1 at a concentration of about 10-200 μg/ml;
(ii) serum IgG2a at a concentration of about 0-500 μg/ml;
(iii) serum IgG2b at a concentration of about 20-400 μg/ml; and
(iv) serum IgM at a concentration of about 50-700 μg/ml;
as determined by Ig capture on a plate followed by incubation (eg, for one hour at RT, eg, for one hour at 20° C.) with anti-mouse isotype-specific labeled antibodies and quantification of Ig using the label (eg, using anti-mouse Ig isotype specific antibodies each conjugated to horseradish peroxidase conjugated at a ratio of 1/10000 in PBS with 0.1% Tween™, followed by development of the label with tetramethylbenzidine substrate (TM B) for 4-5 minutes in the dark at room temperature (eg, 20° C.), adding sulfuric acid to stop development of the label and reading of the label at 450 nm).
Thus, in one aspect it is expected that mice according to the invention can for example express Ig in the relative proportions of
(i) serum IgG1 at a concentration of about 25-150 μg/ml;
(ii) serum IgG2a at a concentration of about 0-200 μg/ml;
(iii) serum IgG2b at a concentration of about 30-300 μg/ml; and
(iv) serum IgM at a concentration of about 50-200 μg/ml;
or
(i) serum IgG1 at a concentration of about 10-200 μg/ml;
(ii) serum IgG2a at a concentration of about 0-500 82 g/ml;
(iii) serum IgG2b at a concentration of about 20-400 μg/ml; and
(iv) serum IgM at a concentration of about 50-700 μg/ml;
as determined by Ig capture on a plate followed by incubation (eg, for one hour at RT, eg, for one hour at 20° C.) with anti-mouse isotype-specific labeled antibodies and quantification of Ig using the label (eg, using anti-mouse Ig isotype specific antibodies each conjugated to horseradish peroxidase conjugated at a ratio of 1/10000 in PBS with 0.1% Tween™, followed by development of the label with tetramethylbenzidine substrate (TMB) for 4-5 minutes in the dark at room temperature (eg, 20° C.), adding sulfuric acid to stop development of the label and reading of the label at 450 nm).
Thus, in one aspect it is expected that mice according to the invention can for example express heavy chains from splenic B-cells in a mouse that produces a normal proportion or percentage of mature splenic B-cells, eg as determined by FACS.
By “normal” is meant comparable to mature splenic B-cell production in a mouse (eg, a naïve mouse) expressing only mouse antibody chains, eg, a mouse whose genome comprises only wild-type functional Ig heavy and light chain loci, eg, a wild-type mouse.
For example, at least 40, 50, 60 or 70% of total splenic B-cells produced by the mouse of the invention are mature B-cells. Splenic B-cells are B220+ and express B220 at relatively high levels as the skilled person will know. Mature splenic B-cells express B220 and IgD, both at relatively high levels as will be known by the skilled person. IgM expression is relatively low in mature splenic B-cells, again as is known in the art. For example, see J Exp Med. 1999 Jul. 5; 190(1):75-89; “B cell development in the spleen takes place in discrete steps and is determined by the quality of B cell receptor-derived signals”; Loder F et al.
Optionally the mouse produces a normal ratio of T1, T2 and mature splenic B-cells, eg, as determined by FACS. For example, the mouse of the invention produces about 40-70% mature splenic B-cells, 15-35% splenic T1 cells; and 5-10% splenic T2 cells (percentage with reference to the total splenic B220-positive (high) population). For example, about 40-60% mature splenic B-cells, 15-30% splenic T1 cells; and 5-10% splenic T2 cells. By “normal” is meant comparable to a T1/T2/mature splenic B-cell proportion in a mouse (eg, a naïve mouse) expressing only mouse antibody chains, eg, a mouse whose genome comprises only wild-type functional Ig heavy and light chain loci, eg, a wild-type mouse.
Thus, in one aspect it is expected that mice according to the invention can for example express heavy chains in a mouse that produces a normal proportion or percentage of bone marrow B-cell progenitor cells (eg as determined by FACS).
In one embodiment, the mouse is for expressing said heavy chains in a mouse that produces a normal proportion or percentage of bone marrow pre-, pro and prepro-B-cells (eg as determined by FACS). See J Exp Med. 1991 May 1; 173(5):1213-25; “Resolution and characterization of pro-B and pre-pro-B cell stages in normal mouse bone marrow”; Hardy R R et al for more discussion on progenitor cells.
By “normal” is meant comparable to bone marrow B-cell production in a mouse (eg, a naïve mouse) expressing only mouse antibody chains, eg, a mouse whose genome comprises only wild-type functional Ig heavy and light chain loci, eg, a wild-type mouse.
In one example of such a mouse, at least 90% of the heavy chains are heavy chains comprising human variable regions. For example, at least 90, 95, 96, 97, 98, 99 or 99.5% or 100% of the heavy chains comprise human variable regions, ie, variable regions derived from the recombination of human VH with human D and JH gene segments.
In one embodiment, the genome of the vertebrate, mouse or cell comprises human kappa gene segments
(i) Vκ1-5, Vκ1-6, Vκ1-8 and Vκ1-9 (and optionally Vκ5-2 and Vκ4-1); or
(ii) Vκ1-5, Vκ1-6, Vκ1-8, Vκ1-9, Vκ3-11, Vκ1-12, Vκ3-15, Vκ1-16, Vκ1-17, Vκ3-20 (and optionally Vκ2-24 and/or Vκ1-13); or
(III) Vκ1-5, Vκ1-6, Vκ1-8, Vκ1-9, Vκ3-11, Vκ1-12, Vκ3-15, Vκ1-16, Vκ1-17, Vκ3-20, Vκ2-24, Vκ1-27, Vκ2-28, Vκ2-30 and Vκ1-33 (and optionally Vκ2-29 and/or Vκ1-40 and/or Vκ1-39);
and optionally
(iv) Jκ1, Jκ2, Jκ3, Jκ4 and Jκ5.
In one embodiment, the genome also comprises (i) at least human VH gene segments VH2-5, 7-4-1, 4-4, 1-3, 1-2, 6-1, and all the human D and JH gene segments D1-1, 2-2, 3-3, 4-4, 5-5, 6-6, 1-7, 2-8, 3-9, 5-12, 6-13, 2-15, 3-16, 4-17, 6-19, 1-20, 2-21, 3-22, 6-25, 1-26 and 7-27; and .11, J2, J3, J4, J5 and J6 and (ii) at least human gene segments Via-24, Vκ3-20, Vκ1-17, Vκ1-16, Vκ3-15, Vκ1-13, Vκ1-12, Vκ3-11, Vκ1-9, Vκ1-8, Vκ1-6, Vκ1-5, Vκ5-2, Vκ4-1, Jκ1, Jκ2, Jκ3, Jκ4 and Jκ5.
Lox Sites
Novel Lox variants are described in the examples below (lox2272/66 and lox2272/71). These are useful for site-specific recombination (eg, in ES cells or other nucleic acid sources). Furthermore, since these sites are not compatible, they can be used for RMCE (recombinase-mediated cassette exchange). Thus, the invention comprises
A site specific recombination site which is lox2272/66. The sequence is given below.
A site specific recombination site which is lox2272/71. The sequence is given below.
A DNA vector or DNA sequence comprising lox2272/66 and/or lox2272/71. For example, the vector or sequence comprises a nucleotide sequence (eg, a gene or gene segment sequence) flanked by lox2272/66 and lox2272/71; optionally wherein the lox sites are inverse to each other (which is useful for locking in sequences inserted into genomes, as explained in the examples). In this sense, lox2272/66 is 5′ (eg, immediately 5′) of the nucleotide sequence and lox2272/71 is 3′ (eg, immediately 3′) of the sequence. In another example, lox2272/71 is 5′ (eg, immediately 5′) of the nucleotide sequence and lox2272/66 is 3′ (eg, immediately 3′) of the sequence. In an example, the DNA sequence is part of a cell genome, eg, an ES cell genome or a B-cell genome or a hybridoma genome or an iPS cell genome.
STATEMENTS OF INVENTIONAspects of the invention are set out in the following clauses.
-
- 1.
- Multivalent
- A non-human vertebrate (eg, a mouse or a rat), wherein the vertebrate comprises lymphocytic cells, each cell genome comprising
- (i) an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region, a first switch, a mu constant region, a second switch and a non-mu (eg, gamma) constant region; wherein the heavy chain locus of each cell is capable of undergoing IgM to the non-mu (eg, IgG) isotype switching; and
- wherein
- (ii) the non-mu constant region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, wherein following isotype switching the vertebrate expresses multivalent polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the heavy chain locus, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes.
- or
- In vivo Guided Selection
- A non-human vertebrate (eg, a mouse or a rat) whose genome comprises an Ig locus comprising (in 5′ to 3′ orientation) (i) an unrearranged human variable region (eg, a heavy chain variable region) for encoding a first variable domain, (ii) a sequence encoding an optional linker and (iii) a rearranged sequence of a second variable domain (eg, a VL domain), wherein sequence (i) is capable of undergoing rearrangement so that the vertebrate produces antibody chains each having an epitope binding site that comprises first and second variable domains derived from sequences (i) and (iii), wherein there is no further antibody domain between the first and second variable domains.
- Optionally, (i), (ii) and (iii) are 5′ of S-mu when the locus is a heavy chain locus. Optionally, Optionally, (i) is 5′ of S-mu when the locus is a heavy chain locus and (ii) and (iii) are downstream of S-mu.
- or
- A non-human vertebrate (eg, a mouse or a rat), wherein the vertebrate comprises lymphocytic cells, each cell genome comprising
- (i) an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region (eg, a heavy chain variable region), a first switch, a mu constant region, a second switch and a non-mu (eg, gamma) constant region; wherein the heavy chain locus of each cell is capable of undergoing IgM to the non-mu (eg, IgG) isotype switching; and
- wherein
- (ii) the non-mu constant region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and a first variable domain (eg, a VL domain), wherein following isotype switching the vertebrate expresses polypeptide chains comprising (in N- to C-terminal direction) an epitope binding site comprising first and second antibody variable domains derived respectively from the first variable domain nucleotide sequence said from said variable region of the heavy chain locus.
- 2.
- Multivalent
- A non-human vertebrate cell (eg, a mouse cell or a rat cell), the cell genome comprising
- (i) an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region, a first switch, a mu constant region, a second switch and a non-mu (eg, gamma) constant region; wherein the heavy chain locus of each cell is capable of undergoing IgM to a non-mu (eg, IgG) isotype switching; and
- wherein
- (ii) the non-mu constant region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, for expressing a multivalent polypeptide chain comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the heavy chain locus, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes.
- or
- In vivo Guided Selection
- A non-human vertebrate cell (eg, a mouse cell or a rat cell) whose genome comprises an Ig locus comprising (in 5′ to 3′ orientation) (i) an unrearranged human variable region (eg, a heavy chain variable region) for encoding a first variable domain, (ii) a sequence encoding an optional linker and (iii) a rearranged sequence of a second variable domain (eg, a VL domain), wherein sequence (i) is capable of undergoing rearrangement so that the cell produces antibody chains each having an epitope binding site that comprises first and second variable domains derived from sequences (i) and (iii), wherein there is no further antibody domain between the first and second variable domains.
- or
- A non-human vertebrate cell (eg, a mouse cell or a rat cell), the cell genome comprising
- (i) an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region (eg, a heavy chain variable region), a first switch, a mu constant region, a second switch and a non-mu (eg, gamma) constant region; wherein the heavy chain locus of each cell is capable of undergoing IgM to the non-mu (eg, IgG) isotype switching; and
- wherein
- (ii) the non-mu constant region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and a first variable domain (eg, a VL domain), for expressing polypeptide chains comprising (in N- to C-terminal direction) an epitope binding site comprising first and second antibody variable domains derived respectively from the first variable domain nucleotide sequence said from said variable region of the heavy chain locus.
- 3. The vertebrate of clause 1 or the cell of clause 2, wherein the genome comprises a functional antibody light chain locus for expressing light chains; wherein the cells can express IgM antibodies comprising IgM-type heavy chains and light chains.
- 4. The vertebrate or cell of clause 3, wherein the light chain locus comprises means for turning off light chain expression, wherein functional light chains are not expressed after IgM to non-mu isotype switching.
- 5. The vertebrate or cell of any preceding clause, wherein the vertebrate expresses polypeptide chains comprising (in N- to C-terminal direction) (a) an antibody variable domain derived from said variable region of the heavy chain locus, an optional linker, an epitope binding moiety and a non-mu (eg, gamma) constant domain (eg, gamma Fc) or (b) an antibody variable domain derived from said variable region of the heavy chain locus, a non-mu (eg, gamma) constant domain (eg, gamma Fc), an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind the respective first and second epitopes.
- 6. The vertebrate or cell of any preceding clause, wherein the non-mu constant region is a gamma constant region and the heavy chain locus is capable of undergoing isotype switching to produce IgG antibodies comprising one or more IgG heavy chains in the absence of light chains, each heavy chain lacking a CH1 domain.
- 7.
- Multivalent
- A non-human vertebrate (eg, a mouse or a rat), wherein the vertebrate comprises lymphocytic cells whose genomes comprise an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged variable region and a non-mu (eg, gamma) constant region;
- wherein
- the non-mu constant region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, wherein the vertebrate expresses multivalent polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the heavy chain locus, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes.
- In an embodiment, there is no mu constant region between the rearranged variable region and the non-mu constant region.
- or
- In Vivo Guided Selection
- A non-human vertebrate (eg, a mouse or a rat), wherein the vertebrate comprises lymphocytic cells whose genomes comprise an antibody heavy or light chain locus comprising (in 5′ to 3′ direction) a rearranged variable region and a non-mu constant region;
- wherein
- the non-mu constant region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and the rearranged variable region which encodes a first variable domain, wherein following isotype switching the vertebrate expresses polypeptide chains comprising (in N- to C-terminal direction) an epitope binding site comprising second and first antibody variable domains derived respectively from a rearranged second variable domain nucleotide sequence and from the first variable domain nucleotide sequence, wherein the second nucleotide sequence has been rearranged in the vertebrate.
- 8. A non-human vertebrate cell (eg, a mouse cell or a rat cell) or a hybridoma, the cell genome comprising (in 5′ to 3′ direction) a rearranged variable region and a non-mu constant region;
- wherein
- the non-mu constant region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and the rearranged variable region which encodes a first variable domain, for expressing polypeptide chains comprising (in N- to C-terminal direction) an epitope binding site comprising second and first antibody variable domains derived respectively from a rearranged second variable domain nucleotide sequence and from the first variable domain nucleotide sequence, wherein the second nucleotide sequence has been rearranged in the cell.
- In an embodiment of the vertebrate or cell, there is no mu constant region between the rearranged variable region encoding the first variable domain and the non-mu constant region.
- 9. The vertebrate of clause 7 or the cell of clause 8, wherein the heavy chain locus has undergone IgM to non-mu (eg, IgG) isotype switching.
- 10. The vertebrate or cell of any preceding clause, wherein the linker and/or epitope binding moiety nucleotide sequence is provided in place of a CH1 domain gene segment in the non-mu constant region.
- or
- The vertebrate or cell of any preceding clause, wherein said linker or first variable domain nucleotide sequence is provided in place of a CH1 domain gene segment in the non-mu constant region.
- 11.
- Multivalent
- A non-human vertebrate (eg, a mouse or a rat), wherein the vertebrate comprises lymphocytic cells, the genome of each cell comprising an antibody light chain locus which comprises (in 5′ to 3′ direction) a rearranged or unrearranged variable region and a second region;
- wherein
- the second region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, wherein following immunisation the vertebrate expresses polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the light chain locus, an optional linker and an epitope binding moiety , wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes.
- or
- In Vivo Guided Selection
- A non-human vertebrate (eg, a mouse or a rat), wherein the vertebrate comprises lymphocytic cells, the genome of each cell comprising an antibody light chain locus which comprises (in 5′ to 3′ direction) an unrearranged variable region (eg, a heavy chain variable region) and a second region (which is a non-mu constant region);
- wherein
- the second region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and a first variable domain (eg, a VL domain), wherein following immunisation the vertebrate expresses polypeptide chains comprising (in N- to C-terminal direction) an epitope binding site comprising first and second antibody variable domains derived respectively from the first variable domain nucleotide sequence said from said variable region of the light chain locus.
- 12.
- Multivalent
- A non-human vertebrate cell (eg, a mouse cell or a rat cell) or a hybridoma, wherein the cell genome comprises an antibody light chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region and a second region;
- wherein
- the second region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, for expressing a polypeptide chain comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the light chain locus, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes.
- or
- In Vivo Guided Selection
- A non-human vertebrate cell (eg, a mouse cell or a rat cell) or a hybridoma, wherein the cell genome comprises an antibody light chain locus comprising (in 5′ to 3′ direction) an unrearranged or rearranged variable region (eg, a heavy chain variable region) and a second region;
- wherein
- the second region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and a first variable domain (eg, a VL domain), for expressing polypeptide chains comprising (in N- to C-terminal direction) an epitope binding site comprising first and second antibody variable domains derived respectively from the first variable domain nucleotide sequence said from said variable region of the light chain locus.
- 13. The vertebrate of clause 11 or the cell of clause 12, which is according to the vertebrate or cell of any one of clauses 1 to 10.
- 14. A non-human vertebrate or cell according to clause 13, wherein the genome comprises said heavy and light chain loci, wherein said polypeptide chain variable domains derived from the heavy chain locus form binding sites with the polypeptide chain variable domains derived from the light chain locus, wherein the binding sites specifically bind the first epitope.
- 15. The vertebrate or cell of clause 14, wherein the epitope binding moieties of the polypeptide chains derived from the heavy and light chain loci are antibody variable domains, wherein the epitope binding domains of the chains derived from the heavy chain locus associate with the epitope binding domains of the chains derived from the light chain locus to form binding sites that specifically bind the second epitope.
- 16. A method of producing multivalent polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes, the method comprising
- (a) expressing in a non-human vertebrate (eg, a mouse or a rat) IgM antibodies in immature B-cells, wherein the antibodies comprise heavy and light chains expressed from heavy and light chain loci respectively;
- (b) immunising the vertebrate with a first predetermined antigen bearing the first epitope and obtaining isotype switching to expression from a non-mu (eg, gamma) constant region in at least some of the heavy chain loci and expression of variable regions that have undergone somatic hypermutation; and
- (c) selecting one or more polypeptide chains from said immunised vertebrate by selection for variable regions that bind said first epitope, wherein each selected chain comprises a somatically hypermutated variable region that specifically binds the epitope; and
- wherein the method comprises
- (d) providing the nucleotide sequence of the epitope binding moiety in the non-mu constant region of heavy chain loci in the genome of the vertebrate, wherein the polypeptide chains selected in step (c) bind the first and second epitopes.
- 17. The method of clause 16, wherein each somatically mutated variable region in step (b) is provided by an non-mu-type (eg, IgG-type) heavy chain that lacks a CH1 domain.
- 18. The method of clause 16 or 17, wherein step (b) comprises expressing the somatically mutated variable regions in the absence of light chain expression.
- 19. A method of producing in a non-human vertebrate (eg, a mouse or a rat) multivalent polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes), the method comprising
- (a) immunising the vertebrate with a first predetermined antigen bearing the first epitope, obtaining isotype switching to expression from a non-mu (eg, gamma) constant region in at least some of the heavy chain loci of the vertebrate and expression of variable regions that have undergone somatic hypermutation; and
- (b) selecting one or more polypeptide chains from said immunised vertebrate by selection for variable regions that bind said first epitope, wherein each selected chain comprises a somatically hypermutated variable region that specifically binds the epitope; and
- wherein
- (d) providing the nucleotide sequence of the epitope binding moiety in the non-mu constant region of heavy chain loci in the genome of the vertebrate, wherein the polypeptide chains selected in step (b) bind the first and second epitopes.
- 20. The method of clause 19, wherein each somatically mutated variable region in step (a) is provided by a non-mu-type (eg, IgG-type) heavy chain that lacks a CH1 domain.
- 21. The method of clause 19 or 20, wherein step (a) comprises expressing the somatically mutated variable regions in the absence of light chain expression.
- 22. The method of any one of clauses 19 to 21, wherein the vertebrate is according to any one of clauses 1 to 15.
- 23. The method of any one of clauses 19 to 22, further comprising isolating or synthesizing a nucleic acid comprising a nucleotide sequence encoding a polypeptide chain selected in the method; and optionally humanising the sequence.
- 24. A multispecific polypeptide chain obtained by the method of any one of clauses 19 to 23 or a derivative thereof that specifically binds the first and second epitopes.
- 25. A multivalent (eg, multispecific) polypeptide chain having (in N- to C-terminal direction) the structure V-X-L-E-L-C, where
- (i) V is an antibody variable domain that specifically binds a first epitope,
- (ii) X is absent, an antibody hinge region or an antibody constant region comprising a constant domain,
- (iii) Each L is an optional linker,
- (iv) E is an epitope binding moiety that specifically binds a second epitope, and
- (v) C is absent or an antibody constant region comprising a constant domain (eg, C is a human gamma Fc),
- wherein V is a rearranged antibody variable domain derived from the rearrangement of variable region gene segments in vivo in a non-human vertebrate with somatic hypermutation of the resulting variable region gene in a nucleotide sequence also encoding for the epitope binding moiety; and
- wherein the rearranged antibody variable domain comprises endogenous AID-pattern somatic hypermutations.
- 26. A method of producing a polypeptide chain of clause 25, the method comprising immunising a non-human vertebrate (eg, a mouse or a rat) with the first epitope and causing somatic hypermutation of a variable region gene in a nucleotide sequence also encoding for the epitope binding moiety (E), the variable region gene encoding V; and isolating said polypeptide chain comprising V and E.
- 27. The polypeptide of clause 25 or the method of clause 26, wherein the epitope binding moiety lacks endogenous AID-pattern somatic hypermutations.
- 28. The polypeptide of clause 25 or the method of clause 26, wherein the epitope binding moiety comprises endogenous AID-pattern somatic hypermutations.
- 29. A dimer of polypeptides according to any one of clauses 25 to 28, wherein the dimer lacks antibody light chains.
- 30. A polypeptide, dimer or method according to any one of clauses 25 to 29, wherein the polypeptide has (in N- to C-terminal direction) the structure V-N-E; V-CH1-M-CH2-CH3-L-E; or V-M-CH2-CH3-L-E, wherein N is L together with an optional antibody hinge region; and M is an optional antibody hinge region.
- 31. A polypeptide, dimer or method according to any one of clauses 25 to 30, wherein V is peptide bonded to a second antibody variable domain (V2) to form a binding site comprising first and second variable domains that specifically binds the first epitope; optionally wherein V and V2 are provided as an scFv.
- 32. The polypeptide, dimer or method of any one of clauses 25 to 31, wherein the polypeptide lacks a CH1 domain.
- 33. A polypeptide, dimer or method according to any one of clauses 25 to 31, wherein the polypeptide comprises a CH1 domain and the polypeptide is present in first and second copies in antibody, the first polypeptide being associated with a first antibody light chain, and the second copy being associated with a second antibody light chain.
- 34. An antibody comprising the dimer, polypeptide chain or a humanised version thereof as recited in any one of clauses 25 to 33.
- 35. A bivalent (eg, bispecific) antibody comprising a dimer of a heavy chain, wherein each heavy chain is a polypeptide according to any one of clauses 25, 27, 28 and 30 to 33 and has in N- to C-terminal direction) the structure
- V-CH1-M-CH2-CH3-L-E,
- V-M-CH2-CH3-L-E,
- V-L-E-L-CH1-M-CH2-CH3,
- V-L-E-L-M-CH2-CH3,
- V-CH1-N-E,
- V-L-E-N-CH1, or
- V-N-E-L-CH1,
- wherein N is L together with an optional antibody hinge region; M is an optional antibody hinge region;
- optionally wherein the constant domains are human constant domains.
- 36. The antibody of clause 35, wherein the antibody comprises two copies of a light chain, each heavy chain being associated with a respective light chain, wherein V in each heavy chain forms an antigen binding site with the variable domain of its respective light chain and the variable domain of each light chain comprises endogenous AID-pattern somatic hypermutations.
- 37. A multivalent (eg, multispecific) antibody comprising heavy chains associated with light chains,
- wherein
- Each heavy chain is a polypeptide chain as recited in any one of clauses 25 and 27 to 35, wherein E is an antibody variable domain;
- Each light chain is a polypeptide chain having (in N- to C-terminal direction) the structure V′-L′-E′-L′-C′, where
- (i) V′ is an antibody variable domain,
- (ii) Each L′ is an optional linker,
- (iv) E′ is an epitope binding moiety, and
- (v) C′ is absent or an antibody constant region comprising a constant domain (eg, C′ is a human CL);
- wherein
- V′ is a rearranged antibody variable domain derived from the rearrangement of variable region gene segments in vivo in a non-human vertebrate with somatic hypermutation of the resulting variable region gene in a nucleotide sequence also encoding for E′; and
- V′ comprises endogenous AID-pattern somatic hypermutations;
- V and V′ form a first binding site that specifically binds a first epitope; and
- Optionally E and E′ form a second binding site that specifically binds a second epitope when E′ is an antibody variable domain.
- 38. An antigen-binding polypeptide comprising a protein scaffold which is linked to one or more epitope binding moieties wherein the antigen-binding polypeptide comprises at least two epitope binding sites at least one of which is provided by an epitope binding moiety and at least one of which is provided by a first antibody variable domain paired with a second antibody variable domain,
- wherein each variable domain is a rearranged antibody variable domain derived from the rearrangement of variable region gene segments in vivo in a non-human vertebrate with somatic hypermutation of the resulting variable region gene in a nucleotide sequence also encoding for one or more of the epitope binding moiety(ies); and
- wherein the rearranged antibody variable domains comprise endogenous AID-pattern somatic hypermutations.
- or
- An antigen-binding polypeptide comprising a protein scaffold which is linked to one or more epitope binding moieties wherein the antigen-binding polypeptide comprises at least two epitope binding sites at least one of which is provided by an epitope binding moiety and at least one of which is provided by a first antibody variable domain paired with a second antibody variable domain,
- wherein the first variable domain is a rearranged antibody variable domain derived from the rearrangement of variable region gene segments in vivo in a non-human vertebrate with somatic hypermutation of the resulting variable region gene in a nucleotide sequence also encoding for the second variable domain and the one or more of the epitope binding moiety(ies); and
- wherein the rearranged first antibody variable domain comprises endogenous AID-pattern somatic hypermutations.
- 39. The polypeptide of clause 38, comprising at least one of said epitope binding moiety linked to the protein scaffold by a peptide linker which comprises at least 10 amino acids (eg, between 10 and 50 amino acids).
- 40. A multispecific antigen binding polypeptide, dimer or antibody according to any one of clauses 25 and 27 to 39, which is capable of recruiting the activity of a human immune effector cell by specifically binding to an effector antigen (eg, human CD3) located on the human immune effector cell, a first of the epitope binding sites of the polypeptide, dimer or antibody being capable of specifically binding to said effector antigen, and a second of the epitope binding sites of the polypeptide, dimer or antibody being capable of specifically binding to a target antigen (eg, human EpCAM or human CD19) other than the effector antigen; optionally wherein said target antigen is located on a target cell other than said human immune effector cell.
- 41. The vertebrate, cell polypeptide, dimer or antibody of any preceding clause, wherein the second epitope is provided by human immune effector cell antigen (eg, human CD3).
- 42. The vertebrate, cell polypeptide, dimer or antibody of any preceding clause, wherein the first epitope is provided by a target antigen (eg, human EpCAM or human CD19) other than the effector antigen; optionally wherein said target antigen is an antigen of a target cell other than said human immune effector cell.
- 43. The vertebrate, cell polypeptide, dimer or antibody of any preceding clause, wherein the epitope binding moiety is selected from the group consisting of an antibody variable domain (eg, a VL or a VH, an antibody single variable domain (domain antibody or dAb), a camelid VHH antibody single variable domain, a shark immunoglobulin single variable domain (NARV), a Nanobody™ or a camelised VH single variable domain); a T-cell receptor binding domain; an immunoglobulin superfamily domain; an agnathan variable lymphocyte receptor; a fibronectin domain (eg, an Adnectin™); an antibody constant domain (eg, a CH3 domain, eg, a CH2 and/or CH3 of an Fcab™) wherein the constant domain is not a functional CH1 domain; an scFv; an (scFv)2; an sc-diabody; an scFab; a centyrin and an epitope binding domain derived from a scaffold selected from CTLA-4 (Evibody™); a lipocalin domain; Protein A such as Z-domain of Protein A (eg, an Affibody™ or SpA); an A-domain (eg, an Avimer™ or Maxibody™); a heat shock protein (such as and epitope binding domain derived from GroEI and GroES); a transferrin domain (eg, a trans-body); ankyrin repeat protein (eg, a DARPin™); peptide aptamer; C-type lectin domain (eg, Tetranectin™); human γ-crystallin or human ubiquitin (an affilin); a PDZ domain; scorpion toxin; and a kunitz type domain of a human protease inhibitor.
- 44. The vertebrate, cell polypeptide, dimer or antibody of any preceding clause, wherein the or each N-terminal variable domain or 5′-terminal variable region is a human variable domain or region.
- 45. The vertebrate, cell polypeptide, dimer or antibody of any preceding clause, wherein each constant region or domain is an endogenous non-human vertebrate constant region or domain.
- 46. A non-human vertebrate (eg, a mouse or a rat), wherein
- (a) the vertebrate expresses IgM antibodies comprising heavy and light chains encoded by antibody heavy and light chain loci respectively;
- (b) the vertebrate is capable of expressing non-mu (eg, IgG) antibodies, each non-mu antibody heavy chain lacking a functional CH1 domain; and
- (c) the IgM antibodies are expressed by lymphocytic cells, each cell comprising a functional light chain locus for expressing light chains of IgM antibodies expressed by the cell; and
- wherein
- (d) the non-mu antibodies are expressed by lymphocytic cells, each cell lacking a functional light chain locus wherein non-mu antibodies are expressed by the cell in the absence of light chain expression.
- 47. A non-human vertebrate (eg, a mouse or a rat), wherein the vertebrate comprises lymphocytic cells whose genomes comprise
- (i) an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region, a first switch, a mu constant region, a second switch and a non-mu (eg, gamma) constant region lacking a CH1 gene segment;
- (ii) a functional antibody light chain locus for expressing light chains;
- wherein the cells can express IgM antibodies comprising IgM-type heavy chains and light chains;
- wherein the heavy chain locus of each cell is capable of undergoing isotype switching to produce non-mu (eg, IgG) antibodies comprising one or more non-mu-type (eg, IgG-type) heavy chains in the absence of light chains, each heavy chain lacking a CH1 domain; and
- (iii) means for turning off light chain expression, wherein functional light chains are not expressed after isotype switching to said non-mu-type antibodies.
- 48. A non-human vertebrate cell (eg, a mouse cell or a rat cell), wherein the cell genome comprises
- (i) a functional antibody light chain locus for expressing light chains;
- (ii) an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region, a first switch, a mu constant region, a second switch and a non-mu (eg, gamma) constant region lacking a CH1 gene segment for expressing IgM antibodies comprising IgM-type heavy chains and light chains; and for IgM to non-mu (eg, IgG) isotype switching to produce non-mu (eg, IgG) antibodies comprising one or more non-mu-type heavy chains in the absence of light chains, each heavy chain lacking a CH1 domain; and
- (iii) means for turning off light chain expression, wherein functional light chains are not expressed after isotype switching to said non-mu-type antibodies.
- 49. The vertebrate or cell of any one of clauses 46 to 48, wherein the means for turning off light chain expression comprises a nucleotide sequence (eg, a light chain variable region or a CL region of the light chain locus) that is essential for functional light chain expression from said light chain locus, wherein the nucleotide sequence is functional in immature B-cells expressing IgM, but the nucleotide sequence is absent or substantially non-functional in mature B-cells expressing said non-mu-type antibodies.
- 50. The vertebrate or cell of any one of clauses 46 to 49, wherein the means for turning off light chain expression comprises a nucleotide sequence comprising a regulatory element (eg, a promoter) for driving light chain expression from said light chain locus in immature B-cells expressing IgM, and wherein the regulatory element is substantially inactive or absent in mature B-cells expressing said non-mu-type antibodies.
- 51. The vertebrate or cell of clause 49 or 50, wherein the nucleotide sequence or regulatory element is flanked by first and second combination elements (eg, site-specific recombination elements) and wherein the genome comprises a gene(s) that encodes a corresponding recombinase(s) or transposase(s), wherein the gene is inactive in immature B-cells expressing IgM, but active to cut at the first and second recombination elements and inactivate the nucleotide sequence or regulatory element in mature B-cells expressing said non-mu-type antibodies.
- 52. The vertebrate or cell of clause 50, wherein the regulatory element is induced in immature B-cells expressing IgM and/or repressed in mature B-cells expressing said non-mu-type antibodies.
- 53. The vertebrate or cell of any one of clauses 46 to 48, wherein the means for turning off light chain expression is another locus in the genome for expressing a polypeptide chain comprising a rearranged light chain variable domain.
- 54. The vertebrate or cell of clause 53, wherein said another locus is a heavy chain locus as defined in clause 47 or 48, wherein following said isotype switching the heavy chain locus encodes an antibody chain comprising said rearranged light chain variable domain.
- 55. The vertebrate or cell of clause 54, wherein the antibody chain further comprises a second antibody variable domain; optionally wherein the light chain variable domain and said second antibody variable domain specifically bind respective first and second epitopes that are different.
- 56. The vertebrate or cell of any one of clauses 53 to 55, wherein the rearranged light chain variable domain is derived from said unrearranged variable region of the heavy chain locus as defined in clause 47 or 48, wherein the unrearranged variable region of the heavy chain locus comprises one or more light chain V gene segments 5′ of one or more light chain J gene segments.
- 57. The vertebrate or cell of clause 54 or 55, wherein the antibody chain comprises (in 5′ to 3′ direction) a variable domain derived from said variable region of the heavy chain locus as defined in clause 47 or 48, an optional linker and said rearranged light chain variable domain.
- 58. The vertebrate or cell of any one of clauses 47, 48 and 49 to 57 when dependent from clause 47 or 48, wherein the non-mu constant region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, wherein following isotype switching the vertebrate expresses multivalent polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the heavy chain locus, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes.
- 59. The vertebrate of clause 58, wherein non-mu constant region comprises one or more non-mu constant region gene segments (eg, CH2 and CH3 gene segments) 3′ of said epitope binding moiety, wherein following isotype switching the vertebrate expresses multivalent polypeptide chains each comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the heavy chain locus, an optional linker, an epitope binding moiety and said one or more non-mu constant region gene segments.
- 60. The vertebrate or cell of clause 58 or 59, wherein a poly(A) site is 3′ of the nucleotide sequence encoding the epitope binding moiety, wherein following isotype switching the vertebrate expresses multivalent polypeptide chains having or consisting of (in N- to C-terminal direction) the structure V-X-L-E, where V is an antibody variable domain derived from said variable region of the heavy chain locus, X is absent an antibody hinge region or a polypeptide encoded by the gamma constant region, L is the optional linker and E is the epitope binding moiety; optionally wherein the vertebrate expresses V-X-L-E or V-L-E dimers.
- 61. The vertebrate or cell of clause 58 or 59, wherein a poly(A) site is 3′ of the nucleotide sequence encoding the one or more non-mu constant region gene segments, wherein following isotype switching the vertebrate expresses multivalent polypeptide chains having or consisting of (in N- to C-terminal direction) the structure V-X-L-E-L-C, where V is an antibody variable domain derived from said variable region of the heavy chain locus, X is absent an antibody hinge region or a polypeptide encoded by the non-mu constant region, L is the optional linker, E is the epitope binding moiety and C, is the one or more non-mu constant region gene segments (eg, gamma Fc); optionally wherein the vertebrate expresses V-X-L-E-L-C or V-L-E-L-C dimers.
- 62. The vertebrate or cell of any one of clauses 46 to 61, wherein the epitope binding moiety is selected from the group consisting of an antibody variable domain (eg, a VL or a VH, an antibody single variable domain (domain antibody or dAb), a camelid VHH antibody single variable domain, a shark immunoglobulin single variable domain (NARV), a Nanobody™ or a camelised VH single variable domain); a T-cell receptor binding domain; an immunoglobulin superfamily domain; an agnathan variable lymphocyte receptor; a fibronectin domain (eg, an Adnectin™); an antibody constant domain (eg, a CH3 domain, eg, a CH2 and/or CH3 of an Fcab™) wherein the constant domain is not a functional CH1 domain; an scFv; an (scFv)2; an sc-diabody; an scFab; a centyrin and an epitope binding domain derived from a scaffold selected from CTLA-4 (Evibody™); a lipocalin domain; Protein A such as Z-domain of Protein A (eg, an Affibody™ or SpA); an A-domain (eg, an Avimer™ or Maxibody™); a heat shock protein (such as and epitope binding domain derived from GroEI and GroES); a transferrin domain (eg, a trans-body); ankyrin repeat protein (eg, a DARPin™); peptide aptamer; C-type lectin domain (eg, Tetranectin™); human γ-crystallin or human ubiquitin (an affilin); a PDZ domain; scorpion toxin; and a kunitz type domain of a human protease inhibitor.
- 63. The vertebrate or cell of any one of clauses 46 to 62, wherein the vertebrate comprises lymphocytic cells that have undergone isotype switching to produce said non-mu-type (eg, IgG-type) antibodies; or the cell has undergone isotype switching to produce said non-mu-type (eg, IgG-type) antibodies.
- 64. The vertebrate or cell of any one of clauses 46 to 63, wherein the vertebrate has been immunised with a predetermined antigen, the vertebrate expressing non-mu-type (eg, IgG-type) antibodies lacking a CH1 domain and comprising a variable domain that specifically binds the predetermined antigen; or the cell is isolated from such a vertebrate.
- 65. The vertebrate or cell of any one of clauses 46 to 64, wherein the or each N-terminal variable domain or 5′-terminal variable region is a human variable domain or region.
- 66. The vertebrate or cell of any one of clauses 46 to 65, wherein each constant region or domain is an endogenous non-human vertebrate constant region or domain.
- 67. The vertebrate or cell of any one of clauses 46 to 66, wherein the lymphocytic cells comprise B-cells expressing said non-mu antibodies or bivalent polypeptide chains, wherein the non-mu antibodies or multivalent chains are specific for an antigen that is foreign to said non-human vertebrate; or wherein said non-human vertebrate cell is such a B-cell.
- 68. An immortalised B-cell or hybridoma produced from a B-cell recited in clause 67.
- 69. A non-mu-type (eg, IgG-type) antibody or multivalent chain isolated from a B-cell or hybridoma of clause 67 or 68; or a humanised version thereof wherein non-human constant domains have been replaced with human constant domains.
- 70. A method of producing polypeptide chains comprising somatically hypermutated variable regions in a non-human vertebrate (eg, a mouse or a rat), the method comprising
- (a) expressing in the vertebrate IgM antibodies in immature B-cells, wherein the antibodies comprise heavy and light chains expressed from heavy and light chain loci respectively;
- (b) immunising the vertebrate with a predetermined epitope and obtaining isotype switching in at least some of the heavy chain loci and expression of non-mu (eg, IgG) antibodies that have undergone somatic hypermutation, wherein the antibodies comprise heavy chains that lack a CH1 domain and comprise variable regions that specifically bind the antigen; and
- (c) selecting one or more polypeptide chains from said immunised vertebrate by selection for variable regions that bind said epitope, wherein each selected chain comprises a somatically hypermutated variable region that specifically binds the epitope; and
- the method further comprising expressing the non-mu antibodies in step (b) in the absence of light chain expression.
- 71. The method of clause 70, comprising isolating from the immunised vertebrate a B-cell that expresses a polypeptide chain comprising a somatically hypermutated variable region that binds the epitope; and optionally immortalising the cell or producing a hybridoma therefrom.
- 72. The method of clause 70 or 71, comprising obtaining a nucleotide sequence that encodes a selected polypeptide chain comprising a somatically hypermutated variable region that binds the epitope, and introducing the nucleotide sequence into a expression vector for expression of the polypeptide chain or a humanised version thereof; optionally wherein vector is in a host cell.
- 73. The method of any one of clauses 70 to 72, wherein the vertebrate is according to any one of clauses 46 to 69.
- 74. A multispecific polypeptide chain obtained by the method of any one of clauses 70 to 73 or a derivative thereof that specifically binds the epitope.
- 75. A non-human vertebrate (eg, a mouse or a rat) whose genome comprises an antibody heavy chain locus and an antibody light chain locus,
- (a) the light chain locus comprising (in 5′ to 3′ direction) a light chain variable region and a constant region for expressing light chains in lymphocytic cells expressing IgM antibodies; and
- (b) means for turning off light chain expression in lymphocytic cells expressing non-mu (eg, IgG) antibodies.
- 76. A non-human vertebrate cell (eg, a mouse cell or a rat cell) or hybridoma whose genome comprises an antibody heavy chain locus and an antibody light chain locus, the light chain locus comprising
- (a) (in 5′ to 3′ direction) a light chain variable region and a constant region for expressing light chains in lymphocytic cells expressing IgM antibodies; and
- (b) means for turning off light chain expression in lymphocytic cells expressing non-mu (eg, IgG) antibodies.
- 77. The vertebrate of clause 73 or cell of clause 74, wherein the means for turning off light chain expression is as recited in any one of clauses 49 to 56.
- 78. A non-human vertebrate (eg, a mouse or a rat), wherein the vertebrate comprises lymphocytic cells, each cell genome comprising an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region and a mu constant region comprising a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, wherein the vertebrate expresses multivalent polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the heavy chain locus, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes.
- 79. A non-human vertebrate cell (eg, a mouse cell or a rat cell), wherein the cell genome comprises an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region and a mu constant region comprising a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, wherein the cell expresses multivalent polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the heavy chain locus, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes.
- 80. A non-human (eg, rat or mouse) vertebrate or cell that expresses multivalent, multispecific heavy chains (or dimers thereof) comprising the structure V-L-E or V-L-E-L (eg, V-L-E-Fc or V-L-E-L-Fc), where V is an N-terminal antibody variable domain, L is an optional linker and E is an epitope binding moiety, wherein V and E specifically bind respective first and second antigens, wherein the antigens are different.
- 81. The vertebrate or cell of clause 80, wherein V is a human variable domain.
- 82. A multivalent (eg, multispecific) light chain having (in N- to C-terminal direction) the structure V-X-L-E-L-C, where
- (i) V is an antibody variable domain (eg, a VL) that specifically binds a first epitope,
- (ii) X is absent, or an antibody constant region comprising a constant domain (eg, a CL),
- (iii) Each L is an optional linker,
- (iv) E is an epitope binding moiety that specifically binds a second epitope, and
- (v) C is absent or an antibody constant region comprising a constant domain (eg, C is a CL),
- wherein V is a rearranged antibody variable domain derived from the rearrangement of variable region gene segments in vivo in a non-human vertebrate with somatic hypermutation of the resulting variable region gene in a nucleotide sequence also encoding for the epitope binding moiety; and
- wherein the rearranged antibody variable domain comprises endogenous AID-pattern somatic hypermutations.
- 83. A dimer of light chains according to clause 82.
- 84. A non-human vertebrate (eg, a mouse or a rat), wherein the vertebrate comprises lymphocytic cells, each cell genome comprising
- (i) an antibody light chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region, a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, and a CL gene segment, wherein the vertebrate expresses multivalent light chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the light chain locus, an optional linker, an epitope binding moiety and a CL domain, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes (which can be any epitopes as defined herein); or
- (ii) an antibody light chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region, a CL gene segment, a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, wherein the vertebrate expresses multivalent light chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the light chain locus, a CL domain, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes (which can be any epitopes as defined herein).
- 85. A non-human vertebrate cell (eg, a mouse cell or a rat cell), the cell genome comprising
- (i) an antibody light chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region, a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, and a CL gene segment, wherein the cell expresses multivalent light chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the light chain locus, an optional linker, an epitope binding moiety and a CL domain, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes (which can be any epitopes as defined herein); or
- (ii) an antibody light chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region, a CL gene segment, a nucleotide sequence encoding an optional linker and a predetermined epitope binding moiety, wherein the cell expresses multivalent light chains comprising (in N- to C-terminal direction) an antibody variable domain derived from said variable region of the light chain locus, a CL domain, an optional linker and an epitope binding moiety, wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes (which can be any epitopes as defined herein).
- 86. A polypeptide comprising a binding site specific for an epitope, the binding site having the structure V1-L-E (optionally V1-L-V2), where V1 and V2 are antibody variable domains (eg, VH and VL respectively or each a VH), E is an epitope binding moiety and L is an optional peptide linker (eg, of 20, 15 or 10 or less amino acids); and wherein V1 is derived from the rearrangement of human variable region gene segments in vivo in a non-human vertebrate with somatic hypermutation of the resulting variable region gene in a nucleotide sequence also encoding E, wherein V1 comprises endogenous AID-pattern somatic hypermutations. Here “endogenous” refers to a pattern caused by AID that is endogenous to the vertebrate (eg, caused by mouse AID where the vertebrate is a mouse).
- 87. A method of producing a polypeptide according to clause 86, the method comprising immunising a non-human vertebrate with said epitope and obtaining somatic hypermutation by endogenous AID of an Ig locus to produce a mutated Ig locus encoding V1 and E; and isolating the polypeptide and/or a nucleic acid encoding the polypeptide.
- 88. A non-human vertebrate (eg, a mouse or a rat) or cell (eg, a mouse cell or a rat cell), wherein an Ig heavy or light chain locus of the genome of the vertebrate or cell comprises (in 5′ to 3′ orientation) (i) an unrearranged human variable region for encoding a first variable domain, (ii) a sequence encoding an optional linker and (iii) a sequence encoding an epitope binding moiety (optionally a rearranged sequence of a second variable domain).
- In an example, the vertebrate is according to clause 1, 7 or 11. In an embodiment, the polypeptide or nucleic acid is modified or mutated after isolation to produce (or encode) a polypeptide derivative that specifically binds the epitope.
- 89. Use of first and second rearranged antibody variable domains in the manufacture of an antigen-binding polypeptide comprising a protein scaffold which is linked to one or more epitope binding moieties wherein the antigen-binding polypeptide comprises at least two epitope binding sites at least one of which is provided by an epitope binding moiety and at least one of which is provided by a first antibody variable domain paired with a second antibody variable domain, wherein the use comprises (i) obtaining the sequence of the first variable domain by rearrangement of variable region gene segments in vivo in a non-human vertebrate with somatic hypermutation of the resulting variable region gene in a nucleotide sequence also encoding for the second variable domain and the one or more of the epitope binding moiety(ies); and isolating the variable domain sequences wherein the rearranged first antibody variable domain sequence comprises endogenous AID-pattern somatic hypermutations; (ii expressing and combining the variable domains with the protein scaffold and one or more epitope binding moieties to produce said antigen-binding polypeptide; and (iii) isolating said polypeptide.
- Optionally, the second variable domain used in step (ii) comprises endogenous AID-pattern somatic hypermutations.
- 90. A method of producing a vertebrate of a non-human species, the method comprising breeding two vertebrates of said species together, wherein both of the vertebrates are according to any one of the clauses above.
- 91. The vertebrate, cell or method of any preceding clause, wherein a common light chain is expressed at the IgM stage.
- 92. The vertebrate or cell of any preceding clause, whose genome comprises means for expressing a common light chain at the IgM stage.
- The common light chain comprises, for example, a human Vκ1-39Jκ or Vκ3-20Jκ (eg, Vκ1-39Jκ5 or Vκ3-20Jκ1) or VpreB (such as human VpreB). These variable domains pair promiscuously with VH, so are useful for producing a repertoire of binding sites during antibody development in the vertebrate or cell.
- 1.
In an embodiment of any of the multivalent aspects of the invention, the first epitope is a human CD19 epitope and the second epitope is a human CD3 or CD16 epitope.
It will be understood that particular embodiments described herein are shown by way of illustration and not as limitations of the invention and (unless the context states otherwise) embodiments can be applied to any of the configurations of the invention described herein. The principal features of this invention can be employed in various embodiments without departing from the scope of the invention. Those skilled in the art will recognize, or be able to ascertain using no more than routine study, numerous equivalents to the specific procedures described herein. Such equivalents are considered to be within the scope of this invention and are covered by the claims. All publications and patent applications mentioned in the specification are indicative of the level of skill of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference. The use of the word “a” or “an” when used in conjunction with the term “comprising” in the claims and/or the specification may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one,” and “one or more than one.” The use of the term “or” in the claims is used to mean “and/or” unless explicitly indicated to refer to alternatives only or the alternatives are mutually exclusive, although the disclosure supports a definition that refers to only alternatives and “and/or.” Throughout this application, the term “about” is used to indicate that a value includes the inherent variation of error for the device, the method being employed to determine the value, or the variation that exists among the study subjects.
As used in this specification and claim(s), the words “comprising” (and any form of comprising, such as “comprise” and “comprises”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “includes” and “include”) or “containing” (and any form of containing, such as “contains” and “contain”) are inclusive or open-ended and do not exclude additional, unrecited elements or method steps
The term “or combinations thereof” as used herein refers to all permutations and combinations of the listed items preceding the term. For example, “A, B, C, or combinations thereof is intended to include at least one of: A, B, C, AB, AC, BC, or ABC, and if order is important in a particular context, also BA, CA, CB, CBA, BCA, ACB, BAC, or CAB. Continuing with this example, expressly included are combinations that contain repeats of one or more item or term, such as BB, AAA, MB, BBC, AAABCCCC, CBBAAA, CABABB, and so forth. The skilled artisan will understand that typically there is no limit on the number of items or terms in any combination, unless otherwise apparent from the context.
Any part of this disclosure may be read in combination with any other part of the disclosure, unless otherwise apparent from the context.
All of the compositions, populations, vertebrates, antibodies, repertoires and/or methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and/or methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.
The present invention is described in more detail in the following non limiting prophetic Examples.
EXAMPLES Example 1 Improved Production of Heavy Chain-Only AntibodiesFour-chain IgM antibodies (H2L2) can be produced by the combination of heavy chains from the heavy chain loci with light chains expressed from light chain loci in the vertebrates, such as during B-cell development (eg, for surface expression on immature splenic B-cells). By enabling a normal IgM stage, the invention provides for the development of normal B-cell compartments and primary variable region repertoires.
According to the invention, during the subsequent isotype (class) switching stage, such as following immunisation with target antigen, light chain expression is switched off by means of a conditional light chain knock-out (as further exemplified below). Thus, heavy chains expressed from the isotype-switched heavy chain locus can form heavy chain dimers lacking CH1 and light chains (ie, H2 antibodies). Thus, heavy chain-only expression and maturation during these later stages are performed by the vertebrate in vivo without being hampered by light chain expression (and avoiding the risk of heavy chain use being directed to undesirable 4-chain H2L2 antibody production and thus reduction of useful H2 yield and repertoire). This is, therefore, advantageous for maximising the production and repertoire of isotype-switched and matured heavy chain-only antibodies produced following immunisation of the vertebrate. In this way, the variable domains of the H2 antibodies are matured and selected without the influence of any light chain variable domain pairing, and thus the H2 variable domains are selected for performance in the H2 format. This is useful for selection of H2 antibodies for desirable antigen-binding affinity and also H2 solubility and expression in vivo. Thus, these H2 antibodies can provide a good source of antibody single variable domains (dAbs).
Furthermore, by accommodating a normal IgM early stage, the chances of maximising the heavy chain variable region repertoire (primary repertoire) are retained, and this provides a good repertoire from which H2 antibody V domains can subsequently be selected.
Example 2 Conditional Light Chain ExpressionConditional, or stage-specific, expression can be performed according to the invention during early stages of B-cell compartment and V repertoire development. As explained in Example 1, the invention provides for light chain expression to be switched off when isotype-switched (non-mu) heavy chains are being expressed.
(a) Generation of Cre Expression by AID Regulatory Elements
A landing pad identical to the one used for engineering the IGγ1 locus (see below) is targeted to the AID locus to replace a sequence comprising the 5th exon of the AID gene, a stop codon and 3′ UTR (mouse chromosome 6: coordinates 12256576-122564230) (
T2A is a self-cleaving peptide identified from Thosea asigna virus. T2A-mediated cleavage is a universal phenomenon in eukaryotic cells. Insertion of a T2A sequence between proteins allows stoichiometric expression of multiple proteins (Szymczak A L et al; “Development of 2A peptide-based strategies in the design of multicistronic vectors”; Expert Opin Biol Ther. 5: 627-638.).
The resulting genomic structure is shown at the foot of
(b) Generation of a Conditional IGκ Allele
A landing pad is targeted to the IGκ locus downstream of the intronic IGκ enhancer (iEκ) to replace the exon encoding the Cκ region (mouse chromosome 6: coordinates 70724743-70727043) in a mouse ES cell (
In an alternative design, other or additional portions of the kappa locus are flanked by lox sites so that they are deleted on expression of cre. For example, the scheme in
In one embodiment, only kappa chain expression is inactivated during the isotype-switched stage. In mice lambda chain expression is relatively low (on the order of only 5% of light chains normally), so it may be acceptable to provide conditional kappa chain expression only. In another embodiment, both kappa and lambda chain expression are conditional (eg, the genome also comprises Cλ flanked by lox sites), in that they occur in a stage-specific manner during the early IgM stage but not during expression of isotype-switched non-mu heavy chains.
Example 3 Genetic Engineering of the IGγ1 Locus & Multivalent Heavy Chains and AntibodiesReference is made to
At the top of
-
- Linker (eg, (GGGGS)3)-VH, where VH is an antibody single variable domain (dAb) of known antigen-binding specificity; or
- an scFv (VH-Linker-VL or VL-Linker-VH) of known antigen-binding specificity; or
- dAb-Linker-scFv.
Thus the binding moiety(ies) of BM are functional without need for light chain pairing.
Following VDJ rearrangement, IgM are expressed as 4-chain (H2L2) antibodies. Subsequently, following isotype (class) switching (eg, following immunisation with a target antigen) in a stage-specific light chain knock-out background (see Example 2), H2 antibodies of gamma-1 type are produced as dimers of multispecific heavy chains. Each heavy chain bears an affinity matured N-terminal VH domain which specifically binds the target antigen. Furthermore, each heavy chain comprises one or other antigen binding sites with the predetermined specificities chosen for BM. In this example, each BM is immediately N-terminal to a hinge-gammal Fc. Thus, the multispecific antibody usefully retains Fc function (such as FcRn binding and recycling and ADCC and/or CDC function).
In an alternative embodiment (where there is not stage-specific light chain knock-out), the isotype-switched heavy chains are expressed together with light chains as part of 4-chain (H2L2) antibodies. CH1 is present in the non-mu (eg, gamma) constant region of the heavy chain locus. In these antibodies, the N-terminal VH/VL pairs are matured and selected against target antigen that has been used for immunisation. In embodiments, it is desirable to position BM downstream of the non-mu CH1 gene segment or hinge so that the CH1 is free to pair with CL in light chains, the BM being present on a part of the constant region that does not require pairing with light chain domains. For example, the BM nucleotide sequence can be positioned immediately 5′ of the CH2 gene segment in the non-mu constant region (and thus immediately N-terminal of the CH2 or Fc in the product heavy chain and antibodies), or it can replace CH2 or CH3, or it can be 3′ of CH3 (ie, at the C-terminus of the Fc in a resulting product). For the latter, for example, the BM can encode optional linker-dAb (where the dAb is of known antigen binding specificity); the resulting 4-chain product is a mAb with a dAb at the C-terminus of each heavy chain.
Similar arrangements can be made for light chain loci, so that multivalent (eg, bispecific) light chains can be produced according to the invention.
Example 4 Producing Secreted Isotype-Switched & Matured Multivalent, Multispecific Antibodies & ChainsThe inventors have devised a method of enabling normal cell surface expression of membrane-bound 4-chain IgM during early stages of B-cell compartment and V repertoire development, and then followed by secretion of specifically designed multivalent heavy chains and antibodies of the invention that are class switched and matured (eg, following immunisation).
Reference is made to
Early during B-cell development, IgM is surface-expressed by virtue of heavy chains comprising membrane-anchor domains (encoded by M in the heavy chain loci).
Later, during the plasmablast and plasma cell stages, antibodies are secreted instead. This arises due to the stopping of transcription short of M and the activity of a polyA signal between CH3 and M (which is different to the polyA 3′ of M, as shown in
According to the present example of the invention, a stop codon (transcription termination site) and polyA can be inserted immediately 3′ of the sequence encoding the epitope binding moiety (or the 3′-most moiety). In
As shown in
Reference is made to
Inactivation of Endogenous Variable Region
Inversion of the endogenous mouse Vκ-Jκ gene segments inactivates endogenous kappa variable region expression.
Insertion of Conditional Vκ
Reference is made to
Use of a common light chain variable region human Vκ1-39Jκ or Vκ3-20Jκ (eg, Vκ1-39Jκ5 or Vκ3-20Jκ1) or VpreB (such as human VpreB) is, the inventors believe, useful since such variable regions promiscuously pair with human VH regions, and thus may have a scaffolding ability that is advantageous to the selection (in the 4-chain IgM stage) of human VH domain sequences that can provide a useful primary repertoire for subsequent selection of VH domains that perform in H2 antibodies following class switching, wherein the VH domains are not paired with VL domains.
The sequence comprises the following components (numbers relate to positions in the sequence):
-
- 1. Human Vκ1-39 promoter: 1894-2000
- 2. Rearranged human Vκ1-39/Jκ5: 2026-2537
- a. Leader exon: 2026-2080
- b. Vκ1-39/Jκ5 exon: 2205-2537
- 3. Mouse intronic sequence: 2538-4891
- 4. Lox2272/66: 4892-4925
- 5. Mouse CK exon: 5083-5402
- 6. Lox2272/71: 5425-5458
In another embodiment, the initial step of inverting the mouse variable region DNA is not carried out, but instead mouse Vκ expression is substantially inactivated by insertion of the common Vκ as described above.
Example 6 Common VL Domain Multispecifics: Generation of a Tandem ScFv Allele within the Cγ1 LocusReference is made to
A DNA fragment including an exon encoding the structure “linker (L1) -common human light chain VκJκ-linker (L2) -binding module” and a intron containing “alternative splicing site-polyadenylation site” is synthesized and inserted between loxP-PB3′LTR and PB3′LTR-promoter-less PuroΔTK gene-lox5171 cassettes to generate the insertion vector (
By placing the epitope binding moiety sequence (binding module) downstream of the mu switch and mu constant region (in this case in a gamma-1 region), this sequence is shielded away from the AID mutation hotspots in the locus.
During the naïve B-cell stage, the resulting locus can produce a membrane-bound heavy chain (eg, as part of a H2 antibody) consisting of the following structure in N- to C-terminal direction:
VH-L1-Common VL-L2-Binding Module-Hinge-Fc-Membrane Anchoring Region
In the present example, the Binding Module is an scFv that specifically binds human CD3 or human CD16A (eg, as further described below).
Following immunisation of a mouse with a target antigen (eg, human CD19 or human EpCAM), plasmablasts and plasma B-cells express secreted heavy chains (eg, as part of secreted H2 antibodies) of the structure shown by the penultimate line at the bottom of
scFv1-L2-Binding Module
Here, scFv1 is provided by “VH-L1-VL” where the VL is based on the common VL and scFv1 specifically binds the target antigen (eg, CD19 or EpCAM) used for immunisation. In the present example, a second scFv (Binding Module) specifically binds CD3 or CD16A.
Alternatively, there is secreted (see bottom line of
scFv1-L2-Binding Module-Hinge-Fc
It is possible to delete the polyA site between CH3 and M1, in order to eliminate production of this product, and thus favouring production of secreted scFv1-L2-Binding Module.
Advantageously, the binding domains have been combined and selected completely in vivo which avoids problems in the art that rely on one or more in vitro steps for such combination and selection.
Biobetters
In an example, a biobetter version of an existing antibody is produced, where the antibody is specific for an antigen. In this embodiment, the Binding Module comprises an scFv (or other binding format) that specifically binds the antigen and comprises the VH and VL pairing found in a binding site of the antibody. The common VL is the VL found in that pairing. The locus comprises human V, D and J gene segments 5′ of the common VL sequence. After production of non-human vertebrate from the resulting ES cell, the vertebrate is immunised with the antigen, and VDJ recombination and maturation is effected in vivo. Thus, matured VH is combined with the common VL and the Binding Module scFv to produce a product scFv-linker-scFv where each scFv is specific for the antigen. Using this method, products can be obtained that bind the antigen and a product can be chosen that has higher binding affinity to the target and/or binds a different epitope than the original starting antibody, or has more desirable therapeutic efficacy, expression or biophysical characteristics.
Thus, in an aspect of the invention, the epitopes bound by the product of the invention are epitopes found on the same antigen species.
In another example, the 3′ scFv Binding Module is omitted, so that a single scFv binding site at the N-terminus is produced, this being a binding site that has undergone guided selection in the presence of the VL from the pre-existing (original) antibody. As discussed above, the selected VH/VL pairing can be used for cloning into heavy and light chain expression vectors for producing an antibody that is a biobetter version of the original antibody.
Example 7 Common VL Domain Multispecifics: Anti-CD19/Anti-CD3/Anti-CD16 Bispecific ConstructsThe invention relates to multispecific polypeptides that are useful for recruiting immune effector cells in patients. Thus, the invention provides a multispecific antigen binding polypeptide, dimer or antibody which is capable of recruiting the activity of a human immune effector cell by specifically binding to (i) an effector antigen (eg, human CD3) located on a human immune effector cell and (ii) a target antigen (eg, human EpCAM or human CD19) other than the effector antigen; optionally wherein said target antigen is located on a target cell other than said human immune effector cell. An anti-CD19/anti-CD3 product is useful, for example, for treating cancer in a patient, such as leukemia or non-Hodgkin's lymphoma. To this end, the present example provides for such a product. Examples are shown in Table 1.
In alternative embodiments, each of L2 and L3 is separately selected from
Other alternatives are provided below.
See
The common VL and L1 (linker that is 5′ of the common VL as shown in
In another example, the Binding Module sequence is inserted 3′ of CH3 (
In an example, all Binding Module variable regions are human. Additionally or alternatively, the common VL is human. Thus, where human V, D and J gene segments are present in the IgH locus 5′ of the common VL sequence, following immunisation with the antigen, there are produced bispecific products whose binding domains are all human (the product would have a 5′ scFv specific for the antigen used for immunisation and a 3′ scFv specific for the other antigen). The 5′ binding domains would be selected and matured in vivo in response to immunisation. The 3′ binding domains would retain specificity for the antigen (eg, CD3 or CD16) against which they originally bound.
The general concept of linking V-regions with suitable linkers and connecting such created scFv or binding units with other binding modules to generate mono- or bispecific binding entities and the otpimisation of such linkers is described extensively in the literature (for example, see Neri D, Momo M, Prospero T, Winter G. J Mol Biol. 1995 Feb. 24; 246(3):367-73); Wright M J, Deonarain M P. Mol Immunol. 2007 April; 44(11):2860-9). The linker length can influence the molecular format that is preferentially produced. For example, monomeric bispecific tandem scFvs or so-called diabody formats where V regions form a VH-VL binding module are provided by two independent polypepeptide chains.
Examples for L3 sequences are:
Examples for L2 sequences are:
Examples of human anti-CD3 variable regions that can be employed in such bispecific therapeutics are: (see WO2010132872, the sequences of which are incorporated herein by reference for use in the present invention)
VL (which is SEQ ID NO: 4 in WO2010132872)
Human Anti CD3VH
Human Anti-CD3 VL
Further examples of CD3 binding VH and VLs are shown below
Anti CD3 VH
Anti CD3 VH
Anti CD3 VL
Anti CD3 VL
A suitable scFv binding module to CD3 could therefore be encoded by:
Translating into a polypeptide sequence of
Alternatively, VH and VL sequences that constitute binding moieties for CD16 effector cell recruitment could be used, which favours the recruitment of NK-cells rather than T-cells. Examples of human anti-CD16 variable regions are described in US2009021474.
Human Anti-CD16A VH
Human Anti-CD16A VL
Further examples of CD16 binding V-regions are described in EP1314741, the sequences of which are incorporated herein by reference for use in the present invention.
Anti-CD16 Binding VL
Anti-CD16 Binding VH
An example of a CD19 binding scFv VL-VH including a linker coding for GGGGSGGGGSGGGGS (G4S)3 (highlighted in bold)
An example of a CD19 binding scFv VH-VL including a linker coding for GGGGSGGGGSGGGGS (G4S)3 (highlighted in bold)
An example module as described in Table x with a fixed VL from a CD19 binding antibody and a scFv specific for human CD3 is encoded as:
Resulting in an amino acid sequence of
to which an N-terminal human VH domain generated in vivo in the vertebrate or cell of the invention will be fused in vivo as described above. VH domains for pairing with the encoded VL specific for CD19 can be generated for example by immunising transgenic vertebrates of the invention with human CD19. In vivo recombination of VDJ gene segments of the heavy chain locus in the vertebrate (eg, mouse) genome will then generate an scFv module consisting of a VH selected in vivo in the animal and a VL encoded in the genome of the vertebrate, that is specific for human CD19 connected via a linker to a binding module specific to human CD3 as outlined above.
Immunisation Procedures
Immunisation procedures for CD19 cell surface antigen have been described for the generation of monoclonal antibodies (PEZZUTTO, A., DORKEN, B., RABINOVITCH, P. S., LEDBETTER, J. A., MOLDENHAUER, G. and CLARK, E. A., CD19 monoclonal antibody HD37 inhibits anti-immunoglobulin-induced B cell activation and proliferation. J. Immunol.; Pezzutto A, Dorken B, Feller A, Moldenhauer G, Schwartz R, Wernet P, et al. HD37 monoclonal antibody: a useful reagent for further characterization of “non-T, non-B” lymphoid malignancies. In: Reinherz E L, Haynes B F, Nadler L M, Bernstein I D, editors. Leukocyte typing II. Proceedings of the 2nd International Workshop on Human Leukocyte Differentiation Antigens; 1984 Sep. 17-20; Boston, USA. New York, Berlin, Heidelberg, Tokyo: Springer-Verlag; 1986. Volume 2. p. 391-402. 138, 2793-2799 (1987).
Screening for CD19-Specific scFvs
Screening for molecules of the invention that are specific for human CD19 can be screened from culture supernatant of hybridoma cells generated by the fusion of mouse (or other vertebrate) spleenocytes with myeloma lines as described by Köhler and Milstein. This can be achieved for example by screening for binding to primary cells or immortalised cell lines that express human CD19 on the cell surface using flow cytometry or immunoassay techniques such as cell-based ELISA or imaging techniques such as Li-Cor Odysee™. Equally, bispecific ELISA and SPR screens can be carried out using recombinant proteins as for example described in Moore et al 2011 (Moore P A, Zhang W, Rainey G J, et al. Application of dual-affinity re-targeting molecules to achieve optimal redirected T-cell killing of B-cell lymphoma. Blood. 2011; 117(17):4542-4551). Hybridoma clones positive for binding to human CD19 would be selected and subjected to secondary screening for binding to human CD19 and human CD3 separately using the same techniques. Functional analysis of these selected clones would involve the CD19-mediated killing of B-cell lymphoma lines or the depletion of B-cells from human PBMC preparations both also described for example in Moore et al 2011.
Example 8 Transgenic Non-Human VertebratesEngineering Mouse IgG1 Constant Region (Landing Pad Insertion)
To allow for the in-vivo selection of multivalent (eg, multispecific or bispecific) polypeptide chains having a structure VH1-L1-VL1-L2-VH2-L3-VL2-Hinge-CH2-CH3 as an example, the mouse IgG1 constant region was engineered as detailed below.
An entry vector termed R232 was constructed for targeting into the mouse IgG1 constant region containing features detailed in
Mouse 129 BAC bMQ263j18 purchased from Source BioScience LifeSciences containing IgG1 constant region was used to retrieve by recombineering the 5′ and 3′ homology arms (HA). The 5′-HA was 2707 bp and the 3′-HA was 3001 bp and retrieval was done in plasmid pBR322. The oligos used for retrieval contained incorporated restriction sites to facilitate downstream cloning. The 5′-HA contained restriction sites NotI and MluI, whereas the 3′-HA contained restriction sites EcoRI and KpnI. The respective homology arms were cloned sequentially into vector R3, which contained an inactive piggyBAC transposon element with two PB5′LTRs and within it a PGK promoter and HPRT gene split into two portions (5′HPRT and 3′HPRT). The 3′-HPRT portion was flanked by loxP and mutant lox5171 sites. Cloning of the 5′ and 3′-HA into R3 yielded the entry vector R232.
The entry vector was prepared for targeting into ES cells by linearising with NotI restriction enzyme. Approximately 10 μg of linearised R232 plasmid DNA was used for targeting into ES cells containing human VDJ gene segments at an IgH locus. Targeted ES clones were selected on medium containing hypoxanthine-aminopterin-thymidine (HAT) and correctly targeted clones were genotyped by PCR.
Binding Module Vector Construction
The binding module vector was constructed using standard molecular cloning techniques unless otherwise stated. The IgG1 constant region containing the Hinge, CH2, CH3, M1 and M2 domains was retrieved from BAC bMQ263j18 by recombineering. scFv from the bispecific single chain antibody construct comprising binding domains specific for human CD3 and human CD19 as documented in WO2004/106381, was used as a fixed binding module against CD3. The overall binding module structure was similar to that of construct 2 (Sequence ID no. 1; protein ID no. 2) documented in WO2004/106381 except the variable heavy chain for CD19 was not included and the variable light chain for CD19 was replaced with a single rearranged common light chain. It was documented in EP2505654 that mice genetically engineered to express reverse chimeric immunoglobulin heavy chains associated with a single rearranged light chain (e.g. Vk1-39/J or Vk3-20/J), when immunised with an antigen of interest, generated B cells that comprised a diversity of human V segment rearrangements and expressed a diversity of high-affinity antigen specific antibodies. To this end, we used a rearranged Vk1-39Jk5 in the absence of a VH to form part of the binding module for a second antigen (this would combine with the VH produced by rearrangement of the human variable region gene segments at the 5′ of the locus). Downstream of the fixed CD3 binding domain, intronic sequence located between mouse IgG1 CH1 and hinge domains was included to allow splicing of the CD3 binding domain to the hinge domain and thus the rest of the IgG1 constant region. The binding module domains and the intronic DNA was synthetically constructed through GeneArt (Invitrogen), which had the following structure:
L1-VL(Vk1-39Jk5)-L2-VH(CD3)-L3-VL(CD3)-Intronic-Seq
L1 is linker 1:
L2 is linker 2:
L3 is linker 3:
VL(Vk1-39Jk5):
VH(CD3):
VL(CD3):
The retrieved mouse IgG1 constant region containing hinge, CH2, CH3, M1 and M2 was cloned downstream of the synthetically constructed binding module domains via NdeI and MluI restriction sites. The resulting binding module and IgG1 constant region was cloned as a single fragment into vector R217 via HindIII and MluI and in between two PB 3′LTRs, which also contained puro-delta-TK selection cassette and compatible lox sites to the entry vector to allow RMCE. The final structure of the binding module is shown in
Targeting of the binding module vector R246 into ES cells containing the landing pad was achieved by RMCE with transient expression of Cre recombinase and selection of clones in medium containing puromycin. Correctly targeted binding module vector in ES cells replaced the landing pad and reconstitutes two functional piggyBAC transposons at the 5′ and 3′ ends to the inserted binding module. The two functional transposons flank the modifying elements and the selection cassettes and thus these were conveniently excised simultaneously by transient expression of hyper-piggyBac transposase. Targeting of the binding module vector and the subsequent double excision were analysed sequentially by PCR.
Progeny mice were generated using standard procedures from the ES cells.
Bispecific Transcripts Amplification from Chimeric Mice
Two chimeric mouse (Table 2) were sacrificed 25 days after birth and their spleen and lymph nodes were collected and total RNA was extracted using Trizol reagent (Life Technologies) according to the manufacturer's protocol (
The spleen was sectioned into 3 equal portions from which total RNA was extracted. A reverse primer specific for mouse IgG1 CH2 domain was used for first strand cDNA synthesis from approx 5 μg total RNA with 5′-RACE second generation kit (Roche). The cDNA was purified with High Pure PCR Purification Kit (Roche). Poly(A) tailing was added to the first-strand cDNA using recombinant terminal transferase and dATP according to the manufacturer's protocol. The dA-tailed cDNA was used directly for PCR amplification using oligo dT-anchored primer and an internal reverse primer 1 specific for mouse IgG1 CH2 domain (1st round single semi-nested PCR) (
Results
Bispecific Antibody Transgenic Mice Generation
A transgenic mouse containing inserted human VDJ genes was further engineered. The IgG1 constant region was replaced initially by targeting in a landing pad. The landing pad facilitated the insertion of a binding module via RMCE containing the following structure L1-VL1-L2-VH2-L3-VL2-Hinge-CH2-CH3-Intronic-Seq-M1-M2, which lacked CH1 domain. To allow RNA splicing of V genes selected in-vivo to linker 1 (L1), a splice acceptor was placed at the 5′ end of L1. In addition, the intragenic region located between the endogenous mouse IgG1 CH1 and hinge, was engineered between the VL2 and hinge region within the binding module to allow correct splicing of the two domains. Furthermore to allow universal selection and rearrangement of VH genes to L1 and thus heavy and light chain pairing, a common light chain was used (Vκ1-39/Jk5) as VL1.
Young naïve chimeric mice (25 days old) were analysed for mRNA transcripts corresponding to the expected size of novel bispecific antibodies using 5′-RACE. Using three rounds of sequential semi-nested PCR on cDNA synthesised from total RNA harvested from spleen and bone marrow using primers specific for IgG1 CH2 domain, transcripts with size corresponding to the expected size of novel bispecific antibodies (approx. 1.7 kb) could be detected in RNA extracted from lymph node of mouse KMBS2.1d. These transcripts were distinct in size from those amplified from the germ line allele (approx. 850 bp) (
The inventors believe that they have provided a method for generating products of guided selection that are stable and that can be generated in vivo via natural selection, VDJ rearrangement and class-switch recombination, and further wherein the constant region can be altered without adversely affecting VDJ rearrangement and class-switch recombination in the absence of a CH1 domain.
Claims
1. A mouse, wherein the genome of B cells of said mouse comprises: wherein
- (i) an immunoglobulin heavy (IgH) chain locus comprising DNA encoding (in 5′ to 3′ direction) a rearranged or unrearranged variable region, a first switch, a mu constant region, a second switch and a non-mu constant region; wherein the IgH chain locus is capable of undergoing IgM to the non-mu isotype switching; and
- (ii) the non-mu mutant constant region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding a predetermined epitope binding moiety comprising a CH3 of an antigen binding Fc fragment (Fcab), wherein following isotype switching the mouse expresses multivalent polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain comprising a heavy chain variable region encoded by said variable region of the heavy chain locus, and an epitope binding moiety comprising a CH3 of an antigen binding Fc fragment (Fcab), wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes.
2. A mouse cell, the mouse cell genome comprising wherein
- (i) an antibody heavy chain locus comprising (in 5′ to 3′ direction) a rearranged or unrearranged variable region, a first switch, a mu constant region, a second switch and a non-mu constant region; wherein the heavy chain locus of each cell is capable of undergoing IgM to a non-mu isotype switching; and
- (ii) the non-mu constant region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding a predetermined epitope binding moiety comprising a CH3 of an antigen binding Fc fragment (Fcab), for expressing a multivalent polypeptide chain comprising (in N- to C-terminal direction) an antibody variable domain encoded by said variable region of the heavy chain locus, and an epitope binding moiety comprising a CH3 of an antigen binding Fc fragment (Fcab), wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes.
3. A mouse, wherein the mouse comprises lymphocytic cells whose genomes comprise an antibody heavy or light chain locus comprising (in 5′ to 3′ direction) a rearranged variable region and a non-mu constant region;
- wherein
- the non-mu constant region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an and a predetermined epitope binding moiety comprising a CH3 of an antigen binding Fc fragment (Fcab), wherein the mouse expresses multivalent polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain encoded by said variable region of the chain locus, an and an epitope binding moiety comprising a CH3 of an antigen binding Fc fragment (Fcab), wherein the variable domain and the epitope binding moietyspecifically bind respective first and second epitopes.
4. A mouse cell or a hybridoma, the mouse cell genome comprising an antibody heavy or light chain locus comprising (in 5′ to 3′ direction) a rearranged variable region and a non-mu constant region;
- wherein the non-mu constant region comprises (in 5′ to 3′ direction) a nucleotide sequence encoding an and a predetermined epitope binding moiety comprising a CH3 of an antigen binding Fc fragment (Fcab), wherein the mouse cell expresses a multivalent polypeptide chain comprising (in N- to C-terminal direction) an antibody variable domain encoded by said variable region of the locus, an and an epitope binding moiety comprising a CH3 of an antigen binding Fc fragment (Fcab), wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes.
5. A method of producing in a mouse multivalent polypeptide chains comprising (in N- to C-terminal direction) an antibody variable domain, an and an epitope binding moiety comprising a CH3 of an antigen binding Fc fragment (Fcab), wherein the variable domain and the epitope binding moiety specifically bind respective first and second epitopes, the method comprising:
- (a) immunising the mouse with a first predetermined antigen bearing the first epitope, obtaining isotype switching to expression from a non-mu constant region in at least some of the heavy chain loci of the mouse and expression of variable regions that have undergone somatic hypermutation; and
- (b) selecting one or more polypeptide chains from said immunised mouse by selection for variable regions that bind said first epitope, wherein each selected chain comprises a somatically hypermutated variable region that specifically binds the epitope and wherein each selected chain binds the first and second epitopes; and
- (c) providing the nucleotide sequence of the epitope binding moiety in the non-mu constant region of heavy chain loci in the genome of the mouse, wherein the polypeptide chains selected in step (b) bind the first and second epitopes.
6. A multispecific polypeptide chain obtained by the method of claim 5, that specifically binds the first and second epitopes.
7. The mouse of claim 1, wherein the N-terminal variable domain and/or the 5′-terminal variable region is a human variable domain or region.
8. The mouse cell of claim 2, wherein the N-terminal variable domain and/or the 5′-terminal variable region is a human variable domain or region.
9. The mouse of claim 3, wherein the N-terminal variable domain and/or the 5′-terminal variable region is a human variable domain or region.
10. The mouse cell or hybridoma of claim 4, wherein the N-terminal variable domain and/or the 5′-terminal variable region is a human variable domain or region.
11. The method of claim 5, wherein the N-terminal variable domain and/or the 5′-terminal variable region is a human variable domain or region.
12. The multispecific polypeptide of claim 6, wherein the N-terminal variable domain and/or the 5′-terminal variable region is a human variable domain or region.
13. The mouse of claim 1, wherein the heavy chain variable region and the epitope binding moiety are connected via a linker.
14. The mouse cell of claim 2, wherein the heavy chain variable region and the epitope binding moiety are connected via a linker.
15. The mouse of claim 3, wherein the antibody variable domain and the epitope binding moiety are connected via a linker.
16. The mouse cell or hybridoma of claim 4 wherein the antibody variable domain and the epitope binding moiety are connected via a linker.
17. The method of claim 5, wherein the antibody variable domain and the epitope binding moiety are connected via a linker.
18. The multispecific polypeptide of claim 6, wherein the antibody variable domain and the epitope binding moiety are connected via a linker.
19. The mouse cell of claim 2, wherein the non-mu constant region is a gamma constant region and the heavy chain locus is capable of undergoing isotype switching to produce IgG antibodies comprising one or more IgG heavy chains in the absence of light chains, each heavy chain lacking a CH1domain.
20. The method of claim 5, wherein each somatically mutated variable region in step (a) is provided by a non-mu-type heavy chain that lacks a CH1 domain.
21. The method of claim 20, further comprising isolating or synthesizing a nucleic acid comprising a nucleotide sequence encoding a polypeptide chain selected in the method.
22. The method of claim 21, further comprising humanising the nucleotide sequence encoding the polypeptide chain selected.
Type: Application
Filed: May 7, 2020
Publication Date: Aug 27, 2020
Inventors: Volker Germaschewski (Cambridge), E-Chiang Lee (Cambridge), Hanif Ali (Cambridge), Jasper Clube (Cambridge)
Application Number: 16/869,416
