Malaria vaccines
The invention provides isolated placental P. falciparum polypeptides comprising an amino acid sequence selected from the group consisting of SEQ ID NOs:1-4 and 6-24, and immunogenic derivatives thereof. The invention also provides isolated nucleic acid molecules encoding the placental P. falciparum polypeptides of the invention, compositions comprising one or more placental P. falciparum polypeptides of the invention, methods for inducing an immune response against the placental P. falciparum polypeptides, and methods for treating and diagnosing placental malaria.
This application claims the benefit of U.S. Provisional Application No. 60/706,733, filed Aug. 9, 2005, and U.S. Provisional Application No. 60/726,584, filed Oct. 14, 2005, both of which are incorporated herein by reference.
STATEMENT OF GOVERNMENT LICENSE RIGHTSThe U.S. Government has a paid-up license in this invention and the right in limited circumstances to require the patent owner to license others on reasonable terms as provided for by the terms of RO1 AI 43680-04 and RO1 AI 52059 awarded by the National Institutes of Health.
FIELD OF THE INVENTIONThis invention relates to proteins that are expressed on the surface of Plasmodium parasites and/or the surface of red blood cells infected by Plasmodium parasites, and their use in the diagnosis, treatment, and prevention of malaria.
BACKGROUND OF THE INVENTIONMalaria has a tremendous impact on human health, killing millions annually and the disease is a major impediment for social and economic development of nations in malaria-endemic areas, particularly in sub-Saharan Africa (Sachs & Malaney (2002) Nature 415:680-85). Malaria is a mosquito-borne disease that is transmitted by inoculation of the Plasmodium parasite sporozoite stage. Sporozoites invade hepatocytes (Kappe et al. (2003) Trends Parasitol. 19:135-43), transform into liver stages, and subsequent liver stage development ultimately results in release of pathogenic merozoites that initiate the blood stage cycle of infection (Shortt & Garnham (1948) Nature 161:126).
Protection against blood stage malaria can be passively transferred by antibodies. Effectiveness of passive transfer of IgG between adults and children living in different geographic regions indicate that the antigens that are targeted by antibodies that protect against blood stage malaria are conserved (see Duffy et al. (2005) Vaccine 23 (17-18):2235-42). The best evidence that naturally occurring immunity against blood stage malaria targets the IRBC surface comes from studies of pregnancy malaria. In areas of stable malaria transmission, adults enjoy immunity that limits parasitemia and prevents disease. Women become more susceptible during pregnancy, and previously this was ascribed to pregnancy-related immunomodulation that develops to prevent rejection of the fetal allograft. However, susceptibility is greatest in primigravid women and diminishes over successive pregnancies, suggesting an acquired immune response to an antigenically distinct microbe. Placental isolates of P. falciparum commonly bind to chondroitin sulfate A (CSA) expressed on the surface of the syncytiotrophoblast (the cells lining the maternal vascular space in the placenta), and this phenotype is uncommon among isolates obtained from non-pregnant individuals (Fried & Duffy (1996) Science 272:1502-4). The distinct binding phenotype renders pregnant women naive to this parasite population during their first pregnancy (primigravidas). Women with multiple pregnancies (multigravidas) residing in areas of stable malaria transmission develop antibodies that inhibit parasite adhesion to CSA (Fried et al. (1998) Nature 395:851-2). These anti-adhesion antibodies are associated with a reduced mass of parasites in the placenta, and substantial improvements in fetal development (Duffy & Fried (2003) Infect. Immun. 71:6620-3). Because CSA-binding parasites cross-react with sera donated by mothers throughout Asia and Africa, the antigen targeted by protective antibodies is presumed to have conserved features or limited diversity.
There is a need in the art for vaccines that protect against malaria infection and disease. There is also a need in the art for diagnostic markers for malaria. The present invention addresses these needs and others.
SUMMARY OF THE INVENTIONOne aspect of the invention provides isolated placental P. falciparum polypeptides. In some embodiments, the isolated placental P. falciparum polypeptides comprise an amino acid sequence selected from the group consisting of SEQ ID NOs:1-4 and 6-24. In some embodiments, the placental P. falciparum proteins are preferentially recognized by sera from multigravidas than by sera from primigravidas and/or sera from males. The isolated placental P. falciparum polypeptides of the invention be recombinant or synthetic polypeptides. In some embodiments, the polypeptides of the invention are immunogenic derivatives of polypeptides comprising an amino acid sequence selected from the group consisting of SEQ ID NOs:1-4 and 6-24.
Another aspect of the invention provides isolated nucleic acid molecules encoding the placental P. falciparum polypeptides of the invention. Thus, some embodiments provide an isolated nucleic acid molecule encoding a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs:1-4 and 6-24, and immunogenic derivatives thereof.
A further aspect of the invention provides compositions comprising one or more placental P. falciparum polypeptides of the invention and a pharmaceutically acceptable carrier. Thus, some embodiments provide an immunogenic composition comprising an isolated polypeptide and a pharmaceutically acceptable carrier, wherein the isolated polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NOs:1-4 and 6-24, and immunogenic derivatives thereof. In some embodiments, the compositions of the invention are immunogenic compositions for inducing immune responses, such as vaccine compositions.
In another aspect, the invention provides methods for inducing an immune response against placental P. falciparum parasites, comprising administering an immunogenic composition comprising an effective amount of one or more placental P. falciparum polypeptides of the invention. Thus, in some embodiments the invention provides a method for inducing an immune response in a mammalian subject against Plasmodium falciparum, comprising administering to the host a composition comprising an effect amount of at least one isolated polypeptide selected from the group consisting of SEQ ID NOs:1-4 and 6-24, and immunogenic derivatives thereof.
Yet another aspect of the invention provides methods for treating a subject in need thereof, comprising administering to a subject in need thereof an immunogenic composition comprising an effective amount of one or more placental P. falciparum polypeptides of the invention. Thus, in some embodiments the invention provides a method for treating a human subject in need thereof, comprising administering to a human subject an immunogenic composition comprising at least one isolated polypeptide selected from the group consisting of SEQ ID NOs:1-4 and 6-24, and immunogenic derivatives thereof. The invention also provides expression vectors encoding the placental P. falciparum polypeptides of the invention, host cells comprising such expression vectors; antibodies that bind specifically to the placental P. falciparum polypeptides of the invention, or immunogenic derivatives thereof; and diagnostic assays for detecting the presence of the placental P. falciparum polypeptides of the invention, or nucleic acid molecules encoding them.
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTIn one aspect, the invention provides novel proteins expressed by placental P. falciparum parasites. In some embodiments, these proteins are expressed on the surface of red blood cells infected by Plasmodium falciparum parasite, as shown in EXAMPLE 1. In some embodiments, the genes encoding these proteins are upregulated in placental P. falciparum parasites, as shown in EXAMPLE 4. Placental P. falciparum proteins are preferentially recognized by sera from multigravidas than by sera from primigravidas and/or sera from males, as shown in EXAMPLES 2 and 5.
Thus, one aspect of the invention provides isolated placental P. falciparum polypeptides. In some embodiments, the isolated placental P. falciparum polypeptides comprise an amino acid sequence selected from the group consisting of SEQ ID NOs:1-4 and 6-24. The sequences of these proteins, the nucleotide sequences encoding them, and annotation information may be obtained from the Plasmodium Genome Database (http://plasmodb.org/; Kissinger et. al (2002) Nature 419: 490-492) under the protein/gene 30 ID numbers provided in Tables 1, 2 and 4, and are herein incorporated by reference. The isolated placental P. falciparum polypeptides of the invention be recombinant or synthetic full-length polypeptides, or immunogenic derivatives thereof, as further described below. Accordingly, some embodiments of the invention provide an isolated polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs:1-4 and 6-24, and immunogenic derivatives thereof.
As used herein, the term “polypeptide” refers to a polymer of amino acids and does not refer to a specific length of the product; thus, peptides, oligopeptides, and proteins are included within the definition of polypeptide. This term also includes post-expression modifications of the polypeptide, for example, glycosylations, acetylations, phosphorylations, and the like. Included within the definition are, for example, polypeptides containing one or more analogues of an amino acid (including, for example, unnatural amino acids, PNA, etc.), polypeptides with substituted linkages, as well as other modifications known in the art, both naturally occurring and non-naturally occurring.
The placental P. falciparum polypeptides of the invention may be full-length polypeptides, immunogenic derivatives or domains of full-length polypeptides, or immunogenic variants thereof. As used herein, the term “immunogenic” refers to the ability of a polypeptide to elicit a humoral and/or cellular immune response, whether alone or when linked to a carrier, in the presence or absence of an adjuvant. Thus, an immunogenic portion of a full-length placental P. falciparum polypeptide of the invention refers to a portion of the full-length polypeptide that is capable of eliciting an immune response against the corresponding full-length polypeptide. The term “immunogenic derivative or domain” encompasses any polypeptide that includes at least 5 to 8 amino acids (such as, for example, 10 to 50 amino acids or 30 to 200 amino acids) and that is capable of inducing an immune response to the full-length polypeptide, such as a truncated form, epitope, or other derivative. The term “epitope” refers to a linear array of 3 to 10 amino acids aligned along the surface of a protein. In a linear epitope, the amino acids are joined sequentially and follow the primary structure of the protein. In a conformational epitope, residues are not joined sequentially, but lie linearly along the surface due to the conformation (folding) of the protein. With respect to conformational epitopes, the length of the epitope-defining sequence can be subject to wide variations. The portions of the primer structure of the antigen between the residues defining the epitope may not be critical to the structure of the conformational epitope. For example, deletion or substitution of these intervening sequences may not affect the conformational epitope provided sequences critical to epitope conformation are maintained (e.g., cysteines involved in disulfide bonding, glycosylation sites, etc.). A conformational epitope may also be formed by 2 or more essential regions of subunits of a homo-oligomer or hetero-oligomer. Other immunogenic derivatives may be prepared by the addition, deletion, substitution, or rearrangement of amino acids or by chemical modifications thereof.
Methods of predicting immunogenic regions in a polypeptide are well-known in the art. For example, a polypeptide sequence may be analyzed using the DNASTAR program by several algorithms, including prediction of hydrophilicity according to the Kyte-Doolittle method, surface probabability according to the Emini method, and antigenicity according to the Jameson-Wolf method. Other epitope prediction approaches are known in the art (see, e.g., Moise & De Groot (2006) Nat. Biotechnol. 24(7):791-2).
In some embodiments, the immunogenic derivatives of the placental P. falciparum proteins of the invention include 5 to 10, 10 to 50, 20 to 200, or 40 to 300 contiguous amino acids of a full-length polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs:1-4 and 6-24. Exemplary immunogenic derivatives of the polypeptides of the invention include, but are not limited to, polypeptides comprising amino acids 572 to 877 of SEQ ID NO:1 1, amino acids 1 to 500 of SEQ ID NO:3, amino acids 50 to 750 of SEQ ID NO:4, amino acids 751-1471 of SEQ ID NO:4, amino acids 370 to 670 of SEQ ID NO:8, amino acids 2000 to 2500 of SEQ ID NO:8, or amino acids 34 to 347 of SEQ ID NO:13.
Immunogenic derivatives of the polypeptides of the invention, which may be useful in the preparation of vaccines, may be prepared by expression of the appropriate gene fragments or by peptide synthesis, using methods well known in the art, as further described below. Exemplary methods for recombinant expression of immunogenic derivatives of the invention are provided in EXAMPLES 3 and 5.
An immunogenic derivative may be a fusion polypeptide containing additional sequences encoding one or more epitopes for other Plasmodium immunogens, or other non-Plasmodium immunogens. Alternatively, the immunogenic derivative of the invention can be fused to a carrier polypeptide (such as Hepatitis B surface or core antigen) or to another carrier that has immunostimulating properties, as in the case of an adjuvant, or that otherwise enhances the immune response to the protein or derivative thereof, or that is useful in expressing, purifying or formulating the protein or derivative thereof. The proteins or immunogenic derivatives thereof which are useful in the invention may be chemically conjugated to a macromolecule using a conventional linking agent such as glutaraldehyde (Geerlings et al. (1988) J Immunol Methods 106: 239-244).
In some embodiments, the placental P. falciparum polypeptides of the invention include immunogenic derivatives with more than 80% amino acid sequence identity (such as more than 90% sequence identity, more than 95% amino acid sequence identity, or more than 99% sequence identity) to the sequences defined in SEQ ID NOs:1-4 and 6-23. The terms “identical” or percent “identity”, in the context of two or more amino acid sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues that are the same, when compared and aligned for maximum correspondence over a comparison window, as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection.
It is recognized that amino acid positions that are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule. Where sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Means for making this adjustment are well known to those of skill in the art. The scoring of conservative substitutions can be calculated according to, for example, the algorithm of Meyers & Millers (1988) Computer Applic. Biol Sci. 4:11-17.
A “comparison window” includes reference to a segment of contiguous positions, such as between about 25 and about 600 positions, or between about 50 to 200 positions, or between about 100 and 150 positions, over which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequences for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, for example, by a local homology algorithm (Smith & Waterman (1981) Adv. Appl. Math. 2:482), by a global alignment algorithm (Needleman & Wunsch (1970) J Mol. Biol. 48:443), by search for similarity methods (Pearson & Lipman (1988) Proc. Natl. Acad Sci. USA. 85:2444; Altschul et al. (1997) NucL Acids Res. 25(17):3389-402), by computerized implementations of these algorithms (e.g., GAP, BESTFIT, FASTA, and BLAST in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), typically using the default settings, or by manual alignment and visual inspection (see, e.g., Current Protocols in Molecular Biology (1994) Ausubel et al., eds.). For example, BLAST protein searches can be performed using the XBLAST program, score=50, wordlength=3 to obtain amino acid sequences that are more than 80% identical to the amino acid sequence of SEQ ID NOs:1-4 and 6-24.
One example of a useful algorithm implementation is PILEUP. PILEUP creates a multiple sequence alignment from a group of related sequences using progressive, pairwise alignments. It can also plot a dendrogram showing the clustering relationships used to create the alignment. PILEUP uses a simplification of the progressive alignment method of Feng & Doolittle (1987) J Mol. Evol. 35:351-60. The method used is similar to the method described by Higgins & Sharp (1989) CABIOS 5:151-3. The multiple alignment procedure begins with the pairwise alignment of the two most similar sequences, producing a cluster of two aligned sequences. This cluster can then be aligned to the next most related sequence or cluster of aligned sequences. Two clusters of sequences can be aligned by a simple extension of the pairwise alignment of two individual sequences. A series of such pairwise alignments that includes increasingly dissimilar sequences and clusters of sequences at each iteration produces the final alignment.
In some embodiments, the placental P. falciparum polypeptides of the invention include variants of the wild-type polypeptides. These variants fall into one or more of three classes: substitutional, insertional or deletional variants. These variants may be naturally occurring allelic or interspecies variants (e.g., variants from different P. falciparum strains), or they may be prepared by site-specific mutagenesis of nucleotides in the DNA encoding protein. Site-specific mutagenesis may be performed using cassette or PCR mutagenesis or other techniques well known in the art, to produce DNA encoding the variant, and thereafter expressing the DNA in recombinant cell culture. Variant target protein fragments having up to about 100-150 amino acid residues may be prepared by in vitro synthesis using established techniques. Conservative substitution tables providing functionally similar amino acids are well known in the art (Henikoff & Henikoff (1992) Proc. Natl. Acad. Sci. U.S.A. 89:10915-9)
Amino acid substitutions are typically of single residues. Insertions usually will be on the order of from about 1 to about 20 amino acids, although considerably longer insertions may be tolerated. Deletions range from about 1 to about 20 residues, although in some cases, deletions may be much longer. Substitutions, deletions, and insertions or any combinations thereof may be used to arrive at a final derivative.
In some embodiments, the placental P. falciparum polypeptides of the invention are recombinant polypeptides. The term “recombinant polypeptide” refers to a protein produced by recombinant expression methods, such as, for example, in prokaryotic or eukaryotic host cells, or in cell-free in vitro expression systems, as described in detail below.
The placental P. falciparum polypeptides of the invention are typically expressed using an expression vector and purified. Expression vectors may be either self-replicating extrachromosomal vectors or vectors which integrate into a host genome. Generally, expression vectors include transcriptional and translational regulatory nucleic acid operably linked to the nucleic acid encoding the target protein. The term “control sequences” refers to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism. The control sequences that are suitable for prokaryotes, for example, include a promoter, optionally an operator sequence, and a ribosome binding site. Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers. Nucleic acid is “operably linked” when it is placed into a finctional relationship with another nucleic acid sequence. For example, DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide; a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation. Operably linked DNA sequences may be contiguous or non-contiguous. Methods for linking DNA sequences are well-known in the art and include use of the polymerase chain reaction and ligation. The transcriptional and translational regulatory nucleic acid will generally be appropriate to the host cell used to express the target protein; for example, transcriptional and translational regulatory nucleic acid sequences from E. coli are preferably used to express the target protein in E. coli.
Numerous types of appropriate expression vectors, and suitable regulatory sequences are known in the art for a variety of host cells. Methods for expressing polypeptides are well known in the art (e.g., Sambrook et al. (1989) Molecular Cloning, A Laboratory Manual, 2nd ed., vol. 1-3, Cold Spring Harbor Laboratory; Berger and Kimmel (1987) Guide to Molecular Cloning Techniques, Methods in Enzymology, vol. 152, Academic Press, Inc., San Diego, Calif.; Ausubel et al. (1995) Current Protocols in Molecular Biology, John Wiley & Sons, Inc., NY)
In general, the transcriptional and translational regulatory sequences may include, but are not limited to, promoter sequences, ribosomal binding sites, transcriptional start and stop sequences, translational start and stop sequences, and enhancer or activator sequences. Promoter sequences encode either constitutive or inducible promoters. The promoters may be either naturally occurring promoters or hybrid promoters. Hybrid promoters, which combine elements of more than one promoter, are also known in the art.
An expression vector may comprise additional elements. For example, the expression vector may have two replication systems, thus allowing it to be maintained in two organisms, for example in mammalian or insect cells for expression and in a prokaryotic host for cloning and amplification. Furthermore, for integrating expression vectors, the expression vector contains at least one sequence homologous to a sequence in the host cell genome, and preferably two homologous sequences that flank the expression construct. The integrating vector may be directed to a specific locus in the host cell by selecting the appropriate homologous sequence for inclusion in the vector. Constructs for integrating vectors are well known in the art.
In addition, an expression vector may include a selectable marker gene to allow the selection of transformed host cells. Selection genes are well known in the art and will vary depending on the host cell used.
The placental P. falciparum polypeptides of the invention may be produced by culturing a host cell transformed with an expression vector containing nucleic acid encoding a placental P. falciparum polypeptide, under the appropriate conditions to induce or cause expression of the placental P. falciparum polypeptide. The conditions appropriate for protein expression will vary with the choice of the expression vector and the host cell, and will be easily ascertained by one skilled in the art using routine experimentation. For example, the growth and proliferation of the host cell may be optimized for the use of constitutive promoters in the expression vector, and appropriate growth conditions for induction are provided for use of an inducible promoter. In addition, in some embodiments, the timing of the harvest is important, for example, when using baculoviral systems. One of skill in the art will recognize that the coding sequences may be optimized for expression in the selected host cells.
Appropriate host cells include yeast, bacteria, archaebacteria, fungi, and insect and animal cells, including mammalian cells. Host cells include, but are not limited to, Drosophila melanogaster cells, Saccharomyces cerevisiae and other yeasts, E. coli, Bacillus subtilis, Sf9 cells, C129 cells, 293 cells, Neurospora, BHK, CHO, COS, HeLa cells, Hep G2 cells, THP1 cell line (a macrophage cell line), and human cells and cell lines.
In some embodiments, the placental P. falciparum polypeptides are expressed in mammalian cells. Mammalian expression systems are also known in the art, and include retroviral systems. Promoters from viral genes are frequently used in mammalian expression systems, because the viral genes are often highly expressed and have a broad host range. Examples include the SV40 early promoter, mouse mammary tumor virus LTR promoter, adenovirus major late promoter, herpes simplex virus promoter, and the CMV promoter. Typically, transcription termination and polyadenylation sequences recognized by mammalian cells are regulatory regions located 3′ to the translation stop codon and thus, together with the promoter elements, flank the coding sequence. Examples of transcription terminator and polyadenylation signals include those derived from SV40.
The placental P. falciparum polypeptides of the invention may be cloned using DNA amplification methods, such as the polymerase chain method (PCR) (see e.g., Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbour, N.Y.; Berger & Kimmel (1987) Methods in Enzymology. Vol. 152: Guide to Molecular Cloning Techniques, Academic Press, Inc., San Diego, Calif.; Co et al. (1992) J. Immunol. 148:1149). Thus, for example, a nucleic acid molecule encoding a placental P. falciparum polypeptide may be PCR amplified using a sense primer containing one restriction site and an antisense primer containing another restriction site. This will produce a nucleic acid encoding the desired sequence or subsequence having terminal restriction sites. This nucleic acid can then easily be ligated into a vector having appropriate corresponding restriction sites. Suitable PCR primers are easily chosen by one of skill in the art based on the sequence to be expressed. Appropriate restriction sites can also be added by site-directed mutagenesis (see Gillman & Smith (1979) Gene 8: 81-97; Roberts et al. (1987) Nature 328: 731-4).
The methods of introducing exogenous nucleic acid into host cells are well known in the art, and will vary with the host cell used. Suitable techniques include, but are not limited to, dextran-mediated transfection, calcium phosphate precipitation, polybrene mediated transfection, protoplast fusion, electroporation, viral infection, encapsulation of the polynucleotide(s) in liposomes, and direct microinjection of the DNA into nuclei.
In some embodiments, the placental P. falciparum polypeptides of the invention are expressed in bacterial systems. Bacterial expression systems are well known in the art. Promoters from bacteriophage may also be used and are known in the art. In addition, synthetic promoters and hybrid promoters are also useful; for example, the tac promoter is a hybrid of the trp and lac promoter sequences. Furthermore, a bacterial promoter can include naturally occurring promoters of non-bacterial origin that have the ability to bind bacterial RNA polymerase and initiate transcription. In addition to a functioning promoter sequence, an efficient ribosome binding site is desirable. The expression vector may also include a signal peptide sequence that provides for secretion of the target protein in bacteria. The placental P. falciparum polypeptide is either secreted into the growth media (gram-positive bacteria) or into the periplasmic space, located between the inner and outer membrane of the cell (gram-negative bacteria). The expression vector may also include an epitope tag providing for affinity purification of the target protein. The bacterial expression vector may also include a selectable marker gene to allow for the selection of bacterial strains that have been transformed. Suitable selection genes include genes that render the bacteria resistant to drugs such as ampicillin, chloramphenicol, erythromycin, kanamycin, neomycin and tetracycline. Selectable markers also include biosynthetic genes, such as those in the histidine, tryptophan, and leucine biosynthetic pathways. These components are assembled into expression vectors. Expression vectors for bacteria are well known in the art, and include vectors for Bacillus subtilis, E. coli, Streptococcus cremoris, and Streptococcus lividans, among others. The bacterial expression vectors are transformed into bacterial host cells using techniques well known in the art, such as calcium chloride treatment, electroporation, and others. An exemplary method for expressing placental P. falciparum polypeptides of the invention using a bacterial expression system is described in EXAMPLES 2 and 3.
The placental P. falciparum polypeptides of the invention may also be produced in insect cells. Expression vectors for the transformation of insect cells, and in particular, baculovirus-based expression vectors, are well known in the art. The placental P. falciparum polypeptides may also be produced in yeast cells. Yeast expression systems are well known in the art, and include expression vectors for Saccharomyces cerevisiae, Candida albicans and C. maltosa, Hansenula polymorpha, Kluyveromyces fragilis and K lactis, Pichia guillerimondii and P. pastoris, Schizosaccharomycespombe, and Yarrowia lipolytica.
The placental P. falciparum polypeptides of the invention may be produced in a cell-free expression system in vitro using an expression vector containing nucleic acid encoding a placental P. falciparum polypeptide, under the appropriate conditions to induce or cause expression of the placental P. falciparum polypeptide in vitro. Cell-free in vitro expression systems are well known in the art. An exemplary method for expressing placental P. falciparum polypeptides of the invention using a cell-free in vitro expression system is described in EXAMPLE 3.
The placental P. falciparum polypeptides of the invention may also be made as a fusion proteins, using techniques that are well known in the art. For example, a placental P. falciparum polypeptides may be made as a fusion protein to increase expression or to link it with a tag polypeptide that provides an epitope to which an anti-tag antibody can selectively bind. Exemplary tags include the myc epitope and 6-histidine. The epitope tag is generally placed at the amino-or carboxyl-terminus of the target protein. The presence of such epitope-tagged forms of a target protein can be detected using an antibody against the tag polypeptide. Thus, the epitope tag enables the target proteins to be readily purified by affinity purification using an anti-tag antibody or another type of affinity matrix that binds to the epitope tag. Various tag polypeptides and their respective antibodies are well known in the art. Examples include poly-histidine (poly-his) or poly-histidine-glycine (poly-his-gly) tags; the flu HA tag polypeptide and its antibody 12CA5 (Field et al. (1988) Mol. Cell. Biol. 8:2159-65); the c-myc tag and the 8F9, 3C7, 6E10, G4, B7 and 9E10 antibodies theret (Evan et al. (1985) Mol. Cell. Biol. 5:3610-6); and the Herpes Simplex virus glycoprotein D (gD) tag and its antibody (Paborsky et al. (1990) Prot. Eng. 3(6):547-53). Other tag polypeptides include the Flag-peptide (Hopp et al. (1988) BioTechnol. 6:1204-10); the KT3 epitope peptide (Martin et al. (1992) Science 255:192-4); tubulin epitope peptide (Skinner et al. (1991) J. Biol. Chem. 266:15163-6); and the T7 gene 10 protein peptide tag (Lutz-Freyermuth et al. (1990) Proc. Natl. Acad. Sci. U.S.A. 87:6393-7).
Covalent modifications of placental P. falciparum polypeptides are included within the scope of this invention. One type of covalent modification includes reacting targeted amino acid residues of a target protein with an organic derivatizing agent that is capable of reacting with selected side chains or the N- or C-terminal residues of a target protein. Derivatization with bifinctional agents is useful, for instance, for crosslinking a target protein to a water-insoluble support matrix or surface for use in screening assays. Commonly used crosslinking agents include, but are not limited to, 1,1-bis(diazoacetyl)-2-phenylethane, glutaraldehyde, N-hydroxysuccinimide esters, for example, esters with 4-azidosalicylic acid, homobifinctional imidoesters, including disuccinimidyl esters such as 3,3′-dithiobis(succinimidylpropionate), bifinctional maleimides such as bis-N-maleimido-1,8-octane and agents such as methyl-3-[(p-azidophenyl)dithio]propioimidate.
The placental P. falciparum polypeptides of the invention may be purified or isolated after expression. The terms “isolated” “purified” or “biologically pure” refer to material that is substantially or essentially free from components which normally accompany it as found in its native state. Purity and homogeneity are typically determined using analytical chemistry techniques such as polyacrylamide gel electrophoresis or high performance liquid chromatography. A protein that is the predominant species present in a preparation is substantially purified. The term “purified” denotes that a protein gives rise to essentially one band in an electrophoretic gel. For example, it means that the protein is at least 85% pure, such as at least 95% pure, such as at least 99% pure. The term “isolated polypeptides” also includes polypeptides in situ within recombinant host cells, since at least one component of the polypeptide natural environment will not be present. Generally, however, isolated polypeptide will be prepared by at least one purification step.
The placental P. falciparum polypeptides of the invention may be isolated or purified in a variety of ways known to those skilled in the art depending on what other components are present in the sample. Standard purification methods include electrophoretic, molecular, immunological and chromatographic techniques, including ion exchange, hydrophobic, affinity, and reverse-phase HPLC chromatography, and chromatofocusing. For example, the target protein may be purified using an antibody column. Ultrafiltration and diafiltration techniques, in conjunction with protein concentration, are also useful. Suitable purification techniques are standard in the art (see generally R. Scopes (1982) Protein Purification, Springer-Verlag, N.Y.; Deutcher (1990) Methods in Enzymology vol. 182: Guide to Protein Purification, Academic Press, Inc. N.Y.). The degree of purification necessary will vary depending on the use of the polypeptide. In some instances no purification may be necessary.
Some embodiments of the invention provide synthetic placental P. falciparum polypeptides. Polypeptides having up to about 100-150 amino acid residues may be prepared by in vitro synthesis using established techniques. Synthetic polypeptides may be prepared by chemical synthesis (such as solid phase peptide synthesis) using methods known in the art, such as those described in Merrifield et al. (1964) J. Am. Chem. Soc. 85:2149, Houghten et al. (1985) Proc. Natl. Acad. Sci. USA, 82:51:32, and Stewart & Young (1984) Solid phase peptide synthesis, Pierce Chem Co., Rockford, Ill. Such polypeptides can be synthesized with or without a methionine on the amino terminus. Chemically synthesized placental P. falciparum proteins of the invention and immunogenic derivatives thereof may be oxidized using methods set forth in these references to form disulfide bridges. Further, peptidomimetics that structurally and/or functionally resemble a polypeptide embodiment may be made. Several approaches to make peptidomimetics that resemble polypeptides have been described (see, e.g., U.S. Pat. Nos. 5,288,707; 5,552,534; 5,811,515; 5,817,626; 5,817,879; 5,821,231; and 5, 874,529).
Another aspect of the invention provides isolated nucleic acid molecules encoding the placental P. falciparum polypeptides of the invention. Thus, some embodiments provide an isolated nucleic acid molecule encoding a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs:1-4 and 6-24, and immunogenic derivatives thereof. The term “isolated nucleic acid molecule(s)” refers to a nucleic acid molecule, DNA or RNA, that has been removed from its native environment. For example, recombinant DNA molecules contained in a vector are considered isolated for the purposes of the present invention. Further examples of isolated DNA molecules include recombinant DNA molecules maintained in heterologous host cells or purified (partially or substantially) DNA molecules in solution. Isolated RNA molecules include in vivo or in vitro RNA transcripts of the DNA molecules of the present invention. Isolated nucleic acid molecules according to the present invention further include such molecules produced synthetically.
Isolated nucleic acid molecules of the present invention include DNA molecules comprising an open reading frame (ORF) encoding placental P. falciparum polypeptides or immunogenic derivatives thereof. The sequence of these nucleic acid molecules may be different to the any naturally-occurring sequences encoding the placental P. falciparum polypeptides of the invention but that, due to the degeneracy of the genetic code, still encode a placental P. falciparum polypeptide. Of course, the genetic code is well known in the art. Thus, it would be routine for one skilled in the art to generate such degenerate variants.
Another aspect of the invention provides expression vectors encoding the placental P. falciparum polypeptides of the invention. Another aspect of the invention provides host cells comprising expression vectors encoding the placental P. falciparum polypeptides of the invention.
Another aspect of the invention provides antibodies that bind specifically to the placental P. falciparum polypeptides of the invention, or immunogenic derivatives thereof. The term “antibody” refers to an intact immunoglobulin, or to an antigen-binding portion of an immunoglobulin that competes with the intact antibody for specific binding to a protein or fragment of a protein of the present invention. Exemplary antibodies include polyclonal, monoclonal, humanized, bispecific, and heteroconjugate antibodies. Antigen-binding portions of an immunoglobulin of the present invention can be produced by various techniques including, but not limited to recombinant DNA techniques and enzymatic or chemical cleavage of intact antibodies.
An “isolated antibody” as used herein is an antibody that (1) is not associated with naturally-associated components, including other naturally-associated antibodies, that accompany it in its native state, (2) is free of other proteins from the same species, (3) is expressed by a cell from a different species, or (4) does not occur in nature. The terms “bind specifically” and “specific binding” refer to the ability of an antibody of the present invention to bind to a first molecular species in preference to binding to other molecular species with which the antibody and first molecular species are admixed. An antibody is said specifically to “recognize” a first molecular species when it can bind specifically to that first molecular species. In the present invention the first molecular species is a placental P. falciparum polypeptide of the invention, or immunogenic derivative thereof.
Methods of preparing polyclonal antibodies are known to the skilled artisan. Polyclonal antibodies can be raised in a mammal, for example, by one or more injections of an immunizing agent and, if desired, an adjuvant. Typically, the immunizing agent and/or adjuvant will be injected in the mammal by multiple subcutaneous or intraperitoneal injections. The immunizing agent may include a placental P. falciparum polypeptide of the invention, or an immunogenic derivative thereof. It may be useful to conjugate the immunizing agent to a protein known to be immunogenic in the mammal being immunized. Examples of such immunogenic proteins include but are not limited to keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. Examples of adjuvants which may be employed include Freund's complete adjuvant and MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate). The immunization protocol may be selected by one skilled in the art without undue experimentation.
Monoclonal antibodies may be prepared using hybridoma methods, such as those described by Kohler & Milstein (1975) Nature 256:495. In a hybridoma method, a mouse, hamster, or other appropriate host animal, is typically immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent. Alternatively, the lymphocytes may be immunized in vitro. Suitable immortalized cell lines for the production of monoclonal antibodies are well-known in the art (see, e.g., Goding (1986) Monoclonal Antibodies: Principles and Practice, Academic Press, pp. 59-103; Kozbor (1984) J. Immunol. 133:3001; Brodeuret al. (1987) Monoclonal Antibody Production Techniques and Applications, Marcel Dekker, Inc., New York, pp. 51-63).
The binding specificity of monoclonal antibodies produced by the hybridoma cells may be determined by immunoprecipitation or by an in vitro binding assay, such as radioimmunoassay (RIA) or enzyme-linked immunoabsorbent assay (ELISA). Such techniques and assays are known in the art. The binding affinity of the monoclonal antibody may, for example, be determined by the Scatchard analysis of Munson & Pollard (1980) Anal. Biochem. 107:220.
The monoclonal antibodies may be isolated or purified from the culture medium or ascites fluid by conventional immunoglobulin purification procedures such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography.
The monoclonal antibodies may also be made by recombinant DNA methods, such as those described in U.S. Pat. No. 4,816,567, herein incorporated by reference. Monoclonal antibodies may be isolated using phage display libraries (Hoogenboom & Winter (1991) J. Mol. Biol. 227:381; Marks et al. (1991) J. Mol. Biol. 222:581).
The antibodies may be monovalent antibodies. Methods for preparing monovalent antibodies are well known in the art. For example, one method involves recombinant expression of immunoglobulin light chain and modified heavy chain. The heavy chain is truncated generally at any point in the Fc region so as to prevent heavy chain crosslinking. Alternatively, the relevant cysteine residues are substituted with another amino acid residue or are deleted so as to prevent crosslinking. In vitro methods are also suitable for preparing monovalent antibodies. Digestion of antibodies to produce fragments thereof, particularly, Fab fragments, can be accomplished using routine techniques known in the art.
The antibodies may also be human or humanized antibodies, bispecific antibodies, or heteroconjugate antibodies. Methods for preparing human or humanized antibodies, bispecific antibodies, or heteroconjugate antibodies are well known in the art and described, for example, in Desnoyers et al., U.S. Pat. No. 7,084,258, herein incorporated by reference.
The antibodies that specifically bind to the placental P. falciparum polypeptides of the invention may be used in diagnostic assays, for example, to detect the presence of placental malaria parasites, or as therapeutic or prophylactic agents for treating or preventing infection by P. falciparum. The term “therapeutic agent” refers to an agent capable of treating a malaria infection. The term “prophylactic agent” refers to an agent capable of preventing an infection by P. falciparum. In some embodiments, the antibodies may be used to treat subjects at risk of developing or suffering from pregnancy malaria by passive immunization.
In general, this will comprise administering a therapeutically or prophylactically effective amount of one or more antibodies of the present invention to a subject susceptible to malaria or a subject exhibiting a malaria infection. Any active form of the antibody can be administered, including Fab and F(ab′)2 fragments. Treatment of individuals having malaria infection may comprise the administration of a therapeutically effective amount of antibodies of the present invention. The dosage of administered antibodies will vary depending upon such factors as the patient's age, weight, height, sex, general medical condition, previous medical history, as well as other factors know to those of skill in the art. An appropriate effective amount can be readily determined using only routine experimentation. Effective amounts and routes of administration for therapeutic and prophylactic applications are further described below.
Another aspect of the invention provides compositions comprising one or more placental P. falciparum polypeptides of the invention and a pharmaceutically acceptable carrier. Thus, some embodiments provide an immunogenic composition comprising an isolated polypeptide and a pharmaceutically acceptable carrier, wherein the isolated polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NOs:1-4 and 6-24, and immunogenic derivatives thereof. In some embodiments, the compositions of the invention are immunogenic compositions for inducing immune responses, such as vaccine compositions. A “vaccine” is an immunogenic composition capable of eliciting protection against infection by Plasmodium parasites and/or malarial disease, whether partial or complete. A vaccine that is used for treatment of an infected individual may be referred to as a therapeutic vaccine. The immunogenic compositions of the invention may also be used to elicit antibodies in a species that is not infectable by P. falciparum, for example to raise antibodies in rabbits or mice.
The invention further provides methods for preparing an immunogenic composition, by suspending and packaging one or more placental P. falciparum polypeptides of the invention in a suitable pharmaceutically acceptable carrier. Suitable pharmaceutically acceptable carrier include sterile water or sterile physiological salt solution, particularly phosphate buffered saline (PBS), as well known in the art.
The immunogenic compositions of the invention generally also include an adjuvant. Adjuvants are well known in the art (see, for example, Vaccine Design-The Subunit and Adjuvant Approach (1995) Pharmaceutical Biotechnology, Volume 6 (eds. Powell, M. F., & Newman, M. J.) Plenum Press, New York and London, ISBN 0-306-44867-X). Exemplary adjuvants include complete Freund's adjuvant (CFA) that is not used in humans, incomplete Freund's adjuvant (IFA), squalene, squalane and alum (e.g., Alhydrogel™, Superfos, Denmark), which are materials well known in the art, and are available commercially from several sources. Other exemplary adjuvants include the adjuvants described in Lanar et al., U.S. Pat. No. 7,029,685, and U.S. Patent Publication No. 2006/0073171, herein incorporated by reference.
In some embodiments, the immunogenic composition is a vaccine composition. Vaccine preparation is generally described in New Trends and Developments in Vaccine (eds. Voller et al.), University Park Press, Baltimore, Md., U.S.A., 1978. Encapsulation within liposomes is described, for example, by Fullerton, U.S. Pat. No. 4,235,877. Conjugation of proteins to macromolecules is disclosed, for example, by Likhite, U.S. Pat. No. 4,372,945 and by Armor et al., U.S. Pat. No. 4,474,757.
The amount of immunogen(s) present in each vaccine dose is selected as an amount that induces an immune response (such as an immunoprotective response) without significant, adverse side effects in typical vaccines. The term “immune response” refers to an acquired and enhanced degree of protective immunity against Plasmodium infection or malarial disease, for example, complete or partial protection against infection or disease following subsequent exposure to malaria parasites. The amount of immunogen present in each dose will vary depending upon which specific immunogens are employed, and other factors. Generally, it is expected that each dose will comprise a total of 1-1000 micrograms of protein, such as 1-200 micrograms or 10-100 micrograms or 5-50 micrograms. Following an initial vaccination, subjects will generally receive one or more boosts. An optimal amount for a particular vaccine, as well as the number and frequency of boosts, can be determined empirically by standard studies involving observation of immune responses in subjects.
The vaccine compositions of the invention may be administered by any suitable method of administration known in the art, including, but not limited to, intradermally, subcutaneously, intramuscularly, intraperitoneally, orally, ocularly (e.g., as an eye spray), and intravenously. Vaccines are conventionally administered parenterally, by injection, for example, either subcutaneously or intramuscularly. Additional formulations that are suitable for other modes of administration include suppositories and, in some cases, oral formulation or by nasal spray. For suppositories, traditional binders and carriers can include, for example, polyalkalene glycols or triglycerides. Oral formulations include such normally employed excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate and the like.
In some embodiments, the vaccine compositions of the invention are DNA vaccines comprising a nucleic acid molecule encoding one or more placental P. falciparum polypeptides of the invention. Thus, some embodiments provide an immunogenic composition comprising a nucleic acid molecule encoding a polypeptide and a pharmaceutically acceptable carrier, wherein the polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NOs:1-4 and 6-24, and immunogenic derivatives thereof. Methods for preparing and administering a DNA vaccine expressing Plasmodium proteins are known in the art and have been previously described (see, e.g., Doolan & Hoffinan (2001) Int. J. Parasitol. 31:753-62; Narum et al., U.S. Pat. No. 7,078,507, herein incorporated by reference. In some embodiments, the vaccine compositions of the invention are viral vaccines comprising a viral vector encoding one or more placental P. falciparum polypeptides of the invention. Exemplary viral vectors for use in the vaccine compositions of the invention include, but are not limited to, vaccinia viral vectors (such as vectors based on modified vaccinia virus or avian pox viruses), adenoviral vectors, and yellow fever viral vectors (see, e.g., Imoukhuede et al. (2006) Vaccine, in press; Miao et al. (2006) Vaccine, in press; Tao et al. (2005) J. Exp. Med. 201:201-9), Methods for preparing and administering viral vaccine expressing Plasmodium proteins are known in the art and have been previously (see, e.g., Imoukhuede et al. (2006) Vaccine, in press; Miao et al. (2006) Vaccine, in press; Tao et al. (2005) J Exp. Med. 201:201-9).
Another aspect of the invention provides methods for inducing an immune response against placental P. falciparum parasites, comprising administering an immunogenic composition comprising an effective amount of one or more placental P. falciparum polypeptides of the invention. Thus, in some embodiments the invention provides a method for inducing an immune response in a mammalian subject against Plasmodium falciparum, comprising administering to the host a composition comprising an effect amount of at least one isolated polypeptide selected from the group consisting of SEQ ID NOs:1-4 and 6-24, and immunogenic derivatives thereof. Exemplary mammalian subjects for the methods of inducing an immune response include, but are not limited to, humans, goats, rabbits, and mice. In some embodiments the mammalian subject is a human subject.
Another aspect of the invention provides methods for treating a subject in need thereof, comprising administering to a subject in need thereof an immunogenic composition comprising an effective amount of one or more placental P. falciparum polypeptides of the invention. Thus, in some embodiments the invention provides a method for treating a human subject in need thereof, comprising administering to a human subject an immunogenic composition comprising at least one isolated polypeptide selected from the group consisting of SEQ ID NOs:1-4 and 6-24, and immunogenic derivatives thereof.
The term “treating” refers to both therapeutic treatment and prophylactic or preventative measures, wherein the object is to prevent or slow down (lessen) the targeted pathologic condition or disorder. Those in need of treatment include those already with the disorder as well as those prone to have the disorder or those in whom the disorder is to be prevented. In some embodiments, the subjects to be treated are human subjects suffering from malaria, such as, for example, placental malaria. In some embodiments, the subjects to be treated are human subjects at risk for contracting malaria, including, but not limited to women at risk for contracting placental malaria. The subjects to be treated may or may not have previously been infected by P. falciparum parasites.
The term “effective amount” for a therapeutic or prophylactic treatment refers to an amount or dosage of a composition sufficient to induce a desired response (e.g., an immunogenic response) in the individual to which it is administered. Preferably, the effective amount is sufficient to effect treatment, as defined above. The effective amount and method of administration of a particular therapeutic or prophylactic treatment may vary based on the individual patient and the stage of the disease, as well as other factors known to those of skill in the art. Therapeutic efficacy and toxicity of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., ED50 (the dose therapeutically effective in 50% of the population) and LD50 (the dose lethal to 50% of the population). The dose ratio of toxic to therapeutic effects is the therapeutic index, and it can be expressed as the ratio, LD50/ED50. Pharmaceutical compositions that exhibit large therapeutic indices are preferred. The data obtained from cell culture assays and animal studies is used in formulating a range of dosage for human use. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage varies within this range depending upon the dosage form employed, sensitivity of the patient, and the route of administration.
The exact dosage is chosen by the individual physician in view of the patient to be treated. Dosage and administration are adjusted to provide sufficient levels of the active moiety or to maintain the desired effect. Additional factors that may be taken into account include the prevalence of P. falciparum in the geographical vicinity of the patient, the severity of the disease state of the patient, age, and weight of the patient; diet, time and frequency of administration, drug combination(s), reaction sensitivities, and tolerance/response to therapy. An appropriate effective amount can be readily determined using only routine experimentation. Several doses may be needed per individual in order to achieve a sufficient response to effect treatment. Suitable regimes for initial administration and follow-up administration (e.g., booster shots) are also variable, but are typified by an initial administration followed in intervals (weeks or months) by a subsequent administration.
The production of antibodies elicited by a treatment is readily ascertained by obtaining a plasma or serum sample from the subject to which an immunogenic composition is administered and assaying the antibodies therein for their ability to bind to the polypeptide(s) used to elicit the immune response to P. falciparum parasites, such as placental parasites. Exemplary methods include, but are not limited to, ELISA assays or by other immunoassays such as a Western blots, as is well known in the art. Another method for measuring the production of antibodies is by using an indirect immunofluorescence assay (IFA).
Antibodies to one or more of the placental P. falciparum parasites of the invention may be isolated from the blood of the host mammal using well known techniques, and then reconstituted into a second vaccine for passive immunization, as is also well known. Similar techniques are used for gamma-globulin immunizations of humans. For example, antiserum from one or a number of immunized hosts can be precipitated in aqueous ammonium sulfate (typically at 40-50 percent of saturation), and the precipitated antibodies purified chromatographically (e.g., affinity chromatography).
In another aspect, the invention provides diagnostic and screening agents and assays, which may be protein-based or nucleic acid-based. These agents and assays may be used to detect the presence of the placental P. falciparum polypeptides of the invention, or nucleic acid molecules encoding them, in order to determine whether a subject is suffering from or is likely to suffer from malaria, particularly pregnancy malaria. Many techniques may be used, including, but not limited to, ELISA, sandwich assays, immunoprecipation, immunoblots, hybridization techniques, and PCR.
In some embodiments, the placental P. falciparum polypeptides of the invention are used for the detection of antibodies in a subject. In some embodiments, antibodies to the placental P. falciparum polypeptides of the invention are used to detect the presence of these polypeptides. Diagnostic immunoassay procedures are standard in the art (see, e.g., Basic and Clinical Immunology (1991) 7th ed., Stites, D., & Terr, A.) Exemplary methods may, for example, use solid supports, or immunoprecipitation. Most assays involve the use of labeled antibody or polypeptide. Such labels may be, for example, enzymatic, fluorescent, chemiluminescent, radioactive, or dye molecules. Assays that amplify the signals from the immune complex are also known, such as assays that utilize biotin and avidin or streptavidin, and enzyme-labeled and mediated immunoassays, such as ELISA assays.
Some embodiments provide methods for the in vitro diagnosis of malaria in a subject likely to be infected by P. falciparum, comprising (a) contacting a biological sample comprising antibodies from a subject with one or more placental P. falciparum polypeptides of the invention under conditions enabling the formation of antigen/antibody complexes between the polypeptides and the antibodies, and (b) detecting the formation of antigen/antibody complexes. Examples of biological samples that may be used to perform this method are red blood cells, white blood cells, serum or urine. Conditions enabling the formation of antigen/antibody complexes are well known in the art.
The invention also provides methods for monitoring the immune status of a subject vaccinated against infection or disease caused by P. falciparum, comprising (a) contacting a biological sample comprising antibodies from a subject with one or more placental P. falciparum polypeptides of the invention under conditions enabling the formation of antigen/antibody complexes between the polypeptides and the antibodies, and (b) detecting the formation of antigen/antibody complexes.
In the diagnostic and monitoring methods described above, the biological sample may be further contacted with one or several antigenic peptides originating from other Plasmodium antigens.
In some embodiments, the diagnostic and screening agents and assays are nucleic acid-based. Exemplary diagnostic and screening agents for use in nucleic acid-based assays include nucleic acid probes complementary to nucleic acid molecules encoding P. falciparum polypeptides of the invention. Nucleic-acid based diagnostic and screening assays are well known in the art. Exemplary diagnostic and screening assays to be used in this aspect of the invention are described in Scherf et al., U.S. Pat. No. 6,855,323, herein incorporated by reference.
The invention also provides kits which are useful for carrying out the present invention. The kits may include a first container means containing the vaccine or antibodies of the invention. The kit may also include other container means containing solutions necessary or convenient for carrying out the invention. The container means can be made of glass, plastic or foil and can be a vial, bottle, pouch, tube, bag, etc. The kit may also contain written information, such as procedures for carrying out the present invention or analytical information, such as the amount of reagent contained in the first container means. The container means may be in another container means, e.g. a box or a bag, along with the written information.
The following-examples illustrate representative embodiments now contemplated for practicing the invention, but should not be construed to limit the invention.
EXAMPLE 1This Example describes proteomic studies to identify parasite proteins displayed on the surface of infected red blood cells (IRBCs).
Electron microscopy studies previously demonstrated that the “knob” structures on the surface of IRBC are the point of attachment of IRBC to the vascular endothelium. One of the characteristics of knob-associated proteins is that they are insoluble in non-ionic detergent and soluble in ionic detergent. Therefore, the following approach was used: enriching for knob-associated proteins by sequential extraction of parasites with non-ionic detergent followed by extraction with ionic detergent, and further separating peptide fragments of these proteins by gel electrophoresis or liquid chromatography, to be used in tandem mass spectrometry (MS/MS) studies.
Materials and methods
a. Sample preparation: Parasite samples were collected from pregnant women and their children recruited to the MOMS project in Muheza Tanzania. The study was performed on 18 samples collected from infected placenta and 21 isolates collected from infected children that attended MOMS clinic in Muheza. Peripheral blood from infected children contains parasites at the ring stage of development. The parasites were allowed to mature to the trophozoite-schizonts stages in culture for 12-20 hr as previously described (Trager & Jensen (1976) Science 193:673-5). Mature forms of the parasites were concentrated on percoll gradient. Enriched samples contained more than 90% infected red blood cells (IRBCs).
Enrichment for membrane proteins was performed by sequential extraction with detergent (Fried et al. (2004) Proteomics 4:1086-93). Parasite were incubated in lysis buffer A (10 mM Tris-HCl pH 7.4, 5 mM EDTA, 1% Triton X-100) for 30 min at 4° C., the lysate was centrifuge for 20 min at 12,000×g at 4° C. Supernatant containing soluble proteins was removed and lysis buffer B (10 mM Tris-HCl pH 7.4, SmM EDTA, 2% SDS, 6 M Urea) was added to the pellet containing insoluble proteins.
Trypsin digestion of protein mixture: Proteins were reduced with 10 mM DTT for 1 hr at 37° C. followed by alkylation with 20 mM iodoacetamide for 1 hr at 25° C. The sample was diluted to 0.05% SDS with 25 mM NH4CO3 and Trypsin was add to a final enzyme:substrate ratio of 1:50 (w:w) (Fried et al. (2004) Proteomics 4:1086-93). The samples were digested over night at 37° C. After trypsin digestion, peptides were cleaned using HILIC (The Nest Group Inc., Southboro, Mass.) according to the manufacturer's instructions.
b. LC-MS/MS analysis using ion trap: LC-MS/MS was performed using a LCQ Deca XP (ThermoFinnigan) ion trap mass spectrometer (ThermoFinnigan) or LTQ-MS (ThermoFinnigan, San Jose, Calif.). A total of 5 μg (1 μg/,μL) of total peptide (as determined by BCA assay) were loaded onto the reversed phase column using a two mobile-phase solvent system consisting of 0.4% acetic acid in water (A) an 0.4% acetic acid in acetonitrile (B).
The mass spectrometer operated in a data-dependent MS/MS mode over a m/z range of 400-2000. For each cycle, the three most abundant ions from each MS scan were selected for MS/MS analysis using 45% collision energy. Dynamic exclusion was used to discriminate against previously analyzed ions in a one minute window.
c. Data analysis: The Sequest algorithm was used to match MS/MS spectra to peptides in the database (Eng et al. (1994) Mass Spectrom. 5:976-89). The database included P. falciparum 3D7 genome sequence and other Plasmodium sequences submitted to NCBI, as well as the sequences from the non-redundant human database. Spectra/peptide matches were retained according to the following criteria: a deltaCn value of 0.1 and for charge state +1, X corr>1.5 for full tryptic peptides and Xcorr>3.1 for partially cleaved peptides. For charge state +2, X corr>1.9 for full tryptic peptides and Xcorr>3.8 for partially cleaved peptides. For charge state +3, × corr>2.9 for full tryptic peptides and Xcorr>4.5 for partially cleaved peptides (Qian et al 2005. J Proteome Research 4:53-62).
d. Accurate mass and time tag (AMT) by Fourier transform ion cyclotron resonance (FTICR-MS): 5 μg of peptide mixtures were separated by HPLC using reversed-phase capillary column (150 μm i.d.×360 jm o.d. Polymico Technologies, Phoenix Ariz.) using a two mobile-phase solvent system consisting of 0.2% acetic acid and 0.05% trifluoroacetic acid (TFA) in water and 0.1% TFA in 90% acetonitrile/10% water. FTICR mass spectrometer was used for detection. Peptides identified in LC-MS/MS were used as potential mass and time tags (PMTs) were matched to peptides detected by MS-FTICR. The FTICR data was analyzed using software developed in-house.
Quantitative analysis was performed using Acuity software on normalized values (Cluster program). Statistical analysis for comparison between placental samples and children samples was performed using non-parametric method (Mann Whitney).
e. Quantitative RT-PCR: For quantitative PCR, total RNA was extracted from placenta parasites and mature forms parasite collected from infected children using RNAwiz (Ambion, Calif.). Reverse transcription was performed using oligodT20 primer and Superscript II enzyme (Invitrogen, Calif.). Quantitative RT-PCR was performed using SYBR green master mix in an ABI Prism 7000 thermal cycler (Applied Biosystems). Primers were validated using both gDNA and a pool of cDNA. Threshold cycles (CT) were calculated and normalized (AACT method) using CT values for P. falciparum housekeeping gene seryl-tRNA synthetase. The results are expressed as fold change from the control gene and statistical significance was determined using t-test.
Results
Protein profiles of placental parasites (i.e., parasites that bind to CSA) were compared with protein profiles of parasites from infected children (i.e., parasites that do not bind to CSA). This study identified peptides from several P. falciparum proteins with unknown functions and predicted trans-membrane domains. These are believed to be novel proteins displayed on the IRBC surface. The list of unique proteins expressed in 2 or more placental isolates is shown in Table 1, except for PF13—0137 and PFL1200c for which peptides have been identified in one isolate by LC-MS/MS. Confirmation was obtained by FTICR-MS which is a more accurate and sensitive technology than LC-MS/MS (Smith et al. (2002) Proteomics 2:513-23).
SP = Signal peptide
TM = Transmembrane domain
PEXEL = Plasmodium Export Element (Hiller et al. (2004) Science 306: 1934-7; Marti et al. (2004) Science 306: 1930-3)
Using quantitative analysis (quantitative proteomics and quantitative RT-PCR), 5 of these proteins were at significantly higher levels in placenta parasites compared to isolates collected from infected children, as shown in Table 2. Using a quantitative proteomics approach, an additional protein expressed specifically by placental parasites was identified (Protein ID PFBO280w in Table 2).
This Example describes studies to show the immunogenicity of exemplary recombinant proteins identified by proteomic studies.
Materials and Methods
a. Expression of PFBO280w (SEQ ID NO:11) and PF13—0137 (SEQ ID NO:3): Recombinant proteins were prepared by cloning the genes into an expression vector pET28b (Novagen) according to the manufacturer instructions. Proteins expression in prokaryotic vector pET28b was carried out by growing bacteria to the logarithmic phase of growth, inducing expression of the recombinant protein with 1 mM IPTG and continuing to grow the bacteria culture to saturation. The culture was spun down and bacteria cell pellets were washed 3 times in solution A (50 mM Tris, 10 mM EDTA, 5 mM DTT, 2% Triton X-100, 500 mM NaCl pH 7.5). Proteins were solubilized for 2 hours in solution B (6 M guandium-HCI, 50 mM Tris pH8.0, 5 mM DTT). Cell debris were removed by centrifugation, and protein solution is loaded onto Nickel column to purify the His-tagged recombinant protein according to the manufacturer's specification (Novagen).
b. Immune recognition studies: ELISA assays were used for the analysis of the immune recognition of the recombinant proteins by sera from immune and non-immune subjects according to the protocol in Antibodies: A Laboratory Manual (1988) Ed Harlow, David Lane Ed. 96-well ELISA plates (Immulon 3) were coated with recombinant protein diluted to a concentration of 10 μg/ml in carbonate/bicarbonate buffer pH 8.6. The plates were incubated over-night at 4° C. The plates were washed 3 times in PBS-Tween buffer. Remaining sites for protein binding on the ELISA plates were saturated by incubating with blocking buffer (2% BSA in PBS-Tween) for 2 hours at room temperature. Sera samples from immune women (multigravid), non-immune women (primnigravid), and non-immune males were diluted 1:100 and added to the wells. The plates were incubated for 2 hours at room temperature, followed by washing 3 times with PBS-Tween buffer. Mouse anti-human IgG conjugated to HRP (enzyme labeled reagent) was added at dilution of 1:1000 and the plates were incubated for 1 hour at room temperature followed by 3 washes with PBS-Tween buffer. The detection was performed using peroxide substrate ABTS (Pierce) and the absorbance was measured in Elisa reader (Molecular Devices) at 405 nm.
Results
The recombinant proteins were analyzed for their recognition by sera from immune women (multigravidas) and non-immune women (primigravidas) as well as males residing in the same area. As shown in Table 3, sera from multigravidas had significantly higher levels of antibodies directed toward these proteins, similarly to the pattern of natural acquired immunity to placental parasites. It is expected that pregnancy malaria vaccine candidates will be better recognized by sera from multigravid women than primigravid women, indicating that these two properties of pregnancy malaria candidates.
This Example describes studies to show the immunogenicity of recombinant proteins derived from cell surface proteins identified by proteomic and/or microarray studies.
Materials and Methods
a. Analyses of protein sequences: Large molecular weight proteins that cannot be expressed as full length proteins may be expressed as predicted immunogenic domains. Such immunogenic domains are predicted from the sequence of the proteins identified by proteomic studies in EXAMPLE 1, or the microarray studies in EXAMPLE 4, and used for animal immunization studies. Protein sequences were analyzed using the DNASTAR program by several algorithms, including prediction of hydrophilicity according to Kyte-Doolittle method, surface probability according to Emini method, and antigenicity according to Jameson-Wolf method (DNASTAR, Inc).
Protein PFBO280w (SEQ ID NO:1) is a predicted 302 kD protein. Analysis using DNASTAR program suggested that the region between amino acids 572-877 contains several hydrophilic and antigenic epitopes. A domain including amino acids 572-877 is expressed as further described below.
Using a similar approach, the first 500 amino acids of protein PF13—0137 (SEQ ID NO:3) is expressed as further described below.
PFA0180w (SEQ ID NO:4) contains a signal peptide sequence, the sequence downstream is predicted to be surface expressed and contain multiple antigenic epitopes. This protein is expressed as two domains; the first domain includes amino acids 50-750, the second domain includes amino acids 751-1471. Each of these domains is predicted to be about 70 kD, which is amenable to expression in both prokaryotic and eukaryotic expression systems.
PFI0805w (SEQ ID NO:8) is a large molecular weight protein of 304 kD. Based on protein analysis as described, two domains are expressed. The first domain contains amino acids 370-670, the second domain includes amino acids 2000-2500.
PFL1200c (SEQ ID NO:10) is a small molecular weight protein of 12 kD. The full length protein is expressed as described below.
b. Protein expression in E. coli: Protein expression in prokaryotic vector pET28b is carried out by growing bacteria to the logarithmic phase of growth, inducing expression of the recombinant protein with 1 mM IPTG and continuing to grow the bacteria culture to saturation. The culture is spun down and the bacteria cell pellet is washed 3 times in solution A (50 mM Tris, 10 mM EDTA, 5 mM DTT, 2% Triton X-100, 500 mM NaCl pH7.5). Proteins are solubilized for 2 hours in solution B (6 M guandium-HCI, 50 mM Tris pH8.0, 5 mM DTT). Cell debris are removed by centrifugation, and the protein solution is loaded onto Nickel columns to purify the His-tagged recombinant protein according to the manufacturer's specification (Novagen).
c. In vitro protein expression: Because some of the malaria antigens may be difficult to express in cellular systems and are conformation dependent, an alternative method is also used to express the proteins identified in EXAMPLES 1 and 4, by using a cell-free in-vitro protein synthesis system (ENDEXT Technology) produced by CellFree Sciences. This method utilizes wheat germ lysate free of translation inhibitors, that allows stable translation of eukaryotic proteins, including conformation-dependent malaria antigens. The genes encoding these proteins are cloned into pEU-E01-His-TEV-MCS vector (Cell Free Systems, Inc.), followed by protein synthesis according to the manufacturer (CellFree Sciences). The His-tag proteins are purified using anti-His beads according to the manufacturer (Dynal).
d. Immune recognition of proteins: The recombinant proteins are analyzed for their recognition by sera from immune women (multigravidas) and non-immune women (primigravidas) as well as male residing in the same area, as described in EXAMPLE 2.
It is expected that the proteins that are used to immunize rabbits are immunogenic, and elicit antibodies that recognized the surface of the IRBC. Proteins that elicit antibodies that bind specifically only to CSA-binding parasites and not to other parasites are likely to be unique surface proteins of placental parasites.
Proteins that react with sera from multigravidas at significantly higher levels compared to sera from primigrivadas and males are expected to be good immunogens for use in a pregnancy malaria vaccine.
EXAMPLE 4This Example describes microarray studies to identify genes that are upregulated in placental parasites and that encode proteins predicted to be surface antigens.
Materials and Methods
Two-color spotted microarrays were used for all experiments. The microarrays were prepared using 70mer oligonucleotides spotted onto gamma amino propyl silane coated glass slides. The 70mers were obtained from Operon and consist of the complete set of commercially available P. falciparum probes. In addition, 70mers from predicted open reading frames that were not represented in the commercially available probe set as well as probes for PfEMP1 genes sequenced from field isolates of P. falciparum, were designed by the Duffy lab and synthesized by Illumina. A total of 8596 70mers were spotted twice on each slide using Gene Machine OGR-04 Omnigrid oligonucleotide arrayer.
Microarray analysis was performed using RNA prepared from parasites isolated from clinical specimens collected from area (name) hospital in Muheza Tanzania. RNA was prepared from both peripheral blood parasites and placental parasites collected from women with pregnancy malaria. Peripheral blood from children with malaria was collected for comparison of gene expression profiles to identify genes that are up-regulated in parasites causing pregnancy malaria. RNA quality was evaluated by Bioanalyzer (Agilent Technologies). RNA from each sample was amplified to generate antisense RNA using the Message Amp II kit (Ambion). Amplified RNA product was quantified and its quality further assessed using the Bioanalyzer. Antisense RNA was then cross-linked to CY3 and CY5 monoesters to generate fluorescent probes. The specific activity of each probe was measured. 5 μg of labeled probe RNA from samples to be compared were combined. The combined probes were fragmented at 70° C. using RNA fragmentation reagent (Ambion) to approximately 100 bp. Competitive hybridization using probe RNA derived from pregnant women and RNA from children's parasites was performed. In practice, when maternal parasite RNA was labeled with CY3 the children's RNA was labeled with CY5 Dye swaps were conducted to minimize dye bias and to provide replicate hybridizations. Microarrays were hybridized for 16-20 hours at 63° C. Following hybridization, the slides were washed to remove unincorporated probe and scanned at 532 nm and 634 nm using the Gene Pix 400A scanner (Axon).
Hybridization of fluorescent probes to each oligonucleotide spot was quantified using Gene Pix Pro Software (Axon). After performing Loess normalization, differential expression was assess by quantifying Log2 CY5/CY3 ratios using single sample, and Student's t-test as well as ANOVA statistical packages on Acuity 4.0 microarray data analysis software (Axon).
Quantitative RT-PCR was performed as described in EXAMPLE 1.
Results
Comparing the transcriptional profiles of placental parasites, peripheral parasites from pregnant women and children with malaria identified potential genes involved in binding placental tissue, as shown in Table 4. Up-regulated genes were examined for potential transmembrane domains, signal sequence and PEXEL (Plasmodium export element) sequences (Hiller et al. (2004) Science 306:1934-7; Marti et al. (2004) Science 306:1930-3) that could be used to indicate that these genes encode proteins at the red blood cell surface that are involved directly in parasite adhesion to placental tissue or are potentially immunogenic. The genes described in Table 4 are designated by their PlasmoDB gene identification names. The fold change in expression, and the presence of transmembrane domains and PEXEL sequences are also indicated in Table 4.
TM = Transmembrane domain
PEXEL = Plasmodium Export Element (Hiller et al. (2004) Science 306: 1934-7; Marti et al. (2004) Science 306: 1930-3)
This Example describes studies to show the inmmunogenicity of an exemplary recombinant protein identified by microarray studies.
Materials and Methods
Amino acids 34 to 347 of PFD1140w (SEQ ID NO:13) were expressed by in vitro translation, as described in EXAMPLE 3. Immune recognition studies were performed as described as described in EXAMPLE 2.
Results
The recombinant protein was analyzed for its recognition by sera from immune women (multigravidas) and males residing in the same area. As shown in Table 5, sera from multigravidas had significantly higher levels of antibodies directed toward these proteins, similarly to the pattern of natural acquired immunity to placental parasites.
Each of the scientific or patent references cited herein is hereby incorporated by reference.
While the preferred embodiment of the invention has been illustrated and described, it will be appreciated that various changes can be made therein without departing from the spirit and scope of the invention.
Claims
1. An isolated polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs:1-4 and 6-24, and immunogenic derivatives thereof.
2. An immunogenic composition comprising an isolated polypeptide and a pharmaceutically acceptable carrier, wherein the isolated polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NOs:1-4 and 6-24, and immunogenic derivatives thereof.
3. An isolated nucleic acid molecule encoding a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs:1-4 and 6-24, and immunogenic derivatives thereof.
Type: Application
Filed: Aug 8, 2006
Publication Date: Feb 15, 2007
Inventors: Michal Fried (Seattle, WA), Patrick Duffy (Seattle, WA), Susan Francis (Seattle, WA), Jason Wendler (Lincoln, NE), Theonest Mutabingwa (Muheza)
Application Number: 11/501,465
International Classification: A61K 39/002 (20060101); C07H 21/04 (20060101); C07K 14/445 (20070101);
