INCREASING ATOH1 LIFE TO DRIVE SENSORINEURAL HAIR CELL DIFFERENTIANTION
The present disclosure provides compositions and methods for treating subjects at risk for or with sensorineural hearing loss by modulating the rate of Atoh1 protein degradation to increase levels of Atoh1 protein.
This application claims priority under 35 USC §119(e) to U.S. Patent Application Ser. No. 62/034,040, filed on Aug. 6, 2014; and U.S. Patent Application Ser. No. 62/034,459, filed on Aug. 7, 2014, the entire contents of which applications are incorporated herein by reference.
TECHNICAL FIELDThis invention relates to the generation of sensorineural hair cells, and more particularly to the use of modulation of Atoh1 expression to generate sensorineural hair cells.
BACKGROUNDThere are six distinct sensory organs in the mammalian inner ear: the three cristae of the semicircular canals, the two maculae of the saccule and utricle, and the organ of Corti of the cochlea. The organ of Corti is the organ of hearing. The receptor cell for hearing is the hair cell of the cochlea (referred to herein as a hair cell, a sensory hair cell, or a sensorineural hair cell). Hair cells are limited in number and do not regenerate in mammals; damage or death of these cells leads to hearing loss (Edge and Chen, Curr. Opin. Neurobiol., 18:377-382 (2008)). Therapeutic compositions and methods to increase sensorineural hair cell number and/or function in the cochlea are required to address hearing loss.
SUMMARYThe present disclosure provides compositions and methods for generating hair cells by modulating expression of Atoh1 by inhibiting proteasome degradation of the Atoh1 protein. The data presented herein shows a role of the ubiquitin proteasome pathway in post-translational regulation of Atoh1, identifies several amino acids in the N terminus as important in determining lifespan of the Atoh1 protein, and identifies the HECT, UBA and WWE domain containing 1 (Huwe1) protein as an E3 ubiquitin ligase for Atoh1.
Thus, in a first aspect the invention provides methods for treating a disorder, e.g., sensorineural hearing loss or vestibular dysfunction, associated with loss of auditory hair cells in a subject. The methods include administering a therapeutically effective amount of proteasome inhibitor to the subject, e.g., to the inner ear of the subject. Also provided herein is the use of a proteasome inhibitor for the treatment of sensorineural hearing loss associated with loss of auditory hair cells in a subject.
In some embodiments, the proteasome inhibitor is selected from the group consisting of Bortezomib, Carfilzomib, NPI-0052, MLN9708, CEP-18770, and ONX0912.
In some embodiments, the methods include comprising administering an HDAC inhibitor, an EZH2/HMT inhibitor, or a DNMT inhibitor, in combination with a proteasome inhibitor, to the subject, e.g., to the inner ear of the subject.
Also provided herein is the use of one or more of an HDAC inhibitor, an EZH2/HMT inhibitor, or a DNMT inhibitor, in combination with a proteasome inhibitor, for the treatment of sensorineural hearing loss associated with loss of auditory hair cells in a subject.
In some embodiments, the HDAC inhibitor is selected from the group consisting of: Sodium Butyrate, Trichostatin A, hydroxamic acids, cyclic tetrapeptides, trapoxin B, depsipeptides, benzamides, electrophilic ketones, aliphatic acid compounds, phenylbutyrate, valproic acid, hydroxamic acids, vorinostat (SAHA), belinostat (PXD101), LAQ824, panobinostat (LBH589), entinostat (MS275), romidepsin, C1994, and mocetinostat (MGCD0103). In some embodiments, the EZH2/HMT inhibitor is selected from the group consisting of Deazaneplanocin A; GSK J1; GSK126; EPZ005687; E7438; EI1 (Qi et al., 2012, supra); EPZ-6438; GSK343; BIX-01294, UNC0638, BRD4770, EPZ004777, AZ505 and PDB 4e47, and those described in Garapaty-Rao et al., Chem. Biol. 20(11):1329-1339 (2013); 20130303555; and WO2012/005805; see, e.g., Wagner and Jung, Nature Biotechnology 30:622-623(2012). In some embodiments, the DNMT inhibitor is selected from the group consisting of azacytidine, decitabine, Zebularine (1-(β-D-ribofuranosyl)-1,2-dihydropyrimidin-2-one), procainamide, procaine, (−)-epigallocatechin-3-gallate, MG98, hydralazine, RG108, and Chlorogenic acid. In some embodiments, the proteasome inhibitor is selected from the group consisting of Bortezomib, Carfilzomib, NPI-0052, MLN9708, CEP-18770, and ONX0912.
In some embodiments, the methods uses include application of the HDAC inhibitor, DNMT inhibitor, the EZH2/HMT inhibitor, or the proteasome inhibitor, to the round window membrane, e.g., intra-tympanic injection, intra-labyrinthine delivery, or direct delivery into the inner ear fluids, e.g., using a microfluidic device or infusion pump.
In another aspect, the invention provides long-lived human Atoh1 variant polypeptides comprising mutations at amino acids 328, 331, and/or 334. In some embodiments, the long-lived human Atoh1 variant polypeptide is at least 80% identical to SEQ ID NO:1.
In some embodiments, the long-lived human Atoh1 variant polypeptide comprises SEQ ID NO:1 with a mutation selected from the group consisting of S328A, S331A, S334A, S328A/S331A, S328A/S331A, S331A/S334A, and S328A/S331A/S334A.
In some embodiments, the long-lived human Atoh1 variant polypeptide comprises SEQ ID NO:1 with a mutation at 5334, e.g., S334A.
In another aspect, the invention provides nucleic acids encoding the long-lived human Atoh1 variant polypeptides described herein, and expression vectors comprising the nucleic acids; in some embodiments, the nucleic acid encoding the long-lived human Atoh1 variant polypeptide is operably linked with an inducible promoter or a tissue specific promoter, e.g., a Lgr5, GFAP, Sox2, p27Kip, FGFR3, Prox1, or Sox2 promoter. Also provided are cells and transgenic animals harboring the nucleic acids and optionally expressing the long-lived human Atoh1 variant polypeptide comprises.
In a further aspect, the invention provides methods for treating a subject suffering from a disorder, e.g., sensorineural hearing loss or vestibular dysfunction, associated with loss of auditory hair cells. The methods include administering a therapeutically effective amount of a nucleic acid encoding a long-lived human Atoh1 variant polypeptide described herein to the subject, e.g., to the inner ear of the subject.
In yet another aspect, the invention features methods for treating a subject suffering from a disorder, e.g., sensorineural hearing loss or vestibular dysfunction, associated with loss of auditory hair cells. The methods include administering a therapeutically effective amount of an inhibitory nucleic acid targeting Huwe1 to the subject, e.g., to the inner ear of the subject. In some embodiments, the inhibitory nucleic acid is selected from the group consisting of antisense oligonucleotides; small interfering RNA (siRNA); and short, hairpin RNA (shRNA).
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Methods and materials are described herein for use in the present invention; other, suitable methods and materials known in the art can also be used. The materials, methods, and examples are illustrative only and not intended to be limiting. All publications, patent applications, patents, sequences, database entries, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control.
Other features and advantages of the invention will be apparent from the following detailed description and figures, and from the claims.
The present disclosure is based, at least in part, on the surprising discovery that inhibition of protein degradation increases levels of Atoh1 protein, which is expected to increase generation of hair cells from inner ear progenitor cells. As shown herein reducing proteasome activity led to an increase in levels of Atoh1 protein. As increased Atoh1 leads to an increase in generation of hair cells, these methods are expected to increase generation of hair cells from progenitors.
It is widely accepted that although cells capable of generating hair cells are present in the inner ear, natural hair cell regeneration in the inner ear is low (Li et al., Trends Mol. Med., 10, 309-315 (2004); Li et al., Nat. Med., 9, 1293-1299 (2003); Rask-Andersen et al., Hear. Res., 203, 180-191 (2005)). As a result, lost or damaged hair cells may not be adequately replaced by natural physiological processes (e.g., cell differentiation), and a loss of hair cells occurs. In many individuals, such hair cell loss can result in, e.g., sensorineural hearing loss, hearing impairment, and balance disorders. Therapeutic strategies that increase the number of hair cells in the inner ear will benefit a subject with hair cell loss, e.g., with one or more of these conditions.
In some embodiments, the present disclosure provides compositions and methods for preventing and/or treating auditory disease in a subject by increasing the number of sensory hair cells of the inner ear (e.g., hair cells), e.g., in the inner ear of the subject, by administering to the subject (e.g., to the inner ear of the subject) compositions that decrease protein degradation, e.g., Atoh1 degradation, in target cells.
Atoh1 is important for specifying hair cell fate and its expression is tightly regulated (Kelly et al., Nat. Rev. Neurosci., 7:837-849 (2006)). Once activated, Atoh1 interacts with its 3′ enhancer in a positive feedback loop to maintain expression (Helms et al., Development, 127: 1185-1196 (2000)). Despite the reported importance of Atoh1 for hair cell differentiation (Bermingham et al., Science, 284:1837-1841 (1999); Zheng and Gao, Nat. Neurosci., 3:580-586 (2000); Izumikawa et al., Nat. Med., 11:271-276 (2005); Kelly et al., Nat. Rev. Neurosci., 7:837-849 (2006); Gubbels et al., Nature, 455:537-541 (2008); Jeon et al., J. Neurosci., 31:8351-8358 (2011)), pathways and factors involved in its regulation are reportedly poorly understood (Fritzsch et al., Dev. Dyn., 233:570-583 (2005)).
As described herein, targeted modulation of protein degradation can be used to regulate Atoh1 and promote hair cell differentiation.
Post-Translational Regulation—the Ubiquitin-Proteasome Pathway
Post-translational modification is the chemical modification of a protein after its translation, which can include phosphorylation, acetylation, sumoylation, and ubiquitylation.
The ubiquitin-proteasome pathway plays an important role in biological processes integral to the development and physiology of eukaryotic cells. Specific proteins are labeled by polyubiquitin chains in an energy-consuming process and then targeted to the proteasome where they are degraded to small peptides. The system is highly selective and precisely regulated; it not only degrades misfolded or damaged proteins but also is essential for regulation of cell-signaling pathways, determining the half-lives ranging from minutes to days.
Ubiquitin, a 76 amino acid protein with a molecular weight of 8.5 kD, is involved in several biological processes. Isopeptide linkages to its 7 lysine residues generate a diverse set of monubiquitin or polyubiquitin chains. While K48-linked polyubiquitin chains signal for proteasomal degradation, monoubiquitylation is a signal for endocytosis or nuclear trafficking. K63-linked polyubiquitin chains signal endocytosis, ribosome modification and DNA repair (Pickart, Molecular cell. Sep. 1 2001; 8(3):499-504).
The ubiquitin system consists of three critical enzymes: ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2), and ubiquitin ligase (E3). E3 catalyzes the formation of polyubiquitin chains (and occasional monoubiquitin chains) by transferring ubiquitins that have been activated by E1 and E2 to internal lysine residues on specific substrates.
E3 ligases are classified by the occurrence of HECT (homologous to the E6-AP COOH terminus) or RING (Really Interesting New Gene) domains. The human genome encodes over 600 E3 ligases, most belonging to the RING family (Deshaies and Joazeiro, Annual review of biochemistry. 2009:78:399-434). HECT domain ligases form a transient and covalent linkage with ubiquitin via a conserved cysteine, while RING domain ligases transfer ubiquitin from E2 to the substrate, without direct ubiquitylation.
RING domain E3 ligases can be further classified into single subunit, dimeric RING finger (RF), and modular classes. Modular RING E3 ligases function as part of a multi-protein complex and substrate proteins are recruited by separate subunits. Examples of modular E3 ligases include the cullin-RING ligase (CRL) superfamily, comprised of Cul1, 2, 3, 4A, 4B, 5 and 7 (Jin et al., Genes Dev. 2004; 18(21):2573-2580). Cullin serves as a scaffold for assembly of the multiple subunits and transfer of ubiquitin from E2 to the substrate protein. The C-terminus of cullin binds the ring-finger protein (RING box, Rbx1) to form the core E3 ubiquitin ligase, while the N-terminus binds the adaptor module protein to mediate the interaction between cullin and its specific substrate. Cul4A E3 ubiquitin ligases contain the cullin 4A scaffold and the DDB1 (damaged DNA binding protein 1) adaptor protein. Substrate specificity is conferred by a set of substrate receptors, DDB1-and-CUL4A-associated factors (DCAF).
Although various pathways have been shown to upregulate Atoh1 expression at the transcriptional level (Jeon et al., The Journal of neuroscience: the official journal of the Society for Neuroscience. 2011; 31(23):8351-8358; Shi et al., Journal of biological chemistry. 2010; 285(1):392-400; Examples 1-10, below), post-transcriptional regulation of Atoh1 is largely unexplored. The present inventors hypothesized that inhibition of post-translational degradation could increase the level of Atoh1 protein and force progenitors toward a hair cell fate. There was a seemingly contradictory role of Sox2 in regulation of Atoh1, as Sox2 increased expression of Atoh1 mRNA but did not increase the level of Atoh1 protein. Example 11 herein shows a role of the ubiquitin proteasome pathway in the post-translational regulation of Atoh1.
Long-Lived Atoh1 ProteinsIn one aspect, the invention provides long-lived Atoh1 variant polypeptides comprising one or more mutations at amino acids 328, 331, and/or 334, i.e., mutations at amino acids 328, 331, and/or 334 to any amino acid other than serine, e.g., alanine, asparagine, glutamine, threonine, tyrosine, or cysteine, preferably alanine or glycine, wherein the variant is resistant to proteasome degradation and thus has a longer half life. Also provided are isolated nucleic acid molecules that encode a long-lived Atoh1 variant polypeptide as described herein.
The sequence of human Atoh1, also known as ATH1; HATH1; MATH-1; and bHLHa14, is available in GenBank at Acc. No. NM_005172.1 (mRNA) and NP_005163.1 (protein). SEQ ID NO:1 shows the long-lived Atoh1 variant human protein sequence with the mutation sites at amino acids 328, 331 and/or 334 shown as
In one embodiment, the protein includes an amino acid sequence at least about 80%, 85%, 90%, 95%, 98% or more identical to SEQ ID NO:1, wherein one or more of amino acids 328, 331 and/or 334 are not serine. For use in the methods described herein, the protein must retain the ability to promote differentiation of a supporting cell into an auditory hair cell.
In some embodiments, an isolated nucleic acid molecule of the invention includes a nucleotide sequence encoding a variant Atoh1 human protein shown in SEQ ID NO:1, wherein one or more of amino acids 328, 331 and/or 334 are not serine, i.e., are alanine, glycine, or another amino acid. In some embodiments, the nucleic acid molecule includes sequences encoding the variant Atoh1 human protein (i.e., “the coding region” or “open reading frame”), as well as 5′ untranslated sequences. Alternatively, the nucleic acid molecule can include only a coding region and, e.g., no flanking sequences that normally accompany the subject sequence. The protein includes one of the following mutations: S328A, S331A, S334A, S328A/S331A, S328A/S331A, S331A/S334A, or S328A/S331A/S334A. An exemplary nucleic acid sequence is shown in SEQ ID NO:2, with the codons encoding amino acids 328, 331 and 334 shown as NNN.
In some embodiments, an isolated nucleic acid molecule encoding a variant Atoh1 human protein described herein includes a nucleotide sequence that is at least about 85% or more identical to the entire length of a nucleotide sequence shown in SEQ ID NO:2. In some embodiments, the nucleotide sequence is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to SEQ ID NO:2. The encoded protein includes at least one of the following mutations: S328A, S331A, S334A, S328A/S331A, S328A/S331A, S331A/S334A, or S328A/S331A/S334A.
Calculations of homology between sequences are performed as follows. To determine the percent identity of two amino acid sequences, or of two nucleic acid sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes). The length of a reference sequence aligned for comparison purposes is at least 80% of the length of the reference sequence, and in some embodiments is at least 90% or 100%. The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences. In another embodiment, the percent identity of two amino acid sequences can be assessed as a function of the conservation of amino acid residues within the same family of amino acids (e.g., positive charge, negative charge, polar and uncharged, hydrophobic) at corresponding positions in both amino acid sequences (e.g., the presence of an alanine residue in place of a valine residue at a specific position in both sequences shows a high level of conservation, but the presence of an arginine residue in place of an aspartate residue at a specific position in both sequences shows a low level of conservation).
For purposes of the present invention, the comparison of sequences and determination of percent identity between two sequences can be accomplished using blastn with Match/Mismatch scores of 1 and −2, respectively, and a linear gap penalty. See Zhang et al., J Comput Biol 2000; 7(1-2):203-14.
Recombinant Expression Vectors, Host Cells and Genetically Engineered CellsIn another aspect, the invention includes vectors, preferably expression vectors, containing a nucleic acid encoding a long-lived Atoh1 variant polypeptide described herein. As used herein, the term “vector” refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked and can include a plasmid, cosmid or viral vector. The vector can be capable of autonomous replication or it can integrate into a host DNA. Viral vectors include, e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses. Additional information regarding vectors is provided below.
A vector can include a long-lived Atoh1 variant-encoding nucleic acid in a form suitable for expression of the nucleic acid in a host cell. Preferably the recombinant expression vector includes one or more regulatory sequences operatively linked to the nucleic acid sequence to be expressed. The term “regulatory sequence” includes promoters, enhancers and other expression control elements (e.g., polyadenylation signals). Regulatory sequences include those which direct constitutive expression of a nucleotide sequence, as well as tissue-specific regulatory and/or inducible sequences. The design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, and the like. The expression vectors of the invention can be introduced into host cells to thereby produce long-lived Atoh1 variants as described herein.
The recombinant expression vectors of the invention can be designed for expression of long-lived Atoh1 variant proteins in prokaryotic or eukaryotic cells. For example, polypeptides of the invention can be expressed in E. coli, insect cells (e.g., using baculovirus expression vectors), yeast cells or mammalian cells. Suitable host cells are discussed further in Goeddel, (1990) Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. Alternatively, the recombinant expression vector can be transcribed and translated in vitro, e.g., using T7 promoter regulatory sequences and T7 polymerase.
When used in mammalian cells, the expression vector's control functions are often provided by viral regulatory elements. For example, commonly used promoters are derived from polyoma, Adenovirus 2, cytomegalovirus and Simian Virus 40.
In another embodiment, the recombinant mammalian expression vector is capable of directing expression of the nucleic acid preferentially in a particular cell type (e.g., tissue-specific regulatory elements are used to express the nucleic acid). For example, promoters that are primarily or only active in auditory or supporting cells can be used, e.g., a Lgr5, GFAP, Sox2, p27Kip, FGFR3, Prox1, or Sox2 promoter.
Another aspect the invention provides a host cell which includes a nucleic acid molecule described herein, e.g., a long-lived Atoh1 variant-encoding nucleic acid molecule within a recombinant expression vector or a long-lived Atoh1 variant-encoding nucleic acid molecule containing sequences which allow it to homologously recombine into a specific site of the host cell's genome. The terms “host cell” and “recombinant host cell” are used interchangeably herein. Such terms refer not only to the particular subject cell but to the progeny or potential progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.
A host cell can be any prokaryotic or eukaryotic cell. For example, a long-lived Atoh1 variant protein can be expressed in bacterial cells such as E. coli, insect cells, yeast or mammalian cells (e.g., Chinese hamster ovary cells (CHO) or COS cells). Other suitable host cells are known to those skilled in the art.
Vector DNA can be introduced into host cells via conventional transformation or transfection techniques. As used herein, the terms “transformation” and “transfection” are intended to refer to a variety of art-recognized techniques for introducing foreign nucleic acid (e.g., DNA) into a host cell, including calcium phosphate or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, lipofection, or electroporation.
A host cell of the invention can be used to produce (i.e., express) a long-lived Atoh1 variant protein. Accordingly, the invention further provides methods for producing a long-lived Atoh1 variant protein using the host cells of the invention. In one embodiment, the method includes culturing the host cell of the invention (into which a recombinant expression vector encoding a long-lived Atoh1 variant protein has been introduced) in a suitable medium such that a long-lived Atoh1 variant protein is produced. In another embodiment, the method further includes isolating a long-lived Atoh1 variant protein from the medium or the host cell.
In another aspect, the invention features, a cell or purified preparation of cells which include a long-lived Atoh1 variant transgene, and that optionally express the long-lived Atoh1 variant. The cell preparation can consist of human or non-human cells, e.g., rodent cells, e.g., mouse or rat cells, rabbit cells, or pig cells. In some embodiments, the long-lived Atoh1 variant transgene is under control of an inducible promoter as is known in the art. Such cells can serve as a model for studying disorders that are related to Atoh1 expression.
In another aspect, the invention features a cell transformed with nucleic acid which encodes a long-lived Atoh1 variant polypeptide. The cell can be, e.g., a mammalian cell, e.g., a mesenchymal stem cell, human embryonic stem cell, inner ear-derived stem cell (see, e.g., Li et al., Nat Med. 9(10):1293-9 (2003)), hair cell progenitor, or induced pluripotent stem cell, or a cell derived therefrom, e.g., an endodermal/mesodermal progenitor that expresses Brachyury and GATA6, or an inner ear progenitor cell that expresses Sox2, which could be made from an ES cell or induced pluripotent stem cell derived from a blood cell or fibroblast, e.g., as described in Li et al., Proc Natl Acad Sci USA. 100(23):13495-500 (2003); or Oshima et al., Cell. 141(4): 704-716 (2010); see also Breuskin et al., Hear Res. 236(1-2):1-10 (2008); Bodson et al., Acta Otolaryngol. 130(3):312-7 (2010); and Jahan et al., Hear Res. 297:30-41 (2013). Alternatively, the cell can be a more differentiated cell, e.g., a fibroblast or other non-auditory cell type.
Cells, e.g., progenitor cells, expressing a long-lived human Atoh1 variant polypeptide as described herein can be introduced into an individual subject to increase the number of hair cells and treat sensorineural hearing loss or vestibular dysfunction associated with loss of auditory hair cells in the subject. Preferably, the cells are injected into the cochlea as described herein. Once implanted in an individual, the cells produce a long-lived human Atoh1 variant polypeptide described herein and differentiate into hair cells. In some embodiments, the Atoh1 is under the control of an inducible promoter, and the cells are implanted into the subject in a progenitor state, and induced to express the long-lived Atoh1 once in situ. A number of inducible promoters are known in the art, e.g., metallothionein, heat shock protein, tetracycline or minocycline promoters. See, e.g., U.S. Pat. No. 8,673,634 and Devarajan et al., J. Funct. Biomater. 2:249-270 (2011) for a review of gene delivery and stem cell based therapies for regenerating inner ear hair cells.
Transgenic animals expressing the long-lived human Atoh1 variant polypeptides described herein are also within the present invention. As used herein, a “transgenic animal” is a non-human animal, preferably a mammal, more preferably a rodent such as a rat or mouse, in which one or more of the cells of the animal includes a long-lived human Atoh1 variant transgene. Other examples of transgenic animals include non-human primates, sheep, dogs, cows, goats, chickens, amphibians, and the like. A long-lived human Atoh1 variant transgene is exogenous DNA encoding a long-lived human Atoh1 variant described herein that preferably is integrated into or occurs in the genome of the cells of a transgenic animal. A long-lived human Atoh1 variant transgene can direct the expression of the encoded gene product in one or more cell types or tissues of the transgenic animal, e.g., in cells of the inner ear of the animal. Thus, a transgenic animal can be one in which an endogenous Atoh1 gene has been altered by, e.g., by homologous recombination between the endogenous gene and an exogenous long-lived human Atoh1 variant-encoding DNA molecule introduced into a cell of the animal, e.g., an embryonic cell of the animal, prior to development of the animal.
Intronic sequences and polyadenylation signals can also be included in the transgene to increase the efficiency of expression of the transgene. A tissue-specific regulatory sequence, e.g. as described above, can be operably linked to a transgene of the invention to direct expression of a long-lived human Atoh1 variant protein to particular cells. A transgenic founder animal can be identified based upon the presence of a long-lived human Atoh1 variant-encoding transgene in its genome and/or expression of long-lived human Atoh1 variant mRNA in tissues or cells of the animals. A transgenic founder animal can then be used to breed additional animals carrying the transgene. Moreover, transgenic animals carrying a transgene encoding a long-lived human Atoh1 variant protein can further be bred to other transgenic animals carrying other transgenes.
Methods of TreatmentThe compounds and methods described herein are appropriate for the treatment of mammalian (e.g., human) subjects who have or are at risk of developing hearing disorders resulting from cochlear hair cell loss, preferably post-neonatal (e.g., child, adolescent or adult, e.g., above the age of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or 13 years) subjects. The methods described herein can be used to treat cochlear hair cell loss and any disorder that arises as a consequence of hair cell loss in the ear, such as hearing impairments or deafness. These subjects can receive treatment with an agent described herein. The approach may be optimal for treatment of acute hearing loss shortly after the damage has occurred, and may be less effective after longer time periods when Notch signaling has returned to its baseline level in the adult.
In some instances, methods include selecting a subject. Subjects suitable for treatment include those at risk of hair cell loss or with hair cell loss and/or those at risk of sensorineural hearing loss or with sensorineural hearing loss. Any subject experiencing or at risk for developing hearing loss is a candidate for the treatment methods described herein. A human subject having or at risk for developing a hearing loss can hear less well than the average human being, or less well than a human before experiencing the hearing loss. For example, hearing can be diminished by at least 5, 10, 30, 50% or more.
The subject can have hearing loss associated with cochlear hair cell loss for any reason, or as a result of any type of event. For example, a subject can be deaf or hard-of-hearing as a result of an infection or physical ototoxic insult, e.g., a traumatic event, such as a physical trauma to a structure of the ear that does not irreversibly damage the supporting cells. In preferred embodiments, the subject can have (or be at risk of developing) hearing loss as result of exposure to a sudden loud noise, or a prolonged exposure to loud noises. For example, prolonged or repeated exposures to concert venues, airport runways, and construction areas can cause inner ear damage and subsequent hearing loss; subjects who are subjected to high levels of environmental noise, e.g., in the home or workplace, can be treated using the methods described herein. A subject can have a hearing disorder that results from aging, e.g., presbycusis, which is generally associated with normal aging processes; see, e.g., Huang, Minn Med. 90(10):48-50 (2007) and Frisina, Annals of the New York Academy of Sciences, 1170: 708-717 (2009), and can occur in subjects as young as 18, but is generally more marked in older subjects, e.g., subjects over age 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or 90. A subject can have tinnitus (characterized by ringing in the ears) due to loss of hair cells. A subject can experience a chemical ototoxic insult, wherein ototoxins include therapeutic drugs including antineoplastic agents, salicylates, quinines, and aminoglycoside antibiotics, e.g., as described further below, contaminants in foods or medicinals, and environmental or industrial pollutants. In general, subjects who have a known genetic disease associated with hearing loss (e.g., mutations in connexin 26, Alport, and so on), or a known cause of hearing loss that is associated with structural damage to the inner ear (e.g. penetrating trauma), that would not be correctable or ameliorated by the present methods are excluded from the present methods.
In some embodiments, the methods include administering to the subject a compound described herein within one, two, three, four, five, six, or seven days, or one, two, three, four, five, or six weeks of exposure to an ototoxic insult, e.g., a physical (noise, trauma) or chemical (ototoxin) insult that results in or could result in a loss of hair cells, and causes an increase in Notch signaling in the subject.
In some embodiments, a subject suitable for the treatment using the compounds and methods featured in the invention can include a subject having a vestibular dysfunction, including bilateral and unilateral vestibular dysfunction; the methods include administering a therapeutically effective amount of an agent described herein, e.g., by systemic administration or administration via the endolymphatic sac (ES). Vestibular dysfunction is an inner ear dysfunction characterized by symptoms that include dizziness, imbalance, vertigo, nausea, and fuzzy vision and may be accompanied by hearing problems, fatigue and changes in cognitive functioning. Vestibular dysfunctions that can be treated by the methods described herein can be the result of a genetic or congenital defect; an infection, such as a viral or bacterial infection; or an injury, such as a traumatic or nontraumatic injury, that results in a loss of vestibular hair cells. In some embodiments, balance disorders or Meniere's disease (idiopathic endolymphatic hydrops) may be treated by the methods described herein. Vestibular dysfunction is most commonly tested by measuring individual symptoms of the disorder (e.g., vertigo, nausea, and fuzzy vision).
Alternatively or in addition, the compounds and methods featured in the invention can be used prophylactically, such as to prevent, reduce or delay progression of hearing loss, deafness, or other auditory disorders associated with loss of hair cells. For example, a composition containing one or more compounds can be administered with (e.g., before, after or concurrently with) an ototoxic therapy, i.e., a therapeutic that has a risk of hair cell toxicity and thus a risk of causing a hearing disorder. Ototoxic drugs include the antibiotics neomycin, kanamycin, amikacin, viomycin, gentamycin, tobramycin, erythromycin, vancomycin, and streptomycin; chemotherapeutics such as cisplatin; nonsteroidal anti-inflammatory drugs (NSAIDs) such as choline magnesium trisalicylate, diclofenac, diflunisal, fenoprofen, flurbiprofen, ibuprofen, indomethacin, ketoprofen, meclofenamate, nabumetone, naproxen, oxaprozin, phenylbutazone, piroxicam, salsalate, sulindac, and tolmetin; diuretics; salicylates such as aspirin; and certain malaria treatments such as quinine and chloroquine. For example, a subject undergoing chemotherapy can be treated using the compounds and methods described herein. The chemotherapeutic agent cisplatin, for example, is known to cause hearing loss. Therefore, a composition containing one or more compounds can be administered with cisplatin therapy (e.g., before, after or concurrently with) to prevent or lessen the severity of the cisplatin side effect. Such a composition can be administered before, after and/or simultaneously with the second therapeutic agent. The two agents may be administered by different routes of administration.
In general, the compounds and methods described herein can be used to generate hair cell growth in the ear and/or to increase the number of hair cells in the ear (e.g., in the inner, middle, and/or outer ear). For example, the number of hair cells in the ear can be increased about 2-, 3-, 4-, 6-, 8-, or 10-fold, or more, as compared to the number of hair cells before treatment. This new hair cell growth can effectively restore or establish at least a partial improvement in the subject's ability to hear. For example, administration of an agent can improve hearing loss by about 5, 10, 15, 20, 40, 60, 80, 100% or more.
In some instances, compositions can be administered to a subject, e.g., a subject identified as being in need of treatment, using a systemic route of administration. Systemic routes of administration can include, but are not limited to, parenteral routes of administration, e.g., intravenous injection, intramuscular injection, and intraperitoneal injection; enteral routes of administration e.g., administration by the oral route, lozenges, compressed tablets, pills, tablets, capsules, drops (e.g., ear drops), syrups, suspensions and emulsions; transdermal routes of administration; and inhalation (e.g., nasal sprays).
In some instances, compositions can be administered to a subject, e.g., a subject identified as being in need of treatment, using a systemic or local route of administration. Such local routes of administration include administering one or more compounds into the ear of a subject and/or the inner ear of a subject, for example, by injection and/or using a pump.
In some instances, compositions can be can be injected into the ear (e.g., auricular administration), such as into the luminae of the cochlea (e.g., the Scala media, Sc vestibulae, and Sc tympani). For example, compositions can be administered by intratympanic injection (e.g., into the middle ear), intralabyrinthine delivery (e.g., to the stapes foot plate), and/or injections into the outer, middle, and/or inner ear. Such methods are routinely used in the art, for example, for the administration of steroids and antibiotics into human ears. Injection can be, for example, through the round window of the ear or through the cochlea capsule. In another exemplary mode of administration, compositions can be administered in situ, via a catheter or pump. A catheter or pump can, for example, direct a pharmaceutical composition into the cochlea luminae or the round window of the ear. Exemplary drug delivery apparatus and methods suitable for administering one or more compounds into an ear, e.g., a human ear, are described by McKenna et al., (U.S. Publication No. 2006/0030837) and Jacobsen et al., (U.S. Pat. No. 7,206,639). In some embodiments, a catheter or pump can be positioned, e.g., in the ear (e.g., the outer, middle, and/or inner ear) of a subject during a surgical procedure. In some embodiments, a catheter or pump can be positioned, e.g., in the ear (e.g., the outer, middle, and/or inner ear) of a subject without the need for a surgical procedure.
In some instances, compositions can be administered in combination with a mechanical device such as a cochlea implant or a hearing aid, which is worn in the outer ear. An exemplary cochlea implant that is suitable for use with the present invention is described by Edge et al., (U.S. Publication No. 2007/0093878).
In some instances, compositions can be administered according to any of the Food and Drug Administration approved methods, for example, as described in CDER Data Standards Manual, version number 004 (which is available at fda.give/cder/dsm/DRG/drg00301.htm).
In some instances, the present disclosure includes treating a subject by administering to the subject cells produced using the compositions and methods disclosed herein. In general, such methods can be used to promote complete or partial differentiation of a cell to or towards a mature cell type of the inner ear (e.g., a hair cell) in vitro. Cells resulting from such methods can then be transplanted or implanted into a subject in need of such treatment. Cell culture methods required to practice these methods, including methods for identifying and selecting suitable cell types, methods for promoting complete or partial differentiation of selected cells, methods for identifying complete or partially differentiated cell types, and methods for implanting complete or partially differentiated cells are described herein. Target cells suitable for use in these methods are described above.
In some instances, methods can include administering one or more compositions disclosed herein and cells produced using the compositions and methods disclosed herein to a subject.
Administration of cells to a subject, whether alone or in combination with compounds or compositions disclosed herein, can include administration of undifferentiated, partially differentiated, and fully differentiated cells, including mixtures of undifferentiated, partially differentiated, and fully differentiated cells. As disclosed herein, less than fully differentiated cells can continue to differentiate into fully differentiated cells following administration to the subject.
Where appropriate, following treatment, the subject can be tested for an improvement in hearing or in other symptoms related to inner ear disorders. Methods for measuring hearing are well-known and include pure tone audiometry, air conduction, and bone conduction tests. These exams measure the limits of loudness (intensity) and pitch (frequency) that a subject can hear. Hearing tests in humans include behavioral observation audiometry (for infants to seven months), visual reinforcement orientation audiometry (for children 7 months to 3 years); play audiometry for children older than 3 years; and standard audiometric tests for older children and adults, e.g., whispered speech, pure tone audiometry; tuning fork tests; brain stem auditory evoked response (BAER) testing or auditory brain stem evoked potential (ABEP) testing. Oto-acoustic emission testing can be used to test the functioning of the cochlear hair cells, and electro-cochleography provides information about the functioning of the cochlea and the first part of the nerve pathway to the brain. In some embodiments, treatment can be continued with or without modification or can be stopped.
Modulation of Post-Translational Degradation of Atoh1 ProteinThe present disclosure provides that the levels of Atoh1 can be modulated to promote hair cell differentiation. Accordingly, the present disclosure provides compositions and methods for modulating Atoh1 protein levels in a target cell to promote differentiation of the target cell towards or to a hair cell. Modification of Atoh1 protein levels can be achieved, e.g., by increasing the half-life of Atoh1 protein.
Thus, the methods described herein include the administration of compounds that decrease degradation of Atoh1. Such compounds include proteasome inhibitors.
Based on chemical structure and active moiety, proteasome inhibitors can be classified into a number of groups: boronates (e.g., Bortezomib, MLN9708 (Ixazomib citrate), MLN2238, and CEP-18770 (Piva et al., Blood. 2008 Mar. 1; 111(5):2765-75), Delanzomib), epoxyketones (Carfilzomib, ONX 0912 (Oprozomib), and epoxomicin), aldehydes (e.g., MG-132, PSI (Figueiredo-Pereira et al., J. Neurochem. 63, 1578-1581 (1994)), and fellutamide), alpha-ketoaldehydes, beta-lactones (e.g., lactacystin, omuralide, PS-519, belactosin A, and Marizomib (NPI-0052)), vinyl sulfones (e.g., NIP-L3VS and MV151), syrbactins (SylA and GlbA), and bacterial (e.g., HT1171 and GL5i. A number of other proteasome inhibitors are known in the art, including disulfiram, PR-924 (Kuhn et al., Blood. 2009; 113:4667-4676) and ISPI-101 (Hurchla et al., Leukemia. 2013; 27:430-440). See, e.g., Crawford et al., J Cell Commun Signal. 2011; 5(2): 101-110; Gupta et al., “Novel Proteasome Inhibitors for Multiple Myeloma,” Contemporary oncology, summer 2013, available onine at onclive.com/publications/contemporary-oncology/2013/Summer-2013/Novel-Proteasome-Inhibitors-for-Multiple-Myeloma; Moreau et al., Blood August 2012, 120 (5) 947-959; Kisselev et al., Chemistry & Biology 19:99-115 (2012); and Metcalf et al., Proteasome inhibitor patents (2010—present), informa healthcare doi:10.1517/13543776.2014.877444.
Gene Therapy Using Nucleic Acids Encoding Long-Lived Atoh1 ProteinsNucleic acids encoding a long-lived Atoh1 variant polypeptide as described herein comprising mutations at amino acids 328, 331, and/or 334, i.e., mutations at amino acids 328, 331, and/or 334 to any amino acid other than serine, e.g., alanine, asparagine, glutamine, threonine, tyrosine, or cysteine, preferably alanine or glycine, can be incorporated into a gene construct to be used as a part of a gene therapy protocol to treat subjects suffering from sensorineural hearing loss or vestibular dysfunction as a result of loss of auditory hair cells.
The present invention includes vectors, e.g., targeted expression vectors, for in vivo transfection and expression of a polynucleotide that encodes a long-lived Atoh1 variant as described herein, preferably in particular cell types, especially supporting cells. For example, promoters that are primarily or only active in auditory or supporting cells can be used, e.g., a Lgr5, GFAP, Sox2, p27Kip, FGFR3, Prox1, or Sox2 promoter. Expression constructs of such components can be administered in any effective carrier, e.g., any formulation or composition capable of effectively delivering the component gene to cells in vivo. Approaches include insertion of the gene in viral vectors, including recombinant retroviruses, adenovirus, adeno-associated virus, lentivirus, and herpes simplex virus-1, or recombinant bacterial or eukaryotic plasmids. Viral vectors transfect cells directly; plasmid DNA can be delivered naked or with the help of, for example, cationic liposomes (lipofectamine) or derivatized (e.g., antibody conjugated), polylysine conjugates, gramacidin S, artificial viral envelopes or other such intracellular carriers, as well as direct injection of the gene construct or CaPO4 precipitation carried out in vivo.
A preferred approach for in vivo introduction of nucleic acid into a cell is by use of a viral vector containing nucleic acid, e.g., a cDNA. Infection of cells with a viral vector has the advantage that a large proportion of the targeted cells can receive the nucleic acid. Additionally, molecules encoded within the viral vector, e.g., by a cDNA contained in the viral vector, are expressed efficiently in cells that have taken up viral vector nucleic acid.
Retrovirus vectors and adeno-associated virus vectors can be used as a recombinant gene delivery system for the transfer of exogenous genes in vivo, particularly into humans. These vectors provide efficient delivery of genes into cells, and the transferred nucleic acids are stably integrated into the chromosomal DNA of the host. The development of specialized cell lines (termed “packaging cells”) which produce only replication-defective retroviruses has increased the utility of retroviruses for gene therapy, and defective retroviruses are characterized for use in gene transfer for gene therapy purposes (for a review see Miller, Blood 76:271 (1990)). A replication defective retrovirus can be packaged into virions, which can be used to infect a target cell through the use of a helper virus by standard techniques. Protocols for producing recombinant retroviruses and for infecting cells in vitro or in vivo with such viruses can be found in Ausubel, et al., eds., Current Protocols in Molecular Biology, Greene Publishing Associates, (1989), Sections 9.10-9.14, and other standard laboratory manuals. Examples of suitable retroviruses include pLJ, pZIP, pWE and pEM which are known to those skilled in the art. Examples of suitable packaging virus lines for preparing both ecotropic and amphotropic retroviral systems include ΨCrip, ΨCre, Ψ2 and ΨAm. Retroviruses have been used to introduce a variety of genes into many different cell types, including epithelial cells, in vitro and/or in vivo (see for example Eglitis, et al. (1985) Science 230:1395-1398; Danos and Mulligan (1988) Proc. Natl. Acad. Sci. USA 85:6460-6464; Wilson et al. (1988) Proc. Natl. Acad. Sci. USA 85:3014-3018; Armentano et al. (1990) Proc. Natl. Acad. Sci. USA 87:6141-6145; Huber et al. (1991) Proc. Natl. Acad. Sci. USA 88:8039-8043; Ferry et al. (1991) Proc. Natl. Acad. Sci. USA 88:8377-8381; Chowdhury et al. (1991) Science 254:1802-1805; van Beusechem et al. (1992) Proc. Natl. Acad. Sci. USA 89:7640-7644; Kay et al. (1992) Human Gene Therapy 3:641-647; Dai et al. (1992) Proc. Natl. Acad. Sci. USA 89:10892-10895; Hwu et al. (1993) J. Immunol. 150:4104-4115; U.S. Pat. No. 4,868,116; U.S. Pat. No. 4,980,286; PCT Application WO 89/07136; PCT Application WO 89/02468; PCT Application WO 89/05345; and PCT Application WO 92/07573).
Another viral gene delivery system useful in the present methods utilizes adenovirus-derived vectors. The genome of an adenovirus can be manipulated such that it encodes and expresses a gene product of interest but is inactivated in terms of its ability to replicate in a normal lytic viral life cycle. See, for example, Berkner et al., BioTechniques 6:616 (1988); Rosenfeld et al., Science 252:431-434 (1991); and Rosenfeld et al., Cell 68:143-155 (1992); and Crystal, Human Gene Therapy 25:3-11 (2014). Suitable adenoviral vectors derived from the adenovirus strain Ad type 5 (e.g., d1324) or other strains of adenovirus (e.g., Ad2, Ad3, or Ad7 etc.), with E1 (and optionally one or both of E3 and E4) deleted, are known to those skilled in the art. Recombinant adenoviruses can be advantageous in certain circumstances, in that they are not capable of infecting non-dividing cells and can be used to infect a wide variety of cell types, including epithelial cells (Rosenfeld et al., (1992) supra). Furthermore, the virus particle is relatively stable and amenable to purification and concentration, and as above, can be modified so as to affect the spectrum of infectivity. Additionally, introduced adenoviral DNA (and foreign DNA contained therein) is not integrated into the genome of a host cell but remains episomal, thereby avoiding potential problems that can occur as a result of insertional mutagenesis in situ, where introduced DNA becomes integrated into the host genome (e.g., retroviral DNA). Moreover, the carrying capacity of the adenoviral genome for foreign DNA is large (up to 8 kilobases) relative to other gene delivery vectors (Berkner et al., supra; Haj-Ahmand and Graham, J. Virol. 57:267 (1986). In some embodiments, the viral vector is an AAV5, e.g., an E1, E3, E4-deleted Adenovirus serotype 5 (Ad5) vector, or Ad28 adenovector. Exemplary viral vectors comprising wild type Atoh1 are described in Parker et al., Human Gene Therapy Methods 25(1): 1-13 (2014); Atkinson et al. PLoS ONE 9(7): e102077 (2014); Izumikawa et al. Nature Medicine, 11(3): 271-276 (2005); Schlecker et al. Gene Therapy, 2011, 18: 884-890, and in US20040237127 and US20140005257; the entire contents of 20040237127 and US20140005257 are specifically incorporated herein. See also Devarajan et al., J. Funct. Biomater. 2:249-270 (2011) for a review of gene delivery and stem cell based therapies for regenerating inner ear hair cells.
Yet another viral vector system useful for delivery of nucleic acids is the adeno-associated virus (AAV). Adeno-associated virus is a naturally occurring defective virus that requires another virus, such as an adenovirus or a herpes virus, as a helper virus for efficient replication and a productive life cycle. (For a review see Muzyczka et al., Curr. Topics in Micro. and Immunol. 158:97-129 (1992). It is also one of the few viruses that may integrate its DNA into non-dividing cells, and exhibits a high frequency of stable integration (see for example Flotte et al., Am. J. Respir. Cell. Mol. Biol. 7:349-356 (1992); Samulski et al., J. Virol. 63:3822-3828 (1989); and McLaughlin et al., J. Virol. 62:1963-1973 (1989). Vectors containing as little as 300 base pairs of AAV can be packaged and can integrate. Space for exogenous DNA is limited to about 4.5 kb. An AAV vector such as that described in Tratschin et al., Mol. Cell. Biol. 5:3251-3260 (1985) can be used to introduce DNA into cells. A variety of nucleic acids have been introduced into different cell types using AAV vectors (see for example Hermonat et al., Proc. Natl. Acad. Sci. USA 81:6466-6470 (1984); Tratschin et al., Mol. Cell. Biol. 4:2072-2081 (1985); Wondisford et al., Mol. Endocrinol. 2:32-39 (1988); Tratschin et al., J. Virol. 51:611-619 (1984); and Flotte et al., J. Biol. Chem. 268:3781-3790 (1993).
In addition to viral transfer methods, such as those illustrated above, non-viral methods can also be employed to cause expression of a nucleic acid compound described herein (e.g., a long-lived Atoh1 variant as described herein) in the tissue of a subject. Typically non-viral methods of gene transfer rely on the normal mechanisms used by mammalian cells for the uptake and intracellular transport of macromolecules. In some embodiments, non-viral gene delivery systems can rely on endocytic pathways for the uptake of the subject gene by the targeted cell. Exemplary gene delivery systems of this type include liposomal derived systems, poly-lysine conjugates, and artificial viral envelopes. Other embodiments include plasmid injection systems such as are described in Meuli et al., J. Invest. Dermatol. 116(1):131-135 (2001); Cohen et al., Gene Ther. 7(22):1896-905 (2000); or Tam et al., Gene Ther. 7(21):1867-74 (2000).
In some embodiments, a gene encoding a compound described herein, e.g., a long-lived Atoh1 variant as described herein, is entrapped in liposomes bearing positive charges on their surface (e.g., lipofectins), which can be tagged with antibodies against cell surface antigens of the target tissue (Mizuno et al., No Shinkei Geka 20:547-551 (1992); PCT publication WO91/06309; Japanese patent application 1047381; and European patent publication EP-A-43075).
In clinical settings, the gene delivery systems for the therapeutic gene can be introduced into a subject by any of a number of methods, each of which is familiar in the art. For instance, a pharmaceutical preparation of the gene delivery system can be introduced systemically, e.g., by intravenous injection, and specific transduction of the protein in the target cells will occur predominantly from specificity of transfection, provided by the gene delivery vehicle, cell-type or tissue-type expression due to the transcriptional regulatory sequences controlling expression of the receptor gene, or a combination thereof.
In some embodiments, initial delivery of the recombinant gene is more limited, with introduction into the subject being quite localized, i.e., into the inner ear or cochlea of the subject. For example, the gene delivery vehicle can be introduced by injection through the round window membrane, e.g., by intra-tympanic injection of a liquid or gel formulation or by direct delivery into the inner ear fluids, e.g., using a microfluidic device. Injection can be, for example, through the round window of the ear or through the cochlea capsule, into the liquid of the inner ear, or into the scala media. Alternatively, in some embodiments, the compound can be administered onto the round window membrane, which can be reached from the middle ear: the injection can be through the ear drum into the middle ear to allow passage of the formulation through the round window membrane. In another exemplary mode of administration, compositions can be administered in situ, via a catheter or pump, e.g., an infusion pump. A catheter or pump can, for example, direct a pharmaceutical composition into the cochlea luminae or the round window of the ear. Exemplary drug delivery apparatus and methods suitable for administering one or more compounds into an ear, e.g., a human ear, are described by McKenna et al., (U.S. Publication No. 2006/0030837) and Jacobsen et al., (U.S. Pat. No. 7,206,639). In some embodiments, a catheter or pump can be positioned, e.g., in the ear (e.g., the outer, middle, and/or inner ear) of a subject during a surgical procedure. In some embodiments, a catheter or pump can be positioned, e.g., in the ear (e.g., the outer, middle, and/or inner ear) of a subject without the need for a surgical procedure. In some embodiments, the compositions are delivered via a pump, e.g., a mini-osmotic pump, see, e.g., Takemura et al., Hear Res. 2004 October; 196(1-2):58-68, or a catheter, see, e.g., Charabi et al., Acta Otolaryngol Suppl. 2000; 543:108-10.
In some instances, compositions can be administered in combination with a mechanical device such as a cochlea implant or a hearing aid, which is worn in the outer ear. An exemplary cochlea implant that is suitable for use with the present invention is described by Edge et al., (U.S. Publication No. 2007/0093878).
In some instances, compositions can be administered according to any of the Food and Drug Administration approved methods, for example, as described in CDER Data Standards Manual, version number 004 (which is available at fda.give/cder/dsm/DRG/drg00301.htm).
The pharmaceutical preparation of the gene therapy construct can consist essentially of the gene delivery system in an acceptable diluent, or can comprise a slow release matrix in which the gene delivery vehicle is embedded. Alternatively, where the complete gene delivery system can be produced intact from recombinant cells, e.g., retroviral vectors, the pharmaceutical preparation can comprise one or more cells, which produce the gene delivery system.
Targeting Huwe1 Using Inhibitory Nucleic acids
As shown herein, reducing Huwe1 expression extends the half-life of Atoh1. Thus, the methods described herein can include reducing Huwe1 expression using inhibitory nucleic acids that target the Huwe1 gene or mRNA; the sequence of the human Huwe1 mRNA is in GenBank at Acc. No. NM_031407.6; the genomic sequence is at NP_113584.3. Inhibitory nucleic acids useful in the present methods and compositions include antisense oligonucleotides, ribozymes, external guide sequence (EGS) oligonucleotides, siRNA compounds, single- or double-stranded RNA interference (RNAi) compounds such as siRNA compounds, modified bases/locked nucleic acids (LNAs), antagomirs, peptide nucleic acids (PNAs), and other oligomeric compounds or oligonucleotide mimetics which hybridize to at least a portion of the target Huwe1 nucleic acid and modulate its function. In some embodiments, the inhibitory nucleic acids include antisense oligonucleotides, e.g., antisense RNA, antisense DNA, chimeric antisense oligonucleotides, or antisense oligonucleotides comprising modified linkages or nucleotide; interfering RNA (RNAi), e.g., small interfering RNA (siRNA), or a short hairpin RNA (shRNA); or combinations thereof. The inhibitory nucleic acids can be modified, e.g., to include a modified nucleotide (e.g., locked nucleic acid) or backbone (e.g., backbones that do not include a phosphorus atom therein), or can by mixmers or gapmers; see, e.g., WO2013/006619, which is incorporated herein by reference for its teachings related to modifications of oligonucleotides. siRNAs directed against Huwe1 are commercially available, e.g., from Origene and Santa Cruz Biotechnology, Inc.
Pharmaceutical FormulationsThe methods described herein include the manufacture and use of pharmaceutical compositions that include proteasome inhibitors, inhibitory nucleic acids targeting Huwe1, or long-lived Atoh1 proteins or nucleic acids as active ingredients. Also included are the pharmaceutical compositions themselves.
Pharmaceutical compositions typically include a pharmaceutically acceptable carrier. As used herein the language “pharmaceutically acceptable carrier” includes saline, solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration. Supplementary active compounds can also be incorporated into the compositions, e.g., dexamethasone; prednisone; gentamicin; brain-derived neurotrophic factor (BDNF); recombinant human insulin-like growth factor 1 (rhIGF-1), FGF, R-spondin. Alternatively or in addition, the one or more supplementary active compounds can include histone deacetylase (HDAC) inhibitors and/or DNMT inhibitors and/or Ezh2 Histone Methyl Transferase (HMT) inhibitors, e.g., as described in U.S. Provisional Patent Application No. 61/985,170, filed on Apr. 28, 2014, which is incorporated herein by reference in its entirety.
The present pharmaceutical compositions are formulated to be compatible with the intended route of administration.
In some embodiments, the compositions are delivered systemically, e.g., by parenteral, e.g., intravenous, intradermal, or subcutaneous administration.
In some embodiments, the compositions are administered by application to the round window membrane, e.g., application of a liquid or gel formulation to the round window membrane. Application to the round window membrane can be accomplished using methods known in the art, e.g., intra-tympanic injection of a liquid or gel formulation or by direct delivery into the inner ear fluids, e.g., using a microfluidic device.
In some embodiments, the compositions are delivered via a pump, e.g., a mini-osmotic pump, see, e.g., Takemura et al., Hear Res. 2004 October; 196(1-2):58-68, or a catheter, see, e.g., Charabi et al., Acta Otolaryngol Suppl. 2000; 543:108-10.
Methods of formulating suitable pharmaceutical compositions are known in the art, see, e.g., Remington: The Science and Practice of Pharmacy, 21st ed., 2005; and the books in the series Drugs and the Pharmaceutical Sciences: a Series of Textbooks and Monographs (Dekker, N.Y.). For example, solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide. The parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.
Pharmaceutical compositions suitable for injectable use can include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion. For intravenous administration, suitable carriers include physiological saline, bacteriostatic water, Cremophor EL™ (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS). In all cases, the composition must be sterile and should be fluid to the extent that easy syringability exists. It should be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyetheylene glycol, and the like), and suitable mixtures thereof. The proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars, polyalcohols such as mannitol, sorbitol, sodium chloride in the composition. Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent that delays absorption, for example, aluminum monostearate and gelatin.
Sterile injectable solutions can be prepared by incorporating the active compound in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle, which contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum drying and freeze-drying, which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
In some embodiments, the therapeutic compounds are prepared with carriers that will protect the therapeutic compounds against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems. Liposomal suspensions (including liposomes targeted to selected cells with monoclonal antibodies to cellular antigens) can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art, for example, as described in U.S. Pat. No. 4,522,811. Nanoparticles, e.g., poly lactic/glycolic acid (PLGA) nanoparticles (see Tamura et al., Laryngoscope. 2005 November; 115(11):2000-5; Ge et al., Otolaryngol Head Neck Surg. 2007 October; 137(4):619-23; Horie et al., Laryngoscope. 2010 February; 120(2):377-83; Sakamoto et al., Acta Otolaryngol Suppl. 2010 November (563):101-4) can also be used.
In some embodiments, the carrier comprises a polymer, e.g., a hydrogel, that increases retention of the compound on the round window and provides local and sustained release of the active ingredient. Such polymers and hydrogels are known in the art, see, e.g., Paulson et al., Laryngoscope. 2008 April; 118(4):706-11 (describing a chitosan-glycerophosphate (CGP)-hydrogel based drug delivery system); other carriers can include thermo-reversible triblock copolymer poloxamer 407 (see, e.g., Wang et al., Audiol Neurootol. 2009; 14(6):393-401. Epub 2009 Nov. 16, and Wang et al., Laryngoscope. 2011 February; 121(2):385-91); poloxamer-based hydrogels such as the one used in OTO-104 (see, e.g., GB2459910; Wang et al., Audiol Neurotol 2009; 14:393-401; and Piu et al., Otol Neurotol. 2011 January; 32(1):171-9); Pluronic F-127 (see, e.g., Escobar-Chavez et al., J Pharm Pharm Sci. 2006; 9(3):339-5); Pluronic F68, F88, or F108; polyoxyethylene-polyoxypropylene triblock copolymer (e.g., a polymer composed of polyoxypropylene and polyoxyethylene, of general formula E106 P70 E106; see GB2459910, US20110319377 and US20100273864); MPEG-PCL diblock copolymers (Hyun et al., Biomacromolecules. 2007 April; 8(4):1093-100. Epub 2007 Feb. 28); hyaluronic acid hydrogels (Borden et al., Audiol Neurootol. 2011; 16(1):1-11); gelfoam cubes (see, e.g., Havenith et al., Hearing Research, February 2011; 272(1-2):168-177); and gelatin hydrogels (see, e.g., Inaoka et al., Acta Otolaryngol. 2009 April; 129(4):453-7); other biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Tunable self-assembling hydrogels made from natural amino acids L and D can also be used, e.g., as described in Hauser et al e.g. Ac-LD6-COOH (L) e.g. Biotechnol Adv. 2012 May-June; 30(3):593-603. Such formulations can be prepared using standard techniques, or obtained commercially, e.g., from Alza Corporation and Nova Pharmaceuticals, Inc.
The pharmaceutical compositions can be included in a container, pack, or dispenser together with instructions for administration.
Dosage
An “effective amount” is an amount sufficient to effect beneficial or desired therapeutic effect. This amount can be the same or different from a prophylactically effective amount, which is an amount necessary to prevent onset of disease or disease symptoms. An effective amount can be administered in one or more administrations, applications or dosages. A therapeutically effective amount of a therapeutic compound (i.e., an effective dosage) depends on the therapeutic compounds selected. The compositions can be administered one from one or more times per day to one or more times per week; including once every other day. The skilled artisan will appreciate that certain factors may influence the dosage and timing required to effectively treat a subject, including but not limited to the severity of the disease or disorder, previous treatments, the general health and/or age of the subject, and other diseases present. Moreover, treatment of a subject with a therapeutically effective amount of the therapeutic compounds described herein can include a single treatment or a series of treatments. In some embodiments, e.g., in subjects exposed to prolonged or repeated exposures to noise, e.g., normal noises such as are associated with activities of daily life (such as lawnmowers, trucks, motorcycles, airplanes, music (e.g., from personal listening devices), sporting events, etc.), or loud noises, e.g., at concert venues, airports, and construction areas, that can cause inner ear damage and subsequent hearing loss; e.g., subjects who are subjected to high levels of environmental noise, e.g., in the home or workplace, can be treated with repeated, e.g., periodic, doses of the pharmaceutical compositions, e.g., to prevent (reduce the risk of) or delay progression or hearing loss.
Dosage, toxicity and therapeutic efficacy of the therapeutic compounds can be determined by standard pharmaceutical procedures, e.g., in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50/ED50. Compounds that exhibit high therapeutic indices are preferred. While compounds that exhibit toxic side effects may be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue in order to minimize potential damage to uninfected cells and, thereby, reduce side effects.
The data obtained from cell culture assays and animal studies can be used in formulating a range of dosage for use in humans. For example, samples of the perilymph or endolymph can be obtained to evaluate pharmacokinetics and approximate an effective dosage, e.g., in animal models, e.g., after administration to the round window. The dosage of such compounds lies preferably within a range of concentrations that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. For any compound used in the method of the invention, the therapeutically effective dose can be estimated from cell culture assays, and/or a dose may be formulated in animal models; alternatively, for those compounds that have been previously used in humans, clinically desirable concentrations can be used as a starting point. Such information can be used to more accurately determine useful doses in humans. An exemplary dose for gene therapy using an adenoviral vector is between about 1010 and 5×1010, delivered in a volume between 10-100 μl, preferably between 20 and 40 μl.
KitsThe compositions and/or cells disclosed herein can be provided in a kit. For example, kits can include one or more active compounds as described herein, such as in a composition that includes the compound(s), and optionally informational material. The informational material can be descriptive, instructional, marketing or other material that relates to the methods described herein and/or to the use of the agent for the methods described herein. For example, the informational material relates to the use of the compound to treat a subject who has, or who is at risk for developing, an auditory hair cell loss hearing. The kits can also include paraphernalia for administering one or more compounds to a cell (in culture or in vivo) and/or for administering to a patient, and any combination of the methods described herein.
In one embodiment, the informational material can include instructions for administering the pharmaceutical composition and/or cell(s) in a suitable manner to treat a human, e.g., in a suitable dose, dosage form, or mode of administration (e.g., a dose, dosage form, or mode of administration described herein). In another embodiment, the informational material can include instructions to administer the pharmaceutical composition to a suitable subject, e.g., a human, e.g., a human having, or at risk for developing, auditory hair cell loss.
The informational material of the kits is not limited in its form. In many cases, the informational material (e.g., instructions) is provided in printed matter, such as in a printed text, drawing, and/or photograph, such as a label or printed sheet. However, the informational material can also be provided in other formats, such as Braille, computer readable material, video recording, or audio recording. Of course, the informational material can also be provided in any combination of formats.
In addition to the compound(s), the composition of the kit can include other ingredients, such as a solvent or buffer, a stabilizer, a preservative, a fragrance or other cosmetic ingredient, and/or a second agent for treating a condition or disorder described herein. Alternatively, the other ingredients can be included in the kit, but in different compositions or containers than the compound. In such embodiments, the kit can include instructions for admixing the agent and the other ingredients, or for using one or more compounds together with the other ingredients.
The kit can include one or more containers for the pharmaceutical composition. In some embodiments, the kit contains separate containers, dividers or compartments for the composition and informational material. For example, the composition can be contained in a bottle (e.g., a dropper bottle, such as for administering drops into the ear), vial, or syringe, and the informational material can be contained in a plastic sleeve or packet. In other embodiments, the separate elements of the kit are contained within a single, undivided container. For example, the composition is contained in a bottle, vial or syringe that has attached thereto the informational material in the form of a label. In some embodiments, the kit includes a plurality (e.g., a pack) of individual containers, each containing one or more unit dosage forms (e.g., a dosage form described herein) of the pharmaceutical composition. For example, the kit can include a plurality of syringes, ampoules, foil packets, or blister packs, each containing a single unit dose of the pharmaceutical composition. The containers of the kits can be air tight and/or waterproof, and the containers can be labeled for a particular use. For example, a container can be labeled for use to treat a hearing disorder.
As noted above, the kits optionally include a device suitable for administration of the composition (e.g., a syringe, pipette, forceps, dropper (e.g., ear dropper), swab (e.g., a cotton swab or wooden swab), or any such delivery device).
ExamplesThe invention is further described in the following examples, which do not limit the scope of the invention described in the claims.
MethodsThe following materials and methods were used in the Examples below.
Cell Culture
HEK cells, FLAG-HA-Atoh1 293T cells and HeLa cells were grown in DMEM supplemented with 10% heat-inactivated fetal bovine serum, 2 mM Glutamax and penicillin (100 U/ml)/streptomycin (100 μg/ml) (all from Invitrogen). All cultures were maintained in a 5% CO2/20% humidified incubator (Forma Scientific).
Generation of Atoh1 Plasmids and Stably Expressing Cell Line
To generate FLAG-Atoh1 plasmids, a construct consisting of Atoh1 cDNA modified to include two consecutive FLAG-tag sequences (GATTACAAGGATGACGA) preceding the start codon, was subcloned into pcDNA3.1(+) (Parker et al., 2014).
Atoh1 mutants, including deletions (410-93 for deletion 1, Δ94-105 for deletion 2, Δ214-305 for deletion 3 and Δ306-347 deletion 4) and mutations at the C-terminus (serine 309, 325, 328, 331 or 334 to alanine) were generated using the QuickChange Site-directed Mutagenesis Kit (Stratagene). All mutants were sequenced in their entirety.
To generate FLAG-HA-Atoh1 plasmids, sequence-verified Atoh1 clones in pDONR223 were recombined into the Gateway destination vector pHAGE-N-Flag-HA (Invitrogen) using 2, recombinase (Sowa et al., 2009). To generate lentivirus for the 293T cell line stably expressing Atoh1, 1 μg of pHAGE-N-FLAG-HA-Atoh1 cDNA was co-transfected with 4 helper plasmids (2 μg of VSVG, 1 μg each of Tat1b, Mgpm2, and CMV-Rev) using Lipofectamine 2000 (Invitrogen) in 10 cm dishes of 293T cells. Virus particles were harvested 48 hours post-transfection and used to infect 293T cells. Puromycin (Sigma, 1 μg/ml) was used for the selection of infected cells (Sowa et al., 2009). See
Western Blotting
Proteins extracted with RIPA buffer from whole cells were separated on 4-12% NuPAGE Bis-Tris gels (Invitrogen) and electrotransferred to 0.2 μm nitrocellulose membranes (BioRad). The membranes were probed with mouse anti-FLAG (Sigma-Aldrich), mouse anti-HA (Sigma-Aldrich), mouse anti-ubiquitin (Santa Cruz), mouse anti-β-actin (Sigma-Aldrich), or mouse anti-HSC70 (1:10,000, Santa Cruz Biotechnology) antibodies, followed by HRP-conjugated, anti-rabbit or anti-mouse IgG, or anti-mouse light chain antibody (Jackson Immunoresearch Laboratories). The blots were processed with ECL or ECL-Plus Western Blot Substrates (Thermo). Band intensity was quantified by densitometry using Quantity One software (Bio-Rad). Each band was normalized to β-actin or HSC70 and expressed as a ratio to the control.
Cycloheximide Chase Assays for Stability
HEK cells were transfected with either FLAG-Atoh1 (wild-type), or indicated mutant FLAG-Atoh1 plasmids (1 mg/ml) using Lipofectamine 2000 (3 μl per 1 mg of cDNA, Invitrogen). Forty-eight hours after transfection, 100 mg/ml cycloheximide (Sigma) was added to block protein synthesis. Cells were harvested at 0, 30, 60, 120, and 240 minutes. Equal amounts of protein from each treatment were taken for Western blotting. Protein bands were quantified by densitometry. The half-lives of indicated proteins were calculated using GraphPad Prism 6 software and a one-phase exponential-decay model.
Co-Immunoprecipitation
To determine if the ubiquitin-proteasome pathway was involved in Atoh1 degradation, HEK cells were transfected with FLAG-Atoh1 (1 μg/ml) using Lipofectamine 2000 (Invitrogen) for 48 hours and either DMSO or MG132 (10 μM) for 6 hours. Transfected cells were lysed in Pierce IP Lysis Buffer (Thermo) containing 1× complete protease inhibitors and 1×PhosSTOP phosphatase inhibitors (Roche). Lysates were immunoprecipitated with Anti-FLAG M2 Affinity Gel (Sigma-Aldrich) and immunoblotted by the procedures mentioned above.
To determine K48 polyubiquitylation, HEK cells were co-transfected with FLAG-Atoh1 (1 μg/ml) and wild-type, K48 ubiquitin plasmids or empty vector (0.5 mg/ml, from Addgene) using Lipofectamine 2000 (Invitrogen). At 48 hours post-transfection, cells were lysed and immunoprecipitated with anti-FLAG M2 Affinity gel and immunoblotted.
Luciferase Assay
105 HEK cells were seeded into a 96-well plate 1 day before transfection. 50 ng of firefly report construct with an Atoh1 E-box associated motif (AtEAM), 5 ng of Renilla-luciferase construct, and 50 ng of wild-type or mutated Atoh1 plasmids were mixed 0.3 ul of Lipofectamine 2000 and incubated with the cells for 48 hours, until cells were lysed. Luciferase activity were measure by the Dual Luciferase Reporter Assay System (Promega) in a Victor3 plate reader (Perkin Elmer).
Protein Purification
HEK293T cells with stable expression of Atoh1 from 15-cm tissue culture dishes at approximately 80% confluence were lysed in a total volume of 4 ml of lysis buffer (50 mM Tris pH 7.8, 150 mM sodium chloride, 0.5% NP40 plus EDTA-free protease inhibitor cocktail (Roche) and incubated at 4° C. for 45 minutes. Lysates were centrifuged at 13,000 rpm for 10 minutes at 4° C. and filtered through 0.45 nm spin filters (Millipore) to remove cell debris. Sixty n1 of immobilized anti-HA resin (Sigma; 50% slurry) were used to immunoprecipitate the cleared lysates by gentle inversion overnight. Once the binding was complete, resin containing immuno-complex was washed with lysis buffer 4 times, followed by PBS 4 times. Atoh1 was eluted with HA peptide (250 μg/ml) in PBS for 30 minutes (3×50 μl) at room temperature. Ten percent of the eluate was electrophoresed on a NuPAGE Novex 4-12% Bis-Tris gel and silver stained to confirm immunoprecipitation of Atoh1 and the remaining eluate was subjected to trichloroacetic acid (TCA) precipitation for subsequent IP-MS/MS analysis.
In other experiments, specific bands stained for Commassie blue after elution were excised for peptide mass spectrometric sequencing at the core facility of Harvard Medical School.
Mass Spectrometry
For identification of Atoh1 interacting proteins, the TCA-precipitated protein pellet was re-suspended in 25 μg/μl of sequencing grade trypsin (25 μg/μl in 30 μl 100 mM ammonium bicarbonate pH 8.0 with 10% acetonitrile) and incubated at 37° C. for 4 hours. Digested samples were loaded onto stagetips and washed. Peptides were eluted with 50% formic acid/5% acetonitrile to neutralize the trypsin, followed by drying and re-suspension in 10 μl of 5% formic acid/5% acetonitrile. The resulting spectra were analyzed against a human database by SEQUEST, a tandem mass spectrometry data analysis program for peptide sequencing and protein identification (Eng et al. Journal of the American Society for Mass Spectrometry 5:976-989 (1994). The list of proteins was loaded into CompPASS for further processing and analysis (Sowa et al., 2009).
Co-Immunoprecipitation
FLAG-HA-Atoh1 293T were lysed with IP buffer and the lysates were immunoprecipitated with HA-resin (Sigma), IgG conjugated A/G agarose, or empty A/G agarose (Santa Cruz Biotechnology) and immunoblotted with antibodies against HA and Huwe1. For reciprocal immunoprecipitation, similar lysates were immunoprecipitated with A/G agarose conjugated with rabbit anti-Huwe1 antibody (Novus Biological) and immunoblotted with antibodies against HA or Huwe1.
To explore the role of Huwe1 on ubiquitylation of Atoh1, we generated Myc-Huwe1 with cysteine 4341 mutated to alanine (Myc-Huwe1-C4341) by recombining Huwe1 pENTR plasmids (Addgene) into pDEST-CMV-N-Myc using Gateway cloning. FLAG-HA-Atoh1 293T cells were transfected with wild-type Huwe1, Huwe1 shRNA (Sigma) or empty vector for 48 hours and treated with MG132 (10 μM) or vehicle for 6 hours. Cell lysates were immunoprecipitated with anti-FLAG-resin (Sigma) and immunoblotted with mouse anti-ubiquitin antibody (Santa Cruz Biotechnology) or reblotted with mouse anti-FLAG or rabbit anti-Huwe1 antibodies.
Wild-type or mutant Myc-Huwe1, wild-type or K48 HA-ubiquitin, and FLAG-Atoh1 plasmids were co-transfected into HeLa cells. After 48 hours, cell lysates were immunoprecipitated with anti-FLAG resin and immunoblotted with mouse anti-HA, mouse anti-FLAG and rabbit anti-Huwe1 antibodies. Input was blotted with mouse anti-Myc, mouse anti-FLAG, and mouse anti-β-actin antibodies as loading controls.
Neonatal Cochlear Explant Culture
Cochlear tissues were dissected from 1-day postnatal CD-1 mice (Charles River Laboratories). Spiral ganglion, Reissner's membrane, and the hook region of the organ of Corti were removed to obtain a flat cochlear surface preparation (Parker et al., 2010). Explants were plated onto 4-well plates (Greiner Bio-One) coated with Matrigel (BD Biosciences) diluted 1:10 in DMEM supplemented with 10% fetal bovine serum overnight.
Huwe1 Knockdown in the Organ of Corti
As described previously, postnatal day 1 mouse organs of Corti were cultured on Matrigel-coated coverslips overnight. The organs were incubated with Huwe1 or scrambled siRNA (IDT-DNA, 100 nM) for 72 hours.
Detection of Proliferation by Incorporation of 5-Ethynyl-2′-Deoxyuridine (EdU)
To evaluate cell proliferation, organs of Corti were incubated with 3 μM 5-ethynyl-2′-deoxyuridine (EdU) in combination with siRNA treatment and replenished after 36 hours. The tissue was fixed, blocked and permealized as described.
RNA Preparation for Quantitative RT-PCR
Total RNA was extracted with the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. 1 μg RNA was reverse transcribed to cDNA using the Improm-II Reverse Transcription System (Promega). The reverse transcription conditions were 25° C. for 10 min followed by 37° C. for 60 min; the reaction was terminated at 95° C. for 5 min. The cDNA products were mixed with LightCycler Taqman Master Mix (Roche) and Taqman primers (Invitrogen) in a 96-well plate according to the manufacturer's instructions. The qPCR was run in triplicate on an ABI 7700 Real-Time PCR machine (Applied Biosystems, Inc.) with the initial denaturation at 95° C. for 2 min, denaturation at 95° C. for 15 s, and annealing/extension at 60° C. for 1 min for 45 cycles. Huwe1 gene expression was calculated relative to 18S RNA, and the amount of cDNA applied was adjusted to bring the Ct value for 18S RNA to within one half-cycle.
Detection of Proliferation by Incorporation of EdU
To evaluate cell proliferation, organ of Corti tissue was incubated with EdU in combination with siRNA treatment and replenished after 36 hours. The tissue was fixed, blocked and permeabilized as described. 70 μl of Alexa-Flour 488-conjugated azide cocktail (Invitrogen) was added to each well and incubated in a light-proof chamber at room temperature for 30 minutes. Tissues were washed with PBS before adding secondary antibodies.
Imaging and Cell Counting
Organs of Corti were analyzed using a Leica TCS SP5 confocal microscope. Inner and outer hair cells and supporting cells (in the outer hair cell region) were counted in cochlear whole mounts. High-power fluorescent images of the organ of Corti were merged in Adobe Illustrator CS6; total length and cell counts were determined with ImageJ software (NIH). Organs of Corti were divided into four regions (apex, mid-apex, mid-base, and base) and hair cell and supporting cells counts were obtained per 100 μm. Each counted segment was 1200-1400 μm.
Mouse Genotyping
The Sox2-Cre-ER mouse was described previously (Arnold et al., Cell Stem Cell 9, 317-329 (2011); Bramhall et al., Stem Cell Reports 2, 311-322 (2014)). The Sox2-flox mice were obtained from the Jackson Laboratory. The Huwe1-flox mouse was also previously described (Hao et al., J Exp Med 209, 173-186 (2012)). The Sox2-Cre-ER mouse was genotyped with Cre primers: forward, 5′-TGG GCG GCA TGG TGC AAG TT-3′ and reverse, 5′-CGG TGC TAA CCA GCG TTT TC-3′). The Huwe1-flox mouse was genotyped with the following primers: forward, 5′ GTA TGG TCA TGA TTG AGT GCT TGG AAC T 3′ and reverse, 5′ TAT ACC TGA ACA CAT GGG CAT ATA CAT 3′. The Sox2-flox mice were genotyped by PCR according to Jackson Laboratory recommendations.
Cochlear Function Tests
Distortion product otoacoustic emissions (DPOAEs) and auditory brainstem responses (ABRs) were recorded as described previously52. The ABR stimuli were 5-ms tone pips with a 0.5 ms rise-fall time delivered at 30/s. Sound level was incremented in 5-dB steps, from 25 dB below threshold to 80 dB sound pressure level (SPL). DPOAEs were recorded for primary tones with a frequency ratio of 1.2 and with the level of the f2 primary 10 dB less than f1 level, incremented together in 5-dB steps. The 2f1-f2 DPOAE amplitude and surrounding noise floor were extracted. DPOAE threshold is defined as the f1 level required to produce a response amplitude of 0 dB SPL.
Statistical Analysis
The mean values and standard error of the mean were calculated and analyzed for significance by an unpaired two-tailed Student's t-test with indicated alpha (0.05, 0.01 or 0.001) with Prism 6 software.
Example 1: Atoh1 is a Short-Lived ProteinTo determine the half-life of Atoh1, we used cycloheximide to prevent new protein synthesis and followed the time course of disappearance of previously synthesized Atoh1 by Western blotting during a chase period. We transfected 293T cells with FLAG-HA-Atoh1 and treated with cycloheximide at 48 hours after transfection.
Pre-existing Atoh1 was completely degraded by 2 hours after inhibition of new protein synthesis. The half-life, as measured by densitometry in three experiments was 35.31 minutes (95% confidence interval: 24.11+/−65.97 minutes;
Since Atoh1 is a highly unstable protein with a turnover rate of less than 1 hour, we assessed the mechanism of degradation. When treated with MG132, a potent proteasome inhibitor, the level of Atoh1 was significantly increased (
We then assessed polyubiquitylation of Atoh1 in the presence of a proteasome inhibitor which would prevent degradation of the ubiquitinated protein. We prepared HEK cells stably transfected with FLAG-HA-Atoh1 and treated with MG132 to inhibit proteasomal degradation. The cell lysates were immunoprecipitated with anti-FLAG antibody, and the pattern of ubiquitylation was assessed with an anti-ubiquitin antibody. Western blotting of immunoprecipitated FLAG-Atoh1 revealed high molecular weight forms of Atoh1, indicating polyubiquitylation (
To determine if Atoh1 forms K48-linked polyubiquitin, the form of ubiquitin chain targeted for proteasomal degradation, we co-transfected HEK cells with FLAG-Atoh1 and ubiquitin plasmid with mutations in all lysines except K48, or without mutations. The formation of high molecular weight bands above the Atoh1 bands on immunoblots suggested that K48 ubiquitin chains were formed on Atoh1 in both cases (
We next generated a panel of two N-terminal (410-93 for deletion 1 and 494-105 for deletion 2) and two C-terminal (4214-305 for deletion 3 and 4306-347 deletion 4) deletions of Atoh1 plasmids (
Cross-species sequence comparison by MegaAlign (DNAstar, Madison, Wis.) indicated that serines 309, 325, 328, 331 and 334 were conserved across species (
To generate FLAG-Atoh1 plasmids, construct consisting of the Atoh1 sequence modified by cloning to include two consecutive FLAG-tag sequences (GATTACAAGGATGACGA) preceding the start codon, was subcloned into pcDNA3.1(+) (Parker et al., Hum Gene Ther Methods 25, 1-13 (2014)).
Atoh1 mutants including deletions (410-93 for deletion 1, 494-105 for deletion 2, Δ214-305 for deletion 3 and Δ306-347 deletion 4) and mutations at the C-terminus (serine 309, 325, 328, 331 or 334 to alanine) were generated using the QuickChange Site-directed Mutagenesis Kit (Stratagene). All mutants were sequenced in their entirety.
To generate FLAG-HA-Atoh1 plasmids, sequence-verified Atoh1 clones in pDONR223 were recombined into the Gateway destination vector pHAGE-N-Flag-HA using λ, recombinase (Sowa et al., Cell 138, 389-403 (2009)). To generate lentivirus for the 293T cell line stably expressing Atoh1, 1 ug of pHAGE-N-FLAG-HA-Atoh1 cDNA was co-transfected with 4 helper plasmids (2 ug of VSVG, 1 ug of Tat1b, Mgpm2, and CMV-Rev) using Lipofectamine 2000 transfection agent (Invitrogen) in 10 cm dishes of 293T cells. Virus particles were harvested 48 hours post-transfection and used to infect 293T cells. Puromycin (Sigma, 1 ug/ml) was used for selection of infected cells (Sowa et al., Cell 138, 389-403 (2009)).
Example 5. Stability Assays—Cycloheximide ChaseHEK cells were transfected with either FLAG-Atoh1 (wild type), or indicated mutant FLAG-Atoh1 plasmids (1 ug/ml) using Lipofectamine 2000 (3 ul per 1 ug of cDNA, Invitrogen). Forty eight hours after transfection, 100 ug/ml cycloheximide (C4859, Sigma) was added to block protein synthesis. Cells were harvested at 0, 30, 60, 120, and 240 minutes. Equal amounts of proteins from each treatment were taken for Western blotting. Protein bands were quantified by densitometry using Quantity One Software (Bio-Rad), with β-actin for normalization. The half-lives of indicated proteins were calculated using GraphPad Prism 6 software and a one-phase exponential-decay model.
Example 6. Identifying Atoh1-Interacting Proteins by Mass SpectrometryWe performed immuoprecipitation followed by mass spectrometry (IP/MS), to identify binding partners of Atoh1 and searched the partners for E3 ubiquitin ligases that could be involved in the ubiquitin-proteasomal degradation (Sowa et al., Cell 138, 389-403 (2009)). We used a stably expressing 293T cell line prepared by lentiviral infection of pHAGE-FLAG-HA-Atoh1. Lysates of FLAG-HA-Atoh1 293T cells immunoprecipitated with HA antibody were subjected to LC-MS/MS analysis to identify proteins associated with Atoh1. We used ComPASS, an unbiased comparative approach for identifying high-confidence candidate interacting proteins, to interrogate datasets for parallel mass spectral studies (Sowa et al., Cell 138, 389-403 (2009)). The scoring metrics, DN and Z, were used to assign scores to each protein. Proteins with a DN score greater one and a Z score great than 3.5 were considered high confidence interacting partners (Table I).
E-proteins, E12 and E47 (TCF3 products), which are known interacting partners of Atoh1, were obtained in the high confidence candidates and validated the IP/MS approach. Another E-protein, TCF12, which has not been reported to bind Atoh1, was also found as Atoh1 binding partner.
Two de-ubiquitinating enzymes, USP11 and USP47, were observed associated with Atoh1. These enzymes cleave the bond between ubiquitin and substrate protein. E3 ubiquitin ligase, Huwe1, was also observed in the high confidence proteins and was the only ligase that passed the criteria for DN and Z scores among the Atoh1 interactors.
We first asked whether Huwe1 formed a physical complex with Atoh1 in HEK cells through reciprocal co-immunoprecipitation analyses (
To determine whether Huwe1 can act as an E3 ubiquitin ligase for Atoh1, we performed an in vivo ubiquitylation assay. Increased ubiquitylation of Atoh1 was observed after transfecting Huwe1 plasmids into FLAG-HA-Atoh1 293T cells, after co-immunoprecipitation, indicating a role of Huwe1 as an E3 ubiquitin ligase (
We also tested whether the ability of Huwe1 to transfer ubiquitin to Atoh1 was affected when a mutant form of Huwe1 that had serine in the place of a critical cysteine in the HECT domain (Huwe1 C4341S) (ref) was used (
To determine whether Huwe1 affected the stability of Atoh1, FLAG-HA-Atoh1 293T cells were transfected with Huwe1 plasmids or Huwe1 shRNA for gain- or loss-of-function experiments respectively. Huwe1 overexpression reduced Atoh1, while Huwe1 knockdown stabilized Atoh1 (
The half-life of Atoh1 measured by a cycloheximide-chase assay also revealed that Huwe1 shRNA extended the half-life of Atoh1 in FLAG-HA-Atoh1 293T cells (
To test whether proteasomal activity regulated Atoh1 in the cochlea we treated P1 organ of Corti explants with proteasome inhibitor, MG132 (10 uM). Atoh1 was increased by the treatment indicating that it was stabilized by the treatment (
Treatment of organ of Corti explants from P1 mice with 100 nM Huwe1 siRNA for 72 hours suppressed Huwe1 gene expression by 59.5% as measured by real-time qRT-PCR (
Since Huwe1 knockdown stabilized Atoh1, we assessed its effect on hair cell generation in the cochlea. Treatment of organ of Corti explants with 100 nM Huwe1 siRNA significantly increased the number of myosin VIIa-positive cells in the outer hair cell region (
Supporting cells and hair cells were not labeled by 5-ethynyl-2′-deoxyuridine (EdU), a marker for cell division 72 hours after siRNA treatment of organ of Corti explants (
As described previously, postnatal day 1 mouse organs of Corti were cultured on Matrigel-coated coverslips overnight. Huwe1 or scrambled siRNA (from IDT-DNA, 100 nM) were incubated for 72 hours.
Example 15. Detection of Proliferation by Incorporation of 5-Ethynyl-2′-Deoxyuridine (EdU)To evaluate cell proliferation, organs of Corti were incubated with 3 uM 5-ethynyl-2′-deoxyuridine (EdU) in combination with siRNA treatment and replenished after 36 hours. The tissue was fixed, blocked and permealized as described.
Example 16. RNA Preparation for Quantitative RT-PCRTotal RNA was extracted with the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. 1 ug RNA was reverse transcribed to cDNA using improm-II Reverse Transcription System (Promega). The reverse transcription conditions were 25° C. for 10 min followed by 37° C. for 60 min; the reaction was terminated at 95° C. for 5 min. The cDNA products were mixed with LightCycler Taqman Master Mix (Roche, 04535286001) and Taqman primers (Invitrogen) in 96-well plate according to the manufacturer's instructions. The qPCR was run in triplicate on an ABI 7700 Real-Time PCR machine (Applied Biosystem, Inc.) with initial denaturation at 95° C. for 2 min, denaturation at 95° C. for 15 s, and annealing/extension at 60° C. for 1 min for 45 cycles. Huwe1 gene expression was calculated relative to 18S RNA, and the amount of cDNA applied was adjusted to bring the Ct value for 18S RNA to within one half-cycle.
Example 17. Huwe1 is Required for Cochlear FunctionTo assess the role of Huwe1 in cochlear development, we induced the conditional deletion of Huwe1 using a Cre driven by Sox2 expression, which is specific for the prosensory progenitors in the developing cochlea and is subsequently expressed in the developing spiral ganglion and cochlear supporting cells. Disruption of Huwe1 at E15.5 stimulated generation of a single extra row of inner hair cells at E18.5 (
Deletion of Sox2 at E12 in earlier studies resulted in the abolition of hair cells, consistent with a role for Sox2 in the expression of Atoh1( ) We reasoned that its deletion at a later time point would prevent the Huwe1 induction and degradation of Atoh1. The phenotype obtained when Sox2 was deleted at E15.5 was, indeed, similar to the deletion of Huwe1; an extra row of inner hair cells could be seen in the knockout mice. An identical phenotype was seen after deletion at E17.5.
Example 19. Post-Translational Dampening of bHLH Transcription Factors by Sox2 Extends to Neurod1 and Neurog1Since proneural bHLH transcription factors share homologies in sequence and regulation (see, e.g., Akagi et al., J Biol Chem 279, 28492-28498 (2004); Lo et al., Development 129, 1553-1567 (2002); Ross et al., Neuron 39, 13-25 (2003)), we asked whether other bHLH proneural transcription factors were regulated by Sox2 destabilization after initial upregulation, as we had observed for Atoh1. qPCR analysis showed that overexpression of Sox2 led to significant upregulation of all three tested bHLH transcription factors, Atoh1, Neurog1 and Neurod1, in HEK cells. Like Atoh1, Sox2 also downregulated Neurog1 and Neurod1 proteins post-translationally, and, again, proteasome inhibition rescued the level of each transcription factor after Sox2 overexpression.
REFERENCES
- Abbott D W, Yang Y, Hutti J E, Madhavarapu S, Kelliher M A, Cantley L C (2007) Coordinated regulation of Toll-like receptor and NOD2 signaling by K63-linked polyubiquitin chains. Molecular and Cellular Biology 27:6012-6025.
- Adhikary S, Marinoni F, Hock A, Hulleman E, Popov N, Beier R, Bernard S, Quarto M, Capra M, Goettig S, Kogel U, Scheffner M, Helin K, Eilers M (2005) The ubiquitin ligase HectH9 regulates transcriptional activation by Myc and is essential for tumor cell proliferation. Cell 123:409-421.
- Adler H J, Raphael Y (1996) New hair cells arise from supporting cell conversion in the acoustically damaged chick inner ear. Neuroscience letters 205:17-20.
- Barker N, van Es J, Kuipers J, Kujala P, van den Born M, Cozijnsen M, Haegebarth A, Korving J, Begthel H, Peters P (2007) Identification of stem cells in small intestine and colon by marker gene Lgr5. Nature 449:1003-1007.
- Ben-Arie N, Bellen H J, Armstrong D L, McCall A E, Gordadze P R, Guo Q, Matzuk M M, Zoghbi HY (1997) Math1 is essential for genesis of cerebellar granule neurons. Nature 390:169-172.
- Ben-Arie N, Hassan B A, Bermingham N A, Malicki D M, Armstrong D, Matzuk M, Bellen H J, Zoghbi H Y (2000) Functional conservation of atonal and Math1 in the CNS and PNS. Development (Cambridge, England) 127:1039-1048.
- Bermingham N A, Hassan B A, Price S D, Vollrath M A, Ben-Arie N, Eatock R A, Bellen H J, Lysakowski A, Zoghbi H Y (1999) Math1: an essential gene for the generation of inner ear hair cells. Science (New York, N.Y.) 284:1837-1841.
- Bertrand N, Castro D, Guillemot F (2002) Proneural genes and the specification of neural cell types. Nature Reviews Neuroscience 3:517-530.
- Bossuyt W, Kazanjian A, De Geest N, Van Kelst S, De Hertogh G, Geboes K, Boivin G P, Luciani J, Fuks F, Chuah M, VandenDriessche T, Marynen P, Cools J, Shroyer N F, Hassan B A (2009) Atonal homolog 1 is a tumor suppressor gene. PLoS biology 7:e39.
- Bramhall N F, Shi F, Arnold K, Hochedlinger K, Edge A S B (2014) Lgr5-positive supporting cells generate new hair cells in the postnatal cochlea. Stem cell reports 2:311-322.
- Brooker R, Hozumi K, Lewis J (2006) Notch ligands with contrasting functions: Jagged1 and Delta1 in the mouse inner ear. Development (Cambridge, England) 133:1277-1286.
- Cafaro J, Lee G S, Stone J S (2007) Atoh1 expression defines activated progenitors and differentiating hair cells during avian hair cell regeneration. Developmental dynamics: an official publication of the American Association of Anatomists 236:156-170.
- Cai T, Seymour M L, Zhang H, Pereira FA, Groves A K (2013) Conditional deletion of Atoh1 reveals distinct critical periods for survival and function of hair cells in the organ of Corti. The Journal of neuroscience: the official journal of the Society for Neuroscience 33:10110-10122.
- Chen D, Kon N, Li M, Zhang W, Qin J, Gu W (2005) ARF-BP1/Mule is a critical mediator of the ARF tumor suppressor. Cell 121:1071-1083.
- Chen P, Johnson J E, Zoghbi H Y, Segil N (2002) The role of Math1 in inner ear development: Uncoupling the establishment of the sensory primordium from hair cell fate determination. Development (Cambridge, England) 129:2495-2505
- Clevers H (2006) Wnt/beta-catenin signaling in development and disease. Cell 127:469-480.
- Corwin J T, Cotanche D A (1988) Regeneration of sensory hair cells after acoustic trauma. Science (New York, N.Y.) 240:1772-1774.
- D'Arca D, Zhao X, Xu W, Ramirez-Martinez N C, Iavarone A, Lasorella A (2010) Huwe1 ubiquitin ligase is essential to synchronize neuronal and glial differentiation in the developing cerebellum. Proceedings of the National Academy of Sciences of the United States of America 107:5875-5880.
- Davis A C (1983) Hearing disorders in the population: first phase findings of the MRC National Study of Hearing. Hearing science and hearing disorders 35.
- de Groot R E A, Ganji R S, Bernatik O, Lloyd-Lewis B, Seipel K, {hacek over (S)}edová K, Zdráhal Z, Dhople V M, Dale T C, Korswagen H C, Bryja V (2014) Huwe1-mediated ubiquitylation of dishevelled defines a negative feedback loop in the Wnt signaling pathway. Science signaling 7:ra26.
- Deshaies R J, Joazeiro C A P (2009) RING domain E3 ubiquitin ligases. Annual review of biochemistry 78:399-434.
- Eng J K, McCormack A L, Yates J R (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. Journal of the American Society for Mass Spectrometry 5:976-989.
- Flora A, Garcia J, Thaller C, Zoghbi H (2007) The E-protein Tcf4 interacts with Math1 to regulate differentiation of a specific subset of neuronal progenitors. Proceedings of the National Academy of Sciences 104:15382.
- Flora A, Klisch T J, Schuster G, Zoghbi H Y (2009) Deletion of Atoh1 disrupts Sonic Hedgehog signaling in the developing cerebellum and prevents medulloblastoma. Science (New York, N.Y.) 326:1424-1427.
- Forge A, Li L, Corwin J T, Nevill G (1993) Ultrastructural evidence for hair cell regeneration in the mammalian inner ear. Science (New York, N.Y.) 259:1616-1619.
- Fritzsch B (2003) Development of inner ear afferent connections: forming primary neurons and connecting them to the developing sensory epithelia. Brain research bulletin 60:423-433.
- Gao D, Inuzuka H, Tan M-K M, Fukushima H, Locasale J W, Liu P, Wan L, Zhai B, Chin Y R, Shaik S, Lyssiotis C A, Gygi S P, Toker A, Cantley L C, Asara J M, Harper J W, Wei W (2011a) mTOR drives its own activation via SCF(βTrCP)-dependent degradation of the mTOR inhibitor DEPTOR. Molecular cell 44:290-303.
- Gao S S, Xia A, Yuan T, Raphael P D, Shelton R L, Applegate B E, Oghalai J S (2011b) Quantitative imaging of cochlear soft tissues in wild-type and hearing-impaired transgenic mice by spectral domain optical coherence tomography. Optics express 19:15415-15428.
- Gregorieff A, Clevers H (2005) Wnt signaling in the intestinal epithelium: from endoderm to cancer. Genes & development 19:877-890.
- Gubbels S P, Woessner D W, Mitchell J C, Ricci A J, Brigande J V (2008) Functional auditory hair cells produced in the mammalian cochlea by in utero gene transfer. Nature 455:537-541.
- Herold S, Hock A, Herkert B, Berns K, Mullenders J, Beijersbergen R, Bernards R, Eilers M (2008) Miz1 and HectH9 regulate the stability of the checkpoint protein, TopBP1. The EMBO Journal 27:2851-2861.
- Hirabayashi Y, Itoh Y, Tabata H, Nakajima K, Akiyama T, Masuyama N, Gotoh Y (2004) The Wnt/beta-catenin pathway directs neuronal differentiation of cortical neural precursor cells. Development (Cambridge, England) 131:2791-2801
- Hu Z, Ulfendahl M (2006) Cell replacement therapy in the inner ear. Stem cells and development 15:449-459.
- Hu Z, Andang M, Ni D, Ulfendahl M (2005) Neural cograft stimulates the survival and differentiation of embryonic stem cells in the adult mammalian auditory system. Brain Research 1051:137-144.
- Huang F, Zeng X, Kim W, Balasubramani M, Fortian A, Gygi S P, Yates N A, Sorkin A (2013) Lysine 63-linked polyubiquitination is required for EGF receptor degradation. Proceedings of the National Academy of Sciences of the United States of America 110:15722-15727.
- Huibregtse J M, Scheffner M, Beaudenon S, Howley P M (1995) A family of proteins structurally and functionally related to the E6-AP ubiquitin-protein ligase. Proceedings of the National Academy of Sciences of the United States of America 92:5249.
- Husseman J, Raphael Y (2009) Gene therapy in the inner ear using adenovirus vectors. Advances in oto-rhino-laryngology 66:37-51.
- Ikeda F, Dikic I (2008) Atypical ubiquitin chains: new molecular signals. “Protein Modifications: Beyond the Usual Suspects” review series. EMBO Reports 9:536-542.
- Incesulu A, Nadol JB (1998) Correlation of acoustic threshold measures and spiral ganglion cell survival in severe to profound sensorineural hearing loss: implications for cochlear implantation. The Annals of otology, rhinology, and laryngology 107:906-911.
- Inoue S et al. (2013) Mule/Huwe1/Arf-BP1 suppresses Ras-driven tumorigenesis by preventing c-Myc/Miz1-mediated down-regulation of p21 and p15. Genes & development 27:1101-1114.
- Inuzuka H, Shaik S, Onoyama I, Gao D, Tseng A, Maser RS, Zhai B, Wan L, Gutierrez A, Lau A W, Xiao Y, Christie A L, Aster J, Settleman J, Gygi S P, Kung A L, Look T, Nakayama K I, Depinho R A, Wei W (2012) SCFFBW7 regulates cellular apoptosis by targeting MCL1 for ubiquitylation and destruction. Nature 470:104-109.
- Ivan M, Kondo K, Yang H, Kim W, Valiando J, Ohh M, Salic A, Asara J M, Lane W S, Kaelin W G (2001) HlFalpha targeted for VHL-mediated destruction by proline hydroxylation: implications for 02 sensing. Science (New York, N.Y.) 292:464-468.
- Izumikawa M, Minoda R, Kawamoto K, Abrashkin K A, Swiderski D L, Dolan D F, Brough D E, Raphael Y (2005) Auditory hair cell replacement and hearing improvement by Atoh1 gene therapy in deaf mammals. Nature Medicine 11:271-276.
- Jaakkola P, Mole D R, Tian Y M, Wilson M I, Gielbert J, Gaskell S J, von Kriegsheim A, Hebestreit H F, Mukherji M, Schofield C J, Maxwell P H, Pugh C W, Ratcliffe P J (2001) Targeting of HIF-alpha to the von Hippel-Lindau ubiquitylation complex by 02-regulated prolyl hydroxylation. Science (New York, N.Y.) 292:468-472.
- Jarriault S, Brou C, Logeat F, Schroeter E H, Kopan R, Israel A (1995) Signalling downstream of activated mammalian Notch. Nature 377:355-358.
- Jeon S-J, Oshima K, Heller S, Edge A S B (2007) Bone marrow mesenchymal stem cells are progenitors in vitro for inner ear hair cells. Molecular and cellular neurosciences 34:59-68.
- Jeon S-J, Fujioka M, Kim S-C, Edge A S B (2011) Notch signaling alters sensory or neuronal cell fate specification of inner ear stem cells. The Journal of neuroscience: the official journal of the Society for Neuroscience 31:8351-8358.
- Kawamoto K, Izumikawa M, Beyer L A, Atkin G M, Raphael Y (2009) Spontaneous hair cell regeneration in the mouse utricle following gentamicin ototoxicity. Hearing research 247:17-26.
- Kelley M W (2006) Regulation of cell fate in the sensory epithelia of the inner ear. Nature Reviews Neuroscience 7:837-849.
- Klisch T J, Xi Y, Flora A, Wang L, Li W, Zoghbi H Y (2011) In vivo Atoh1 targetome reveals how a proneural transcription factor regulates cerebellar development. Proceedings of the National Academy of Sciences of the United States of America.
- Knippschild U, Kruger M, Richter J, Xu P, Garcia-Reyes B, Peifer C, Halekotte J, Bakulev V, Bischof J (2014) The CK1 Family: Contribution to Cellular Stress Response and Its Role in Carcinogenesis. Frontiers in oncology 4:96.
- Kondo T, Matsuoka A J, Shimomura A, Koehler K R, Chan R J, Miller J M, Srour E F, Hashino E (2011) Wnt Signaling Promotes Neuronal Differentiation From Mesenchymal Stem Cells Through Activation of Tlx3. Stem cells (Dayton, Ohio).
- Kurokawa M, Kim J, Geradts J, Matsuura K, Liu L, Ran X, Xia W, Ribar T J, Henao R, Dewhirst M W, Kim W-J, Lucas J E, Wang S, Spector N L, Kornbluth S (2013) A network of substrates of the E3 ubiquitin ligases MDM2 and HUWE1 control apoptosis independently of p53. Science signaling 6:ra32.
- Lanford P J, Lan Y, Jiang R, Lindsell C, Weinmaster G, Gridley T, Kelley MW (1999) Notch signalling pathway mediates hair cell development in mammalian cochlea. Nature Genetics 21:289-292.
- Latres E, Chiaur D S, Pagano M (1999) The human F box protein beta-Trcp associates with the Cul1/Skp1 complex and regulates the stability of beta-catenin. Oncogene 18:849-854.
- Ledent V, Paquet O, Vervoort M (2002) Phylogenetic analysis of the human basic helix-loop-helix proteins. Genome biology 3:RESEARCH0030.
- Lee J M, Lee J S, Kim H, Kim K, Park H, Kim J-Y, Lee S H, Kim I S, Kim J, Lee M, Chung C H, Seo S-B, Yoon J-B, Ko E, Noh D-Y, Kim K I, Kim K K, Baek S H (2012) EZH2 generates a methyl degron that is recognized by the DCAF1/DDB1/CUL4 E3 ubiquitin ligase complex. Molecular cell 48:572-586.
- Lin V, Golub J S, Nguyen T B, Hume C R, Oesterle E C, Stone J S (2011) Inhibition of notch activity promotes nonmitotic regeneration of hair cells in the adult mouse utricles. The Journal of neuroscience: the official journal of the Society for Neuroscience 31:15329-15339.
- Lo L C, Johnson J E, Wuenschell C W, Saito T, Anderson D J (1991) Mammalian achaete-scute homolog 1 is transiently expressed by spatially restricted subsets of early neuroepithelial and neural crest cells. Genes & development 5:1524-1537.
- Ma E Y, Raible D W (2009) Signaling pathways regulating zebrafish lateral line development. Current biology: CB 19:R381-386.
- Maksimovic S, Nakatani M, Baba Y, Nelson A M, Marshall K L, Wellnitz S A, Firozi P, Woo S-H, Ranade S, Patapoutian A, Lumpkin E A (2014) Epidermal Merkel cells are mechanosensory cells that tune mammalian touch receptors. Nature 509:617-621.
- Markkanen E, van Loon B, Ferrari E, Parsons J L, Dianov G L, Hiibscher U (2012) Regulation of oxidative DNA damage repair by DNA polymerase and MutYH by cross-talk of phosphorylation and ubiquitination. Proceedings of the National Academy of Sciences of the United States of America 109:437-442.
- Meierhofer D, Wang X, Huang L, Kaiser P (2008) Quantitative analysis of global ubiquitination in HeLa cells by mass spectrometry. Journal of proteome research 7:4566-4576.
- Miesegaes G R, Klisch T J, Thaller C, Ahmad K A, Atkinson R C, Zoghbi H Y (2009) Identification and subclassification of new Atoh1 derived cell populations during mouse spinal cord development. Developmental Biology 327:339-351.
- Mizutari K, Fujioka M, Hosoya M, Bramhall N, Okano H J, Okano H, Edge A S B (2013) Notch inhibition induces cochlear hair cell regeneration and recovery of hearing after acoustic trauma. Neuron 77:58-69.
- Morrison K M, Miesegaes G R, Lumpkin E A, Maricich S M (2009) Mammalian Merkel cells are descended from the epidermal lineage. Developmental Biology 336:76-83.
- Murre C, McCaw P S, Vaessin H, Caudy M, Jan L Y, Jan Y N, Cabrera C V, Buskin J N, Hauschka S D, Lassar A B (1989) Interactions between heterologous helix-loop-helix proteins generate complexes that bind specifically to a common DNA sequence. Cell 58:537-544.
- Naujokat C, {hacek over (S)}arić T (2007) Concise review: role and function of the ubiquitin-proteasome system in mammalian stem and progenitor cells. Stem cells (Dayton, Ohio) 25:2408-2418.
- Noy T, Suad O, Taglicht D, Ciechanover A (2012) HUWE1 ubiquitinates MyoD and targets it for proteasomal degradation. Biochemical and Biophysical Research Communications 418:408-413.
- Ohyama T, Mohamed O A, Taketo M M, Dufort D, Groves A K (2006) Wnt signals mediate a fate decision between otic placode and epidermis. Development (Cambridge, England) 133:865-875.
- Pan N, Jahan I, Kersigo J, Duncan JS, Kopecky B, Fritzsch B (2012) A novel Atoh1 “self-terminating” mouse model reveals the necessity of proper Atoh1 level and duration for hair cell differentiation and viability. PloS one 7:e30358.
- Pandya R K, Partridge J R, Love K R, Schwartz T U, Ploegh H L (2010) A structural element within the HUWE1 HECT domain modulates self-ubiquitination and substrate ubiquitination activities. The Journal of biological chemistry 285:5664-5673.
- Parker M, Brugeaud A, Edge A S B (2010) Primary culture and plasmid electroporation of the murine organ of Corti. Journal of Visualized Experiments.
- Parker M A (2011) Biotechnology in the treatment of sensorineural hearing loss: foundations and future of hair cell regeneration. Journal of speech, language, and hearing research: JSLHR 54:1709-1731.
- Parker M A, Cheng Y-f, Kinouchi H, Bieber R, Edge A S B (2014) An independent construct for conditional expression of atonal homolog-1. Human gene therapy methods 25:1-13.
- Peng J, Schwartz D, Elias J E, Thoreen C C, Cheng D, Marsischky G, Roelofs J, Finley D, Gygi S P (2003) A proteomics approach to understanding protein ubiquitination. Nature Biotechnology 21:921-926.
- Qyang Y, Martin-Puig S, Chiravuri M, Chen S, Xu H, Bu L, Jiang X, Lin L, Granger A, Moretti A, Caron L, Wu X, Clarke J, Taketo M M, Laugwitz K-L, Moon R T, Gruber P, Evans S M, Ding S, Chien K R (2007) The renewal and differentiation of Isl1+ cardiovascular progenitors are controlled by a Wnt/beta-catenin pathway. Cell stem cell 1:165-179.
- Riccomagno M, Takada S, Epstein D (2005) Wnt-dependent regulation of inner ear morphogenesis is balanced by the opposing and supporting roles of Shh. Genes & development 19:1612-1623.
- Roberson D W, Alosi J A, Cotanche D A (2004) Direct transdifferentiation gives rise to the earliest new hair cells in regenerating avian auditory epithelium. Journal of neuroscience research 78:461-471.
- Ross S E, Greenberg M E, Stiles C D (2003) Basic helix-loop-helix factors in cortical development. Neuron 39:13-25.
- Rotin D, Kumar S (2009) Physiological functions of the HECT family of ubiquitin ligases. Nature Reviews Molecular Cell Biology 10:398-409.
- Scheffner M, Staub O (2007) HECT E3s and human disease. BMC biochemistry 8 Suppl 1:S6.
Schwarz S E, Rosa J L, Scheffner M (1998) Characterization of human hect domain family members and their interaction with UbcH5 and UbcH7. The Journal of biological chemistry 273:12148-12154.
- Shi F, Kempfle J S, Edge A S B (2012) Wnt-responsive Lgr5-expressing stem cells are hair cell progenitors in the cochlea. The Journal of neuroscience: the official journal of the Society for Neuroscience 32:9639-9648.
- Shi F, Cheng Y-f, Wang X L, Edge A S B (2010) Beta-catenin up-regulates Atoh1 expression in neural progenitor cells by interaction with an Atoh1 3′ enhancer. The Journal of biological chemistry 285:392-400.
- Shi F, Hu L, Jacques B E, Mulvaney J F, Dabdoub A, Edge A S B (2014) β-Catenin is required for hair-cell differentiation in the cochlea. The Journal of neuroscience: the official journal of the Society for Neuroscience 34:6470-6479.
- Skowyra D, Craig K L, Tyers M, Elledge S J, Harper J W (1997) F-box proteins are receptors that recruit phosphorylated substrates to the SCF ubiquitin-ligase complex. Cell 91:209-219.
- Sowa M E, Bennett E J, Gygi S P, Harper J W (2009) Defining the human deubiquitinating enzyme interaction landscape. Cell 138:389-403.
- Spence J, Sadis S, Haas A L, Finley D (1995) A ubiquitin mutant with specific defects in DNA repair and multiubiquitination. Molecular and Cellular Biology 15:1265-1273.
- Staecker H, Praetorius M, Baker K, Brough D E (2007) Vestibular hair cell regeneration and restoration of balance function induced by mathl gene transfer. Otology & neurotology 28:223-231.
- Stevens C B, Davies A L, Battista S, Lewis J H, Fekete D M (2003) Forced activation of Wnt signaling alters morphogenesis and sensory organ identity in the chicken inner ear. Developmental Biology 261:149-164.
- Stone J S, Cotanche D A (1994) Identification of the timing of S phase and the patterns of cell proliferation during hair cell regeneration in the chick cochlea. The Journal of Comparative Neurology 341:50-67.
- Tai H-C, Schuman E M (2008) Ubiquitin, the proteasome and protein degradation in neuronal function and dysfunction. Nature Reviews Neuroscience 9:826-838.
- Takebayashi S, Yamamoto N, Yabe D, Fukuda H, Kojima K, Ito J, Honjo T (2007) Multiple roles of Notch signaling in cochlear development. Developmental Biology 307:165-178.
- Tan M-KM, Lim H-J, Bennett E J, Shi Y, Harper J W (2013) Parallel SCF adaptor capture proteomics reveals a role for SCFFBXL17 in NRF2 activation via BACH1 repressor turnover. Molecular cell 52:9-24.
- Tiveron M C, Pattyn A, Hirsch M R, Brunet J F (2003) Role of Phox2b and Mash1 in the generation of the vestibular efferent nucleus. Developmental Biology 260:46-57.
- Tsuchiya K, Nakamura T, Okamoto R, Kanai T, Watanabe M (2007) Reciprocal targeting of Hathl and beta-catenin by Wnt glycogen synthase kinase 3beta in human colon cancer. Gastroenterology 132:208-220.
- Varshaysky A (1991) Naming a targeting signal. Cell 64:13-15. Wang X, Lu G, Li L, Yi J, Yan K, Wang Y, Zhu B, Kuang J, Lin M, Zhang S, Shao G (2013) HUWE1 interacts with BRCA1 and promotes its degradation in the ubiquitin-proteasome pathway. Biochemical and Biophysical Research Communications.
- Warchol M E, Lambert P R, Goldstein B J, Forge A, Corwin J T (1993) Regenerative proliferation in inner ear sensory epithelia from adult guinea pigs and humans. Science (New York, N.Y.) 259:1619-1622.
- WHO In.
- Woods C, Montcouquiol M, Kelley MW (2004) Math1 regulates development of the sensory epithelium in the mammalian cochlea. Nature Neuroscience 7:1310.
- Wu G, Xu G, Schulman B A, Jeffrey P D, Harper J W, Pavletich N P (2003) Structure of a beta-TrCP1-Skp1-beta-catenin complex: destruction motif binding and lysine specificity of the SCF(beta-TrCP1) ubiquitin ligase. Molecular cell 11:1445-1456.
- Yamamoto N, Tanigaki K, Tsuji M, Yabe D, Ito J, Honjo T (2006) Inhibition of Notch/RBP-J signaling induces hair cell formation in neonate mouse cochleas. Journal of Molecular Medicine 84:37-45.
- Yang H, Xie X, Deng M, Chen X, Gan L (2010a) Generation and characterization of Atoh1-Cre knock-in mouse line. Genesis (New York, N.Y.: 2000) 48:407-413.
- Yang Q, Bermingham N, Finegold M, Zoghbi H (2001) Requirement of Math1 for Secretory Cell Lineage Commitment in the Mouse Intestine. Science (New York, N.Y.) 294:2155.
- Yang Y, Do H, Tian X, Zhang C, Liu X, Dada L A, Sznajder J I, Liu J (2010b) E3 ubiquitin ligase Mule ubiquitinates Miz1 and is required for TNFalpha-induced JNK activation. Proceedings of the National Academy of Sciences of the United States of America 107:13444-13449.
- Ye X, Nalepa G, Welcker M, Kessler B M, Spooner E, Qin J, Elledge S J, Clurman B E, Harper J W (2004) Recognition of phosphodegron motifs in human cyclin E by the SCF(Fbw7) ubiquitin ligase. The Journal of biological chemistry 279:50110-50119.
- Zhang J, Kan S, Huang B, Hao Z, Mak T W, Zhong Q (2011) Mule determines the apoptotic response to HDAC inhibitors by targeted ubiquitination and destruction of HDAC2. Genes & development 25:2610-2618.
- Zhao X, Heng J I-T, Guardavaccaro D, Jiang R, Pagano M, Guillemot F, Iavarone A, Lasorella A (2008) The HECT-domain ubiquitin ligase Huwe1 controls neural differentiation and proliferation by destabilizing the N-Myc oncoprotein. Nature Cell Biology 10:643-653.
- Zhao X, D'Arca D, Lim W K, Brahmachary M, Carro M S, Ludwig T, Cardo C C, Guillemot F, Aldape K, Califano A, Iavarone A, Lasorella A (2009) The N-Myc-DLL3 cascade is suppressed by the ubiquitin ligase Huwe1 to inhibit proliferation and promote neurogenesis in the developing brain. Developmental cell 17:210-221.
- Zheng J L, Gao W-Q (2000) Overexpression of Math1 induces robust production of extra hair cells in postnatal rat inner ears. Nature Neuroscience 3:580.
- Zhong Q, Gao W, Du F, Wang X (2005) Mule/ARF-BP1, a BH3-only E3 ubiquitin ligase, catalyzes the polyubiquitination of Mcl-1 and regulates apoptosis. Cell 21:1085-1095.
It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.
Claims
1. A method for treating sensorineural hearing loss or vestibular dysfunction associated with loss of auditory hair cells in a subject, the method comprising administering a therapeutically effective amount of proteasome inhibitor to the subject, optionally to the inner ear of the subject.
2. (canceled)
3. The method of claim 1, wherein the proteasome inhibitor is selected from the group consisting of Bortezomib, Carfilzomib, NPI-0052, MLN9708, CEP-18770, and ONX0912.
4. The method of claim 1, further comprising administering to the subject an HDAC inhibitor, an EZH2/HMT inhibitor, or a DNMT inhibitor, in combination with a proteasome inhibitor, optionally to the inner ear of the subject.
5. (canceled)
6. The method of claim 4, wherein: the HDAC inhibitor is selected from the group consisting of: Sodium Butyrate, Trichostatin A, hydroxamic acids, cyclic tetrapeptides, trapoxin B, depsipeptides, benzamides, electrophilic ketones, ROMIDEPSIN, aliphatic acid compounds, phenylbutyrate, valproic acid, hydroxamic acids, vorinostat (SAHA), belinostat (PXD101), LAQ824, panobinostat (LBH589), entinostat (MS275), C1994, and mocetinostat (MGCD0103); the EZH2/HMT inhibitor is selected from the group consisting of Deazaneplanocin A; GSK J1; GSK126; EPZ005687; E7438; EI1; EPZ-6438; GSK343; BIX-01294, UNC0638, BRD4770, EPZ004777, AZ505 and PDB 4e47; the DNMT inhibitor is selected from the group consisting of azacytidine, decitabine, Zebularine (1-(β-D-ribofuranosyl)-1,2-dihydropyrimidin-2-one), procainamide, procaine, (−)-epigallocatechin-3-gallate, MG98, hydralazine, RG108, and Chlorogenic acid; and the proteasome inhibitor is selected from the group consisting of Bortezomib, Carfilzomib, NPI-0052, MLN9708, CEP-18770, and ONX0912.
7. The method of claim 1, comprising application of the proteasome inhibitor to the round window membrane or direct delivery into the inner ear fluids.
8. A long-lived human Atoh1 variant polypeptide comprising mutations at amino acids 328, 331, and/or 334.
9. The long-lived human Atoh1 variant polypeptide of claim 8 which is at least 80% identical to SEQ ID NO:1.
10. The long-lived human Atoh1 variant polypeptide of claim 8, comprising SEQ ID NO:1 with a mutation selected from the group consisting of S328A, S331A, S334A, S328A/S331A, S328A/S331A, S331A/S334A, and S328A/S331A/S334A.
11. The long-lived human Atoh1 variant polypeptide of claim 8, comprising SEQ ID NO:1 with a mutation at 5334.
12. A nucleic acid encoding the long-lived human Atoh1 variant polypeptide of claim 8.
13. An expression vector comprising the nucleic acid of claim 12.
14. The expression vector of claim 12, wherein the nucleic acid encoding the long-lived human Atoh1 variant polypeptide is operably linked with an inducible promoter or a tissue specific promoter.
15. The expression vector of claim 14, wherein the promoter is a Lgr5, GFAP, Sox2, p27Kip, FGFR3, Prox1, or Sox2 promoter.
16. A cell harboring the nucleic acid of claim 12, and optionally expressing the long-lived human Atoh1 variant polypeptide of claim 8.
17. A method of treating a subject suffering from a sensorineural hearing loss or vestibular dysfunction associated with loss of auditory hair cells, the method comprising administering a therapeutically effective amount of the nucleic acid of claim 12 to the subject.
18. The method of claim 17, wherein the nucleic acid is delivered to the inner ear of the subject.
19. (canceled)
20. A method of treating a subject suffering from a sensorineural hearing loss or vestibular dysfunction associated with loss of auditory hair cells, the method comprising administering a therapeutically effective amount of an inhibitory nucleic acid targeting Huwe1 to the subject.
21. (canceled)
22. The method of claim 20, wherein the inhibitory nucleic acid is delivered to the inner ear of the subject.
23. The method of claim 20, wherein the inhibitory nucleic acid is selected from the group consisting of antisense oligonucleotides; small interfering RNA (siRNA); and short, hairpin RNA (shRNA).
24. A cell harboring the expression vector of claim 13, and optionally expressing the long-lived human Atoh1 variant polypeptide of claim 8.
Type: Application
Filed: Aug 6, 2015
Publication Date: Nov 2, 2017
Inventors: Albert Edge (Brookline, MA), Yen-Fu Cheng (Boston, MA), Judith Kempfle (Brookline, MA), Dunia Abdul-Aziz (Boston, MA)
Application Number: 15/502,113
