U.S. patent application number 16/178776 was filed with the patent office on 2019-06-27 for pathways to generate hair cells.
The applicant listed for this patent is Massachusetts Eye and Ear Infirmary. Invention is credited to Albert Edge, Fuxin Shi.
Application Number | 20190192575 16/178776 |
Document ID | / |
Family ID | 42198853 |
Filed Date | 2019-06-27 |
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United States Patent
Application |
20190192575 |
Kind Code |
A1 |
Edge; Albert ; et
al. |
June 27, 2019 |
Pathways to Generate Hair Cells
Abstract
This disclosure relates to methods and compositions for
modulating (e.g., increasing) Atoh1 activity (e.g., biological
activity) and/or expression (e.g., transcription and/or
translation) in vivo and/or in vitro, e.g., in a biological cell
and/or in a subject. The methods and compositions described herein
can be used in the treatment of diseases and/or disorders that
would benefit from increased Atoh1 expression in a biological
cell.
Inventors: |
Edge; Albert; (Brookline,
MA) ; Shi; Fuxin; (Winchester, MA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Massachusetts Eye and Ear Infirmary |
Boston |
MA |
US |
|
|
Family ID: |
42198853 |
Appl. No.: |
16/178776 |
Filed: |
November 2, 2018 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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13130607 |
Aug 26, 2011 |
10143711 |
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PCT/US2009/065747 |
Nov 24, 2009 |
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16178776 |
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61117515 |
Nov 24, 2008 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
A61P 27/16 20180101;
A61K 38/1709 20130101; A61P 25/02 20180101; A61K 31/16 20130101;
A61K 35/30 20130101; A61P 43/00 20180101; A61K 45/06 20130101; A61K
38/1709 20130101; A61K 2300/00 20130101; A61K 35/30 20130101; A61K
2300/00 20130101 |
International
Class: |
A61K 35/30 20060101
A61K035/30; A61K 38/17 20060101 A61K038/17; A61K 31/16 20060101
A61K031/16; A61K 45/06 20060101 A61K045/06 |
Claims
1.-43. (canceled)
44. A method of treating a subject who has hearing loss as a result
of loss of auditory hair cells, the method comprising: identifying
a subject who has hearing loss as a result of loss of auditory hair
cells; and administering to the middle or inner ear of the subject
a composition comprising a glycogen synthase kinase 3.beta.
(GSK3.beta.) inhibitor and a proteasome inhibitor in an amount
effective to increase the number of auditory hair cells in the
subject; thereby treating the hearing loss as a result of loss of
auditory hair cells in the subject.
45. The method of claim 44, wherein the subject has sensorineural
hearing loss, auditory neuropathy, or both, as a result of loss of
auditory hair cells.
46. The method of claim 44, wherein the composition further
comprises a .beta.-catenin polypeptide.
47. The method of claim 44, wherein the composition is injected
into the luminae of the cochlea.
48. The method of claim 44, wherein the one or more GSK3.beta.
inhibitors is selected from the group consisting of lithium
chloride, purvalanol A, olomoucine, alsterpaullone, kenpaullone,
benzyl-2-methyl-1,2,4-thiadiazolidine-3,5-dione,
2-thio(3-iodobenzyl)-5-(1-pyridyl)-[1,3,4 ]-oxadiazole,
2,4-dibenzyl-5-oxothiadiazolidine-3-thione,
(2'Z,3'E)-6-bromoindirubin-3'-oxime (BIO), .alpha. 4
dibromoacetophenone,
2-chloro-1-(4,5-dibromo-thiophen-2-yl)-ethanone,
N-(4-nethoxybenzyl)-N'-(5-nitro-1,3-thiazol-2-yl)urea,
4-benzyl-2-methyl-1,2,4-thiadiazolidine-3,5-dione,
2-thio(3-iodobenzyl)-5-(1-pyridyl)-[1,3,4]-oxadiazole,
2,4-dibenzyl-5-oxothiadiazolidine-3-thione,
.alpha.-4-dibromoacetophenone, 2-chloro-1-(4,
5-dibromo-thiophen-2-yl)-ethanone, and
N-(4-Methoxybenzyl)-N'-(5-nitro-1,3-thiazol-2-yl)urea.
49. The method of claim 44, wherein the one or more GSK3.beta.
inhibitor is an indirubin.
50. The method of claim 49, wherein the indirubin is selected from
the group consisting of: indirubin-5-sulfonamide,
indirubin-5-sulfonic acid (2-hydroxyethyl)-amide,
indirubin-3'-monoxime; 5-iodo-indirubin-3'-monoxime,
5-fluoroindirubin, 5, 5'-dibromoindirubin, 5-nitroindirubin,
5-chloroindirubin, 5-methylindirubin, and 5-bromoindirubin.
51. The method of claim 44, wherein the method comprises
administering the composition to the middle ear of the subject.
52. The method of claim 44, wherein the method comprises
administering the composition to the inner ear of the subject.
53. The method of claim 48, wherein the GSK3.beta. inhibitor is
(2'Z,3'E)-6-bromoindirubin-3'-oxime (BIO).
54. The method of claim 44, wherein the proteasome inhibitor is
selected from the group consisting of Bortezomib, MG132,
lactacystin, and proteasome inhibitor PSI.
55. The method of claim 44, wherein the auditory hair cell
expresses atonal protein homologue 1 (Atoh1).
56. The method of claim 44, wherein the composition further
comprises an inhibitor of the Notch signaling pathway.
57. The method of claim 56, wherein the inhibitor of the Notch
signaling pathway is a .gamma.-secretase inhibitor.
Description
CLAIM OF PRIORITY
[0001] This application is a continuation of U.S. patent
application Ser. No. 13/130,607, filed Aug. 26, 2011, which is the
National Stage of International Application No. PCT/US2009/065747,
filed Nov. 24, 2009, and claims priority under 35 USC .sctn.119(e)
to U.S. Provisional Patent Application Ser. No. 61/117,515, filed
on Nov. 24, 2008. The entire contents of the foregoing applications
are hereby incorporated by reference.
TECHNICAL FIELD
[0002] This disclosure relates to methods and compositions for
modulating (e.g., increasing) Atoh1 activity (e.g., biological
activity) and/or expression (e.g., transcription and/or
translation) in vivo and/or in vitro, e.g., in a biological cell
and/or in a subject. More specifically, the methods and
compositions described herein can be used in the treatment of
diseases and/or disorders that would benefit from increased Atoh1
expression in a biological cell.
BACKGROUND
[0003] Atonal protein homologue 1 (Atoh1 or atonal) is a proneural
gene that encodes a basic helix-loop-helix (bHLH) domain-containing
protein that seems to play an important role in cell fate
determination in the development of the Drosophila nervous system
(Jarman et al., Cell, 73:1307-1321, 1993). Atoh1 is evolutionarily
conserved, with homologs identified in Tribolium castenium (the red
flour beetle), Fugu rubripes (puffer fish), chicken (Cath1), mouse
(Math1), and human (Hath1) (Ben-Arie et al., Hum. Mol. Gene.,
5:1207-1216, 1996). Each of these homologs contain a bHLH domain
that is identical in length and have high sequence identity to the
Atoh1 bHLH domain. For example, the Hath1 and Math1 genes are
almost identical in length.
[0004] These molecules also have highly similar nucleotide
sequences (86% identity) and highly similar bHLH amino acid
sequences (89%). The bHLH domain of Cath1 is 97% and 95% identical
to the bHLH domain of Hath1 and Math1, respectively. The bHLH of
Cath1 is 67% identical to the Atoh1 bHLH domain. In contrast, the
bHLH domains of other Drosophila encoded proteins share only 40-50%
sequence identity.
[0005] Each of the mammalian Atoh1 homologs function as
transcription factors that activate E box (CANNTG (SEQ ID NO:1))
dependent transcription (Arie et al., supra; Akazawa et al., J.
Biol. Chem., 270:8730-8738, 1995) and function as critical positive
regulators of cell fate determination in neural tissue and the
gastrointestinal (GI) tract (Helms et al., Development,
125:919-928, 1998; Isaka et al., Eur. J. Neurosci., 11:2582-2588,
1999; Ben-Arie et al., Development, 127:1039-1048, 2000). In
addition, Atoh1 is critical for auditory hair cell development from
inner ear progenitor cells, as demonstrated by the absence of
auditory hair cells in Atoh1 knockout animals (Bermingham et al.,
Science, 284:1837-1841, 1999).
[0006] Once activated, Atoh1 transcription is self perpetuating due
to the binding of Atoh1 to the Atoh1 3' enhancer (Helms et al.,
Development, 127:1185-1196, 2000), and the Atoh1 promoter is
switched on in Atoh1 knockout mice (Bermingham et al., Science,
284:1837-1841, 1999; Tsuchiya et al., Gastroenterology,
132:208-220, 2007). These observation indicate that mechanisms to
activate Atoh1, such as upstream regulators of Atoh1, must exist.
Such upstream regulators of Atoh1 are likely to have important
roles in the regulation of development in the central and
peripheral nervous systems and in the intestinal epithelium, all of
which rely on Atoh1 for differentiation.
SUMMARY
[0007] The present disclosure features methods and compositions for
modulating (e.g., increasing) Atoh1 expression (e.g., transcription
and/or translation) and/or activity (e.g., biological activity) a
subject and/or target cell.
[0008] Thus, in one aspect, the invention provides methods for
treating a subject who has or is at risk of developing hearing loss
or vestibular dysfunction. The methods include identifying a
subject who has experienced, or is at risk for developing, hearing
loss or vestibular dysfunction; and administering to the ear of the
subject a composition comprising one or more compounds that
increase .beta.-catenin expression or activity in a cell in the
subject's ear; thereby treating the hearing loss or vestibular
dysfunction in the subject.
[0009] In some embodiments, the subject has or is at risk for
developing sensorineural hearing loss, auditory neuropathy, or
both. In some embodiments, the subject has or is at risk for
developing a vestibular dysfunction that results in dizziness,
imbalance, or vertigo.
[0010] In some embodiments, the composition is administered
systemically. In some embodiments, the composition is administered
locally to the inner ear.
[0011] In some embodiments, the composition comprises a
.beta.-catenin polypeptide. In some embodiments, the composition
comprises one or more Wnt/.beta.-catenin pathway agonists. In some
embodiments, the composition comprises one or more glycogen
synthase kinase 3.beta. (GSK3.beta.) inhibitors. In some
embodiments, the composition comprises one or more casein kinase 1
(CK1) inhibitors.
[0012] In some embodiments, the methods further include
administering an inhibitor of the Notch signaling pathway to the
subject. In some embodiments, the inhibitor of the Notch signaling
pathway is a gamma secretase inhibitor.
[0013] In some embodiments, the composition comprises a
pharmaceutically acceptable excipient.
[0014] In another aspect, the invention provides methods for
treating a subject who has or is at risk of developing hearing loss
or vestibular dysfunction, the method comprising selecting a
subject in need of treatment, obtaining a population of cells
capable of differentiating into hair cells, contacting the
population of cells in vitro with an effective amount of a
composition comprising one or more compounds that increase
.beta.-catenin expression or activity for a time sufficient to
induce at least some of the cells to express one or more of
p27.sub.kip, p75, S100A, Jagged-1, Prox1, myosin VIIa, atonal
homolog 1 (Atoh1) or homologues thereof, .alpha.9 acetylcholine
receptor, espin, parvalbumin 3 and F-actin (phalloidin), optionally
purifying the population of cells, e.g., to a purity of at least
50%, 60%, 70%, 80%, 90%, or more, and administering the population
of cells, or a subset thereof, to the subjects's ear.
[0015] In some embodiments, the subject has or is at risk for
developing sensorineural hearing loss, auditory neuropathy, or
both.
[0016] In some embodiments, the population of cells capable of
differentiating into auditory hair cells includes cells selected
from the group consisting of stem cells, progenitor cells, support
cells, Deiters' cells, pillar cells, inner phalangeal cells, tectal
cells, Hensen's cells, and germ cells.
[0017] In some embodiments, the stem cells are adult stem cells,
e.g., adult stem cells are derived from the inner ear, bone marrow,
mesenchyme, skin, fat, liver, muscle, or blood, or embryonic stem
cells or stem cells obtained from a placenta or umbilical cord.
[0018] In some embodiments, the progenitor cells are derived from
the inner ear, bone marrow, mesenchyme, skin, fat, liver, muscle,
or blood.
[0019] In some embodiments, the composition comprises DNA encoding
.beta.-catenin; a .beta.-catenin polypeptide; one or more
Wnt/.beta.-catenin pathway agonists; one or more glycogen synthase
kinase 3.beta. (GSK3.beta.) inhibitors; and/or one or more casein
kinase 1 (CK1) inhibitors.
[0020] In some embodiments, administering the population of cells
comprises (a) injecting the cells into the luminae of the cochlea,
into the auditory nerve trunk in the internal auditory meatus, or
into the scala tympani or (b) implanting the cells within a cochlea
implant.
[0021] In some embodiments, the methods further include contacting
the cells with an inhibitor of the Notch signaling pathway, e.g., a
gamma secretase inhibitor, e.g., one or more of an arylsulfonamide,
a dibenzazepine, a benzodiazepine,
N-[N-(3,5-difluorophenacetyl)-L-alanyl]-(S)-phenylglycine t-butyl
ester (DAPT), L-685,458, or MK0752.
[0022] In some embodiments, the methods further include
administering to the ear of the subject a composition comprising
one or more compounds capable of increasing .beta.-catenin
expression or activity in a cell in the subject's ear, e.g., DNA
encoding .beta.-catenin, a .beta.-catenin polypeptide, one or more
Wnt/.beta.-catenin pathway agonist, one or more glycogen synthase
kinase 3 (GSK3.beta.) inhibitors, and/or one or more casein kinase
1 (CK1) inhibitors.
[0023] In some embodiments, the methods further include
administering to the ear of the subject a composition comprising
one or more inhibitors of the Notch signaling pathway, e.g., a
gamma secretase inhibitor.
[0024] In yet a further aspect, the invention provides methods for
treating a subject who has or is at risk of developing hearing loss
or vestibular dysfunction including identifying a subject who has
experienced, or is at risk for developing, hearing loss or
vestibular dysfunction; administering to the ear of the subject a
composition comprising one or more compounds that specifically
increase .beta.-catenin expression or activity in a cell in the
subject's ear; and administering an inhibitor of the Notch
signaling pathway, e.g., a gamma secretase inhibitor, to the
subject; thereby treating the hearing loss or vestibular
dysfunction in the subject.
[0025] In some embodiments, the composition includes one or more
Wnt/.beta.-catenin pathway agonists. In some embodiments, the
composition comprises one or more glycogen synthase kinase 3.beta.
(GSK3.beta.) inhibitors. In some embodiments, composition comprises
one or more casein kinase 1 (CK1) inhibitors.
[0026] In some embodiments, the one or more CK1 inhibitors is
antisense RNA or siRNA that binds specifically to CK1 mRNA
[0027] In some embodiments, the composition comprises one or more
proteasome inhibitors.
[0028] In some aspects, the present disclosure provides methods for
treating a subject or subjects that have or are at risk of
developing hearing loss or vestibular dysfunction. These methods
include methods for treating hearing loss or vestibular dysfunction
in the subject steps by identifying a subject who has experienced,
or is at risk for developing, hearing loss or vestibular
dysfunction, and administering to the ear of the subject a
composition comprising one or more compounds capable of increasing
.beta.-catenin expression or activity in a cell in the subject's
ear.
[0029] In another aspect, the present disclosure provides methods
of treating a subject who has or is at risk of developing hearing
loss or vestibular dysfunction. These methods include selecting a
subject in need of treatment, obtaining a population of cells
capable of differentiating into auditory hair cells, contacting the
population of cells in vitro with an effective amount of a
composition comprising one or more compounds capable of increasing
.beta.-catenin expression or activity for a time sufficient to
induce at least some of the cells to express: (a) one or more of
p27.sub.kip, p75, S100A, Jagged-1, Prox1, myosin VIIa, atonal
homolog 1 (Atoh1) or homologues thereof, .alpha.9 acetylcholine
receptor, espin, parvalbumin 3 and F-actin (phalloidin); or (b) one
or more of myosin VIIa, atonal homolog 1 (Atoh1) or homologues
thereof, and administering the population of cells, or a subset
thereof, to the subject's ear. In some embodiments, the population
of cells capable of differentiating into hair cells expresses one
or more of p27.sub.kip, p75, S100A, Jagged-1, Prox1, myosin VIIa,
atonal homolog 1 (Atoh1) or homologues thereof, .alpha.9
acetylcholine receptor, espin, parvalbumin 3 and F-actin
(phalloidin).
[0030] In yet another aspect, the present disclosure provides
methods of increasing the number of cells that express one or more
of (a) p27.sub.kip, p75, S100A, Jagged-1, Prox1, myosin VIIa,
atonal homolog 1 (Atoh1) or homologues thereof, .alpha.9
acetylcholine receptor, espin, parvalbumin 3 and F-actin
(phalloidin), or (b) one or more of myosin VIIa, atonal homolog 1
(Atoh1) or homologues thereof, e.g., in vitro. These methods
include steps of obtaining a population of cells capable of
differentiating into cells that express one or more of (a)
p27.sub.kip, p75, S100A, Jagged-1, Prox1, myosin VIIa, atonal
homolog 1 (Atoh1) or homologues thereof, .alpha.9 acetylcholine
receptor, espin, parvalbumin 3 and F-actin (phalloidin), or (b) one
or more of myosin VIIa, atonal homolog 1 (Atoh1) or homologues
thereof, and contacting the population of cells in vitro with an
effective amount of a composition comprising one or more compounds
capable of increasing .beta.-catenin expression or activity for a
time sufficient to increase the number of cells with the
characteristics of auditory hair cells in the population of
cells.
[0031] In a further aspect, the present disclosure provides a
population of cells in which the number of cells that express one
or more of (a) p27.sub.kip, p75, S100A, Jagged-1, Prox1, myosin
VIIa, atonal homolog 1 (Atoh1) or homologues thereof, .alpha.9
acetylcholine receptor, espin, parvalbumin 3 and F-actin
(phalloidin), or (b) one or more of myosin VIIa, atonal homolog 1
(Atoh1) or homologues thereof, is increased. In some embodiments,
this population of cells is obtained by obtaining a population of
cells capable of differentiating into cells that express one or
more of (a) p27.sub.kip, p75, S100A, Jagged-1, Prox1, myosin VIIa,
atonal homolog 1 (Atoh1) or homologues thereof, .alpha.9
acetylcholine receptor, espin, parvalbumin 3 and F-actin
(phalloidin), or (b) one or more of myosin VIIa, atonal homolog 1
(Atoh1) or homologues thereof, contacting the population of cells
in vitro with an effective amount of a composition comprising one
or more compounds capable of increasing .beta.-catenin expression
or activity for a time sufficient to increase the number of cells
with the characteristics of auditory hair cells in the population
of cells.
[0032] In some embodiments, this population of cells contacted
expresses one or more of p27kip, p75, A100AS100A, Jagged-1, Prox1,
.alpha.9 acetylcholine receptor, espin, parvalbumin 3 and F-actin
(phalloidin).
[0033] In a further aspect, the present disclosure includes kits
that include a composition comprising one or more compounds capable
of increasing .beta.-catenin expression or activity and
informational material. In some embodiments, the these kits include
DNA encoding .beta.-catenin.
[0034] In an additional aspect, the present disclosure provides
methods of treating a subject who has or is at risk of developing
hearing loss or vestibular dysfunction. Such methods include steps
of identifying a subject who has experienced, or is at risk for
developing, hearing loss or vestibular dysfunction, administering
to the ear of the subject a composition comprising one or more
compounds capable of increasing .beta.-catenin expression or
activity in a cell in the subject's ear, and administering an
inhibitor of the Notch signaling pathway to the subject.
[0035] In some aspects, the subject selected for any of the methods
disclosed herein is at risk for developing sensorineural hearing
loss, auditory neuropathy, or both. For example, the subject is at
risk for developing a vestibular dysfunction that results in
dizziness, imbalance, or vertigo. Alternatively or in addition, the
subject can be a subject that has been or will be treated with an
orthotoxic agent
[0036] In some aspects, the methods disclosed herein effectively
increases the expression of one or more of (a) nestin, sox2,
musashi, Brn3c, islet 1, Pax2, p27.sub.kip, p75, S100A, Jagged-1,
Prox1, myosin VIIa, Atoh1 or homologues thereof, .alpha.9
acetylcholine receptor, espin, parvalbumin 3, and F-actin
(phalloidin); (b) myosin VIIa, Atoh1 in cells in the subject's
inner ear; (c) one or more of p27.sub.kip, p75, S100A, Jagged-1,
and Prox1 in cells in the subject's inner ear; (d) one or more of
murine atonal gene 1 myosin VIIa, Atoh1 or homologues thereof,
.alpha.9 acetylcholine receptor, espin, parvalbumin 3, and F-actin
(phalloidin) in cells in the patient's inner ear.
[0037] In some aspects, any composition disclosed herein can be
administered systemically, for example, using a systemic route of
administration is selected from the group consisting of parenteral
administration, intravenous injection, intramuscular injection,
intraperitoneal injection, oral administration, lozenges,
compressed tablets, pills, tablets, capsules, drops, ear drops,
syrups, suspensions, emulsions, rectal administration, a rectal
suppository, an enema, a vaginal suppository, a urethral
suppository, transdermal administration, inhalation, nasal sprays,
and administration using a catheter or pump.
[0038] In some aspects, any composition disclosed herein can be
administered locally to the inner ear. For example, using injection
into the luminae of the cochlea, into the auditory nerve trunk in
the internal auditory meatus, and/or into the scala tympani. Such
methods can also include, for example, administered to the middle,
or the inner ear, or both, e.g., using a catheter or pump.
[0039] In some aspects, any composition disclosed herein can be
administered by a route of administration selected from the group
consisting of an intratympanic injection, an injection into the
outer, middle, or inner ear, an injection through the round window
of the ear, and an injection through the cochlear capsule.
[0040] In some aspects, the compositions administered in the
methods disclosed herein include one or more of DNA encoding
.beta.-catenin (e.g., naked DNA encoding .beta.-catenin, plasmid
expression vectors encoding .beta.-catenin, viral expression
vectors encoding .beta.-catenin), .beta.-catenin polypeptides, one
or more Wnt/.beta.-catenin pathway agonists (e.g., selected from
the group consisting of Wnt ligands, DSH/DVL1, 2, 3, LRP6N, WNT3A,
WNT5A, and WNT3A, 5A), one or more glycogen synthase kinase 3.beta.
(GSK3.beta.) inhibitors (e.g., selected from the group consisting
of lithium chloride (LiCl), Purvalanol A, olomoucine,
alsterpaullone, kenpaullone,
benzyl-2-methyl-1,2,4-thiadiazolidine-3,5-dione (TDZD-8),
2-thio(3-iodobenzyl)-5-(1-pyridyl)-[1,3,4]-oxadiazole (GSK3
inhibitor II), 2,4-dibenzyl-5-oxothiadiazolidine-3-thione (OTDZT),
(2'Z,3'E)-6-Bromoindirubin-3'-oxime (BIO),
.alpha.-4-Dibromoacetophenone (i.e., Tau Protein Kinase I (TPK I)
Inhibitor), 2-Chloro-1-(4,5-dibromo-thiophen-2-yl)-ethanone,
N-(4-Methoxybenzyl)-N'-(5-nitro-1,3-thiazol-2-yl)urea (AR-A014418),
indirubin-5-sulfonamide; indirubin-5-sulfonic acid
(2-hydroxyethyl)-amide indirubin-3'-monoxime;
5-iodo-indirubin-3'-monoxime; 5-fluoroindirubin;
5,5'-dibromoindirubin; 5-nitroindirubin; 5-chloroindirubin;
5-methylindirubin, 5-bromoindirubin,
4-Benzyl-2-methyl-1,2,4-thiadiazolidine-3,5-dione (TDZD-8),
2-thio(3-iodobenzyl)-5-(1-pyridyl)-[1,3,4]-oxadiazole (GSK3
inhibitor II), 2,4-Dibenzyl-5-oxothiadiazolidine-3-thione (OTDZT),
(2'Z,3'E)-6-Bromoindirubin-3'-oxime (BIO),
.alpha.-4-Dibromoacetophenone (i.e., Tau Protein Kinase I (TPK I)
Inhibitor), 2-Chloro-1-(4,5-dibromo-thiophen-2-yl)-ethanone, (vi)
N-(4-Methoxybenzyl)-N'-(5-nitro-1,3-thiazol-2-yl)urea (AR-A014418),
H-KEAPPAPPQSpP-NH2 (L803) (SEQ ID NO: 40) and
Myr-N-GKEAPPAPPQSpP-NH2 (L803-mts) (SEQ ID NO: 41)), one or more
anti-sense RNA or siRNA that bind specifically to GSK3.beta. mRNA,
one or more casein kinase 1 (CK1) inhibitors (e.g., antisense RNA
or siRNA that binds specifically to CK1 mRNA), one or more protease
inhibitors, one or more proteasome inhibitors. The compositions and
methods disclosed herein can also further include the use or
administration of an inhibitor of the Notch signaling pathway
(e.g., one or more of a gamma secretase inhibitor (e.g., one or
more of an arylsulfonamide, a dibenzazepine, a benzodiazepine,
N-[N-(3,5-difluorophenacetyl)-L-alanyl]-(S)-phenylglycine t-butyl
ester (DAPT), L-685,458, or MK0752, and an inhibitory nucleic acid
including small interfering RNA, an antisense
oligonucleotideoligonucleotides, and a morpholino oligo oligoss).
Where an inhibitor of Notch signaling is administered, it can be
administered administered systemically (e.g., selected from the
group consisting of parenteral administration, intravenous
injection, intramuscular injection, intraperitoneal injection, oral
administration, lozenges, compressed tablets, pills, tablets,
capsules, drops, ear drops, syrups, suspensions, emulsions, rectal
administration, a rectal suppository, an enema, a vaginal
suppository, a urethral suppository, transdermal administration,
inhalation, nasal sprays, and administration using a catheter or
pump) and or locally (e.g., locally to the ear, for example, by
injection into the luminae of the cochlea, into the auditory nerve
trunk in the internal auditory meatus, and/or into the scala
tympani). In some aspects, the inhibitor of Notch signaling can be
administered by a route of administration selected from the group
consisting of an intratympanic injection, an injection into the
outer, middle, or inner ear, an injection through the round window
of the ear, injection through the cochlear capsule, and/or to the
middle, or the inner ear, or both using a catheter or pump.
[0041] In some aspects, the methods disclosed herein include the
use of single cells (i.e., an isolated cell) and/or populations of
cells, wherein the cell or population of cells are capable of
differentiating (e.g., can, when subjected to the methods disclosed
herein, differentiate into) auditory hair cells selected from the
group consisting of stem cells (e.g., adult stem cells (e.g., adult
stem cells obtained from the inner ear, bone marrow, mesenchyme,
skin, fat, liver, muscle, or blood of a subject, e.g., the subject
to be treated), embryonic stem cells, or stem cells obtained from a
placenta or umbilical cord), progenitor cells (e.g., progenitor
cells derived from the inner ear, bone marrow, mesenchyme, skin,
fat, liver, muscle, or blood), support cells, Deiters' cells,
pillar cells, inner phalangeal cells, tectal cells, Hensen's cells,
and germ cells.
Definitions
[0042] As used herein, "Atoh1" refers to any and all
Atoh1-associated nucleic acid or protein sequences and includes any
sequence that is orthologous or homologous to, or has significant
sequence similarity to, an Atoh 1 nucleic acid or amino acid
sequence, respectively. The sequence can be present in any animal
including mammals (e.g., humans) and insects. Examples of Atoh1
associated sequences include, but are not limited to Atoh1 (e.g.,
GenBank Accession Number NM_001012432.1), Hath1 (e.g.,
NM_005172.1), Math1 (e.g., NM_007500.4), and Cath1 (e.g., U61149.1
and AF467292.1), as well as all other synonyms that may be used to
refer to this protein, e.g., atonal, atonal homolog 1, Ath1, and
helix-loop-helix protein Hath1. Furthermore, multiple homologous or
similar sequences can exist in an animal.
[0043] As used herein, "treatment" means any manner in which one or
more of the symptoms of a disease or disorder are ameliorated or
otherwise beneficially altered. As used herein, amelioration of the
symptoms of a particular disorder refers to any lessening, whether
permanent or temporary, lasting or transient that can be attributed
to or associated with treatment by the compositions and methods of
the present invention.
[0044] The terms "effective amount" and "effective to treat," as
used herein, refer to an amount or a concentration of one or more
compounds or a pharmaceutical composition described herein utilized
for a period of time (including acute or chronic administration and
periodic or continuous administration) that is effective within the
context of its administration for causing an intended effect or
physiological outcome.
[0045] Effective amounts of one or more compounds or a
pharmaceutical composition for use in the present invention include
amounts that promote increased .beta.-catenin levels (e.g., protein
levels) and/or activity (e.g., biological activity) in target
cells, increased .beta.-catenin levels (e.g. protein levels) and/or
activity (e.g., biological activity) in the nucleus of target
cells, increased Atoh1 expression or activity, and/or that promote
complete or partial differentiation of one or more cells to treat a
disease that would benefit from increased Atoh1 expression, e.g.,
prevent or delay the onset, delay the progression, ameliorate the
effects of, or generally improve the prognosis of a subject
diagnosed with one or more diseases that would benefit from
increased Atoh1 expression, e.g., one or more of the diseases
described herein. For example, in the treatment of hearing
impairment, a compound which improves hearing to any degree or
arrests any symptom of hearing impairment would be therapeutically
effective. A therapeutically effective amount of a compound is not
required to cure a disease but will provide a treatment for a
disease.
[0046] The term "subject" is used throughout the specification to
describe an animal, human or non-human, to whom treatment according
to the methods of the present invention is provided. Veterinary and
non-veterinary applications are contemplated.
[0047] The term includes, but is not limited to, birds and mammals,
e.g., humans, other primates, pigs, rodents such as mice and rats,
rabbits, guinea pigs, hamsters, cows, horses, cats, dogs, sheep and
goats. Typical subjects include humans, farm animals, and domestic
pets such as cats and dogs.
[0048] As used herein "target cell" and "target cells" refers to a
cell or cells that are capable of undergoing conversion (e.g.,
differentiation) to or towards a cell or cells that have
characteristics of auditory hair cells. Target cells include, but
are not limited to, e.g., stem cells (e.g., inner ear stem cells,
adult stem cells, bone marrow derived stem cells, embryonic stem
cells, mesenchymal stem cells, skin stem cells, and fat derived
stem cells), progenitor cells (e.g., inner ear progenitor cells),
support cells (e.g., Deiters' cells, pillar cells, inner phalangeal
cells, tectal cells and Hensen's cells), support cells expressing
one or more of p27.sub.kip, p75, S100A, Jagged-1, Prox1, and/or
germ cells. As described herein, prior to treatment with the
methods, compounds, and compositions described herein, each of
these target cells can be identified using a defined set of one or
more markers (e.g., cell surface markers) that is unique to the
target cell. A different set of one or more markers (e.g., cell
surface markers) can also be used to identify target cells that
have a partial or complete conversion (e.g., partial or complete
differentiation) to or towards a cell that has characteristics of
auditory hair cells or an auditory hair cell.
[0049] Target cells can be generated from stem cells isolated from
a mammal, such as a mouse or human, and the cells can be embryonic
stem cells or stem cells derived from mature (e.g., adult) tissue,
such as the inner ear, central nervous system, blood, skin, eye or
bone marrow. Unless stated otherwise, any of the methods described
below for culturing stem cells and inducing differentiation into
ear cells (e.g., hair cells) can be used.
[0050] As used herein, ".beta.-catenin" refers to any and all
.beta.-catenin-associated nucleic acid or protein sequences and
includes any sequence that is orthologous or homologous to, or has
significant sequence similarity to, a .beta.-catenin nucleic acid
or amino acid sequence.
[0051] In some embodiments, .beta.-catenin, as used herein, refers
to .beta.-catenin (e.g., mammalian .beta.-catenin), .alpha.-catenin
(e.g., mammalian .alpha.-catenin), .gamma.-catenin (e.g., mammalian
.gamma.-catenin), .delta.-catenin (e.g., mammalian
.delta.-catenin).
[0052] As used herein, ".beta.-catenin modulating compounds" or
simply "compounds" include any compound that can increase
.beta.-catenin levels (e.g., protein levels) and/or activity (e.g.,
biological activity) in target cells. Alternatively or in addition,
the strategies can promote an increase in the levels (e.g. protein
levels) and/or activity (e.g., biological activity) of
.beta.-catenin in the nucleus of target cells.
[0053] As used herein, the term "expression" means protein and/or
nucleic acid expression and/or protein activity.
[0054] 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.
[0055] Other features and advantages of the invention will be
apparent from the following detailed description and figures, and
from the claims.
DESCRIPTION OF DRAWINGS
[0056] The patent or application file contains at least one drawing
executed in color.
[0057] Copies of this patent or patent application publication with
color drawing(s) will be provided by the Office upon request and
payment of the necessary fee.
[0058] FIGS. 1A and 1B are images of an agarose gel showing Atoh1
and GAPDH mRNA expression in HEK and HT29 cells, respectively.
"None" indicates that the cells were untransfected.
[0059] FIG. 1C is an image of a gel showing mRNA expression levels
of Atoh1 and GAPDH in Neuro2a and neural progenitor cells
transfected with Atoh1, .beta.-catenin, or green fluorescent
protein (GFP) (as shown).
[0060] FIGS. 1D and 1F are bar graphs showing relative Atoh1
expression as assessed by RT-PCR. Atoh1 levels were normalized
against the S18 housekeeping gene.
[0061] FIG. 1E is an image of a gel showing mRNA expression levels
of Atoh1 and GAPDH in Neuro2a and neural progenitor cells
transfected with siRNA targeted against Atoh1 or .beta.-catenin
mRNA or non-targeted siRNA as a control.
[0062] FIG. 1G is a line graph showing luciferase reporter
expression levels.\
[0063] FIG. 1H is an image of a Western blot gel showing Atoh1 and
nuclear unphosphorylated .beta.-catenin expression levels from the
nuclear fraction.
[0064] FIG. 2A is a bar graph showing Atoh1 expression in HEK cells
quantified using real-time polymerase chain reaction (RT-PCR).
Columns represent the mean of two independent experiments each
performed in triplicate. Atoh1 levels are shown relative to control
cells without transfection and are normalized to S18.
[0065] FIG. 2B is a schematic representation of the Atoh1 3'
enhancer and an image of a gel showing Atoh1 bound to
.beta.-catenin, Tcf/Lef, or serum. Input (DNA without antibody
precipitation) is shown as control.
[0066] FIG. 3 is an image of an immunoblot showing Atoh1 protein
expression in untransfected HEK cells and HEK cells transfected
with Atoh1, .beta.-catenin or GFP each of which was under the
control of a CMV promoter.
[0067] FIGS. 4A and 4B are images of an agarose gel showing Atoh1
and GAPDH mRNA expression in Neuro2a and mouse progenitor cells
derived from mouse embryonic stem (ES) cells (mES), respectively.
None indicates that cells are untransfected.
[0068] FIG. 5 is a bar graph showing Atoh1 expression in Neuro2a
cells quantified using RT-PCR. Columns represent the mean of two
independent experiments each performed in triplicate. Atoh1 levels
are shown relative to control cells without transfection and are
normalized to S18.
[0069] FIG. 6 is an image of an agarose gel showing Atoh1 enhancer
region from HEK cells amplified using chromatin immunoprecipitation
(ChIP).
[0070] FIGS. 7A and 7B are images of immunoblots showing
.beta.-catenin and Tcf-Lef detection following DNA pull down. Left
lanes show proteins pulled down using probe 309 (7A) and probe 966
(7B). Center lanes show probe 309 (7A) and probe 966 (7B)
competition pull downs. Right lane show proteins pulled down using
mutant probe 309 (7A) and mutant probe 966 (7B).
[0071] FIG. 7C is an image of gels showing Western blotting of
.beta.-catenin and Tcf-Lef.
[0072] FIG. 7D is a bar graph showing the expression of Atoh1 in
untransfected Neuo2a cells and neural progenitors.
[0073] FIGS. 8A-8E are schematics showing luciferase reporter
expression cassettes encoded by the luciferase vector pGL3. (8A)
control luciferase reporter expression cassette encoding a
.beta.-globin promoter (BGZA) and a firefly luciferase gene (Luc+)
in the absence of a Atoh1 3' enhancer. (8B) Wild type luciferase
reporter expression cassette encoding a BGZA promoter (BGZA), Luc+,
and a wild type Atoh1 3' enhancer. (8C) Mutant luciferase reporter
expression cassette encoding a BGZA promoter (BGZA), Luc+, and a
Atoh1 3' enhancer encoding a mutated first .beta.-catenin binding
site located at nucleotides 309-315 of AF218258. (8D) Mutant
luciferase reporter expression cassette encoding a BGZA promoter
(BGZA), Luc+, and a Atoh1 3' enhancer encoding a mutated second
.beta.-catenin binding site located at nucleotides 966-972 of
AF218258. (8E) Mutant luciferase reporter expression cassette
encoding a BGZA promoter (BGZA), Luc+, and a Atoh1 3' enhancer
encoding mutated first and second .beta.-catenin binding sites at
nucleotides 309-315 and 966-972 of AF218258. Nucleotides encoded by
the first and second .beta.-catenin binding sites at nucleotides
309-315 and 966-972 of AF218258 are shown in upper case font. *
indicates a mutated nucleotide. Nucleotides shown with * are mutant
nucleotides.
[0074] FIG. 9 is a bar graph showing relative luciferase expression
in murine Neuro2a cells alone (open bars) or in the presence of
.beta.-catenin (solid bars). Cells were transfected with luciferase
constructs (A)-(E) depicted in FIGS. 8A-8E.
[0075] FIGS. 10A, C, and E are images of gels showing the
expression levels of .beta.-catenin, Atoh1, and .beta.-actin
following treatment of cells with the .gamma.-secretase inhibitor
DAPT (used at 10 .mu.M and 50 .mu.M), GSK3.beta. inhibitor, and/or
siRNA targeted against .beta.-catenin.
[0076] FIG. 10B is a bar graph showing the effect of two siRNAs
directed against .beta.-catenin as evaluated by RT-PCR.
[0077] FIG. 10D is a bar graph showing data collected using
Pofut1-/- cells in which Notch signaling is inhibited.
[0078] FIG. 10F is an image of a gel showing .beta.-catenin
expression in cells following treatment with .beta.-catenin
agonists and Notch signaling inhibitors.
[0079] FIGS. 11A-11C are images of inner ear stem cells expressing
fluorescent markers. (11A) Cells infected with adenoviruses
encoding GFP. Left panel shows inner ear stem cells expressing
green fluorescent protein (GFP); center panel shows cells stained
with the nuclear stain 4'-6-Diamidino-2-phenylindole (DAPI-blue);
right panel shows a merge of the left and center panels. (11B) and
(11C) left panels show cells stained for myosin VIIa (red); second
panels show Atoh1-nGFP positive cells (green); third panels show
cells stained with DAPI; right panels show merged cells (red, green
and blue). Triple stained cells are shown with arrows. (11B) cells
infected with empty adenovirus vector. (11C) cells infected with
adenoviruses encoding human .beta.-catenin.
[0080] FIG. 11D is a bar graph showing quantification of Atoh1 and
myosin VIIa double stained cells. Data represents three independent
experiments in which 5000 cells were counted.
[0081] FIGS. 12A and 12B are images of inner ear stem cells
expressing .beta.-catenin-IRES-DsRed (12A) and IRES-DsRed in the
absence of .beta.-catenin (12B). (i) shows cells expressing
.beta.-catenin-IRES-DsRed or IRES-DsRed (red). One cell is shown
for both (12A) and (12B). (ii) shows Atoh1 expression (green) in
the same field of view as (i). (iii) shows a phase contrast image
of the same field of view as (i) and (ii). (iv) shows a merged
image of (i), (ii), and (iii). Co-stained cells are shown with
arrows.
[0082] FIGS. 13A-13D are images of hair cells in the organ of corti
dissected at E16 in Atoh1-nGFP mice. (13A) untreated control hair
cells; (13B) hair cells infected with empty adenoviral vector for 5
days; (13C and D) hair cells infected with adenovirus encoding
.beta.-catenin for 5 days. Green cells are Atoh-1 positive hair
cells.
[0083] FIGS. 14A and 14B are images of different organs of corti
dissected from Atoh1-nGFP mice. (14A) shows a dissected organ of
corti 2 days post infected with .beta.-catenin. (14B) shows an
uninfected organ of corti.
[0084] FIGS. 15A and 15B are images showing putative
WNT/.beta.-catenin signaling pathways. 15B illustrates regulation
of Atoh1 by .beta.-catenin according to the data presented
herein.
DETAILED DESCRIPTION
[0085] The present disclosure provides, inter alia, methods and
pharmaceutical compositions for treating subjects for the
conditions noted below. Accordingly, the present disclosure is
based, at least in part, on the discovery that differentiation of a
cell to or towards a mature cell of the inner ear, e.g., an
auditory hair cell can be promoted through .beta.-catenin-dependent
WNT signaling. In other words, the present disclosure provides
methods and compositions relating to the WNT/.beta.-catenin
signaling pathway for generating cells that have characteristics of
auditory hair cells.
[0086] While the treatment methods are not limited to those in
which particular underlying cellular events occur, the present
compounds and compositions may increase the expression of an Atoh1
gene in a subject and/or target cell.
[0087] As shown herein, .beta.-catenin, the intracellular mediator
of the canonical Wnt signaling pathway, is capable of increasing
Atoh1 expression in a biological cell. Characterization of this
effect revealed that .beta.-catenin increases Atoh1 expression
through a direct interaction with two distinct .beta.-catenin
binding domains encoded in the Atoh1 3' enhancer region (e.g., at
nucleotides 309-315 and nucleotides 966-972 of GenBank Accession
No. AF218258 (e.g., AF218258.1; G17677269)). These two
.beta.-catenin binding domains also interact with T-cell factor
(TCF) and lymphoid enhancer-binding protein (LEF), which are
transcription factors that normally maintain target genes of the
WNT signaling pathway in a repressed state by interacting, in
combination with other co-repressors, with the promoter or enhancer
regions of Wnt target genes. Thus, the data presented herein
demonstrates that .beta.-catenin serves as an upstream regulator of
Atoh1. Additionally, the data presented herein demonstrates that
.beta.-catenin dependent Atoh1 expression promotes the
differentiation of inner ear progenitor cells to or towards cells
that have characteristics of auditory hair cells.
Catenins
[0088] Catenins are a group of proteins that are commonly found in
complex with cadherin cell adhesion molecules, e.g., in animal
cells. Four catenins have been identified to date, namely:
.alpha.-catenin, .beta.-catenin, .delta.-catenin, and
.gamma.-catenin.
[0089] .alpha.-catenin is an actin-binding protein at the adherens
junction, that has overall similarity to vinculin, another
actin-binding protein present at adhesional complexes.
.alpha.-catenin is about 100 kDa (e.g., 102 kDa) as detected by
Western Blotting (see, e.g., Nagafuchi et al., Cell, 65:849-857,
1991). .alpha.-catenin is detectable by Western blotting using,
e.g., anti-alpha catenin monoclonal antibody available from GenWay
(e.g., catalogue number 20-272-191447).
[0090] .beta.-catenin is capable of binding to the subdomain of
some cadherins and is implicated in the WNT signaling pathway. The
ability of .beta.-catenin to bind to other proteins is regulated by
tyrosine kinases and serine kinases such as GSK-3 (see, e.g.,
Lilien et al., Current Opinion in Cell Biology, 17:459-465, 2005).
.beta.-catenin is about a 80-100 kDa (e.g., 88 kDa-92 kDa, e.g., 92
kDa) as detected by Western Blotting. .beta.-catenin is detectable
by Western blotting using, e.g., anti-beta catenin monoclonal
antibody available from Abcam (e.g., catalogue number Ab2982).
[0091] .delta.-catenin (e.g., .delta.1-catenin and
.delta.2-catenin) is a member of a family of proteins with ten
armadillo repeats (the p120 catenin subfamily of catenins).
.delta.-catenin is expressed predominantly in neural tissue where
it interacts with presenilins (see, e.g., Israely et al., Current
Biology, 14:1657-1663, 2004 and Rubio et al., Mol. And Cell.
Neurosci., 4:611-623, 2005). .delta.-catenin is about a 100-150 kDa
(e.g., about 125 kDa) as detected by Western Blotting.
.delta.1-catenin is detectable by Western blotting using, e.g.,
anti-delta catenin antibody available from Sigma Aldrich (e.g.,
catalogue number C4989). .delta.2-catenin is detectable by Western
blotting using, e.g., anti-delta catenin antibody available from
Abcam (e.g., catalogue number ab54578).
[0092] .gamma.-catenin is commonly found as a component of
desmosomes and can bind to desmoglein I (see e.g., Franke et al.,
Proc. Natl. Acad. Sci. USA., 86:4027-31, 1989). .gamma.-catenin is
about a 80-100 kDa (e.g., about 80 kDa) as detected by Western
Blotting. .gamma.-catenin is detectable by Western blotting using,
e.g., anti-gamma catenin monoclonal antibody available from Abcam
(e.g., catalogue number Ab11799).
WNT/.beta.-Catenin Signaling
[0093] The expression of bHLH transcription factors, such as Atoh1,
is partly regulated by various components of the Notch pathway.
However, Notch may be only a part of the complex regulatory
circuits governing the timing and amount of bHLH transcription
factor expression as well as the tissue specificity of
expression.
[0094] WNT signaling pathways (see, e.g., FIG. 14) play a key role
in early development of several tissues, including but not limited
to, for example, the intestinal epithelium and the inner ear
(Clevers, Cell, 127:469-480, 2006; Ohyama et al., Development,
133:865-875, 2006; Pinto et al., Exp. Cell. Res., 306:357-363,
2005; Stevens et al., Dev. Biol., 261:149-164, 2003; van ES et al.,
Nat. Cell. Biol., 7:381-386, 2005; van ES et al., Nature,
435:959-963, 2005). Furthermore, disruption of Wnt signaling
prevents intestinal epithelial differentiation to mature cell types
accompanied by decreased Atoh1 expression (Pinto et al.,
supra).
[0095] WNTs are secreted cysteine-rich glycoproteins that act as
short-range ligands to locally activate receptor-mediated signaling
pathways. In mammals, 19 members of the WNT protein family have
been identified. WNTs activate more than one signaling pathway
(Veerman et al., Dev. Cell., 5:367-377, 2003) including both
.beta.-catenin-dependent and .beta.-catenin-independent pathways.
The best understood of the WNT-activated pathways, however, is the
WNT/.beta.-catenin pathway, and the list of proteins identified as
being involved in the WNT/.beta.-catenin pathway is extensive and
expanding.
[0096] Wnt signaling is transduced intracellularly by the frizzled
(Fzd) family of receptors (Hendrickx and Leyns, Dev. Growth
Differ., 50:229-243, 2008). Activation of the WNT/.beta.-catenin
pathway leads to an increase in the post-translational stability of
.beta.-catenin. As .beta.-catenin levels rise, it accumulates in
the nucleus, where it interacts and forms a complex with DNA-bound
TCF and LEF family members to activate the transcription of target
genes. Conversely, in the absence of WNT signaling, .beta.-catenin
is recruited to a destruction complex containing adenomatous
polyposis coli (APC) and AXIN, which together serve to facilitate
the phosphorylation of .beta.-catenin by casein kinase 1 (CK1) and
then glycogen synthase kinase 3 (GSK3). This process leads to the
ubiquitination and proteosomal degradation of .beta.-catenin. As a
result, in the absence of WNT signaling, cells maintain low
cytoplasmic and nuclear .beta.-catenin levels. Some .beta.-catenin
is spared from proteosomal degradation through an association with
cadherins at the plasma membrane (Nelson et al., Science, 303,
1483-1487, 2004).
[0097] .beta.-catenin expression is involved in maintaining the
balance between stem cell proliferation and stem cell
differentiation (Chenn and Walsh, Science, 297:365-369, 2002). A
role for .beta.-catenin in the development of mouse auditory
epithelia has also been described and it has been shown that
.beta.-catenin expression was linked with auditory epithelia
development in mouse models (Takebayashi et al., Acta. Otolaryngol
Suppl., 551:18-21, 2004). Other studies also support a role for
.beta.-catenin in promoting cell proliferation in the developing
auditory epithelia of mice (Takebyashi et al., Neuroreport,
16:431-434, 2005; Warchol, J. Neurosci., 22:2607-2616, 2002) and
rat utricles (Kim et al., Acta. Otolaryngol Suppl., 551:22-25,
2004). A further study performed in rat embryos also reports that
suppression of .beta.-catenin using antisense technology reduced
the number of cells in the otic cup, which the authors concluded
demonstrated that .beta.-catenin plays a role in cell proliferation
in the otic placodes and in differentiation in acoustic neurons
within the acoustic neural crest complex (Matsuda and Keino, Anat.
Embryol. (Berl)., 202:39-48, 2000). In addition, it is reported
that the Wnt/.beta.-catenin pathway is involved in defining and
maintaining the sensory/neurosensory boundaries in the cochlea duct
(Stevens et al., Dev. Biol., 261:149-164, 2003). Together,
previously published data indicated that .beta.-catenin is involved
in promoting stem cell proliferation, not differentiation.
Methods of Treatment
[0098] In some embodiments, the present disclosure provides novel
therapeutic strategies for treating diseases that would benefit
from an increase in Atoh1 expression and/or activity. In some
embodiments, such strategies can promote an increase in the levels
(e.g., protein levels) and/or activity (e.g., biological activity)
of .beta.-catenin in target cells, thereby promoting
differentiation of a target cell to or towards a mature cell of the
inner ear, e.g., an auditory hair cell. Alternatively or in
addition, the strategies can promote an increase in the levels
(e.g. protein levels) and/or activity (e.g., biological activity)
of .beta.-catenin in the nucleus of target cells, thereby promoting
differentiation of a target cell to or towards a mature cell of the
inner ear, e.g., an auditory hair cell.
[0099] In some embodiments, the methods and compositions described
herein promote differentiation of target cells to or towards mature
cells of the inner ear, e.g., auditory hair cells without promoting
substantial cellular proliferation. In some embodiments, 0, 0.5, 1,
3, 5, 10, 15, 20, 25, 30, 40, or 50% of the target cells undergo
proliferation upon treatment with the methods and compositions
described herein.
[0100] Compositions and Methods for Modulating .beta.-Catenin
Expression
[0101] In some embodiments, the present disclosure includes the use
of compounds, compositions (referred to collectively herein as
.beta.-catenin modulating compounds) and methods that increase the
levels (e.g., protein levels) and/or activity (e.g., biological
activity) of .beta.-catenin in target cells. Exemplary
.beta.-catenin modulating compounds and methods include, but are
not limited to compositions and methods for increasing
.beta.-catenin expression (e.g., transcription and/or translation)
or levels (e.g., concentration) in target cells include the use
of:
[0102] (i) DNA encoding .beta.-catenin. .beta.-catenin can be
expressed using one or more expression constructs. Such expression
constructs include, but are not limited to, naked DNA, viral, and
non-viral expression vectors). Exemplary .beta.-catenin nucleic
acid sequences that may be usefully expressed include, but are not
limited to, for example, NM_001098209 (e.g., NM_001098209.1),
GI:148233337, NM_001904 (e.g., NM_001904.3), GI:148228165,
NM_001098210 (e.g., NM_001098210.1), GI:148227671, NM_007614 (e.g.,
NM_007614.2), GI:31560726, NM_007614 (e.g., NM_007614.2), and
GI:31560726.
[0103] In some embodiments, .beta.-catenin nucleic acid can include
nucleic acid encoding .alpha.-catenin (e.g., NM_001903.2),
.delta.-catenin (e.g., NM_001085467.1 (.delta.1) and NM_01332.2
(S2)), and .gamma.-catenin (e.g., AY243535.1 and GI:29650758)
[0104] In some embodiments, DNA encoding .beta.-catenin can be an
unmodified wild type sequence. Alternatively, DNA encoding
.beta.-catenin can be modified using standard molecular biological
techniques. For example, DNA encoding .beta.-catenin can be altered
or mutated, e.g., to increase the stability of the DNA or resulting
polypeptide. Polypeptides resulting from such altered DNAs will
retain the biological activity of wild type .beta.-catenin. In some
embodiments, DNA encoding .beta.-catenin can be altered to increase
nuclear translocation of the resulting polypeptide. In some
embodiments, DNA encoding .beta.-catenin can be modified using
standard molecular biological techniques to include an additional
DNA sequence that can encode one or more of, e.g., detectable
polypeptides, signal peptides, and protease cleavage sites.
[0105] (ii) .beta.-catenin encoding polypeptides. Exemplary useful
.beta.-catenin polypeptides include, but are not limited to, for
example, NP_001091679 (e.g., NP_001091679.1), GI:148233338,
NP_001895 (e.g., NP_001895.1), GI:4503131, NP_001091680 (e.g.,
NP_001091680.1), GI:148227672, NP_031640 (e.g., NP_031640.1), and
GI:6671684. Such .beta.-catenin encoding polypeptides can be used
in combination with compositions to enhance uptake of the
polypeptides into biological cells. In some embodiments,
.beta.-catenin encoding polypeptides can be mutated to include
amino acid sequences that enhance uptake of the polypeptides into a
biological cell. In some embodiments, .beta.-catenin encoding
polypeptides can be altered or mutated to increase the stability
and/or activity of the polypeptide (e.g., .beta.-catenin point
mutants. In some embodiments, .beta.-catenin encoding polypeptides
can be altered to increase nuclear translocation of the
polypeptide. In some embodiments, altered polypeptides will retain
the biological activity of wild type .beta.-catenin.
[0106] In some embodiments, useful .beta.-catenin nucleic acid
sequences and .beta.-catenin encoding polypeptides include modified
.beta.-catenin nucleic acid sequences and .beta.-catenin encoding
polypeptides. Such modified .beta.-catenin nucleic acid sequences
and .beta.-catenin encoding polypeptides can be nucleic acids
and/or polypeptide having sequences that are substantially
identical to the nucleic acid or amino acid sequences of
NM_001098209 (e.g., NM_001098209.1), GI:148233337, NM_001904 (e.g.,
NM_001904.3), GI:148228165, NM_001098210 (e.g., NM_001098210.1),
GI:148227671, NM_007614 (e.g., NM_007614.2), GI:31560726, NM_007614
(e.g., NM_007614.2), GI:31560726, NP_001091679 (e.g.,
NP_001091679.1), GI:148233338, NP_001895 (e.g., NP_001895.1),
GI:4503131, NP_001091680 (e.g., NP_001091680.1), GI:148227672,
NP_031640 (e.g., NP_031640.1), and GI:6671684. In some embodiments,
useful .beta.-catenin nucleic acid sequences can be 50%, 60%, 70%,
80%, 85%, 90%, 95%, 98%, 99%, or 100% homologous to NM_001098209
(e.g., NM_001098209.1), GI:148233337, NM_001904 (e.g.,
NM_001904.3), GI:148228165, NM_001098210 (e.g., NM_001098210.1),
GI:148227671, NM_007614 (e.g., NM_007614.2), GI:31560726, NM_007614
(e.g., NM_007614.2), and GI:31560726. In some embodiments, useful
.beta.-catenin encoding polypeptides sequences can be 50%, 60%,
70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% homologous to
NP_001091679 (e.g., NP_001091679.1), GI:148233338, NP_001895 (e.g.,
NP_001895.1), GI:4503131, NP_001091680 (e.g., NP_001091680.1),
GI:148227672, NP_031640 (e.g., NP_031640.1), and GI:6671684. In
some embodiments, molecules encoded by useful modified
.beta.-catenin nucleic acid sequences and .beta.-catenin encoding
polypeptide sequences will possess at least a portion of the
activity (e.g., biological activity) of the molecules encoded by
the corresponding, e.g., unmodified .beta.-catenin nucleic acid
sequences and .beta.-catenin encoding polypeptide sequences. For
example, molecules encoded by modified .beta.-catenin nucleic acid
sequences and .beta.-catenin encoding polypeptides can retain 50%,
60%, 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% of the activity
(e.g., biological activity) of the molecules encoded by the
corresponding, e.g., unmodified .beta.-catenin nucleic acid
sequences and .beta.-catenin encoding polypeptide sequences. The
methods required to assess the activity of .beta.-catenin or a
.beta.-catenin-like molecule are described herein.
[0107] 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). In a
preferred embodiment, the length of a reference sequence aligned
for comparison purposes is at least 30%, preferably at least 40%,
more preferably at least 50%, even more preferably at least 60%,
and even more preferably at least 70%, 80%, 90%, or 100% of the
length of the reference sequence. 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 determination of percent
identity between two amino acid sequences is accomplished using the
BLAST 2.0 program. Sequence comparison is performed using an
ungapped alignment and using the default parameters (Blossom 62
matrix, gap existence cost of 11, per residue gapped cost of 1, and
a lambda ratio of 0.85). The mathematical algorithm used in BLAST
programs is described in Altschul et al. (Nucleic Acids Res.
25:3389-3402, 1997). Useful .beta.-catenin encoding polypeptide
sequences or polypeptide fragments can have up to about 20 (e.g.,
up to about 10, 5, or 3) amino acid deletions, additions, or
substitutions, such as conservative substitutions, to be useful for
the compositions and methods described herein. Conservative amino
acid substitutions are known in the art.
[0108] (iii) Wnt/.beta.-catenin pathway agonists. In some
embodiments, .beta.-catenin levels (e.g., protein levels) and/or
activity (e.g., biological activity) can be modulated (e.g.,
increased) using compounds or compositions that target one or more
components of the WNT/.beta.-catenin pathway. For example, suitable
compounds or compositions can target two, three, four, five or more
components of the WNT/.beta.-catenin pathway. In some embodiments,
components with opposing effects on .beta.-catenin levels (e.g.,
protein levels) and/or activity (e.g., biological activity) can be
targeted. For example, a first component that increases
.beta.-catenin levels (e.g., protein levels) and/or activity (e.g.,
biological activity) can be targeted in combination with a second
target that inhibits .beta.-catenin levels (e.g., protein levels)
and/or activity (e.g., biological activity). In this example, the
first target would be activated and the second target would be
inhibited.
[0109] Exemplary useful .beta.-catenin pathway agonists increase
.beta.-catenin expression (e.g., transcription and/or translation),
levels (e.g., concentration), or activity by acting on one or more
components of the Wnt/.beta.-catenin signaling pathway. For
example, suitable Wnt/.beta.-catenin pathway agonists can act
indirectly (e.g., on upstream modulators or inhibitors
of.beta.-catenin or on components of cellular transcription
machinery), by increasing the stability of .beta.-catenin (e.g., by
decreasing the degradation of .beta.-catenin, such as through the
inhibition of casein kinase 1 (CK1) and glycogen synthase kinase
3.beta. (GSK3.beta.)), and/or by promoting the release of
sequestered endogenous intracellular .beta.-catenin. Exemplary
Wnt/.beta.-catenin pathway agonists include, but are not limited
to, e.g., Wnt ligands, DSH/DVL1, 2, 3, LRP6AN, WNT3A, WNTSA, and
WNT3A, 5A. Additional Wnt/.beta.-catenin pathway activators and
inhibitors are reviewed in the art (Moon et al., Nature Reviews
Genetics, 5:689-699, 2004). In some embodiments, suitable
Wnt/.beta.-catenin pathway agonists can include antibodies and
antigen binding fragments thereof, and peptides that bind
specifically to frizzled (Fzd) family of receptors.
[0110] (iv) Kinase inhibitors, e.g., casein kinase 1 (CK1) and
glycogen synthase kinase 3.beta. (GSK3.beta.) inhibitors. In some
embodiments, useful kinase inhibitors can increase .beta.-catenin
levels by reducing the degradation of .beta.-catenin. In some
embodiments, exemplary useful kinase inhibitors, e.g., GSK3.beta.
inhibitors include, but are not limited to, lithium chloride
(LiCl), Purvalanol A, olomoucine, alsterpaullone, kenpaullone,
benzyl-2-methyl-1,2,4-thiadiazolidine-3,5-dione (TDZD-8),
2-thio(3-iodobenzyl)-5-(1-pyridyl)-[1,3,4]-oxadiazole (GSK3
inhibitor II), 2,4-dibenzyl-5-oxothiadiazolidine-3-thione (OTDZT),
(2'Z,3'E)-6-Bromoindirubin-3'-oxime (BIO),
.alpha.-4-Dibromoacetophenone (i.e., Tau Protein Kinase I (TPK I)
Inhibitor), 2-Chloro-1-(4,5-dibromo-thiophen-2-yl)-ethanone,
N-(4-Methoxybenzyl)-N'-(5-nitro-1,3-thiazol-2-yl)urea (AR-A014418),
and indirubins (e.g., indirubin-5-sulfonamide; indirubin-5-sulfonic
acid (2-hydroxyethyl)-amide indirubin-3'-monoxime;
5-iodo-indirubin-3'-monoxime; 5-fluoroindirubin; 5,
5'-dibromoindirubin; 5-nitroindirubin; 5-chloroindirubin;
5-methylindirubin, 5-bromoindirubin),
4-Benzyl-2-methyl-1,2,4-thiadiazolidine-3,5-dione (TDZD-8),
2-thio(3-iodobenzyl)-5-(1-pyridyl)-[1,3,4]-oxadiazole (GSK3
inhibitor II), 2,4-Dibenzyl-5-oxothiadiazolidine-3-thione (OTDZT),
(2'Z,3'E)-6-Bromoindirubin-3'-oxime (BIO),
.alpha.-4-Dibromoacetophenone (i.e., Tau Protein Kinase I (TPK I)
Inhibitor), 2-Chloro-1-(4,5-dibromo-thiophen-2-yl)-ethanone, (vi)
N-(4-Methoxybenzyl)-N'-(5-nitro-1,3-thiazol-2-yl)urea (AR-A014418),
and H-KEAPPAPPQSpP-NH2 (L803) (SEQ ID NO: 40) or its cell-permeable
derivative Myr-N-GKEAPPAPPQSpP-NH2 (L803-mts) (SEQ ID NO: 41).
Other GSK3.beta. inhibitors are disclosed in U.S. Pat. Nos.
6,417,185; 6,489,344; 6,608,063 and Published U.S. Applications
Nos. 690497, filed Oct. 20, 2003; 468605, filed Aug. 19, 2003;
646625, filed Aug. 21, 2003; 360535, filed Feb. 6, 2003; 447031,
filed May 28, 2003; and 309535 filed Dec. 3, 2002. In some
embodiments, suitable kinase inhibitors can include RNAi and siRNA
designed to decrease GSK3.beta. and/or CK1 protein levels. In some
embodiments, useful kinase inhibitors include FGF pathway
inhibitors. In some embodiments, FGF pathway inhibitors include,
for example, SU5402.
[0111] (v) Protease inhibitors and Proteasome inhibitors. In some
embodiments, useful protease inhibitors can increase .beta.-catenin
levels by reducing the degradation of .beta.-catenin. Suitable
protease inhibitors are known in the art (see e.g., Shargel et al.,
Comprehensive Pharmacy Review, Fifth Edition, published by
Lippincott Williams, and Wilkins, at, e.g., pages 373 and 872-874).
In some embodiments, useful protease inhibitors can include, for
example, natural protease inhibitors, synthetic protease
inhibitors, antiretroviral protease inhibitors, and protease
inhibitor cocktails.
[0112] In some embodiments, useful protease inhibitors can include
inhibitors of the proteasome or proteasome inhibitors. Suitable
proteasome inhibitors include, but are not limited to, for example,
Velcade.RTM. (e.g., bortezomib, Millenium Pharmaceuticals), MG132
(Calbiochem), lactacystin (Calbiochem), and proteasome inhibitor
(PSI). In some embodiments, useful protease inhibitors can include
inhibitors of the ubiquitin pathway.
[0113] (vi) Any combination of (i)-(v).
[0114] (vii) Any combination of (i)-(v) in combination with an
inhibitor of the Notch signaling pathway, e.g., a gamma-secretase
inhibitor or inhibitory nucleic acid. Exemplary gamma secretase
inhibitors include, but are not limited to, e.g., arylsulfonamides,
dibenzazepines, benzodiazepines,
N-[N-(3,5-difluorophenacetyl)-L-alanyl]-(S)-phenylglycine t-butyl
ester (DAPT), L-685,458, or MK0752. Other exemplary Notch pathway
inhibitors and methods for identifying inhibitors of the Notch
signaling pathway are disclosed in, e.g., PCT/US2007/084654, U.S.
P.G. Pub. No. 2005/0287127, and U.S. application Ser. No.
61/027,032.
[0115] In some embodiments, the present disclosure provides methods
whereby:
[0116] (a) one or more .beta.-catenin modulating compounds are
administered to a subject, e.g., to the ear of a subject (direct
therapy);
[0117] (b) one or more target cells are contacted, e.g., in vitro,
with one or more .beta.-catenin modulating compounds to promote
complete or partial conversion (e.g., differentiation) of those
cells to or toward a mature cell type, e.g., a hair cell.
[0118] (c) one or more target cells that have been treated
according to method (b) (e.g., one or more cells resulting from
method (b)) is administered to a subject, e.g., to the ear of a
subject (cell therapy); and
[0119] (d) methods whereby one or more target cells that have been
treated according to method (b) (e.g., one or more cells resulting
from method (b)) are administered to a subject in combination with
one or more .beta.-catenin modulating compounds administered to a
subject, e.g., to the ear of a subject (combination therapy).
[0120] Subject Selection
[0121] 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 imbalance 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.
[0122] The importance of Atoh1 in hair cell genesis is well
documented. For example, Atoh1 is required for hair cell
development and the differentiation of inner ear progenitor cells
to inner ear support cells and/or hair cells (Bermingham et al.,
Science, 284:1837-1841, 1999). In addition, adenovirus mediated
Math1 overexpression in the endolymph of the mature guinea pig
results in the differentiation of non-sensory cells in the mature
cochlea into immature hair cells (Kawamoto et al., The Journal of
Neuroscience, 23:4395-4400, 2003;). The implications of these
studies are twofold. First, they demonstrate that non-sensory cells
of the mature cochlea retain the ability to differentiate into
sensory cells, e.g., hair cells. Second, they demonstrate that
Math1 overexpression is necessary and sufficient to direct hair
cell differentiation from non-sensory cells. A later study
furthered these findings by demonstrating that adenovirus mediated
Atoh1 overexpression induces hair cell regeneration and
substantially improves hearing thresholds in an experimentally
deafened animal model (Izumikawa et al., Nat. Med., 11:271-276,
2005).
[0123] In some embodiments, the methods, compounds, and
compositions described herein can be used for treating subjects who
have, or who are at risk for developing, an auditory disorder
resulting from a loss of auditory hair cells, e.g., sensorineural
hair cell loss.
[0124] Subjects with sensorineural hair cell loss experience the
degeneration of cochlea hair cells, which frequently results in the
loss of spiral ganglion neurons in regions of hair cell loss. Such
subjects may also experience loss of supporting cells in the organ
of Corti, and degeneration of the limbus, spiral ligament, and
stria vascularis in the temporal bone material.
[0125] In some embodiments, the present invention can be used to
treat hair cell loss and any disorder that arises as a consequence
of cell loss in the ear, such as hearing impairments, deafness, and
vestibular disorders, for example, by promoting differentiation
(e.g., complete or partial differentiation) of one or more cells
into one or more cells capable of functioning as sensory cells of
the ear, e.g., hair cells.
[0126] In some embodiments, the methods include steps of selecting
a subject at risk of hair cell loss and/or a subject with hair cell
loss. Alternatively or in addition, the methods include steps of
selecting a subject at risk of sensorineural hearing loss and/or a
subject 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.
[0127] In some embodiments, the subject can have sensorineural
hearing loss, which results from damage or malfunction of the
sensory part (the cochlea) or the neural part (the auditory nerve)
of the ear, or conductive hearing loss, which is caused by blockage
or damage in the outer and/or middle ear. Alternatively or in
addition, the subject can have mixed hearing loss caused by a
problem in both the conductive pathway (in the outer or middle ear)
and in the nerve pathway (the inner ear). An example of a mixed
hearing loss is a conductive loss due to a middle-ear infection
combined with a sensorineural loss due to damage associated with
aging.
[0128] In some embodiments, the subject can be deaf or have a
hearing loss for any reason, or as a result of any type of event.
For example, a subject can be deaf because of a genetic or
congenital defect; for example, a human subject can have been deaf
since birth, or can be deaf or hard-of-hearing as a result of a
gradual loss of hearing due to a genetic or congenital defect. In
another example, a human subject can be deaf or hard-of-hearing as
a result of a traumatic event, such as a physical trauma to a
structure of the ear, or a sudden loud noise, or a prolonged
exposure to loud noises. For example, prolonged exposures to
concert venues, airport runways, and construction areas can cause
inner ear damage and subsequent hearing loss.
[0129] In some embodiments, a subject can experience
chemical-induced ototoxicity, wherein ototoxins include therapeutic
drugs including antineoplastic agents, salicylates, quinines, and
aminoglycoside antibiotics, contaminants in foods or medicinals,
and environmental or industrial pollutants.
[0130] In some embodiments, a subject can have a hearing disorder
that results from aging. Alternatively or in addition, the subject
can have tinnitus (characterized by ringing in the ears).
[0131] In some embodiments, a subject suitable for the treatment
using the methods and .beta.-catenin modulating compounds featured
in this disclosure can include a subject having a vestibular
dysfunction, including bilateral and unilateral vestibular
dysfunction. 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
dysfunction 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. Vestibular dysfunction
is most commonly tested by measuring individual symptoms of the
disorder (e.g., vertigo, nausea, and fuzzy vision).
[0132] In some embodiments, the methods and .beta.-catenin
modulating compounds provided herein can be used prophylactically,
such as to prevent hearing loss, deafness, or other auditory
disorders associated with loss of inner ear function. For example,
a composition containing one or more compounds can be administered
with a second therapeutic, such as a therapeutic that may affect a
hearing disorder. Such 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 human undergoing
chemotherapy can be treated using 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 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 can be
administered by different routes of administration.
[0133] In some embodiments, the treatment of auditory hair cell
loss includes steps whereby one or more .beta.-catenin modulating
compounds are administered to a subject to promote the formation of
auditory hair cells (e.g., an inner ear and/or outer ear hair
cells) and/or increase the number of hair cells (e.g., an inner ear
and/or outer ear hair cells) in the ear of a subject by promoting
complete or partial hair cell differentiation from non-hair cell
types naturally present in the inner ear of a subject. This method
of treatment is referred to as direct therapy.
[0134] In some embodiments, the treatment of auditory hair cell
loss includes steps whereby one or more target cells are contacted,
e.g., in vitro, with one or more .beta.-catenin modulating
compounds to promote complete or partial differentiation of those
cells to or toward a mature cell type of the inner ear, e.g., a
hair cell (e.g., an inner ear and/or outer ear hair cell).
[0135] Alternatively or in addition, the methods include steps
whereby one or more target cells that have been contacted with one
or more .beta.-catenin modulating compounds, e.g., in vitro, are
administered to the ear (e.g., the inner ear) of the subject. This
method of therapy is referred to as cell therapy.
[0136] In some embodiments, the methods include steps whereby one
or more target cells that have been contacted with one or more
.beta.-catenin modulating compounds, e.g., in vitro are
administered to the ear (e.g., inner ear) of a subject in
combination with one or more .beta.-catenin modulating compounds.
This method of treatment is referred to as combination therapy.
[0137] In general, 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.
[0138] Where appropriate, following treatment, the human 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 human 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) and play audiometry
for children older than 3 years. Oto-acoustic emission testing can
be used to test the functioning of the cochlea 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.
Routes of Administration
[0139] Direct Therapy
[0140] The route of administration will vary depending on the
disease being treated. Hair cell loss, sensorineural hearing loss,
and vestibular disorders can be treated using direct therapy using
systemic administration and/or local administration. In some
embodiments, the route of administration can be determined by a
subject's health care provider or clinician, for example following
an evaluation of the subject. In some embodiments, a individual
subject's therapy may be customized, e.g., one or more
.beta.-catenin modulating compounds, the routes of administration,
and the frequency of administration can be personalized.
Alternatively, therapy may be performed using a standard course of
treatment, e.g., using one or more pre-selected .beta.-catenin
modulating compounds and pre-selected routes of administration and
frequency of administration.
[0141] In some embodiments, one or more .beta.-catenin modulating
compounds can be administered to a subject, e.g., a subject
identified as being in need of treatment for hair cell loss, 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; rectal
administration, e.g., a rectal suppository or enema; a vaginal
suppository; a urethral suppository; transdermal routes of
administration; and inhalation (e.g., nasal sprays).
[0142] Alternatively or in addition, one or more .beta.-catenin
modulating compounds can be administered to a subject, e.g., a
subject identified as being in need of treatment for hair cell
loss, using a 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.
[0143] In some embodiments, one or more .beta.-catenin modulating
compounds 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, one or
more .beta.-catenin modulating compounds can be administered by
intratympanic injection (e.g., into the middle ear), 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.
[0144] In another mode of administration, one or more
.beta.-catenin modulating compounds 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.
[0145] Alternatively or in addition, one or more compounds 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).
[0146] In some embodiments, the modes of administration described
above may be combined in any order and can be simultaneous or
interspersed.
[0147] Alternatively or in addition, the present invention may 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).
[0148] .beta.-catenin Expression Constructs
[0149] In some aspects, .beta.-catenin can be expressed using
expression constructs, e.g., naked DNA constructs, DNA vector based
constructs, and/or viral vector and/or viral based constructs.
[0150] The present application also provides such expression
constructs formulated as a pharmaceutical composition, e.g., for
administration to a subject. Such pharmaceutical compositions are
not limited to one expression construct and rather can include two
or more expression constructs (e.g., two, three, four, five, six,
seven, eight, nine, ten or more expression constructs).
[0151] Naked DNA constructs and the therapeutic use of such
constructs are well known to those of skill in the art (see, e.g.,
Chiarella et al., Recent Patents Anti-Infect. Drug Disc.,3:93-101,
2008; Gray et al., Expert Opin. Biol. Ther., 8:911-922, 2008;
Melman et al., Hum. Gene Ther., 17:1165-1176, 2008). Typically,
naked DNA constructs include one or more therapeutic nucleic acids
(e.g., DNA encoding .beta.-catenin) and a promoter sequence. A
naked DNA construct can be a DNA vector, commonly referred to as
pDNA. Naked DNA typically do not incorporate into chromosomal DNA.
Generally, naked DNA constructs do not require, or are not used in
conjunction with, the presence of lipids, polymers, or viral
proteins. Such constructs may also include one or more of the
non-therapeutic components described herein.
[0152] DNA vectors are known in the art and typically are circular
double stranded DNA molecules. DNA vectors usually range in size
from three to five kilo-base pairs (e.g., including inserted
therapeutic nucleic acids). Like naked DNA, DNA vectors can be used
to deliver and express one or more therapeutic proteins in target
cells. DNA vectors do not incorporate into chromosomal DNA.
[0153] Generally, DNA vectors include at least one promoter
sequence that allows for replication in a target cell. Uptake of a
DNA vector may be facilitated (e.g., improved) by combining the DNA
vector with, for example, a cationic lipid, and forming a DNA
complex.
[0154] Also useful are viral vectors, which are also well known to
those of skill in the art. Typically, viral vectors are double
stranded circular DNA molecules that are derived from a virus.
Viral vectors are typically larger in size than naked DNA and DNA
vector constructs and have a greater capacity for the introduction
of foreign (i.e., not virally encoded) genes. Like naked DNA and
DNA vectors, viral vectors can be used to deliver and express one
or more therapeutic nucleic acids in target cells. Unlike naked DNA
and DNA vectors, certain viral vectors stably incorporate
themselves into chromosomal DNA.
[0155] Typically, viral vectors include at least one promoter
sequence that allows for replication of one or more vector encoded
nucleic acids, e.g., a therapeutic nucleic acid, in a host cell.
Viral vectors may optionally include one or more non-therapeutic
components described herein. Advantageously, uptake of a viral
vector into a target cell does not require additional components,
e.g., cationic lipids. Rather, viral vectors transfect or infect
cells directly upon contact with a target cell.
[0156] The approaches described herein include the use of
retroviral vectors, adenovirus-derived vectors, and/or
adeno-associated viral vectors as recombinant gene delivery systems
for the transfer of exogenous genes in vivo, particularly into
humans. Protocols for producing recombinant retroviruses and for
infecting cells in vitro or in vivo with such viruses can be found
in Current Protocols in Molecular Biology, Ausubel, F. M. et al.
(eds.) Greene Publishing Associates, (1989), Sections 9.10-9.14,
and other standard laboratory manuals.
[0157] 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. Suitable adenoviral vectors derived from the
adenovirus strain Ad type 5 d1324 or other strains of adenovirus
(e.g., Ad2, Ad3, Ad7 etc.) are known to those skilled in the art.
Recombinant adenoviruses can be advantageous in certain
circumstances in that they are not capable of infecting nondividing
cells and can be used to infect a wide variety of cell types,
including epithelial cells (Rosenfeld et al. (1992) cited 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. cited supra; Haj-Ahmand and Graham, J. Virol.,
57:267, 1986).
[0158] 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. Skilled practitioners will appreciate that the use of any
number of viral vectors in the presently described methods is
possible.
[0159] All the molecular biological techniques required to generate
an expression construct described herein are standard techniques
that will be appreciated by one of skill in the art. Detailed
methods may also be found, e.g., Current Protocols in Molecular
Biology, Ausubel et al. (eds.) Greene Publishing Associates,
(1989), Sections 9.10-9.14 and other standard laboratory manuals.
DNA encoding altered .beta.-catenin can be generated using, e.g.,
site directed mutagenesis techniques.
[0160] Polypeptides Encoding .beta.-Catenin
[0161] Polypeptides encoding .beta.-catenin can be generated using
recombinant techniques or using chemical synthesis. Methods for
generating such polypeptides, and the methods required for the
purification of such polypeptides will be appreciated by one of
skill in the art.
[0162] Pharmaceutical Compositions
[0163] In some embodiments, one or more .beta.-catenin modulating
compounds can be formulated as a pharmaceutical composition.
Pharmaceutical compositions containing one or more .beta.-catenin
modulating compounds can be formulated according to the intended
method of administration.
[0164] One or more .beta.-catenin modulating compounds can be
formulated as pharmaceutical compositions for direct administration
to a subject. Pharmaceutical compositions containing one or more
compounds can be formulated in a conventional manner using one or
more physiologically acceptable carriers or excipients. For
example, a pharmaceutical composition can be formulated for local
or systemic administration, e.g., administration by drops or
injection into the ear, insufflation (such as into the ear),
intravenous, topical, or oral administration.
[0165] The nature of the pharmaceutical compositions for
administration is dependent on the mode of administration and can
readily be determined by one of ordinary skill in the art. In some
embodiments, the pharmaceutical composition is sterile or
sterilizable. The therapeutic compositions featured in the
invention can contain carriers or excipients, many of which are
known to skilled artisans. Excipients that can be used include
buffers (for example, citrate buffer, phosphate buffer, acetate
buffer, and bicarbonate buffer), amino acids, urea, alcohols,
ascorbic acid, phospholipids, polypeptides (for example, serum
albumin), EDTA, sodium chloride, liposomes, mannitol, sorbitol,
water, and glycerol. The nucleic acids, polypeptides, small
molecules, and other modulatory compounds featured in the invention
can be administered by any standard route of administration. For
example, administration can be parenteral, intravenous,
subcutaneous, or oral.
[0166] A pharmaceutical composition can be formulated in various
ways, according to the corresponding route of administration. For
example, liquid solutions can be made for administration by drops
into the ear, for injection, or for ingestion; gels or powders can
be made for ingestion or topical application. Methods for making
such formulations are well known and can be found in, for example,
Remington's Pharmaceutical Sciences, 18th Ed., Gennaro, ed., Mack
Publishing Co., Easton, Pa., 1990.
[0167] One or more .beta.-catenin modulating compounds can be
administered, e.g., as a pharmaceutical composition, directly
and/or locally by injection or through surgical placement, e.g., to
the inner ear. The amount of the pharmaceutical composition may be
described as the effective amount or the amount of a cell-based
composition may be described as a therapeutically effective amount.
Where application over a period of time is advisable or desirable,
the compositions of the invention can be placed in sustained
released formulations or implantable devices (e.g., a pump).
[0168] Alternatively or in addition, the pharmaceutical
compositions can be formulated for systemic parenteral
administration by injection, for example, by bolus injection or
continuous infusion. Such formulations can be presented in unit
dosage form, for example, in ampoules or in multi-dose containers,
with an added preservative. The compositions may take such forms as
suspensions, solutions or emulsions in oily or aqueous vehicles,
and may contain formulatory agents such as suspending, stabilizing
and/or dispersing agents. Alternatively, the active ingredient may
be in powder form for constitution with a suitable vehicle, for
example, sterile pyrogen-free water, before use.
[0169] In addition to the formulations described previously, the
compositions can also be formulated as a depot preparation. Such
long acting formulations can be administered by implantation (e.g.,
subcutaneously). Thus, for example, the compositions can be
formulated with suitable polymeric or hydrophobic materials (for
example as an emulsion in an acceptable oil) or ion exchange
resins, or as sparingly soluble derivatives, for example, as a
sparingly soluble salt.
[0170] Pharmaceutical compositions formulated for systemic oral
administration can take the form of tablets or capsules prepared by
conventional means with pharmaceutically acceptable excipients such
as binding agents (for example, pregelatinised maize starch,
polyvinylpyrrolidone or hydroxypropyl methylcellulose); fillers
(for example, lactose, microcrystalline cellulose or calcium
hydrogen phosphate); lubricants (for example, magnesium stearate,
talc or silica); disintegrants (for example, potato starch or
sodium starch glycolate); or wetting agents (for example, sodium
lauryl sulphate). The tablets can be coated by methods well known
in the art. Liquid preparations for oral administration may take
the form of, for example, solutions, syrups or suspensions, or they
may be presented as a dry product for constitution with water or
other suitable vehicle before use. Such liquid preparations may be
prepared by conventional means with pharmaceutically acceptable
additives such as suspending agents (for example, sorbitol syrup,
cellulose derivatives or hydrogenated edible fats); emulsifying
agents (for example, lecithin or acacia); non-aqueous vehicles (for
example, almond oil, oily esters, ethyl alcohol or fractionated
vegetable oils); and preservatives (for example, methyl or
propyl-p-hydroxybenzoates or sorbic acid). The preparations may
also contain buffer salts, flavoring, coloring and sweetening
agents as appropriate. Preparations for oral administration may be
suitably formulated to give controlled release of the active
compound.
[0171] In some embodiments, the pharmaceutical compositions
described herein can include one or more of the compounds
formulated according to any of the methods described above, and one
or more cells obtained to the methods described herein.
[0172] Cell Therapy
[0173] In general, the cell therapy methods described herein 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 be transplanted or
implanted into a subject in need of such treatment. The 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 below.
[0174] Cell Selection
[0175] Target cells suitable for use in the present invention
include, but are not limited to, cells that are capable of
differentiating completely or partially into a mature cell of the
inner ear, e.g., a hair cell (e.g., an inner ear and/or outer ear
hair cell), when contacted, e.g., in vitro, with one or more
.beta.-catenin modulating compounds. Exemplary cells that are
capable of differentiating into a hair cell include, but are not
limited to stem cells (e.g., inner ear stem cells, adult stem
cells, bone marrow derived stem cells, embryonic stem cells,
mesenchymal stem cells, skin stem cells, and fat derived stem
cells), progenitor cells (e.g., inner ear progenitor cells),
support cells (e.g., Deiters' cells, pillar cells, inner phalangeal
cells, tectal cells and Hensen's cells), and/or germ cells. The use
of stem cells for the replacement of inner ear sensory cells is
described, e.g., in Li et al., (U.S. Publication No. 2005/0287127)
and Li et al., (U.S. patent Ser. No. 11/953,797). The use of bone
marrow derived stem cells for the replacement of inner ear sensory
cells is described, e.g., in Edge et al., PCT/US2007/084654.
[0176] Such suitable cells can be identified by analyzing (e.g.,
qualitatively or quantitatively) the presence of one or more tissue
specific genes. For example, gene expression can be detected by
detecting the protein product of one or more tissue-specific genes.
Protein detection techniques involve staining proteins (e.g., using
cell extracts or whole cells) using antibodies against the
appropriate antigen. In this case, the appropriate antigen is the
protein product of the tissue-specific gene expression. Although,
in principle, a first antibody (i.e., the antibody that binds the
antigen) can be labeled, it is more common (and improves
visualization) to use a second antibody directed against the first
(e.g., an anti-IgG). This second antibody is conjugated either with
fluorochromes, or appropriate enzymes for colorimetric reactions,
or gold beads (for electron microscopy), or with the biotin-avidin
system, so that the location of the primary antibody, and thus the
antigen, can be recognized.
[0177] Tissue-specific gene expression can also be assayed by
detection of RNA transcribed from the gene. RNA detection methods
include reverse transcription coupled to polymerase chain reaction
(RT-PCR), Northern blot analysis, and RNAse protection assays.
[0178] Exemplary tissue specific genes that may be used to identify
a stem cell (e.g., an undifferentiated cell) include, but are not
limited to, e.g., nestin, sox1, sox2, or musashi, NeuroD, Atoh1,
and neurogenin1. Alternatively or in addition, stem cells can be
selected based on one or more of the unique properties that such
cell types present in vitro. For example, in vitro, stem cells
often show a distinct potential for forming spheres by
proliferation of single cells. Thus, the identification and
isolation of spheres can aid in the process of isolating stem cells
from mature tissue for use in making differentiated cells of the
inner ear. For example, stem cells can be cultured in serum free
DMEM/high-glucose and F12 media (mixed 1:1), and supplemented with
N2 and B27 solutions and growth factors. Growth factors such as
EGF, IGF-1, and bFGF have been demonstrated to augment sphere
formation in culture.
[0179] Exemplary tissue specific genes that may be used to identify
a progenitor cells and/or an inner ear progenitor cell (e.g., a
less than fully differentiated or partially differentiated cell)
include but are not limited to, e.g., nestin, sox2, and musashi, in
addition to certain inner-ear specific marker genes such as Brn3c,
islet1 and Pax2
[0180] Exemplary tissue specific genes that may be used to identify
fully differentiated support cells include, but are not limited to,
e.g., p27.sub.kip, p75, S100A, Jagged-1, and Prox1.
[0181] Exemplary tissue specific genes that may be used to identify
fully differentiated cells capable of functioning as inner ear
sensory cells) include, but are not limited to, e.g., myosin VIIa,
Math1 (Atoh1), .alpha.9 acetylcholine receptor, espin, parvalbumin
3, and F-actin (phalloidin).
[0182] Alternatively or in addition, cells suspected as being fully
differentiated (e.g., cells capable of functioning as inner ear
sensory cells) may be subjected to physiological testing to
determine whether conductance channels that would be present in
mature hair cells are present and active.
[0183] Alternatively or in addition, inner ear hair cells may be
distinguished from other fully differentiated cells of the inner
ear (e.g., spiral ganglia) by analyzing the expression of markers
that are specific to spiral ganglia, which include but are not
limited to ephrinB2, ephrinB3, trkB, trkC, GATA3, and BF1. In some
embodiments, cells identified as expressing one or more markers
that are specific to spiral ganglia, e.g., ephrinB2, ephrinB3,
trkB, trkC, GATA3, and BF1 will be isolated and removed.
[0184] In some embodiments, suitable cells can be derived from a
mammal, such as a human, mouse, rat, pig, sheep, goat, or non-human
primate. For example, stem cells have been identified and isolated
from the mouse utricular macula (Li et al., Nature Medicine
9:1293-1299, 2003). The cells can also be obtained from a subject
to whom they will subsequently be readministered.
[0185] In some embodiments, target cells can be isolated from the
inner ear of an animal. More specifically, a suitable cells can be
obtained from the cochlea organ of Corti, the modiolus (center) of
the cochlea, the spiral ganglion of the cochlea, the vestibular
sensory epithelia of the saccular macula, the utricular macula, or
the cristae of the semicircular canals.
[0186] In some embodiments, target cells can be any cell that
expresses or can express Atoh1. In some embodiments, target cells
can be obtained from tissues such as bone marrow, blood, skin, or
an eye. In some embodiments, target cells can be obtained from any
tissue that expresses or can express Atoh1, for example, intestinal
tissue, skin (e.g., Merkel's cells), and cerebellum.
[0187] In some embodiments, target cells can be obtained from a
single source (e.g., the ear or a structure or tissue within the
ear) or a combination of sources (e.g., the ear and one or more
peripheral tissues (e.g., bone marrow, blood, skin, or an
eye)).
[0188] Alternatively or in addition, methods include obtaining
tissue from the inner ear of the animal, where the tissue includes
at least a portion of the utricular maculae. The animal can be a
mammal, such as a mouse, rat, pig, rabbit, goat, horse, cow, dog,
cat, primate, or human. The isolated tissue can be suspended in a
neutral buffer, such as phosphate buffered saline (PBS), and
subsequently exposed to a tissue-digesting enzyme (e.g., trypsin,
leupeptin, chymotrypsin, and the like) or a combination of enzymes,
or a mechanical (e.g., physical) force, such as trituration, to
break the tissue into smaller pieces. Alternatively, or in
addition, both mechanisms of tissue disruption can be used. For
example, the tissue can be incubated in about 0.05% enzyme (e.g.,
about 0.001%, 0.01%, 0.03%, 0.07%, or 1.0% of enzyme) for about 5,
10, 15, 20, or 30 minutes, and following incubation, the cells can
be mechanically disrupted. The disrupted tissue can be passed
through a device, such as a filter or bore pipette, that separates
a stem cell or progenitor cell from a differentiated cell or
cellular debris. The separation of the cells can include the
passage of cells through a series of filters having progressively
smaller pore size. For example, the filter pore size can range from
about 80 .mu.m or less, about 70 .mu.m or less, about 60 .mu.m or
less, about 50 .mu.m or less, about 40 .mu.m or less, about 30
.mu.m or less, about 35 .mu.m or less, or about 20 .mu.m or
less.
[0189] The cells obtained may constitute an enriched population of
stem cells and/or progenitor cells; isolation from all (or
essentially all) differentiated cells or other cellular material
within the tissue may be achieved but is not required to meet the
definition of "isolated." Absolute purity is not required. The
invention encompasses cells obtained by the isolation procedures
described herein. The cells may be mixed with a cryoprotectant and
stored or packaged into kits. Once obtained, the stem cells and/or
progenitor cells can be expanded in culture.
[0190] Where a mixed population of cells is used, the proportion of
stem cells within the test population can vary. For example, the
population can contain few stem cells (e.g., about 1-10%) a
moderate proportion of stem cells (e.g., about 10-90% (e.g., about
20, 25, 30, 40, 50, 60, 70, 75, 80, or 85% stem cells)) or many
stem cells (e.g., at least 90% of the population (e.g., 92, 94, 96,
97, 98, or 99%) can be stem cells). The cells will have the
potential to differentiate into a completely or partially
differentiated cell of the inner ear (e.g., the cell can be a
pluripotent stem cell that differentiates into a cell that
expresses one or more auditory proteins). Partially differentiated
cells are useful in the treatment methods (whether therapeutic or
prophylactic) so long as they express a sufficient number and type
of auditory-specific proteins to confer a benefit on the subject
(e.g., improved hearing).
[0191] Differentiation Methods
[0192] In general, differentiation can be promoted by contacting a
suitable target cell and/or cell population with one or more
.beta.-catenin modulating compounds for a time sufficient to
promote complete or partial conversion (e.g., differentiation) of
the target cells to or towards a mature sensory cell of the inner
ear, e.g., a hair cell.
[0193] Suitable target cells, e.g., identified according to the
methods described above, can be cultured in vitro. In general,
standard culture methods are used in the methods described herein.
Appropriate culture medium is described in the art, such as in Li
et al. Nature Medicine 9:1293-1299, 2003. The growth medium for
cultured stem cells can contain one or more or any combination of
growth factors. For example, growth media can contain leukemia
inhibitory factor (LIF), which prevents stem cells from
differentiating.
[0194] Target cells can be separated into individual well of a
culture dish and cultured. Formation of spheres (clonal floating
colonies) from the isolated cells can be monitored, and the spheres
can be amplified by disrupting them (e.g., by physically means) to
separate the cells, and the cells can be cultured again to form
additional spheres. Such cultured cells can then be contacted with
one or more .beta.-catenin modulating compounds.
[0195] Alternatively or in addition, target cells may be contacted
with one or more .beta.-catenin modulating compounds in combination
with an additional induction protocol. There are a number of
induction protocols known in the art for inducing differentiation
of stem cells with neurogenic potential into neural progenitor
cells, including growth factor treatment (e.g., treatment with EGF,
FGF, and IGF, as described herein) and neurotrophin treatment
(e.g., treatment with NT3 and BDNF, as described herein). Other
differentiation protocols are known in the art; see, e.g., Corrales
et al., J. Neurobiol. 66(13):1489-500 (2006); Kim et al., Nature
418, 50-6 (2002); Lee et al., Nat Biotechnol 18, 675-9 (2000); and
Li et al., Nat Biotechnol., 23, 215-21 (2005).
[0196] As one example of an additional induction protocol, target
cells are grown in the presence of supplemental growth factors that
induce differentiation into progenitor cells. These supplemental
growth factors are added to the culture medium. The type and
concentration of the supplemental growth factors is be adjusted to
modulate the growth characteristics of the cells (e.g., to
stimulate or sensitize the cells to differentiate) and to permit
the survival of the differentiated cells such as neurons, glial
cells, supporting cells or hair cells.
[0197] Exemplary supplementary growth factors include, but are not
limited to basic fibroblast growth factor (bFGF), insulin-like
growth factor (IGF), and epidermal growth factor (EGF).
Alternatively, the supplemental growth factors can include the
neurotrophic factors neurotrophin-3 (NT3) and brain derived
neurotrophic factor (BDNF). Concentrations of growth factors can
range from about 100 ng/mL to about 0.5 ng/mL (e.g., from about 80
ng/mL to about 3 ng/mL, such as about 60 ng/mL, about 50 ng/mL,
about 40 ng/mL, about 30 ng/mL, about 20 ng/mL, about 10 ng/mL, or
about 5 ng/mL).
[0198] Alternatively or in addition, the medium can be exchanged
for medium lacking growth factors. For example, the medium can be
serum-free DMEM/high glucose and F12 media (mixed 1:1) supplemented
with N2 and B27 solutions. Equivalent alternative media and
nutrients can also be used. Culture conditions can be optimized
using methods known in the art.
[0199] Methods for Analyzing Complete or Partial
Differentiation
[0200] Target cells that have been contacted with one or more
.beta.-catenin modulating compounds can be analyzed to determine if
complete of partial differentiation has occurred. Such a
determination can be performed by analyzing the presence or absence
of tissue specific genes, as described above (see Cell Selection).
Alternatively or in addition, a hair cell can be identified by
physiological testing to determine if the cells generate
conductance channels characteristic of mature hair or spiral
ganglion cells. Such cells can be distinguished from spiral ganglia
cells using the markers described above.
[0201] Secondary assays can be used to confirm, or provide
additional evidence, that a cell has differentiated into a cell of
the inner ear. For example, a gene useful as a marker for
identifying a cell of the inner ear can be expressed exclusively in
a particular cell type (e.g., exclusively in a hair cell or
exclusively in cells of the spiral ganglion), or the cell may also
be expressed in a few other cell types (preferably not more than
one, two, three, four, or five other cell types). For example,
ephrinB1 and ephrinB2 are expressed in spiral ganglion cells, and
also in retinal cells. Thus detection of ephrinB1 or ephrinB2
expression is not definitive proof that a stem cell has
differentiated into a cell of the spiral ganglion. Secondary assays
can be used to confirm that a cell has developed into a cell of the
spiral ganglion. Such assays include detection of multiple genes
known to be expressed in the suspected cell type. For example, a
cell that expresses ephrinB1 and/or ephrinB2, can also be assayed
for expression of one or more of GATA3, trkB, trkC, BF1, FGF10,
FGF3, CSP, GFAP, and Islet1. A determination that these additional
genes are expressed is additional evidence that a stem cell has
differentiated into a spiral ganglion cell.
[0202] Secondary assays also include detection of the absence of
gene expression or the absence of proteins that are not typically
expressed in hair cells. Such negative markers include the
pan-cytokeratin gene, which is not expressed in mature hair cells
but is expressed in supporting cells of the inner ear (Li et al.,
Nature Medicine 9:1293-1299, 2003).
[0203] Cells that are confirmed to have undergone complete or
partial differentiation towards a inner ear sensory cell, e.g., a
hair cell can be transplanted or implanted into a subject.
[0204] Implantation Methods
[0205] Partially and/or fully differentiated cells, e.g., generated
by the methods described above, can be transplanted or implanted,
such as in the form of a cell suspension, into the ear by
injection, such as into the luminae of the cochlea. Injection can
be, for example, through the round window of the ear or through the
bony capsule surrounding the cochlea. The cells can be injected
through the round window into the auditory nerve trunk in the
internal auditory meatus or into the scala tympani.
[0206] To improve the ability of transplanted or implanted cells to
engraft, cells can be modified prior to differentiation. For
example, the cells can be engineered to overexpress one or more
anti-apoptotic genes in the progenitor or differentiated cells. The
Fak tyrosine kinase or Akt genes are candidate anti-apoptotic genes
that can be useful for this purpose; overexpression of FAK or Akt
can prevent cell death in spiral ganglion cells and encourage
engraftment when transplanted into another tissue, such as an
explanted organ of Corti (see for example, Mangi et al., Nat. Med.
9:1195-201, 2003). Neural progenitor cells overexpressing
.alpha..sub.v.beta..sub.3 integrin may have an enhanced ability to
extend neurites into a tissue explant, as the integrin has been
shown to mediate neurite extension from spiral ganglion neurons on
laminin substrates (Aletsee et al., Audiol. Neurootol. 6:57-65,
2001). In another example, ephrinB2 and ephrinB3 expression can be
altered, such as by silencing with RNAi or overexpression with an
exogenously expressed cDNA, to modify EphA4 signaling events.
Spiral ganglion neurons have been shown to be guided by signals
from EphA4 that are mediated by cell surface expression of
ephrin-B2 and -B3 (Brors et al., J. Comp. Neurol. 462:90-100,
2003). Inactivation of this guidance signal may enhance the number
of neurons that reach their target in an adult inner ear. Exogenous
factors such as the neurotrophins BDNF and NT3, and LIF can be
added to tissue transplants to enhance the extension of neurites
and their growth towards a target tissue in vivo and in ex vivo
tissue cultures. Neurite extension of sensory neurons can be
enhanced by the addition of neurotrophins (BDNF, NT3) and LIF
(Gillespie et al., NeuroReport 12:275-279, 2001).
[0207] In some embodiments, the cells described herein can be used
in a cochlea implant, for example, as described in Edge et al.,
(U.S. Publication No. 2007/0093878). A cochlea implant is an
electronic device that is used to improve hearing in humans who
have experienced hearing loss, particularly severe to profound
hearing loss. These devices typically include an "external" and an
"internal" part. The external part includes a microphone, which can
be placed behind the ear, that detects sounds in the environment.
The sounds are then digitized and processed by a small computer
called a speech processor. The external components may be referred
to as a processor unit. In addition to the microphone and speech
processor, the external portion of the implant can include a power
source, such as a battery and an external antenna transmitter coil.
The internal part is an electronic device that is put under the
skin in the vicinity of the ear and is commonly referred to as a
stimulator/receiver unit (see FIG. 1). The coded signal output by
the speech processor is transmitted transcutaneously to the
implanted stimulator/receiver unit situated within a recess of the
temporal bone of the implantee. This transcutaneous transmission
occurs through use of an inductive coupling provided between the
external antenna transmitter coil which is positioned to
communicate with the implanted antenna receiver coil provided with
the stimulator/receiver unit. The communication is typically
provided by a radio frequency (RF) link, but other such links have
been proposed and implemented with varying degrees of success.
[0208] The implanted stimulator/receiver unit typically includes
the antenna receiver coil that receives the coded signal and power
from the external processor component, and a stimulator that
processes the coded signal and outputs a stimulation signal to an
electrode assembly, which applies the electrical stimulation
directly to the auditory nerve producing a hearing sensation
corresponding to the original detected sound.
[0209] An electrode connected to the electronic device is inserted
into the inner ear. The electrode can be a bundle of wires that
have open contacts spread along the length of the cochlea and
represent different frequencies of sounds. The number of electrodes
can vary from 1 to about 30 electrodes, such as about 5, 10, 15,
18, 20, 22, 24, 26, or 28 electrodes.
[0210] Combination Therapies
[0211] In some embodiments, the present invention provides methods
for treating a subject with one or more compounds using the direct
administration and cell therapy methods described above.
[0212] Effective Dose
[0213] Toxicity and therapeutic efficacy of the compounds and
pharmaceutical compositions described herein can be determined by
standard pharmaceutical procedures, using either cells in culture
or experimental animals to determine the LD.sub.50 (the dose lethal
to 50% of the population) and the ED.sub.50 (the dose
therapeutically effective in 50% of the population). The dose ratio
between toxic and therapeutic effects is the therapeutic index and
can be expressed as the ratio LD.sub.50/ED.sub.50. Polypeptides or
other compounds that exhibit large therapeutic indices are
preferred.
[0214] Data obtained from cell culture assays and further animal
studies can be used in formulating a range of dosage for use in
humans. The dosage of such compounds lies preferably within a range
of circulating concentrations that include the ED.sub.50 with
little or no toxicity, and with little or no adverse effect on a
human's ability to hear. 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 methods
described herein, the therapeutically effective dose can be
estimated initially from cell culture assays. A dose can be
formulated in animal models to achieve a circulating plasma
concentration range that includes the IC.sub.50 (that is, the
concentration of the test compound which achieves a half-maximal
inhibition of symptoms) as determined in cell culture. Such
information can be used to more accurately determine useful doses
in humans. Exemplary dosage amounts of a differentiation agent are
at least from about 0.01 to 3000 mg per day, e.g., at least about
0.00001, 0.0001, 0.001, 0.01, 0.1, 1, 2, 5, 10, 25, 50, 100, 200,
500, 1000, 2000, or 3000 mg per kg per day, or more.
[0215] The formulations and routes of administration can be
tailored to the disease or disorder being treated, and for the
specific human being treated. A subject can receive a dose of the
agent once or twice or more daily for one week, one month, six
months, one year, or more. The treatment can continue indefinitely,
such as throughout the lifetime of the human. Treatment can be
administered at regular or irregular intervals (once every other
day or twice per week), and the dosage and timing of the
administration can be adjusted throughout the course of the
treatment. The dosage can remain constant over the course of the
treatment regimen, or it can be decreased or increased over the
course of the treatment.
[0216] Generally the dosage facilitates an intended purpose for
both prophylaxis and treatment without undesirable side effects,
such as toxicity, irritation or allergic response. Although
individual needs may vary, the determination of optimal ranges for
effective amounts of formulations is within the skill of the art.
Human doses can readily be extrapolated from animal studies (Katocs
et al., Chapter 27 In: Remington's Pharmaceutical Sciences, 18th
Ed., Gennaro, ed., Mack Publishing Co., Easton, Pa., 1990).
Generally, the dosage required to provide an effective amount of a
formulation, which can be adjusted by one skilled in the art, will
vary depending on several factors, including the age, health,
physical condition, weight, type and extent of the disease or
disorder of the recipient, frequency of treatment, the nature of
concurrent therapy, if required, and the nature and scope of the
desired effect(s) (Nies et al., Chapter 3, In: Goodman &
Gilman's "The Pharmacological Basis of Therapeutics", 9th Ed.,
Hardman et al., eds., McGraw-Hill, New York, N.Y., 1996).
[0217] Methods of Screening
[0218] In some embodiments, a candidate compound can be tested for
its ability to increase .beta.-catenin levels (e.g., protein
levels) and/or activity (e.g., biological activity) in target cells
and/or to promote an increase in the levels (e.g. protein levels)
and/or activity (e.g., biological activity) of .beta.-catenin in
the nucleus of target cells using cells (e.g., stem cells) that
have been engineered to express a .beta.-catenin reporter
construct. These engineered cells make up a reporter cell line. A
reporter construct includes (1) any gene or nucleic acid sequence
whose expression may be indirectly or directly detected and/or
assayed; and (2) a .beta.-catenin reporter sequence (e.g., any
nucleic acid sequence whose expression is specifically correlated
with .beta.-catenin activity or expression), wherein (2) is
operably linked to (1) such that (2) drives the expression of (1).
S Examples of (1) include, without limitation, green fluorescent
protein (GFP), .alpha.-glucuronidase (GUS), luciferase,
chloramphenicol transacetylase (CAT), horseradish peroxidase (HRP),
alkaline phosphatase, acetylcholinesterase and (3-galactosidase.
Other optional fluorescent reporter genes include but are not
limited to red fluorescent protein (RFP), cyan fluorescent protein
(CFP) and blue fluorescent protein (BFP), or any paired combination
thereof, provided the paired proteins fluoresce at distinguishable
wavelengths. Examples of a .beta.-catenin reporter sequence include
.beta.-catenin transcriptional binding sequences (e.g., nucleic
acid sequences that can be bound (e.g., specifically bound) by
.beta.-catenin, wherein binding of .beta.-catenin to the sequence
modulates expression of the sequence (e.g., a promoter sequence
that can be bound by .beta.-catenin)). In some embodiments, a
candidate compound can be assessed using the TOPflash genetic
reporter system (Chemicon).
[0219] Alternatively or in addition, a reporter gene can be under
control of a promoter that is active in cells of the inner ear,
including progenitor cells and cells at varying degrees of
differentiation, but not in stem cells. In such cases, ideally, the
promoter is stably upregulated in the differentiated cells or
progenitors cells to allow assessment of the partially or fully
differentiated phenotype (e.g., expression of the reporter gene and
further identification of genes known to be expressed in the inner
ear).
Methods for Assessing .beta.-Catenin Levels and/or Activity
[0220] .beta.-catenin levels (e.g., protein levels) and/or activity
(e.g., biological activity) in target cells and/or in the nucleus
of target cells can be assessed using standard methods such as
Western Blotting, reverse transcriptase polymerase chain reaction,
immunocytochemistry, and genetic reporter assays, examples of each
of which are provided herein. Increases in .beta.-catenin levels
(e.g., protein levels) and/or activity (e.g., biological activity)
in target cells and/or in the nucleus of target cells can be
assessed by comparing .beta.-catenin levels and/or activity in a
first sample or a standard with .beta.-catenin levels and/or
activity in a second sample, e.g., after treatment of the sample
using a method or composition expected to increase .beta.-catenin
levels and/or activity.
Kits
[0221] The compounds and pharmaceutical compositions described
herein can be provided in a kit, as can cells that have been
induced to differentiate (e.g., stem cells, progenitor cells,
and/or support cells that have differentiated into, for example,
hair cells or hair-like cells) and/or that are capable of
differentiating into hair cells. The kit can also include
combinations of the compounds, pharmaceutical compositions, and
cells described herein. The kit can include (a) one or more
compounds, such as in a composition that includes the compound, (b)
cells that have been induced to differentiate (e.g., stem cells,
progenitor cells, and/or support cells that have differentiated
into, for example, hair cells or hair-like cells) and/or that are
capable of differentiating into hair cells, (c) informational
material, and any combination of (a)-(c). 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, a 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 a cell to a patient, and any
combination of the methods described herein.
[0222] 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.
[0223] 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.
[0224] In addition to the compound, 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.
[0225] 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.
[0226] 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).
EXAMPLES
[0227] The invention is further described in the following
examples, which do not limit the scope of the invention described
in the claims.
[0228] An adenoviral library was employed to test the affect of a
number of gene on Atoh1 expression. Preliminary data generated
using this method indicated that .beta.-catenin modulated the
expression of Atoh1. To confirm and characterize these findings,
.beta.-catenin was expressed in various human and non-human cell
lines and animal models as described in the subsequent
Examples.
Example 1
.beta.-Catenin Modulates Atoh1 mRNA Expression in Human Cells
[0229] Human embryonic kidney (HEK) cells and the human intestinal
epithelial cell line HT29 (Human colon adenocarcinoma grade II cell
line) were maintained in culture media containing Dulbecco's
Modified Eagles Medium (DMEM) supplemented with 10% heat
inactivated fetal calf serum (FCS), 2 mM Glutamax, penicillin (50
U/mL), and streptomycin (50 .mu.g/mL) using standard cell culture
methods. For .beta.-catenin overexpression experiments, 10.sup.6
HEK and HT29 cells were seeding per 10 cm dish.
[0230] .beta.-catenin overexpression was achieved by transfecting
HEK and HT29 cells seeded as described above with 5 .mu.g of pcDNA3
(Invitrogen) encoding human .beta.-catenin under the control of a
cytomegalovirus (CMV) promoter (Michiels et al., Nature
Biotechnology, 20:1154-1157, 2002). Negative control cells included
untransfected cells and cells transfected with 5 .mu.g green
fluorescent protein, under the control of a CMV promoter (GFP:
Michiels et al., supra). Positive control cells were transfected
with 5 .mu.g of Atoh1 under the control of a CMV promoter (Lumpkin
et al., Gene Expr. Patterns, 3:389-395, 2003). All transfections
were performed using 15 .mu.L Lipofectamine.TM. 2000 for four
hours, according to the manufacturer's instruction (Invitrogen). At
the four hour time point, the transfection solution was replaced
with culture media. Cells were then cultured for a total of 24
hours before RNA extractions were performed using the RNeasy Mini
kit, according to the manufacturer's instruction (Qiagen). 1 .mu.g
RNA was then subjected to reverse transcriptase polymerase chain
reaction using SuperTranscript.TM. III and Taq DNA polymerase,
according to the manufacturer's instruction (New England Biolabs),
using the following primer pairs:
TABLE-US-00001 Atoh1 (human): (SEQ ID NO: 2) Sense:
5'-GCGCAATGTTATCCCGTCGTT-3' (SEQ ID NO: 3) Antisense:
5'-AAAATTCCCCGTCGCTTCTGTG-3' Glyceraldehyde 3-phosphate
dehydrogenase (GAPDH-human) (SEQ ID NO: 4) Sense:
5'-CTTTTAACTCTGGTAAAGTGG-3' (SEQ ID NO: 5) Antisense:
5'-TTTTGGCTCCCCCCTGCAAAT-3'
[0231] Annealing temperatures and cycles were optimized for each
primer pair. The polymerase chain reaction (PCR) products that
resulted from the above Atoh1 and GAPDH primer pairs were 479 base
pairs (bp) and 287 bp, respectively. PCR products were resolved and
analyzed by agarose gel electrophoresis.
[0232] As shown in FIGS. 1A and 1B, .beta.-catenin expression
promoted an increase in Atoh1 mRNA expression in HEK and HT29,
respectively, which was similar to the increase promoted by cells
transfected with Atoh1 as a positive control in each cell line. In
contrast, untransfected and GFP transfected cells did not show an
increase in Atoh1 mRNA expression.
[0233] The Atoh1 upregulation observed in FIG. 1 was quantified in
HEK cells using real-time PCR (RT-PCR). Briefly, cells were
cultured and transfected as described above. RT-PCR primers Atoh1
and S18 were purchased from Applied Biosystems and RT-PCR was
performed using a Perkin Elmer ABI PRISM.TM. 7700 Sequence Detector
(PE Applied Biosystems). Two independent experiments were performed
in triplicate and Atoh1 expression was expressed as the mean value
relative to the expression of the housekeeping gene, S18.
[0234] As shown in FIG. 1B, Atoh1 expression increased in HEK cells
36.02.+-.4.46 fold compared to untreated control cells.
[0235] Similar experiments were also performed using neural
progenitor cells.
[0236] Neural progenitor cells were obtained using ROSA26 mouse
embryonic stem cells (Zambrowicz et al., Proc. Natl. Acad. Sci.
USA., 94:3789-3794, 1997) using the methods described in Li et al.
(BMC Neurosci., 10:122, 2009). .beta.-catenin was overexpressed as
described above.
[0237] Atoh1 and .beta.-catenin levels were determined following
.beta.-catenin overexpression by subjecting 1 .mu.g of RNA to
RT-PCR using SuperTranscript.TM. III and Taq DNA polymerase (New
England Biolabs), as described above. GAPDH levels were assessed as
control. Levels of each of the markers were assessed using the
following oligonucleotide primers:
TABLE-US-00002 Atoh1: (SEQ ID NO: 6) Sense:
5'-AGATCTACATCAACGCTCTGTC'-3' (SEQ ID NO: 7) Antisense:
5'-ACTGGCCTCATCAGAGTCACTG-3' .beta.-catenin: (SEQ ID NO: 8) Sense:
5'-ATGCGCTCCCCTCAGATGGTGTC-3' (SEQ ID NO: 9) Antisense:
5'-TCGCGGTGGTGAGAAAGGTTGTGC-3' GAPDH: (SEQ ID NO: 10) Sense:
5'-AACGGGAAGCCCATCACC-3' (SEQ ID NO: 11) Antisense:
5'-TCGCGGTGGTGAGAAAGGTTGTGC-3'
[0238] As shown in FIGS. 1C and 1D, Atoh1 mRNA expression was
upregulated in neural progenitor cells following .beta.-catenin
expression (741.2.+-.218.2) compared to untransfected control cells
or cells transfected with GFP (1.+-.0.2). As expected, Atoh1
expression also increased following transfection with Atoh1.
[0239] These observations suggest that .beta.-catenin increases
Atoh1 mRNA expression in human cell lines.
Example 2
.beta.-Catenin Modulates Atoh1 Protein Expression in Human
Cells
[0240] Atoh1 protein expression was analyzed in HEK cells
transfected as described in Example 1. Following transfection,
cells were cultured for 72 hours. Proteins were then resolved on
4-12% nuPAGE.RTM. Bis-Tris gels (Invitrogen) and transferred to 0.2
.mu.m nitrocellulose membranes (BioRad). Membranes were then
immunoblotted with mouse anti-Atoh1 antibody (Developmental Studies
Hybridoma bank) followed by HRP-conjugated anti-mouse antibody
(Sigma). Immunoblots were processed using ECL.TM., according to the
manufacturer instructions (Amersham Pharmacia).
[0241] As shown in FIG. 3, Atoh1 was not detectable in
untransfected control HEK cells or GFP transfected cells. In
contrast, Atoh1 was detectable in HEK cells transfected with
.beta.-catenin and Atoh1.
[0242] These observations suggest that .beta.-catenin increases
Atoh1 protein expression in human cell lines. Atoh1 expression also
increased following transfection with Atoh1 possibly due to the
activation of endogenous Atoh1 via an Atoh1 auto-feedback loop
(Helms et al., Development, 127:1185-1196, 2000).
Example 3
.beta.-Catenin Modulates Atoh1 mRNA Expression in Mouse Cells
[0243] Murine Neuro2a cells and mouse neural progenitor cells
derived from mouse ES cells (mES) were cultured and transfected as
described in Example 1. Atoh1 and GAPDH mRNA was amplified using
PCR and the following primer pairs:
TABLE-US-00003 Atoh1 (mouse) (SEQ ID NO: 12) Sense:
5'-GCGCAATGTTATCCCGTCGTT-3' (SEQ ID NO: 13) Antisense:
5'-AAAATTCCCCGTCGCTTCTGTG-3' GAPDH (mouse) (SEQ ID NO: 14) Sense:
5'-CTTTTAACTCTGGTAAAGTGG-3' (SEQ ID NO: 15) Antisense:
5'-TTTTGGCTCCCCCCTGCAAAT-3'
[0244] Annealing temperatures and cycles were optimized for each
primer pair. The polymerase chain reaction (PCR) products that
resulted from the above Atoh1 and GAPDH primer pairs were 479 base
pairs (bp) and 287 bp, respectively. PCR products were resolved and
analyzed by agarose gel electrophoresis.
[0245] As shown in FIGS. 4A and 4B, .beta.-catenin expression
promoted an increase in Atoh1 mRNA expression in Neuro2a and mES
cells, respectively. This increase was similar to the increase
promoted by cells transfected with Atoh1 as a positive control in
both cell lines. In contrast, untransfected and GFP transfected
cells did not show an increase in Atoh1 mRNA expression.
[0246] The Atoh1 upregulation observed in FIG. 4 was quantified in
Neuro2a cells using real-time PCR (RT-PCR), as described in Example
1.
[0247] As shown in FIG. 5, Atoh1 expression increased in Neuro2a
cells 871.86.+-.141.31 fold compared to untreated control
cells.
[0248] Neuro2a data is also shown in FIGS. 1C and 1D.
[0249] These observations suggest that .beta.-catenin increases
Atoh1 mRNA expression in murine cell lines.
[0250] The data shown in Examples 1-3 was corroborated using gene
silencing. Briefly, siRNA were designed to silence Atoh1
(NM_007500.4, NM_005172.1) and .beta.-catenin (NM_007614.2 and
NM_001904.3), as shown below:
TABLE-US-00004 Atoh1: (SEQ ID NO: 16)
GCAACGUUAUCCCGUCCUUUAACAGCGAUGAUGGCACA .beta.-catenin: (SEQ ID NO:
17) GCGCUUGGCUGAACCAUCAUUGUGAAAUUCUUGGCUAUUAUU
[0251] 200 nM of each siRNA were transfected using the
GeneSilencer.TM. transfection reagent at 5 .mu.L/mL. Cells were
incubated in the presence of the transfection mix for 16 hours and
were harvested following a total of 48 hours. Non-targeting siRNA
was used as control. Gene silencing was confirmed using RT-PCR.
Cells were also transfected with Atoh1, .beta.-catenin, or GFP
using the methods described above.
[0252] As shown in FIGS. 1E and F, Atoh1 expression was decreased
by siRNA directed against Atoh1 and .beta.-catenin in both neural
progenitor cells (see Example 2) and Neuro2a (Atoh1 expression in
the presence of Atoh1 siRNA decreased by about 45%. Atoh1
expression in the presence of.beta.-catenin decreased by about
40%). .beta.-catenin also suppressed .beta.-catenin expression
levels in all cell types tested.
[0253] The correlation between .beta.-catenin and Atoh1 was also
corroborated using genetic reporter assays. Briefly, 10.sup.5
Neuro2a cells were seeded into a 24-well plate one day prior to
transfection. 0.125 .mu.g of Atoh1-luciferase reporter construct
and 0.125 .mu.g o CBFI-luciferase reporter construct (Hseih et al.,
Mol. Cell. Biol., 16(3):952-959, 1996) TOPFlash or FOPFlas
(Addgene) or 0.125 .mu.g of Renilla-luciferase were mixed in the
presence or absence of 0.25 .mu.g .beta.-catenin and 0.5 .mu.L
lipofectamine 2000 in 0.125 mL of opti-MEM. This transfection
mixture was then incubated on the cells for 4 hours. Cells were
lysed after 48 hours and luciferase activity was measured using the
Dual Luciferase Reporter Assay System (Promega) in a TD-20/20
Luminometer (Turner Designs).
[0254] As shown in FIGS. 1G and H, reporter activity of TOPFlash
(which contains multiple .beta.-catenin binding sites) was
comparable to reporter activity of the Atoh1 reporter, indicating
that Atoh1 is regulated by .beta.-catenin (FIG. 1G). Increased
.beta.-catenin expression also raised the level of the active
fraction of nuclear .beta.-catenin as detected using an antibody
that binds specifically to the unphosphorylated form (FIG. 1H)
(unphosphorylated .beta.-catenin was detected using the
anti-unphosphorylated 13-catenin antibody disclosed by van Noort et
al., Blood, 110(7):2778-2779, 2007).
[0255] Nuclear unphosphorylated.beta.-catenin and Atoh1 levels were
also increased when cells were incubated in Wnt3a conditioned media
(FIG. 1H). In contrast, overexpression of dominant negative Tcf4,
which lacks the .beta.-catenin binding site, decreased the level of
Atoh1.
Example 4
.beta.-Catenin Directly Interacts with the Atoh1 Enhancer
Region
[0256] To investigate whether .beta.-catenin, in combination with
Tcf-Lef factor, has a direct interaction with regulatory regions of
the Atoh1 gene, DNA binding to .beta.-catenin was analyzed using
chromatin immunoprecipitation (ChIP).
[0257] 10.sup.7 HEK cells were crosslinked in DMEM containing 1%
formaldehyde for 10 minutes followed by 5 minutes at 37.degree. C.
in formaldehyde saturated with 0.125 M glycine. Crosslinked cells
were harvested, rinsed in phosphate buffered saline (PBS), and
centrifuged for 5 minutes at 160 g at 4.degree. C. in cold PBS.
Samples were then resuspended in sonication buffer (1% Triton.RTM.
X-100, 0.1% deoxycholate, 50 mM Tris pH 8.1, 150 mM NaCl, 5 mM
ethylenediaminetetraacetic acid (EDTA), 2 mM
phenylmethanesulphonylfluoride (PMSF), and a 1:100 dilution of
fresh proteinase inhibitor cocktail (Sigma)) and genomic DNA was
sheared using 15 pulses (5 seconds/pulse) in a sonication bath.
Cell extracts were pelleted and resuspended in 1 ml
radioimmunoprecipitation assay (RIPA) buffer supplemented with
fresh proteinase inhibitors (Sigma). Each sample was then separated
into one 200 .mu.L aliquot and two 400 .mu.L aliquots. The 200
.mu.L aliquot was not subjected to immunoprecipitation, but was
used as the input control for the subsequent PCR reaction (input).
The first 400 .mu.L aliquot was immunoprecipitated using mouse
anti-.beta.-catenin antibody (Upstate, 05-601) as the primary
antibody at a dilution of 1:100. The second 400 .mu.L aliquot was
immunoprecipitated using nonimmune IgG as the primary antibody at a
concentration of 1:6000 (Sigma, M5905). Immunoprecipitations were
performed using the primary antibodies at 4.degree. C. for 16
hours. Protein A agarose (Amersham Pharmacia) and 2 .mu.L herrin
sperm DNA (10 mg/mL) were then added to the samples for 2 hours.
Immunoprecipitates were then washed and heated at 65.degree. C. for
3 minutes in RIPA buffer. DNA was recovered from immunoprecipitates
and input using ethanol precipitation and phenol extraction. Atoh1
enhancer DNA was amplified using PCR and following primer pair:
TABLE-US-00005 (SEQ ID NO: 18) Sense: 5'-GGGGAGAGGCAGGGGAGGAGAG-3'
(SEQ ID NO: 19) Antisense: 5'-AGGCCGGGGAGGGTGACGA-3'
[0258] Samples were then analyzed using agarose gel
electrophoresis. As shown in FIG. 6, Atoh1 enhancer DNA was
detected in the .beta.-catenin precipitated samples and input
samples. Atoh1 enhancer DNA was not amplified from control
chromatin immunoprecipitated with nonimmune IgG. These observations
suggest that .beta.-catenin binds directly to the Atoh1
enhancer.
[0259] Similar chromatin immunoprecipitation experiments were also
performed using Neuro2a cells. Such methods are as described above
except that harvested cells were pelleted for 10 minutes at 720 g
at 4.degree. C. Nuclei were then released in a Dounce homogenizer
in PBS containing protease inhibitors (see above) and collected at
4.degree. C. by centrifugation at 2400 g. Sheared chromatin was
collected in the supernatant by centrifugation (8,000 g at
4.degree. C. for 10 minutes) after treatment of the nuclei with the
enzymatic cocktail from the ChIP-IT.TM. Express kit (Active Motif)
for 10 minutes at 37.degree. C. 1 .mu.g of sheared DNA was used for
immunoprecipitation using 1 .mu.g of mouse anti-.beta.-catenin
antibody (Upstate, 05-601, 1:100), mouse anti-LEF-1 antibody (Sigma
L7901) or nonimmune mouse serum (Sigma). Precipitated chromatin was
recovered after reversing cross-links and the proteins were
digested with proteinase K. Target Atoh1 regulatory DNA (AF218258)
was amplified by PCR using the following primers, which cover the
entire 1.3 kB sequence in overlapping segments (as indicated)
TABLE-US-00006 Sense 1 (nucleotides 33-272): (SEQ ID NO: 20)
ACGTTTGGCAGCTCCCTCTC Anti-sense 1: (SEQ ID NO: 21)
ATAGTTGATGCCTTTGGTAGTA Sense 2 (nucleotides 148-434): (SEQ ID NO:
22) ATTCCCCATATGCCAGACCAC Anti-sense 2: (SEQ ID NO: 23)
GGCAAAGACAGAATATAAAACAAG Sense 3 (nucleotides 349-609): (SEQ ID NO:
24) AATCGGGTTAGTTCTTTG Antisense 3: (SEQ ID NO: 25)
ACTCCCCCTCCCTTTCTGGTA Sense 4 (nucleotides 501-742): (SEQ ID NO:
26) CAGGGGGAGCTGAAGGAAG Anti-sense 4: (SEQ ID NO: 27)
TTTTAAGTTAGCAGAGGAGATTA Sense 5 (nucleotides 675-939): (SEQ ID NO:
28) CTGAGCCCCAAAGTTGTAATGTT Anti-sense 5: (SEQ ID NO: 29)
TGGGGTGCAGAGAAGACTAAA Sense 6 (nucleotides 926-1161): (SEQ ID NO:
30) ACCCCAGGCCTAGTGTCTCC Anti-sense 6: (SEQ ID NO: 31)
TGCCAGCCCCTCTATTGTCAG Sense 7 (nucleotides 1094-1367): (SEQ ID NO:
32) GTGGGGGTAGTTTGCCGTAATGTG Anti-sense 7: (SEQ ID NO: 33)
GGCTCTGGCTTCTGTAAACTCTGC
[0260] As shown in FIG. 2B, .beta.-catenin and Tcf-Lef antibody
immunoprecipitated DNA at the 5' and 3' ends of the 1.3 kB
sequence. This observation indicates that DNA in these regions has
an affinity for both proteins. These sequences were not seen in
control samples exposed to serum.
[0261] Atoh1 has a 1.7 kb regulatory enhancer located 3' to its
coding region. This 3' Atoh1 enhancer is sufficient to direct
expression of a heterologous reporter gene in transgenic mice
(Helms et al., Development, 127:1185-1196, 2000). To define the
binding sites on the mouse Atoh1 enhancer, the murine Atoh1 3'
enhancer sequence (AF218258) was searched using MatInspector
(Genomatix) software. These searches identified two candidate
binding sites for .beta.-catenin in combination with Tcf-Lef
transcriptional coactivators at nucleotides 309-315 and 966-972 of
AF218258. To determine whether these candidate sites had binding
affinity for .beta.-catenin we performed DNA pulldown assays with
two biotin-labeled oligonucleotides probes, termed probe 309 and
probe 966. Each of these probes contain sequence homologous to the
candidate sites at nucleotides 309-315 and 966-972 of AF218258 and
surrounding nucleotides. Probe 309 spans nucleotides 297-326 and
probe 966 spans nucleotides 956-985 of AF218258. The sequences of
probes 309 and 966 are as follows:
TABLE-US-00007 Probe 309 (SEQ ID NO: 34)
5'-ATCACCCAAACAAACAAAGAGTCAGAACTT-3' Probe 966 (SEQ ID NO: 35)
5'-GTTAGGAGCCAGAAGCAAAGGGGGTGACAC-3'
[0262] Both probe 309 and 966 encode five prime termini biotin
labels. The sequences of the candidate .beta.-catenin/Tcf-Lef
binding sites (309-315 and 966-972) are shown in bold.
[0263] Pulldown assays were performed as follows. Nuclei were
isolated from 10.sup.6 HEK and Neuro2a cells following mechanical
disruption with a 20 gauge needle.
[0264] Proteins were extracted from nuclei in 200 .mu.l RIPA buffer
with fresh proteinase inhibitors at 4.degree. C. for 60 minutes.
Chromatin DNA was pelleted at 14,000 g for 15 min at 4.degree. C.
and the nuclear lysate (supernatant) was collected. Biotin-labeled
DNA probe (0.3 .mu.g) with or without 10 .mu.g unlabeled DNA probe
was incubated with 40 .mu.l nuclear lysate for 30 min at room
temperature with gentle shake in binding buffer (10 mM Tris, 50 mM
KCl, 1 mM DTT, 5% glycerol, pH 7.5, 40 mM 20 mer poly A and poly C)
with proteinase inhibitors. Probe-bound proteins were collected
with 50 .mu.l Streptavidin magnetic beads (Amersham Pharmacia).
Precipitated proteins were washed five times with binding buffer
and boiled in 50 .mu.l 2.times. sample buffer (BioRad), and the
supernatant was collected for Western blotting.
[0265] Western blots were performed to detect proteins interacting
with probes 309 and 966. Briefly, proteins were separated on 4-12%
NuPAGE Bis-Tris gels (Invitrogen) and electotransferred to 0.2
.mu.m nitrocellulose membranes (BioRad). The membranes were probed
with mouse anti-Atoh1 antibody (Developmental Studies Hybridoma
Bank), anti-Lef-1/Tcf antibody (Sigma L4270), or rabbit
anti-.beta.-catenin antibody (Sigma C2206), followed by
HRP-conjugated anti-mouse (Sigma), anti-goat (Santa-Cruz) or
anti-rabbit (Chemicon) antibodies. The blots were processed with
ECL.TM. (Amersham Pharmacia) according to the manufacturer's
instructions.
[0266] As shown in FIGS. 7A and 7B, left columns, both
.beta.-catenin and Tcf-Lef, respectively, were detected following
DNA pull down using Western blotting. As shown in the center column
of FIGS. 7A and 7B, binding of .beta.-catenin and Tcf-Lef to the
probes was reduced by competition with unlabeled probe. As shown in
the right column of FIGS. 7A and 7B, mutation of the candidate
binding sites (see SEQ ID NOs: 11 and 12) of probes 309 and 966
also reduced binding of .beta.-catenin and Tcf-Lef to the probes.
The sequences of the mutant 309 and 966 probes are as follows:
TABLE-US-00008 Mutant Probe 309 (SEQ ID NO: 36)
5'-ATCACCCAAACACATACGAAGTCAGAACTT-3' Mutant Probe 966 (SEQ ID NO:
37) 5'-GTTAGGAGCCAGAGGATCGTGGGGTGACAC-3' The sequences of the wild
type probes are as follows: Wild Type Probe 309 (nucleotides
297-326) (SEQ ID NO: 38) 5'-ATCACCCAAACAAACAAGAGTCAGCACTT-3' Wild
Type Probe 966 (SEQ ID NO: 39)
5'-GTTAGGAGCCAGAAGCAAAGGGGGTGACTC-3'
[0267] The sequences of the mutated candidate
.beta.-catenin/Tcf-Lef binding sites (309-315 and 966-972) are
shown in bold. Both mutant probes 309 and 966 encode five prime
termini biotin labels. Thus, probe bound proteins were collected
with Streptavidin magnetic beads (50 .mu.L; Amersham-Pharmacia).
Precipitated proteins were washed five times with binding buffer
and boiled in 50 .mu.L sample buffer. Supernatant was collected for
Western blotting with anti-.beta.-catenin antibody and
anti-Lef-1-Tcf antibody.
[0268] The precise sequences within Atoh1 that have binding
affinity for .beta.-catenin and Tcf-Lef were identified using the
above described DNA pulldown. Consistent with the observation
reported above in HEK cells, in Neuro2a cell, as shown in FIG. 7C,
probe 309 and 966 interacted with .beta.-catenin and Tcf-Lef and
this interaction was reduced by competition and destroyed by
mutation.
[0269] The competition and mutation assays confirm the specificity
of the DNA pull down assay.
[0270] These data suggest that both of the candidate binding sites
identified in the Atoh1 enhancer region bound to .beta.-catenin in
the Tcf/Lef complex.
[0271] As shown in FIG. 7D, dominant negative Tcf4 suppressed
.beta.-catenin induced Atoh1 expression. Furthermore, inhibition
was almost complete at higher levels, indicating that a complex
between .beta.-catenin and Tcf-Lef is required for activation of
Atoh1 by .beta.-catenin.
Example 5
.beta.-Catenin Modulates the Activity of the Atoh1 Enhancer
Region
[0272] To determine whether the two confirmed .beta.-catenin
binding sites on the Atoh1 enhancer increased the functional
activity of the Atoh1 enhancer, we constructed multiple Atoh1
enhancer-reporter genes with intact or mutated Atoh1 3'
enhancers.
[0273] A construct with the Atoh1 3' enhancer controlling
expression of the firefly luciferase gene (Luc) was made as
follows. A BamH1/NcoI fragment containing the Atoh1 3' enhancer
region (containing the .beta.-catenin/Tcf-Lef binding sites
identified above) with a basic .beta.-globin promoter was excised
from an Atoh1-GFP construct (Lumpkin et al., supra) and inserted
into the luciferase vector, pGL3 (Promega), at BglII/NcoI in the
multiple cloning region to create a Atoh1-luc vector.
[0274] A control Luc construct was made using the Atoh1-luc vector
by excising the Atoh1 enhancer with BgII/EcoR1, followed by blunt
end ligation. All the sequences were confirmed by sequencing.
[0275] Site-directed mutagenesis was performed using the
QuickChange.RTM. II Site-Directed Mutagenesis Kit (Stratagene),
according to the manufacturer's instructions. In short, the vector
containing the target gene was denatured and annealed to the
oligonucleotide primers that were designed according to the
manufacturer's instructions, with the desired mutations in the
complimentary strands. Following temperature cycling, circular DNA
was generated from the template vector containing the incorporated
mutagenic primers using PfuTurbo DNA polymerase, and methylated,
parental DNA was digested with Dpn1 endonuclease. Finally the
circular, nicked dsDNA was transformed into competent cells for
repair. All mutations were confirmed after amplification by
sequencing. Each of the .beta.-catenin binding sites on the Atoh1
enhancer were mutated, alone or together, in a luciferase reporter
construct, as indicated in FIGS. 8A-8E.
[0276] The wild type (WT) and mutant (MUT) constructs illustrated
in FIG. 8 were then used to assess the functional activity of the
Atoh1 enhancer by luciferase assay. Briefly, 10.sup.5 murine
Neuro2a cells were seeded into a 24 well plate one day before
transfection. 0.125 .mu.g Atoh1-Luciferase reporter construct,
0.125 .mu.g Renilla-Luciferase construct with or without 0.25 .mu.g
.beta.-catenin expression construct were mixed with 0.5 .mu.pl
Lipofectamine.TM. 2000 transfection reagent in 0.125 ml opti-MEM
and incubated with the cells for 4 hr. Cells were lysed after 24 hr
and luciferase activity was measured using the Dual Luciferase
Reporter Assay System (Promega) in a TD-20/20 Luminometer (Turner
Designs).
[0277] As shown in FIG. 9, .beta.-catenin had no effect on the
control luciferase construct, which does not include the Atoh1 3'
enhancer. Conversely, .beta.-catenin increased reporter gene
expression from the luciferase construct encoding the WT Atoh1 3'
enhancer. .beta.-catenin mediated Atoh1 3' enhancer reporter gene
expression was reduced in the presence of .beta.-catenin in all
mutant constructs. .beta.-catenin mediated upregulation was
abolished in the double mutant construct.
[0278] These data indicate that .beta.-catenin binding to the Atoh1
3' enhancer increases activity of the enhancer and that both of the
.beta.-catenin binding sites are required for maximum enhancer
activity.
Example 6
A Combination of Notch Signaling Inhibition and .beta.-Catenin
Activity Promotes Enhanced Atoh1 Expression
[0279] Notch signaling was inhibited using a .gamma.-secretase
inhibitor (DAPT) and .beta.-catenin was activated using a
GSK3.beta. inhibitor (GSKi). Briefly, bone marrow derived MSCs that
exhibit increased Atoh1 activity following the inhibition of Notch
signaling were exposed to a .gamma.-secretase inhibitor and a
GSK3.beta. inhibitor. Altered Notch activity was confirmed using
CBF-1 luciferase reporter.
[0280] Mesenchymal stem cells (MSCs) were isolated from human bone
marrow using the methods described by Jeon et al. (Mol. Cell.
Neurosci., 34(1):59-68, (2007)). Cells were expanded once before
use and cultured in MEM-a cell culture media (Sigma-Aldrich)
supplemented with 9% horse serum, 9% fetal calf serum, and
penicillin (100 U/mL) and streptomycin (100 .mu.g/mL).
[0281] As shown in FIG. 10A, .beta.-catenin expression was
increased in cells exposed to .gamma.-secretase inhibitor.
Furthermore, as noted above, Atoh1 expression is increased by
.beta.-catenin. As shown in FIG. 10A, Atoh1 expression is further
increased by a combination of .beta.-catenin and Notch inhibition.
To confirm the role of .beta.-catenin in this observation,
.beta.-catenin expression was modulated using siRNA (as described
in Example 3 above). The decrease in .beta.-catenin is shown in
FIG. 10B. As shown in FIG. 10C, suppression of .beta.-catenin
prevented any .beta.-catenin expression following .gamma.-secretase
treatment and reduced Atoh1 expression. Similar results were also
observed when Notch signaling was inhibited using
non-.gamma.-secretase inhibitors (see FIG. 10D). This result
demonstrates the relationship between the inhibition of Notch
signaling and .beta.-catenin activity is not limited to the use of
.gamma.-secretase inhibitors.
[0282] Disruption of .beta.-catenin mediated transcription by
overexpression of dominant negative Tcf (dn Tcf) also reversed the
increase in Atoh1 expression observed in cells treated with the
inhibitor of Notch signaling (see FIG. 10E). Conversely, whereas
.beta.-catenin and Atoh1 expression were diminished following the
elevation of Notch signaling, activation of .beta.-catenin by Wnt3a
rescued Atoh1 expression (see FIG. 10E).
[0283] These results suggest that the inhibition of Notch signaling
combined with .beta.-catenin activity may function synergistically
to increase Atoh1 expression. Accordingly, combined therapy using
Notch signaling inhibition and a .beta.-catenin modulating
compound, such as a .beta.-catenin agonist, can be used to promote
Atoh1 expression.
Example 7
.beta.-Catenin Promotes the Conversion of Inner Ear Stem Cells to
Atoh1 Positive Cells in Transgenic Mice
[0284] Mice that express nuclear green fluorescent protein (GFP)
under the control of the Atoh1 enhancer (Atoh1-nGFP mice (Lumpkin
et al., supra)) were used to assess the conversion of inner ear
stem cells into hair cells. Increased expression of GFP in these
animals indicates an increase in the activity of the Atoh1 3'
enhancer. Inner ear stem cells derived from the transgenic animals
were transduced with adenoviruses containing .beta.-catenin or GFP
under the control of a CMV promoter (Michiels et al., Nat. Biotec.,
20:1154-1157, 2002).
[0285] Inner ear stem cells were isolated from Atoh1-nGFP as
previously described (Li et al., Nat. Med., 9:1293-1299, 2003).
Briefly utricles were dissected from 4 Atoh1-nGFP mice at postnatal
day four (P4) and were trypsinized into a single cell suspension.
The released cells were then grown in suspension for seven days in
DMEM/FD12 medium (1:1) supplemented with N2/B27, 10 ng/mL FGF-2
(Chemicon), 50 ng/mL IGF (Chemicon), and 20 ng/mL EGF (Chemicon) to
obtain spheres.
[0286] Inner ear stem cells isolated as spheres were seeded into a
four-compartment 35 mm tissue culture dish and grown as a monolayer
in DMEM/N2 medium. 10.sup.6 cells were infected with
.beta.-catenin, GFP or empty adenoviruses (9.times.10.sup.7 viral
particles) in 100 .mu.L Opti-MEM for 16 hours.
[0287] As shown in FIG. 11A, transduction of inner ear stem cells
with the control GFP adenovirus resulted in GFP expression in 68%
of the cells. As shown in FIG. 5C, transduction of inner ear stem
cells with .beta.-catenin adenovirus increased the number of Atoh1
positive cells compared to inner ear stem cells transduced with
empty virus. This data suggests that .beta.-catenin increased Atoh
1 activity in inner ear stem cells obtained from Atoh1-nGFP mice.
This observation is consistent with the differentiation of inner
ear stem cells to hair cells. To further confirm the
differentiation of the inner ear stem cells to hair cells,
transduced cells were analyzed using immunocytochemistry to detect
hair cell specific markers. Immunostaining was performed using
rabbit antibody to myosin VII1 (Proteus Bioscience) at a 1:1000
dilution or mouse monoclonal antibody PC10 to detect PCNA
(eBioscience) at a 1:100 dilution. Positively stained cells were
counted using MetaMorph Imaging 7.0 and statistics were performed
from three independent experiments.
[0288] As shown in FIG. 11D, when 5000 cells were counted in three
independent experiments, the number of cells staining positive for
Atoh1 and myosin VIIa doubled in cells expressing .beta.-catenin
(Atoh1 positive cells increased from 8.9% to 15.8% and myosin VIIa
positive cells increased from 3.3% to 6.6%). As Atoh1 and myosin
VIIa are known specific hair cell markers, this observation
confirms that .beta.-catenin promotes the differentiation of inner
ear stem cells into hair cells. To correlate .beta.-catenin
overexpression with the conversion of inner ear progenitor cells
into Atoh1 positive cells, an expression vector encoding the
.beta.-catenin coding region followed by the reporter sequence
IRES-DsRed was constructed.
[0289] The .beta.-catenin-IRES-DsRed construct was by cloning human
.beta.-catenin cDNA containing Xba I (enzymes from New England
Biolabs) sticky ends into pIRES2-DsRed Express (Clontech) at the
Nhe I site.
[0290] Inner ear stem cells isolated and seeded as described above
where transfected with 4 .mu.g IRES-DsRed empty vector or 4 .mu.g
.beta.-catenin-IRES-DsRed using 3 .mu.L Lipofectamine.TM. 2000
transfection reagent in 100 .mu.L Opti-MEM for 4 hours. Transfected
cells were then analyzed by immunocytochemistry after 5 days.
Immunostaining was performed as described above.
[0291] As shown in FIG. 12B and Table 1, none of the 14 cells
expressing IRES-DsRed empty vector stained positively for Atoh1. In
contrast, as shown in FIG. 12A and table 1, 8 of 15 cells
expressing .beta.-catenin-IRES-DsRed stained positively for
Atoh1.
TABLE-US-00009 TABLE 1 Quantification of .beta.-Catenin-Mediated
Atoh1 Expression in Inner Ear Stem Cells DsRed Atoh1 Positive
Positive Cells Cells Transfection (Red) (Green)
.beta.-catenin-IRES-DsRed 14 8 IRES-DsRed 15 0 N = 3; cells counted
= 1000.
[0292] To ascertain whether the increase in Atoh1 positive cells
observed above was due to increased proliferation of the inner ear
stem cells, as has been reported for other neural progenitor cells
(Adachi et al., Stem Cells, 25:2827-36, 2007; Woodhead et al., J.
Neurosci., 26:12620-12630, 2006), labeling for PCNA was assessed in
.beta.-catenin expressing cells.
[0293] Adenovirus mediated .beta.-catenin expression resulted in
68.+-.7.9% PCNA positive cells, which was not significantly
different (p>0.05) from cells transduced with empty adenovirus
(69.7.+-.5.2% PCNA positive cells) and non-transduced cells
(72.+-.8.8% PCNA positive cells) based on three independent
experiments in which 5000 cells were counted.
[0294] This data suggests that cell proliferation was not required
for .beta.-catenin mediated cell differentiation.
Example 8
.beta.-Catenin Mediated Hair Cell Formation
[0295] As shown in FIG. 13, .beta.-catenin expression promoted the
formation of extra rows of outer hair cells at E16. 8.1 E+07
adenovirus particles were applied to organ of Corti dissected from
E16 Atoh1-nGFP embryos and cultured for 5 days. Adenovirus encoding
As shown in FIGS. 13C and 12D, .beta.-catenin increased the number
of Atoh1 positive outer hair cells compared to untreated (A) or
cells treated with empty adenovirus (B).
[0296] As shown in FIG. 14 and table 2, 8.1E+07 adenovirus
particles were used to infect organs of Corti dissected from E16
Atoh1-nGFP embryos that were then cultured for 5 days. Images were
captured prior to infected (see FIG. 13B) and 5 days post-infected
(see FIG. 13A). The results were quantified and are shown in Table
2. As shown in Table 2, a 32.+-.3.1% increase was observed
following treatment.
TABLE-US-00010 TABLE 2 Treatment with Ad-.beta.-catenin
Pre-infected Post-infection IHC 256 249 OHC 768 1014 N = 3.
Example 9
Assessment of the Combined Affect of .beta.-Catenin and Inhibitors
of the Notch Signaling Pathway on the Conversion of Inner Ear Stem
Cells to Atoh1 Positive Cells in Transgenic Mice
[0297] Mice that express nuclear green fluorescent protein (GFP)
under the control of the Atoh1 enhancer (Atoh1-nGFP mice (Lumpkin
et al., supra)) were processed as described in Example 9.
[0298] Inner ear stem cells isolated as spheres were seeded into a
four-compartment 35 mm tissue culture dish and grown as a monolayer
in DMEM/N2 medium. 10.sup.6 cells were infected with combinations
of a .beta.-catenin adenovirus or one or more .beta.-catenin
modulating compounds, GFP adenovirus, empty adenoviruses
(9.times.10.sup.7 viral particles) and an inhibitor of the Notch
signaling pathway in 100 .mu.L Opti-MEM for 16 hours, as shown in
Table 3 (X indicates cells are treated):
TABLE-US-00011 TABLE 3 Well GFP Empty Notch No. .beta.-catenin
adenovirus Adenovirus inhibitor 1 X 2 X 3 X 4 X 5 X X 6 X X 7 X
X
[0299] Following treatment, cells were analyzed for Atoh1 and
myosin VIIa expression.
Other Embodiments
[0300] 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.
Sequence CWU 1
1
4116DNAArtificial Sequencesynthetically generated
oligonucleotidesmisc_feature3, 4n = A,T,C or G 1canntg
6221DNAArtificial Sequencesynthetically generated oligonucleotides
2gcgcaatgtt atcccgtcgt t 21322DNAArtificial Sequencesynthetically
generated oligonucleotides 3aaaattcccc gtcgcttctg tg
22421DNAArtificial Sequencesynthetically generated oligonucleotides
4cttttaactc tggtaaagtg g 21521DNAArtificial Sequencesynthetically
generated oligonucleotides 5ttttggctcc cccctgcaaa t
21622DNAArtificial Sequencesynthetically generated oligonucleotides
6agatctacat caacgctctg tc 22722DNAArtificial Sequencesynthetically
generated oligonucleotides 7actggcctca tcagagtcac tg
22823DNAArtificial Sequencesynthetically generated oligonucleotides
8atgcgctccc ctcagatggt gtc 23924DNAArtificial Sequencesynthetically
generated oligonucleotides 9tcgcggtggt gagaaaggtt gtgc
241018DNAArtificial Sequencesynthetically generated
oligonucleotides 10aacgggaagc ccatcacc 181124DNAArtificial
Sequencesynthetically generated oligonucleotides 11tcgcggtggt
gagaaaggtt gtgc 241221DNAArtificial Sequencesynthetically generated
oligonucleotides 12gcgcaatgtt atcccgtcgt t 211322DNAArtificial
Sequencesynthetically generated oligonucleotides 13aaaattcccc
gtcgcttctg tg 221421DNAArtificial Sequencesynthetically generated
oligonucleotides 14cttttaactc tggtaaagtg g 211521DNAArtificial
Sequencesynthetically generated oligonucleotides 15ttttggctcc
cccctgcaaa t 211638RNAArtificial Sequencesynthetically generated
oligonucleotides 16gcaacguuau cccguccuuu aacagcgaug auggcaca
381742RNAArtificial Sequencesynthetically generated
oligonucleotides 17gcgcuuggcu gaaccaucau ugugaaauuc uuggcuauua uu
421822DNAArtificial Sequencesynthetically generated
oligonucleotides 18ggggagaggc aggggaggag ag 221919DNAArtificial
Sequencesynthetically generated oligonucleotides 19aggccgggga
gggtgacga 192020DNAArtificial Sequencesynthetically generated
oligonucleotides 20acgtttggca gctccctctc 202122DNAArtificial
Sequencesynthetically generated oligonucleotides 21atagttgatg
cctttggtag ta 222221DNAArtificial Sequencesynthetically generated
oligonucleotides 22attccccata tgccagacca c 212324DNAArtificial
Sequencesynthetically generated oligonucleotides 23ggcaaagaca
gaatataaaa caag 242418DNAArtificial Sequencesynthetically generated
oligonucleotides 24aatcgggtta gttctttg 182521DNAArtificial
Sequencesynthetically generated oligonucleotides 25actccccctc
cctttctggt a 212619DNAArtificial Sequencesynthetically generated
oligonucleotides 26cagggggagc tgaaggaag 192723DNAArtificial
Sequencesynthetically generated oligonucleotides 27ttttaagtta
gcagaggaga tta 232823DNAArtificial Sequencesynthetically generated
oligonucleotides 28ctgagcccca aagttgtaat gtt 232921DNAArtificial
Sequencesynthetically generated oligonucleotides 29tggggtgcag
agaagactaa a 213020DNAArtificial Sequencesynthetically generated
oligonucleotides 30accccaggcc tagtgtctcc 203121DNAArtificial
Sequencesynthetically generated oligonucleotides 31tgccagcccc
tctattgtca g 213224DNAArtificial Sequencesynthetically generated
oligonucleotides 32gtgggggtag tttgccgtaa tgtg 243324DNAArtificial
Sequencesynthetically generated oligonucleotides 33ggctctggct
tctgtaaact ctgc 243430DNAArtificial Sequencesynthetically generated
oligonucleotides 34atcacccaaa caaacaaaga gtcagaactt
303530DNAArtificial Sequencesynthetically generated
oligonucleotides 35gttaggagcc agaagcaaag ggggtgacac
303630DNAArtificial Sequencesynthetically generated
oligonucleotides 36atcacccaaa cacatacgaa gtcagaactt
303730DNAArtificial Sequencesynthetically generated
oligonucleotides 37gttaggagcc agaggatcgt ggggtgacac
303829DNAArtificial Sequencesynthetically generated
oligonucleotides 38atcacccaaa caaacaagag tcagcactt
293930DNAArtificial Sequencesynthetically generated
oligonucleotides 39gttaggagcc agaagcaaag ggggtgactc
304011PRTArtificial SequenceSynthetic Peptide L803VARIANT10Xaa =
Phospho-Serine 40Lys Glu Ala Pro Pro Ala Pro Pro Gln Xaa Pro1 5
104112PRTArtificial SequenceSynthetic Peptide L803-mtsVARIANT1Xaa =
Myristoylated GlyineVARIANT11Xaa = Phospho-SerineVARIANT12Xaa =
C-terminal amide 41Xaa Lys Glu Ala Pro Pro Ala Pro Pro Gln Xaa Xaa1
5 10
* * * * *