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Wu SR, Butts JC, Caudill MS, Revelli JP, Dhindsa RS, Durham MA, Zoghbi HY. Atoh1 drives the heterogeneity of the pontine nuclei neurons and promotes their differentiation. SCIENCE ADVANCES 2023; 9:eadg1671. [PMID: 37390208 PMCID: PMC10313176 DOI: 10.1126/sciadv.adg1671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 05/26/2023] [Indexed: 07/02/2023]
Abstract
Pontine nuclei (PN) neurons mediate the communication between the cerebral cortex andthe cerebellum to refine skilled motor functions. Prior studies showed that PN neurons fall into two subtypes based on their anatomic location and region-specific connectivity, but the extent of their heterogeneity and its molecular drivers remain unknown. Atoh1 encodes a transcription factor that is expressed in the PN precursors. We previously showed that partial loss of Atoh1 function in mice results in delayed PN development and impaired motor learning. In this study, we performed single-cell RNA sequencing to elucidate the cell state-specific functions of Atoh1 during PN development and found that Atoh1 regulates cell cycle exit, differentiation, migration, and survival of PN neurons. Our data revealed six previously not known PN subtypes that are molecularly and spatially distinct. We found that the PN subtypes exhibit differential vulnerability to partial loss of Atoh1 function, providing insights into the prominence of PN phenotypes in patients with ATOH1 missense mutations.
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Affiliation(s)
- Sih-Rong Wu
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
| | - Jessica C. Butts
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX, USA
| | - Matthew S. Caudill
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
| | - Jean-Pierre Revelli
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ryan S. Dhindsa
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Mark A. Durham
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
- Medical Student Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Huda Y. Zoghbi
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
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2
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Iyer AA, Hosamani I, Nguyen JD, Cai T, Singh S, McGovern MM, Beyer L, Zhang H, Jen HI, Yousaf R, Birol O, Sun JJ, Ray RS, Raphael Y, Segil N, Groves AK. Cellular reprogramming with ATOH1, GFI1, and POU4F3 implicate epigenetic changes and cell-cell signaling as obstacles to hair cell regeneration in mature mammals. eLife 2022; 11:e79712. [PMID: 36445327 PMCID: PMC9708077 DOI: 10.7554/elife.79712] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 11/16/2022] [Indexed: 11/30/2022] Open
Abstract
Reprogramming of the cochlea with hair-cell-specific transcription factors such as ATOH1 has been proposed as a potential therapeutic strategy for hearing loss. ATOH1 expression in the developing cochlea can efficiently induce hair cell regeneration but the efficiency of hair cell reprogramming declines rapidly as the cochlea matures. We developed Cre-inducible mice to compare hair cell reprogramming with ATOH1 alone or in combination with two other hair cell transcription factors, GFI1 and POU4F3. In newborn mice, all transcription factor combinations tested produced large numbers of cells with the morphology of hair cells and rudimentary mechanotransduction properties. However, 1 week later, only a combination of ATOH1, GFI1 and POU4F3 could reprogram non-sensory cells of the cochlea to a hair cell fate, and these new cells were less mature than cells generated by reprogramming 1 week earlier. We used scRNA-seq and combined scRNA-seq and ATAC-seq to suggest at least two impediments to hair cell reprogramming in older animals. First, hair cell gene loci become less epigenetically accessible in non-sensory cells of the cochlea with increasing age. Second, signaling from hair cells to supporting cells, including Notch signaling, can prevent reprogramming of many supporting cells to hair cells, even with three hair cell transcription factors. Our results shed light on the molecular barriers that must be overcome to promote hair cell regeneration in the adult cochlea.
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Affiliation(s)
- Amrita A Iyer
- Department of Molecular & Human Genetics, Baylor College of MedicineHoustonUnited States
| | - Ishwar Hosamani
- Department of Molecular & Human Genetics, Baylor College of MedicineHoustonUnited States
| | - John D Nguyen
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Biology at USCLos AngelesUnited States
| | - Tiantian Cai
- Program in Developmental Biology, Baylor College of MedicineHoustonUnited States
| | - Sunita Singh
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
| | - Melissa M McGovern
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
| | - Lisa Beyer
- Department of Otolaryngology-Head and Neck Surgery, University of MichiganAnn ArborUnited States
| | - Hongyuan Zhang
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
| | - Hsin-I Jen
- Program in Developmental Biology, Baylor College of MedicineHoustonUnited States
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
| | - Rizwan Yousaf
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
| | - Onur Birol
- Program in Developmental Biology, Baylor College of MedicineHoustonUnited States
| | - Jenny J Sun
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
| | - Russell S Ray
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
| | - Yehoash Raphael
- Department of Otolaryngology-Head and Neck Surgery, University of MichiganAnn ArborUnited States
| | - Neil Segil
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Biology at USCLos AngelesUnited States
- Caruso Department of Otolaryngology-Head and Neck Surgery, Keck School of Medicine of the University of Southern CaliforniaLos AngelesUnited States
| | - Andrew K Groves
- Department of Molecular & Human Genetics, Baylor College of MedicineHoustonUnited States
- Program in Developmental Biology, Baylor College of MedicineHoustonUnited States
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
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3
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Višnjar T, Maver A, Writzl K, Maloku O, Bergant G, Jaklič H, Neubauer D, Fogolari F, Pečarič Meglič N, Peterlin B. Biallelic ATOH1 Gene Variant in Siblings With Pontocerebellar Hypoplasia, Developmental Delay, and Hearing Loss. Neurol Genet 2022; 8:e677. [PMID: 35518571 PMCID: PMC9067583 DOI: 10.1212/nxg.0000000000000677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/04/2022] [Indexed: 11/15/2022]
Abstract
Background and Objectives To report on the novel association of biallelic variant in atonal basic helix-loop-helix transcription factor 1 (ATOH1) gene and pontocerebellar hypoplasia (PCH), severe global developmental delay, intellectual disability, and hearing loss in a family with 2 affected siblings. Methods A detailed clinical assessment and exome sequencing of peripheral blood sample were performed. Segregation analysis with Sanger sequencing and structural modeling of the variant was performed to support the pathogenicity of the variant. Results A homozygous missense variant (NM_005172.1:c.481C>G) in the ATOH1 gene was identified in the proband and his affected sister. The segregation analysis subsequently confirmed its segregation with an apparently recessive PCH in this family. ATOH1 encodes for the atonal basic helix-loop-helix (bHLH) transcription factor 1, a core transcription factor in the developing cerebellum, brainstem, and dorsal spinal cord, and in the ear. The identified variant results in the p.(Arg161Gly) amino acid substitution in the evolutionarily conserved DNA-binding bHLH domain of the ATOH1 protein. Biallelic missense variants in this domain were previously reported to result in disordered cerebellar development and hearing loss in animal models. In silico homology modeling revealed that p.Arg161Gly in ATOH1 protein probably disrupts a salt bridge with DNA backbone phosphate and increases the flexibility of the bHLH helix-both of which together affect the binding capability of the bHLH domain to the DNA. Discussion Based on the sequencing results and evidence from structural modeling of the identified variant, as well as with previous reports of ATOH1 gene disruption, we conclude that ATOH1 may represent a novel candidate gene associated with the phenotype of PCH, global developmental delay, and hearing loss in humans.
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Affiliation(s)
- Tanja Višnjar
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Aleš Maver
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Karin Writzl
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Ornela Maloku
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Gaber Bergant
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Helena Jaklič
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - David Neubauer
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Federico Fogolari
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Nuška Pečarič Meglič
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
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4
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Miyashita S, Owa T, Seto Y, Yamashita M, Aida S, Sone M, Ichijo K, Nishioka T, Kaibuchi K, Kawaguchi Y, Taya S, Hoshino M. Cyclin D1 controls development of cerebellar granule cell progenitors through phosphorylation and stabilization of ATOH1. EMBO J 2021; 40:e105712. [PMID: 34057742 PMCID: PMC8280807 DOI: 10.15252/embj.2020105712] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 03/28/2021] [Accepted: 04/01/2021] [Indexed: 12/27/2022] Open
Abstract
During development, neural progenitors are in proliferative and immature states; however, the molecular machinery that cooperatively controls both states remains elusive. Here, we report that cyclin D1 (CCND1) directly regulates both proliferative and immature states of cerebellar granule cell progenitors (GCPs). CCND1 not only accelerates cell cycle but also upregulates ATOH1 protein, an essential transcription factor that maintains GCPs in an immature state. In cooperation with CDK4, CCND1 directly phosphorylates S309 of ATOH1, which inhibits additional phosphorylation at S328 and consequently prevents S328 phosphorylation-dependent ATOH1 degradation. Additionally, PROX1 downregulates Ccnd1 expression by histone deacetylation of Ccnd1 promoter in GCPs, leading to cell cycle exit and differentiation. Moreover, WNT signaling upregulates PROX1 expression in GCPs. These findings suggest that WNT-PROX1-CCND1-ATOH1 signaling cascade cooperatively controls proliferative and immature states of GCPs. We revealed that the expression and phosphorylation levels of these molecules dynamically change during cerebellar development, which are suggested to determine appropriate differentiation rates from GCPs to GCs at distinct developmental stages. This study contributes to understanding the regulatory mechanism of GCPs as well as neural progenitors.
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Affiliation(s)
- Satoshi Miyashita
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Tomoo Owa
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Yusuke Seto
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan.,Laboratory of Developmental Systems, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Mariko Yamashita
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Shogo Aida
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan.,Department of Biomolecular Science, Faculty of Science, Toho University, Chiba, Japan
| | - Masaki Sone
- Department of Biomolecular Science, Faculty of Science, Toho University, Chiba, Japan
| | - Kentaro Ichijo
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan.,Department of Otolaryngology and Head and Neck Surgery, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoki Nishioka
- Department of Cell Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kozo Kaibuchi
- Department of Cell Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiya Kawaguchi
- Department of Life Science Frontiers, Center for iPS cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Shinichiro Taya
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Mikio Hoshino
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
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5
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Iyer AA, Groves AK. Transcription Factor Reprogramming in the Inner Ear: Turning on Cell Fate Switches to Regenerate Sensory Hair Cells. Front Cell Neurosci 2021; 15:660748. [PMID: 33854418 PMCID: PMC8039129 DOI: 10.3389/fncel.2021.660748] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/08/2021] [Indexed: 12/15/2022] Open
Abstract
Non-mammalian vertebrates can restore their auditory and vestibular hair cells naturally by triggering the regeneration of adjacent supporting cells. The transcription factor ATOH1 is a key regulator of hair cell development and regeneration in the inner ear. Following the death of hair cells, supporting cells upregulate ATOH1 and give rise to new hair cells. However, in the mature mammalian cochlea, such natural regeneration of hair cells is largely absent. Transcription factor reprogramming has been used in many tissues to convert one cell type into another, with the long-term hope of achieving tissue regeneration. Reprogramming transcription factors work by altering the transcriptomic and epigenetic landscapes in a target cell, resulting in a fate change to the desired cell type. Several studies have shown that ATOH1 is capable of reprogramming cochlear non-sensory tissue into cells resembling hair cells in young animals. However, the reprogramming ability of ATOH1 is lost with age, implying that the potency of individual hair cell-specific transcription factors may be reduced or lost over time by mechanisms that are still not clear. To circumvent this, combinations of key hair cell transcription factors have been used to promote hair cell regeneration in older animals. In this review, we summarize recent findings that have identified and studied these reprogramming factor combinations for hair cell regeneration. Finally, we discuss the important questions that emerge from these findings, particularly the feasibility of therapeutic strategies using reprogramming factors to restore human hearing in the future.
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Affiliation(s)
- Amrita A. Iyer
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Program in Genetics & Genomics, Houston, TX, United States
| | - Andrew K. Groves
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Program in Genetics & Genomics, Houston, TX, United States
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
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6
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Brownstein Z, Gulsuner S, Walsh T, Martins FTA, Taiber S, Isakov O, Lee MK, Bordeynik-Cohen M, Birkan M, Chang W, Casadei S, Danial-Farran N, Abu-Rayyan A, Carlson R, Kamal L, Arnþórsson ÁÖ, Sokolov M, Gilony D, Lipschitz N, Frydman M, Davidov B, Macarov M, Sagi M, Vinkler C, Poran H, Sharony R, Samara N, Zvi N, Baris-Feldman H, Singer A, Handzel O, Hertzano R, Ali-Naffaa D, Ruhrman-Shahar N, Madgar O, Sofrin E, Peleg A, Khayat M, Shohat M, Basel-Salmon L, Pras E, Lev D, Wolf M, Steingrimsson E, Shomron N, Kelley MW, Kanaan M, Allon-Shalev S, King MC, Avraham KB. Spectrum of genes for inherited hearing loss in the Israeli Jewish population, including the novel human deafness gene ATOH1. Clin Genet 2020; 98:353-364. [PMID: 33111345 PMCID: PMC8045518 DOI: 10.1111/cge.13817] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 12/26/2022]
Abstract
Mutations in more than 150 genes are responsible for inherited hearing loss, with thousands of different, severe causal alleles that vary among populations. The Israeli Jewish population includes communities of diverse geographic origins, revealing a wide range of deafness-associated variants and enabling clinical characterization of the associated phenotypes. Our goal was to identify the genetic causes of inherited hearing loss in this population, and to determine relationships among genotype, phenotype, and ethnicity. Genomic DNA samples from informative relatives of 88 multiplex families, all of self-identified Jewish ancestry, with either non-syndromic or syndromic hearing loss, were sequenced for known and candidate deafness genes using the HEar-Seq gene panel. The genetic causes of hearing loss were identified for 60% of the families. One gene was encountered for the first time in human hearing loss: ATOH1 (Atonal), a basic helix-loop-helix transcription factor responsible for autosomal dominant progressive hearing loss in a five-generation family. Our results show that genomic sequencing with a gene panel dedicated to hearing loss is effective for genetic diagnoses in a diverse population. Comprehensive sequencing enables well-informed genetic counseling and clinical management by medical geneticists, otolaryngologists, audiologists, and speech therapists and can be integrated into newborn screening for deafness.
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Affiliation(s)
- Zippora Brownstein
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Suleyman Gulsuner
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, WA, USA
| | - Tom Walsh
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, WA, USA
| | - Fábio Tadeu Arrojo Martins
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Shahar Taiber
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Ofer Isakov
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ming K. Lee
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, WA, USA
| | - Mor Bordeynik-Cohen
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Maria Birkan
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Raphael Recanati Genetic Institute, Rabin Medical Center–Beilinson Hospital, Tel Aviv University Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Weise Chang
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communications Disorders, NIH, Bethesda, MD, USA
| | - Silvia Casadei
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, WA, USA
| | - Nada Danial-Farran
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Genetics Institute, Ha'Emek Medical Center, Afula, Israel
- Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Amal Abu-Rayyan
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Department of Biological Sciences, Bethlehem University, Bethlehem, Palestine
| | - Ryan Carlson
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, WA, USA
| | - Lara Kamal
- Department of Biological Sciences, Bethlehem University, Bethlehem, Palestine
| | - Ásgeir Örn Arnþórsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Meirav Sokolov
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Department of Otolaryngology - Head and Neck Surgery, Schneider Children's Medical Center, Petach Tikva, Israel
| | - Dror Gilony
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Department of Otolaryngology - Head and Neck Surgery, Schneider Children's Medical Center, Petach Tikva, Israel
| | - Noga Lipschitz
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Department of Otolaryngology - Head and Neck Surgery, Sheba Medical Center, Tel Hashomer, Israel
| | - Moshe Frydman
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Bella Davidov
- Raphael Recanati Genetic Institute, Rabin Medical Center–Beilinson Hospital, Tel Aviv University Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Michal Macarov
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Michal Sagi
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Chana Vinkler
- Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel
| | - Hana Poran
- Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Reuven Sharony
- Genetics Institute, Meir Medical Center, Kfar Saba and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Na’ama Zvi
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | | | - Amihood Singer
- Community Genetics Department, Public Health Services, Ministry of Health, Ramat Gan, Israel
| | - Ophir Handzel
- Department of Otolaryngology Head and Neck Surgery and Maxillofacial Surgery, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Ronna Hertzano
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Doaa Ali-Naffaa
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Human Genetics Institute, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Noa Ruhrman-Shahar
- Raphael Recanati Genetic Institute, Rabin Medical Center–Beilinson Hospital, Tel Aviv University Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Ory Madgar
- Department of Otolaryngology - Head and Neck Surgery, Sheba Medical Center, Tel Hashomer, Israel
| | - Efrat Sofrin
- Raphael Recanati Genetic Institute, Rabin Medical Center–Beilinson Hospital, Tel Aviv University Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Amir Peleg
- Human Genetics Institute, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Morad Khayat
- Genetics Institute, Ha'Emek Medical Center, Afula, Israel
| | - Mordechai Shohat
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel
- Institute of Medical Genetics, Maccabi HMO, Rehovot, Israel
| | - Lina Basel-Salmon
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Raphael Recanati Genetic Institute, Rabin Medical Center–Beilinson Hospital, Tel Aviv University Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Elon Pras
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Dorit Lev
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel
| | - Michael Wolf
- Department of Otolaryngology - Head and Neck Surgery, Sheba Medical Center, Tel Hashomer, Israel
| | - Eirikur Steingrimsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Noam Shomron
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Matthew W. Kelley
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communications Disorders, NIH, Bethesda, MD, USA
| | - Moien Kanaan
- Department of Biological Sciences, Bethlehem University, Bethlehem, Palestine
| | - Stavit Allon-Shalev
- Genetics Institute, Ha'Emek Medical Center, Afula, Israel
- Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Mary-Claire King
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, WA, USA
| | - Karen B. Avraham
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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7
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Zheng L, Yuan H, Zhang M, Wang C, Cai X, Liu J, Xu XQ. Rbm24 regulates inner-ear-specific alternative splicing and is essential for maintaining auditory and motor coordination. RNA Biol 2020; 18:468-480. [PMID: 32887533 DOI: 10.1080/15476286.2020.1817265] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Tissue-specific alternative splicing (AS) is emerging as one of the most exciting types of mechanisms associated with organ development and disease. In the auditory system, many hearing-related genes undergo AS, and errors in this process result in syndromic or non-syndromic hearing loss. However, little is known about the factors and mechanisms directing AS in the inner ear. In the present study, we identified a novel RNA-binding protein, Rbm24, which was critically involved in regulating inner-ear-specific AS. Rbm24 deletion resulted in hearing loss and defects in motor coordination. Global splicing analysis showed Rbm24 was required for correct splicing of a subset of pre-mRNA transcripts with essential roles in stereocilia integrity and survival of hair cells. Furthermore, we identified that Rbm24 directly regulated the splicing of Cdh23, a known disease gene responsible for human Usher syndrome 1D and non-syndromic autosomal recessive deafness DFNB12. In conclusion, our findings demonstrated that Rbm24 was a critical factor in regulating inner-ear-specific splicing and maintaining the hearing and motor coordination function of the inner ear. Our data not only offer mechanistic insights but also provide functional annotation of Rbm24 splicing targets that contribute to hearing loss.
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Affiliation(s)
- Longqing Zheng
- The Institute of Stem Cell and Regenerative Medicine, School of Medicine, Xiamen University, Xiamen, China
| | - Huijun Yuan
- Medical Genetics Center, Southwest Hospital, Army Medical University, Chongqing, China
| | - Mengkai Zhang
- The Institute of Stem Cell and Regenerative Medicine, School of Medicine, Xiamen University, Xiamen, China
| | - Cuicui Wang
- Medical Genetics Center, Southwest Hospital, Army Medical University, Chongqing, China
| | - Xuemin Cai
- The Institute of Stem Cell and Regenerative Medicine, School of Medicine, Xiamen University, Xiamen, China
| | - Jing Liu
- The Institute of Stem Cell and Regenerative Medicine, School of Medicine, Xiamen University, Xiamen, China.,Shenzhen Research Institute, Xiamen University, P.R. China
| | - Xiu Qin Xu
- The Institute of Stem Cell and Regenerative Medicine, School of Medicine, Xiamen University, Xiamen, China
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8
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Nadar-Ponniah PT, Taiber S, Caspi M, Koffler-Brill T, Dror AA, Siman-Tov R, Rubinstein M, Padmanabhan K, Luxenburg C, Lang RA, Avraham KB, Rosin-Arbesfeld R. Striatin Is Required for Hearing and Affects Inner Hair Cells and Ribbon Synapses. Front Cell Dev Biol 2020; 8:615. [PMID: 32766247 PMCID: PMC7381154 DOI: 10.3389/fcell.2020.00615] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 06/22/2020] [Indexed: 12/22/2022] Open
Abstract
Striatin, a subunit of the serine/threonine phosphatase PP2A, is a core member of the conserved striatin-interacting phosphatase and kinase (STRIPAK) complexes. The protein is expressed in the cell junctions between epithelial cells, which play a role in maintaining cell-cell adhesion. Since the cell junctions are crucial for the function of the mammalian inner ear, we examined the localization and function of striatin in the mouse cochlea. Our results show that in neonatal mice, striatin is specifically expressed in the cell-cell junctions of the inner hair cells, the receptor cells in the mammalian cochlea. Auditory brainstem response measurements of striatin-deficient mice indicated a progressive, high-frequency hearing loss, suggesting that striatin is essential for normal hearing. Moreover, scanning electron micrographs of the organ of Corti revealed a moderate degeneration of the outer hair cells in the middle and basal regions, concordant with the high-frequency hearing loss. Additionally, striatin-deficient mice show aberrant ribbon synapse maturation. Loss of the outer hair cells, combined with the aberrant ribbon synapse distribution, may lead to the observed auditory impairment. Together, these results suggest a novel function for striatin in the mammalian auditory system.
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Affiliation(s)
- Prathamesh T. Nadar-Ponniah
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shahar Taiber
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Michal Caspi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tal Koffler-Brill
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Amiel A. Dror
- Department of Otolaryngology, Head and Neck Surgery, Galilee Medical Center, Nahariya, Israel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Ronen Siman-Tov
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Moran Rubinstein
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Goldschleger Eye Research Institute, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Krishnanand Padmanabhan
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chen Luxenburg
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Richard A. Lang
- Visual Systems Group, Abrahamson Pediatric Eye Institute, Division of Pediatric Ophthalmology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Karen B. Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Rina Rosin-Arbesfeld
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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9
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Homeostatic maintenance and age-related functional decline in the Drosophila ear. Sci Rep 2020; 10:7431. [PMID: 32366993 PMCID: PMC7198581 DOI: 10.1038/s41598-020-64498-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/13/2020] [Indexed: 01/12/2023] Open
Abstract
Age-related hearing loss (ARHL) is a threat to future human wellbeing. Multiple factors contributing to the terminal auditory decline have been identified; but a unified understanding of ARHL - or the homeostatic maintenance of hearing before its breakdown - is missing. We here present an in-depth analysis of homeostasis and ageing in the antennal ears of the fruit fly Drosophila melanogaster. We show that Drosophila, just like humans, display ARHL. By focusing on the phase of dynamic stability prior to the eventual hearing loss we discovered a set of evolutionarily conserved homeostasis genes. The transcription factors Onecut (closest human orthologues: ONECUT2, ONECUT3), Optix (SIX3, SIX6), Worniu (SNAI2) and Amos (ATOH1, ATOH7, ATOH8, NEUROD1) emerged as key regulators, acting upstream of core components of the fly’s molecular machinery for auditory transduction and amplification. Adult-specific manipulation of homeostatic regulators in the fly’s auditory neurons accelerated - or protected against - ARHL.
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10
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Gennarino VA, Palmer EE, McDonell LM, Wang L, Adamski CJ, Koire A, See L, Chen CA, Schaaf CP, Rosenfeld JA, Panzer JA, Moog U, Hao S, Bye A, Kirk EP, Stankiewicz P, Breman AM, McBride A, Kandula T, Dubbs HA, Macintosh R, Cardamone M, Zhu Y, Ying K, Dias KR, Cho MT, Henderson LB, Baskin B, Morris P, Tao J, Cowley MJ, Dinger ME, Roscioli T, Caluseriu O, Suchowersky O, Sachdev RK, Lichtarge O, Tang J, Boycott KM, Holder JL, Zoghbi HY. A Mild PUM1 Mutation Is Associated with Adult-Onset Ataxia, whereas Haploinsufficiency Causes Developmental Delay and Seizures. Cell 2019; 172:924-936.e11. [PMID: 29474920 DOI: 10.1016/j.cell.2018.02.006] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 08/23/2017] [Accepted: 02/01/2018] [Indexed: 02/06/2023]
Abstract
Certain mutations can cause proteins to accumulate in neurons, leading to neurodegeneration. We recently showed, however, that upregulation of a wild-type protein, Ataxin1, caused by haploinsufficiency of its repressor, the RNA-binding protein Pumilio1 (PUM1), also causes neurodegeneration in mice. We therefore searched for human patients with PUM1 mutations. We identified eleven individuals with either PUM1 deletions or de novo missense variants who suffer a developmental syndrome (Pumilio1-associated developmental disability, ataxia, and seizure; PADDAS). We also identified a milder missense mutation in a family with adult-onset ataxia with incomplete penetrance (Pumilio1-related cerebellar ataxia, PRCA). Studies in patient-derived cells revealed that the missense mutations reduced PUM1 protein levels by ∼25% in the adult-onset cases and by ∼50% in the infantile-onset cases; levels of known PUM1 targets increased accordingly. Changes in protein levels thus track with phenotypic severity, and identifying posttranscriptional modulators of protein expression should identify new candidate disease genes.
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Affiliation(s)
- Vincenzo A Gennarino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA.
| | - Elizabeth E Palmer
- Sydney Children's Hospital, Randwick, NSW 2031, Australia; School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, NSW 2031, Australia; Genetics of Learning Disability Service, Waratah, NSW 2298, Australia
| | - Laura M McDonell
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Li Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Carolyn J Adamski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amanda Koire
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lauren See
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chun-An Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jessica A Panzer
- Department of Pediatrics, Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ute Moog
- Institute of Human Genetics, Heidelberg University, Im Neuenheimer Feld 440, 69120 Heidelberg, Germany
| | - Shuang Hao
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ann Bye
- Sydney Children's Hospital, Randwick, NSW 2031, Australia; School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, NSW 2031, Australia
| | - Edwin P Kirk
- Sydney Children's Hospital, Randwick, NSW 2031, Australia; School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, NSW 2031, Australia; Genetics Laboratory, NSW Health Pathology East Randwick, Sydney, NSW, Australia
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratories, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amy M Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratories, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arran McBride
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Tejaswi Kandula
- Sydney Children's Hospital, Randwick, NSW 2031, Australia; School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, NSW 2031, Australia
| | - Holly A Dubbs
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | - Michael Cardamone
- Sydney Children's Hospital, Randwick, NSW 2031, Australia; School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, NSW 2031, Australia
| | - Ying Zhu
- Genetics Laboratory, NSW Health Pathology East Randwick, Sydney, NSW, Australia
| | - Kevin Ying
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Kerith-Rae Dias
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Megan T Cho
- GeneDx, 207 Perry Pkwy Gaithersburg, MD 20877, USA
| | | | | | - Paula Morris
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Jiang Tao
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Mark J Cowley
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Marcel E Dinger
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Tony Roscioli
- Sydney Children's Hospital, Randwick, NSW 2031, Australia; Genetics Laboratory, NSW Health Pathology East Randwick, Sydney, NSW, Australia; Neuroscience Research Australia and Prince of Wales Clinical School, University of New South Wales, Randwick, NSW 2031, Australia
| | - Oana Caluseriu
- Department of Medical Genetics, University of Alberta, AB T6G 2H7, Canada
| | - Oksana Suchowersky
- Department of Medical Genetics, University of Alberta, AB T6G 2H7, Canada; Departments of Medicine (Neurology) and Pediatrics, University of Alberta, AB, Canada
| | - Rani K Sachdev
- Sydney Children's Hospital, Randwick, NSW 2031, Australia; School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, NSW 2031, Australia
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jianrong Tang
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - J Lloyd Holder
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Huda Y Zoghbi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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11
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Atkinson PJ, Kim GS, Cheng AG. Direct cellular reprogramming and inner ear regeneration. Expert Opin Biol Ther 2019; 19:129-139. [PMID: 30584811 DOI: 10.1080/14712598.2019.1564035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
INTRODUCTION Sound is integral to communication and connects us to the world through speech and music. Cochlear hair cells are essential for converting sounds into neural impulses. However, these cells are highly susceptible to damage from an array of factors, resulting in degeneration and ultimately irreversible hearing loss in humans. Since the discovery of hair cell regeneration in birds, there have been tremendous efforts to identify therapies that could promote hair cell regeneration in mammals. AREAS COVERED Here, we will review recent studies describing spontaneous hair cell regeneration and direct cellular reprograming as well as other factors that mediate mammalian hair cell regeneration. EXPERT OPINION Numerous combinatorial approaches have successfully reprogrammed non-sensory supporting cells to form hair cells, albeit with limited efficacy and maturation. Studies on epigenetic regulation and transcriptional network of hair cell progenitors may accelerate discovery of more promising reprogramming regimens.
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Affiliation(s)
- Patrick J Atkinson
- a Department of Otolaryngology-Head and Neck Surgery , Stanford University School of Medicine , Stanford , CA , USA
| | - Grace S Kim
- a Department of Otolaryngology-Head and Neck Surgery , Stanford University School of Medicine , Stanford , CA , USA
| | - Alan G Cheng
- a Department of Otolaryngology-Head and Neck Surgery , Stanford University School of Medicine , Stanford , CA , USA
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12
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Zeng X, Kirkpatrick R, Hofmann G, Grillot D, Linhart V, Viviani F, Marino J, Boyer J, Graham TL, Lu Q, Wu Z, Benowitz A, Cousins R. Screen for modulators of atonal homolog 1 gene expression using notch pathway-relevant gene transcription based cellular assays. PLoS One 2018; 13:e0207140. [PMID: 30540745 PMCID: PMC6291236 DOI: 10.1371/journal.pone.0207140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 10/25/2018] [Indexed: 12/11/2022] Open
Abstract
Atonal homolog 1 (Atoh1) is a basic helix-loop-helix 9 (bHLH) transcription factor acting downstream of Notch and is required for the differentiation of sensory hair cells in the inner ear and the specification of secretory cells during the intestinal crypt cell regeneration. Motivated by the observations that the upregulation of Atoh1 gene expression, through genetic manipulation or pharmacological inhibition of Notch signaling (e.g. γ-secretase inhibitors, GSIs), induces ectopic hair cell growth in the cochlea of the inner ear and partially restores hearing after injuries in experimental models, we decided to identify small molecule modulators of the Notch-Atoh1 pathway, which could potentially regenerate hair cells. However, the lack of cellular models of the inner ear has precluded the screening and characterization of such modulators. Here we report using a colon cancer cell line LS-174T, which displays Notch inhibition-dependent Atoh1 expression as a surrogate cellular model to screen for inducers of Atoh1 expression. We designed an Atoh1 promoter-driven luciferase assay to screen a target-annotated library of ~6000 compounds. We further developed a medium throughput, real-time quantitative RT-PCR assay measuring the endogenous Atoh1 gene expression to confirm the hits and eliminate false positives from the reporter-based screen. This strategy allowed us to successfully recover GSIs of known chemotypes. This LS-174T cell-based assay directly measures Atoh1 gene expression induced through Notch-Hes1 inhibition, and therefore offers an opportunity to identify novel cellular modulators along the Notch-Atoh1 pathway.
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Affiliation(s)
- Xin Zeng
- R&D Target Sciences, GlaxoSmithKline, Upper Providence, Collegeville, United States of America
- * E-mail: (XZ); (RC)
| | - Robert Kirkpatrick
- R&D Alternative Discovery and Development, GlaxoSmithKline, Upper Providence, Collegeville, United States of America
| | - Glenn Hofmann
- R&D Platform Technology Sciences, Drug Design and Selection, GlaxoSmithKline, Upper Providence, Collegeville, United States of America
| | - Didier Grillot
- R&D Flexible Discovery Unit, Villebon-sur-Yvette, Paris, France
| | - Valerie Linhart
- R&D Flexible Discovery Unit, Villebon-sur-Yvette, Paris, France
| | - Fabrice Viviani
- R&D Flexible Discovery Unit, Villebon-sur-Yvette, Paris, France
| | - Joseph Marino
- R&D Alternative Discovery and Development, GlaxoSmithKline, Upper Providence, Collegeville, United States of America
| | - Joseph Boyer
- R&D Statistical sciences, GlaxoSmithKline, Upper Providence, Collegeville, United States of America
| | - Taylor L. Graham
- R&D Target Sciences, GlaxoSmithKline, Upper Providence, Collegeville, United States of America
| | - Quinn Lu
- R&D Target Sciences, GlaxoSmithKline, Upper Providence, Collegeville, United States of America
| | - Zining Wu
- R&D Platform Technology Sciences, Drug Design and Selection, GlaxoSmithKline, Upper Providence, Collegeville, United States of America
| | - Andrew Benowitz
- R&D Alternative Discovery and Development, GlaxoSmithKline, Upper Providence, Collegeville, United States of America
| | - Rick Cousins
- R&D Alternative Discovery and Development, GlaxoSmithKline, Stevenage, Hertfordshire, United Kingdom
- * E-mail: (XZ); (RC)
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13
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Molecular therapy for genetic and degenerative vestibular disorders. Curr Opin Otolaryngol Head Neck Surg 2018; 26:307-311. [PMID: 30045104 DOI: 10.1097/moo.0000000000000477] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE OF REVIEW The primary purpose of this review is to summarize current literature in the field of vestibular regeneration with a focus on recent developments in molecular and gene therapies. RECENT FINDINGS Since the discovery of limited vestibular hair cell regeneration in mammals in the 1990s, many elegant studies have improved our knowledge of mechanisms of development and regeneration of the vestibular system. A better understanding of the developmental pathways of the vestibular organs has fueled various biological strategies to enhance regeneration, including novel techniques in deriving vestibular hair cells from embryonic and induced pluripotent stem cells. In addition, the identification of specific genetic mutations responsible for vestibular disorders has opened various opportunities for gene replacement therapy. SUMMARY Vestibular dysfunction is a significant clinical problem with limited therapeutic options, warranting research on biological strategies to repair/regenerate the vestibular organs to restore function. The use of gene therapy appears promising in animal models of vestibular dysfunction.
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14
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Baker NE, Brown NL. All in the family: proneural bHLH genes and neuronal diversity. Development 2018; 145:145/9/dev159426. [PMID: 29720483 DOI: 10.1242/dev.159426] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Proneural basic Helix-Loop-Helix (bHLH) proteins are required for neuronal determination and the differentiation of most neural precursor cells. These transcription factors are expressed in vastly divergent organisms, ranging from sponges to primates. Here, we review proneural bHLH gene evolution and function in the Drosophila and vertebrate nervous systems, arguing that the Drosophila gene atonal provides a useful platform for understanding proneural gene structure and regulation. We also discuss how functional equivalency experiments using distinct proneural genes can reveal how proneural gene duplication and divergence are interwoven with neuronal complexity.
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Affiliation(s)
- Nicholas E Baker
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
| | - Nadean L Brown
- Department of Cell Biology and Human Anatomy, University of California, One Shields Avenue, Davis, CA 95616 USA
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15
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Dennis DJ, Han S, Schuurmans C. bHLH transcription factors in neural development, disease, and reprogramming. Brain Res 2018; 1705:48-65. [PMID: 29544733 DOI: 10.1016/j.brainres.2018.03.013] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/07/2018] [Accepted: 03/10/2018] [Indexed: 01/16/2023]
Abstract
The formation of functional neural circuits in the vertebrate central nervous system (CNS) requires that appropriate numbers of the correct types of neuronal and glial cells are generated in their proper places and times during development. In the embryonic CNS, multipotent progenitor cells first acquire regional identities, and then undergo precisely choreographed temporal identity transitions (i.e. time-dependent changes in their identity) that determine how many neuronal and glial cells of each type they will generate. Transcription factors of the basic-helix-loop-helix (bHLH) family have emerged as key determinants of neural cell fate specification and differentiation, ensuring that appropriate numbers of specific neuronal and glial cell types are produced. Recent studies have further revealed that the functions of these bHLH factors are strictly regulated. Given their essential developmental roles, it is not surprising that bHLH mutations and de-regulated expression are associated with various neurological diseases and cancers. Moreover, the powerful ability of bHLH factors to direct neuronal and glial cell fate specification and differentiation has been exploited in the relatively new field of cellular reprogramming, in which pluripotent stem cells or somatic stem cells are converted to neural lineages, often with a transcription factor-based lineage conversion strategy that includes one or more of the bHLH genes. These concepts are reviewed herein.
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Affiliation(s)
- Daniel J Dennis
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N3M5, Canada
| | - Sisu Han
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Carol Schuurmans
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
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Miesfeld JB, Glaser T, Brown NL. The dynamics of native Atoh7 protein expression during mouse retinal histogenesis, revealed with a new antibody. Gene Expr Patterns 2018; 27:114-121. [PMID: 29225067 PMCID: PMC5835195 DOI: 10.1016/j.gep.2017.11.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/17/2017] [Accepted: 11/28/2017] [Indexed: 12/19/2022]
Abstract
The Atoh7 transcription factor catalyzes the rate-limiting step in the specification of retinal ganglion cells (RGCs). As a tool to study vertebrate retinal development, we validate an antibody that recognizes human and mouse Atoh7 polypeptide, using informative knockout and transgenic mouse tissues and overexpression experiments. The transient features of Atoh7 protein expression during retinal neurogenesis match the expected pattern at the tissue and cellular level. Further, we compare endogenous Atoh7 to established RGC markers, reporter mouse lines and cell cycle markers, demonstrating the utility of the antibody to investigate molecular mechanisms of retinal histogenesis.
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Affiliation(s)
- Joel B Miesfeld
- Department of Cell Biology & Human Anatomy, University of California, Davis School of Medicine, One Shields Avenue, Davis, CA 95616, United States
| | - Tom Glaser
- Department of Cell Biology & Human Anatomy, University of California, Davis School of Medicine, One Shields Avenue, Davis, CA 95616, United States
| | - Nadean L Brown
- Department of Cell Biology & Human Anatomy, University of California, Davis School of Medicine, One Shields Avenue, Davis, CA 95616, United States.
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