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Cepeda AP, Ninov M, Neef J, Parfentev I, Kusch K, Reisinger E, Jahn R, Moser T, Urlaub H. Proteomic Analysis Reveals the Composition of Glutamatergic Organelles of Auditory Inner Hair Cells. Mol Cell Proteomics 2024; 23:100704. [PMID: 38128648 PMCID: PMC10832297 DOI: 10.1016/j.mcpro.2023.100704] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 11/08/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023] Open
Abstract
In the ear, inner hair cells (IHCs) employ sophisticated glutamatergic ribbon synapses with afferent neurons to transmit auditory information to the brain. The presynaptic machinery responsible for neurotransmitter release in IHC synapses includes proteins such as the multi-C2-domain protein otoferlin and the vesicular glutamate transporter 3 (VGluT3). Yet, much of this likely unique molecular machinery remains to be deciphered. The scarcity of material has so far hampered biochemical studies which require large amounts of purified samples. We developed a subcellular fractionation workflow combined with immunoisolation of VGluT3-containing membrane vesicles, allowing for the enrichment of glutamatergic organelles that are likely dominated by synaptic vesicles (SVs) of IHCs. We have characterized their protein composition in mice before and after hearing onset using mass spectrometry and confocal imaging and provide a fully annotated proteome with hitherto unidentified proteins. Despite the prevalence of IHC marker proteins across IHC maturation, the profiles of trafficking proteins differed markedly before and after hearing onset. Among the proteins enriched after hearing onset were VAMP-7, syntaxin-7, syntaxin-8, syntaxin-12/13, SCAMP1, V-ATPase, SV2, and PKCα. Our study provides an inventory of the machinery associated with synaptic vesicle-mediated trafficking and presynaptic activity at IHC ribbon synapses and serves as a foundation for future functional studies.
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Affiliation(s)
- Andreia P Cepeda
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Momchil Ninov
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Jakob Neef
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany; Auditory Neuroscience & Synaptic Nanophysiology Group Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Iwan Parfentev
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Kathrin Kusch
- Functional Auditory Genomics Group, Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Ellen Reisinger
- Gene Therapy for Hearing Impairment and Deafness, Department for Otolaryngology, Head & Neck Surgery, University Hospital Tübingen, Tübingen, Germany
| | - Reinhard Jahn
- Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
| | - Tobias Moser
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany; Auditory Neuroscience & Synaptic Nanophysiology Group Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
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2
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A V, Kumar A, Mahala S, Chandra Janga S, Chauhan A, Mehrotra A, Kumar De A, Ranjan Sahu A, Firdous Ahmad S, Vempadapu V, Dutt T. Revelation of genetic diversity and genomic footprints of adaptation in Indian pig breeds. Gene 2024; 893:147950. [PMID: 37918549 DOI: 10.1016/j.gene.2023.147950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/16/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
In the present study, the genetic diversity measures among four Indian domestic breeds of pig namely Agonda Goan, Ghurrah, Ghungroo, and Nicobari, of different agro-climatic regions of country were explored and compared with European commercial breeds, European wild boar and Chinese domestic breeds. The double digest restriction site-associated DNA sequencing (ddRADseq) data of Indian pigs (102) and Landrace (10 animals) were generated and whole genome sequencing data of exotic pigs (60 animals) from public data repository were used in the study. The principal component analysis (PCA), admixture analysis and phylogenetic analysis revealed that Indian breeds were closer in ancestry to Chinese breeds than European breeds. European breeds exhibited highest genetic diversity measures among all the considered breeds. Among Indian breeds, Agonda Goan and Ghurrah were found to be more genetically diverse than Nicobari and Ghungroo. The selection signature regions in Indian pigs were explored using iHS and XP-EHH, and during iHS analysis, it was observed that genes related to growth, reproduction, health, meat quality, sensory perception and behavior were found to be under selection pressure in Indian pig breeds. Strong selection signatures were recorded in 24.25-25.25 Mb region of SSC18, 123.25-124 Mb region of SSC15 and 118.75-119.5 Mb region of SSC2 in most of the Indian breeds upon pairwise comparison with European commercial breeds using XP-EHH. These regions were harboring some important genes such as EPHA4 for thermotolerance, TAS2R16, FEZF1, CADPS2 and PTPRZ1 for adaptability to scavenging system of rearing, TRIM36 and PGGT1B for disease resistance and CCDC112, PIAS1, FEM1B and ITGA11 for reproduction.
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Affiliation(s)
- Vani A
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Amit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India.
| | - Sudarshan Mahala
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Sarath Chandra Janga
- Luddy School of Informatics, Computing, and Engineering, Indiana University, IUPUI, Indianapolis, IN, USA
| | - Anuj Chauhan
- Livestock Production and Management, Indian Veterinary Research Institute, Bareilly, UP, India
| | | | - Arun Kumar De
- Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Amiya Ranjan Sahu
- Central Coastal Agricultural Research Institute, Old Goa, Goa, India
| | - Sheikh Firdous Ahmad
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Varshini Vempadapu
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Triveni Dutt
- Livestock Production and Management, Indian Veterinary Research Institute, Bareilly, UP, India
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Baxi AB, Nemes P, Moody SA. Time-resolved quantitative proteomic analysis of the developing Xenopus otic vesicle reveals putative congenital hearing loss candidates. iScience 2023; 26:107665. [PMID: 37670778 PMCID: PMC10475516 DOI: 10.1016/j.isci.2023.107665] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/16/2023] [Accepted: 08/14/2023] [Indexed: 09/07/2023] Open
Abstract
Over 200 genes are known to underlie human congenital hearing loss (CHL). Although transcriptomic approaches have identified candidate regulators of otic development, little is known about the abundance of their protein products. We used a multiplexed quantitative mass spectrometry-based proteomic approach to determine protein abundances over key stages of Xenopus otic morphogenesis to reveal a dynamic expression of cytoskeletal, integrin signaling, and extracellular matrix proteins. We correlated these dynamically expressed proteins to previously published lists of putative downstream targets of human syndromic hearing loss genes: SIX1 (BOR syndrome), CHD7 (CHARGE syndrome), and SOX10 (Waardenburg syndrome). We identified transforming growth factor beta-induced (Tgfbi), an extracellular integrin-interacting protein, as a putative target of Six1 that is required for normal otic vesicle formation. Our findings demonstrate the application of this Xenopus dataset to understanding the dynamic regulation of proteins during otic development and to discovery of additional candidates for human CHL.
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Affiliation(s)
- Aparna B. Baxi
- Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
| | - Peter Nemes
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Sally A. Moody
- Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
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Asaad M, Mahfood M, Al Mutery A, Tlili A. Loss-of-function mutations in MYO15A and OTOF cause non-syndromic hearing loss in two Yemeni families. Hum Genomics 2023; 17:42. [PMID: 37189200 DOI: 10.1186/s40246-023-00489-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 05/06/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND Hearing loss is a rare hereditary deficit that is rather common among consanguineous populations. Autosomal recessive non-syndromic hearing loss is the predominant form of hearing loss worldwide. Although prevalent, hearing loss is extremely heterogeneous and poses a pitfall in terms of diagnosis and screening. Using next-generation sequencing has enabled a rapid increase in the identification rate of genes and variants in heterogeneous conditions, including hearing loss. We aimed to identify the causative variants in two consanguineous Yemeni families affected with hearing loss using targeted next-generation sequencing (clinical exome sequencing). The proband of each family was presented with sensorineural hearing loss as indicated by pure-tone audiometry results. RESULTS We explored variants obtained from both families, and our analyses collectively revealed the presence and segregation of two novel loss-of-function variants: a frameshift variant, c.6347delA in MYO15A in Family I, and a splice site variant, c.5292-2A > C, in OTOF in Family II. Sanger sequencing and PCR-RFLP of DNA samples from 130 deaf and 50 control individuals confirmed that neither variant was present in our in-house database. In silico analyses predicted that each variant has a pathogenic effect on the corresponding protein. CONCLUSIONS We describe two novel loss-of-function variants in MYO15A and OTOF that cause autosomal recessive non-syndromic hearing loss in Yemeni families. Our findings are consistent with previously reported pathogenic variants in the MYO15A and OTOF genes in Middle Eastern individuals and suggest their implication in hearing loss.
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Affiliation(s)
- Maria Asaad
- Department of Applied Biology, College of Sciences, University of Sharjah, Building W8 - Room 107, P.O. Box 27272, Sharjah, UAE
| | - Mona Mahfood
- Department of Applied Biology, College of Sciences, University of Sharjah, Building W8 - Room 107, P.O. Box 27272, Sharjah, UAE
| | - Abdullah Al Mutery
- Department of Applied Biology, College of Sciences, University of Sharjah, Building W8 - Room 107, P.O. Box 27272, Sharjah, UAE
- Human Genetics and Stem Cells Research Group, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah, UAE
| | - Abdelaziz Tlili
- Department of Applied Biology, College of Sciences, University of Sharjah, Building W8 - Room 107, P.O. Box 27272, Sharjah, UAE.
- Human Genetics and Stem Cells Research Group, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah, UAE.
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Chohra I, Chung K, Giri S, Malgrange B. ATP-Dependent Chromatin Remodellers in Inner Ear Development. Cells 2023; 12:cells12040532. [PMID: 36831199 PMCID: PMC9954591 DOI: 10.3390/cells12040532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
During transcription, DNA replication and repair, chromatin structure is constantly modified to reveal specific genetic regions and allow access to DNA-interacting enzymes. ATP-dependent chromatin remodelling complexes use the energy of ATP hydrolysis to modify chromatin architecture by repositioning and rearranging nucleosomes. These complexes are defined by a conserved SNF2-like, catalytic ATPase subunit and are divided into four families: CHD, SWI/SNF, ISWI and INO80. ATP-dependent chromatin remodellers are crucial in regulating development and stem cell biology in numerous organs, including the inner ear. In addition, mutations in genes coding for proteins that are part of chromatin remodellers have been implicated in numerous cases of neurosensory deafness. In this review, we describe the composition, structure and functional activity of these complexes and discuss how they contribute to hearing and neurosensory deafness.
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Shahbazi M, Zhang X, Dinh PC, Sanchez VA, Trendowski MR, Shuey MM, Nguyen T, Feldman DR, Vaughn DJ, Fung C, Kollmannsberger C, Martin NE, Einhorn LH, Cox NJ, Frisina RD, Travis LB, Dolan ME. Comprehensive association analysis of speech recognition thresholds after cisplatin-based chemotherapy in survivors of adult-onset cancer. Cancer Med 2023; 12:2999-3012. [PMID: 36097363 PMCID: PMC9939144 DOI: 10.1002/cam4.5218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/14/2022] [Accepted: 08/17/2022] [Indexed: 11/05/2022] Open
Abstract
PURPOSE Deficits in speech understanding constitute one of the most severe consequences of hearing loss. Here we investigate the clinical and genetic risk factors for symmetric deterioration of speech recognition thresholds (SRT) among cancer survivors treated with cisplatin. METHODS SRT was measured using spondaic words and calculating the mean of measurements for both ears with symmetric SRT values. For clinical associations, SRT-based hearing disability (SHD) was defined as SRT≥15 dB hearing loss and clinical variables were derived from the study dataset. Genotyped blood samples were used for GWAS with rank-based inverse normal transformed SRT values as the response variable. Age was used as a covariate in association analyses. RESULTS SHD was inversely associated with self-reported health (p = 0.004). Current smoking (p = 0.002), years of smoking (p = 0.02), BMI (p < 0.001), and peripheral motor neuropathy (p = 0.003) were positively associated with SHD, while physical activity was inversely associated with SHD (p = 0.005). In contrast, cumulative cisplatin dose, peripheral sensory neuropathy, hypertension, and hypercholesterolemia were not associated with SHD. Although no genetic variants had an association p value < 5 × 10-8 , 22 genetic variants were suggestively associated (p < 10-5 ) with SRT deterioration. Three of the top variants in 10 respective linkage disequilibrium regions were either positioned within the coding sequence or were eQTLs for genes involved in neuronal development (ATE1, ENAH, and ZFHX3). CONCLUSION Current results improve our understanding of risk factors for SRT deterioration in cancer survivors. Higher BMI, lower physical activity, and smoking are associated with SHD. Larger samples would allow for expansion of the current findings on the genetic architecture of SRT.
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Affiliation(s)
| | - Xindi Zhang
- Department of MedicineUniversity of ChicagoChicagoIllinoisUSA
| | - Paul C. Dinh
- Department of Medical OncologyIndiana UniversityIndianapolisIndianaUSA
| | - Victoria A. Sanchez
- Department of Otolaryngology—Head and Neck SurgeryUniversity of South FloridaTampaFloridaUSA
| | | | - Megan M. Shuey
- Department of Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Tessa Nguyen
- Center for Audiology, Speech, Language and LearningNorthwesthern UniversityChicagoIllinoisUSA
| | | | - Darren R. Feldman
- Department of Medical Oncology, Memorial Sloan‐Kettering Cancer CenterNew YorkNew YorkUSA
| | - David J. Vaughn
- Department of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Chunkit Fung
- J.P. Wilmot Cancer Institute, University of Rochester Medical CenterRochesterNew YorkUSA
| | | | - Neil E. Martin
- Department of Radiation OncologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
| | | | - Nancy J. Cox
- Department of Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Robert D. Frisina
- Departments of Medical Engineering and Communication Sciences and Disorders, Global Center for Hearing and Speech ResearchUniversity of South FloridaTampaFloridaUSA
| | - Lois B. Travis
- Department of Medical OncologyIndiana UniversityIndianapolisIndianaUSA
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Rutherford MA, Bhattacharyya A, Xiao M, Cai HM, Pal I, Rubio ME. GluA3 subunits are required for appropriate assembly of AMPAR GluA2 and GluA4 subunits on cochlear afferent synapses and for presynaptic ribbon modiolar-pillar morphology. eLife 2023; 12:e80950. [PMID: 36648432 PMCID: PMC9891727 DOI: 10.7554/elife.80950] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 01/16/2023] [Indexed: 01/18/2023] Open
Abstract
Cochlear sound encoding depends on α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptors (AMPARs), but reliance on specific pore-forming subunits is unknown. With 5-week-old male C57BL/6J Gria3-knockout mice (i.e., subunit GluA3KO) we determined cochlear function, synapse ultrastructure, and AMPAR molecular anatomy at ribbon synapses between inner hair cells (IHCs) and spiral ganglion neurons. GluA3KO and wild-type (GluA3WT) mice reared in ambient sound pressure level (SPL) of 55-75 dB had similar auditory brainstem response (ABR) thresholds, wave-1 amplitudes, and latencies. Postsynaptic densities (PSDs), presynaptic ribbons, and synaptic vesicle sizes were all larger on the modiolar side of the IHCs from GluA3WT, but not GluA3KO, demonstrating GluA3 is required for modiolar-pillar synapse differentiation. Presynaptic ribbons juxtaposed with postsynaptic GluA2/4 subunits were similar in quantity, however, lone ribbons were more frequent in GluA3KO and GluA2-lacking synapses were observed only in GluA3KO. GluA2 and GluA4 immunofluorescence volumes were smaller on the pillar side than the modiolar side in GluA3KO, despite increased pillar-side PSD size. Overall, the fluorescent puncta volumes of GluA2 and GluA4 were smaller in GluA3KO than GluA3WT. However, GluA3KO contained less GluA2 and greater GluA4 immunofluorescence intensity relative to GluA3WT (threefold greater mean GluA4:GluA2 ratio). Thus, GluA3 is essential in development, as germline disruption of Gria3 caused anatomical synapse pathology before cochlear output became symptomatic by ABR. We propose the hearing loss in older male GluA3KO mice results from progressive synaptopathy evident in 5-week-old mice as decreased abundance of GluA2 subunits and an increase in GluA2-lacking, GluA4-monomeric Ca2+-permeable AMPARs.
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Affiliation(s)
- Mark A Rutherford
- Department of Otolaryngology, Washington University School of MedicineSt LouisUnited States
| | - Atri Bhattacharyya
- Department of Otolaryngology, Washington University School of MedicineSt LouisUnited States
| | - Maolei Xiao
- Department of Otolaryngology, Washington University School of MedicineSt LouisUnited States
| | - Hou-Ming Cai
- Department of Neurobiology, University of Pittsburgh School of MedicinePittsburghUnited States
| | - Indra Pal
- Department of Neurobiology, University of Pittsburgh School of MedicinePittsburghUnited States
| | - Maria Eulalia Rubio
- Department of Neurobiology, University of Pittsburgh School of MedicinePittsburghUnited States
- Department of Otolaryngology, University of Pittsburgh School of MedicinePittsburghUnited States
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Ramirez MA, Ninoyu Y, Miller C, Andrade LR, Edassery S, Bomba-Warczak E, Ortega B, Manor U, Rutherford MA, Friedman RA, Savas JN. Cochlear ribbon synapse maturation requires Nlgn1 and Nlgn3. iScience 2022; 25:104803. [PMID: 35992071 PMCID: PMC9386149 DOI: 10.1016/j.isci.2022.104803] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 05/10/2022] [Accepted: 07/15/2022] [Indexed: 01/13/2023] Open
Abstract
Hearing depends on precise synaptic transmission between cochlear inner hair cells and spiral ganglion neurons through afferent ribbon synapses. Neuroligins (Nlgns) facilitate synapse maturation in the brain, but they have gone unstudied in the cochlea. We report Nlgn3 and Nlgn1 knockout (KO) cochleae have fewer ribbon synapses and have impaired hearing. Nlgn3 KO is more vulnerable to noise trauma with limited activity at high frequencies one day after noise. Furthermore, Nlgn3 KO cochleae have a 5-fold reduction in synapse number compared to wild type after two weeks of recovery. Double KO cochlear phenotypes are more prominent than the KOs, for example, 5-fold smaller synapses, 25% reduction in synapse density, and 30% less synaptic output. These observations indicate Nlgn3 and Nlgn1 are essential to cochlear ribbon synapse maturation and function.
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Affiliation(s)
- Miguel A. Ramirez
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yuzuru Ninoyu
- Division of Otolaryngology, Department of Surgery, University of California, San Diego, 9500 Gilman Drive, Mail Code 0666, La Jolla, CA 92093, USA
| | - Cayla Miller
- Waitt Advanced Biophotonics Core, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Leonardo R. Andrade
- Waitt Advanced Biophotonics Core, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Seby Edassery
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ewa Bomba-Warczak
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Briana Ortega
- Division of Otolaryngology, Department of Surgery, University of California, San Diego, 9500 Gilman Drive, Mail Code 0666, La Jolla, CA 92093, USA
| | - Uri Manor
- Waitt Advanced Biophotonics Core, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Mark A. Rutherford
- Department of Otolaryngology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Rick A. Friedman
- Division of Otolaryngology, Department of Surgery, University of California, San Diego, 9500 Gilman Drive, Mail Code 0666, La Jolla, CA 92093, USA
| | - Jeffrey N. Savas
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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Smith RS, Takagishi SR, Amici DR, Metz K, Gayatri S, Alasady MJ, Wu Y, Brockway S, Taiberg SL, Khalatyan N, Taipale M, Santagata S, Whitesell L, Lindquist S, Savas JN, Mendillo ML. HSF2 cooperates with HSF1 to drive a transcriptional program critical for the malignant state. SCIENCE ADVANCES 2022; 8:eabj6526. [PMID: 35294249 PMCID: PMC8926329 DOI: 10.1126/sciadv.abj6526] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 01/25/2022] [Indexed: 05/14/2023]
Abstract
Heat shock factor 1 (HSF1) is well known for its role in the heat shock response (HSR), where it drives a transcriptional program comprising heat shock protein (HSP) genes, and in tumorigenesis, where it drives a program comprising HSPs and many noncanonical target genes that support malignancy. Here, we find that HSF2, an HSF1 paralog with no substantial role in the HSR, physically and functionally interacts with HSF1 across diverse types of cancer. HSF1 and HSF2 have notably similar chromatin occupancy and regulate a common set of genes that include both HSPs and noncanonical transcriptional targets with roles critical in supporting malignancy. Loss of either HSF1 or HSF2 results in a dysregulated response to nutrient stresses in vitro and reduced tumor progression in cancer cell line xenografts. Together, these findings establish HSF2 as a critical cofactor of HSF1 in driving a cancer cell transcriptional program to support the anabolic malignant state.
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Affiliation(s)
- Roger S. Smith
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Seesha R. Takagishi
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Biochemistry and Biophysics, UCSF, San Francisco, CA 94158, USA
- Tetrad Graduate Program, UCSF, San Francisco, CA 94143, USA
| | - David R. Amici
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kyle Metz
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Sitaram Gayatri
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Milad J. Alasady
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yaqi Wu
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Master of Biotechnology Program, Northwestern University, Evanston, IL 60208, USA
| | - Sonia Brockway
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Stephanie L. Taiberg
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Natalia Khalatyan
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Mikko Taipale
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Molecular Architecture of Life Program, Canadian Institute for Advanced Research (CIFAR), Toronto, ON, Canada
| | - Sandro Santagata
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Ludwig Center at Harvard, Boston, MA 02115, USA
| | - Luke Whitesell
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Jeffrey N. Savas
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Marc L. Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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10
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Mahshid SS, Higazi AM, Ogier JM, Dabdoub A. Extracellular Biomarkers of Inner Ear Disease and Their Potential for Point-of-Care Diagnostics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2104033. [PMID: 34957708 PMCID: PMC8948604 DOI: 10.1002/advs.202104033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 11/09/2021] [Indexed: 06/14/2023]
Abstract
Rapid diagnostic testing has become a mainstay of patient care, using easily obtained samples such as blood or urine to facilitate sample analysis at the point-of-care. These tests rely on the detection of disease or organ-specific biomarkers that have been well characterized for a particular disorder. Currently, there is no rapid diagnostic test for hearing loss, which is one of the most prevalent sensory disorders in the world. In this review, potential biomarkers for inner ear-related disorders, their detection, and quantification in bodily fluids are described. The authors discuss lesion-specific changes in cell-free deoxyribonucleic acids (DNAs), micro-ribonucleic acids (microRNAs), proteins, and metabolites, in addition to recent biosensor advances that may facilitate rapid and precise detection of these molecules. Ultimately, these biomarkers may be used to provide accurate diagnostics regarding the site of damage in the inner ear, providing practical information for individualized therapy and assessment of treatment efficacy in the future.
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Affiliation(s)
- Sahar Sadat Mahshid
- Biological SciencesSunnybrook Research InstituteSunnybrook Health Sciences CentreTorontoONM4N 3M5Canada
| | - Aliaa Monir Higazi
- Biological SciencesSunnybrook Research InstituteSunnybrook Health Sciences CentreTorontoONM4N 3M5Canada
- Department of Clinical and Chemical PathologyMinia UniversityMinia61519Egypt
| | - Jacqueline Michelle Ogier
- Biological SciencesSunnybrook Research InstituteSunnybrook Health Sciences CentreTorontoONM4N 3M5Canada
| | - Alain Dabdoub
- Biological SciencesSunnybrook Research InstituteSunnybrook Health Sciences CentreTorontoONM4N 3M5Canada
- Department of Otolaryngology–Head & Neck SurgeryUniversity of TorontoTorontoONM5G 2C4Canada
- Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoONM5S 1A8Canada
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11
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Martín-de-Saavedra MD, Dos Santos M, Culotta L, Varea O, Spielman BP, Parnell E, Forrest MP, Gao R, Yoon S, McCoig E, Jalloul HA, Myczek K, Khalatyan N, Hall EA, Turk LS, Sanz-Clemente A, Comoletti D, Lichtenthaler SF, Burgdorf JS, Barbolina MV, Savas JN, Penzes P. Shed CNTNAP2 ectodomain is detectable in CSF and regulates Ca 2+ homeostasis and network synchrony via PMCA2/ATP2B2. Neuron 2022; 110:627-643.e9. [PMID: 34921780 PMCID: PMC8857041 DOI: 10.1016/j.neuron.2021.11.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/11/2021] [Accepted: 11/19/2021] [Indexed: 11/29/2022]
Abstract
Although many neuronal membrane proteins undergo proteolytic cleavage, little is known about the biological significance of neuronal ectodomain shedding (ES). Here, we show that the neuronal sheddome is detectable in human cerebrospinal fluid (hCSF) and is enriched in neurodevelopmental disorder (NDD) risk factors. Among shed synaptic proteins is the ectodomain of CNTNAP2 (CNTNAP2-ecto), a prominent NDD risk factor. CNTNAP2 undergoes activity-dependent ES via MMP9 (matrix metalloprotease 9), and CNTNAP2-ecto levels are reduced in the hCSF of individuals with autism spectrum disorder. Using mass spectrometry, we identified the plasma membrane Ca2+ ATPase (PMCA) extrusion pumps as novel CNTNAP2-ecto binding partners. CNTNAP2-ecto enhances the activity of PMCA2 and regulates neuronal network dynamics in a PMCA2-dependent manner. Our data underscore the promise of sheddome analysis in discovering neurobiological mechanisms, provide insight into the biology of ES and its relationship with the CSF, and reveal a mechanism of regulation of Ca2+ homeostasis and neuronal network synchrony by a shed ectodomain.
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Affiliation(s)
| | - Marc Dos Santos
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Lorenza Culotta
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Olga Varea
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Benjamin P Spielman
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Euan Parnell
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Marc P Forrest
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ruoqi Gao
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Sehyoun Yoon
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Emmarose McCoig
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Hiba A Jalloul
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kristoffer Myczek
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Natalia Khalatyan
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Elizabeth A Hall
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Liam S Turk
- Child Health Institute of New Jersey, New Brunswick, NJ 08901, USA; Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Antonio Sanz-Clemente
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Davide Comoletti
- Child Health Institute of New Jersey, New Brunswick, NJ 08901, USA; Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA; Department of Pediatrics, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA; School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Stefan F Lichtenthaler
- German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany; Department of Neuroproteomics, School of Medicine, Klinikum rechts der Isar, and Institute for Advanced Study, Technical University of Munich, 81675 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
| | - Jeffrey S Burgdorf
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Autism and Neurodevelopment, Northwestern University, Chicago, IL 60611, USA; Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Maria V Barbolina
- Department of Biopharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Jeffrey N Savas
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Peter Penzes
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Autism and Neurodevelopment, Northwestern University, Chicago, IL 60611, USA; Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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12
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Hogan AK, Sathyan KM, Willis AB, Khurana S, Srivastava S, Zasadzińska E, Lee AS, Bailey AO, Gaynes MN, Huang J, Bodner J, Rosencrance CD, Wong KA, Morgan MA, Eagen KP, Shilatifard A, Foltz DR. UBR7 acts as a histone chaperone for post-nucleosomal histone H3. EMBO J 2021; 40:e108307. [PMID: 34786730 PMCID: PMC8672181 DOI: 10.15252/embj.2021108307] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 09/24/2021] [Accepted: 10/22/2021] [Indexed: 12/13/2022] Open
Abstract
Histone chaperones modulate the stability of histones beginning from histone synthesis, through incorporation into DNA, and during recycling during transcription and replication. Following histone removal from DNA, chaperones regulate histone storage and degradation. Here, we demonstrate that UBR7 is a histone H3.1 chaperone that modulates the supply of pre-existing post-nucleosomal histone complexes. We demonstrate that UBR7 binds to post-nucleosomal H3K4me3 and H3K9me3 histones via its UBR box and PHD. UBR7 binds to the non-nucleosomal histone chaperone NASP. In the absence of UBR7, the pool of NASP-bound post-nucleosomal histones accumulate and chromatin is depleted of H3K4me3-modified histones. We propose that the interaction of UBR7 with NASP and histones opposes the histone storage functions of NASP and that UBR7 promotes reincorporation of post-nucleosomal H3 complexes.
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Affiliation(s)
- Ann K Hogan
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Kizhakke M Sathyan
- R. D. Berlin Center for Cell Analysis and ModelingThe University of Connecticut School of MedicineFarmingtonCTUSA
| | - Alexander B Willis
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Sakshi Khurana
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Shashank Srivastava
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Ewelina Zasadzińska
- Drug Substance TechnologiesProcess Development, Amgen Inc.Thousand OaksCAUSA
| | - Alexander S Lee
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Aaron O Bailey
- Department of Biochemistry and Molecular BiologyUniversity of Texas Medical BranchGalvestonTXUSA
| | - Matthew N Gaynes
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Jiehuan Huang
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Justin Bodner
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Celeste D Rosencrance
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Kelvin A Wong
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Marc A Morgan
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
- Robert H. Lurie Comprehensive Cancer CenterNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Kyle P Eagen
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
- Robert H. Lurie Comprehensive Cancer CenterNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
- Robert H. Lurie Comprehensive Cancer CenterNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Daniel R Foltz
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
- Robert H. Lurie Comprehensive Cancer CenterNorthwestern University Feinberg School of MedicineChicagoILUSA
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13
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Morgan MAJ, Popova IK, Vaidya A, Burg JM, Marunde MR, Rendleman EJ, Dumar ZJ, Watson R, Meiners MJ, Howard SA, Khalatyan N, Vaughan RM, Rothbart SB, Keogh MC, Shilatifard A. A trivalent nucleosome interaction by PHIP/BRWD2 is disrupted in neurodevelopmental disorders and cancer. Genes Dev 2021; 35:1642-1656. [PMID: 34819353 PMCID: PMC8653789 DOI: 10.1101/gad.348766.121] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/09/2021] [Indexed: 11/24/2022]
Abstract
Mutations in the PHIP/BRWD2 chromatin regulator cause the human neurodevelopmental disorder Chung-Jansen syndrome, while alterations in PHIP expression are linked to cancer. Precisely how PHIP functions in these contexts is not fully understood. Here we demonstrate that PHIP is a chromatin-associated CRL4 ubiquitin ligase substrate receptor and is required for CRL4 recruitment to chromatin. PHIP binds to chromatin through a trivalent reader domain consisting of a H3K4-methyl binding Tudor domain and two bromodomains (BD1 and BD2). Using semisynthetic nucleosomes with defined histone post-translational modifications, we characterize PHIPs BD1 and BD2 as respective readers of H3K14ac and H4K12ac, and identify human disease-associated mutations in each domain and the intervening linker region that likely disrupt chromatin binding. These findings provide new insight into the biological function of this enigmatic chromatin protein and set the stage for the identification of both upstream chromatin modifiers and downstream targets of PHIP in human disease.
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Affiliation(s)
- Marc A J Morgan
- Simpson Querrey Center for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | | | - Anup Vaidya
- EpiCypher, Inc., Durham, North Carolina 27709, USA
| | | | | | - Emily J Rendleman
- Simpson Querrey Center for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Zachary J Dumar
- Simpson Querrey Center for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | | | | | | | - Natalia Khalatyan
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Robert M Vaughan
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, Minnesota 49503, USA
| | - Scott B Rothbart
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, Minnesota 49503, USA
| | | | - Ali Shilatifard
- Simpson Querrey Center for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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14
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Norrie disease protein is essential for cochlear hair cell maturation. Proc Natl Acad Sci U S A 2021; 118:2106369118. [PMID: 34544869 DOI: 10.1073/pnas.2106369118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2021] [Indexed: 11/18/2022] Open
Abstract
Mutations in the gene for Norrie disease protein (Ndp) cause syndromic deafness and blindness. We show here that cochlear function in an Ndp knockout mouse deteriorated with age: At P3-P4, hair cells (HCs) showed progressive loss of Pou4f3 and Gfi1, key transcription factors for HC maturation, and Myo7a, a specialized myosin required for normal function of HC stereocilia. Loss of expression of these genes correlated to increasing HC loss and profound hearing loss by 2 mo. We show that overexpression of the Ndp gene in neonatal supporting cells or, remarkably, up-regulation of canonical Wnt signaling in HCs rescued HCs and cochlear function. We conclude that Ndp secreted from supporting cells orchestrates a transcriptional network for the maintenance and survival of HCs and that increasing the level of β-catenin, the intracellular effector of Wnt signaling, is sufficient to replace the functional requirement for Ndp in the cochlea.
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15
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Roman-Naranjo P, Moleon MDC, Aran I, Escalera-Balsera A, Soto-Varela A, Bächinger D, Gomez-Fiñana M, Eckhard AH, Lopez-Escamez JA. Rare coding variants involving MYO7A and other genes encoding stereocilia link proteins in familial meniere disease. Hear Res 2021; 409:108329. [PMID: 34391192 DOI: 10.1016/j.heares.2021.108329] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/27/2021] [Accepted: 07/27/2021] [Indexed: 11/25/2022]
Abstract
The MYO7A gene encodes a motor protein with a key role in the organization of stereocilia in auditory and vestibular hair cells. Rare variants in the MYO7A (myosin VIIA) gene may cause autosomal dominant (AD) or autosomal recessive (AR) sensorineural hearing loss (SNHL) accompanied by vestibular dysfunction or retinitis pigmentosa (Usher syndrome type 1B). Familial Meniere's disease (MD) is a rare inner ear syndrome mainly characterized by low-frequency sensorineural hearing loss and episodic vertigo associated with tinnitus. Familial aggregation has been found in 6-8% of sporadic cases, and most of the reported genes were involved in single families. Thus, this study aimed to search for relevant genes not previously linked to familial MD. Through exome sequencing and segregation analysis in 62 MD families, we have found a total of 1 novel and 8 rare heterozygous variants in the MYO7A gene in 9 non-related families. Carriers of rare variants in MYO7A showed autosomal dominant or autosomal recessive SNHL in familial MD. Additionally, some novel and rare variants in other genes involved in the organization of the stereocilia links such as CDH23, PCDH15 or ADGRV1 co-segregated in the same patients. Our findings reveal a co-segregation of rare variants in the MYO7A gene and other structural myosin VIIA binding proteins involved in the tip and ankle links of the hair cell stereocilia. We suggest that recessive digenic inheritance involving these genes could affect the ultrastructure of the stereocilia links in familial MD.
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Affiliation(s)
- P Roman-Naranjo
- Otology & Neurotology Group CTS 495, Department of Genomic Medicine, Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica, GENYO, Granada, Spain
| | - M D C Moleon
- Otology & Neurotology Group CTS 495, Department of Genomic Medicine, Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica, GENYO, Granada, Spain; Department of Otolaryngology, Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria, ibs.GRANADA, Granada, Spain
| | - I Aran
- Department of Otolaryngology, Complexo Hospitalario de Pontevedra, Pontevedra, Spain
| | - A Escalera-Balsera
- Otology & Neurotology Group CTS 495, Department of Genomic Medicine, Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica, GENYO, Granada, Spain
| | - A Soto-Varela
- Division of Otoneurology, Department of Otorhinolaryngology, Complexo Hospitalario Universitario, Santiago de Compostela, Spain
| | - D Bächinger
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Zurich, Zurich, Switzerland; University of Zurich, Zurich, Switzerland
| | - M Gomez-Fiñana
- Department of Otolaryngology, Hospital de Poniente, El Ejido, Almeria, Spain
| | - A H Eckhard
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Zurich, Zurich, Switzerland; University of Zurich, Zurich, Switzerland
| | - J A Lopez-Escamez
- Otology & Neurotology Group CTS 495, Department of Genomic Medicine, Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica, GENYO, Granada, Spain; Department of Otolaryngology, Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria, ibs.GRANADA, Granada, Spain; Department of Surgery, Division of Otolaryngology, Universidad de Granada, Granada, Spain.
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16
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Moreira A, Croze M, Delehelle F, Cussat-Blanc S, Luga H, Mollereau C, Balaresque P. Hearing Sensitivity of Primates: Recurrent and Episodic Positive Selection in Hair Cells and Stereocilia Protein-Coding Genes. Genome Biol Evol 2021; 13:6302699. [PMID: 34137817 PMCID: PMC8358225 DOI: 10.1093/gbe/evab133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2021] [Indexed: 12/29/2022] Open
Abstract
The large spectrum of hearing sensitivity observed in primates results from the impact of environmental and behavioral pressures to optimize sound perception and localization. Although evidence of positive selection in auditory genes has been detected in mammals including in Hominoids, selection has never been investigated in other primates. We analyzed 123 genes highly expressed in the inner ear of 27 primate species and tested to what extent positive selection may have shaped these genes in the order Primates tree. We combined both site and branch-site tests to obtain a comprehensive picture of the positively selected genes (PSGs) involved in hearing sensitivity, and drew a detailed description of the most affected branches in the tree. We chose a conservative approach, and thus focused on confounding factors potentially affecting PSG signals (alignment, GC-biased gene conversion, duplications, heterogeneous sequencing qualities). Using site tests, we showed that around 12% of these genes are PSGs, an α selection value consistent with average human genome estimates (10-15%). Using branch-site tests, we showed that the primate tree is heterogeneously affected by positive selection, with the black snub-nosed monkey, the bushbaby, and the orangutan, being the most impacted branches. A large proportion of these genes is inclined to shape hair cells and stereocilia, which are involved in the mechanotransduction process, known to influence frequency perception. Adaptive selection, and more specifically recurrent adaptive evolution, could have acted in parallel on a set of genes (ADGRV1, USH2A, PCDH15, PTPRQ, and ATP8A2) involved in stereocilia growth and the whole complex of bundle links connecting them, in species across different habitats, including high altitude and nocturnal environments.
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Affiliation(s)
- Andreia Moreira
- Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Faculté de Médecine Purpan, CNRS UMR5288, Université de Toulouse, Université Toulouse III Paul Sabatier, France.,Institut de Recherche en Informatique de Toulouse (IRIT), CNRS UMR5505, Université Toulouse III Paul Sabatier, France
| | - Myriam Croze
- Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Faculté de Médecine Purpan, CNRS UMR5288, Université de Toulouse, Université Toulouse III Paul Sabatier, France
| | - Franklin Delehelle
- Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Faculté de Médecine Purpan, CNRS UMR5288, Université de Toulouse, Université Toulouse III Paul Sabatier, France.,Institut de Recherche en Informatique de Toulouse (IRIT), CNRS UMR5505, Université Toulouse III Paul Sabatier, France
| | - Sylvain Cussat-Blanc
- Institut de Recherche en Informatique de Toulouse (IRIT), CNRS UMR5505, Université Toulouse III Paul Sabatier, France
| | - Hervé Luga
- Institut de Recherche en Informatique de Toulouse (IRIT), CNRS UMR5505, Université Toulouse III Paul Sabatier, France
| | - Catherine Mollereau
- Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Faculté de Médecine Purpan, CNRS UMR5288, Université de Toulouse, Université Toulouse III Paul Sabatier, France
| | - Patricia Balaresque
- Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Faculté de Médecine Purpan, CNRS UMR5288, Université de Toulouse, Université Toulouse III Paul Sabatier, France
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17
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Ivarsdottir EV, Holm H, Benonisdottir S, Olafsdottir T, Sveinbjornsson G, Thorleifsson G, Eggertsson HP, Halldorsson GH, Hjorleifsson KE, Melsted P, Gylfason A, Arnadottir GA, Oddsson A, Jensson BO, Jonasdottir A, Jonasdottir A, Juliusdottir T, Stefansdottir L, Tragante V, Halldorsson BV, Petersen H, Thorgeirsson G, Thorsteinsdottir U, Sulem P, Hinriksdottir I, Jonsdottir I, Gudbjartsson DF, Stefansson K. The genetic architecture of age-related hearing impairment revealed by genome-wide association analysis. Commun Biol 2021; 4:706. [PMID: 34108613 PMCID: PMC8190123 DOI: 10.1038/s42003-021-02224-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 05/17/2021] [Indexed: 02/05/2023] Open
Abstract
Age-related hearing impairment (ARHI) is the most common sensory disorder in older adults. We conducted a genome-wide association meta-analysis of 121,934 ARHI cases and 591,699 controls from Iceland and the UK. We identified 21 novel sequence variants, of which 13 are rare, under either additive or recessive models. Of special interest are a missense variant in LOXHD1 (MAF = 1.96%) and a tandem duplication in FBF1 covering 4 exons (MAF = 0.22%) associating with ARHI (OR = 3.7 for homozygotes, P = 1.7 × 10-22 and OR = 4.2 for heterozygotes, P = 5.7 × 10-27, respectively). We constructed an ARHI genetic risk score (GRS) using common variants and showed that a common variant GRS can identify individuals at risk comparable to carriers of rare high penetrance variants. Furthermore, we found that ARHI and tinnitus share genetic causes. This study sheds a new light on the genetic architecture of ARHI, through several rare variants in both Mendelian deafness genes and genes not previously linked to hearing.
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Affiliation(s)
- Erna V Ivarsdottir
- deCODE Genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Hilma Holm
- deCODE Genetics/Amgen, Reykjavik, Iceland
| | | | | | | | | | | | - Gisli H Halldorsson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Kristjan E Hjorleifsson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Pall Melsted
- deCODE Genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | | | | | | | | | - Bjarni V Halldorsson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- School of Technology, Reykjavik University, Reykjavik, Iceland
| | - Hannes Petersen
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Akureyri Hospital, Akureyri, Iceland
| | - Gudmundur Thorgeirsson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Division of Cardiology, Department of Internal Medicine, Landspitali University Hospital, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | - Ingileif Jonsdottir
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Department of Immunology, Landspitali University Hospital, Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Reykjavik, Iceland.
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland.
| | - Kari Stefansson
- deCODE Genetics/Amgen, Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
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18
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Srivastava S, Sahu U, Zhou Y, Hogan AK, Sathyan KM, Bodner J, Huang J, Wong KA, Khalatyan N, Savas JN, Ntziachristos P, Ben-Sahra I, Foltz DR. NOTCH1-driven UBR7 stimulates nucleotide biosynthesis to promote T cell acute lymphoblastic leukemia. SCIENCE ADVANCES 2021; 7:eabc9781. [PMID: 33571115 PMCID: PMC7840127 DOI: 10.1126/sciadv.abc9781] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
Ubiquitin protein ligase E3 component N-recognin 7 (UBR7) is the most divergent member of UBR box-containing E3 ubiquitin ligases/recognins that mediate the proteasomal degradation of its substrates through the N-end rule. Here, we used a proteomic approach and found phosphoribosyl pyrophosphate synthetases (PRPSs), the essential enzymes for nucleotide biosynthesis, as strong interacting partners of UBR7. UBR7 stabilizes PRPS catalytic subunits by mediating the polyubiquitination-directed degradation of PRPS-associated protein (PRPSAP), the negative regulator of PRPS. Loss of UBR7 leads to nucleotide biosynthesis defects. We define UBR7 as a transcriptional target of NOTCH1 and show that UBR7 is overexpressed in NOTCH1-driven T cell acute lymphoblastic leukemia (T-ALL). Impaired nucleotide biosynthesis caused by UBR7 depletion was concomitant with the attenuated cell proliferation and oncogenic potential of T-ALL. Collectively, these results establish UBR7 as a critical regulator of nucleotide metabolism through the regulation of the PRPS enzyme complex and uncover a metabolic vulnerability in NOTCH1-driven T-ALL.
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Affiliation(s)
- Shashank Srivastava
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Umakant Sahu
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yalu Zhou
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ann K Hogan
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kizhakke Mattada Sathyan
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Justin Bodner
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jiehuan Huang
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kelvin A Wong
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Natalia Khalatyan
- Department of Neurology Northwestern University, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jeffrey N Savas
- Department of Neurology Northwestern University, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Panagiotis Ntziachristos
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Issam Ben-Sahra
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Daniel R Foltz
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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19
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Jongkamonwiwat N, Ramirez MA, Edassery S, Wong ACY, Yu J, Abbott T, Pak K, Ryan AF, Savas JN. Noise Exposures Causing Hearing Loss Generate Proteotoxic Stress and Activate the Proteostasis Network. Cell Rep 2020; 33:108431. [PMID: 33238128 PMCID: PMC7722268 DOI: 10.1016/j.celrep.2020.108431] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 09/24/2020] [Accepted: 11/04/2020] [Indexed: 12/20/2022] Open
Abstract
Exposure to excessive sound causes noise-induced hearing loss through complex mechanisms and represents a common and unmet neurological condition. We investigate how noise insults affect the cochlea with proteomics and functional assays. Quantitative proteomics reveals that exposure to loud noise causes proteotoxicity. We identify and confirm hundreds of proteins that accumulate, including cytoskeletal proteins, and several nodes of the proteostasis network. Transcriptomic analysis reveals that a subset of the genes encoding these proteins also increases acutely after noise exposure, including numerous proteasome subunits. Global cochlear protein ubiquitylation levels build up after exposure to excess noise, and we map numerous posttranslationally modified lysines residues. Several collagen proteins decrease in abundance, and Col9a1 specifically localizes to pillar cell heads. After two weeks of recovery, the cochlea selectively elevates the abundance of the protein synthesis machinery. We report that overstimulation of the auditory system drives a robust cochlear proteotoxic stress response.
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Affiliation(s)
- Nopporn Jongkamonwiwat
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Miguel A Ramirez
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Seby Edassery
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ann C Y Wong
- Departments of Surgery and Neuroscience, University of California San Diego and Veterans Administration Medical Center, La Jolla, CA 92093, USA; Translational Neuroscience Facility, Department of Physiology, NSW Australia, Sydney, NSW 2052, Australia
| | - Jintao Yu
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Tirzah Abbott
- Northwestern University Atomic and Nanoscale Characterization Experimental (NUANCE) Center, Northwestern University, Evanston, IL 60208, USA
| | - Kwang Pak
- Departments of Surgery and Neuroscience, University of California San Diego and Veterans Administration Medical Center, La Jolla, CA 92093, USA
| | - Allen F Ryan
- Departments of Surgery and Neuroscience, University of California San Diego and Veterans Administration Medical Center, La Jolla, CA 92093, USA
| | - Jeffrey N Savas
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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20
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Rickels R, Wang L, Iwanaszko M, Ozark PA, Morgan MA, Piunti A, Khalatyan N, Soliman SHA, Rendleman EJ, Savas JN, Smith ER, Shilatifard A. A small UTX stabilization domain of Trr is conserved within mammalian MLL3-4/COMPASS and is sufficient to rescue loss of viability in null animals. Genes Dev 2020; 34:1493-1502. [PMID: 33033055 PMCID: PMC7608747 DOI: 10.1101/gad.339762.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 09/09/2020] [Indexed: 12/19/2022]
Abstract
Catalytic-inactivating mutations within the Drosophila enhancer H3K4 mono-methyltransferase Trr and its mammalian homologs, MLL3/4, cause only minor changes in gene expression compared with whole-gene deletions for these COMPASS members. To identify essential histone methyltransferase-independent functions of Trr, we screened to identify a minimal Trr domain sufficient to rescue Trr-null lethality and demonstrate that this domain binds and stabilizes Utx in vivo. Using the homologous MLL3/MLL4 human sequences, we mapped a short ∼80-amino-acid UTX stabilization domain (USD) that promotes UTX stability in the absence of the rest of MLL3/4. Nuclear UTX stability is enhanced when the USD is fused with the MLL4 HMG-box. Thus, COMPASS-dependent UTX stabilization is an essential noncatalytic function of Trr/MLL3/MLL4, suggesting that stabilizing UTX could be a therapeutic strategy for cancers with MLL3/4 loss-of-function mutations.
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Affiliation(s)
- Ryan Rickels
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Lu Wang
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Marta Iwanaszko
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Patrick A Ozark
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Marc A Morgan
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Andrea Piunti
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Natalia Khalatyan
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Shimaa H A Soliman
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Emily J Rendleman
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Jeffrey N Savas
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Edwin R Smith
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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21
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Sadler E, Ryals MM, May LA, Martin D, Welsh N, Boger ET, Morell RJ, Hertzano R, Cunningham LL. Cell-Specific Transcriptional Responses to Heat Shock in the Mouse Utricle Epithelium. Front Cell Neurosci 2020; 14:123. [PMID: 32528249 PMCID: PMC7247426 DOI: 10.3389/fncel.2020.00123] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/15/2020] [Indexed: 12/21/2022] Open
Abstract
Sensory epithelia of the inner ear contain mechanosensory hair cells (HCs) and glia-like supporting cells (SCs), both of which are required for hearing and balance functions. Each of these cell types has unique responses to ototoxic and cytoprotective stimuli. Non-lethal heat stress in the mammalian utricle induces heat shock proteins (HSPs) and protects against ototoxic drug-induced hair cell death. Induction of HSPs in the utricle demonstrates cell-type specificity at the protein level, with HSP70 induction occurring primarily in SCs, while HSP32 (also known as heme oxygenase 1, HMOX1) is induced primarily in resident macrophages. Neither of these HSPs are robustly induced in HCs, suggesting that HCs may have little capacity for induction of stress-induced protective responses. To determine the transcriptional responses to heat shock of these different cell types, we performed cell-type-specific transcriptional profiling using the RiboTag method, which allows for immunoprecipitation (IP) of actively translating mRNAs from specific cell types. RNA-Seq differential gene expression analyses demonstrated that the RiboTag method identified known cell type-specific markers as well as new markers for HCs and SCs. Gene expression differences suggest that HCs and SCs exhibit differential transcriptional heat shock responses. The chaperonin family member Cct8 was significantly enriched only in heat-shocked HCs, while Hspa1l (HSP70 family), and Hspb1 and Cryab (HSP27 and HSP20 families, respectively) were enriched only in SCs. Together our data indicate that HCs exhibit a limited but unique heat shock response, and SCs exhibit a broader and more robust transcriptional response to protective heat stress.
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Affiliation(s)
- Erica Sadler
- Section on Sensory Cell Biology, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, United States
| | - Matthew M Ryals
- Section on Sensory Cell Biology, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, United States.,Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Lindsey A May
- Section on Sensory Cell Biology, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, United States
| | - Daniel Martin
- Genomics and Computational Biology Core, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, United States.,Genomics and Computational Biology Core, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, United States
| | - Nora Welsh
- Section on Sensory Cell Biology, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, United States
| | - Erich T Boger
- Genomics and Computational Biology Core, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, United States
| | - Robert J Morell
- Genomics and Computational Biology Core, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, United States
| | - Ronna Hertzano
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States.,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States.,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Lisa L Cunningham
- Section on Sensory Cell Biology, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, United States
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22
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Hayward JJ, Kelly-Smith M, Boyko AR, Burmeister L, De Risio L, Mellersh C, Freeman J, Strain GM. A genome-wide association study of deafness in three canine breeds. PLoS One 2020; 15:e0232900. [PMID: 32413090 PMCID: PMC7228063 DOI: 10.1371/journal.pone.0232900] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 04/23/2020] [Indexed: 12/17/2022] Open
Abstract
Congenital deafness in the domestic dog is usually related to the presence of white pigmentation, which is controlled primarily by the piebald locus on chromosome 20 and also by merle on chromosome 10. Pigment-associated deafness is also seen in other species, including cats, mice, sheep, alpacas, horses, cows, pigs, and humans, but the genetic factors determining why some piebald or merle dogs develop deafness while others do not have yet to be determined. Here we perform a genome-wide association study (GWAS) to identify regions of the canine genome significantly associated with deafness in three dog breeds carrying piebald: Dalmatian, Australian cattle dog, and English setter. We include bilaterally deaf, unilaterally deaf, and matched control dogs from the same litter, phenotyped using the brainstem auditory evoked response (BAER) hearing test. Principal component analysis showed that we have different distributions of cases and controls in genetically distinct Dalmatian populations, therefore GWAS was performed separately for North American and UK samples. We identified one genome-wide significant association and 14 suggestive (chromosome-wide) associations using the GWAS design of bilaterally deaf vs. control Australian cattle dogs. However, these associations were not located on the same chromosome as the piebald locus, indicating the complexity of the genetics underlying this disease in the domestic dog. Because of this apparent complex genetic architecture, larger sample sizes may be needed to detect the genetic loci modulating risk in piebald dogs.
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Affiliation(s)
- Jessica J. Hayward
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Maria Kelly-Smith
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Adam R. Boyko
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | | | - Luisa De Risio
- Animal Health Trust, Newmarket, Suffolk, England, United Kingdom
| | - Cathryn Mellersh
- Animal Health Trust, Newmarket, Suffolk, England, United Kingdom
| | - Julia Freeman
- Animal Health Trust, Newmarket, Suffolk, England, United Kingdom
| | - George M. Strain
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, United States of America
- * E-mail:
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23
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Kelly-Smith M, Strain GM. STRING data mining of GWAS data in canine hereditary pigment-associated deafness. Vet Anim Sci 2020; 9:100118. [PMID: 32734119 PMCID: PMC7386748 DOI: 10.1016/j.vas.2020.100118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/06/2020] [Indexed: 02/06/2023] Open
Abstract
Genome-wide association studies may fail to identify significant associations between a disorder and causative genes in complex hereditary disorders. STRING software is a bioinformatics data mining tool that identifies known and predicted physical and functional relationship networks among the proteins of candidate genes. STRING analysis provides a mechanism to identify gene-gene interactions that might not otherwise have been recognized. Relationships identified from STRING analysis can uncover function-based gene-gene relationships that may not be easily extracted from literature, thereby providing genes for pursuit as a cause of a complex hereditary disorder. In this study STRING analysis was applied to identification of candidate genes to pursue as the cause of pigment-associated hereditary deafness in dogs.
Most canine deafness is linked to white pigmentation caused by the piebald locus, shown to be the gene MITF (melanocyte inducing transcription factor), but studies have failed to identify a deafness cause. The coding regions of MITF have not been shown to be mutated in deaf dogs, leading us to pursue genes acting on or controlled by MITF. We have genotyped DNA from 502 deaf and hearing Australian cattle dogs, Dalmatians, and English setters, breeds with a high deafness prevalence. Genome-wide significance was not attained in any of our analyses, but we did identify several suggestive associations. Genome-wide association studies (GWAS) in complex hereditary disorders frequently fail to identify causative gene variants, so advanced bioinformatics data mining techniques are needed to extract information to guide future studies. STRING diagrams are graphical representations of known and predicted networks of protein-protein interactions, identifying documented relationships between gene proteins based on the scientific literature, to identify functional gene groupings to pursue for further scrutiny. The STRING program predicts associations at a preset confidence level and suggests biological functions based on the identified genes. Starting with (1) genes within 500 kb of GWAS-suggested SNPs, (2) known pigmentation genes, (3) known human deafness genes, and (4) genes identified from proteomic analysis of the cochlea, we generated STRING diagrams that included these genes. We then reduced the number of genes by excluding genes with no relationship to auditory function, pigmentation, or relevant structures, and identified clusters of genes that warrant further investigation.
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Affiliation(s)
- Maria Kelly-Smith
- Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803 USA
| | - George M Strain
- Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803 USA
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24
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Liu P, Xie X, Jin J. Isotopic Nitrogen-15 Labeling of Mice Identified Long-lived Proteins of the Renal Basement Membranes. Sci Rep 2020; 10:5317. [PMID: 32210336 PMCID: PMC7093503 DOI: 10.1038/s41598-020-62348-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/12/2020] [Indexed: 12/20/2022] Open
Abstract
The kidney is comprised of highly complex structures that rely on self-maintenance for their functions, and tissue repair and regeneration in renal diseases. We devised a proteomics assay to measure the turnover of individual proteins in mouse kidney. Mice were metabolically labeled with a specially formulated chow containing nitrogen-15 (15N) with the absence of normal 14N atoms. Newly synthesized proteins with 15N contents were distinguished from their 14N counterparts by mass spectrometry. In total, we identified over 4,000 proteins from the renal cortex with a majority of them contained only 15N. About 100 proteins had both 14N- and 15N-contents. Notably, the long-lived proteins that had large 14N/15N ratios were mostly matrix proteins. These included proteins such as type IV and type VI collagen, laminin, nidogen and perlecan/HSPG2 that constitute the axial core of the glomerular basement membrane (GBM). In contrast, the surface lamina rara proteins such as agrin and integrin had much shorter longevity, suggesting their faster regeneration cycle. The data illustrated matrix proteins that constitute the basement membranes in the renal cortex are constantly renewed in an ordered fashion. In perspective, the global profile of protein turnover is usefully in understanding the protein-basis of GBM maintenance and repair.
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Affiliation(s)
- Pan Liu
- Feinberg Cardiovascular and Renal Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Xinfang Xie
- Feinberg Cardiovascular and Renal Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.,Department of Nephrology, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, China
| | - Jing Jin
- Feinberg Cardiovascular and Renal Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
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25
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Piunti A, Smith ER, Morgan MAJ, Ugarenko M, Khaltyan N, Helmin KA, Ryan CA, Murray DC, Rickels RA, Yilmaz BD, Rendleman EJ, Savas JN, Singer BD, Bulun SE, Shilatifard A. CATACOMB: An endogenous inducible gene that antagonizes H3K27 methylation activity of Polycomb repressive complex 2 via an H3K27M-like mechanism. SCIENCE ADVANCES 2019; 5:eaax2887. [PMID: 31281901 PMCID: PMC6609211 DOI: 10.1126/sciadv.aax2887] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 05/28/2019] [Indexed: 05/16/2023]
Abstract
Using biochemical characterization of fusion proteins associated with endometrial stromal sarcoma, we identified JAZF1 as a new subunit of the NuA4 acetyltransferase complex and CXORF67 as a subunit of the Polycomb Repressive Complex 2 (PRC2). Since CXORF67's interaction with PRC2 leads to decreased PRC2-dependent H3K27me2/3 deposition, we propose a new name for this gene: CATACOMB (catalytic antagonist of Polycomb; official gene name: EZHIP ). We map CATACOMB's inhibitory function to a short highly conserved region and identify a single methionine residue essential for diminution of H3K27me2/3 levels. Remarkably, the amino acid sequence surrounding this critical methionine resembles the oncogenic histone H3 Lys27-to-methionine (H3K27M) mutation found in high-grade pediatric gliomas. As CATACOMB expression is regulated through DNA methylation/demethylation, we propose CATACOMB as the potential interlocutor between DNA methylation and PRC2 activity. We raise the possibility that similar regulatory mechanisms could exist for other methyltransferase complexes such as Trithorax/COMPASS.
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Affiliation(s)
- Andrea Piunti
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Edwin R. Smith
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Marc A. J. Morgan
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Michal Ugarenko
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Natalia Khaltyan
- Department of Neurology, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Kathryn A. Helmin
- Division of Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Caila A. Ryan
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - David C. Murray
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Ryan A. Rickels
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Bahar D. Yilmaz
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Emily J. Rendleman
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Jeffrey N. Savas
- Department of Neurology, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Benjamin D. Singer
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
- Division of Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Serdar E. Bulun
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
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26
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Zhao Z, Wang L, Bartom E, Marshall S, Rendleman E, Ryan C, Shilati A, Savas J, Chandel N, Shilatifard A. β-Catenin/Tcf7l2-dependent transcriptional regulation of GLUT1 gene expression by Zic family proteins in colon cancer. SCIENCE ADVANCES 2019; 5:eaax0698. [PMID: 31392276 PMCID: PMC6669021 DOI: 10.1126/sciadv.aax0698] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/25/2019] [Indexed: 05/04/2023]
Abstract
The zinc finger of the cerebellum (ZIC) proteins has been implicated to function in normal tissue development. Recent studies have described the critical functions of Zic proteins in cancers and the potential tumor-suppressive functions in colon cancer development and progression. To elucidate the functional roles of Zic proteins in colorectal cancer, we knocked out the Zic5 gene and analyzed the chromatin localization pattern and transcriptional regulation of target gene expression. We found that Zic5 regulates glucose metabolism, and Zic5 knockout is accompanied by an increased glycolytic state and tolerance to a low-glucose condition. Furthermore, loss of β-catenin or TCF7l2 diminishes the chromatin binding of Zic5 globally. Our studies suggest that the Wnt/β-catenin signaling pathway has a strong influence on the function of Zic proteins and glucose metabolism in colorectal cancers through GLUT1. Interfering Wnt/-catenin-Zic5 axis-regulated aerobic glycolysis represents a potentially effective strategy to selectively target colon cancer cells.
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Affiliation(s)
- Zibo Zhao
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Lu Wang
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Elizabeth Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Stacy Marshall
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Emily Rendleman
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Caila Ryan
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Anthony Shilati
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jeffrey Savas
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Navdeep Chandel
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie NCI Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie NCI Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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27
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Jen HI, Hill MC, Tao L, Sheng K, Cao W, Zhang H, Yu HV, Llamas J, Zong C, Martin JF, Segil N, Groves AK. Transcriptomic and epigenetic regulation of hair cell regeneration in the mouse utricle and its potentiation by Atoh1. eLife 2019; 8:e44328. [PMID: 31033441 PMCID: PMC6504235 DOI: 10.7554/elife.44328] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/28/2019] [Indexed: 12/30/2022] Open
Abstract
The mammalian cochlea loses its ability to regenerate new hair cells prior to the onset of hearing. In contrast, the adult vestibular system can produce new hair cells in response to damage, or by reprogramming of supporting cells with the hair cell transcription factor Atoh1. We used RNA-seq and ATAC-seq to probe the transcriptional and epigenetic responses of utricle supporting cells to damage and Atoh1 transduction. We show that the regenerative response of the utricle correlates with a more accessible chromatin structure in utricle supporting cells compared to their cochlear counterparts. We also provide evidence that Atoh1 transduction of supporting cells is able to promote increased transcriptional accessibility of some hair cell genes. Our study offers a possible explanation for regenerative differences between sensory organs of the inner ear, but shows that additional factors to Atoh1 may be required for optimal reprogramming of hair cell fate.
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Affiliation(s)
- Hsin-I Jen
- Program in Developmental BiologyBaylor College of MedicineHoustonUnited States
| | - Matthew C Hill
- Program in Developmental BiologyBaylor College of MedicineHoustonUnited States
| | - Litao Tao
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
- Caruso Department of Otolaryngology - Head and Neck Surgery, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
| | - Kuanwei Sheng
- Program in Integrative Molecular and Biomedical SciencesBaylor College of MedicineHoustonUnited States
| | - Wenjian Cao
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
| | - Hongyuan Zhang
- Department of NeuroscienceBaylor College of MedicineHoustonUnited States
| | - Haoze V Yu
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
- Caruso Department of Otolaryngology - Head and Neck Surgery, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
| | - Juan Llamas
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
- Caruso Department of Otolaryngology - Head and Neck Surgery, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
| | - Chenghang Zong
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
| | - James F Martin
- Program in Developmental BiologyBaylor College of MedicineHoustonUnited States
- Department of Molecular Physiology and BiophysicsBaylor College of MedicineHoustonUnited States
- The Texas Heart InstituteHoustonUnited States
| | - Neil Segil
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
- Caruso Department of Otolaryngology - Head and Neck Surgery, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
| | - Andrew K Groves
- Program in Developmental BiologyBaylor College of MedicineHoustonUnited States
- Department of NeuroscienceBaylor College of MedicineHoustonUnited States
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28
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Celaya AM, Sánchez-Pérez I, Bermúdez-Muñoz JM, Rodríguez-de la Rosa L, Pintado-Berninches L, Perona R, Murillo-Cuesta S, Varela-Nieto I. Deficit of mitogen-activated protein kinase phosphatase 1 (DUSP1) accelerates progressive hearing loss. eLife 2019; 8:39159. [PMID: 30938680 PMCID: PMC6464786 DOI: 10.7554/elife.39159] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 04/01/2019] [Indexed: 12/12/2022] Open
Abstract
Mitogen-activated protein kinases (MAPK) such as p38 and the c-Jun N-terminal kinases (JNKs) are activated during the cellular response to stress signals. Their activity is regulated by the MAPK-phosphatase 1 (DUSP1), a key component of the anti-inflammatory response. Stress kinases are well-described elements of the response to otic injury and the otoprotective potential of JNK inhibitors is being tested in clinical trials. By contrast, there are no studies exploring the role of DUSP1 in hearing and hearing loss. Here we show that Dusp1 expression is age-regulated in the mouse cochlea. Dusp1 gene knock-out caused premature progressive hearing loss, as confirmed by auditory evoked responses in Dusp1-/- mice. Hearing loss correlated with cell death in hair cells, degeneration of spiral neurons and increased macrophage infiltration. Dusp1-/- mouse cochleae showed imbalanced redox status and dysregulated expression of cytokines. These data suggest that DUSP1 is essential for cochlear homeostasis in the response to stress during ageing.
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Affiliation(s)
- Adelaida M Celaya
- Institute for Biomedical Research "Alberto Sols" (IIBM), Spanish National Research Council-Autonomous University of Madrid (CSIC-UAM), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), CIBER, ISCIII, Madrid, Spain
| | - Isabel Sánchez-Pérez
- Institute for Biomedical Research "Alberto Sols" (IIBM), Spanish National Research Council-Autonomous University of Madrid (CSIC-UAM), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), CIBER, ISCIII, Madrid, Spain.,Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain.,Biochemistry Department, Faculty of Medicine, Autonomous University of Madrid, Madrid, Spain.,Biomedicine Unit UCLM-CSIC, Madrid, Spain
| | - Jose M Bermúdez-Muñoz
- Institute for Biomedical Research "Alberto Sols" (IIBM), Spanish National Research Council-Autonomous University of Madrid (CSIC-UAM), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), CIBER, ISCIII, Madrid, Spain
| | - Lourdes Rodríguez-de la Rosa
- Institute for Biomedical Research "Alberto Sols" (IIBM), Spanish National Research Council-Autonomous University of Madrid (CSIC-UAM), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), CIBER, ISCIII, Madrid, Spain.,Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Laura Pintado-Berninches
- Institute for Biomedical Research "Alberto Sols" (IIBM), Spanish National Research Council-Autonomous University of Madrid (CSIC-UAM), Madrid, Spain.,Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Rosario Perona
- Institute for Biomedical Research "Alberto Sols" (IIBM), Spanish National Research Council-Autonomous University of Madrid (CSIC-UAM), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), CIBER, ISCIII, Madrid, Spain.,Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Silvia Murillo-Cuesta
- Institute for Biomedical Research "Alberto Sols" (IIBM), Spanish National Research Council-Autonomous University of Madrid (CSIC-UAM), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), CIBER, ISCIII, Madrid, Spain
| | - Isabel Varela-Nieto
- Institute for Biomedical Research "Alberto Sols" (IIBM), Spanish National Research Council-Autonomous University of Madrid (CSIC-UAM), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), CIBER, ISCIII, Madrid, Spain
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29
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Wilson RS, Nairn AC. Cell-Type-Specific Proteomics: A Neuroscience Perspective. Proteomes 2018; 6:51. [PMID: 30544872 PMCID: PMC6313874 DOI: 10.3390/proteomes6040051] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 12/18/2022] Open
Abstract
Cell-type-specific analysis has become a major focus for many investigators in the field of neuroscience, particularly because of the large number of different cell populations found in brain tissue that play roles in a variety of developmental and behavioral disorders. However, isolation of these specific cell types can be challenging due to their nonuniformity and complex projections to different brain regions. Moreover, many analytical techniques used for protein detection and quantitation remain insensitive to the low amounts of protein extracted from specific cell populations. Despite these challenges, methods to improve proteomic yield and increase resolution continue to develop at a rapid rate. In this review, we highlight the importance of cell-type-specific proteomics in neuroscience and the technical difficulties associated. Furthermore, current progress and technological advancements in cell-type-specific proteomics research are discussed with an emphasis in neuroscience.
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Affiliation(s)
- Rashaun S Wilson
- Yale/NIDA Neuroproteomics Center, 300 George St., New Haven, CT 06511, USA.
| | - Angus C Nairn
- Yale/NIDA Neuroproteomics Center, 300 George St., New Haven, CT 06511, USA.
- Department of Psychiatry, Yale School of Medicine, Connecticut Mental Health Center, New Haven, CT 06511, USA.
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30
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Gene expression dataset for whole cochlea of Macaca fascicularis. Sci Rep 2018; 8:15554. [PMID: 30349143 PMCID: PMC6197234 DOI: 10.1038/s41598-018-33985-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/09/2018] [Indexed: 11/17/2022] Open
Abstract
Macaca fascicularis is a highly advantageous model in which to study human cochlea with regard to both evolutionary proximity and physiological similarity of the auditory system. To better understand the properties of primate cochlear function, we analyzed the genes predominantly expressed in M. fascicularis cochlea. We compared the cochlear transcripts obtained from an adult male M. fascicularis by macaque and human GeneChip microarrays with those in multiple macaque and human tissues or cells and identified 344 genes with expression levels more than 2-fold greater than in the other tissues. These “cochlear signature genes” included 35 genes responsible for syndromic or nonsyndromic hereditary hearing loss. Gene set enrichment analysis revealed groups of genes categorized as “ear development” and “ear morphogenesis” in the top 20 gene ontology categories in the macaque and human arrays, respectively. This dataset will facilitate both the study of genes that contribute to primate cochlear function and provide insight to discover novel genes associated with hereditary hearing loss that have yet to be established using animal models.
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31
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Li J, Akil O, Rouse SL, McLaughlin CW, Matthews IR, Lustig LR, Chan DK, Sherr EH. Deletion of Tmtc4 activates the unfolded protein response and causes postnatal hearing loss. J Clin Invest 2018; 128:5150-5162. [PMID: 30188326 DOI: 10.1172/jci97498] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 08/30/2018] [Indexed: 12/16/2022] Open
Abstract
Hearing loss is a significant public health concern, affecting over 250 million people worldwide. Both genetic and environmental etiologies are linked to hearing loss, but in many cases the underlying cellular pathophysiology is not well understood, highlighting the importance of further discovery. We found that inactivation of the gene Tmtc4 (transmembrane and tetratricopeptide repeat 4), which was broadly expressed in the mouse cochlea, caused acquired hearing loss in mice. Our data showed Tmtc4 enriched in the endoplasmic reticulum, and that it functioned by regulating Ca2+ dynamics and the unfolded protein response (UPR). Given this genetic linkage of the UPR to hearing loss, we demonstrated a direct link between the more common noise-induced hearing loss (NIHL) and the UPR. These experiments suggested a novel approach to treatment. We demonstrated that the small-molecule UPR and stress response modulator ISRIB (integrated stress response inhibitor), which activates eIF2B, prevented NIHL in a mouse model. Moreover, in an inverse genetic complementation approach, we demonstrated that mice with homozygous inactivation of both Tmtc4 and Chop had less hearing loss than knockout of Tmtc4 alone. This study implicated a novel mechanism for hearing impairment, highlighting a potential treatment approach for a broad range of human hearing loss disorders.
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Affiliation(s)
| | - Omar Akil
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco (UCSF), San Francisco, California, USA
| | - Stephanie L Rouse
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco (UCSF), San Francisco, California, USA
| | - Conor W McLaughlin
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco (UCSF), San Francisco, California, USA
| | - Ian R Matthews
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco (UCSF), San Francisco, California, USA
| | - Lawrence R Lustig
- Department of Otolaryngology - Head and Neck Surgery, College of Physicians and Surgeons, Columbia University and New York Presbyterian Hospital, New York, New York, USA
| | - Dylan K Chan
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco (UCSF), San Francisco, California, USA
| | - Elliott H Sherr
- Department of Neurology and.,Department of Pediatrics, Institute of Human Genetics, Weill Institute for Neurosciences, UCSF, San Francisco, California, USA
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32
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The Key Transcription Factor Expression in the Developing Vestibular and Auditory Sensory Organs: A Comprehensive Comparison of Spatial and Temporal Patterns. Neural Plast 2018; 2018:7513258. [PMID: 30410537 PMCID: PMC6205106 DOI: 10.1155/2018/7513258] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/31/2018] [Accepted: 09/06/2018] [Indexed: 11/17/2022] Open
Abstract
Inner ear formation requires that a series of cell fate decisions and morphogenetic events occur in a precise temporal and spatial pattern. Previous studies have shown that transcription factors, including Pax2, Sox2, and Prox1, play important roles during the inner ear development. However, the temporospatial expression patterns among these transcription factors are poorly understood. In the current study, we present a comprehensive description of the temporal and spatial expression profiles of Pax2, Sox2, and Prox1 during auditory and vestibular sensory organ development in mice. Using immunohistochemical analyses, we show that Sox2 and Pax2 are both expressed in the prosensory cells (the developing hair cells), but Sox2 is later restricted to only the supporting cells of the organ of Corti. In the vestibular sensory organ, however, the Pax2 expression is localized in hair cells at postnatal day 7, while Sox2 is still expressed in both the hair cells and supporting cells at that time. Prox1 was transiently expressed in the presumptive hair cells and developing supporting cells, and lower Prox1 expression was observed in the vestibular sensory organ compared to the organ of Corti. The different expression patterns of these transcription factors in the developing auditory and vestibular sensory organs suggest that they play different roles in the development of the sensory epithelia and might help to shape the respective sensory structures.
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33
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Darville LNF, Sokolowski BHA. Label-free quantitative mass spectrometry analysis of differential protein expression in the developing cochlear sensory epithelium. Proteome Sci 2018; 16:15. [PMID: 30127667 PMCID: PMC6091194 DOI: 10.1186/s12953-018-0144-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 07/26/2018] [Indexed: 12/27/2022] Open
Abstract
Background The sensory epithelium of the inner ear converts the mechanical energy of sound to electro-chemical energy recognized by the central nervous system. This process is mediated by receptor cells known as hair cells that express proteins in a timely fashion with the onset of hearing. Methods The proteomes of 3, 14, and 30 day-old mice cochlear sensory epithelia were revealed, using label-free quantitative mass spectrometry (LTQ-Orbitrap). Statistical analysis using a one-way ANOVA followed by Bonferroni’s post-hoc test was used to show significant differences in protein expression. Ingenuity Pathway Analysis was used to observe networks of differentially expressed proteins, their biological processes, and associated diseases, while Cytoscape software was used to determine putative interactions with select biomarker proteins. These candidate biomarkers were further verified using Western blotting, while coimmunoprecipitation was used to verify putative partners determined using bioinformatics. Results We show that a comparison across all three proteomes shows that there are 447 differentially expressed proteins, with 387 differentially expressed between postnatal day 3 and 30. Ingenuity Pathway Analysis revealed ~ 62% of postnatal day 3 downregulated proteins are involved in neurological diseases. Several proteins are expressed exclusively on P3, including Parvin α, Drebrin1 (Drb1), Secreted protein acidic and cysteine rich (SPARC), Transmembrane emp24 domain-containing protein 10 (Tmed10). Coimmunoprecipitations showed that Parvin and SPARC interact with integrin-linked protein kinase and the large conductance calcium-activated potassium channel, respectively. Conclusions Quantitative mass spectrometry revealed the identification of numerous differentially regulated proteins over three days of postnatal development. These data provide insights into functional pathways regulating normal sensory and supporting cell development in the cochlea that include potential biomarkers. Interacting partners of two of these markers suggest the importance of these complexes in regulating cellular structure and synapse development. Electronic supplementary material The online version of this article (10.1186/s12953-018-0144-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lancia N F Darville
- Morsani College of Medicine, Department of Otolaryngology-HNS, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612 USA
| | - Bernd H A Sokolowski
- Morsani College of Medicine, Department of Otolaryngology-HNS, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612 USA
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34
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Uncovering Discrete Synaptic Proteomes to Understand Neurological Disorders. Proteomes 2018; 6:proteomes6030030. [PMID: 30029459 PMCID: PMC6161107 DOI: 10.3390/proteomes6030030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/10/2018] [Accepted: 07/13/2018] [Indexed: 12/20/2022] Open
Abstract
The mammalian nervous system is an immensely heterogeneous organ composed of a diverse collection of neuronal types that interconnect in complex patterns. Synapses are highly specialized neuronal cell-cell junctions with common and distinct functional characteristics that are governed by their protein composition or synaptic proteomes. Even a single neuron can possess a wide-range of different synapse types and each synapse contains hundreds or even thousands of proteins. Many neurological disorders and diseases are caused by synaptic dysfunction within discrete neuronal populations. Mass spectrometry (MS)-based proteomic analysis has emerged as a powerful strategy to characterize synaptic proteomes and potentially identify disease driving synaptic alterations. However, most traditional synaptic proteomic analyses have been limited by molecular averaging of proteins from multiple types of neurons and synapses. Recently, several new strategies have emerged to tackle the ‘averaging problem’. In this review, we summarize recent advancements in our ability to characterize neuron-type specific and synapse-type specific proteomes and discuss strengths and limitations of these emerging analysis strategies.
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35
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Mass spectrometry quantitation of proteins from small pools of developing auditory and vestibular cells. Sci Data 2018; 5:180128. [PMID: 30015805 PMCID: PMC6049031 DOI: 10.1038/sdata.2018.128] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/20/2018] [Indexed: 01/15/2023] Open
Abstract
Hair cells of the inner ear undergo postnatal development that leads to formation of their sensory organelles, synaptic machinery, and in the case of cochlear outer hair cells, their electromotile mechanism. To examine how the proteome changes over development from postnatal days 0 through 7, we isolated pools of 5000 Pou4f3-Gfp positive or negative cells from the cochlea or utricles; these cell pools were analysed by data-dependent and data-independent acquisition (DDA and DIA) mass spectrometry. DDA data were used to generate spectral libraries, which enabled identification and accurate quantitation of specific proteins using the DIA datasets. DIA measurements were extremely sensitive; we were able to detect proteins present at less than one part in 100,000 from only 312 hair cells. The DDA and DIA datasets will be valuable for accurately quantifying proteins in hair cells and non-hair cells over this developmental window.
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36
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Matern MS, Beirl A, Ogawa Y, Song Y, Paladugu N, Kindt KS, Hertzano R. Transcriptomic Profiling of Zebrafish Hair Cells Using RiboTag. Front Cell Dev Biol 2018; 6:47. [PMID: 29765956 PMCID: PMC5939014 DOI: 10.3389/fcell.2018.00047] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 04/13/2018] [Indexed: 01/27/2023] Open
Abstract
The zebrafish inner ear organs and lateral line neuromasts are comprised of a variety of cell types, including mechanosensitive hair cells. Zebrafish hair cells are evolutionarily homologous to mammalian hair cells, and have been particularly useful for studying normal hair cell development and function. However, the relative scarcity of hair cells within these complex organs, as well as the difficulty of fine dissection at early developmental time points, makes hair cell-specific gene expression profiling technically challenging. Cell sorting methods, as well as single-cell RNA-Seq, have proved to be very informative in studying hair cell-specific gene expression. However, these methods require that tissues are dissociated, the processing for which can lead to changes in gene expression prior to RNA extraction. To bypass this problem, we have developed a transgenic zebrafish model to evaluate the translatome of the inner ear and lateral line hair cells in their native tissue environment; the Tg(myo6b:RiboTag) zebrafish. This model expresses both GFP and a hemagglutinin (HA) tagged rpl10a gene under control of the myo6b promoter (myo6b:GFP-2A-rpl10a-3xHA), resulting in HA-tagged ribosomes expressed specifically in hair cells. Consequently, intact zebrafish larvae can be used to enrich for actively translated hair cell mRNA via an immunoprecipitation protocol using an antibody for the HA-tag (similar to the RiboTag mice). We demonstrate that this model can be used to reliably enrich for actively translated zebrafish hair cell mRNA. Additionally, we perform a global hair cell translatome analysis using RNA-Seq and show enrichment of known hair cell expressed transcripts and depletion of non-hair cell expressed transcripts in the immunoprecipitated material compared with mRNA extracted from whole fish (input). Our results show that our model can identify novel hair cell expressed genes in intact zebrafish, without inducing changes to gene expression that result from tissue dissociation and delays during cell sorting. Overall, we believe that this model will be highly useful for studying changes in zebrafish hair cell-specific gene expression in response to developmental progression, mutations, as well as hair cell damage by noise or ototoxic drug exposure.
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Affiliation(s)
- Maggie S. Matern
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Alisha Beirl
- Section on Sensory Cell Development and Function, National Institute on Deafness and Other Communication Disorders, Bethesda, MD, United States
| | - Yoko Ogawa
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Yang Song
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Nikhil Paladugu
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Katie S. Kindt
- Section on Sensory Cell Development and Function, National Institute on Deafness and Other Communication Disorders, Bethesda, MD, United States
| | - Ronna Hertzano
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States,*Correspondence: Ronna Hertzano
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37
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Morgan MAJ, Rickels RA, Collings CK, He X, Cao K, Herz HM, Cozzolino KA, Abshiru NA, Marshall SA, Rendleman EJ, Sze CC, Piunti A, Kelleher NL, Savas JN, Shilatifard A. A cryptic Tudor domain links BRWD2/PHIP to COMPASS-mediated histone H3K4 methylation. Genes Dev 2017; 31:2003-2014. [PMID: 29089422 PMCID: PMC5710144 DOI: 10.1101/gad.305201.117] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/05/2017] [Indexed: 01/22/2023]
Abstract
In this study, Morgan et al. identify an evolutionarily conserved factor, BRWD2/PHIP, that localizes with histone H3K4 methylation genome-wide in human cells, mouse embryonic stem cells, and Drosophila. Depletion of the Drosophila sole homolog dBRWD3 results in altered histone H3 Lys27 acetylation patterns at enhancers and promoters and changes in gene expression, suggesting a cross-talk between these epigenetic modifications and transcription through the BRWD family. Histone H3 Lys4 (H3K4) methylation is a chromatin feature enriched at gene cis-regulatory sequences such as promoters and enhancers. Here we identify an evolutionarily conserved factor, BRWD2/PHIP, which colocalizes with histone H3K4 methylation genome-wide in human cells, mouse embryonic stem cells, and Drosophila. Biochemical analysis of BRWD2 demonstrated an association with the Cullin-4–RING ubiquitin E3 ligase-4 (CRL4) complex, nucleosomes, and chromatin remodelers. BRWD2/PHIP binds directly to H3K4 methylation through a previously unidentified chromatin-binding module related to Royal Family Tudor domains, which we named the CryptoTudor domain. Using CRISPR–Cas9 genetic knockouts, we demonstrate that COMPASS H3K4 methyltransferase family members differentially regulate BRWD2/PHIP chromatin occupancy. Finally, we demonstrate that depletion of the single Drosophila homolog dBRWD3 results in altered gene expression and aberrant patterns of histone H3 Lys27 acetylation at enhancers and promoters, suggesting a cross-talk between these chromatin modifications and transcription through the BRWD protein family.
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Affiliation(s)
- Marc A J Morgan
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Ryan A Rickels
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Clayton K Collings
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Xiaolin He
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Kaixiang Cao
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Hans-Martin Herz
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | | | - Nebiyu A Abshiru
- Department of Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Stacy A Marshall
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Emily J Rendleman
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Christie C Sze
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Andrea Piunti
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Neil L Kelleher
- Department of Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | | | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
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Avenarius MR, Krey JF, Dumont RA, Morgan CP, Benson CB, Vijayakumar S, Cunningham CL, Scheffer DI, Corey DP, Müller U, Jones SM, Barr-Gillespie PG. Heterodimeric capping protein is required for stereocilia length and width regulation. J Cell Biol 2017; 216:3861-3881. [PMID: 28899994 PMCID: PMC5674897 DOI: 10.1083/jcb.201704171] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 07/21/2017] [Accepted: 08/08/2017] [Indexed: 02/07/2023] Open
Abstract
Control of the dimensions of actin-rich processes like filopodia, lamellipodia, microvilli, and stereocilia requires the coordinated activity of many proteins. Each of these actin structures relies on heterodimeric capping protein (CAPZ), which blocks actin polymerization at barbed ends. Because dimension control of the inner ear's stereocilia is particularly precise, we studied the CAPZB subunit in hair cells. CAPZB, present at ∼100 copies per stereocilium, concentrated at stereocilia tips as hair cell development progressed, similar to the CAPZB-interacting protein TWF2. We deleted Capzb specifically in hair cells using Atoh1-Cre, which eliminated auditory and vestibular function. Capzb-null stereocilia initially developed normally but later shortened and disappeared; surprisingly, stereocilia width decreased concomitantly with length. CAPZB2 expressed by in utero electroporation prevented normal elongation of vestibular stereocilia and irregularly widened them. Together, these results suggest that capping protein participates in stereocilia widening by preventing newly elongating actin filaments from depolymerizing.
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MESH Headings
- Animals
- Auditory Threshold
- Behavior, Animal
- Brain Stem/metabolism
- Brain Stem/physiopathology
- CapZ Actin Capping Protein/deficiency
- CapZ Actin Capping Protein/genetics
- CapZ Actin Capping Protein/metabolism
- Chick Embryo
- Cilia/metabolism
- Cilia/ultrastructure
- Evoked Potentials, Auditory, Brain Stem
- Gene Expression Regulation, Developmental
- Genotype
- Hair Cells, Auditory/metabolism
- Hair Cells, Auditory/ultrastructure
- Intracellular Signaling Peptides and Proteins/genetics
- Intracellular Signaling Peptides and Proteins/metabolism
- Mass Spectrometry
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Microfilament Proteins/genetics
- Microfilament Proteins/metabolism
- Otoacoustic Emissions, Spontaneous
- Phenotype
- Vestibular Evoked Myogenic Potentials
- Vestibule, Labyrinth/metabolism
- Vestibule, Labyrinth/physiopathology
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Affiliation(s)
- Matthew R Avenarius
- Oregon Hearing Research Center and Vollum Institute, Oregon Health and Science University, Portland, OR
| | - Jocelyn F Krey
- Oregon Hearing Research Center and Vollum Institute, Oregon Health and Science University, Portland, OR
| | - Rachel A Dumont
- Oregon Hearing Research Center and Vollum Institute, Oregon Health and Science University, Portland, OR
| | - Clive P Morgan
- Oregon Hearing Research Center and Vollum Institute, Oregon Health and Science University, Portland, OR
| | - Connor B Benson
- Oregon Hearing Research Center and Vollum Institute, Oregon Health and Science University, Portland, OR
| | - Sarath Vijayakumar
- Department of Special Education and Communication Disorders, University of Nebraska-Lincoln, Lincoln, NE
| | | | | | - David P Corey
- Department of Neurobiology, Harvard Medical School, Boston, MA
| | - Ulrich Müller
- Department of Neuroscience, Johns Hopkins University, Baltimore, MD
| | - Sherri M Jones
- Department of Special Education and Communication Disorders, University of Nebraska-Lincoln, Lincoln, NE
| | - Peter G Barr-Gillespie
- Oregon Hearing Research Center and Vollum Institute, Oregon Health and Science University, Portland, OR
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