Single-cell RNA-sequencing of zebrafish hair cells reveals novel genes potentially involved in hearing loss.
Hair cell
Zebrafish
scRNA-seq
Journal
Cellular and molecular life sciences : CMLS
ISSN: 1420-9071
Titre abrégé: Cell Mol Life Sci
Pays: Switzerland
ID NLM: 9705402
Informations de publication
Date de publication:
26 Jun 2022
26 Jun 2022
Historique:
received:
08
01
2022
accepted:
01
06
2022
revised:
18
05
2022
entrez:
26
6
2022
pubmed:
27
6
2022
medline:
29
6
2022
Statut:
epublish
Résumé
Hair cells play key roles in hearing and balance, and hair cell loss would result in hearing loss or vestibular dysfunction. Cellular and molecular research in hair cell biology provides us a better understanding of hearing and deafness. Zebrafish, owing to their hair cell-enriched organs, have been widely applied in hair cell-related research worldwide. Similar to mammals, zebrafish have inner ear hair cells. In addition, they also have lateral line neuromast hair cells. These different types of hair cells vary in morphology and function. However, systematic analysis of their molecular characteristics remains lacking. In this study, we analyzed the GFP+ cells isolated from Tg(Brn3c:mGFP) larvae with GFP expression in all hair cells using single-cell RNA-sequencing (scRNA-seq). Three subtypes of hair cells, namely macula hair cell (MHC), crista hair cell (CHC), and neuromast hair cell (NHC), were characterized and validated by whole-mount in situ hybridization analysis of marker genes. The hair cell scRNA-seq data revealed hair cell-specific genes, including hearing loss genes that have been identified in humans and novel genes potentially involved in hair cell formation and function. Two novel genes were discovered to specifically function in NHCs and MHCs, corresponding to their specific expression in NHCs and MHCs. This study allows us to understand the specific genes in hair cell subpopulations of zebrafish, which will shed light on the genetics of both human vestibular and cochlear hair cell function.
Identifiants
pubmed: 35753015
doi: 10.1007/s00018-022-04410-2
pii: 10.1007/s00018-022-04410-2
doi:
Substances chimiques
Zebrafish Proteins
0
RNA
63231-63-0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
385Subventions
Organisme : National Natural Science Foundation of China
ID : 2018YFA0801004
Organisme : National Natural Science Foundation of China
ID : 81870359
Organisme : National Natural Science Foundation of China
ID : 31900484
Organisme : Natural Science Foundation of Jiangsu Province
ID : BK20180048
Organisme : Natural Science Foundation of Jiangsu Province
ID : BRA2019278
Organisme : Natural Science Foundation of Jiangsu Province
ID : BK20190924
Organisme : Natural Science Foundation of Jiangsu Province
ID : BK20190920
Commentaires et corrections
Type : ErratumIn
Informations de copyright
© 2022. The Author(s), under exclusive licence to Springer Nature Switzerland AG.
Références
Taylor RR, Filia A, Paredes U, Asai Y, Holt JR, Lovett M, Forge A (2018) Regenerating hair cells in vestibular sensory epithelia from humans. Elife. https://doi.org/10.7554/eLife.34817
doi: 10.7554/eLife.34817
pubmed: 30558713
pmcid: 6298766
Kurima K, Ebrahim S, Pan B, Sedlacek M, Sengupta P, Millis BA, Cui R, Nakanishi H, Fujikawa T, Kawashima Y, Choi BY, Monahan K, Holt JR, Griffith AJ, Kachar B (2015) TMC1 and TMC2 localize at the site of mechanotransduction in mammalian inner ear hair cell stereocilia. Cell Rep 12(10):1606–1617
pubmed: 26321635
pmcid: 4569002
doi: 10.1016/j.celrep.2015.07.058
Wagner EL, Shin JB (2019) Mechanisms of hair cell damage and repair. Trends Neurosci 42(6):414–424
pubmed: 30992136
pmcid: 6556399
doi: 10.1016/j.tins.2019.03.006
Nordang L, Cestreicher E, Arnold W, Anniko M (2000) Glutamate is the afferent neurotransmitter in the human cochlea. Acta Otolaryngol 120(3):359–362
pubmed: 10894409
doi: 10.1080/000164800750000568
Dalet A, Bonsacquet J, Gaboyard-Niay S, Calin-Jageman I, Chidavaenzi RL, Venteo S, Desmadryl G, Goldberg JM, Lysakowski A, Chabbert C (2012) Glutamate transporters EAAT4 and EAAT5 are expressed in vestibular hair cells and calyx endings. PLoS ONE 7(9):e46261
pubmed: 23049999
pmcid: 3457983
doi: 10.1371/journal.pone.0046261
Highstein SM, Holstein GR, Mann MA, Rabbitt RD (2014) Evidence that protons act as neurotransmitters at vestibular hair cell-calyx afferent synapses. Proc Natl Acad Sci USA 111(14):5421–5426
pubmed: 24706862
pmcid: 3986198
doi: 10.1073/pnas.1319561111
Dallos P (1992) The active cochlea. J Neurosci 12(12):4575–4585
pubmed: 1464757
pmcid: 6575778
doi: 10.1523/JNEUROSCI.12-12-04575.1992
Burns JC, Stone JS (2017) Development and regeneration of vestibular hair cells in mammals. Semin Cell Dev Biol 65:96–105
pubmed: 27864084
doi: 10.1016/j.semcdb.2016.11.001
Day BL, Fitzpatrick RC (2005) The vestibular system. Curr Biol 15(15):R583–R586
pubmed: 16085475
doi: 10.1016/j.cub.2005.07.053
Patton EE, Zon LI, Langenau DM (2021) Zebrafish disease models in drug discovery: from preclinical modelling to clinical trials. Nat Rev Drug Discov. https://doi.org/10.1038/s41573-021-00210-8 (1474-1784 (Electronic))
doi: 10.1038/s41573-021-00210-8
pubmed: 34117457
pmcid: 9210578
Riley BB, Moorman SJ (2000) Development of utricular otoliths, but not saccular otoliths, is necessary for vestibular function and survival in zebrafish. J Neurobiol 43(4):329–337
pubmed: 10861559
doi: 10.1002/1097-4695(20000615)43:4<329::AID-NEU2>3.0.CO;2-H
Yao Q, DeSmidt AA, Tekin M, Liu X, Lu Z (2016) Hearing assessment in zebrafish during the first week postfertilization. Zebrafish 13(2):79–86
pubmed: 26982161
pmcid: 4799700
doi: 10.1089/zeb.2015.1166
Smith ET, Pacentine I, Shipman A, Hill M, Nicolson T (2020) Disruption of tmc1/2a/2b genes in zebrafish reveals subunit requirements in subtypes of inner ear hair cells. J Neurosci 40(23):4457–4468
pubmed: 32371604
pmcid: 7275854
doi: 10.1523/JNEUROSCI.0163-20.2020
Pacentine IV, Nicolson T (2019) Subunits of the mechano-electrical transduction channel, Tmc1/2b, require Tmie to localize in zebrafish sensory hair cells. PLoS Genet 15(2):e1007635
pubmed: 30726219
pmcid: 6380590
doi: 10.1371/journal.pgen.1007635
Erickson T, Pacentine IV, Venuto A, Clemens R, Nicolson T (2019) The lhfpl5 Ohnologs lhfpl5a and lhfpl5b are required for mechanotransduction in distinct populations of sensory hair cells in zebrafish. Front Mol Neurosci 12:320
pubmed: 32009898
doi: 10.3389/fnmol.2019.00320
Navajas Acedo J, Voas MG, Alexander R, Woolley T, Unruh JR, Li H, Moens C, Piotrowski T (2019) PCP and Wnt pathway components act in parallel during zebrafish mechanosensory hair cell orientation. Nat Commun 10(1):3993
pubmed: 31488837
pmcid: 6728366
doi: 10.1038/s41467-019-12005-y
Lush ME, Diaz DC, Koenecke N, Baek S, Boldt H, St Peter MK, Gaitan-Escudero T, Romero-Carvajal A, Busch-Nentwich EM, Perera AG, Hall KE, Peak A, Haug JS, Piotrowski T (2019) scRNA-Seq reveals distinct stem cell populations that drive hair cell regeneration after loss of Fgf and Notch signaling. Elife. https://doi.org/10.7554/eLife.44431
doi: 10.7554/eLife.44431
pubmed: 30681411
pmcid: 6363392
Kozlovskaja-Gumbriene A, Yi R, Alexander R, Aman A, Jiskra R, Nagelberg D, Knaut H, McClain M, Piotrowski T (2017) Proliferation-independent regulation of organ size by Fgf/Notch signaling. Elife. https://doi.org/10.7554/eLife.21049
doi: 10.7554/eLife.21049
pubmed: 28085667
pmcid: 5235355
Xiao T, Roeser T, Staub W, Baier H (2005) A GFP-based genetic screen reveals mutations that disrupt the architecture of the zebrafish retinotectal projection. Development 132(13):2955–2967
pubmed: 15930106
doi: 10.1242/dev.01861
Huo L, Jiao Li J, Chen L, Yu Z, Hutvagner G, Li J (2021) Single-cell multi-omics sequencing: application trends, COVID-19, data analysis issues and prospects. Brief Bioinform. https://doi.org/10.1093/bib/bbab229
doi: 10.1093/bib/bbab229
pubmed: 34117739
pmcid: 8575021
Yang CH, Cheng CH, Chen GD, Liao WH, Chen YC, Huang KY, Hwang PP, Hwang SP, Huang CJ (2011) Zona pellucida domain-containing protein β-tectorin is crucial for zebrafish proper inner ear development. PLoS ONE 6(8):e23078
pubmed: 21829695
pmcid: 3149068
doi: 10.1371/journal.pone.0023078
Kozak EL, Palit S, Miranda-Rodriguez JR, Janjic A, Bottcher A, Lickert H, Enard W, Theis FJ, Lopez-Schier H (2020) Epithelial planar bipolarity emerges from notch-mediated asymmetric inhibition of Emx2. Curr Biol 30(6):1142-1151 e6
pubmed: 32109392
doi: 10.1016/j.cub.2020.01.027
Pistocchi A, Feijoo CG, Cabrera P, Villablanca EJ, Allende ML, Cotelli F (2009) The zebrafish prospero homolog prox1 is required for mechanosensory hair cell differentiation and functionality in the lateral line. BMC Dev Biol 9:58
pubmed: 19948062
pmcid: 2794270
doi: 10.1186/1471-213X-9-58
Aman A, Piotrowski T (2008) Wnt/beta-catenin and Fgf signaling control collective cell migration by restricting chemokine receptor expression. Dev Cell 15(5):749–761
pubmed: 19000839
doi: 10.1016/j.devcel.2008.10.002
Seiler C, Ben-David O, Sidi S, Hendrich O, Rusch A, Burnside B, Avraham KB, Nicolson T (2004) Myosin VI is required for structural integrity of the apical surface of sensory hair cells in zebrafish. Dev Biol 272(2):328–338
pubmed: 15282151
doi: 10.1016/j.ydbio.2004.05.004
Ernest S, Rosa FM (2015) A genomic region encompassing a newly identified exon provides enhancing activity sufficient for normal myo7aa expression in zebrafish sensory hair cells. Dev Neurobiol 75(9):961–983
pubmed: 25556989
doi: 10.1002/dneu.22263
Wu Z, Muller U (2016) Molecular identity of the mechanotransduction channel in hair cells: not quiet there yet. J Neurosci 36(43):10927–10934
pubmed: 27798175
pmcid: 5098834
doi: 10.1523/JNEUROSCI.1149-16.2016
Qiu X, Muller U (2018) Mechanically gated ion channels in mammalian hair cells. Front Cell Neurosci 12:100
pubmed: 29755320
pmcid: 5932396
doi: 10.3389/fncel.2018.00100
Xiong W, Grillet N, Elledge HM, Wagner TF, Zhao B, Johnson KR, Kazmierczak P, Muller U (2012) TMHS is an integral component of the mechanotransduction machinery of cochlear hair cells. Cell 151(6):1283–1295
pubmed: 23217710
pmcid: 3522178
doi: 10.1016/j.cell.2012.10.041
Giese APJ, Tang YQ, Sinha GP, Bowl MR, Goldring AC, Parker A, Freeman MJ, Brown SDM, Riazuddin S, Fettiplace R, Schafer WR, Frolenkov GI, Ahmed ZM (2017) CIB2 interacts with TMC1 and TMC2 and is essential for mechanotransduction in auditory hair cells. Nat Commun 8(1):43
pubmed: 28663585
pmcid: 5491523
doi: 10.1038/s41467-017-00061-1
Wang Y, Li J, Yao X, Li W, Du H, Tang M, Xiong W, Chai R, Xu Z (2017) Loss of CIB2 causes profound hearing loss and abolishes mechanoelectrical transduction in mice. Front Mol Neurosci 10:401
pubmed: 29255404
pmcid: 5722843
doi: 10.3389/fnmol.2017.00401
Sollner C, Rauch GJ, Siemens J, Geisler R, Schuster SC, Muller U, Nicolson T (2004) Tubingen screen, consortium, mutations in cadherin 23 affect tip links in zebrafish sensory hair cells. Nature 428(6986):955–959
pubmed: 15057246
doi: 10.1038/nature02484
Sakaguchi H, Tokita J, Muller U, Kachar B (2009) Tip links in hair cells: molecular composition and role in hearing loss. Curr Opin Otolaryngol Head Neck Surg 17(5):388–393
pubmed: 19633555
pmcid: 2921850
doi: 10.1097/MOO.0b013e3283303472
Choudhary D, Narui Y, Neel BL, Wimalasena LN, Klanseck CF, De-la-Torre P, Chen C, Araya-Secchi R, Tamilselvan E, Sotomayor M (2020) Structural determinants of protocadherin-15 mechanics and function in hearing and balance perception. Proc Natl Acad Sci USA 117(40):24837–24848
pubmed: 32963095
pmcid: 7547225
doi: 10.1073/pnas.1920444117
Zhang S, Dong Y, Qiang R, Zhang Y, Zhang X, Chen Y, Jiang P, Ma X, Wu L, Ai J, Gao X, Wang P, Chen J, Chai R (2021) Characterization of strip1 expression in mouse cochlear hair cells. Front Genet 12:625867
pubmed: 33889175
pmcid: 8056008
doi: 10.3389/fgene.2021.625867
Cossins AR, Williams DR, Foulkes NS, Berenbrink M, Kipar A (2009) Diverse cell-specific expression of myoglobin isoforms in brain, kidney, gill and liver of the hypoxia-tolerant carp and zebrafish. J Exp Biol 212(5):627–638
pubmed: 19218513
doi: 10.1242/jeb.026286
Quinting T, Heymann AK, Bicker A, Nauth T, Bernardini A, Hankeln T, Fandrey J, Schreiber T (2021) Myoglobin protects breast cancer cells due to Its ROS and NO scavenging properties. Front Endocrinol (Lausanne) 12:732190
pubmed: 34671319
doi: 10.3389/fendo.2021.732190
Chen ZF, Huang ZH, Chen SJ, Jiang YD, Qin ZK, Zheng SB, Chen T (2021) Oncogenic potential of macrophage-capping protein in clear cell renal cell carcinoma. Mol Med Rep. https://doi.org/10.3892/mmr.2020.11718
doi: 10.3892/mmr.2020.11718
pubmed: 34935056
pmcid: 8767549
Jiang S, Yang Y, Zhang Y, Ye Q, Song J, Zheng M, Li X (2022) Overexpression of CAPG Is associated with poor prognosis and immunosuppressive cell infiltration in ovarian cancer. Dis Markers 2022:9719671
pubmed: 35186171
pmcid: 8849939
doi: 10.1155/2022/9719671
Lang Z, Chen Y, Zhu H, Sun Y, Zhang H, Huang J, Zou Z (2019) Prognostic and clinicopathological significance of CapG in various cancers: Evidence from a meta-analysis. Pathol Res Pract 215(12):152683
pubmed: 31685300
doi: 10.1016/j.prp.2019.152683
Nader JS, Boissard A, Henry C, Valo I, Verrièle V, Grégoire M, Coqueret O, Guette C, Pouliquen DL (2020) Cross-species proteomics identifies CAPG and SBP1 as crucial invasiveness biomarkers in rat and human malignant mesothelioma. Cancers (Basel) 12(9):2430
pubmed: 32867073
doi: 10.3390/cancers12092430
Prescher N, Hänsch S, Knobbe-Thomsen CB, Stühler K, Poschmann G (2021) The migration behavior of human glioblastoma cells is influenced by the redox-sensitive human macrophage capping protein CAPG. Free Radic Biol Med 167:81–93
pubmed: 33711419
doi: 10.1016/j.freeradbiomed.2021.02.038
Lahbib S, Leblond CS, Hamza M, Regnault B, Lemee L, Mathieu A, Jaouadi H, Mkaouar R, Youssef-Turki IB, Belhadj A, Kraoua I, Bourgeron T, Abdelhak S (2019) Homozygous 2p11.2 deletion supports the implication of ELMOD3 in hearing loss and reveals the potential association of CAPG with ASD/ID etiology. J Appl Genet 60(1):49–56
pubmed: 30284680
doi: 10.1007/s13353-018-0472-3
Shi J, Fok KL, Dai P, Qiao F, Zhang M, Liu H, Sang M, Ye M, Liu Y, Zhou Y, Wang C, Sun F, Xie G, Chen H (2021) Spatio-temporal landscape of mouse epididymal cells and specific mitochondria-rich segments defined by large-scale single-cell RNA-seq. Cell Discov 7(1):34
pubmed: 34001862
pmcid: 8129088
doi: 10.1038/s41421-021-00260-7
Yu G, Wang LG, Han Y, He QY (2012) clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16(5):284–287
pubmed: 22455463
pmcid: 3339379
doi: 10.1089/omi.2011.0118
Qian F, Wang X, Yin Z, Xie G, Yuan H, Liu D, Chai R (2020) The slc4a2b gene is required for hair cell development in zebrafish. Aging (Albany NY) 12(19):18804–18821
pubmed: 33044947
doi: 10.18632/aging.103840
Zhang L, Gao Y, Zhang R, Sun F, Cheng C, Qian F, Duan X, Wei G, Sun C, Pang X, Chen P, Chai R, Yang T, Wu H, Liu D (2020) THOC1 deficiency leads to late-onset nonsyndromic hearing loss through p53-mediated hair cell apoptosis. PLoS Genet 16(8):e1008953
pubmed: 32776944
pmcid: 7444544
doi: 10.1371/journal.pgen.1008953
Wang C, Zhong Z, Sun P, Zhong H, Li H, Chen F (2017) Evaluation of the hair cell regeneration in zebrafish larvae by measuring and quantifying the startle responses. Neural Plast 2017:8283075
pubmed: 28250994
pmcid: 5303594
doi: 10.1155/2017/8283075
Gong J, Qian P, Hu Y, Guo C, Wei G, Wang C, Cai C, Wang H, Liu D, Claudin H (2021) Is essential for hair cell morphogenesis and auditory function in zebrafish. Front Cell Dev Biol 9:663995
pubmed: 34046408
pmcid: 8147561
doi: 10.3389/fcell.2021.663995
Sun P, Zhang Y, Zhao F, Wu JP, Pun SH, Peng C, Du M, Vai MI, Liu D, Chen F (2018) An assay for systematically quantifying the vestibulo-ocular reflex to assess vestibular function in zebrafish larvae. Front Cell Neurosci 12:257
pubmed: 30186115
pmcid: 6113563
doi: 10.3389/fncel.2018.00257