Cell Type–Specific Transcriptome Analysis Reveals a Major Role for and miR-200b in Mouse Inner Ear Morphogenesis

English version České info

Cellular heterogeneity hinders the extraction of functionally significant results and inference of regulatory networks from wide-scale expression profiles of complex mammalian organs. The mammalian inner ear consists of the auditory and vestibular systems that are each composed of hair cells, supporting cells, neurons, mesenchymal cells, other epithelial cells, and blood vessels. We developed a novel protocol to sort auditory and vestibular tissues of newborn mouse inner ears into their major cellular components. Transcriptome profiling of the sorted cells identified cell type–specific expression clusters. Computational analysis detected transcription factors and microRNAs that play key roles in determining cell identity in the inner ear. Specifically, our analysis revealed the role of the Zeb1/miR-200b pathway in establishing epithelial and mesenchymal identity in the inner ear. Furthermore, we detected a misregulation of the ZEB1 pathway in the inner ear of Twirler mice, which manifest, among other phenotypes, malformations of the auditory and vestibular labyrinth. The association of misregulation of the ZEB1/miR-200b pathway with auditory and vestibular defects in the Twirler mutant mice uncovers a novel mechanism underlying deafness and balance disorders. Our approach can be employed to decipher additional complex regulatory networks underlying other hearing and balance mouse mutants.

Vyšlo v časopise: Cell Type–Specific Transcriptome Analysis Reveals a Major Role for and miR-200b in Mouse Inner Ear Morphogenesis. PLoS Genet 7(9): e32767. doi:10.1371/journal.pgen.1002309
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1002309

Souhrn

Zdroje

1. FriedmanTBSchultzJMBen-YosefTPryorSPLagzielA 2003 Recent advances in the understanding of syndromic forms of hearing loss. Ear Hear 24 289 302

2. RavivDDrorAAAvrahamKB 2010 Hearing loss: a common disorder caused by many rare alleles. Ann NY Acad Sci 1214 168 79

3. FriedmanLMDrorAAAvrahamKB 2007 Mouse models to study inner ear development and hereditary hearing loss. Int J Dev Biol 51 609 631

4. HertzanoRPuligillaCChanSLTimothyCDepireuxDA 2010 CD44 is a marker for the outer pillar cells in the early postnatal mouse inner ear. J Assoc Res Otolaryngol 11 407 418

5. NielsenJSMcNagnyKM 2008 Novel functions of the CD34 family. J Cell Sci 121 3683 3692

6. PavlidisP 2003 Using ANOVA for gene selection from microarray studies of the nervous system. Methods 31 282 289

7. DoJHChoiDK 2008 Clustering approaches to identifying gene expression patterns from DNA microarray data. Mol Cells 25 279 288

8. OchsMFPetersonAJKossenkovABidautG 2007 Incorporation of gene ontology annotations to enhance microarray data analysis. Methods Mol Biol 377 243 254

9. SchoenCJEmerySBThorneMCAmmanaHRSliwerskaE 2010 Increased activity of Diaphanous homolog 3 (DIAPH3)/diaphanous causes hearing defects in humans with auditory neuropathy and in Drosophila. Proc Natl Acad Sci U S A 107 13396 13401

10. UlitskyIShamirR 2007 Identification of functional modules using network topology and high-throughput data. BMC Syst Biol 1 8

11. MenciaAModamio-HoybjorSRedshawNMorinMMayo-MerinoF 2009 Mutations in the seed region of human miR-96 are responsible for nonsyndromic progressive hearing loss. Nat Genet 41 609 613

12. LewisMAQuintEGlazierAMFuchsHDe AngelisMH 2009 An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice. Nat Genet 41 614 618

13. WestonMDPierceMLRocha-SanchezSBeiselKWSoukupGA 2006 MicroRNA gene expression in the mouse inner ear. Brain Res 1111 95 104

14. ElkonRAgamiR 2008 Removal of AU bias from microarray mRNA expression data enhances computational identification of active microRNAs. PLoS Comput Biol 4 e1000189

15. Van DongenSAbreu-GoodgerCEnrightAJ 2008 Detecting microRNA binding and siRNA off-target effects from expression data. Nat Methods 5 1023 1025

16. SmirnovaLGrafeASeilerASchumacherSNitschR 2005 Regulation of miRNA expression during neural cell specification. Eur J Neurosci 21 1469 1477

17. SacheliRNguyenLBorgsLVandenboschRBodsonM 2009 Expression patterns of miR-96, miR-182 and miR-183 in the development inner ear. Gene Expr Patterns 9 364 370

18. LinhartCHalperinYShamirR 2008 Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets. Genome Res 18 1180 1189

19. IkedaKKawakamiK 1995 DNA binding through distinct domains of zinc-finger-homeodomain protein AREB6 has different effects on gene transcription. Eur J Biochem 233 73 82

20. PostigoAAWardESkeathJBDeanDC 1999 zfh-1, the Drosophila homologue of ZEB, is a transcriptional repressor that regulates somatic myogenesis. Mol Cell Biol 19 7255 7263

21. SpoelstraNSManningNGHigashiYDarlingDSinghM 2006 The transcription factor ZEB1 is aberrantly expressed in aggressive uterine cancers. Cancer Res 66 3893 3902

22. BurkUSchubertJWellnerUSchmalhoferOVincanE 2008 A reciprocal repression between ZEB1 and members of the miR-200 family promotes EMT and invasion in cancer cells. EMBO Rep 9 6 582 9

23. LyonMF 1958 Twirler: a mutant affecting the inner ear of the house mouse. J Embryol Exp Morphol 6 105 116

24. KurimaKHertzanoRGavrilovaOMonahanKShpargelKB 2011 A Noncoding Point Mutation of Zeb1 Causes Multiple Developmental Malformations and Obesity in Twirler mice. PLoS Genetics, accepted

25. GoodyearRJRichardsonGP 2002 Extracellular matrices associated with the apical surfaces of sensory epithelia in the inner ear: molecular and structural diversity. J Neurobiol 53 212 227

26. ZhaoXYangHYamoahENLundbergYW 2007 Gene targeting reveals the role of Oc90 as the essential organizer of the otoconial organic matrix. Dev Biol 304 508 524

27. WangWCherryJMNochomovitzYJollyEBotsteinD 2005 Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation. Proc Natl Acad Sci U S A 102 1998 2003

28. PilpelYSudarsanamPChurchGM 2001 Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet 29 153 159

29. HornsteinEShomronN 2006 Canalization of development by microRNAs. Nat Genet 38 Suppl S20 24

30. LiuYPengXTanJDarlingDSKaplanHJ 2008 Zeb1 mutant mice as a model of posterior corneal dystrophy. Invest Ophthalmol Vis Sci 49 1843 1849

31. ParkPJ 2009 ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10 669 680

32. VerpyELeiboviciMPetitC 1999 Characterization of otoconin-95, the major protein of murine otoconia, provides insights into the formation of these inner ear biominerals. Proc Natl Acad Sci USA 96 529 534

33. Cohen-SalmonMEl-AmraouiALeiboviciMPetitC 1997 Otogelin: a glycoprotein specific to the acellular membranes of the inner ear. Proc Natl Acad Sci USA 94 14450 14455

34. LeganPKLukashkinaVAGoodyearRJKossiMRussellIJ 2000 A targeted deletion in alpha-tectorin reveals that the tectorial membrane is required for the gain and timing of cochlear feedback. Neuron 28 273 285

35. DriverECKelleyMW 2010 Transfection of mouse cochlear explants by electroporation. Curr Protoc Neurosci Chapter 4 Unit 4 34 31 10

36. UlitskyIMaron-KatzAShavitSSagirDLinhartC 2010 Expander: from expression microarrays to networks and functions. Nat Protoc 5 303 322

37. LewisBPBurgeCBBartelDP 2005 Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120 15 20

38. SayersEWBarrettTBensonDABoltonEBryantSH 2011 Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 38 D5 16

39. FriedmanLMDrorAAMorETenneTTorenG 2009 MicroRNAs are essential for development and function of inner ear hair cells in vertebrates. Proc Natl Acad Sci U S A 106 7915 7920

40. SubramanianATamayoPMoothaVKMukherjeeSEbertBL 2005 Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102 15545 15550