Advanced Omics Techniques for Understanding Cochlear Genome, Epigenome, and Transcriptome in Health and Disease.
cochlea
epigenomics
genomics
omics
organ of Corti
single-cell omics
spatial omics
transcriptomics
Journal
Biomolecules
ISSN: 2218-273X
Titre abrégé: Biomolecules
Pays: Switzerland
ID NLM: 101596414
Informations de publication
Date de publication:
17 10 2023
17 10 2023
Historique:
received:
24
08
2023
revised:
10
10
2023
accepted:
13
10
2023
medline:
30
10
2023
pubmed:
28
10
2023
entrez:
28
10
2023
Statut:
epublish
Résumé
Advanced genomics, transcriptomics, and epigenomics techniques are providing unprecedented insights into the understanding of the molecular underpinnings of the central nervous system, including the neuro-sensory cochlea of the inner ear. Here, we report for the first time a comprehensive and updated overview of the most advanced omics techniques for the study of nucleic acids and their applications in cochlear research. We describe the available in vitro and in vivo models for hearing research and the principles of genomics, transcriptomics, and epigenomics, alongside their most advanced technologies (like single-cell omics and spatial omics), which allow for the investigation of the molecular events that occur at a single-cell resolution while retaining the spatial information.
Identifiants
pubmed: 37892216
pii: biom13101534
doi: 10.3390/biom13101534
pmc: PMC10605747
pii:
doi:
Types de publication
Journal Article
Review
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Références
Nat Genet. 2005 Aug;37(8):853-62
pubmed: 16007088
Proc Natl Acad Sci U S A. 2016 Jul 26;113(30):8508-13
pubmed: 27402757
Proteomics. 2018 Sep;18(18):e1700312
pubmed: 29644800
J Vis Exp. 2015 Jan 12;(95):52260
pubmed: 25651458
Cell. 2020 Dec 10;183(6):1665-1681.e18
pubmed: 33188776
Genome Biol. 2021 Jun 30;22(1):195
pubmed: 34193237
Development. 2019 Feb 15;146(4):
pubmed: 30770379
Cell Rep. 2021 Mar 23;34(12):108900
pubmed: 33761346
Nucleic Acids Res. 2017 Jun 2;45(10):e77
pubmed: 28126923
J Neurobiol. 2002 Nov 5;53(2):306-18
pubmed: 12382283
Acta Otolaryngol Suppl. 1991;482:7-12; discussion 13
pubmed: 1897363
Genet Test Mol Biomarkers. 2013 Aug;17(8):581-7
pubmed: 23738631
Science. 2016 Jul 1;353(6294):78-82
pubmed: 27365449
Development. 2018 Feb 21;145(4):
pubmed: 29437831
Science. 2015 Apr 24;348(6233):aaa6090
pubmed: 25858977
Elife. 2017 Jan 16;6:
pubmed: 28079019
Int J Dev Biol. 2007;51(6-7):609-31
pubmed: 17891721
Cell. 2022 Nov 10;185(23):4448-4464.e17
pubmed: 36272405
Nat Genet. 1998 May;19(1):60-2
pubmed: 9590290
Cell Res. 2016 Mar;26(3):304-19
pubmed: 26902283
Science. 2019 Mar 29;363(6434):1463-1467
pubmed: 30923225
Cell. 2015 May 21;161(5):1202-1214
pubmed: 26000488
Cell Rep. 2021 Sep 28;36(13):109758
pubmed: 34592158
Brain Res Bull. 2003 Jun 15;60(5-6):397-422
pubmed: 12787864
Front Genet. 2018 Feb 07;9:20
pubmed: 29467791
Anat Rec (Hoboken). 2012 Nov;295(11):1791-811
pubmed: 23044521
Cell Biosci. 2023 May 20;13(1):93
pubmed: 37210555
Curr Protoc Mol Biol. 2018 Apr;122(1):e57
pubmed: 29851283
Nat Rev Genet. 2016 Mar;17(3):175-88
pubmed: 26806412
Brain Res. 1981 May 11;212(1):17-30
pubmed: 7225854
Pharmacol Ther. 2019 Aug;200:190-209
pubmed: 31075354
Nat Genet. 2002 Mar;30(3):257-8
pubmed: 11850623
Front Neurosci. 2023 May 03;17:1177791
pubmed: 37207182
Hum Mutat. 2019 Oct 23;:
pubmed: 31646703
J Hum Genet. 2022 Mar;67(3):157-164
pubmed: 34719681
Stem Cell Reports. 2019 Jul 9;13(1):147-162
pubmed: 31204303
Comput Struct Biotechnol J. 2022 Jun 02;20:2895-2908
pubmed: 35765645
Cell Rep. 2022 Apr 12;39(2):110665
pubmed: 35417713
Dev Cell. 2021 Sep 13;56(17):2471-2485.e5
pubmed: 34331868
Front Bioeng Biotechnol. 2022 Apr 12;10:842299
pubmed: 35497361
Hear Res. 2022 Dec;426:108440
pubmed: 35063312
Front Neurosci. 2022 Apr 27;16:867034
pubmed: 35573297
Nat Methods. 2014 Apr;11(4):360-1
pubmed: 24681720
Cell Rep. 2015 Jun 9;11(9):1385-99
pubmed: 26027927
Quant Imaging Med Surg. 2019 May;9(5):858-881
pubmed: 31281781
BMC Res Notes. 2015 Nov 18;8:691
pubmed: 26582541
Nat Med. 2020 May;26(5):792-802
pubmed: 32405060
Nat Rev Genet. 2015 Dec;16(12):716-26
pubmed: 26460349
J Anat. 2016 Feb;228(2):255-69
pubmed: 26403558
J Biol Chem. 1997 Mar 28;272(13):8791-801
pubmed: 9079715
Ann Transl Med. 2021 Sep;9(17):1393
pubmed: 34733945
Nat Methods. 2015 Apr;12(4):351-6
pubmed: 25686389
Mol Biotechnol. 2023 Feb;65(2):227-242
pubmed: 35474409
Hear Res. 2016 Mar;333:266-274
pubmed: 26341477
Front Genet. 2023 Jan 04;13:1100016
pubmed: 36685871
Nat Protoc. 2017 Mar;12(3):566-580
pubmed: 28207000
Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):19802-7
pubmed: 24248345
Nat Biotechnol. 2014 Oct;32(10):1053-8
pubmed: 25086649
Signal Transduct Target Ther. 2023 Jan 16;8(1):36
pubmed: 36646687
Hear Res. 2019 Oct;382:107785
pubmed: 31493568
Nat Commun. 2017 May 11;8:15046
pubmed: 28492243
Nat Biotechnol. 2021 Aug;39(8):968-977
pubmed: 33875865
Nat Protoc. 2017 Jan;12(1):44-73
pubmed: 27929523
Otolaryngol Clin North Am. 2015 Dec;48(6):1041-61
pubmed: 26443487
Mol Genet Genomic Med. 2019 Aug;7(8):e808
pubmed: 31250571
Genome Biol. 2016 Apr 18;17:72
pubmed: 27091476
Nat Genet. 2004 Sep;36(9):955-7
pubmed: 15300250
Audiol Neurootol. 2001 Nov-Dec;6(6):305-18
pubmed: 11847461
Cell Res. 2011 Mar;21(3):381-95
pubmed: 21321607
J Cell Biochem. 2018 Apr;119(4):3545-3553
pubmed: 29143984
Cell Genom. 2022 Sep 14;2(9):
pubmed: 36212030
Biomedicines. 2022 Nov 15;10(11):
pubmed: 36428503
Indian J Radiol Imaging. 2009 Apr-Jun;19(2):99-106
pubmed: 19881062
Elife. 2022 Nov 29;11:
pubmed: 36445327
Annu Rev Genomics Hum Genet. 2021 Aug 31;22:171-197
pubmed: 33722077
Front Cell Dev Biol. 2021 Feb 12;9:637779
pubmed: 33644075
Sci Rep. 2022 Dec 7;12(1):21196
pubmed: 36476755
Clin Genet. 2020 Oct;98(4):353-364
pubmed: 33111345
Trends Genet. 2017 Feb;33(2):155-168
pubmed: 28089370
J Acoust Soc Am. 2019 Nov;146(5):3646
pubmed: 31795692
Sci China Life Sci. 2013 Oct;56(10):960-7
pubmed: 24091688
Genome Med. 2022 Jun 27;14(1):68
pubmed: 35761361
Curr Protoc Mol Biol. 2015 Jan 05;109:21.29.1-21.29.9
pubmed: 25559105
Am J Hum Genet. 2010 Mar 12;86(3):378-88
pubmed: 20170899
Opt Express. 2011 Aug 1;19(16):15415-28
pubmed: 21934905
Hear Res. 2007 Sep;231(1-2):1-12
pubmed: 17475424
Elife. 2020 Jan 08;9:
pubmed: 31913118
Front Mol Neurosci. 2022 Mar 16;15:832813
pubmed: 35370544
Oxid Med Cell Longev. 2022 Feb 9;2022:4127238
pubmed: 35186184
Nat Methods. 2013 Sep;10(9):857-60
pubmed: 23852452
Adv Exp Med Biol. 2011;720:15-25
pubmed: 21901615
Cold Spring Harb Protoc. 2010 Feb;2010(2):pdb.prot5384
pubmed: 20150147
Proc Natl Acad Sci U S A. 2014 Nov 25;111(47):16919-24
pubmed: 25385613
Nature. 2021 Feb;590(7845):344-350
pubmed: 33505024
Int J Mol Sci. 2023 Apr 25;24(9):
pubmed: 37175547
Mol Cells. 2018 Jul 31;41(7):695-702
pubmed: 30008200
PLoS One. 2016 Jun 28;11(6):e0157768
pubmed: 27351484
Methods. 2021 Mar;187:104-113
pubmed: 32645449
Brief Bioinform. 2023 Jan 19;24(1):
pubmed: 36545790
Oncol Lett. 2020 Sep;20(3):2595-2605
pubmed: 32782577
Cell Rep. 2019 Mar 12;26(11):3160-3171.e3
pubmed: 30865901
Nat Biotechnol. 2020 May;38(5):586-599
pubmed: 32393914
Adv Biochem Eng Biotechnol. 2002;77:75-101
pubmed: 12227738
Front Oncol. 2022 Jun 29;12:890410
pubmed: 35847846
Nat Biotechnol. 2021 Mar;39(3):313-319
pubmed: 33288904
Science. 2021 Feb 26;371(6532):
pubmed: 33384301
Nat Neurosci. 2021 Mar;24(3):425-436
pubmed: 33558695
Proc Natl Acad Sci U S A. 2006 May 9;103(19):7240-5
pubmed: 16648246
Mol Cell. 2015 May 21;58(4):598-609
pubmed: 26000845
Methods Cell Biol. 2016;135:299-307
pubmed: 27443932
Nature. 2022 Sep;609(7926):375-383
pubmed: 35978191
Genome Biol. 2021 Mar 22;22(1):86
pubmed: 33752742
Front Cell Neurosci. 2021 Feb 26;15:643517
pubmed: 33716676
Hear Res. 2016 Feb;332:17-28
pubmed: 26688175
Lab Chip. 2020 Aug 11;20(16):3011-3023
pubmed: 32700707
BMC Bioinformatics. 2022 Nov 3;23(1):459
pubmed: 36329406
Hear Res. 2015 Sep;327:102-8
pubmed: 25987504
Matrix Biol. 2020 Sep;91-92:152-166
pubmed: 32416243
Nature. 2011 Apr 7;472(7341):90-4
pubmed: 21399628
Genes (Basel). 2021 Aug 20;12(8):
pubmed: 34440452
Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7
pubmed: 271968
Biomedicines. 2023 Jun 01;11(6):
pubmed: 37371710
Neurology. 2013 Feb 26;80(9):824-8
pubmed: 23365052
Front Cell Dev Biol. 2022 Jun 23;10:884240
pubmed: 35813214
Methods Mol Biol. 2018;1675:167-181
pubmed: 29052192
Nat Biotechnol. 2018 Jun;36(5):428-431
pubmed: 29644997
Clin Transl Med. 2022 Mar;12(3):e694
pubmed: 35352511
PLoS Genet. 2019 Jul 5;15(7):e1008254
pubmed: 31276493
Elife. 2019 Jan 25;8:
pubmed: 30681411
Nat Rev Genet. 2023 Aug;24(8):494-515
pubmed: 36864178
Hear Res. 2017 May;348:87-97
pubmed: 28263850
Curr Biol. 2019 Aug 5;29(15):2477-2487.e6
pubmed: 31353184
Nat Methods. 2020 Jan;17(1):14-17
pubmed: 31907463
Clin Pharmacol Ther. 2017 Apr;101(4):491-500
pubmed: 28002638
Science. 2022 Feb 11;375(6581):681-686
pubmed: 35143307
BMC Genomics. 2012 Jul 24;13:341
pubmed: 22827831
Genes (Basel). 2021 Apr 13;12(4):
pubmed: 33924653
Front Cell Dev Biol. 2021 Apr 21;9:664317
pubmed: 33968938
Nature. 2022 Aug;608(7924):733-740
pubmed: 35978187
Small. 2020 Mar;16(9):e1903905
pubmed: 31544338
Nat Commun. 2023 Sep 12;14(1):5618
pubmed: 37699885
Development. 2016 Nov 1;143(21):4003-4015
pubmed: 27633988
Acta Otolaryngol. 2022 Feb;142(2):132-139
pubmed: 35148225
PLoS Genet. 2015 Feb 13;11(2):e1004994
pubmed: 25679813
Dev Dyn. 2011 Feb;240(2):372-83
pubmed: 21246654
ACS Nano. 2022 Jan 25;16(1):211-220
pubmed: 34559518
Nat Commun. 2019 Apr 29;10(1):1930
pubmed: 31036827
Biomed Pharmacother. 2023 Jan;157:114045
pubmed: 36455457
Exp Mol Med. 2018 Aug 7;50(8):1-14
pubmed: 30089861
Development. 2019 Sep 2;146(17):
pubmed: 31477580
Front Med (Lausanne). 2022 Jul 01;9:911861
pubmed: 35860739
Otol Neurotol. 2021 Aug 1;42(7):e849-e857
pubmed: 33617194
Hear Res. 2017 Jun;349:138-147
pubmed: 28087419
Front Mol Neurosci. 2020 Feb 05;13:13
pubmed: 32116546
Front Cell Dev Biol. 2021 Jul 22;9:714687
pubmed: 34368164
Nat Protoc. 2013 Nov;8(11):2281-2308
pubmed: 24157548
Otolaryngol Head Neck Surg. 2015 Aug;153(2):175-82
pubmed: 26084827
Proc Natl Acad Sci U S A. 2023 Jun 27;120(26):e2221744120
pubmed: 37339214
Genomics Proteomics Bioinformatics. 2022 Oct;20(5):836-849
pubmed: 36581065
J Neurosurg. 2014 Sep;121(3):554-63
pubmed: 24995779
Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):E1383-92
pubmed: 24706903
Nat Biotechnol. 2023 Feb;41(2):222-231
pubmed: 36138169
Epigenetics. 2006 Jul-Sep;1(3):146-52
pubmed: 17965615
Cell. 2020 Sep 17;182(6):1641-1659.e26
pubmed: 32822575
Acta Otorrinolaringol Esp (Engl Ed). 2020 May - Jun;71(3):166-174
pubmed: 31706454
Ear Hear. 2021 Nov 8;43(3):1049-1066
pubmed: 34753855
Nature. 2018 Jan 11;553(7687):217-221
pubmed: 29258297
Brain Sci. 2021 Dec 21;12(1):
pubmed: 35053747
Science. 2005 Sep 9;309(5741):1728-32
pubmed: 16081699
J Appl Genet. 2020 Feb;61(1):51-65
pubmed: 31912450
Nat Methods. 2022 Feb;19(2):139
pubmed: 35145316
Brain Res. 2006 May 26;1091(1):113-21
pubmed: 16600193
Nat Methods. 2017 Apr;14(4):395-398
pubmed: 28192419
Stem Cell Reports. 2017 Nov 14;9(5):1516-1529
pubmed: 29033307
PLoS One. 2016 Feb 09;11(2):e0148339
pubmed: 26859490
J Big Data. 2021;8(1):53
pubmed: 33816053
J Assoc Res Otolaryngol. 2017 Dec;18(6):751-769
pubmed: 28717876
J Pharm Anal. 2023 Jul;13(7):694-710
pubmed: 37577383
JAMA Netw Open. 2022 Jul 1;5(7):e2220986
pubmed: 35816303
Cell. 2022 May 12;185(10):1777-1792.e21
pubmed: 35512705
Curr Opin Neurobiol. 2018 Jun;50:242-249
pubmed: 29738987
Arch Pathol Lab Med. 2017 Jun;141(6):798-805
pubmed: 28362156
Cell. 2021 Dec 22;184(26):6361-6377.e24
pubmed: 34875226