Identification of differentially expressed genomic repeats in primary hepatocellular carcinoma and their potential links to biological processes and survival.
RNA sequencing
hepatocellular carcinoma
retroelements
satellite RNA
transposable elements
Liver cancer
Journal
Turkish journal of biology = Turk biyoloji dergisi
ISSN: 1303-6092
Titre abrégé: Turk J Biol
Pays: Turkey
ID NLM: 9434434
Informations de publication
Date de publication:
2021
2021
Historique:
received:
05
04
2021
accepted:
19
06
2021
entrez:
22
11
2021
pubmed:
23
11
2021
medline:
23
11
2021
Statut:
epublish
Résumé
Hepatocellular carcinoma (HCC) is one of the deadliest cancers. Research on HCC so far primarily focused on genes and provided limited information on genomic repeats, which constitute more than half of the human genome and contribute to genomic stability. In line with this, repeat dysregulation was significantly shown to be pathological in various cancers and other diseases. In this study, we aimed to determine the full repeat expression profile of HCC for the first time. We utilised two independent RNA-seq datasets obtained from primary HCC tumours with matched normal tissues of 20 and 17 HCC patients, respectively. We quantified repeat expressions and analysed their differential expression. We also identified repeats that are cooperatively expressed with genes by constructing a gene coexpression network. Our results indicated that HCC tumours in both datasets harbour 24 differentially expressed repeats and even more elements were coexpressed with genes involved in various metabolic pathways. We discovered that two L1 elements (L1M3b, L1M3de) were downregulated and a handful of HERV subfamily repeats (HERV-Fc1-int, HERV3-int, HERVE_a-int, HERVK11D-int, HERVK14C-int, HERVL18-int) were upregulated with the exception of HERV1_LTRc, which was downregulated. Various LTR elements (LTR32, LTR9, LTR4, LTR52-int, LTR70) and MER elements (MER11C, MER11D, MER57C1, MER9a1, MER74C) were implicated along with few other subtypes including Charlie12, MLT2A2, Tigger15a, Tigger 17b. The only satellite repeat differentially expressed in both datasets was GSATII, whose expression was upregulated in 33 (>90%) out of 37 patients. Notably, GSATII expression correlated with HCC survival genes. Elements discovered here promise future studies to be considered for biomarker and HCC therapy research. The coexpression pattern of the GSATII satellite with HCC survival genes and the fact that it has been upregulated in the vast majority of patients make this repeat particularly stand out for HCC.
Identifiants
pubmed: 34803457
doi: 10.3906/biy-2104-13
pmc: PMC8574195
doi:
Types de publication
Journal Article
Langues
eng
Pagination
599-612Informations de copyright
Copyright © 2021 The Author(s).
Déclaration de conflit d'intérêts
CONFLICT OF INTEREST: none declared
Références
Clin Transl Med. 2019 May 6;8(1):13
pubmed: 31056726
Mob DNA. 2015 Jun 02;6:11
pubmed: 26045719
PeerJ. 2019 Dec 19;7:e8277
pubmed: 31875158
OMICS. 2012 May;16(5):284-7
pubmed: 22455463
Cell. 2017 Jun 15;169(7):1327-1341.e23
pubmed: 28622513
Nat Commun. 2016 Sep 26;7:13006
pubmed: 27667193
BMC Bioinformatics. 2014 Mar 29;15:91
pubmed: 24678608
Hepatol Res. 2009 Mar;39(3):266-73
pubmed: 19054153
Bioinformatics. 2008 Mar 1;24(5):719-20
pubmed: 18024473
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Front Chem. 2016 May 11;4:21
pubmed: 27242996
World J Hepatol. 2015 Jul 28;7(15):1964-70
pubmed: 26244070
PLoS One. 2019 May 6;14(5):e0216374
pubmed: 31059558
Cancer Res. 2020 Mar 1;80(5):976-987
pubmed: 31874857
Bioinformatics. 2014 Apr 1;30(7):923-30
pubmed: 24227677
JHEP Rep. 2020 Aug 07;2(6):100167
pubmed: 33134907
Science. 2011 Feb 4;331(6017):593-6
pubmed: 21233348
Nucleic Acids Res. 2017 Jul 3;45(W1):W98-W102
pubmed: 28407145
Nucleic Acids Res. 2016 Jan 4;44(D1):D81-9
pubmed: 26612867
BMC Genomics. 2019 May 31;20(1):439
pubmed: 31151386
Clin Epigenetics. 2019 Oct 21;11(1):145
pubmed: 31639042
Front Aging Neurosci. 2018 Aug 27;10:259
pubmed: 30210331
Philos Trans R Soc Lond B Biol Sci. 2020 Mar 30;375(1795):20190330
pubmed: 32075561
J Pathol. 2017 Dec;243(4):418-430
pubmed: 28862757
Curr Biol. 2017 Sep 11;27(17):2652-2660.e4
pubmed: 28844647
Cell Rep. 2017 Apr 18;19(3):584-600
pubmed: 28423321
Nature. 2011 Sep 07;477(7363):179-84
pubmed: 21901007
Mol Biol (Mosk). 2014 Nov-Dec;48(6):999-1007
pubmed: 25845241
World J Gastroenterol. 2016 Nov 7;22(41):9069-9095
pubmed: 27895396
Genome Biol. 2010;11(3):R25
pubmed: 20196867
Nature. 2019 Feb;566(7742):73-78
pubmed: 30728521
Nucleic Acids Res. 2011 Jan;39(Database issue):D19-21
pubmed: 21062823
Proc Natl Acad Sci U S A. 2015 Dec 8;112(49):15148-53
pubmed: 26575630
Bioinformatics. 2010 Jan 1;26(1):139-40
pubmed: 19910308
Nucleic Acids Res. 2019 May 7;47(8):e47
pubmed: 30783653
Genome Res. 2009 Apr;19(4):533-44
pubmed: 19141594
Genome Res. 2018 May;28(5):639-653
pubmed: 29643204
Biol Rev Camb Philos Soc. 2005 May;80(2):227-50
pubmed: 15921050
Chromosome Res. 2015 Sep;23(3):415-20
pubmed: 26514350
Elife. 2017 Aug 01;6:
pubmed: 28760198
Cancer Genet. 2019 Nov;239:36-45
pubmed: 31536958
BMC Genomics. 2011 Oct 28;12:531
pubmed: 22035034
Hepatology. 2019 Jan;69(1):359-375
pubmed: 30014619
Hepatology. 2001 Mar;33(3):561-8
pubmed: 11230735
Stat Appl Genet Mol Biol. 2005;4:Article17
pubmed: 16646834
Nat Genet. 2014 Jan;46(1):24-32
pubmed: 24316982
Cell Rep. 2018 Apr 10;23(2):512-521
pubmed: 29642008
Microbiol Mol Biol Rev. 2008 Dec;72(4):686-727
pubmed: 19052325
Nat Commun. 2017 Feb 13;8:14421
pubmed: 28194035
Dev Cell. 2010 Oct 19;19(4):625-38
pubmed: 20951352
Elife. 2017 Aug 01;6:
pubmed: 28760199
BMC Bioinformatics. 2008 Dec 29;9:559
pubmed: 19114008
Oncotarget. 2014 Nov 15;5(21):10621-35
pubmed: 25301737
J Virol. 2012 Apr;86(7):3713-22
pubmed: 22278236
Nat Rev Genet. 2011 Nov 29;13(1):36-46
pubmed: 22124482
Genome Biol. 2016 Jan 26;17:13
pubmed: 26813401
Genome Res. 2015 Dec;25(12):1812-24
pubmed: 26510915
Nat Rev Cancer. 2017 Jul;17(7):415-424
pubmed: 28642606
Trends Cancer. 2018 Aug;4(8):583-597
pubmed: 30064665
Brief Bioinform. 2019 Nov 27;20(6):2044-2054
pubmed: 30099484
Nat Rev Dis Primers. 2016 Apr 14;2:16018
pubmed: 27158749
Sci Rep. 2017 Mar 31;7:45846
pubmed: 28361988