Identification of a Putative Enhancer RNA for EGFR in Hyper-Accessible Regions in Esophageal Squamous Cell Carcinoma Cells by Analysis of Chromatin Accessibility Landscapes.
AP-1
ATAC-seq
digital droplet PCR
enhancer RNA (eRNA)
esophageal cancer
non-coding RNA (ncRNA)
transcription factor binding
tyrosine kinase inhibitor (TKI)
Journal
Frontiers in oncology
ISSN: 2234-943X
Titre abrégé: Front Oncol
Pays: Switzerland
ID NLM: 101568867
Informations de publication
Date de publication:
2021
2021
Historique:
received:
14
06
2021
accepted:
20
09
2021
entrez:
1
11
2021
pubmed:
2
11
2021
medline:
2
11
2021
Statut:
epublish
Résumé
Abnormal genetic and epigenetic modifications play a key role in esophageal cancer. By Assay for Transposase-Accessible Chromatin by sequencing (ATAC-seq), this study compared chromatin accessibility landscapes among two esophageal squamous cell carcinoma (ESCC) cell lines, KYSE-30 and KYSE-150, and a non-cancerous esophageal epithelial cell line, HET-1A. Data showed that hyper-accessible regions in ESCC cells contained genes related with cancer hallmarks, such as epidermal growth factor receptor (EGFR). Multi-omics analysis and digital-droplet PCR results demonstrated that several non-coding RNAs in EGFR upstream were upregulated in ESCC cells. Among them, one appeared to act as an enhancer RNA responsible for EGFR overexpression. Further motif analysis and pharmacological data suggested that AP-1 family transcription factors were able to bind the hyper-accessible regions and thus to regulate cancer cell proliferation and migration. This study discovered a putative enhancer RNA for EGFR gene and the reliance of ESCC on AP-1 transcription factor.
Identifiants
pubmed: 34722266
doi: 10.3389/fonc.2021.724687
pmc: PMC8554337
doi:
Types de publication
Journal Article
Langues
eng
Pagination
724687Informations de copyright
Copyright © 2021 Choi, Sathe, Mathé, Xing and Pan.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Références
FASEB J. 2018 Jan;32(1):404-416
pubmed: 28928244
Oncotarget. 2014 Jun 15;5(11):3455-71
pubmed: 24797725
BMC Cancer. 2009 Sep 16;9:329
pubmed: 19758438
JAMA Oncol. 2017 Nov 1;3(11):1520-1528
pubmed: 28687830
Gene. 2018 Jun 30;661:169-175
pubmed: 29604464
Trends Mol Med. 2012 Jan;18(1):13-26
pubmed: 22177734
World J Surg Oncol. 2013 Oct 16;11:278
pubmed: 24131756
Nucleic Acids Res. 2021 Jan 8;49(D1):D325-D334
pubmed: 33290552
Science. 2018 Oct 26;362(6413):
pubmed: 30361341
Nucleic Acids Res. 2020 Jan 8;48(D1):D845-D855
pubmed: 31680165
J Clin Oncol. 2017 Jul 10;35(20):2279-2287
pubmed: 28537764
Front Oncol. 2014 Jun 04;4:129
pubmed: 24926435
Bioinformatics. 2009 Jan 15;25(2):288-9
pubmed: 19033274
Cancer Res. 2018 Mar 15;78(6):1418-1430
pubmed: 29339538
Nature. 2014 Mar 27;507(7493):455-461
pubmed: 24670763
PLoS Genet. 2017 Aug 31;13(8):e1006879
pubmed: 28859074
Cancer Lett. 2018 Sep 28;432:169-179
pubmed: 29908962
Nucleic Acids Res. 2019 Jul 2;47(W1):W199-W205
pubmed: 31114916
Biochim Biophys Acta Rev Cancer. 2019 Aug;1872(1):11-23
pubmed: 31034924
Nucleic Acids Res. 2019 Jul 2;47(W1):W556-W560
pubmed: 31114875
EMBO Rep. 2018 Dec;19(12):
pubmed: 30413482
Oncotarget. 2016 Jun 7;7(23):34371-83
pubmed: 27144339
J Biol Chem. 2018 Sep 7;293(36):13795-13804
pubmed: 29507097
Nat Genet. 2013 Jun;45(6):632-8
pubmed: 23644492
Epigenetics. 2011 Oct 1;6(10):1217-27
pubmed: 21946330
Nucleic Acids Res. 2017 Jan 4;45(D1):D353-D361
pubmed: 27899662
Nucleic Acids Res. 2021 Jan 8;49(D1):D613-D621
pubmed: 33211851
Nucleic Acids Res. 2020 Jan 8;48(D1):D498-D503
pubmed: 31691815
Gastroenterology. 2012 Sep;143(3):675-686.e12
pubmed: 22705009
J Physiol Pharmacol. 2018 Aug;69(4):
pubmed: 30415238
Nat Methods. 2013 Dec;10(12):1213-8
pubmed: 24097267
Genome Biol. 2008;9(9):R137
pubmed: 18798982
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Bioinformatics. 2015 Jul 15;31(14):2382-3
pubmed: 25765347
Mol Genet Genomics. 2018 Feb;293(1):1-15
pubmed: 28894972
Mol Cell. 2010 May 28;38(4):576-89
pubmed: 20513432
Cancer Res. 1991 Jan 1;51(1):365-71
pubmed: 1703038
Nucleic Acids Res. 2019 Jan 8;47(D1):D106-D112
pubmed: 30247654
Cancer. 1992 Jan 15;69(2):277-84
pubmed: 1728357
Int J Cancer. 1994 Jul 15;58(2):291-7
pubmed: 7913084
Nature. 2013 Jun 27;498(7455):516-20
pubmed: 23728302
Lancet Oncol. 2014 Jul;15(8):894-904
pubmed: 24950987