Genomic instability-associated lncRNA signature predicts prognosis and distinct immune landscape in gastric cancer.
Gastric cancer (GC)
The Cancer Genome Atlas (TCGA)
genomic instability
immune landscape
long non-coding RNAs (lncRNAs)
Journal
Annals of translational medicine
ISSN: 2305-5839
Titre abrégé: Ann Transl Med
Pays: China
ID NLM: 101617978
Informations de publication
Date de publication:
Aug 2021
Aug 2021
Historique:
received:
17
06
2021
accepted:
05
08
2021
entrez:
17
9
2021
pubmed:
18
9
2021
medline:
18
9
2021
Statut:
ppublish
Résumé
Characterized by multiple features, genomic stability-related markers, such as microsatellite instability (MSI), were regulated as an important predictor of chemotherapy and immunity responses in cancer treatment. The aim of our study was to identify a genomic instability-associated long non-coding RNA (lncRNA) signature to help predict the survival and therapy response of gastric cancers (GCs). We used RNA sequencing and single nucleotide variant (SNV) data from The Cancer Genome Atlas-stomach adenocarcinoma (TCGA-STAD) datasets to explore genomic instability-associated lncRNAs. Hierarchical cluster analyses of 197 differentially expressed genomic instability-associated lncRNAs were performed to separate GC patients into two groups, namely, the genomically unstable (GU)-like group and the genomically stable (GS)-like group. Cox regression analysis was conducted to finally identify six lncRNAs (LINC02678, HOXA10-AS, RHOXF1-AS1, AC010789.1, LINC01150, and TGFB2-AS1) with independent prognostic value to establish the genomic instability-associated lncRNA signature (GILncSig). Based on the SNV analysis, GILncSig was correlated with accumulation of gene mutation counts. Further comparisons between different risk score groups were performed to assess chemotherapy drug sensitivity and immune landscape variations. Our study not only revealed the genomic instability-associated lncRNAs in GCs, but provided a key method and resource for further studies of the role of these lncRNAs play, and introduced a potential new way to identify genomic instability-associated cancer biomarkers.
Sections du résumé
BACKGROUND
BACKGROUND
Characterized by multiple features, genomic stability-related markers, such as microsatellite instability (MSI), were regulated as an important predictor of chemotherapy and immunity responses in cancer treatment. The aim of our study was to identify a genomic instability-associated long non-coding RNA (lncRNA) signature to help predict the survival and therapy response of gastric cancers (GCs).
METHODS
METHODS
We used RNA sequencing and single nucleotide variant (SNV) data from The Cancer Genome Atlas-stomach adenocarcinoma (TCGA-STAD) datasets to explore genomic instability-associated lncRNAs. Hierarchical cluster analyses of 197 differentially expressed genomic instability-associated lncRNAs were performed to separate GC patients into two groups, namely, the genomically unstable (GU)-like group and the genomically stable (GS)-like group.
RESULTS
RESULTS
Cox regression analysis was conducted to finally identify six lncRNAs (LINC02678, HOXA10-AS, RHOXF1-AS1, AC010789.1, LINC01150, and TGFB2-AS1) with independent prognostic value to establish the genomic instability-associated lncRNA signature (GILncSig). Based on the SNV analysis, GILncSig was correlated with accumulation of gene mutation counts. Further comparisons between different risk score groups were performed to assess chemotherapy drug sensitivity and immune landscape variations.
CONCLUSIONS
CONCLUSIONS
Our study not only revealed the genomic instability-associated lncRNAs in GCs, but provided a key method and resource for further studies of the role of these lncRNAs play, and introduced a potential new way to identify genomic instability-associated cancer biomarkers.
Identifiants
pubmed: 34532463
doi: 10.21037/atm-21-3569
pii: atm-09-16-1326
pmc: PMC8422092
doi:
Types de publication
Journal Article
Langues
eng
Pagination
1326Informations de copyright
2021 Annals of Translational Medicine. All rights reserved.
Déclaration de conflit d'intérêts
Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://dx.doi.org/10.21037/atm-21-3569). The authors have no conflicts of interest to declare.
Références
Gastroenterology. 2003 Nov;125(5):1330-40
pubmed: 14598249
Front Oncol. 2020 Aug 06;10:1300
pubmed: 32850406
BMC Genomics. 2019 Nov 13;20(1):846
pubmed: 31722674
Cancer Lett. 2019 May 28;450:14-21
pubmed: 30807784
Oncologist. 2019 Oct;24(10):1340-1347
pubmed: 31040255
Cancer Discov. 2016 Jul;6(7):784-801
pubmed: 27147598
Int J Biol Markers. 2010 Oct-Dec;25(4):219-28
pubmed: 21161944
Cell Death Differ. 2019 Mar;26(3):516-530
pubmed: 29899380
Cell Rep. 2019 Sep 17;28(12):3182-3198.e11
pubmed: 31533040
J Gastrointest Oncol. 2020 Aug;11(4):760-769
pubmed: 32953159
Genome Biol. 2014 Mar 03;15(3):R47
pubmed: 24580837
Neoplasma. 2019 Jul 23;66(4):564-575
pubmed: 30943745
Science. 2014 Jan 10;343(6167):189-193
pubmed: 24336570
JAMA Oncol. 2018 Dec 1;4(12):1691-1698
pubmed: 30098163
Cell. 2019 Jan 24;176(3):505-519.e22
pubmed: 30612738
Nat Commun. 2021 Jun 16;12(1):3663
pubmed: 34135330
Cancer Cell. 2021 Feb 8;39(2):154-173
pubmed: 33125859
J Nanobiotechnology. 2021 Jan 12;19(1):22
pubmed: 33436002
J Clin Oncol. 2019 Dec 10;37(35):3392-3400
pubmed: 31513484
Mol Cancer. 2017 Nov 21;16(1):174
pubmed: 29162158
J Cell Biochem. 2019 Oct;120(10):17898-17911
pubmed: 31135068
Nat Med. 2018 Sep;24(9):1441-1448
pubmed: 30082870
JAMA Surg. 2020 Jul 1;155(7):572-579
pubmed: 32520332
Front Oncol. 2020 Mar 13;10:314
pubmed: 32232003
Front Cell Dev Biol. 2020 Oct 15;8:565355
pubmed: 33178684
Ann Oncol. 2019 Jan 1;30(1):44-56
pubmed: 30395155
Brief Bioinform. 2020 Sep 25;21(5):1742-1755
pubmed: 31665214
Nat Rev Cancer. 2014 Feb;14(2):135-46
pubmed: 24457417
Cancer Sci. 2018 Jul;109(7):2093-2100
pubmed: 29774630
Clin Transl Med. 2020 Aug;10(4):e155
pubmed: 32898332
Development. 2020 Jun 11;147(11):
pubmed: 32527937
Ann Oncol. 2006 Jun;17 Suppl 7:vii97-102
pubmed: 16760303