Genomic and transcriptomic analyses identify a prognostic gene signature and predict response to therapy in pleural and peritoneal mesothelioma.
WES
mesothelioma
response to therapy
synthetic lethality
transcriptome
Journal
Cell reports. Medicine
ISSN: 2666-3791
Titre abrégé: Cell Rep Med
Pays: United States
ID NLM: 101766894
Informations de publication
Date de publication:
21 02 2023
21 02 2023
Historique:
received:
25
04
2022
revised:
23
08
2022
accepted:
19
01
2023
pubmed:
12
2
2023
medline:
25
2
2023
entrez:
11
2
2023
Statut:
ppublish
Résumé
Malignant mesothelioma is an aggressive cancer with limited treatment options and poor prognosis. A better understanding of mesothelioma genomics and transcriptomics could advance therapies. Here, we present a mesothelioma cohort of 122 patients along with their germline and tumor whole-exome and tumor RNA sequencing data as well as phenotypic and drug response information. We identify a 48-gene prognostic signature that is highly predictive of mesothelioma patient survival, including CCNB1, the expression of which is highly predictive of patient survival on its own. In addition, we analyze the transcriptomics data to study the tumor immune microenvironment and identify synthetic-lethality-based signatures predictive of response to therapy. This germline and somatic whole-exome sequencing as well as transcriptomics data from the same patient are a valuable resource to address important biological questions, including prognostic biomarkers and determinants of treatment response in mesothelioma.
Identifiants
pubmed: 36773602
pii: S2666-3791(23)00030-7
doi: 10.1016/j.xcrm.2023.100938
pmc: PMC9975319
pii:
doi:
Types de publication
Journal Article
Research Support, N.I.H., Intramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
100938Subventions
Organisme : Intramural NIH HHS
ID : ZIA BC010816
Pays : United States
Informations de copyright
Published by Elsevier Inc.
Déclaration de conflit d'intérêts
Declaration of interests E.R. is a co-founder of Medaware, Metabomed, and Pangea Biomed (divested from the latter). He serves as a non-paid scientific consultant to Pangea Biomed under a collaboration agreement between Pangea Biomed and the NCI. R.H. has received funding for conduct of clinical trials via a cooperative research and development agreement between NCI and Bayer AG and TCR2 Therapeutics. J.S.L. is a scientific consultant of Pangea Therapeutics.
Références
Med Sci Monit. 2018 Nov 26;24:8553-8564
pubmed: 30476929
Cancer Res. 2006 Mar 15;66(6):2970-9
pubmed: 16540645
J Thorac Oncol. 2008 Jul;3(7):764-71
pubmed: 18594323
Clin Cancer Res. 2004 Feb 1;10(3):849-59
pubmed: 14871960
Bioinformatics. 2010 Jan 1;26(1):139-40
pubmed: 19910308
Cancer Res. 2000 Aug 1;60(15):4000-4
pubmed: 10945597
Cancer Med. 2016 May;5(5):950-9
pubmed: 26860323
J Clin Oncol. 2000 Dec 1;18(23):3912-7
pubmed: 11099320
JAMA Oncol. 2019 Nov 01;5(11):1614-1618
pubmed: 31436822
Nucleic Acids Res. 2019 Jan 8;47(D1):D559-D563
pubmed: 30357367
Lancet. 2021 Jan 30;397(10272):375-386
pubmed: 33485464
Mol Syst Biol. 2019 Mar 11;15(3):e8323
pubmed: 30858180
Nat Med. 2019 Oct;25(10):1519-1525
pubmed: 31591589
J Cell Biol. 2003 Sep 15;162(6):1017-29
pubmed: 12963707
Cell. 2021 Apr 29;184(9):2487-2502.e13
pubmed: 33857424
Nat Rev Genet. 2017 Oct;18(10):613-623
pubmed: 28649135
Lancet Oncol. 2017 May;18(5):623-630
pubmed: 28291584
Cancer Res. 2017 Nov 1;77(21):e31-e34
pubmed: 29092934
J Thorac Oncol. 2013 Jun;8(6):783-7
pubmed: 23571475
Nat Biotechnol. 2016 Feb;34(2):184-191
pubmed: 26780180
Carcinogenesis. 2008 Feb;29(2):307-15
pubmed: 18048386
Blood. 2017 Jul 27;130(4):453-459
pubmed: 28600341
Lung Cancer. 2014 Jun;84(3):265-70
pubmed: 24321581
Clin Exp Metastasis. 2015 Apr;32(4):301-11
pubmed: 25759210
Br J Ind Med. 1992 Aug;49(8):566-75
pubmed: 1325180
Transl Lung Cancer Res. 2020 Feb;9(Suppl 1):S120-S132
pubmed: 32206577
Nat Methods. 2015 May;12(5):453-7
pubmed: 25822800
Exp Cell Res. 2018 Jun 15;367(2):216-221
pubmed: 29608915
J Natl Cancer Inst. 2003 Apr 16;95(8):598-605
pubmed: 12697852
J Thorac Oncol. 2012 Sep;7(9):1449-56
pubmed: 22895142
J Clin Oncol. 2003 Jul 15;21(14):2636-44
pubmed: 12860938
Lancet Oncol. 2013 Oct;14(11):1104-1111
pubmed: 24035405
Cancer Causes Control. 2017 Sep;28(9):971-979
pubmed: 28755241
Cancer Discov. 2020 Aug;10(8):1103-1120
pubmed: 32690542
Genome Med. 2019 Mar 26;11(1):18
pubmed: 30914057
Nat Biotechnol. 2020 Jun;38(6):675-678
pubmed: 32444850
Nat Genet. 2016 Apr;48(4):407-16
pubmed: 26928227
Lancet Respir Med. 2015 Apr;3(4):301-9
pubmed: 25819643
Oncotarget. 2017 May 2;8(18):29935-29950
pubmed: 28404898
Genet Med. 2015 May;17(5):405-24
pubmed: 25741868
Proc Natl Acad Sci U S A. 2019 Apr 30;116(18):9008-9013
pubmed: 30975761
Cell Rep Med. 2020 Apr 21;1(1):
pubmed: 32483558
Lung Cancer. 2014 Oct;86(1):35-40
pubmed: 25174276
JAMA Netw Open. 2020 Oct 1;3(10):e2025109
pubmed: 33119110
Nucleic Acids Res. 2019 Jan 8;47(D1):D607-D613
pubmed: 30476243
J Thorac Oncol. 2011 Nov;6(11):1950-4
pubmed: 22005473
Front Oncol. 2021 Jun 23;11:660039
pubmed: 34249695
iScience. 2020 Jun 26;23(6):101192
pubmed: 32521508
Nucleic Acids Res. 2018 Jan 4;46(D1):D380-D386
pubmed: 29087512
Cell. 2021 Oct 14;184(21):5482-5496.e28
pubmed: 34597583
Cancer Discov. 2018 Dec;8(12):1548-1565
pubmed: 30322867
Mutat Res. 2015 Jan;771:6-12
pubmed: 25771974
Dig Dis Sci. 2015 Dec;60(12):3681-90
pubmed: 26280083
Oncogene. 2013 Jan 24;32(4):462-70
pubmed: 22370640
CA Cancer J Clin. 2019 Sep;69(5):402-429
pubmed: 31283845
J Clin Oncol. 2003 Apr 15;21(8):1556-61
pubmed: 12697881
Nat Genet. 2017 Dec;49(12):1779-1784
pubmed: 29083409
Cancer Lett. 2016 Aug 10;378(2):120-30
pubmed: 27181379
Nat Commun. 2021 Jun 23;12(1):3880
pubmed: 34162872
Oncotarget. 2017 Jan 10;8(2):2224-2232
pubmed: 27903976
Immunity. 2014 Jul 17;41(1):49-61
pubmed: 25035953
Trends Cell Biol. 2013 Mar;23(3):135-40
pubmed: 23182110
J Toxicol Environ Health B Crit Rev. 2016;19(5-6):231-249
pubmed: 27705543
Clin Cancer Res. 2005 Mar 15;11(6):2300-4
pubmed: 15788680
Nucleic Acids Res. 2018 Jan 4;46(D1):D1074-D1082
pubmed: 29126136