Genomic and Transcriptomic Analyses of Malignant Pleural Mesothelioma (MPM) Samples Reveal Crucial Insights for Preclinical Testing.
genomic analysis
malignant pleural mesothelioma
patient-derived cell lines
preclinical models
transcriptomic analysis
Journal
Cancers
ISSN: 2072-6694
Titre abrégé: Cancers (Basel)
Pays: Switzerland
ID NLM: 101526829
Informations de publication
Date de publication:
18 May 2023
18 May 2023
Historique:
received:
19
04
2023
revised:
15
05
2023
accepted:
15
05
2023
medline:
22
6
2023
pubmed:
22
6
2023
entrez:
22
6
2023
Statut:
epublish
Résumé
Cell lines are extensively used to study cancer biology. However, the use of highly passaged commercial cell lines has to be questioned, as they do not closely resemble the originating tumor. To understand the reliability of preclinical models for Malignant pleural mesothelioma (MPM) studies, we have performed whole transcriptome and whole exome analyses of fresh frozen MPM tumors and compared them to cell lines generated from these tumors, as well as commercial cell lines and a preclinical MPM mouse model. Patient-derived cell lines were generated from digested fresh tumors and whole exome sequencing was performed on DNA isolated from formalin-fixed, paraffin-embedded (FFPE) tumor samples, corresponding patient-derived cell lines, and normal tissue. RNA sequencing libraries were prepared from 10 fresh frozen tumor samples, the 10 corresponding patient-derived cell lines, and 7 commercial cell lines. Our results identified alterations in tumor suppressor genes such as
Identifiants
pubmed: 37345150
pii: cancers15102813
doi: 10.3390/cancers15102813
pmc: PMC10216513
pii:
doi:
Types de publication
Journal Article
Langues
eng
Subventions
Organisme : Swiss Cancer League
ID : KLS-4538-08-2018
Organisme : Stiftung für wissenschaftliche Forschung an der UZH/Erbschaft Bühler
ID : UZH STEB-22, -001
Organisme : Stiftung für angewandte Krebsforschung (SAKF)
ID : UFR20070801
Références
Semin Immunol. 2020 Feb;47:101391
pubmed: 31952903
J Clin Oncol. 2005 Jun 10;23(17):3923-31
pubmed: 15897550
Nucleic Acids Res. 2013 May 1;41(10):e108
pubmed: 23558742
Cell Syst. 2015 Dec 23;1(6):417-425
pubmed: 26771021
Br J Cancer. 2022 Nov;127(11):1997-2005
pubmed: 36138075
Br J Cancer. 2021 Jan;124(1):259-269
pubmed: 33299129
Oncogene. 2018 May;37(20):2645-2659
pubmed: 29507420
J Transl Med. 2016 Feb 29;14:61
pubmed: 26928703
Cancer Res. 2002 Sep 1;62(17):4963-7
pubmed: 12208747
Clin Cancer Res. 2009 Apr 15;15(8):2818-28
pubmed: 19351772
Breast Cancer Res. 2011 Jun 10;13(3):R59
pubmed: 21663619
Cancer Res. 1989 Dec 1;49(23):6449-65
pubmed: 2684393
BMC Genomics. 2016 Aug 22;17 Suppl 7:525
pubmed: 27556158
Cancers (Basel). 2021 Jun 14;13(12):
pubmed: 34198671
Lancet. 2021 Jan 30;397(10272):375-386
pubmed: 33485464
Cell. 2008 May 16;133(4):704-15
pubmed: 18485877
Am J Pathol. 2005 Jun;166(6):1827-40
pubmed: 15920167
Methods Mol Biol. 2019;1979:25-44
pubmed: 31028630
J Biol Chem. 2016 Dec 23;291(52):26750-26761
pubmed: 27756837
Front Oncol. 2022 Jun 28;12:869485
pubmed: 35837106
Oncogene. 2001 Jan 25;20(4):461-70
pubmed: 11313977
J Thorac Oncol. 2009 Feb;4(2):149-60
pubmed: 19179889
Nat Rev Cancer. 2018 Nov;18(11):696-705
pubmed: 30293088
Front Oncol. 2020 Feb 21;10:187
pubmed: 32154179
Cancer Cell. 2006 May;9(5):391-403
pubmed: 16697959
Genome Biol. 2021 Apr 12;22(1):102
pubmed: 33845875
Am J Respir Cell Mol Biol. 2001 Nov;25(5):562-8
pubmed: 11713097
F1000Res. 2020 Jan 29;9:63
pubmed: 32269765
PLoS One. 2009 Jun 12;4(6):e5884
pubmed: 19536353
Genome Res. 2010 Sep;20(9):1297-303
pubmed: 20644199
Cell Rep Med. 2023 Feb 21;4(2):100938
pubmed: 36773602
Nat Rev Cancer. 2003 Dec;3(12):952-9
pubmed: 14737125
Mod Pathol. 2023 Jan;36(1):100036
pubmed: 36788071
Nucleic Acids Res. 2019 Jan 8;47(D1):D923-D929
pubmed: 30260411
Lung Cancer. 2010 Jun;68(3):309-18
pubmed: 20079948
Bioinformatics. 2018 Sep 1;34(17):i884-i890
pubmed: 30423086
Cell Rep. 2017 Nov 14;21(7):1936-1952
pubmed: 29141224
Oncol Lett. 2016 Aug;12(2):977-982
pubmed: 27446380
Transl Lung Cancer Res. 2017 Jun;6(3):350-365
pubmed: 28713680
Cancer Res. 1980 Jan;40(1):181-5
pubmed: 7349896
Nat Rev Mol Cell Biol. 2019 Feb;20(2):69-84
pubmed: 30459476
PLoS One. 2017 May 11;12(5):e0177459
pubmed: 28494014
Bioinformatics. 2012 Feb 1;28(3):423-5
pubmed: 22155870
Nat Methods. 2012 Jun 28;9(7):676-82
pubmed: 22743772
Mol Cell Biol. 2002 Nov;22(21):7405-16
pubmed: 12370288
Thorax. 2020 Nov;75(11):1004-1008
pubmed: 32943495
Oncotarget. 2016 Apr 19;7(16):21272-86
pubmed: 26848772
Cell Death Differ. 2016 Jul;23(7):1152-64
pubmed: 26891694
PLoS Comput Biol. 2016 Apr 21;12(4):e1004873
pubmed: 27100738
Lung Cancer. 2018 May;119:64-70
pubmed: 29656754
Cell Rep Methods. 2021 Jun 21;1(2):100039
pubmed: 35475239
Gastroenterology. 2006 Sep;131(3):830-40
pubmed: 16952552
Lancet Oncol. 2019 Feb;20(2):239-253
pubmed: 30660609
Breast Cancer Res. 2015 Aug 20;17:114
pubmed: 26289960
Bioinformatics. 2010 Jan 1;26(1):139-40
pubmed: 19910308
Nat Commun. 2013;4:2126
pubmed: 23839242
J Cell Physiol. 2018 Apr;233(4):2889-2901
pubmed: 28543438
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Oncogene. 2023 Feb;42(8):572-585
pubmed: 36550359
Nat Biotechnol. 2017 Apr 11;35(4):316-319
pubmed: 28398311
In Vitro Cell Dev Biol Anim. 2015 Aug;51(7):714-21
pubmed: 25877069
Cancer Res. 1997 Aug 1;57(15):3200-7
pubmed: 9242450
Front Oncol. 2021 Nov 11;11:748444
pubmed: 34900693
Drug Des Devel Ther. 2015 Aug 10;9:4479-99
pubmed: 26309397
Cell Rep. 2018 Apr 3;23(1):1-10
pubmed: 29617651
Nat Rev Cancer. 2008 Nov;8(11):851-64
pubmed: 18846101
Oncotarget. 2018 Oct 2;9(77):34495-34505
pubmed: 30349644
Thorax. 2021 Nov;76(11):1154-1162
pubmed: 33692175
Mod Pathol. 2023 Mar;36(3):100030
pubmed: 36788094
Cell Rep. 2019 Feb 5;26(6):1627-1640.e7
pubmed: 30726743
PLoS One. 2011;6(7):e21320
pubmed: 21789168
Front Genet. 2017 May 29;8:70
pubmed: 28611824
Genome Med. 2021 Jul 14;13(1):113
pubmed: 34261524
BMC Med Genomics. 2015;8 Suppl 2:S5
pubmed: 26043652
Oncotarget. 2017 Oct 6;8(58):98280-98297
pubmed: 29228689
Cancers (Basel). 2019 Jan 27;11(2):
pubmed: 30691229
Nature. 2018 Aug;560(7718):325-330
pubmed: 30089904
J Ovarian Res. 2011 Apr 26;4(1):7
pubmed: 21521521
Nat Commun. 2020 Nov 6;11(1):5650
pubmed: 33159064
Oncotarget. 2016 Oct 18;7(42):68721-68733
pubmed: 27626682
J Natl Cancer Inst. 2013 Apr 3;105(7):452-8
pubmed: 23434901
Sci Rep. 2022 Jan 19;12(1):1007
pubmed: 35046456
Clin Cancer Res. 2017 Feb 15;23(4):1060-1067
pubmed: 27683181
Int J Mol Sci. 2021 Nov 11;22(22):
pubmed: 34830097