Profile of Basal Cell Carcinoma Mutations and Copy Number Alterations - Focus on Gene-Associated Noncoding Variants.
DPH3
TERT
basal cell carcinoma (BCC)
cancer drivers
cancer somatic mutations
copy number alterations
immune checkpoint
noncoding mutations
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:
03
08
2021
accepted:
08
11
2021
entrez:
13
12
2021
pubmed:
14
12
2021
medline:
14
12
2021
Statut:
epublish
Résumé
Basal cell carcinoma (BCC) of the skin is the most common cancer in humans, characterized by the highest mutation rate among cancers, and is mostly driven by mutations in genes involved in the hedgehog pathway. To date, almost all BCC genetic studies have focused exclusively on protein-coding sequences; therefore, the impact of noncoding variants on the BCC genome is unrecognized. In this study, with the use of whole-exome sequencing of 27 tumor/normal pairs of BCC samples, we performed an analysis of somatic mutations in both protein-coding sequences and gene-associated noncoding regions, including 5'UTRs, 3'UTRs, and exon-adjacent intron sequences. Separately, in each region, we performed hotspot identification, mutation enrichment analysis, and cancer driver identification with OncodriveFML. Additionally, we performed a whole-genome copy number alteration analysis with GISTIC2. Of the >80,000 identified mutations, ~50% were localized in noncoding regions. The results of the analysis generally corroborated the previous findings regarding genes mutated in coding sequences, including
Identifiants
pubmed: 34900699
doi: 10.3389/fonc.2021.752579
pmc: PMC8656283
doi:
Types de publication
Journal Article
Langues
eng
Pagination
752579Informations de copyright
Copyright © 2021 Nawrocka, Galka-Marciniak, Urbanek-Trzeciak, M-Thirusenthilarasan, Szostak, Philips, Susok, Sand and Kozlowski.
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
Biol Res. 2020 Mar 14;53(1):11
pubmed: 32169117
Oncotarget. 2014 Oct 30;5(20):9864-76
pubmed: 25296969
Diagnostics (Basel). 2019 Jun 12;9(2):
pubmed: 31212865
Biochim Biophys Acta. 2014 Dec;1846(2):297-311
pubmed: 25072963
FASEB J. 2020 Nov;34(11):14602-14614
pubmed: 32941657
Proc Natl Acad Sci U S A. 2020 Jul 7;117(27):15591-15598
pubmed: 32576697
Science. 2013 Feb 22;339(6122):957-9
pubmed: 23348506
Nature. 2013 Jul 11;499(7457):214-218
pubmed: 23770567
Am J Med Genet A. 2010 Feb;152A(2):327-32
pubmed: 20082463
PLoS One. 2012;7(2):e32193
pubmed: 22363815
Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9435-40
pubmed: 19478061
Mod Pathol. 2014 Apr;27(4):516-23
pubmed: 24030752
Nat Genet. 2009 Feb;41(2):211-5
pubmed: 19169253
Neurochem Int. 2017 Oct;109:141-161
pubmed: 28461171
JAMA Oncol. 2016 Jul 1;2(7):962-3
pubmed: 27054919
EMBO Mol Med. 2016 May 02;8(5):442-57
pubmed: 26992833
J Biol Chem. 2005 Nov 4;280(44):37118-29
pubmed: 16118219
Carcinogenesis. 2007 Sep;28(9):2028-35
pubmed: 17389615
Nat Genet. 2019 Mar;51(3):517-528
pubmed: 30692681
EBioMedicine. 2020 Nov;61:103051
pubmed: 33038763
BMC Bioinformatics. 2018 Jun 14;19(1):224
pubmed: 29898651
Genome Biol. 2011;12(4):R41
pubmed: 21527027
J Invest Dermatol. 2006 Mar;126(3):614-20
pubmed: 16397523
J Dermatol Sci. 2017 May;86(2):142-148
pubmed: 28187958
Sci Rep. 2017 Sep 7;7(1):10909
pubmed: 28883623
Br J Dermatol. 2006 Aug;155(2):401-7
pubmed: 16882181
Science. 2013 Feb 22;339(6122):959-61
pubmed: 23348503
J Am Acad Dermatol. 2012 May;66(5):e167-78
pubmed: 20800318
Nucleic Acids Res. 2020 Jan 8;48(D1):D148-D154
pubmed: 31647101
Cancer Res. 2016 Jun 1;76(11):3145-55
pubmed: 27013197
Cells. 2019 May 22;8(5):
pubmed: 31121896
Clin Cancer Res. 2011 Oct 1;17(19):6356-66
pubmed: 21849418
Nat Rev Cancer. 2008 Oct;8(10):743-54
pubmed: 18813320
J Am Acad Dermatol. 1985 Jun;12(6):997-1000
pubmed: 3874217
J Cell Mol Med. 2018 Nov;22(11):5188-5195
pubmed: 30145807
Int J Dermatol. 1985 Dec;24(10):660-3
pubmed: 3910595
NPJ Genom Med. 2016;1:
pubmed: 27942391
Nat Med. 2008 Feb;14(2):144-53
pubmed: 18223655
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W429-34
pubmed: 16845041
Pigment Cell Melanoma Res. 2020 May;33(3):466-479
pubmed: 31663663
Carcinogenesis. 2010 Sep;31(9):1567-75
pubmed: 20631058
Sci Rep. 2021 Jun 24;11(1):13206
pubmed: 34168209
BMC Bioinformatics. 2014 Jun 12;15:182
pubmed: 24925680
Cell Cycle. 2009 Sep 1;8(17):2819-27
pubmed: 19667759
Sci Rep. 2020 May 14;10(1):8005
pubmed: 32409749
Oncol Lett. 2019 May;17(5):4197-4206
pubmed: 30944615
Oncol Rep. 2017 May;37(5):2920-2928
pubmed: 28393234
Mol Cancer Res. 2011 Nov;9(11):1509-19
pubmed: 21896638
Eur J Dermatol. 1998 Jun;8(4):256-60
pubmed: 9649682
Oncogene. 2020 Jan;39(4):754-766
pubmed: 31570788
Cancer Invest. 2010 Jul;28(6):649-53
pubmed: 20210522
Histopathology. 1998 May;32(5):393-8
pubmed: 9639112
Br J Dermatol. 2012 Oct;167(4):847-55
pubmed: 22540308
Nat Cell Biol. 2018 Jul;20(7):775-781
pubmed: 29941933
Nature. 2014 Jan 23;505(7484):495-501
pubmed: 24390350
Cell. 1997 Oct 17;91(2):231-41
pubmed: 9346240
Genome Biol. 2020 Jun 9;21(1):127
pubmed: 32513296
J Cutan Med Surg. 2005 Jan;9(1):10-5
pubmed: 16208438
J Am Acad Dermatol. 2019 Feb;80(2):564-566
pubmed: 30145186
Oncogene. 2005 Feb 3;24(6):1111-6
pubmed: 15690057
Sci Rep. 2019 Jan 30;9(1):987
pubmed: 30700785
Bioinformatics. 2020 Aug 1;36(15):4348-4349
pubmed: 32502231
J Biol Chem. 2012 Aug 31;287(36):30468-76
pubmed: 22787160
Br J Dermatol. 2017 Aug;177(2):359-372
pubmed: 28220485
Oncogene. 2016 Apr 21;35(16):2040-51
pubmed: 26189798
J Biol Chem. 2003 Oct 10;278(41):40330-6
pubmed: 12835323
Cell Oncol (Dordr). 2020 Jun;43(3):335-352
pubmed: 32219702
Cell. 1995 Jan 27;80(2):285-91
pubmed: 7834748
Nucleic Acids Res. 2019 Jan 8;47(D1):D506-D515
pubmed: 30395287
PLoS One. 2013 Nov 18;8(11):e80354
pubmed: 24260374
Nat Commun. 2019 Jul 2;10(1):2924
pubmed: 31266950
Blood. 2013 Oct 31;122(18):3165-8
pubmed: 24052547
Nat Commun. 2016 Jan 29;7:10582
pubmed: 26822383
Oncogenesis. 2019 Sep 24;8(10):52
pubmed: 31551419
BMC Med Genet. 2019 Dec 9;20(Suppl 2):190
pubmed: 31815613
Oncotarget. 2014 May 30;5(10):2912-7
pubmed: 24913145
Lancet Neurol. 2015 Mar;14(3):274-82
pubmed: 25662902
Nucleic Acids Res. 2003 Jul 1;31(13):3406-15
pubmed: 12824337
Nature. 2003 Aug 21;424(6951):952-6
pubmed: 12931191
J Am Acad Dermatol. 1990 Dec;23(6 Pt 1):1118-26
pubmed: 2273112
Nature. 2020 Feb;578(7793):94-101
pubmed: 32025018
Mol Cell. 2009 Feb 13;33(3):377-88
pubmed: 19217411
Cell Death Differ. 2014 Dec;21(12):1936-49
pubmed: 25215949
J Natl Cancer Inst. 1996 Mar 20;88(6):349-54
pubmed: 8609643
Nat Genet. 2016 Jan;48(1):4-6
pubmed: 26711108
Nat Rev Mol Cell Biol. 2018 Mar;19(3):158-174
pubmed: 29165424
Clin Transl Oncol. 2015 Jul;17(7):497-503
pubmed: 25643667
Genome Res. 2019 Feb;29(2):159-170
pubmed: 30587507
Histol Histopathol. 1993 Apr;8(2):219-26
pubmed: 7683937
Eur J Dermatol. 2014 Jan-Feb;24(1):41-5
pubmed: 24413452
Cell. 2014 Mar 13;156(6):1324-1335
pubmed: 24630730
PLoS One. 2015 Aug 12;10(8):e0135750
pubmed: 26267899
J Biol Chem. 2003 Nov 21;278(47):46832-9
pubmed: 12954646
BMC Cancer. 2019 May 2;19(1):411
pubmed: 31046734
Fly (Austin). 2012 Apr-Jun;6(2):80-92
pubmed: 22728672
Pigment Cell Melanoma Res. 2014 May;27(3):442-53
pubmed: 24472175
J Cutan Pathol. 1990 Apr;17(2):65-71
pubmed: 2187024
Eur J Cancer. 2019 Sep;118:10-34
pubmed: 31288208
Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17761-6
pubmed: 22006338
Cell. 2005 Jan 14;120(1):15-20
pubmed: 15652477
Bioinformatics. 1998 Jun;14(5):384-90
pubmed: 9682051
Nucleic Acids Res. 2021 Jan 25;49(2):601-620
pubmed: 33406242
PLoS One. 2009;4(4):e5227
pubmed: 19384417
J Biol Chem. 2001 Jun 1;276(22):19414-9
pubmed: 11259441
Cell Physiol Biochem. 2019;53(5):760-773
pubmed: 31647206
Nature. 2002 Jun 20;417(6891):861-6
pubmed: 12075355
Sci Immunol. 2018 Mar 2;3(21):
pubmed: 29500225
Mitochondrion. 2015 Jan;20:43-51
pubmed: 25315652
BMC Bioinformatics. 2013;14 Suppl 2:S4
pubmed: 23369107
Nat Rev Cancer. 2009 Nov;9(11):810-20
pubmed: 19851316
Biomedicines. 2020 Nov 25;8(12):
pubmed: 33255617
Hum Mutat. 2014 Nov;35(11):1301-10
pubmed: 25113440
J Skin Cancer. 2011;2011:328615
pubmed: 21152128
Int J Mol Med. 2015 Apr;35(4):1081-7
pubmed: 25653146
Nat Commun. 2019 Jun 12;10(1):2569
pubmed: 31189880
Cell Death Differ. 2015 Jun;22(6):1035-46
pubmed: 25476776
J Invest Dermatol. 2020 Feb;140(2):390-394.e1
pubmed: 31425705
ScientificWorldJournal. 2010 Oct 12;10:2003-18
pubmed: 20953551
Actas Dermosifiliogr (Engl Ed). 2018 Apr;109(3):207-217
pubmed: 29373110
Clin Cancer Res. 2021 Jul 15;27(14):3845-3853
pubmed: 33727259
Nature. 2020 Feb;578(7793):102-111
pubmed: 32025015
J Am Acad Dermatol. 1991 May;24(5 Pt 1):715-9
pubmed: 1869642
Comp Med. 2017 Oct 1;67(5):407-415
pubmed: 28935002
PLoS One. 2014 Apr 09;9(4):e92712
pubmed: 24718257
Nature. 2013 Aug 22;500(7463):415-21
pubmed: 23945592
J Invest Dermatol. 2015 Dec;135(12):3197-3200
pubmed: 26348826
Nat Genet. 2014 Oct;46(10):1060-2
pubmed: 25194279
Pigment Cell Melanoma Res. 2011 Jun;24(3):525-37
pubmed: 21435193
Dermatol Surg. 1996 Mar;22(3):301-4
pubmed: 8599743
Proc Int Conf Intell Syst Mol Biol. 1997;5:234-6
pubmed: 9322042
J Neuropathol Exp Neurol. 2005 Aug;64(8):695-705
pubmed: 16106218
J Biol Chem. 2004 Oct 1;279(40):42240-9
pubmed: 15231831
Am J Dermatopathol. 2019 Apr;41(4):264-272
pubmed: 30211730
Int J Mol Sci. 2017 Nov 22;18(11):
pubmed: 29165358
Nat Cell Biol. 2009 Dec;11(12):1427-32
pubmed: 19935652
Nature. 2011 Mar 24;471(7339):518-22
pubmed: 21430780
N Engl J Med. 1991 Sep 19;325(12):884-7
pubmed: 1875975
Blood Cells Mol Dis. 2004 Jan-Feb;32(1):143-54
pubmed: 14757430
Genome Res. 2018 Nov;28(11):1611-1620
pubmed: 30341163
BMC Bioinformatics. 2011 Dec 30;12:495
pubmed: 22208852
Tumour Biol. 2017 Mar;39(3):1010428317691427
pubmed: 28345455
Nat Genet. 2016 Apr;48(4):398-406
pubmed: 26950094
J Invest Dermatol. 2014 Jan;134(1):213-220
pubmed: 23774526
N Engl J Med. 2005 Nov 24;353(21):2262-9
pubmed: 16306523
Cell Death Dis. 2020 Oct 15;11(10):862
pubmed: 33060568
Nature. 2017 May 11;545(7653):175-180
pubmed: 28467829
Cell Rep. 2018 Jun 19;23(12):3621-3634
pubmed: 29925003
Hum Genet. 2007 May;121(3-4):389-400
pubmed: 17287951
J Cell Biol. 2009 Mar 9;184(5):707-19
pubmed: 19255249
Genome Biol. 2016 Jun 16;17(1):128
pubmed: 27311963
Hum Pathol. 1996 Apr;27(4):355-9
pubmed: 8617478
Mod Pathol. 2006 Feb;19 Suppl 2:S127-47
pubmed: 16446711
Genes Chromosomes Cancer. 2007 Jul;46(7):661-9
pubmed: 17420988