DNA methylome combined with chromosome cluster-oriented analysis provides an early signature for cutaneous melanoma aggressiveness.
DNA methylation
cancer biology
chromosome clusters
chromosomes
epigenomics
gene expression
human
melanoma
oriented approach
patient outcome
Journal
eLife
ISSN: 2050-084X
Titre abrégé: Elife
Pays: England
ID NLM: 101579614
Informations de publication
Date de publication:
20 09 2022
20 09 2022
Historique:
received:
11
03
2022
accepted:
18
09
2022
pubmed:
21
9
2022
medline:
5
10
2022
entrez:
20
9
2022
Statut:
epublish
Résumé
Aberrant DNA methylation is a well-known feature of tumours and has been associated with metastatic melanoma. However, since melanoma cells are highly heterogeneous, it has been challenging to use affected genes to predict tumour aggressiveness, metastatic evolution, and patients' outcomes. We hypothesized that common aggressive hypermethylation signatures should emerge early in tumorigenesis and should be shared in aggressive cells, independent of the physiological context under which this trait arises. We compared paired melanoma cell lines with the following properties: (i) each pair comprises one aggressive counterpart and its parental cell line and (ii) the aggressive cell lines were each obtained from different host and their environment (human, rat, and mouse), though starting from the same parent cell line. Next, we developed a multi-step genomic pipeline that combines the DNA methylome profile with a chromosome cluster-oriented analysis. A total of 229 differentially hypermethylated genes was commonly found in the aggressive cell lines. Genome localization analysis revealed hypermethylation peaks and clusters, identifying eight hypermethylated gene promoters for validation in tissues from melanoma patients. Five Cytosine-phosphate-Guanine (CpGs) identified in primary melanoma tissues were transformed into a DNA methylation score that can predict survival (log-rank test, p=0.0008). This strategy is potentially universally applicable to other diseases involving DNA methylation alterations.
Identifiants
pubmed: 36125262
doi: 10.7554/eLife.78587
pii: 78587
pmc: PMC9525058
doi:
pii:
Substances chimiques
Phosphates
0
Guanine
5Z93L87A1R
Cytosine
8J337D1HZY
Banques de données
GEO
['GSE155856']
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© 2022, Carrier et al.
Déclaration de conflit d'intérêts
AC, CD, LP, LL, MB, JT, RH, CJ, LL, AD, GF, AD, FB, DH, JT, CE, JR, PA No competing interests declared
Références
Biochem J. 1996 Dec 1;320 ( Pt 2):473-8
pubmed: 8973555
Leukemia. 2011 Dec;25(12):1910-3
pubmed: 21760590
Clin Epigenetics. 2019 Jan 16;11(1):9
pubmed: 30651148
Nat Rev Genet. 2006 Jan;7(1):21-33
pubmed: 16369569
Pigment Cell Melanoma Res. 2013 Jul;26(4):542-54
pubmed: 23590314
J Pathol. 2011 Feb;223(3):400-9
pubmed: 21171085
Cytogenet Genome Res. 2006;113(1-4):81-9
pubmed: 16575166
Tumour Biol. 2014 Jul;35(7):6783-90
pubmed: 24729088
Sci Rep. 2019 Oct 31;9(1):15790
pubmed: 31673075
Int J Oncol. 2009 Aug;35(2):393-400
pubmed: 19578755
J Thorac Oncol. 2011 Oct;6(10):1632-8
pubmed: 21694641
Br J Dermatol. 2018 Aug;179(2):394-404
pubmed: 29278418
J Transl Med. 2012 Sep 05;10:185
pubmed: 22950745
Sci Rep. 2013 Oct 16;3:2962
pubmed: 24129253
Anticancer Res. 2007 Sep-Oct;27(5A):3441-9
pubmed: 17970093
Cell. 2011 Mar 4;144(5):646-74
pubmed: 21376230
Breast Cancer Res. 2005;7(6):R965-74
pubmed: 16280046
Nat Cell Biol. 2010 Mar;12(3):235-46
pubmed: 20173741
Clin Cancer Res. 2007 May 15;13(10):2905-15
pubmed: 17504990
Nat Rev Clin Oncol. 2017 Aug;14(8):463-482
pubmed: 28374786
JAMA. 2015 Sep 15;314(11):1129-30
pubmed: 26372577
Oncogene. 2005 Nov 24;24(53):7821-9
pubmed: 16027728
Int J Oncol. 2007 Mar;30(3):689-94
pubmed: 17273770
Elife. 2022 Sep 20;11:
pubmed: 36125262
Trends Immunol. 2019 Apr;40(4):328-344
pubmed: 30853334
Nature. 2000 Aug 3;406(6795):532-5
pubmed: 10952316
PLoS One. 2013;8(1):e54958
pubmed: 23383013
Gene. 2013 Dec 10;532(1):1-12
pubmed: 23246696
Cancers (Basel). 2020 Apr 27;12(5):
pubmed: 32349217
Elife. 2019 Jun 06;8:
pubmed: 31169496
Annu Rev Genet. 2011;45:379-403
pubmed: 21942369
Clin Cancer Res. 2019 Sep 1;25(17):5191-5201
pubmed: 30923036
Nat Rev Mol Cell Biol. 2019 Oct;20(10):573-589
pubmed: 31270442
Clin Epigenetics. 2017 Apr 4;9:34
pubmed: 28396701
Eur J Cancer. 2022 Jun;168:1-11
pubmed: 35421838
Clin Cancer Res. 2009 Mar 1;15(5):1801-7
pubmed: 19223509
Epigenomics. 2010 Aug;2(4):575-85
pubmed: 22121975
PLoS One. 2010 Aug 23;5(8):e12334
pubmed: 20808801
Int J Cancer. 1991 Nov 11;49(5):750-7
pubmed: 1937961
World J Surg Oncol. 2019 Jul 25;17(1):129
pubmed: 31345228
Oncol Rep. 2010 Jun;23(6):1701-8
pubmed: 20428828
CA Cancer J Clin. 2017 Nov;67(6):472-492
pubmed: 29028110
Cancer Res. 2005 Feb 1;65(3):828-34
pubmed: 15705880
Nat Protoc. 2007;2(9):2265-75
pubmed: 17853883
Semin Cancer Biol. 2018 Aug;51:80-88
pubmed: 29074395
Epigenomics. 2015;7(8):1303-11
pubmed: 26638944
Cancer Lett. 1995 Jan 27;88(2):221-5
pubmed: 7874696
Oncotarget. 2017 Jan 24;8(4):6085-6101
pubmed: 28030832
Nat Genet. 2006 May;38(5):540-9
pubmed: 16642018
Hum Mol Genet. 2014 Jan 1;23(1):226-38
pubmed: 24014427
Lab Invest. 2012 Mar;92(3):458-65
pubmed: 22157715
Epigenomics. 2012 Jun;4(3):325-41
pubmed: 22690668