Locus-Specific Bisulfate NGS Sequencing of GSTP1, RNF219, and KIAA1539 Genes in the Total Pool of Cell-Free and Cell-Surface-Bound DNA in Prostate Cancer: A Novel Approach for Prostate Cancer Diagnostics.
cell-free DNA
cell-surface-bound DNA
locus-specific NGS sequencing
methylation
prostate cancer
Journal
Cancers
ISSN: 2072-6694
Titre abrégé: Cancers (Basel)
Pays: Switzerland
ID NLM: 101526829
Informations de publication
Date de publication:
09 Jan 2023
09 Jan 2023
Historique:
received:
18
11
2022
revised:
27
12
2022
accepted:
27
12
2022
entrez:
21
1
2023
pubmed:
22
1
2023
medline:
22
1
2023
Statut:
epublish
Résumé
The locus-specific methylation of three genes (GSTP1, RNF219, and KIAA1539, also known as FAM214B) in the total pool of blood cell-free DNA, including cell-free DNA from plasma and cell-surface-bound DNA, of patients with prostate cancer and healthy donors was studied on the MiSeq platform. Our study found a higher methylation index of loci for total cell-free DNA compared with cell-free DNA. For total cell-free DNA, the methylation of GSTP1 in each of the 11 positions provided a complete separation of cancer patients from healthy donors, whereas for cell-free DNA, there were no positions in the three genes allowing for such separation. Among the prostate cancer patients, the minimum proportion of GSTP1 genes methylated in any of the 17 positions was 12.1% of the total circulated DNA fragments, and the minimum proportion of GSTP1 genes methylated in any of the 11 diagnostically specific positions was 8.4%. Total cell-free DNA was shown to be more convenient and informative as a source of methylated DNA molecules circulating in the blood than cell-free DNA.
Identifiants
pubmed: 36672380
pii: cancers15020431
doi: 10.3390/cancers15020431
pmc: PMC9856824
pii:
doi:
Types de publication
Journal Article
Langues
eng
Subventions
Organisme : the Russian state budget project via the ICBFM SB RAS
ID : 121030200173-6
Organisme : program for fundamental scientific research of the Siberian Branch of the Russian Academy of Sciences
ID : FWNF-2022-0009
Références
J Biomark. 2014;2014:321680
pubmed: 26317031
Genome Res. 2008 Jan;18(1):19-29
pubmed: 18032725
ISME J. 2012 Aug;6(8):1621-4
pubmed: 22402401
Nat Rev Genet. 2019 Feb;20(2):71-88
pubmed: 30410101
Ann N Y Acad Sci. 2001 Sep;945:36-50
pubmed: 11708493
Dis Markers. 2016;2016:4358292
pubmed: 27594734
Biomed Khim. 2015 Jul-Aug;61(4):409-26
pubmed: 26350732
Tumour Biol. 2013 Jun;34(3):1337-47
pubmed: 23504524
J Natl Compr Canc Netw. 2019 May 1;17(5):479-505
pubmed: 31085757
Int J Mol Sci. 2022 Aug 10;23(16):
pubmed: 36012175
Int J Mol Sci. 2021 Jul 08;22(14):
pubmed: 34298969
Epigenomics. 2010 Aug;2(4):561-73
pubmed: 22121974
J Urol. 2008 Apr;179(4):1587-92
pubmed: 18295257
Mol Biol (Mosk). 2017 Jul-Aug;51(4):622-628
pubmed: 28900080
Clin Chem Lab Med. 2018 Apr 25;56(5):702-717
pubmed: 29305565
Cancers (Basel). 2021 Aug 21;13(16):
pubmed: 34439363
Expert Rev Mol Diagn. 2021 Jan;21(1):63-75
pubmed: 33270495
Int J Mol Sci. 2013 Jun 17;14(6):12620-49
pubmed: 23774836
Cancer Treat Rev. 2002 Oct;28(5):255-71
pubmed: 12435372
Eur Urol. 2008 Nov;54(5):1081-8
pubmed: 18602209
PLoS One. 2017 May 24;12(5):e0177406
pubmed: 28542303
J Clin Immunol. 1995 Nov;15(6):284-92
pubmed: 8576314
Nat Med. 2017 Mar;23(3):386-395
pubmed: 28134926
Biomark Cancer. 2018 Jan 08;10:1179299X17751920
pubmed: 29343995
CA Cancer J Clin. 2021 May;71(3):209-249
pubmed: 33538338
Cancer J. 2017 Sep/Oct;23(5):257-261
pubmed: 28926425
Hum Mol Genet. 2012 Aug 15;21(16):3619-31
pubmed: 22619380
Br J Cancer. 2006 May 22;94(10):1492-5
pubmed: 16641902
Pediatr Res. 2017 Jan;81(1-1):68-74
pubmed: 27653086
Lung Cancer. 2016 Sep;99:127-30
pubmed: 27565927
Int J Mol Sci. 2022 Jun 29;23(13):
pubmed: 35806228
Biochemistry (Mosc). 2013 Nov;78(11):1201-15
pubmed: 24460935
Ann N Y Acad Sci. 2008 Aug;1137:222-5
pubmed: 18837951
Prostate. 2010 May 15;70(7):765-76
pubmed: 20054818
J Natl Cancer Inst. 2008 Aug 20;100(16):1144-54
pubmed: 18695132
Cancer Res. 1999 Jan 1;59(1):67-70
pubmed: 9892187
Epigenetics. 2016 Dec;11(12):881-888
pubmed: 27748645
Nucleic Acids Res. 2015 Dec 15;43(22):e154
pubmed: 26304549
Oncotarget. 2017 Jan 17;8(3):5629-5637
pubmed: 27895318
IUBMB Life. 2019 Sep;71(9):1201-1210
pubmed: 31091350
Acta Naturae. 2015 Apr-Jun;7(2):115-8
pubmed: 26085953
G3 (Bethesda). 2015 Jul 02;5(8):1543-50
pubmed: 26139844
PLoS One. 2017 Oct 16;12(10):e0186321
pubmed: 29036193
Cold Spring Harb Perspect Med. 2019 Apr 1;9(4):
pubmed: 29959132
Mol Biol (Mosk). 2017 Mar-Apr;51(2):195-214
pubmed: 28537228
Biochimie. 2012 Nov;94(11):2314-37
pubmed: 22847185
Ann Intern Med. 2012 Jul 17;157(2):120-34
pubmed: 22801674
Genome Res. 2011 Jul;21(7):1028-41
pubmed: 21724842
Mutat Res Rev Mutat Res. 2019 Jan - Mar;779:45-57
pubmed: 31097151
Expert Rev Mol Diagn. 2010 May;10(4):481-8
pubmed: 20465502
Anal Biochem. 2011 Jan 15;408(2):354-6
pubmed: 20828533
Ann N Y Acad Sci. 2008 Aug;1137:226-31
pubmed: 18837952
Iran Red Crescent Med J. 2011 Feb;13(2):80-98
pubmed: 22737441
Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):18761-8
pubmed: 24191000
Cancer Res. 2014 Apr 15;74(8):2160-70
pubmed: 24737128
Expert Opin Pharmacother. 2000 Dec;1(7):1399-411
pubmed: 11249473
Nat Methods. 2016 Oct;13(10):833-6
pubmed: 27525975
Mol Cancer Res. 2016 Oct;14(10):898-908
pubmed: 27422709
Nat Genet. 2014 Mar;46(3):214-5
pubmed: 24569233
Cancers (Basel). 2021 Dec 12;13(24):
pubmed: 34944854
Eur J Cancer Prev. 2011 Nov;20(6):453-5
pubmed: 21795979