Locus-specific methylation of gstp1, rnf219, and kiaa1539 genes with single molecule resolution in cell-free dna from healthy donors and prostate tumor patients: Application in diagnostics

Locus-specific methylation of gstp1, rnf219, and kiaa1539 genes with single molecule resolution in cell-free dna from healthy donors and prostate tumor patients: Application in diagnostics Full article

Journal

Cancers
ISSN: 2072-6694

Output data

Year: 2021, Volume: 13, Number: 24, Article number : 6234, Pages count : 24 DOI: 10.3390/cancers13246234

Tags

Benign prostatic hyperplasia; Cell-free DNA; Locus-specific NGS sequencing; Methylation; Prostate cancer

Authors

Bryzgunova Olga ¹ , Bondar Anna ¹ , Ruzankin Pavel ^2,3 , Laktionov Petr ^4,5 , Tarasenko Anton ^2,3 , Kurilshikov Alexander ¹ , Epifanov Rostislav ⁴ , Zaripov Marat ¹ , Kabilov Marsel ¹ , Laktionov Pavel ¹

Affiliations

1	Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
2	Sobolev Institute of Mathematics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
3	Department of Mathematics and Mechanics, Novosibirsk State University
4	Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
5	Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia

The locus-specific methylation of three genes (GSTP1, RNF219, and KIAA1539 (also known as FAM214B)) in the blood plasma cell-free DNA (cfDNA) of 20 patients with prostate cancer (PCa), 18 healthy donors (HDs), and 17 patients with benign prostatic hyperplasia (BPH) was studied via the MiSeq platform. The methylation status of two CpGs within the same loci were used as the diagnostic feature for discriminating the patient groups. Many variables had good diagnostic characteristics, e.g., each of the variables GSTP1.C3.C9, GSTP1.C9, and GSTP1.C9.T17 demonstrated an 80% sensitivity at a 100% specificity for PCa patients vs. the others comparison. The analysis of RNF219 gene loci methylation allowed discriminating BPH patients with absolute sensitivity and specificity. The data on the methylation of the genes GSTP1 and RNF219 allowed discriminating PCa patients, as well as HDs, with absolute sensitivity and specificity. Thus, the data on the locus-specific methylation of cfDNA (with single-molecule resolution) combined with a diagnostic approach considering the simultaneous methylation of several CpGs in one locus enabled the discrimination of HD, BPH, and PCa patients.

Bryzgunova O. , Bondar A. , Ruzankin P. , Laktionov P. , Tarasenko A. , Kurilshikov A. , Epifanov R. , Zaripov M. , Kabilov M. , Laktionov P.
Locus-specific methylation of gstp1, rnf219, and kiaa1539 genes with single molecule resolution in cell-free dna from healthy donors and prostate tumor patients: Application in diagnostics
Cancers. 2021. V.13. N24. 6234 :1-24. DOI: 10.3390/cancers13246234 WOS Scopus OpenAlex

Submitted:	Nov 9, 2021
Accepted:	Dec 10, 2021
Published online:	Dec 12, 2021

Web of science:	WOS:000736163900001
Scopus:	2-s2.0-85120990310
OpenAlex:	W4200074335

DB	Citing
Scopus	8
OpenAlex	9
Web of science	9