Epigenetic Probes for Lung Cancer Monitoring:
Line-1 Methylation Pattern in Blood-Circulating DNA

A. A. Ponomaryovaa, c, E. Y. Rykovab, N. V. Cherdyntsevaa, d, A. A. Bondarb,
A. Y. Dobrodeev
a, A. A. Zavyalova, S. A. Tuzikova, L. O. Bryzgalove,
T. I. Merkulova
e, V. V. Vlassovb, and P. P. Laktionovb

aFederal Government Budget Institute Tomsk Cancer Research Institute, Tomsk, Russia

bFederal Government Budget Institute of Science Institute of Chemical Biology and Fundamental Medicine,
Russian Academy of Sciences, Siberian Brunch, Novosibirsk, Russia

cFederal Government Autonomous Educational Institute of Higher Professional Education the National Research
Tomsk Polytechnic University, Tomsk, Russia

dFederal Government Autonomous Educational Institute of Higher Education National Research
Tomsk State University, Tomsk, Russia

eFederal Government Budget Institute of Science Institute of Cytology and Genetics,
Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia

e-mail: rykova@niboch.nsc.ru

Received October 20, 2014; in final form, December 15, 2014

Abstract—The main components of DNA aberrant methylation in malignant cells are promoter hypermethy-
lation of specific genes and hypomethylation of the main part of DNA, in particular, the repeated sequences of
retrotransposons. The hypomethylation of retrotransposons from the LINE-1 family was revealed in the lung
cancer (LC) tissue. The composition of circulating DNA (cirDNA) from the plasma and blood cell surface
bound circulating DNA (csb-cirDNA) was shown earlier to be altered in the blood of cancer patients due to the
accumulation of tumor-specific aberrantly methylated DNA fragments, which are currently considered to be
valuable cancer markers. The present study compares LINE-1 retrotransposon methylation patterns in the cir-
DNA and csb-cirDNA plasma from 21 untreated LC patients and 23 healthy donors. Concentrations of methy-
lated LINE-1 region 1 copies (LINE-1met) were assessed by quantitative real-time methylation-specific PCR.
In order to normalize the LINE-1 methylation level, the LINE-1 region 2 concentration was evaluated, which
was independent of the methylation status (LINE-1Ind). The LINE-1met concentration in csb-cirDNA tended
to decrease (by a factor of 1.4) in blood from LC patients compared to healthy donors (Mann–Whitney test, P
= 0.16). The LINE-1Ind (methylation-independent) concentration in csb-cirDNA was found to be lower by a
factor of three in LC patients and by a factor of four in patients with adenocarcinoma than in healthy donors.
Thus, along with the expected decrease in the LINE-1met concentration in csb-cirDNA from LC patients’
blood, we recorded an unexpected statistically significant increase of the LINE-1 methylation index determined
as (LINE-1met/LINE-1Ind) due to the profound decrease of the total LINE-1Ind number. There were no differ-
ences between the plasma cirDNA LINE-1 methylation indexes in the LC patients and healthy donors (Mann–
Whitney test, P = 0.40). The data obtained agreed with our earlier results, which showed that csb-cirDNA was
highly informative material for lung cancer diagnostics.

Keywords: blood-circulating DNA, aberrant methylation, LINE-1 retrotransposons, diagnostics, lung cancer

DOI: 10.1134/S2079059716010111

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