A novel quantitative method for the detection of individual L1 copies methylation patterns in circulating cell-free DNA - 11th International Symposium on Circulating Nucleic Acids in Plasma and Serum (CNAPS)

Ilgar Mamedov ^1,5 Alexander Komkov ^1,5 Maria Shamshuvarova ¹ Maria Salutina ¹ Anastasia Ponomareva ² Yuri Lebedev ¹ Elena Rykova ^3,4 Tatyana Azhikina ¹

¹Genomics of Adaptive Immunity, Shemyakin–Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia
²Oncology, Tomsk National Research Medical Center, Tomsk, Russia
³Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine, Russia
⁴Ecology, Novosibirsk State Technical University, Russia
⁵Molecular Biology, Dmitry Rogachev National Research Center Of Pediatric Hematology, Oncology and Immunology, Russia

Activation of retroelements (RE) including long interspersed nuclear elements (LINE1, L1) is shown in several types of cancer. Hypomethylation of promoter region of full-length L1 elements is one of the key mechanisms of their de-repression leading to increased transcription and retrotransposition of both autonomous and non-autonomous RE. L1 methylation profiles can be used as a prognostic marker for the monitoring of disease progression and post-therapy. RE activity is associated with anticancer immune response particularly in course of demethylation drugs therapy. Thus, deep L1 methylation profiling in non-invasive manner can become a useful tool in cancer therapy.

According to our recent study (Gainetdinov, et al, 2016), L1 human-specific family elements are characterized by hypomethylation in circulating cell-free DNA from lung cancer patients versus healthy individuals. Here, we developed a novel method to determine methylation status of individual L1 copies in cfDNA. The method combines bisulfite modification with further targeted enrichment for active L1 elements and high-throughput sequencing. Unique molecular identifiers (UMI) are introduced at the first step of library preparation and are used for the direct quantification of methylated/hypomethylated molecules for each individual L1 insertion. UMI are also used to attribute each bisulfit modified sequence to its unmodified template molecule.The method was used to compare methylation profiles of a set of active full-length L1 copies in blood plasma samples of several lung cancer patients and healthy donors. Using this approach we determined a set of particular L1 insertions intensively hypomethylated in lung cancer and other types of malignancies.

This study was supported by RFBR 18-29-09124, 18-315-20038, GACR 19-11299S and RSF 18-14-00244 grants