Integration activity of evolutionarily recent human retroelements Alu and LINE in tumors

The activity of mobile elements can be considered as one of the aspects of tumor genomic instability. From that perspective, it has a potential as a prognostic or diagnostic marker. In this work we attempted to assess the levels of integration activity of evolutionarily recent human retroelements (RE) in tumors and their relationship with RE transcriptional activity as well as other potential regulatory factors.To determine the integration activity of RE in tumors and to assess its correlation with RE transcriptional activity we performed a genome-wide search for tumor-specific inserts. For that we selected 20 tumor samples with higher and 20 samples with lower LINE L1 L1Hs and L1PA2 expression for further sequencing of genomic flanks of L1Hs L1PA2 and AluYa5/8 elements. Corresponding matched norm samples were used as a control. Overall design: All experimental biosamples were FFPE tumor tissue blocks. Histological materials were assessed by a pathologist and selected areas with at least 50% of tumor cells were dissected for further nucleic acids extraction. In some cases, adjacent non-tumour tissue was also marked and dissected. Total RNA was extracted from FFPE samples with RNeasy FFPE Kit (Qiagen) following the manufacturer's protocol. For depletion of ribosomal RNA and library preparation, the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche) was used. KAPA single-indexed adaptors (Roche) or KAPA unique dual indexed primers (Roche) were used for multiplexing samples in one sequencing run. Sequencing was performed on Illumina NextSeq 550(Illumina) with equipment for single-end 75-bp read length sequencing, for approximately 30 million raw reads per sample.