NearTrans Can Identify Correlated Expression Changes Between Retrotransposons and Surrounding Genes in Human Cancer

Recent studies using high-throughput sequencing technologies have demonstrated that transposable elements (TEs) seem to be involved not only in some cancer onset but also in cancer development. New dedicated tools have been recently designed to quantify the global expression of the different families of TEs from RNA-seq data, but the identification of the particular, differentially expressed TEs would provide more profitable results. To fill the gap, here it is presented NearTrans, a bioinformatic workflow that takes advantage of gEVE (a database of endogenous viral elements) to determine differentially expressed TEs as well as the activity of genes surrounding them to study if changes in TE expression is correlated with nearby genes. An especial requirement is that input RNA-seq reads must derive from normal and cancerous tissue from the same patient. NearTrans has been tested using RNA-seq data from 14 patients with prostate cancer, where two HERVs (HERVH-int and HERV17-int) and three LINE-1 (L1PA3, L1PA4 and L1PA7) were over-expressed in separate positions of the genome. Only one of the nearby genes (ACSM1) is over-expressed in prostate cancer, in agreement with the literature. Three (PLA2G5, UBE2MP1 and MIR4675) change their expression between normal and tumor cell, although the change is not statistically significant. The fifth (LOC101928437) is highly distant to the L1PA7 and their correlation is unlikely. These results are supporting that, in some cases such as the HERVs, TE expression can be governed by the genome context related with cancer, while in others, such as the LINEs, their expression is less related with the genome context, even though they are surrounded by genes potentially involved in cancer. Therefore, NearTrans seems to be a suitable and useful workflow to discover or corroborate genes involved in cancer that might be used as specific biomarkers for the diagnosis, prognosis or treatment of cancer.