Analysis of the influence of retroelements on activation of oncogenes in primary human lymphomas using high-throughput sequencing

Endogenous retroviruses (ERVs) are viral DNA sequences that have repeatedly inserted themselves through the course of primate evolution and in turn become an integral part of the human genome. The human genome contains more than 200 families of ERVs, which together comprise approximately 8 percent of our chromosomal DNA. A growing body of evidence indicates that ERVs have been a major player in molecular evolution and continue to impact the mammalian genome by acting as insertional mutagens, inducing DNA rearrangements and altering gene regulation. Given the potential for harmful effects, it is not surprising that mammals have evolved multiple lines of defense against these endogenous retroviruses, such as modifying the DNA or chromatin structure to prevent the genes from being expressed. In theory, if the ERVs are de-repressed, they could become active and then cause disruptive events leading to cancer. Although the structure, function and impact of human ERVs (HERVs) on the human genome has been studied in detail, their potential contribution to cancer has not been systematically examined. Dr. Mohammed Mahdi Karimi will be applying his experience in bioinformatics methods and high-throughput epigenetic analyses to study HERV families in human cancers. He will examine gene expression patterns and different types of epigenetic modifications, including histone modifications and DNA methylation, in primary lymphocytes isolated from lymphoma patients as well as in cell lines. By identifying the epigenetic changes in the genomes of HERV families, he hopes to determine how abnormal gene expression leads to the development of human lymphomas. Dr. Karimi expects that the results from this initial analysis will reveal genes that are misregulated in cancer as a result of the de-repression of HERVs, and this misregulation will be reflected in changes to the DNA or chromatin modification. The ultimate goal of Dr. Karimi's research is to identify molecular or epigenetic pathways that are perturbed in different types of human lymphomas, which in turn may potentially be targeted with new therapeutic strategies.