Characterization of the Human Endogenous Retrovirus (HERV) HML-6 group and identification of HERV differential expression in immunity

Human Endogenous retroviruses (HERVs) are remnants of ancient retroviral infections that represent a large fraction of our genome. The HERV transcriptional activity is finely regulated in late developmental stages and the HERV expression is modulated in different cell types and tissues. The consequences of such activity may have an impact on both human physiology and pathology. Anyway, up to date, the HERVs contribution to our biology is only partially understood, often due to the poor characterization of the involved loci. For this reason, the comprehensive identification, classification and characterization of the HERV loci lay the foundations for studies of HERV expression and modulation. Moreover, novel high-throughput sequencing tools have recently allowed a great advancement in elucidating the various HERV expression patterns in different tissues, the control mechanisms of their transcription, and it overall helped in getting better insights in an all-inclusive understanding of the impact of HERVs in the biology of the host. In this work, we firstly focused on the analysis of the HML-6 group, a member of the class II Betaretrovirus-like. This group includes several proviral loci with an increased transcriptional activity in cancer. One HML-6 locus encodes the small protein ERVK3-1, expressed in various healthy tissues. Moreover, another HML-6 locus encodes HERV-K-MEL, a small Env peptide expressed in samples of cutaneous and ocular melanoma, but not in normal tissues. We characterized the group, reporting the distribution and genetic composition of 66 HML-6 elements. We analyzed the phylogeny of the HML-6 sequences and identified two main clusters. We provided the first description of a Rec domain within the env sequence of 23 HML-6 elements. A Rec domain was also predicted within the ERVK3-1 transcript sequence, revealing its expression in various healthy tissues. We reported the co-localization of 19 HML-6 elements with functional human genes. Indeed, we provided the first complete overview of the HML-6 elements in GRCh37(hg19), describing the structure, phylogeny and genomic context of insertion of each locus. Secondarily, we used a bioinformatic approach, based on RNA-sequencing (RNA-seq), to study the expression and modulation of HERVs in a scenario of immune system activation. We analyzed a dataset of Human Peripheral Blood Mononuclear Cells (PBMCs) RNA-seq from i) 15 healthy participants before and after the exposure to Lipopolysaccharide (LPS) ii) 19 subjects before and after the administration of an inactivated vaccine. We described the HERV transcriptome in PBMCs, finding that about 8 % of the HERV/MaLR loci were expressed, and identifying the Beta-retrovirus HERVs as those with the highest percentage of expressed loci. We found loci that were modulated as a result of both stimulation with LPS and vaccine administration. The HERV-H group showed the highest number of differentially expressed most intact proviruses. We characterized the HERV loci differentially expressed, checking their genomic context of insertion. In case of the LPS stimulation, that induces a strong activation of innate immune response, we observed a general co-localization with genes that are involved and modulated in the immunity. The analyses showed that HERVs and MaLRs are expressed in PBMCs and regulated in inflammatory settings. The modulation patterns of HERVs and MaLRs are different after LPS stimulation and vaccine administration, presumably indicating that such modulation patterns differ among innate and adaptive immune response.