"Project 1" KSHV short and long noncoding RNAs and alteration of host IncRNA expression

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PROJECT SUMMARY Kaposi's sarcoma-associated herpesvirus (KSHV), a human gamma-herpesvirus, is the causative agent of AIDS malignancies like KS and primary effusion lymphomas (PEL). In recent years it became clear that pathogenic herpesviruses including EBV, KSHV, and MHV68 express numerous long non-coding RNAs (lncRNAs) many of which are in antisense orientation to protein coding transcripts. The function and structure of these RNAs is largely unknown. In addition, these viruses express microRNAs (miRNAs). While characterizing the KSHV miRNA targetomes using a modified Crosslinking and Sequencing of Hybrids (qCLASH) protocol, we identified several hundred host cellular lncRNAs as putative miRNA targets. These data strongly suggest that both KSHV encoded proteins and miRNAs contribute to dysregulation of host lncRNAs. Importantly, 34 lncRNAs that are perturbed following KSHV infection, including MALAT1, HOTTIP, ANRIL, Meg3, UCA1 and GAS-5 are reported to be associated with human cancers. We also linked both mRNA and lncRNA targets to cancer hallmark phenotypes such as proliferation, migration, angiogenesis, and glucose metabolism, and started to identify signaling pathways that are perturbed by KSHV miRNAs in human endothelial cells as a model for KS. We also identified aberrant splicing as an additional cancer hallmark phenotype. Here we propose to extend our studies by integrating multi-omics data sets from qCLASH, RNAseq and miRNAseq data to comprehensively analyze miRNA-regulated gene regulatory networks in KSHV infected endothelial cells. Moreover, we propose to validate our findings in a significant number of human tumor samples and by generating the first KS tumor miRNA targetome by qCLASH. These studies will be performed in a comparative fashion with Projects 2 and 3 and furthermore will be supported by Cores B, C, and D. In addition, we are functionally studying the role of the antisense LANA transcript (ALT) for which we have identified 81 putative binding proteins using a highly innovative RNA-pulldown assay. Moreover, we will study the role of a newly identified class of viral circular RNAs that has been discovered by this program. In summary, the goal of this project is to delineate the role of viral lncRNAs and host cellular lncRNAs that are perturbed by viral infection in AIDS malignancies.