Contribution of the Virome to HIV/AIDS pathogenesis

点击翻译按钮获取中文摘要

The proposed project stems from two decades of my research experience in Neuro-Virology and Neuro- Immunology, but involves a new and bold line of investigation. This new direction will allow me not only to contribute to HIV/AIDS research, but it will also help develop the nascent field of “Viromics, and define its impact to elucidate the pathogenesis associated with drug use. The key gap in our knowledge is the contribution of ALL viruses, defined as the “Virome”, to HIV/AIDS pathogenesis, and whether it is associated with drug use. However, deep sequencing alone (also called Next Gen sequencing) is sub-optimal for viral studies due to the enormous imbalance between size and abundance of human genomic DNA/RNA and viral nucleic acids. Furthermore, accessing brain areas of interest or CSF samples for targeted virological studies in the CNS represents another major obstacle. We have developed a novel target-enrichment deep sequencing-based platform for detection of the entire Virome in clinical samples, named “ViroFind”. This assay can detect all 561 DNA or RNA viruses known to infect humans, and potentially, yet undiscovered viruses. Compared to deep sequencing alone, ViroFind could enrich viral sequences present in brain samples up to 127-fold. We will define the entire Virome in the brain, CSF and blood of HIV/AIDS patients with and without drug use, using ViroFind. These include known viruses, viral variants and potentially yet unknown viruses. We will use banked samples of several cohorts of HIV/AIDS patients, as well as CSF samples from HIV+ patients seen at Rush University Medical Center (RUMC) and at my Global Neurology Program in Zambia. We will also determine the expression pattern of viral species formalin-fixed, paraffin-embedded samples, and characterize their cellular localization in the brain. The major challenge that needs to be addressed is to go beyond the mere characterization of viral sequences, and to develop the nascent field of “Viromics”. This will allow us to integrate virological data together with genomics, transcriptomics, metabolomics, immunomics and pathobiology in the human host using a systems biology approach, aiming to define possible interventions and therapeutic targets. The Avant-Garde mechanism will allow me to leverage my previous research achievements and my access to collections of post mortem samples as well cohorts of HIV-infected patients with and without drug use at RUMC and Zambia. It is also suited to my new position as Chair of Department of Neurology at RUMC, and will give me the freedom to move the field of Viromics forward in a truly transformative way. By integrating the field of Viromics with other “omics” these studies will not only advance HIV/AIDS and drug use research, but also pave the way for delineating druggable targets and developing novel therapies for viral diseases. The proposed studies are in line with the Office of AIDS Research new priorities including HIV co-infections, co-morbidities and complications (CCC).