Data Mining and Functional Validation of SCORCH Datasets

Scripps Research Institute, The, La Jolla CA

Investigators

Abstract

Summary The abuse of drugs is associated with treatment non-compliance, greater risk of viral transmission, and more rapid clinical progression of HIV disease. The overarching hypothesis behind the present project is that the exploration of gene regulatory networks in single cells will elucidate key pathogenic mechanisms that underlie the effects of HIV and substance use disorder (SUD) and their detrimental interactions that will indicate novel therapeutic targets for neuroinflammation, neurodegeneration, virus expression and persistence, and cognitive impairment in the setting of HIV and SUD. To test the present hypothesis, we propose a data mining campaign centered on a comparative analysis of cell type-specific gene regulatory networks or interactomes reconstructed from the human and animal model single cell/single nucleus RNA-Seq (sc/snRNA- Seq) and single nucleus assay for transposase-accessible chromatin-sequencing (snATAC-seq) from the SCORCH program. To this end we will use a validated systems biology strategy for the reconstruction and interrogation of a genome-scale gene regulatory network that proved exceptionally effective in deconvolving molecular interactions in cancer, Alzheimer's disease, development, substance abuse (by our group), as well as in the identification of therapeutic targets, mechanisms of action and synergistic activities of therapeutics. The occasional but limited use of a drug is clinically distinct from dependent drug use, which is characterized by the emergence of dependence and a negative emotional state when access to the drug is prevented that drives negative reinforcement, a powerful source of motivation for drug seeking. Therefore, we will validate the key genes identified both in vitro and in vivo in a state-of-the-art paradigm of voluntary intravenous drug self-administration under long access (LgA) conditions, which leads to escalated (dependent) drug intake that we implemented in HIV transgenic rats. Escalated drug intake in this paradigm is highly relevant to human SUD as it has been suggested that it models all 7 of the criteria for drug addiction in the Diagnostic and Statistical Manual of Mental Disorders (DSM)-IV and 7 of the 11 criteria in the DSM-V. HIV Tg rats self-administering drugs in this paradigm display increased neural injury and neuroinflammation. Overall, this collaborative interdisciplinary proposal integrating systems biology data mining centered on the deconvolution of the gene regulatory networks at the single cell level, hierarchical validation strategies including state-of-the-art behavioral paradigms of volitional drug intake, single cell level transcriptomics, and state-of-the-art behavior methods in HIV Tg and wild-type rats, will elucidate key mechanisms that underlie the detrimental interactions of HIV and SUD on disease progression, virus expression and persistence. The results will indicate transformative new mechanistic hypotheses that may lead to novel therapeutic concepts for SUD in the setting of HIV and will establish key resources for the neuroHIV field to be made publicly available through the SCORCH data coordination center and other public repositories.