Single Chromatin Fiber Sequencing and Longitudinal Epigenomic Profiling in HIV+ Brain Cells Exposed to Narcotic and Stimulant

HIV-associated neurocognitive disorders persist in the era of combination antiretroviral therapy (cART) while HIV latency, and cell-specific expression of HIV transcript in human CNS remains incompletely understood. There is high prevalence of HIV-associated neurologic disease and increasing recognition of CNS viral escape in people stably suppressed with cART, often further complicated by the co-registered epidemic of substance use disorders (SUD) in people living with HIV/AIDS (PLWHA), as SUD also have profound impact on CNS function. Ongoing work in our laboratory is providing first assessments of cell-type specific HIV 'molecular signatures', including genome integration patterns and alterations on the level of the transcriptome and epigenome in reward- and addiction circuitry of the human postmortem brain. However, like virtually all other genomic approaches in the field, our ongoing studies face two massive limitations: (A) Exclusively cross-sectional design, limited to a snapshot of genome organization and function at a single time point – the time of death of the brain donor. The very same limitation obviously applies to cell culture and animals. This is extremely unfortunate as such types of endpoint epigenome and transcriptome mappings in infected and non-infected brain cells cannot inform about cell-specific chromatin status during earlier periods in the life of the cell (B) Conventional brain neurogenomics is thus far limited to short read sequencing of chromatin, typically extending 150 base pairs or less per read. However, it would be much more informative to profile, at base pair resolution, epigenomic chromatin landscapes across a wider window encompassing full length retroviral insertion sites, which are two orders of magnitude above current read length. In this Avant-Garde project, we will, for the first time, for each brain, embark on retrospective/longitudinal epigenomic profiling, using a xenograft model well established in the HIV field, together with genetically engineered human iPSC- derived hematopoietic progenitor cells (HPC). We will, for the first time, embark on the longitudinal epigenomic tagging of single chromatin fibers, and explore dynamic changes and even reversibility (or progressive deterioration) of the epigenomic dysregulation in HIV infected myeloid derived cells residing in brain and blood.