Discovery and functional characterization of long non-coding RNAs in opioid use disorder within the context of HIV at single cell resolution - ABSTRACT Opioid use disorder (OUD) is a significant public health threat that affects millions of people and is associated with high rates of co-occurring conditions such as HIV. Approximately 17% of the 15 million people who inject drugs globally are HIV-positive. Conversely, HIV-positive individuals often experience chronic pain, which leads to increased opioid use and a higher risk of addiction. OUD causes persistent molecular changes in the brain, potentially further altering or exacerbating HIV-related brain impairment. However, transcriptional alterations by alternative mechanisms remain understudied in the human brain and may be a major factor in OUD and HIV. Constituting over 70% of the human genome, long non-coding RNAs (lncRNAs) are increasingly recognized for their significant roles in gene regulation and disease pathogenesis, including OUD and HIV-related neurocognitive disorders. However, lncRNAs have not yet been well studied in either OUD or HIV, let alone in the coexistence of OUD and HIV. Our pilot study suggests that lncRNAs are especially abundant in the brain. Some of these lncRNAs are also conserved between humans and mice. We also found that conserved OUD- dysregulated lncRNAs exhibit cell type-specific expression in neurons and non-neurons in the brain. Therefore, we hypothesize that lncRNAs may regulate brain functions in a cell type-specific manner, and these lncRNAs might also potentially modulate brain functions in individuals with OUD, HIV, or co-occurring OUD and HIV. Several NIH programs, such as SCORCH and BICAN, have generated large amounts of single-cell (sc) RNA sequencing (scRNA-seq) data in human and rodent brains with or without OUD or HIV exposure. These data offer excellent opportunities to test our hypothesis. However, current approaches cannot comprehensively study cell type-specific lncRNAs at single-cell resolution because most disease-, tissue-, or cell type-specific lncRNAs have not yet been discovered. Therefore, to test our hypothesis, (1) we will expand our current lncRNA study methods to systematically discover and characterize lncRNAs in OUD and HIV at the single-cell level by analyzing large-scale omics data of human and mouse brains obtained from SCORCH, BRAIN, and other public data sources; (2) we will functionally characterize conserved lncRNAs in mouse models to uncover lncRNAs as potential new molecular mechanisms in OUD and HIV, as well as in their co-occurrence. This study will discover novel lncRNAs as potential molecular factors at the single-cell level in key brain regions involved in OUD, HIV, and their co-occurrence. Understanding lncRNAs in key brain regions affected by OUD and HIV is likely to reveal novel drug targets for treating patients who suffer from one or both conditions. Additionally, this study will provide a new computational framework broadly applicable to existing and future scRNA-seq datasets for understanding lncRNAs in other substance use disorders at single-cell resolution, and consequently, it will improve the utility of datasets from NIH SCORCH, HuBMAP, and BICAN programs.
