Multi-Omic Atlas reveals cytotoxic phenotype and ROS-linked metabolic quiescence as key features of CTL-resistant HIV-infected CD4+ T-cells

HIV, although manageable as a chronic condition, currently lacks a safe or scalable cure. Antiretroviral therapy (ART) effectively suppresses HIV replication, preventing disease progression and transmission to sexual partners. However, ART does not affect established 'reservoirs', which are rare cell populations harboring integrated, intact proviruses that can reignite viral replication if ART is discontinued. Cytotoxic T-lymphocytes (CTL) exert sustained pressure on reservoirs of HIV-infected cells that persist through years of antiretroviral therapy (ART). This selects for latently-infected cells, but also potentially for cells that express HIV but possess intrinsic CTL resistance. In this study we confirm the existence of HIV-infected CD4+ T-cells that survive rigorous CTL attack and map CTL susceptibility to cell identities and states defined by single-cell multi-omics (using 10X based ECCITE-seq) and functional metabolic profiling. Our results provide an atlas for elucidating features of CTL resistance in HIV reservoirs, and identify oxidative stress as a therapeutic target to facilitate reservoir elimination. Overall design: ECCITE-seq gene expression and antibody derived tag profiles (from 4 donors), and TCR clonotype profiles (from 1 donor) were constructed from 'surviving' and 'bystander' HIV-infected CD4+ T-cells using a wild-type clinical HIV stain and the same strain but with a single CTL epitope escape mutation respectively after co-culture together with a HLA-matched CTL clone targeting the escaped epitope in the second virus.