Single-cell multi-omics profiling uncovers the immune heterogeneity in HIV-infected immunological non-responders

BACKGROUND: T cells increase the risk of opportunistic infections and non-AIDS-related morbidity and mortality. Understanding the mechanisms driving this immune dysfunction is critical for developing targeted therapies. METHODS: We performed single-cell RNA sequencing (scRNA-seq) and single-cell VDJ sequencing (scVDJ-seq) on peripheral blood mononuclear cells (PBMCs) from INRs, immune responders (IRs), and healthy controls (HCs). We developed scGeneANOVA, a novel mixed model differential gene analysis tool, to detect differentially expressed genes and pathways. In addition, we developed the Viral Identification and Load Detection Analysis (VILDA) tool to quantify HIV-1 transcripts and investigate their relationship with interferon (IFN) pathway activation. FINDINGS: T cell exhaustion and immune recovery failure. The scGeneANOVA tool identified critical genes and pathways that were missed by traditional analysis methods, while VILDA showed higher levels of HIV-1 transcripts in INRs, which may drive the heightened IFN response. These findings support a potential contribution of IFN signalling in INR-related immune dysfunction. INTERPRETATION: T cell exhaustion. The identification of key genes and pathways offers potential biomarkers and therapeutic targets for improving immune recovery in this vulnerable population. FUNDING: This study was supported by the grants from Special Research Fund for the Central High-level Hospitals of Peking Union Medical College Hospital (Grant No. 2022-PUMCH-D-008), Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (Grant No. 2021-I2M-1-037), National Key Technologies R&D Program for the 13th Five-year Plan (Grant No. 2017ZX10202101-001). The funders played no role in the design, experiment conduction, data analysis and preparation of the manuscript of this work.