Single-cell sequencing reveals NK cell dysregulation during chronic HIV infection and identifies transitional NK cell cytotoxicity related to HIV reservoir decay
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE332837 | GEO | 2026/07/22
REPOSITORIES: GEO
Similar Datasets
Project description:Treatment with latency-reversing agents (LRAs) alone has been ineffective in reducing HIV-1 reservoirs in people living with HIV-1 (PLWH) who are on antiretroviral therapy (ART), due to inefficiencies in reservoir reactivation and adaptive immune responses. However, NK cells activated with cytokines may be able to target HIV-1 reservoirs more effectively. To explore the therapeutic potential of NK cells, we expanded blood NK cells from multiple donors ex vivo into CD56brightCD16+ “eNK” cells using artificial antigen-presenting cells (aAPCs) expressing membrane-bound IL21. eNK cells express multiple activating receptors and are highly cytotoxic against specific target cells. They can also kill HIV-infected CD4+ T cells via antibody-dependent cell-mediated cytotoxicity (ADCC) using broadly neutralizing antibodies (bNAbs) against HIV-1 Env gp120/gp41. Notably, eNK cells from PLWH on ART efficiently killed autologous HIV-1+ T cells reactivated by a combination of vorinostat (SAHA) and IL-15 or an IL-15 superagonist (N-803), as evidenced by declines in proviral load, inducible HIV-1 mRNA, and virus release. Adoptive immunotherapy with eNK cells combined with LRA treatment thus presents a promising strategy to reduce the latent HIV-1 reservoir in PLWH.
2025-12-29 | GSE312273 | GEO
Project description:Antiretroviral therapy (ART) in human immunodeficiency virus (HIV) improved life expectancy in people living with HIV (PLWH) but cardiac diseases have emerged as a leading cause of death in this population. There is a notable increase in diastolic dysfunction and HF with preserved ejection fraction (HFpEF) attributed to the altered metabolic milieu seen in PLWH on ART. However, the specific role(s) that HIV itself, and/or ART may have on the cardiomyocyte phenotype is unknown. We investigated molecular pathways altered in cardiomyocytes in vitro in response to serum from ART-naïve and after ART-treated patients. Cardiomyocytes were treated for 24 hours with serum obtained longitudinally from HIV patients before and after receiving ART for 6 months. RNA sequencing revealed that differences between pre- and post-treatment with ART were related to processes involving cell death, cardiomyocyte calcium handling, and adverse remodeling. Apoptotic death was increased in cardiomyocytes treated with serum obtained from ART naïve HIV patients whereas those treated with serum from the same patients 6 months after ART presented changes in calcium-handling proteins and profibrotic markers, indicating altered contraction and relaxation, and adverse remodeling. These findings demonstrate altered molecular pathways in cardiomyocytes in response to active viremia and ART.
2025-11-06 | GSE268983 | GEO
Project description:Persons living with HIV (PLWH) are at increased risk of tuberculosis (TB). HIV-associated TB is mainly the result of recent infection with Mycobacterium tuberculosis (Mtb) followed by rapid progression to disease. Alveolar macrophages (AM) are the first cells of the innate immune system that engage Mtb, but how HIV and antiretroviral therapy (ART) impact on the anti-mycobacterial response of AM is not known. In this study AM were challenged in vitro with Mtb, and their epigenetic and transcriptomic responses were determined for PLWH receiving ART, control subjects who were HIV-free (HC) and subjects who received pre-exposure prophylaxis (PrEP) with ART to prevent HIV infection. Compared to HC subjects’ response to Mtb, we showed that AM isolated from PLWH and PrEP subjects displayed substantially weaker transcriptomic response and no significant changes in their chromatin state. These findings revealed a previously unknown adverse effect of ART.
2021-09-03 | GSE165708 | GEO
Project description:Persons living with HIV (PLWH) are at increased risk of tuberculosis (TB). HIV-associated TB is mainly the result of recent infection with Mycobacterium tuberculosis (Mtb) followed by rapid progression to disease. Alveolar macrophages (AM) are the first cells of the innate immune system that engage Mtb, but how HIV and antiretroviral therapy (ART) impact on the anti-mycobacterial response of AM is not known. In this study AM were challenged in vitro with Mtb, and their epigenetic and transcriptomic responses were determined for PLWH receiving ART, control subjects who were HIV-free (HC) and subjects who received pre-exposure prophylaxis (PrEP) with ART to prevent HIV infection. Compared to HC subjects’ response to Mtb, we showed that AM isolated from PLWH and PrEP subjects displayed substantially weaker transcriptomic response and no significant changes in their chromatin state. These findings revealed a previously unknown adverse effect of ART.
2021-09-03 | GSE165705 | GEO
Project description:Persons living with HIV (PLWH) are at increased risk of tuberculosis (TB). HIV-associated TB is mainly the result of recent infection with Mycobacterium tuberculosis (Mtb) followed by rapid progression to disease. Alveolar macrophages (AM) are the first cells of the innate immune system that engage Mtb, but how HIV and antiretroviral therapy (ART) impact on the anti-mycobacterial response of AM is not known. In this study AM were challenged in vitro with Mtb, and their epigenetic and transcriptomic responses were determined for PLWH receiving ART, control subjects who were HIV-free (HC) and subjects who received pre-exposure prophylaxis (PrEP) with ART to prevent HIV infection. Compared to HC subjects’ response to Mtb, we showed that AM isolated from PLWH and PrEP subjects displayed substantially weaker transcriptomic response and no significant changes in their chromatin state. These findings revealed a previously unknown adverse effect of ART.
2021-09-03 | GSE165703 | GEO
Project description:The crosstalk between intestinal epithelial cells (IEC) and Th17-polarized CD4+ T-cells is critical for mucosal homeostasis, with HIV-1 causing major alterations in people living with HIV (PLWH) despite antiretroviral therapy (ART). Here, we used a model of IEC:T-cell co-culture to investigate the effects of IL-17A and TNF, two cytokines produced by Th17-cells, in regulating IEC ability to promote de novo infection and viral outgrowth from reservoir cells. Our results demonstrated that IL-17A in the presence/absence of TNF acts on IEC to increase HIV capture and trans infection of CD3/CD28-activated T-cells from uninfected individuals. Also, IL-17A-exposed IEC significantly increased HIV replication and outgrowth in CD3/CD28-activated T-cells infected with HIV in vitro and isolated from ART-treated PLWH, respectively. Exposure of IEC to IL-17A resulted in decreased type I IFN levels, as measured using the 293T-KEK cell based assay. Illumina RNA sequencing performed on cytokine-activated IEC before/after co-culture with T-cells of ART-treated PLWH revealed a molecular signature associated with IL-17A-mediated proviral effects. This signature includes decreased expression of transcripts linked to type I IFN production/response (DDX60, IRF7, STAT1) and HIV restriction (IFITM1, TRIM5, IF2AK2, MX1, MX2, IFIT1,3,5, PARP12, HERC6, ISG15, viperin, BST2, OAS2/3), and increased expression of Th17-attracting chemokines (CCL20).
2021-03-01 | GSE147045 | GEO
Project description:Understanding the complexity of the long-lived HIV reservoir during antiretroviral therapy (ART) remains a major impediment for HIV cure research. To address this, we developed single-cell viral ASAPseq to precisely define the unperturbed peripheral blood HIV-infected memory CD4+ T cell reservoir from antiretroviral treated people living with HIV (ART-PLWH) via the presence of integrated accessible proviral DNA in concert with epigenetic and cell surface protein profiling. We identified profound reservoir heterogeneity within and between ART-PLWH, characterized by novel and known surface markers within total and individual memory CD4+ T cell subsets. We further uncovered novel epigenetic profiles and transcription factor motifs enriched in HIV-infected cells that suggest infected cells with accessible provirus, irrespective of reservoir distribution, are poised for reactivation during ART treatment. Together, our findings reveal the extensive inter- and intrapersonal cellular heterogeneity of the HIV reservoir, and establish an initial multiomic atlas to develop targeted reservoir elimination strategies.
2022-10-21 | GSE199727 | GEO
Project description:People living with HIV (PLWH) experience chronic intestinal barrier dysfunction (gut leakage), which persists despite viral suppression by antiretroviral therapy (ART) and contributes to chronic inflammation and its comorbidities. The mechanisms underlying this phenomenon remain unclear and are likely multifactorial. We hypothesize that living with HIV compromises the intestinal barrier’s resilience to injurious agents, increasing susceptibility to leakage upon exposure to common exogenous or endogenous disruptors, such as alcohol or pro-inflammatory cytokines, respectively. Using 3D intestinal organoids (colonoids and enteroids) derived from PLWH on ART and HIV-negative controls, we assessed the impact of alcohol and inflammatory cytokines on barrier integrity. Organoids from PLWH exhibited reduced resilience to disruption compared to controls, correlating with alterations in pathways critical to epithelial integrity, including epithelial-mesenchymal transition, DNA repair, and oxidative stress-related pathways. These findings reveal a novel mechanism underlying intestinal dysfunction in PLWH and highlight potential molecular targets to mitigate these complications.
2025-12-17 | GSE284761 | GEO
Project description:People living with HIV (PLWH) experience chronic intestinal barrier dysfunction (gut leakage), which persists despite viral suppression by antiretroviral therapy (ART) and contributes to chronic inflammation and its comorbidities. The mechanisms underlying this phenomenon remain unclear and are likely multifactorial. We hypothesize that living with HIV compromises the intestinal barrier’s resilience to injurious agents, increasing susceptibility to leakage upon exposure to common exogenous or endogenous disruptors, such as alcohol or pro-inflammatory cytokines, respectively. Using 3D intestinal organoids (colonoids and enteroids) derived from PLWH on ART and HIV-negative controls, we assessed the impact of alcohol and inflammatory cytokines on barrier integrity. Organoids from PLWH exhibited reduced resilience to disruption compared to controls, correlating with alterations in pathways critical to epithelial integrity, including epithelial-mesenchymal transition, DNA repair, and oxidative stress-related pathways. These findings reveal a novel mechanism underlying intestinal dysfunction in PLWH and highlight potential molecular targets to mitigate these complications.
2025-12-17 | GSE284755 | GEO
Project description:In study NCT00594880, we successfully administered weekly doses of pegylated interferon-α-2a (Peg-IFN-α2a) with antiretroviral therapy (ART) for 5 weeks, before continued Peg-IFN-α2a monotherapy to 12 weeks (primary endpoint) in chronic HIV-infected subjects. Subjects maintaining HIV viral load <400 copies/ml by primary endpoint were defined as responders. We now describe innate immune correlates and transcriptional profiles associated with viral control and decrease in integrated HIV DNA after Peg-IFN-α2a immunotherapy. Peripheral blood samples were obtained prior to Peg-IFN-α2a administration (ART), after 5 weeks of ART+Peg-IFN-α2a dual treatment, and after 12 weeks of Peg-IFN-α2a monotherapy. Cell subset modulation, natural killer cell (NK) function and signaling, as well as inflammatory mediators and gene expression were assessed. Results were analyzed using R.2.5.1 or MATLAB 7.10.0. Five weeks of ART+Peg-IFN-α2a preserved the frequency of immune subsets and NK cytotoxicity, while increased the levels of inflammatory mediators, and decreased cell-responsiveness to in vitro IFN-α re-stimulation. Gene expression analysis showed that induction of host restriction factors after ART+Peg-IFN-α2a was not solely predictive of a virologic response, and revealed a 108 gene signature that identified subjects who did not modulate genes after ART+Peg-IFN-α2a. A 29 gene signature along with higher NK cell activation and IFN-γ-induced protein 10 (IP-10) levels on ART, as well as higher in vitro responses to IFN-γ-induced NK cytotoxicity, and decrease in the frequency of NK bearing inhibitory receptors [i.e. killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail 1 (KIR2DL1) or KIR2DL2/DL3] and C-C chemokine receptor type 7+ (CCR7) myeloid dendritic cells after ART+Peg-IFN-α2a distinguished responders from non-responders. Reductions in integrated HIV DNA after immunotherapy were associated with expression patterns of genes that are associated with activated cell-mediated response and NK cytotoxicity. In summary, innate activation and NK cell cytotoxicity are identified as correlates of HIV control and reduction after Peg-IFN-α2a immunotherapy in ART-suppressed subjects.
2019-06-03 | GSE107549 | GEO