Despite the success of antiretroviral therapy,human immunodeficiency virus(HIV)cannot be cured because of a reservoir of latently infected cells that evades therapy.To understand the mechanisms of HIV latency,we emplo...Despite the success of antiretroviral therapy,human immunodeficiency virus(HIV)cannot be cured because of a reservoir of latently infected cells that evades therapy.To understand the mechanisms of HIV latency,we employed an integrated single-cell RNA sequencing(scRNA-seq)and single-cell assay for transposase-accessible chromatin with sequencing(scATAC-seq)approach to simultaneously profile the transcriptomic and epigenomic characteristics of~125,000 latently infected primary CD4^(+)T cells after reactivation using three different latency reversing agents.Differentially expressed genes and differentially accessible motifs were used to examine transcriptional pathways and transcription factor(TF)activities across the cell population.We identified cellular transcripts and TFs whose expression/activity was correlated with viral reactivation and demonstrated that a machine learning model trained on these data was 75%-79%accurate at predicting viral reactivation.Finally,we validated the role of two candidate HIV-regulating factors,FOXP1 and GATA3,in viral transcription.These data demonstrate the power of integrated multimodal single-cell analysis to uncover novel relationships between host cell factors and HIV latency.展开更多
基金supported by the following grants from the National Institutes of Health:the National Institute of Allergy and Infectious Diseases(NIAID)(Grant No.R01 AI143381)to Edward P.Brownethe NIAID(Grant No.UM1 AI164567)to David M.Murdoch,the National Institute on Drug Abuse(NIDA)(Grant No.R61 DA047023)to Edward P.Browne+2 种基金the NIAID(Grant No.T32 AI007419)to Jackson J.Petersonthe UNC-Chapel Hill Molecular Biology of Viral Diseases T32 to Jackson J.Peterson,the National Institute of General Medical Sciences(NIGMS)(Grant No.R35 GM138342)to Yuchao Jiangthe NIDA(Grant No.R01 DA054994)to Cynthia D.Rudin.
文摘Despite the success of antiretroviral therapy,human immunodeficiency virus(HIV)cannot be cured because of a reservoir of latently infected cells that evades therapy.To understand the mechanisms of HIV latency,we employed an integrated single-cell RNA sequencing(scRNA-seq)and single-cell assay for transposase-accessible chromatin with sequencing(scATAC-seq)approach to simultaneously profile the transcriptomic and epigenomic characteristics of~125,000 latently infected primary CD4^(+)T cells after reactivation using three different latency reversing agents.Differentially expressed genes and differentially accessible motifs were used to examine transcriptional pathways and transcription factor(TF)activities across the cell population.We identified cellular transcripts and TFs whose expression/activity was correlated with viral reactivation and demonstrated that a machine learning model trained on these data was 75%-79%accurate at predicting viral reactivation.Finally,we validated the role of two candidate HIV-regulating factors,FOXP1 and GATA3,in viral transcription.These data demonstrate the power of integrated multimodal single-cell analysis to uncover novel relationships between host cell factors and HIV latency.
