hiv-seq reveals global host gene expression differences between hiv-transcribing cells from viremic and suppressed people with hiv

In our study, we aimed to improve the identification of active reservoir cells producing HIV in individuals undergoing antiretroviral therapy (ART). We developed a technique called HIV-Seq to enhance the efficiency of capturing HIV transcripts during single-cell RNA sequencing (scRNAseq) analysis. By applying this technique and surface phenotyping using CITE-seq, we compared the transcriptional features of HIV RNA+ cells before and after ART initiation. Our findings highlight distinct transcriptional signatures of active reservoir cells during viremia and suppression, demonstrating the utility of HIV-Seq in elucidating the mechanisms underlying reservoir persistence during ART. Overall design: Paired and longitudinal, archived PBMC samples were obtained from different cohort. Samples were collected prior to ART initiation (Week 0) and following ART suppression (week 24 or week 45). PBMCs were thawed, CD4+ T cells were purified by negative selection using the EasySep Human CD4 T cell enrichment kit (StemCell) and then stained with TotalSeq-C antibodiesfollowed by 10X libraries (ADT and GEX) preparation. ----------------------------------------- ADT Barcode sequence TotalSeq™-C0390 anti-human CD127 (IL-7Ra) Antibody GTGTGTTGTCCTATG TotalSeq™-C0081 anti-human CD14 Antibody TCTCAGACCTCCGTA TotalSeq™-C0050 anti-human CD19 Antibody CTGGGCAATTACTCG TotalSeq™-C0148 anti-human CD197 (CCR7) Antibody AGTTCAGTCAACCGA TotalSeq™-C0100 anti-human CD20 Antibody TTCTGGGTCCCTAGA TotalSeq™-C0088 anti-human CD279 (PD-1) Antibody ACAGCGCCGTATTTA TotalSeq™-C0034 anti-human CD3 Antibody CTCATTGTAACTCCT TotalSeq™-C0045 anti-human CD4 Antibody GAGGTTAGTGATGGA TotalSeq™-C0048 anti-human CD45 Antibody TCCCTTGCGATTTAC TotalSeq™-C0063 anti-human CD45RA Antibody TCAATCCTTCCGCTT TotalSeq™-C0087 anti-human CD45RO Antibody CTCCGAATCATGTTG TotalSeq™-C0046 anti-human CD8 Antibody GCGCAACTTGATGAT TotalSeq™-C0154 anti-human CD27 Antibody GCACTCCTGCATGTA TotalSeq™-C0576 anti-human CD49d Antibody CCATTCAACTTCCGG TotalSeq™-C0147 anti-human CD62L Antibody GTCCCTGCAACTTGA