Single-cell TCR profiling of CSF and blood cells of PWH reveals persistent and shared infected T cell clones across tissue compartments even after ART
The brain is a site of persistent infected cells during HIV infection. However, the dynamics of central nervous system (CNS) infection and T cell trafficking in people living with HIV (PWH) are incompletely understood. We profiled the single cell T cell repertoire and host transcriptome from paired blood and cerebrospinal fluid (CSF) from PWH and uninfected controls. We detected HIV RNA-producing cells in 8/11 (72.7 %) CSF samples and 6/11 (54.5 %) blood samples, with a higher frequency of infected single CD4 T cells in CSF than in blood. Infected CSF T cells displayed a unique transcriptional profile compared to uninfected CSF T cells. Most infected T cell clones were not shared across tissue; however, in a subset of participants we detected identical T cell clones that were infected in both CSF and blood. Longitudinally following one PWH before and at three time points after initiating ART, we found infected T cell clones that persisted after ART initiation, in both CSF and blood, including a T cell clone that expanded in the CSF several months after ART initiation. Our findings suggest that infected T cells traffic to the CNS where they undergo clonal expansion despite ART, contributing to the CNS reservoir. Overall design: Asymptomatic PWH P2 - P7 were enrolled (n = 7), and all were stable on ART (median 16 years) with suppressed plasma viral loads (< 50 copies/mL) and a median CD4 count of 503. One additional PWH was enrolled (P1) with newly diagnosed HIV and not yet on ART, and had a plasma viral load of 257,000 copies/mL. Control participants C1 - C6 were healthy volunteers recruited from the surrounding community for research sampling (n = 6) plus one hospitalized individual C1 undergoing a workup for gait instability. All control participants were confirmed HIV-negative by plasma enzyme immunoassay and screened for confounding neurological conditions. All participants consented to large-volume lumbar puncture (up to 30cc CSF removed) and blood draw for research purposes, or to donate additional CSF and blood samples collected during clinical standard-of-care procedures. Participant P1 underwent longitudinal study visits and consented to provide blood and CSF samples at HIV diagnosis/baseline and three, six, and nine months after initiating ART. The gene expression and T cell receptors of the peripheral blood and CSF samples were then measured using 5' V(D)J 10x Genomics paired scRNA-seq and TCR-seq. Sequencing data for C1 - C3 was previously published on SRA (study accession: SRP312293, C1_BLD_RNA: SRR14076861, C1_BLD_TCR: SRR14076833, C1_CSF_RNA: SRR14076871, C1_CSF_TCR: SRR14076842, C2_BLD_RNA: SRR14076860, C2_BLD_TCR: SRR14076832, C2_CSF_RNA: SRR14076869, C2_CSF_TCR: SRR14076841, C3_BLD_RNA: SRR14076858, C3_BLD_TCR: SRR14076831, C3_CSF_RNA: SRR14076868, C3_CSF_TCR: SRR14076840).