Cellular proliferation maintains genetically intact and defective HIV-1 over time

Phenotypic characterization of single CD4+ T cells harboring genetically intact and inducible HIV genomes

“…Unexpectedly, individual p24+ cells belonging to a given clonally expanded population expressed highly variable levels of most cellular markers analyzed (Figure 4B), with the highest variations observed for α4, b1 and CCR7 (standard deviation of 1.18, 0.42 and 0.38, respectively, Figure 4A). Clonal expansions were more frequently found in CD4+ T cells expressing TIGIT, HLA-DR and displaying an effector memory phenotype (86.5%, 84.8%, 81.4% clonal, respectively), and less common in central memory cells (65.4% clonal) (Figure 4C), in line with previous studies [25,31,49].…”

“…Single HIV genome approaches have provided extremely valuable information on the chromosomal location of proviral integration sites [8, 21, 24, 34-37, 64, 71], on the T cell receptor repertoire and antigen specificity of HIV-infected cells [31,[33][34][35]72] as well as on the integrity and clonality of viral genomes [8,25,26,29,30,36,37,49,57,59,64].…”

“…PMA/ionomycin was used to induce p24 production from latent proviruses. The expression levels of 8 cellular markers previously described to enrich in HIV-infected cells (PD-1, TIGIT, HLA-DR, ICOS, α4, β1, CD45RA and CCR7 [18,45,49,50]) and which expression were not modified by the stimulation in the presence of brefeldin A (BFA), were simultaneously recorded (Figure 1B). We obtained a total of 309 NFL sequences from single-sorted p24+ cells (range: 41-59 sequences per participant).…”

“…Stop codons (2) ψ defects (49) Intact (8) 0.007 HXB2 Inversion (3) Hypermutations (8) Large deletions (67) Identical sequence (16) p24+ single-sorted cell (59) p24-cell ( 76)…”

“…Several cellular markers that enrich in HIV reservoirs have been identified [reviewed in 40]. Within the CD4+ T cell compartment, HIV is enriched in cells displaying a memory phenotype [18-20, 25, 41-44], in cells expressing the immune checkpoint molecules PD-1 (programmed death-1), TIGIT (T-cell immunoglobulin and ITIM domain) and LAG-3 (lymphocyte activation gene 3) [18,[45][46][47][48], as well as the activation marker HLA-DR [49,50]. Other cell-surface markers enriching in persistent HIV genomes include the adhesion molecule CD2 [51], the TNF receptor CD30 [52], the FC gamma receptor CD32 [53,54], the homing receptor VLA-4 [50] and the B cell marker CD20 [55].…”