Deep Phenotypic Analysis of Blood and Lymphoid T and NK Cells From HIV+ Controllers and ART-Suppressed Individuals

Abstract

T and natural killer (NK) cells are effector cells with key roles in anti-HIV immunity, including in lymphoid tissues, the major site of HIV persistence. However, little is known about the features of these effector cells from people living with HIV (PLWH), particularly from those who initiated antiretroviral therapy (ART) during acute infection. Our study design was to use 42-parameter CyTOF to conduct deep phenotyping of paired blood- and lymph node (LN)-derived T and NK cells from three groups of HIV+ aviremic individuals: elite controllers (N = 5), and ART-suppressed individuals who had started therapy during chronic (N = 6) vs. acute infection (N = 8), the latter of which is associated with better outcomes. We found that acute-treated individuals are enriched for specific subsets of T and NK cells, including blood-derived CD56-CD16+ NK cells previously associated with HIV control, and LN-derived CD4+ T follicular helper cells with heightened expansion potential. An in-depth comparison of the features of the cells from blood vs. LNs of individuals from our cohort revealed that T cells from blood were more activated than those from LNs. By contrast, LNs were enriched for follicle-homing CXCR5+ CD8+ T cells, which expressed increased levels of inhibitory receptors and markers of survival and proliferation as compared to their CXCR5- counterparts. In addition, a subset of memory-like CD56brightTCF1+ NK cells was enriched in LNs relative to blood. These results together suggest unique T and NK cell features in acute-treated individuals, and highlight the importance of examining effector cells not only in blood but also the lymphoid tissue compartment, where the reservoir mostly persists, and where these cells take on distinct phenotypic features.

Long COVID manifests with T cell dysregulation, inflammation, and an uncoordinated adaptive immune response to SARS-CoV-2

“…A second limitation was our focus on blood specimens, when the source of immune dysregulation, including SARS-CoV-2 persistence, likely originates from tissues. The infrastructure supporting LIINC has the ability for non-invasive tissue sampling via gut biopsies and fine needle aspirates 62,63 , and future studies will take advantage of these capabilities to better understand the tissue-based mechanisms underlying the immune dysregulation that manifests in LC.…”

“…The optimal clustering resolution parameters were determined using Random Forests 70 and a silhouette score-based assessment of clustering validity and subject-wise cross-validation. This procedure is described in greater detail in George et al 62 . A generalized linear mixed model (GLMM) (implemented in the lme4 71 package in R with family argument set to the binomial probability distribution) was used to estimate the association between cluster membership and LC status and the gender of the participant, with the participant modeled as a random effect.…”

Advances in HIV Research Using Mass Cytometry

“…CyTOF analysis has identified subsets of NK and T cells enriched in individuals who initiated treatment during acute as compared to chronic infection. In particular, acutely treated PLWH harbored higher frequencies of a subset of bloodderived CD56-CD16 + NK cells [4], which are also found in PLWH that produce broadly neutralizing antibodies (bnAbs) against HIV and which have been implicated in HIV control [53]. Analysis of specimens from fine needle aspirates of lymph nodes of these individuals has also revealed higher numbers of lymphoid CD4 + Tfh expressing the homeostatic proliferation marker CD127 in the acute group, suggesting that early treatment with HIV can preserve long-lived Tfh responses in the tissue compartment [4].…”

“…In particular, acutely treated PLWH harbored higher frequencies of a subset of bloodderived CD56-CD16 + NK cells [4], which are also found in PLWH that produce broadly neutralizing antibodies (bnAbs) against HIV and which have been implicated in HIV control [53]. Analysis of specimens from fine needle aspirates of lymph nodes of these individuals has also revealed higher numbers of lymphoid CD4 + Tfh expressing the homeostatic proliferation marker CD127 in the acute group, suggesting that early treatment with HIV can preserve long-lived Tfh responses in the tissue compartment [4]. Future studies should compare the immune features of acute-vs. chronic-treated individuals within mucosal tissues, where HIV initiates infection and which likely harbors a large proportion of the reservoir during ART suppression [27].…”

Cytolytic CD8 + T cells infiltrate germinal centers to limit ongoing HIV replication in spontaneous controller lymph nodes

“…Whereas pathogens in nonlymphoid tissues are typically contained or cleared by tissue-resident and circulating cytotoxic CD8 + T cells (7,8), follicular GCs within lymphoid tissues represent a semiprivileged niche with limited immune surveillance (9). Nonetheless, accumulation of follicular CD8 + T cells (fCD8) has been associated with immune control of pathogenic viral infections and cancers, including lymphocytic choriomeningitis virus (10)(11)(12), HIV (11)(12)(13)(14)(15)(16), simian immunodeficiency virus (17)(18)(19)(20)(21), Epstein-Barr virus infectious mononucleosis (12,(22)(23)(24), B cell lymphoma (25)(26)(27), and hepatitis B virus-related carcinoma (28), as well as lung (29), pancreatic (30), and colorectal cancers (31,32).…”