Mass cytometry identifies distinct CD4+ T cell clusters distinguishing HIV-1–infected patients according to antiretroviral therapy initiation

Abstract

Recent guidelines recommend antiretroviral therapy (ART) to be administered as early as possible during HIV-1 infection. Few studies addressed the immunological benefit of commencing ART during the acute phase of infection. We used mass cytometry to characterize blood CD4 + T cells from HIV-1-infected patients who initiated ART during acute or chronic phase of infection. Using this method, we analyzed a large number of markers on millions of individual immune cells. The results revealed that CD4 + T cell clusters with high expression of CD27, CD28, CD127, and CD44, whose function involves T cell migration to inflamed tissues and survival, are more abundant in healthy controls and patients initiating ART during the acute phase; on the contrary, CD4 + T cell clusters in patients initiating ART during the chronic phase had reduced expression of these markers. The results are suggestive of a better preserved immune function in HIV-1-infected patients initiating ART during acute infection.

Single-Cell Technologies Applied to HIV-1 Research: Reaching Maturity

“…Compared to Thelper responses identified in HIV-1 elite controllers, ART did not fully reverse the dysregulated transcriptional program identified in viremic progressors before initiation of therapy (Morou et al, 2019). This is consistent with mass cytometry studies of the total CD8 + and CD4 + T cell subsets conducted on other HIV-1 + cohorts, which showed incomplete restoration of clusters of exhausted T cells on suppressive ART (Bengsch et al, 2018b;Bekele et al, 2019). A precise map of the corrected versus persistently altered gene modules will be key to understand residual T cell dysfunction in people living with HIV-1.…”

“…Current high-end platforms are designed to achieve high dimensionality (up to >30 parameters for cytometers and >40 parameters for CyTOF, accordingly to manufacturers). While technical considerations usually slightly reduce the number of channels useable simultaneously compared to the limit of parameters available, the depth of single-cell profiling achieved is still remarkable (Cavrois et al, 2017;Bengsch et al, 2018a;Buggert et al, 2018;Bekele et al, 2019). For both technologies analytical tools, rather than instrument performance, can still be bottlenecks preventing full exploitation of the data.…”

“…Time-of-flight cytometry based on heavy ion metal tags with minimal spectral overlap Evaluate the susceptibility of CD4 + T subsets to productive HIV-1 infection (Cavrois et al, 2017) Define the phenotypic landscape of exhausted T cells (Bengsch et al, 2018a;Bekele et al, 2019) Link new CD8 + T cell subsets to HIV-1 pathogenesis (Buggert et al, 2018) Imaging of subcellular molecular dynamics Fluorescent tags Temporal interrogation of bioengineered fluorescently tagged proteins of interest in primary cells Dissect, in live cells viral entry (Miyauchi et al, 2009), uncoating (Arhel et al, 2006;Mamede et al, 2017;Francis and Melikyan, 2018b), nuclear import (Chin et al, 2015), and assembly (Ivanchenko et al, 2009) Estimate the timeline of gene expression (Holmes et al, 2015) Branched DNA signal amplification for RNA/DNA single-cell microscopy…”

“…The extent to which these findings also apply to CD4 + T cells remains to be determined, and single-cell technologies applied to CD4 + T cell biology will be informative. Mass cytometry data revealed a complex network of CD4 + T cells clusters that correlated with functional decline and was associated with late ART initiation (Bekele et al, 2019). Most high-dimensional studies on T cell dysfunction in HIV infection have thus far been focused on T cell subsets, not HIV-specific T cells, a step required to delineate antigen-specific immune dysfunction from broader dysregulation in the context of HIV-1 infection and associated chronic immune activation.…”

Progress and applications of mass cytometry in sketching immune landscapes

“…Viral infections pose a constant challenge to the hosts' immune system. Researchers have applied CyTOF to explore the immune alterations of patients infected with influenza, 124 HIV, [125][126][127][128][129][130][131][132][133] Japanese Encephalitis, 134 Ebola, 135 Gammaherpesvirus, 136 chikungunya, 137 hepatitis B, 138,139 as well as the mosquito-borne human viral pathogens, including dengue [140][141][142] and Zika, 143,144 and elucidated the fates of immune cells across viral infections. The use of CyTOF has also supported recent findings in COVID-19 pathogenesis and immune perturbations, 145,146 where the results showed immunosuppression and dysfunction in PBMCs of COVID-19-infected patients.…”