HIV efficiently infects T cells from the endometrium and remodels them to promote systemic viral spread

Abstract

The female reproductive tract (FRT) is the most common site of infection during HIV transmission to women, but viral remodeling complicates characterization of cells targeted for infection. Here, we report extensive phenotypic analyses of HIV-infected endometrial cells by CyTOF, and use a ‘nearest neighbor’ bioinformatics approach to trace cells to their original pre-infection phenotypes. Like in blood, HIV preferentially targets memory CD4+ T cells in the endometrium, but these cells exhibit unique phenotypes and sustain much higher levels of infection. Genital cell remodeling by HIV includes downregulating TCR complex components and modulating chemokine receptor expression to promote dissemination of infected cells to lymphoid follicles. HIV also upregulates the anti-apoptotic protein BIRC5, which when blocked promotes death of infected endometrial cells. These results suggest that HIV remodels genital T cells to prolong viability and promote viral dissemination and that interfering with these processes might reduce the likelihood of systemic viral spread.

SARS-CoV-2-specific T cells exhibit phenotypic features reflecting robust helper function, lack of terminal differentiation, and high proliferative potential

“…Overlapping 15mer peptides from spike, an immunodominant SARS-CoV-2 antigen (Braun et al, 2020;Grifoni et al, 2020), were used for characterization of the SARS-CoV-2-specific response, while overlapping peptides against pp65, an immunodominant CMV antigen (Sylwester et al, 2005), were used for comparison. To enable high-parameter phenotyping of antigen-specific cells, we modified a recently developed human T cell CyTOF panel (Ma et al, 2020b) so it would detect cells producing the cytokines IFNg, IL4, or IL17 (Table S2). CD4+ and CD8+ T cells were identified by sequential gating on live, singlet CD3+ cells expressing the corresponding coreceptor ( Fig.…”

“…We believe that to not be the case because 1) ICOS-CXCR5-cells do not upregulate either ICOS or CXCR5 during 6 hours of in vitro stimulation (Bentebibel et al, 2013;Morita et al, 2011), and 2) SARS-CoV-2-specific CD4+ T cells had higher ICOS expression than CMV-specific CD4+ T cells which were similarly stimulated. To verify that SARS-CoV-2-specific cells at baseline express high levels of ICOS, we implemented Predicted Precursor as determined by SLIDE (PP-SLIDE) (Cavrois et al, 2017;Ma et al, 2020b), a bioinformatics pseudotime analysis approach that can predict the original phenotypes of cells before cellular perturbations. SARS-CoV-2-and CMV-specific CD4+ T cells were traced back to their predicted original states by matching their high-dimensional CyTOF profiles against the "atlas" of all CD4+ T cells phenotyped by CyTOF at baseline (prior to the 6 hours of stimulation).…”

“…PBMCs were isolated from blood using Lymphoprep TM (StemCell Technologies) within 2 hours of blood collection. Six million cells were then immediately treated with cisplatin (Sigma-Aldrich) as a Live/Dead marker and fixed with paraformaldehyde (PFA) as previously described (Ma et al, 2020b). Briefly, 6x10 6 cells were resuspended at room temperature in 2 ml PBS (Rockland) with 2 mM EDTA (Corning).…”

“…This was achieved by combining detection of SARS-CoV-2-specific T cells together with CyTOF, a mass spectrometry-based single-cell phenotyping method that uses antibodies conjugated to metal lanthanides to quantify expression levels of both surface and intracellular proteins (Bendall et al, 2011). As spectral overlap is not a limitation with CyTOF, large phenotyping panels of nearly 40 parameters can be implemented, allowing for a highresolution view of immune cells and the use of high-dimensional analytical methods to monitor cellular remodeling (Cavrois et al, 2017;Ma et al, 2020b). We report here that SARS-CoV-2specific CD4+ and CD8+ T cells from convalescent individuals are diverse, exhibit features different from antigen-specific T cells against CMV, include cells with both lymphoid and tissue homing potential, harbor phenotypic features of functional effector cells, and are long-lived and capable of homeostatic proliferation.…”

“…D) ICOS is expressed at high levels onpredicted precursors of IFNg-producing SARS-CoV-2-specific CD4+ T cells. PP-SLIDE(Cavrois et al, 2017;Ma et al, 2020b) was conducted to predict the original phenotypic features of SARS-CoV-2-specific (red) and CMV-specific (blue) cells prior to IFNg induction. Expression levels of ICOS on these cells were compared to those on total CD4+ T cells phenotyped by CyTOF immediately following PBMC isolation.…”