Background:
CD8 T-cell responses to HIV/SIV infection critically contribute to control of viremia, but lymph node (LN) CD8 T-cells have been shown to be phenotypically and functionally distinct from those in blood.
Methods:
To characterize the unique populations in LN, we obtained LN samples from rhesus macaques during early chronic SIV infection (D42 post-infection) and performed flow cytometry, scRNA-seq and imaging to explore the dynamics of LN CD8 T-cells expressing Tox, TCF1 and CD39, three well-described markers delineating exhausted, stem-like and terminally-differentiated populations.
Results:
Tox is upregulated after SIV infection and primarily expressed in PD-1+ and TIGIT+ cells. Notably, we observed high expression of Tox on a previously undescribed TCF1+CD39+ population, distinct from the known TCF1+CD39- stem-like and TCF1-CD39+ effector/exhausted CD8 T-cells, that significantly expands after infection. These TCF1+CD39+ cells expressed inhibitory receptors, intermediate levels of Ki-67, and are uniquely high in GzmK but low in GzmB, a profile consistent with a precursor effector cell. After SIV peptide stimulation, TCF1+CD39+ cells degranulated at similar levels to TCF1-CD39+ cells but produce less IFNy. scRNA-seq of SIV-specific CD8 T-cells revealed an intermediate profile of TCF1+CD39+ cells between the stem-like TCF1+CD39- cells and the differentiated TCF1-CD39+ cells. Importantly, a higher frequency of both Tox+ (p< 0.0001) and TCF1+CD39+ (p=0.0003) CD8 T-cells in LN at d42 p.i. was strongly associated with lower plasma viremia, lower levels of cell-associated SIV-DNA (Tox p=0.0007; TCF1+CD39+ p=0.01) and better CD4 preservation (Tox p=0.02; TCF1+CD39+ p=0.065). After more than 1 year of ART, the level of TCF1+CD39+ LN CD8 T cells is associated with lower frequency of CD4 T cells harboring intact SIV-DNA (IPDA). Investigations into potential mechanisms contributing to viral control revealed that TCF1+CD39+ cells expressed elevated levels of CXCR5 compared to traditional effector cells, and expression of CXCR5 within TCF1+CD39+ cells was associated with lower plasma viremia. Imaging analysis confirmed increased presence of TCF1+Tox+ CD8 T-cells within B cell follicles compared to TCF1-Tox+ and TCF1+Tox- cells.
Conclusions:
Overall, these data are consistent with a unique precursor effector CD8 T-cell population that expands in LN after SIV infection, have a better ability to access the LN BCF, and is associated with increased viral control and reduced disease progression.