Identification of unique memory T cell populations associated with protection against Chlamydia trachomatis reinfection in the peripheral blood of highly exposed women

Abstract Chlamydia trachomatis (Ct) is an obligate intracellular bacterium that annually infects 100 million people globally and leaves 1 million women infertile, making vaccine development a priority. While repeated infections are common, they can elicit partial protective immunity. To better determine protective T cell responses elicited by natural infection to guide rational vaccine design, we performed single-cell RNA sequencing (scRNA-seq) on sorted CD3+ T cells from PBMC samples of two uninfected and four infected women, two who remained uninfected (F/U−; n=2) and two who became reinfected (F/U+; n=2) when tested at intervals over a year. We detected enrichment of two CD4 and two CD8 subpopulations in the F/U− subgroup, compared to F/U+ or uninfected controls. The CD4 T cell populations were characterized by differential expression of genes involved in cell activation, tissue homing, memory, and Th1/17 differentiation (LMNA, S100A11/10/4, ANXA1/2, LGALS1/3, TIMP1, CD29, CD161, IL7R), and the CD8 T cell populations differentially expressed markers of cell growth, activation, cytokine signaling, and cytotoxicity (CCL4/5, GRZMA/K, NKG7, CST7, HLA-DRA/B1, CD74). Both CD8 subsets expressed fewer markers of terminal differentiation, suggestive of memory and/or transitional effector phenotypes. These pilot data demonstrate that, even though Ct is mucosally restricted, differential T cell responses are detectable in peripheral blood by scRNA-seq and can improve understanding of T cell heterogeneity, activation, differentiation, and functional responses that promote protection.