Functional, Antigen-Specific Stem Cell Memory (T_SCM) CD4⁺ T Cells Are Induced by Human <i>Mycobacterium tuberculosis</i> Infection

Background Maintenance of long-lasting immunity is thought to depend on stem cell memory T cells (T SCM ), which have superior self-renewing capacity, longevity and proliferative potential compared with central memory (T CM ) or effector (T EFF ) T cells. Our knowledge of T SCM derives primarily from studies of virus-specific CD8 + T SCM . We aimed to determine if infection with Mycobacterium tuberculosis ( M. tb ), the etiological agent of tuberculosis, generates antigen-specific CD4 + T SCM and to characterize their functional ontology. Methods We studied T cell responses to natural M. tb infection in a longitudinal adolescent cohort of recent QuantiFERON-TB Gold (QFT) converters and three cross-sectional QFT + adult cohorts; and to bacillus Calmette-Guerin (BCG) vaccination in infants. M. tb and/or BCG-specific CD4 T cells were detected by flow cytometry using major histocompatibility complex class II tetramers bearing Ag85, CFP-10, or ESAT-6 peptides, or by intracellular cytokine staining. Transcriptomic analyses of M. tb -specific tetramer + CD4 + T SCM (CD45RA + CCR7 + CD27 + ) were performed by microfluidic qRT-PCR, and functional and phenotypic characteristics were confirmed by measuring expression of chemokine receptors, cytotoxic molecules and cytokines using flow cytometry. Results M. tb -specific T SCM were not detected in QFT-negative persons. After QFT conversion frequencies of T SCM increased to measurable levels and remained detectable thereafter, suggesting that primary M. tb infection induces T SCM cells. Gene expression (GE) profiling of tetramer + T SCM showed that these cells were distinct from bulk CD4 + naïve T cells (T N ) and shared features of bulk T SCM and M. tb -specific tetramer + T CM and T EFF cells. These T SCM were predominantly CD95 + and CXCR3 + , markers typical of CD8 + T SCM . Tetramer + T SCM expressed significantly higher protein levels of CCR5, CCR6, CXCR3, granzyme A, granzyme K, and granulysin than bulk T N and T SCM cells. M. tb -specific T SCM were also functional, producing IL-2, IFN-γ, and TNF-α upon antigen stimulation, and their frequencies correlated positively with long-term BCG-specific CD4 + T cell proliferative potential after infant vaccination. Conclusion Human infection with M. tb induced distinct, antigen-specific CD4 + T SCM cells endowed with effector functions, including expression of cytotoxic molecules and Th1 cytokines, and displayed chemokine receptor profiles consistent with memory Th1/17 cells. Induction of CD4 + T SCM should be considered for vaccination approaches that aim to generate long-lived memory T cells against M. tb .