MicroRNA-29a enhances and preserves stem-like CD8 T cell differentiation by regulating master epigenetic circuits of exhaustion.

Abstract

CD8 T cells mediate protective immune responses. However, persisting antigens such as chronic viruses or tumors redirect CD8 T cell differentiation to a sub-optimal, epigenetically defined state called exhaustion. Exhausted T cells (TEX) lose their ability to persist long-term and to initiate functional memory responses. Checkpoint inhibitor blockade temporarily restores effector functions, but immune reinvigoration is not long-lasting, due to the epigenetic stability of TEX. Therefore, epigenetic reprogramming of TEX leading to durable T cell responses is essential to improve disease control. Here, we demonstrate that a single microRNA (miR), miR-29a, epigenetically re-directs TEX differentiation and preserves TEX into a stem-like state, leading to long-term persisting progenitor TEX. MiR-29a rewires epigenetic maintenance programs, including downregulation of key exhaustion-associated regulators (Dnmt1, Dnmt3a, and Dnmt3b), alongside increased expression of progenitor- and stemness-associated genes such as Tcf7 and Il7r. These reprogrammed CD8 T cells are more sensitive to PD-L1 checkpoint blockade. Ectopic expression of miR-29a combined with aPD-L1 treatments enhances effector responses, while preserving T cell stemness. Together, our findings suggest that miR-29a can be leveraged to overcome current barriers to immune checkpoint blockade. HighlightsO_LIMiR-29a rewires key exhaustion-associated epigenetic maintenance programs, while enhancing stemness-associated transcriptional circuits. C_LIO_LIMiR-29a drives extensive remodeling of accessible chromatin in TEX. C_LIO_LIMiR-29a preserves newly generated progenitor TEX in a durable, epigenetically defined stem-like state with increased effector function. C_LIO_LIMiR-29a synergizes with aPD-L1; while miR-29a preserves progenitor TEX state, addition of aPD-L1 enhances the cytotoxic potential of these progenitor TEX cells. C_LI