Tumour-specific CD8 T cells in solid tumours are dysfunctional, allowing tumours to progress. The epigenetic regulation of T cell dysfunction and therapeutic reprogrammability (for example, to immune checkpoint blockade) is not well understood. Here we show that T cells in mouse tumours differentiate through two discrete chromatin states: a plastic dysfunctional state from which T cells can be rescued, and a fixed dysfunctional state in which the cells are resistant to reprogramming. We identified surface markers associated with each chromatin state that distinguished reprogrammable from non-reprogrammable PD1hi dysfunctional T cells within heterogeneous T cell populations from tumours in mice; these surface markers were also expressed on human PD1hi tumour-infiltrating CD8 T cells. Our study has important implications for cancer immunotherapy as we define key transcription factors and epigenetic programs underlying T cell dysfunction and surface markers that predict therapeutic reprogrammability.

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The cytoplasm is compartmentalized into different translation environments. mRNAs use their 3′UTRs to localize to distinct cytoplasmic compartments, including TIS granules (TGs). Many transcription factors, including MYC, are translated in TGs. It was shown that translation of proteins in TGs enables the formation of protein complexes that cannot be established when these proteins are translated in the cytosol, but the mechanism is poorly understood. Here we show that MYC protein complexes that involve binding to the intrinsically disordered region (IDR) of MYC are only formed when MYC is translated in TGs. TG-dependent protein complexes require TG-enriched mRNAs for assembly. These mRNAs bind to a new and widespread RNA-binding domain in neutral or negatively charged IDRs in several transcription factors, including MYC. RNA-IDR interaction changes the conformational ensemble of the IDR, enabling the formation of MYC protein complexes that act in the nucleus and control functions that cannot be accomplished by cytosolically-translated MYC. We propose that certain mRNAs have IDR chaperone activity as they control IDR conformations. In addition to post-translational modifications, we found a novel mode of protein activity regulation. Since RNA-IDR interactions are prevalent, we suggest that mRNA-dependent control of protein functional states is widespread.

The cytoplasm is highly compartmentalized, but the extent of subcytoplasmic mRNA localization in non-polarized cells is largely unknown. We used fluorescent particle sorting to determine mRNA enrichment in three unenclosed cytoplasmic compartments: the canonical rough endoplasmic reticulum (CRER), the TIS granule-associated rough endoplasmic reticulum (TGER), and the cytosol. Focusing our analysis on non-membrane protein-encoding mRNAs, we observed that 53% have a unique subcytoplasmic localization pattern which is determined by a combinatorial code of 3′UTR-bound RNA-binding proteins. Compartment-enriched mRNAs differed in production and degradation rates and the expression levels and functional classes of their encoded proteins. The TGER domain enriches mRNAs that encode transcription factors, the CRER highly expressed proteins, and the cytosol unstable mRNAs. The rough ER environment is stimulatory as redirecting cytosolic mRNAs to the ER increases their protein expression by two-fold, independently of the bound RNA-binding proteins. We show that local translation environments functionally compartmentalize the cytoplasm.