Metabolic Programs of T Cell Tissue Residency Empower Tumor Immunity [RNA-seq II]

Tissue-resident memory CD8 T cells (TRM) offer fast, robust, and long-term protection at sites of re-infection1. Tumor-infiltrating lymphocytes (TIL) with characteristics of TRM maintain enhanced effector functions, predict responses to immunotherapy, and accompany better prognoses2,3. Thus, an improved understanding of the metabolic strategies that enable tissue residency could inform new approaches to empower T cell responses in tissues and solid tumors. To systematically define the basis for the metabolic reprogramming supporting TRM differentiation, survival, and function, we leveraged in vivo functional genomics, untargeted metabolomics, and transcriptomics of virus-specific memory CD8 T cell populations. We found that memory CD8 T cells deployed a range of adaptations to tissue residency, including a marked reliance on non-steroidal products of the mevalonate/cholesterol pathway, such as Coenzyme Q (CoQ), driven by increased activity of the transcription factor Srebp2. This metabolic adaptation was most pronounced in the small intestine (SI), where TRM interface with dietary cholesterol and maintain a heightened state of activation4, and was shared by functional TIL in diverse tumor types in mice and humans. Enforcing CoQ synthesis through Fdft1 deletion or Pdss2 overexpression promoted mitochondrial respiration, memory formation upon viral infection, and enhanced antitumor immunity. In sum, through a systematic exploration of TRM metabolism, we reveal how these programs can be leveraged to empower CD8 T cell memory formation in the context of acute infections and enhance antitumor immunity. Mouse previously infected (> 30 days) with LCMV and transferred with P14 CD8 T cells were fed a low or high cholesterol diet for 7 days. 3 replicates per condition. Each replicate contains 1000 cells re-sorted from a first sort of 5000 cells pooled from at least 2 different mice. After preparation of single-cell suspensions, 5 x 103 iv- P14 CD8 T cells were sorted from the IEL, into PBS + 5% BSA + 2% FBS + 0.5 M EDTA. 1 x 103 cells were then resorted into 5 ul of 1x TCL lysis buffer + 1% 2-mercaptoethanol. Library preparation for ULI RNA-seq was performed as described online at Immgen (“ImmGenULI_RNAseq_methods.pdf”).