A functional single cell metabolic survey identifies Elovl1 as a target to enhance CD8+ T cell fitness in solid tumors. [in vivo]

Rewiring T cell metabolism can improve intratumoral infiltration and function. By performing a CRISPR/Cas9 metabolic survey in CD8+ T cells, we identified 83 targets enriched at the primary and/or metastatic niche in the context of pancreatic cancer. We applied single-cell RNA sequencing to disclose transcriptome changes associated with each metabolic perturbation. This revealed Elongation of Very-Long-chain fatty acids protein 1 (Elovl1) as a metabolic target to sustain proliferation and both effector and memory functions in CD8+ T cells. Accordingly, Elovl1 inactivation in adoptively transferred T cells combined with αPD-1 showed therapeutic efficacy in resistant pancreatic and melanoma tumors. Loss of Elovl1 in T cells rewired lipid metabolism and changed the plasma membrane composition mainly through SREBP2 activation, leading to higher cholesterol content and stronger TCR signaling. Finally, ELOVL1 in CD8+ T cells correlated with αPD-1 response in melanoma patients. Altogether, Elovl1 targeting synergizes with αPD-1 to promote effective anti-tumor T cell responses OT-I T cells transduced with a lentiviral vector containing a non-targeting guide or a sgRNA targeting Elovl1, were used to perferm adoptive cell transfer in mice bearing orthotopic KPC_OVA tumors. The day after aPD-1 therapy was initiated. 7 days from ACT, control and Elovl1 KO OT-I T cells were sorted from the primary tumor. Sorting via Flow cytometry (FACS), was based on CD90.1 expression (CD90.1 being the reporter gene of the lentiviral vector). Sorted cells underwent bulk RNA sequencing. Each replicate represent cells sorted from a different mouse. Sample 1 (pool of T46 and T47) and sample 2 (pool of T49 and T51) are pool of cells sorted from 2 tumors each. We sorted and isolated the cells separately and pooled the extracted RNA to increase the RNA quantity.