A functional single cell metabolic survey identifies Elovl1 as a target to enhance CD8+ T cell fitness in solid tumors [CROPseq]
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 aPD-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 aPD-1 response in melanoma patients. Altogether, Elovl1 targeting synergizes with aPD-1 to promote effective anti-tumor T cell responses Overall design: OT-I T cells transduced with a metabolic CRISPR library were sorted from the primary tumor of ova expressing Pancreatic cancer (KPC_OVA) bearing mice. Sorting via Flow cytometry (FACS), was based on CD90.1 expression (CD90.1 being the reporter gene of the library vector). Sorted cells underwent scRNA sequencing.