TFAP2C and HNRNPK control cellular bioenergetic metabolism and prion propagation [RNA-seq]

Heterogenous Nuclear Ribonucleoprotein K (HNRNPK) is a limiting factor for prion propagation. However, little is known about the function of hnRNP_K other that it is essential to cell survival. Here, we performed a synthetic-viability CRISPR ablation screen to identify functional epistatic interactors of HNRNPK. We found that deletion of Transcription Factor AP-2γ (TFAP2C) mitigated the survival of hnRNP_K-depleted LN-229 and U-251MG cells, whereas its overexpression hypersensitized cells to the loss of hnRNP_K. HNRNPK ablation induced downregulation of genes related to lipid and glucose metabolism, decreased cellular ATP and enhanced catabolism through modulation of the mTOR and AMPK pathways. Conversely, TFAP2C overexpression promoted mTOR anabolic activity, and its deletion countered the energetic crisis resulting from HNRNPK ablation. We then found that TFAP2C overexpression reduced prion propagation in wild-type cells and neutralized prion accumulation in HNRNPK-suppressed cells. We conclude that TFAP2C and HNRNPK are genetic interactors controlling cell metabolism, bioenergy and prion propagation. To investigate the molecular basis of the genetic epistatic interaction between HNRNPK and TFAP2C, we performed RNA-seq analysis on LN-229 cells depleted of hnRNP K, Tfap2c, or both proteins. Non-targeting controls (NT and NT3) were used in combination with HNRNPK- and TFAP2C-targeting CRISPR knockout guides. Three biological replicates were run for each condition, but replicate 2 for the NT3/NT, NT/HNRNPK, and TFAP2C/NT conditions was excluded from the analysis due to low RNA quality