Identification of a Lipid Oxygen Radical Defense pathway and its epigenetic control [RNA-Seq]

Membrane phospholipids are vulnerable to oxidative radicals, and uncontrolled lipid peroxidation affects cell viability. Cells have evolved quality control and defense mechanisms, of which the genetic regulation is not fully understood. Here, we identify what we have coined the Lipid Oxygen Radical Defense (LORD) pathway. It is epigenetically repressed by a complex comprising the KRAB-zinc finger protein ZNF354A, the scaffold protein KAP1/TRIM28, the histone methyltransferase SETDB1, and the transcriptional activator ATF2. Upon lipid peroxide accumulation, p38- and JNK-dependent phosphorylation of ATF2, KAP1/TRIM28, and ZNF354A leads to disassembly of the repressive complex, releasing ZNF354A from specific DNA loci and activating a network of protective genes, including NRF2 targets. The pathway affects the cellular sensitivity to oxidative stress and ferroptosis, revealing a previously uncharacterized layer of epigenetic control in lipid quality control and damage repair. This positions the LORD pathway as a promising therapeutic target for diseases linked to chronic inflammation, neurodegeneration and cancer. Overall design: U2OS human osteosarcoma cells were transfected with control siRNA (siCtrl) or siRNA targeting ZNF354A (siZNF354A). Four independent biological replicates were prepared per condition. Total RNA was extracted 72 hours after transfection for mRNA sequencing to identify transcriptional changes upon ZNF354A depletion. For human ZNF354A, 3 different siRNA in 3'-UTR were tested and validated, from Qiagen: ZNF354A (TACATCCTTGAGAGAGATGTA), from Santa Cruz (sc-91974), ZNF354A (GTCACGTGATCATCAGAAA), and from Origene , ZNF354A (GAGGTTTATCCATGGAATTAAATACCT). A control siRNA, a sequence targeting the viral glycoprotein VSV-G (5'-ATTGAACAAACGAAACAAGGA-3') was used.