C/EBPα confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia [ATAC-seq]

While transcription factor C/AAT-enhancer binding protein α (C/EBPα) is critical for normal and leukemic differentiation, its role on cell and metabolic homeostasis is largely unknown in cancer. Here, multi-omics analyses uncovered a coordinated activation of C/EBPα and Fms-like tyrosine kinase 3 (FLT3) that increased lipid anabolism in vivo and in patients with FLT3-mutant acute myeloid leukemia (AML). Mechanistically, C/EBPα regulated FASN-SCD axis to promote fatty acid (FA) biosynthesis and desaturation. We further demonstrated that FLT3 or C/EBPα inactivation decreased mono-unsaturated FAs incorporation to membrane phospholipids through SCD downregulation. Consequently, SCD inhibition enhanced susceptibility to lipid redox stress, which was exploited by combining FLT3 and glutathione peroxidase 4 inhibition to trigger lipid oxidative stress, enhancing ferroptotic death of FLT3-mutant AML cells. Altogether, our study reveals a C/EBPα function in lipid homeostasis and adaptation to redox stress, and a previously unreported vulnerability of FLT3-mutant AML to ferroptosis with promising therapeutic application. shCTL and shC/EBPα MOLM14 cells (in biological duplicates) were FACS-sorted, and ATAC-seq was performed as previously described (94) with minor modifications. Briefly, 50 000 cells were lysed in ice-cold lysis buffer and the transposition reaction was performed using the Tn5 transposase at 37°C for 30 min. DNA was purified using the QIAGEN MinElute kit (QIAGEN). The libraries were prepared using Tagment DNA Enzyme and Buffer kits (Illumina), NEBNext High-Fidelity 2X PCR Master Mix (NEB, catalog # M0541S) with custom sequencing primers (95–98). The libraries were purified twice using AMPure XP beads (Beckman) following a double-sided protocol to remove primer dimers and large fragments. Libraries quality was assessed using the NGS High Sensitivity Kit on the Fragment Analyzer (Agilent Technologies, Santa Clara, USA). Only high-quality libraries were subsequently equimolarly pooled and sequencing was performed at the Pôle Technologique du CRCT – Plateau de Génomique et Transcriptomique (Inserm-UMR1037, Toulouse, France). The pool of libraries was quantified by qPCR using the KAPA Library Quantification Kit (Roche, Basel, Switzerland) to obtain an accurate quantification. Sequencing was then performed on one flowcell of the Illumina NextSeq 550 instrument (Illumina, San Diego, USA), using the NextSeq 500/550 High Output Kit v2.5 (150 Cycles), and a paired-end 2 x 75 pb strategy. A minimum of 2x80 million raw reads were produced per sample.