CHAF1A Blocks Neuronal Differentiation and Promotes Neuroblastoma Oncogenesis via Metabolic Reprogramming

Neuroblastoma (NB) arises from neural crest cells (NCCs) secondary to a block in differentiation. Retinoic acid (RA) differentiation therapy has limited therapeutic efficacy, and the mechanisms preventing terminal differentiation remain elusive. We found that the chromatin modifier CHAF1A restricts neuronal differentiation and promotes NB oncogenesis. CHAF1A blocks NC differentiation into mature neurons in both human NCCs and zebrafish models. CHAF1A gain-of-function promotes cell malignancy, blocks RA-induced differentiation, and is sufficient to induce NB tumor formation. Mechanistically, CHAF1A blocks NB differentiation by repressing gene expression programs promoting neuronal development and differentiation, and rewiring polyamine metabolism. Targeting polyamine synthesis restores NB sensitivity to RA therapy. Our results demonstrate that CHAF1A critically contributes to NB oncogenesis by blocking neuronal differentiation and reprogramming cell metabolism. To address the mechanisms through which CHAF1A promotes oncogenesis, we carried out gene expression profiling of SHEP cells upon conditional CHAF1A overexpression over time (0, 24, 72, and 96 h). Total RNA was extracted and processed by the random primed RT-IVT-RT method using the GeneChip WT cDNA Synthesis and Amplification Kit (Affymetrix, Santa Clara CA). cDNA was synthesized from 200 ng of total RNA by reverse transcription using T7 promoter-(N6) oligonucleotides as primers. cDNA was then fragmented and hybridized for 17 h at 45oC to GeneChip® Human Gene 2.0 ST Arrays (Affymetrix). Raw microarray CEL files were processed in R (3.4.1) using the biocLite Affy package (Gautier et al., 2004) function rma and the hugene.2.0st annotation.