Amino acid stress response genes promote L-asparaginase resistance in pediatric acute lymphoblastic leukemia [ChIP-seq]

Understanding the genomic and epigenetic mechanisms of drug resistance in pediatric acute lymphoblastic leukemia (ALL) is critical for further improving treatment. The role of transcriptomic response in conferring resistance to l-asparaginase (LASP) is poorly understood, beyond asparagine synthetase (ASNS). We defined reproducible LASP response genes in LASP resistant and sensitive ALL cells lines as well as primary leukemia samples from newly diagnosed patients. Defining ATF4 target genes in ALL cell lines using ChIP-seq revealed 25% of genes that changed expression after LASP treatment were direct targets of the ATF4 transcription factor. SLC7A11 was found to be a response gene in cell lines and patient samples as well as a direct target of ATF4. SLC7A11 was also one of only 2.4% of response genes with basal level gene expression that also correlated with LASP ex vivo resistance in primary leukemia cells. Experiments using chemical inhibition of SLC7A11 with sulfasalazine, gene overexpression, and partial gene knockout recapitulated LASP resistance or sensitivity in ALL cell lines. These findings show the importance of assessing changes in gene expression following treatment with antileukemic agent for their association with drug resistance and highlight that many response genes may not differ in their basal expression in drug resistant leukemia cells. Overall design: ATF4 ChIP-seq performed in Nalm6 cells with or without L-asparaginase treatment. Cells grown in standard culture conditions were treated with L-asparaginase (1IU/ml) for 2 hrs. Twenty million cells were cross-linked for each replicate and 5ug of ATF4 antibody were used for IP. Three independent experiments were conducted for each condition