Deciphering the role of non-coding sequence variants predisposing to pediatric B-ALL

Most trait- and disease-associated sequence variants map at non-coding regions, modulating transcription factor (TF) binding and transcription of the associated gene. Multiple genome-wide association studies linked several non-coding germline variants to increased risk of pediatric B-ALL, particularly at the IKZF1 locus. However, the consequence of intergenic variants at IKZF1 and the mechanism of disease predisposition remain largely unknown. Here, we established IKZF1-GFP reporter NALM6 and REH cell lines and a multi-scale screening approach to map the regulatory network of IKZF1, identify top regulators, and elucidate the effect of disease-associated variants at TF binding motifs. To uncover putative cis-regulatory elements, we applied a CRISPRi screen tiling ~400kb at the IKZF1 locus, including its promoter, 3’ UTR, proximal and distal enhancers. In this screen, we identified two distal enhancers as well as a cis-regulatory sequence located at the IKZF1 3’ UTR. In parallel, to identify trans-regulators of IKZF1, we performed a KO screen, targeting 635 TFs expressed in the hematopoietic lineage, and identified a shortlist of high-confidence IKZF1 regulators.

Publication History

Article published online:
09 May 2025