Genetic Mechanisms of Transcriptional Regulation in Childhood Acute Lymphoblastic Leukemia

Introduction. Advances in genomic profiling and sequencing studies have identified germline and somatic variations that are associated with childhood ALL, improving our understanding of the genetic basis of childhood acute lymphoblastic leukemia (ALL). Recent genome-wide association studies (GWAS) have identified germline genetic variations of ARID5B and, more recently, IGF2BP1 that are associated with susceptibility to ALL. Genome-wide sequencing studies also discovered a new ALL subtype characterized of ZNF384-mediated chromosomal translocations, providing new insights into genetic heterogeneity in childhood ALL. However, the underlying mechanism by which these genetic variants contribute to the transcriptional regulatory circuitries of ALL is still poorly understood. We tested these hypotheses: 1) A low ARID5B expression will increase the relapse risk of ALL, 2) Genetic variants of ARID5B will affect its expression and thus influence susceptibility to childhood ALL, 3) IGF2BP1 is transcriptionally suppressed by ETV6, 4) ZNF384-mediated fusion genes transcriptionally upregulate FLT3 expression as being a therapeutic target. Specific aims in this study include: 1) identifying the causal variant of ARID5B, 2) identifying molecular mechanism underlying drug resistance, 3) identifying molecular mechanism of transcriptional regulation of IGF2BP1 by ETV6, and 4) identifying molecular mechanism of transcriptional regulation of FLT3 by EP300-ZNF384 fusion protein. Methods. We analyzed association of ARID5B expression in primary human ALL blasts with different molecular subtypes and treatment outcomes. Subsequent mechanistic studies were performed in ALL cell lines by manipulating ARID5B expression isogenically, in which we evaluated drug sensitivity, metabolism, and molecular signaling events. We performed ARID5B targeted sequencing in 5,008 children with ALL and conducted high throughput CRISPR/dCas9 screening in an engineered ARID5B mCherry knock-in cell line. Effects of genetic polymorphism on binding affinity of transcription factor and chromatin accessibility were subsequently assessed. We applied CRISPR/dCas9 to investigate transcriptional regulation of IGF2BP1 by ETV6 in ALL cell lines. We stably knocked down EP300-ZNF384 fusion gene by CRISPR editing in ALL cell line, in which we analyzed FLT3 expression and drug sensitivity. Results. ARID5B expression varied substantially by ALL subtype, with the highest level being observed in hyperdiploid ALL. Lower ARID5B expression at diagnosis was associated with the risk of ALL relapse, and further reduction was noted at ALL relapse. In isogenic ALL cell models in vitro, ARID5B knockdown led to resistance specific to antimetabolite drugs. ARID5B downregulation significantly inhibited ALL cell proliferation and caused partial cell-cycle arrest partially through upregulating expression the cell-cycle checkpoint regulator p21 (encoded by CDKN1A). Using targeted sequencing in germline DNA of 5,008 children with ALL and high throughput CRISPR/dCas9 screening in an engineered ARID5B mCherry knock-in cell line, we nominated ALL risk variant (rs7090445, P = 1.82 × 10-10) as the causal variant. And its polymorphisms disrupted binding of transcription factor MEF2C and local chromosome accessibility as confirmed by ChIP-Sanger-seq and ATAC-seq. Although it was previously reported that IGF2BP1 expression was significantly higher in ETV6-RUNX1 ALL as well as other cancers, the underlying transcriptional regulatory mechanism remains elusive. In ALL cell models, we identified a cis-regulatory element (CRE) blocking of which by dCas9-KRAB strongly influenced transcription of IGF2BP1. Moreover, we presented a CRISPR-based approach to comprehensively investigate the transcriptional regulatory mechanism of IGF2BP1 by identifying its CREs and upstream transcriptional regulators. In tissue-specific overexpression mouse models, we demonstrated that role of Igf2bp1 in B-cell development was stage-specific. In a novel ALL subtype characterized of ZNF384-mediated rearrangements, for the first time we reported overexpression of FLT3 in this new ALL subtype, providing a novel therapeutic target for ALL patient with high expression of FLT3. Furthermore, we defined EP300-ZNF384 fusion protein as a transcriptional activator of FLT3 gene with direct binding at its 5’UTRand knocking down this fusion gene led to downregulation of FLT3 expression as well as decreased sensitivity to FLT3 inhibitor in vitro. Conclusions. Our studies have demonstrated that a causal variant of ARID5B affected its transcription in-cis and that a low expression of ARID5B increased ALL relapse risk. As a downstream effector of ETV6, IGF2BP1 expression influenced B-cell development in vivo in a stage-specific manner. Moreover, expression of FLT3 was transcriptionally upregulated by ZNF384-mediated fusion genes. This study sheds light on the underlying mechanism by which genetic variations altered transcriptional programs in childhood ALL and refined our understanding of the genetic basis of childhood ALL, providing new molecular targets which can be harnessed for development of new therapies for patients with ALL.