Identifying Relapse Predictors and Therapeutic Vulnerabilities in Ph+ and Ph-like Acute Lymphoblastic Leukemia

Abstract Our overarching goal is to systematically uncover the genomic heterogeneity of pediatric and adolescent/young adult (AYA) Philadelphia chromosome-positive (Ph+) and ABL-class Ph-like acute lymphoblastic leukemia (ALL) to 1) identify genetic predictors of relapse and 2) therapeutic vulnerabilities. While the long-term survival rate of childhood ALL exceeds 90% with contemporary chemotherapy, the outcome of pediatric and AYA patients with BCR::ABL1-driven acute leukemia remains poor, even with the addition of tyrosine kinase inhibitors. BCR::ABL1 constitutes the canonical oncogenic driver of two hematologic malignancies: chronic myeloid leukemia (CML) and Ph+ALL. Since 2012, a myriad of ABL-class fusions involving ABL1, ABL2, CSF1R, KIT, LYN, PDGFRA and PDGFRB was discovered. Patients with ABL-class Ph-like ALL also have poor outcomes, with 5-year event free survival (EFS) <60%. In addition, a recently recognized Ph+ ALL subset with discordant end-of-induction minimal residual disease (MRD) response, characterized by the absence of IgH/TCR clones with persistent BCR::ABL1 fusion transcript in non-leukemic cell subpopulations, suggests that the BCR::ABL1 fusion arises from a multipotent hematopoietic progenitor cell reminiscent of CML. Consequently, these patients are designated as CML-like and fare poorly with intensive chemotherapy and TKI. There is thus a critical unmet need to improve outcomes for patients diagnosed with these aggressive leukemias. Our central hypothesis is that genetic alterations mediating therapeutic resistance leading to clinical relapse can be identified via a comprehensive multi-omics profiling of a large cohort of patients uniformly treated on a clinical trial, and these resistance drivers will harbor novel therapeutic targets. We will leverage the unique resource of patient samples and clinical data collected on Children's Oncology Group (COG) AALL1631, the largest prospective international study for pediatric/AYA Ph+ and ABL-class Ph-like ALL to date. Using comprehensive genomic data (funded from other sources) generated from paired diagnostic/germline samples collected on AALL1631, we will first identify predictors of relapse in Ph+ and ABL-class Ph-like ALL and further determine the therapeutic value of major secondary events via cell proliferation and pharmacologic inhibitor screens in engineered cell line models of Ph+ and ABL-class Ph-like ALL harboring these secondary events. We will test the efficacy of the most compelling candidate compounds in patient-derived xenograft (PDX) models established from samples collected on AALL1631. Second, we will decipher the molecular and cellular heterogeneity of CML-like versus typical Ph+ALL via single-cell genomics and functional assays. We hypothesize that CML-like patients exhibit distinct transcriptomic signatures, mutational profiles, and cellular heterogeneity compared to typical Ph+ ALL patients that may account for their differential treatment responses, and we will investigate CML-like phenotypes by performing single-cell RNA-sequencing to determine distinct transcriptomic and expression profiles that will provide novel opportunities for diagnostic and therapeutic interventions.