Refractoriness to initial
chemotherapy and relapse after remission are the main obstacles to cure in T-cell
Acute Lymphoblastic Leukemia (
T-ALL).
Biomarker guided risk stratification and targeted
therapy have the potential to improve outcomes in high-risk
T-ALL; however, cellular and genetic factors contributing to treatment resistance remain unknown. Previous bulk genomic studies in
T-ALL have implicated
tumor heterogeneity as an unexplored mechanism for treatment failure. To link
tumor subpopulations with clinical outcome, we created an atlas of healthy pediatric hematopoiesis and applied single-cell multiomic (CITE-seq/snATAC-seq) analysis to a cohort of 40 cases of
T-ALL treated on the Children's Oncology Group AALL0434 clinical trial. The cohort was carefully selected to capture the immunophenotypic diversity of
T-ALL, with early T-cell precursor (ETP) and Near/Non-ETP subtypes represented, as well as enriched with both relapsed and treatment refractory cases. Integrated analyses of
T-ALL blasts and normal T-cell precursors identified a bone-marrow progenitor-like (BMP-like)
leukemia sub-population associated with treatment failure and poor overall survival. The single-cell-derived molecular signature of BMP-like blasts predicted poor outcome across multiple subtypes of
T-ALL within two independent patient cohorts using bulk
RNA-sequencing data from over 1300 patients. We defined the mutational landscape of BMP-like
T-ALL, finding that NOTCH1 mutations additively drive
T-ALL blasts away from the BMP-like state. We transcriptionally matched BMP-like blasts to early thymic seeding progenitors that have low NR3C1 expression and high stem cell gene expression, corresponding to a
corticosteroid and conventional cytotoxic resistant phenotype we observed in ex vivo
drug screening. To identify novel targets for BMP-like blasts, we performed in silico and in vitro
drug screening against the BMP-like signature and prioritized BMP-like overexpressed cell-surface (CD44, ITGA4,
LGALS1) and intracellular
proteins (BCL-2, MCL-1, BTK, NF-κB) as candidates for precision targeted
therapy. We established patient derived xenograft models of BMP-high and BMP-low
leukemias, which revealed vulnerability of BMP-like blasts to apoptosis-inducing agents,
TEC-kinase inhibitors, and
proteasome inhibitors. Our study establishes the first multi-omic signatures for rapid risk-stratification and targeted treatment of high-risk
T-ALL.