Identification and targeting of treatment resistant progenitor populations in T-cell Acute Lymphoblastic Leukemia
Authors: Tan Kai , Xu Jason , Chen Changya , Vincent Tiffaney , Pölönen Petri , Hu Jianzhong , Yoshimura Satoshi , Yu Wenbao , Sussman Jonathan , Chen Chia-hui , Li Elizabeth , Diorio Caroline , Shraim Rawan , Newman Haley , Uppuluri Lahari , Li Alexander , Chen Gregory , Bandyopadhyay Shovik , Wu David , Ding Yang-yang , Xu Jessica , Lim Tristan , Hsu Miles , Thadi Anusha , Ahn Kyung Jin , Wu Chi-Yun , Peng Jacqueline , Sun Yusha , Wang Alice , Mehta Rushabh , Frank David , Meyer Lauren , Loh Mignon , Raetz Elizabeth , Chen Zhiguo , Wood Brent , Devidas Meenakshi , Dunsmore Kimberly , Winter Stuart , Chang Ti-Cheng , Wu Gang , Pounds Stanley , Zhang Nancy , Carroll William , Hunger Stephen , Bernt Kathrin , Yang Jun , Mullighan Charles , Teachey David 
Published: October 2023

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.