-Author name in bold denotes the presenting author
-Asterisk * with author name denotes a Non-ASH member
Clinically Relevant Abstract denotes an abstract that is clinically relevant.

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717 Progenitor Sub-Populations in Treatment Resistant T-ALLClinically Relevant Abstract

Program: Oral and Poster Abstracts
Type: Oral
Session: 618. Acute Lymphoblastic Leukemias: Biomarkers, Molecular Markers and Minimal Residual Disease in Diagnosis and Prognosis: High-risk T-ALL and Prognostic Biomarkers
Hematology Disease Topics & Pathways:
Research, Fundamental Science, Lymphoid Leukemias, ALL, Translational Research, Diseases, Lymphoid Malignancies, Minimal Residual Disease
Monday, December 12, 2022: 11:00 AM

Jason Xu, PhD1, Changya Chen, Ph.D.2*, Tiffaney L. Vincent3*, Petri Pölönen, PhD4, Abdelrahman Elsayed, PhD4*, Jianzhong Hu, PhD5*, Satoshi Yoshimura6*, Wenbao Yu, PhD7*, Chia-hui Chen7*, Elizabeth Li8*, Rawan Shraim, MSc9*, Marieke Lavaert, Ph.D10*, Haley Newman, MD3, Yang-yang Ding7*, Anusha Thadi11*, Kyung Jin Ahn, BS11*, Jacqueline Peng11*, Chujie Gong12*, Yusha Sun13*, Shovik Bandyopadhyay, MSTP Candidate14*, David Frank15*, Mignon L. Loh, MD16,17, Elizabeth A. Raetz, MD18, Zhiguo Chen19*, Brent L. Wood, MD PhD20, Meenakshi Devidas, PhD, MBA21, Kimberly P. Dunsmore, MD22*, Stuart S. Winter, MD23*, Gang Wu, PhD24*, Avinash Bhandoola, M.B., B.S., Ph.D.10*, Stanley B. Pounds, PhD25*, Stephen P. Hunger, MD26, Jun J. Yang, PhD5, Charles G. Mullighan, MBBS, MD27, David T. Teachey, MD28 and Kai Tan, PhD2,29

1Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
2Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
3Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA
4St. Jude Children's Research Hospital, Memphis, TN
5Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN
6Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
7Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA
8Yale School of Medicine, New Haven, CT
9Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
10National Institutes of Health, Bethesda, MD
11Children’s Hospital of Philadelphia, Philadelphia, PA
12University of Pennsylvania, Philadelphia, PA
13Perelman School of Medicine, Medical Scientist Training Program, Philadelphia, PA
14Graduate Group in Cell & Molecular Biology, University of Pennsylvania, Philadelphia, PA
15Division of Cardiology, Children’s Hospital of Philadelphia, Philadelphia, PA
16Division of Hematology, Oncology, BMT, and Cellular Therapies, Seattle Children's Hospital, Seattle, WA
17The Ben Town Center for Childhood Cancer Research, Seattle Children's Hospital, Seattle, WA
18Division of Pediatric Hematology and Oncology, Stephen D. Hassenfeld Children's Center for Cancer and Blood Disorders, NYU Langone Health, New York, NY
19Department of Biostatistics, University of Florida, Gainesville, FL
20Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA
21Department of Global Pediatric Medicine, St Jude Children's Research Hospital, Memphis, TN
22Division of Oncology, University of Virginia Children’s Hospital, Charlottesville, VA
23Children's Minnesota, Minneapolis, MN
24Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN
25Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
26Department of Pediatrics, Division of Oncology and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
27Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
28Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Rutledge, PA
29Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive lymphoid malignancy for which optimal therapeutic approaches for relapsed/refractory disease and biomarkers for upfront risk stratification are currently unknown. Comprehensive, large-cohort bulk-level profiling of T-ALL is currently underway with the promise to reveal novel drivers and associate genetics with treatment response. To synergize with these studies, we designed a single-cell (sc) genomics study powered to comprehensively characterize intra-tumoral arrest states in T-ALL.

Using integrated scRNA and scATAC-seq analysis on 40 T-ALL cases alongside a novel, single cell atlas of pediatric T-cell development, we identified and characterized a bone-marrow progenitor-like (BMP-like) tumor sub-population associated with resistance to conventional therapy across distinct immunophenotypic subtypes of T-ALL. We first compared 10 treatment-refractory ETP-ALL patients (End of Induction MRD > 20%) to 10 treatment sensitive ETP-ALL patients (EOI MRD negative), where we identified a strong and consistent enrichment of ETP-ALL blasts that were transcriptomically and epigenetically analogous to multipotent BMP. BMP-like blasts had higher surface protein expression of myeloid and stem cell markers, such as CD33, CD123, HLA-DR, and CD34, and lowered expression of T-lineage surface protein markers, such as sCD3, CD4, CD2, and CD10. The top differentially expressed (DE) genes for BMP-like blasts included stem cell markers (C1QTNF4, CD44, LGALS1, HOPX), myeloid-lineage (S100A4, SPINK2), and B-lineage markers (IGLL1, IGKC, IGHM). The top DE transcription factors (TFs) in BMP-like blasts included TFs associated with self-renewal (MEF2C, HOXA3/4/5/6/9/10/11, MEIS1, HHEX, SPI1) and recovery from genotoxic stress (BCL11A). Several of the genes involved in self renewal (MEF2C, HOXA9, FLI1), or T-cell developmental block (SPI1) also had increased motif accessibility. We integrated these signatures with large-cohort bulk-genomic results of 1300+ T-ALL patients treated in the Children’s Oncology Group (COG) AALL0434 clinical trial. The molecular signature of BMP-like blasts predicted poor outcome across multiple subtypes of T-ALL (ETP & Non-ETP) and were validated in two independent COG trials (AALL0434, full cohort sequenced; AALL1231, partially sequenced cohort) with corresponding bulk-RNAseq data (Panel A, ETP-ALL patient stratification). We also utilized single-cell derived transcriptional signatures in conjunction with bulk-sample-derived mutation calls to identify fusion drivers (eg, MLLT10, KMT2A, NUP98, NUP214) and gene mutations (eg, NOTCH1 WT, IL7R WT, ETV6 mut, and SAT1B mut) that are associated with the BMP-like state and poor outcome.

Computational analysis and in vitro experiments indicated that BMP-like tumors would be highly resistant to conventional ALL-directed cytotoxics. To address the pressing need for targeted therapy in chemo-refractory T-ALL, we performed multi-database drug screening against the BMP-like signature derived from our single cell data, nominating a number of surface markers (CD44, ITGA4, LGALS1) and intracellular targets (BCL-2, MCL-1, BTK, NFKB) for experimental follow-up in patient derived xenografts (PDX) which we generated and characterized in our single cell study. Notably, experimental studies of PDX expanded blasts indicated consistent and selective vulnerability of BMP-like blasts to apoptosis-inducing agents (Panel B). Other agents with potent activity in this population included TEC-kinase inhibitors and proteasome inhibitors. Follow-up in-vivo studies in PDX are underway with the promise to bridge these therapies to the clinic.

Our work comprehensively defines the developmental arrest states of T-ALL in reference to human early T-cell development. By doing so, we reveal a previously unappreciated sub-population level overlap between patients with distinct subtypes of T-ALL and identify one common BMP-like sub-population that associates with poor response to current therapy. As T-ALL thus far is solely defined by bulk-sample immuno-phenotype, we propose the prospective identification of BMP-like sub-populations and use of non-conventional cytotoxic agents for upfront-risk-stratification and targeted therapy to be realized in high-risk T-ALL.

JX & CC, as well as DTT & KT, contributed equally to the work.

Disclosures: Raetz: Pfizer: Research Funding; BMS: Other: Data and Safety Monitoring Board. Hunger: Amgen: Current equity holder in private company, Honoraria; Jazz: Honoraria; Servier: Honoraria. Yang: Takeda: Research Funding. Teachey: BEAM Therapeutics: Consultancy; Sobi: Consultancy.

*signifies non-member of ASH