Dose-Dependent Metabolic and Proteomic Determinants of Chemotherapy Resistance in KMT2A-Rearranged Pediatric ALL
Presenter Status
Fellow
Abstract Type
Translational Research
Primary Mentor or Principal Investigator
John Perry, PhD
Presentation Type
Poster
Start Date
20-5-2026 12:00 PM
End Date
20-5-2026 1:00 PM
Abstract Text
Background:
KMT2A-rearranged pediatric acute lymphoblastic leukemia (ALL) is a biologically aggressive subtype characterized by early relapse and poor response to conventional chemotherapy¹. Leveraging publicly available pediatric leukemia multi-omic datasets—including the Pediatric Dependency Map (PedDep/DepMap)⁴, FORALL quantitative proteomics³, PRISM drug response screening, and the Pediatric Single-Cell Leukemia Atlas⁵—we systematically characterized metabolic, proteomic, and drug dependency signatures across KMT2A-rearranged leukemia models (RS4;11, SEM, KOPN-8) relative to non-KMT2A B-ALL cell lines (NALM-6, REH, 697) and healthy hematopoietic controls. Integrative analyses revealed KMT2A-specific metabolic reprogramming marked by enhanced oxidative phosphorylation, amino acid utilization, and redox homeostasis, consistent with transcriptionally regulated metabolic dependencies in B-lineage leukemias², alongside proteome-level adaptations involving mitochondrial function, protein homeostasis, and epigenetic regulation³. These molecular features were associated with reduced chemotherapy sensitivity and distinct drug dependency profiles, defining convergent mechanisms underlying treatment resistance in KMT2A-driven leukemia.
Objectives/Goal:
This work aims to identify clinically actionable vulnerabilities that may inform rational chemotherapy dose optimization, improve risk stratification, and support the development of targeted therapeutic strategies for children with KMT2A-rearranged ALL.
Methods/Design:
Using publicly available pediatric leukemia datasets, metabolomic signatures were curated from published mass spectrometry–based profiling studies of pediatric ALL and leukemia stem cell metabolism². Quantitative proteomic data were obtained from FORALL, enabling comparative protein abundance analyses across pediatric ALL subtypes³. Drug sensitivity and dependency profiles were extracted from the Pediatric Dependency Map (PedDep/DepMap) and PRISM repurposing datasets⁴. Comparative analyses focused on KMT2A-rearranged models (RS4;11, SEM, KOPN-8) versus non-KMT2A B-ALL controls (NALM-6, REH, 697). To contextualize developmental state and lineage identity, transcriptional information was integrated from the Pediatric Single-Cell Leukemia Atlas, which provides single-cell–resolved molecular landscapes across pediatric leukemia subtypes⁵.
Results:
Metabolomic Profiling of KMT2A-Rearranged Leukemia
Metabolomic analyses demonstrate that KMT2A-rearranged cell lines exhibit increased reliance on oxidative phosphorylation, amino acid metabolism, and redox balance compared with non-KMT2A controls². RS4;11 and SEM display enrichment of glutamine, arginine, and lipid metabolic pathways, consistent with stem-like metabolic programs linked to chemotherapy tolerance.
Proteomic Signatures Associated with Chemotherapy Resistance
Proteomic profiling reveals that KMT2A-rearranged cell lines cluster distinctly based on protein abundance patterns³. Elevated expression of mitochondrial enzymes, molecular chaperones, and chromatin-associated regulators is observed in RS4;11, SEM, and KOPN-8. These proteomic features align with enhanced stress adaptation and reduced sensitivity to anthracyclines.
Drug Dependency and Sensitivity Analysis
Analysis of PedDep and PRISM datasets reveals that KMT2A-rearranged models display reduced sensitivity to standard cytotoxic agents, including doxorubicin, and increased dependency on pathways governing apoptosis, mitochondrial integrity, and protein homeostasis⁴. In contrast, non-KMT2A B-ALL cell lines such as NALM-6 and 697 demonstrate greater sensitivity to apoptosis-inducing agents.
Conclusions and Future Directions:
Integrated metabolomic, proteomic, and drug dependency analyses identify KMT2A-specific mechanisms of chemotherapy resistance in pediatric ALL. These findings underscore the central role of metabolic and mitochondrial adaptations in shaping chemotherapy response and support future development of patient-matched experimental systems to mechanistically dissect resistance pathways. Integration of single-cell pediatric leukemia atlases further enables alignment of in vitro models with patient-relevant developmental states, advancing precision therapeutic strategies for high-risk KMT2A-rearranged leukemia⁵.
To enable mechanistic validation and accelerate clinical translation, we are developing a human iPSC-based hematopoietic differentiation platform that generates functional, multilineage hematopoietic stem and progenitor cells (HSPCs) and permits precise temporal control of KMT2A::AFF1 expression across defined stages of hematopoietic ontogeny. Integration of this system with single-cell transcriptomic profiling of lymphoid progenitors—building on prior evidence that KMT2A-rearranged infant ALL reflects a distinct developmental state⁵—and planned CRISPR-based functional screens will allow identification of stage-specific metabolic and proteomic dependencies that govern leukemia initiation, progression, and therapy resistance.
References
- Pui, C.-H., Nichols, K. E. & Yang, J. J. Somatic and germline genomics in pediatric acute lymphoblastic leukemia. Nat. Rev. Clin. Oncol. 16, 227–240 (2019).
- Chan, L. N. et al. Metabolic gatekeeper function of B-lymphoid transcription factors. Nature 542, 479–483 (2017).
- Pushel, I., Clark, Z., Rekowski, M.J., Lansdon, L.A., Yoo, B., August, K.J., Gamis, A.S., Guest, E.M., Washburn, M.P., & Farooqi, M.S. (2024). Proteomic Characterization of Pediatric Acute Lymphoblastic Leukemias Sheds Light on Subtype-Specific Molecular Mechanisms. Blood.
- Tsherniak, A. et al. Defining a cancer dependency map. Cell 170, 564–576.e16 (2017).
- Khabirova E, Jardine L, Coorens THH, Webb S, Treger TD, Engelbert J, Porter T, Prigmore E, Collord G, Piapi A, Teichmann SA, Inglott S, Williams O, Heidenreich O, Young MD, Straathof K, Bomken S, Bartram J, Haniffa M, Behjati S. Single-cell transcriptomics reveals a distinct developmental state of KMT2A-rearranged infant B-cell acute lymphoblastic leukemia. Nat Med. 2022 Apr;28(4):743-751.
Dose-Dependent Metabolic and Proteomic Determinants of Chemotherapy Resistance in KMT2A-Rearranged Pediatric ALL
Background:
KMT2A-rearranged pediatric acute lymphoblastic leukemia (ALL) is a biologically aggressive subtype characterized by early relapse and poor response to conventional chemotherapy¹. Leveraging publicly available pediatric leukemia multi-omic datasets—including the Pediatric Dependency Map (PedDep/DepMap)⁴, FORALL quantitative proteomics³, PRISM drug response screening, and the Pediatric Single-Cell Leukemia Atlas⁵—we systematically characterized metabolic, proteomic, and drug dependency signatures across KMT2A-rearranged leukemia models (RS4;11, SEM, KOPN-8) relative to non-KMT2A B-ALL cell lines (NALM-6, REH, 697) and healthy hematopoietic controls. Integrative analyses revealed KMT2A-specific metabolic reprogramming marked by enhanced oxidative phosphorylation, amino acid utilization, and redox homeostasis, consistent with transcriptionally regulated metabolic dependencies in B-lineage leukemias², alongside proteome-level adaptations involving mitochondrial function, protein homeostasis, and epigenetic regulation³. These molecular features were associated with reduced chemotherapy sensitivity and distinct drug dependency profiles, defining convergent mechanisms underlying treatment resistance in KMT2A-driven leukemia.
Objectives/Goal:
This work aims to identify clinically actionable vulnerabilities that may inform rational chemotherapy dose optimization, improve risk stratification, and support the development of targeted therapeutic strategies for children with KMT2A-rearranged ALL.
Methods/Design:
Using publicly available pediatric leukemia datasets, metabolomic signatures were curated from published mass spectrometry–based profiling studies of pediatric ALL and leukemia stem cell metabolism². Quantitative proteomic data were obtained from FORALL, enabling comparative protein abundance analyses across pediatric ALL subtypes³. Drug sensitivity and dependency profiles were extracted from the Pediatric Dependency Map (PedDep/DepMap) and PRISM repurposing datasets⁴. Comparative analyses focused on KMT2A-rearranged models (RS4;11, SEM, KOPN-8) versus non-KMT2A B-ALL controls (NALM-6, REH, 697). To contextualize developmental state and lineage identity, transcriptional information was integrated from the Pediatric Single-Cell Leukemia Atlas, which provides single-cell–resolved molecular landscapes across pediatric leukemia subtypes⁵.
Results:
Metabolomic Profiling of KMT2A-Rearranged Leukemia
Metabolomic analyses demonstrate that KMT2A-rearranged cell lines exhibit increased reliance on oxidative phosphorylation, amino acid metabolism, and redox balance compared with non-KMT2A controls². RS4;11 and SEM display enrichment of glutamine, arginine, and lipid metabolic pathways, consistent with stem-like metabolic programs linked to chemotherapy tolerance.
Proteomic Signatures Associated with Chemotherapy Resistance
Proteomic profiling reveals that KMT2A-rearranged cell lines cluster distinctly based on protein abundance patterns³. Elevated expression of mitochondrial enzymes, molecular chaperones, and chromatin-associated regulators is observed in RS4;11, SEM, and KOPN-8. These proteomic features align with enhanced stress adaptation and reduced sensitivity to anthracyclines.
Drug Dependency and Sensitivity Analysis
Analysis of PedDep and PRISM datasets reveals that KMT2A-rearranged models display reduced sensitivity to standard cytotoxic agents, including doxorubicin, and increased dependency on pathways governing apoptosis, mitochondrial integrity, and protein homeostasis⁴. In contrast, non-KMT2A B-ALL cell lines such as NALM-6 and 697 demonstrate greater sensitivity to apoptosis-inducing agents.
Conclusions and Future Directions:
Integrated metabolomic, proteomic, and drug dependency analyses identify KMT2A-specific mechanisms of chemotherapy resistance in pediatric ALL. These findings underscore the central role of metabolic and mitochondrial adaptations in shaping chemotherapy response and support future development of patient-matched experimental systems to mechanistically dissect resistance pathways. Integration of single-cell pediatric leukemia atlases further enables alignment of in vitro models with patient-relevant developmental states, advancing precision therapeutic strategies for high-risk KMT2A-rearranged leukemia⁵.
To enable mechanistic validation and accelerate clinical translation, we are developing a human iPSC-based hematopoietic differentiation platform that generates functional, multilineage hematopoietic stem and progenitor cells (HSPCs) and permits precise temporal control of KMT2A::AFF1 expression across defined stages of hematopoietic ontogeny. Integration of this system with single-cell transcriptomic profiling of lymphoid progenitors—building on prior evidence that KMT2A-rearranged infant ALL reflects a distinct developmental state⁵—and planned CRISPR-based functional screens will allow identification of stage-specific metabolic and proteomic dependencies that govern leukemia initiation, progression, and therapy resistance.
References
- Pui, C.-H., Nichols, K. E. & Yang, J. J. Somatic and germline genomics in pediatric acute lymphoblastic leukemia. Nat. Rev. Clin. Oncol. 16, 227–240 (2019).
- Chan, L. N. et al. Metabolic gatekeeper function of B-lymphoid transcription factors. Nature 542, 479–483 (2017).
- Pushel, I., Clark, Z., Rekowski, M.J., Lansdon, L.A., Yoo, B., August, K.J., Gamis, A.S., Guest, E.M., Washburn, M.P., & Farooqi, M.S. (2024). Proteomic Characterization of Pediatric Acute Lymphoblastic Leukemias Sheds Light on Subtype-Specific Molecular Mechanisms. Blood.
- Tsherniak, A. et al. Defining a cancer dependency map. Cell 170, 564–576.e16 (2017).
- Khabirova E, Jardine L, Coorens THH, Webb S, Treger TD, Engelbert J, Porter T, Prigmore E, Collord G, Piapi A, Teichmann SA, Inglott S, Williams O, Heidenreich O, Young MD, Straathof K, Bomken S, Bartram J, Haniffa M, Behjati S. Single-cell transcriptomics reveals a distinct developmental state of KMT2A-rearranged infant B-cell acute lymphoblastic leukemia. Nat Med. 2022 Apr;28(4):743-751.
Comments
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Poster Board Number: 26