Intra-subtype heterogeneity shapes treatment response in KMT2A-rearranged ALL across all age groups

Hartmann, A. M.; Bastian, L.; Barz, M. J.; Haas, J.; Amelunxen, E.; Ehm, P.; Lenk, L.; Kotrova, M.; Beder, T.; Steffen, F.; Rauwolf, K.; Wolgast, N.; Bendig, S.; Bozzetti, C.; Alten, J.; Mondal, M.; Rademacher, A.; Heymann, J.; Walter, W.; Haferlach, C.; Ströh, A.-S.; Bergmann, A. K.; Burmeister, T.; Gökbuget, N.; Bornhauser, B.; Bourquin, J.-P.; Brüggemann, M.; Schrappe, M.; Cario, G.; Baldus, C. D.

doi:10.1101/2025.06.05.657589

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bioRxiv · 10.1101/2025.06.05.657589

Intra-subtype heterogeneity shapes treatment response in KMT2A-rearranged ALL across all age groups

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Abstract

BackgroundKMT2A-rearranged B-cell acute lymphoblastic leukemia (KMT2Ar B-ALL) exhibits significant heterogeneity in age of onset, developmental origins, and clinical outcomes. The interplay of individual factors influencing early treatment response within this high-risk molecular subtype remains poorly elucidated. We aimed to comprehensively assess how leukemic developmental state, fusion partner, and patient age jointly influence early treatment response and drug sensitivity. MethodsTo identify determinants of early treatment response to induction chemotherapy, we analysed 465 KMT2Ar B-ALL cases spanning a wide age range (1 month to 89 years) by integrating transcriptomic and genomic profiling with functional drug response and measurable residual disease (MRD) kinetics. Transcriptomic profiling was used to derive a developmental maturity score based on proximity to physiological B-cell differentiation from a normal B-lymphopoiesis reference. Using an ordinal regression model we identify gene expression programs associated with early MRD response. ResultsWe observed a strong inverse correlation between MRD clearance with advancing age (p=2.1E-04), proximity to early B-cell-precursor developmental state (low maturity score, p=1.3E-03) and AFF1 as fusion partner (p=7.0E-04). A combined model confirmed the predominate impact of both maturity and KMT2A fusion partner on MRD response, supporting the concept that the cells developmental state defines therapy response. Gene expression analysis identified cellular traits that relate to MRD response (e.g. chromatin organization, immune modulation and proliferation). This gene expression classifier grouped cases by MRD response but also by ex-vivo induction drug sensitivity. Notably, good responders to ex-vivo induction drugs were characterized by a higher maturity score (p=1.8E-03), whereas for less mature KMT2Ar B-ALL cases response profiles suggested higher Venetoclax sensitivity. ConclusionsOur study provides an integrative framework linking developmental phenotype, fusion partner, and MRD kinetics across the full age spectrum of KMT2Ar B-ALL. The maturity score, derived from bulk transcriptome data, offers a biologically relevant predictor of early treatment response and drug sensitivity. These insights may support future risk-adapted strategies and therapeutic targeting, particularly in immature KMT2Ar B-ALL.

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Hartmann, A. M., Bastian, L., Barz, M. J., Haas, J., Amelunxen, E., Ehm, P., Lenk, L., Kotrova, M., Beder, T., Steffen, F., Rauwolf, K., Wolgast, N., Bendig, S., Bozzetti, C., Alten, J., Mondal, M., Rademacher, A., Heymann, J., Walter, W., Haferlach, C., Ströh, A.-S., Bergmann, A. K., Burmeister, T., Gökbuget, N., Bornhauser, B., Bourquin, J.-P., Brüggemann, M., Schrappe, M., Cario, G., Baldus, C. D.. 2025-06-09. Intra-subtype heterogeneity shapes treatment response in KMT2A-rearranged ALL across all age groups. https://doi.org/10.1101/2025.06.05.657589

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