CD180 identifies chemoresistant stem-like blasts and reveals a KMT2A-driven vulnerability in acute myeloid leukaemia

Eltoukhy, M. M.; Winton, A.; Fasanella Masci, F.; Kania, E.; Scott, M. T.; Smith, A. L.; Rigby, E.; Curran, A.; Gouma, A.; Cassels, J.; Liu, L.; Stevens, T.; Dunn, K.; Rattigan, K. M.; almowaled, M.; Wheeler, L.; Helgason, G. V.; Roy, A.; Kearns, P.; Wetherell, p.; Milne, T. A.; Gibson, B.; Vyas, P.; Harrison, C. J.; Vetrie, D.; Keeshan, K.

doi:10.64898/2026.04.23.720316

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bioRxiv · 10.64898/2026.04.23.720316

CD180 identifies chemoresistant stem-like blasts and reveals a KMT2A-driven vulnerability in acute myeloid leukaemia

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Abstract

Relapse and chemoresistance remain major challenges in paediatric acute myeloid leukaemia (PAML), particularly in KMT2A-rearranged (KMT2A-r) subtypes where conventional markers such as CD34 are often absent, complicating measurable residual disease (MRD) detection. Leukaemia stem/regenerating cells (LSC/LRC) drive disease initiation, progression, and relapse, sharing stemness and chemoresistance properties that make them critical therapeutic targets. Using high-dimensional spectral flow cytometry, we identified CD180, a Toll-like receptor-like surface protein, as highly expressed on blasts and stem-like populations in KMT2A-r AML, while near absent on normal haematopoietic stem cells (HSCs). PAML KMT2A-r exhibits an unconventional immunophenotype dominated by CD34-CD180 populations. Integrated single-cell transcriptomics and functional profiling revealed CD180high clusters enriched for quiescence, oxidative phosphorylation, and KMT2A/LSC stemness signatures. CD180 cells demonstrated robust leukaemia-initiating capacity in xenograft models and persisted through therapy, re-emerging at relapse with phenotypic plasticity. Epigenomic analysis showed CD180 is a direct transcriptional target of the KMT2A::MLLT3 fusion complex, regulated by intragenic enhancers and downregulated by menin and BET inhibitors. Longitudinal single-cell analysis confirmed persistence and clonal evolution of CD180 populations during treatment and relapse, underscoring their mechanistic role in chemoresistance and disease progression. In summary, CD180 marks dynamic, relapse-driving populations in KMT2A-r PAML, persists through therapy, and importantly is near absent on normal HSCs, offering a selective therapeutic window. These findings position CD180 as a clinically actionable biomarker for MRD detection and a compelling therapeutic target for eradicating chemoresistant, stem-like cells in paediatric AML. Main PointsO_LICD180 marks chemoresistant, relapse-driving stem-like blasts in KMT2A-r paediatric AML, overcoming CD34-based MRD limitations. C_LIO_LIAbsent on normal HSCs, CD180 is a KMT2A::MLLT3 target and actionable for MRD, relapse prediction, and CD180-directed therapies. C_LI NoveltyThis study introduces CD180 as a novel biomarker and therapeutic target in AML, particularly KMT2A-rearranged subtypes where conventional markers are often absent. Unlike MRD strategies focused on bulk blasts, CD180 marks chemoresistant, stem-like populations driving relapse, critical reservoirs poorly defined in paediatric AML. This work fills a major gap in prognostic assessment and therapy by enabling precise detection of relapse-driving cells and offering a selective therapeutic window.

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Eltoukhy, M. M., Winton, A., Fasanella Masci, F., Kania, E., Scott, M. T., Smith, A. L., Rigby, E., Curran, A., Gouma, A., Cassels, J., Liu, L., Stevens, T., Dunn, K., Rattigan, K. M., almowaled, M., Wheeler, L., Helgason, G. V., Roy, A., Kearns, P., Wetherell, p., Milne, T. A., Gibson, B., Vyas, P., Harrison, C. J., Vetrie, D., Keeshan, K.. 2026-04-27. CD180 identifies chemoresistant stem-like blasts and reveals a KMT2A-driven vulnerability in acute myeloid leukaemia. https://doi.org/10.64898/2026.04.23.720316

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