DNMT3A-R882 mutations intrinsically drive dysfunctional neutropoiesis from human haematopoietic stem cells

Giovanna Mantica; Aditi Vedi; Amos Tuval; Hector Huerga Encabo; Daniel Hayler; Aleksandra Krzywon; Emily Mitchell; William G. Dunn; Tamir Biezuner; Hugo P. Bastos; Kendig Sham; Antonella Santoro; Joe Lee; Nick Williams; Adi Danin; Noa Chapal-Ilani; Yoni Moskovitz; Andrea Arruda; Edoardo Fiorillo; Valeria Orrù; Michele Marongiu; Eoin F. McKinney; Francesco Cucca; Matthew Collin; Mark David Minden; Peter J. Campbell; George S. Vassiliou; Margarete A. Fabre; Jyoti Nangalia; Dominique A. Bonnet

doi:10.1101/2025.10.08.679225

Cell BiologybioRxivOct 8, 2025

Preprint

DNMT3A-R882 mutations intrinsically drive dysfunctional neutropoiesis from human haematopoietic stem cells

Giovanna Mantica iD, Aditi Vedi iD, Amos Tuval iD, Hector Huerga Encabo iD, Daniel Hayler, Aleksandra Krzywon iD, Emily Mitchell iD, William G. Dunn iD, Tamir Biezuner iD, Hugo P. Bastos iD, Kendig Sham iD, Antonella Santoro iD, Joe Lee iD, Nick Williams iD, Adi Danin, Noa Chapal-Ilani, Yoni Moskovitz iD, Andrea Arruda iD, Edoardo Fiorillo iD, Valeria Orrù iD, Michele Marongiu iD, Eoin F. McKinney iD, Francesco Cucca iD, Matthew Collin iD, Mark David Minden iD, , Elisa Laurenti iD

Abstract

Clonal haematopoiesis (CH) arises from the expansion of hematopoietic stem cells (HSCs) carrying leukaemia-associated somatic mutations. CH is linked to pathological immune dysregulation and a greater risk of age-related inflammatory diseases. Yet, how CH mutations impact HSC differentiation into immune effector cells remains understudied. Here, we report a single-cell resolution functional and multi-omic investigation of HSC clonal and differentiation dynamics in individuals with DNMT3A-R882 CH. DNMT3A-R882 reshapes the clonal architecture of haematopoiesis towards an aged phylogenetic structure. Functionally, DNMT3A-R882 HSCs produce decreased monocytic output but more abundant and mature neutrophil progeny compared to WT HSCs in the same individual. Whereas DNMT3A-R882 myeloid progenitors display attenuated inflammatory transcriptional programmes, DNMT3A- R882 mature neutrophils acquire proinflammatory and immunomodulatory features typical of maladaptive immunity and CH co-morbidities. Our findings, validated in humanised mice, identify aberrant DNMT3A-R882 HSC-driven neutropoiesis as a key link between CH, immune dysregulation and risk of inflammatory disease.

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