Human iPSCs-based modeling unveils SETBP1 as a driver of chromatin rewiring in GATA2 deficiency

Abstract

Patients with GATA2 deficiency are predisposed to developing myelodysplastic neoplasms (MDS), which can progress to acute myeloid leukemia. This progression is often associated with cytogenetic and somatic alterations. Mutations in SETBP1 and ASXL1 genes are recurrently observed in GATA2 patients, although their roles remain poorly understood. Here we develop a hiPSC-based system to investigate the impact of SETBP1 and ASXL1 mutations in GATA2 deficiency. Using precise genome editing, we recreate stepwise mutational trajectories observed in GATA2-related MDS. We demonstrate that GATA2 mutation has limited impact on hematopoietic progenitors, while the co-occurrence of SETBP1 or ASXL1 mutations impairs myeloid differentiation. The combination of all three mutations severely depletes myeloid progenitors, recapitulating GATA2-related MDS and highlighting their synergistic interplay. Notably, SETBP1 mutation plays a dominant role in establishing a stable chromatin accessibility landscape, even when co-occurring with ASXL1. Our study establishes an iPSC-based model of GATA2 deficiency, offering new insights into myeloid disease progression and a platform for testing future therapeutic strategies.

We thank Dr. M.A. Mulaw - Ulm University and Dr. J. Pozniak - KU Leuven for their valuable advice and suggestions regarding the scATAC-seq analysis. This work was supported by ERA PerMed GATA2-HuMo Funding Mechanism (Spain: Acció Instrumental de SLT011/18/00006 of the Department of Health of the Government of Catalonia), Fondazione Pisana per la Scienza ONLUS (FPS-G01/2018), Ministerio de Ciencia e Innovación, which is part of Agencia Estatal de Investigación (AEI), through the Retos Investigación grant, number PID2020-115591RB-I00 / https://doi.org/10.13039/501100011033, Fundació La Marató TV3 228/C/2020, Award no. AC23_2/00040 by ISCIII through AES 2023 and within the European Joint Programme Rare Diseases framework, by Instituto de Salud Carlos III (ISCIII), "Programa FORTALECE del Ministerio de Ciencia e Innovación", through the project number FORT23/00032, and Finançat per el Departament de Recerca i Universitats de la Generalitat de Catalunya i l'AGAUR (expedient 2021 SGR 00888) to AG. Funding for this project was provided in part by an EHA Research Grant award granted by the European Hematology Association (KOG-202109-01162). J.P. and M.D. were supported by Fundació La Marató TV3 228/C/2020. Z.Q. and Z.L. are supported by funding from the Shenzhen Bay Laboratory Startup Fund. D.R.M. was supported by Deutsche José Carreras Leukämie-Stiftung, DJCLS 13 R/2022. O.M.-B. was supported by 101029927-scGATA2track (H2020-MSCA-IF-2020) and he is currently supported by the Ramón y Cajal contract (RYC2021-032129-I) funded by AEI/European Social Fund UE. P.S. received the support of a fellowship from "la Caixa" Foundation (ID 100010434). The fellowship code is LCF/BQ/DI22/11940009. M.M.M. was supported by the Government of Andorra with the predoctoral fellowship, ATC030-AND/2022. The work in the LP laboratory was supported by "la Caixa" Foundation, LCF-PR-HR24-00150 and by PID2023-151556OB-I00 and CNS2024-154742 funded by MICIU/AEI/10.13039/501100011033 and, as appropriate, by "ESF Investing in your future", by "ESF+" or by "European Union NextGenerationEU/PRTR". MCF received funding from "la Caixa" Foundation (ID 100010434), under the agreement LCF/PR/HR20/52400014, PIXEL - TRANSCAN3-2021 (FAECC&ISCIII) and 2021 SGR 00888 - AGAUR 2022. The work in AB laboratory was funded by ERA PerMed-Departament de Salut, Generalitat de Catalunya (SLT011/18/00007) and the EJP RD-Instituto de Salud Carlos III (AC23_2/00014). This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 101029927. We thank Dr. Pablo Menendez and Dr. Clara Bueno group for technical support and expertise during experimental procedures. We thank the CERCA Programme/Generalitat de Catalunya for institutional support.