Induced pluripotent stem cell models of hematopoiesis in development and disease

Hematopoiesis is a tightly regulated process that sustains the production of blood cells. Disruption in hematopoietic stem and progenitor cells (HSPCs) can impair differentiation, promote clonal expansion, and lead to myeloid malignancies such as myelodysplastic neoplasms (MDS) and acute myeloid leukemia (AML). Mechanistic studies and drug discovery are often limited by the availability, heterogeneity, and limited ex vivo stability of primary patient material. In this thesis, patient-derived induced pluripotent stem cells (iPSCs), together with isogenic wild-type controls, were used to model hematopoietic differentiation and link recurrent disease-defining lesions to downstream mechanisms and therapeutic vulnerabilities. In Study I, we investigated SF3B1-mutant MDS, a distinct subgroup characterized by RNA mis-splicing and erythroid dysplasia. Isogenic SF3B1K700E and SF3B1WT iPSCs from an MDS patient were differentiated into hematopoietic cells and analyzed by full-length RNA sequencing, uncovering mutated SF3B1-specific mis-splicing of UBA1, which encodes the major E1 enzyme at the apex of the ubiquitination cascade. While the mis-spliced UBA1 transcript was stable, its protein product was rapidly degraded, lowering total UBA1 levels and rendering SF3B1-mutant cells particularly sensitive to the UBA1 inhibitor TAK-243. CD34+ RNA sequencing from an MDS patient cohort confirmed UBA1 mis-splicing as a prevalent feature of MDS-SF3B1, absent in other spliceosome-mutant MDS cases and healthy controls. Functionally, TAK-243 selectively reduced SF3B1-mutant primary CD34+ cells and decreased mutant colony output, sparing wild-type hematopoietic progenitors. In Study II, we addressed epigenetic and transcriptional deregulation in KMT2A- rearranged (KMT2A-r) AML using patient-derived iPSCs. Transcriptional analysis during iPSC-directed hematopoietic development identified key activators and repressors contributing to the altered regulatory landscape in KMT2A-r AML. Integration with chromatin immunoprecipitation sequencing analyses indicated that a substantial fraction of genes downregulated in AML iPSC-derived HSPCs were direct targets of Polycomb Repressive Complex 2 (PRC2). Pharmacologic inhibition PRC2 via EZH1/2 using UNC1999, in combination with 5-azacitidine, reactivated PRC2 target genes specifically in AML-HSPCs, shifting expression toward a more normal hematopoietic program and reducing leukemic properties in KMT2A-r cells. Together, these findings support targeting Polycomb-associated repression as a potential epigenetic strategy in KMT2A-rearranged AML. List of scientific papers I. SF3B1-mutant models of RNA mis-splicing uncover UBA1 as a therapeutic target in myelodysplastic neoplasms. Thier J, Hofmann S, Kirchhof KM, Todisco G, Mortera-Blanco T, Barbosa I, Björklund AC, Deslauriers AG, Papaemmanuil E, Papapetrou EP, Hellström-Lindberg E, Moura PL, Lundin V. Leukemia 2025; 39:2801-2811. https://doi.org/10.1038/s41375-025-02740-1 II. Targeting dysregulated epigenetic and transcription factor networks in KMT2A-rearranged AML using iPSC models. Palau A#, Thier J#, Naughton A#, Tae-Jun Kwon A, Kaczkowski B, Cabrerizo Granados D, Hofmann S, Kaczkowski B, Zhong X, Lehmann S, Arner E, Lundin V*, Lennartsson A *. Blood Neoplasia 2025; 3(1):100172. #Equal contribution. *Shared last authorship https://doi.org/10.1016/j.bneo.2025.100172