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Sarchi M, Clough CA, Crosse EI, Kim J, Baquero Galvis LD, Aydinyan N, Wellington R, Yang F, Gallì A, Creamer JP, Stewart S, Bradley RK, Malcovati L, Doulatov S. Mis-splicing of Mitotic Regulators Sensitizes SF3B1-Mutated Human HSCs to CHK1 Inhibition. Blood Cancer Discov 2024; 5:353-370. [PMID: 38856693 PMCID: PMC11369594 DOI: 10.1158/2643-3230.bcd-23-0230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 04/18/2024] [Accepted: 06/06/2024] [Indexed: 06/11/2024] Open
Abstract
Splicing factor SF3B1 mutations are frequent somatic lesions in myeloid neoplasms that transform hematopoietic stem cells (HSCs) by inducing mis-splicing of target genes. However, the molecular and functional consequences of SF3B1 mutations in human HSCs and progenitors (HSPCs) remain unclear. Here, we identify the mis-splicing program in human HSPCs as a targetable vulnerability by precise gene editing of SF3B1 K700E mutations in primary CD34+ cells. Mutant SF3B1 induced pervasive mis-splicing and reduced expression of genes regulating mitosis and genome maintenance leading to altered differentiation, delayed G2/M progression, and profound sensitivity to CHK1 inhibition (CHK1i). Mis-splicing or reduced expression of mitotic regulators BUBR1 and CDC27 delayed G2/M transit and promoted CHK1i sensitivity. Clinical CHK1i prexasertib selectively targeted SF3B1-mutant immunophenotypic HSCs and abrogated engraftment in vivo. These findings identify mis-splicing of mitotic regulators in SF3B1-mutant HSPCs as a targetable vulnerability engaged by pharmacological CHK1 inhibition. Significance: In this study, we engineer precise SF3B1 mutations in human HSPCs and identify CHK1 inhibition as a selective vulnerability promoted by mis-splicing of mitotic regulators. These findings uncover the mis-splicing program induced by mutant SF3B1 in human HSPCs and show that it can be therapeutically targeted by clinical CHK1 inhibitors.
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Affiliation(s)
- Martina Sarchi
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, Washington.
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.
| | - Courtnee A. Clough
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, Washington.
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington.
| | - Edie I. Crosse
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington.
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington.
| | - Jason Kim
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, Washington.
| | - Laura D. Baquero Galvis
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, Washington.
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington.
| | - Nelli Aydinyan
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, Washington.
| | - Rachel Wellington
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, Washington.
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington.
| | - Feini Yang
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.
| | - Anna Gallì
- Department of Hematology, IRCCS S. Matteo Hospital Foundation, Pavia, Italy.
| | - J. Philip Creamer
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, Washington.
| | - Sintra Stewart
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, Washington.
| | - Robert K. Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington.
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington.
- Department of Genome Sciences, University of Washington, Seattle, Washington.
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.
- Department of Hematology, IRCCS S. Matteo Hospital Foundation, Pavia, Italy.
| | - Sergei Doulatov
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, Washington.
- Department of Genome Sciences, University of Washington, Seattle, Washington.
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington.
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2
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Ng ES, Sarila G, Li JY, Edirisinghe HS, Saxena R, Sun S, Bruveris FF, Labonne T, Sleebs N, Maytum A, Yow RY, Inguanti C, Motazedian A, Calvanese V, Capellera-Garcia S, Ma F, Nim HT, Ramialison M, Bonifer C, Mikkola HKA, Stanley EG, Elefanty AG. Long-term engrafting multilineage hematopoietic cells differentiated from human induced pluripotent stem cells. Nat Biotechnol 2024:10.1038/s41587-024-02360-7. [PMID: 39223325 DOI: 10.1038/s41587-024-02360-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 07/20/2024] [Indexed: 09/04/2024]
Abstract
Hematopoietic stem cells (HSCs) derived from human induced pluripotent stem cells (iPS cells) have important biomedical applications. We identified differentiation conditions that generate HSCs defined by robust long-term multilineage engraftment in immune-deficient NOD,B6.Prkdcscid Il2rgtm1Wjl/SzJ KitW41/W41 mice. We guided differentiating iPS cells, as embryoid bodies in a defined culture medium supplemented with retinyl acetate, through HOXA-patterned mesoderm to hemogenic endothelium specified by bone morphogenetic protein 4 and vascular endothelial growth factor (VEGF). Removal of VEGF facilitated an efficient endothelial-to-hematopoietic transition, evidenced by release into the culture medium of CD34+ blood cells, which were cryopreserved. Intravenous transplantation of two million thawed CD34+ cells differentiated from four independent iPS cell lines produced multilineage bone marrow engraftment in 25-50% of immune-deficient recipient mice. These functionally defined, multipotent CD34+ hematopoietic cells, designated iPS cell-derived HSCs (iHSCs), produced levels of engraftment similar to those achieved following umbilical cord blood transplantation. Our study provides a step toward the goal of generating HSCs for clinical translation.
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Grants
- GNT1117596,GNT1068866, GNT1129861,GNT2012535 Department of Health | National Health and Medical Research Council (NHMRC)
- GNT1164577, GNT2012936 Department of Health | National Health and Medical Research Council (NHMRC)
- GNT2012535 Department of Health | National Health and Medical Research Council (NHMRC)
- GNT1186019 Department of Health | National Health and Medical Research Council (NHMRC)
- GNT1068866, GNT1129861, GNT2012535 Department of Health | National Health and Medical Research Council (NHMRC)
- GNT1068866, GNT1129861, GNT1186019 Department of Health | National Health and Medical Research Council (NHMRC)
- GNT1079004, GNT1068866, GNT1129861, GNT1186019 Department of Health | National Health and Medical Research Council (NHMRC)
- RT3-07763 California Institute for Regenerative Medicine (CIRM)
- NNF21CC0073729 Novo Nordisk Fonden (Novo Nordisk Foundation)
- NIH 1RO1DK125097-01 Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)
- IPD2 2018-06635 Vetenskapsrådet (Swedish Research Council)
- BB/R014809/1 RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
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Affiliation(s)
- Elizabeth S Ng
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia.
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia.
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Parkville, Victoria, Australia.
| | - Gulcan Sarila
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Jacky Y Li
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Hasindu S Edirisinghe
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Ritika Saxena
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Shicheng Sun
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Changping Laboratory, Beijing, China
| | - Freya F Bruveris
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Tanya Labonne
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Nerida Sleebs
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Alexander Maytum
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Raymond Y Yow
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Chantelle Inguanti
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Ali Motazedian
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Vincenzo Calvanese
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
- Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Sandra Capellera-Garcia
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
| | - Feiyang Ma
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
| | - Hieu T Nim
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Mirana Ramialison
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Constanze Bonifer
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Hanna K A Mikkola
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
| | - Edouard G Stanley
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Andrew G Elefanty
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia.
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia.
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Parkville, Victoria, Australia.
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3
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Moura PL, Mortera-Blanco T, Hofman IJ, Todisco G, Kretzschmar WW, Björklund AC, Creignou M, Hagemann-Jensen M, Ziegenhain C, Cabrerizo Granados D, Barbosa I, Walldin G, Jansson M, Ashley N, Mead AJ, Lundin V, Dimitriou M, Yoshizato T, Woll PS, Ogawa S, Sandberg R, Jacobsen SEW, Hellström-Lindberg E. Erythroid Differentiation Enhances RNA Mis-Splicing in SF3B1-Mutant Myelodysplastic Syndromes with Ring Sideroblasts. Cancer Res 2024; 84:211-225. [PMID: 37921711 PMCID: PMC10790130 DOI: 10.1158/0008-5472.can-23-3038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/04/2023]
Abstract
Myelodysplastic syndromes with ring sideroblasts (MDS-RS) commonly develop from hematopoietic stem cells (HSC) bearing mutations in the splicing factor SF3B1 (SF3B1mt). Direct studies into MDS-RS pathobiology have been limited by a lack of model systems that fully recapitulate erythroid biology and RS development and the inability to isolate viable human RS. Here, we combined successful direct RS isolation from patient samples, high-throughput multiomics analysis of cells encompassing the SF3B1mt stem-erythroid continuum, and functional assays to investigate the impact of SF3B1mt on erythropoiesis and RS accumulation. The isolated RS differentiated, egressed into the blood, escaped traditional nonsense-mediated decay (NMD) mechanisms, and leveraged stress-survival pathways that hinder wild-type hematopoiesis through pathogenic GDF15 overexpression. Importantly, RS constituted a contaminant of magnetically enriched CD34+ cells, skewing bulk transcriptomic data. Mis-splicing in SF3B1mt cells was intensified by erythroid differentiation through accelerated RNA splicing and decreased NMD activity, and SF3B1mt led to truncations in several MDS-implicated genes. Finally, RNA mis-splicing induced an uncoupling of RNA and protein expression, leading to critical abnormalities in proapoptotic p53 pathway genes. Overall, this characterization of erythropoiesis in SF3B1mt RS provides a resource for studying MDS-RS and uncovers insights into the unexpectedly active biology of the "dead-end" RS. SIGNIFICANCE Ring sideroblast isolation combined with state-of-the-art multiomics identifies survival mechanisms underlying SF3B1-mutant erythropoiesis and establishes an active role for erythroid differentiation and ring sideroblasts themselves in SF3B1-mutant myelodysplastic syndrome pathogenesis.
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Affiliation(s)
- Pedro L. Moura
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Teresa Mortera-Blanco
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Isabel J. Hofman
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Gabriele Todisco
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Warren W. Kretzschmar
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Ann-Charlotte Björklund
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Maria Creignou
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Medicine, Division of Hematology, Karolinska University Hospital, Huddinge, Sweden
| | - Michael Hagemann-Jensen
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
- Xpress Genomics AB, Stockholm, Sweden
| | - Christoph Ziegenhain
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
- Xpress Genomics AB, Stockholm, Sweden
| | - David Cabrerizo Granados
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Indira Barbosa
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Gunilla Walldin
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Monika Jansson
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Neil Ashley
- Hematopoietic Stem Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Adam J. Mead
- Hematopoietic Stem Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Vanessa Lundin
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Marios Dimitriou
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Tetsuichi Yoshizato
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Petter S. Woll
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Seishi Ogawa
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Rickard Sandberg
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
- Xpress Genomics AB, Stockholm, Sweden
| | - Sten Eirik W. Jacobsen
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
- Department of Medicine, Division of Hematology, Karolinska University Hospital, Huddinge, Sweden
- Hematopoietic Stem Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Eva Hellström-Lindberg
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Medicine, Division of Hematology, Karolinska University Hospital, Huddinge, Sweden
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4
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Tatwavedi D, Pellagatti A, Boultwood J. Recent advances in the application of induced pluripotent stem cell technology to the study of myeloid malignancies. Adv Biol Regul 2024; 91:100993. [PMID: 37827894 DOI: 10.1016/j.jbior.2023.100993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/14/2023]
Abstract
Acquired myeloid malignancies are a spectrum of clonal disorders known to be caused by sequential acquisition of genetic lesions in hematopoietic stem and progenitor cells, leading to their aberrant self-renewal and differentiation. The increasing use of induced pluripotent stem cell (iPSC) technology to study myeloid malignancies has helped usher a paradigm shift in approaches to disease modeling and drug discovery, especially when combined with gene-editing technology. The process of reprogramming allows for the capture of the diversity of genetic lesions and mutational burden found in primary patient samples into individual stable iPSC lines. Patient-derived iPSC lines, owing to their self-renewal and differentiation capacity, can thus be a homogenous source of disease relevant material that allow for the study of disease pathogenesis using various functional read-outs. Furthermore, genome editing technologies like CRISPR/Cas9 enable the study of the stepwise progression from normal to malignant hematopoiesis through the introduction of specific driver mutations, individually or in combination, to create isogenic lines for comparison. In this review, we survey the current use of iPSCs to model acquired myeloid malignancies including myelodysplastic syndromes (MDS), myeloproliferative neoplasms (MPN), acute myeloid leukemia and MDS/MPN overlap syndromes. The use of iPSCs has enabled the interrogation of the underlying mechanism of initiation and progression driving these diseases. It has also made drug testing, repurposing, and the discovery of novel therapies for these diseases possible in a high throughput setting.
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Affiliation(s)
- Dharamveer Tatwavedi
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| | - Andrea Pellagatti
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jacqueline Boultwood
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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5
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Cortés-López M, Chamely P, Hawkins AG, Stanley RF, Swett AD, Ganesan S, Mouhieddine TH, Dai X, Kluegel L, Chen C, Batta K, Furer N, Vedula RS, Beaulaurier J, Drong AW, Hickey S, Dusaj N, Mullokandov G, Stasiw AM, Su J, Chaligné R, Juul S, Harrington E, Knowles DA, Potenski CJ, Wiseman DH, Tanay A, Shlush L, Lindsley RC, Ghobrial IM, Taylor J, Abdel-Wahab O, Gaiti F, Landau DA. Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths. Cell Stem Cell 2023; 30:1262-1281.e8. [PMID: 37582363 PMCID: PMC10528176 DOI: 10.1016/j.stem.2023.07.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 05/28/2023] [Accepted: 07/18/2023] [Indexed: 08/17/2023]
Abstract
RNA splicing factors are recurrently mutated in clonal blood disorders, but the impact of dysregulated splicing in hematopoiesis remains unclear. To overcome technical limitations, we integrated genotyping of transcriptomes (GoT) with long-read single-cell transcriptomics and proteogenomics for single-cell profiling of transcriptomes, surface proteins, somatic mutations, and RNA splicing (GoT-Splice). We applied GoT-Splice to hematopoietic progenitors from myelodysplastic syndrome (MDS) patients with mutations in the core splicing factor SF3B1. SF3B1mut cells were enriched in the megakaryocytic-erythroid lineage, with expansion of SF3B1mut erythroid progenitor cells. We uncovered distinct cryptic 3' splice site usage in different progenitor populations and stage-specific aberrant splicing during erythroid differentiation. Profiling SF3B1-mutated clonal hematopoiesis samples revealed that erythroid bias and cell-type-specific cryptic 3' splice site usage in SF3B1mut cells precede overt MDS. Collectively, GoT-Splice defines the cell-type-specific impact of somatic mutations on RNA splicing, from early clonal outgrowths to overt neoplasia, directly in human samples.
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Affiliation(s)
- Mariela Cortés-López
- New York Genome Center, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Paulina Chamely
- New York Genome Center, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Allegra G Hawkins
- Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Philadelphia, PA, USA
| | - Robert F Stanley
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ariel D Swett
- New York Genome Center, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Saravanan Ganesan
- New York Genome Center, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Tarek H Mouhieddine
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xiaoguang Dai
- Oxford Nanopore Technologies Inc., New York, NY, USA
| | - Lloyd Kluegel
- New York Genome Center, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Celine Chen
- New York Genome Center, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Tri-Institutional MD-PhD Program, Weill Cornell Medicine, Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kiran Batta
- Division of Cancer Sciences, The University of Manchester, Manchester, UK
| | - Nili Furer
- Weizmann Institute of Science, Department of Molecular Cell Biology, Rehovot, Israel
| | - Rahul S Vedula
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Scott Hickey
- Oxford Nanopore Technologies Inc., San Francisco, CA, USA
| | - Neville Dusaj
- New York Genome Center, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Tri-Institutional MD-PhD Program, Weill Cornell Medicine, Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gavriel Mullokandov
- New York Genome Center, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Adam M Stasiw
- New York Genome Center, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Jiayu Su
- New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA
| | - Ronan Chaligné
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sissel Juul
- Oxford Nanopore Technologies Inc., New York, NY, USA
| | | | - David A Knowles
- New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA; Department of Computer Science, Columbia University, New York, NY, USA
| | - Catherine J Potenski
- New York Genome Center, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Daniel H Wiseman
- Division of Cancer Sciences, The University of Manchester, Manchester, UK
| | - Amos Tanay
- Weizmann Institute of Science, Department of Computer Science and Applied Mathematics, Rehovot, Israel
| | - Liran Shlush
- Weizmann Institute of Science, Department of Molecular Cell Biology, Rehovot, Israel
| | - Robert C Lindsley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Irene M Ghobrial
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Justin Taylor
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Federico Gaiti
- University Health Network, Princess Margaret Cancer Centre, Toronto, ON, Canada; University of Toronto, Medical Biophysics, Toronto, ON, Canada.
| | - Dan A Landau
- New York Genome Center, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
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6
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Kotini AG, Carcamo S, Cruz-Rodriguez N, Olszewska M, Wang T, Demircioglu D, Chang CJ, Bernard E, Chao MP, Majeti R, Luo H, Kharas MG, Hasson D, Papapetrou EP. Patient-Derived iPSCs Faithfully Represent the Genetic Diversity and Cellular Architecture of Human Acute Myeloid Leukemia. Blood Cancer Discov 2023; 4:318-335. [PMID: 37067914 PMCID: PMC10320625 DOI: 10.1158/2643-3230.bcd-22-0167] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/30/2023] [Accepted: 03/10/2023] [Indexed: 04/18/2023] Open
Abstract
The reprogramming of human acute myeloid leukemia (AML) cells into induced pluripotent stem cell (iPSC) lines could provide new faithful genetic models of AML, but is currently hindered by low success rates and uncertainty about whether iPSC-derived cells resemble their primary counterparts. Here we developed a reprogramming method tailored to cancer cells, with which we generated iPSCs from 15 patients representing all major genetic groups of AML. These AML-iPSCs retain genetic fidelity and produce transplantable hematopoietic cells with hallmark phenotypic leukemic features. Critically, single-cell transcriptomics reveal that, upon xenotransplantation, iPSC-derived leukemias faithfully mimic the primary patient-matched xenografts. Transplantation of iPSC-derived leukemias capturing a clone and subclone from the same patient allowed us to isolate the contribution of a FLT3-ITD mutation to the AML phenotype. The results and resources reported here can transform basic and preclinical cancer research of AML and other human cancers. SIGNIFICANCE We report the generation of patient-derived iPSC models of all major genetic groups of human AML. These exhibit phenotypic hallmarks of AML in vitro and in vivo, inform the clonal hierarchy and clonal dynamics of human AML, and exhibit striking similarity to patient-matched primary leukemias upon xenotransplantation. See related commentary by Doulatov, p. 252. This article is highlighted in the In This Issue feature, p. 247.
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Affiliation(s)
- Andriana G. Kotini
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Saul Carcamo
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Bioinformatics for Next-Generation Sequencing Shared Resource Facility, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Nataly Cruz-Rodriguez
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Malgorzata Olszewska
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Tiansu Wang
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Deniz Demircioglu
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Bioinformatics for Next-Generation Sequencing Shared Resource Facility, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Chan-Jung Chang
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Elsa Bernard
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark P. Chao
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California
- Cancer Institute, Stanford University School of Medicine, Stanford, California
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California
| | - Ravindra Majeti
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California
- Cancer Institute, Stanford University School of Medicine, Stanford, California
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California
| | - Hanzhi Luo
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael G. Kharas
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Bioinformatics for Next-Generation Sequencing Shared Resource Facility, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Eirini P. Papapetrou
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
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7
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Pellagatti A, Boultwood J. Splicing factor mutations in the myelodysplastic syndromes: Role of key aberrantly spliced genes in disease pathophysiology and treatment. Adv Biol Regul 2023; 87:100920. [PMID: 36216757 DOI: 10.1016/j.jbior.2022.100920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 03/01/2023]
Abstract
Mutations of splicing factor genes (including SF3B1, SRSF2, U2AF1 and ZRSR2) occur in more than half of all patients with myelodysplastic syndromes (MDS), a heterogeneous group of myeloid neoplasms. Splicing factor mutations lead to aberrant pre-mRNA splicing of many genes, some of which have been shown in functional studies to impact on hematopoiesis and to contribute to the MDS phenotype. This clearly demonstrates that impaired spliceosome function plays an important role in MDS pathophysiology. Recent studies that harnessed the power of induced pluripotent stem cell (iPSC) and CRISPR/Cas9 gene editing technologies to generate new iPSC-based models of splicing factor mutant MDS, have further illuminated the role of key downstream target genes. The aberrantly spliced genes and the dysregulated pathways associated with splicing factor mutations in MDS represent potential new therapeutic targets. Emerging data has shown that IRAK4 is aberrantly spliced in SF3B1 and U2AF1 mutant MDS, leading to hyperactivation of NF-κB signaling. Pharmacological inhibition of IRAK4 has shown efficacy in pre-clinical studies and in MDS clinical trials, with higher response rates in patients with splicing factor mutations. Our increasing knowledge of the effects of splicing factor mutations in MDS is leading to the development of new treatments that may benefit patients harboring these mutations.
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Affiliation(s)
- Andrea Pellagatti
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom.
| | - Jacqueline Boultwood
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom.
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