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Barbosa K, Deshpande A, Perales M, Xiang P, Murad R, Pramod AB, Minkina A, Robertson N, Schischlik F, Lei X, Sun Y, Brown A, Amend D, Jeremias I, Doench JG, Humphries RK, Ruppin E, Shendure J, Mali P, Adams PD, Deshpande AJ. Transcriptional control of leukemogenesis by the chromatin reader SGF29. Blood 2024; 143:697-712. [PMID: 38048593 PMCID: PMC10900139 DOI: 10.1182/blood.2023021234] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 11/15/2023] [Accepted: 11/27/2023] [Indexed: 12/06/2023] Open
Abstract
ABSTRACT Aberrant expression of stem cell-associated genes is a common feature in acute myeloid leukemia (AML) and is linked to leukemic self-renewal and therapy resistance. Using AF10-rearranged leukemia as a prototypical example of the recurrently activated "stemness" network in AML, we screened for chromatin regulators that sustain its expression. We deployed a CRISPR-Cas9 screen with a bespoke domain-focused library and identified several novel chromatin-modifying complexes as regulators of the TALE domain transcription factor MEIS1, a key leukemia stem cell (LSC)-associated gene. CRISPR droplet sequencing revealed that many of these MEIS1 regulators coordinately controlled the transcription of several AML oncogenes. In particular, we identified a novel role for the Tudor-domain-containing chromatin reader protein SGF29 in the transcription of AML oncogenes. Furthermore, SGF29 deletion impaired leukemogenesis in models representative of multiple AML subtypes in multiple AML subtype models. Our studies reveal a novel role for SGF29 as a nononcogenic dependency in AML and identify the SGF29 Tudor domain as an attractive target for drug discovery.
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Affiliation(s)
- Karina Barbosa
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Anagha Deshpande
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Marlenne Perales
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Ping Xiang
- British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Rabi Murad
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Akula Bala Pramod
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Anna Minkina
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Neil Robertson
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Fiorella Schischlik
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Xue Lei
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Younguk Sun
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Adam Brown
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Munich, Germany
| | - Diana Amend
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Munich, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Munich, Germany
| | | | | | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, San Diego, CA
| | - Peter D. Adams
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Aniruddha J. Deshpande
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
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2
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Coulombe P, Cole G, Fentiman A, Parker JDK, Yung E, Bilenky M, Degefie L, Lac P, Ling MYM, Tam D, Humphries RK, Karsan A. Meis1 establishes the pre-hemogenic endothelial state prior to Runx1 expression. Nat Commun 2023; 14:4537. [PMID: 37500618 PMCID: PMC10374625 DOI: 10.1038/s41467-023-40283-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/20/2023] [Indexed: 07/29/2023] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) originate from an endothelial-to-hematopoietic transition (EHT) during embryogenesis. Characterization of early hemogenic endothelial (HE) cells is required to understand what drives hemogenic specification and to accurately define cells capable of undergoing EHT. Using Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), we define the early subpopulation of pre-HE cells based on both surface markers and transcriptomes. We identify the transcription factor Meis1 as an essential regulator of hemogenic cell specification in the embryo prior to Runx1 expression. Meis1 is expressed at the earliest stages of EHT and distinguishes pre-HE cells primed towards the hemogenic trajectory from the arterial endothelial cells that continue towards a vascular fate. Endothelial-specific deletion of Meis1 impairs the formation of functional Runx1-expressing HE which significantly impedes the emergence of pre-HSPC via EHT. Our findings implicate Meis1 in a critical fate-determining step for establishing EHT potential in endothelial cells.
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Affiliation(s)
- Patrick Coulombe
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Experimental Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Grace Cole
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Amanda Fentiman
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Jeremy D K Parker
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Eric Yung
- Terry Fox Laboratory, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Misha Bilenky
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Lemlem Degefie
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Patrick Lac
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Maggie Y M Ling
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Derek Tam
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - R Keith Humphries
- Terry Fox Laboratory, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Aly Karsan
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada.
- Department of Experimental Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada.
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, V6T 2B5, Canada.
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In Vitro Human Haematopoietic Stem Cell Expansion and Differentiation. Cells 2023; 12:cells12060896. [PMID: 36980237 PMCID: PMC10046976 DOI: 10.3390/cells12060896] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/17/2023] Open
Abstract
The haematopoietic system plays an essential role in our health and survival. It is comprised of a range of mature blood and immune cell types, including oxygen-carrying erythrocytes, platelet-producing megakaryocytes and infection-fighting myeloid and lymphoid cells. Self-renewing multipotent haematopoietic stem cells (HSCs) and a range of intermediate haematopoietic progenitor cell types differentiate into these mature cell types to continuously support haematopoietic system homeostasis throughout life. This process of haematopoiesis is tightly regulated in vivo and primarily takes place in the bone marrow. Over the years, a range of in vitro culture systems have been developed, either to expand haematopoietic stem and progenitor cells or to differentiate them into the various haematopoietic lineages, based on the use of recombinant cytokines, co-culture systems and/or small molecules. These approaches provide important tractable models to study human haematopoiesis in vitro. Additionally, haematopoietic cell culture systems are being developed and clinical tested as a source of cell products for transplantation and transfusion medicine. This review discusses the in vitro culture protocols for human HSC expansion and differentiation, and summarises the key factors involved in these biological processes.
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Elucidating the importance and regulation of key enhancers for human MEIS1 expression. Leukemia 2022; 36:1980-1989. [PMID: 35624144 PMCID: PMC9343249 DOI: 10.1038/s41375-022-01602-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 05/05/2022] [Accepted: 05/12/2022] [Indexed: 11/20/2022]
Abstract
Myeloid ecotropic virus insertion site 1 (MEIS1) is essential for normal hematopoiesis and is a critical factor in the pathogenesis of a large subset of acute myeloid leukemia (AML). Despite the clinical relevance of MEIS1, its regulation is largely unknown. To understand the transcriptional regulatory mechanisms contributing to human MEIS1 expression, we created a knock-in green florescent protein (GFP) reporter system at the endogenous MEIS1 locus in a human AML cell line. Using this model, we have delineated and dissected a critical enhancer region of the MEIS1 locus for transcription factor (TF) binding through in silico prediction in combination with oligo pull-down, mass-spectrometry and knockout analysis leading to the identification of FLI1, an E-twenty-six (ETS) transcription factor, as an important regulator of MEIS1 transcription. We further show direct binding of FLI1 to the MEIS1 locus in human AML cell lines as well as enrichment of histone acetylation in MEIS1-high healthy and leukemic cells. We also observe a positive correlation between high FLI1 transcript levels and worse overall survival in AML patients. Our study expands the role of ETS factors in AML and our model constitutes a feasible tool for a more detailed understanding of transcriptional regulatory elements and their interactome.
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Lehnertz B, Chagraoui J, MacRae T, Tomellini E, Corneau S, Mayotte N, Boivin I, Durand A, Gracias D, Sauvageau G. HLF expression defines the human hematopoietic stem cell state. Blood 2021; 138:2642-2654. [PMID: 34499717 DOI: 10.1182/blood.2021010745] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 08/11/2021] [Indexed: 12/30/2022] Open
Abstract
Hematopoietic stem cells (HSCs) sustain blood cell homeostasis throughout life and can regenerate all blood lineages after transplantation. Despite this clear functional definition, highly enriched isolation of human HSCs can currently only be achieved through combinatorial assessment of multiple surface antigens. Although several transgenic HSC reporter mouse strains have been described, no analogous approach to prospectively isolate human HSCs has been reported. To identify genes with the most selective expression in human HSCs, we profiled population and single-cell transcriptomes of unexpanded and ex vivo cultured cord blood-derived hematopoietic stem and progenitor cells as well as peripheral blood, adult bone marrow, and fetal liver. On the basis of these analyses, we propose the master transcription factor HLF (hepatic leukemia factor) as one of the most specific HSC marker genes. To directly track its expression in human hematopoietic cells, we developed a genomic HLF reporter strategy, capable of selectively labeling the most immature blood cells on the basis of a single engineered parameter. Most importantly, HLF-expressing cells comprise all stem cell activity in culture and in vivo during serial transplantation. Taken together, these results experimentally establish HLF as a defining gene of the human HSC state and outline a new approach to continuously mark these cells with high fidelity.
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Affiliation(s)
- Bernhard Lehnertz
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Jalila Chagraoui
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Tara MacRae
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Elisa Tomellini
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Sophie Corneau
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Nadine Mayotte
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Isabel Boivin
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Aurélie Durand
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Deanne Gracias
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Guy Sauvageau
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
- Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada; and
- Department of Medicine, Faculty of Medicine, University of Montreal, Montreal, QC, Canada
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González-Romero E, Martínez-Valiente C, García-Ruiz C, Vázquez-Manrique RP, Cervera J, Sanjuan-Pla A. CRISPR to fix bad blood: a new tool in basic and clinical hematology. Haematologica 2019; 104:881-893. [PMID: 30923099 PMCID: PMC6518885 DOI: 10.3324/haematol.2018.211359] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/19/2019] [Indexed: 12/13/2022] Open
Abstract
Advances in genome engineering in the last decade, particularly in the development of programmable nucleases, have made it possible to edit the genomes of most cell types precisely and efficiently. Chief among these advances, the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system is a novel, versatile and easy-to-use tool to edit genomes irrespective of their complexity, with multiple and broad applications in biomedicine. In this review, we focus on the use of CRISPR/Cas9 genome editing in the context of hematologic diseases and appraise the major achievements and challenges in this rapidly moving field to gain a clearer perspective on the potential of this technology to move from the laboratory to the clinic. Accordingly, we discuss data from studies editing hematopoietic cells to understand and model blood diseases, and to develop novel therapies for hematologic malignancies. We provide an overview of the applications of gene editing in experimental, preclinical and clinical hematology including interrogation of gene function, target identification and drug discovery and chimeric antigen receptor T-cell engineering. We also highlight current limitations of CRISPR/Cas9 and the possible strategies to overcome them. Finally, we consider what advances in CRISPR/Cas9 are needed to move the hematology field forward.
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Affiliation(s)
| | | | | | - Rafael P Vázquez-Manrique
- Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Instituto de Investigación Sanitaria La Fe, Valencia
- CIBER de Enfermedades Raras, Madrid
| | - José Cervera
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia
- CIBER de Oncología, Madrid, Spain
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