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Lara-Astiaso D, Goñi-Salaverri A, Mendieta-Esteban J, Narayan N, Del Valle C, Gross T, Giotopoulos G, Beinortas T, Navarro-Alonso M, Aguado-Alvaro LP, Zazpe J, Marchese F, Torrea N, Calvo IA, Lopez CK, Alignani D, Lopez A, Saez B, Taylor-King JP, Prosper F, Fortelny N, Huntly BJP. In vivo screening characterizes chromatin factor functions during normal and malignant hematopoiesis. Nat Genet 2023; 55:1542-1554. [PMID: 37580596 PMCID: PMC10484791 DOI: 10.1038/s41588-023-01471-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 07/11/2023] [Indexed: 08/16/2023]
Abstract
Cellular differentiation requires extensive alterations in chromatin structure and function, which is elicited by the coordinated action of chromatin and transcription factors. By contrast with transcription factors, the roles of chromatin factors in differentiation have not been systematically characterized. Here, we combine bulk ex vivo and single-cell in vivo CRISPR screens to characterize the role of chromatin factor families in hematopoiesis. We uncover marked lineage specificities for 142 chromatin factors, revealing functional diversity among related chromatin factors (i.e. barrier-to-autointegration factor subcomplexes) as well as shared roles for unrelated repressive complexes that restrain excessive myeloid differentiation. Using epigenetic profiling, we identify functional interactions between lineage-determining transcription factors and several chromatin factors that explain their lineage dependencies. Studying chromatin factor functions in leukemia, we show that leukemia cells engage homeostatic chromatin factor functions to block differentiation, generating specific chromatin factor-transcription factor interactions that might be therapeutically targeted. Together, our work elucidates the lineage-determining properties of chromatin factors across normal and malignant hematopoiesis.
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Affiliation(s)
- David Lara-Astiaso
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK.
| | | | | | - Nisha Narayan
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Cynthia Del Valle
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | | | - George Giotopoulos
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Tumas Beinortas
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Mar Navarro-Alonso
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | | | - Jon Zazpe
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Francesco Marchese
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Natalia Torrea
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Isabel A Calvo
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Cecile K Lopez
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Diego Alignani
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Aitziber Lopez
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Borja Saez
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | | | - Felipe Prosper
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Nikolaus Fortelny
- Department of Biosciences & Medical Biology, University of Salzburg, Salzburg, Austria.
| | - Brian J P Huntly
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK.
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