A genome-wide screen identifies genes required for erythroid differentiation
Abstract The complete array of genes required for terminal erythroid differentiation remains unknown. To address this knowledge gap, we perform a genome-scale CRISPR knock-out screen in the human erythroid progenitor cell line HUDEP-2 and validate candidate regulators of erythroid differentiation in...
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Nature Portfolio
2025-04-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-58739-w |
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| author | Greggory Myers Ann Friedman Lei Yu Narges Pourmandi Claire Kerpet Masaki A. Ito Rilie Saba Vi Tang Ayse Bilge Ozel Ingrid L. Bergin Craig N. Johnson Chia-Jui Ku Yu Wang Ginette Balbin-Cuesta Kim-Chew Lim Zesen Lin Claire Drysdale Beth McGee Ryo Kurita Yukio Nakamura Xiaofang Liu David Siemieniak Sharon A. Singh Costas A. Lyssiotis Ivan Maillard Lois S. Weisman James Douglas Engel Rami Khoriaty |
| author_facet | Greggory Myers Ann Friedman Lei Yu Narges Pourmandi Claire Kerpet Masaki A. Ito Rilie Saba Vi Tang Ayse Bilge Ozel Ingrid L. Bergin Craig N. Johnson Chia-Jui Ku Yu Wang Ginette Balbin-Cuesta Kim-Chew Lim Zesen Lin Claire Drysdale Beth McGee Ryo Kurita Yukio Nakamura Xiaofang Liu David Siemieniak Sharon A. Singh Costas A. Lyssiotis Ivan Maillard Lois S. Weisman James Douglas Engel Rami Khoriaty |
| author_sort | Greggory Myers |
| collection | DOAJ |
| description | Abstract The complete array of genes required for terminal erythroid differentiation remains unknown. To address this knowledge gap, we perform a genome-scale CRISPR knock-out screen in the human erythroid progenitor cell line HUDEP-2 and validate candidate regulators of erythroid differentiation in a custom secondary screen. Comparison of sgRNA abundance in the CRISPR library, proerythroblasts, and orthochromatic erythroblasts, resulted in the identification of genes that are essential for proerythroblast survival and genes that are required for terminal erythroid differentiation. Among the top genes identified are known regulators of erythropoiesis, underscoring the validity of this screen. Notably, using a Log2 fold change of <−1 and false discovery rate of <0.01, the screen identified 277 genes that are required for terminal erythroid differentiation, including multiple genes not previously nominated through GWAS. NHLRC2, which was previously implicated in hemolytic anemia, was a highly ranked gene. We suggest that anemia due to NHLRC2 mutation results at least in part from a defect in erythroid differentiation. Another highly ranked gene in the screen is VAC14, which we validated for its requirement in erythropoiesis in vitro and in vivo. Thus, data from this CRISPR screen may help classify the underlying mechanisms that contribute to erythroid disorders. |
| format | Article |
| id | doaj-art-a4b3dbed174840db95690033ec40db4e |
| institution | OA Journals |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-a4b3dbed174840db95690033ec40db4e2025-08-20T02:16:59ZengNature PortfolioNature Communications2041-17232025-04-0116111510.1038/s41467-025-58739-wA genome-wide screen identifies genes required for erythroid differentiationGreggory Myers0Ann Friedman1Lei Yu2Narges Pourmandi3Claire Kerpet4Masaki A. Ito5Rilie Saba6Vi Tang7Ayse Bilge Ozel8Ingrid L. Bergin9Craig N. Johnson10Chia-Jui Ku11Yu Wang12Ginette Balbin-Cuesta13Kim-Chew Lim14Zesen Lin15Claire Drysdale16Beth McGee17Ryo Kurita18Yukio Nakamura19Xiaofang Liu20David Siemieniak21Sharon A. Singh22Costas A. Lyssiotis23Ivan Maillard24Lois S. Weisman25James Douglas Engel26Rami Khoriaty27Department of Cell and Developmental Biology, University of MichiganDepartment of Internal Medicine, University of MichiganDepartment of Internal Medicine, University of MichiganCellular and Molecular Biology Program, University of MichiganDepartment of Internal Medicine, University of MichiganDepartment of Internal Medicine, University of MichiganDepartment of Internal Medicine, University of MichiganDepartment of Genetics, Harvard Medical SchoolDepartment of Human Genetics, University of MichiganUnit for Laboratory Animal Medicine, University of MichiganDepartment of Cell and Developmental Biology, University of MichiganDepartment of Cell and Developmental Biology, University of MichiganDepartment of Cell and Developmental Biology, University of MichiganCellular and Molecular Biology Program, University of MichiganDepartment of Cell and Developmental Biology, University of MichiganDepartment of Pharmacology, University of MichiganDepartment of Cell and Developmental Biology, University of MichiganDepartment of Cell and Developmental Biology, University of MichiganDepartment of Research and Development, Central Blood Institute, Blood Service Headquarters, Japanese Red Cross SocietyCell Engineering Division, RIKEN BioResource Research CenterDepartment of Cell and Developmental Biology, University of MichiganLife Sciences Institute, University of MichiganDepartment of Pediatrics, University of MichiganDepartment of Cell and Developmental Biology, University of MichiganDivision of Hematologic Malignancies, Department of Medicine, Memorial Sloan Kettering Cancer CenterDepartment of Cell and Developmental Biology, University of MichiganDepartment of Cell and Developmental Biology, University of MichiganDepartment of Cell and Developmental Biology, University of MichiganAbstract The complete array of genes required for terminal erythroid differentiation remains unknown. To address this knowledge gap, we perform a genome-scale CRISPR knock-out screen in the human erythroid progenitor cell line HUDEP-2 and validate candidate regulators of erythroid differentiation in a custom secondary screen. Comparison of sgRNA abundance in the CRISPR library, proerythroblasts, and orthochromatic erythroblasts, resulted in the identification of genes that are essential for proerythroblast survival and genes that are required for terminal erythroid differentiation. Among the top genes identified are known regulators of erythropoiesis, underscoring the validity of this screen. Notably, using a Log2 fold change of <−1 and false discovery rate of <0.01, the screen identified 277 genes that are required for terminal erythroid differentiation, including multiple genes not previously nominated through GWAS. NHLRC2, which was previously implicated in hemolytic anemia, was a highly ranked gene. We suggest that anemia due to NHLRC2 mutation results at least in part from a defect in erythroid differentiation. Another highly ranked gene in the screen is VAC14, which we validated for its requirement in erythropoiesis in vitro and in vivo. Thus, data from this CRISPR screen may help classify the underlying mechanisms that contribute to erythroid disorders.https://doi.org/10.1038/s41467-025-58739-w |
| spellingShingle | Greggory Myers Ann Friedman Lei Yu Narges Pourmandi Claire Kerpet Masaki A. Ito Rilie Saba Vi Tang Ayse Bilge Ozel Ingrid L. Bergin Craig N. Johnson Chia-Jui Ku Yu Wang Ginette Balbin-Cuesta Kim-Chew Lim Zesen Lin Claire Drysdale Beth McGee Ryo Kurita Yukio Nakamura Xiaofang Liu David Siemieniak Sharon A. Singh Costas A. Lyssiotis Ivan Maillard Lois S. Weisman James Douglas Engel Rami Khoriaty A genome-wide screen identifies genes required for erythroid differentiation Nature Communications |
| title | A genome-wide screen identifies genes required for erythroid differentiation |
| title_full | A genome-wide screen identifies genes required for erythroid differentiation |
| title_fullStr | A genome-wide screen identifies genes required for erythroid differentiation |
| title_full_unstemmed | A genome-wide screen identifies genes required for erythroid differentiation |
| title_short | A genome-wide screen identifies genes required for erythroid differentiation |
| title_sort | genome wide screen identifies genes required for erythroid differentiation |
| url | https://doi.org/10.1038/s41467-025-58739-w |
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