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Scimone C, Donato L, Alibrandi S, Conti A, Bortolotti C, Germanò A, Alafaci C, Vinci SL, D'Angelo R, Sidoti A. Methylome analysis of endothelial cells suggests new insights on sporadic brain arteriovenous malformation. Heliyon 2024; 10:e35126. [PMID: 39170526 PMCID: PMC11336478 DOI: 10.1016/j.heliyon.2024.e35126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Accepted: 07/23/2024] [Indexed: 08/23/2024] Open
Abstract
Arteriovenous malformation of the brain (bAVM) is a vascular phenotype related to brain defective angiogenesis. Involved vessels show impaired expression of vascular differentiation markers resulting in the arteriolar to venule direct shunt. In order to clarify aberrant gene expression occurring in bAVM, here we describe results obtained by methylome analysis performed on endothelial cells (ECs) isolated from bAVM specimens, compared to human cerebral microvascular ECs. Results were validated by quantitative methylation-specific PCR and quantitative realtime-PCR. Differential methylation events occur in genes already linked to bAVM onset, as RBPJ and KRAS. However, among differentially methylated genes, we identified EPHB1 and several other loci involved in EC adhesion as well as in EC/vascular smooth muscle cell (VSMC) crosstalk, suggesting that only endothelial dysfunction might not be sufficient to trigger the bAVM phenotype. Moreover, aberrant methylation pattern was reported for many lncRNA genes targeting transcription factors expressed during neurovascular development. Among these, the YBX1 that was recently shown to target the arteridin coding gene. Finally, in addition to the conventional CpG methylation, we further considered the role of impaired CHG methylation, mainly occurring in brain at embryo stage. We showed as differentially CHG methylated genes are clustered in pathways related to EC homeostasis, as well as to VSMC-EC crosstalk, suggesting as impairment of this interaction plays a prominent role in loss of vascular differentiation, in bAVM phenotype.
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Affiliation(s)
- Concetta Scimone
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125, Messina, Italy
- Department of Biomolecular Strategies, Genetics, Cutting-edge Therapies, I.E.ME.S.T., Via Michele Miraglia 20, Palermo, 90139, Italy
| | - Luigi Donato
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125, Messina, Italy
- Department of Biomolecular Strategies, Genetics, Cutting-edge Therapies, I.E.ME.S.T., Via Michele Miraglia 20, Palermo, 90139, Italy
| | - Simona Alibrandi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125, Messina, Italy
- Department of Biomolecular Strategies, Genetics, Cutting-edge Therapies, I.E.ME.S.T., Via Michele Miraglia 20, Palermo, 90139, Italy
| | - Alfredo Conti
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Bologna, Via Altura 3, 40123, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), Alma Mater Studiorum – University of Bologna, Bologna, Italy
| | - Carlo Bortolotti
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Bologna, Via Altura 3, 40123, Bologna, Italy
| | - Antonino Germanò
- Neurosurgery Unit, Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125, Messina, Italy
| | - Concetta Alafaci
- Neurosurgery Unit, Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125, Messina, Italy
| | - Sergio Lucio Vinci
- Neuroradiology Unit, Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Rosalia D'Angelo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125, Messina, Italy
- Department of Biomolecular Strategies, Genetics, Cutting-edge Therapies, I.E.ME.S.T., Via Michele Miraglia 20, Palermo, 90139, Italy
| | - Antonina Sidoti
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125, Messina, Italy
- Department of Biomolecular Strategies, Genetics, Cutting-edge Therapies, I.E.ME.S.T., Via Michele Miraglia 20, Palermo, 90139, Italy
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2
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Feng C, Tie R, Xin S, Chen Y, Li S, Chen Y, Hu X, Zhou Y, Liu Y, Hu Y, Hu Y, Pan H, Wu Z, Chao H, Zhang S, Ni Q, Huang J, Luo W, Huang H, Chen M. Systematic single-cell analysis reveals dynamic control of transposable element activity orchestrating the endothelial-to-hematopoietic transition. BMC Biol 2024; 22:143. [PMID: 38937802 PMCID: PMC11209969 DOI: 10.1186/s12915-024-01939-5] [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: 08/02/2023] [Accepted: 06/14/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND The endothelial-to-hematopoietic transition (EHT) process during definitive hematopoiesis is highly conserved in vertebrates. Stage-specific expression of transposable elements (TEs) has been detected during zebrafish EHT and may promote hematopoietic stem cell (HSC) formation by activating inflammatory signaling. However, little is known about how TEs contribute to the EHT process in human and mouse. RESULTS We reconstructed the single-cell EHT trajectories of human and mouse and resolved the dynamic expression patterns of TEs during EHT. Most TEs presented a transient co-upregulation pattern along the conserved EHT trajectories, coinciding with the temporal relaxation of epigenetic silencing systems. TE products can be sensed by multiple pattern recognition receptors, triggering inflammatory signaling to facilitate HSC emergence. Interestingly, we observed that hypoxia-related signals were enriched in cells with higher TE expression. Furthermore, we constructed the hematopoietic cis-regulatory network of accessible TEs and identified potential TE-derived enhancers that may boost the expression of specific EHT marker genes. CONCLUSIONS Our study provides a systematic vision of how TEs are dynamically controlled to promote the hematopoietic fate decisions through transcriptional and cis-regulatory networks, and pre-train the immunity of nascent HSCs.
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Affiliation(s)
- Cong Feng
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Bioinformatics Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Ruxiu Tie
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 310058, China
- Institute of Hematology, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou, 310058, China
- Department of Hematology, The Second Clinical Medical College of Shanxi Medical University, Shanxi Medical University, Taiyuan, 030000, China
- Department of Hematology-Oncology, Taizhou Hospital of Zhejiang Province, Linhai, 317000, China
| | - Saige Xin
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yuhao Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Sida Li
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yifan Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaotian Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yincong Zhou
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yongjing Liu
- Bioinformatics Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yueming Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yanshi Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hang Pan
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, 310058, China
| | - Zexu Wu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Haoyu Chao
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shilong Zhang
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qingyang Ni
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jinyan Huang
- Bioinformatics Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Wenda Luo
- Department of Hematology-Oncology, Taizhou Hospital of Zhejiang Province, Linhai, 317000, China.
| | - He Huang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 310058, China.
- Institute of Hematology, Zhejiang University, Hangzhou, 310058, China.
- Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou, 310058, China.
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
- Bioinformatics Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
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3
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Bobrovskikh AV, Zubairova US, Doroshkov AV. Fishing Innate Immune System Properties through the Transcriptomic Single-Cell Data of Teleostei. BIOLOGY 2023; 12:1516. [PMID: 38132342 PMCID: PMC10740722 DOI: 10.3390/biology12121516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
The innate immune system is the first line of defense in multicellular organisms. Danio rerio is widely considered a promising model for IIS-related research, with the most amount of scRNAseq data available among Teleostei. We summarized the scRNAseq and spatial transcriptomics experiments related to the IIS for zebrafish and other Teleostei from the GEO NCBI and the Single-Cell Expression Atlas. We found a considerable number of scRNAseq experiments at different stages of zebrafish development in organs such as the kidney, liver, stomach, heart, and brain. These datasets could be further used to conduct large-scale meta-analyses and to compare the IIS of zebrafish with the mammalian one. However, only a small number of scRNAseq datasets are available for other fish (turbot, salmon, cavefish, and dark sleeper). Since fish biology is very diverse, it would be a major mistake to use zebrafish alone in fish immunology studies. In particular, there is a special need for new scRNAseq experiments involving nonmodel Teleostei, e.g., long-lived species, cancer-resistant fish, and various fish ecotypes.
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Affiliation(s)
- Aleksandr V. Bobrovskikh
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (U.S.Z.); (A.V.D.)
| | - Ulyana S. Zubairova
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (U.S.Z.); (A.V.D.)
- Department of Information Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexey V. Doroshkov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (U.S.Z.); (A.V.D.)
- Department of Genomics and Bioinformatics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036 Krasnoyarsk, Russia
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4
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Li Y, Ding J, Araki D, Zou J, Larochelle A. Modulation of WNT, Activin/Nodal, and MAPK Signaling Pathways Increases Arterial Hemogenic Endothelium and Hematopoietic Stem/Progenitor Cell Formation During Human iPSC Differentiation. Stem Cells 2023; 41:685-697. [PMID: 37220178 PMCID: PMC10346406 DOI: 10.1093/stmcls/sxad040] [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: 02/21/2023] [Accepted: 05/03/2023] [Indexed: 05/25/2023]
Abstract
Several differentiation protocols enable the emergence of hematopoietic stem and progenitor cells (HSPCs) from human-induced pluripotent stem cells (iPSCs), yet optimized schemes to promote the development of HSPCs with self-renewal, multilineage differentiation, and engraftment potential are lacking. To improve human iPSC differentiation methods, we modulated WNT, Activin/Nodal, and MAPK signaling pathways by stage-specific addition of small-molecule regulators CHIR99021, SB431542, and LY294002, respectively, and measured the impact on hematoendothelial formation in culture. Manipulation of these pathways provided a synergy sufficient to enhance formation of arterial hemogenic endothelium (HE) relative to control culture conditions. Importantly, this approach significantly increased production of human HSPCs with self-renewal and multilineage differentiation properties, as well as phenotypic and molecular evidence of progressive maturation in culture. Together, these findings provide a stepwise improvement in human iPSC differentiation protocols and offer a framework for manipulating intrinsic cellular cues to enable de novo generation of human HSPCs with functionality in vivo.
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Affiliation(s)
- Yongqin Li
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Jianyi Ding
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Daisuke Araki
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Jizhong Zou
- iPSC Core Facility, NHLBI, NIH, Bethesda, MD, USA
| | - Andre Larochelle
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
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5
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Feng X, Wang AH, Juan AH, Ko KD, Jiang K, Riparini G, Ciuffoli V, Kaba A, Lopez C, Naz F, Jarnik M, Aliberti E, Hu S, Segalés J, Khateb M, Acevedo-Luna N, Randazzo D, Cheung TH, Muñoz-Cánoves P, Dell'Orso S, Sartorelli V. Polycomb Ezh1 maintains murine muscle stem cell quiescence through non-canonical regulation of Notch signaling. Dev Cell 2023; 58:1052-1070.e10. [PMID: 37105173 PMCID: PMC10330238 DOI: 10.1016/j.devcel.2023.04.005] [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: 12/16/2022] [Revised: 03/08/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023]
Abstract
Organismal homeostasis and regeneration are predicated on committed stem cells that can reside for long periods in a mitotically dormant but reversible cell-cycle arrest state defined as quiescence. Premature escape from quiescence is detrimental, as it results in stem cell depletion, with consequent defective tissue homeostasis and regeneration. Here, we report that Polycomb Ezh1 confers quiescence to murine muscle stem cells (MuSCs) through a non-canonical function. In the absence of Ezh1, MuSCs spontaneously exit quiescence. Following repeated injuries, the MuSC pool is progressively depleted, resulting in failure to sustain proper muscle regeneration. Rather than regulating repressive histone H3K27 methylation, Ezh1 maintains gene expression of the Notch signaling pathway in MuSCs. Selective genetic reconstitution of the Notch signaling corrects stem cell number and re-establishes quiescence of Ezh1-/- MuSCs.
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Affiliation(s)
- Xuesong Feng
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
| | - A Hongjun Wang
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
| | - Aster H Juan
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
| | - Kyung Dae Ko
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
| | - Kan Jiang
- Biodata Mining & Discovery Section, NIAMS, NIH, Bethesda, MD, USA
| | - Giulia Riparini
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
| | - Veronica Ciuffoli
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
| | - Aissah Kaba
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
| | - Christopher Lopez
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
| | - Faiza Naz
- Genomic Technology Section, NIAMS, NIH, Bethesda, MD, USA
| | - Michal Jarnik
- Cell Biology and Neurobiology Branch, NICHD, NIH, Bethesda, MD, USA
| | - Elizabeth Aliberti
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
| | - Shenyuan Hu
- Division of Life Sciences, State Key Laboratory of Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jessica Segalés
- Department of Medicine and Life Sciences (MELIS), Pompeu Fabra University (UPF), Barcelona, Spain
| | - Mamduh Khateb
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
| | - Natalia Acevedo-Luna
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
| | | | - Tom H Cheung
- Division of Life Sciences, State Key Laboratory of Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Pura Muñoz-Cánoves
- Department of Medicine and Life Sciences (MELIS), Pompeu Fabra University (UPF), Barcelona, Spain; Altos Labs Inc, San Diego, CA, USA
| | | | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA.
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6
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Wang D, Li Y, Xu C, Wang H, Huang X, Jin X, Ren S, Gao J, Tong J, Liu J, Zhou J, Shi L. SETD7 promotes lateral plate mesoderm formation by modulating the Wnt/β-catenin signaling pathway. iScience 2023; 26:106917. [PMID: 37378343 PMCID: PMC10291335 DOI: 10.1016/j.isci.2023.106917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 02/16/2023] [Accepted: 05/14/2023] [Indexed: 06/29/2023] Open
Abstract
The role of SET domain containing 7 (SETD7) during human hematopoietic development remains elusive. Here, we found that deletion of SETD7 attenuated the generation of hematopoietic progenitor cells (HPCs) during the induction of hematopoietic differentiation from human embryonic stem cells (hESCs). Further analysis specified that SETD7 was required for lateral plate mesoderm (LPM) specification but dispensable for the generation of endothelial progenitor cells (EPCs) and HPCs. Mechanistically, rather than depending on its histone methyltransferase activity, SETD7 interacted with β-catenin at lysine residue 180 facilitated its degradation. Diminished SETD7 expression led to the accumulation of β-catenin and the consequent activation of the Wnt signaling pathway, which altered LPM patterning and facilitated the production of paraxial mesoderm (PM). Taken together, the findings indicate that SETD7 is related to LPM and PM patterning via posttranslational regulation of the Wnt/β-catenin signaling pathway, providing novel insights into mesoderm specification during hematopoietic differentiation from hESCs.
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Affiliation(s)
- Ding Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Yapu Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Changlu Xu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Hongtao Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Xin Huang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Xu Jin
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Sirui Ren
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Jie Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Jingyuan Tong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Jinhua Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Jiaxi Zhou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Lihong Shi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
- CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
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7
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Li Y, Ding J, Araki D, Zou J, Larochelle A. Modulation of WNT, Activin/Nodal and MAPK Signaling Pathways Increases Arterial Hemogenic Endothelium and Hematopoietic Stem/Progenitor Cell Formation During Human iPSC Differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.21.529379. [PMID: 36865308 PMCID: PMC9980074 DOI: 10.1101/2023.02.21.529379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Several differentiation protocols enable the emergence of hematopoietic stem and progenitor cells (HSPCs) from human induced pluripotent stem cells (iPSCs), yet optimized schemes to promote the development of HSPCs with self-renewal, multilineage differentiation and engraftment potential are lacking. To improve human iPSC differentiation methods, we modulated WNT, Activin/Nodal and MAPK signaling pathways by stage-specific addition of small molecule regulators CHIR99021, SB431542 and LY294002, respectively, and measured the impact on hematoendothelial formation in culture. Manipulation of these pathways provided a synergy sufficient to enhance formation of arterial hemogenic endothelium (HE) relative to control culture conditions. Importantly, this approach significantly increased production of human HSPCs with self-renewal and multilineage differentiation properties, as well as phenotypic and molecular evidence of progressive maturation in culture. Together, these findings provide a stepwise improvement in human iPSC differentiation protocols and offer a framework for manipulating intrinsic cellular cues to enable de novo generation of human HSPCs with functionality in vivo . Significance Statement The ability to produce functional HSPCs by differentiation of human iPSCs ex vivo holds enormous potential for cellular therapy of human blood disorders. However, obstacles still thwart translation of this approach to the clinic. In keeping with the prevailing arterial-specification model, we demonstrate that concurrent modulation of WNT, Activin/Nodal and MAPK signaling pathways by stage-specific addition of small molecules during human iPSC differentiation provides a synergy sufficient to promote arterialization of HE and production of HSPCs with features of definitive hematopoiesis. This simple differentiation scheme provides a unique tool for disease modeling, in vitro drug screening and eventual cell therapies.
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8
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Hanot M, Raby L, Völkel P, Le Bourhis X, Angrand PO. The Contribution of the Zebrafish Model to the Understanding of Polycomb Repression in Vertebrates. Int J Mol Sci 2023; 24:ijms24032322. [PMID: 36768643 PMCID: PMC9916924 DOI: 10.3390/ijms24032322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 01/26/2023] Open
Abstract
Polycomb group (PcG) proteins are highly conserved proteins assembled into two major types of complexes, PRC1 and PRC2, involved in the epigenetic silencing of a wide range of gene expression programs regulating cell fate and tissue development. The crucial role of PRC1 and PRC2 in the fundamental cellular processes and their involvement in human pathologies such as cancer attracted intense attention over the last few decades. Here, we review recent advancements regarding PRC1 and PRC2 function using the zebrafish model. We point out that the unique characteristics of the zebrafish model provide an exceptional opportunity to increase our knowledge of the role of the PRC1 and PRC2 complexes in tissue development, in the maintenance of organ integrity and in pathology.
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Affiliation(s)
- Mariette Hanot
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Ludivine Raby
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Pamela Völkel
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Xuefen Le Bourhis
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Pierre-Olivier Angrand
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
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9
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De Novo Generation of Human Hematopoietic Stem Cells from Pluripotent Stem Cells for Cellular Therapy. Cells 2023; 12:cells12020321. [PMID: 36672255 PMCID: PMC9857267 DOI: 10.3390/cells12020321] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/02/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
The ability to manufacture human hematopoietic stem cells (HSCs) in the laboratory holds enormous promise for cellular therapy of human blood diseases. Several differentiation protocols have been developed to facilitate the emergence of HSCs from human pluripotent stem cells (PSCs). Most approaches employ a stepwise addition of cytokines and morphogens to recapitulate the natural developmental process. However, these protocols globally lack clinical relevance and uniformly induce PSCs to produce hematopoietic progenitors with embryonic features and limited engraftment and differentiation capabilities. This review examines how key intrinsic cues and extrinsic environmental inputs have been integrated within human PSC differentiation protocols to enhance the emergence of definitive hematopoiesis and how advances in genomics set the stage for imminent breakthroughs in this field.
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10
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Jing R, Scarfo I, Najia MA, Lummertz da Rocha E, Han A, Sanborn M, Bingham T, Kubaczka C, Jha DK, Falchetti M, Schlaeger TM, North TE, Maus MV, Daley GQ. EZH1 repression generates mature iPSC-derived CAR T cells with enhanced antitumor activity. Cell Stem Cell 2022; 29:1181-1196.e6. [PMID: 35931029 PMCID: PMC9386785 DOI: 10.1016/j.stem.2022.06.014] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/31/2022] [Accepted: 06/29/2022] [Indexed: 01/12/2023]
Abstract
Human induced pluripotent stem cells (iPSCs) provide a potentially unlimited resource for cell therapies, but the derivation of mature cell types remains challenging. The histone methyltransferase EZH1 is a negative regulator of lymphoid potential during embryonic hematopoiesis. Here, we demonstrate that EZH1 repression facilitates in vitro differentiation and maturation of T cells from iPSCs. Coupling a stroma-free T cell differentiation system with EZH1-knockdown-mediated epigenetic reprogramming, we generated iPSC-derived T cells, termed EZ-T cells, which display a highly diverse T cell receptor (TCR) repertoire and mature molecular signatures similar to those of TCRαβ T cells from peripheral blood. Upon activation, EZ-T cells give rise to effector and memory T cell subsets. When transduced with chimeric antigen receptors (CARs), EZ-T cells exhibit potent antitumor activities in vitro and in xenograft models. Epigenetic remodeling via EZH1 repression allows efficient production of developmentally mature T cells from iPSCs for applications in adoptive cell therapy.
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Affiliation(s)
- Ran Jing
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Irene Scarfo
- Cellular Immunotherapy Program, Massachusetts General Hospital Cancer Center, Charlestown, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Mohamad Ali Najia
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Health Sciences & Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Edroaldo Lummertz da Rocha
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, SC 88040-900, Brazil
| | - Areum Han
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Sanborn
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Trevor Bingham
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Caroline Kubaczka
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Deepak K Jha
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Marcelo Falchetti
- Graduate Program of Pharmacology, Center for Biological Sciences, Federal University of Santa Catarina, Florianópolis, SC 88040-900, Brazil
| | - Thorsten M Schlaeger
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
| | - Trista E North
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA; Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA 02115, USA
| | - Marcela V Maus
- Cellular Immunotherapy Program, Massachusetts General Hospital Cancer Center, Charlestown, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - George Q Daley
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA; Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA 02115, USA.
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11
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Raby L, Völkel P, Hasanpour S, Cicero J, Toillon RA, Adriaenssens E, Van Seuningen I, Le Bourhis X, Angrand PO. Loss of Polycomb Repressive Complex 2 Function Alters Digestive Organ Homeostasis and Neuronal Differentiation in Zebrafish. Cells 2021; 10:cells10113142. [PMID: 34831364 PMCID: PMC8620594 DOI: 10.3390/cells10113142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 11/16/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) mediates histone H3K27me3 methylation and the stable transcriptional repression of a number of gene expression programs involved in the control of cellular identity during development and differentiation. Here, we report on the generation and on the characterization of a zebrafish line harboring a null allele of eed, a gene coding for an essential component of the PRC2. Homozygous eed-deficient mutants present a normal body plan development but display strong defects at the level of the digestive organs, such as reduced size of the pancreas, hepatic steatosis, and a loss of the intestinal structures, to die finally at around 10-12 days post fertilization. In addition, we found that PRC2 loss of function impairs neuronal differentiation in very specific and discrete areas of the brain and increases larval activity in locomotor assays. Our work highlights that zebrafish is a suited model to study human pathologies associated with PRC2 loss of function and H3K27me3 decrease.
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Affiliation(s)
- Ludivine Raby
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR 9020-U 1277 – CANTHER – Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France; (L.R.); (P.V.); (J.C.); (R.-A.T.); (E.A.); (I.V.S.); (X.L.B.)
| | - Pamela Völkel
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR 9020-U 1277 – CANTHER – Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France; (L.R.); (P.V.); (J.C.); (R.-A.T.); (E.A.); (I.V.S.); (X.L.B.)
| | - Shaghayegh Hasanpour
- Department of Fisheries and Animal Sciences, Faculty of Natural Resources, University of Tehran, Karaj 31587-77871, Iran;
| | - Julien Cicero
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR 9020-U 1277 – CANTHER – Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France; (L.R.); (P.V.); (J.C.); (R.-A.T.); (E.A.); (I.V.S.); (X.L.B.)
- Univ. Artois, UR 2465, Laboratoire de la Barrière Hémato-Encéphalique (LBHE), F-62300 Lens, France
| | - Robert-Alain Toillon
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR 9020-U 1277 – CANTHER – Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France; (L.R.); (P.V.); (J.C.); (R.-A.T.); (E.A.); (I.V.S.); (X.L.B.)
| | - Eric Adriaenssens
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR 9020-U 1277 – CANTHER – Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France; (L.R.); (P.V.); (J.C.); (R.-A.T.); (E.A.); (I.V.S.); (X.L.B.)
| | - Isabelle Van Seuningen
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR 9020-U 1277 – CANTHER – Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France; (L.R.); (P.V.); (J.C.); (R.-A.T.); (E.A.); (I.V.S.); (X.L.B.)
| | - Xuefen Le Bourhis
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR 9020-U 1277 – CANTHER – Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France; (L.R.); (P.V.); (J.C.); (R.-A.T.); (E.A.); (I.V.S.); (X.L.B.)
| | - Pierre-Olivier Angrand
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR 9020-U 1277 – CANTHER – Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France; (L.R.); (P.V.); (J.C.); (R.-A.T.); (E.A.); (I.V.S.); (X.L.B.)
- Correspondence: ; Tel.: +33-3-2033-6222
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12
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Sugden WW, North TE. Making Blood from the Vessel: Extrinsic and Environmental Cues Guiding the Endothelial-to-Hematopoietic Transition. Life (Basel) 2021; 11:life11101027. [PMID: 34685398 PMCID: PMC8539454 DOI: 10.3390/life11101027] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 01/10/2023] Open
Abstract
It is increasingly recognized that specialized subsets of endothelial cells carry out unique functions in specific organs and regions of the vascular tree. Perhaps the most striking example of this specialization is the ability to contribute to the generation of the blood system, in which a distinct population of “hemogenic” endothelial cells in the embryo transforms irreversibly into hematopoietic stem and progenitor cells that produce circulating erythroid, myeloid and lymphoid cells for the lifetime of an animal. This review will focus on recent advances made in the zebrafish model organism uncovering the extrinsic and environmental factors that facilitate hemogenic commitment and the process of endothelial-to-hematopoietic transition that produces blood stem cells. We highlight in particular biomechanical influences of hemodynamic forces and the extracellular matrix, metabolic and sterile inflammatory cues present during this developmental stage, and outline new avenues opened by transcriptomic-based approaches to decipher cell–cell communication mechanisms as examples of key signals in the embryonic niche that regulate hematopoiesis.
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Affiliation(s)
- Wade W. Sugden
- Stem Cell Program, Department of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA;
- Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA 02115, USA
| | - Trista E. North
- Stem Cell Program, Department of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA;
- Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA 02115, USA
- Correspondence:
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