1
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Salignon J, Millan-Ariño L, Garcia MU, Riedel CG. Cactus: A user-friendly and reproducible ATAC-Seq and mRNA-Seq analysis pipeline for data preprocessing, differential analysis, and enrichment analysis. Genomics 2024; 116:110858. [PMID: 38735595 DOI: 10.1016/j.ygeno.2024.110858] [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: 02/09/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/14/2024]
Abstract
The ever decreasing cost of Next-Generation Sequencing coupled with the emergence of efficient and reproducible analysis pipelines has rendered genomic methods more accessible. However, downstream analyses are basic or missing in most workflows, creating a significant barrier for non-bioinformaticians. To help close this gap, we developed Cactus, an end-to-end pipeline for analyzing ATAC-Seq and mRNA-Seq data, either separately or jointly. Its Nextflow-, container-, and virtual environment-based architecture ensures efficient and reproducible analyses. Cactus preprocesses raw reads, conducts differential analyses between conditions, and performs enrichment analyses in various databases, including DNA-binding motifs, ChIP-Seq binding sites, chromatin states, and ontologies. We demonstrate the utility of Cactus in a multi-modal and multi-species case study as well as by showcasing its unique capabilities as compared to other ATAC-Seq pipelines. In conclusion, Cactus can assist researchers in gaining comprehensive insights from chromatin accessibility and gene expression data in a quick, user-friendly, and reproducible manner.
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Affiliation(s)
- Jérôme Salignon
- Department of Bioscience and Nutrition, Karolinska Institute, Blickagången 16, Huddinge SE-141 83, Sweden.
| | - Lluís Millan-Ariño
- Department of Bioscience and Nutrition, Karolinska Institute, Blickagången 16, Huddinge SE-141 83, Sweden
| | - Maxime U Garcia
- National Genomics Infrastructure, Science for Life Laboratory, Tomtebodavägen 23A, Solna SE-171 65, Sweden; Department of Oncology-Pathology, Karolinska Institute, Visionsgatan 4, Solna SE-171 64, Sweden
| | - Christian G Riedel
- Department of Bioscience and Nutrition, Karolinska Institute, Blickagången 16, Huddinge SE-141 83, Sweden.
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2
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Shin YJ, Lee JH. Exploring the Molecular and Developmental Dynamics of Endothelial Cell Differentiation. Int J Stem Cells 2024; 17:15-29. [PMID: 37879853 PMCID: PMC10899884 DOI: 10.15283/ijsc23086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/06/2023] [Accepted: 09/05/2023] [Indexed: 10/27/2023] Open
Abstract
The development and differentiation of endothelial cells (ECs) are fundamental processes with significant implications for both health and disease. ECs, which are found in all organs and blood vessels, play a crucial role in facilitating nutrient and waste exchange and maintaining proper vessel function. Understanding the intricate signaling pathways involved in EC development holds great promise for enhancing vascularization, tissue engineering, and vascular regeneration. Hematopoietic stem cells originating from hemogenic ECs, give rise to diverse immune cell populations, and the interaction between ECs and immune cells is vital for maintaining vascular integrity and regulating immune responses. Dysregulation of vascular development pathways can lead to various diseases, including cancer, where tumor-specific ECs promote tumor growth through angiogenesis. Recent advancements in single-cell genomics and in vivo genetic labeling have shed light on EC development, plasticity, and heterogeneity, uncovering tissue-specific gene expression and crucial signaling pathways. This review explores the potential of ECs in various applications, presenting novel opportunities for advancing vascular medicine and treatment strategies.
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Affiliation(s)
- Yu Jung Shin
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Jung Hyun Lee
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Dermatology, School of Medicine, University of Washington, Seattle, WA, USA
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3
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Silvério-Alves R, Kurochkin I, Rydström A, Vazquez Echegaray C, Haider J, Nicholls M, Rode C, Thelaus L, Lindgren AY, Ferreira AG, Brandão R, Larsson J, de Bruijn MFTR, Martin-Gonzalez J, Pereira CF. GATA2 mitotic bookmarking is required for definitive haematopoiesis. Nat Commun 2023; 14:4645. [PMID: 37580379 PMCID: PMC10425459 DOI: 10.1038/s41467-023-40391-x] [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: 08/08/2022] [Accepted: 07/26/2023] [Indexed: 08/16/2023] Open
Abstract
In mitosis, most transcription factors detach from chromatin, but some are retained and bookmark genomic sites. Mitotic bookmarking has been implicated in lineage inheritance, pluripotency and reprogramming. However, the biological significance of this mechanism in vivo remains unclear. Here, we address mitotic retention of the hemogenic factors GATA2, GFI1B and FOS during haematopoietic specification. We show that GATA2 remains bound to chromatin throughout mitosis, in contrast to GFI1B and FOS, via C-terminal zinc finger-mediated DNA binding. GATA2 bookmarks a subset of its interphase targets that are co-enriched for RUNX1 and other regulators of definitive haematopoiesis. Remarkably, homozygous mice harbouring the cyclin B1 mitosis degradation domain upstream Gata2 partially phenocopy knockout mice. Degradation of GATA2 at mitotic exit abolishes definitive haematopoiesis at aorta-gonad-mesonephros, placenta and foetal liver, but does not impair yolk sac haematopoiesis. Our findings implicate GATA2-mediated mitotic bookmarking as critical for definitive haematopoiesis and highlight a dependency on bookmarkers for lineage commitment.
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Affiliation(s)
- Rita Silvério-Alves
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
- CNC - Centre for Neuroscience and Cell Biology, University of Coimbra, Largo Marquês do Pombal, 3004-517, Coimbra, Portugal
- Doctoral Programme in Experimental Biology and Biomedicine, University of Coimbra, Largo Marquês do Pombal, 3004-517, Coimbra, Portugal
| | - Ilia Kurochkin
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Anna Rydström
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Camila Vazquez Echegaray
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Jakob Haider
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Matthew Nicholls
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Christina Rode
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Louise Thelaus
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Aida Yifter Lindgren
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Alexandra Gabriela Ferreira
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
- CNC - Centre for Neuroscience and Cell Biology, University of Coimbra, Largo Marquês do Pombal, 3004-517, Coimbra, Portugal
- Doctoral Programme in Experimental Biology and Biomedicine, University of Coimbra, Largo Marquês do Pombal, 3004-517, Coimbra, Portugal
| | - Rafael Brandão
- Core Facility for Transgenic Mice, Department of Experimental Medicine, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Jonas Larsson
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Marella F T R de Bruijn
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Javier Martin-Gonzalez
- Core Facility for Transgenic Mice, Department of Experimental Medicine, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Carlos-Filipe Pereira
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden.
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden.
- CNC - Centre for Neuroscience and Cell Biology, University of Coimbra, Largo Marquês do Pombal, 3004-517, Coimbra, Portugal.
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4
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Reprogramming cell fates towards novel cancer immunotherapies. Curr Opin Pharmacol 2022; 67:102312. [PMID: 36335715 DOI: 10.1016/j.coph.2022.102312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/18/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
Abstract
Recent advances in our understanding of host immune and cancer cells interactions have made immunotherapy a prominent choice in cancer treatment. Despite such promise, cell-based immunotherapies remain inapplicable to many patients due to severe limitations in the availability and quality of immune cells isolated from donors. Reprogramming technologies that facilitate the engineering of cell types of interest, are emerging as a putative solution to such challenges. Here we focus on the recent progress being made in reprogramming technologies with respect to the immune system and their potential for clinical applications.
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5
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Bigas A, Galán Palma L, Kartha GM, Giorgetti A. Using Pluripotent Stem Cells to Understand Normal and Leukemic Hematopoietic Development. Stem Cells Transl Med 2022; 11:1123-1134. [PMID: 36398586 PMCID: PMC9672852 DOI: 10.1093/stcltm/szac071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/29/2022] [Indexed: 12/02/2023] Open
Abstract
Several decades have passed since the generation of the first embryonic stem cell (ESC) lines both in mice and in humans. Since then, stem cell biologists have tried to understand their potential biological and clinical uses for their implementation in regenerative medicine. The hematopoietic field was a pioneer in establishing the potential use for the development of blood cell products and clinical applications; however, early expectations have been truncated by the difficulty in generating bonafide hematopoietic stem cells (HSCs). Despite some progress in understanding the origin of HSCs during embryonic development, the reproduction of this process in vitro is still not possible, but the knowledge acquired in the embryo is slowly being implemented for mouse and human pluripotent stem cells (PSCs). In contrast, ESC-derived hematopoietic cells may recapitulate some leukemic transformation processes when exposed to oncogenic drivers. This would be especially useful to model prenatal leukemia development or other leukemia-predisposing syndromes, which are difficult to study. In this review, we will review the state of the art of the use of PSCs as a model for hematopoietic and leukemia development.
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Affiliation(s)
- Anna Bigas
- Program in Cancer Research, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), CIBERONC, Barcelona, Spain
- Josep Carreras Leukemia Research Institute (IJC), Barcelona, Spain
| | - Luis Galán Palma
- Program in Cancer Research, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), CIBERONC, Barcelona, Spain
- Josep Carreras Leukemia Research Institute (IJC), Barcelona, Spain
| | - Gayathri M Kartha
- Program in Cancer Research, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), CIBERONC, Barcelona, Spain
- Josep Carreras Leukemia Research Institute (IJC), Barcelona, Spain
| | - Alessandra Giorgetti
- Regenerative Medicine Program, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), Barcelona, Spain
- Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences, Barcelona University, Barcelona, Spain
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6
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Kotmayer L, Romero‐Moya D, Marin‐Bejar O, Kozyra E, Català A, Bigas A, Wlodarski MW, Bödör C, Giorgetti A. GATA2 deficiency and MDS/AML: Experimental strategies for disease modelling and future therapeutic prospects. Br J Haematol 2022; 199:482-495. [PMID: 35753998 PMCID: PMC9796058 DOI: 10.1111/bjh.18330] [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: 04/07/2022] [Revised: 06/10/2022] [Accepted: 06/11/2022] [Indexed: 12/30/2022]
Abstract
The importance of predisposition to leukaemia in clinical practice is being increasingly recognized. This is emphasized by the establishment of a novel WHO disease category in 2016 called "myeloid neoplasms with germline predisposition". A major syndrome within this group is GATA2 deficiency, a heterogeneous immunodeficiency syndrome with a very high lifetime risk to develop myelodysplastic syndrome (MDS) and acute myeloid leukaemia (AML). GATA2 deficiency has been identified as the most common hereditary cause of MDS in adolescents with monosomy 7. Allogenic haematopoietic stem cell transplantation is the only curative option; however, chances of survival decrease with progression of immunodeficiency and MDS evolution. Penetrance and expressivity within families carrying GATA2 mutations is often variable, suggesting that co-operating extrinsic events are required to trigger the disease. Predictive tools are lacking, and intrafamilial heterogeneity is poorly understood; hence there is a clear unmet medical need. On behalf of the ERAPerMed GATA2 HuMo consortium, in this review we describe the genetic, clinical, and biological aspects of familial GATA2-related MDS, highlighting the importance of developing robust disease preclinical models to improve early detection and clinical decision-making of GATA2 carriers.
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Affiliation(s)
- Lili Kotmayer
- HCEMM‐SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer ResearchSemmelweis UniversityBudapestHungary
| | - Damia Romero‐Moya
- Regenerative Medicine ProgramInstitut d'Investigació Biomèdica de Bellvitge (IDIBELL)BarcelonaSpain
| | - Oskar Marin‐Bejar
- Regenerative Medicine ProgramInstitut d'Investigació Biomèdica de Bellvitge (IDIBELL)BarcelonaSpain
| | - Emilia Kozyra
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of MedicineUniversity of FreiburgFreiburgGermany,Faculty of BiologyUniversity of FreiburgFreiburgGermany
| | - Albert Català
- Department of Hematology and OncologyInstitut de Recerca Sant Joan de DéuHospital Sant Joan de DeuBarcelonaSpain,Biomedical Network Research Centre on Rare DiseasesInstituto de Salud Carlos IIIMadridSpain
| | - Anna Bigas
- Cancer Research ProgramInstitut Hospital del Mar d'Investigacions Mèdiques, CIBERONC, Hospital del MarBarcelonaSpain,Josep Carreras Research Institute (IJC), BadalonaBarcelonaSpain
| | - Marcin W. Wlodarski
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of MedicineUniversity of FreiburgFreiburgGermany,Department of HematologySt. Jude Children's Research HospitalMemphisTennesseeUSA
| | - Csaba Bödör
- HCEMM‐SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer ResearchSemmelweis UniversityBudapestHungary
| | - Alessandra Giorgetti
- Regenerative Medicine ProgramInstitut d'Investigació Biomèdica de Bellvitge (IDIBELL)BarcelonaSpain,Fondazione Pisana Per la Scienza ONLUS (FPS)San Giuliano TermeItaly,Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health SciencesBarcelona UniversityBarcelonaSpain
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7
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Quek H, White AR. Patient-specific monocyte-derived microglia as a screening tool for neurodegenerative diseases. Neural Regen Res 2022; 18:955-958. [PMID: 36254974 PMCID: PMC9827786 DOI: 10.4103/1673-5374.355740] [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] [Indexed: 11/05/2022] Open
Abstract
Microglia, the main driver of neuroinflammation, play a central role in the initiation and exacerbation of various neurodegenerative diseases and are now considered a promising therapeutic target. Previous studies on in vitro human microglia and in vivo rodent models lacked scalability, consistency, or physiological relevance, which deterred successful therapeutic outcomes for the past decade. Here we review human blood monocyte-derived microglia-like cells as a robust and consistent approach to generate a patient-specific microglia-like model that can be used in extensive cohort studies for drug testing. We will highlight the strength and applicability of human blood monocyte-derived microglia-like cells to increase translational outcomes by reviewing the advantages of human blood monocyte-derived microglia-like cells in addressing patient heterogeneity and stratification, the basis of personalized medicine.
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Affiliation(s)
- Hazel Quek
- Mental Health and Neuroscience, QIMR Berghofer Medical Research Institute, The University of Queensland, Brisbane, QLD, Australia,School of Biomedical Science, The University of Queensland, Brisbane, QLD, Australia,Correspondence to: Hazel Quek, .
| | - Anthony R. White
- Mental Health and Neuroscience, QIMR Berghofer Medical Research Institute, The University of Queensland, Brisbane, QLD, Australia,School of Biomedical Science, The University of Queensland, Brisbane, QLD, Australia
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8
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Hörnblad A, Remeseiro S. Epigenetics, Enhancer Function and 3D Chromatin Organization in Reprogramming to Pluripotency. Cells 2022; 11:cells11091404. [PMID: 35563711 PMCID: PMC9105757 DOI: 10.3390/cells11091404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 12/22/2022] Open
Abstract
Genome architecture, epigenetics and enhancer function control the fate and identity of cells. Reprogramming to induced pluripotent stem cells (iPSCs) changes the transcriptional profile and chromatin landscape of the starting somatic cell to that of the pluripotent cell in a stepwise manner. Changes in the regulatory networks are tightly regulated during normal embryonic development to determine cell fate, and similarly need to function in cell fate control during reprogramming. Switching off the somatic program and turning on the pluripotent program involves a dynamic reorganization of the epigenetic landscape, enhancer function, chromatin accessibility and 3D chromatin topology. Within this context, we will review here the current knowledge on the processes that control the establishment and maintenance of pluripotency during somatic cell reprogramming.
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Affiliation(s)
- Andreas Hörnblad
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, 901 87 Umeå, Sweden
- Correspondence: (A.H.); (S.R.)
| | - Silvia Remeseiro
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, 901 87 Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, 901 87 Umeå, Sweden
- Correspondence: (A.H.); (S.R.)
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9
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Rosa FF, Pires CF, Kurochkin I, Halitzki E, Zahan T, Arh N, Zimmermannová O, Ferreira AG, Li H, Karlsson S, Scheding S, Pereira CF. Single-cell transcriptional profiling informs efficient reprogramming of human somatic cells to cross-presenting dendritic cells. Sci Immunol 2022; 7:eabg5539. [PMID: 35245086 DOI: 10.1126/sciimmunol.abg5539] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Type 1 conventional dendritic cells (cDC1s) are rare immune cells critical for the induction of antigen-specific cytotoxic CD8+ T cells, although the genetic program driving human cDC1 specification remains largely unexplored. We previously identified PU.1, IRF8, and BATF3 transcription factors as sufficient to induce cDC1 fate in mouse fibroblasts, but reprogramming of human somatic cells was limited by low efficiency. Here, we investigated single-cell transcriptional dynamics during human cDC1 reprogramming. Human induced cDC1s (hiDC1s) generated from embryonic fibroblasts gradually acquired a global cDC1 transcriptional profile and expressed antigen presentation signatures, whereas other DC subsets were not induced at the single-cell level during the reprogramming process. We extracted gene modules associated with successful reprogramming and identified inflammatory signaling and the cDC1-inducing transcription factor network as key drivers of the process. Combining IFN-γ, IFN-β, and TNF-α with constitutive expression of cDC1-inducing transcription factors led to improvement of reprogramming efficiency by 190-fold. hiDC1s engulfed dead cells, secreted inflammatory cytokines, and performed antigen cross-presentation, key cDC1 functions. This approach allowed efficient hiDC1 generation from adult fibroblasts and mesenchymal stromal cells. Mechanistically, PU.1 showed dominant and independent chromatin targeting at early phases of reprogramming, recruiting IRF8 and BATF3 to shared binding sites. The cooperative binding at open enhancers and promoters led to silencing of fibroblast genes and activation of a cDC1 program. These findings provide mechanistic insights into human cDC1 specification and reprogramming and represent a platform for generating patient-tailored cDC1s, a long-sought DC subset for vaccination strategies in cancer immunotherapy.
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Affiliation(s)
- Fábio F Rosa
- Molecular Medicine and Gene Therapy, Lund Stem Cell Centre, Lund University, BMC A12, 221 84 Lund, Sweden.,Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84 Lund, Sweden.,Centre for Neuroscience and Cell Biology, University of Coimbra, Largo Marquês do Pombal 3004-517 Coimbra, Portugal.,Doctoral Programme in Experimental Biology and Biomedicine, University of Coimbra, Coimbra, Portugal
| | - Cristiana F Pires
- Molecular Medicine and Gene Therapy, Lund Stem Cell Centre, Lund University, BMC A12, 221 84 Lund, Sweden.,Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84 Lund, Sweden.,Centre for Neuroscience and Cell Biology, University of Coimbra, Largo Marquês do Pombal 3004-517 Coimbra, Portugal
| | - Ilia Kurochkin
- Molecular Medicine and Gene Therapy, Lund Stem Cell Centre, Lund University, BMC A12, 221 84 Lund, Sweden.,Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84 Lund, Sweden.,Skolkovo Institute of Science and Technology, Nobel Street, Building 3, Moscow 143026, Russia
| | - Evelyn Halitzki
- Molecular Medicine and Gene Therapy, Lund Stem Cell Centre, Lund University, BMC A12, 221 84 Lund, Sweden.,Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84 Lund, Sweden
| | - Tasnim Zahan
- Molecular Medicine and Gene Therapy, Lund Stem Cell Centre, Lund University, BMC A12, 221 84 Lund, Sweden.,Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84 Lund, Sweden
| | - Nejc Arh
- Molecular Medicine and Gene Therapy, Lund Stem Cell Centre, Lund University, BMC A12, 221 84 Lund, Sweden.,Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84 Lund, Sweden
| | - Olga Zimmermannová
- Molecular Medicine and Gene Therapy, Lund Stem Cell Centre, Lund University, BMC A12, 221 84 Lund, Sweden.,Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84 Lund, Sweden
| | - Alexandra G Ferreira
- Molecular Medicine and Gene Therapy, Lund Stem Cell Centre, Lund University, BMC A12, 221 84 Lund, Sweden.,Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84 Lund, Sweden.,Centre for Neuroscience and Cell Biology, University of Coimbra, Largo Marquês do Pombal 3004-517 Coimbra, Portugal.,Doctoral Programme in Experimental Biology and Biomedicine, University of Coimbra, Coimbra, Portugal
| | - Hongzhe Li
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund University, BMC B12, 221 84 Lund, Sweden
| | - Stefan Karlsson
- Molecular Medicine and Gene Therapy, Lund Stem Cell Centre, Lund University, BMC A12, 221 84 Lund, Sweden
| | - Stefan Scheding
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund University, BMC B12, 221 84 Lund, Sweden.,Department of Hematology, Skåne University Hospital Lund, Skåne, 222 42 Lund, Sweden
| | - Carlos-Filipe Pereira
- Molecular Medicine and Gene Therapy, Lund Stem Cell Centre, Lund University, BMC A12, 221 84 Lund, Sweden.,Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84 Lund, Sweden.,Centre for Neuroscience and Cell Biology, University of Coimbra, Largo Marquês do Pombal 3004-517 Coimbra, Portugal
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10
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Mack R, Zhang L, Breslin Sj P, Zhang J. The Fetal-to-Adult Hematopoietic Stem Cell Transition and its Role in Childhood Hematopoietic Malignancies. Stem Cell Rev Rep 2021; 17:2059-2080. [PMID: 34424480 DOI: 10.1007/s12015-021-10230-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 01/07/2023]
Abstract
As with most organ systems that undergo continuous generation and maturation during the transition from fetal to adult life, the hematopoietic and immune systems also experience dynamic changes. Such changes lead to many unique features in blood cell function and immune responses in early childhood. The blood cells and immune cells in neonates are a mixture of fetal and adult origin due to the co-existence of both fetal and adult types of hematopoietic stem cells (HSCs) and progenitor cells (HPCs). Fetal blood and immune cells gradually diminish during maturation of the infant and are almost completely replaced by adult types of cells by 3 to 4 weeks after birth in mice. Such features in early childhood are associated with unique features of hematopoietic and immune diseases, such as leukemia, at these developmental stages. Therefore, understanding the cellular and molecular mechanisms by which hematopoietic and immune changes occur throughout ontogeny will provide useful information for the study and treatment of pediatric blood and immune diseases. In this review, we summarize the most recent studies on hematopoietic initiation during early embryonic development, the expansion of both fetal and adult types of HSCs and HPCs in the fetal liver and fetal bone marrow stages, and the shift from fetal to adult hematopoiesis/immunity during neonatal/infant development. We also discuss the contributions of fetal types of HSCs/HPCs to childhood leukemias.
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Affiliation(s)
- Ryan Mack
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA
| | - Lei Zhang
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA
| | - Peter Breslin Sj
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA.,Departments of Molecular/Cellular Physiology and Biology, Loyola University Medical Center and Loyola University Chicago, Chicago, IL, 60660, USA
| | - Jiwang Zhang
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA.
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11
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Wang N, Lefaudeux D, Mazumder A, Li JJ, Hoffmann A. Identifying the combinatorial control of signal-dependent transcription factors. PLoS Comput Biol 2021; 17:e1009095. [PMID: 34166361 PMCID: PMC8263068 DOI: 10.1371/journal.pcbi.1009095] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 07/07/2021] [Accepted: 05/18/2021] [Indexed: 12/13/2022] Open
Abstract
The effectiveness of immune responses depends on the precision of stimulus-responsive gene expression programs. Cells specify which genes to express by activating stimulus-specific combinations of stimulus-induced transcription factors (TFs). Their activities are decoded by a gene regulatory strategy (GRS) associated with each response gene. Here, we examined whether the GRSs of target genes may be inferred from stimulus-response (input-output) datasets, which remains an unresolved model-identifiability challenge. We developed a mechanistic modeling framework and computational workflow to determine the identifiability of all possible combinations of synergistic (AND) or non-synergistic (OR) GRSs involving three transcription factors. Considering different sets of perturbations for stimulus-response studies, we found that two thirds of GRSs are easily distinguishable but that substantially more quantitative data is required to distinguish the remaining third. To enhance the accuracy of the inference with timecourse experimental data, we developed an advanced error model that avoids error overestimates by distinguishing between value and temporal error. Incorporating this error model into a Bayesian framework, we show that GRS models can be identified for individual genes by considering multiple datasets. Our analysis rationalizes the allocation of experimental resources by identifying most informative TF stimulation conditions. Applying this computational workflow to experimental data of immune response genes in macrophages, we found that a much greater fraction of genes are combinatorially controlled than previously reported by considering compensation among transcription factors. Specifically, we revealed that a group of known NFκB target genes may also be regulated by IRF3, which is supported by chromatin immuno-precipitation analysis. Our study provides a computational workflow for designing and interpreting stimulus-response gene expression studies to identify underlying gene regulatory strategies and further a mechanistic understanding.
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Affiliation(s)
- Ning Wang
- Institute for Quantitative and Computational Biosciences (QCBio), University of California, Los Angeles, California, United States of America
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, United States of America
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, California, United States of America
| | - Diane Lefaudeux
- Institute for Quantitative and Computational Biosciences (QCBio), University of California, Los Angeles, California, United States of America
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, United States of America
| | - Anup Mazumder
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, United States of America
| | - Jingyi Jessica Li
- Institute for Quantitative and Computational Biosciences (QCBio), University of California, Los Angeles, California, United States of America
- Department of Statistics, University of California, Los Angeles, California, United States of America
| | - Alexander Hoffmann
- Institute for Quantitative and Computational Biosciences (QCBio), University of California, Los Angeles, California, United States of America
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, United States of America
- * E-mail:
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12
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Lange L, Morgan M, Schambach A. The hemogenic endothelium: a critical source for the generation of PSC-derived hematopoietic stem and progenitor cells. Cell Mol Life Sci 2021; 78:4143-4160. [PMID: 33559689 PMCID: PMC8164610 DOI: 10.1007/s00018-021-03777-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 12/16/2020] [Accepted: 01/15/2021] [Indexed: 12/02/2022]
Abstract
In vitro generation of hematopoietic cells and especially hematopoietic stem cells (HSCs) from human pluripotent stem cells (PSCs) are subject to intensive research in recent decades, as these cells hold great potential for regenerative medicine and autologous cell replacement therapies. Despite many attempts, in vitro, de novo generation of bona fide HSCs remains challenging, and we are still far away from their clinical use, due to insufficient functionality and quantity of the produced HSCs. The challenges of generating PSC-derived HSCs are already apparent in early stages of hemato-endothelial specification with the limitation of recapitulating complex, dynamic processes of embryonic hematopoietic ontogeny in vitro. Further, these current shortcomings imply the incompleteness of our understanding of human ontogenetic processes from embryonic mesoderm over an intermediate, specialized hemogenic endothelium (HE) to their immediate progeny, the HSCs. In this review, we examine the recent investigations of hemato-endothelial ontogeny and recently reported progress for the conversion of PSCs and other promising somatic cell types towards HSCs with the focus on the crucial and inevitable role of the HE to achieve the long-standing goal—to generate therapeutically applicable PSC-derived HSCs in vitro.
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Affiliation(s)
- Lucas Lange
- Institute of Experimental Hematology, Hannover Medical School, 30625, Hannover, Germany.,REBIRTH, Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625, Hannover, Germany
| | - Michael Morgan
- Institute of Experimental Hematology, Hannover Medical School, 30625, Hannover, Germany.,REBIRTH, Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625, Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, 30625, Hannover, Germany. .,REBIRTH, Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625, Hannover, Germany. .,Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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13
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Elsaid R, Soares-da-Silva F, Peixoto M, Amiri D, Mackowski N, Pereira P, Bandeira A, Cumano A. Hematopoiesis: A Layered Organization Across Chordate Species. Front Cell Dev Biol 2020; 8:606642. [PMID: 33392196 PMCID: PMC7772317 DOI: 10.3389/fcell.2020.606642] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/19/2020] [Indexed: 12/12/2022] Open
Abstract
The identification of distinct waves of progenitors during development, each corresponding to a specific time, space, and function, provided the basis for the concept of a "layered" organization in development. The concept of a layered hematopoiesis was established by classical embryology studies in birds and amphibians. Recent progress in generating reliable lineage tracing models together with transcriptional and proteomic analyses in single cells revealed that, also in mammals, the hematopoietic system evolves in successive waves of progenitors with distinct properties and fate. During embryogenesis, sequential waves of hematopoietic progenitors emerge at different anatomic sites, generating specific cell types with distinct functions and tissue homing capacities. The first progenitors originate in the yolk sac before the emergence of hematopoietic stem cells, some giving rise to progenies that persist throughout life. Hematopoietic stem cell-derived cells that protect organisms against environmental pathogens follow the same sequential strategy, with subsets of lymphoid cells being only produced during embryonic development. Growing evidence indicates that fetal immune cells contribute to the proper development of the organs they seed and later ensure life-long tissue homeostasis and immune protection. They include macrophages, mast cells, some γδ T cells, B-1 B cells, and innate lymphoid cells, which have "non-redundant" functions, and early perturbations in their development or function affect immunity in the adult. These observations challenged the view that all hematopoietic cells found in the adult result from constant and monotonous production from bone marrow-resident hematopoietic stem cells. In this review, we evaluate evidence for a layered hematopoietic system across species. We discuss mechanisms and selective pressures leading to the temporal generation of different cell types. We elaborate on the consequences of disturbing fetal immune cells on tissue homeostasis and immune development later in life.
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Affiliation(s)
- Ramy Elsaid
- Unit of Lymphocytes and Immunity, Immunology Department, Institut Pasteur, Paris, France
- INSERM U1223, Paris, France
- Université de Paris, Céllule Pasteur, Paris, France
| | - Francisca Soares-da-Silva
- Unit of Lymphocytes and Immunity, Immunology Department, Institut Pasteur, Paris, France
- INSERM U1223, Paris, France
- Université de Paris, Céllule Pasteur, Paris, France
- I3S—Instituto de Investigação e Inovação em Saúde and INEB—Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
- Graduate Program in Areas of Basic and Applied Biology, Instituto de Ciências Biomeìdicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Marcia Peixoto
- Unit of Lymphocytes and Immunity, Immunology Department, Institut Pasteur, Paris, France
- INSERM U1223, Paris, France
- Université de Paris, Céllule Pasteur, Paris, France
- I3S—Instituto de Investigação e Inovação em Saúde and INEB—Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Dali Amiri
- Unit of Lymphocytes and Immunity, Immunology Department, Institut Pasteur, Paris, France
- INSERM U1223, Paris, France
- Université de Paris, Céllule Pasteur, Paris, France
| | - Nathan Mackowski
- Unit of Lymphocytes and Immunity, Immunology Department, Institut Pasteur, Paris, France
- INSERM U1223, Paris, France
- Université de Paris, Céllule Pasteur, Paris, France
| | - Pablo Pereira
- Unit of Lymphocytes and Immunity, Immunology Department, Institut Pasteur, Paris, France
- INSERM U1223, Paris, France
- Université de Paris, Céllule Pasteur, Paris, France
| | - Antonio Bandeira
- Unit of Lymphocytes and Immunity, Immunology Department, Institut Pasteur, Paris, France
- INSERM U1223, Paris, France
- Université de Paris, Céllule Pasteur, Paris, France
| | - Ana Cumano
- Unit of Lymphocytes and Immunity, Immunology Department, Institut Pasteur, Paris, France
- INSERM U1223, Paris, France
- Université de Paris, Céllule Pasteur, Paris, France
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14
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Arumugam K, Shin W, Schiavone V, Vlahos L, Tu X, Carnevali D, Kesner J, Paull EO, Romo N, Subramaniam P, Worley J, Tan X, Califano A, Cosma MP. The Master Regulator Protein BAZ2B Can Reprogram Human Hematopoietic Lineage-Committed Progenitors into a Multipotent State. Cell Rep 2020; 33:108474. [PMID: 33296649 DOI: 10.1016/j.celrep.2020.108474] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/25/2020] [Accepted: 11/12/2020] [Indexed: 01/03/2023] Open
Abstract
Bi-species, fusion-mediated, somatic cell reprogramming allows precise, organism-specific tracking of unknown lineage drivers. The fusion of Tcf7l1-/- murine embryonic stem cells with EBV-transformed human B cell lymphocytes, leads to the generation of bi-species heterokaryons. Human mRNA transcript profiling at multiple time points permits the tracking of the reprogramming of B cell nuclei to a multipotent state. Interrogation of a human B cell regulatory network with gene expression signatures identifies 8 candidate master regulator proteins. Of these 8 candidates, ectopic expression of BAZ2B, from the bromodomain family, efficiently reprograms hematopoietic committed progenitors into a multipotent state and significantly enhances their long-term clonogenicity, stemness, and engraftment in immunocompromised mice. Unbiased systems biology approaches let us identify the early driving events of human B cell reprogramming.
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Affiliation(s)
- Karthik Arumugam
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - William Shin
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Valentina Schiavone
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Lukas Vlahos
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Xiaochuan Tu
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Davide Carnevali
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Jordan Kesner
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Evan O Paull
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Neus Romo
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Prem Subramaniam
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Jeremy Worley
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Xiangtian Tan
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, J.P. Sulzberger Columbia Genome Center, Department of Biomedical Informatics, Department of Biochemistry and Molecular Biophysics, Department of Medicine, Columbia University, New York, NY, USA.
| | - Maria Pia Cosma
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain; Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China; CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
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15
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Caldwell AB, Liu Q, Schroth GP, Galasko DR, Yuan SH, Wagner SL, Subramaniam S. Dedifferentiation and neuronal repression define familial Alzheimer's disease. SCIENCE ADVANCES 2020; 6:6/46/eaba5933. [PMID: 33188013 PMCID: PMC7673760 DOI: 10.1126/sciadv.aba5933] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 09/23/2020] [Indexed: 05/05/2023]
Abstract
Identifying the systems-level mechanisms that lead to Alzheimer's disease, an unmet need, is an essential step toward the development of therapeutics. In this work, we report that the key disease-causative mechanisms, including dedifferentiation and repression of neuronal identity, are triggered by changes in chromatin topology. Here, we generated human induced pluripotent stem cell (hiPSC)-derived neurons from donor patients with early-onset familial Alzheimer's disease (EOFAD) and used a multiomics approach to mechanistically characterize the modulation of disease-associated gene regulatory programs. We demonstrate that EOFAD neurons dedifferentiate to a precursor-like state with signatures of ectoderm and nonectoderm lineages. RNA-seq, ATAC-seq, and ChIP-seq analysis reveals that transcriptional alterations in the cellular state are orchestrated by changes in histone methylation and chromatin topology. Furthermore, we demonstrate that these mechanisms are observed in EOFAD-patient brains, validating our hiPSC-derived neuron models. The mechanistic endotypes of Alzheimer's disease uncovered here offer key insights for therapeutic interventions.
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Affiliation(s)
- Andrew B Caldwell
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Qing Liu
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | | | - Douglas R Galasko
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Shauna H Yuan
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Steven L Wagner
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- VA San Diego Healthcare System, La Jolla, CA, USA
| | - Shankar Subramaniam
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Nanoengineering, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
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16
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Beauchemin H, Möröy T. Multifaceted Actions of GFI1 and GFI1B in Hematopoietic Stem Cell Self-Renewal and Lineage Commitment. Front Genet 2020; 11:591099. [PMID: 33193732 PMCID: PMC7649360 DOI: 10.3389/fgene.2020.591099] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/23/2020] [Indexed: 12/15/2022] Open
Abstract
Growth factor independence 1 (GFI1) and the closely related protein GFI1B are small nuclear proteins that act as DNA binding transcriptional repressors. Both recognize the same consensus DNA binding motif via their C-terminal zinc finger domains and regulate the expression of their target genes by recruiting chromatin modifiers such as histone deacetylases (HDACs) and demethylases (LSD1) by using an N-terminal SNAG domain that comprises only 20 amino acids. The only region that is different between both proteins is the region that separates the zinc finger domains and the SNAG domain. Both proteins are co-expressed in hematopoietic stem cells (HSCs) and, to some extent, in multipotent progenitors (MPPs), but expression is specified as soon as early progenitors and show signs of lineage bias. While expression of GFI1 is maintained in lymphoid primed multipotent progenitors (LMPPs) that have the potential to differentiate into both myeloid and lymphoid cells, GFI1B expression is no longer detectable in these cells. By contrast, GFI1 expression is lost in megakaryocyte precursors (MKPs) and in megakaryocyte-erythrocyte progenitors (MEPs), which maintain a high level of GFI1B expression. Consequently, GFI1 drives myeloid and lymphoid differentiation and GFI1B drives the development of megakaryocytes, platelets, and erythrocytes. How such complementary cell type- and lineage-specific functions of GFI1 and GFI1B are maintained is still an unresolved question in particular since they share an almost identical structure and very similar biochemical modes of actions. The cell type-specific accessibility of GFI1/1B binding sites may explain the fact that very similar transcription factors can be responsible for very different transcriptional programming. An additional explanation comes from recent data showing that both proteins may have additional non-transcriptional functions. GFI1 interacts with a number of proteins involved in DNA repair and lack of GFI1 renders HSCs highly susceptible to DNA damage-induced death and restricts their proliferation. In contrast, GFI1B binds to proteins of the beta-catenin/Wnt signaling pathway and lack of GFI1B leads to an expansion of HSCs and MKPs, illustrating the different impact that GFI1 or GFI1B has on HSCs. In addition, GFI1 and GFI1B are required for endothelial cells to become the first blood cells during early murine development and are among those transcription factors needed to convert adult endothelial cells or fibroblasts into HSCs. This role of GFI1 and GFI1B bears high significance for the ongoing effort to generate hematopoietic stem and progenitor cells de novo for the autologous treatment of blood disorders such as leukemia and lymphoma.
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Affiliation(s)
| | - Tarik Möröy
- Institut de recherches cliniques de Montréal, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
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17
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Wei C, Yu P, Cheng L. Hematopoietic Reprogramming Entangles with Hematopoiesis. Trends Cell Biol 2020; 30:752-763. [PMID: 32861580 DOI: 10.1016/j.tcb.2020.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/24/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023]
Abstract
Hematopoiesis generally refers to hematopoietic development in fetuses and adults, as well as to hematopoietic stem cell differentiation into progeny lineages. The multiple processes that generate diverse hematopoietic cells have been considered to be unidirectional. However, many reports have recently demonstrated that these processes are not only reversible but also interconvertible via cell reprogramming. The cell reprogramming that occurs in hematopoietic cells is termed hematopoietic reprogramming. We focus on both autogenous and artificial hematopoietic reprogramming under physiological and pathological conditions that is mainly directed by the actions of transcription factors (TFs), chemical compounds, or extracellular cytokines. A comprehensive understanding of hematopoietic reprogramming will help us not only to generate desirable cells for cell therapy but also to further analyze normal and malignant hematopoiesis.
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Affiliation(s)
- Chuijin Wei
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Pei Yu
- Department of Orthopaedics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lin Cheng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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18
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Okeke C, Silas U, Okeke C, Chikwendu C. Current Trends on Hemopoietic Stem Cells. Curr Stem Cell Res Ther 2020; 16:199-208. [PMID: 32729427 DOI: 10.2174/1574888x15999200729162021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/29/2020] [Accepted: 05/13/2020] [Indexed: 11/22/2022]
Abstract
Advances in single-cell technology and genetic mouse models have resulted in the identification of new types of hemopoietic stem cells (HSC), resulting in baffling observations, suggesting a reconsideration of the long-held notion that all hematopoietic cells in the adult are derived from HSCs. The existence of long-lived HSC-independent hematopoiesis has led to the conclusion that despite the single hierarchical differentiation route that generates functional blood types, other differentiation routes exist in-vivo. Heterogeneity in the HSC population and the evolving knowledge around HSC has translated to it's improved application as a therapeutic tool for various blood disorders. The reprogramming of non-hematopoietic somatic and mature blood cells to pluripotency with their subsequent differentiation into hematopoietic stem cells/progenitor cells and the introduction of new generation sequencing holds the potential for the resolution of ambiguities involved in HSC bone marrow transplantation. There is a change in the paradigm for HSC transplantation donor selection. Donor choice favors haploidentical HCT than cord blood. This review provides a general overview of the current events around hemopoietic stem cells, with emphasis on the rising trend of HSC transplantation, especially haploidentical stem cell transplantation.
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Affiliation(s)
- Chinwe Okeke
- Medical Laboratory Science Department, Faculty of Health Science and Tech. University of Nigeria, Nsukka, Nigeria
| | - Ufele Silas
- Medical Laboratory Science Department, Faculty of Health Science and Tech. University of Nigeria, Nsukka, Nigeria
| | - Chinedu Okeke
- Haematology Department, College of Medicine,University of Abuja, Abuja, Nigeria
| | - Chiedozie Chikwendu
- Medical Laboratory Science Department, Faculty of Health Science and Tech. University of Nigeria, Nsukka, Nigeria
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19
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Pires CF, Rosa FF, Kurochkin I, Pereira CF. Understanding and Modulating Immunity With Cell Reprogramming. Front Immunol 2019; 10:2809. [PMID: 31921109 PMCID: PMC6917620 DOI: 10.3389/fimmu.2019.02809] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/15/2019] [Indexed: 12/30/2022] Open
Abstract
Cell reprogramming concepts have been classically developed in the fields of developmental and stem cell biology and are currently being explored for regenerative medicine, given its potential to generate desired cell types for replacement therapy. Cell fate can be experimentally reversed or modified by enforced expression of lineage specific transcription factors leading to pluripotency or attainment of another somatic cell type identity. The possibility to reprogram fibroblasts into induced dendritic cells (DC) competent for antigen presentation creates a paradigm shift for understanding and modulating the immune system with direct cell reprogramming. PU.1, IRF8, and BATF3 were identified as sufficient and necessary to impose DC fate in unrelated cell types, taking advantage of Clec9a, a C-type lectin receptor with restricted expression in conventional DC type 1. The identification of such minimal gene regulatory networks helps to elucidate the molecular mechanisms governing development and lineage heterogeneity along the hematopoietic hierarchy. Furthermore, the generation of patient-tailored reprogrammed immune cells provides new and exciting tools for the expanding field of cancer immunotherapy. Here, we summarize cell reprogramming concepts and experimental approaches, review current knowledge at the intersection of cell reprogramming with hematopoiesis, and propose how cell fate engineering can be merged to immunology, opening new opportunities to understand the immune system in health and disease.
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Affiliation(s)
- Cristiana F. Pires
- Cell Reprogramming in Hematopoiesis and Immunity Laboratory, Lund Stem Cell Center, Molecular Medicine and Gene Therapy, Lund University, Lund, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Fábio F. Rosa
- Cell Reprogramming in Hematopoiesis and Immunity Laboratory, Lund Stem Cell Center, Molecular Medicine and Gene Therapy, Lund University, Lund, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Ilia Kurochkin
- Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Carlos-Filipe Pereira
- Cell Reprogramming in Hematopoiesis and Immunity Laboratory, Lund Stem Cell Center, Molecular Medicine and Gene Therapy, Lund University, Lund, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
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20
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Barcia Durán JG, Lis R, Rafii S. Haematopoietic stem cell reprogramming and the hope for a universal blood product. FEBS Lett 2019; 593:3253-3265. [PMID: 31725897 DOI: 10.1002/1873-3468.13681] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/31/2019] [Accepted: 11/12/2019] [Indexed: 12/13/2022]
Abstract
Haematopoietic stem cells (HSCs) are the only adult stem cells with a demonstrated clinical use, even though a tractable method to maintain and expand human HSCs in vitro has not yet been found. Owing to the introduction of transplantation strategies for the treatment of haematological malignancies and, more recently, the promise of gene therapy, the need to improve the generation, manipulation and scalability of autologous or allogeneic HSCs has risen steeply over the past decade. In that context, reprogramming strategies based on the expression of exogenous transcription factors have emerged as a means to produce functional HSCs in vitro. These approaches largely stem from the assumption that key master transcription factors direct the expression of downstream target genes thereby triggering haematopoiesis. Both somatic and pluripotent cells have been used to this end, yielding variable results in terms of haematopoietic phenotype and functionality. Here, we present an overview of the haematopoietic reprogramming methods reported to date, provide the appropriate historical context and offer some critical insight about where the field stands at present.
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Affiliation(s)
- José Gabriel Barcia Durán
- Division of Regenerative Medicine, Department of Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA
| | - Raphaël Lis
- Division of Regenerative Medicine, Department of Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA.,Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine and Infertility, Weill Cornell Medicine, New York, NY, USA
| | - Shahin Rafii
- Division of Regenerative Medicine, Department of Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA
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21
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Daniel MG, Rapp K, Schaniel C, Moore KA. Induction of developmental hematopoiesis mediated by transcription factors and the hematopoietic microenvironment. Ann N Y Acad Sci 2019; 1466:59-72. [PMID: 31621095 DOI: 10.1111/nyas.14246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/30/2019] [Accepted: 09/13/2019] [Indexed: 12/11/2022]
Abstract
The induction of hematopoiesis in various cell types via transcription factor (TF) reprogramming has been demonstrated by several strategies. The eventual goal of these approaches is to generate a product for unmet needs in hematopoietic cell transplantation therapies. The most successful strategies hew closely to clues provided from developmental hematopoiesis in terms of factor expression and environmental cues. In this review, we aim to summarize the TFs that play important roles in developmental hematopoiesis primarily and to also touch on adult hematopoiesis. Several aspects of cellular and molecular biology coalesce in this process, with TFs and surrounding cellular signals playing a major role in the overall development of the hematopoietic lineage. We attempt to put these elements into the context of reprogramming and highlight their roles.
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Affiliation(s)
- Michael G Daniel
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York City, New York.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York City, New York.,The Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Katrina Rapp
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York City, New York.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Christoph Schaniel
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York City, New York.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York City, New York.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York.,Mount Sinai Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Kateri A Moore
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York City, New York.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York City, New York
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22
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Daniel MG, Sachs D, Bernitz JM, Fstkchyan Y, Rapp K, Satija N, Law K, Patel F, Gomes AM, Kim HS, Pereira CF, Chen B, Lemischka IR, Moore KA. Induction of human hemogenesis in adult fibroblasts by defined factors and hematopoietic coculture. FEBS Lett 2019; 593:3266-3287. [PMID: 31557312 DOI: 10.1002/1873-3468.13621] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 09/20/2019] [Accepted: 09/23/2019] [Indexed: 12/13/2022]
Abstract
Transcription factor (TF)-based reprogramming of somatic tissues holds great promise for regenerative medicine. Previously, we demonstrated that the TFs GATA2, GFI1B, and FOS convert mouse and human fibroblasts to hemogenic endothelial-like precursors that generate hematopoietic stem progenitor (HSPC)-like cells over time. This conversion is lacking in robustness both in yield and biological function. Herein, we show that inclusion of GFI1 to the reprogramming cocktail significantly expands the HSPC-like population. AFT024 coculture imparts functional potential to these cells and allows quantification of stem cell frequency. Altogether, we demonstrate an improved human hemogenic induction protocol that could provide a valuable human in vitro model of hematopoiesis for disease modeling and a platform for cell-based therapeutics. DATABASE: Gene expression data are available in the Gene Expression Omnibus (GEO) database under the accession number GSE130361.
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Affiliation(s)
- Michael G Daniel
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David Sachs
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey M Bernitz
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zurich, Basel, Switzerland
| | - Yesai Fstkchyan
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katrina Rapp
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Namita Satija
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kenneth Law
- Rocket Pharmaceuticals Ltd, New York, NY, USA
| | - Foram Patel
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andreia M Gomes
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Cantanhede, Portugal
| | - Huen-Suk Kim
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlos-Filipe Pereira
- Division of Molecular Medicine and Gene Therapy, Lund University, Sweden.,Wallenberg Center for Molecular Medicine, Lund University, Sweden
| | - Benjamin Chen
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ihor R Lemischka
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine, New York, NY, USA
| | - Kateri A Moore
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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23
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Castaño J, Aranda S, Bueno C, Calero-Nieto FJ, Mejia-Ramirez E, Mosquera JL, Blanco E, Wang X, Prieto C, Zabaleta L, Mereu E, Rovira M, Jiménez-Delgado S, Matson DR, Heyn H, Bresnick EH, Göttgens B, Di Croce L, Menendez P, Raya A, Giorgetti A. GATA2 Promotes Hematopoietic Development and Represses Cardiac Differentiation of Human Mesoderm. Stem Cell Reports 2019; 13:515-529. [PMID: 31402335 PMCID: PMC6742600 DOI: 10.1016/j.stemcr.2019.07.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 02/02/2023] Open
Abstract
In vertebrates, GATA2 is a master regulator of hematopoiesis and is expressed throughout embryo development and in adult life. Although the essential role of GATA2 in mouse hematopoiesis is well established, its involvement during early human hematopoietic development is not clear. By combining time-controlled overexpression of GATA2 with genetic knockout experiments, we found that GATA2, at the mesoderm specification stage, promotes the generation of hemogenic endothelial progenitors and their further differentiation to hematopoietic progenitor cells, and negatively regulates cardiac differentiation. Surprisingly, genome-wide transcriptional and chromatin immunoprecipitation analysis showed that GATA2 bound to regulatory regions, and repressed the expression of cardiac development-related genes. Moreover, genes important for hematopoietic differentiation were upregulated by GATA2 in a mostly indirect manner. Collectively, our data reveal a hitherto unrecognized role of GATA2 as a repressor of cardiac fates, and highlight the importance of coordinating the specification and repression of alternative cell fates.
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Affiliation(s)
- Julio Castaño
- Center of Regenerative Medicine in Barcelona (CMRB), Hospital Duran i Reynals, Gran Via de L'Hospitalet, 199-203, Hospitalet de Llobregat, Barcelona 08908, Spain; Center for Networked Biomedical Research on Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Madrid 28029, Spain
| | - Sergi Aranda
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Clara Bueno
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona 08036, Spain
| | - Fernando J Calero-Nieto
- Department of Hematology, Wellcome and MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Eva Mejia-Ramirez
- Center of Regenerative Medicine in Barcelona (CMRB), Hospital Duran i Reynals, Gran Via de L'Hospitalet, 199-203, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Jose Luis Mosquera
- Bioinformatics Unit, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, 08908 Spain
| | - Enrique Blanco
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Xiaonan Wang
- Department of Hematology, Wellcome and MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Cristina Prieto
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona 08036, Spain
| | - Lorea Zabaleta
- Laboratory of Hematological Diseases, Fundación Inbiomed, San Sebastian, 20009, Spain
| | - Elisabetta Mereu
- CNAG-CRG, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Meritxell Rovira
- Center of Regenerative Medicine in Barcelona (CMRB), Hospital Duran i Reynals, Gran Via de L'Hospitalet, 199-203, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Senda Jiménez-Delgado
- Center of Regenerative Medicine in Barcelona (CMRB), Hospital Duran i Reynals, Gran Via de L'Hospitalet, 199-203, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Daniel R Matson
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Holger Heyn
- CNAG-CRG, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain
| | - Emery H Bresnick
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Berthold Göttgens
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona 08036, Spain
| | - Luciano Di Croce
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Universitat Pompeu Fabra, Barcelona 08003, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | - Pablo Menendez
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona 08036, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain; Centro de Investigación Biomedica en Red en Cancer (CIBERONIC) ISCIII, Barcelona, Spain
| | - Angel Raya
- Center of Regenerative Medicine in Barcelona (CMRB), Hospital Duran i Reynals, Gran Via de L'Hospitalet, 199-203, Hospitalet de Llobregat, Barcelona 08908, Spain; Center for Networked Biomedical Research on Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Madrid 28029, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | - Alessandra Giorgetti
- Center of Regenerative Medicine in Barcelona (CMRB), Hospital Duran i Reynals, Gran Via de L'Hospitalet, 199-203, Hospitalet de Llobregat, Barcelona 08908, Spain.
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24
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Current Advances in Red Blood Cell Generation Using Stem Cells from Diverse Sources. Stem Cells Int 2019; 2019:9281329. [PMID: 31467565 PMCID: PMC6701316 DOI: 10.1155/2019/9281329] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 06/02/2019] [Accepted: 07/01/2019] [Indexed: 12/29/2022] Open
Abstract
Blood transfusions hold an indispensable part in the modern healthcare system. Up to date, the blood supply is largely dependent on donations. Unfortunately, collecting the clinical-grade blood products has become a challenging mission due to accelerated population aging, which not only increases the need for blood transfusions but also decreases the number of healthy donors. Moreover, individuals with severe hematological abnormalities or rare blood phenotypes need alternative therapeutic approaches instead of conventional blood transfusion. In these aspects, the concept of in vitro/ex vivo production of blood cells has been emerging and many attempts have been focused on manufacturing mature erythrocytes, so-called red blood cells (RBCs), the most common and important component among the blood derivatives. In this review, we provide a general overview regarding the current strategies for generating RBCs from various stem cell sources including pluripotent stem cells (PSCs) as well as circulating blood stem cells and the remaining challenges that must be overcome prior to their practical application.
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25
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Mahony CB, Bertrand JY. How HSCs Colonize and Expand in the Fetal Niche of the Vertebrate Embryo: An Evolutionary Perspective. Front Cell Dev Biol 2019; 7:34. [PMID: 30915333 PMCID: PMC6422921 DOI: 10.3389/fcell.2019.00034] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/25/2019] [Indexed: 12/18/2022] Open
Abstract
Rare hematopoietic stem cells (HSCs) can self-renew, establish the entire blood system and represent the basis of regenerative medicine applied to hematological disorders. Clinical use of HSCs is however limited by their inefficient expansion ex vivo, creating a need to further understand HSC expansion in vivo. After embryonic HSCs are born from the hemogenic endothelium, they migrate to the embryonic/fetal niche, where the future adult HSC pool is established by considerable expansion. This takes place at different anatomical sites and is controlled by numerous signals. HSCs then migrate to their adult niche, where they are maintained throughout adulthood. Exactly how HSC expansion is controlled during embryogenesis remains to be characterized and is an important step to improve the therapeutic use of HSCs. We will review the current knowledge of HSC expansion in the different fetal niches across several model organisms and highlight possible clinical applications.
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Affiliation(s)
- Christopher B Mahony
- Department of Pathology and Immunology, Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland
| | - Julien Y Bertrand
- Department of Pathology and Immunology, Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland
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26
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Alsayegh K, Cortés-Medina LV, Ramos-Mandujano G, Badraiq H, Li M. Hematopoietic Differentiation of Human Pluripotent Stem Cells: HOX and GATA Transcription Factors as Master Regulators. Curr Genomics 2019; 20:438-452. [PMID: 32194342 PMCID: PMC7062042 DOI: 10.2174/1389202920666191017163837] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 09/04/2019] [Accepted: 09/27/2019] [Indexed: 02/07/2023] Open
Abstract
Numerous human disorders of the blood system would directly or indirectly benefit from therapeutic approaches that reconstitute the hematopoietic system. Hematopoietic stem cells (HSCs), either from matched donors or ex vivo manipulated autologous tissues, are the most used cellular source of cell therapy for a wide range of disorders. Due to the scarcity of matched donors and the difficulty of ex vivo expansion of HSCs, there is a growing interest in harnessing the potential of pluripotent stem cells (PSCs) as a de novo source of HSCs. PSCs make an ideal source of cells for regenerative medicine in general and for treating blood disorders in particular because they could expand indefinitely in culture and differentiate to any cell type in the body. However, advancement in deriving functional HSCs from PSCs has been slow. This is partly due to an incomplete understanding of the molecular mechanisms underlying normal hematopoiesis. In this review, we discuss the latest efforts to generate human PSC (hPSC)-derived HSCs capable of long-term engraftment. We review the regulation of the key transcription factors (TFs) in hematopoiesis and hematopoietic differentiation, the Homeobox (HOX) and GATA genes, and the interplay between them and microRNAs. We also propose that precise control of these master regulators during the course of hematopoietic differentiation is key to achieving functional hPSC-derived HSCs.
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Affiliation(s)
- Khaled Alsayegh
- King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia.,Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Lorena V Cortés-Medina
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Gerardo Ramos-Mandujano
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Heba Badraiq
- King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Mo Li
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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