1
|
Nelson TA, Tommasini S, Fretz JA. Deletion of the transcription factor EBF1 in perivascular stroma disrupts skeletal homeostasis and precipitates premature aging of the marrow microenvironment. Bone 2024; 187:117198. [PMID: 39002837 DOI: 10.1016/j.bone.2024.117198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 06/26/2024] [Accepted: 07/07/2024] [Indexed: 07/15/2024]
Abstract
Early B cell factor 1 (EBF1) is a transcription factor expressed by multiple lineages of stromal cells within the bone marrow. While cultures of Ebf1-deficient cells have been demonstrated to have impaired differentiation into either the osteoblast or adipogenic lineage in vitro by several groups, in vivo there has been a nominal consequence of the loss of EBF1 on skeletal development. In this study we used Prx-cre driven deletion of Ebf1 to eliminate EBF1 from the entire mesenchymal lineage of the skeleton and resolve this discrepancy. We report here that EBF1 is expressed primarily in the Mesenchymal Stem and Progenitor Cell (MSPC)-Adipo, MSPC-Osteo, and the Early Mesenchymal Progenitors, and that loss of EBF1 has a plethora of consequences to maintenance of the skeleton throughout adulthood. Stroma from the Prx-cre;Ebf1fl/fl bones had impaired osteogenic differentiation, an age-dependent loss of CFU-F, and elevated senescence accompanying Ebf1-deletion. New bone formation was reduced after 3 months, and resulted in a quiescent bone environment with fewer osteoblasts and an accompanied reduction in osteoclast-mediated remodeling. Consequently, bones were less ductile at a younger age, and deletion of EBF1 dramatically impaired fracture repair. Disruption of EBF1 in perivascular populations also rearranged the vascular network within these bones and disrupted cytokine signaling from key hematopoietic niches resulting in anemia, reductions in B cells, and myeloid skewing of marrow hematopoietic lineages. Mechanistically we observed disrupted BMP signaling within Ebf1-deficient progenitors with reduced SMAD1-phosphorylation, and elevated secretion of the soluble BMP-inhibitor Gremlin from the MSPC-Adipo cells. Ebf1-deficient progenitors also exhibited posttranslational suppression of glucocorticoid receptor expression. Together, these results suggest that EBF1 signaling is required for mesenchymal progenitor mobilization to maintain the adult skeleton, and that the primary action of EBF1 in the early mesenchymal lineage is to promote proliferation, and differentiation of these perivascular cells to sustain a healthy tissue.
Collapse
Affiliation(s)
- Tracy A Nelson
- Yale School of Medicine, Department of Orthopaedics and Rehabilitation, New Haven, CT 06510, United States of America
| | - Stephen Tommasini
- Yale School of Medicine, Department of Orthopaedics and Rehabilitation, New Haven, CT 06510, United States of America
| | - Jackie A Fretz
- Yale School of Medicine, Department of Orthopaedics and Rehabilitation, New Haven, CT 06510, United States of America.
| |
Collapse
|
2
|
Wang G, Wen B, Guo M, Li E, Zhang Y, Whitsett JA, Kalin TV, Kalinichenko VV. Identification of endothelial and mesenchymal FOXF1 enhancers involved in alveolar capillary dysplasia. Nat Commun 2024; 15:5233. [PMID: 38898031 PMCID: PMC11187179 DOI: 10.1038/s41467-024-49477-6] [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: 07/26/2023] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Mutations in the FOXF1 gene, a key transcriptional regulator of pulmonary vascular development, cause Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins, a lethal lung disease affecting newborns and infants. Identification of new FOXF1 upstream regulatory elements is critical to explain why frequent non-coding FOXF1 deletions are linked to the disease. Herein, we use multiome single-nuclei RNA and ATAC sequencing of mouse and human patient lungs to identify four conserved endothelial and mesenchymal FOXF1 enhancers. We demonstrate that endothelial FOXF1 enhancers are autoactivated, whereas mesenchymal FOXF1 enhancers are regulated by EBF1 and GLI1. The cell-specificity of FOXF1 enhancers is validated by disrupting these enhancers in mouse embryonic stem cells using CRISPR/Cpf1 genome editing followed by lineage-tracing of mutant embryonic stem cells in mouse embryos using blastocyst complementation. This study resolves an important clinical question why frequent non-coding FOXF1 deletions that interfere with endothelial and mesenchymal enhancers can lead to the disease.
Collapse
Affiliation(s)
- Guolun Wang
- Division of Neonatology and Pulmonary Biology, Perinatal Institute, Cincinnati Children's Research Foundation, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Bingqiang Wen
- Phoenix Children's Research Institute, Department of Child Health, University of Arizona, College of Medicine - Phoenix, Phoenix, AZ, USA
| | - Minzhe Guo
- Division of Neonatology and Pulmonary Biology, Perinatal Institute, Cincinnati Children's Research Foundation, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Enhong Li
- Phoenix Children's Research Institute, Department of Child Health, University of Arizona, College of Medicine - Phoenix, Phoenix, AZ, USA
| | - Yufang Zhang
- Division of Neonatology and Pulmonary Biology, Perinatal Institute, Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Jeffrey A Whitsett
- Division of Neonatology and Pulmonary Biology, Perinatal Institute, Cincinnati Children's Research Foundation, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Tanya V Kalin
- Phoenix Children's Research Institute, Department of Child Health, University of Arizona, College of Medicine - Phoenix, Phoenix, AZ, USA
| | - Vladimir V Kalinichenko
- Phoenix Children's Research Institute, Department of Child Health, University of Arizona, College of Medicine - Phoenix, Phoenix, AZ, USA.
- Division of Neonatology, Phoenix Children's Hospital, Phoenix, AZ, USA.
| |
Collapse
|
3
|
Amoedo-Leite C, Parv K, Testini C, Herrera-Hidalgo C, Xu F, Giraud A, Malaquias M, Fasterius E, Holl D, Seignez C, Göritz C, Christoffersson G, Phillipson M. Macrophages upregulate mural cell-like markers and support healing of ischemic injury by adopting functions important for vascular support. NATURE CARDIOVASCULAR RESEARCH 2024; 3:685-700. [PMID: 39196227 PMCID: PMC11358018 DOI: 10.1038/s44161-024-00478-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/25/2024] [Indexed: 08/29/2024]
Abstract
Sterile inflammation after injury is important for tissue restoration. In injured human and mouse tissues, macrophages were recently found to accumulate perivascularly. This study investigates if macrophages adopt a mural cell phenotype important for restoration after ischemic injury. Single-cell RNA sequencing of fate-mapped macrophages from ischemic mouse muscles demonstrates a macrophage-toward-mural cell switch of a subpopulation of macrophages with downregulated myeloid cell genes and upregulated mural cell genes, including PDGFRβ. This observation was further strengthened when including unspliced transcripts in the analysis. The macrophage switch was proven functionally relevant, as induction of macrophage-specific PDGFRβ deficiency prevented their perivascular macrophage phenotype, impaired vessel maturation and increased vessel leakiness, which ultimately reduced limb function. In conclusion, macrophages in adult ischemic tissue were demonstrated to undergo a cellular program to morphologically, transcriptomically and functionally resemble mural cells while weakening their macrophage identity. The macrophage-to-mural cell-like phenotypic switch is crucial for restoring tissue function and warrants further exploration as a potential target for immunotherapies to enhance healing.
Collapse
Affiliation(s)
| | - Kristel Parv
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Chiara Testini
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | | | - Feifei Xu
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Antoine Giraud
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Marta Malaquias
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Erik Fasterius
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Daniel Holl
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Cedric Seignez
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Christian Göritz
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, Shatin, Hong Kong
| | - Gustaf Christoffersson
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mia Phillipson
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden.
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| |
Collapse
|
4
|
Weinand K, Sakaue S, Nathan A, Jonsson AH, Zhang F, Watts GFM, Al Suqri M, Zhu Z, Rao DA, Anolik JH, Brenner MB, Donlin LT, Wei K, Raychaudhuri S. The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis. Nat Commun 2024; 15:4650. [PMID: 38821936 PMCID: PMC11143375 DOI: 10.1038/s41467-024-48620-7] [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: 03/29/2023] [Accepted: 05/02/2024] [Indexed: 06/02/2024] Open
Abstract
Synovial tissue inflammation is a hallmark of rheumatoid arthritis (RA). Recent work has identified prominent pathogenic cell states in inflamed RA synovial tissue, such as T peripheral helper cells; however, the epigenetic regulation of these states has yet to be defined. Here, we examine genome-wide open chromatin at single-cell resolution in 30 synovial tissue samples, including 12 samples with transcriptional data in multimodal experiments. We identify 24 chromatin classes and predict their associated transcription factors, including a CD8 + GZMK+ class associated with EOMES and a lining fibroblast class associated with AP-1. By integrating with an RA tissue transcriptional atlas, we propose that these chromatin classes represent 'superstates' corresponding to multiple transcriptional cell states. Finally, we demonstrate the utility of this RA tissue chromatin atlas through the associations between disease phenotypes and chromatin class abundance, as well as the nomination of classes mediating the effects of putatively causal RA genetic variants.
Collapse
Affiliation(s)
- Kathryn Weinand
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Saori Sakaue
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aparna Nathan
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anna Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Fan Zhang
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine Division of Rheumatology and Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Gerald F M Watts
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Majd Al Suqri
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zhu Zhu
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jennifer H Anolik
- Division of Allergy, Immunology and Rheumatology, Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Michael B Brenner
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Laura T Donlin
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.
| |
Collapse
|
5
|
Tang W, Lo CWS, Ma W, Chu ATW, Tong AHY, Chung BHY. Revealing the role of SPP1 + macrophages in glioma prognosis and therapeutic targeting by investigating tumor-associated macrophage landscape in grade 2 and 3 gliomas. Cell Biosci 2024; 14:37. [PMID: 38515213 PMCID: PMC10956315 DOI: 10.1186/s13578-024-01218-4] [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: 10/27/2023] [Accepted: 03/13/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Glioma is a highly heterogeneous brain tumor categorized into World Health Organization (WHO) grades 1-4 based on its malignancy. The suppressive immune microenvironment of glioma contributes significantly to unfavourable patient outcomes. However, the cellular composition and their complex interplays within the glioma environment remain poorly understood, and reliable prognostic markers remain elusive. Therefore, in-depth exploration of the tumor microenvironment (TME) and identification of predictive markers are crucial for improving the clinical management of glioma patients. RESULTS Our analysis of single-cell RNA-sequencing data from glioma samples unveiled the immunosuppressive role of tumor-associated macrophages (TAMs), mediated through intricate interactions with tumor cells and lymphocytes. We also discovered the heterogeneity within TAMs, among which a group of suppressive TAMs named TAM-SPP1 demonstrated a significant association with Epidermal Growth Factor Receptor (EGFR) amplification, impaired T cell response and unfavourable patient survival outcomes. Furthermore, by leveraging genomic and transcriptomic data from The Cancer Genome Atlas (TCGA) dataset, two distinct molecular subtypes with a different constitution of TAMs, EGFR status and clinical outcomes were identified. Exploiting the molecular differences between these two subtypes, we developed a four-gene-based prognostic model. This model displayed strong associations with an elevated level of suppressive TAMs and could be used to predict anti-tumor immune response and prognosis in glioma patients. CONCLUSION Our findings illuminated the molecular and cellular mechanisms that shape the immunosuppressive microenvironment in gliomas, providing novel insights into potential therapeutic targets. Furthermore, the developed prognostic model holds promise for predicting immunotherapy response and assisting in more precise risk stratification for glioma patients.
Collapse
Affiliation(s)
- Wenshu Tang
- Hong Kong Genome Institute, 2/F, Building 20E, Hong Kong Science Park, Hong Kong, China
| | - Cario W S Lo
- Hong Kong Genome Institute, 2/F, Building 20E, Hong Kong Science Park, Hong Kong, China
| | - Wei Ma
- Hong Kong Genome Institute, 2/F, Building 20E, Hong Kong Science Park, Hong Kong, China
| | - Annie T W Chu
- Hong Kong Genome Institute, 2/F, Building 20E, Hong Kong Science Park, Hong Kong, China
| | - Amy H Y Tong
- Hong Kong Genome Institute, 2/F, Building 20E, Hong Kong Science Park, Hong Kong, China
| | - Brian H Y Chung
- Hong Kong Genome Institute, 2/F, Building 20E, Hong Kong Science Park, Hong Kong, China.
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
| |
Collapse
|
6
|
Girolamo DD, Benavente-Diaz M, Murolo M, Grimaldi A, Lopes PT, Evano B, Kuriki M, Gioftsidi S, Laville V, Tinevez JY, Letort G, Mella S, Tajbakhsh S, Comai G. Extraocular muscle stem cells exhibit distinct cellular properties associated with non-muscle molecular signatures. Development 2024; 151:dev202144. [PMID: 38240380 DOI: 10.1242/dev.202144] [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: 06/29/2023] [Accepted: 12/27/2023] [Indexed: 02/22/2024]
Abstract
Skeletal muscle stem cells (MuSCs) are recognised as functionally heterogeneous. Cranial MuSCs are reported to have greater proliferative and regenerative capacity when compared with those in the limb. A comprehensive understanding of the mechanisms underlying this functional heterogeneity is lacking. Here, we have used clonal analysis, live imaging and single cell transcriptomic analysis to identify crucial features that distinguish extraocular muscle (EOM) from limb muscle stem cell populations. A MyogeninntdTom reporter showed that the increased proliferation capacity of EOM MuSCs correlates with deferred differentiation and lower expression of the myogenic commitment gene Myod. Unexpectedly, EOM MuSCs activated in vitro expressed a large array of extracellular matrix components typical of mesenchymal non-muscle cells. Computational analysis underscored a distinct co-regulatory module, which is absent in limb MuSCs, as driver of these features. The EOM transcription factor network, with Foxc1 as key player, appears to be hardwired to EOM identity as it persists during growth, disease and in vitro after several passages. Our findings shed light on how high-performing MuSCs regulate myogenic commitment by remodelling their local environment and adopting properties not generally associated with myogenic cells.
Collapse
Affiliation(s)
- Daniela Di Girolamo
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Maria Benavente-Diaz
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
- Sorbonne Universités, Complexité du Vivant, F-75005 Paris, France
| | - Melania Murolo
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Alexandre Grimaldi
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
- Sorbonne Universités, Complexité du Vivant, F-75005 Paris, France
| | - Priscilla Thomas Lopes
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Brendan Evano
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Mao Kuriki
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Stamatia Gioftsidi
- Université Paris-Est, 77420 Champs-sur- Marne, France
- Freie Universität Berlin, 14195 Berlin, Germany
- Inserm, IMRB U955-E10, 94000 Créteil, France
| | - Vincent Laville
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Jean-Yves Tinevez
- Institut Pasteur, Université Paris Cité, Image Analysis Hub, 75015 Paris, France
| | - Gaëlle Letort
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris Cité, CNRS UMR 3738, 25 rue du Dr Roux, 75015 Paris, France
| | - Sebastian Mella
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Shahragim Tajbakhsh
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Glenda Comai
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| |
Collapse
|
7
|
Chai YC, To SK, Simorgh S, Zaunz S, Zhu Y, Ahuja K, Lemaitre A, Ramezankhani R, van der Veer BK, Wierda K, Verhulst S, van Grunsven LA, Pasque V, Verfaillie C. Spatially Self-Organized Three-Dimensional Neural Concentroid as a Novel Reductionist Humanized Model to Study Neurovascular Development. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2304421. [PMID: 38037510 PMCID: PMC10837345 DOI: 10.1002/advs.202304421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 10/15/2023] [Indexed: 12/02/2023]
Abstract
Although human pluripotent stem cell (PSC)-derived brain organoids have enabled researchers to gain insight into human brain development and disease, these organoids contain solely ectodermal cells and are not vascularized as occurs during brain development. Here it is created less complex and more homogenous large neural constructs starting from PSC-derived neuroprogenitor cells (NPC), by fusing small NPC spheroids into so-called concentroids. Such concentroids consisted of a pro-angiogenic core, containing neuronal and outer radial glia cells, surrounded by an astroglia-dense outer layer. Incorporating PSC-derived endothelial cells (EC) around and/or in the concentroids promoted vascularization, accompanied by differential outgrowth and differentiation of neuronal and astroglia cells, as well as the development of ectodermal-derived pericyte-like mural cells co-localizing with EC networks. Single nucleus transcriptomic analysis revealed an enhanced neural cell subtype maturation and diversity in EC-containing concentroids, which better resemble the fetal human brain compared to classical organoids or NPC-only concentroids. This PSC-derived "vascularized" concentroid brain model will facilitate the study of neurovascular/blood-brain barrier development, neural cell migration, and the development of effective in vitro vascularization strategies of brain mimics.
Collapse
Affiliation(s)
- Yoke Chin Chai
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - San Kit To
- Stem Cell Institute LeuvenDepartment of Development and RegenerationLeuven Institute for Single Cell Omics (LISCO)KU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Susan Simorgh
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Samantha Zaunz
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - YingLi Zhu
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Karan Ahuja
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Alix Lemaitre
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Roya Ramezankhani
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Bernard K. van der Veer
- Laboratory for Stem Cell and Developmental EpigeneticsDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Keimpe Wierda
- Electrophysiology Expert UnitVIB‐KU Leuven Center for Brain & Disease ResearchLeuven3000Belgium
| | - Stefaan Verhulst
- Liver Cell Biology Research GroupVrije Universiteit Brussel (VUB)Brussels1090Belgium
| | - Leo A. van Grunsven
- Liver Cell Biology Research GroupVrije Universiteit Brussel (VUB)Brussels1090Belgium
| | - Vincent Pasque
- Stem Cell Institute LeuvenDepartment of Development and RegenerationLeuven Institute for Single Cell Omics (LISCO)KU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Catherine Verfaillie
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| |
Collapse
|
8
|
Kim EE, Shekhar A, Ramachandran J, Khodadadi-Jamayran A, Liu FY, Zhang J, Fishman GI. The transcription factor EBF1 non-cell-autonomously regulates cardiac growth and differentiation. Development 2023; 150:dev202054. [PMID: 37787076 PMCID: PMC10652039 DOI: 10.1242/dev.202054] [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: 06/01/2023] [Accepted: 09/18/2023] [Indexed: 10/04/2023]
Abstract
Reciprocal interactions between non-myocytes and cardiomyocytes regulate cardiac growth and differentiation. Here, we report that the transcription factor Ebf1 is highly expressed in non-myocytes and potently regulates heart development. Ebf1-deficient hearts display myocardial hypercellularity and reduced cardiomyocyte size, ventricular conduction system hypoplasia, and conduction system disease. Growth abnormalities in Ebf1 knockout hearts are observed as early as embryonic day 13.5. Transcriptional profiling of Ebf1-deficient embryonic cardiac non-myocytes demonstrates dysregulation of Polycomb repressive complex 2 targets, and ATAC-Seq reveals altered chromatin accessibility near many of these same genes. Gene set enrichment analysis of differentially expressed genes in cardiomyocytes isolated from E13.5 hearts of wild-type and mutant mice reveals significant enrichment of MYC targets and, consistent with this finding, we observe increased abundance of MYC in mutant hearts. EBF1-deficient non-myocytes, but not wild-type non-myocytes, are sufficient to induce excessive accumulation of MYC in co-cultured wild-type cardiomyocytes. Finally, we demonstrate that BMP signaling induces Ebf1 expression in embryonic heart cultures and controls a gene program enriched in EBF1 targets. These data reveal a previously unreported non-cell-autonomous pathway controlling cardiac growth and differentiation.
Collapse
Affiliation(s)
- Eugene E. Kim
- Leon H. Charney Division of Cardiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Akshay Shekhar
- Leon H. Charney Division of Cardiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jayalakshmi Ramachandran
- Leon H. Charney Division of Cardiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | | | - Fang-Yu Liu
- Leon H. Charney Division of Cardiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jie Zhang
- Leon H. Charney Division of Cardiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Glenn I. Fishman
- Leon H. Charney Division of Cardiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| |
Collapse
|
9
|
Lemcke R, Egebjerg C, Berendtsen NT, Egerod KL, Thomsen AR, Pers TH, Christensen JP, Kornum BR. Molecular consequences of peripheral Influenza A infection on cell populations in the murine hypothalamus. eLife 2023; 12:RP87515. [PMID: 37698546 PMCID: PMC10497288 DOI: 10.7554/elife.87515] [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] [Indexed: 09/13/2023] Open
Abstract
Infection with Influenza A virus (IAV) causes the well-known symptoms of the flu, including fever, loss of appetite, and excessive sleepiness. These responses, mediated by the brain, will normally disappear once the virus is cleared from the system, but a severe respiratory virus infection may cause long-lasting neurological disturbances. These include encephalitis lethargica and narcolepsy. The mechanisms behind such long lasting changes are unknown. The hypothalamus is a central regulator of the homeostatic response during a viral challenge. To gain insight into the neuronal and non-neuronal molecular changes during an IAV infection, we intranasally infected mice with an H1N1 virus and extracted the brain at different time points. Using single-nucleus RNA sequencing (snRNA-seq) of the hypothalamus, we identify transcriptional effects in all identified cell populations. The snRNA-seq data showed the most pronounced transcriptional response at 3 days past infection, with a strong downregulation of genes across all cell types. General immune processes were mainly impacted in microglia, the brain resident immune cells, where we found increased numbers of cells expressing pro-inflammatory gene networks. In addition, we found that most neuronal cell populations downregulated genes contributing to the energy homeostasis in mitochondria and protein translation in the cytosol, indicating potential reduced cellular and neuronal activity. This might be a preventive mechanism in neuronal cells to avoid intracellular viral replication and attack by phagocytosing cells. The change of microglia gene activity suggest that this is complemented by a shift in microglia activity to provide increased surveillance of their surroundings.
Collapse
Affiliation(s)
- René Lemcke
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Christine Egebjerg
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Nicolai T Berendtsen
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Kristoffer L Egerod
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Allan R Thomsen
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Tune H Pers
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Jan P Christensen
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Birgitte R Kornum
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| |
Collapse
|
10
|
Sun J, Lin Y, Ha N, Zhang J, Wang W, Wang X, Bian Q. Single-cell RNA-Seq reveals transcriptional regulatory networks directing the development of mouse maxillary prominence. J Genet Genomics 2023; 50:676-687. [PMID: 36841529 DOI: 10.1016/j.jgg.2023.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/15/2023] [Accepted: 02/08/2023] [Indexed: 02/27/2023]
Abstract
During vertebrate embryonic development, neural crest-derived ectomesenchyme within the maxillary prominences undergoes precisely coordinated proliferation and differentiation to give rise to diverse craniofacial structures, such as tooth and palate. However, the transcriptional regulatory networks underpinning such an intricate process have not been fully elucidated. Here, we perform single-cell RNA-Seq to comprehensively characterize the transcriptional dynamics during mouse maxillary development from embryonic day (E) 10.5-E14.5. Our single-cell transcriptome atlas of ∼28,000 cells uncovers mesenchymal cell populations representing distinct differentiating states and reveals their developmental trajectory, suggesting that the segregation of dental from the palatal mesenchyme occurs at E11.5. Moreover, we identify a series of key transcription factors (TFs) associated with mesenchymal fate transitions and deduce the gene regulatory networks directed by these TFs. Collectively, our study provides important resources and insights for achieving a systems-level understanding of craniofacial morphogenesis and abnormality.
Collapse
Affiliation(s)
- Jian Sun
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai 200011, China
| | - Yijun Lin
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Nayoung Ha
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai 200011, China
| | - Jianfei Zhang
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai 200011, China
| | - Weiqi Wang
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai 200011, China
| | - Xudong Wang
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai 200011, China.
| | - Qian Bian
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Shanghai Institute of Precision Medicine, Shanghai 200125, China; Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| |
Collapse
|
11
|
Lurje I, Gaisa NT, Weiskirchen R, Tacke F. Mechanisms of organ fibrosis: Emerging concepts and implications for novel treatment strategies. Mol Aspects Med 2023; 92:101191. [PMID: 37236017 DOI: 10.1016/j.mam.2023.101191] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023]
Abstract
Fibrosis, or tissue scarring, develops as a pathological deviation from the physiological wound healing response and can occur in various organs such as the heart, lung, liver, kidney, skin, and bone marrow. Organ fibrosis significantly contributes to global morbidity and mortality. A broad spectrum of etiologies can cause fibrosis, including acute and chronic ischemia, hypertension, chronic viral infection (e.g., viral hepatitis), environmental exposure (e.g., pneumoconiosis, alcohol, nutrition, smoking) and genetic diseases (e.g., cystic fibrosis, alpha-1-antitrypsin deficiency). Common mechanisms across organs and disease etiologies involve a sustained injury to parenchymal cells that triggers a wound healing response, which becomes deregulated in the disease process. A transformation of resting fibroblasts into myofibroblasts with excessive extracellular matrix production constitutes the hallmark of disease, however, multiple other cell types such as immune cells, predominantly monocytes/macrophages, endothelial cells, and parenchymal cells form a complex network of profibrotic cellular crosstalk. Across organs, leading mediators include growth factors like transforming growth factor-β and platelet-derived growth factor, cytokines like interleukin-10, interleukin-13, interleukin-17, and danger-associated molecular patterns. More recently, insights into fibrosis regression and resolution of chronic conditions have deepened our understanding of beneficial, protective effects of immune cells, soluble mediators and intracellular signaling. Further in-depth insights into the mechanisms of fibrogenesis can provide the rationale for therapeutic interventions and the development of targeted antifibrotic agents. This review gives insight into shared responses and cellular mechanisms across organs and etiologies, aiming to paint a comprehensive picture of fibrotic diseases in both experimental settings and in human pathology.
Collapse
Affiliation(s)
- Isabella Lurje
- Department of Hepatology and Gastroenterology, Campus Charité Mitte and Campus Virchow-Klinikum, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Nadine T Gaisa
- Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH Aachen University Hospital, Aachen, Germany
| | - Frank Tacke
- Department of Hepatology and Gastroenterology, Campus Charité Mitte and Campus Virchow-Klinikum, Charité-Universitätsmedizin Berlin, Berlin, Germany.
| |
Collapse
|
12
|
Hickey JW, Becker WR, Nevins SA, Horning A, Perez AE, Zhu C, Zhu B, Wei B, Chiu R, Chen DC, Cotter DL, Esplin ED, Weimer AK, Caraccio C, Venkataraaman V, Schürch CM, Black S, Brbić M, Cao K, Chen S, Zhang W, Monte E, Zhang NR, Ma Z, Leskovec J, Zhang Z, Lin S, Longacre T, Plevritis SK, Lin Y, Nolan GP, Greenleaf WJ, Snyder M. Organization of the human intestine at single-cell resolution. Nature 2023; 619:572-584. [PMID: 37468586 PMCID: PMC10356619 DOI: 10.1038/s41586-023-05915-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/02/2023] [Indexed: 07/21/2023]
Abstract
The intestine is a complex organ that promotes digestion, extracts nutrients, participates in immune surveillance, maintains critical symbiotic relationships with microbiota and affects overall health1. The intesting has a length of over nine metres, along which there are differences in structure and function2. The localization of individual cell types, cell type development trajectories and detailed cell transcriptional programs probably drive these differences in function. Here, to better understand these differences, we evaluated the organization of single cells using multiplexed imaging and single-nucleus RNA and open chromatin assays across eight different intestinal sites from nine donors. Through systematic analyses, we find cell compositions that differ substantially across regions of the intestine and demonstrate the complexity of epithelial subtypes, and find that the same cell types are organized into distinct neighbourhoods and communities, highlighting distinct immunological niches that are present in the intestine. We also map gene regulatory differences in these cells that are suggestive of a regulatory differentiation cascade, and associate intestinal disease heritability with specific cell types. These results describe the complexity of the cell composition, regulation and organization for this organ, and serve as an important reference map for understanding human biology and disease.
Collapse
Affiliation(s)
- John W Hickey
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
| | - Winston R Becker
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | | | - Aaron Horning
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Almudena Espin Perez
- Department of Biomedical Data Science, Stanford School of Medicine, Stanford, CA, USA
| | - Chenchen Zhu
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Bokai Zhu
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
| | - Bei Wei
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Roxanne Chiu
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Derek C Chen
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Daniel L Cotter
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Edward D Esplin
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Annika K Weimer
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Chiara Caraccio
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
| | | | - Christian M Schürch
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Sarah Black
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
| | - Maria Brbić
- Department of Computer Science, Stanford University, Stanford, CA, USA
- School of Computer and Communication Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Kaidi Cao
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Shuxiao Chen
- Department of Statistics and Data Science, University of Pennsylvania, Pennsylvania, PA, USA
| | - Weiruo Zhang
- Department of Biomedical Data Science, Stanford School of Medicine, Stanford, CA, USA
| | - Emma Monte
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Nancy R Zhang
- Department of Statistics and Data Science, University of Pennsylvania, Pennsylvania, PA, USA
| | - Zongming Ma
- Department of Statistics and Data Science, University of Pennsylvania, Pennsylvania, PA, USA
| | - Jure Leskovec
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Zhengyan Zhang
- Department of Surgery, Washington University, St Louis, MO, USA
| | - Shin Lin
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Teri Longacre
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
| | - Sylvia K Plevritis
- Department of Biomedical Data Science, Stanford School of Medicine, Stanford, CA, USA
| | - Yiing Lin
- Department of Surgery, Washington University, St Louis, MO, USA
| | - Garry P Nolan
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA.
| | | | - Michael Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA.
| |
Collapse
|
13
|
Weinand K, Sakaue S, Nathan A, Jonsson AH, Zhang F, Watts GFM, Zhu Z, Rao DA, Anolik JH, Brenner MB, Donlin LT, Wei K, Raychaudhuri S. The Chromatin Landscape of Pathogenic Transcriptional Cell States in Rheumatoid Arthritis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.536026. [PMID: 37066336 PMCID: PMC10104143 DOI: 10.1101/2023.04.07.536026] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Synovial tissue inflammation is the hallmark of rheumatoid arthritis (RA). Recent work has identified prominent pathogenic cell states in inflamed RA synovial tissue, such as T peripheral helper cells; however, the epigenetic regulation of these states has yet to be defined. We measured genome-wide open chromatin at single cell resolution from 30 synovial tissue samples, including 12 samples with transcriptional data in multimodal experiments. We identified 24 chromatin classes and predicted their associated transcription factors, including a CD8+ GZMK+ class associated with EOMES and a lining fibroblast class associated with AP-1. By integrating an RA tissue transcriptional atlas, we found that the chromatin classes represented 'superstates' corresponding to multiple transcriptional cell states. Finally, we demonstrated the utility of this RA tissue chromatin atlas through the associations between disease phenotypes and chromatin class abundance as well as the nomination of classes mediating the effects of putatively causal RA genetic variants.
Collapse
Affiliation(s)
- Kathryn Weinand
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Saori Sakaue
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aparna Nathan
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anna Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Fan Zhang
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology and the Center for Health Artificial Intelligence, University of Colorado School of Medicine, Aurora, CO, USA
| | - Gerald F. M. Watts
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Zhu Zhu
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Deepak A. Rao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Jennifer H. Anolik
- Division of Allergy, Immunology and Rheumatology; Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Michael B. Brenner
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Laura T. Donlin
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| |
Collapse
|
14
|
Ciavarella C, Valente S, Pasquinelli G. The Characteristics and Survival Potential Under Sub-lethal Stress of Mesenchymal Stromal/Stem Cells Isolated from the Human Vascular Wall. Stem Cells 2022; 40:1071-1077. [PMID: 36099050 PMCID: PMC9806765 DOI: 10.1093/stmcls/sxac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/30/2022] [Indexed: 01/05/2023]
Abstract
Mesenchymal stromal/stem cells (MSCs) have been identified in multiple human tissues, including the vascular wall. High proliferative potential, multilineage, and immunomodulatory properties make vascular MSCs promising candidates for regenerative medicine. Indeed, their location is strategic for controlling vascular and extra-vascular tissue homeostasis. However, the clinical application of MSCs, and in particular vascular MSCs, is still challenging. Current studies are focused on developing strategies to improve MSC therapeutic applications, like priming MSCs with stress conditions (hypoxia, nutrient deprivation) to achieve a higher therapeutic potential. The goal of the present study is to review the main findings regarding the MSCs isolated from the human vascular wall. Further, the main priming strategies tested on MSCs from different sources are reported, together with the experience on vascular MSCs isolated from healthy cryopreserved and pathological arteries. Stress induction can be a priming approach able to improve MSC effectiveness through several mechanisms that are discussed in this review. Nevertheless, these issues have not been completely explored in vascular MSCs and potential side effects need to be investigated.
Collapse
Affiliation(s)
| | - Sabrina Valente
- Corresponding author: Sabrina Valente, PhD, DIMES - Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Via Massarenti, 9, 40138 Bologna, Italy. Tel: +39 0512144520;
| | - Gianandrea Pasquinelli
- DIMES - Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy,Subcellular Nephro-Vascular Diagnostic Program, Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| |
Collapse
|
15
|
Taatjes DJ, Roth J. In focus in HCB. Histochem Cell Biol 2021; 156:297-299. [PMID: 34626215 DOI: 10.1007/s00418-021-02035-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Douglas J Taatjes
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA.
| | - Jürgen Roth
- University of Zurich, 8091, Zurich, Switzerland
| |
Collapse
|