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Escarrer-Garau G, Martín-Medina A, Truyols-Vives J, Gómez-Bellvert C, Elowsson L, Westergren-Thorsson G, Molina-Molina M, Mercader-Barceló J, Sala-Llinàs E. In Vivo and In Vitro Pro-Fibrotic Response of Lung-Resident Mesenchymal Stem Cells from Patients with Idiopathic Pulmonary Fibrosis. Cells 2024; 13:160. [PMID: 38247851 PMCID: PMC10814068 DOI: 10.3390/cells13020160] [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: 11/28/2023] [Revised: 01/05/2024] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Lung-resident mesenchymal stem cells (LR-MSC) are thought to participate in idiopathic pulmonary fibrosis (IPF) by differentiating into myofibroblasts. On the other hand, LR-MSC in IPF patients present senescence-related features. It is unclear how they respond to a profibrotic environment. Here, we investigated the profibrotic response of LR-MSC isolated from IPF and control (CON) patients. LR-MSC were inoculated in mice 48 h after bleomycin (BLM) instillation to analyze their contribution to lung damage. In vitro, LR-MSC were exposed to TGFβ. Mice inoculated with IPF LR-MSC exhibited worse maintenance of their body weight. The instillation of either IPF or CON LR-MSC sustained BLM-induced histological lung damage, bronchoalveolar lavage fluid cell count, and the expression of the myofibroblast marker, extracellular matrix (ECM) proteins, and proinflammatory cytokines in the lungs. In vitro, IPF LR-MSC displayed higher basal protein levels of aSMA and fibronectin than CON LR-MSC. However, the TGFβ response in the expression of TGFβ, aSMA, and ECM genes was attenuated in IPF LR-MSC. In conclusion, IPF LR-MSC have acquired myofibroblastic features, but their capacity to further respond to profibrotic stimuli seems to be attenuated. In an advanced stage of the disease, LR-MSC may participate in disease progression owing to their limited ability to repair epithelial damage.
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Affiliation(s)
| | - Aina Martín-Medina
- iRESPIRE Research Group, Health Research Institute of the Balearic Islands (IdISBa), 07120 Palma, Spain
| | - Joan Truyols-Vives
- MolONE Research Group, University of the Balearic Islands (UIB), 07122 Palma, Spain
| | | | - Linda Elowsson
- Lung Biology, Department of Experimental Medical Science, Lund University, 08908 Lund, Sweden
| | | | - Maria Molina-Molina
- ILD Unit, Respiratory Department, University Hospital of Bellvitge-Bellvitge Biomedical Research Institute (IDIBELL), 08908 Hospitalet de Llobregat, Barcelona, Spain
- Centre of Biomedical Research Network in Respiratory Diseases (CIBERES), 28029 Madrid, Spain
| | - Josep Mercader-Barceló
- MolONE Research Group, University of the Balearic Islands (UIB), 07122 Palma, Spain
- iRESPIRE Research Group, Health Research Institute of the Balearic Islands (IdISBa), 07120 Palma, Spain
- Centre of Biomedical Research Network in Respiratory Diseases (CIBERES), 28029 Madrid, Spain
| | - Ernest Sala-Llinàs
- iRESPIRE Research Group, Health Research Institute of the Balearic Islands (IdISBa), 07120 Palma, Spain
- Centre of Biomedical Research Network in Respiratory Diseases (CIBERES), 28029 Madrid, Spain
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Budeus B, Unger K, Hess J, Sentek H, Klein D. Comparative computational analysis to distinguish mesenchymal stem cells from fibroblasts. Front Immunol 2023; 14:1270493. [PMID: 37822926 PMCID: PMC10562561 DOI: 10.3389/fimmu.2023.1270493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 08/30/2023] [Indexed: 10/13/2023] Open
Abstract
Introduction Mesenchymal stem cells (MSCs) are considered to be the most promising stem cell type for cell-based therapies in regenerative medicine. Based on their potential to home to diseased body sites following a therapeutically application, these cells could (i) differentiate then into organ-specific cell types to locally restore injured cells or, most prominently, (ii) foster tissue regeneration including immune modulations more indirectly by secretion of protective growth factors and cytokines. As tissue-resident stem cells of mesenchymal origin, these cells are morphologically and even molecularly- at least concerning the classical marker genes- indistinguishable from similar lineage cells, particularly fibroblasts. Methods Here we used microarray-based gene expression and global DNA methylation analyses as well as accompanying computational tools in order to specify differences between MSCs and fibroblasts, to further unravel potential identity genes and to highlight MSC signaling pathways with regard to their trophic and immunosuppressive action. Results We identified 1352 differentially expressed genes, of which in the MSCs there is a strong signature for e.g., KRAS signaling, known to play essential role in stemness maintenance, regulation of coagulation and complement being decisive for resolving inflammatory processes, as well as of wound healing particularly important for their regenerative capacity. Genes upregulated in fibroblasts addressed predominately transcription and biosynthetic processes and mapped morphological features of the tissue. Concerning the cellular identity, we specified the already known HOX code for MSCs, established a potential HOX code for fibroblasts, and linked certain HOX genes to functional cell-type-specific properties. Accompanied methylation profiles revealed numerous regions, especially in HOX genes, being differentially methylated, which might provide additional biomarker potential. Discussion Conclusively, transcriptomic together with epigenetic signatures can be successfully be used for the definition (cellular identity) of MSCs versus fibroblasts as well as for the determination of the superior functional properties of MSCs, such as their immunomodulatory potential.
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Affiliation(s)
- Bettina Budeus
- Institute for Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kristian Unger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- Clinical Cooperation Group Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Julia Hess
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- Clinical Cooperation Group Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Hanna Sentek
- Institute for Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Diana Klein
- Institute for Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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3
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Mercader-Barceló J, Martín-Medina A, Truyols-Vives J, Escarrer-Garau G, Elowsson L, Montes-Worboys A, Río-Bocos C, Muncunill-Farreny J, Velasco-Roca J, Cederberg A, Kadefors M, Molina-Molina M, Westergren-Thorsson G, Sala-Llinàs E. Mitochondrial Dysfunction in Lung Resident Mesenchymal Stem Cells from Idiopathic Pulmonary Fibrosis Patients. Cells 2023; 12:2084. [PMID: 37626894 PMCID: PMC10453747 DOI: 10.3390/cells12162084] [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: 07/22/2023] [Revised: 08/09/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is characterized by an aberrant repair response with uncontrolled turnover of extracellular matrix involving mesenchymal cell phenotypes, where lung resident mesenchymal stem cells (LRMSC) have been supposed to have an important role. However, the contribution of LRMSC in lung fibrosis is not fully understood, and the role of LRMSC in IPF remains to be elucidated. Here, we performed transcriptomic and functional analyses on LRMSC isolated from IPF and control patients (CON). Both over-representation and gene set enrichment analyses indicated that oxidative phosphorylation is the major dysregulated pathway in IPF LRMSC. The most relevant differences in biological processes included complement activation, mesenchyme development, and aerobic electron transport chain. Compared to CON LRMSC, IPF cells displayed impaired mitochondrial respiration, lower expression of genes involved in mitochondrial dynamics, and dysmorphic mitochondria. These changes were linked to an impaired autophagic response and a lower mRNA expression of pro-apoptotic genes. In addition, IPF TGFβ-exposed LRMSC presented different expression profiles of mitochondrial-related genes compared to CON TGFβ-treated cells, suggesting that TGFβ reinforces mitochondrial dysfunction. In conclusion, these results suggest that mitochondrial dysfunction is a major event in LRMSC and that their occurrence might limit LRMSC function, thereby contributing to IPF development.
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Affiliation(s)
- Josep Mercader-Barceló
- iRESPIRE Research Group, Health Research Institute of the Balearic Islands (IdISBa), 07120 Palma, Spain
- MolONE Research Group, University of the Balearic Islands, 07122 Palma, Spain
| | - Aina Martín-Medina
- iRESPIRE Research Group, Health Research Institute of the Balearic Islands (IdISBa), 07120 Palma, Spain
| | - Joan Truyols-Vives
- MolONE Research Group, University of the Balearic Islands, 07122 Palma, Spain
| | | | - Linda Elowsson
- Lung Biology, Department of Experimental Medical Science, Lund University, 08908 Lund, Sweden
| | - Ana Montes-Worboys
- ILD Unit, Respiratory Department, University Hospital of Bellvitge-Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Carlos Río-Bocos
- iRESPIRE Research Group, Health Research Institute of the Balearic Islands (IdISBa), 07120 Palma, Spain
| | | | - Julio Velasco-Roca
- Health Research Institute of the Balearic Islands (IdISBa), 07120 Palma, Spain
| | - Anna Cederberg
- Lung Biology, Department of Experimental Medical Science, Lund University, 08908 Lund, Sweden
| | - Måns Kadefors
- Lung Biology, Department of Experimental Medical Science, Lund University, 08908 Lund, Sweden
| | - Maria Molina-Molina
- ILD Unit, Respiratory Department, University Hospital of Bellvitge-Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, 08908 Barcelona, Spain
- Centre of Biomedical Research Network in Respiratory Diseases (CIBERES), 28029 Madrid, Spain
| | | | - Ernest Sala-Llinàs
- iRESPIRE Research Group, Health Research Institute of the Balearic Islands (IdISBa), 07120 Palma, Spain
- Centre of Biomedical Research Network in Respiratory Diseases (CIBERES), 28029 Madrid, Spain
- Respiratory Department, Son Espases University Hospital, 07120 Palma, Spain
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4
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Ghabriel M, El Hosseiny A, Moustafa A, Amleh A. Computational comparative analysis identifies potential stemness-related markers for mesenchymal stromal/stem cells. Front Cell Dev Biol 2023; 11:1065050. [PMID: 36936690 PMCID: PMC10014615 DOI: 10.3389/fcell.2023.1065050] [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: 10/09/2022] [Accepted: 02/16/2023] [Indexed: 03/05/2023] Open
Abstract
Mesenchymal stromal/stem cells (MSCs) are multipotent cells that reside in multiple tissues are capable of self-renewal and differentiation into various cell types. These properties make them promising candidates for regenerative therapies. MSC identification is critical in yielding pure populations for successful therapeutic applications; however, the criteria for MSC identification proposed by the International Society for Cellular Therapy (ISCT) are inconsistent across different tissue sources. This study aimed to identify potential markers to be used together with the ISCT criteria to provide a more accurate means of MSC identification. Thus, we carried out a computational comparative analysis of the gene expression in human and mouse MSCs derived from multiple tissues to identify the differentially expressed genes that are shared between the two species. We show that six members of the proteasome degradation system are similarly expressed across MSCs derived from bone marrow, adipose tissue, amnion, and umbilical cord. Additionally, with the help of predictive models, we found that the expression profile of these genes correctly validated the identity of the MSCs across all the tissue sources tested. Moreover, using genetic interaction networks, we showed a possible link between these genes and antioxidant enzymes in the MSC antioxidant defense system, thereby pointing to their potential role in prolonging the life span of MSCs. According to our findings, members of the proteasome degradation system may serve as stemness-related markers.
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Affiliation(s)
- Myret Ghabriel
- Biotechnology Graduate Program, American University in Cairo, New Cairo, Egypt
| | - Ahmed El Hosseiny
- Biotechnology Graduate Program, American University in Cairo, New Cairo, Egypt
- Department of Biology, American University in Cairo, New Cairo, Egypt
- Systems Genomics Laboratory, American University in Cairo, New Cairo, Egypt
| | - Ahmed Moustafa
- Biotechnology Graduate Program, American University in Cairo, New Cairo, Egypt
- Department of Biology, American University in Cairo, New Cairo, Egypt
- Systems Genomics Laboratory, American University in Cairo, New Cairo, Egypt
- *Correspondence: Ahmed Moustafa, ; Asma Amleh,
| | - Asma Amleh
- Biotechnology Graduate Program, American University in Cairo, New Cairo, Egypt
- Department of Biology, American University in Cairo, New Cairo, Egypt
- *Correspondence: Ahmed Moustafa, ; Asma Amleh,
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5
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Kay AG, Fox JM, Hewitson JP, Stone AP, Robertson S, James S, Wang XN, Kapasa E, Yang XB, Genever PG. CD317-Positive Immune Stromal Cells in Human "Mesenchymal Stem Cell" Populations. Front Immunol 2022; 13:903796. [PMID: 35734183 PMCID: PMC9207511 DOI: 10.3389/fimmu.2022.903796] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/04/2022] [Indexed: 12/31/2022] Open
Abstract
Heterogeneity of bone marrow mesenchymal stromal cells (MSCs, frequently referred to as "mesenchymal stem cells") clouds biological understanding and hampers their clinical development. In MSC cultures most commonly used in research and therapy, we have identified an MSC subtype characterized by CD317 expression (CD317pos (29.77 ± 3.00% of the total MSC population), comprising CD317dim (28.10 ± 4.60%) and CD317bright (1.67 ± 0.58%) MSCs) and a constitutive interferon signature linked to human disease. We demonstrate that CD317pos MSCs induced cutaneous tissue damage when applied a skin explant model of inflammation, whereas CD317neg MSCs had no effect. Only CD317neg MSCs were able to suppress proliferative cycles of activated human T cells in vitro, whilst CD317pos MSCs increased polarization towards pro-inflammatory Th1 cells and CD317neg cell lines did not. Using an in vivo peritonitis model, we found that CD317neg and CD317pos MSCs suppressed leukocyte recruitment but only CD317neg MSCs suppressed macrophage numbers. Using MSC-loaded scaffolds implanted subcutaneously in immunocompromised mice we were able to observe tissue generation and blood vessel formation with CD317neg MSC lines, but not CD317pos MSC lines. Our evidence is consistent with the identification of an immune stromal cell, which is likely to contribute to specific physiological and pathological functions and influence clinical outcome of therapeutic MSCs.
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Affiliation(s)
- Alasdair G. Kay
- York Biomedical Research Institute and Department of Biology, University of York, York, United Kingdom,*Correspondence: Paul G. Genever, ; Alasdair G. Kay,
| | - James M. Fox
- York Biomedical Research Institute and Department of Biology, University of York, York, United Kingdom
| | - James P. Hewitson
- York Biomedical Research Institute and Department of Biology, University of York, York, United Kingdom
| | - Andrew P. Stone
- York Biomedical Research Institute and Department of Biology, University of York, York, United Kingdom
| | - Sophie Robertson
- York Biomedical Research Institute and Department of Biology, University of York, York, United Kingdom
| | - Sally James
- York Biomedical Research Institute and Department of Biology, University of York, York, United Kingdom
| | - Xiao-nong Wang
- Translational and Clinical Research Institute, Newcastle University, Newcastle, United Kingdom
| | - Elizabeth Kapasa
- Department of Oral Biology, School of Dentistry, University of Leeds, St James’s University Hospital, Leeds, United Kingdom
| | - Xuebin B. Yang
- Department of Oral Biology, School of Dentistry, University of Leeds, St James’s University Hospital, Leeds, United Kingdom
| | - Paul G. Genever
- York Biomedical Research Institute and Department of Biology, University of York, York, United Kingdom,*Correspondence: Paul G. Genever, ; Alasdair G. Kay,
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6
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Brügger M, Démoulins T, Barut GT, Zumkehr B, Oliveira Esteves BI, Mehinagic K, Haas Q, Schögler A, Rameix-Welti MA, Eléouët JF, Moehrlen U, Marti TM, Schmid RA, Summerfield A, Posthaus H, Ruggli N, Hall SRR, Alves MP. Pulmonary mesenchymal stem cells are engaged in distinct steps of host response to respiratory syncytial virus infection. PLoS Pathog 2021; 17:e1009789. [PMID: 34320038 PMCID: PMC8351988 DOI: 10.1371/journal.ppat.1009789] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 08/09/2021] [Accepted: 07/08/2021] [Indexed: 02/06/2023] Open
Abstract
Lung-resident (LR) mesenchymal stem and stromal cells (MSCs) are key elements of the alveolar niche and fundamental regulators of homeostasis and regeneration. We interrogated their function during virus-induced lung injury using the highly prevalent respiratory syncytial virus (RSV) which causes severe outcomes in infants. We applied complementary approaches with primary pediatric LR-MSCs and a state-of-the-art model of human RSV infection in lamb. Remarkably, RSV-infection of pediatric LR-MSCs led to a robust activation, characterized by a strong antiviral and pro-inflammatory phenotype combined with mediators related to T cell function. In line with this, following in vivo infection, RSV invades and activates LR-MSCs, resulting in the expansion of the pulmonary MSC pool. Moreover, the global transcriptional response of LR-MSCs appears to follow RSV disease, switching from an early antiviral signature to repair mechanisms including differentiation, tissue remodeling, and angiogenesis. These findings demonstrate the involvement of LR-MSCs during virus-mediated acute lung injury and may have therapeutic implications.
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Affiliation(s)
- Melanie Brügger
- Institute of Virology and Immunology, University of Bern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Thomas Démoulins
- Institute of Virology and Immunology, University of Bern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - G. Tuba Barut
- Institute of Virology and Immunology, University of Bern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Beatrice Zumkehr
- Institute of Virology and Immunology, University of Bern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Blandina I. Oliveira Esteves
- Institute of Virology and Immunology, University of Bern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Kemal Mehinagic
- Institute of Virology and Immunology, University of Bern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Quentin Haas
- Institute of Pharmacology, University of Bern, Bern, Switzerland
| | - Aline Schögler
- Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Marie-Anne Rameix-Welti
- Université Paris-Saclay, INSERM, Université de Versailles St. Quentin, UMR 1173 (2I), Versailles, France
| | | | - Ueli Moehrlen
- Pediatric Surgery, University Children’s Hospital Zurich, Zurich, Switzerland
| | - Thomas M. Marti
- Department of Biomedical Research, University of Bern, Bern, Switzerland
- Department of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Ralph A. Schmid
- Department of Biomedical Research, University of Bern, Bern, Switzerland
- Department of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Artur Summerfield
- Institute of Virology and Immunology, University of Bern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Horst Posthaus
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nicolas Ruggli
- Institute of Virology and Immunology, University of Bern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Sean R. R. Hall
- Department of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Gillies McIndoe Research Institute, Wellington, New Zealand
| | - Marco P. Alves
- Institute of Virology and Immunology, University of Bern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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7
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Grotheer V, Skrynecki N, Oezel L, Windolf J, Grassmann J. Osteogenic differentiation of human mesenchymal stromal cells and fibroblasts differs depending on tissue origin and replicative senescence. Sci Rep 2021; 11:11968. [PMID: 34099837 PMCID: PMC8184777 DOI: 10.1038/s41598-021-91501-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
The need for an autologous cell source for bone tissue engineering and medical applications has led researchers to explore multipotent mesenchymal stromal cells (MSC), which show stem cell plasticity, in various human tissues. However, MSC with different tissue origins vary in their biological properties and their capability for osteogenic differentiation. Furthermore, MSC-based therapies require large-scale ex vivo expansion, accompanied by cell type-specific replicative senescence, which affects osteogenic differentiation. To elucidate cell type-specific differences in the osteogenic differentiation potential and replicative senescence, we analysed the impact of BMP and TGF-β signaling in adipose-derived stromal cells (ASC), fibroblasts (FB), and dental pulp stromal cells (DSC). We used inhibitors of BMP and TGF-β signaling, such as SB431542, dorsomorphin and/or a supplemental addition of BMP-2. The expression of high-affinity binding receptors for BMP-2 and calcium deposition with alizarin red S were evaluated to assess osteogenic differentiation potential. Our study demonstrated that TGF-β signaling inhibits osteogenic differentiation of ASC, DSC and FB in the early cell culture passages. Moreover, DSC had the best osteogenic differentiation potential and an activation of BMP signaling with BMP-2 could further enhance this capacity. This phenomenon is likely due to an increased expression of activin receptor-like kinase-3 and -6. However, in DSC with replicative senescence (in cell culture passage 10), osteogenic differentiation sharply decreased, and the simultaneous use of BMP-2 and SB431542 did not result in further improvement of this process. In comparison, ASC retain a similar osteogenic differentiation potential regardless of whether they were in the early (cell culture passage 3) or later (cell culture passage 10) stages. Our study elucidated that ASC, DSC, and FB vary functionally in their osteogenic differentiation, depending on their tissue origin and replicative senescence. Therefore, our study provides important insights for cell-based therapies to optimize prospective bone tissue engineering strategies.
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Affiliation(s)
- Vera Grotheer
- Clinic for Orthopedics and Trauma Surgery, Medical Faculty of the Heinrich Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany.
| | - Nadine Skrynecki
- Clinic for Orthopedics and Trauma Surgery, Medical Faculty of the Heinrich Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Lisa Oezel
- Clinic for Orthopedics and Trauma Surgery, Medical Faculty of the Heinrich Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Joachim Windolf
- Clinic for Orthopedics and Trauma Surgery, Medical Faculty of the Heinrich Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Jan Grassmann
- Clinic for Orthopedics and Trauma Surgery, Medical Faculty of the Heinrich Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany
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Dzobo K. Recent Trends in Multipotent Human Mesenchymal Stem/Stromal Cells: Learning from History and Advancing Clinical Applications. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:342-357. [PMID: 34115524 DOI: 10.1089/omi.2021.0049] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Early cell biology reports demonstrated the presence of cells with stem-like properties in bone marrow, with both hematopoietic and mesenchymal lineages. Over the years, various investigations have purified and characterized mesenchymal stromal/stem cells (MSCs) from different human tissues as cells with multilineage differentiation potential under the appropriate conditions. Due to their appealing characteristics and versatile potentials, MSCs are leveraged in many applications in medicine such as oncology, bioprinting, and as recent as therapeutics discovery and innovation for COVID-19. To date, studies indicate that MSCs have varied differentiation capabilities into different cell types, and demonstrate immunomodulating and anti-inflammatory properties. Different microenvironments or niche for MSCs and their resulting heterogeneity may influence attendant cellular behavior and differentiation capacity. The potential clinical applications of MSCs and exosomes derived from these cells have led to an avalanche of research reports on their properties and hundreds of clinical trials being undertaken. There is ample reason to think, as discussed in this expert review that the future looks bright and promising for MSC research, with many clinical trials under way to ascertain their clinical utility. This review provides a synthesis of the latest advances and trends in MSC research to allow for broad and critically informed use of MSCs. Early observations of the presence of these cells in the bone marrow and their remarkable differentiation capabilities and immunomodulation are also presented.
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Affiliation(s)
- Kevin Dzobo
- International Center for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Cape Town, South Africa.,Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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9
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Gorodetsky R, Aicher WK. Allogenic Use of Human Placenta-Derived Stromal Cells as a Highly Active Subtype of Mesenchymal Stromal Cells for Cell-Based Therapies. Int J Mol Sci 2021; 22:5302. [PMID: 34069909 PMCID: PMC8157571 DOI: 10.3390/ijms22105302] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/14/2021] [Accepted: 05/14/2021] [Indexed: 12/13/2022] Open
Abstract
The application of mesenchymal stromal cells (MSCs) from different sources, including bone marrow (BM, bmMSCs), adipose tissue (atMSCs), and human term placenta (hPSCs) has been proposed for various clinical purposes. Accumulated evidence suggests that the activity of the different MSCs is indirect and associated with paracrine release of pro-regenerative and anti-inflammatory factors. A major limitation of bmMSCs-based treatment for autologous application is the limited yield of cells harvested from BM and the invasiveness of the procedure. Similar effects of autologous and allogeneic MSCs isolated from various other tissues were reported. The easily available fresh human placenta seems to represent a preferred source for harvesting abundant numbers of human hPSCs for allogenic use. Cells derived from the neonate tissues of the placenta (f-hPSC) can undergo extended expansion with a low risk of senescence. The low expression of HLA class I and II on f-hPSCs reduces the risk of rejection in allogeneic or xenogeneic applications in normal immunocompetent hosts. The main advantage of hPSCs-based therapies seems to lie in the secretion of a wide range of pro-regenerative and anti-inflammatory factors. This renders hPSCs as a very competent cell for therapy in humans or animal models. This review summarizes the therapeutic potential of allogeneic applications of f-hPSCs, with reference to their indirect pro-regenerative and anti-inflammatory effects and discusses clinical feasibility studies.
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Affiliation(s)
- Raphael Gorodetsky
- Biotechnology and Radiobiology Laboratory, Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Wilhelm K. Aicher
- Center of Medical Research, Department of Urology at UKT, Eberhard-Karls-University, 72076 Tuebingen, Germany
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10
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Identification and characterisation of maternal perivascular SUSD2 + placental mesenchymal stem/stromal cells. Cell Tissue Res 2021; 385:803-815. [PMID: 33961124 DOI: 10.1007/s00441-021-03453-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/16/2021] [Indexed: 12/12/2022]
Abstract
Mesenchymal stem cells (MSCs) that meet the International Society for Cellular Therapy (ISCT) criteria are obtained from placental tissue by plastic adherence. Historically, no known single marker was available for isolating placental MSCs (pMSCs) from the decidua basalis. As the decidua basalis is derived from the regenerative endometrium, we hypothesised that SUSD2, an endometrial perivascular MSC marker, would purify maternal perivascular pMSC. Perivascular pMSCs were isolated from the maternal placenta using SUSD2 magnetic bead sorting and assessed for the colony-forming unit-fibroblasts (CFU-F), surface markers, and in vitro differentiation into mesodermal lineages. Multi-colour immunofluorescence was used to colocalise SUSD2 and α-SMA, a perivascular marker in the decidua basalis. Placental stromal cell suspensions comprised 5.1%SUSD2+ cells. SUSD2 magnetic bead sorting of the placental stromal cells increased their purity approximately two-fold. SUSD2+ pMSCs displayed greater CFU-F activity than SUSD2- stromal fibroblasts (pSFs). However, both SUSD2+ pMSC and SUSD2- pSF underwent mesodermal differentiation in vitro, and both expressed the ISCT surface markers. Higher percentages of cultured SUSD2+ pMSCs expressed the perivascular markers CD146, CD140b, and SUSD2 than SUSD2- pSFs. These findings suggest that SUSD2 is a single marker that enriches maternal pMSCs, suggesting they may originate from eMSC. Placental decidua basalis can be used as an alternative source of MSC for clinical translation in situations where there is no access to endometrial tissue.
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11
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Kulthong K, Hooiveld GJEJ, Duivenvoorde L, Miro Estruch I, Marin V, van der Zande M, Bouwmeester H. Transcriptome comparisons of in vitro intestinal epithelia grown under static and microfluidic gut-on-chip conditions with in vivo human epithelia. Sci Rep 2021; 11:3234. [PMID: 33547413 PMCID: PMC7864925 DOI: 10.1038/s41598-021-82853-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/22/2021] [Indexed: 02/06/2023] Open
Abstract
Gut-on-chip devices enable exposure of cells to a continuous flow of culture medium, inducing shear stresses and could thus better recapitulate the in vivo human intestinal environment in an in vitro epithelial model compared to static culture methods. We aimed to study if dynamic culture conditions affect the gene expression of Caco-2 cells cultured statically or dynamically in a gut-on-chip device and how these gene expression patterns compared to that of intestinal segments in vivo. For this we applied whole genome transcriptomics. Dynamic culture conditions led to a total of 5927 differentially expressed genes (3280 upregulated and 2647 downregulated genes) compared to static culture conditions. Gene set enrichment analysis revealed upregulated pathways associated with the immune system, signal transduction and cell growth and death, and downregulated pathways associated with drug metabolism, compound digestion and absorption under dynamic culture conditions. Comparison of the in vitro gene expression data with transcriptome profiles of human in vivo duodenum, jejunum, ileum and colon tissue samples showed similarities in gene expression profiles with intestinal segments. It is concluded that both the static and the dynamic gut-on-chip model are suitable to study human intestinal epithelial responses as an alternative for animal models.
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Affiliation(s)
- Kornphimol Kulthong
- Division of Toxicology, Wageningen University, P.O. box 8000, 6700 EA, Wageningen, The Netherlands.
- Wageningen Food Safety Research, P.O. Box 230, 6700 AE, Wageningen, The Netherlands.
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand.
| | - Guido J E J Hooiveld
- Nutrition, Metabolism and Genomics group, Division of Human Nutrition and Health, Wageningen University, Wageningen, The Netherlands
| | - Loes Duivenvoorde
- Wageningen Food Safety Research, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
| | - Ignacio Miro Estruch
- Division of Toxicology, Wageningen University, P.O. box 8000, 6700 EA, Wageningen, The Netherlands
| | - Victor Marin
- Wageningen Food Safety Research, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
| | - Meike van der Zande
- Wageningen Food Safety Research, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
| | - Hans Bouwmeester
- Division of Toxicology, Wageningen University, P.O. box 8000, 6700 EA, Wageningen, The Netherlands.
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12
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Steens J, Unger K, Klar L, Neureiter A, Wieber K, Hess J, Jakob HG, Klump H, Klein D. Direct conversion of human fibroblasts into therapeutically active vascular wall-typical mesenchymal stem cells. Cell Mol Life Sci 2020; 77:3401-3422. [PMID: 31712992 PMCID: PMC7426315 DOI: 10.1007/s00018-019-03358-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 09/27/2019] [Accepted: 10/28/2019] [Indexed: 12/11/2022]
Abstract
Cell-based therapies using adult stem cells are promising options for the treatment of a number of diseases including autoimmune and cardiovascular disorders. Among these, vascular wall-derived mesenchymal stem cells (VW-MSCs) might be particularly well suited for the protection and curative treatment of vascular damage because of their tissue-specific action. Here we report a novel method for the direct conversion of human skin fibroblasts towards MSCs using a VW-MSC-specific gene code (HOXB7, HOXC6 and HOXC8) that directs cell fate conversion bypassing pluripotency. This direct programming approach using either a self-inactivating (SIN) lentiviral vector expressing the VW-MSC-specific HOX-code or a tetracycline-controlled Tet-On system for doxycycline-inducible gene expressions of HOXB7, HOXC6 and HOXC8 successfully mediated the generation of VW-typical MSCs with classical MSC characteristics in vitro and in vivo. The induced VW-MSCs (iVW-MSCs) fulfilled all criteria of MSCs as defined by the International Society for Cellular Therapy (ISCT). In terms of multipotency and clonogenicity, which are important specific properties to discriminate MSCs from fibroblasts, iVW-MSCs behaved like primary ex vivo isolated VW-MSCs and shared similar molecular and DNA methylation signatures. With respect to their therapeutic potential, these cells suppressed lymphocyte proliferation in vitro, and protected mice against vascular damage in a mouse model of radiation-induced pneumopathy in vivo, as well as ex vivo cultured human lung tissue. The feasibility to obtain patient-specific VW-MSCs from fibroblasts in large amounts by a direct conversion into induced VW-MSCs could potentially open avenues towards novel, MSC-based therapies.
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Affiliation(s)
- Jennifer Steens
- Institute for Cell Biology (Cancer Research), University Hospital Essen, Medical Faculty, University of Duisburg-Essen, Virchowstr. 173, Ger-45122, Essen, Germany
| | - Kristian Unger
- Research Unit Radiation Cytogenetics and Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Lea Klar
- Institute for Cell Biology (Cancer Research), University Hospital Essen, Medical Faculty, University of Duisburg-Essen, Virchowstr. 173, Ger-45122, Essen, Germany
| | - Anika Neureiter
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Karolin Wieber
- Institute for Cell Biology (Cancer Research), University Hospital Essen, Medical Faculty, University of Duisburg-Essen, Virchowstr. 173, Ger-45122, Essen, Germany
| | - Julia Hess
- Research Unit Radiation Cytogenetics and Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Heinz G Jakob
- Department of Thoracic and Cardiovascular Surgery, West-German Heart and Vascular Center Essen, University Duisburg-Essen, Essen, Germany
| | - Hannes Klump
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Diana Klein
- Institute for Cell Biology (Cancer Research), University Hospital Essen, Medical Faculty, University of Duisburg-Essen, Virchowstr. 173, Ger-45122, Essen, Germany.
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13
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Angel PW, Rajab N, Deng Y, Pacheco CM, Chen T, Lê Cao KA, Choi J, Wells CA. A simple, scalable approach to building a cross-platform transcriptome atlas. PLoS Comput Biol 2020; 16:e1008219. [PMID: 32986694 PMCID: PMC7544119 DOI: 10.1371/journal.pcbi.1008219] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 10/08/2020] [Accepted: 08/04/2020] [Indexed: 12/21/2022] Open
Abstract
Gene expression atlases have transformed our understanding of the development, composition and function of human tissues. New technologies promise improved cellular or molecular resolution, and have led to the identification of new cell types, or better defined cell states. But as new technologies emerge, information derived on old platforms becomes obsolete. We demonstrate that it is possible to combine a large number of different profiling experiments summarised from dozens of laboratories and representing hundreds of donors, to create an integrated molecular map of human tissue. As an example, we combine 850 samples from 38 platforms to build an integrated atlas of human blood cells. We achieve robust and unbiased cell type clustering using a variance partitioning method, selecting genes with low platform bias relative to biological variation. Other than an initial rescaling, no other transformation to the primary data is applied through batch correction or renormalisation. Additional data, including single-cell datasets, can be projected for comparison, classification and annotation. The resulting atlas provides a multi-scaled approach to visualise and analyse the relationships between sets of genes and blood cell lineages, including the maturation and activation of leukocytes in vivo and in vitro. In allowing for data integration across hundreds of studies, we address a key reproduciblity challenge which is faced by any new technology. This allows us to draw on the deep phenotypes and functional annotations that accompany traditional profiling methods, and provide important context to the high cellular resolution of single cell profiling. Here, we have implemented the blood atlas in the open access Stemformatics.org platform, drawing on its extensive collection of curated transcriptome data. The method is simple, scalable and amenable for rapid deployment in other biological systems or computational workflows.
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Affiliation(s)
- Paul W. Angel
- Centre for Stem Cell Systems, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nadia Rajab
- Centre for Stem Cell Systems, The University of Melbourne, Melbourne, Victoria, Australia
| | - Yidi Deng
- Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Chris M. Pacheco
- Centre for Stem Cell Systems, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tyrone Chen
- Centre for Stem Cell Systems, The University of Melbourne, Melbourne, Victoria, Australia
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jarny Choi
- Centre for Stem Cell Systems, The University of Melbourne, Melbourne, Victoria, Australia
| | - Christine A. Wells
- Centre for Stem Cell Systems, The University of Melbourne, Melbourne, Victoria, Australia
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14
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Wiese DM, Braid LR. Transcriptome profiles acquired during cell expansion and licensing validate mesenchymal stromal cell lineage genes. Stem Cell Res Ther 2020; 11:357. [PMID: 32795342 PMCID: PMC7427746 DOI: 10.1186/s13287-020-01873-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/09/2020] [Accepted: 08/03/2020] [Indexed: 12/31/2022] Open
Abstract
Background Mesenchymal stromal cells (MSCs) are rapidly advancing as commercial therapeutics. However, there are still no adequate tools to validate the identity of MSCs and support standardization of MSC-based products. Currently accepted metrics include cell surface marker profiling and tri-lineage differentiation assays, neither of which is definitive. Transcript profiling represents a cost- and time-effective approach amenable to MSC manufacturing processes. Two independent labs recently reported non-overlapping MSC-specific transcriptomic signatures of 489 and 16 genes. Methods Here, we interrogated our repository of transcriptome data to determine whether routine culture manipulations including cell expansion and immune activation affect expression of the reported MSC lineage genes. These data sets comprise 4 donor populations of human umbilical cord (UC) MSCs serially cultured from cryopreservation thaw through pre-senescence, and 3 donor populations each of naïve UC and bone marrow (BM) MSCs and licensed by 3 different cytokines. Results Overall, 437 of 456 proposed signature genes assessed in these data sets were reliably expressed, representing an enduring lineage profile in 96% agreement with the previous studies. Serial passaging resulted in the downregulation of 3 signature genes, and one was silenced. Cytokine stimulation downregulated expression of 16 signature genes, and 3 were uniformly silenced in one or the other MSC type. Fifteen additional genes were unreliably detected, independent of culture manipulation. Conclusion These results validate and refine the proposed transcriptomic tools for reliable identification of MSCs after isolation through cell expansion and after inflammatory activation. We propose a 24-gene signature to support standardized and accessible MSC characterization.
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Affiliation(s)
- Danielle M Wiese
- Aurora BioSolutions Inc., Crescent Heights PO Box 21053, Medicine Hat, AB, T1A 6N0, Canada
| | - Lorena R Braid
- Aurora BioSolutions Inc., Crescent Heights PO Box 21053, Medicine Hat, AB, T1A 6N0, Canada.
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15
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Choi J, Pacheco CM, Mosbergen R, Korn O, Chen T, Nagpal I, Englart S, Angel PW, Wells CA. Stemformatics: visualize and download curated stem cell data. Nucleic Acids Res 2020; 47:D841-D846. [PMID: 30407577 PMCID: PMC6323943 DOI: 10.1093/nar/gky1064] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/03/2018] [Indexed: 12/21/2022] Open
Abstract
Stemformatics is an established gene expression data portal containing over 420 public gene expression datasets derived from microarray, RNA sequencing and single cell profiling technologies. Developed for the stem cell community, it has a major focus on pluripotency, tissue stem cells, and staged differentiation. Stemformatics includes curated ‘collections’ of data relevant to cell reprogramming, as well as hematopoiesis and leukaemia. Rather than simply rehosting datasets as they appear in public repositories, Stemformatics uses a stringent set of quality control metrics and its own pipelines to process handpicked datasets from raw files. This means that about 30% of datasets processed by Stemformatics fail the quality control metrics and never make it to the portal, ensuring that Stemformatics data are of high quality and have been processed in a consistent manner. Stemformatics provides easy-to-use and intuitive tools for biologists to visually explore the data, including interactive gene expression profiles, principal component analysis plots and hierarchical clusters, among others. The addition of tools that facilitate cross-dataset comparisons provides users with snapshots of gene expression in multiple cell and tissues, assisting the identification of cell-type restricted genes, or potential housekeeping genes. Stemformatics is freely available at stemformatics.org.
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Affiliation(s)
- Jarny Choi
- Centre for Stem Cell Systems, Anatomy and Neuroscience, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Chris M Pacheco
- Centre for Stem Cell Systems, Anatomy and Neuroscience, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Rowland Mosbergen
- Centre for Stem Cell Systems, Anatomy and Neuroscience, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Othmar Korn
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
| | - Tyrone Chen
- Centre for Stem Cell Systems, Anatomy and Neuroscience, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Isha Nagpal
- Centre for Stem Cell Systems, Anatomy and Neuroscience, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Steve Englart
- Centre for Stem Cell Systems, Anatomy and Neuroscience, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Paul W Angel
- Centre for Stem Cell Systems, Anatomy and Neuroscience, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Christine A Wells
- Centre for Stem Cell Systems, Anatomy and Neuroscience, The University of Melbourne, Melbourne, Victoria 3010, Australia.,Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
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16
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Wells CA, Choi J. Transcriptional Profiling of Stem Cells: Moving from Descriptive to Predictive Paradigms. Stem Cell Reports 2020; 13:237-246. [PMID: 31412285 PMCID: PMC6700522 DOI: 10.1016/j.stemcr.2019.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 12/24/2022] Open
Abstract
Transcriptional profiling is a powerful tool commonly used to benchmark stem cells and their differentiated progeny. As the wealth of stem cell data builds in public repositories, we highlight common data traps, and review approaches to combine and mine this data for new cell classification and cell prediction tools. We touch on future trends for stem cell profiling, such as single-cell profiling, long-read sequencing, and improved methods for measuring molecular modifications on chromatin and RNA that bring new challenges and opportunities for stem cell analysis.
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Affiliation(s)
- Christine A Wells
- Centre for Stem Cell Systems, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville 3010, Australia.
| | - Jarny Choi
- Centre for Stem Cell Systems, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville 3010, Australia
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17
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Attia N, Mashal M. Mesenchymal Stem Cells: The Past Present and Future. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1312:107-129. [PMID: 33159306 DOI: 10.1007/5584_2020_595] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The biomedical applications of mesenchymal stem cells (MSCs) have gained expanding attention over the past three decades. MSCs are easily obtained from various tissue types (e.g. bone marrow, fat, cord blood, etc.), are capable of self-renewal, and could be induced to differentiate into several cell lineages for countless biomedical applications. In addition, when transplanted, MSCs are not detected by immune surveillance, thus do not lead to graft rejection. Moreover, they can home towards affected tissues and induce their therapeutic effect in a cell-base and/or a cell-free manner. These properties, and many others, have made MSCs appealing therapeutic cell candidates (for cell and/or gene therapy) in myriad clinical conditions. However, similar to any other therapeutic tool, MSCs still have their own limitations and grey areas that entail more research for better understanding and optimization. Herein, we present a brief overview of various pre-clinical/clinical applications of MSCs in regenerative medicine and discuss limitations and future challenges.
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Affiliation(s)
- Noha Attia
- Department of Basic Sciences, The American University of Antigua-College of Medicine, Coolidge, Antigua and Barbuda. .,The Center of research and evaluation, The American University of Antigua-College of Medicine, Coolidge, Antigua and Barbuda. .,Histology and Cell Biology Department, Faculty of Medicine, University of Alexandria, Alexandria, Egypt. .,NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain.
| | - Mohamed Mashal
- The Center of research and evaluation, The American University of Antigua-College of Medicine, Coolidge, Antigua and Barbuda.,NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
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18
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Mesenchymal stem cell perspective: cell biology to clinical progress. NPJ Regen Med 2019; 4:22. [PMID: 31815001 PMCID: PMC6889290 DOI: 10.1038/s41536-019-0083-6] [Citation(s) in RCA: 1001] [Impact Index Per Article: 200.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 09/20/2019] [Indexed: 02/07/2023] Open
Abstract
The terms MSC and MSCs have become the preferred acronym to describe a cell and a cell population of multipotential stem/progenitor cells commonly referred to as mesenchymal stem cells, multipotential stromal cells, mesenchymal stromal cells, and mesenchymal progenitor cells. The MSCs can differentiate to important lineages under defined conditions in vitro and in limited situations after implantation in vivo. MSCs were isolated and described about 30 years ago and now there are over 55,000 publications on MSCs readily available. Here, we have focused on human MSCs whenever possible. The MSCs have broad anti-inflammatory and immune-modulatory properties. At present, these provide the greatest focus of human MSCs in clinical testing; however, the properties of cultured MSCs in vitro suggest they can have broader applications. The medical utility of MSCs continues to be investigated in over 950 clinical trials. There has been much progress in understanding MSCs over the years, and there is a strong foundation for future scientific research and clinical applications, but also some important questions remain to be answered. Developing further methods to understand and unlock MSC potential through intracellular and intercellular signaling, biomedical engineering, delivery methods and patient selection should all provide substantial advancements in the coming years and greater clinical opportunities. The expansive and growing field of MSC research is teaching us basic human cell biology as well as how to use this type of cell for cellular therapy in a variety of clinical settings, and while much promise is evident, careful new work is still needed.
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19
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Cruz T, López-Giraldo A, Noell G, Guirao A, Casas-Recasens S, Garcia T, Saco A, Sellares J, Agustí A, Faner R. Smoking Impairs the Immunomodulatory Capacity of Lung-Resident Mesenchymal Stem Cells in Chronic Obstructive Pulmonary Disease. Am J Respir Cell Mol Biol 2019; 61:575-583. [DOI: 10.1165/rcmb.2018-0351oc] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Tamara Cruz
- Centro Investigación Biomédica en Red Enfermedades Respiratorias, Barcelona, Spain
| | - Alejandra López-Giraldo
- Centro Investigación Biomédica en Red Enfermedades Respiratorias, Barcelona, Spain
- Respiratory Institute, Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Guillaume Noell
- Centro Investigación Biomédica en Red Enfermedades Respiratorias, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain; and
| | - Angela Guirao
- Respiratory Institute, Hospital Clinic, University of Barcelona, Barcelona, Spain
| | | | - Tamara Garcia
- Centro Investigación Biomédica en Red Enfermedades Respiratorias, Barcelona, Spain
| | - Adela Saco
- Department of Pathology, Hospital Clinic, Barcelona, Spain
| | - Jacobo Sellares
- Respiratory Institute, Hospital Clinic, University of Barcelona, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain; and
| | - Alvar Agustí
- Centro Investigación Biomédica en Red Enfermedades Respiratorias, Barcelona, Spain
- Respiratory Institute, Hospital Clinic, University of Barcelona, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain; and
| | - Rosa Faner
- Centro Investigación Biomédica en Red Enfermedades Respiratorias, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain; and
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20
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Larson BL, Yu SN, Park H, Estes BT, Moutos FT, Bloomquist CJ, Wu PB, Welter JF, Langer R, Guilak F, Freed LE. Chondrogenic, hypertrophic, and osteochondral differentiation of human mesenchymal stem cells on three-dimensionally woven scaffolds. J Tissue Eng Regen Med 2019; 13:1453-1465. [PMID: 31115161 DOI: 10.1002/term.2899] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/30/2019] [Accepted: 05/09/2019] [Indexed: 12/18/2022]
Abstract
The development of mechanically functional cartilage and bone tissue constructs of clinically relevant size, as well as their integration with native tissues, remains an important challenge for regenerative medicine. The objective of this study was to assess adult human mesenchymal stem cells (MSCs) in large, three-dimensionally woven poly(ε-caprolactone; PCL) scaffolds in proximity to viable bone, both in a nude rat subcutaneous pouch model and under simulated conditions in vitro. In Study I, various scaffold permutations-PCL alone, PCL-bone, "point-of-care" seeded MSC-PCL-bone, and chondrogenically precultured Ch-MSC-PCL-bone constructs-were implanted in a dorsal, ectopic pouch in a nude rat. After 8 weeks, only cells in the Ch-MSC-PCL constructs exhibited both chondrogenic and osteogenic gene expression profiles. Notably, although both tissue profiles were present, constructs that had been chondrogenically precultured prior to implantation showed a loss of glycosaminoglycan (GAG) as well as the presence of mineralization along with the formation of trabecula-like structures. In Study II of the study, the GAG loss and mineralization observed in Study I in vivo were recapitulated in vitro by the presence of either nearby bone or osteogenic culture medium additives but were prevented by a continued presence of chondrogenic medium additives. These data suggest conditions under which adult human stem cells in combination with polymer scaffolds synthesize functional and phenotypically distinct tissues based on the environmental conditions and highlight the potential influence that paracrine factors from adjacent bone may have on MSC fate, once implanted in vivo for chondral or osteochondral repair.
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Affiliation(s)
- Benjamin L Larson
- Institute for Medical Engineering and Science, David H. Koch Institute for Integrative Cancer Research, and Media Lab, Massachusetts Institute of Technology, Cambridge, MA
| | - Sarah N Yu
- Institute for Medical Engineering and Science, David H. Koch Institute for Integrative Cancer Research, and Media Lab, Massachusetts Institute of Technology, Cambridge, MA
| | - Hyoungshin Park
- Institute for Medical Engineering and Science, David H. Koch Institute for Integrative Cancer Research, and Media Lab, Massachusetts Institute of Technology, Cambridge, MA
| | | | | | | | - Patrick B Wu
- Institute for Medical Engineering and Science, David H. Koch Institute for Integrative Cancer Research, and Media Lab, Massachusetts Institute of Technology, Cambridge, MA
| | - Jean F Welter
- Skeletal Research Center and Case Center for Multimodal Evaluation of Engineered Cartilage, Department of Biology, Case Western Reserve University, Cleveland, OH
| | - Robert Langer
- Institute for Medical Engineering and Science, David H. Koch Institute for Integrative Cancer Research, and Media Lab, Massachusetts Institute of Technology, Cambridge, MA
| | - Farshid Guilak
- Cytex Therapeutics, Inc., Durham, NC.,Department of Orthopaedic Surgery, Washington University in St. Louis, St. Louis, MO.,Shriners Hospitals for Children-St. Louis, St. Louis, MO.,Center of Regenerative Medicine, Washington University in St. Louis, St. Louis, MO
| | - Lisa E Freed
- Institute for Medical Engineering and Science, David H. Koch Institute for Integrative Cancer Research, and Media Lab, Massachusetts Institute of Technology, Cambridge, MA
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21
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Jin W, Liang X, Brooks A, Futrega K, Liu X, Doran MR, Simpson MJ, Roberts MS, Wang H. Modelling of the SDF-1/CXCR4 regulated in vivo homing of therapeutic mesenchymal stem/stromal cells in mice. PeerJ 2018; 6:e6072. [PMID: 30564525 PMCID: PMC6286806 DOI: 10.7717/peerj.6072] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/05/2018] [Indexed: 01/12/2023] Open
Abstract
Background Mesenchymal stem/stromal cells (MSCs) are a promising tool for cell-based therapies in the treatment of tissue injury. The stromal cell-derived factor-1 (SDF-1)/CXC chemokine receptor 4 (CXCR4) axis plays a significant role in directing MSC homing to sites of injury. However in vivo MSC distribution following intravenous transplantation remains poorly understood, potentially hampering the precise prediction and evaluation of therapeutic efficacy. Methods A murine model of partial ischemia/reperfusion (I/R) is used to induce liver injury, increase the hepatic levels of SDF-1, and study in vivo MSC distribution. Hypoxia-preconditioning increases the expression of CXCR4 in human bone marrow-derived MSCs. Quantitative assays for human DNA using droplet digital PCR (ddPCR) allow us to examine the in vivo kinetics of intravenously infused human MSCs in mouse blood and liver. A mathematical model-based system is developed to characterize in vivo homing of human MSCs in mouse models with SDF-1 levels in liver and CXCR4 expression on the transfused MSCs. The model is calibrated to experimental data to provide novel estimates of relevant parameter values. Results Images of immunohistochemistry for SDF-1 in the mouse liver with I/R injury show a significantly higher SDF-1 level in the I/R injured liver than that in the control. Correspondingly, the ddPCR results illustrate a higher MSC concentration in the I/R injured liver than the normal liver. CXCR4 is overexpressed in hypoxia-preconditioned MSCs. An increased number of hypoxia-preconditioned MSCs in the I/R injured liver is observed from the ddPCR results. The model simulations align with the experimental data of control and hypoxia-preconditioned human MSC distribution in normal and injured mouse livers, and accurately predict the experimental outcomes with different MSC doses. Discussion The modelling results suggest that SDF-1 in organs is an effective in vivo attractant for MSCs through the SDF-1/CXCR4 axis and reveal the significance of the SDF-1/CXCR4 chemotaxis on in vivo homing of MSCs. This in vivo modelling approach allows qualitative characterization and prediction of the MSC homing to normal and injured organs on the basis of clinically accessible variables, such as the MSC dose and SDF-1 concentration in blood. This model could also be adapted to abnormal conditions and/or other types of circulating cells to predict in vivo homing patterns.
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Affiliation(s)
- Wang Jin
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Xiaowen Liang
- Therapeutics Research Centre, The University of Queensland Diamantina Institute, University of Queensland, Translational Research Institute, Brisbane, Australia
| | - Anastasia Brooks
- Therapeutics Research Centre, The University of Queensland Diamantina Institute, University of Queensland, Translational Research Institute, Brisbane, Australia
| | - Kathryn Futrega
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Brisbane, Australia
| | - Xin Liu
- Therapeutics Research Centre, The University of Queensland Diamantina Institute, University of Queensland, Translational Research Institute, Brisbane, Australia
| | - Michael R Doran
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Brisbane, Australia.,Mater Research Institute, University of Queensland, Translational Research Institute, Brisbane, Australia.,Australian National Centre for the Public Awareness of Science, Australian National University, Canberra, Australia
| | - Matthew J Simpson
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Michael S Roberts
- Therapeutics Research Centre, The University of Queensland Diamantina Institute, University of Queensland, Translational Research Institute, Brisbane, Australia.,School of Pharmacy and Medical Science, University of South Australia, Adelaide, Australia
| | - Haolu Wang
- Therapeutics Research Centre, The University of Queensland Diamantina Institute, University of Queensland, Translational Research Institute, Brisbane, Australia
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22
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Rohart F, Gautier B, Singh A, Lê Cao KA. mixOmics: An R package for 'omics feature selection and multiple data integration. PLoS Comput Biol 2017; 13:e1005752. [PMID: 29099853 PMCID: PMC5687754 DOI: 10.1371/journal.pcbi.1005752] [Citation(s) in RCA: 1683] [Impact Index Per Article: 240.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 11/15/2017] [Accepted: 08/31/2017] [Indexed: 02/07/2023] Open
Abstract
The advent of high throughput technologies has led to a wealth of publicly available 'omics data coming from different sources, such as transcriptomics, proteomics, metabolomics. Combining such large-scale biological data sets can lead to the discovery of important biological insights, provided that relevant information can be extracted in a holistic manner. Current statistical approaches have been focusing on identifying small subsets of molecules (a 'molecular signature') to explain or predict biological conditions, but mainly for a single type of 'omics. In addition, commonly used methods are univariate and consider each biological feature independently. We introduce mixOmics, an R package dedicated to the multivariate analysis of biological data sets with a specific focus on data exploration, dimension reduction and visualisation. By adopting a systems biology approach, the toolkit provides a wide range of methods that statistically integrate several data sets at once to probe relationships between heterogeneous 'omics data sets. Our recent methods extend Projection to Latent Structure (PLS) models for discriminant analysis, for data integration across multiple 'omics data or across independent studies, and for the identification of molecular signatures. We illustrate our latest mixOmics integrative frameworks for the multivariate analyses of 'omics data available from the package.
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Affiliation(s)
- Florian Rohart
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Benoît Gautier
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Amrit Singh
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kim-Anh Lê Cao
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
- Melbourne Integrative Genomics and School of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, Australia
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23
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Désert R, Rohart F, Canal F, Sicard M, Desille M, Renaud S, Turlin B, Bellaud P, Perret C, Clément B, Lê Cao KA, Musso O. Human hepatocellular carcinomas with a periportal phenotype have the lowest potential for early recurrence after curative resection. Hepatology 2017; 66:1502-1518. [PMID: 28498607 DOI: 10.1002/hep.29254] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/03/2017] [Accepted: 05/03/2017] [Indexed: 12/25/2022]
Abstract
UNLABELLED Hepatocellular carcinomas (HCCs) exhibit a diversity of molecular phenotypes, raising major challenges in clinical management. HCCs detected by surveillance programs at an early stage are candidates for potentially curative therapies (local ablation, resection, or transplantation). In the long term, transplantation provides the lowest recurrence rates. Treatment allocation is based on tumor number, size, vascular invasion, performance status, functional liver reserve, and the prediction of early (<2 years) recurrence, which reflects the intrinsic aggressiveness of the tumor. Well-differentiated, potentially low-aggressiveness tumors form the heterogeneous molecular class of nonproliferative HCCs, characterized by an approximate 50% β-catenin mutation rate. To define the clinical, pathological, and molecular features and the outcome of nonproliferative HCCs, we constructed a 1,133-HCC transcriptomic metadata set and validated findings in a publically available 210-HCC RNA sequencing set. We show that nonproliferative HCCs preserve the zonation program that distributes metabolic functions along the portocentral axis in normal liver. More precisely, we identified two well-differentiated, nonproliferation subclasses, namely periportal-type (wild-type β-catenin) and perivenous-type (mutant β-catenin), which expressed negatively correlated gene networks. The new periportal-type subclass represented 29% of all HCCs; expressed a hepatocyte nuclear factor 4A-driven gene network, which was down-regulated in mouse hepatocyte nuclear factor 4A knockout mice; were early-stage tumors by Barcelona Clinic Liver Cancer, Cancer of the Liver Italian Program, and tumor-node-metastasis staging systems; had no macrovascular invasion; and showed the lowest metastasis-specific gene expression levels and TP53 mutation rates. Also, we identified an eight-gene periportal-type HCC signature, which was independently associated with the highest 2-year recurrence-free survival by multivariate analyses in two independent cohorts of 247 and 210 patients. CONCLUSION Well-differentiated HCCs display mutually exclusive periportal or perivenous zonation programs. Among all HCCs, periportal-type tumors have the lowest intrinsic potential for early recurrence after curative resection. (Hepatology 2017;66:1502-1518).
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Affiliation(s)
- Romain Désert
- INSERM, INRA, Univ Rennes, CHU Rennes, Nutrition Metabolisms and Cancer (NuMeCan), CRB-Santé, Biosit, Biogenouest, UBL, Rennes, France
| | - Florian Rohart
- Diamantina Institute and Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Frédéric Canal
- INSERM, CNRS, Université de Paris Descartes, Sorbonne Paris Cité, Institut Cochin, Paris, France
| | - Marie Sicard
- INSERM, INRA, Univ Rennes, CHU Rennes, Nutrition Metabolisms and Cancer (NuMeCan), CRB-Santé, Biosit, Biogenouest, UBL, Rennes, France
| | - Mireille Desille
- INSERM, INRA, Univ Rennes, CHU Rennes, Nutrition Metabolisms and Cancer (NuMeCan), CRB-Santé, Biosit, Biogenouest, UBL, Rennes, France
| | - Stéphanie Renaud
- INSERM, INRA, Univ Rennes, CHU Rennes, Nutrition Metabolisms and Cancer (NuMeCan), CRB-Santé, Biosit, Biogenouest, UBL, Rennes, France
| | - Bruno Turlin
- INSERM, INRA, Univ Rennes, CHU Rennes, Nutrition Metabolisms and Cancer (NuMeCan), CRB-Santé, Biosit, Biogenouest, UBL, Rennes, France
| | - Pascale Bellaud
- INSERM, INRA, Univ Rennes, CHU Rennes, Nutrition Metabolisms and Cancer (NuMeCan), CRB-Santé, Biosit, Biogenouest, UBL, Rennes, France
| | - Christine Perret
- INSERM, CNRS, Université de Paris Descartes, Sorbonne Paris Cité, Institut Cochin, Paris, France
| | - Bruno Clément
- INSERM, INRA, Univ Rennes, CHU Rennes, Nutrition Metabolisms and Cancer (NuMeCan), CRB-Santé, Biosit, Biogenouest, UBL, Rennes, France
| | - Kim-Anh Lê Cao
- Diamantina Institute and Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Orlando Musso
- INSERM, INRA, Univ Rennes, CHU Rennes, Nutrition Metabolisms and Cancer (NuMeCan), CRB-Santé, Biosit, Biogenouest, UBL, Rennes, France
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24
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Rohart F, Eslami A, Matigian N, Bougeard S, Lê Cao KA. MINT: a multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms. BMC Bioinformatics 2017; 18:128. [PMID: 28241739 PMCID: PMC5327533 DOI: 10.1186/s12859-017-1553-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 02/16/2017] [Indexed: 12/12/2022] Open
Abstract
Background Molecular signatures identified from high-throughput transcriptomic studies often have poor reliability and fail to reproduce across studies. One solution is to combine independent studies into a single integrative analysis, additionally increasing sample size. However, the different protocols and technological platforms across transcriptomic studies produce unwanted systematic variation that strongly confounds the integrative analysis results. When studies aim to discriminate an outcome of interest, the common approach is a sequential two-step procedure; unwanted systematic variation removal techniques are applied prior to classification methods. Results To limit the risk of overfitting and over-optimistic results of a two-step procedure, we developed a novel multivariate integration method, MINT, that simultaneously accounts for unwanted systematic variation and identifies predictive gene signatures with greater reproducibility and accuracy. In two biological examples on the classification of three human cell types and four subtypes of breast cancer, we combined high-dimensional microarray and RNA-seq data sets and MINT identified highly reproducible and relevant gene signatures predictive of a given phenotype. MINT led to superior classification and prediction accuracy compared to the existing sequential two-step procedures. Conclusions MINT is a powerful approach and the first of its kind to solve the integrative classification framework in a single step by combining multiple independent studies. MINT is computationally fast as part of the mixOmics R CRAN package, available at http://www.mixOmics.org/mixMINT/and http://cran.r-project.org/web/packages/mixOmics/. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1553-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Florian Rohart
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, 4102, QLD, Australia
| | - Aida Eslami
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Nicholas Matigian
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, 4102, QLD, Australia
| | - Stéphanie Bougeard
- French agency for food, environmental and occupational health safety (Anses), Department of Epidemiology, Ploufragan, 22440, France
| | - Kim-Anh Lê Cao
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, 4102, QLD, Australia.
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25
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Godwin JW, Pinto AR, Rosenthal NA. Chasing the recipe for a pro-regenerative immune system. Semin Cell Dev Biol 2016; 61:71-79. [PMID: 27521522 DOI: 10.1016/j.semcdb.2016.08.008] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 08/08/2016] [Accepted: 08/09/2016] [Indexed: 02/07/2023]
Abstract
Identification of the key ingredients and essential processes required to achieve perfect tissue regeneration in humans has so far remained elusive. Injury in vertebrates induces an obligatory wound response that will precede or overlap any regeneration specific program or scarring outcome. This process shapes the cellular and molecular landscape of the tissue, influencing the success of endogenous repair pathways or for potential clinical intervention. The involvement of immune cells is also required for aspects of development extending beyond the initial inflammatory phase of wounding. It has now become clear from amphibian, fish and mammalian models of tissue injury that the type of immune response and the profile of immune cells attending the site of injury can act as the gatekeepers that determine wound repair quality. The heterogeneity among innate and adaptive immune cell populations, along with the developmental origin of these cells, form key ingredients affecting the potential for downstream repair and the suppression of fibrosis. Cell-to-cell interactions between immune cells, such as macrophages and T cells, with stem cells and mesenchymal cells are critically important for shaping this process and these exchanges, are in turn influenced by the type of injury, tissue location and developmental stage of the organism. Developmentally, mouse cardiac regeneration is restricted to early stages of postnatal life where the balance of innate to adaptive immune cells may be poised towards regeneration. In the injured adult mouse liver, specific macrophage subsets improve repair while other bone marrow derived cells can exacerbate injury. Other studies using genetically diverse mice have shown enhanced regeneration in certain strains, restricted to specific tissues. This enhanced repair is linked with expression of genes such as Insulin-like Growth Factor- 1 (IGF-1) and activin (Act 1), that both play important roles in shaping the immune system. Immune cells are now appreciated to have powerful influences on critical cell types required for regeneration success. The winning recipe for tissue regeneration is likely to be found ultimately by identifying the genetic elements and specific cell populations that limit or allow intrinsic potential. This will be essential for developing therapeutic strategies for tissue regeneration in humans.
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Affiliation(s)
- James W Godwin
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA; MDI Biological Laboratory, Salisbury Cove, ME 04672, USA; Australian Regenerative Medicine Institute, Monash University, Victoria, 3800, Australia.
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26
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Sinclair KA, Yerkovich ST, Hopkins PMA, Chambers DC. Characterization of intercellular communication and mitochondrial donation by mesenchymal stromal cells derived from the human lung. Stem Cell Res Ther 2016; 7:91. [PMID: 27406134 PMCID: PMC4942965 DOI: 10.1186/s13287-016-0354-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/14/2016] [Accepted: 06/23/2016] [Indexed: 12/22/2022] Open
Abstract
Background Bone marrow-derived mesenchymal stromal cells (BM-MSCs) are capable of repairing wounded lung epithelial cells by donating cytoplasmic material and mitochondria. Recently, we characterized two populations of human lung-derived mesenchymal stromal cells isolated from digested parenchymal lung tissue (LT-MSCs) from healthy individuals or from lung transplant recipients’ bronchoalveolar lavage fluid (BAL-MSCs). The aim of this study was to determine whether LT-MSCs and BAL-MSCs are also capable of donating cytoplasmic content and mitochondria to lung epithelial cells. Methods Cytoplasmic and mitochondrial transfer was assessed by co-culturing BEAS2B epithelial cells with Calcein AM or Mitotracker Green FM-labelled MSCs. Transfer was then measured by flow cytometry and validated by fluorescent microscopy. Molecular inhibitors were used to determine the contribution of microtubules/tunnelling nanotubes (TNTs, cytochalasin D), gap junctions (carbenoxolone), connexin-43 (gap26) and microvesicles (dynasore). Results F-actin microtubules/TNTs extending from BM-MSCs, LT-MSCs and BAL-MSCs to bronchial epithelial cells formed within 45 minutes of co-culturing cells. Each MSC population transferred a similar volume of cytoplasmic content to epithelial cells. Inhibiting microtubule/TNTs, gap junction formation and microvesicle endocytosis abrogated the transfer of cytoplasmic material from BM-MSCs, LT-MSCs and BAL-MSCs to epithelial cells. In contrast, blocking connexin-43 gap junction formation had no effect on cytoplasmic transfer. All MSC populations donated mitochondria to bronchial epithelial cells with similar efficiency. Mitochondrial transfer was reduced in all co-cultures after microtubule/TNT or endocytosis inhibition. Gap junction formation inhibition reduced mitochondrial transfer in BM-MSC and BAL-MSC co-cultures but had no effect on transfer in LT-MSC co-cultures. Connexin-43 inhibition did not impact mitochondrial transfer. Finally, bronchial epithelial cells were incapable of donating cytoplasmic content or mitochondria to any MSC population. Conclusion Similar to their bone marrow counterparts, LT-MSCs and BAL-MSCs can donate cytoplasmic content and mitochondria to bronchial epithelial cells via multiple mechanisms. Given that BM-MSCs utilize these mechanisms to mediate the repair of damaged bronchial epithelial cells, both LT-MSCs and BAL-MSCs will probably function similarly. Electronic supplementary material The online version of this article (doi:10.1186/s13287-016-0354-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kenneth Andrew Sinclair
- School of Medicine, University of Queensland, Brisbane, QLD, Australia. .,Queensland Lung Transplant Service, Ground Floor, Clinical Sciences Building, The Prince Charles Hospital, Rode Road, Chermside, Brisbane, QLD, 4032, Australia.
| | - Stephanie Terase Yerkovich
- School of Medicine, University of Queensland, Brisbane, QLD, Australia.,Queensland Lung Transplant Service, Ground Floor, Clinical Sciences Building, The Prince Charles Hospital, Rode Road, Chermside, Brisbane, QLD, 4032, Australia
| | - Peter Mark-Anthony Hopkins
- School of Medicine, University of Queensland, Brisbane, QLD, Australia.,Queensland Lung Transplant Service, Ground Floor, Clinical Sciences Building, The Prince Charles Hospital, Rode Road, Chermside, Brisbane, QLD, 4032, Australia
| | - Daniel Charles Chambers
- School of Medicine, University of Queensland, Brisbane, QLD, Australia.,Queensland Lung Transplant Service, Ground Floor, Clinical Sciences Building, The Prince Charles Hospital, Rode Road, Chermside, Brisbane, QLD, 4032, Australia
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27
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Sinclair KA, Yerkovich ST, Chen T, McQualter JL, Hopkins PMA, Wells CA, Chambers DC. Mesenchymal Stromal Cells are Readily Recoverable from Lung Tissue, but not the Alveolar Space, in Healthy Humans. Stem Cells 2016; 34:2548-2558. [PMID: 27352824 DOI: 10.1002/stem.2419] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 04/14/2016] [Accepted: 05/06/2016] [Indexed: 12/17/2022]
Abstract
Stromal support is critical for lung homeostasis and the maintenance of an effective epithelial barrier. Despite this, previous studies have found a positive association between the number of mesenchymal stromal cells (MSCs) isolated from the alveolar compartment and human lung diseases associated with epithelial dysfunction. We hypothesised that bronchoalveolar lavage derived MSCs (BAL-MSCs) are dysfunctional and distinct from resident lung tissue MSCs (LT-MSCs). In this study, we comprehensively interrogated the phenotype and transcriptome of human BAL-MSCs and LT-MSCs. We found that MSCs were rarely recoverable from the alveolar space in healthy humans, but could be readily isolated from lung transplant recipients by bronchoalveolar lavage. BAL-MSCs exhibited a CD90Hi , CD73Hi , CD45Neg , CD105Lo immunophenotype and were bipotent, lacking adipogenic potential. In contrast, MSCs were readily recoverable from healthy human lung tissue and were CD90Hi or Lo , CD73Hi , CD45Neg , CD105Int and had full tri-lineage potential. Transcriptional profiling of the two populations confirmed their status as bona fide MSCs and revealed a high degree of similarity between each other and the archetypal bone-marrow MSC. 105 genes were differentially expressed; 76 of which were increased in BAL-MSCs including genes involved in fibroblast activation, extracellular matrix deposition and tissue remodelling. Finally, we found the fibroblast markers collagen 1A1 and α-smooth muscle actin were increased in BAL-MSCs. Our data suggests that in healthy humans, lung MSCs reside within the tissue, but in disease can differentiate to acquire a profibrotic phenotype and migrate from their in-tissue niche into the alveolar space. Stem Cells 2016;34:2548-2558.
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Affiliation(s)
- K A Sinclair
- School of Medicine, The Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia. .,Queensland Lung Transplant Service, The Prince Charles Hospital, Brisbane, Queensland, Australia.
| | - S T Yerkovich
- School of Medicine, The Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia.,Queensland Lung Transplant Service, The Prince Charles Hospital, Brisbane, Queensland, Australia
| | - T Chen
- The Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
| | - J L McQualter
- Lung and Regenerative Medical Institutes, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - P M-A Hopkins
- School of Medicine, The Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia.,Queensland Lung Transplant Service, The Prince Charles Hospital, Brisbane, Queensland, Australia
| | - C A Wells
- The Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
| | - D C Chambers
- School of Medicine, The Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia.,Queensland Lung Transplant Service, The Prince Charles Hospital, Brisbane, Queensland, Australia
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Wagner W, Frobel J, Goetzke R. Epigenetic quality check - how good are your mesenchymal stromal cells? Epigenomics 2016; 8:889-94. [PMID: 27366986 DOI: 10.2217/epi-2016-0054] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology & Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Joana Frobel
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology & Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Roman Goetzke
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology & Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
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