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Liu S, Li Y, Wu C. Paeoniflorin suppresses the apoptosis and inflammation of human coronary artery endothelial cells induced by oxidized low-density lipoprotein by regulating the Wnt/β-catenin pathway. PHARMACEUTICAL BIOLOGY 2023; 61:1454-1461. [PMID: 37674320 PMCID: PMC10486282 DOI: 10.1080/13880209.2023.2220360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 04/24/2023] [Accepted: 05/27/2023] [Indexed: 09/08/2023]
Abstract
CONTEXT Paeoniflorin (PF) contributes to improving coronary artery disease (CAD). OBJECTIVE This study clarified the efficiency of PF in CAD and the molecular mechanism. MATERIALS AND METHODS Human coronary artery endothelial cells (HCAECs) were treated with oxidized low-density lipoprotein (ox-LDL; 20, 40, 80 and 160 μg/mL) and PF (0.05, 0.1 0.2 and 0.4 mM). To study cell phenotypes, HCAECs were treated with 80 μg/mL ox-LDL with or without 0.1 mM PF for 24 h, and cell viability and apoptosis were evaluated using the methyl thiazolyl tetrazolium (MTT) assay and flow cytometry, respectively. In addition, inflammatory cytokines levels were measured by enzyme-linked immunosorbent assay (ELISA). Western blot evaluated the Wnt/β-catenin pathway-related factors. RESULTS ox-LDL and PF (0.2 and 0.4 mM) suppressed cell viability in a dose-dependent manner. The IC50 value of PF was 722.9 nM. PF facilitated cell viability (115.76%), inhibited apoptosis (46.28%), reduced IL-6 (63.43%) and IL-8 (66.70%) levels and increased IL-10 levels (181.15%) of ox-LDL-treated HCAECs. Additionally, PF inactivated the Wnt/β-catenin pathway, and XAV939 treatment further promoted cell viability (120.54%), suppressed apoptosis (56.92%), reduced the levels of IL-6 (76.16%) and IL-8 (86.82%) and increased the IL-10 levels (120.22%) of ox-LDL-induced HCAECs after PF treatment. Moreover, PF alleviated plaque lesions of the aorta and aorta root and serum lipid of ApoE-/- mice with a high-fat diet. DISCUSSION AND CONCLUSIONS This study first revealed that PF inhibited ox-LDL-induced HCAECs apoptosis and inflammation via the Wnt/β-catenin pathway and alleviated CAD, suggesting the potential of PF as a drug for CAD treatment.
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Affiliation(s)
- Shasha Liu
- Department of Geriatrics, Sichuan People’s Hospital, Sichuan Academy of Medical Sciences, Chengdu, Sichuan, China
| | - Ying Li
- Department of Geriatrics, Sichuan People’s Hospital, Sichuan Academy of Medical Sciences, Chengdu, Sichuan, China
| | - Caojie Wu
- Department of Geriatrics, Sichuan People’s Hospital, Sichuan Academy of Medical Sciences, Chengdu, Sichuan, China
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2
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Bhat SM, Prasad PR, Joshi MB. Novel insights into DNA methylation-based epigenetic regulation of breast tumor angiogenesis. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 380:63-96. [PMID: 37657860 DOI: 10.1016/bs.ircmb.2023.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
Breast tumors are highly vascularized and dependent on angiogenesis for growth, progression and metastasis. Like other solid tumors, vasculature in breast tumors also display leaky and tortuous phenotype and hence inhibit immune cell infiltration, show reduced efficacy to anticancer drugs and radiotherapy. Epigenetic reprogramming including significant alterations in DNA methylation in tumor and stromal cells generate an imbalance in expression of pro- and anti-angiogenic factors and subsequently lead to disordered angiogenesis. Hence, understanding DNA methylation-based regulation of angiogenesis in breast tumors may open new avenues for designing therapeutic targets. Our present review manuscript summarized contemporary knowledge of influence of DNA methylation in regulating angiogenesis. Further, we identified novel set of pro-angiogenic genes enriched in endothelial cells which are coregulated with DNMT isoforms in breast tumors and harboring CpG islands. Our analysis revealed promoters of pro-angiogenic genes were hypomethylated and anti-angiogenic genes were hypermethylated in tumors and further reflected on their expression patterns. Interestingly, promoter DNA methylation intensities of novel set of pro-angiogenic genes significantly correlated to patient survival outcome.
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Affiliation(s)
- Sharath Mohan Bhat
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Palla Ranga Prasad
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Manjunath B Joshi
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India.
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3
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Yao Y, Du Jiang P, Chao BN, Cagdas D, Kubo S, Balasubramaniyam A, Zhang Y, Shadur B, NaserEddin A, Folio LR, Schwarz B, Bohrnsen E, Zheng L, Lynberg M, Gottlieb S, Leney-Greene MA, Park AY, Tezcan I, Akdogan A, Gocmen R, Onder S, Rosenberg A, Soilleux EJ, Johnson E, Jackson PK, Demeter J, Chauvin SD, Paul F, Selbach M, Bulut H, Clatworthy MR, Tuong ZK, Zhang H, Stewart BJ, Bosio CM, Stepensky P, Clare S, Ganesan S, Pascall JC, Daumke O, Butcher GW, McMichael AJ, Simon AK, Lenardo MJ. GIMAP6 regulates autophagy, immune competence, and inflammation in mice and humans. J Exp Med 2022; 219:213217. [PMID: 35551368 PMCID: PMC9111091 DOI: 10.1084/jem.20201405] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 01/18/2022] [Accepted: 03/16/2022] [Indexed: 11/26/2022] Open
Abstract
Inborn errors of immunity (IEIs) unveil regulatory pathways of human immunity. We describe a new IEI caused by mutations in the GTPase of the immune-associated protein 6 (GIMAP6) gene in patients with infections, lymphoproliferation, autoimmunity, and multiorgan vasculitis. Patients and Gimap6−/− mice show defects in autophagy, redox regulation, and polyunsaturated fatty acid (PUFA)–containing lipids. We find that GIMAP6 complexes with GABARAPL2 and GIMAP7 to regulate GTPase activity. Also, GIMAP6 is induced by IFN-γ and plays a critical role in antibacterial immunity. Finally, we observed that Gimap6−/− mice died prematurely from microangiopathic glomerulosclerosis most likely due to GIMAP6 deficiency in kidney endothelial cells.
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Affiliation(s)
- Yikun Yao
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Ping Du Jiang
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Brittany N Chao
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD.,Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Deniz Cagdas
- Division of Immunology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey.,Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey.,Ihsan Dogramaci Childrens Hospital, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Satoshi Kubo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Arasu Balasubramaniyam
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Yu Zhang
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Bella Shadur
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel.,The Garvan Institute of Medical Research, Immunology Division, Darlinghurst, Sydney, Australia.,St Vincent's Clinical School, University of New South Wales, Darlinghurst, Sydney, Australia
| | - Adeeb NaserEddin
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel
| | - Les R Folio
- Clinical Center, National Institutes of Health, Bethesda, MD
| | - Benjamin Schwarz
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Eric Bohrnsen
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Lixin Zheng
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Matthew Lynberg
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Simone Gottlieb
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Michael A Leney-Greene
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Ann Y Park
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Ilhan Tezcan
- Division of Immunology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey.,Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey.,Ihsan Dogramaci Childrens Hospital, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Ali Akdogan
- Division of Rheumatology, Department of Internal Medicine, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Rahsan Gocmen
- Department of Radiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Sevgen Onder
- Department of Pathology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Avi Rosenberg
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD.,Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
| | | | - Errin Johnson
- The Dunn School of Pathology, South Parks Road, Oxford, UK
| | - Peter K Jackson
- Baxter Laboratory, Departments of Microbiology & Immunology and Pathology Stanford University School of Medicine, Stanford, CA
| | - Janos Demeter
- Baxter Laboratory, Departments of Microbiology & Immunology and Pathology Stanford University School of Medicine, Stanford, CA
| | - Samuel D Chauvin
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Florian Paul
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Matthias Selbach
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Haydar Bulut
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Menna R Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Zewen K Tuong
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Hanlin Zhang
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Catharine M Bosio
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Polina Stepensky
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel
| | - Simon Clare
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Sundar Ganesan
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - John C Pascall
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Oliver Daumke
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Geoffrey W Butcher
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Andrew J McMichael
- Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anna Katharina Simon
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Michael J Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
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4
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Multimerin-1 and cancer: a review. Biosci Rep 2022; 42:230760. [PMID: 35132992 PMCID: PMC8881648 DOI: 10.1042/bsr20211248] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/29/2022] [Accepted: 02/01/2022] [Indexed: 11/21/2022] Open
Abstract
Multimerin-1 (MMRN1) is a platelet protein with a role in haemostasis and coagulation. It is also present in endothelial cells (ECs) and the extracellular matrix (ECM), where it may be involved in cell adhesion, but its molecular functions and protein–protein interactions in these cellular locations have not been studied in detail yet. In recent years, MMRN1 has been identified as a differentially expressed gene (DEG) in various cancers and it has been proposed as a possible cancer biomarker. Some evidence suggest that MMRN1 expression is regulated by methylation, protein interactions, and non-coding RNAs (ncRNAs) in different cancers. This raises the questions if a functional role of MMRN1 is being targeted during cancer development, and if MMRN1’s differential expression pattern correlates with cancer progression. As a result, it is timely to review the current state of what is known about MMRN1 to help inform future research into MMRN1’s molecular mechanisms in cancer.
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5
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Chen H, Xia K, Huang W, Li H, Wang C, Ma Y, Chen J, Luo P, Zheng S, Wang J, Wang Y, Dong L, Tan Z, Lai X, Mao FF, Li W, Liang X, Wang T, Xiang AP, Ke Q. Autologous transplantation of thecal stem cells restores ovarian function in nonhuman primates. Cell Discov 2021; 7:75. [PMID: 34462432 PMCID: PMC8405815 DOI: 10.1038/s41421-021-00291-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/21/2021] [Indexed: 02/07/2023] Open
Abstract
Premature ovarian insufficiency (POI) is defined as the loss of ovarian activity under the age of 40. Theca cells (TCs) play a vital role during folliculogenesis and TCs dysfunction participate in the pathogenesis of POI. Therefore, transplantation of thecal stem cells (TSCs), which are capable of self-renewal and differentiation into mature TCs, may provide a new strategy for treating POI. To investigate the feasibility, safety, and efficacy of TSCs transplantation in clinically relevant non-human primate (NHP) models, we isolate TSCs from cynomolgus monkeys, and these cells are confirmed to expand continuously and show potential to differentiate into mature TCs. In addition, engraftment of autologous TSCs into POI monkeys significantly improves hormone levels, rescues the follicle development, promotes the quality of oocytes and boosts oocyte maturation/fertilization rate. Taken together, these results for the first time suggest that autologous TSCs can ameliorate POI symptoms in primate models and shed new light on developing stem cell therapy for POI.
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Affiliation(s)
- Hong Chen
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Kai Xia
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Weijun Huang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of Genetics and Cell Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Huijian Li
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Chao Wang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yuanchen Ma
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jianhui Chen
- Center for Reproductive Medicine, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Peng Luo
- Department of Andrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shuwei Zheng
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiancheng Wang
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Yi Wang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lin Dong
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhipeng Tan
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xingqiang Lai
- Cardiovascular Department, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Frank Fuxiang Mao
- State Key Laboratory of Ophthalmology, Zhong Shan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Weiqiang Li
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaoyan Liang
- Center for Reproductive Medicine, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Tao Wang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Andy Peng Xiang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Qiong Ke
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Department of Genetics and Cell Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.
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6
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The secretome mouse provides a genetic platform to delineate tissue-specific in vivo secretion. Proc Natl Acad Sci U S A 2021; 118:2005134118. [PMID: 33431665 DOI: 10.1073/pnas.2005134118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
At present, it remains difficult to deconvolute serum in order to identify the cell or tissue origin of a given circulating protein. Here, by exploiting the properties of proximity biotinylation, we describe a mouse model that enables the elucidation of the in vivo tissue-specific secretome. As an example, we demonstrate how we can readily identify in vivo endothelial-specific secretion as well as how this model allows for the characterization of muscle-derived serum proteins that either increase or decrease with exercise. This genetic platform should, therefore, be of wide utility in understanding normal and disease physiology and for the rational design of tissue-specific disease biomarkers.
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7
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Lammerts RGM, Lagendijk LM, Tiller G, Dam WA, Lancaster HL, Daha MR, Seelen MA, Hepkema BG, Pol RA, Leuvenink HGD, Molema G, van den Born J, Berger SP. Machine-perfused donor kidneys as a source of human renal endothelial cells. Am J Physiol Renal Physiol 2021; 320:F947-F962. [PMID: 33719571 DOI: 10.1152/ajprenal.00541.2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Renal endothelial cells (ECs) play crucial roles in vasorelaxation, ultrafiltration, and selective transport of electrolytes and water, but also in leakage of the glomerular filtration barrier and inflammatory processes like complement activation and leukocyte recruitment. In addition, they are target cells for both cellular and antibody-mediated rejection in the transplanted kidney. To study the molecular and cellular processes underlying EC behavior in renal disease, well-characterized primary renal ECs are indispensible. In this report, we describe a straightforward procedure to isolate ECs from the perfusion fluid of human donor kidneys by a combination of negative selection of monocytes/macrophages, positive selection by CD31 Dynabeads, and propagation in endothelium-specific culture medium. Thus, we isolated and propagated renal ECs from 102 donor kidneys, representative of all blood groups and major human leukocyte antigen (HLA) class I and II antigens. The obtained ECs were positive for CD31 and von Willebrand factor, expressed other endothelial markers such as CD34, VEGF receptor-2, TIE2, and plasmalemmal vesicle associated protein-1 to a variable extent, and were negative for the monocyte marker CD14 and lymphatic endothelial marker podoplanin. HLA class II was either constitutively expressed or could be induced by interferon-γ. Furthermore, as a proof of principle, we showed the diagnostic value of this renal endothelial biobank in renal endothelium-specific cross-matching tests for HLA antibodies.NEW & NOTEWORTHY We describe a new and widely accessible approach to obtain human primary renal endothelial cells in a standardized fashion, by isolating from the perfusate of machine-perfused donor kidneys. Characterization of the cells showed a mixed population originating from different compartments of the kidney. As a proof of principle, we demonstrated a possible diagnostic application in an endothelium-specific cross-match. Next to transplantation, we foresee further applications in the field renal endothelial research.
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Affiliation(s)
- Rosa G M Lammerts
- Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Lisanne M Lagendijk
- Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Gesa Tiller
- Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Wendy A Dam
- Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Harriet L Lancaster
- Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Mohamed R Daha
- Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marc A Seelen
- Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Bouke G Hepkema
- Transplantation Immunology, Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Robert A Pol
- Department of Surgery, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Henri G D Leuvenink
- Department of Surgery, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Grietje Molema
- Medical Biology Section, Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Jacob van den Born
- Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Stefan P Berger
- Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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8
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Maurya MR, Gupta S, Li JYS, Ajami NE, Chen ZB, Shyy JYJ, Chien S, Subramaniam S. Longitudinal shear stress response in human endothelial cells to atheroprone and atheroprotective conditions. Proc Natl Acad Sci U S A 2021; 118:e2023236118. [PMID: 33468662 PMCID: PMC7848718 DOI: 10.1073/pnas.2023236118] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The two main blood flow patterns, namely, pulsatile shear (PS) prevalent in straight segments of arteries and oscillatory shear (OS) observed at branch points, are associated with atheroprotective (healthy) and atheroprone (unhealthy) vascular phenotypes, respectively. The effects of blood flow-induced shear stress on endothelial cells (ECs) and vascular health have generally been studied using human umbilical vein endothelial cells (HUVECs). While there are a few studies comparing the differential roles of PS and OS across different types of ECs at a single time point, there is a paucity of studies comparing the temporal responses between different EC types. In the current study, we measured OS and PS transcriptomic responses in human aortic endothelial cells (HAECs) over 24 h and compared these temporal responses of HAECs with our previous findings on HUVECs. The measurements were made at 1, 4, and 24 h in order to capture the responses at early, mid, and late time points after shearing. The results indicate that the responses of HAECs and HUVECs are qualitatively similar for endothelial function-relevant genes and several important pathways with a few exceptions, thus demonstrating that HUVECs can be used as a model to investigate the effects of shear on arterial ECs, with consideration of the differences. Our findings show that HAECs exhibit an earlier response or faster kinetics as compared to HUVECs. The comparative analysis of HAECs and HUVECs presented here offers insights into the mechanisms of common and disparate shear stress responses across these two major endothelial cell types.
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Affiliation(s)
- Mano R Maurya
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
| | - Shakti Gupta
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
| | - Julie Yi-Shuan Li
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
- Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA 92093
| | - Nassim E Ajami
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92023
| | - Zhen B Chen
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, CA 91010
| | - John Y-J Shyy
- Department of Medicine, University of California San Diego, La Jolla, CA 92093;
| | - Shu Chien
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093;
- Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA 92093
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Shankar Subramaniam
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093;
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
- Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA 92093
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92023
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
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9
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Gunawardana H, Romero T, Yao N, Heidt S, Mulder A, Elashoff DA, Valenzuela NM. Tissue-specific endothelial cell heterogeneity contributes to unequal inflammatory responses. Sci Rep 2021; 11:1949. [PMID: 33479269 PMCID: PMC7820348 DOI: 10.1038/s41598-020-80102-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/16/2020] [Indexed: 12/30/2022] Open
Abstract
Endothelial cells (EC) coordinate vascular homeostasis and inflammation. In organ transplantation, EC are a direct alloimmune target. We posited that tissue specific heterogeneity of vascular EC may partly underlie the disparate organ-specific alloimmune risk. We examined the vascular endothelial response to inflammation across six primary endothelial beds from four major transplanted organs: the heart, lung, kidney and liver. First, we reanalyzed a public dataset of cardiac allograft rejection and found that endothelial inflammatory response genes were elevated in human cardiac allograft biopsies undergoing rejection compared with stable grafts. Next, the inducible inflammatory phenotypes of EC from heart, lung, kidney, and liver were characterized in vitro, focused on expression of adhesion molecules and chemokines, and recruitment of allogeneic peripheral blood mononuclear immune cells. Large vessel cardiac EC most highly upregulated VCAM-1, particularly compared with hepatic EC, supported greater leukocyte adhesion and had distinct chemokine profiles after stimulation with cytokines and complement. Differentially expressed gene candidates that are known regulators of cytokine signaling and inflammatory programming were verified in publicly available datasets of organ-specific endothelial transcriptomes. In summary, differential baseline expression of immune regulating genes may contribute to differential vascular inflammatory responses depending on organ.
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Affiliation(s)
- Hasitha Gunawardana
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, 1000 Veteran Avenue, Room 1-520, Los Angeles, CA, 90095, USA
| | - Tahmineh Romero
- Statistics Core, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Ning Yao
- Statistics Core, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Sebastiaan Heidt
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Arend Mulder
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - David A Elashoff
- Statistics Core, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Nicole M Valenzuela
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, 1000 Veteran Avenue, Room 1-520, Los Angeles, CA, 90095, USA.
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10
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Lee J, Henderson K, Massidda MW, Armenta-Ochoa M, Im BG, Veith A, Lee BK, Kim M, Maceda P, Yoon E, Samarneh L, Wong M, Dunn AK, Kim J, Baker AB. Mechanobiological conditioning of mesenchymal stem cells for enhanced vascular regeneration. Nat Biomed Eng 2021; 5:89-102. [PMID: 33483713 PMCID: PMC8875880 DOI: 10.1038/s41551-020-00674-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 12/09/2020] [Indexed: 01/30/2023]
Abstract
Using endogenous mesenchymal stem cells for treating myocardial infarction and other cardiovascular conditions typically results in poor efficacy, in part owing to the heterogeneity of the harvested cells and of the patient responses. Here, by means of high-throughput screening of the combinatorial space of mechanical-strain level and of the presence of particular kinase inhibitors, we show that human mesenchymal stem cells can be mechanically and pharmacologically conditioned to enhance vascular regeneration in vivo. Mesenchymal stem cells conditioned to increase the activation of signalling pathways mediated by Smad2/3 (mothers against decapentaplegic homolog 2/3) and YAP (Yes-associated protein) expressed markers that are associated with pericytes and endothelial cells, displayed increased angiogenic activity in vitro, and enhanced the formation of vasculature in mice after subcutaneous implantation and after implantation in ischaemic hindlimbs. These effects were mediated by the crosstalk of endothelial-growth-factor receptors, transforming-growth-factor-beta receptor type 1 and vascular-endothelial-growth-factor receptor 2. Mechanical and pharmacological conditioning can significantly enhance the regenerative properties of mesenchymal stem cells.
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Affiliation(s)
- Jason Lee
- University of Texas at Austin, Department of Biomedical Engineering, Austin, TX
| | - Kayla Henderson
- University of Texas at Austin, Department of Biomedical Engineering, Austin, TX
| | - Miles W. Massidda
- University of Texas at Austin, Department of Biomedical Engineering, Austin, TX
| | | | - Byung Gee Im
- University of Texas at Austin, Department of Biomedical Engineering, Austin, TX
| | - Austin Veith
- University of Texas at Austin, Department of Biomedical Engineering, Austin, TX
| | - Bum-Kyu Lee
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX
| | - Mijeong Kim
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX
| | - Pablo Maceda
- University of Texas at Austin, Department of Biomedical Engineering, Austin, TX
| | - Eun Yoon
- University of Texas at Austin, Department of Biomedical Engineering, Austin, TX
| | - Lara Samarneh
- University of Texas at Austin, Department of Biomedical Engineering, Austin, TX
| | - Mitchell Wong
- University of Texas at Austin, Department of Biomedical Engineering, Austin, TX
| | - Andrew K. Dunn
- University of Texas at Austin, Department of Biomedical Engineering, Austin, TX
| | - Jonghwan Kim
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX
| | - Aaron B. Baker
- University of Texas at Austin, Department of Biomedical Engineering, Austin, TX,Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX,The Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, TX,Institute for Biomaterials, Drug Delivery and Regenerative Medicine, University of Texas at Austin, Austin, TX
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11
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Jamil MA, Singer H, Al-Rifai R, Nüsgen N, Rath M, Strauss S, Andreou I, Oldenburg J, El-Maarri O. Molecular Analysis of Fetal and Adult Primary Human Liver Sinusoidal Endothelial Cells: A Comparison to Other Endothelial Cells. Int J Mol Sci 2020; 21:E7776. [PMID: 33096636 PMCID: PMC7589710 DOI: 10.3390/ijms21207776] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/14/2020] [Accepted: 10/16/2020] [Indexed: 01/27/2023] Open
Abstract
In humans, Factor VIII (F8) deficiency leads to hemophilia A and F8 is largely synthesized and secreted by the liver sinusoidal endothelial cells (LSECs). However, the specificity and characteristics of these cells in comparison to other endothelial cells is not well known. In this study, we performed genome wide expression and CpG methylation profiling of fetal and adult human primary LSECs together with other fetal primary endothelial cells from lung (micro-vascular and arterial), and heart (micro-vascular). Our results reveal expression and methylation markers distinguishing LSECs at both fetal and adult stages. Differential gene expression of fetal LSECs in comparison to other fetal endothelial cells pointed to several differentially regulated pathways and biofunctions in fetal LSECs. We used targeted bisulfite resequencing to confirm selected top differentially methylated regions. We further designed an assay where we used the selected methylation markers to test the degree of similarity of in-house iPS generated vascular endothelial cells to primary LSECs; a higher similarity was found to fetal than to adult LSECs. In this study, we provide a detailed molecular profile of LSECs and a guide to testing the effectiveness of production of in vitro differentiated LSECs.
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Affiliation(s)
- Muhammad Ahmer Jamil
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany; (M.A.J.); (H.S.); (R.A.-R.); (N.N.); (M.R.); (J.O.)
| | - Heike Singer
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany; (M.A.J.); (H.S.); (R.A.-R.); (N.N.); (M.R.); (J.O.)
| | - Rawya Al-Rifai
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany; (M.A.J.); (H.S.); (R.A.-R.); (N.N.); (M.R.); (J.O.)
| | - Nicole Nüsgen
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany; (M.A.J.); (H.S.); (R.A.-R.); (N.N.); (M.R.); (J.O.)
| | - Melanie Rath
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany; (M.A.J.); (H.S.); (R.A.-R.); (N.N.); (M.R.); (J.O.)
| | | | | | - Johannes Oldenburg
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany; (M.A.J.); (H.S.); (R.A.-R.); (N.N.); (M.R.); (J.O.)
| | - Osman El-Maarri
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany; (M.A.J.); (H.S.); (R.A.-R.); (N.N.); (M.R.); (J.O.)
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12
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DeBiasse MB, Colgan WN, Harris L, Davidson B, Ryan JF. Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata. Genome Biol Evol 2020; 12:948-964. [PMID: 32211845 PMCID: PMC7337526 DOI: 10.1093/gbe/evaa060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2020] [Indexed: 12/21/2022] Open
Abstract
Tunicates, the closest living relatives of vertebrates, have served as a foundational model of early embryonic development for decades. Comparative studies of tunicate phylogeny and genome evolution provide a critical framework for analyzing chordate diversification and the emergence of vertebrates. Toward this goal, we sequenced the genome of Corella inflata (Ascidiacea, Phlebobranchia), so named for the capacity to brood self-fertilized embryos in a modified, "inflated" atrial chamber. Combining the new genome sequence for Co. inflata with publicly available tunicate data, we estimated a tunicate species phylogeny, reconstructed the ancestral Hox gene cluster at important nodes in the tunicate tree, and compared patterns of gene loss between Co. inflata and Ciona robusta, the prevailing tunicate model species. Our maximum-likelihood and Bayesian trees estimated from a concatenated 210-gene matrix were largely concordant and showed that Aplousobranchia was nested within a paraphyletic Phlebobranchia. We demonstrated that this relationship is not an artifact due to compositional heterogeneity, as had been suggested by previous studies. In addition, within Thaliacea, we recovered Doliolida as sister to the clade containing Salpida and Pyrosomatida. The Co. inflata genome provides increased resolution of the ancestral Hox clusters of key tunicate nodes, therefore expanding our understanding of the evolution of this cluster and its potential impact on tunicate morphological diversity. Our analyses of other gene families revealed that several cardiovascular associated genes (e.g., BMP10, SCL2A12, and PDE2a) absent from Ci. robusta, are present in Co. inflata. Taken together, our results help clarify tunicate relationships and the genomic content of key ancestral nodes within this phylogeny, providing critical insights into tunicate evolution.
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Affiliation(s)
- Melissa B DeBiasse
- Whitney Laboratory for Marine Bioscience, University of Florida
- Department of Biology, University of Florida, Gainesville
| | - William N Colgan
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania
| | - Lincoln Harris
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania
| | - Bradley Davidson
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida
- Department of Biology, University of Florida, Gainesville
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13
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Yan G, Yan R, Chen C, Chen C, Zhao Y, Qin W, Veldman MB, Li S, Lin S. Engineering vascularized skeletal muscle tissue with transcriptional factor ETV2-induced autologous endothelial cells. Protein Cell 2020; 10:217-222. [PMID: 29687363 PMCID: PMC6338622 DOI: 10.1007/s13238-018-0542-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Guanrong Yan
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen University Town, Shenzhen, 518055, China
| | - Ruibin Yan
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen University Town, Shenzhen, 518055, China
| | - Cheng Chen
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen University Town, Shenzhen, 518055, China
| | - Cheng Chen
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen University Town, Shenzhen, 518055, China
| | - Yanqiu Zhao
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen University Town, Shenzhen, 518055, China
| | - Wei Qin
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen University Town, Shenzhen, 518055, China
| | - Matthew B Veldman
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095-1555, USA
| | - Song Li
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen University Town, Shenzhen, 518055, China
| | - Shuo Lin
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen University Town, Shenzhen, 518055, China. .,Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095-1555, USA.
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14
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Grangeon L, Guey S, Schwitalla JC, Bergametti F, Arnould M, Corpechot M, Hadjadj J, Riant F, Aloui C, Drunat S, Vidaud D, Tournier-Lasserve E, Kraemer M. Clinical and Molecular Features of 5 European Multigenerational Families With Moyamoya Angiopathy. Stroke 2020; 50:789-796. [PMID: 30908154 DOI: 10.1161/strokeaha.118.023972] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background and Purpose Moyamoya angiopathy (MMA) is a rare cerebral vasculopathy outside of Asia. In Japanese patients, a vast majority of patients carry the founder p.R4810K variant in the RNF213 gene, and familial cases are around 10%. In European patients, data about familial occurrence are limited. The aim of this study was to characterize the clinical and molecular features of several European families with a parent-to-child transmission of MMA. Methods Out of 126 MMA probands referred, we identified 113 sporadic probands and 13 familial probands. Segregation analysis showed a vertical parent-to-child pattern of inheritance in the families of 5 of these probands. All 5 families were of German or Dutch ancestry. We investigated the clinical features of affected members and used whole-exome sequencing to screen RNF213 and 13 genes involved in Mendelian MMA and to identify genes recurrently mutated in these families. Results Twelve affected MMA patients were identified, including 9 females and 3 males. Age at clinical onset ranged from 11 to 65 years. In 3 of 5 families, associated livedo racemosa was found. We did not detect any deleterious variants in the 13 known MMA genes. RNF213 rare missense variants predicted to be pathogenic were detected in all affected members of 2 of these families, as well as 2 candidate variants of the PALD1 gene. Conclusions Nonsyndromic MMA was identified in 5 European families, including 2 to 3 clinically affected cases segregating with a parent-to-child pattern of inheritance in each family. Molecular screening detected rare deleterious variants within RNF213 and PALD1 in all affected members of 2 of these 5 families, as well as in some clinically unaffected members. Altogether these data raise the difficult and, to date unanswered, question of the medical indication of presymptomatic screening.
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Affiliation(s)
- Lou Grangeon
- From the Sorbonne Paris Cité, Inserm UMR-S1161, Génétique et physiopathologie des maladies cérébro-vasculaires, Université Paris Diderot, France (L.G., S.G., F.B., M.A., C.A. E.T.-L.)
| | - Stéphanie Guey
- From the Sorbonne Paris Cité, Inserm UMR-S1161, Génétique et physiopathologie des maladies cérébro-vasculaires, Université Paris Diderot, France (L.G., S.G., F.B., M.A., C.A. E.T.-L.)
| | | | - Françoise Bergametti
- From the Sorbonne Paris Cité, Inserm UMR-S1161, Génétique et physiopathologie des maladies cérébro-vasculaires, Université Paris Diderot, France (L.G., S.G., F.B., M.A., C.A. E.T.-L.)
| | - Minh Arnould
- From the Sorbonne Paris Cité, Inserm UMR-S1161, Génétique et physiopathologie des maladies cérébro-vasculaires, Université Paris Diderot, France (L.G., S.G., F.B., M.A., C.A. E.T.-L.)
| | - Michaelle Corpechot
- AP-HP, Service de génétique moléculaire neurovasculaire, Centre de Référence des Maladies Vasculaires Rares du Cerveau et de l'œil, Groupe Hospitalier Saint-Louis Lariboisière, Paris, France (M.C., J.H., F.R., E.T.-L.)
| | - Jessica Hadjadj
- AP-HP, Service de génétique moléculaire neurovasculaire, Centre de Référence des Maladies Vasculaires Rares du Cerveau et de l'œil, Groupe Hospitalier Saint-Louis Lariboisière, Paris, France (M.C., J.H., F.R., E.T.-L.)
| | - Florence Riant
- AP-HP, Service de génétique moléculaire neurovasculaire, Centre de Référence des Maladies Vasculaires Rares du Cerveau et de l'œil, Groupe Hospitalier Saint-Louis Lariboisière, Paris, France (M.C., J.H., F.R., E.T.-L.)
| | - Chaker Aloui
- From the Sorbonne Paris Cité, Inserm UMR-S1161, Génétique et physiopathologie des maladies cérébro-vasculaires, Université Paris Diderot, France (L.G., S.G., F.B., M.A., C.A. E.T.-L.)
| | - Severine Drunat
- AP-HP, Service de génétique, Groupe Hospitalier Robert Debré, Paris, France (S.D.)
| | - Dominique Vidaud
- AP-HP, Service de génétique, Groupe hospitalier Cochin, Paris, France (D.V.)
| | - Elisabeth Tournier-Lasserve
- From the Sorbonne Paris Cité, Inserm UMR-S1161, Génétique et physiopathologie des maladies cérébro-vasculaires, Université Paris Diderot, France (L.G., S.G., F.B., M.A., C.A. E.T.-L.).,AP-HP, Service de génétique moléculaire neurovasculaire, Centre de Référence des Maladies Vasculaires Rares du Cerveau et de l'œil, Groupe Hospitalier Saint-Louis Lariboisière, Paris, France (M.C., J.H., F.R., E.T.-L.)
| | - Markus Kraemer
- Department of Neurology, Alfried Krupp Hospital Essen, Germany (J.C.S., M.K.).,Department of Neurology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Germany (M.K.)
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15
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The in vivo endothelial cell translatome is highly heterogeneous across vascular beds. Proc Natl Acad Sci U S A 2019; 116:23618-23624. [PMID: 31712416 DOI: 10.1073/pnas.1912409116] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Endothelial cells (ECs) are highly specialized across vascular beds. However, given their interspersed anatomic distribution, comprehensive characterization of the molecular basis for this heterogeneity in vivo has been limited. By applying endothelial-specific translating ribosome affinity purification (EC-TRAP) combined with high-throughput RNA sequencing analysis, we identified pan EC-enriched genes and tissue-specific EC transcripts, which include both established markers and genes previously unappreciated for their presence in ECs. In addition, EC-TRAP limits changes in gene expression after EC isolation and in vitro expansion, as well as rapid vascular bed-specific shifts in EC gene expression profiles as a result of the enzymatic tissue dissociation required to generate single-cell suspensions for fluorescence-activated cell sorting or single-cell RNA sequencing analysis. Comparison of our EC-TRAP with published single-cell RNA sequencing data further demonstrates considerably greater sensitivity of EC-TRAP for the detection of low abundant transcripts. Application of EC-TRAP to examine the in vivo host response to lipopolysaccharide (LPS) revealed the induction of gene expression programs associated with a native defense response, with marked differences across vascular beds. Furthermore, comparative analysis of whole-tissue and TRAP-selected mRNAs identified LPS-induced differences that would not have been detected by whole-tissue analysis alone. Together, these data provide a resource for the analysis of EC-specific gene expression programs across heterogeneous vascular beds under both physiologic and pathologic conditions.
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16
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Peghaire C, Dufton NP, Lang M, Salles-Crawley II, Ahnström J, Kalna V, Raimondi C, Pericleous C, Inuabasi L, Kiseleva R, Muzykantov VR, Mason JC, Birdsey GM, Randi AM. The transcription factor ERG regulates a low shear stress-induced anti-thrombotic pathway in the microvasculature. Nat Commun 2019; 10:5014. [PMID: 31676784 PMCID: PMC6825134 DOI: 10.1038/s41467-019-12897-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 09/30/2019] [Indexed: 12/30/2022] Open
Abstract
Endothelial cells actively maintain an anti-thrombotic environment; loss of this protective function may lead to thrombosis and systemic coagulopathy. The transcription factor ERG is essential to maintain endothelial homeostasis. Here, we show that inducible endothelial ERG deletion (ErgiEC-KO) in mice is associated with spontaneous thrombosis, hemorrhages and systemic coagulopathy. We find that ERG drives transcription of the anticoagulant thrombomodulin (TM), as shown by reporter assays and chromatin immunoprecipitation. TM expression is regulated by shear stress (SS) via Krüppel-like factor 2 (KLF2). In vitro, ERG regulates TM expression under low SS conditions, by facilitating KLF2 binding to the TM promoter. However, ERG is dispensable for TM expression in high SS conditions. In ErgiEC-KO mice, TM expression is decreased in liver and lung microvasculature exposed to low SS but not in blood vessels exposed to high SS. Our study identifies an endogenous, vascular bed-specific anticoagulant pathway in microvasculature exposed to low SS.
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Affiliation(s)
- C Peghaire
- National Heart and Lung Institute, Imperial College London, London, UK
| | - N P Dufton
- National Heart and Lung Institute, Imperial College London, London, UK
| | - M Lang
- National Heart and Lung Institute, Imperial College London, London, UK
| | - I I Salles-Crawley
- Centre for Haematology, Hammersmith Hospital Campus, Imperial College London, London, UK
| | - J Ahnström
- Centre for Haematology, Hammersmith Hospital Campus, Imperial College London, London, UK
| | - V Kalna
- National Heart and Lung Institute, Imperial College London, London, UK
| | - C Raimondi
- National Heart and Lung Institute, Imperial College London, London, UK
| | - C Pericleous
- National Heart and Lung Institute, Imperial College London, London, UK
| | - L Inuabasi
- National Heart and Lung Institute, Imperial College London, London, UK
| | - R Kiseleva
- Department of Pharmacology, Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, USA
| | - V R Muzykantov
- Department of Pharmacology, Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, USA
| | - J C Mason
- National Heart and Lung Institute, Imperial College London, London, UK
| | - G M Birdsey
- National Heart and Lung Institute, Imperial College London, London, UK
| | - A M Randi
- National Heart and Lung Institute, Imperial College London, London, UK.
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17
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Comparative Transcriptomics of Ex Vivo, Patient-Derived Endothelial Cells Reveals Novel Pathways Associated With Type 2 Diabetes Mellitus. JACC Basic Transl Sci 2019; 4:567-574. [PMID: 31768474 PMCID: PMC6872769 DOI: 10.1016/j.jacbts.2019.05.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 05/23/2019] [Accepted: 05/23/2019] [Indexed: 12/18/2022]
Abstract
Endothelial cells can be harvested directly from humans, rapidly sorted and subjected to RNA-sequencing to study global gene expression. In endothelial cells isolated from patients with type 2 diabetes mellitus, pathways involved in TGF-β and Cyclin-D1 signaling were positively enriched while androgen signaling and oxidative phosphorylation were negatively enriched compared to healthy individuals. Patient-derived endothelial cells can be used to discover and validate disease-associated pathways.
In this study low-input RNA-sequencing was used to annotate the molecular identity of endothelial cells isolated and immunopurified with CD144 microbeads. Using this technique, comparative gene expression profiling from healthy subjects and patients with type 2 diabetes mellitus identified both known and novel pathways linked with EC dysfunction. Modeling of diabetes by treating cultured ECs with high glucose identified shared changes in gene expression in diabetic cells. Overall, the data demonstrate how purified ECs from patients can be used to generate new hypotheses about mechanisms of human vascular disease.
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Key Words
- BSA, bovine serum albumin
- EC, endothelial cell
- EDTA, ethylenediamine tetra-acetic acid
- FACS, fluorescence activated cell sorting
- FDR, false discovery rate
- GSEA, gene set enrichment analysis
- HUVEC, human umbilical vein endothelial cell
- IV, intravenous
- PBS, phosphate buffered saline
- Seq, sequencing
- T2DM, type 2 diabetes mellitus
- TGFβ, transforming growth factor beta
- VEGF, vascular endothelial growth factor
- VUMC, Vanderbilt University Medical Center
- WBC, white blood cell
- ddCt, delta-delta cycle threshold
- diabetes mellitus
- endothelial cell dysfunction
- endothelial cells
- gene expression
- qPCR, quantitative polymerase chain reaction
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18
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Saatcioglu HD, Kano M, Horn H, Zhang L, Samore W, Nagykery N, Meinsohn MC, Hyun M, Suliman R, Poulo J, Hsu J, Sacha C, Wang D, Gao G, Lage K, Oliva E, Morris Sabatini ME, Donahoe PK, Pépin D. Single-cell sequencing of neonatal uterus reveals an Misr2+ endometrial progenitor indispensable for fertility. eLife 2019; 8:46349. [PMID: 31232694 PMCID: PMC6650247 DOI: 10.7554/elife.46349] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/24/2019] [Indexed: 12/16/2022] Open
Abstract
The Mullerian ducts are the anlagen of the female reproductive tract, which regress in the male fetus in response to MIS. This process is driven by subluminal mesenchymal cells expressing Misr2, which trigger the regression of the adjacent Mullerian ductal epithelium. In females, these Misr2+ cells are retained, yet their contribution to the development of the uterus remains unknown. Here, we report that subluminal Misr2+ cells persist postnatally in the uterus of rodents, but recede by week 37 of gestation in humans. Using single-cell RNA sequencing, we demonstrate that ectopic postnatal MIS administration inhibits these cells and prevents the formation of endometrial stroma in rodents, suggesting a progenitor function. Exposure to MIS during the first six days of life, by inhibiting specification of the stroma, dysregulates paracrine signals necessary for uterine development, eventually resulting in apoptosis of the Misr2+ cells, uterine hypoplasia, and complete infertility in the adult female. In the womb, mammals possess all of the preliminary sexual structures necessary to become either male or female. This includes the Mullerian duct, which develops into the Fallopian tubes, uterus, cervix, and vagina in female fetuses. In male fetuses, the testis secretes a hormone called Mullerian inhibiting substance (MIS). This triggers the activity of a small group of cells, known as Misr2+ cells, that cause the Mullerian duct to degenerate, preventing males from developing female sexual organs. It was not clear what happens to Misr2+ cells in female fetuses or if they affect how the uterus develops. Saatcioglu et al. now show that in newborn female mice and rats, a type of Misr2+ cell that sits within a thin inner layer of the developing uterus still responds to MIS. At this time, the uterus is in a critical early period of development. Treating the mice and rats with MIS protein during their first six days of life eventually caused the Misr2+ cells to die. The treatment also prevented a layer of connective tissue, known as the endometrial stroma, from forming in the uterus. As a result, the mice and rats were infertile and had severely underdeveloped uteri. While the Misr2+ cells are present in newborn rats and mice, Saatcioglu et al. found that they disappeared before birth in humans. However, the overall results suggest that Misr2+ cells act as progenitor cells that develop into the cells of the endometrial stroma. Future work could investigate the roles these cells play in causing uterine developmental disorders and infertility disorders. Furthermore, the finding that MIS inhibits the Misr2+ cells could help researchers to develop treatments for uterine cancer and other conditions where the cells of the uterus grow and divide too much.
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Affiliation(s)
- Hatice Duygu Saatcioglu
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, United States.,Department of Surgery, Harvard Medical School, Boston, United States
| | - Motohiro Kano
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, United States.,Department of Surgery, Harvard Medical School, Boston, United States
| | - Heiko Horn
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, United States.,Department of Surgery, Harvard Medical School, Boston, United States.,Stanley Center, Broad Institute of MIT and Harvard, Cambridge, United States
| | - Lihua Zhang
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, United States.,Department of Surgery, Harvard Medical School, Boston, United States
| | - Wesley Samore
- Department of Pathology, Massachusetts General Hospital, Boston, United States
| | - Nicholas Nagykery
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, United States.,Department of Surgery, Harvard Medical School, Boston, United States
| | - Marie-Charlotte Meinsohn
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, United States.,Department of Surgery, Harvard Medical School, Boston, United States
| | - Minsuk Hyun
- Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Rana Suliman
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, United States.,Department of Surgery, Harvard Medical School, Boston, United States
| | - Joy Poulo
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, United States.,Department of Surgery, Harvard Medical School, Boston, United States.,Stanley Center, Broad Institute of MIT and Harvard, Cambridge, United States
| | - Jennifer Hsu
- Department of Gynecology and Reproductive Biology, Massachussets General Hospital, Boston, United States
| | - Caitlin Sacha
- Department of Gynecology and Reproductive Biology, Massachussets General Hospital, Boston, United States
| | - Dan Wang
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, United States
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, United States
| | - Kasper Lage
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, United States.,Department of Surgery, Harvard Medical School, Boston, United States.,Stanley Center, Broad Institute of MIT and Harvard, Cambridge, United States
| | - Esther Oliva
- Department of Pathology, Massachusetts General Hospital, Boston, United States
| | - Mary E Morris Sabatini
- Department of Gynecology and Reproductive Biology, Massachussets General Hospital, Boston, United States
| | - Patricia K Donahoe
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, United States.,Department of Surgery, Harvard Medical School, Boston, United States
| | - David Pépin
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, United States.,Department of Surgery, Harvard Medical School, Boston, United States
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19
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Identification of Macrophage Genotype and Key Biological Pathways in Circulating Angiogenic Cell Transcriptome. Stem Cells Int 2019; 2019:9545261. [PMID: 31191690 PMCID: PMC6525806 DOI: 10.1155/2019/9545261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 01/14/2019] [Accepted: 02/13/2019] [Indexed: 11/17/2022] Open
Abstract
Background Circulating angiogenic cells (CAC) have been identified as important regulators of vascular biology. However, there is still considerable debate about the genotype and function of CAC. Methods and Results Data from publicly available gene expression data sets were used to analyse the transcriptome of in vitro cultured CAC (CACiv). Genes and pathways of interest were further evaluated using qPCR comparing CACiv versus CD14+ monocytic cells. The CACiv transcriptome strongly related to tissue macrophages, and more specifically to regulatory M2c macrophages. The cytokine expression profile of CACiv was predominantly immune modulatory and resembled the cytokine expression of tumor-associated macrophages (TAM). Pathway analysis revealed previously unrecognized biological processes in CACiv, such as riboflavin metabolism and liver X receptor (LXR)/retinoid X receptor (RXR) and farnesoid X receptor (FXR)/retinoid X receptor (RXR) pathways. Analysis of endothelial-specific genes did not show evidence for endothelial transdifferentiation. Conclusions CACiv are genotypically similar to regulatory M2c macrophages and lack signs of endothelial differentiation.
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20
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Endothelial Cell Aging: How miRNAs Contribute? J Clin Med 2018; 7:jcm7070170. [PMID: 29996516 PMCID: PMC6068727 DOI: 10.3390/jcm7070170] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/04/2018] [Accepted: 07/09/2018] [Indexed: 12/19/2022] Open
Abstract
Endothelial cells (ECs) form monolayers and line the interior surfaces of blood vessels in the entire body. In most mammalian systems, the capacity of endothelial cells to divide is limited and endothelial cells are prone to be senescent. Aging of ECs and resultant endothelial dysfunction lead to a variety of vascular diseases such as atherosclerosis, diabetes mellites, hypertension, and ischemic injury. However, the mechanism by which ECs get old and become senescent and the impact of endothelial senescence on the vascular function are not fully understood. Recent research has unveiled the crucial roles of miRNAs, which are small non-coding RNAs, in regulating endothelial cellular functions, including nitric oxide production, vascular inflammation, and anti-thromboformation. In this review, how senescent-related miRNAs are involved in controlling the functions of ECs will be discussed.
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21
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McGarrity S, Anuforo Ó, Halldórsson H, Bergmann A, Halldórsson S, Palsson S, Henriksen HH, Johansson PI, Rolfsson Ó. Metabolic systems analysis of LPS induced endothelial dysfunction applied to sepsis patient stratification. Sci Rep 2018; 8:6811. [PMID: 29717213 PMCID: PMC5931560 DOI: 10.1038/s41598-018-25015-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 04/13/2018] [Indexed: 12/24/2022] Open
Abstract
Endothelial dysfunction contributes to sepsis outcome. Metabolic phenotypes associated with endothelial dysfunction are not well characterised in part due to difficulties in assessing endothelial metabolism in situ. Here, we describe the construction of iEC2812, a genome scale metabolic reconstruction of endothelial cells and its application to describe metabolic changes that occur following endothelial dysfunction. Metabolic gene expression analysis of three endothelial subtypes using iEC2812 suggested their similar metabolism in culture. To mimic endothelial dysfunction, an in vitro sepsis endothelial cell culture model was established and the metabotypes associated with increased endothelial permeability and glycocalyx loss after inflammatory stimuli were quantitatively defined through metabolomics. These data and transcriptomic data were then used to parametrize iEC2812 and investigate the metabotypes of endothelial dysfunction. Glycan production and increased fatty acid metabolism accompany increased glycocalyx shedding and endothelial permeability after inflammatory stimulation. iEC2812 was then used to analyse sepsis patient plasma metabolome profiles and predict changes to endothelial derived biomarkers. These analyses revealed increased changes in glycan metabolism in sepsis non-survivors corresponding to metabolism of endothelial dysfunction in culture. The results show concordance between endothelial health and sepsis survival in particular between endothelial cell metabolism and the plasma metabolome in patients with sepsis.
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Affiliation(s)
- Sarah McGarrity
- Center for Systems Biology, University of Iceland, Sturlugata 8, Reykjavik, Iceland
| | - Ósk Anuforo
- Center for Systems Biology, University of Iceland, Sturlugata 8, Reykjavik, Iceland
| | - Haraldur Halldórsson
- Medical Department, University of Iceland, Sturlugata 8, Reykjavik, Iceland
- Landspitali, Læknagarður, Hringbraut, Reykjavik, Iceland
| | - Andreas Bergmann
- Center for Systems Biology, University of Iceland, Sturlugata 8, Reykjavik, Iceland
| | | | - Sirus Palsson
- Center for Systems Biology, University of Iceland, Sturlugata 8, Reykjavik, Iceland
| | | | - Pär Ingemar Johansson
- Center for Systems Biology, University of Iceland, Sturlugata 8, Reykjavik, Iceland
- Rigshospitalet, Blegdamsvej 9, 2100, Kobenhavn O, Denmark
| | - Óttar Rolfsson
- Center for Systems Biology, University of Iceland, Sturlugata 8, Reykjavik, Iceland.
- Medical Department, University of Iceland, Sturlugata 8, Reykjavik, Iceland.
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22
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Lipps C, Klein F, Wahlicht T, Seiffert V, Butueva M, Zauers J, Truschel T, Luckner M, Köster M, MacLeod R, Pezoldt J, Hühn J, Yuan Q, Müller PP, Kempf H, Zweigerdt R, Dittrich-Breiholz O, Pufe T, Beckmann R, Drescher W, Riancho J, Sañudo C, Korff T, Opalka B, Rebmann V, Göthert JR, Alves PM, Ott M, Schucht R, Hauser H, Wirth D, May T. Expansion of functional personalized cells with specific transgene combinations. Nat Commun 2018. [PMID: 29520052 PMCID: PMC5843645 DOI: 10.1038/s41467-018-03408-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Fundamental research and drug development for personalized medicine necessitates cell cultures from defined genetic backgrounds. However, providing sufficient numbers of authentic cells from individuals poses a challenge. Here, we present a new strategy for rapid cell expansion that overcomes current limitations. Using a small gene library, we expanded primary cells from different tissues, donors, and species. Cell-type-specific regimens that allow the reproducible creation of cell lines were identified. In depth characterization of a series of endothelial and hepatocytic cell lines confirmed phenotypic stability and functionality. Applying this technology enables rapid, efficient, and reliable production of unlimited numbers of personalized cells. As such, these cell systems support mechanistic studies, epidemiological research, and tailored drug development. Personalised medicine requires cell cultures from defined genetic backgrounds, but providing sufficient numbers of cells is a challenge. Here the authors develop gene cocktails to expand primary cells from a variety of different tissues and species, and show that expanded endothelial and hepatic cells retain properties of the differentiated phenotype.
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Affiliation(s)
- Christoph Lipps
- Model Systems for Infection and Immunity, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany.,Experimental Cardiology, Justus-Liebig University Giessen, Aulweg 129, 35392, Giessen, Germany
| | - Franziska Klein
- Department of Gene Regulation and Differentiation, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Tom Wahlicht
- Model Systems for Infection and Immunity, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Virginia Seiffert
- Department of Gene Regulation and Differentiation, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Milada Butueva
- Model Systems for Infection and Immunity, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | | | | | - Martin Luckner
- InSCREENeX GmbH, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Mario Köster
- Department of Gene Regulation and Differentiation, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Roderick MacLeod
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Jörn Pezoldt
- Experimental Immunology, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Jochen Hühn
- Experimental Immunology, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Qinggong Yuan
- Department of Gastroenterology, Hepatology, Endocrinology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.,Translational Research Group Cell and Gene Therapy, Twincore - Centre for Experimental and Clinical Infection Research GmbH, Feodor-Lynen-Str. 7, 30625, Hannover, Germany
| | - Peter Paul Müller
- Department of Gene Regulation and Differentiation, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Henning Kempf
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Hannover Medical School, MHH, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Robert Zweigerdt
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Hannover Medical School, MHH, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | | | - Thomas Pufe
- Department of Anatomy and Cell Biology, RWTH Aachen University, 52074, Aachen, Germany
| | - Rainer Beckmann
- Department of Anatomy and Cell Biology, RWTH Aachen University, 52074, Aachen, Germany
| | - Wolf Drescher
- Department of Orthopaedics, Aachen University Hospital, RWTH Aachen University, Aachen, 52074, Germany.,Department of Orthopedic Surgery of the Lower Limb and Arthroplasty, Rummelsberg Hospital, Schwarzenbruck, 90592, Germany
| | - Jose Riancho
- Department of Internal Medicine, Hospital U.M. Valdecilla, University of Cantabria, IDIVAL, 39008, Santander, Spain
| | - Carolina Sañudo
- Department of Internal Medicine, Hospital U.M. Valdecilla, University of Cantabria, IDIVAL, 39008, Santander, Spain
| | - Thomas Korff
- Institute of Physiology and Pathophysiology, RG Blood Vessel Remodeling, University Heidelberg, Im Neuenheimer Feld 326, 69120, Heidelberg, Germany
| | - Bertram Opalka
- Department of Hematology, West German Cancer Center (WTZ), University Hospital Essen, Hufelandstr. 55, 45147, Essen, Germany
| | - Vera Rebmann
- Institute for Transfusion Medicine, University Hospital Essen, Virchowstr. 179, 45147, Essen, Germany
| | - Joachim R Göthert
- Department of Hematology, West German Cancer Center (WTZ), University Hospital Essen, Hufelandstr. 55, 45147, Essen, Germany
| | - Paula M Alves
- Instituto de Biologia Experimental e Tecnologica, Universidade Nova de Lisboa, Oeiras, 2781-901, Portugal
| | - Michael Ott
- Department of Gastroenterology, Hepatology, Endocrinology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.,Translational Research Group Cell and Gene Therapy, Twincore - Centre for Experimental and Clinical Infection Research GmbH, Feodor-Lynen-Str. 7, 30625, Hannover, Germany
| | - Roland Schucht
- InSCREENeX GmbH, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Hansjörg Hauser
- Department of Gene Regulation and Differentiation, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Dagmar Wirth
- Model Systems for Infection and Immunity, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany. .,Experimental Hematology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
| | - Tobias May
- InSCREENeX GmbH, Inhoffenstr. 7, 38124, Braunschweig, Germany.
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23
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Angiogenic patterning by STEEL, an endothelial-enriched long noncoding RNA. Proc Natl Acad Sci U S A 2018; 115:2401-2406. [PMID: 29467285 DOI: 10.1073/pnas.1715182115] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Endothelial cell (EC)-enriched protein coding genes, such as endothelial nitric oxide synthase (eNOS), define quintessential EC-specific physiologic functions. It is not clear whether long noncoding RNAs (lncRNAs) also define cardiovascular cell type-specific phenotypes, especially in the vascular endothelium. Here, we report the existence of a set of EC-enriched lncRNAs and define a role for spliced-transcript endothelial-enriched lncRNA (STEEL) in angiogenic potential, macrovascular/microvascular identity, and shear stress responsiveness. STEEL is expressed from the terminus of the HOXD locus and is transcribed antisense to HOXD transcription factors. STEEL RNA increases the number and integrity of de novo perfused microvessels in an in vivo model and augments angiogenesis in vitro. The STEEL RNA is polyadenylated, nuclear enriched, and has microvascular predominance. Functionally, STEEL regulates a number of genes in diverse ECs. Of interest, STEEL up-regulates both eNOS and the transcription factor Kruppel-like factor 2 (KLF2), and is subject to feedback inhibition by both eNOS and shear-augmented KLF2. Mechanistically, STEEL up-regulation of eNOS and KLF2 is transcriptionally mediated, in part, via interaction of chromatin-associated STEEL with the poly-ADP ribosylase, PARP1. For instance, STEEL recruits PARP1 to the KLF2 promoter. This work identifies a role for EC-enriched lncRNAs in the phenotypic adaptation of ECs to both body position and hemodynamic forces and establishes a newer role for lncRNAs in the transcriptional regulation of EC identity.
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24
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Identification of Novel Hemangioblast Genes in the Early Chick Embryo. Cells 2018; 7:cells7020009. [PMID: 29385069 PMCID: PMC5850097 DOI: 10.3390/cells7020009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 01/17/2018] [Accepted: 01/27/2018] [Indexed: 12/20/2022] Open
Abstract
During early vertebrate embryogenesis, both hematopoietic and endothelial lineages derive from a common progenitor known as the hemangioblast. Hemangioblasts derive from mesodermal cells that migrate from the posterior primitive streak into the extraembryonic yolk sac. In addition to primitive hematopoietic cells, recent evidence revealed that yolk sac hemangioblasts also give rise to tissue-resident macrophages and to definitive hematopoietic stem/progenitor cells. In our previous work, we used a novel hemangioblast-specific reporter to isolate the population of chick yolk sac hemangioblasts and characterize its gene expression profile using microarrays. Here we report the microarray profile analysis and the identification of upregulated genes not yet described in hemangioblasts. These include the solute carrier transporters SLC15A1 and SCL32A1, the cytoskeletal protein RhoGap6, the serine protease CTSG, the transmembrane receptor MRC1, the transcription factors LHX8, CITED4 and PITX1, and the previously uncharacterized gene DIA1R. Expression analysis by in situ hybridization showed that chick DIA1R is expressed not only in yolk sac hemangioblasts but also in particular intraembryonic populations of hemogenic endothelial cells, suggesting a potential role in the hemangioblast-derived hemogenic lineage. Future research into the function of these newly identified genes may reveal novel important regulators of hemangioblast development.
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25
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Borisov N, Tkachev V, Suntsova M, Kovalchuk O, Zhavoronkov A, Muchnik I, Buzdin A. A method of gene expression data transfer from cell lines to cancer patients for machine-learning prediction of drug efficiency. Cell Cycle 2018; 17:486-491. [PMID: 29251172 DOI: 10.1080/15384101.2017.1417706] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Personalized medicine implies that distinct treatment methods are prescribed to individual patients according several features that may be obtained from, e.g., gene expression profile. The majority of machine learning methods suffer from the deficiency of preceding cases, i.e. the gene expression data on patients combined with the confirmed outcome of known treatment methods. At the same time, there exist thousands of various cell lines that were treated with hundreds of anti-cancer drugs in order to check the ability of these drugs to stop the cell proliferation, and all these cell line cultures were profiled in terms of their gene expression. Here we present a new approach in machine learning, which can predict clinical efficiency of anti-cancer drugs for individual patients by transferring features obtained from the expression-based data from cell lines. The method was validated on three datasets for cancer-like diseases (chronic myeloid leukemia, as well as lung adenocarcinoma and renal carcinoma) treated with targeted drugs - kinase inhibitors, such as imatinib or sorafenib.
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Affiliation(s)
- Nicolas Borisov
- a National Research Centre "Kurchatov Institute" , Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow , Russia.,b Department of R&D , First Oncology Research and Advisory Center, Moscow , Russia
| | - Victor Tkachev
- b Department of R&D , First Oncology Research and Advisory Center, Moscow , Russia.,c Department of R&D , OmicsWay Corporation, Walnut , CA , USA
| | - Maria Suntsova
- b Department of R&D , First Oncology Research and Advisory Center, Moscow , Russia.,d Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia.,e Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology , Oncology and Immunology, Moscow , 117198 , Russia
| | - Olga Kovalchuk
- f Department of Biological Sciences , University of Lethbridge , Lethbridge , AB , Canada.,g Canada Cancer and Aging Research Laboratories , Lethbridge , AB , Canada
| | - Alex Zhavoronkov
- h Insilico Medicine, Inc, ETC, Johns Hopkins University , Baltimore , MD , USA
| | - Ilya Muchnik
- i Rutgers University , Hill Center, Busch Campus, Piscataway , NJ , USA
| | - Anton Buzdin
- a National Research Centre "Kurchatov Institute" , Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow , Russia.,b Department of R&D , First Oncology Research and Advisory Center, Moscow , Russia.,c Department of R&D , OmicsWay Corporation, Walnut , CA , USA.,d Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia.,e Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology , Oncology and Immunology, Moscow , 117198 , Russia
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26
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Prediction of Drug Efficiency by Transferring Gene Expression Data from Cell Lines to Cancer Patients. BRAVERMAN READINGS IN MACHINE LEARNING. KEY IDEAS FROM INCEPTION TO CURRENT STATE 2018. [DOI: 10.1007/978-3-319-99492-5_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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27
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Yamani A, Wu D, Waggoner L, Noah T, Koleske AJ, Finkelman F, Hogan SP. The vascular endothelial specific IL-4 receptor alpha-ABL1 kinase signaling axis regulates the severity of IgE-mediated anaphylactic reactions. J Allergy Clin Immunol 2017; 142:1159-1172.e5. [PMID: 29157947 DOI: 10.1016/j.jaci.2017.08.046] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/04/2017] [Accepted: 08/31/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Severe IgE-mediated, food-induced anaphylactic reactions are characterized by pulmonary venous vasodilatation and fluid extravasation, which are thought to lead to the life-threatening anaphylactic phenotype. The underlying immunologic and cellular processes involved in driving fluid extravasation and the severe anaphylactic phenotype are not fully elucidated. OBJECTIVE We sought to define the interaction and requirement of IL-4 and vascular endothelial (VE) IL-4 receptor α chain (IL-4Rα) signaling in histamine-abelson murine leukemia viral oncogene homology 1 (ABL1)-mediated VE dysfunction and fluid extravasation in the severity of IgE-mediated anaphylactic reactions in mice. METHODS Mice deficient in VE IL-4Rα and models of passive and active oral antigen- and IgE-induced anaphylaxis were used to define the requirements of the VE IL-4Rα and ABL1 pathway in severe anaphylactic reactions. The human VE cell line (EA.hy926 cells) and pharmacologic (imatinib) and genetic (short hairpin RNA knockdown of IL4RA and ABL1) approaches were used to define the requirement of this pathway in VE barrier dysfunction. RESULTS IL-4 exacerbation of histamine-induced hypovolemic shock in mice was dependent on VE expression of IL-4Rα. IL-4- and histamine-induced ABL1 activation in human VE cells and VE barrier dysfunction was ABL1-dependent. Development of severe IgE-mediated hypovolemia and shock required VE-restricted ABL1 expression. Treatment of mice with a history of food-induced anaphylaxis with the ABL kinase inhibitor imatinib protected the mice from severe IgE-mediated anaphylaxis. CONCLUSION IL-4 amplifies IgE- and histamine-induced VE dysfunction, fluid extravasation, and the severity of anaphylaxis through a VE IL-4Rα/ABL1-dependent mechanism. These studies implicate an important contribution by the VE compartment in the severity of anaphylaxis and identify a new pathway for therapeutic intervention of IgE-mediated reactions.
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Affiliation(s)
- Amnah Yamani
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - David Wu
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Lisa Waggoner
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Taeko Noah
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Anthony J Koleske
- Department of Biological and Biomedical Sciences, Yale University, New Haven, Conn
| | - Fred Finkelman
- Division of Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Simon P Hogan
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio.
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28
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Female mice lacking Pald1 exhibit endothelial cell apoptosis and emphysema. Sci Rep 2017; 7:15453. [PMID: 29133847 PMCID: PMC5684320 DOI: 10.1038/s41598-017-14894-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 10/18/2017] [Indexed: 12/16/2022] Open
Abstract
Paladin (Pald1, mKIAA1274 or x99384) was identified in screens for vascular-specific genes and is a putative phosphatase. Paladin has also been proposed to be involved in various biological processes such as insulin signaling, innate immunity and neural crest migration. To determine the role of paladin we have now characterized the Pald1 knock-out mouse in a broad array of behavioral, physiological and biochemical tests. Here, we show that female, but not male, Pald1 heterozygous and homozygous knock-out mice display an emphysema-like histology with increased alveolar air spaces and impaired lung function with an obstructive phenotype. In contrast to many other tissues where Pald1 is restricted to the vascular compartment, Pald1 is expressed in both the epithelial and mesenchymal compartments of the postnatal lung. However, in Pald1 knock-out females, there is a specific increase in apoptosis and proliferation of endothelial cells, but not in non-endothelial cells. This results in a transient reduction of endothelial cells in the maturing lung. Our data suggests that Pald1 is required during lung vascular development and for normal function of the developing and adult lung in a sex-specific manner. To our knowledge, this is the first report of a sex-specific effect on endothelial cell apoptosis.
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Yue X, Acun A, Zorlutuna P. Transcriptome profiling of 3D co-cultured cardiomyocytes and endothelial cells under oxidative stress using a photocrosslinkable hydrogel system. Acta Biomater 2017. [PMID: 28648749 DOI: 10.1016/j.actbio.2017.06.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Myocardial infarction (MI) is one of the most common among cardiovascular diseases. Endothelial cells (ECs) are considered to have protective effects on cardiomyocytes (CMs) under stress conditions such as MI; however, the paracrine CM-EC crosstalk and the resulting endogenous cellular responses that could contribute to this protective effect are not thoroughly investigated. Here we created biomimetic synthetic tissues containing CMs and human induced pluripotent stem cell (hiPSC)-derived ECs (iECs), which showed improved cell survival compared to single cultures under conditions mimicking the aftermath of MI, and performed high-throughput RNA-sequencing to identify target pathways that could govern CM-iEC crosstalk and the resulting improvement in cell viability. Our results showed that single cultured CMs had different gene expression profiles compared to CMs co-cultured with iECs. More importantly, this gene expression profile was preserved in response to oxidative stress in co-cultured CMs while single cultured CMs showed a significantly different gene expression pattern under stress, suggesting a stabilizing effect of iECs on CMs under oxidative stress conditions. Furthermore, we have validated the in vivo relevance of our engineered model tissues by comparing the changes in the expression levels of several key genes of the encapsulated CMs and iECs with in vivo rat MI model data and clinical data, respectively. We conclude that iECs have protective effects on CMs under oxidative stress through stabilizing mitochondrial complexes, suppressing oxidative phosphorylation pathway and activating pathways such as the drug metabolism-cytochrome P450 pathway, Rap1 signaling pathway, and adrenergic signaling in cardiomyocytes pathway. STATEMENT OF SIGNIFICANCE Heart diseases are the leading cause of death worldwide. Oxidative stress is a common unwanted outcome that especially occurs due to the reperfusion following heart attack or heart surgery. Standard methods of in vivo analysis do not allow dissecting various intermingled parameters, while regular 2D cell culture approaches often fail to provide a biomimetic environment for the physiologically relevant cellular phenotypes. In this research, a systematic genome-wide transcriptome profiling was performed on myocardial cells in a biomimetic 3D hydrogel-based synthetic model tissue, for identifying possible target genes and pathways as protecting regulators against oxidative stress. Identification of such pathways would be very valuable for new strategies during heart disease treatment by reducing the cellular damage due to reperfusion injury.
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Affiliation(s)
- Xiaoshan Yue
- University of Notre Dame, Department of Aerospace and Mechanical Engineering, Bioengineering Graduate Program, United States
| | - Aylin Acun
- University of Notre Dame, Bioengineering Graduate Program, United States
| | - Pinar Zorlutuna
- University of Notre Dame, Department of Aerospace and Mechanical Engineering, Bioengineering Graduate Program, United States; University of Notre Dame, Bioengineering Graduate Program, United States.
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30
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Lipps C, Badar M, Butueva M, Dubich T, Singh VV, Rau S, Weber A, Kracht M, Köster M, May T, Schulz TF, Hauser H, Wirth D. Proliferation status defines functional properties of endothelial cells. Cell Mol Life Sci 2017; 74:1319-1333. [PMID: 27853834 PMCID: PMC11107763 DOI: 10.1007/s00018-016-2417-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 10/31/2016] [Accepted: 11/09/2016] [Indexed: 12/21/2022]
Abstract
Homeostasis of solid tissue is characterized by a low proliferative activity of differentiated cells while special conditions like tissue damage induce regeneration and proliferation. For some cell types it has been shown that various tissue-specific functions are missing in the proliferating state, raising the possibility that their proliferation is not compatible with a fully differentiated state. While endothelial cells are important players in regenerating tissue as well as in the vascularization of tumors, the impact of proliferation on their features remains elusive. To examine cell features in dependence of proliferation, we established human endothelial cell lines in which proliferation is tightly controlled by a doxycycline-dependent, synthetic regulatory unit. We observed that uptake of macromolecules and establishment of cell-cell contacts was more pronounced in the growth-arrested state. Tube-like structures were formed in vitro in both proliferating and non-proliferating conditions. However, functional vessel formation upon transplantation into immune-compromised mice was restricted to the proliferative state. Kaposi's sarcoma-associated herpes virus (KSHV) infection resulted in reduced expression of endothelial markers. Upon transplantation of infected cells, drastic differences were observed: proliferation arrested cells acquired a high migratory activity while the proliferating counterparts established a tumor-like phenotype, similar to Kaposi Sarcoma lesions. The study gives evidence that proliferation governs endothelial functions. This suggests that several endothelial functions are differentially expressed during angiogenesis. Moreover, since proliferation defines the functional properties of cells upon infection with KSHV, this process crucially affects the fate of virus-infected cells.
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Affiliation(s)
- Christoph Lipps
- Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
- Experimental Cardiology, Justus-Liebig-University, Giessen, Germany
| | - Muhammad Badar
- Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
- Gomal Center of Biochemistry and Biotechnology, Gomal University, D. I. Khan, Pakistan
| | - Milada Butueva
- Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Tatyana Dubich
- Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Vivek Vikram Singh
- Institute for Virology, Medical University in Hannover, Hannover, Germany
- Value Edge Research Services, Noida, India
| | - Sophie Rau
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Axel Weber
- Rudolf-Buchheim Institute for Pharmacology, Schubertstraße 81, 35392, Giessen, Germany
| | - Michael Kracht
- Rudolf-Buchheim Institute for Pharmacology, Schubertstraße 81, 35392, Giessen, Germany
| | - Mario Köster
- Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Tobias May
- Inscreenex GmbH, Inhoffenstr. 7, 38124, Brunswick, Germany
| | - Thomas F Schulz
- Institute for Virology, Medical University in Hannover, Hannover, Germany
| | - Hansjörg Hauser
- Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Dagmar Wirth
- Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany.
- Institute for Experimental Hematology, Medical University in Hannover, Hannover, Germany.
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Li JB, Wang HY, Yao Y, Sun QF, Liu ZH, Liu SQ, Zhuang JL, Wang YP, Liu HY. Overexpression of microRNA-138 alleviates human coronary artery endothelial cell injury and inflammatory response by inhibiting the PI3K/Akt/eNOS pathway. J Cell Mol Med 2017; 21:1482-1491. [PMID: 28371277 PMCID: PMC5542903 DOI: 10.1111/jcmm.13074] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 11/29/2016] [Indexed: 12/24/2022] Open
Abstract
This study aimed to investigate the role of miR‐138 in human coronary artery endothelial cell (HCAEC) injury and inflammatory response and the involvement of the PI3K/Akt/eNOS signalling pathway. Oxidized low‐density lipoprotein (OX‐LDL)‐induced HCAEC injury models were established and assigned to blank, miR‐138 mimic, miR‐138 inhibitor, LY294002 (an inhibitor of the PI3K/Akt/eNOS pathway), miR‐138 inhibitor + LY294002 and negative control (NC) groups. qRT‐PCR and Western blotting were performed to detect the miR‐138, PI3K, Akt and eNOS levels and the protein expressions of PI3K, Akt, eNOS, p‐Akt, p‐eNOS, Bcl‐2, Bax and caspase‐3. ELISAs were employed to measure the expressions of TNF‐α, IL‐4, IL‐6, IL‐8, IL‐10 and nitric oxide (NO) and the activities of lactate dehydrogenase (LDH) and eNOS. MTT and flow cytometry were performed to assess the proliferation and apoptosis of HCAECs. Compared to the blank group, PI3K, Akt and eNOS were down‐regulated in the miR‐138 mimic and LY294002 groups but were up‐regulated in the miR‐138 inhibitor group. The miR‐138 mimic and LY294002 groups showed decreased concentrations of TNF‐α, IL‐6, IL‐8 and NO and reduced activities of LDH and eNOS, while opposite trends were observed in the miR‐138 inhibitor group. The concentrations of IL‐4 and IL‐10 increased in the miR‐138 mimic and LY294002 groups but decreased in the miR‐138 inhibitor group. The miR‐138 mimic and LY294002 groups had significantly decreased cell proliferation and increased cell apoptosis compared to the blank group. These findings indicate that up‐regulation of miR‐138 alleviates HCAEC injury and inflammatory response by inhibiting the PI3K/Akt/eNOS signalling pathway.
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Affiliation(s)
- Jing-Bo Li
- Department of Cardiac Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hai-Yang Wang
- Department of Vascular Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Ye Yao
- Department of Vascular Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qing-Feng Sun
- Department of Vascular Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zong-Hong Liu
- Department of Cardiac Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Si-Qi Liu
- Department of Vascular Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jun-Li Zhuang
- Department of Vascular Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yun-Peng Wang
- Department of Vascular Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hong-Yu Liu
- Department of Cardiac Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
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32
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Spatiotemporal genomic architecture informs precision oncology in glioblastoma. Nat Genet 2017; 49:594-599. [PMID: 28263318 DOI: 10.1038/ng.3806] [Citation(s) in RCA: 182] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 02/10/2017] [Indexed: 12/13/2022]
Abstract
Precision medicine in cancer proposes that genomic characterization of tumors can inform personalized targeted therapies. However, this proposition is complicated by spatial and temporal heterogeneity. Here we study genomic and expression profiles across 127 multisector or longitudinal specimens from 52 individuals with glioblastoma (GBM). Using bulk and single-cell data, we find that samples from the same tumor mass share genomic and expression signatures, whereas geographically separated, multifocal tumors and/or long-term recurrent tumors are seeded from different clones. Chemical screening of patient-derived glioma cells (PDCs) shows that therapeutic response is associated with genetic similarity, and multifocal tumors that are enriched with PIK3CA mutations have a heterogeneous drug-response pattern. We show that targeting truncal events is more efficacious than targeting private events in reducing the tumor burden. In summary, this work demonstrates that evolutionary inference from integrated genomic analysis in multisector biopsies can inform targeted therapeutic interventions for patients with GBM.
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Butler LM, Hallström BM, Fagerberg L, Pontén F, Uhlén M, Renné T, Odeberg J. Analysis of Body-wide Unfractionated Tissue Data to Identify a Core Human Endothelial Transcriptome. Cell Syst 2016; 3:287-301.e3. [PMID: 27641958 DOI: 10.1016/j.cels.2016.08.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 05/23/2016] [Accepted: 08/03/2016] [Indexed: 12/11/2022]
Abstract
Endothelial cells line blood vessels and regulate hemostasis, inflammation, and blood pressure. Proteins critical for these specialized functions tend to be predominantly expressed in endothelial cells across vascular beds. Here, we present a systems approach to identify a panel of human endothelial-enriched genes using global, body-wide transcriptomics data from 124 tissue samples from 32 organs. We identified known and unknown endothelial-enriched gene transcripts and used antibody-based profiling to confirm expression across vascular beds. The majority of identified transcripts could be detected in cultured endothelial cells from various vascular beds, and we observed maintenance of relative expression in early passage cells. In summary, we describe a widely applicable method to determine cell-type-specific transcriptome profiles in a whole-organism context, based on differential abundance across tissues. We identify potential vascular drug targets or endothelial biomarkers and highlight candidates for functional studies to increase understanding of the endothelium in health and disease.
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Affiliation(s)
- Lynn Marie Butler
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany; Clinical Chemistry and Blood Coagulation, Department of Molecular Medicine and Surgery, Karolinska Institute, 171 76 Stockholm, Sweden.
| | - Björn Mikael Hallström
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology (KTH), 171 21 Stockholm, Sweden
| | - Linn Fagerberg
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology (KTH), 171 21 Stockholm, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology (KTH), 171 21 Stockholm, Sweden
| | - Thomas Renné
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany; Clinical Chemistry and Blood Coagulation, Department of Molecular Medicine and Surgery, Karolinska Institute, 171 76 Stockholm, Sweden
| | - Jacob Odeberg
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology (KTH), 171 21 Stockholm, Sweden; Coagulation Unit, Centre for Hematology, Karolinska University Hospital, 171 76 Stockholm, Sweden
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Shah AV, Birdsey GM, Randi AM. Regulation of endothelial homeostasis, vascular development and angiogenesis by the transcription factor ERG. Vascul Pharmacol 2016; 86:3-13. [PMID: 27208692 PMCID: PMC5404112 DOI: 10.1016/j.vph.2016.05.003] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/08/2016] [Accepted: 05/16/2016] [Indexed: 01/06/2023]
Abstract
Over the last few years, the ETS transcription factor ERG has emerged as a major regulator of endothelial function. Multiple studies have shown that ERG plays a crucial role in promoting angiogenesis and vascular stability during development and after birth. In the mature vasculature ERG also functions to maintain endothelial homeostasis, by transactivating genes involved in key endothelial functions, while repressing expression of pro-inflammatory genes. Its homeostatic role is lineage-specific, since ectopic expression of ERG in non-endothelial tissues such as prostate is detrimental and contributes to oncogenesis. This review summarises the main roles and pathways controlled by ERG in the vascular endothelium, its transcriptional targets and its functional partners and the emerging evidence on the pathways regulating ERG's activity and expression.
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Affiliation(s)
- Aarti V Shah
- Vascular Sciences, Imperial Centre for Translational and Experimental Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Graeme M Birdsey
- Vascular Sciences, Imperial Centre for Translational and Experimental Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Anna M Randi
- Vascular Sciences, Imperial Centre for Translational and Experimental Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom.
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35
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Sulaiman RS, Merrigan S, Quigley J, Qi X, Lee B, Boulton ME, Kennedy B, Seo SY, Corson TW. A novel small molecule ameliorates ocular neovascularisation and synergises with anti-VEGF therapy. Sci Rep 2016; 6:25509. [PMID: 27148944 PMCID: PMC4857741 DOI: 10.1038/srep25509] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 04/18/2016] [Indexed: 01/18/2023] Open
Abstract
Ocular neovascularisation underlies blinding eye diseases such as retinopathy of prematurity, proliferative diabetic retinopathy, and wet age-related macular degeneration. These diseases cause irreversible vision loss, and provide a significant health and economic burden. Biologics targeting vascular endothelial growth factor (VEGF) are the major approach for treatment. However, up to 30% of patients are non-responsive to these drugs and they are associated with ocular and systemic side effects. Therefore, there is a need for small molecule ocular angiogenesis inhibitors to complement existing therapies. We examined the safety and therapeutic potential of SH-11037, a synthetic derivative of the antiangiogenic homoisoflavonoid cremastranone, in models of ocular neovascularisation. SH-11037 dose-dependently suppressed angiogenesis in the choroidal sprouting assay ex vivo and inhibited ocular developmental angiogenesis in zebrafish larvae. Additionally, intravitreal SH-11037 (1 μM) significantly reduced choroidal neovascularisation (CNV) lesion volume in the laser-induced CNV mouse model, comparable to an anti-VEGF antibody. Moreover, SH-11037 synergised with anti-VEGF treatments in vitro and in vivo. Up to 100 μM SH-11037 was not associated with signs of ocular toxicity and did not interfere with retinal function or pre-existing retinal vasculature. SH-11037 is thus a safe and effective treatment for murine ocular neovascularisation, worthy of further mechanistic and pharmacokinetic evaluation.
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Affiliation(s)
- Rania S Sulaiman
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States of America.,Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States of America.,Department of Biochemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Stephanie Merrigan
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Judith Quigley
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States of America
| | - Xiaoping Qi
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States of America
| | - Bit Lee
- College of Pharmacy, Gachon University, Incheon 406-840, South Korea
| | - Michael E Boulton
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States of America.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States of America
| | - Breandán Kennedy
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Seung-Yong Seo
- College of Pharmacy, Gachon University, Incheon 406-840, South Korea
| | - Timothy W Corson
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States of America.,Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States of America.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States of America
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36
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Alonso A, Pulido R. The extended human PTPome: a growing tyrosine phosphatase family. FEBS J 2015; 283:1404-29. [PMID: 26573778 DOI: 10.1111/febs.13600] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 10/02/2015] [Accepted: 11/13/2015] [Indexed: 12/13/2022]
Abstract
Tyr phosphatases are, by definition, enzymes that dephosphorylate phospho-Tyr (pTyr) from proteins. This activity is found in several structurally diverse protein families, including the protein Tyr phosphatase (PTP), arsenate reductase, rhodanese, haloacid dehalogenase (HAD) and His phosphatase (HP) families. Most of these families include members with substrate specificity for non-pTyr substrates, such as phospho-Ser/phospho-Thr, phosphoinositides, phosphorylated carbohydrates, mRNAs, or inorganic moieties. A Cys is essential for catalysis in PTPs, rhodanese and arsenate reductase enzymes, whereas this work is performed by an Asp in HAD phosphatases and by a His in HPs, via a catalytic mechanism shared by all of the different families. The category that contains most Tyr phosphatases is the PTP family, which, although it received its name from this activity, includes Ser, Thr, inositide, carbohydrate and RNA phosphatases, as well as some inactive pseudophosphatase proteins. Here, we propose an extended collection of human Tyr phosphatases, which we call the extended human PTPome. The addition of new members (SACs, paladin, INPP4s, TMEM55s, SSU72, and acid phosphatases) to the currently categorized PTP group of enzymes means that the extended human PTPome contains up to 125 proteins, of which ~ 40 are selective for pTyr. We set criteria to ascribe proteins to the extended PTPome, and summarize the more important features of the new PTPome members in the context of their phosphatase activity and their relationship with human disease.
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Affiliation(s)
- Andrés Alonso
- Instituto de Biología y Genética Molecular (IBGM), CSIC-Universidad de Valladolid, Valladolid, Spain
| | - Rafael Pulido
- Biocruces Health Research Institute, Barakaldo, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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Chu LH, Vijay CG, Annex BH, Bader JS, Popel AS. PADPIN: protein-protein interaction networks of angiogenesis, arteriogenesis, and inflammation in peripheral arterial disease. Physiol Genomics 2015; 47:331-43. [PMID: 26058837 DOI: 10.1152/physiolgenomics.00125.2014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 06/04/2015] [Indexed: 11/22/2022] Open
Abstract
Peripheral arterial disease (PAD) results from an obstruction of blood flow in the arteries other than the heart, most commonly the arteries that supply the legs. The complexity of the known signaling pathways involved in PAD, including various growth factor pathways and their cross talks, suggests that analyses of high-throughput experimental data could lead to a new level of understanding of the disease as well as novel and heretofore unanticipated potential targets. Such bioinformatic analyses have not been systematically performed for PAD. We constructed global protein-protein interaction networks of angiogenesis (Angiome), immune response (Immunome), and arteriogenesis (Arteriome) using our previously developed algorithm GeneHits. The term "PADPIN" refers to the angiome, immunome, and arteriome in PAD. Here we analyze four microarray gene expression datasets from ischemic and nonischemic gastrocnemius muscles at day 3 posthindlimb ischemia (HLI) in two genetically different C57BL/6 and BALB/c mouse strains that display differential susceptibility to HLI to identify potential targets and signaling pathways in angiogenesis, immune, and arteriogenesis networks. We hypothesize that identification of the differentially expressed genes in ischemic and nonischemic muscles between the strains that recovers better (C57BL/6) vs. the strain that recovers more poorly (BALB/c) will help for the prediction of target genes in PAD. Our bioinformatics analysis identified several genes that are differentially expressed between the two mouse strains with known functions in PAD including TLR4, THBS1, and PRKAA2 and several genes with unknown functions in PAD including EphA4, TSPAN7, SLC22A4, and EIF2a.
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Affiliation(s)
- Liang-Hui Chu
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland;
| | - Chaitanya G Vijay
- Cardiovascular Medicine, Department of Medicine, and the Robert M. Berne Cardiovascular Research Center University of Virginia School of Medicine, Charlottesville, Virginia; and
| | - Brian H Annex
- Cardiovascular Medicine, Department of Medicine, and the Robert M. Berne Cardiovascular Research Center University of Virginia School of Medicine, Charlottesville, Virginia; and
| | - Joel S Bader
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland; High-Throughput Biology Center, Johns Hopkins University, Baltimore, Maryland
| | - Aleksander S Popel
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland
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Dhahbi JM. Circulating small noncoding RNAs as biomarkers of aging. Ageing Res Rev 2014; 17:86-98. [PMID: 24607831 DOI: 10.1016/j.arr.2014.02.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 02/17/2014] [Accepted: 02/24/2014] [Indexed: 12/31/2022]
Abstract
Small noncoding RNAs (sncRNAs) mediate a variety of cellular functions in animals and plants. Deep sequencing has made it possible to obtain highly detailed information on the types and abundance of sncRNAs in biological specimens, leading to the discovery that sncRNAs circulate in the blood of humans and mammals. The most abundant types of circulating sncRNAs are microRNAs (miRNAs), 5' transfer RNA (tRNA) halves, and YRNA fragments, with minute amounts of other types that may nevertheless be significant. Of the more abundant circulating sncRNAs only miRNAs have well described functions, but characteristics of the others suggest specific processing and secretion as complexes that protect the RNA from degradation. The properties of circulating sncRNAs are consistent with their serving as signaling molecules, and investigations of circulating miRNAs support the view that they can enter cells and regulate cellular functions. The serum levels of specific sncRNAs change markedly with age, and these changes can be mitigated by calorie restriction (CR), indicating that levels are under physiologic control. The ability of circulating sncRNAs to transmit functions between cells and to regulate a broad spectrum of cellular functions, and the changes in their levels with age, implicate them in the manifestations of aging. Our understanding of the functions of circulating sncRNA, particularly in relation to aging, is currently at a very early stage; results to date suggest that more extensive investigation will yield important insights into mechanisms of aging.
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Affiliation(s)
- Joseph M Dhahbi
- Department of Biochemistry, University of California at Riverside, Riverside, CA 92521, USA; Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA.
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Kalamohan K, Periasamy J, Bhaskar Rao D, Barnabas GD, Ponnaiyan S, Ganesan K. Transcriptional coexpression network reveals the involvement of varying stem cell features with different dysregulations in different gastric cancer subtypes. Mol Oncol 2014; 8:1306-25. [PMID: 24917244 DOI: 10.1016/j.molonc.2014.04.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 03/22/2014] [Accepted: 04/14/2014] [Indexed: 01/29/2023] Open
Abstract
Despite the advancements in the cancer therapeutics, gastric cancer ranks as the second most common cancers with high global mortality rate. Integrative functional genomic investigation is a powerful approach to understand the major dysregulations and to identify the potential targets toward the development of targeted therapeutics for various cancers. Intestinal and diffuse type gastric tumors remain the major subtypes and the molecular determinants and drivers of these distinct subtypes remain unidentified. In this investigation, by exploring the network of gene coexpression association in gastric tumors, mRNA expressions of 20,318 genes across 200 gastric tumors were categorized into 21 modules. The genes and the hub genes of the modules show gastric cancer subtype specific expression. The expression patterns of the modules were correlated with intestinal and diffuse subtypes as well as with the differentiation status of gastric tumors. Among these, G1 module has been identified as a major driving force of diffuse type gastric tumors with the features of (i) enriched mesenchymal, mesenchymal stem cell like, and mesenchymal derived multiple lineages, (ii) elevated OCT1 mediated transcription, (iii) involvement of Notch activation, and (iv) reduced polycomb mediated epigenetic repression. G13 module has been identified as key factor in intestinal type gastric tumors and found to have the characteristic features of (i) involvement of embryonic stem cell like properties, (ii) Wnt, MYC and E2F mediated transcription programs, and (iii) involvement of polycomb mediated repression. Thus the differential transcription programs, differential epigenetic regulation and varying stem cell features involved in two major subtypes of gastric cancer were delineated by exploring the gene coexpression network. The identified subtype specific dysregulations could be optimally employed in developing subtype specific therapeutic targeting strategies for gastric cancer.
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Affiliation(s)
- Kalaivani Kalamohan
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, India
| | - Jayaprakash Periasamy
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, India
| | - Divya Bhaskar Rao
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, India
| | - Georgina D Barnabas
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, India
| | - Srigayatri Ponnaiyan
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, India
| | - Kumaresan Ganesan
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, India.
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Basavarajappa HD, Lee B, Fei X, Lim D, Callaghan B, Mund JA, Case J, Rajashekhar G, Seo SY, Corson TW. Synthesis and mechanistic studies of a novel homoisoflavanone inhibitor of endothelial cell growth. PLoS One 2014; 9:e95694. [PMID: 24752613 PMCID: PMC3994091 DOI: 10.1371/journal.pone.0095694] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 03/30/2014] [Indexed: 12/13/2022] Open
Abstract
Preventing pathological ocular angiogenesis is key to treating retinopathy of prematurity, diabetic retinopathy and age-related macular degeneration. At present there is no small molecule drug on the market to target this process and hence there is a pressing need for developing novel small molecules that can replace or complement the present surgical and biologic therapies for these neovascular eye diseases. Previously, an antiangiogenic homoisoflavanone was isolated from the bulb of a medicinal orchid, Cremastra appendiculata. In this study, we present the synthesis of a novel homoisoflavanone isomer of this compound. Our compound, SH-11052, has antiproliferative activity against human umbilical vein endothelial cells, and also against more ocular disease-relevant human retinal microvascular endothelial cells (HRECs). Tube formation and cell cycle progression of HRECs were inhibited by SH-11052, but the compound did not induce apoptosis at effective concentrations. SH-11052 also decreased TNF-α induced p38 MAPK phosphorylation in these cells. Intriguingly, SH-11052 blocked TNF-α induced IκB-α degradation, and therefore decreased NF-κB nuclear translocation. It decreased the expression of NF-κB target genes and the pro-angiogenic or pro-inflammatory markers VCAM-1, CCL2, IL8, and PTGS2. In addition SH-11052 inhibited VEGF induced activation of Akt but not VEGF receptor autophosphorylation. Based on these results we propose that SH-11052 inhibits inflammation induced angiogenesis by blocking both TNF-α and VEGF mediated pathways, two major pathways involved in pathological angiogenesis. Synthesis of this novel homoisoflavanone opens the door to structure-activity relationship studies of this class of compound and further evaluation of its mechanism and potential to complement existing antiangiogenic drugs.
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Affiliation(s)
- Halesha D. Basavarajappa
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Bit Lee
- College of Pharmacy, Gachon University, Incheon, South Korea
| | - Xiang Fei
- College of Pharmacy, Gachon University, Incheon, South Korea
| | - Daesung Lim
- College of Pharmacy, Gachon University, Incheon, South Korea
| | - Breedge Callaghan
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Julie A. Mund
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States Of America
| | - Jamie Case
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States Of America
| | - Gangaraju Rajashekhar
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Seung-Yong Seo
- College of Pharmacy, Gachon University, Incheon, South Korea
- * E-mail: (S-YS); (TWC)
| | - Timothy W. Corson
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States Of America
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail: (S-YS); (TWC)
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Pascall JC, Rotondo S, Mukadam AS, Oxley D, Webster J, Walker SA, Piron J, Carter C, Ktistakis NT, Butcher GW. The immune system GTPase GIMAP6 interacts with the Atg8 homologue GABARAPL2 and is recruited to autophagosomes. PLoS One 2013; 8:e77782. [PMID: 24204963 PMCID: PMC3804274 DOI: 10.1371/journal.pone.0077782] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 09/12/2013] [Indexed: 12/22/2022] Open
Abstract
The GIMAPs (GTPases of the immunity-associated proteins) are a family of small GTPases expressed prominently in the immune systems of mammals and other vertebrates. In mammals, studies of mutant or genetically-modified rodents have indicated important roles for the GIMAP GTPases in the development and survival of lymphocytes. No clear picture has yet emerged, however, of the molecular mechanisms by which they perform their function(s). Using biotin tag-affinity purification we identified a major, and highly specific, interaction between the human cytosolic family member GIMAP6 and GABARAPL2, one of the mammalian homologues of the yeast autophagy protein Atg8. Chemical cross-linking studies performed on Jurkat T cells, which express both GIMAP6 and GABARAPL2 endogenously, indicated that the two proteins in these cells readily associate with one another in the cytosol under normal conditions. The GIMAP6-GABARAPL2 interaction was disrupted by deletion of the last 10 amino acids of GIMAP6. The N-terminal region of GIMAP6, however, which includes a putative Atg8-family interacting motif, was not required. Over-expression of GIMAP6 resulted in increased levels of endogenous GABARAPL2 in cells. After culture of cells in starvation medium, GIMAP6 was found to localise in punctate structures with both GABARAPL2 and the autophagosomal marker MAP1LC3B, indicating that GIMAP6 re-locates to autophagosomes on starvation. Consistent with this finding, we have demonstrated that starvation of Jurkat T cells results in the degradation of GIMAP6. Whilst these findings raise the possibility that the GIMAPs play roles in the regulation of autophagy, we have been unable to demonstrate an effect of GIMAP6 over-expression on autophagic flux.
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Affiliation(s)
- John C. Pascall
- The Babraham Institute, Cambridge, Cambridgeshire, United Kingdom
| | - Sergio Rotondo
- The Babraham Institute, Cambridge, Cambridgeshire, United Kingdom
| | - Aamir S. Mukadam
- The Babraham Institute, Cambridge, Cambridgeshire, United Kingdom
| | - David Oxley
- Laboratory of Lymphocyte Signalling and Development, the Mass Spectrometry Facility, the Babraham Institute, Cambridge, Cambridgeshire, United Kingdom
| | - Judith Webster
- Laboratory of Lymphocyte Signalling and Development, the Mass Spectrometry Facility, the Babraham Institute, Cambridge, Cambridgeshire, United Kingdom
| | - Simon A. Walker
- The Imaging Facility, the Babraham Institute, Cambridge, Cambridgeshire, United Kingdom
| | - Jerry Piron
- The Monoclonal Antibody Unit, the Babraham Institute, Cambridge, Cambridgeshire, United Kingdom
| | - Christine Carter
- The Babraham Institute, Cambridge, Cambridgeshire, United Kingdom
| | - Nicholas T. Ktistakis
- The Inositide Laboratory, the Babraham Institute, Cambridge, Cambridgeshire, United Kingdom
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Boesten DMPHJ, Berger A, de Cock P, Dong H, Hammock BD, den Hartog GJM, Bast A. Multi-targeted mechanisms underlying the endothelial protective effects of the diabetic-safe sweetener erythritol. PLoS One 2013; 8:e65741. [PMID: 23755276 PMCID: PMC3673924 DOI: 10.1371/journal.pone.0065741] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 04/26/2013] [Indexed: 02/07/2023] Open
Abstract
Diabetes is characterized by hyperglycemia and development of vascular pathology. Endothelial cell dysfunction is a starting point for pathogenesis of vascular complications in diabetes. We previously showed the polyol erythritol to be a hydroxyl radical scavenger preventing endothelial cell dysfunction onset in diabetic rats. To unravel mechanisms, other than scavenging of radicals, by which erythritol mediates this protective effect, we evaluated effects of erythritol in endothelial cells exposed to normal (7 mM) and high glucose (30 mM) or diabetic stressors (e.g. SIN-1) using targeted and transcriptomic approaches. This study demonstrates that erythritol (i.e. under non-diabetic conditions) has minimal effects on endothelial cells. However, under hyperglycemic conditions erythritol protected endothelial cells against cell death induced by diabetic stressors (i.e. high glucose and peroxynitrite). Also a number of harmful effects caused by high glucose, e.g. increased nitric oxide release, are reversed. Additionally, total transcriptome analysis indicated that biological processes which are differentially regulated due to high glucose are corrected by erythritol. We conclude that erythritol protects endothelial cells during high glucose conditions via effects on multiple targets. Overall, these data indicate a therapeutically important endothelial protective effect of erythritol under hyperglycemic conditions.
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A mechanistic role for DNA methylation in endothelial cell (EC)-enriched gene expression: relationship with DNA replication timing. Blood 2013; 121:3531-40. [PMID: 23449636 DOI: 10.1182/blood-2013-01-479170] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Proximal promoter DNA methylation has been shown to be important for regulating gene expression. However, its relative contribution to the cell-specific expression of endothelial cell (EC)-enriched genes has not been defined. We used methyl-DNA immunoprecipitation and bisulfite conversion to analyze the DNA methylation profile of EC-enriched genes in ECs vs nonexpressing cell types, both in vitro and in vivo. We show that prototypic EC-enriched genes exhibit functional differential patterns of DNA methylation in proximal promoter regions of most (eg, CD31, von Willebrand factor [vWF], VE-cadherin, and intercellular adhesion molecule-2), but not all (eg, VEGFR-1 and VEGFR-2), EC-enriched genes. Comparable findings were evident in cultured ECs, human blood origin ECs, and murine aortic ECs. Promoter-reporter episomal transfection assays for endothelial nitric oxide synthase, VE-cadherin, and vWF indicated functional promoter activity in cell types where the native gene was not active. Inhibition of DNA methyltransferase activity indicated important functional relevance. Importantly, profiling DNA replication timing patterns indicated that EC-enriched gene promoters with differentially methylated regions replicate early in S-phase in both expressing and nonexpressing cell types. Collectively, these studies highlight the functional importance of promoter DNA methylation in controlling vascular EC gene expression.
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Transcriptional patterns in peritoneal tissue of encapsulating peritoneal sclerosis, a complication of chronic peritoneal dialysis. PLoS One 2013; 8:e56389. [PMID: 23418565 PMCID: PMC3572070 DOI: 10.1371/journal.pone.0056389] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 12/27/2012] [Indexed: 12/26/2022] Open
Abstract
Encapsulating peritoneal sclerosis (EPS) is a devastating complication of peritoneal dialysis (PD), characterized by marked inflammation and severe fibrosis of the peritoneum, and associated with high morbidity and mortality. EPS can occur years after termination of PD and, in severe cases, leads to intestinal obstruction and ileus requiring surgical intervention. Despite ongoing research, the pathogenesis of EPS remains unclear. We performed a global transcriptome analysis of peritoneal tissue specimens from EPS patients, PD patients without EPS, and uremic patients without history of PD or EPS (Uremic). Unsupervised and supervised bioinformatics analysis revealed distinct transcriptional patterns that discriminated these three clinical groups. The analysis identified a signature of 219 genes expressed differentially in EPS as compared to PD and Uremic groups. Canonical pathway analysis of differentially expressed genes showed enrichment in several pathways, including antigen presentation, dendritic cell maturation, B cell development, chemokine signaling and humoral and cellular immunity (P value<0.05). Further interactive network analysis depicted effects of EPS-associated genes on networks linked to inflammation, immunological response, and cell proliferation. Gene expression changes were confirmed by qRT-PCR for a subset of the differentially expressed genes. EPS patient tissues exhibited elevated expression of genes encoding sulfatase1, thrombospondin 1, fibronectin 1 and alpha smooth muscle actin, among many others, while in EPS and PD tissues mRNAs encoding leptin and retinol-binding protein 4 were markedly down-regulated, compared to Uremic group patients. Immunolocalization of Collagen 1 alpha 1 revealed that Col1a1 protein was predominantly expressed in the submesothelial compact zone of EPS patient peritoneal samples, whereas PD patient peritoneal samples exhibited homogenous Col1a1 staining throughout the tissue samples. The results are compatible with the hypothesis that encapsulating peritoneal sclerosis is a distinct pathological process from the simple peritoneal fibrosis that accompanies all PD treatment.
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Guduric-Fuchs J, O'Connor A, Cullen A, Harwood L, Medina RJ, O'Neill CL, Stitt AW, Curtis TM, Simpson DA. Deep sequencing reveals predominant expression of miR-21 amongst the small non-coding RNAs in retinal microvascular endothelial cells. J Cell Biochem 2012; 113:2098-111. [PMID: 22298343 PMCID: PMC3708110 DOI: 10.1002/jcb.24084] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The retinal vascular endothelium is essential for angiogenesis and is involved in maintaining barrier selectivity and vascular tone. The aim of this study was to identify and quantify microRNAs and other small regulatory non-coding RNAs (ncRNAs) which may regulate these crucial functions. Primary bovine retinal microvascular endothelial cells (RMECs) provide a well-characterized in vitro system for studying angiogenesis. RNA extracted from RMECs was used to prepare a small RNA library for deep sequencing (Illumina Genome Analyzer). A total of 6.8 million reads were mapped to 250 known microRNAs in miRBase (release 16). In many cases, the most frequent isomiR differed from the sequence reported in miRBase. In addition, five novel microRNAs, 13 novel bovine orthologs of known human microRNAs and multiple new members of the miR-2284/2285 family were detected. Several ∼30 nucleotide sno-miRNAs were identified, with the most highly expressed being derived from snoRNA U78. Highly expressed microRNAs previously associated with endothelial cells included miR-126 and miR-378, but the most highly expressed was miR-21, comprising more than one-third of all mapped reads. Inhibition of miR-21 with an LNA inhibitor significantly reduced proliferation, migration, and tube-forming capacity of RMECs. The independence from prior sequence knowledge provided by deep sequencing facilitates analysis of novel microRNAs and other small RNAs. This approach also enables quantitative evaluation of microRNA expression, which has highlighted the predominance of a small number of microRNAs in RMECs. Knockdown of miR-21 suggests a role for this microRNA in regulation of angiogenesis in the retinal microvasculature. J. Cell. Biochem. 113: 2098–2111, 2012. © 2012 Wiley Periodicals, Inc.
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Affiliation(s)
- Jasenka Guduric-Fuchs
- Centre for Vision and Vascular Science, Queen's University Belfast, Belfast, Northern Ireland, UK
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Wallgard E, Nitzsche A, Larsson J, Guo X, Dieterich LC, Dimberg A, Olofsson T, Pontén FC, Mäkinen T, Kalén M, Hellström M. Paladin (X99384) is expressed in the vasculature and shifts from endothelial to vascular smooth muscle cells during mouse development. Dev Dyn 2012; 241:770-86. [PMID: 22354871 DOI: 10.1002/dvdy.23753] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2012] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Angiogenesis is implicated in many pathological conditions. The role of the proteins involved remains largely unknown, and few vascular-specific drug targets have been discovered. Previously, in a screen for angiogenesis regulators, we identified Paladin (mouse: X99384, human: KIAA1274), a protein containing predicted S/T/Y phosphatase domains. RESULTS We present a mouse knockout allele for Paladin with a β-galactosidase reporter, which in combination with Paladin antibodies demonstrate that Paladin is expressed in the vasculature. During mouse embryogenesis, Paladin is primarily expressed in capillary and venous endothelial cells. In adult mice Paladin is predominantly expressed in arterial pericytes and vascular smooth muscle cells. Paladin also displays vascular-restricted expression in human brain, astrocytomas, and glioblastomas. CONCLUSIONS Paladin, a novel putative phosphatase, displays a dynamic expression pattern in the vasculature. During embryonic stages it is broadly expressed in endothelial cells, while in the adult it is selectively expressed in arterial smooth muscle cells.
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Affiliation(s)
- Elisabet Wallgard
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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McCall MN, Kent OA, Yu J, Fox-Talbot K, Zaiman AL, Halushka MK. MicroRNA profiling of diverse endothelial cell types. BMC Med Genomics 2011; 4:78. [PMID: 22047531 PMCID: PMC3223144 DOI: 10.1186/1755-8794-4-78] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 11/02/2011] [Indexed: 01/25/2023] Open
Abstract
Background MicroRNAs are ~22-nt long regulatory RNAs that serve as critical modulators of post-transcriptional gene regulation. The diversity of miRNAs in endothelial cells (ECs) and the relationship of this diversity to epithelial and hematologic cells is unknown. We investigated the baseline miRNA signature of human ECs cultured from the aorta (HAEC), coronary artery (HCEC), umbilical vein (HUVEC), pulmonary artery (HPAEC), pulmonary microvasculature (HPMVEC), dermal microvasculature (HDMVEC), and brain microvasculature (HBMVEC) to understand the diversity of miRNA expression in ECs. Results We identified 166 expressed miRNAs, of which 3 miRNAs (miR-99b, miR-20b and let-7b) differed significantly between EC types and predicted EC clustering. We confirmed the significance of these miRNAs by RT-PCR analysis and in a second data set by Sylamer analysis. We found wide diversity of miRNAs between endothelial, epithelial and hematologic cells with 99 miRNAs shared across cell types and 31 miRNAs unique to ECs. We show polycistronic miRNA chromosomal clusters have common expression levels within a given cell type. Conclusions EC miRNA expression levels are generally consistent across EC types. Three microRNAs were variable within the dataset indicating potential regulatory changes that could impact on EC phenotypic differences. MiRNA expression in endothelial, epithelial and hematologic cells differentiate these cell types. This data establishes a valuable resource characterizing the diverse miRNA signature of ECs.
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Affiliation(s)
- Matthew N McCall
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, USA
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Dhahbi JM, Atamna H, Boffelli D, Magis W, Spindler SR, Martin DIK. Deep sequencing reveals novel microRNAs and regulation of microRNA expression during cell senescence. PLoS One 2011; 6:e20509. [PMID: 21637828 PMCID: PMC3102725 DOI: 10.1371/journal.pone.0020509] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 04/29/2011] [Indexed: 11/19/2022] Open
Abstract
In cell senescence, cultured cells cease proliferating and acquire aberrant gene expression patterns. MicroRNAs (miRNAs) modulate gene expression through translational repression or mRNA degradation and have been implicated in senescence. We used deep sequencing to carry out a comprehensive survey of miRNA expression and involvement in cell senescence. Informatic analysis of small RNA sequence datasets from young and senescent IMR90 human fibroblasts identifies many miRNAs that are regulated (either up or down) with cell senescence. Comparison with mRNA expression profiles reveals potential mRNA targets of these senescence-regulated miRNAs. The target mRNAs are enriched for genes involved in biological processes associated with cell senescence. This result greatly extends existing information on the role of miRNAs in cell senescence and is consistent with miRNAs having a causal role in the process.
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Affiliation(s)
- Joseph M. Dhahbi
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, California, United States of America
- Department of Biochemistry, University of California Riverside, Riverside, California, United States of America
- * E-mail: (JMD); (HA); (DIKM)
| | - Hani Atamna
- Department of Basic Sciences, Neuroscience, The Commonwealth Medical College, Scranton, Pennsylvania, United States of America
- * E-mail: (JMD); (HA); (DIKM)
| | - Dario Boffelli
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Wendy Magis
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Stephen R. Spindler
- Department of Biochemistry, University of California Riverside, Riverside, California, United States of America
| | - David I. K. Martin
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, California, United States of America
- * E-mail: (JMD); (HA); (DIKM)
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Kenagy RD, Min SK, Mulvihill E, Clowes AW. A link between smooth muscle cell death and extracellular matrix degradation during vascular atrophy. J Vasc Surg 2011; 54:182-191.e24. [PMID: 21493032 DOI: 10.1016/j.jvs.2010.12.070] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Revised: 12/07/2010] [Accepted: 12/11/2010] [Indexed: 12/12/2022]
Abstract
OBJECTIVE High blood flow induces neointimal atrophy in polytetrafluoroethylene (PTFE) aortoiliac grafts and a tight external PTFE wrap of the iliac artery induces medial atrophy. In both nonhuman primate models, atrophy with loss of smooth muscle cells and extracellular matrix (ECM) begins at ≤4 days. We hypothesized that matrix loss would be linked to cell death, but the factors and mechanisms involved are not known. The purpose of this study was to determine commonly regulated genes in these two models, which we hypothesized would be a small set of genes that might be key regulators of vascular atrophy. METHODS DNA microarray analysis (Sentrix Human Ref 8; Illumina, San Diego, Calif; ∼23,000 genes) was performed on arterial tissue from the wrap model (n = 9) and graft neointima from the graft model (n = 5) 1 day after wrapping or the switch to high flow, respectively. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) was also performed. Expression of this vascular atrophy gene set was also studied after Fas ligand-induced cell death in cultured smooth muscle cells and organ cultured arteries. RESULTS Microarray analysis showed 15 genes were regulated in the same direction in both atrophy models: 9 upregulated and 6 downregulated. Seven of nine upregulated genes were confirmed by qRT-PCR in both models. Upregulated genes included the ECM-degrading enzymes ADAMTS4, tissue plasminogen activator (PLAT), and hyaluronidase 2; possible growth regulatory factors, including chromosome 8 open reading frame 4 and leucine-rich repeat family containing 8; a differentiation regulatory factor (musculoskeletal embryonic nuclear protein 1); a dead cell removal factor (ficolin 3); and a prostaglandin transporter (solute carrier organic anion transporter family member 2A1). Five downregulated genes were confirmed but only in one or the other model. Of the seven upregulated genes, ADAMTS4, PLAT, hyaluronidase 2, solute carrier organic anion transporter family member 2A1, leucine-rich repeat family containing 8, and chromosome 8 open reading frame 4 were also upregulated in vitro in cultured smooth muscle cells or cultured iliac artery by treatment with FasL, which causes cell death. However, blockade of caspase activity with Z-VAD inhibited FasL-mediated cell death, but not gene induction. CONCLUSION Seven gene products were upregulated in two distinctly different in vivo nonhuman primate vascular atrophy models. Induction of cell death by FasL in vitro induced six of these genes, including the ECM-degrading factors ADAMTS4, hyaluronidase 2, and PLAT, suggesting a mechanism by which the program of tissue atrophy coordinately removes extracellular matrix as cells die. These genes may be key regulators of vascular atrophy.
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Affiliation(s)
- Richard D Kenagy
- Department of Surgery, University of Washington, Seattle, WA 98195-6410, USA
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50
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Ståhlberg A, Andersson D, Aurelius J, Faiz M, Pekna M, Kubista M, Pekny M. Defining cell populations with single-cell gene expression profiling: correlations and identification of astrocyte subpopulations. Nucleic Acids Res 2010; 39:e24. [PMID: 21112872 PMCID: PMC3045576 DOI: 10.1093/nar/gkq1182] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Single-cell gene expression levels show substantial variations among cells in seemingly homogenous populations. Astrocytes perform many control and regulatory functions in the central nervous system. In contrast to neurons, we have limited knowledge about functional diversity of astrocytes and its molecular basis. To study astrocyte heterogeneity and stem/progenitor cell properties of astrocytes, we used single-cell gene expression profiling in primary mouse astrocytes and dissociated mouse neurosphere cells. The transcript number variability for astrocytes showed lognormal features and revealed that cells in primary cultures to a large extent co-express markers of astrocytes and neural stem/progenitor cells. We show how subpopulations of cells can be identified at single-cell level using unsupervised algorithms and that gene correlations can be used to identify differences in activity of important transcriptional pathways. We identified two subpopulations of astrocytes with distinct gene expression profiles. One had an expression profile very similar to that of neurosphere cells, whereas the other showed characteristics of activated astrocytes in vivo.
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Affiliation(s)
- Anders Ståhlberg
- Center for Brain Repair and Rehabilitation, Department of Clinical Neuroscience and Rehabilitation, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 9A, 413 90 Gothenburg, Sweden.
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