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Chavkin NW, Hirschi KK. Single Cell Analysis in Vascular Biology. Front Cardiovasc Med 2020; 7:42. [PMID: 32296715 PMCID: PMC7137757 DOI: 10.3389/fcvm.2020.00042] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/05/2020] [Indexed: 12/12/2022] Open
Abstract
The ability to quantify DNA, RNA, and protein variations at the single cell level has revolutionized our understanding of cellular heterogeneity within tissues. Via such analyses, individual cells within populations previously thought to be homogeneous can now be delineated into specific subpopulations expressing unique sets of genes, enabling specialized functions. In vascular biology, studies using single cell RNA sequencing have revealed extensive heterogeneity among endothelial and mural cells even within the same vessel, key intermediate cell types that arise during blood and lymphatic vessel development, and cell-type specific responses to disease. Thus, emerging new single cell analysis techniques are enabling vascular biologists to elucidate mechanisms of vascular development, homeostasis, and disease that were previously not possible. In this review, we will provide an overview of single cell analysis methods and highlight recent advances in vascular biology made possible through single cell RNA sequencing.
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Affiliation(s)
- Nicholas W Chavkin
- Department of Cell Biology, Developmental Genomics Center, School of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Karen K Hirschi
- Department of Cell Biology, Developmental Genomics Center, School of Medicine, University of Virginia, Charlottesville, VA, United States.,Departments of Medicine and Genetics, Cardiovascular Research Center, School of Medicine, Yale University, New Haven, CT, United States
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2
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Feng W, Chen L, Nguyen PK, Wu SM, Li G. Single Cell Analysis of Endothelial Cells Identified Organ-Specific Molecular Signatures and Heart-Specific Cell Populations and Molecular Features. Front Cardiovasc Med 2019; 6:165. [PMID: 31850371 PMCID: PMC6901932 DOI: 10.3389/fcvm.2019.00165] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/30/2019] [Indexed: 12/03/2022] Open
Abstract
Endothelial cells line the inner surface of vasculature and play an important role in normal physiology and disease progression. Although most tissue is known to have a heterogeneous population of endothelial cells, transcriptional differences in organ specific endothelial cells have not been systematically analyzed at the single cell level. The Tabula Muris project profiled mouse single cells from 20 organs. We found 10 of the organs profiled by this Consortium have endothelial cells. Unsupervised analysis of these endothelial cells revealed that they were mainly grouped by organs, and organ-specific cells were further partially correlated by germ layers. Unexpectedly, we found all lymphatic endothelial cells grouped together regardless of their resident organs. To further understand the cellular heterogeneity in organ-specific endothelial cells, we used the heart as an example. As a pump of the circulation system, the heart has multiple types of endothelial cells. Detailed analysis of these cells identified an endocardial endothelial cell population, a coronary vascular endothelial cell population, and an aorta-specific cell population. Through integrated analysis of the single cell data from another two studies analyzing the aorta, we identified conserved cell populations and molecular markers across the datasets. In summary, by reanalyzing the existing endothelial cell single-cell data, we identified organ-specific molecular signatures and heart-specific subpopulations and molecular markers. We expect these findings will pave the way for a deeper understanding of vascular biology and endothelial cell-related diseases.
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Affiliation(s)
- Wei Feng
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Lyuqin Chen
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, United States.,Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA, United States
| | - Patricia K Nguyen
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, United States.,Veterans Affairs Palo Alto Health Care Administration, Palo Alto, CA, United States.,Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Sean M Wu
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, United States.,Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Guang Li
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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Li G, Tian L, Goodyer W, Kort EJ, Buikema JW, Xu A, Wu JC, Jovinge S, Wu SM. Single cell expression analysis reveals anatomical and cell cycle-dependent transcriptional shifts during heart development. Development 2019; 146:dev.173476. [PMID: 31142541 DOI: 10.1242/dev.173476] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 05/15/2019] [Indexed: 01/06/2023]
Abstract
The heart is a complex organ composed of multiple cell and tissue types. Cardiac cells from different regions of the growing embryonic heart exhibit distinct patterns of gene expression, which are thought to contribute to heart development and morphogenesis. Single cell RNA sequencing allows genome-wide analysis of gene expression at the single cell level. Here, we have analyzed cardiac cells derived from early stage developing hearts by single cell RNA-seq and identified cell cycle gene expression as a major determinant of transcriptional variation. Within cell cycle stage-matched CMs from a given heart chamber, we found that CMs in the G2/M phase downregulated sarcomeric and cytoskeletal markers. We also identified cell location-specific signaling molecules that may influence the proliferation of other nearby cell types. Our data highlight how variations in cell cycle activity selectively promote cardiac chamber growth during development, reveal profound chamber-specific cell cycle-linked transcriptional shifts, and open the way to deeper understanding of pathogenesis of congenital heart disease.
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Affiliation(s)
- Guang Li
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA .,Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, USA
| | - Lei Tian
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William Goodyer
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eric J Kort
- DeVos Cardiovascular Research Program of Spectrum Health and Van Andel Research Institute, 100 Michigan Street NE, Grand Rapids, MI 49503, USA.,Michigan State University, College of Human Medicine, 15 Michigan Street NE, Grand Rapids, MI 49503, USA
| | - Jan W Buikema
- Department of Cardiology, Utrecht Regenerative Medicine Center, University Medical Center Utrecht, Utrecht University, 3508 GA Utrecht, The Netherlands
| | - Adele Xu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph C Wu
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.,Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.,Deparment of Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stefan Jovinge
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA .,DeVos Cardiovascular Research Program of Spectrum Health and Van Andel Research Institute, 100 Michigan Street NE, Grand Rapids, MI 49503, USA.,Michigan State University, College of Human Medicine, 15 Michigan Street NE, Grand Rapids, MI 49503, USA
| | - Sean M Wu
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA .,Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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Yin L, Zhang Z, Liu Y, Gao Y, Gu J. Recent advances in single-cell analysis by mass spectrometry. Analyst 2019; 144:824-845. [PMID: 30334031 DOI: 10.1039/c8an01190g] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cells are the most basic structural units that play vital roles in the functioning of living organisms. Analysis of the chemical composition and content of a single cell plays a vital role in ensuring precise investigations of cellular metabolism, and is a crucial aspect of lipidomic and proteomic studies. In addition, structural knowledge provides a better understanding of cell behavior as well as the cellular and subcellular mechanisms. However, single-cell analysis can be very challenging due to the very small size of each cell as well as the large variety and extremely low concentrations of substances found in individual cells. On account of its high sensitivity and selectivity, mass spectrometry holds great promise as an effective technique for single-cell analysis. Numerous mass spectrometric techniques have been developed to elucidate the molecular profiles at the cellular level, including electrospray ionization mass spectrometry (ESI-MS), secondary ion mass spectrometry (SIMS), laser-based mass spectrometry and inductively coupled plasma mass spectrometry (ICP-MS). In this review, the recent advances in single-cell analysis by mass spectrometry are summarized. The strategies of different ionization modes to achieve single-cell analysis are classified and discussed in detail.
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Affiliation(s)
- Lei Yin
- Research Institute of Translational Medicine, The First Hospital of Jilin University, Jilin University, Dongminzhu Street, Changchun 130061, PR China.
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Khoury P, Akuthota P, Ackerman SJ, Arron JR, Bochner BS, Collins MH, Kahn JE, Fulkerson PC, Gleich GJ, Gopal-Srivastava R, Jacobsen EA, Leiferman KM, Francesca LS, Mathur SK, Minnicozzi M, Prussin C, Rothenberg ME, Roufosse F, Sable K, Simon D, Simon HU, Spencer LA, Steinfeld J, Wardlaw AJ, Wechsler ME, Weller PF, Klion AD. Revisiting the NIH Taskforce on the Research needs of Eosinophil-Associated Diseases (RE-TREAD). J Leukoc Biol 2018; 104:69-83. [PMID: 29672914 PMCID: PMC6171343 DOI: 10.1002/jlb.5mr0118-028r] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 02/21/2018] [Accepted: 02/21/2018] [Indexed: 02/05/2023] Open
Abstract
Eosinophil-associated diseases (EADs) are rare, heterogeneous disorders characterized by the presence of eosinophils in tissues and/or peripheral blood resulting in immunopathology. The heterogeneity of tissue involvement, lack of sufficient animal models, technical challenges in working with eosinophils, and lack of standardized histopathologic approaches have hampered progress in basic research. Additionally, clinical trials and drug development for rare EADs are limited by the lack of primary and surrogate endpoints, biomarkers, and validated patient-reported outcomes. Researchers with expertise in eosinophil biology and eosinophil-related diseases reviewed the state of current eosinophil research, resources, progress, and unmet needs in the field since the 2012 meeting of the NIH Taskforce on the Research of Eosinophil-Associated Diseases (TREAD). RE-TREAD focused on gaps in basic science, translational, and clinical research on eosinophils and eosinophil-related pathogenesis. Improved recapitulation of human eosinophil biology and pathogenesis in murine models was felt to be of importance. Characterization of eosinophil phenotypes, the role of eosinophil subsets in tissues, identification of biomarkers of eosinophil activation and tissue load, and a better understanding of the role of eosinophils in human disease were prioritized. Finally, an unmet need for tools for use in clinical trials was emphasized. Histopathologic scoring, patient- and clinician-reported outcomes, and appropriate coding were deemed of paramount importance for research collaborations, drug development, and approval by regulatory agencies. Further exploration of the eosinophil genome, epigenome, and proteome was also encouraged. Although progress has been made since 2012, unmet needs in eosinophil research remain a priority.
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Affiliation(s)
- Paneez Khoury
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Praveen Akuthota
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, La Jolla, California, USA
| | - Steven J Ackerman
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Joseph R Arron
- Immunology Discovery, Genentech, Inc., South San Francisco, California, USA
| | - Bruce S Bochner
- Department of Medicine, Division of Allergy and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Margaret H Collins
- Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio, USA
| | | | - Patricia C Fulkerson
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Gerald J Gleich
- Departments of Dermatology and Medicine, University of Utah Health, Salt Lake City, Utah, USA
| | - Rashmi Gopal-Srivastava
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Kristen M Leiferman
- Department of Dermatology, University of Utah Health, Salt Lake City, Utah, USA
| | - Levi-Schaffer Francesca
- Pharmacology and Experimental Therapeutics Unit, Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Sameer K Mathur
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Michael Minnicozzi
- Division of Allergy, Immunology and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Marc E Rothenberg
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | | | - Kathleen Sable
- American Partnership For Eosinophilic Disorders, Atlanta, Georgia, USA
| | - Dagmar Simon
- Department of Dermatology, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Hans-Uwe Simon
- Institute of Pharmacology, University of Bern, Bern, Switzerland
| | - Lisa A Spencer
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Andrew J Wardlaw
- Institute for Lung Health, University of Leicester, Leicester, England
| | | | - Peter F Weller
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Amy D Klion
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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Alekseyev YO, Fazeli R, Yang S, Basran R, Maher T, Miller NS, Remick D. A Next-Generation Sequencing Primer-How Does It Work and What Can It Do? Acad Pathol 2018; 5:2374289518766521. [PMID: 29761157 PMCID: PMC5944141 DOI: 10.1177/2374289518766521] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 02/14/2018] [Accepted: 02/16/2018] [Indexed: 12/28/2022] Open
Abstract
Next-generation sequencing refers to a high-throughput technology that determines the nucleic acid sequences and identifies variants in a sample. The technology has been introduced into clinical laboratory testing and produces test results for precision medicine. Since next-generation sequencing is relatively new, graduate students, medical students, pathology residents, and other physicians may benefit from a primer to provide a foundation about basic next-generation sequencing methods and applications, as well as specific examples where it has had diagnostic and prognostic utility. Next-generation sequencing technology grew out of advances in multiple fields to produce a sophisticated laboratory test with tremendous potential. Next-generation sequencing may be used in the clinical setting to look for specific genetic alterations in patients with cancer, diagnose inherited conditions such as cystic fibrosis, and detect and profile microbial organisms. This primer will review DNA sequencing technology, the commercialization of next-generation sequencing, and clinical uses of next-generation sequencing. Specific applications where next-generation sequencing has demonstrated utility in oncology are provided.
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Affiliation(s)
- Yuriy O Alekseyev
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Roghayeh Fazeli
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Shi Yang
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Raveen Basran
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Thomas Maher
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Nancy S Miller
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Daniel Remick
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
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Doppler SA, Lange R, Laugwitz KL, Krane M. Cardiac development: from current understanding to new regenerative concepts. J Thorac Dis 2017; 9:S1-S4. [PMID: 28446962 DOI: 10.21037/jtd.2017.03.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Stefanie A Doppler
- Department of Cardiovascular Surgery, Division of Experimental Surgery, German Heart Center Munich, Technische Universität München, Munich, Germany
| | - Rüdiger Lange
- Department of Cardiovascular Surgery, Division of Experimental Surgery, German Heart Center Munich, Technische Universität München, Munich, Germany.,DZHK (German Center for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Karl-Ludwig Laugwitz
- DZHK (German Center for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,I. Department of Medicine (Cardiology), Klinikum rechts der Isar der Technischen Universität München, Munich, Germany
| | - Markus Krane
- Department of Cardiovascular Surgery, Division of Experimental Surgery, German Heart Center Munich, Technische Universität München, Munich, Germany.,DZHK (German Center for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
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