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Younesi FS, Miller AE, Barker TH, Rossi FMV, Hinz B. Fibroblast and myofibroblast activation in normal tissue repair and fibrosis. Nat Rev Mol Cell Biol 2024; 25:617-638. [PMID: 38589640 DOI: 10.1038/s41580-024-00716-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2024] [Indexed: 04/10/2024]
Abstract
The term 'fibroblast' often serves as a catch-all for a diverse array of mesenchymal cells, including perivascular cells, stromal progenitor cells and bona fide fibroblasts. Although phenotypically similar, these subpopulations are functionally distinct, maintaining tissue integrity and serving as local progenitor reservoirs. In response to tissue injury, these cells undergo a dynamic fibroblast-myofibroblast transition, marked by extracellular matrix secretion and contraction of actomyosin-based stress fibres. Importantly, whereas transient activation into myofibroblasts aids in tissue repair, persistent activation triggers pathological fibrosis. In this Review, we discuss the roles of mechanical cues, such as tissue stiffness and strain, alongside cell signalling pathways and extracellular matrix ligands in modulating myofibroblast activation and survival. We also highlight the role of epigenetic modifications and myofibroblast memory in physiological and pathological processes. Finally, we discuss potential strategies for therapeutically interfering with these factors and the associated signal transduction pathways to improve the outcome of dysregulated healing.
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Affiliation(s)
- Fereshteh Sadat Younesi
- Keenan Research Institute for Biomedical Science of the St. Michael's Hospital, Toronto, Ontario, Canada
- Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Andrew E Miller
- Department of Biomedical Engineering, School of Engineering and Applied Science, University of Virginia, Charlottesville, VA, USA
| | - Thomas H Barker
- Department of Biomedical Engineering, School of Engineering and Applied Science, University of Virginia, Charlottesville, VA, USA
| | - Fabio M V Rossi
- School of Biomedical Engineering and Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Boris Hinz
- Keenan Research Institute for Biomedical Science of the St. Michael's Hospital, Toronto, Ontario, Canada.
- Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada.
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Mancini A, Gentile MT, Pentimalli F, Cortellino S, Grieco M, Giordano A. Multiple aspects of matrix stiffness in cancer progression. Front Oncol 2024; 14:1406644. [PMID: 39015505 PMCID: PMC11249764 DOI: 10.3389/fonc.2024.1406644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/27/2024] [Indexed: 07/18/2024] Open
Abstract
The biophysical and biomechanical properties of the extracellular matrix (ECM) are crucial in the processes of cell differentiation and proliferation. However, it is unclear to what extent tumor cells are influenced by biomechanical and biophysical changes of the surrounding microenvironment and how this response varies between different tumor forms, and over the course of tumor progression. The entire ensemble of genes encoding the ECM associated proteins is called matrisome. In cancer, the ECM evolves to become highly dysregulated, rigid, and fibrotic, serving both pro-tumorigenic and anti-tumorigenic roles. Tumor desmoplasia is characterized by a dramatic increase of α-smooth muscle actin expressing fibroblast and the deposition of hard ECM containing collagen, fibronectin, proteoglycans, and hyaluronic acid and is common in many solid tumors. In this review, we described the role of inflammation and inflammatory cytokines, in desmoplastic matrix remodeling, tumor state transition driven by microenvironment forces and the signaling pathways in mechanotransduction as potential targeted therapies, focusing on the impact of qualitative and quantitative variations of the ECM on the regulation of tumor development, hypothesizing the presence of matrisome drivers, acting alongside the cell-intrinsic oncogenic drivers, in some stages of neoplastic progression and in some tumor contexts, such as pancreatic carcinoma, breast cancer, lung cancer and mesothelioma.
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Affiliation(s)
- Alessandro Mancini
- Department of Translational Medical Sciences, University of Campania “Luigi Vanvitelli”, Naples, Italy
- BioUp Sagl, Lugano, Switzerland
| | - Maria Teresa Gentile
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Caserta, Italy
| | - Francesca Pentimalli
- Department of Medicine and Surgery, LUM University “Giuseppe De Gennaro,” Casamassima, Bari, Italy
| | - Salvatore Cortellino
- Laboratory of Molecular Oncology, Responsible Research Hospital, Campobasso, Italy
- Scuola Superiore Meridionale (SSM), Clinical and Translational Oncology, Naples, NA, Italy
- Sbarro Health Research Organization (S.H.R.O.) Italia Foundation ETS, Candiolo, TO, Italy
| | - Michele Grieco
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Caserta, Italy
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, United States
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
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Cox BP, Hannan RT, Batrash N, Raichura P, Sperling AI, Shim YM, Sturek JM. Local, Quantitative Morphometry of Fibroproliferative Lung Injury Using Laminin. Am J Respir Cell Mol Biol 2024; 71:23-29. [PMID: 38593005 PMCID: PMC11225868 DOI: 10.1165/rcmb.2023-0294ma] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 04/09/2024] [Indexed: 04/11/2024] Open
Abstract
Investigations into the mechanisms of injury and repair in fibroproliferative disease require consideration of the spatial heterogeneity inherent in the disease. Most scoring of fibrotic remodeling in preclinical animal models relies on the modified Ashcroft score, which is an ordinal rubric of macroscopic resolution. The obvious limitations of manual histopathologic scoring have generated an unmet need for unbiased, repeatable scoring of fibroproliferative burden in tissue. Using computer vision approaches on immunofluorescence imaging of the extracellular matrix component laminin, we generated a robust and repeatable quantitative remodeling scorer. In the bleomycin lung injury model, the quantitative remodeling scorer shows significant agreement with the modified Ashcroft scale. This antibody-based approach is easily integrated into larger multiplex immunofluorescence experiments, which we demonstrate by testing the spatial apposition of tertiary lymphoid structures to fibroproliferative tissue, a poorly characterized phenomenon observed in both human interstitial lung diseases and preclinical models of lung fibrosis. The tool reported in this article is available as a stand-alone application that is usable without programming knowledge.
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Affiliation(s)
| | | | - Noora Batrash
- University of Virginia School of Medicine, University of Virginia, Charlottesville, Virginia
| | | | - Anne I. Sperling
- Division of Pulmonary and Critical Care Medicine
- Beirne B. Carter Center for Immunology Research, and
| | | | - Jeffrey M. Sturek
- Division of Pulmonary and Critical Care Medicine
- Beirne B. Carter Center for Immunology Research, and
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4
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Du P, Fan R, Zhang N, Wu C, Zhang Y. Advances in Integrated Multi-omics Analysis for Drug-Target Identification. Biomolecules 2024; 14:692. [PMID: 38927095 PMCID: PMC11201992 DOI: 10.3390/biom14060692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/08/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
As an essential component of modern drug discovery, the role of drug-target identification is growing increasingly prominent. Additionally, single-omics technologies have been widely utilized in the process of discovering drug targets. However, it is difficult for any single-omics level to clearly expound the causal connection between drugs and how they give rise to the emergence of complex phenotypes. With the progress of large-scale sequencing and the development of high-throughput technologies, the tendency in drug-target identification has shifted towards integrated multi-omics techniques, gradually replacing traditional single-omics techniques. Herein, this review centers on the recent advancements in the domain of integrated multi-omics techniques for target identification, highlights the common multi-omics analysis strategies, briefly summarizes the selection of multi-omics analysis tools, and explores the challenges of existing multi-omics analyses, as well as the applications of multi-omics technology in drug-target identification.
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Affiliation(s)
- Peiling Du
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Rui Fan
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Nana Zhang
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Chenyuan Wu
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Yingqian Zhang
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
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5
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Al-Husinat L, Azzam S, Al Sharie S, Al Sharie AH, Battaglini D, Robba C, Marini JJ, Thornton LT, Cruz FF, Silva PL, Rocco PRM. Effects of mechanical ventilation on the interstitial extracellular matrix in healthy lungs and lungs affected by acute respiratory distress syndrome: a narrative review. Crit Care 2024; 28:165. [PMID: 38750543 PMCID: PMC11094887 DOI: 10.1186/s13054-024-04942-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/06/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Mechanical ventilation, a lifesaving intervention in critical care, can lead to damage in the extracellular matrix (ECM), triggering inflammation and ventilator-induced lung injury (VILI), particularly in conditions such as acute respiratory distress syndrome (ARDS). This review discusses the detailed structure of the ECM in healthy and ARDS-affected lungs under mechanical ventilation, aiming to bridge the gap between experimental insights and clinical practice by offering a thorough understanding of lung ECM organization and the dynamics of its alteration during mechanical ventilation. MAIN TEXT Focusing on the clinical implications, we explore the potential of precise interventions targeting the ECM and cellular signaling pathways to mitigate lung damage, reduce inflammation, and ultimately improve outcomes for critically ill patients. By analyzing a range of experimental studies and clinical papers, particular attention is paid to the roles of matrix metalloproteinases (MMPs), integrins, and other molecules in ECM damage and VILI. This synthesis not only sheds light on the structural changes induced by mechanical stress but also underscores the importance of cellular responses such as inflammation, fibrosis, and excessive activation of MMPs. CONCLUSIONS This review emphasizes the significance of mechanical cues transduced by integrins and their impact on cellular behavior during ventilation, offering insights into the complex interactions between mechanical ventilation, ECM damage, and cellular signaling. By understanding these mechanisms, healthcare professionals in critical care can anticipate the consequences of mechanical ventilation and use targeted strategies to prevent or minimize ECM damage, ultimately leading to better patient management and outcomes in critical care settings.
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Affiliation(s)
- Lou'i Al-Husinat
- Department of Clinical Sciences, Faculty of Medicine, Yarmouk University, Irbid, Jordan
| | - Saif Azzam
- Faculty of Medicine, Yarmouk University, Irbid, Jordan
| | | | - Ahmed H Al Sharie
- Department of Pathology and Microbiology, Jordan University of Science and Technology, Irbid, Jordan
| | - Denise Battaglini
- Anesthesia and Intensive Care, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Chiara Robba
- Anesthesia and Intensive Care, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Dipartimento di Scienze Chirurgiche e Diagnostiche, Università Degli Studi di Genova, Genoa, Italy
| | - John J Marini
- Department of Pulmonary and Critical Care Medicine, University of Minnesota, Minneapolis, St Paul, MN, USA
| | - Lauren T Thornton
- Department of Pulmonary and Critical Care Medicine, University of Minnesota, Minneapolis, St Paul, MN, USA
| | - Fernanda F Cruz
- Laboratory of Pulmonary Investigation, Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Pedro L Silva
- Laboratory of Pulmonary Investigation, Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Patricia R M Rocco
- Laboratory of Pulmonary Investigation, Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
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Macdonald JK, Mehta AS, Drake RR, Angel PM. Molecular analysis of the extracellular microenvironment: from form to function. FEBS Lett 2024; 598:602-620. [PMID: 38509768 PMCID: PMC11049795 DOI: 10.1002/1873-3468.14852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
The extracellular matrix (ECM) proteome represents an important component of the tissue microenvironment that controls chemical flux and induces cell signaling through encoded structure. The analysis of the ECM represents an analytical challenge through high levels of post-translational modifications, protease-resistant structures, and crosslinked, insoluble proteins. This review provides a comprehensive overview of the analytical challenges involved in addressing the complexities of spatially profiling the extracellular matrix proteome. A synopsis of the process of synthesizing the ECM structure, detailing inherent chemical complexity, is included to present the scope of the analytical challenge. Current chromatographic and spatial techniques addressing these challenges are detailed. Capabilities for multimodal multiplexing with cellular populations are discussed with a perspective on developing a holistic view of disease processes that includes both the cellular and extracellular microenvironment.
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Affiliation(s)
- Jade K Macdonald
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC
| | - Anand S Mehta
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC
| | - Peggi M. Angel
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC
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7
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Piga I, Magni F, Smith A. The journey towards clinical adoption of MALDI-MS-based imaging proteomics: from current challenges to future expectations. FEBS Lett 2024; 598:621-634. [PMID: 38140823 DOI: 10.1002/1873-3468.14795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/06/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023]
Abstract
Among the spatial omics techniques available, mass spectrometry imaging (MSI) represents one of the most promising owing to its capability to map the distribution of hundreds of peptides and proteins, as well as other classes of biomolecules, within a complex sample background in a multiplexed and relatively high-throughput manner. In particular, matrix-assisted laser desorption/ionisation (MALDI-MSI) has come to the fore and established itself as the most widely used technique in clinical research. However, the march of this technique towards clinical utility has been hindered by issues related to method reproducibility, appropriate biocomputational tools, and data storage. Notwithstanding these challenges, significant progress has been achieved in recent years regarding multiple facets of the technology and has rendered it more suitable for a possible clinical role. As such, there is now more robust and extensive evidence to suggest that the technology has the potential to support clinical decision-making processes under appropriate circumstances. In this review, we will discuss some of the recent developments that have facilitated this progress and outline some of the more promising clinical proteomics applications which have been developed with a clear goal towards implementation in mind.
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Affiliation(s)
- Isabella Piga
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro, Italy
| | - Fulvio Magni
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro, Italy
| | - Andrew Smith
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro, Italy
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8
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Diedrich AM, Daneshgar A, Tang P, Klein O, Mohr A, Onwuegbuchulam OA, von Rueden S, Menck K, Bleckmann A, Juratli MA, Becker F, Sauer IM, Hillebrandt KH, Pascher A, Struecker B. Proteomic analysis of decellularized mice liver and kidney extracellular matrices. J Biol Eng 2024; 18:17. [PMID: 38389090 PMCID: PMC10885605 DOI: 10.1186/s13036-024-00413-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 02/07/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND The extracellular matrix (ECM) is a three-dimensional network of proteins that encases and supports cells within a tissue and promotes physiological and pathological cellular differentiation and functionality. Understanding the complex composition of the ECM is essential to decrypt physiological processes as well as pathogenesis. In this context, the method of decellularization is a useful technique to eliminate cellular components from tissues while preserving the majority of the structural and functional integrity of the ECM. RESULTS In this study, we employed a bottom-up proteomic approach to elucidate the intricate network of proteins in the decellularized extracellular matrices of murine liver and kidney tissues. This approach involved the use of a novel, perfusion-based decellularization protocol to generate acellular whole organ scaffolds. Proteomic analysis of decellularized mice liver and kidney ECM scaffolds revealed tissue-specific differences in matrisome composition, while we found a predominantly stable composition of the core matrisome, consisting of collagens, glycoproteins, and proteoglycans. Liver matrisome analysis revealed unique proteins such as collagen type VI alpha-6, fibrillin-2 or biglycan. In the kidney, specific ECM-regulators such as cathepsin z were detected. CONCLUSION The identification of distinct proteomic signatures provides insights into how different matrisome compositions might influence the biological properties of distinct tissues. This experimental workflow will help to further elucidate the proteomic landscape of decellularized extracellular matrix scaffolds of mice in order to decipher complex cell-matrix interactions and their contribution to a tissue-specific microenvironment.
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Affiliation(s)
- Anna-Maria Diedrich
- Department of General, Visceral, and Transplant Surgery, University Hospital Muenster, 48149, Muenster, Germany
| | - Assal Daneshgar
- Department of Surgery, Charité Mitte | Campus Virchow-Klinikum, Charité -Universitaetsmedizin Berlin, Campus, 13353, Berlin, Germany
- Berlin Institute of Health at Charité - Universitaetsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Charitéplatz 1, 10117, Berlin, Germany
| | - Peter Tang
- Department of Surgery, Charité Mitte | Campus Virchow-Klinikum, Charité -Universitaetsmedizin Berlin, Campus, 13353, Berlin, Germany
| | - Oliver Klein
- Berlin Institute of Health at Charité - Universitaetsmedizin Berlin, Core Facility Imaging Mass Spectrometry, 13353, Berlin, Germany
| | - Annika Mohr
- Department of General, Visceral, and Transplant Surgery, University Hospital Muenster, 48149, Muenster, Germany
| | - Olachi A Onwuegbuchulam
- Department of General, Visceral, and Transplant Surgery, University Hospital Muenster, 48149, Muenster, Germany
| | - Sabine von Rueden
- Department of General, Visceral, and Transplant Surgery, University Hospital Muenster, 48149, Muenster, Germany
| | - Kerstin Menck
- Department of Medicine A for Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Muenster, 48149, Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149, Muenster, Germany
| | - Annalen Bleckmann
- Department of Medicine A for Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Muenster, 48149, Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149, Muenster, Germany
| | - Mazen A Juratli
- Department of General, Visceral, and Transplant Surgery, University Hospital Muenster, 48149, Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149, Muenster, Germany
| | - Felix Becker
- Department of General, Visceral, and Transplant Surgery, University Hospital Muenster, 48149, Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149, Muenster, Germany
| | - Igor M Sauer
- Department of Surgery, Charité Mitte | Campus Virchow-Klinikum, Charité -Universitaetsmedizin Berlin, Campus, 13353, Berlin, Germany
| | - Karl H Hillebrandt
- Department of Surgery, Charité Mitte | Campus Virchow-Klinikum, Charité -Universitaetsmedizin Berlin, Campus, 13353, Berlin, Germany
- Berlin Institute of Health at Charité - Universitaetsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Charitéplatz 1, 10117, Berlin, Germany
| | - Andreas Pascher
- Department of General, Visceral, and Transplant Surgery, University Hospital Muenster, 48149, Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149, Muenster, Germany
| | - Benjamin Struecker
- Department of General, Visceral, and Transplant Surgery, University Hospital Muenster, 48149, Muenster, Germany.
- West German Cancer Center, University Hospital Muenster, 48149, Muenster, Germany.
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Bingham GC, Muehling LM, Li C, Huang Y, Ma SF, Abebayehu D, Noth I, Sun J, Woodfolk JA, Barker TH, Bonham CA. High-dimensional comparison of monocytes and T cells in post-COVID and idiopathic pulmonary fibrosis. Front Immunol 2024; 14:1308594. [PMID: 38292490 PMCID: PMC10824838 DOI: 10.3389/fimmu.2023.1308594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/19/2023] [Indexed: 02/01/2024] Open
Abstract
Introduction Up to 30% of hospitalized COVID-19 patients experience persistent sequelae, including pulmonary fibrosis (PF). Methods We examined COVID-19 survivors with impaired lung function and imaging worrisome for developing PF and found within six months, symptoms, restriction and PF improved in some (Early-Resolving COVID-PF), but persisted in others (Late-Resolving COVID-PF). To evaluate immune mechanisms associated with recovery versus persistent PF, we performed single-cell RNA-sequencing and multiplex immunostaining on peripheral blood mononuclear cells from patients with Early- and Late-Resolving COVID-PF and compared them to age-matched controls without respiratory disease. Results and discussion Our analysis showed circulating monocytes were significantly reduced in Late-Resolving COVID-PF patients compared to Early-Resolving COVID-PF and non-diseased controls. Monocyte abundance correlated with pulmonary function forced vital capacity and diffusion capacity. Differential expression analysis revealed MHC-II class molecules were upregulated on the CD8 T cells of Late-Resolving COVID-PF patients but downregulated in monocytes. To determine whether these immune signatures resembled other interstitial lung diseases, we analyzed samples from Idiopathic Pulmonary Fibrosis (IPF) patients. IPF patients had a similar marked decrease in monocyte HLA-DR protein expression compared to Late-Resolving COVID-PF patients. Our findings indicate decreased circulating monocytes are associated with decreased lung function and uniquely distinguish Late-Resolving COVID-PF from Early-Resolving COVID-PF, IPF, and non-diseased controls.
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Affiliation(s)
- Grace C. Bingham
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, United States
| | - Lyndsey M. Muehling
- Division of Asthma, Allergy and Immunology, Department of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Chaofan Li
- Carter Immunology Center, University of Virginia, Charlottesville, VA, United States
- Division of Infectious Disease and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Yong Huang
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, VA, United States
| | - Shwu-Fan Ma
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, VA, United States
| | - Daniel Abebayehu
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, United States
| | - Imre Noth
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, VA, United States
| | - Jie Sun
- Carter Immunology Center, University of Virginia, Charlottesville, VA, United States
- Division of Infectious Disease and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, United States
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN, United States
| | - Judith A. Woodfolk
- Division of Asthma, Allergy and Immunology, Department of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Thomas H. Barker
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, United States
| | - Catherine A. Bonham
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, VA, United States
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10
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Chen D, Rehfeld JF, Watts AG, Rorsman P, Gundlach AL. History of key regulatory peptide systems and perspectives for future research. J Neuroendocrinol 2023; 35:e13251. [PMID: 37053148 DOI: 10.1111/jne.13251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/10/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023]
Abstract
Throughout the 20th Century, regulatory peptide discovery advanced from the identification of gut hormones to the extraction and characterization of hypothalamic hypophysiotropic factors, and to the isolation and cloning of multiple brain neuropeptides. These discoveries were followed by the discovery of G-protein-coupled and other membrane receptors for these peptides. Subsequently, the systems physiology associated with some of these multiple regulatory peptides and receptors has been comprehensively elucidated and has led to improved therapeutics and diagnostics and their approval by the US Food and Drug Administration. In light of this wealth of information and further potential, it is truly a time of renaissance for regulatory peptides. In this perspective, we review what we have learned from the pioneers in exemplified fields of gut peptides, such as cholecystokinin, enterochromaffin-like-cell peptides, and glucagon, from the trailblazing studies on the key stress hormone, corticotropin-releasing factor, as well as from more recently characterized relaxin-family peptides and receptors. The historical viewpoints are based on our understanding of these topics in light of the earliest phases of research and on subsequent studies and the evolution of knowledge, aiming to sharpen our vision of the current state-of-the-art and those studies that should be prioritized in the future.
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Affiliation(s)
- Duan Chen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Jens F Rehfeld
- Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Alan G Watts
- Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California, USA
| | - Patrik Rorsman
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew L Gundlach
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Melbourne, VIC, Australia
- Florey Department of Neuroscience and Mental Health and Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
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11
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Lu H, Zhang H, Li L. Chemical tagging mass spectrometry: an approach for single-cell omics. Anal Bioanal Chem 2023; 415:6901-6913. [PMID: 37466681 PMCID: PMC10729908 DOI: 10.1007/s00216-023-04850-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
Single-cell (SC) analysis offers new insights into the study of fundamental biological phenomena and cellular heterogeneity. The superior sensitivity, high throughput, and rich chemical information provided by mass spectrometry (MS) allow MS to emerge as a leading technology for molecular profiling of SC omics, including the SC metabolome, lipidome, and proteome. However, issues such as ionization suppression, low concentration, and huge span of dynamic concentrations of SC components lead to poor MS response for certain types of molecules. It is noted that chemical tagging/derivatization has been adopted in SCMS analysis, and this strategy has been proven an effective solution to circumvent these issues in SCMS analysis. Herein, we review the basic principle and general strategies of chemical tagging/derivatization in SCMS analysis, along with recent applications of chemical derivatization to single-cell metabolomics and multiplexed proteomics, as well as SCMS imaging. Furthermore, the challenges and opportunities for the improvement of chemical derivatization strategies in SCMS analysis are discussed.
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Affiliation(s)
- Haiyan Lu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Hua Zhang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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12
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Dunne J, Griner J, Romeo M, Macdonald J, Krieg C, Lim M, Yagnik G, Rothschild KJ, Drake RR, Mehta AS, Angel PM. Evaluation of antibody-based single cell type imaging techniques coupled to multiplexed imaging of N-glycans and collagen peptides by matrix-assisted laser desorption/ionization mass spectrometry imaging. Anal Bioanal Chem 2023; 415:7011-7024. [PMID: 37843548 PMCID: PMC10632234 DOI: 10.1007/s00216-023-04983-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/07/2023] [Accepted: 09/18/2023] [Indexed: 10/17/2023]
Abstract
The integration of matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) with single cell spatial omics methods allows for a comprehensive investigation of single cell spatial information and matrisomal N-glycan and extracellular matrix protein imaging. Here, the performance of the antibody-directed single cell workflows coupled with MALDI-MSI are evaluated. Miralys™ photocleavable mass-tagged antibody probes (MALDI-IHC, AmberGen, Inc.), GeoMx DSP® (NanoString, Inc.), and Imaging Mass Cytometry (IMC, Standard BioTools Inc.) were used in series with MALDI-MSI of N-glycans and extracellular matrix peptides on formalin-fixed paraffin-embedded tissues. Single cell omics protocols were performed before and after MALDI-MSI. The data suggests that for each modality combination, there is an optimal order for performing both techniques on the same tissue section. An overall conclusion is that MALDI-MSI studies may be completed on the same tissue section as used for antibody-directed single cell modalities. This work increases access to combined cellular and extracellular information within the tissue microenvironment to enhance research on the pathological origins of disease.
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Affiliation(s)
- Jaclyn Dunne
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Avenue BSB 358, Charleston, SC, 29425, USA
| | - Jake Griner
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Avenue BSB 358, Charleston, SC, 29425, USA
| | - Martin Romeo
- Translational Science Laboratory, Hollings Cancer Center, Charleston, SC, 29425, USA
| | - Jade Macdonald
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Avenue BSB 358, Charleston, SC, 29425, USA
| | - Carsten Krieg
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Mark Lim
- AmberGen, Inc, 44 Manning Road, Billerica, MA, 01821, USA
| | - Gargey Yagnik
- AmberGen, Inc, 44 Manning Road, Billerica, MA, 01821, USA
| | - Kenneth J Rothschild
- AmberGen, Inc, 44 Manning Road, Billerica, MA, 01821, USA
- Department of Physics and Photonics Center, Boston University, Boston, MA, 02215, USA
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Avenue BSB 358, Charleston, SC, 29425, USA
| | - Anand S Mehta
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Avenue BSB 358, Charleston, SC, 29425, USA
| | - Peggi M Angel
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Avenue BSB 358, Charleston, SC, 29425, USA.
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13
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Tisi A, Palaniappan S, Maccarrone M. Advanced Omics Techniques for Understanding Cochlear Genome, Epigenome, and Transcriptome in Health and Disease. Biomolecules 2023; 13:1534. [PMID: 37892216 PMCID: PMC10605747 DOI: 10.3390/biom13101534] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Advanced genomics, transcriptomics, and epigenomics techniques are providing unprecedented insights into the understanding of the molecular underpinnings of the central nervous system, including the neuro-sensory cochlea of the inner ear. Here, we report for the first time a comprehensive and updated overview of the most advanced omics techniques for the study of nucleic acids and their applications in cochlear research. We describe the available in vitro and in vivo models for hearing research and the principles of genomics, transcriptomics, and epigenomics, alongside their most advanced technologies (like single-cell omics and spatial omics), which allow for the investigation of the molecular events that occur at a single-cell resolution while retaining the spatial information.
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Affiliation(s)
- Annamaria Tisi
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Sakthimala Palaniappan
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Mauro Maccarrone
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
- Laboratory of Lipid Neurochemistry, European Center for Brain Research (CERC), Santa Lucia Foundation IRCCS, 00143 Rome, Italy
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14
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Wang Q, Zhi Y, Zi M, Mo Y, Wang Y, Liao Q, Zhang S, Gong Z, Wang F, Zeng Z, Guo C, Xiong W. Spatially Resolved Transcriptomics Technology Facilitates Cancer Research. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2302558. [PMID: 37632718 PMCID: PMC10602551 DOI: 10.1002/advs.202302558] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/16/2023] [Indexed: 08/28/2023]
Abstract
Single cell RNA sequencing (scRNA-seq) provides a great convenience for studying tumor occurrence and development for its ability to study gene expression at the individual cell level. However, patient-derived tumor tissues are composed of multiple types of cells including tumor cells and adjacent non-malignant cells such as stromal cells and immune cells. The spatial locations of various cells in situ tissues plays a pivotal role in the occurrence and development of tumors, which cannot be elucidated by scRNA-seq alone. Spatially resolved transcriptomics (SRT) technology emerges timely to explore the unrecognized relationship between the spatial background of a particular cell and its functions, and is increasingly used in cancer research. This review provides a systematic overview of the SRT technologies that are developed, in particular the more widely used cutting-edge SRT technologies based on next-generation sequencing (NGS). In addition, the main achievements by SRT technologies in precisely unveiling the underappreciated spatial locations on gene expression and cell function with unprecedented high-resolution in cancer research are emphasized, with the aim of developing more effective clinical therapeutics oriented to a deeper understanding of the interaction between tumor cells and surrounding non-malignant cells.
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Affiliation(s)
- Qian Wang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer MetabolismHunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaHunan410008P. R. China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
| | - Yuan Zhi
- Department of Oral and Maxillofacial SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaHunan410012P. R. China
| | - Moxin Zi
- Department of Oral and Maxillofacial SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaHunan410012P. R. China
| | - Yongzhen Mo
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
- Department of Otolaryngology Head and Neck SurgeryXiangya HospitalCentral South UniversityChangshaHunan410008P. R. China
| | - Yumin Wang
- Department of Otolaryngology Head and Neck SurgeryXiangya HospitalCentral South UniversityChangshaHunan410008P. R. China
| | - Qianjin Liao
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer MetabolismHunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaHunan410008P. R. China
| | - Shanshan Zhang
- Department of Otolaryngology Head and Neck SurgeryXiangya HospitalCentral South UniversityChangshaHunan410008P. R. China
| | - Zhaojian Gong
- Department of Oral and Maxillofacial SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaHunan410012P. R. China
| | - Fuyan Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer MetabolismHunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaHunan410008P. R. China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
| | - Can Guo
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer MetabolismHunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaHunan410008P. R. China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer MetabolismHunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaHunan410008P. R. China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
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15
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Zhou Y, Jiang X, Wang X, Huang J, Li T, Jin H, He J. Promise of spatially resolved omics for tumor research. J Pharm Anal 2023; 13:851-861. [PMID: 37719191 PMCID: PMC10499658 DOI: 10.1016/j.jpha.2023.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 09/19/2023] Open
Abstract
Tumors are spatially heterogeneous tissues that comprise numerous cell types with intricate structures. By interacting with the microenvironment, tumor cells undergo dynamic changes in gene expression and metabolism, resulting in spatiotemporal variations in their capacity for proliferation and metastasis. In recent years, the rapid development of histological techniques has enabled efficient and high-throughput biomolecule analysis. By preserving location information while obtaining a large number of gene and molecular data, spatially resolved metabolomics (SRM) and spatially resolved transcriptomics (SRT) approaches can offer new ideas and reliable tools for the in-depth study of tumors. This review provides a comprehensive introduction and summary of the fundamental principles and research methods used for SRM and SRT techniques, as well as a review of their applications in cancer-related fields.
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Affiliation(s)
- Yanhe Zhou
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Xinyi Jiang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Xiangyi Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jianpeng Huang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Tong Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Hongtao Jin
- New Drug Safety Evaluation Center, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
- NMPA Key Laboratory for Safety Research and Evaluation of Innovative Drug, Beijing, 10050, China
| | - Jiuming He
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
- NMPA Key Laboratory for Safety Research and Evaluation of Innovative Drug, Beijing, 10050, China
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16
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Fangma Y, Liu M, Liao J, Chen Z, Zheng Y. Dissecting the brain with spatially resolved multi-omics. J Pharm Anal 2023; 13:694-710. [PMID: 37577383 PMCID: PMC10422112 DOI: 10.1016/j.jpha.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 08/15/2023] Open
Abstract
Recent studies have highlighted spatially resolved multi-omics technologies, including spatial genomics, transcriptomics, proteomics, and metabolomics, as powerful tools to decipher the spatial heterogeneity of the brain. Here, we focus on two major approaches in spatial transcriptomics (next-generation sequencing-based technologies and image-based technologies), and mass spectrometry imaging technologies used in spatial proteomics and spatial metabolomics. Furthermore, we discuss their applications in neuroscience, including building the brain atlas, uncovering gene expression patterns of neurons for special behaviors, deciphering the molecular basis of neuronal communication, and providing a more comprehensive explanation of the molecular mechanisms underlying central nervous system disorders. However, further efforts are still needed toward the integrative application of multi-omics technologies, including the real-time spatial multi-omics analysis in living cells, the detailed gene profile in a whole-brain view, and the combination of functional verification.
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Affiliation(s)
- Yijia Fangma
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Mengting Liu
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jie Liao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhong Chen
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yanrong Zheng
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
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17
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Naba A. 10 years of extracellular matrix proteomics: Accomplishments, challenges, and future perspectives. Mol Cell Proteomics 2023; 22:100528. [PMID: 36918099 PMCID: PMC10152135 DOI: 10.1016/j.mcpro.2023.100528] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/13/2023] Open
Abstract
The extracellular matrix (ECM) is a complex assembly of hundreds of proteins forming the architectural scaffold of multicellular organisms. In addition to its structural role, the ECM conveys signals orchestrating cellular phenotypes. Alterations of ECM composition, abundance, structure, or mechanics, have been linked to diseases and disorders affecting all physiological systems, including fibrosis and cancer. Deciphering the protein composition of the ECM and how it changes in pathophysiological contexts is thus the first step toward understanding the roles of the ECM in health and disease and toward the development of therapeutic strategies to correct disease-causing ECM alterations. Potentially, the ECM also represents a vast, yet untapped reservoir of disease biomarkers. ECM proteins are characterized by unique biochemical properties that have hindered their study: they are large, heavily and uniquely post-translationally modified, and highly insoluble. Overcoming these challenges, we and others have devised mass-spectrometry-based proteomic approaches to define the ECM composition, or "matrisome", of tissues. This review provides a historical overview of ECM proteomics research and presents the latest advances that now allow the profiling of the ECM of healthy and diseased tissues. The second part highlights recent examples illustrating how ECM proteomics has emerged as a powerful discovery pipeline to identify prognostic cancer biomarkers. The third part discusses remaining challenges limiting our ability to translate findings to clinical application and proposes approaches to overcome them. Last, the review introduces readers to resources available to facilitate the interpretation of ECM proteomics datasets. The ECM was once thought to be impenetrable. MS-based proteomics has proven to be a powerful tool to decode the ECM. In light of the progress made over the past decade, there are reasons to believe that the in-depth exploration of the matrisome is within reach and that we may soon witness the first translational application of ECM proteomics.
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Affiliation(s)
- Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA; University of Illinois Cancer Center, Chicago, IL 60612, USA.
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18
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Pal D, Ghatak S, Singh K, Abouhashem AS, Kumar M, El Masry MS, Mohanty SK, Palakurti R, Rustagi Y, Tabasum S, Khona DK, Khanna S, Kacar S, Srivastava R, Bhasme P, Verma SS, Hernandez E, Sharma A, Reese D, Verma P, Ghosh N, Gorain M, Wan J, Liu S, Liu Y, Castro NH, Gnyawali SC, Lawrence W, Moore J, Perez DG, Roy S, Yoder MC, Sen CK. Identification of a physiologic vasculogenic fibroblast state to achieve tissue repair. Nat Commun 2023; 14:1129. [PMID: 36854749 PMCID: PMC9975176 DOI: 10.1038/s41467-023-36665-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 02/13/2023] [Indexed: 03/02/2023] Open
Abstract
Tissue injury to skin diminishes miR-200b in dermal fibroblasts. Fibroblasts are widely reported to directly reprogram into endothelial-like cells and we hypothesized that miR-200b inhibition may cause such changes. We transfected human dermal fibroblasts with anti-miR-200b oligonucleotide, then using single cell RNA sequencing, identified emergence of a vasculogenic subset with a distinct fibroblast transcriptome and demonstrated blood vessel forming function in vivo. Anti-miR-200b delivery to murine injury sites likewise enhanced tissue perfusion, wound closure, and vasculogenic fibroblast contribution to perfused vessels in a FLI1 dependent manner. Vasculogenic fibroblast subset emergence was blunted in delayed healing wounds of diabetic animals but, topical tissue nanotransfection of a single anti-miR-200b oligonucleotide was sufficient to restore FLI1 expression, vasculogenic fibroblast emergence, tissue perfusion, and wound healing. Augmenting a physiologic tissue injury adaptive response mechanism that produces a vasculogenic fibroblast state change opens new avenues for therapeutic tissue vascularization of ischemic wounds.
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Affiliation(s)
- Durba Pal
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, 140001, India
| | - Subhadip Ghatak
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Kanhaiya Singh
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Ahmed Safwat Abouhashem
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Manishekhar Kumar
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Mohamed S El Masry
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Sujit K Mohanty
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Ravichand Palakurti
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Yashika Rustagi
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Saba Tabasum
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Dolly K Khona
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Savita Khanna
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Sedat Kacar
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Rajneesh Srivastava
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Pramod Bhasme
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Sumit S Verma
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Edward Hernandez
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Anu Sharma
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Diamond Reese
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Priyanka Verma
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Nandini Ghosh
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Mahadeo Gorain
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Jun Wan
- Center for Computational Biology and Bioinformatics (CCBB), Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Sheng Liu
- Center for Computational Biology and Bioinformatics (CCBB), Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Yunlong Liu
- Center for Computational Biology and Bioinformatics (CCBB), Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Natalia Higuita Castro
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Surya C Gnyawali
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - William Lawrence
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Jordan Moore
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Daniel Gallego Perez
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Sashwati Roy
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Mervin C Yoder
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Chandan K Sen
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA.
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH, 43210, USA.
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19
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Patkulkar P, Subbalakshmi AR, Jolly MK, Sinharay S. Mapping Spatiotemporal Heterogeneity in Tumor Profiles by Integrating High-Throughput Imaging and Omics Analysis. ACS OMEGA 2023; 8:6126-6138. [PMID: 36844580 PMCID: PMC9948167 DOI: 10.1021/acsomega.2c06659] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/05/2023] [Indexed: 05/14/2023]
Abstract
Intratumoral heterogeneity associates with more aggressive disease progression and worse patient outcomes. Understanding the reasons enabling the emergence of such heterogeneity remains incomplete, which restricts our ability to manage it from a therapeutic perspective. Technological advancements such as high-throughput molecular imaging, single-cell omics, and spatial transcriptomics allow recording of patterns of spatiotemporal heterogeneity in a longitudinal manner, thus offering insights into the multiscale dynamics of its evolution. Here, we review the latest technological trends and biological insights from molecular diagnostics as well as spatial transcriptomics, both of which have witnessed burgeoning growth in the recent past in terms of mapping heterogeneity within tumor cell types as well as the stromal constitution. We also discuss ongoing challenges, indicating possible ways to integrate insights across these methods to have a systems-level spatiotemporal map of heterogeneity in each tumor and a more systematic investigation of the implications of heterogeneity for patient outcomes.
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20
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Zhang Z, Bao C, Jiang L, Wang S, Wang K, Lu C, Fang H. When cancer drug resistance meets metabolomics (bulk, single-cell and/or spatial): Progress, potential, and perspective. Front Oncol 2023; 12:1054233. [PMID: 36686803 PMCID: PMC9854130 DOI: 10.3389/fonc.2022.1054233] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/20/2022] [Indexed: 01/07/2023] Open
Abstract
Resistance to drug treatment is a critical barrier in cancer therapy. There is an unmet need to explore cancer hallmarks that can be targeted to overcome this resistance for therapeutic gain. Over time, metabolic reprogramming has been recognised as one hallmark that can be used to prevent therapeutic resistance. With the advent of metabolomics, targeting metabolic alterations in cancer cells and host patients represents an emerging therapeutic strategy for overcoming cancer drug resistance. Driven by technological and methodological advances in mass spectrometry imaging, spatial metabolomics involves the profiling of all the metabolites (metabolomics) so that the spatial information is captured bona fide within the sample. Spatial metabolomics offers an opportunity to demonstrate the drug-resistant tumor profile with metabolic heterogeneity, and also poses a data-mining challenge to reveal meaningful insights from high-dimensional spatial information. In this review, we discuss the latest progress, with the focus on currently available bulk, single-cell and spatial metabolomics technologies and their successful applications in pre-clinical and translational studies on cancer drug resistance. We provide a summary of metabolic mechanisms underlying cancer drug resistance from different aspects; these include the Warburg effect, altered amino acid/lipid/drug metabolism, generation of drug-resistant cancer stem cells, and immunosuppressive metabolism. Furthermore, we propose solutions describing how to overcome cancer drug resistance; these include early detection during cancer initiation, monitoring of clinical drug response, novel anticancer drug and target metabolism, immunotherapy, and the emergence of spatial metabolomics. We conclude by describing the perspectives on how spatial omics approaches (integrating spatial metabolomics) could be further developed to improve the management of drug resistance in cancer patients.
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Affiliation(s)
- Zhiqiang Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chaohui Bao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lu Jiang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kankan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chang Lu
- MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,*Correspondence: Hai Fang,
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21
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Schuster R, Younesi F, Ezzo M, Hinz B. The Role of Myofibroblasts in Physiological and Pathological Tissue Repair. Cold Spring Harb Perspect Biol 2023; 15:cshperspect.a041231. [PMID: 36123034 PMCID: PMC9808581 DOI: 10.1101/cshperspect.a041231] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Myofibroblasts are the construction workers of wound healing and repair damaged tissues by producing and organizing collagen/extracellular matrix (ECM) into scar tissue. Scar tissue effectively and quickly restores the mechanical integrity of lost tissue architecture but comes at the price of lost tissue functionality. Fibrotic diseases caused by excessive or persistent myofibroblast activity can lead to organ failure. This review defines myofibroblast terminology, phenotypic characteristics, and functions. We will focus on the central role of the cell, ECM, and tissue mechanics in regulating tissue repair by controlling myofibroblast action. Additionally, we will discuss how therapies based on mechanical intervention potentially ameliorate wound healing outcomes. Although myofibroblast physiology and pathology affect all organs, we will emphasize cutaneous wound healing and hypertrophic scarring as paradigms for normal tissue repair versus fibrosis. A central message of this review is that myofibroblasts can be activated from multiple cell sources, varying with local environment and type of injury, to either restore tissue integrity and organ function or create an inappropriate mechanical environment.
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Affiliation(s)
- Ronen Schuster
- Faculty of Dentistry, University of Toronto, Toronto, M5S 3E2 Ontario, Canada
| | - Fereshteh Younesi
- Faculty of Dentistry, University of Toronto, Toronto, M5S 3E2 Ontario, Canada.,Laboratory of Tissue Repair and Regeneration, Keenan Research Centre for Biomedical Science of the St. Michael's Hospital, Toronto, Ontario M5B 1T8, Canada
| | - Maya Ezzo
- Faculty of Dentistry, University of Toronto, Toronto, M5S 3E2 Ontario, Canada.,Laboratory of Tissue Repair and Regeneration, Keenan Research Centre for Biomedical Science of the St. Michael's Hospital, Toronto, Ontario M5B 1T8, Canada
| | - Boris Hinz
- Faculty of Dentistry, University of Toronto, Toronto, M5S 3E2 Ontario, Canada.,Laboratory of Tissue Repair and Regeneration, Keenan Research Centre for Biomedical Science of the St. Michael's Hospital, Toronto, Ontario M5B 1T8, Canada
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22
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Long X, Yuan X, Du J. Single-cell and spatial transcriptomics: Advances in heart development and disease applications. Comput Struct Biotechnol J 2023; 21:2717-2731. [PMID: 37181659 PMCID: PMC10173363 DOI: 10.1016/j.csbj.2023.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/11/2023] [Accepted: 04/11/2023] [Indexed: 05/16/2023] Open
Abstract
Current transcriptomics technologies, including bulk RNA-seq, single-cell RNA sequencing (scRNA-seq), single-nucleus RNA-sequencing (snRNA-seq), and spatial transcriptomics (ST), provide novel insights into the spatial and temporal dynamics of gene expression during cardiac development and disease processes. Cardiac development is a highly sophisticated process involving the regulation of numerous key genes and signaling pathways at specific anatomical sites and developmental stages. Exploring the cell biological mechanisms involved in cardiogenesis also contributes to congenital heart disease research. Meanwhile, the severity of distinct heart diseases, such as coronary heart disease, valvular disease, cardiomyopathy, and heart failure, is associated with cellular transcriptional heterogeneity and phenotypic alteration. Integrating transcriptomic technologies in the clinical diagnosis and treatment of heart diseases will aid in advancing precision medicine. In this review, we summarize applications of scRNA-seq and ST in the cardiac field, including organogenesis and clinical diseases, and provide insights into the promise of single-cell and spatial transcriptomics in translational research and precision medicine.
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Affiliation(s)
- Xianglin Long
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Xin Yuan
- Department of Nephrology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
- Correspondence to: Department of Nephrology, The Second Affiliated Hospital of Chongqing Medical University, 74 Lin Jiang Road Chongqing 4000l0, China.
| | - Jianlin Du
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
- Correspondence to: Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, 74 Lin Jiang Road Chongqing 400010, China.
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23
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Essential Role of Multi-Omics Approaches in the Study of Retinal Vascular Diseases. Cells 2022; 12:cells12010103. [PMID: 36611897 PMCID: PMC9818611 DOI: 10.3390/cells12010103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
Retinal vascular disease is a highly prevalent vision-threatening ocular disease in the global population; however, its exact mechanism remains unclear. The expansion of omics technologies has revolutionized a new medical research methodology that combines multiple omics data derived from the same patients to generate multi-dimensional and multi-evidence-supported holistic inferences, providing unprecedented opportunities to elucidate the information flow of complex multi-factorial diseases. In this review, we summarize the applications of multi-omics technology to further elucidate the pathogenesis and complex molecular mechanisms underlying retinal vascular diseases. Moreover, we proposed multi-omics-based biomarker and therapeutic strategy discovery methodologies to optimize clinical and basic medicinal research approaches to retinal vascular diseases. Finally, the opportunities, current challenges, and future prospects of multi-omics analyses in retinal vascular disease studies are discussed in detail.
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24
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Denti V, Capitoli G, Piga I, Clerici F, Pagani L, Criscuolo L, Bindi G, Principi L, Chinello C, Paglia G, Magni F, Smith A. Spatial Multiomics of Lipids, N-Glycans, and Tryptic Peptides on a Single FFPE Tissue Section. J Proteome Res 2022; 21:2798-2809. [PMID: 36259755 PMCID: PMC9639202 DOI: 10.1021/acs.jproteome.2c00601] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Mass spectrometry
imaging (MSI) is an emerging technology
that
is capable of mapping various biomolecules within their native spatial
context, and performing spatial multiomics on formalin-fixed paraffin-embedded
(FFPE) tissues may further increase the molecular characterization
of pathological states. Here we present a novel workflow which enables
the sequential MSI of lipids, N-glycans, and tryptic peptides on a
single FFPE tissue section and highlight the enhanced molecular characterization
that is offered by combining the multiple spatial omics data sets.
In murine brain and clear cell renal cell carcinoma (ccRCC) tissue,
the three molecular levels provided complementary information and
characterized different histological regions. Moreover, when the spatial
omics data was integrated, the different histopathological regions
of the ccRCC tissue could be better discriminated with respect to
the imaging data set of any single omics class. Taken together, these
promising findings demonstrate the capability to more comprehensively
map the molecular complexity within pathological tissue.
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Affiliation(s)
- Vanna Denti
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Giulia Capitoli
- Bicocca Bioinformatics Biostatistics and Bioimaging B4 Center, School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Isabella Piga
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Francesca Clerici
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Lisa Pagani
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Lucrezia Criscuolo
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Greta Bindi
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Lucrezia Principi
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Clizia Chinello
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Giuseppe Paglia
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Fulvio Magni
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Andrew Smith
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
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25
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Misra P, Jadhav AR, Bapat SA. Single-cell sequencing: A cutting edge tool in molecular medical research. Med J Armed Forces India 2022; 78:S7-S13. [PMID: 36147383 PMCID: PMC9485843 DOI: 10.1016/j.mjafi.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/18/2022] [Indexed: 10/15/2022] Open
Abstract
The rapid development of advanced high throughput technologies and introduction of high resolution "omics" data through analysis of biological molecules has revamped medical research. Single-cell sequencing in recent years, is in fact revolutionising the field by providing a deeper, spatio-temporal analyses of individual cells within tissues and their relevance to disease. Like conventional sequencing, the single-cell approach deciphers the sequence of nucleotides in a given Deoxyribose Nucleic Acid (DNA), Ribose Nucleic Acid (RNA), Micro Ribose Nucleic Acid (miRNA), epigenetically modified DNA or chromatin DNA; however, the unit of analyses is changed to single cells rather than the entire tissue. Further, a large number of single cells analysed from a single tissue generate a unique holistic perception capturing all kinds of perturbations across different cells in the tissue that increases the precision of data. Inherently, execution of the technique generates a large amount of data, which is required to be processed in a specific manner followed by customised bioinformatic analysis to produce meaningful results. The most crucial role of single-cell sequencing technique is in elucidating the inter-cell genetic, epigenetic, transcriptomic and proteomic heterogeneity in health and disease. The current review presents a brief overview of this cutting-edge technology and its applications in medical research.
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Affiliation(s)
- Pratibha Misra
- Senior Advisor (Pathology & Biochemistry), 151 Base Hospital, Guwahati, India
| | - Amruta R. Jadhav
- Senior Research Fellow, National Centre for Cell Science (NCCS), Pune, India
| | - Sharmila A. Bapat
- Professor & Head, Ovarian Cancer Program, National Centre for Cell Science, (NCCS), Pune, India
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26
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Vishnoi M, Upadhyay R, Cho WC. Editorial: The role of the extracellular matrix in tumor progression and therapeutic resistance. Front Mol Biosci 2022; 9:994506. [PMID: 36120554 PMCID: PMC9472207 DOI: 10.3389/fmolb.2022.994506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/05/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Monika Vishnoi
- Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, United States
- *Correspondence: Monika Vishnoi,
| | - Rohit Upadhyay
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - William C. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong SAR, China
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27
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Liu Y, Xu P. Quantitative and analytical tools to analyze the spatiotemporal population dynamics of microbial consortia. Curr Opin Biotechnol 2022; 76:102754. [PMID: 35809433 DOI: 10.1016/j.copbio.2022.102754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 12/27/2022]
Abstract
Microorganisms occupy almost every niche on earth. They play critical roles in maintaining ecological balance, atmospheric C/N cycle, and human health. Microbes live in consortia with metabolite exchange or signal communication. Quantitative and analytical tools are becoming increasingly important to study microbial consortia dynamics. We argue that a combined reductionist and holistic approach will be important to understanding the assembly rules and spatiotemporal population dynamics of the microbial community (MICOM). Reductionism allows us to reconstruct complex MICOM from isolated or simple synthetic consortia. Holism allows us to understand microbes as a community with cooperation and competition. Here we review the recent development of quantitative and analytical tools to uncover the underlying principles in microbial communities that govern their spatiotemporal change and interaction dynamics. Mathematical models and analytical tools will continue to provide essential knowledge and expand our capability to manipulate and control microbial consortia.
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Affiliation(s)
- Yugeng Liu
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology, Shantou, Guangdong 515063, China
| | - Peng Xu
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology, Shantou, Guangdong 515063, China; Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion-Israel Institute of Technology, Shantou, Guangdong 515063, China.
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28
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Burnum-Johnson KE, Conrads TP, Drake RR, Herr AE, Iyengar R, Kelly RT, Lundberg E, MacCoss MJ, Naba A, Nolan GP, Pevzner PA, Rodland KD, Sechi S, Slavov N, Spraggins JM, Van Eyk JE, Vidal M, Vogel C, Walt DR, Kelleher NL. New Views of Old Proteins: Clarifying the Enigmatic Proteome. Mol Cell Proteomics 2022; 21:100254. [PMID: 35654359 PMCID: PMC9256833 DOI: 10.1016/j.mcpro.2022.100254] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/09/2022] [Accepted: 05/27/2022] [Indexed: 11/23/2022] Open
Abstract
All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide a >10 years of projection for technologies to meet the challenges that protein biology presents. With a broad perspective, we discuss grand opportunities to transition the science of proteomics into a more propulsive enterprise. Extrapolating recent trends, we describe a next generation of approaches to define, quantify, and visualize the multiple dimensions of the proteome, thereby transforming our understanding and interactions with human disease in the coming decade.
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Affiliation(s)
- Kristin E Burnum-Johnson
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA.
| | - Thomas P Conrads
- Inova Women's Service Line, Inova Health System, Falls Church, Virginia, USA
| | - Richard R Drake
- Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Amy E Herr
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Ravi Iyengar
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Emma Lundberg
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California at San Diego, San Diego, California, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Salvatore Sechi
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Nikolai Slavov
- Department of Bioengineering, Northeastern University, Boston, Massachusetts, USA
| | - Jeffrey M Spraggins
- Department of Cell and Developmental Biology, Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Institute in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Marc Vidal
- Department of Genetics, Harvard University, Cambridge, Massachusetts, USA
| | - Christine Vogel
- New York University Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - David R Walt
- Department of Pathology, Harvard Medical School, Brigham and Women's Hospital, Wyss Institute at Harvard University, Boston, Massachusetts, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA.
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29
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van den Bosch T, Vermeulen L, Miedema DM. Quantitative models for the inference of intratumor heterogeneity. COMPUTATIONAL AND SYSTEMS ONCOLOGY 2022. [DOI: 10.1002/cso2.1034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Tom van den Bosch
- Laboratory for Experimental Oncology and Radiobiology Center for Experimental and Molecular Medicine Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism Amsterdam University Medical Centers Amsterdam The Netherlands
- Oncode Institute Amsterdam The Netherlands
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology Center for Experimental and Molecular Medicine Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism Amsterdam University Medical Centers Amsterdam The Netherlands
- Oncode Institute Amsterdam The Netherlands
| | - Daniël M. Miedema
- Laboratory for Experimental Oncology and Radiobiology Center for Experimental and Molecular Medicine Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism Amsterdam University Medical Centers Amsterdam The Netherlands
- Oncode Institute Amsterdam The Netherlands
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30
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Dong C, Donnarumma F, Murray KK. Infrared Laser Ablation Microsampling for Small Volume Proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1003-1010. [PMID: 35536596 DOI: 10.1021/jasms.2c00063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Infrared (IR) laser ablation was used to remove localized tissue regions from which proteins were extracted and processed with a low volume sample preparation workflow for bottom-up proteomics by liquid chromatography tandem mass spectrometry (LC-MS/MS). A polytetrafluoroethylene (PTFE) coated glass slide with 2 mm diameter microwells was used to capture ablated rat brain tissue for in situ protein digestion with submicroliter solution volumes. The resulting peptides were analyzed with LC-MS/MS for protein identification and label-free quantification. The method was used to identify an average of 600, 1350, and 1900 proteins from ablation areas of 0.01, 0.04, and 0.1 mm2, respectively, from a 50 μm thick rat brain tissue section. Differential proteomics of 0.01 mm2 regions captured from cerebral cortex and corpus callosum was accomplished to demonstrate the capabilities of the approach.
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Affiliation(s)
- Chao Dong
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Kermit K Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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31
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Unravelling Prostate Cancer Heterogeneity Using Spatial Approaches to Lipidomics and Transcriptomics. Cancers (Basel) 2022; 14:cancers14071702. [PMID: 35406474 PMCID: PMC8997139 DOI: 10.3390/cancers14071702] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 03/11/2022] [Accepted: 03/21/2022] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Prostate cancer is a heterogenous disease in terms of disease aggressiveness and therapy response, leading to dilemmas in treatment decisions. This heterogeneity reflects the multifocal nature of prostate cancer and its diversity in cellular and molecular composition, necessitating spatial molecular approaches. Here in view of the emerging importance of rewired lipid metabolism as a source of biomarkers and therapeutic targets for prostate cancer, we highlight recent advancements in technologies that enable the spatial mapping of lipids and related metabolic pathways associated with prostate cancer development and progression. We also evaluate their potential for future implementation in treatment decision-making in the clinical management of prostate cancer. Abstract Due to advances in the detection and management of prostate cancer over the past 20 years, most cases of localised disease are now potentially curable by surgery or radiotherapy, or amenable to active surveillance without treatment. However, this has given rise to a new dilemma for disease management; the inability to distinguish indolent from lethal, aggressive forms of prostate cancer, leading to substantial overtreatment of some patients and delayed intervention for others. Driving this uncertainty is the critical deficit of novel targets for systemic therapy and of validated biomarkers that can inform treatment decision-making and to select and monitor therapy. In part, this lack of progress reflects the inherent challenge of undertaking target and biomarker discovery in clinical prostate tumours, which are cellularly heterogeneous and multifocal, necessitating the use of spatial analytical approaches. In this review, the principles of mass spectrometry-based lipid imaging and complementary gene-based spatial omics technologies, their application to prostate cancer and recent advancements in these technologies are considered. We put in perspective studies that describe spatially-resolved lipid maps and metabolic genes that are associated with prostate tumours compared to benign tissue and increased risk of disease progression, with the aim of evaluating the future implementation of spatial lipidomics and complementary transcriptomics for prognostication, target identification and treatment decision-making for prostate cancer.
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32
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Moretti L, Stalfort J, Barker TH, Abebayehu D. The interplay of fibroblasts, the extracellular matrix, and inflammation in scar formation. J Biol Chem 2022; 298:101530. [PMID: 34953859 PMCID: PMC8784641 DOI: 10.1016/j.jbc.2021.101530] [Citation(s) in RCA: 114] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/08/2021] [Indexed: 02/06/2023] Open
Abstract
Various forms of fibrosis, comprising tissue thickening and scarring, are involved in 40% of deaths across the world. Since the discovery of scarless functional healing in fetuses prior to a certain stage of development, scientists have attempted to replicate scarless wound healing in adults with little success. While the extracellular matrix (ECM), fibroblasts, and inflammatory mediators have been historically investigated as separate branches of biology, it has become increasingly necessary to consider them as parts of a complex and tightly regulated system that becomes dysregulated in fibrosis. With this new paradigm, revisiting fetal scarless wound healing provides a unique opportunity to better understand how this highly regulated system operates mechanistically. In the following review, we navigate the four stages of wound healing (hemostasis, inflammation, repair, and remodeling) against the backdrop of adult versus fetal wound healing, while also exploring the relationships between the ECM, effector cells, and signaling molecules. We conclude by singling out recent findings that offer promising leads to alter the dynamics between the ECM, fibroblasts, and inflammation to promote scarless healing. One factor that promises to be significant is fibroblast heterogeneity and how certain fibroblast subpopulations might be predisposed to scarless healing. Altogether, reconsidering fetal wound healing by examining the interplay of the various factors contributing to fibrosis provides new research directions that will hopefully help us better understand and address fibroproliferative diseases, such as idiopathic pulmonary fibrosis, liver cirrhosis, systemic sclerosis, progressive kidney disease, and cardiovascular fibrosis.
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Affiliation(s)
- Leandro Moretti
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
| | - Jack Stalfort
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
| | - Thomas Harrison Barker
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
| | - Daniel Abebayehu
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA.
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33
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Lavrador P, Gaspar VM, Mano JF. Engineering mammalian living materials towards clinically relevant therapeutics. EBioMedicine 2021; 74:103717. [PMID: 34839265 PMCID: PMC8628209 DOI: 10.1016/j.ebiom.2021.103717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/28/2021] [Accepted: 11/11/2021] [Indexed: 02/07/2023] Open
Abstract
Engineered living materials represent a new generation of human-made biotherapeutics that are highly attractive for a myriad of medical applications. In essence, such cell-rich platforms provide encodable bioactivities with extended lifetimes and environmental multi-adaptability currently unattainable in conventional biomaterial platforms. Emerging cell bioengineering tools are herein discussed from the perspective of materializing living cells as cooperative building blocks that drive the assembly of multiscale living materials. Owing to their living character, pristine cellular units can also be imparted with additional therapeutically-relevant biofunctionalities. On this focus, the most recent advances on the engineering of mammalian living materials and their biomedical applications are herein outlined, alongside with a critical perspective on major roadblocks hindering their realistic clinical translation. All in all, transposing the concept of leveraging living materials as autologous tissue-building entities and/or self-regulated biotherapeutics opens new realms for improving precision and personalized medicine strategies in the foreseeable future.
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Affiliation(s)
- Pedro Lavrador
- Department of Chemistry, CICECO - Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Vítor M Gaspar
- Department of Chemistry, CICECO - Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - João F Mano
- Department of Chemistry, CICECO - Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
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Lawal RO, Richardson LT, Dong C, Donnarumma F, Solouki T, Murray KK. Deep-ultraviolet laser ablation sampling for proteomic analysis of tissue. Anal Chim Acta 2021; 1184:339021. [PMID: 34625253 DOI: 10.1016/j.aca.2021.339021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/29/2021] [Accepted: 08/30/2021] [Indexed: 01/22/2023]
Abstract
Deep-ultraviolet laser ablation with a pulsed 193 nm ArF excimer laser was used to remove localized regions from tissue sections from which proteins were extracted for spatially resolved proteomic analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS). The ability to capture intact proteins by ablation at 193 nm wavelength was verified by matrix-assisted laser desorption ionization (MALDI) of the protein standard bovine serum albumin (BSA), which showed that BSA was ablated and captured without fragmentation. A Bradford assay of the ablated and captured proteins indicated 90% efficiency for transfer of the intact protein at a laser fluence of 3 kJ/m2. Rat brain tissue sections mounted on quartz microscope slides and ablated in transmission mode yielded 2 μg protein per mm2 as quantified by the Bradford assay. Tissue areas ranging from 0.06 mm2 to 1 mm2 were ablated and the ejected material was collected for proteomic analysis. Extracted proteins were digested and the resulting peptides were analyzed by LC-MS/MS. The proteins extracted from the ablated areas were identified and the average number of identified proteins ranged from 85 in the 0.06 mm2 area to 2400 in the 1 mm2 area of a 50 μm thick tissue. In comparison to infrared laser ablation of equivalent sampled areas, both the protein mass and number of proteins identified using DUV laser ablation sampling were approximately four times larger.
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Affiliation(s)
- Remilekun O Lawal
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Luke T Richardson
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
| | - Chao Dong
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
| | - Kermit K Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA.
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Chen Y, Qian W, Lin L, Cai L, Yin K, Jiang S, Song J, Han RPS, Yang C. Mapping Gene Expression in the Spatial Dimension. SMALL METHODS 2021; 5:e2100722. [PMID: 34927963 DOI: 10.1002/smtd.202100722] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/25/2021] [Indexed: 06/14/2023]
Abstract
The main function and biological processes of tissues are determined by the combination of gene expression and spatial organization of their cells. RNA sequencing technologies have primarily interrogated gene expression without preserving the native spatial context of cells. However, the emergence of various spatially-resolved transcriptome analysis methods now makes it possible to map the gene expression to specific coordinates within tissues, enabling transcriptional heterogeneity between different regions, and for the localization of specific transcripts and novel spatial markers to be revealed. Hence, spatially-resolved transcriptome analysis technologies have broad utility in research into human disease and developmental biology. Here, recent advances in spatially-resolved transcriptome analysis methods are summarized, including experimental technologies and computational methods. Strengths, challenges, and potential applications of those methods are highlighted, and perspectives in this field are provided.
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Affiliation(s)
- Yingwen Chen
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Weizhou Qian
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Li Lin
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Linfeng Cai
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Kun Yin
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Shaowei Jiang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Jia Song
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Ray P S Han
- Jiangxi University of Traditional Chinese Medicine, Nanchang, Jiangxi, 33004, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
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Petukhov V, Xu RJ, Soldatov RA, Cadinu P, Khodosevich K, Moffitt JR, Kharchenko PV. Cell segmentation in imaging-based spatial transcriptomics. Nat Biotechnol 2021; 40:345-354. [PMID: 34650268 DOI: 10.1038/s41587-021-01044-w] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 08/04/2021] [Indexed: 12/14/2022]
Abstract
Single-molecule spatial transcriptomics protocols based on in situ sequencing or multiplexed RNA fluorescent hybridization can reveal detailed tissue organization. However, distinguishing the boundaries of individual cells in such data is challenging and can hamper downstream analysis. Current methods generally approximate cells positions using nuclei stains. We describe a segmentation method, Baysor, that optimizes two-dimensional (2D) or three-dimensional (3D) cell boundaries considering joint likelihood of transcriptional composition and cell morphology. While Baysor can take into account segmentation based on co-stains, it can also perform segmentation based on the detected transcripts alone. To evaluate performance, we extend multiplexed error-robust fluorescence in situ hybridization (MERFISH) to incorporate immunostaining of cell boundaries. Using this and other benchmarks, we show that Baysor segmentation can, in some cases, nearly double the number of cells compared to existing tools while reducing segmentation artifacts. We demonstrate that Baysor performs well on data acquired using five different protocols, making it a useful general tool for analysis of imaging-based spatial transcriptomics.
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Affiliation(s)
- Viktor Petukhov
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rosalind J Xu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Department of Chemistry, Harvard University, Boston, MA, USA
| | - Ruslan A Soldatov
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Paolo Cadinu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Konstantin Khodosevich
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeffrey R Moffitt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA. .,Harvard Stem Cell Institute, Cambridge, MA, USA.
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Tang LJW, Zaseela A, Toh CCM, Adine C, Aydar AO, Iyer NG, Fong ELS. Engineering stromal heterogeneity in cancer. Adv Drug Deliv Rev 2021; 175:113817. [PMID: 34087326 DOI: 10.1016/j.addr.2021.05.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/19/2021] [Accepted: 05/29/2021] [Indexed: 02/09/2023]
Abstract
Based on our exponentially increasing knowledge of stromal heterogeneity from advances in single-cell technologies, the notion that stromal cell types exist as a spectrum of unique subpopulations that have specific functions and spatial distributions in the tumor microenvironment has significant impact on tumor modeling for drug development and personalized drug testing. In this Review, we discuss the importance of incorporating stromal heterogeneity and tumor architecture, and propose an overall approach to guide the reconstruction of stromal heterogeneity in vitro for tumor modeling. These next-generation tumor models may support the development of more precise drugs targeting specific stromal cell subpopulations, as well as enable improved recapitulation of patient tumors in vitro for personalized drug testing.
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Affiliation(s)
- Leon Jia Wei Tang
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Ayshath Zaseela
- Department of Biomedical Engineering, National University of Singapore, Singapore
| | | | - Christabella Adine
- Department of Biomedical Engineering, National University of Singapore, Singapore; The N.1 Institute for Health, National University of Singapore, Singapore
| | - Abdullah Omer Aydar
- Department of Biomedical Engineering, National University of Singapore, Singapore
| | - N Gopalakrishna Iyer
- National Cancer Centre Singapore, Singapore; Duke-NUS Medical School, Singapore.
| | - Eliza Li Shan Fong
- Department of Biomedical Engineering, National University of Singapore, Singapore; The N.1 Institute for Health, National University of Singapore, Singapore.
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38
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Hannan RT, Miller AE, Hung RC, Sano C, Peirce SM, Barker TH. Extracellular matrix remodeling associated with bleomycin-induced lung injury supports pericyte-to-myofibroblast transition. Matrix Biol Plus 2021; 10:100056. [PMID: 34195593 PMCID: PMC8233458 DOI: 10.1016/j.mbplus.2020.100056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/11/2022] Open
Abstract
Of the many origins of pulmonary myofibroblasts, microvascular pericytes are a known source. Prior literature has established the ability of pericytes to transition into myofibroblasts, but provide limited insight into molecular cues that drive this process during lung injury repair and fibrosis. Fibronectin and RGD-binding integrins have long been considered pro-fibrotic factors in myofibroblast biology, and here we test the hypothesis that these known myofibroblast cues coordinate pericyte-to-myofibroblast transitions. Specifically, we hypothesized that αvβ3 integrin engagement on fibronectin induces pericyte transition into myofibroblastic phenotypes in the murine bleomycin lung injury model. Myosin Heavy Chain 11 (Myh11)-CreERT2 lineage tracing in transgenic mice allows identification of cells of pericyte origin and provides a robust tool for isolating pericytes from tissues for further evaluation. We used this murine model to track and characterize pericyte behaviors during tissue repair. The majority of Myh11 lineage-positive cells are positive for the pericyte surface markers, PDGFRβ (55%) and CD146 (69%), and display typical pericyte morphology with spatial apposition to microvascular networks. After intratracheal bleomycin treatment of mice, Myh11 lineage-positive cells showed significantly increased contractile and secretory markers, as well as αv integrin expression. According to RNASeq measurements, many disease and tissue-remodeling genesets were upregulated in Myh11 lineage-positive cells in response to bleomycin-induced lung injury. In vitro, blocking αvβ3 binding through cycloRGDfK prevented expression of the myofibroblastic marker αSMA relative to controls. In response to RGD-containing provisional matrix proteins present in lung injury, pericytes may alter their integrin profile.
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Affiliation(s)
- Riley T. Hannan
- Department of Pathology, University of Virginia, 415 Lane Road, Charlottesville, VA, United States
| | - Andrew E. Miller
- Department of Biomedical Engineering, University of Virginia, 415 Lane Road, Charlottesville, VA, United States
| | - Ruei-Chun Hung
- Department of Biomedical Engineering, University of Virginia, 415 Lane Road, Charlottesville, VA, United States
| | - Catherine Sano
- Department of Chemical Engineering, University of Virginia, 102 Engineer's Way, Charlottesville, VA, United States
| | - Shayn M. Peirce
- Department of Biomedical Engineering, University of Virginia, 415 Lane Road, Charlottesville, VA, United States
| | - Thomas H. Barker
- Department of Biomedical Engineering, University of Virginia, 415 Lane Road, Charlottesville, VA, United States
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39
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Neill T, Kapoor A, Xie C, Buraschi S, Iozzo RV. A functional outside-in signaling network of proteoglycans and matrix molecules regulating autophagy. Matrix Biol 2021; 100-101:118-149. [PMID: 33838253 PMCID: PMC8355044 DOI: 10.1016/j.matbio.2021.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 02/07/2023]
Abstract
Proteoglycans and selected extracellular matrix constituents are emerging as intrinsic and critical regulators of evolutionarily conversed, intracellular catabolic pathways. Often, these secreted molecules evoke sustained autophagy in a variety of cell types, tissues, and model systems. The unique properties of proteoglycans have ushered in a paradigmatic shift to broaden our understanding of matrix-mediated signaling cascades. The dynamic cellular pathway controlling autophagy is now linked to an equally dynamic and fluid signaling network embedded in a complex meshwork of matrix molecules. A rapidly emerging field of research encompasses multiple matrix-derived candidates, representing a menagerie of soluble matrix constituents including decorin, biglycan, endorepellin, endostatin, collagen VI and plasminogen kringle 5. These matrix constituents are pro-autophagic and simultaneously anti-angiogenic. In contrast, perlecan, laminin α2 chain, and lumican have anti-autophagic functions. Mechanistically, each matrix constituent linked to intracellular catabolic events engages a specific cell surface receptor that often converges on a common core of the autophagic machinery including AMPK, Peg3 and Beclin 1. We consider this matrix-evoked autophagy as non-canonical given that it occurs in an allosteric manner and is independent of nutrient availability or prevailing bioenergetics control. We propose that matrix-regulated autophagy is an important outside-in signaling mechanism for proper tissue homeostasis that could be therapeutically leveraged to combat a variety of diseases.
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Affiliation(s)
- Thomas Neill
- Department of Pathology, Anatomy, and Cell Biology, and the Translational Cellular Oncology Program, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA.
| | - Aastha Kapoor
- Department of Pathology, Anatomy, and Cell Biology, and the Translational Cellular Oncology Program, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Christopher Xie
- Department of Pathology, Anatomy, and Cell Biology, and the Translational Cellular Oncology Program, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Simone Buraschi
- Department of Pathology, Anatomy, and Cell Biology, and the Translational Cellular Oncology Program, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Renato V Iozzo
- Department of Pathology, Anatomy, and Cell Biology, and the Translational Cellular Oncology Program, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA.
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Angel PM, Rujchanarong D, Pippin S, Spruill L, Drake R. Mass Spectrometry Imaging of Fibroblasts: Promise and Challenge. Expert Rev Proteomics 2021; 18:423-436. [PMID: 34129411 PMCID: PMC8717608 DOI: 10.1080/14789450.2021.1941893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/09/2021] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Fibroblasts maintain tissue and organ homeostasis through output of extracellular matrix that affects nearby cell signaling within the stroma. Altered fibroblast signaling contributes to many disease states and extracellular matrix secreted by fibroblasts has been used to stratify patient by outcome, recurrence, and therapeutic resistance. Recent advances in imaging mass spectrometry allow access to single cell fibroblasts and their ECM niche within clinically relevant tissue samples. AREAS COVERED We review biological and technical challenges as well as new solutions to proteomic access of fibroblast expression within the complex tissue microenvironment. Review topics cover conventional proteomic methods for single fibroblast analysis and current approaches to accessing single fibroblast proteomes by imaging mass spectrometry approaches. Strategies to target and evaluate the single cell stroma proteome on the basis of cell signaling are presented. EXPERT OPINION The promise of defining proteomic signatures from fibroblasts and their extracellular matrix niches is the discovery of new disease markers and the ability to refine therapeutic treatments. Several imaging mass spectrometry approaches exist to define the fibroblast in the setting of pathological changes from clinically acquired samples. Continued technology advances are needed to access and understand the stromal proteome and apply testing to the clinic.
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Affiliation(s)
- Peggi M. Angel
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston SC USA
| | - Denys Rujchanarong
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston SC USA
| | - Sarah Pippin
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston SC USA
| | - Laura Spruill
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC
| | - Richard Drake
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston SC USA
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Triffitt JT. Orthopaedic tissue engineering and stem cells - an unfulfilled promise. BIOMATERIALS TRANSLATIONAL 2021; 2:89-90. [PMID: 35836964 PMCID: PMC9255783 DOI: 10.12336/biomatertransl.2021.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 12/02/2022]
Affiliation(s)
- James T Triffitt
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
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42
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Modeling of Old Scars: Histopathological, Biochemical and Thermal Analysis of the Scar Tissue Maturation. BIOLOGY 2021; 10:biology10020136. [PMID: 33572335 PMCID: PMC7916157 DOI: 10.3390/biology10020136] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 01/31/2021] [Accepted: 02/04/2021] [Indexed: 12/26/2022]
Abstract
Simple Summary Severe skin scars (i.e., hypertrophic and keloid) induce physical and emotional discomfort and functional disorders such as contractures and body part deformations. Scar’s response to treatment depends on “maturity”, which increases with time but is not merely proportional to it. When “fresh”, scars are relatively more treatable by conservative methods, while the treatment is only partially efficient. In contrast, surgery is a preferred approach for the older scars, but it is associated with a risk of the scar regrowth and worsening after excision if unrecognized immature scar tissue remains in the operated lesion. Therefore, to develop better treatment and diagnostics of scars, understanding of the scar maturation is essential. This requires biologically accurate experimental models of skin scarring. The current models only mimic the early stages of skin scar development. They are useful for testing new scar-preventing approaches while not addressing the problem of the older scars that exist for years. In our study, we demonstrate a new rabbit model of “old” scars and explore what happens to the scar tissue during maturation. We define measurable signs to delineate the scar development stages and discuss how this knowledge can improve scar diagnostics and treatment. Abstract Mature hypertrophic scars (HSs) remain a challenging clinical problem, particularly due to the absence of biologically relevant experimental models as a standard rabbit ear HS model only reflects an early stage of scarring. The current study aims to adapt this animal model for simulation of mature HS by validating the time of the scar stabilization using qualitative and quantitative criteria. The full-thickness skin and perichondrium excision wounds were created on the ventral side of the rabbit ears. The tissue samples were studied on post-operation days (PODs) 30, 60, 90 and 120. The histopathological examination and morphometry were applied in parallel with biochemical analysis of protein and glycosaminoglycans (GAGs) content and amino acid composition. The supramolecular organization of collagen was explored by differential scanning calorimetry. Four stages of the rabbit ear HS maturation were delineated and attributed with the histolomorphometrical and physicochemical parameters of the tissue. The experimental scars formed in 30 days but stabilized structurally and biochemically only on POD 90–120. This evidence-based model can be used for the studies and testing of new treatments of the mature HSs.
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Louie RH, Luciani F. Recent advances in single-cell multimodal analysis to study immune cells. Immunol Cell Biol 2021; 99:157-167. [PMID: 33314406 DOI: 10.1111/imcb.12432] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 12/11/2022]
Abstract
Recent advances in single-cell technologies have enabled the profiling of the genome, epigenome, transcriptome and proteome, along with temporal and spatial information of individual cells. These technologies have provided unique opportunities to understand mechanisms underpinning the immune system, such as characterizations of the molecular cell state, how the cell state evolves along its lineage and the impact of spatial location on cell state. In this review, we discuss how these mechanisms have been studied through recent advances in single-cell multimodal technologies.
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Affiliation(s)
- Raymond Hy Louie
- School of Medical Sciences, The Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Fabio Luciani
- School of Medical Sciences, The Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia
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Wang Z, Kapadia W, Li C, Lin F, Pereira RF, Granja PL, Sarmento B, Cui W. Tissue-specific engineering: 3D bioprinting in regenerative medicine. J Control Release 2021; 329:237-256. [DOI: 10.1016/j.jconrel.2020.11.044] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 12/18/2022]
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Nerurkar SN, Goh D, Cheung CCL, Nga PQY, Lim JCT, Yeong JPS. Transcriptional Spatial Profiling of Cancer Tissues in the Era of Immunotherapy: The Potential and Promise. Cancers (Basel) 2020; 12:E2572. [PMID: 32917035 PMCID: PMC7563386 DOI: 10.3390/cancers12092572] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/05/2020] [Accepted: 09/06/2020] [Indexed: 12/18/2022] Open
Abstract
Intratumoral heterogeneity poses a major challenge to making an accurate diagnosis and establishing personalized treatment strategies for cancer patients. Moreover, this heterogeneity might underlie treatment resistance, disease progression, and cancer relapse. For example, while immunotherapies can confer a high success rate, selective pressures coupled with dynamic evolution within a tumour can drive the emergence of drug-resistant clones that allow tumours to persist in certain patients. To improve immunotherapy efficacy, researchers have used transcriptional spatial profiling techniques to identify and subsequently block the source of tumour heterogeneity. In this review, we describe and assess the different technologies available for such profiling within a cancer tissue. We first outline two well-known approaches, in situ hybridization and digital spatial profiling. Then, we highlight the features of an emerging technology known as Visium Spatial Gene Expression Solution. Visium generates quantitative gene expression data and maps them to the tissue architecture. By retaining spatial information, we are well positioned to identify novel biomarkers and perform computational analyses that might inform on novel combinatorial immunotherapies.
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Affiliation(s)
- Sanjna Nilesh Nerurkar
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore;
| | - Denise Goh
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore 169856, Singapore; (D.G.); (P.Q.Y.N.); (J.C.T.L.)
| | | | - Pei Qi Yvonne Nga
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore 169856, Singapore; (D.G.); (P.Q.Y.N.); (J.C.T.L.)
| | - Jeffrey Chun Tatt Lim
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore 169856, Singapore; (D.G.); (P.Q.Y.N.); (J.C.T.L.)
| | - Joe Poh Sheng Yeong
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore 169856, Singapore; (D.G.); (P.Q.Y.N.); (J.C.T.L.)
- Department of Anatomical Pathology, Singapore General Hospital, Singapore 169856, Singapore
- Singapore Immunology Network (SIgN), Agency of Science, Technology and Research (A*STAR), Singapore 138648, Singapore
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DeLeon-Pennell KY, Barker TH, Lindsey ML. Fibroblasts: The arbiters of extracellular matrix remodeling. Matrix Biol 2020; 91-92:1-7. [PMID: 32504772 PMCID: PMC7434687 DOI: 10.1016/j.matbio.2020.05.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 05/29/2020] [Accepted: 05/29/2020] [Indexed: 12/12/2022]
Abstract
Extracellular matrix (ECM) is the foundation on which all cells and organs converge to orchestrate normal physiological functions. In the setting of pathology, the ECM is modified to incorporate additional roles, with modifications including turnover of existing ECM and deposition of new ECM. The fibroblast is center stage in coordinating both normal tissue homeostasis and response to disease. Understanding how fibroblasts work under normal conditions and are activated in response to injury or stress will provide mechanistic insight that triggers discovery of new therapeutic treatments for a wide range of disease. We highlight here fibroblast roles in the cancer, lung, and heart as example systems where fibroblasts are major contributors to homeostasis and pathology.
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Affiliation(s)
- Kristine Y DeLeon-Pennell
- Division of Cardiology, Department of Medicine, Medical University of South Carolina, and Research Service, Ralph H. Johnson Veterans Affairs Medical Center, Charleston, SC 29425, USA
| | - Thomas H Barker
- Department of Biomedical Engineering, University of Virginia, 415 Lane Road, Charlottesville, VA 22903, USA
| | - Merry L Lindsey
- Department of Cellular and Integrative Physiology, Center for Heart and Vascular Research, University of Nebraska Medical Center, 985850 Nebraska Medical Center, Omaha, NE 68198-5850, USA; and Research Service, Nebraska-Western Iowa Health Care System, Omaha, NE 68105; Research Service, Nebraska-Western Iowa Health Care System, Omaha, NE 68105.
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Cardiac fibroblast activation during myocardial infarction wound healing: Fibroblast polarization after MI. Matrix Biol 2020; 91-92:109-116. [PMID: 32446909 DOI: 10.1016/j.matbio.2020.03.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 12/13/2022]
Abstract
Cardiac wound healing after myocardial infarction (MI) evolves from pro-inflammatory to anti-inflammatory to reparative responses, and the cardiac fibroblast is a central player during the entire transition. The fibroblast mirrors changes seen in the left ventricle infarct by undergoing a continuum of polarization phenotypes that follow pro-inflammatory, anti-inflammatory, and pro-scar producing profiles. The development of each phenotype transition is contingent upon the MI environment into which the fibroblast enters. In this mini-review, we summarize our current knowledge regarding cardiac fibroblast activation during MI and highlight key areas where gaps remain.
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48
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Naba A, Ricard-Blum S. The Extracellular Matrix Goes -Omics: Resources and Tools. EXTRACELLULAR MATRIX OMICS 2020. [DOI: 10.1007/978-3-030-58330-9_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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