1
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Manda V, Pavelka J, Lau E. Proteomics applications in next generation induced pluripotent stem cell models. Expert Rev Proteomics 2024; 21:217-228. [PMID: 38511670 PMCID: PMC11065590 DOI: 10.1080/14789450.2024.2334033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 03/08/2024] [Indexed: 03/22/2024]
Abstract
INTRODUCTION Induced pluripotent stem (iPS) cell technology has transformed biomedical research. New opportunities now exist to create new organoids, microtissues, and body-on-a-chip systems for basic biology investigations and clinical translations. AREAS COVERED We discuss the utility of proteomics for attaining an unbiased view into protein expression changes during iPS cell differentiation, cell maturation, and tissue generation. The ability to discover cell-type specific protein markers during the differentiation and maturation of iPS-derived cells has led to new strategies to improve cell production yield and fidelity. In parallel, proteomic characterization of iPS-derived organoids is helping to realize the goal of bridging in vitro and in vivo systems. EXPERT OPINIONS We discuss some current challenges of proteomics in iPS cell research and future directions, including the integration of proteomic and transcriptomic data for systems-level analysis.
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Affiliation(s)
- Vyshnavi Manda
- Department of Medicine, Division of Cardiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Consortium for Fibrosis Research and Translation, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Jay Pavelka
- Department of Medicine, Division of Cardiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Consortium for Fibrosis Research and Translation, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Edward Lau
- Department of Medicine, Division of Cardiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Consortium for Fibrosis Research and Translation, University of Colorado School of Medicine, Aurora, Colorado, USA
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2
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Fleischer S, Nash TR, Tamargo MA, Lock RI, Venturini G, Morsink M, Li V, Lamberti MJ, Graney PL, Liberman M, Kim Y, Zhuang RZ, Whitehead J, Friedman RA, Soni RK, Seidman JG, Seidman CE, Geraldino-Pardilla L, Winchester R, Vunjak-Novakovic G. An engineered human cardiac tissue model reveals contributions of systemic lupus erythematosus autoantibodies to myocardial injury. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583787. [PMID: 38559188 PMCID: PMC10979865 DOI: 10.1101/2024.03.07.583787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Systemic lupus erythematosus (SLE) is a highly heterogenous autoimmune disease that affects multiple organs, including the heart. The mechanisms by which myocardial injury develops in SLE, however, remain poorly understood. Here we engineered human cardiac tissues and cultured them with IgG fractions containing autoantibodies from SLE patients with and without myocardial involvement. We observed unique binding patterns of IgG from two patient subgroups: (i) patients with severe myocardial inflammation exhibited enhanced binding to apoptotic cells within cardiac tissues subjected to stress, and (ii) patients with systolic dysfunction exhibited enhanced binding to the surfaces of viable cardiomyocytes. Functional assays and RNA sequencing (RNA-seq) revealed that IgGs from patients with systolic dysfunction exerted direct effects on engineered tissues in the absence of immune cells, altering tissue cellular composition, respiration and calcium handling. Autoantibody target characterization by phage immunoprecipitation sequencing (PhIP-seq) confirmed distinctive IgG profiles between patient subgroups. By coupling IgG profiling with cell surface protein analyses, we identified four pathogenic autoantibody candidates that may directly alter the function of cells within the myocardium. Taken together, these observations provide insights into the cellular processes of myocardial injury in SLE that have the potential to improve patient risk stratification and inform the development of novel therapeutic strategies.
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Affiliation(s)
- Sharon Fleischer
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Trevor R Nash
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Manuel A Tamargo
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Roberta I Lock
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | | | - Margaretha Morsink
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Vanessa Li
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Morgan J Lamberti
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Pamela L Graney
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Martin Liberman
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Youngbin Kim
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Richard Z Zhuang
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Jaron Whitehead
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Richard A Friedman
- Biomedical Informatics Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Rajesh K Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Robert Winchester
- Department of Medicine, Columbia University, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Gordana Vunjak-Novakovic
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Department of Medicine, Columbia University, New York, NY, USA
- College of Dental Medicine, Columbia University, New York, NY, USA
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3
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Berg Luecke L, Mesidor R, Littrell J, Carpenter M, Wojtkiewicz M, Gundry RL. Veneer Is a Webtool for Rapid, Standardized, and Transparent Interpretation, Annotation, and Reporting of Mammalian Cell Surface N-Glycocapture Data. J Proteome Res 2024. [PMID: 38412263 DOI: 10.1021/acs.jproteome.3c00800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Currently, no consensus exists regarding criteria required to designate a protein within a proteomic data set as a cell surface protein. Most published proteomic studies rely on varied ontology annotations or computational predictions instead of experimental evidence when attributing protein localization. Consequently, standardized approaches for analyzing and reporting cell surface proteome data sets would increase confidence in localization claims and promote data use by other researchers. Recently, we developed Veneer, a web-based bioinformatic tool that analyzes results from cell surface N-glycocapture workflows─the most popular cell surface proteomics method used to date that generates experimental evidence of subcellular location. Veneer assigns protein localization based on defined experimental and bioinformatic evidence. In this study, we updated the criteria and process for assigning protein localization and added new functionality to Veneer. Results of Veneer analysis of 587 cell surface N-glycocapture data sets from 32 published studies demonstrate the importance of applying defined criteria when analyzing cell surface proteomics data sets and exemplify how Veneer can be used to assess experimental quality and facilitate data extraction for informing future biological studies and annotating public repositories.
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Affiliation(s)
- Linda Berg Luecke
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Roneldine Mesidor
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Jack Littrell
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Morgan Carpenter
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Melinda Wojtkiewicz
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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Dieters-Castator DZ, Manzanillo P, Yang HY, Modak RV, Rardin MJ, Gibson BW. Magnetic Bead-Based Workflow for Sensitive and Streamlined Cell Surface Proteomics. J Proteome Res 2024; 23:618-632. [PMID: 38226771 DOI: 10.1021/acs.jproteome.3c00432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Cell surface proteins represent an important class of molecules for therapeutic targeting and cellular phenotyping. However, their enrichment and detection via mass spectrometry-based proteomics remains challenging due to low abundance, post-translational modifications, hydrophobic regions, and processing requirements. To improve their identification, we optimized a Cell-Surface Capture (CSC) workflow that incorporates magnetic bead-based processing. Using this approach, we evaluated labeling conditions (biotin tags and catalysts), enrichment specificity (streptavidin beads), missed cleavages (lysis buffers), nonenzymatic deamidation (digestion and deglycosylation buffers), and data acquisition methods (DDA, DIA, and TMT). Our findings support the use of alkoxyamine-PEG4-biotin plus 5-methoxy-anthranilic acid, SDS/urea-based lysis buffers, single-pot solid-phased-enhanced sample-preparation (SP3), and streptavidin magnetic beads for maximal surfaceome coverage. Notably, with semiautomated processing, sample handling was simplified and between ∼600 and 900 cell surface N-glycoproteins were identified from only 25-200 μg of HeLa protein. CSC also revealed significant differences between in vitro monolayer cultures and in vivo tumor xenografts of murine CT26 colon adenocarcinoma samples that may aid in target identification for drug development. Overall, the improved efficiency of the magnetic-based CSC workflow identified both previously reported and novel N-glycosites with less material and high reproducibility that should help advance the field of surfaceomics by providing insight in cellular phenotypes not previously documented.
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Affiliation(s)
| | - Paolo Manzanillo
- Inflammation, Amgen Research, South San Francisco, California 94080, United States
| | - Han-Yin Yang
- Discovery Proteomics, Amgen Research, South San Francisco, California 94080, United States
| | - Rucha V Modak
- Inflammation, Amgen Research, South San Francisco, California 94080, United States
| | - Matthew J Rardin
- Discovery Proteomics, Amgen Research, South San Francisco, California 94080, United States
| | - Bradford W Gibson
- Discovery Proteomics, Amgen Research, South San Francisco, California 94080, United States
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5
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Omenn GS, Lane L, Overall CM, Lindskog C, Pineau C, Packer NH, Cristea IM, Weintraub ST, Orchard S, Roehrl MHA, Nice E, Guo T, Van Eyk JE, Liu S, Bandeira N, Aebersold R, Moritz RL, Deutsch EW. The 2023 Report on the Proteome from the HUPO Human Proteome Project. J Proteome Res 2024; 23:532-549. [PMID: 38232391 PMCID: PMC11026053 DOI: 10.1021/acs.jproteome.3c00591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Since 2010, the Human Proteome Project (HPP), the flagship initiative of the Human Proteome Organization (HUPO), has pursued two goals: (1) to credibly identify the protein parts list and (2) to make proteomics an integral part of multiomics studies of human health and disease. The HPP relies on international collaboration, data sharing, standardized reanalysis of MS data sets by PeptideAtlas and MassIVE-KB using HPP Guidelines for quality assurance, integration and curation of MS and non-MS protein data by neXtProt, plus extensive use of antibody profiling carried out by the Human Protein Atlas. According to the neXtProt release 2023-04-18, protein expression has now been credibly detected (PE1) for 18,397 of the 19,778 neXtProt predicted proteins coded in the human genome (93%). Of these PE1 proteins, 17,453 were detected with mass spectrometry (MS) in accordance with HPP Guidelines and 944 by a variety of non-MS methods. The number of neXtProt PE2, PE3, and PE4 missing proteins now stands at 1381. Achieving the unambiguous identification of 93% of predicted proteins encoded from across all chromosomes represents remarkable experimental progress on the Human Proteome parts list. Meanwhile, there are several categories of predicted proteins that have proved resistant to detection regardless of protein-based methods used. Additionally there are some PE1-4 proteins that probably should be reclassified to PE5, specifically 21 LINC entries and ∼30 HERV entries; these are being addressed in the present year. Applying proteomics in a wide array of biological and clinical studies ensures integration with other omics platforms as reported by the Biology and Disease-driven HPP teams and the antibody and pathology resource pillars. Current progress has positioned the HPP to transition to its Grand Challenge Project focused on determining the primary function(s) of every protein itself and in networks and pathways within the context of human health and disease.
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Affiliation(s)
- Gilbert S. Omenn
- University of Michigan, Ann Arbor, Michigan 48109, United States
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and University of Geneva, 1015 Lausanne, Switzerland
| | - Christopher M. Overall
- University of British Columbia, Vancouver, BC V6T 1Z4, Canada, Yonsei University Republic of Korea
| | | | - Charles Pineau
- University Rennes, Inserm U1085, Irset, 35042 Rennes, France
| | | | | | - Susan T. Weintraub
- University of Texas Health Science Center-San Antonio, San Antonio, Texas 78229-3900, United States
| | | | - Michael H. A. Roehrl
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, United States
| | | | - Tiannan Guo
- Westlake Center for Intelligent Proteomics, Westlake Laboratory, Westlake University, Hangzhou 310024, Zhejiang Province, China
| | - Jennifer E. Van Eyk
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, 127 South San Vicente Boulevard, Pavilion, 9th Floor, Los Angeles, CA, 90048, United States
| | - Siqi Liu
- BGI Group, Shenzhen 518083, China
| | - Nuno Bandeira
- University of California, San Diego, La Jolla, CA, 92093, United States
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology in ETH Zurich, 8092 Zurich, Switzerland
- University of Zurich, 8092 Zurich, Switzerland
| | - Robert L. Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Eric W. Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
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6
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Xu X, Yin K, Xu S, Wang Z, Wu R. Mass spectrometry-based methods for investigating the dynamics and organization of the surfaceome: exploring potential clinical implications. Expert Rev Proteomics 2024; 21:99-113. [PMID: 38300624 PMCID: PMC10928381 DOI: 10.1080/14789450.2024.2314148] [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: 11/22/2023] [Accepted: 01/16/2024] [Indexed: 02/02/2024]
Abstract
INTRODUCTION Cell-surface proteins are extremely important for many cellular events, such as regulating cell-cell communication and cell-matrix interactions. Aberrant alterations in surface protein expression, modification (especially glycosylation), and interactions are directly related to human diseases. Systematic investigation of surface proteins advances our understanding of protein functions, cellular activities, and disease mechanisms, which will lead to identifying surface proteins as disease biomarkers and drug targets. AREAS COVERED In this review, we summarize mass spectrometry (MS)-based proteomics methods for global analysis of cell-surface proteins. Then, investigations of the dynamics of surface proteins are discussed. Furthermore, we summarize the studies for the surfaceome interaction networks. Additionally, biological applications of MS-based surfaceome analysis are included, particularly highlighting the significance in biomarker identification, drug development, and immunotherapies. EXPERT OPINION Modern MS-based proteomics provides an opportunity to systematically characterize proteins. However, due to the complexity of cell-surface proteins, the labor-intensive workflow, and the limit of clinical samples, comprehensive characterization of the surfaceome remains extraordinarily challenging, especially in clinical studies. Developing and optimizing surfaceome enrichment methods and utilizing automated sample preparation workflow can expand the applications of surfaceome analysis and deepen our understanding of the functions of cell-surface proteins.
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Affiliation(s)
- Xing Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Kejun Yin
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Senhan Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Zeyu Wang
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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7
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Waknitz M, Berg Luecke L, Mesidor R, Wojtkiewicz M, Castro C, Gundry RL. The GENTIL Method for Isolation of Human Adult Cardiomyocytes from Cryopreserved Tissue for Proteomic Analyses. Methods Mol Biol 2024; 2735:145-167. [PMID: 38038848 DOI: 10.1007/978-1-0716-3527-8_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Heart failure is a serious clinical and economic health care problem, and its clinical progression is linked to pathological cardiac remodeling. Due to the heterogeneity of heart failure, lack of animal models to accurately represent advanced heart failure, and limited access to fresh human cardiac tissue, little is known regarding cell-type-specific mechanisms and context-specific functions of cardiomyocytes during disease development processes. While mass spectrometry has been increasingly applied to unravel changes in the proteome associated with cardiovascular physiology and disease, most studies have used homogenized tissue. Therefore, new studies using isolated cardiomyocytes are necessary to gain a better understanding of the intricate cell-type-specific molecular mechanisms underlying the pathophysiology of heart failure. This chapter describes the GENTIL method, which incorporates recent technological developments in sample handling, for isolation of cardiomyocytes from cryopreserved human cardiac tissues for use in proteomic analyses.
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Affiliation(s)
- Michelle Waknitz
- CardiOmics Program, Center for Heart and Vascular Research; Division of Cardiovascular Medicine; and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Linda Berg Luecke
- CardiOmics Program, Center for Heart and Vascular Research; Division of Cardiovascular Medicine; and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Roneldine Mesidor
- CardiOmics Program, Center for Heart and Vascular Research; Division of Cardiovascular Medicine; and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Melinda Wojtkiewicz
- CardiOmics Program, Center for Heart and Vascular Research; Division of Cardiovascular Medicine; and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Chase Castro
- CardiOmics Program, Center for Heart and Vascular Research; Division of Cardiovascular Medicine; and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research; Division of Cardiovascular Medicine; and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, USA.
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8
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de Haan N, Song M, Grant OC, Ye Z, Khoder Agha F, Koed Møller Aasted M, Woods RJ, Vakhrushev SY, Wandall HH. Sensitive and Specific Global Cell Surface N-Glycoproteomics Shows Profound Differences Between Glycosylation Sites and Subcellular Components. Anal Chem 2023; 95:17328-17336. [PMID: 37956981 PMCID: PMC10688226 DOI: 10.1021/acs.analchem.3c03626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/02/2023] [Indexed: 11/21/2023]
Abstract
Cell surface glycans are essential for establishing cell communication, adhesion, and migration. However, it remains challenging to obtain cell surface-specific information about glycoconjugate structures. Acquiring this information is essential for unraveling the functional role of glycans and for exploiting them as clinical targets. To specifically analyze the N-glycoprotein forms expressed at the cell surface, we developed a C18 liquid chromatography (LC)-mass spectrometry (MS)-based glycoproteomics method in combination with highly specific cell surface protein labeling and enrichment using a biotin label. The surface-specificity of the method was validated by MS-based proteomics of subcellular component marker proteins. Using the human keratinocytes N/TERT-1 as a model system, we identified and quantified the glycosylation of hundreds of cell surface N-glycosylation sites. This approach allowed us to study the glycoforms present at the functional relevant cell surface, omitting immaturely glycosylated proteins present in the secretory pathway. Interestingly, the different stages of N-glycan processing at individual sites displayed at the cell surface were found to correlate with their accessibility for ER-residing processing enzymes, as investigated through molecular dynamics simulations. Using the new approach, we compared N-glycosylation sites of proteins expressed on the cell surface to their counterparts in a total cell lysate, showing profound differences in glycosylation between the subcellular components and indicating the relevance of the method for future studies in understanding contextual glycan functions.
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Affiliation(s)
- Noortje de Haan
- Copenhagen
Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333, ZA, The Netherlands
| | - Ming Song
- Copenhagen
Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Oliver C. Grant
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Zilu Ye
- Novo
Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark
| | - Fawzi Khoder Agha
- Copenhagen
Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | | | - Robert J. Woods
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Sergey Y. Vakhrushev
- Copenhagen
Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Hans H. Wandall
- Copenhagen
Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
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9
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Mahoney SA, Dey AK, Basisty N, Herman AB. Identification and functional analysis of senescent cells in the cardiovascular system using omics approaches. Am J Physiol Heart Circ Physiol 2023; 325:H1039-H1058. [PMID: 37656130 PMCID: PMC10908411 DOI: 10.1152/ajpheart.00352.2023] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023]
Abstract
Cardiovascular disease (CVD) is a leading cause of morbidity and mortality worldwide, and senescent cells have emerged as key contributors to its pathogenesis. Senescent cells exhibit cell cycle arrest and secrete a range of proinflammatory factors, termed the senescence-associated secretory phenotype (SASP), which promotes tissue dysfunction and exacerbates CVD progression. Omics technologies, specifically transcriptomics and proteomics, offer powerful tools to uncover and define the molecular signatures of senescent cells in cardiovascular tissue. By analyzing the comprehensive molecular profiles of senescent cells, omics approaches can identify specific genetic alterations, gene expression patterns, protein abundances, and metabolite levels associated with senescence in CVD. These omics-based discoveries provide insights into the mechanisms underlying senescence-induced cardiovascular damage, facilitating the development of novel diagnostic biomarkers and therapeutic targets. Furthermore, integration of multiple omics data sets enables a systems-level understanding of senescence in CVD, paving the way for precision medicine approaches to prevent or treat cardiovascular aging and its associated complications.
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Affiliation(s)
- Sophia A Mahoney
- Department of Integrative Physiology, University of Colorado at Boulder, Boulder, Colorado, United States
| | - Amit K Dey
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States
| | - Nathan Basisty
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States
| | - Allison B Herman
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States
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10
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Dey AK, Banarjee R, Boroumand M, Rutherford DV, Strassheim Q, Nyunt T, Olinger B, Basisty N. Translating Senotherapeutic Interventions into the Clinic with Emerging Proteomic Technologies. BIOLOGY 2023; 12:1301. [PMID: 37887011 PMCID: PMC10604147 DOI: 10.3390/biology12101301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023]
Abstract
Cellular senescence is a state of irreversible growth arrest with profound phenotypic changes, including the senescence-associated secretory phenotype (SASP). Senescent cell accumulation contributes to aging and many pathologies including chronic inflammation, type 2 diabetes, cancer, and neurodegeneration. Targeted removal of senescent cells in preclinical models promotes health and longevity, suggesting that the selective elimination of senescent cells is a promising therapeutic approach for mitigating a myriad of age-related pathologies in humans. However, moving senescence-targeting drugs (senotherapeutics) into the clinic will require therapeutic targets and biomarkers, fueled by an improved understanding of the complex and dynamic biology of senescent cell populations and their molecular profiles, as well as the mechanisms underlying the emergence and maintenance of senescence cells and the SASP. Advances in mass spectrometry-based proteomic technologies and workflows have the potential to address these needs. Here, we review the state of translational senescence research and how proteomic approaches have added to our knowledge of senescence biology to date. Further, we lay out a roadmap from fundamental biological discovery to the clinical translation of senotherapeutic approaches through the development and application of emerging proteomic technologies, including targeted and untargeted proteomic approaches, bottom-up and top-down methods, stability proteomics, and surfaceomics. These technologies are integral for probing the cellular composition and dynamics of senescent cells and, ultimately, the development of senotype-specific biomarkers and senotherapeutics (senolytics and senomorphics). This review aims to highlight emerging areas and applications of proteomics that will aid in exploring new senescent cell biology and the future translation of senotherapeutics.
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Affiliation(s)
| | | | | | | | | | | | | | - Nathan Basisty
- Translational Geroproteomics Unit, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; (A.K.D.); (R.B.); (M.B.); (D.V.R.); (Q.S.); (T.N.); (B.O.)
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11
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Chua CJ, Morrissette-McAlmon J, Tung L, Boheler KR. Understanding Arrhythmogenic Cardiomyopathy: Advances through the Use of Human Pluripotent Stem Cell Models. Genes (Basel) 2023; 14:1864. [PMID: 37895213 PMCID: PMC10606441 DOI: 10.3390/genes14101864] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/11/2023] [Accepted: 09/16/2023] [Indexed: 10/29/2023] Open
Abstract
Cardiomyopathies (CMPs) represent a significant healthcare burden and are a major cause of heart failure leading to premature death. Several CMPs are now recognized to have a strong genetic basis, including arrhythmogenic cardiomyopathy (ACM), which predisposes patients to arrhythmic episodes. Variants in one of the five genes (PKP2, JUP, DSC2, DSG2, and DSP) encoding proteins of the desmosome are known to cause a subset of ACM, which we classify as desmosome-related ACM (dACM). Phenotypically, this disease may lead to sudden cardiac death in young athletes and, during late stages, is often accompanied by myocardial fibrofatty infiltrates. While the pathogenicity of the desmosome genes has been well established through animal studies and limited supplies of primary human cells, these systems have drawbacks that limit their utility and relevance to understanding human disease. Human induced pluripotent stem cells (hiPSCs) have emerged as a powerful tool for modeling ACM in vitro that can overcome these challenges, as they represent a reproducible and scalable source of cardiomyocytes (CMs) that recapitulate patient phenotypes. In this review, we provide an overview of dACM, summarize findings in other model systems linking desmosome proteins with this disease, and provide an up-to-date summary of the work that has been conducted in hiPSC-cardiomyocyte (hiPSC-CM) models of dACM. In the context of the hiPSC-CM model system, we highlight novel findings that have contributed to our understanding of disease and enumerate the limitations, prospects, and directions for research to consider towards future progress.
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Affiliation(s)
- Christianne J. Chua
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (C.J.C.); (J.M.-M.); (L.T.)
| | - Justin Morrissette-McAlmon
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (C.J.C.); (J.M.-M.); (L.T.)
| | - Leslie Tung
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (C.J.C.); (J.M.-M.); (L.T.)
| | - Kenneth R. Boheler
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (C.J.C.); (J.M.-M.); (L.T.)
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Čaval T, Alisson-Silva F, Schwarz F. Roles of glycosylation at the cancer cell surface: opportunities for large scale glycoproteomics. Theranostics 2023; 13:2605-2615. [PMID: 37215580 PMCID: PMC10196828 DOI: 10.7150/thno.81760] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/13/2023] [Indexed: 05/24/2023] Open
Abstract
Cell surface glycosylation has a variety of functions, and its dysregulation in cancer contributes to impaired signaling, metastasis and the evasion of the immune responses. Recently, a number of glycosyltransferases that lead to altered glycosylation have been linked to reduced anti-tumor immune responses: B3GNT3, which is implicated in PD-L1 glycosylation in triple negative breast cancer, FUT8, through fucosylation of B7H3, and B3GNT2, which confers cancer resistance to T cell cytotoxicity. Given the increased appreciation of the relevance of protein glycosylation, there is a critical need for the development of methods that allow for an unbiased interrogation of cell surface glycosylation status. Here we provide an overview of the broad changes in glycosylation at the surface of cancer cell and describe selected examples of receptors with aberrant glycosylation leading to functional changes, with emphasis on immune checkpoint inhibitors, growth-promoting and growth-arresting receptors. Finally, we posit that the field of glycoproteomics has matured to an extent where large-scale profiling of intact glycopeptides from the cell surface is feasible and is poised for discovery of new actionable targets against cancer.
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