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Ramirez-Sagredo A, Sunny AT, Cupp-Sutton KA, Chowdhury T, Zhao Z, Wu S, Chiao YA. Characterizing age-related changes in intact mitochondrial proteoforms in murine hearts using quantitative top-down proteomics. Clin Proteomics 2024; 21:57. [PMID: 39343872 PMCID: PMC11440756 DOI: 10.1186/s12014-024-09509-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 09/19/2024] [Indexed: 10/01/2024] Open
Abstract
BACKGROUND Cardiovascular diseases (CVDs) are the leading cause of death worldwide, and the prevalence of CVDs increases markedly with age. Due to the high energetic demand, the heart is highly sensitive to mitochondrial dysfunction. The complexity of the cardiac mitochondrial proteome hinders the development of effective strategies that target mitochondrial dysfunction in CVDs. Mammalian mitochondria are composed of over 1000 proteins, most of which can undergo post-translational modifications (PTMs). Top-down proteomics is a powerful technique for characterizing and quantifying proteoform sequence variations and PTMs. However, there are still knowledge gaps in the study of age-related mitochondrial proteoform changes using this technique. In this study, we used top-down proteomics to identify intact mitochondrial proteoforms in young and old hearts and determined changes in protein abundance and PTMs in cardiac aging. METHODS Intact mitochondria were isolated from the hearts of young (4-month-old) and old (24-25-month-old) mice. The mitochondria were lysed, and mitochondrial lysates were subjected to denaturation, reduction, and alkylation. For quantitative top-down analysis, there were 12 runs in total arising from 3 biological replicates in two conditions, with technical duplicates for each sample. The collected top-down datasets were deconvoluted and quantified, and then the proteoforms were identified. RESULTS From a total of 12 LC-MS/MS runs, we identified 134 unique mitochondrial proteins in the different sub-mitochondrial compartments (OMM, IMS, IMM, matrix). 823 unique proteoforms in different mass ranges were identified. Compared to cardiac mitochondria of young mice, 7 proteoforms exhibited increased abundance and 13 proteoforms exhibited decreased abundance in cardiac mitochondria of old mice. Our analysis also detected PTMs of mitochondrial proteoforms, including N-terminal acetylation, lysine succinylation, lysine acetylation, oxidation, and phosphorylation. Data are available via ProteomeXchange with the identifier PXD051505. CONCLUSION By combining mitochondrial protein enrichment using mitochondrial fractionation with quantitative top-down analysis using ultrahigh-pressure liquid chromatography (UPLC)-MS and label-free quantitation, we successfully identified and quantified intact proteoforms in the complex mitochondrial proteome. Using this approach, we detected age-related changes in abundance and PTMs of mitochondrial proteoforms in the heart.
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Affiliation(s)
- Andrea Ramirez-Sagredo
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, MS21, 825 NE 13th St, Oklahoma City, OK, 73104, USA
| | - Anju Teresa Sunny
- Department of Chemistry and Biochemistry, University of Alabama, 250 Hackberry ln, Tuscaloosa, AL, 35487, USA
| | - Kellye A Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Alabama, 250 Hackberry ln, Tuscaloosa, AL, 35487, USA
| | - Trishika Chowdhury
- Department of Chemistry and Biochemistry, University of Alabama, 250 Hackberry ln, Tuscaloosa, AL, 35487, USA
| | - Zhitao Zhao
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 2210, Norman, OK, 73019-5251, USA
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Alabama, 250 Hackberry ln, Tuscaloosa, AL, 35487, USA.
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 2210, Norman, OK, 73019-5251, USA.
| | - Ying Ann Chiao
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, MS21, 825 NE 13th St, Oklahoma City, OK, 73104, USA.
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Karpov OA, Stotland A, Raedschelders K, Chazarin B, Ai L, Murray CI, Van Eyk JE. Proteomics of the heart. Physiol Rev 2024; 104:931-982. [PMID: 38300522 PMCID: PMC11381016 DOI: 10.1152/physrev.00026.2023] [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: 07/03/2023] [Revised: 12/25/2023] [Accepted: 01/14/2024] [Indexed: 02/02/2024] Open
Abstract
Mass spectrometry-based proteomics is a sophisticated identification tool specializing in portraying protein dynamics at a molecular level. Proteomics provides biologists with a snapshot of context-dependent protein and proteoform expression, structural conformations, dynamic turnover, and protein-protein interactions. Cardiac proteomics can offer a broader and deeper understanding of the molecular mechanisms that underscore cardiovascular disease, and it is foundational to the development of future therapeutic interventions. This review encapsulates the evolution, current technologies, and future perspectives of proteomic-based mass spectrometry as it applies to the study of the heart. Key technological advancements have allowed researchers to study proteomes at a single-cell level and employ robot-assisted automation systems for enhanced sample preparation techniques, and the increase in fidelity of the mass spectrometers has allowed for the unambiguous identification of numerous dynamic posttranslational modifications. Animal models of cardiovascular disease, ranging from early animal experiments to current sophisticated models of heart failure with preserved ejection fraction, have provided the tools to study a challenging organ in the laboratory. Further technological development will pave the way for the implementation of proteomics even closer within the clinical setting, allowing not only scientists but also patients to benefit from an understanding of protein interplay as it relates to cardiac disease physiology.
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Affiliation(s)
- Oleg A Karpov
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Aleksandr Stotland
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Koen Raedschelders
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Blandine Chazarin
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Lizhuo Ai
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Christopher I Murray
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Jennifer E Van Eyk
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
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Roberts DS, Loo JA, Tsybin YO, Liu X, Wu S, Chamot-Rooke J, Agar JN, Paša-Tolić L, Smith LM, Ge Y. Top-down proteomics. NATURE REVIEWS. METHODS PRIMERS 2024; 4:38. [PMID: 39006170 PMCID: PMC11242913 DOI: 10.1038/s43586-024-00318-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/24/2024] [Indexed: 07/16/2024]
Abstract
Proteoforms, which arise from post-translational modifications, genetic polymorphisms and RNA splice variants, play a pivotal role as drivers in biology. Understanding proteoforms is essential to unravel the intricacies of biological systems and bridge the gap between genotypes and phenotypes. By analysing whole proteins without digestion, top-down proteomics (TDP) provides a holistic view of the proteome and can decipher protein function, uncover disease mechanisms and advance precision medicine. This Primer explores TDP, including the underlying principles, recent advances and an outlook on the future. The experimental section discusses instrumentation, sample preparation, intact protein separation, tandem mass spectrometry techniques and data collection. The results section looks at how to decipher raw data, visualize intact protein spectra and unravel data analysis. Additionally, proteoform identification, characterization and quantification are summarized, alongside approaches for statistical analysis. Various applications are described, including the human proteoform project and biomedical, biopharmaceutical and clinical sciences. These are complemented by discussions on measurement reproducibility, limitations and a forward-looking perspective that outlines areas where the field can advance, including potential future applications.
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Affiliation(s)
- David S Roberts
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California - Los Angeles, Los Angeles, CA, USA
| | | | - Xiaowen Liu
- Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Si Wu
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, USA
| | | | - Jeffrey N Agar
- Departments of Chemistry and Chemical Biology and Pharmaceutical Sciences, Northeastern University, Boston, MA, USA
| | - Ljiljana Paša-Tolić
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
- Department of Cell and Regenerative Biology, Human Proteomics Program, University of Wisconsin - Madison, Madison, WI, USA
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Opetová M, Tomašovský R, Mikuš P, Maráková K. Transient isotachophoresis-Capillary zone electrophoresis-Mass spectrometry method with off-line microscale solid phase extraction pretreatment for quantitation of intact low molecular mass proteins in various biological fluids. J Chromatogr A 2024; 1718:464697. [PMID: 38341901 DOI: 10.1016/j.chroma.2024.464697] [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] [Received: 11/08/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/13/2024]
Abstract
Quantification of proteins is still predominantly done by the traditional bottom-up approach. Targeting of intact proteins in complex biological matrices is connected with multiple challenges during the sample pretreatment, separation, and detection step of the analytical workflow. In this work, we focused on the development of an on-line hyphenated capillary zone electrophoresis-mass spectrometry method employing off-line microscale solid-phase extraction based on hydrophilic lipophilic balance (HLB) sorbent as a sample pretreatment step for the analysis of low molecular mass intact proteins (<20 kDa) spiked in various biological fluids (human serum, plasma, urine, and saliva). A detailed optimization process involved the selection of a suitable capillary surface, background electrolyte (BGE), and comparison of two in-capillary preconcentration methods, namely transient isotachophoresis (tITP) and dynamic pH junction (DPJ), to enhance the sensitivity of the method. Optimum separation of the analytes was achieved using uncoated bare fused silica capillary employing 500 mM formic acid (pH 1.96) + 5 % (v/v) acetonitrile as BGE. tITP was utilized as an optimum preconcentration technique, achieving a 19- to 127-fold increase in the signal intensity when using 200 mM ammonium formate (adjusted to pH 4.00) as the leading electrolyte and BGE as the terminating electrolyte. Off-line microscale solid-phase extraction with various eluate treatment procedures was evaluated to ensure the compatibility of the sample pretreatment method with the selected in-capillary preconcentration, separation, and detection process. Achieved extraction recoveries of spiked proteins were in the range of 76-100 % for urine, 12-54 % for serum, 21-106 % for plasma, and 25-98 % for saliva when the eluate was evaporated and reconstituted in the solution of the leading electrolyte to achieve the tITP process. The optimum method was validated across different biological matrices, offering good linearity, accuracy, and precision, and making it suitable for proteomic studies (e.g., therapeutic drug monitoring, biomarker research) in different biological samples.
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Affiliation(s)
- Martina Opetová
- Faculty of Pharmacy, Department of Pharmaceutical Analysis and Nuclear Pharmacy, Comenius University Bratislava, Odbojárov 10, SK-832 32, Bratislava, Slovakia; Faculty of Pharmacy, Toxicological and Antidoping Center, Department of Pharmaceutical Analysis and Nuclear Pharmacy, Comenius University Bratislava, Odbojárov 10, SK-832 32, Bratislava, Slovakia
| | - Radovan Tomašovský
- Faculty of Pharmacy, Department of Pharmaceutical Analysis and Nuclear Pharmacy, Comenius University Bratislava, Odbojárov 10, SK-832 32, Bratislava, Slovakia; Faculty of Pharmacy, Toxicological and Antidoping Center, Department of Pharmaceutical Analysis and Nuclear Pharmacy, Comenius University Bratislava, Odbojárov 10, SK-832 32, Bratislava, Slovakia
| | - Peter Mikuš
- Faculty of Pharmacy, Department of Pharmaceutical Analysis and Nuclear Pharmacy, Comenius University Bratislava, Odbojárov 10, SK-832 32, Bratislava, Slovakia; Faculty of Pharmacy, Toxicological and Antidoping Center, Department of Pharmaceutical Analysis and Nuclear Pharmacy, Comenius University Bratislava, Odbojárov 10, SK-832 32, Bratislava, Slovakia
| | - Katarína Maráková
- Faculty of Pharmacy, Department of Pharmaceutical Analysis and Nuclear Pharmacy, Comenius University Bratislava, Odbojárov 10, SK-832 32, Bratislava, Slovakia; Faculty of Pharmacy, Toxicological and Antidoping Center, Department of Pharmaceutical Analysis and Nuclear Pharmacy, Comenius University Bratislava, Odbojárov 10, SK-832 32, Bratislava, Slovakia.
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Ramirez-Sagredo A, Sunny A, Cupp-Sutton K, Chowdhury T, Zhao Z, Wu S, Ann Chiao Y. Characterizing Age-related Changes in Intact Mitochondrial Proteoforms in Murine Hearts using Quantitative Top-Down Proteomics. RESEARCH SQUARE 2024:rs.3.rs-3868218. [PMID: 38313302 PMCID: PMC10836115 DOI: 10.21203/rs.3.rs-3868218/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Cardiovascular diseases (CVDs) are the leading cause of death worldwide, and the prevalence of CVDs increases markedly with age. Due to the high energetic demand, the heart is highly sensitive to mitochondrial dysfunction. The complexity of the cardiac mitochondrial proteome hinders the development of effective strategies that target mitochondrial dysfunction in CVDs. Mammalian mitochondria are composed of over 1000 proteins, most of which can undergo post-translational protein modifications (PTMs). Top-down proteomics is a powerful technique for characterizing and quantifying all protein sequence variations and PTMs. However, there are still knowledge gaps in the study of age-related mitochondrial proteoform changes using this technique. In this study, we used top-down proteomics to identify intact mitochondrial proteoforms in young and old hearts and determined changes in protein abundance and PTMs in cardiac aging. METHODS Intact mitochondria were isolated from the hearts of young (4-month-old) and old (24-25-month-old) mice. The mitochondria were lysed, and mitochondrial lysates were subjected to denaturation, reduction, and alkylation. For quantitative top-down analysis, there were 12 runs in total arising from 3 biological replicates in two conditions, with technical duplicates for each sample. The collected top-down datasets were deconvoluted and quantified, and then the proteoforms were identified. RESULTS From a total of 12 LC-MS/MS runs, we identified 134 unique mitochondrial proteins in the different sub-mitochondrial compartments (OMM, IMS, IMM, matrix). 823 unique proteoforms in different mass ranges were identified. Compared to cardiac mitochondria of young mice, 7 proteoforms exhibited increased abundance and 13 proteoforms exhibited decreased abundance in cardiac mitochondria of old mice. Our analysis also detected PTMs of mitochondrial proteoforms, including N-terminal acetylation, lysine succinylation, lysine acetylation, oxidation, and phosphorylation. CONCLUSION By combining mitochondrial protein enrichment using mitochondrial fractionation with quantitative top-down analysis using ultrahigh-pressure liquid chromatography (UPLC)-MS and label-free quantitation, we successfully identified and quantified intact proteoforms in the complex mitochondrial proteome. Using this approach, we detected age-related changes in abundance and PTMs of mitochondrial proteoforms in the heart.
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Castel J, Delaux S, Hernandez-Alba O, Cianférani S. Recent advances in structural mass spectrometry methods in the context of biosimilarity assessment: from sequence heterogeneities to higher order structures. J Pharm Biomed Anal 2023; 236:115696. [PMID: 37713983 DOI: 10.1016/j.jpba.2023.115696] [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] [Received: 06/28/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/17/2023]
Abstract
Biotherapeutics and their biosimilar versions have been flourishing in the biopharmaceutical market for several years. Structural and functional characterization is needed to achieve analytical biosimilarity through the assessment of critical quality attributes as required by regulatory authorities. The role of analytical strategies, particularly mass spectrometry-based methods, is pivotal to gathering valuable information for the in-depth characterization of biotherapeutics and biosimilarity assessment. Structural mass spectrometry methods (native MS, HDX-MS, top-down MS, etc.) provide information ranging from primary sequence assessment to higher order structure evaluation. This review focuses on recent developments and applications in structural mass spectrometry for biotherapeutic and biosimilar characterization.
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Affiliation(s)
- Jérôme Castel
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Delaux
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France.
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Huang CF, Su P, Fisher TD, Levitsky J, Kelleher NL, Forte E. Mass spectrometry-based proteomics for advancing solid organ transplantation research. FRONTIERS IN TRANSPLANTATION 2023; 2:1286881. [PMID: 38993855 PMCID: PMC11235370 DOI: 10.3389/frtra.2023.1286881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/13/2023] [Indexed: 07/13/2024]
Abstract
Scarcity of high-quality organs, suboptimal organ quality assessment, unsatisfactory pre-implantation procedures, and poor long-term organ and patient survival are the main challenges currently faced by the solid organ transplant (SOT) field. New biomarkers for assessing graft quality pre-implantation, detecting, and predicting graft injury, rejection, dysfunction, and survival are critical to provide clinicians with invaluable prediction tools and guidance for personalized patients' treatment. Additionally, new therapeutic targets are also needed to reduce injury and rejection and improve transplant outcomes. Proteins, which underlie phenotypes, are ideal candidate biomarkers of health and disease statuses and therapeutic targets. A protein can exist in different molecular forms, called proteoforms. As the function of a protein depends on its exact composition, proteoforms can offer a more accurate basis for connection to complex phenotypes than protein from which they derive. Mass spectrometry-based proteomics has been largely used in SOT research for identification of candidate biomarkers and therapeutic intervention targets by so-called "bottom-up" proteomics (BUP). However, such BUP approaches analyze small peptides in lieu of intact proteins and provide incomplete information on the exact molecular composition of the proteins of interest. In contrast, "Top-down" proteomics (TDP), which analyze intact proteins retaining proteoform-level information, have been only recently adopted in transplantation studies and already led to the identification of promising proteoforms as biomarkers for organ rejection and dysfunction. We anticipate that the use of top-down strategies in combination with new technological advancements in single-cell and spatial proteomics could drive future breakthroughs in biomarker and therapeutic target discovery in SOT.
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Affiliation(s)
- Che-Fan Huang
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
| | - Pei Su
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
- Department of Chemistry, Northwestern University, Evanston, IL, United States
| | - Troy D. Fisher
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
| | - Josh Levitsky
- Division of Gastroenterology and Hepatology, Comprehensive Transplant Center Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Neil L. Kelleher
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
- Department of Chemistry, Northwestern University, Evanston, IL, United States
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Surgery, Feinberg School of Medicine, Comprehensive Transplant Center, Northwestern University, Chicago, IL, United States
| | - Eleonora Forte
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
- Department of Surgery, Feinberg School of Medicine, Comprehensive Transplant Center, Northwestern University, Chicago, IL, United States
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Bayne EF, Rossler KJ, Gregorich ZR, Aballo TJ, Roberts DS, Chapman EA, Guo W, Palecek SP, Ralphe JC, Kamp TJ, Ge Y. Top-down proteomics of myosin light chain isoforms define chamber-specific expression in the human heart. J Mol Cell Cardiol 2023; 181:89-97. [PMID: 37327991 PMCID: PMC10528938 DOI: 10.1016/j.yjmcc.2023.06.003] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 05/27/2023] [Accepted: 06/13/2023] [Indexed: 06/18/2023]
Abstract
Myosin functions as the "molecular motor" of the sarcomere and generates the contractile force necessary for cardiac muscle contraction. Myosin light chains 1 and 2 (MLC-1 and -2) play important functional roles in regulating the structure of the hexameric myosin molecule. Each of these light chains has an 'atrial' and 'ventricular' isoform, so called because they are believed to exhibit chamber-restricted expression in the heart. However, recently the chamber-specific expression of MLC isoforms in the human heart has been questioned. Herein, we analyzed the expression of MLC-1 and -2 atrial and ventricular isoforms in each of the four cardiac chambers in adult non-failing donor hearts using top-down mass spectrometry (MS)-based proteomics. Strikingly, we detected an isoform thought to be ventricular, MLC-2v (gene: MYL2), in the atria and confirmed the protein sequence using tandem MS (MS/MS). For the first time, a putative deamidation post-translation modification (PTM) located on MLC-2v in atrial tissue was localized to amino acid N13. MLC-1v (MYL3) and MLC-2a (MYL7) were the only MLC isoforms exhibiting chamber-restricted expression patterns across all donor hearts. Importantly, our results unambiguously show that MLC-1v, not MLC-2v, is ventricle-specific in adult human hearts. Moreover, we found elevated MLC-2 phosphorylation in male hearts compared to female hearts across each cardiac chamber. Overall, top-down proteomics allowed an unbiased analysis of MLC isoform expression throughout the human heart, uncovering previously unexpected isoform expression patterns and PTMs.
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Affiliation(s)
- Elizabeth F Bayne
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kalina J Rossler
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Zachery R Gregorich
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Timothy J Aballo
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Emily A Chapman
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Wei Guo
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sean P Palecek
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - J Carter Ralphe
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Timothy J Kamp
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA; Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.
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Templeton EM, Pilbrow AP, Kleffmann T, Pickering JW, Rademaker MT, Scott NJA, Ellmers LJ, Charles CJ, Endre ZH, Richards AM, Cameron VA, Lassé M. Comparison of SPEED, S-Trap, and In-Solution-Based Sample Preparation Methods for Mass Spectrometry in Kidney Tissue and Plasma. Int J Mol Sci 2023; 24:ijms24076290. [PMID: 37047281 PMCID: PMC10094439 DOI: 10.3390/ijms24076290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/07/2023] [Accepted: 03/11/2023] [Indexed: 03/30/2023] Open
Abstract
Mass spectrometry is a powerful technique for investigating renal pathologies and identifying biomarkers, and efficient protein extraction from kidney tissue is essential for bottom-up proteomic analyses. Detergent-based strategies aid cell lysis and protein solubilization but are poorly compatible with downstream protein digestion and liquid chromatography-coupled mass spectrometry, requiring additional purification and buffer-exchange steps. This study compares two well-established detergent-based methods for protein extraction (in-solution sodium deoxycholate (SDC); suspension trapping (S-Trap)) with the recently developed sample preparation by easy extraction and digestion (SPEED) method, which uses strong acid for denaturation. We compared the quantitative performance of each method using label-free mass spectrometry in both sheep kidney cortical tissue and plasma. In kidney tissue, SPEED quantified the most unique proteins (SPEED 1250; S-Trap 1202; SDC 1197). In plasma, S-Trap produced the most unique protein quantifications (S-Trap 150; SDC 148; SPEED 137). Protein quantifications were reproducible across biological replicates in both tissue (R2 = 0.85–0.90) and plasma (SPEED R2 = 0.84; SDC R2 = 0.76, S-Trap R2 = 0.65). Our data suggest SPEED as the optimal method for proteomic preparation in kidney tissue and S-Trap or SPEED as the optimal method for plasma, depending on whether a higher number of protein quantifications or greater reproducibility is desired.
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Chapman EA, Aballo TJ, Melby JA, Zhou T, Price SJ, Rossler KJ, Lei I, Tang PC, Ge Y. Defining the Sarcomeric Proteoform Landscape in Ischemic Cardiomyopathy by Top-Down Proteomics. J Proteome Res 2023; 22:931-941. [PMID: 36800490 PMCID: PMC10115148 DOI: 10.1021/acs.jproteome.2c00729] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Ischemic cardiomyopathy (ICM) is a prominent form of heart failure, but the molecular mechanisms underlying ICM remain relatively understudied due to marked phenotypic heterogeneity. Alterations in post-translational modifications (PTMs) and isoform switches in sarcomeric proteins play important roles in cardiac pathophysiology. Thus, it is essential to define sarcomeric proteoform landscape to better understand ICM. Herein, we have implemented a top-down liquid chromatography (LC)-mass spectrometry (MS)-based proteomics method for the identification and quantification of sarcomeric proteoforms in the myocardia of donors without heart diseases (n = 16) compared to end-stage ICM patients (n = 16). Importantly, quantification of post-translational modifications (PTMs) and expression reveal significant changes in various sarcomeric proteins extracted from ICM tissues. Changes include altered phosphorylation and expression of cardiac troponin I (cTnI) and enigma homologue 2 (ENH2) as well as an increase in muscle LIM protein (MLP) and calsarcin-1 (Cal-1) phosphorylation in ICM hearts. Our results imply that the contractile apparatus of the sarcomere is severely dysregulated during ICM. Thus, this is the first study to uncover significant molecular changes to multiple sarcomeric proteins in the LV myocardia of the end-stage ICM patients using liquid chromatography-mass spectrometry (LC-MS)-based top-down proteomics. Raw data are available via the PRIDE repository with identifier PXD038066.
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Affiliation(s)
- Emily A. Chapman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Timothy J. Aballo
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Jake A. Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Tianhua Zhou
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Scott J. Price
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Kalina J. Rossler
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Ienglam Lei
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Paul C. Tang
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
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11
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Olaleye O, Spanov B, Bults P, van der Voort A, Govorukhina N, Sonke GS, Horvatovich P, van de Merbel NC, Bischoff R. Biotransformation of Trastuzumab and Pertuzumab in Breast Cancer Patients Assessed by Affinity Enrichment and Ion-Exchange Chromatography. Drug Metab Dispos 2023; 51:249-256. [PMID: 36379709 DOI: 10.1124/dmd.122.001094] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 11/16/2022] Open
Abstract
Therapeutic proteins (TPs) are known to be heterogeneous due to modifications that occur during the production process and storage. Modifications may also occur in TPs after their administration to patients due to in vivo biotransformation. Ligand binding assays, which are widely used in the bioanalysis of TPs in body fluids, are typically unable to distinguish such modifications. Liquid chromatography coupled to mass spectrometry is being increasingly used to study modifications in TPs, but its use to study in vivo biotransformation has been limited until now. We present a novel approach that combines affinity enrichment using Affimer reagents with ion-exchange chromatography (IEX) to analyze charge variants of the TPs trastuzumab and pertuzumab in plasma of patients undergoing therapy for HER2-positive breast cancer. Affimer reagents were immobilized via engineered Cys tags to maleimide beads, and the TPs were eluted under acidic conditions followed by rapid neutralization. The enriched TPs were analyzed by cation-exchange chromatography (IEX) using pH-gradient elution, resulting in the separation of about 20 charge variants for trastuzumab and about five charge variants for pertuzumab. A comparison between in vitro stressed TPs spiked into plasma, and TPs enriched from patient plasma showed that the observed profiles were highly similar. This indicates that in vitro stress testing in plasma can mimic the situation in patient plasma, as far as the generation of charge variants is concerned. SIGNIFICANCE STATEMENT: This research attempts to elucidate the modifications that occur in therapeutic proteins (TPs) after they have been administered to patients. This is important because there is little knowledge about the fate of TPs in this regard, and certain modifications could affect their efficiency. Our results show that the modifications discovered are most likely due to a chemical process and are not patient specific.
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Affiliation(s)
- Oladapo Olaleye
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Baubek Spanov
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Peter Bults
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Anna van der Voort
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Natalia Govorukhina
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Gabe S Sonke
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Nico C van de Merbel
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
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12
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Peripartum cardiomyopathy: a global effort to find the cause and cure for the rare and little understood disease. Biophys Rev 2022; 14:369-379. [PMID: 35340597 PMCID: PMC8921403 DOI: 10.1007/s12551-022-00930-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/06/2022] [Indexed: 12/12/2022] Open
Abstract
Abstract
In this review, we present our current understanding of peripartum cardiomyopathy (PPCM) based on reports of the incidence, diagnosis and current treatment options. We summarise opinions on whether PPCM is triggered by vascular and/or hormonal causes and examine the influence of comorbidities such as preeclampsia. Two articles published in 2021 strongly support the hypothesis that PPCM may be a familial disease. Using large cohorts of PPCM patients, they summarised the available genomic DNA sequence data that are expressed in human cardiomyocytes. While PPCM is considered a disease predominately affecting the left ventricle, there are data to suggest that some cases also involve right ventricular failure. Finally, we conclude that there is sufficient evidence to warrant an RNAseq investigation and that this would be most informative if performed at the cardiomyocytes level rather than analysing genomic DNA from the peripheral circulation. Given the rarity of PPCM, the combined resources of international human heart tissue biobanks have assembled 30 ventricular tissue samples from PPCM patients, and we are actively seeking to enlarge this patient base by collaborating with human heart tissue banks and research laboratories who would like to join this endeavour.
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13
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Progress and challenges in mass spectrometry-based analysis of antibody repertoires. Trends Biotechnol 2021; 40:463-481. [PMID: 34535228 DOI: 10.1016/j.tibtech.2021.08.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 12/22/2022]
Abstract
Humoral immunity is divided into the cellular B cell and protein-level antibody responses. High-throughput sequencing has advanced our understanding of both these fundamental aspects of B cell immunology as well as aspects pertaining to vaccine and therapeutics biotechnology. Although the protein-level serum and mucosal antibody repertoire make major contributions to humoral protection, the sequence composition and dynamics of antibody repertoires remain underexplored. This limits insight into important immunological and biotechnological parameters such as the number of antigen-specific antibodies, which are for example, relevant for pathogen neutralization, microbiota regulation, severity of autoimmunity, and therapeutic efficacy. High-resolution mass spectrometry (MS) has allowed initial insights into the antibody repertoire. We outline current challenges in MS-based sequence analysis of antibody repertoires and propose strategies for their resolution.
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14
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Melby JA, Roberts DS, Larson EJ, Brown KA, Bayne EF, Jin S, Ge Y. Novel Strategies to Address the Challenges in Top-Down Proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1278-1294. [PMID: 33983025 PMCID: PMC8310706 DOI: 10.1021/jasms.1c00099] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Top-down mass spectrometry (MS)-based proteomics is a powerful technology for comprehensively characterizing proteoforms to decipher post-translational modifications (PTMs) together with genetic variations and alternative splicing isoforms toward a proteome-wide understanding of protein functions. In the past decade, top-down proteomics has experienced rapid growth benefiting from groundbreaking technological advances, which have begun to reveal the potential of top-down proteomics for understanding basic biological functions, unraveling disease mechanisms, and discovering new biomarkers. However, many challenges remain to be comprehensively addressed. In this Account & Perspective, we discuss the major challenges currently facing the top-down proteomics field, particularly in protein solubility, proteome dynamic range, proteome complexity, data analysis, proteoform-function relationship, and analytical throughput for precision medicine. We specifically review the major technology developments addressing these challenges with an emphasis on our research group's efforts, including the development of top-down MS-compatible surfactants for protein solubilization, functionalized nanoparticles for the enrichment of low-abundance proteoforms, strategies for multidimensional chromatography separation of proteins, and a new comprehensive user-friendly software package for top-down proteomics. We have also made efforts to connect proteoforms with biological functions and provide our visions on what the future holds for top-down proteomics.
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Affiliation(s)
- Jake A Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Eli J Larson
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Elizabeth F Bayne
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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15
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Clementy N, Bodin A, Bisson A, Teixeira-Gomes AP, Roger S, Angoulvant D, Labas V, Babuty D. The Defibrillation Conundrum: New Insights into the Mechanisms of Shock-Related Myocardial Injury Sustained from a Life-Saving Therapy. Int J Mol Sci 2021; 22:5003. [PMID: 34066832 PMCID: PMC8125879 DOI: 10.3390/ijms22095003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 11/16/2022] Open
Abstract
Implantable cardiac defibrillators (ICDs) are recommended to prevent the risk of sudden cardiac death. However, shocks are associated with an increased mortality with a dose response effect, and a strategy of reducing electrical therapy burden improves the prognosis of implanted patients. We review the mechanisms of defibrillation and its consequences, including cell damage, metabolic remodeling, calcium metabolism anomalies, and inflammatory and pro-fibrotic remodeling. Electrical shocks do save lives, but also promote myocardial stunning, heart failure, and pro-arrhythmic effects as seen in electrical storms. Limiting unnecessary implantations and therapies and proposing new methods of defibrillation in the future are recommended.
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Affiliation(s)
- Nicolas Clementy
- Service de Cardiologie, Hôpital Trousseau, Université de Tours, 37044 Tours, France; (A.B.); (A.B.); (D.A.); (D.B.)
- Transplantation, Immunologie et Inflammation T2I-EA 4245, Université de Tours, 37044 Tours, France;
| | - Alexandre Bodin
- Service de Cardiologie, Hôpital Trousseau, Université de Tours, 37044 Tours, France; (A.B.); (A.B.); (D.A.); (D.B.)
| | - Arnaud Bisson
- Service de Cardiologie, Hôpital Trousseau, Université de Tours, 37044 Tours, France; (A.B.); (A.B.); (D.A.); (D.B.)
- Transplantation, Immunologie et Inflammation T2I-EA 4245, Université de Tours, 37044 Tours, France;
| | - Ana-Paula Teixeira-Gomes
- Plate-forme de Chirurgie et d’Imagerie pour la Recherche et l’Enseignement (CIRE), INRA, Université de Tours, CHU de Tours, 37380 Nouzilly, France; (A.-P.T.-G.); (V.L.)
| | - Sebastien Roger
- Transplantation, Immunologie et Inflammation T2I-EA 4245, Université de Tours, 37044 Tours, France;
| | - Denis Angoulvant
- Service de Cardiologie, Hôpital Trousseau, Université de Tours, 37044 Tours, France; (A.B.); (A.B.); (D.A.); (D.B.)
- Transplantation, Immunologie et Inflammation T2I-EA 4245, Université de Tours, 37044 Tours, France;
| | - Valérie Labas
- Plate-forme de Chirurgie et d’Imagerie pour la Recherche et l’Enseignement (CIRE), INRA, Université de Tours, CHU de Tours, 37380 Nouzilly, France; (A.-P.T.-G.); (V.L.)
| | - Dominique Babuty
- Service de Cardiologie, Hôpital Trousseau, Université de Tours, 37044 Tours, France; (A.B.); (A.B.); (D.A.); (D.B.)
- Transplantation, Immunologie et Inflammation T2I-EA 4245, Université de Tours, 37044 Tours, France;
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16
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Carneiro A, Viana-Gomes D, Macedo-da-Silva J, Lima GHO, Mitri S, Alves SR, Kolliari-Turner A, Zanoteli E, Neto FRDA, Palmisano G, Pesquero JB, Moreira JC, Pereira MD. Risk factors and future directions for preventing and diagnosing exertional rhabdomyolysis. Neuromuscul Disord 2021; 31:583-595. [PMID: 34193371 DOI: 10.1016/j.nmd.2021.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/19/2022]
Abstract
Exertional rhabdomyolysis may occur when an individual is subjected to strenuous physical exercise. It is occasionally associated with myoglobinuria (i.e. "cola-colored" urine) alongside muscle pain and weakness. The pathophysiology of exertional rhabdomyolysis involves striated muscle damage and the release of cellular components into extracellular fluid and bloodstream. This can cause acute renal failure, electrolyte abnormalities, arrhythmias and potentially death. Exertional rhabdomyolysis is observed in high-performance athletes who are subjected to intense, repetitive and/or prolonged exercise but is also observed in untrained individuals and highly trained or elite groups of military personnel. Several risk factors have been reported to increase the likelihood of the condition in athletes, including: viral infection, drug and alcohol abuse, exercise in intensely hot and humid environments, genetic polymorphisms (e.g. sickle cell trait and McArdle disease) and epigenetic modifications. This article reviews several of these risk factors and proposes screening protocols to identify individual susceptibility to exertional rhabdomyolysis as well as the relevance of proteomics for the evaluation of potential biomarkers of muscle damage.
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Affiliation(s)
- Andréia Carneiro
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Brazil; Departamento de Química, Diretoria de Sistemas de Armas da Marinha, Marinha do Brazil, Brazil; Departamento de Parasitologia, Universidade de São Paulo, Instituto de Ciencias Biomédicas, Brazil.
| | - Diego Viana-Gomes
- Departamento de Corridas, Universidade Federal do Rio de Janeiro, Escola de Educação Física, Brazil
| | - Janaina Macedo-da-Silva
- Departamento de Parasitologia, Universidade de São Paulo, Instituto de Ciencias Biomédicas, Brazil
| | - Giscard Humberto Oliveira Lima
- Departamento de Biofísica, Universidade Federal de São Paulo, Brazil; Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Italy
| | - Simone Mitri
- Centro de Ecologia Humana e Saúde do Trabalhador, Fundação Oswaldo Cruz, Brazil
| | | | | | - Edmar Zanoteli
- Departamento de Neurologia, Faculdade de Medicina, Universidade de São Paulo, Brazil
| | | | - Giuseppe Palmisano
- Departamento de Parasitologia, Universidade de São Paulo, Instituto de Ciencias Biomédicas, Brazil
| | - João Bosco Pesquero
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Italy
| | | | - Marcos Dias Pereira
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Brazil.
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17
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Kruszewska J, Zajda J, Matczuk M. How to effectively prepare a sample for bottom-up proteomic analysis of nanoparticle protein corona? A critical review. Talanta 2021; 226:122153. [PMID: 33676702 DOI: 10.1016/j.talanta.2021.122153] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 02/08/2023]
Abstract
Since the interest in the biomedical applications of inorganic nanoparticles (NPs) has rapidly grown over the last decades, there is a need for a thorough characterization of bio-nano interactions. NPs introduced to the body (mostly intravenously) encounter plasma proteins, that instantly create a so-called "protein corona" on the NPs surface, giving the nanomaterial a new biological identity. Type of the proteins that interact with NPs may affect the in vivo fate of NPs. For that reason, it is particularly important to establish analytical methods capable of corona protein identification. Bottom-up proteomics is most often used for that purpose. A crucial part of the experiment is sample preparation, as it is already proven that different protocols may lead to distinct results. This review is aimed at providing a characterization of two main stages of sample preparation: separation of NPs with protein corona from the unbound proteins and the digestion of corona proteins. Separation techniques such as centrifugation, magnetic separation, and chromatography and three digestion methods (in-gel, in-solution, and on-particle) are described with special emphasis paid on their advantages and disadvantages as well as their influence on the result of identification. This paper also indicates the need for standardization of protein corona identification protocols, as some of the proteins may be preferentially detected while applying a particular digestion procedure.
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Affiliation(s)
- Joanna Kruszewska
- Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664, Warsaw, Poland
| | - Joanna Zajda
- Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664, Warsaw, Poland
| | - Magdalena Matczuk
- Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664, Warsaw, Poland.
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18
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Bodin A, Labas V, Bisson A, Teixeira-Gomes AP, Blasco H, Tomas D, Combes-Soia L, Marcelo P, Miquelestorena-Standley E, Baron C, Angoulvant D, Babuty D, Clementy N. Acute pathophysiological myocardial changes following intra-cardiac electrical shocks using a proteomic approach in a sheep model. Sci Rep 2020; 10:20252. [PMID: 33219330 PMCID: PMC7679418 DOI: 10.1038/s41598-020-77346-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/04/2020] [Indexed: 12/18/2022] Open
Abstract
Implantable cardioverter-defibrillators (ICD) are meant to fight life-threatening ventricular arrhythmias and reduce overall mortality. Ironically, life-saving shocks themselves have been shown to be independently associated with an increased mortality. We sought to identify myocardial changes at the protein level immediately after ICD electrical shocks using a proteomic approach. ICD were surgically implanted in 10 individuals of a healthy male sheep model: a control group (N = 5) without any shock delivery and a shock group (N = 5) with the delivery of 5 consecutive shocks at 41 J. Myocardial tissue samples were collected at the right-ventricle apex near to the lead coil and at the right ventricle basal free wall region. Global quantitative proteomics experiments on myocardial tissue samples were performed using mass spectrometry techniques. Proteome was significantly modified after electrical shock and several mechanisms were associated: protein, DNA and membrane damages due to extreme physical conditions induced by ICD-shock but also due to regulated cell death; metabolic remodeling; oxidative stress; calcium dysregulation; inflammation and fibrosis. These proteome modifications were seen in myocardium both "near" and "far" from electrical shock region. N-term acetylated troponin C was an interesting tissular biomarker, significantly decreased after electrical shock in the "far" region (AUC: 0.93). Our data support an acute shock-induced myocardial tissue injury which might be involved in acute paradoxical deleterious effects such as heart failure and ventricular arrhythmias.
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Affiliation(s)
- Alexandre Bodin
- Service de Cardiologie, Centre Hospitalier Universitaire Trousseau Et EA7505, Faculté de Médecine, Université François Rabelais, Tours, France.
- INRAE, CNRS, IFCE, UMR PRC, Université de Tours, 37380, Nouzilly, France.
| | - Valérie Labas
- INRAE, CNRS, IFCE, UMR PRC, Université de Tours, 37380, Nouzilly, France
- INRAE, CHU de Tours, Plate-Forme de Chirurgie Et D'Imagerie Pour La Recherche Et L'Enseignement, Université de Tours, 37380, Nouzilly, France
| | - Arnaud Bisson
- Service de Cardiologie, Centre Hospitalier Universitaire Trousseau Et EA7505, Faculté de Médecine, Université François Rabelais, Tours, France
| | | | - Hélène Blasco
- Imagerie Et Cerveau - UMR 1253, Université de Tours, Tours, France
| | - Daniel Tomas
- INRAE, CNRS, IFCE, UMR PRC, Université de Tours, 37380, Nouzilly, France
- INRAE, CHU de Tours, Plate-Forme de Chirurgie Et D'Imagerie Pour La Recherche Et L'Enseignement, Université de Tours, 37380, Nouzilly, France
| | - Lucie Combes-Soia
- INRAE, CNRS, IFCE, UMR PRC, Université de Tours, 37380, Nouzilly, France
- INRAE, CHU de Tours, Plate-Forme de Chirurgie Et D'Imagerie Pour La Recherche Et L'Enseignement, Université de Tours, 37380, Nouzilly, France
| | - Paulo Marcelo
- Plate-Forme ICAP, Centre Universitaire de Recherche en Santé, Université de Picardie Jules Verne, 80054, Amiens, France
| | | | - Christophe Baron
- Transplantation, Immunologie et Inflammation T2i - EA 4245, Université de Tours, Tours, France
| | - Denis Angoulvant
- Service de Cardiologie, Centre Hospitalier Universitaire Trousseau Et EA7505, Faculté de Médecine, Université François Rabelais, Tours, France
- Transplantation, Immunologie et Inflammation T2i - EA 4245, Université de Tours, Tours, France
| | - Dominique Babuty
- Service de Cardiologie, Centre Hospitalier Universitaire Trousseau Et EA7505, Faculté de Médecine, Université François Rabelais, Tours, France
| | - Nicolas Clementy
- Service de Cardiologie, Centre Hospitalier Universitaire Trousseau Et EA7505, Faculté de Médecine, Université François Rabelais, Tours, France
- Transplantation, Immunologie et Inflammation T2i - EA 4245, Université de Tours, Tours, France
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19
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Vitorino R, Guedes S, Trindade F, Correia I, Moura G, Carvalho P, Santos MAS, Amado F. De novo sequencing of proteins by mass spectrometry. Expert Rev Proteomics 2020; 17:595-607. [PMID: 33016158 DOI: 10.1080/14789450.2020.1831387] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Proteins are crucial for every cellular activity and unraveling their sequence and structure is a crucial step to fully understand their biology. Early methods of protein sequencing were mainly based on the use of enzymatic or chemical degradation of peptide chains. With the completion of the human genome project and with the expansion of the information available for each protein, various databases containing this sequence information were formed. AREAS COVERED De novo protein sequencing, shotgun proteomics and other mass-spectrometric techniques, along with the various software are currently available for proteogenomic analysis. Emphasis is placed on the methods for de novo sequencing, together with potential and shortcomings using databases for interpretation of protein sequence data. EXPERT OPINION As mass-spectrometry sequencing performance is improving with better software and hardware optimizations, combined with user-friendly interfaces, de-novo protein sequencing becomes imperative in shotgun proteomic studies. Issues regarding unknown or mutated peptide sequences, as well as, unexpected post-translational modifications (PTMs) and their identification through false discovery rate searches using the target/decoy strategy need to be addressed. Ideally, it should become integrated in standard proteomic workflows as an add-on to conventional database search engines, which then would be able to provide improved identification.
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Affiliation(s)
- Rui Vitorino
- QOPNA & LAQV-REQUIMTE, Departamento De Química, Institute of Biomedicine - iBiMED , Aveiro, Portugal.,iBiMED, Department of Medical Sciences, University of Aveiro , Aveiro, Portugal.,Unidade De Investigação Cardiovascular, Departamento De Cirurgia E Fisiologia, Faculdade De Medicina, Universidade Do Porto , Porto, Portugal
| | - Sofia Guedes
- QOPNA & LAQV-REQUIMTE, Departamento De Química, Institute of Biomedicine - iBiMED , Aveiro, Portugal
| | - Fabio Trindade
- Unidade De Investigação Cardiovascular, Departamento De Cirurgia E Fisiologia, Faculdade De Medicina, Universidade Do Porto , Porto, Portugal
| | - Inês Correia
- iBiMED, Department of Medical Sciences, University of Aveiro , Aveiro, Portugal
| | - Gabriela Moura
- iBiMED, Department of Medical Sciences, University of Aveiro , Aveiro, Portugal
| | - Paulo Carvalho
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, FIOCRUZ, Laboratory for Proteomics and Protein Engineering , Brazil
| | - Manuel A S Santos
- iBiMED, Department of Medical Sciences, University of Aveiro , Aveiro, Portugal
| | - Francisco Amado
- QOPNA & LAQV-REQUIMTE, Departamento De Química, Institute of Biomedicine - iBiMED , Aveiro, Portugal
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Distinct hypertrophic cardiomyopathy genotypes result in convergent sarcomeric proteoform profiles revealed by top-down proteomics. Proc Natl Acad Sci U S A 2020; 117:24691-24700. [PMID: 32968017 PMCID: PMC7547245 DOI: 10.1073/pnas.2006764117] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is the most common heritable heart disease. Although the genetic cause of HCM has been linked to mutations in genes encoding sarcomeric proteins, the ability to predict clinical outcomes based on specific mutations in HCM patients is limited. Moreover, how mutations in different sarcomeric proteins can result in highly similar clinical phenotypes remains unknown. Posttranslational modifications (PTMs) and alternative splicing regulate the function of sarcomeric proteins; hence, it is critical to study HCM at the level of proteoforms to gain insights into the mechanisms underlying HCM. Herein, we employed high-resolution mass spectrometry-based top-down proteomics to comprehensively characterize sarcomeric proteoforms in septal myectomy tissues from HCM patients exhibiting severe outflow track obstruction (n = 16) compared to nonfailing donor hearts (n = 16). We observed a complex landscape of sarcomeric proteoforms arising from combinatorial PTMs, alternative splicing, and genetic variation in HCM. A coordinated decrease of phosphorylation in important myofilament and Z-disk proteins with a linear correlation suggests PTM cross-talk in the sarcomere and dysregulation of protein kinase A pathways in HCM. Strikingly, we discovered that the sarcomeric proteoform alterations in the myocardium of HCM patients undergoing septal myectomy were remarkably consistent, regardless of the underlying HCM-causing mutations. This study suggests that the manifestation of severe HCM coalesces at the proteoform level despite distinct genotype, which underscores the importance of molecular characterization of HCM phenotype and presents an opportunity to identify broad-spectrum treatments to mitigate the most severe manifestations of this genetically heterogenous disease.
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Brown KA, Tucholski T, Eken C, Knott S, Zhu Y, Jin S, Ge Y. High-Throughput Proteomics Enabled by a Photocleavable Surfactant. Angew Chem Int Ed Engl 2020; 59:8406-8410. [PMID: 32097521 PMCID: PMC7230032 DOI: 10.1002/anie.201915374] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/07/2020] [Indexed: 11/10/2022]
Abstract
Mass spectrometry (MS)-based proteomics provides unprecedented opportunities for understanding the structure and function of proteins in complex biological systems; however, protein solubility and sample preparation before MS remain a bottleneck preventing high-throughput proteomics. Herein, we report a high-throughput bottom-up proteomic method enabled by a newly developed MS-compatible photocleavable surfactant, 4-hexylphenylazosulfonate (Azo) that facilitates robust protein extraction, rapid enzymatic digestion (30 min compared to overnight), and subsequent MS-analysis following UV degradation. Moreover, we developed an Azo-aided bottom-up method for analysis of integral membrane proteins, which are key drug targets and are generally underrepresented in global proteomic studies. Furthermore, we demonstrated the ability of Azo to serve as an "all-in-one" MS-compatible surfactant for both top-down and bottom-up proteomics, with streamlined workflows for high-throughput proteomics amenable to clinical applications.
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Affiliation(s)
- Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Christian Eken
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Samantha Knott
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yanlong Zhu
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
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22
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Brown KA, Tucholski T, Eken C, Knott S, Zhu Y, Jin S, Ge Y. High‐Throughput Proteomics Enabled by a Photocleavable Surfactant. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915374] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Kyle A. Brown
- Department of Chemistry University of Wisconsin-Madison Madison WI 53706 USA
| | - Trisha Tucholski
- Department of Chemistry University of Wisconsin-Madison Madison WI 53706 USA
| | - Christian Eken
- Department of Chemistry University of Wisconsin-Madison Madison WI 53706 USA
| | - Samantha Knott
- Department of Chemistry University of Wisconsin-Madison Madison WI 53706 USA
| | - Yanlong Zhu
- Department of Cell and Regenerative Biology University of Wisconsin-Madison Madison WI 53706 USA
| | - Song Jin
- Department of Chemistry University of Wisconsin-Madison Madison WI 53706 USA
| | - Ying Ge
- Department of Chemistry University of Wisconsin-Madison Madison WI 53706 USA
- Department of Cell and Regenerative Biology University of Wisconsin-Madison Madison WI 53706 USA
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23
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Melby JA, Jin Y, Lin Z, Tucholski T, Wu Z, Gregorich ZR, Diffee GM, Ge Y. Top-Down Proteomics Reveals Myofilament Proteoform Heterogeneity among Various Rat Skeletal Muscle Tissues. J Proteome Res 2020; 19:446-454. [PMID: 31647247 PMCID: PMC7487979 DOI: 10.1021/acs.jproteome.9b00623] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Heterogeneity in skeletal muscle contraction time, peak power output, and resistance to fatigue, among others, is necessary to accommodate the wide range of functional demands imposed on the body. Underlying this functional heterogeneity are a myriad of differences in the myofilament protein isoform expression and post-translational modifications; yet, characterizing this heterogeneity remains challenging. Herein, we have utilized top-down liquid chromatography (LC)-mass spectrometry (MS)-based proteomics to characterize myofilament proteoform heterogeneity in seven rat skeletal muscle tissues including vastus lateralis, vastus medialis, vastus intermedius, rectus femoris, soleus, gastrocnemius, and plantaris. Top-down proteomics revealed that myofilament proteoforms varied greatly across the seven different rat skeletal muscle tissues. Subsequently, we quantified and characterized myofilament proteoforms using online LC-MS. We have comprehensively characterized the fast and slow skeletal troponin I isoforms, which demonstrates the ability of top-down MS to decipher isoforms with high sequence homology. Taken together, we have shown that top-down proteomics can be used as a robust and high-throughput method to characterize the molecular heterogeneity of myofilament proteoforms from various skeletal muscle tissues.
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Affiliation(s)
- Jake A. Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Yutong Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Ziqing Lin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI 53705
| | - Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Zhijie Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Zachery R. Gregorich
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705
| | - Gary M. Diffee
- Department of Kinesiology, University of Wisconsin-Madison, Madison, WI 53706
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI 53705
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24
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Berry JL, Zhu W, Tang YL, Krishnamurthy P, Ge Y, Cooke JP, Chen Y, Garry DJ, Yang HT, Rajasekaran NS, Koch WJ, Li S, Domae K, Qin G, Cheng K, Kamp TJ, Ye L, Hu S, Ogle BM, Rogers JM, Abel ED, Davis ME, Prabhu SD, Liao R, Pu WT, Wang Y, Ping P, Bursac N, Vunjak-Novakovic G, Wu JC, Bolli R, Menasché P, Zhang J. Convergences of Life Sciences and Engineering in Understanding and Treating Heart Failure. Circ Res 2019; 124:161-169. [PMID: 30605412 DOI: 10.1161/circresaha.118.314216] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
On March 1 and 2, 2018, the National Institutes of Health 2018 Progenitor Cell Translational Consortium, Cardiovascular Bioengineering Symposium, was held at the University of Alabama at Birmingham. Convergence of life sciences and engineering to advance the understanding and treatment of heart failure was the theme of the meeting. Over 150 attendees were present, and >40 scientists presented their latest work on engineering human functional myocardium for disease modeling, drug development, and heart failure research. The scientists, engineers, and physicians in the field of cardiovascular sciences met and discussed the most recent advances in their work and proposed future strategies for overcoming the major roadblocks of cardiovascular bioengineering and therapy. Particular emphasis was given for manipulation and using of stem/progenitor cells, biomaterials, and methods to provide molecular, chemical, and mechanical cues to cells to influence their identity and fate in vitro and in vivo. Collectively, these works are profoundly impacting and progressing toward deciphering the mechanisms and developing novel treatments for left ventricular dysfunction of failing hearts. Here, we present some important perspectives that emerged from this meeting.
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Affiliation(s)
- Joel L Berry
- From the Department of Biomedical Engineering (J.L.B., W.Z., P.K., G.Q., J.M.R., J.Z.), University of Alabama at Birmingham
| | - Wuqiang Zhu
- From the Department of Biomedical Engineering (J.L.B., W.Z., P.K., G.Q., J.M.R., J.Z.), University of Alabama at Birmingham
| | - Yao Liang Tang
- Vascular Biology Center, Medical College of Georgia, Augusta University (Y.T.)
| | - Prasanna Krishnamurthy
- From the Department of Biomedical Engineering (J.L.B., W.Z., P.K., G.Q., J.M.R., J.Z.), University of Alabama at Birmingham
| | - Ying Ge
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, (Y.G., T.J.K.)
| | - John P Cooke
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, TX (J.P.C.)
| | - Yabing Chen
- Department of Pathology (Y.C., N.S.R.), University of Alabama at Birmingham
| | - Daniel J Garry
- Lillehei Heart Institute, Department of Medicine, Division of Cardiology, University of Minnesota, Minneapolis (D.J.G.)
| | - Huang-Tian Yang
- Shanghai Institutes for Biological Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), China (H.-T.Y.)
| | | | - Walter J Koch
- Department of Pharmacology, Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA (W.J.K.)
| | - Song Li
- Department of Bioengineering, University of California at Los Angeles (S.L.)
| | - Keitaro Domae
- Department of Cardiovascular Surgery, Graduate School of Medicine, Osaka University, Japan (K.D.)
| | - Gangjian Qin
- From the Department of Biomedical Engineering (J.L.B., W.Z., P.K., G.Q., J.M.R., J.Z.), University of Alabama at Birmingham
| | - Ke Cheng
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh (K.C.)
| | - Timothy J Kamp
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, (Y.G., T.J.K.)
| | - Lei Ye
- National Heart Research Institute Singapore, National Heart Centre Singapore (L.Y.)
| | - Shijun Hu
- Institute for Cardiovascular Science, Medical College of Soochow University, Suzhou, China (S.H.)
| | - Brenda M Ogle
- Department of Biomedical Engineering, University of Minnesota-Twin Cities, Minneapolis, MN (B.M.O.)
| | - Jack M Rogers
- From the Department of Biomedical Engineering (J.L.B., W.Z., P.K., G.Q., J.M.R., J.Z.), University of Alabama at Birmingham
| | - E Dale Abel
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Fraternal Order of Eagles Diabetes Research Center, University of Iowa Carver College of Medicine (E.D.A.)
| | - Michael E Davis
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory University School of Medicine, Atlanta (M.E.D.)
| | - Sumanth D Prabhu
- Division of Cardiovascular Disease and Comprehensive Cardiovascular Center, Department of Medicine (S.D.P.), University of Alabama at Birmingham
| | - Ronglih Liao
- Stanford Cardiovascular Institute, Department of Medicine, Stanford University School of Medicine, CA (R.L., J.C.W.)
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, MA (W.T.P.)
| | - Yibin Wang
- Department of Anesthesiology and Medicine (Y.W.), David Geffen School of Medicine, University of California, Los Angeles
| | - Peipei Ping
- Department of Physiology (P.P.), David Geffen School of Medicine, University of California, Los Angeles
| | - Nenad Bursac
- Department of Biomedical Engineering, Duke University, Durham, NC (N.B.)
| | - Gordana Vunjak-Novakovic
- Department of Biomedical Engineering and Department of Medicine, Columbia University, New York City, NY (G.V.-N.)
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Department of Medicine, Stanford University School of Medicine, CA (R.L., J.C.W.)
| | - Roberto Bolli
- Institute of Molecular Cardiology, Department of Medicine, University of Louisville, KY (R.B.)
| | - Philippe Menasché
- Department of Cardiovascular Surgery, Hôpital Européen Georges Pompidou, Paris, France (P.M.)
| | - Jianyi Zhang
- From the Department of Biomedical Engineering (J.L.B., W.Z., P.K., G.Q., J.M.R., J.Z.), University of Alabama at Birmingham
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25
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Cai W, Zhang J, de Lange WJ, Gregorich ZR, Karp H, Farrell ET, Mitchell SD, Tucholski T, Lin Z, Biermann M, McIlwain SJ, Ralphe JC, Kamp TJ, Ge Y. An Unbiased Proteomics Method to Assess the Maturation of Human Pluripotent Stem Cell-Derived Cardiomyocytes. Circ Res 2019; 125:936-953. [PMID: 31573406 DOI: 10.1161/circresaha.119.315305] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RATIONALE Human pluripotent stem cell (hPSC)-derived cardiomyocytes exhibit the properties of fetal cardiomyocytes, which limits their applications. Various methods have been used to promote maturation of hPSC-cardiomyocytes; however, there is a lack of an unbiased and comprehensive method for accurate assessment of the maturity of hPSC-cardiomyocytes. OBJECTIVE We aim to develop an unbiased proteomics strategy integrating high-throughput top-down targeted proteomics and bottom-up global proteomics for the accurate and comprehensive assessment of hPSC-cardiomyocyte maturation. METHODS AND RESULTS Utilizing hPSC-cardiomyocytes from early- and late-stage 2-dimensional monolayer culture and 3-dimensional engineered cardiac tissue, we demonstrated the high reproducibility and reliability of a top-down proteomics method, which enabled simultaneous quantification of contractile protein isoform expression and associated post-translational modifications. This method allowed for the detection of known maturation-associated contractile protein alterations and, for the first time, identified contractile protein post-translational modifications as promising new markers of hPSC-cardiomyocytes maturation. Most notably, decreased phosphorylation of α-tropomyosin was found to be associated with hPSC-cardiomyocyte maturation. By employing a bottom-up global proteomics strategy, we identified candidate maturation-associated markers important for sarcomere organization, cardiac excitability, and Ca2+ homeostasis. In particular, upregulation of myomesin 1 and transmembrane 65 was associated with hPSC-cardiomyocyte maturation and validated in cardiac development, making these promising markers for assessing maturity of hPSC-cardiomyocytes. We have further validated α-actinin isoforms, phospholamban, dystrophin, αB-crystallin, and calsequestrin 2 as novel maturation-associated markers, in the developing mouse cardiac ventricles. CONCLUSIONS We established an unbiased proteomics method that can provide accurate and specific assessment of the maturity of hPSC-cardiomyocytes and identified new markers of maturation. Furthermore, this integrated proteomics strategy laid a strong foundation for uncovering the molecular pathways involved in cardiac development and disease using hPSC-cardiomyocytes.
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Affiliation(s)
- Wenxuan Cai
- From the Molecular and Cellular Pharmacology Training Program (W.C., S.D.M., T.J.K., Y.G.), University of Wisconsin-Madison.,Department of Cell and Regenerative Biology (W.C., Z.R.G., H.K., S.D.M., Z.L., T.J.K., Y.G.), University of Wisconsin-Madison
| | - Jianhua Zhang
- Department of Medicine (J.Z., Z.R.G., M.B., T.J.K.), University of Wisconsin-Madison
| | - Willem J de Lange
- Department of Pediatrics (W.J.d.L., E.T.F., J.C.R.), University of Wisconsin-Madison
| | - Zachery R Gregorich
- Department of Cell and Regenerative Biology (W.C., Z.R.G., H.K., S.D.M., Z.L., T.J.K., Y.G.), University of Wisconsin-Madison.,Department of Medicine (J.Z., Z.R.G., M.B., T.J.K.), University of Wisconsin-Madison
| | - Hannah Karp
- Department of Cell and Regenerative Biology (W.C., Z.R.G., H.K., S.D.M., Z.L., T.J.K., Y.G.), University of Wisconsin-Madison
| | - Emily T Farrell
- Department of Pediatrics (W.J.d.L., E.T.F., J.C.R.), University of Wisconsin-Madison
| | - Stanford D Mitchell
- From the Molecular and Cellular Pharmacology Training Program (W.C., S.D.M., T.J.K., Y.G.), University of Wisconsin-Madison.,Department of Cell and Regenerative Biology (W.C., Z.R.G., H.K., S.D.M., Z.L., T.J.K., Y.G.), University of Wisconsin-Madison
| | - Trisha Tucholski
- From the Molecular and Cellular Pharmacology Training Program (W.C., S.D.M., T.J.K., Y.G.), University of Wisconsin-Madison.,Department of Chemistry (T.T., Y.G.), University of Wisconsin-Madison.,Department of Biostatistics and Medical Informatics (T.T., S.J.M.), University of Wisconsin-Madison
| | - Ziqing Lin
- Department of Cell and Regenerative Biology (W.C., Z.R.G., H.K., S.D.M., Z.L., T.J.K., Y.G.), University of Wisconsin-Madison.,Human Proteomics Program (Z.L., Y.G.), University of Wisconsin-Madison
| | - Mitch Biermann
- Department of Medicine (J.Z., Z.R.G., M.B., T.J.K.), University of Wisconsin-Madison
| | - Sean J McIlwain
- Department of Biostatistics and Medical Informatics (T.T., S.J.M.), University of Wisconsin-Madison.,UW Carbone Cancer Center (S.J.M.), University of Wisconsin-Madison
| | - J Carter Ralphe
- Department of Pediatrics (W.J.d.L., E.T.F., J.C.R.), University of Wisconsin-Madison
| | - Timothy J Kamp
- From the Molecular and Cellular Pharmacology Training Program (W.C., S.D.M., T.J.K., Y.G.), University of Wisconsin-Madison.,Department of Cell and Regenerative Biology (W.C., Z.R.G., H.K., S.D.M., Z.L., T.J.K., Y.G.), University of Wisconsin-Madison.,Department of Medicine (J.Z., Z.R.G., M.B., T.J.K.), University of Wisconsin-Madison
| | - Ying Ge
- From the Molecular and Cellular Pharmacology Training Program (W.C., S.D.M., T.J.K., Y.G.), University of Wisconsin-Madison.,Department of Cell and Regenerative Biology (W.C., Z.R.G., H.K., S.D.M., Z.L., T.J.K., Y.G.), University of Wisconsin-Madison.,Human Proteomics Program (Z.L., Y.G.), University of Wisconsin-Madison.,Department of Chemistry (T.T., Y.G.), University of Wisconsin-Madison
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26
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Bøtker HE, Hausenloy D, Andreadou I, Antonucci S, Boengler K, Davidson SM, Deshwal S, Devaux Y, Di Lisa F, Di Sante M, Efentakis P, Femminò S, García-Dorado D, Giricz Z, Ibanez B, Iliodromitis E, Kaludercic N, Kleinbongard P, Neuhäuser M, Ovize M, Pagliaro P, Rahbek-Schmidt M, Ruiz-Meana M, Schlüter KD, Schulz R, Skyschally A, Wilder C, Yellon DM, Ferdinandy P, Heusch G. Practical guidelines for rigor and reproducibility in preclinical and clinical studies on cardioprotection. Basic Res Cardiol 2018; 113:39. [PMID: 30120595 PMCID: PMC6105267 DOI: 10.1007/s00395-018-0696-8] [Citation(s) in RCA: 304] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/18/2018] [Accepted: 08/03/2018] [Indexed: 02/07/2023]
Affiliation(s)
- Hans Erik Bøtker
- Department of Cardiology, Aarhus University Hospital, Palle-Juul Jensens Boulevard 99, 8200, Aarhus N, Denmark.
| | - Derek Hausenloy
- The Hatter Cardiovascular Institute, University College London, 67 Chenies Mews, London, WC1E 6HX, UK
- The National Institute of Health Research, University College London Hospitals Biomedial Research Centre, Research and Development, London, UK
- National Heart Research Institute Singapore, National Heart Centre, Singapore, Singapore
- Yon Loo Lin School of Medicine, National University Singapore, Singapore, Singapore
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore, 8 College Road, Singapore, 169857, Singapore
| | - Ioanna Andreadou
- Laboratory of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Salvatore Antonucci
- Department of Biomedical Sciences, CNR Institute of Neuroscience, University of Padova, Via Ugo Bassi 58/B, 35121, Padua, Italy
| | - Kerstin Boengler
- Institute for Physiology, Justus-Liebig University Giessen, Giessen, Germany
| | - Sean M Davidson
- The Hatter Cardiovascular Institute, University College London, 67 Chenies Mews, London, WC1E 6HX, UK
| | - Soni Deshwal
- Department of Biomedical Sciences, CNR Institute of Neuroscience, University of Padova, Via Ugo Bassi 58/B, 35121, Padua, Italy
| | - Yvan Devaux
- Cardiovascular Research Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Fabio Di Lisa
- Department of Biomedical Sciences, CNR Institute of Neuroscience, University of Padova, Via Ugo Bassi 58/B, 35121, Padua, Italy
| | - Moises Di Sante
- Department of Biomedical Sciences, CNR Institute of Neuroscience, University of Padova, Via Ugo Bassi 58/B, 35121, Padua, Italy
| | - Panagiotis Efentakis
- Laboratory of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Saveria Femminò
- Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
| | - David García-Dorado
- Experimental Cardiology, Vall d'Hebron Institut de Recerca (VHIR), Hospital Universitari Vall d'Hebron, Pg. Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Zoltán Giricz
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Pharmahungary Group, Szeged, Hungary
| | - Borja Ibanez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), IIS-Fundación Jiménez Díaz, CIBERCV, Madrid, Spain
| | - Efstathios Iliodromitis
- Second Department of Cardiology, Faculty of Medicine, Attikon University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Nina Kaludercic
- Department of Biomedical Sciences, CNR Institute of Neuroscience, University of Padova, Via Ugo Bassi 58/B, 35121, Padua, Italy
| | - Petra Kleinbongard
- Institute for Pathophysiology, West German Heart and Vascular Center, University of Essen Medical School, Essen, Germany
| | - Markus Neuhäuser
- Department of Mathematics and Technology, Koblenz University of Applied Science, Remagen, Germany
- Institute for Medical Informatics, Biometry, and Epidemiology, University Hospital Essen, Essen, Germany
| | - Michel Ovize
- Explorations Fonctionnelles Cardiovasculaires, Hôpital Louis Pradel, Lyon, France
- UMR, 1060 (CarMeN), Université Claude Bernard, Lyon1, Villeurbanne, France
| | - Pasquale Pagliaro
- Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
| | - Michael Rahbek-Schmidt
- Department of Cardiology, Aarhus University Hospital, Palle-Juul Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Marisol Ruiz-Meana
- Experimental Cardiology, Vall d'Hebron Institut de Recerca (VHIR), Hospital Universitari Vall d'Hebron, Pg. Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | | | - Rainer Schulz
- Institute for Physiology, Justus-Liebig University Giessen, Giessen, Germany
| | - Andreas Skyschally
- Institute for Pathophysiology, West German Heart and Vascular Center, University of Essen Medical School, Essen, Germany
| | - Catherine Wilder
- The Hatter Cardiovascular Institute, University College London, 67 Chenies Mews, London, WC1E 6HX, UK
| | - Derek M Yellon
- The Hatter Cardiovascular Institute, University College London, 67 Chenies Mews, London, WC1E 6HX, UK
| | - Peter Ferdinandy
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Pharmahungary Group, Szeged, Hungary
| | - Gerd Heusch
- Institute for Pathophysiology, West German Heart and Vascular Center, University of Essen Medical School, Essen, Germany.
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27
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Affiliation(s)
- Donna K. Arnett
- From the College of Public Health, University of Kentucky, Lexington
| | - Steven A. Claas
- From the College of Public Health, University of Kentucky, Lexington
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28
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Wang Z, Ma H, Smith K, Wu S. Two-Dimensional Separation Using High-pH and Low-pH Reversed Phase Liquid Chromatography for Top-down Proteomics. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2018; 427:43-51. [PMID: 31097918 PMCID: PMC6516780 DOI: 10.1016/j.ijms.2017.09.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Advancements in chromatographic separation are critical to in-depth top-down proteomics of complex intact protein samples. Reversed-phase liquid chromatography is the most prevalent technique for top-down proteomics. However, in cases of high complexities and large dynamic ranges, 1D-RPLC may not provide sufficient coverage of the proteome. To address these challenges, orthogonal separation techniques are often combined to improve the coverage and the dynamic range of detection. In this study, a "salt-free" high-pH RPLC was evaluated as an orthogonal dimension of separation to conventional low-pH RPLC with top-down MS. The RPLC separations with low-pH conditions (pH=2) and high-pH conditions (pH=10) were compared to confirm the good orthogonality between high-pH and low-pH RPLC's. The offline 2D RPLC-RPLC-MS/MS analyses of intact E. coli samples were evaluated for the improvement of intact protein identifications as well as intact proteoform characterizations. Compared to the 163 proteins and 328 proteoforms identified using a 1D RPLC-MS approach, 365 proteins and 886 proteoforms were identified using the 2D RPLC-RPLC top-down MS approach. Our results demonstrate that the 2D RPLC-RPLC top-down approach holds great potential for in-depth top-down proteomics studies by utilizing the high resolving power of RPLC separations and by using mass spectrometry compatible buffers for easy sample handling for online MS analysis.
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Affiliation(s)
- Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma,
101 Stephenson Parkway, Norman, OK 73019
| | - Hongyan Ma
- Department of Chemistry and Biochemistry, University of Oklahoma,
101 Stephenson Parkway, Norman, OK 73019
| | - Kenneth Smith
- Arthritis & Clinical Immunology Research Program, Oklahoma
Medical Research Foundation, 825 N.E. 13th Street, Oklahoma City, OK 73104
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma,
101 Stephenson Parkway, Norman, OK 73019
- To whom correspondence should be addressed: Si
Wu, Ph.D., Department of Chemistry and Biochemistry, 101 Stephenson
Parkway, Room 2210, Norman, Oklahoma 73019-5251, United States, Phone: (405)
325-6931, , Fax: (405) 325-6111
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29
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Kachuk C, Doucette AA. The benefits (and misfortunes) of SDS in top-down proteomics. J Proteomics 2018; 175:75-86. [DOI: 10.1016/j.jprot.2017.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/19/2017] [Accepted: 03/03/2017] [Indexed: 12/18/2022]
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30
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31
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Senthong V, Kirsop JL, Tang WHW. Clinical Phenotyping of Heart Failure with Biomarkers: Current and Future Perspectives. Curr Heart Fail Rep 2017; 14:106-116. [PMID: 28205040 DOI: 10.1007/s11897-017-0321-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Heart failure (HF) is a complex clinical syndrome with diverse risk factors and etiologies, differing underlying pathophysiology, and large phenotypic heterogeneity. RECENT FINDINGS Advances in imaging techniques coupled with clinical trials that targeted only in those with impaired left ventricular ejection fraction (LVEF) have largely shaped the current management strategy for HF that focuses predominantly in patients with systolic HF. In contrast, there are no effective treatments for HF with preserved ejection fraction (HFpEF). Instead of this "one-size-fits-all" approach to treatment, better precision to define HF phenotypic classifications may lead to more efficient and effective HF disease management. CONCLUSION Integrating variables-including clinical variables, HF biomarkers, imaging, genotypes, metabolomics, and proteomics-can identify different pathophysiologies, lead to more precise phenotypic classification, and warrant investigation in future clinical trials.
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Affiliation(s)
- Vichai Senthong
- Department of Cardiovascular Medicine, Heart and Vascular Institute, 9500 Euclid Avenue, Desk J3-4, Cleveland, OH, 44915, USA.,Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Jennifer L Kirsop
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland, OH, USA
| | - W H Wilson Tang
- Department of Cardiovascular Medicine, Heart and Vascular Institute, 9500 Euclid Avenue, Desk J3-4, Cleveland, OH, 44915, USA. .,Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland, OH, USA. .,Center for Clinical Genomics, Cleveland Clinic, Cleveland, OH, USA.
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Costanzo M, Zacchia M, Bruno G, Crisci D, Caterino M, Ruoppolo M. Integration of Proteomics and Metabolomics in Exploring Genetic and Rare Metabolic Diseases. KIDNEY DISEASES 2017; 3:66-77. [PMID: 28868294 DOI: 10.1159/000477493] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 05/15/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Inherited metabolic disorders or inborn errors of metabolism are caused by deficiency of enzymatic activities in the catabolism of amino acids, carbohydrates, or lipids. These disorders include aminoacidopathies, urea cycle defects, organic acidemias, defects of oxidation of fatty acids, and lysosomal storage diseases. Inborn errors of metabolism constitute a significant proportion of genetic diseases, particularly in children; however, they are individually rare. Clinical phenotypes are very variable, some of them remain asymptomatic, others manifest metabolic decompensation in neonatal age, and others encompass mental retardation at later age. The clinical manifestation of these disorders can involve different organs and/or systems. Some disorders are easily managed if promptly diagnosed and treated, whereas in other cases neither diet, vitamin therapy, nor transplantation appears to prevent multi-organ impairment. SUMMARY Here, we discuss the principal challenges of metabolomics and proteomics in inherited metabolic disorders. We review the recent developments in mass spectrometry-based proteomic and metabolomic strategies. Mass spectrometry has become the most widely used platform in proteomics and metabolomics because of its ability to analyze a wide range of molecules, its optimal dynamic range, and great sensitivity. The fast measurement of a broad spectrum of metabolites in various body fluids, also collected in small samples like dried blood spots, have been facilitated by the use of mass spectrometry-based techniques. These approaches have enabled the timely diagnosis of inherited metabolic disorders, thereby facilitating early therapeutic intervention. Due to its analytical features, proteomics is suited for the basic investigation of inborn errors of metabolism. Modern approaches enable detailed functional characterization of the pathogenic biochemical processes, as achieved by quantification of proteins and identification of their regulatory chemical modifications. KEY MESSAGE Mass spectrometry-based "omics" approaches most frequently used to study the molecular mechanisms underlying inherited metabolic disorders pathophysiology are described.
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Affiliation(s)
- Michele Costanzo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II," Naples, Italy
| | - Miriam Zacchia
- Prima Divisione di Nefrologia, Dipartimento di Scienze Cardio-Toraciche e Respiratorie, Università degli studi della Campania "Luigi Vanvitelli," Scuola di Medicina, Naples, Italy
| | | | - Daniela Crisci
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II," Naples, Italy.,CEINGE - Biotecnologie Avanzate scarl, Naples, Italy
| | - Marianna Caterino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II," Naples, Italy.,CEINGE - Biotecnologie Avanzate scarl, Naples, Italy.,Associazione culturale DiSciMuS RCF, Naples, Italy
| | - Margherita Ruoppolo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II," Naples, Italy.,CEINGE - Biotecnologie Avanzate scarl, Naples, Italy.,Associazione culturale DiSciMuS RCF, Naples, Italy
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Gregorich ZR, Cai W, Lin Z, Chen AJ, Peng Y, Kohmoto T, Ge Y. Distinct sequences and post-translational modifications in cardiac atrial and ventricular myosin light chains revealed by top-down mass spectrometry. J Mol Cell Cardiol 2017; 107:13-21. [PMID: 28427997 DOI: 10.1016/j.yjmcc.2017.04.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 04/15/2017] [Indexed: 01/01/2023]
Abstract
Myosin is the principal component of the thick filaments that, through interactions with the actin thin filaments, mediates force production during muscle contraction. Myosin is a hexamer, consisting of two heavy chains, each associated with an essential (ELC) and a regulatory (RLC) light chain, which bind the lever-arm of the heavy chain and play important modulatory roles in striated muscle contraction. Nevertheless, a comprehensive assessment of the sequences of the ELC and RLC isoforms, as well as their post-translational modifications, in the heart remains lacking. Herein, utilizing top-down high-resolution mass spectrometry (MS), we have comprehensively characterized the sequences and N-terminal modifications of the atrial and ventricular isoforms of the myosin light chains from human and swine hearts, as well as the sites of phosphorylation in the swine proteins. In addition to the correction of disparities in the database sequences of the swine proteins, we show for the first time that, whereas the ventricular isoforms of the ELC and RLC are methylated at their N-termini, which is consistent with previous studies, the atrial isoforms of the ELC and RLC from both human and swine are Nα-methylated and Nα-acetylated, respectively. Furthermore, top-down MS with electron capture dissociation enabled localization of the sites of phosphorylation in swine RLC isoforms from the ventricles and atria to Ser14 and Ser22, respectively. Collectively, these results provide new insights into the sequences and modifications of myosin light chain isoforms in the human and swine hearts, which will pave the way for a better understanding of their functional roles in cardiac physiology and pathophysiology.
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Affiliation(s)
- Zachery R Gregorich
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Wenxuan Cai
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ziqing Lin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Albert J Chen
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ying Peng
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Takushi Kohmoto
- Department of Surgery, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ying Ge
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA; Human Proteomics Program, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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The clinical utility of mass spectrometry based protein assays. Clin Chim Acta 2016; 459:155-161. [DOI: 10.1016/j.cca.2016.05.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/25/2016] [Accepted: 05/30/2016] [Indexed: 11/22/2022]
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Cai W, Tucholski TM, Gregorich ZR, Ge Y. Top-down Proteomics: Technology Advancements and Applications to Heart Diseases. Expert Rev Proteomics 2016; 13:717-30. [PMID: 27448560 DOI: 10.1080/14789450.2016.1209414] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Heart diseases are a leading cause of morbidity and mortality for both men and women worldwide, and impose significant economic burdens on the healthcare systems. Despite substantial effort over the last several decades, the molecular mechanisms underlying diseases of the heart remain poorly understood. AREAS COVERED Altered protein post-translational modifications (PTMs) and protein isoform switching are increasingly recognized as important disease mechanisms. Top-down high-resolution mass spectrometry (MS)-based proteomics has emerged as the most powerful method for the comprehensive analysis of PTMs and protein isoforms. Here, we will review recent technology developments in the field of top-down proteomics, as well as highlight recent studies utilizing top-down proteomics to decipher the cardiac proteome for the understanding of the molecular mechanisms underlying diseases of the heart. Expert commentary: Top-down proteomics is a premier method for the global and comprehensive study of protein isoforms and their PTMs, enabling the identification of novel protein isoforms and PTMs, characterization of sequence variations, and quantification of disease-associated alterations. Despite significant challenges, continuous development of top-down proteomics technology will greatly aid the dissection of the molecular mechanisms underlying diseases of the hearts for the identification of novel biomarkers and therapeutic targets.
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Affiliation(s)
- Wenxuan Cai
- a Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , WI , USA.,b Molecular and Cellular Pharmacology Training Program , University of Wisconsin-Madison , Madison , WI , USA
| | - Trisha M Tucholski
- c Department of Chemistry , University of Wisconsin-Madison , Madison , WI , USA
| | - Zachery R Gregorich
- a Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , WI , USA.,b Molecular and Cellular Pharmacology Training Program , University of Wisconsin-Madison , Madison , WI , USA
| | - Ying Ge
- a Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , WI , USA.,c Department of Chemistry , University of Wisconsin-Madison , Madison , WI , USA.,d Human Proteomics Program , University of Wisconsin-Madison , Madison , WI , USA
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Abstract
Advances in mass spectrometry technology and bioinformatics using clinical human samples have expanded quantitative proteomics in cardiovascular research. There are two major proteomic strategies: namely, "gel-based" or "gel-free" proteomics coupled with either "top-down" or "bottom-up" mass spectrometry. Both are introduced into the proteomic analysis using plasma or serum sample targeting 'biomarker" searches of aortic aneurysm and tissue samples, such as from the aneurysmal wall, calcific aortic valve, or myocardial tissue, investigating pathophysiological protein interactions and post-translational modifications. We summarize the proteomic studies that analyzed human samples taken during cardiovascular surgery to investigate disease processes, in order to better understand the system-wide changes behind known molecular factors and specific signaling pathways.
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Affiliation(s)
- Teiji Oda
- Division of Thoracic and Cardiovascular Surgery, Department of Surgery, Shimane University Faculty of Medicine, 89-1 Enya-cho, Izumo, Shimane, 693-8501, Japan.
| | - Ken-ichi Matsumoto
- Department of Biosignaling and Radioisotope Experiment, Interdisciplinary Center for Science Research, Organization for Research, Shimane University, Izumo, Shimane, Japan
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Chandrasekera PC, Pippin JJ. The human subject: an integrative animal model for 21(st) century heart failure research. Am J Transl Res 2015; 7:1636-47. [PMID: 26550463 PMCID: PMC4626425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/13/2015] [Indexed: 06/05/2023]
Abstract
Heart failure remains a leading cause of death and it is a major cause of morbidity and mortality affecting tens of millions of people worldwide. Despite decades of extensive research conducted at enormous expense, only a handful of interventions have significantly impacted survival in heart failure. Even the most widely prescribed treatments act primarily to slow disease progression, do not provide sustained survival advantage, and have adverse side effects. Since mortality remains about 50% within five years of diagnosis, the need to increase our understanding of heart failure disease mechanisms and development of preventive and reparative therapies remains critical. Currently, the vast majority of basic science heart failure research is conducted using animal models ranging from fruit flies to primates; however, insights gleaned from decades of animal-based research efforts have not been proportional to research success in terms of deciphering human heart failure and developing effective therapeutics for human patients. Here we discuss the reasons for this translational discrepancy which can be equally attributed to the use of erroneous animal models and the lack of widespread use of human-based research methodologies and address why and how we must position our own species at center stage as the quintessential animal model for 21(st) century heart failure research. If the ultimate goal of the scientific community is to tackle the epidemic status of heart failure, the best way to achieve that goal is through prioritizing human-based, human-relevant research.
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Affiliation(s)
| | - John J Pippin
- Physicians Committee for Responsible Medicine Washington, D. C., USA
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Abstract
Heart failure in children is a complex clinical syndrome with multiple aetiologies. The underlying disorders that lead to heart failure in children differ significantly from those in adults. Some clinical biomarkers for heart failure status and prognosis appear to be useful in both age groups. This review outlines the use and the present status of biomarkers for heart failure in paediatric cardiology. Furthermore, clinical scenarios in which development of new biomarkers might address management or prognosis are discussed. Finally, strategies for proteomic discovery of novel biomarkers and application to practice are described.
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Lindsey ML, Mayr M, Gomes AV, Delles C, Arrell DK, Murphy AM, Lange RA, Costello CE, Jin YF, Laskowitz DT, Sam F, Terzic A, Van Eyk J, Srinivas PR. Transformative Impact of Proteomics on Cardiovascular Health and Disease: A Scientific Statement From the American Heart Association. Circulation 2015. [PMID: 26195497 DOI: 10.1161/cir.0000000000000226] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The year 2014 marked the 20th anniversary of the coining of the term proteomics. The purpose of this scientific statement is to summarize advances over this period that have catalyzed our capacity to address the experimental, translational, and clinical implications of proteomics as applied to cardiovascular health and disease and to evaluate the current status of the field. Key successes that have energized the field are delineated; opportunities for proteomics to drive basic science research, facilitate clinical translation, and establish diagnostic and therapeutic healthcare algorithms are discussed; and challenges that remain to be solved before proteomic technologies can be readily translated from scientific discoveries to meaningful advances in cardiovascular care are addressed. Proteomics is the result of disruptive technologies, namely, mass spectrometry and database searching, which drove protein analysis from 1 protein at a time to protein mixture analyses that enable large-scale analysis of proteins and facilitate paradigm shifts in biological concepts that address important clinical questions. Over the past 20 years, the field of proteomics has matured, yet it is still developing rapidly. The scope of this statement will extend beyond the reaches of a typical review article and offer guidance on the use of next-generation proteomics for future scientific discovery in the basic research laboratory and clinical settings.
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Dissecting human skeletal muscle troponin proteoforms by top-down mass spectrometry. J Muscle Res Cell Motil 2015; 36:169-81. [PMID: 25613324 DOI: 10.1007/s10974-015-9404-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 01/07/2015] [Indexed: 01/26/2023]
Abstract
Skeletal muscles are the most abundant tissues in the human body. They are composed of a heterogeneous collection of muscle fibers that perform various functions. Skeletal muscle troponin (sTn) regulates skeletal muscle contraction and relaxation. sTn consists of 3 subunits, troponin I (TnI), troponin T (TnT), and troponin C (TnC). TnI inhibits the actomyosin Mg(2+)-ATPase, TnC binds Ca(2+), and TnT is the tropomyosin (Tm)-binding subunit. The cardiac and skeletal isoforms of Tn share many similarities but the roles of modifications of Tn in the two muscles may differ. The modifications of cardiac Tn are known to alter muscle contractility and have been well-characterized. However, the modification status of sTn remains unclear. Here, we have employed top-down mass spectrometry (MS) to decipher the modifications of human sTnT and sTnI. We have extensively characterized sTnT and sTnI proteoforms, including alternatively spliced isoforms and post-translationally modified forms, found in human skeletal muscle with high mass accuracy and comprehensive sequence coverage. Moreover, we have localized the phosphorylation site of slow sTnT isoform III to Ser1 by tandem MS with electron capture dissociation. This is the first study to comprehensively characterize human sTn and also the first to identify the basal phosphorylation site for human sTnT by top-down MS.
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Ying P, Serife AG, Deyang Y, Ying G. Top-down mass spectrometry of cardiac myofilament proteins in health and disease. Proteomics Clin Appl 2014; 8:554-68. [PMID: 24945106 PMCID: PMC4231170 DOI: 10.1002/prca.201400043] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/21/2014] [Accepted: 06/12/2014] [Indexed: 12/29/2022]
Abstract
Myofilaments are composed of thin and thick filaments that coordinate with each other to regulate muscle contraction and relaxation. PTMs together with genetic variations and alternative splicing of the myofilament proteins play essential roles in regulating cardiac contractility in health and disease. Therefore, a comprehensive characterization of the myofilament proteins in physiological and pathological conditions is essential for better understanding the molecular basis of cardiac function and dysfunction. Due to the vast complexity and dynamic nature of proteins, it is challenging to obtain a holistic view of myofilament protein modifications. In recent years, top-down MS has emerged as a powerful approach to study isoform composition and PTMs of proteins owing to its advantage of complete sequence coverage and its ability to identify PTMs and sequence variants without a priori knowledge. In this review, we will discuss the application of top-down MS to the study of cardiac myofilaments and highlight the insights it provides into the understanding of molecular mechanisms in contractile dysfunction of heart failure. Particularly, recent results of cardiac troponin and tropomyosin modifications will be elaborated. The limitations and perspectives on the use of top-down MS for myofilament protein characterization will also be briefly discussed.
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Affiliation(s)
- Peng Ying
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Ayaz-Guner Serife
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Yu Deyang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Molecular and Environmental Toxicology Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Ge Ying
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
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