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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 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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2
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Chapman EA, Li BH, Krichel B, Chan HJ, Buck KM, Roberts DS, Ge Y. Native Top-Down Mass Spectrometry for Characterizing Sarcomeric Proteins Directly from Cardiac Tissue Lysate. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:738-745. [PMID: 38422011 PMCID: PMC11098619 DOI: 10.1021/jasms.3c00430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Native top-down mass spectrometry (nTDMS) has emerged as a powerful structural biology tool that can localize post-translational modifications (PTMs), explore ligand-binding interactions, and elucidate the three-dimensional structure of proteins and protein complexes in the gas-phase. Fourier-transform ion cyclotron resonance (FTICR) MS offers distinct capabilities for nTDMS, owing to its ultrahigh resolving power, mass accuracy, and robust fragmentation techniques. Previous nTDMS studies using FTICR have mainly been applied to overexpressed recombinant proteins and protein complexes. Here, we report the first nTDMS study that directly analyzes human heart tissue lysate by direct infusion FTICR MS without prior chromatographic separation strategies. We have achieved comprehensive nTDMS characterization of cardiac contractile proteins that play critical roles in heart contraction and relaxation. Specifically, our results reveal structural insights into ventricular myosin light chain 2 (MLC-2v), ventricular myosin light chain 1 (MLC-1v), and alpha-tropomyosin (α-Tpm) in the sarcomere, the basic contractile unit of cardiac muscle. Furthermore, we verified the calcium (Ca2+) binding domain in MLC-2v. In summary, our nTDMS platform extends the application of FTICR MS to directly characterize the structure, PTMs, and metal-binding of endogenous proteins from heart tissue lysate without prior separation methods.
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Affiliation(s)
- Emily A. Chapman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Brad H. Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Boris Krichel
- School of Life Sciences, University of Siegen, 57076, Germany
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Hsin-Ju Chan
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Kevin M. Buck
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - David S. Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, 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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3
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Lambert MR, Gussoni E. Tropomyosin 3 (TPM3) function in skeletal muscle and in myopathy. Skelet Muscle 2023; 13:18. [PMID: 37936227 PMCID: PMC10629095 DOI: 10.1186/s13395-023-00327-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/10/2023] [Indexed: 11/09/2023] Open
Abstract
The tropomyosin genes (TPM1-4) contribute to the functional diversity of skeletal muscle fibers. Since its discovery in 1988, the TPM3 gene has been recognized as an indispensable regulator of muscle contraction in slow muscle fibers. Recent advances suggest that TPM3 isoforms hold more extensive functions during skeletal muscle development and in postnatal muscle. Additionally, mutations in the TPM3 gene have been associated with the features of congenital myopathies. The use of different in vitro and in vivo model systems has leveraged the discovery of several disease mechanisms associated with TPM3-related myopathy. Yet, the precise mechanisms by which TPM3 mutations lead to muscle dysfunction remain unclear. This review consolidates over three decades of research about the role of TPM3 in skeletal muscle. Overall, the progress made has led to a better understanding of the phenotypic spectrum in patients affected by mutations in this gene. The comprehensive body of work generated over these decades has also laid robust groundwork for capturing the multiple functions this protein plays in muscle fibers.
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Affiliation(s)
- Matthias R Lambert
- Division of Genetics and Genomics, Boston Children's Hospital, 300 Longwood Ave., Boston, MA, 02115, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
| | - Emanuela Gussoni
- Division of Genetics and Genomics, Boston Children's Hospital, 300 Longwood Ave., Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- The Stem Cell Program, Boston Children's Hospital, Boston, MA, 02115, USA
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4
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Kopylova GV, Kochurova AM, Yampolskaya DS, Nefedova VV, Tsaturyan AK, Koubassova NA, Kleymenov SY, Levitsky DI, Bershitsky SY, Matyushenko AM, Shchepkin DV. Structural and Functional Properties of Kappa Tropomyosin. Int J Mol Sci 2023; 24:ijms24098340. [PMID: 37176047 PMCID: PMC10179609 DOI: 10.3390/ijms24098340] [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: 03/27/2023] [Revised: 04/27/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
In the myocardium, the TPM1 gene expresses two isoforms of tropomyosin (Tpm), alpha (αTpm; Tpm 1.1) and kappa (κTpm; Tpm 1.2). κTpm is the result of alternative splicing of the TPM1 gene. We studied the structural features of κTpm and its regulatory function in the atrial and ventricular myocardium using an in vitro motility assay. We tested the possibility of Tpm heterodimer formation from α- and κ-chains. Our result shows that the formation of ακTpm heterodimer is thermodynamically favorable, and in the myocardium, κTpm most likely exists as ακTpm heterodimer. Using circular dichroism, we compared the thermal unfolding of ααTpm, ακTpm, and κκTpm. κκTpm had the lowest stability, while the ακTpm was more stable than ααTpm. The differential scanning calorimetry results indicated that the thermal stability of the N-terminal part of κκTpm is much lower than that of ααTpm. The affinity of ααTpm and κκTpm to F-actin did not differ, and ακTpm interacted with F-actin significantly worse. The troponin T1 fragment enhanced the κκTpm and ακTpm affinity to F-actin. κκTpm differently affected the calcium regulation of the interaction of pig and rat ventricular myosin with the thin filament. With rat myosin, calcium sensitivity of thin filaments containing κκTpm was significantly lower than that with ααTpm and with pig myosin, and the sensitivity did not differ. Thin filaments containing κκTpm and ακTpm were better activated by pig atrial myosin than those containing ααTpm.
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Affiliation(s)
- Galina V Kopylova
- Institute of Immunology and Physiology, Russian Academy of Sciences, 620049 Yekaterinburg, Russia
| | - Anastasia M Kochurova
- Institute of Immunology and Physiology, Russian Academy of Sciences, 620049 Yekaterinburg, Russia
| | - Daria S Yampolskaya
- Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Victoria V Nefedova
- Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | | | | | - Sergey Y Kleymenov
- Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Dmitrii I Levitsky
- Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Sergey Y Bershitsky
- Institute of Immunology and Physiology, Russian Academy of Sciences, 620049 Yekaterinburg, Russia
| | | | - Daniil V Shchepkin
- Institute of Immunology and Physiology, Russian Academy of Sciences, 620049 Yekaterinburg, Russia
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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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6
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Tropomyosin Isoform Diversity in the Cynomolgus Monkey Heart and Skeletal Muscles Compared to Human Tissues. Biochem Res Int 2023; 2023:1303500. [PMID: 36733713 PMCID: PMC9889151 DOI: 10.1155/2023/1303500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/26/2022] [Accepted: 11/21/2022] [Indexed: 01/25/2023] Open
Abstract
Old world monkeys separated from the great apes, including the ancestor of humans, about 25 million years ago, but most of the genes in humans and various nonhuman primates are quite similar even though their anatomical appearances are quite different. Like other mammals, primates have four tropomyosin genes (TPM1, TPM2, TPM3, and TPM4) each of which generates a multitude of TPM isoforms via alternative splicing. Only TPM1 produces two sarcomeric isoforms (TPM1α and TPM1κ), and TPM2, TPM3, and TPM4 each generate one sarcomeric isoform. We have cloned and sequenced TPM1α, TPM1κ, TPM2α, TPM3α, and TPM4α with RNA from cynomolgus (Cyn) monkey hearts and skeletal muscle. We believe this is the first report of directly cloning and sequencing of these monkey transcripts. In the Cyn monkey heart, the rank order of TPM isoform expression is TPM1α > TPM2α > TPM1κ > TPM3α > TPM4α. In the Cyn monkey skeletal muscle, the rank order of expression is TPM1α > TPM2α > TPM3α > TPM1κ > TPM4α. The major differences in the human heart are the increased expression of TPM1κ, although TPM1α is still the dominant transcript. In the Cyn monkey heart, the only sarcomeric TPM isoform at the protein level is TPM1α. This is in contrast to human hearts where TPM1α is the major sarcomeric isoform but a lower quantity of TPM1κ, TPM2α, and TPM3α is also detected at the protein level. These differences of tropomyosin and/or other cardiac protein expression in human and Cyn monkey hearts may reflect the differences in physiological activities in daily life.
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7
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Tucholski T, Ge Y. Fourier-transform ion cyclotron resonance mass spectrometry for characterizing proteoforms. MASS SPECTROMETRY REVIEWS 2022; 41:158-177. [PMID: 32894796 PMCID: PMC7936991 DOI: 10.1002/mas.21653] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 08/26/2020] [Accepted: 08/26/2020] [Indexed: 05/05/2023]
Abstract
Proteoforms contribute functional diversity to the proteome and aberrant proteoforms levels have been implicated in biological dysfunction and disease. Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS), with its ultrahigh mass-resolving power, mass accuracy, and versatile tandem MS capabilities, has empowered top-down, middle-down, and native MS-based approaches for characterizing proteoforms and their complexes in biological systems. Herein, we review the features which make FT-ICR MS uniquely suited for measuring proteoform mass with ultrahigh resolution and mass accuracy; obtaining in-depth proteoform sequence coverage with expansive tandem MS capabilities; and unambiguously identifying and localizing post-translational and noncovalent modifications. We highlight examples from our body of work in which we have quantified and comprehensively characterized proteoforms from cardiac and skeletal muscle to better understand conditions such as chronic heart failure, acute myocardial infarction, and sarcopenia. Structural characterization of monoclonal antibodies and their proteoforms by FT-ICR MS and emerging applications, such as native top-down FT-ICR MS and high-throughput top-down FT-ICR MS-based proteomics at 21 T, are also covered. Historically, the information gleaned from FT-ICR MS analyses have helped provide biological insights. We predict FT-ICR MS will continue to enable the study of proteoforms of increasing size from increasingly complex endogenous mixtures and facilitate the benchmarking of sensitive and specific assays for clinical diagnostics. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Trisha Tucholski
- Department of Chemistry, 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, 53706
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53705
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8
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Corbett JR, Robinson DE, Patrie SM. Robustness and Ruggedness of Isoelectric Focusing and Superficially Porous Liquid Chromatography with Fourier Transform Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:346-354. [PMID: 33274937 PMCID: PMC10476448 DOI: 10.1021/jasms.0c00355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
An investigation of a multidimensional proteomics workflow composed of off-gel isoelectric focusing (IEF) and superficially porous liquid chromatography (SPLC) with Fourier transform mass spectrometry (FTMS) was completed in order to assess various figures of merit associated with intact protein measurements. Triplicate analysis performed at both high and low FTMS resolutions on the E. coli proteome resulted in ∼900 redundant proteoforms from 3 to 95 kDa. Normalization of the chromatographic axis to identified proteoforms enabled reproducible physicochemical property measurements between proteome replicates with inter-replicate variances of ±3 ppm mass error for proteoforms <30 kDa, ±1.1 Da for proteins >30 kDa, ±12 s retention time error, and ±0.21 pI units. The results for E. coli and standard proteins revealed a correlation between pI precision and proteoform abundance with species detected in multiple IEF fractions exhibiting pI precisions less than the theoretical resolution of the off-gel system (±0.05 vs ±0.17, respectively). Evaluation of differentially modified proteoforms of standard proteins revealed that high sample loads (100s μgrams) change the IEF pH gradient profile, leading to sample broadening that facilitates resolution of charged post-translational modifications (e.g., phosphorylation, sialylation). Despite the impact of sample load on IEF resolution, results on standard proteins measured directly or after being spiked into E. coli demonstrated that the reproducibility of the workflow permitted recombination of the MS signal across IEF fractions in a manner supporting the evaluation of three label-free quantitation metrics for intact protein studies (proteoforms, proteoform ratios, and protein) over 102-103 sample amount with low femtomole detection limits.
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Affiliation(s)
- John R Corbett
- Department of Pathology, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
- Department of Bioengineering, UT Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
| | - Dana E Robinson
- Department of Pathology, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Steven M Patrie
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Pathology, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
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9
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Melby JA, de Lange WJ, Zhang J, Roberts DS, Mitchell SD, Tucholski T, Kim G, Kyrvasilis A, McIlwain SJ, Kamp TJ, Ralphe JC, Ge Y. Functionally Integrated Top-Down Proteomics for Standardized Assessment of Human Induced Pluripotent Stem Cell-Derived Engineered Cardiac Tissues. J Proteome Res 2021; 20:1424-1433. [PMID: 33395532 DOI: 10.1021/acs.jproteome.0c00830] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Three-dimensional (3D) human induced pluripotent stem cell-derived engineered cardiac tissues (hiPSC-ECTs) have emerged as a promising alternative to two-dimensional hiPSC-cardiomyocyte monolayer systems because hiPSC-ECTs are a closer representation of endogenous cardiac tissues and more faithfully reflect the relevant cardiac pathophysiology. The ability to perform functional and molecular assessments using the same hiPSC-ECT construct would allow for more reliable correlation between observed functional performance and underlying molecular events, and thus is critically needed. Herein, for the first time, we have established an integrated method that permits sequential assessment of functional properties and top-down proteomics from the same single hiPSC-ECT construct. We quantitatively determined the differences in isometric twitch force and the sarcomeric proteoforms between two groups of hiPSC-ECTs that differed in the duration of time of 3D-ECT culture. Importantly, by using this integrated method we discovered a new and strong correlation between the measured contractile parameters and the phosphorylation levels of alpha-tropomyosin between the two groups of hiPSC-ECTs. The integration of functional assessments together with molecular characterization by top-down proteomics in the same hiPSC-ECT construct enables a holistic analysis of hiPSC-ECTs to accelerate their applications in disease modeling, cardiotoxicity, and drug discovery. Data are available via ProteomeXchange with identifier PXD022814.
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Affiliation(s)
- Jake A Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Willem J de Lange
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Jianhua Zhang
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Stanford D Mitchell
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Gina Kim
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Andreas Kyrvasilis
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Sean J McIlwain
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Timothy J Kamp
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - J Carter Ralphe
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin 53705, 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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10
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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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11
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Dube DK, Dube S, Abbott L, Elsekaily O, Sanger JW, Sanger JM, Poiesz BJ. Sarcomeric TPM3 expression in human heart and skeletal muscle. Cytoskeleton (Hoboken) 2020; 77:313-328. [PMID: 32761805 DOI: 10.1002/cm.21629] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/30/2020] [Accepted: 08/03/2020] [Indexed: 01/28/2023]
Abstract
In mammals, four tropomyosin genes TPM1, TPM2, TPM3, and TPM4 are known. One isoform of the TPM3 gene, encoding 285 amino acid residues designated as TPM3α, has been reported. TPM3α protein expression in human hearts is not definitively established. We have cloned from human heart and skeletal muscle transcripts of TPM3α and three novel TPM3 isoforms, TPM3ν, TPM3ξ, and TPM3ο. TPM3ν and TPM3ο are alternatively spliced RNAs with different 3'-UTRs encoding an identical novel protein with 285 amino acid differing from TPM3α and TPM3ξ in exon 6 only. TPM3α and TPM3ξ, which have different 3'UTRs, also encode an identical protein. qRT-PCR data show that the transcripts of TPM3α, TPM3ν, TPM3ξ, and TPM3ο are expressed in both heart and skeletal muscle. We have evaluated the expression of various TPM proteins in fetal and adult human hearts, and also in skeletal muscle samples. Western blots using CG3 antibody show a stronger signal of TPM3 protein in fetal heart and adult skeletal muscle compared to adult heart. LC-MS/MS studies with the protein spots separated and identified by CH1 antibody after 2D Western blot analyses, confirm the expression of TPM3α/TPM3ξ in heart, but some peptides detected could be either TPM3α or TPM3ν. In heart samples, TPM1 protein was the dominant with varying amount of TPM2 and TPM3, while TPM4 expression was not observed. In skeletal muscles, TPM2 was the majority TPM protein expressed. The biological consequences of these varying expression of individual tropomyosin proteins are yet to be established.
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Affiliation(s)
- Dipak K Dube
- Department of Medicine, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Syamalima Dube
- Department of Medicine, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Lynn Abbott
- Department of Medicine, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Omar Elsekaily
- Department of Medicine, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Joseph W Sanger
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Jean M Sanger
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Bernard J Poiesz
- Department of Medicine, SUNY Upstate Medical University, Syracuse, New York, USA
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12
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Nollet EE, Manders EM, Goebel M, Jansen V, Brockmann C, Osinga J, van der Velden J, Helmes M, Kuster DWD. Large-Scale Contractility Measurements Reveal Large Atrioventricular and Subtle Interventricular Differences in Cultured Unloaded Rat Cardiomyocytes. Front Physiol 2020; 11:815. [PMID: 32848817 PMCID: PMC7396550 DOI: 10.3389/fphys.2020.00815] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 06/18/2020] [Indexed: 01/22/2023] Open
Abstract
The chambers of the heart fulfill different hemodynamic functions, which are reflected in their structural and contractile properties. While the atria are highly elastic to allow filling from the venous system, the ventricles need to be able to produce sufficiently high pressures to eject blood into the circulation. The right ventricle (RV) pumps into the low pressure pulmonary circulation, while the left ventricle (LV) needs to overcome the high pressure of the systemic circulation. It is incompletely understood whether these differences can be explained by the contractile differences at the level of the individual cardiomyocytes of the chambers. We addressed this by isolating cardiomyocytes from atria, RV, LV, and interventricular septum (IVS) of five healthy wild-type rats. Using a high-throughput contractility set-up, we measured contractile function of 2,043 cells after overnight culture. Compared to ventricular cardiomyocytes, atrial cells showed a twofold lower contraction amplitude and 1.4- to 1.7-fold slower kinetics of contraction and relaxation. The interventricular differences in contractile function were much smaller; RV cells displayed 12–13% less fractional shortening and 5–9% slower contraction and 3–15% slower relaxation kinetics relative to their LV and IVS counterparts. Aided by a large dataset, we established relationships between contractile parameters and found contraction velocity, fractional shortening and relaxation velocity to be highly correlated. In conclusion, our findings are in line with contractile differences observed at the atrioventricular level, but can only partly explain the interventricular differences that exist at the organ level.
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Affiliation(s)
- Edgar E Nollet
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands
| | | | - Max Goebel
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands
| | - Valentijn Jansen
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands
| | - Cord Brockmann
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands
| | - Jorrit Osinga
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands
| | - Jolanda van der Velden
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands
| | - Michiel Helmes
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands.,CytoCypher BV, Wageningen, Netherlands
| | - Diederik W D Kuster
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands
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13
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Kwon YS, Jung JW, Kim YJ, Park CB, Shon JC, Kim JH, Park JW, Kim SG, Seo JS. Proteomic analysis of whole-body responses in medaka ( Oryzias latipes) exposed to benzalkonium chloride. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2020; 55:1387-1397. [PMID: 32693679 DOI: 10.1080/10934529.2020.1796117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 07/09/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Abstract
Benzalkonium chloride (BAC) is a cationic surfactant commonly used as a disinfectant, and is discharged into the aquatic environment by various water sources such as wastewater. BAC may also interact with potentially toxic substances such as persistent organic chemicals. Although studies of BAC contamination toxicity and bioaccumulation have been widely reported, the biochemical responses to BAC toxicity remain incompletely understood, and the detailed molecular mechanisms are largely unknown. In this study, two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry-based proteomic approaches were applied to investigate the protein profiles in Oryzias latipes (medaka) chronically exposed to BAC. Fish were exposed to three different concentrations of BAC, 0.05, 0.1, and 0.2 mg/L, for 21 days. A total of 20 proteins involved in the cytoskeleton, the oxidative stress response, the nervous and endocrine systems, signaling pathways, and cellular proteolysis were significantly upregulated by BAC exposure. The proteomic information obtained in the present study will be useful in identification of potential biomarkers for BAC toxicity, and begins to elucidate its molecular mechanisms, providing new insights into the ecotoxicity of BAC.
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Affiliation(s)
- Young Sang Kwon
- Environmental Chemistry Research Group, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, Republic of Korea
| | - Jae-Woong Jung
- Environmental Biology Research Group, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, Republic of Korea
| | - Yeong Jin Kim
- Environmental Chemistry Research Group, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, Republic of Korea
| | - Chang-Beom Park
- Ecotoxicology Research Group, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, Republic of Korea
| | - Jong Cheol Shon
- Environmental Chemistry Research Group, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, Republic of Korea
| | - Jong-Hwan Kim
- Environmental Chemistry Research Group, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, Republic of Korea
| | - June-Woo Park
- Environmental Biology Research Group, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, Republic of Korea
| | - Sang Gon Kim
- Gyeongnam Oriental Anti-aging Institute, Sancheong, Republic of Korea
| | - Jong-Su Seo
- Environmental Chemistry Research Group, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, Republic of Korea
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14
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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 2019; 19:446-454. [PMID: 31647247 DOI: 10.1021/acs.jproteome.9b00623] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [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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15
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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: 46] [Impact Index Per Article: 9.2] [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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16
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Thin filament dysfunctions caused by mutations in tropomyosin Tpm3.12 and Tpm1.1. J Muscle Res Cell Motil 2019; 41:39-53. [PMID: 31270709 PMCID: PMC7109180 DOI: 10.1007/s10974-019-09532-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/26/2019] [Indexed: 12/14/2022]
Abstract
Tropomyosin is the major regulator of the thin filament. In striated muscle its function is to bind troponin complex and control the access of myosin heads to actin in a Ca2+-dependent manner. It also participates in the maintenance of thin filament length by regulation of tropomodulin and leiomodin, the pointed end-binding proteins. Because the size of the overlap between actin and myosin filaments affects the number of myosin heads which interact with actin, the filament length is one of the determinants of force development. Numerous point mutations in genes encoding tropomyosin lead to single amino acid substitutions along the entire length of the coiled coil that are associated with various types of cardiomyopathy and skeletal muscle disease. Specific regions of tropomyosin interact with different binding partners; therefore, the mutations affect diverse tropomyosin functions. In this review, results of studies on mutations in the genes TPM1 and TPM3, encoding Tpm1.1 and Tpm3.12, are described. The paper is particularly focused on mutation-dependent alterations in the mechanisms of actin-myosin interactions and dynamics of the thin filament at the pointed end.
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17
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Tucholski T, Knott SJ, Chen B, Pistono P, Lin Z, Ge Y. A Top-Down Proteomics Platform Coupling Serial Size Exclusion Chromatography and Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Anal Chem 2019; 91:3835-3844. [PMID: 30758949 DOI: 10.1021/acs.analchem.8b04082] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mass spectrometry (MS) based top-down proteomics provides rich information about proteoforms arising from combinatorial amino acid sequence variations and post-translational modifications (PTMs). Fourier transform ion cyclotron resonance (FT-ICR) MS affords ultrahigh resolving power and provides high-accuracy mass measurements, presenting a powerful tool for top-down MS characterization of proteoforms. However, the detection and characterization of large proteins from complex mixtures remain challenging due to the exponential decrease in S: N with increasing molecular weight (MW) and coeluting low-MW proteins; thus, size-based fractionation of complex protein mixtures prior to MS analysis is necessary. Here, we directly combine MS-compatible serial size exclusion chromatography (sSEC) fractionation with 12 T FT-ICR MS for targeted top-down characterization of proteins from complex mixtures extracted from human and swine heart tissue. Benefiting from the ultrahigh resolving power of FT-ICR, we isotopically resolved 31 distinct proteoforms (30-50 kDa) simultaneously in a single mass spectrum within a 100 m/ z window. Notably, within a 5 m/ z window, we obtained baseline isotopic resolution for 6 distinct large proteoforms (30-50 kDa). The ultrahigh resolving power of FT-ICR MS combined with sSEC fractionation enabled targeted top-down analysis of large proteoforms (>30 kDa) from the human heart proteome without extensive chromatographic separation or protein purification. Further separation of proteoforms inside the mass spectrometer (in-MS) allowed for isolation of individual proteoforms and targeted electron capture dissociation (ECD), yielding high sequence coverage. sSEC/FT-ICR ECD facilitated the identification and sequence characterization of important metabolic enzymes. This platform, which facilitates deep interrogation of proteoform primary structure, is highly tunable, allows for adjustment of MS and MS/MS parameters in real time, and can be utilized for a variety of complex protein mixtures.
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Affiliation(s)
- Trisha Tucholski
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Human Proteomics Program , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Samantha J Knott
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Human Proteomics Program , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Bifan Chen
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Human Proteomics Program , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Paige Pistono
- Department of Biochemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Ziqing Lin
- Department of Cell and Regenerative Biology , University of Wisconsin-Madison , 1111 Highland Avenue , WIMR II 8551, Madison , Wisconsin 53705 , United States
| | - Ying Ge
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Human Proteomics Program , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States.,Department of Cell and Regenerative Biology , University of Wisconsin-Madison , 1111 Highland Avenue , WIMR II 8551, Madison , Wisconsin 53705 , United States
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18
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Dube DK, Dube S, Shrestha R, Abbott L, Randhawa S, Muthu V, Fan Y, Wang J, Sanger JM, Sanger JW, Poiesz BJ. Qualitative and quantitative evaluation of TPM transcripts and proteins in developing striated chicken muscles indicate TPM4α is the major sarcomeric cardiac tropomyosin from early embryonic life to adulthood. Cytoskeleton (Hoboken) 2018; 75:437-449. [PMID: 30255988 PMCID: PMC6279486 DOI: 10.1002/cm.21495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/13/2018] [Accepted: 07/30/2018] [Indexed: 11/09/2022]
Abstract
The chicken has been used since the 1980s as an animal model for developmental studies regarding tropomyosin isoform diversity in striated muscles, however, the pattern of expression of transcripts as well as the corresponding TPM proteins of various tropomyosin isoforms in avian hearts are not well documented. In this study, using conventional and qRT-PCR, we report the expression of transcripts for various sarcomeric TPM isoforms in striated muscles through development. Transcripts of both TPM1α and TPM1κ, the two sarcomeric isoforms of the TPM1 gene, are expressed in embryonic chicken hearts but disappear in post hatch stages. TPM1α transcripts are expressed in embryonic and adult skeletal muscle. The sarcomeric isoform of the TPM2 gene is expressed mostly in embryonic skeletal muscles. As reported earlier, TPM3α is expressed in embryonic heart and skeletal muscle but significantly lower in adult striated muscle. TPM4α transcripts are expressed from embryonic to adult chicken hearts but not in skeletal muscle. Our 2D Western blot analyses using CH1 monoclonal antibody followed by mass spectra evaluations found TPM4α protein is the major sarcomeric tropomysin expressed in embryonic chicken hearts. However, in 7-day-old embryonic hearts, a minute quantity of TPM1α or TPM1κ is also expressed. This finding suggests that sarcomeric TPM1 protein may play some important role in cardiac contractility and/or cardiac morphogenesis during embryogenesis. Since only the transcripts of TPM4α are expressed in adult chicken hearts, it is logical to presume that TPM4α is the only sarcomeric TPM protein produced in adult cardiac tissues.
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Affiliation(s)
- Dipak K Dube
- Department of Medicine, Upatate Medical University, Syracuse, New York
| | - Syamalima Dube
- Department of Medicine, Upatate Medical University, Syracuse, New York
| | - Runa Shrestha
- Department of Medicine, Upatate Medical University, Syracuse, New York
| | - Lynn Abbott
- Department of Medicine, Upatate Medical University, Syracuse, New York
| | - Samender Randhawa
- Department of Medicine, Upatate Medical University, Syracuse, New York
| | - Vasundhara Muthu
- Department of Medicine, Upatate Medical University, Syracuse, New York
| | - Yingli Fan
- Department of Cell and Developmental Biology, Upatate Medical University, Syracuse, New York
| | - Jushuo Wang
- Department of Cell and Developmental Biology, Upatate Medical University, Syracuse, New York
| | - Jean M Sanger
- Department of Cell and Developmental Biology, Upatate Medical University, Syracuse, New York
| | - Joseph W Sanger
- Department of Cell and Developmental Biology, Upatate Medical University, Syracuse, New York
| | - Bernard J Poiesz
- Department of Medicine, Upatate Medical University, Syracuse, New York
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19
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Śliwinska M, Robaszkiewicz K, Czajkowska M, Zheng W, Moraczewska J. Functional effects of substitutions I92T and V95A in actin-binding period 3 of tropomyosin. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:558-568. [PMID: 29496559 DOI: 10.1016/j.bbapap.2018.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 02/12/2018] [Accepted: 02/23/2018] [Indexed: 01/10/2023]
Affiliation(s)
- Małgorzata Śliwinska
- Department of Biochemistry and Cell Biology, Faculty of Natural Sciences, Kazimierz Wielki University in Bydgoszcz, Ks. J. Poniatowskiego 12 Str., 85-671 Bydgoszcz, Poland
| | - Katarzyna Robaszkiewicz
- Department of Biochemistry and Cell Biology, Faculty of Natural Sciences, Kazimierz Wielki University in Bydgoszcz, Ks. J. Poniatowskiego 12 Str., 85-671 Bydgoszcz, Poland
| | - Marta Czajkowska
- Department of Biochemistry and Cell Biology, Faculty of Natural Sciences, Kazimierz Wielki University in Bydgoszcz, Ks. J. Poniatowskiego 12 Str., 85-671 Bydgoszcz, Poland
| | - Wenjun Zheng
- Department of Physics, University at Buffalo, SUNY, Buffalo, NY 14260, United States
| | - Joanna Moraczewska
- Department of Biochemistry and Cell Biology, Faculty of Natural Sciences, Kazimierz Wielki University in Bydgoszcz, Ks. J. Poniatowskiego 12 Str., 85-671 Bydgoszcz, Poland.
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20
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Wei L, Gregorich ZR, Lin Z, Cai W, Jin Y, McKiernan SH, McIlwain S, Aiken JM, Moss RL, Diffee GM, Ge Y. Novel Sarcopenia-related Alterations in Sarcomeric Protein Post-translational Modifications (PTMs) in Skeletal Muscles Identified by Top-down Proteomics. Mol Cell Proteomics 2017; 17:134-145. [PMID: 29046390 DOI: 10.1074/mcp.ra117.000124] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 10/17/2017] [Indexed: 11/06/2022] Open
Abstract
Sarcopenia, the age-related loss of skeletal muscle mass and strength, is a significant cause of morbidity in the elderly and is a major burden on health care systems. Unfortunately, the underlying molecular mechanisms in sarcopenia remain poorly understood. Herein, we utilized top-down proteomics to elucidate sarcopenia-related changes in the fast- and slow-twitch skeletal muscles of aging rats with a focus on the sarcomeric proteome, which includes both myofilament and Z-disc proteins-the proteins that constitute the contractile apparatuses. Top-down quantitative proteomics identified significant changes in the post-translational modifications (PTMs) of critical myofilament proteins in the fast-twitch skeletal muscles of aging rats, in accordance with the vulnerability of fast-twitch muscles to sarcopenia. Surprisingly, age-related alterations in the phosphorylation of Cypher isoforms, proteins that localize to the Z-discs in striated muscles, were also noted in the fast-twitch skeletal muscle of aging rats. This represents the first report of changes in the phosphorylation of Z-disc proteins in skeletal muscle during aging. In addition, increased glutathionylation of slow skeletal troponin I, a novel modification that may help protect against oxidative damage, was observed in slow-twitch skeletal muscles. Furthermore, we have identified and characterized novel muscle type-specific proteoforms of myofilament proteins and Z-disc proteins, including a novel isoform of the Z-disc protein Enigma. The finding that the phosphorylation of Z-disc proteins is altered in response to aging in the fast-twitch skeletal muscles of aging rats opens new avenues for the investigation of the role of Z-discs in age-related muscle dysfunction.
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Affiliation(s)
- Liming Wei
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705.,§Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, P. R. China
| | - Zachery R Gregorich
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705.,¶Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705
| | - Ziqing Lin
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705.,‖Human Proteomics Program,University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705
| | - Wenxuan Cai
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705.,¶Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705
| | - Yutong Jin
- **Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin, 53706
| | - Susan H McKiernan
- ‡‡Department of Kinesiology, University of Wisconsin-Madison, 2000 Observatory Dr., Madison, Wisconsin, 53705
| | - Sean McIlwain
- §§Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, 600 Highland Ave., Madison, Wisconsin, 53792.,¶¶UW Carbone Cancer Center, University of Wisconsin-Madison, 600 Highland Ave., Madison, Wisconsin, 53792
| | - Judd M Aiken
- ‖‖Departments of Agriculture, Food, and Nutritional Sciences, University of Alberta-Edmonton, Edmonton, AB, Canada
| | - Richard L Moss
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705.,‖Human Proteomics Program,University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705
| | - Gary M Diffee
- ‡‡Department of Kinesiology, University of Wisconsin-Madison, 2000 Observatory Dr., Madison, Wisconsin, 53705
| | - Ying Ge
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705; .,¶Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705.,‖Human Proteomics Program,University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705.,**Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin, 53706
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21
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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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Cloning, Sequencing, and the Expression of the Elusive Sarcomeric TPM4 α Isoform in Humans. Mol Biol Int 2016; 2016:3105478. [PMID: 27703814 PMCID: PMC5040813 DOI: 10.1155/2016/3105478] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/22/2016] [Accepted: 08/10/2016] [Indexed: 01/05/2023] Open
Abstract
In mammals, tropomyosin is encoded by four known TPM genes (TPM1, TPM2, TPM3, and TPM4) each of which can generate a number of TPM isoforms via alternative splicing and/or using alternate promoters. In humans, the sarcomeric isoform(s) of each of the TPM genes, except for the TPM4, have been known for a long time. Recently, on the basis of computational analyses of the human genome sequence, the predicted sequence of TPM4α has been posted in GenBank. We designed primer-pairs for RT-PCR and showed the expression of the transcripts of TPM4α and a novel isoform TPM4δ in human heart and skeletal muscle. qRT-PCR shows that the relative expression of TPM4α and TPM4δ is higher in human cardiac muscle. Western blot analyses using CH1 monoclonal antibodies show the absence of the expression of TPM4δ protein (~28 kDa) in human heart muscle. 2D western blot analyses with the same antibody show the expression of at least nine distinct tropomyosin molecules with a mass ~32 kD and above in adult heart. By Mass spectrometry, we determined the amino acid sequences of the extracted proteins from these spots. Spot “G” reveals the putative expression of TPM4α along with TPM1α protein in human adult heart.
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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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24
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Jin Y, Peng Y, Lin Z, Chen YC, Wei L, Hacker TA, Larsson L, Ge Y. Comprehensive analysis of tropomyosin isoforms in skeletal muscles by top-down proteomics. J Muscle Res Cell Motil 2016; 37:41-52. [PMID: 27090236 PMCID: PMC4955698 DOI: 10.1007/s10974-016-9443-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 04/07/2016] [Indexed: 01/09/2023]
Abstract
Mammalian skeletal muscles are heterogeneous in nature and are capable of performing various functions. Tropomyosin (Tpm) is a major component of the thin filament in skeletal muscles and plays an important role in controlling muscle contraction and relaxation. Tpm is known to consist of multiple isoforms resulting from different encoding genes and alternative splicing, along with post-translational modifications. However, a systematic characterization of Tpm isoforms in skeletal muscles is still lacking. Therefore, we employed top-down mass spectrometry (MS) to identify and characterize Tpm isoforms present in different skeletal muscles from multiple species, including swine, rat, and human. Our study revealed that Tpm1.1 and Tpm2.2 are the two major Tpm isoforms in swine and rat skeletal muscles, whereas Tpm1.1, Tpm2.2, and Tpm3.12 are present in human skeletal muscles. Tandem MS was utilized to identify the sequences of the major Tpm isoforms. Furthermore, quantitative analysis revealed muscle-type specific differences in the abundance of un-modified and modified Tpm isoforms in rat and human skeletal muscles. This study represents the first systematic investigation of Tpm isoforms in skeletal muscles, which not only demonstrates the capabilities of top-down MS for the comprehensive characterization of skeletal myofilament proteins but also provides the basis for further studies on these Tpm isoforms in muscle-related diseases.
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Affiliation(s)
- Yutong Jin
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
| | - Ying Peng
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705, USA
- Human Proteomics Program, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Ziqing Lin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705, USA
- Human Proteomics Program, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Yi-Chen Chen
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
| | - Liming Wei
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705, USA
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, P.R. China
| | - Timothy A Hacker
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Lars Larsson
- Department of Physiology and Pharmacology, Department of Clinical Neuroscience, Clinical Neurophysiology Section, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA.
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705, USA.
- Human Proteomics Program, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705, USA.
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25
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Zhang X, Schulz BL, Punyadeera C. The current status of heart failure diagnostic biomarkers. Expert Rev Mol Diagn 2016; 16:487-500. [PMID: 26788983 DOI: 10.1586/14737159.2016.1144474] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Heart failure (HF) affects approximately 23 million individuals worldwide and this number is increasing, due to an aging and growing population. Early detection of HF is crucial in the management of this debilitating disease. Current diagnostic methods for HF rely heavily on clinical imaging techniques and blood analysis, which makes them less than ideal for population-based screening purposes. Studies focusing on developing novel biomarkers for HF have utilized various techniques and biological fluids, including urine and saliva. Promising results from these studies imply that these body fluids can be used in evaluating the clinical manifestation of HF and will one day be integrated into a clinical workflow and facilitate HF management.
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Affiliation(s)
- Xi Zhang
- a The School of Biomedical Sciences , Institute of Health and Biomedical Innovations, Queensland University of Technology , Brisbane , Queensland , Australia
| | - Benjamin L Schulz
- b School of Chemistry and Molecular Biosciences , The University of Queensland , Brisbane , Queensland , Australia
| | - Chamindie Punyadeera
- a The School of Biomedical Sciences , Institute of Health and Biomedical Innovations, Queensland University of Technology , Brisbane , Queensland , Australia
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26
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Yu D, Peng Y, Ayaz-Guner S, Gregorich ZR, Ge Y. Comprehensive Characterization of AMP-Activated Protein Kinase Catalytic Domain by Top-Down Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:220-32. [PMID: 26489410 PMCID: PMC4840101 DOI: 10.1007/s13361-015-1286-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 09/25/2015] [Accepted: 09/26/2015] [Indexed: 05/12/2023]
Abstract
AMP-activated protein kinase (AMPK) is a serine/threonine protein kinase that is essential in regulating energy metabolism in all eukaryotic cells. It is a heterotrimeric protein complex composed of a catalytic subunit (α) and two regulatory subunits (β and γ). C-terminal truncation of AMPKα at residue 312 yielded a protein that is active upon phosphorylation of Thr172 in the absence of β and γ subunits, which is refered to as the AMPK catalytic domain and commonly used to substitute for the AMPK heterotrimeric complex in in vitro kinase assays. However, a comprehensive characterization of the AMPK catalytic domain is lacking. Herein, we expressed a His-tagged human AMPK catalytic domin (denoted as AMPKΔ) in E. coli, comprehensively characterized AMPKΔ in its basal state and after in vitro phosphorylation using top-down mass spectrometry (MS), and assessed how phosphorylation of AMPKΔ affects its activity. Unexpectedly, we found that bacterially-expressed AMPKΔ was basally phosphorylated and localized the phosphorylation site to the His-tag. We found that AMPKΔ had noticeable basal activity and was capable of phosphorylating itself and its substrates without activating phosphorylation at Thr172. Moreover, our data suggested that Thr172 is the only site phosphorylated by its upstream kinase, liver kinase B1, and that this phosphorylation dramatically increases the kinase activity of AMPKΔ. Importantly, we demonstrated that top-down MS in conjunction with in vitro phosphorylation assay is a powerful approach for monitoring phosphorylation reaction and determining sequential order of phosphorylation events in kinase-substrate systems.
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Affiliation(s)
- Deyang Yu
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Molecular and Environmental Toxicology Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Ying Peng
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Serife Ayaz-Guner
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Zachery R. Gregorich
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Ying Ge
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Molecular and Environmental Toxicology Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Molecular and Cellular Pharmacology Training Program, 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
- Address reprint requests to: Dr. Ying Ge, 1300 University Ave., SMI 130, Madison, Wisconsin, USA. Tel: 608-263-9212, Fax: 608-265-5512,
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27
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Gregorich ZR, Peng Y, Lane NM, Wolff JJ, Wang S, Guo W, Guner H, Doop J, Hacker TA, Ge Y. Comprehensive assessment of chamber-specific and transmural heterogeneity in myofilament protein phosphorylation by top-down mass spectrometry. J Mol Cell Cardiol 2015; 87:102-12. [PMID: 26268593 DOI: 10.1016/j.yjmcc.2015.08.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 08/04/2015] [Accepted: 08/08/2015] [Indexed: 11/28/2022]
Abstract
The heart is characterized by a remarkable degree of heterogeneity, the basis of which is a subject of active investigation. Myofilament protein post-translational modifications (PTMs) represent a critical mechanism regulating cardiac contractility, and emerging evidence shows that pathological cardiac conditions induce contractile heterogeneity that correlates with transmural variations in the modification status of myofilament proteins. Nevertheless, whether there exists basal heterogeneity in myofilament protein PTMs in the heart remains unclear. Here we have systematically assessed chamber-specific and transmural variations in myofilament protein PTMs, specifically, the phosphorylation of cardiac troponin I (cTnI), cardiac troponin T (cTnT), tropomyosin (Tpm), and myosin light chain 2 (MLC2). We show that the phosphorylation of cTnI and αTm vary in the different chambers of the heart, whereas the phosphorylation of MLC2 and cTnT does not. In contrast, no significant transmural differences were observed in the phosphorylation of any of the myofilament proteins analyzed. These results highlight the importance of appropriate tissue sampling-particularly for studies aimed at elucidating disease mechanisms and biomarker discovery-in order to minimize potential variations arising from basal heterogeneity in myofilament PTMs in the heart.
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Affiliation(s)
- Zachery R Gregorich
- Molecular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ying Peng
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nicole M Lane
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA; Cellular and Molecular Pathology Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Sijian Wang
- Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Wei Guo
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Huseyin Guner
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA; Human Proteomics Program, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Justin Doop
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Timothy A Hacker
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ying Ge
- Molecular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA; Cellular and Molecular Pathology Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA; Human Proteomics Program, University of Wisconsin-Madison, Madison, WI 53706, USA.
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28
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Abascal F, Ezkurdia I, Rodriguez-Rivas J, Rodriguez JM, del Pozo A, Vázquez J, Valencia A, Tress ML. Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level. PLoS Comput Biol 2015; 11:e1004325. [PMID: 26061177 PMCID: PMC4465641 DOI: 10.1371/journal.pcbi.1004325] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 05/08/2015] [Indexed: 11/19/2022] Open
Abstract
Alternative splicing of messenger RNA can generate a wide variety of mature RNA transcripts, and these transcripts may produce protein isoforms with diverse cellular functions. While there is much supporting evidence for the expression of alternative transcripts, the same is not true for the alternatively spliced protein products. Large-scale mass spectroscopy experiments have identified evidence of alternative splicing at the protein level, but with conflicting results. Here we carried out a rigorous analysis of the peptide evidence from eight large-scale proteomics experiments to assess the scale of alternative splicing that is detectable by high-resolution mass spectroscopy. We find fewer splice events than would be expected: we identified peptides for almost 64% of human protein coding genes, but detected just 282 splice events. This data suggests that most genes have a single dominant isoform at the protein level. Many of the alternative isoforms that we could identify were only subtly different from the main splice isoform. Very few of the splice events identified at the protein level disrupted functional domains, in stark contrast to the two thirds of splice events annotated in the human genome that would lead to the loss or damage of functional domains. The most striking result was that more than 20% of the splice isoforms we identified were generated by substituting one homologous exon for another. This is significantly more than would be expected from the frequency of these events in the genome. These homologous exon substitution events were remarkably conserved—all the homologous exons we identified evolved over 460 million years ago—and eight of the fourteen tissue-specific splice isoforms we identified were generated from homologous exons. The combination of proteomics evidence, ancient origin and tissue-specific splicing indicates that isoforms generated from homologous exons may have important cellular roles. Alternative splicing is thought to be one means for generating the protein diversity necessary for the whole range of cellular functions. While the presence of alternatively spliced transcripts in the cell has been amply demonstrated, the same cannot be said for alternatively spliced proteins. The quest for alternative protein isoforms has focused primarily on the analysis of peptides from large-scale mass spectroscopy experiments, but evidence for alternative isoforms has been patchy and contradictory. A careful analysis of the peptide evidence is needed to fully understand the scale of alternative splicing detectable at the protein level. Here we analysed peptides from eight large-scale data sets, identifying just 282 splice events among 12,716 genes. This suggests that most genes have a single dominant isoform. Many of the alternative isoforms that we identified were only subtly different from the main splice variant, and one in five was generated by substitution of homologous exons by swapping one related exon for another. Remarkably, the alternative isoforms generated from homologous exons were highly conserved, first appearing 460 million years ago, and several appear to have tissue-specific roles in the brain and heart. Our results suggest that these particular isoforms are likely to have important cellular roles.
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Affiliation(s)
- Federico Abascal
- Structural Biology and Bioinformatics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Iakes Ezkurdia
- Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Juan Rodriguez-Rivas
- Structural Biology and Bioinformatics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Jose Manuel Rodriguez
- National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Angela del Pozo
- Instituto de Genetica Medica y Molecular, Hospital Universitario La Paz, Madrid, Spain
| | - Jesús Vázquez
- Laboratorio de Proteómica Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares (CNIC) Madrid, Spain
| | - Alfonso Valencia
- Structural Biology and Bioinformatics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- * E-mail: (AV); (MLT)
| | - Michael L. Tress
- Structural Biology and Bioinformatics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- * E-mail: (AV); (MLT)
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Phosphorylation of Ser283 enhances the stiffness of the tropomyosin head-to-tail overlap domain. Arch Biochem Biophys 2015; 571:10-5. [PMID: 25726728 DOI: 10.1016/j.abb.2015.02.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 02/19/2015] [Accepted: 02/20/2015] [Indexed: 12/15/2022]
Abstract
The ends of coiled-coil tropomyosin molecules are joined together by nine to ten residue-long head-to-tail "overlapping domains". These short four-chained interconnections ensure formation of continuous tropomyosin cables that wrap around actin filaments. Molecular Dynamics simulations indicate that the curvature and bending flexibility at the overlap is 10-20% greater than over the rest of the molecule, which might affect head-to-tail filament assembly on F-actin. Since the penultimate residue of striated muscle tropomyosin, Ser283, is a natural target of phosphorylating enzymes, we have assessed here if phosphorylation adjusts the mechanical properties of the tropomyosin overlap domain. MD simulations show that phosphorylation straightens the overlap to match the curvature of the remainder of tropomyosin while stiffening it to equal or exceed the rigidity of canonical coiled-coil regions. Corresponding EM data on phosphomimetic tropomyosin S283D corroborate these findings. The phosphorylation-induced change in mechanical properties of tropomyosin likely results from electrostatic interactions between C-terminal phosphoSer283 and N-terminal Lys12 in the four-chain overlap bundle, while promoting stronger interactions among surrounding residues and thus facilitating tropomyosin cable assembly. The stiffening effect of D283-tropomyosin noted correlates with previously observed enhanced actin-tropomyosin activation of myosin S1-ATPase, suggesting a role for the tropomyosin phosphorylation in potentiating muscle contraction.
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30
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Mahr C, Gundry RL. Hold or fold--proteins in advanced heart failure and myocardial recovery. Proteomics Clin Appl 2014; 9:121-33. [PMID: 25331159 DOI: 10.1002/prca.201400100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/17/2014] [Accepted: 10/14/2014] [Indexed: 12/14/2022]
Abstract
Advanced heart failure (AHF) describes the subset of heart failure patients refractory to conventional medical therapy. For some AHF patients, the use of mechanical circulatory support (MCS) provides an intermediary "bridge" step for transplant-eligible patients or an alternative therapy for transplant-ineligible patients. Over the past 20 years, clinical observations have revealed that approximately 1% of patients with MCS undergo significant reverse remodeling to the point where the device can be explanted. Unfortunately, it is unclear why some patients experience durable, sustained myocardial remission, while others redevelop heart failure (i.e. which hearts "hold" and which hearts "fold"). In this review, we outline unmet clinical needs related to treating patients with MCS, provide an overview of protein dynamics in the reverse-remodeling process, and propose specific areas where we expect MS and proteomic analyses will have significant impact on our understanding of disease progression, molecular mechanisms of recovery, and provide new markers with prognostic value that can positively impact patient care. Complimentary perspectives are provided with the goal of making this important topic accessible and relevant to both a clinical and basic science audience, as the intersection of these disciplines is required to advance the field.
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Affiliation(s)
- Claudius Mahr
- Division of Cardiology, University of Washington, Seattle, WA, USA
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31
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Reinwarth M, Avrutina O, Fabritz S, Kolmar H. Fragmentation follows structure: top-down mass spectrometry elucidates the topology of engineered cystine-knot miniproteins. PLoS One 2014; 9:e108626. [PMID: 25303319 PMCID: PMC4193770 DOI: 10.1371/journal.pone.0108626] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 09/02/2014] [Indexed: 12/21/2022] Open
Abstract
Over the last decades the field of pharmaceutically relevant peptides has enormously expanded. Among them, several peptide families exist that contain three or more disulfide bonds. In this context, elucidation of the disulfide patterns is extremely important as these motifs are often prerequisites for folding, stability, and activity. An example of this structure-determining pattern is a cystine knot which comprises three constrained disulfide bonds and represents a core element in a vast number of mechanically interlocked peptidic structures possessing different biological activities. Herein, we present our studies on disulfide pattern determination and structure elucidation of cystine-knot miniproteins derived from Momordica cochinchinensis peptide MCoTI-II, which act as potent inhibitors of human matriptase-1. A top-down mass spectrometric analysis of the oxidised and bioactive peptides is described. Following the detailed sequencing of the peptide backbone, interpretation of the MS(3) spectra allowed for the verification of the knotted topology of the examined miniproteins. Moreover, we found that the fragmentation pattern depends on the knottin's folding state, hence, tertiary structure, which to our knowledge has not been described for a top-down MS approach before.
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Affiliation(s)
- Michael Reinwarth
- Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Olga Avrutina
- Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | | | - Harald Kolmar
- Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
- * E-mail: (SF); (HK)
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32
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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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Peng Y, Gregorich ZR, Valeja SG, Zhang H, Cai W, Chen YC, Guner H, Chen AJ, Schwahn DJ, Hacker TA, Liu X, Ge Y. Top-down proteomics reveals concerted reductions in myofilament and Z-disc protein phosphorylation after acute myocardial infarction. Mol Cell Proteomics 2014; 13:2752-64. [PMID: 24969035 PMCID: PMC4189000 DOI: 10.1074/mcp.m114.040675] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Heart failure (HF) is a leading cause of morbidity and mortality worldwide and is most often precipitated by myocardial infarction. However, the molecular changes driving cardiac dysfunction immediately after myocardial infarction remain poorly understood. Myofilament proteins, responsible for cardiac contraction and relaxation, play critical roles in signal reception and transduction in HF. Post-translational modifications of myofilament proteins afford a mechanism for the beat-to-beat regulation of cardiac function. Thus it is of paramount importance to gain a comprehensive understanding of post-translational modifications of myofilament proteins involved in regulating early molecular events in the post-infarcted myocardium. We have developed a novel liquid chromatography–mass spectrometry-based top-down proteomics strategy to comprehensively assess the modifications of key cardiac proteins in the myofilament subproteome extracted from a minimal amount of myocardial tissue with high reproducibility and throughput. The entire procedure, including tissue homogenization, myofilament extraction, and on-line LC/MS, takes less than three hours. Notably, enabled by this novel top-down proteomics technology, we discovered a concerted significant reduction in the phosphorylation of three crucial cardiac proteins in acutely infarcted swine myocardium: cardiac troponin I and myosin regulatory light chain of the myofilaments and, unexpectedly, enigma homolog isoform 2 (ENH2) of the Z-disc. Furthermore, top-down MS allowed us to comprehensively sequence these proteins and pinpoint their phosphorylation sites. For the first time, we have characterized the sequence of ENH2 and identified it as a phosphoprotein. ENH2 is localized at the Z-disc, which has been increasingly recognized for its role as a nodal point in cardiac signaling. Thus our proteomics discovery opens up new avenues for the investigation of concerted signaling between myofilament and Z-disc in the early molecular events that contribute to cardiac dysfunction and progression to HF.
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Affiliation(s)
- Ying Peng
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Zachery R Gregorich
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706; §Molecular Pharmacology Training Program, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Santosh G Valeja
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Han Zhang
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Wenxuan Cai
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706; §Molecular Pharmacology Training Program, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Yi-Chen Chen
- ¶Department of Chemistry, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Huseyin Guner
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706; ‖Human Proteomics Program, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Albert J Chen
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Denise J Schwahn
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Timothy A Hacker
- ‡‡Department of Medicine, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Xiaowen Liu
- §§Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 719 Indiana Ave., Indianapolis, Indiana 46202; ¶¶Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 West 10th Street, Indianapolis, Indiana 46202
| | - Ying Ge
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706; ¶Department of Chemistry, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706; ‖Human Proteomics Program, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706;
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Gregorich ZR, Chang YH, Ge Y. Proteomics in heart failure: top-down or bottom-up? Pflugers Arch 2014; 466:1199-209. [PMID: 24619480 DOI: 10.1007/s00424-014-1471-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 01/31/2014] [Accepted: 02/04/2014] [Indexed: 01/11/2023]
Abstract
The pathophysiology of heart failure (HF) is diverse, owing to multiple etiologies and aberrations in a number of cellular processes. Therefore, it is essential to understand how defects in the molecular pathways that mediate cellular responses to internal and external stressors function as a system to drive the HF phenotype. Mass spectrometry (MS)-based proteomics strategies have great potential for advancing our understanding of disease mechanisms at the systems level because proteins are the effector molecules for all cell functions and, thus, are directly responsible for determining cell phenotype. Two MS-based proteomics strategies exist: peptide-based bottom-up and protein-based top-down proteomics--each with its own unique strengths and weaknesses for interrogating the proteome. In this review, we will discuss the advantages and disadvantages of bottom-up and top-down MS for protein identification, quantification, and analysis of post-translational modifications, as well as highlight how both of these strategies have contributed to our understanding of the molecular and cellular mechanisms underlying HF. Additionally, the challenges associated with both proteomics approaches will be discussed and insights will be offered regarding the future of MS-based proteomics in HF research.
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Affiliation(s)
- Zachery R Gregorich
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI, USA
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Introducing a special edition of the Journal of Muscle Research and Cell Motility on tropomyosin: form and function. J Muscle Res Cell Motil 2013; 34:151-3. [PMID: 24101402 DOI: 10.1007/s10974-013-9361-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 09/19/2013] [Indexed: 10/26/2022]
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