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Karpov OA, Stotland A, Raedschelders K, Chazarin B, Ai L, Murray CI, Van Eyk JE. Proteomics of the heart. Physiol Rev 2024; 104:931-982. [PMID: 38300522 PMCID: PMC11381016 DOI: 10.1152/physrev.00026.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/25/2023] [Accepted: 01/14/2024] [Indexed: 02/02/2024] Open
Abstract
Mass spectrometry-based proteomics is a sophisticated identification tool specializing in portraying protein dynamics at a molecular level. Proteomics provides biologists with a snapshot of context-dependent protein and proteoform expression, structural conformations, dynamic turnover, and protein-protein interactions. Cardiac proteomics can offer a broader and deeper understanding of the molecular mechanisms that underscore cardiovascular disease, and it is foundational to the development of future therapeutic interventions. This review encapsulates the evolution, current technologies, and future perspectives of proteomic-based mass spectrometry as it applies to the study of the heart. Key technological advancements have allowed researchers to study proteomes at a single-cell level and employ robot-assisted automation systems for enhanced sample preparation techniques, and the increase in fidelity of the mass spectrometers has allowed for the unambiguous identification of numerous dynamic posttranslational modifications. Animal models of cardiovascular disease, ranging from early animal experiments to current sophisticated models of heart failure with preserved ejection fraction, have provided the tools to study a challenging organ in the laboratory. Further technological development will pave the way for the implementation of proteomics even closer within the clinical setting, allowing not only scientists but also patients to benefit from an understanding of protein interplay as it relates to cardiac disease physiology.
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Affiliation(s)
- Oleg A Karpov
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Aleksandr Stotland
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Koen Raedschelders
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Blandine Chazarin
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Lizhuo Ai
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Christopher I Murray
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Jennifer E Van Eyk
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
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Belenichev I, Popazova O, Bukhtiyarova N, Savchenko D, Oksenych V, Kamyshnyi O. Modulating Nitric Oxide: Implications for Cytotoxicity and Cytoprotection. Antioxidants (Basel) 2024; 13:504. [PMID: 38790609 PMCID: PMC11118938 DOI: 10.3390/antiox13050504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 05/26/2024] Open
Abstract
Despite the significant progress in the fields of biology, physiology, molecular medicine, and pharmacology; the designation of the properties of nitrogen monoxide in the regulation of life-supporting functions of the organism; and numerous works devoted to this molecule, there are still many open questions in this field. It is widely accepted that nitric oxide (•NO) is a unique molecule that, despite its extremely simple structure, has a wide range of functions in the body, including the cardiovascular system, the central nervous system (CNS), reproduction, the endocrine system, respiration, digestion, etc. Here, we systematize the properties of •NO, contributing in conditions of physiological norms, as well as in various pathological processes, to the mechanisms of cytoprotection and cytodestruction. Current experimental and clinical studies are contradictory in describing the role of •NO in the pathogenesis of many diseases of the cardiovascular system and CNS. We describe the mechanisms of cytoprotective action of •NO associated with the regulation of the expression of antiapoptotic and chaperone proteins and the regulation of mitochondrial function. The most prominent mechanisms of cytodestruction-the initiation of nitrosative and oxidative stresses, the production of reactive oxygen and nitrogen species, and participation in apoptosis and mitosis. The role of •NO in the formation of endothelial and mitochondrial dysfunction is also considered. Moreover, we focus on the various ways of pharmacological modulation in the nitroxidergic system that allow for a decrease in the cytodestructive mechanisms of •NO and increase cytoprotective ones.
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Affiliation(s)
- Igor Belenichev
- Department of Pharmacology and Medical Formulation with Course of Normal Physiology, Zaporizhzhia State Medical and Pharmaceutical University, 69000 Zaporizhzhia, Ukraine
| | - Olena Popazova
- Department of Histology, Cytology and Embryology, Zaporizhzhia State Medical and Pharmaceutical University, 69000 Zaporizhzhia, Ukraine
| | - Nina Bukhtiyarova
- Department of Clinical Laboratory Diagnostics, Zaporizhzhia State Medical and Pharmaceutical University, 69000 Zaporizhzhia, Ukraine
| | - Dmytro Savchenko
- Department of Pharmacy and Industrial Drug Technology, Bogomolets National Medical University, 01601 Kyiv, Ukraine
| | - Valentyn Oksenych
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
| | - Oleksandr Kamyshnyi
- Department of Microbiology, Virology and Immunology, I. Horbachevsky Ternopil State Medical University, 46001 Ternopil, Ukraine;
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Cai W, Wang Y, Luo Y, Gao L, Zhang J, Jiang Z, Fan X, Li F, Xie Y, Wu X, Li Y, Yuan W. asb5a/ asb5b Double Knockout Affects Zebrafish Cardiac Contractile Function. Int J Mol Sci 2023; 24:16364. [PMID: 38003559 PMCID: PMC10671462 DOI: 10.3390/ijms242216364] [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: 10/08/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Ankyrin repeat and suppression-of-cytokine-signaling box (Asb) proteins, a subset of ubiquitin ligase E3, include Asb5 with six ankyrin-repeat domains. Zebrafish harbor two asb5 gene isoforms, asb5a and asb5b. Currently, the effects of asb5 gene inactivation on zebrafish embryonic development and heart function are unknown. Using CRISPR/Cas9, we generated asb5a-knockout zebrafish, revealing no abnormal phenotypes at 48 h post-fertilization (hpf). In situ hybridization showed similar asb5a and asb5b expression patterns, indicating the functional redundancy of these isoforms. Morpholino interference was used to target asb5b in wild-type and asb5a-knockout zebrafish. Knocking down asb5b in the wild-type had no phenotypic impact, but simultaneous asb5b knockdown in asb5a-knockout homozygotes led to severe pericardial cavity enlargement and atrial dilation. RNA-seq and cluster analyses identified significantly enriched cardiac muscle contraction genes in the double-knockout at 48 hpf. Moreover, semi-automatic heartbeat analysis demonstrated significant changes in various heart function indicators. STRING database/Cytoscape analyses confirmed that 11 cardiac-contraction-related hub genes exhibited disrupted expression, with three modules containing these genes potentially regulating cardiac contractile function through calcium ion channels. This study reveals functional redundancy in asb5a and asb5b, with simultaneous knockout significantly impacting zebrafish early heart development and contraction, providing key insights into asb5's mechanism.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Yongqing Li
- The Laboratary of Heart Development Research, College of Life Science, Hunan Normal University, Changsha 410081, China; (W.C.); (Y.W.); (Y.L.); (L.G.); (J.Z.); (Z.J.); (X.F.); (F.L.); (Y.X.); (X.W.)
| | - Wuzhou Yuan
- The Laboratary of Heart Development Research, College of Life Science, Hunan Normal University, Changsha 410081, China; (W.C.); (Y.W.); (Y.L.); (L.G.); (J.Z.); (Z.J.); (X.F.); (F.L.); (Y.X.); (X.W.)
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Bayne EF, Rossler KJ, Gregorich ZR, Aballo TJ, Roberts DS, Chapman EA, Guo W, Palecek SP, Ralphe JC, Kamp TJ, Ge Y. Top-down proteomics of myosin light chain isoforms define chamber-specific expression in the human heart. J Mol Cell Cardiol 2023; 181:89-97. [PMID: 37327991 PMCID: PMC10528938 DOI: 10.1016/j.yjmcc.2023.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 05/27/2023] [Accepted: 06/13/2023] [Indexed: 06/18/2023]
Abstract
Myosin functions as the "molecular motor" of the sarcomere and generates the contractile force necessary for cardiac muscle contraction. Myosin light chains 1 and 2 (MLC-1 and -2) play important functional roles in regulating the structure of the hexameric myosin molecule. Each of these light chains has an 'atrial' and 'ventricular' isoform, so called because they are believed to exhibit chamber-restricted expression in the heart. However, recently the chamber-specific expression of MLC isoforms in the human heart has been questioned. Herein, we analyzed the expression of MLC-1 and -2 atrial and ventricular isoforms in each of the four cardiac chambers in adult non-failing donor hearts using top-down mass spectrometry (MS)-based proteomics. Strikingly, we detected an isoform thought to be ventricular, MLC-2v (gene: MYL2), in the atria and confirmed the protein sequence using tandem MS (MS/MS). For the first time, a putative deamidation post-translation modification (PTM) located on MLC-2v in atrial tissue was localized to amino acid N13. MLC-1v (MYL3) and MLC-2a (MYL7) were the only MLC isoforms exhibiting chamber-restricted expression patterns across all donor hearts. Importantly, our results unambiguously show that MLC-1v, not MLC-2v, is ventricle-specific in adult human hearts. Moreover, we found elevated MLC-2 phosphorylation in male hearts compared to female hearts across each cardiac chamber. Overall, top-down proteomics allowed an unbiased analysis of MLC isoform expression throughout the human heart, uncovering previously unexpected isoform expression patterns and PTMs.
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Affiliation(s)
- Elizabeth F Bayne
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kalina J Rossler
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Zachery R Gregorich
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Timothy J Aballo
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Emily A Chapman
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Wei Guo
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sean P Palecek
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - J Carter Ralphe
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Timothy J Kamp
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA; Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.
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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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Study on the muscle transcriptome of two diverse Indian backyard poultry breeds acclimatized to different agro-ecological conditions. Mol Biol Rep 2023; 50:2453-2461. [PMID: 36598628 DOI: 10.1007/s11033-022-08223-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/19/2022] [Indexed: 01/05/2023]
Abstract
OBJECTIVE Free-range (FR) poultry production systems are associated with quality products and improved welfare. All the 19 diverse chicken breeds of India have evolved under the FR system and are adapted to different agro-climatic conditions. It is vital to explore indigenous germplasm with modern genomic tools to have insights into genomic characteristics of production traits and adaptation. METHODS In this study, breast tissue transcriptome profiles were generated and analyzed from four biological replicates of two indigenous backyard poultry breeds of India-Ankaleshwar, a breed of the mainland, and Nicobari, a breed adapted to islands. The read quality of sequences was checked by FASTQC and processed reads were aligned to the reference genome (bGalGal1). RESULTS More than 94% mapping to the reference genome was observed for all samples. A total of 12,790 transcripts were common across both groups, while 657 were expressed only in Ankaleshwar and 169 in Nicobari. The highest expressed genes across both groups were associated mainly with muscle structure, contraction, and energy metabolism. The highly expressed genes identified in Ankaleshwar were involved in fatty acid catabolism and oxidative stress mitigation. Functional terms, pathways, and hub genes in Nicobari participated in muscle fiber growth, adipogenesis, and fatty acid anabolism. A key hub gene (RAC1) in Nicobari is a potential candidate affecting the laying rate in chickens. The qRT-PCR results also substantiate the RNA-seq results. CONCLUSION The findings provide a precious molecular resource to advance understanding of the genetic basis of adaptation, meat quality, and egg production in backyard chickens.
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7
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Bayne EF, Rossler KJ, Gregorich ZR, Aballo TJ, Roberts DS, Chapman EA, Guo W, Ralphe JC, Kamp TJ, Ge Y. Top-down Proteomics of Myosin Light Chain Isoforms Define Chamber-Specific Expression in the Human Heart. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525767. [PMID: 36747670 PMCID: PMC9900887 DOI: 10.1101/2023.01.26.525767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Myosin functions as the "molecular motor" of the sarcomere and generates the contractile force necessary for cardiac muscle contraction. Myosin light chains 1 and 2 (MLC-1 and -2) play important functional roles in regulating the structure of the hexameric myosin molecule. Each of these light chains has an "atrial" and "ventricular" isoform, so called because they are believed to exhibit chamber-restricted expression in the heart. However, recently the chamber-specific expression of MLC isoforms in the human heart has been questioned. Herein, we analyzed the expression of MLC-1 and -2 atrial and ventricular isoforms in each of the four cardiac chambers in adult non-failing donor hearts using top-down mass spectrometry (MS)-based proteomics. Strikingly, we detected an isoform thought to be ventricular, MLC-2v, in the atria and confirmed the protein sequence using tandem MS (MS/MS). For the first time, a putative deamidation post-translation modification (PTM) located on MLC-2v in atrial tissue was localized to amino acid N13. MLC-1v and MLC-2a were the only MLC isoforms exhibiting chamber-restricted expression patterns across all donor hearts. Importantly, our results unambiguously show that MLC-1v, not MLC-2v, is ventricle-specific in adult human hearts. Overall, top-down proteomics allowed us an unbiased analysis of MLC isoform expression throughout the human heart, uncovering previously unexpected isoform expression patterns and PTMs.
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8
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Eaton DM, Martin TG, Kasa M, Djalinac N, Ljubojevic-Holzer S, Von Lewinski D, Pöttler M, Kampaengsri T, Krumphuber A, Scharer K, Maechler H, Zirlik A, McKinsey TA, Kirk JA, Houser SR, Rainer PP, Wallner M. HDAC Inhibition Regulates Cardiac Function by Increasing Myofilament Calcium Sensitivity and Decreasing Diastolic Tension. Pharmaceutics 2022; 14:pharmaceutics14071509. [PMID: 35890404 PMCID: PMC9323146 DOI: 10.3390/pharmaceutics14071509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 01/09/2023] Open
Abstract
We recently established a large animal model that recapitulates key clinical features of heart failure with preserved ejection fraction (HFpEF) and tested the effects of the pan-HDAC inhibitor suberoylanilide hydroxamic acid (SAHA). SAHA reversed and prevented the development of cardiopulmonary impairment. This study evaluated the effects of SAHA at the level of cardiomyocyte and contractile protein function to understand how it modulates cardiac function. Both isolated adult feline ventricular cardiomyocytes (AFVM) and left ventricle (LV) trabeculae isolated from non-failing donors were treated with SAHA or vehicle before recording functional data. Skinned myocytes were isolated from AFVM and human trabeculae to assess myofilament function. SAHA-treated AFVM had increased contractility and improved relaxation kinetics but no difference in peak calcium transients, with increased calcium sensitivity and decreased passive stiffness of myofilaments. Mass spectrometry analysis revealed increased acetylation of the myosin regulatory light chain with SAHA treatment. SAHA-treated human trabeculae had decreased diastolic tension and increased developed force. Myofilaments isolated from human trabeculae had increased calcium sensitivity and decreased passive stiffness. These findings suggest that SAHA has an important role in the direct control of cardiac function at the level of the cardiomyocyte and myofilament by increasing myofilament calcium sensitivity and reducing diastolic tension.
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Affiliation(s)
- Deborah M. Eaton
- Cardiovascular Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (D.M.E.); (S.R.H.)
- Penn Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Thomas G. Martin
- Department of Cell and Molecular Physiology, Loyola University Chicago Stritch School of Medicine, Chicago, IL 60153, USA; (T.G.M.); (T.K.); (J.A.K.)
| | - Michael Kasa
- Division of Cardiology, Medical University of Graz, 8036 Graz, Austria; (M.K.); (N.D.); (S.L.-H.); (D.V.L.); (M.P.); (A.K.); (K.S.); (A.Z.); (P.P.R.)
| | - Natasa Djalinac
- Division of Cardiology, Medical University of Graz, 8036 Graz, Austria; (M.K.); (N.D.); (S.L.-H.); (D.V.L.); (M.P.); (A.K.); (K.S.); (A.Z.); (P.P.R.)
| | - Senka Ljubojevic-Holzer
- Division of Cardiology, Medical University of Graz, 8036 Graz, Austria; (M.K.); (N.D.); (S.L.-H.); (D.V.L.); (M.P.); (A.K.); (K.S.); (A.Z.); (P.P.R.)
| | - Dirk Von Lewinski
- Division of Cardiology, Medical University of Graz, 8036 Graz, Austria; (M.K.); (N.D.); (S.L.-H.); (D.V.L.); (M.P.); (A.K.); (K.S.); (A.Z.); (P.P.R.)
| | - Maria Pöttler
- Division of Cardiology, Medical University of Graz, 8036 Graz, Austria; (M.K.); (N.D.); (S.L.-H.); (D.V.L.); (M.P.); (A.K.); (K.S.); (A.Z.); (P.P.R.)
| | - Theerachat Kampaengsri
- Department of Cell and Molecular Physiology, Loyola University Chicago Stritch School of Medicine, Chicago, IL 60153, USA; (T.G.M.); (T.K.); (J.A.K.)
| | - Andreas Krumphuber
- Division of Cardiology, Medical University of Graz, 8036 Graz, Austria; (M.K.); (N.D.); (S.L.-H.); (D.V.L.); (M.P.); (A.K.); (K.S.); (A.Z.); (P.P.R.)
| | - Katharina Scharer
- Division of Cardiology, Medical University of Graz, 8036 Graz, Austria; (M.K.); (N.D.); (S.L.-H.); (D.V.L.); (M.P.); (A.K.); (K.S.); (A.Z.); (P.P.R.)
| | - Heinrich Maechler
- Department of Cardiothoracic Surgery, Medical University of Graz, 8036 Graz, Austria;
| | - Andreas Zirlik
- Division of Cardiology, Medical University of Graz, 8036 Graz, Austria; (M.K.); (N.D.); (S.L.-H.); (D.V.L.); (M.P.); (A.K.); (K.S.); (A.Z.); (P.P.R.)
| | - Timothy A. McKinsey
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA;
- Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jonathan A. Kirk
- Department of Cell and Molecular Physiology, Loyola University Chicago Stritch School of Medicine, Chicago, IL 60153, USA; (T.G.M.); (T.K.); (J.A.K.)
| | - Steven R. Houser
- Cardiovascular Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (D.M.E.); (S.R.H.)
| | - Peter P. Rainer
- Division of Cardiology, Medical University of Graz, 8036 Graz, Austria; (M.K.); (N.D.); (S.L.-H.); (D.V.L.); (M.P.); (A.K.); (K.S.); (A.Z.); (P.P.R.)
- BioTechMed Graz, 8010 Graz, Austria
| | - Markus Wallner
- Cardiovascular Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (D.M.E.); (S.R.H.)
- Division of Cardiology, Medical University of Graz, 8036 Graz, Austria; (M.K.); (N.D.); (S.L.-H.); (D.V.L.); (M.P.); (A.K.); (K.S.); (A.Z.); (P.P.R.)
- Correspondence:
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Wang T, Spahiu E, Osten J, Behrens F, Grünhagen F, Scholz T, Kraft T, Nayak A, Amrute-Nayak M. Cardiac ventricular myosin and slow skeletal myosin exhibit dissimilar chemomechanical properties despite bearing the same myosin heavy chain isoform. J Biol Chem 2022; 298:102070. [PMID: 35623390 PMCID: PMC9243179 DOI: 10.1016/j.jbc.2022.102070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/12/2022] [Accepted: 05/14/2022] [Indexed: 11/29/2022] Open
Abstract
The myosin II motors are ATP-powered force-generating machines driving cardiac and muscle contraction. Myosin II heavy chain isoform-beta (β-MyHC) is primarily expressed in the ventricular myocardium and in slow-twitch muscle fibers, such as M. soleus. M. soleus-derived myosin II (SolM-II) is often used as an alternative to the ventricular β-cardiac myosin (βM-II); however, the direct assessment of biochemical and mechanical features of the native myosins is limited. By employing optical trapping, we examined the mechanochemical properties of native myosins isolated from the rabbit heart ventricle and soleus muscles at the single-molecule level. We found purified motors from the two tissue sources, despite expressing the same MyHC isoform, displayed distinct motile and ATPase kinetic properties. We demonstrate βM-II was approximately threefold faster in the actin filament-gliding assay than SolM-II. The maximum actomyosin (AM) detachment rate derived in single-molecule assays was also approximately threefold higher in βM-II, while the power stroke size and stiffness of the "AM rigor" crossbridge for both myosins were comparable. Our analysis revealed a higher AM detachment rate for βM-II, corresponding to the enhanced ADP release rates from the crossbridge, likely responsible for the observed differences in the motility driven by these myosins. Finally, we observed a distinct myosin light chain 1 isoform (MLC1sa) that associates with SolM-II, which might contribute to the observed kinetics differences between βM-II and SolM-II. These results have important implications for the choice of tissue sources and justify prerequisites for the correct myosin heavy and light chains to study cardiomyopathies.
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Affiliation(s)
- Tianbang Wang
- Institute of Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
| | - Emrulla Spahiu
- Institute of Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
| | - Jennifer Osten
- Institute of Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
| | - Florentine Behrens
- Institute of Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
| | - Fabius Grünhagen
- Institute of Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
| | - Tim Scholz
- Institute of Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
| | - Theresia Kraft
- Institute of Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
| | - Arnab Nayak
- Institute of Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany.
| | - Mamta Amrute-Nayak
- Institute of Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany.
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10
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Drown BS, Jooß K, Melani RD, Lloyd-Jones C, Camarillo JM, Kelleher NL. Mapping the Proteoform Landscape of Five Human Tissues. J Proteome Res 2022; 21:1299-1310. [PMID: 35413190 PMCID: PMC9087339 DOI: 10.1021/acs.jproteome.2c00034] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A functional understanding of the human body requires structure-function studies of proteins at scale. The chemical structure of proteins is controlled at the transcriptional, translational, and post-translational levels, creating a variety of products with modulated functions within the cell. The term "proteoform" encapsulates this complexity at the level of chemical composition. Comprehensive mapping of the proteoform landscape in human tissues necessitates analytical techniques with increased sensitivity and depth of coverage. Here, we took a top-down proteomics approach, combining data generated using capillary zone electrophoresis (CZE) and nanoflow reversed-phase liquid chromatography (RPLC) hyphenated to mass spectrometry to identify and characterize proteoforms from the human lungs, heart, spleen, small intestine, and kidneys. CZE and RPLC provided complementary post-translational modification and proteoform selectivity, thereby enhancing the overall proteome coverage when used in combination. Of the 11,466 proteoforms identified in this study, 7373 (64%) were not reported previously. Large differences in the protein and proteoform level were readily quantified, with initial inferences about proteoform biology operative in the analyzed organs. Differential proteoform regulation of defensins, glutathione transferases, and sarcomeric proteins across tissues generate hypotheses about how they function and are regulated in human health and disease.
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Affiliation(s)
- Bryon S Drown
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Kevin Jooß
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D Melani
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Cameron Lloyd-Jones
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Jeannie M Camarillo
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
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11
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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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12
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Banaszkiewicz M, Olejnik A, Krzywonos-Zawadzka A, Hałucha K, Bil-Lula I. Expression of atrial‑fetal light chains in cultured human cardiomyocytes after chemical ischemia‑reperfusion injury. Mol Med Rep 2021; 24:770. [PMID: 34490485 PMCID: PMC8430302 DOI: 10.3892/mmr.2021.12410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/19/2021] [Indexed: 11/19/2022] Open
Abstract
Atrial light chains (ALC1) are naturally present in adult heart atria, while ventricular light chains (VLC1) are predominant in ventricles. Degradation of VLC1 and re-expression of ALC1 in heart ventricles are associated with heart disorders in response to pressure overload. The aim of the current study was to investigate changes in myosin light chain expression after simulated ischemia and simulated reperfusion (sI/sR). Human cardiomyocytes (HCM) isolated from adult heart ventricles were subjected to chemical ischemia. The control group was maintained under aerobic conditions. Myocyte injury was determined by testing lactate dehydrogenase (LDH) activity. The gene expression of ALC1, VLC1 and MMP-2 were assessed by reverse transcription-quatitive PCR. Additionally, protein synthesis was measured using ELISA kits and MMP-2 activity was measured by zymography. The results revealed that LDH activity was increased in sI/sR cell-conditioned medium (P=0.02), confirming the ischemic damage of HCM. ALC1 gene expression and content in HCM were also increased in the sI/sR group (P=0.03 and P<0.001, respectively), while VLC1 gene expression after sI/sR was decreased (P=0.008). Furthermore, MMP-2 gene expression and synthesis were lower in the sI/sR group when compared with the aerobic control group (P<0.001 and P=0.03, respectively). MMP-2 activity was also increased in sI/sR cell-conditioned medium (P=0.006). In conclusion, sI/sR treatment led to increased ALC1 and decreased VLC1 expression in ventricular cardiomyocytes, which may constitute an adaptive mechanism to altered conditions and contribute to the improvement of heart function.
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Affiliation(s)
- Marta Banaszkiewicz
- Division of Clinical Chemistry and Laboratory Haematology, Department of Medical Laboratory Diagnostics, Faculty of Pharmacy, Wroclaw Medical University, 50‑556 Wroclaw, Poland
| | - Agnieszka Olejnik
- Division of Clinical Chemistry and Laboratory Haematology, Department of Medical Laboratory Diagnostics, Faculty of Pharmacy, Wroclaw Medical University, 50‑556 Wroclaw, Poland
| | - Anna Krzywonos-Zawadzka
- Division of Clinical Chemistry and Laboratory Haematology, Department of Medical Laboratory Diagnostics, Faculty of Pharmacy, Wroclaw Medical University, 50‑556 Wroclaw, Poland
| | - Kornela Hałucha
- Division of Clinical Chemistry and Laboratory Haematology, Department of Medical Laboratory Diagnostics, Faculty of Pharmacy, Wroclaw Medical University, 50‑556 Wroclaw, Poland
| | - Iwona Bil-Lula
- Division of Clinical Chemistry and Laboratory Haematology, Department of Medical Laboratory Diagnostics, Faculty of Pharmacy, Wroclaw Medical University, 50‑556 Wroclaw, Poland
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13
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Khan ZU, Pi D. DeepSSPred: A Deep Learning Based Sulfenylation Site Predictor Via a Novel nSegmented Optimize Federated Feature Encoder. Protein Pept Lett 2021; 28:708-721. [PMID: 33267753 DOI: 10.2174/0929866527666201202103411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 10/14/2020] [Accepted: 10/18/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND S-sulfenylation (S-sulphenylation, or sulfenic acid) proteins, are special kinds of post-translation modification, which plays an important role in various physiological and pathological processes such as cytokine signaling, transcriptional regulation, and apoptosis. Despite these aforementioned significances, and by complementing existing wet methods, several computational models have been developed for sulfenylation cysteine sites prediction. However, the performance of these models was not satisfactory due to inefficient feature schemes, severe imbalance issues, and lack of an intelligent learning engine. OBJECTIVE In this study, our motivation is to establish a strong and novel computational predictor for discrimination of sulfenylation and non-sulfenylation sites. METHODS In this study, we report an innovative bioinformatics feature encoding tool, named DeepSSPred, in which, resulting encoded features is obtained via nSegmented hybrid feature, and then the resampling technique called synthetic minority oversampling was employed to cope with the severe imbalance issue between SC-sites (minority class) and non-SC sites (majority class). State of the art 2D-Convolutional Neural Network was employed over rigorous 10-fold jackknife cross-validation technique for model validation and authentication. RESULTS Following the proposed framework, with a strong discrete presentation of feature space, machine learning engine, and unbiased presentation of the underline training data yielded into an excellent model that outperforms with all existing established studies. The proposed approach is 6% higher in terms of MCC from the first best. On an independent dataset, the existing first best study failed to provide sufficient details. The model obtained an increase of 7.5% in accuracy, 1.22% in Sn, 12.91% in Sp and 13.12% in MCC on the training data and12.13% of ACC, 27.25% in Sn, 2.25% in Sp, and 30.37% in MCC on an independent dataset in comparison with 2nd best method. These empirical analyses show the superlative performance of the proposed model over both training and Independent dataset in comparison with existing literature studies. CONCLUSION In this research, we have developed a novel sequence-based automated predictor for SC-sites, called DeepSSPred. The empirical simulations outcomes with a training dataset and independent validation dataset have revealed the efficacy of the proposed theoretical model. The good performance of DeepSSPred is due to several reasons, such as novel discriminative feature encoding schemes, SMOTE technique, and careful construction of the prediction model through the tuned 2D-CNN classifier. We believe that our research work will provide a potential insight into a further prediction of S-sulfenylation characteristics and functionalities. Thus, we hope that our developed predictor will significantly helpful for large scale discrimination of unknown SC-sites in particular and designing new pharmaceutical drugs in general.
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Affiliation(s)
- Zaheer Ullah Khan
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Dechang Pi
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
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14
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Zhang G, Wu P, Zhou K, He M, Zhang X, Qiu C, Li T, Zhang T, Xie K, Dai G, Wang J. Study on the transcriptome for breast muscle of chickens and the function of key gene RAC2 on fibroblasts proliferation. BMC Genomics 2021; 22:157. [PMID: 33676413 PMCID: PMC7937270 DOI: 10.1186/s12864-021-07453-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 02/19/2021] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Growth performance is significant in broiler production. In the growth process of broilers, gene expression varies at different growth stages. However, limited research has been conducted on the molecular mechanisms of muscle growth and development in yellow-feathered male chickens. RESULTS In the study, we used RNA-seq to study the transcriptome of the breast muscle of male Jinghai yellow chickens at 4 (M4F), 8 (M8F) and 12 weeks (M12F) of age. The results showed that 4608 differentially expressed genes (DEGs) were obtained by comparison in pairs of the three groups with Fold Change (FC) ≥ 2 and False Discovery Rate (FDR) ≤ 0.05, and 83, 3445 and 3903 DEGs were obtained separately from M4FvsM8F, M4FvsM12F and M8FvsM12F. Six genes were found as co-differentially expressed in the three age groups, namely SNCG, MYH1A, ARHGDIB, ENSGALG00000031598, ENSGALG00000035660 and ENSGALG00000030559. The GO analysis showed that 0, 304 and 408 biological process (BP) were significantly enriched in M4FvsM8F, M4FvsM12F and M8FvsM12F groups, respectively. KEGG pathway enrichment showed that 1, 2, 4 and 4 pathways were significantly enriched in M4FvsM8F, M4FvsM12F, M8FvsM12F and all DEGs, respectively. They were steroid biosynthesis, carbon metabolism, focal adhesion, cytokine-cytokine receptor interaction, biosynthesis of amino acids and salmonella infection. We constructed short hairpin RNA (shRNA) to interfere the differentially expressed gene RAC2 in DF-1 cells and detected mRNA and protein expression of the downstream genes PAK1 and MAPK8. Results of qPCR showed that RAC2, PAK1 and MAPK8 mRNA expression significantly decreased in the shRAC2-2 group compared with the negative control (NC) group. Western Blot (WB) results showed that the proteins of RAC2, PAK1 and MAPK8 also decreased in the shRAC2-2 group. Cell Counting Kit-8 (CCK-8) and 5-Ethynyl-2'-deoxyuridine (EdU) assay both showed that the proliferation of DF-1 cells was significantly inhibited after transfection of shRAC2-2. CONCLUSIONS The results of RNA-seq revealed genes, BP terms and KEGG pathways related to growth and development of male Jinghai yellow chickens, and they would have important guiding significance to our production practice. Further research suggested that RAC2 might regulate cell proliferation by regulating PAKs/MAPK8 pathway and affect growth of chickens.
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Affiliation(s)
- Genxi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, 225009, China
| | - Pengfei Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, 225009, China.
| | - Kaizhi Zhou
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, 225009, China
| | - Mingliang He
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, 225009, China
| | - Xinchao Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, 225009, China
| | - Cong Qiu
- Jiangsu Jinghai Poultry Group Co. Ltd., Nantong, 226100, China
| | - Tingting Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, 225009, China
| | - Tao Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, 225009, China
| | - Kaizhou Xie
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, 225009, China
| | - Guojun Dai
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, 225009, China
| | - Jinyu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, 225009, China
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15
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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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16
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Alpha and beta myosin isoforms and human atrial and ventricular contraction. Cell Mol Life Sci 2021; 78:7309-7337. [PMID: 34704115 PMCID: PMC8629898 DOI: 10.1007/s00018-021-03971-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 10/03/2021] [Accepted: 10/08/2021] [Indexed: 01/15/2023]
Abstract
Human atrial and ventricular contractions have distinct mechanical characteristics including speed of contraction, volume of blood delivered and the range of pressure generated. Notably, the ventricle expresses predominantly β-cardiac myosin while the atrium expresses mostly the α-isoform. In recent years exploration of the properties of pure α- & β-myosin isoforms have been possible in solution, in isolated myocytes and myofibrils. This allows us to consider the extent to which the atrial vs ventricular mechanical characteristics are defined by the myosin isoform expressed, and how the isoform properties are matched to their physiological roles. To do this we Outline the essential feature of atrial and ventricular contraction; Explore the molecular structural and functional characteristics of the two myosin isoforms; Describe the contractile behaviour of myocytes and myofibrils expressing a single myosin isoform; Finally we outline the outstanding problems in defining the differences between the atria and ventricles. This allowed us consider what features of contraction can and cannot be ascribed to the myosin isoforms present in the atria and ventricles.
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17
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The challenge of detecting modifications on proteins. Essays Biochem 2020; 64:135-153. [PMID: 31957791 DOI: 10.1042/ebc20190055] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 12/16/2022]
Abstract
Post-translational modifications (PTMs) are integral to the regulation of protein function, characterising their role in this process is vital to understanding how cells work in both healthy and diseased states. Mass spectrometry (MS) facilitates the mass determination and sequencing of peptides, and thereby also the detection of site-specific PTMs. However, numerous challenges in this field continue to persist. The diverse chemical properties, low abundance, labile nature and instability of many PTMs, in combination with the more practical issues of compatibility with MS and bioinformatics challenges, contribute to the arduous nature of their analysis. In this review, we present an overview of the established MS-based approaches for analysing PTMs and the common complications associated with their investigation, including examples of specific challenges focusing on phosphorylation, lysine acetylation and redox modifications.
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18
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Sitbon YH, Yadav S, Kazmierczak K, Szczesna-Cordary D. Insights into myosin regulatory and essential light chains: a focus on their roles in cardiac and skeletal muscle function, development and disease. J Muscle Res Cell Motil 2020; 41:313-327. [PMID: 31131433 PMCID: PMC6879809 DOI: 10.1007/s10974-019-09517-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 05/21/2019] [Indexed: 12/15/2022]
Abstract
The activity of cardiac and skeletal muscles depends upon the ATP-coupled actin-myosin interactions to execute the power stroke and muscle contraction. The goal of this review article is to provide insight into the function of myosin II, the molecular motor of the heart and skeletal muscles, with a special focus on the role of myosin II light chain (MLC) components. Specifically, we focus on the involvement of myosin regulatory (RLC) and essential (ELC) light chains in striated muscle development, isoform appearance and their function in normal and diseased muscle. We review the consequences of isoform switching and knockout of specific MLC isoforms on cardiac and skeletal muscle function in various animal models. Finally, we discuss how dysregulation of specific RLC/ELC isoforms can lead to cardiac and skeletal muscle diseases and summarize the effects of most studied mutations leading to cardiac or skeletal myopathies.
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Affiliation(s)
- Yoel H Sitbon
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, 1600 NW 10th Ave, Miami, FL, 33136, USA
| | - Sunil Yadav
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, 1600 NW 10th Ave, Miami, FL, 33136, USA
| | - Katarzyna Kazmierczak
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, 1600 NW 10th Ave, Miami, FL, 33136, USA
| | - Danuta Szczesna-Cordary
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, 1600 NW 10th Ave, Miami, FL, 33136, USA.
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19
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Cai W, Zhang J, de Lange WJ, Gregorich ZR, Karp H, Farrell ET, Mitchell SD, Tucholski T, Lin Z, Biermann M, McIlwain SJ, Ralphe JC, Kamp TJ, Ge Y. An Unbiased Proteomics Method to Assess the Maturation of Human Pluripotent Stem Cell-Derived Cardiomyocytes. Circ Res 2019; 125:936-953. [PMID: 31573406 DOI: 10.1161/circresaha.119.315305] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RATIONALE Human pluripotent stem cell (hPSC)-derived cardiomyocytes exhibit the properties of fetal cardiomyocytes, which limits their applications. Various methods have been used to promote maturation of hPSC-cardiomyocytes; however, there is a lack of an unbiased and comprehensive method for accurate assessment of the maturity of hPSC-cardiomyocytes. OBJECTIVE We aim to develop an unbiased proteomics strategy integrating high-throughput top-down targeted proteomics and bottom-up global proteomics for the accurate and comprehensive assessment of hPSC-cardiomyocyte maturation. METHODS AND RESULTS Utilizing hPSC-cardiomyocytes from early- and late-stage 2-dimensional monolayer culture and 3-dimensional engineered cardiac tissue, we demonstrated the high reproducibility and reliability of a top-down proteomics method, which enabled simultaneous quantification of contractile protein isoform expression and associated post-translational modifications. This method allowed for the detection of known maturation-associated contractile protein alterations and, for the first time, identified contractile protein post-translational modifications as promising new markers of hPSC-cardiomyocytes maturation. Most notably, decreased phosphorylation of α-tropomyosin was found to be associated with hPSC-cardiomyocyte maturation. By employing a bottom-up global proteomics strategy, we identified candidate maturation-associated markers important for sarcomere organization, cardiac excitability, and Ca2+ homeostasis. In particular, upregulation of myomesin 1 and transmembrane 65 was associated with hPSC-cardiomyocyte maturation and validated in cardiac development, making these promising markers for assessing maturity of hPSC-cardiomyocytes. We have further validated α-actinin isoforms, phospholamban, dystrophin, αB-crystallin, and calsequestrin 2 as novel maturation-associated markers, in the developing mouse cardiac ventricles. CONCLUSIONS We established an unbiased proteomics method that can provide accurate and specific assessment of the maturity of hPSC-cardiomyocytes and identified new markers of maturation. Furthermore, this integrated proteomics strategy laid a strong foundation for uncovering the molecular pathways involved in cardiac development and disease using hPSC-cardiomyocytes.
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Affiliation(s)
- Wenxuan Cai
- From the Molecular and Cellular Pharmacology Training Program (W.C., S.D.M., T.J.K., Y.G.), University of Wisconsin-Madison.,Department of Cell and Regenerative Biology (W.C., Z.R.G., H.K., S.D.M., Z.L., T.J.K., Y.G.), University of Wisconsin-Madison
| | - Jianhua Zhang
- Department of Medicine (J.Z., Z.R.G., M.B., T.J.K.), University of Wisconsin-Madison
| | - Willem J de Lange
- Department of Pediatrics (W.J.d.L., E.T.F., J.C.R.), University of Wisconsin-Madison
| | - Zachery R Gregorich
- Department of Cell and Regenerative Biology (W.C., Z.R.G., H.K., S.D.M., Z.L., T.J.K., Y.G.), University of Wisconsin-Madison.,Department of Medicine (J.Z., Z.R.G., M.B., T.J.K.), University of Wisconsin-Madison
| | - Hannah Karp
- Department of Cell and Regenerative Biology (W.C., Z.R.G., H.K., S.D.M., Z.L., T.J.K., Y.G.), University of Wisconsin-Madison
| | - Emily T Farrell
- Department of Pediatrics (W.J.d.L., E.T.F., J.C.R.), University of Wisconsin-Madison
| | - Stanford D Mitchell
- From the Molecular and Cellular Pharmacology Training Program (W.C., S.D.M., T.J.K., Y.G.), University of Wisconsin-Madison.,Department of Cell and Regenerative Biology (W.C., Z.R.G., H.K., S.D.M., Z.L., T.J.K., Y.G.), University of Wisconsin-Madison
| | - Trisha Tucholski
- From the Molecular and Cellular Pharmacology Training Program (W.C., S.D.M., T.J.K., Y.G.), University of Wisconsin-Madison.,Department of Chemistry (T.T., Y.G.), University of Wisconsin-Madison.,Department of Biostatistics and Medical Informatics (T.T., S.J.M.), University of Wisconsin-Madison
| | - Ziqing Lin
- Department of Cell and Regenerative Biology (W.C., Z.R.G., H.K., S.D.M., Z.L., T.J.K., Y.G.), University of Wisconsin-Madison.,Human Proteomics Program (Z.L., Y.G.), University of Wisconsin-Madison
| | - Mitch Biermann
- Department of Medicine (J.Z., Z.R.G., M.B., T.J.K.), University of Wisconsin-Madison
| | - Sean J McIlwain
- Department of Biostatistics and Medical Informatics (T.T., S.J.M.), University of Wisconsin-Madison.,UW Carbone Cancer Center (S.J.M.), University of Wisconsin-Madison
| | - J Carter Ralphe
- Department of Pediatrics (W.J.d.L., E.T.F., J.C.R.), University of Wisconsin-Madison
| | - Timothy J Kamp
- From the Molecular and Cellular Pharmacology Training Program (W.C., S.D.M., T.J.K., Y.G.), University of Wisconsin-Madison.,Department of Cell and Regenerative Biology (W.C., Z.R.G., H.K., S.D.M., Z.L., T.J.K., Y.G.), University of Wisconsin-Madison.,Department of Medicine (J.Z., Z.R.G., M.B., T.J.K.), University of Wisconsin-Madison
| | - Ying Ge
- From the Molecular and Cellular Pharmacology Training Program (W.C., S.D.M., T.J.K., Y.G.), University of Wisconsin-Madison.,Department of Cell and Regenerative Biology (W.C., Z.R.G., H.K., S.D.M., Z.L., T.J.K., Y.G.), University of Wisconsin-Madison.,Human Proteomics Program (Z.L., Y.G.), University of Wisconsin-Madison.,Department of Chemistry (T.T., Y.G.), University of Wisconsin-Madison
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20
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Fert-Bober J, Murray CI, Parker SJ, Van Eyk JE. Precision Profiling of the Cardiovascular Post-Translationally Modified Proteome: Where There Is a Will, There Is a Way. Circ Res 2019; 122:1221-1237. [PMID: 29700069 DOI: 10.1161/circresaha.118.310966] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
There is an exponential increase in biological complexity as initial gene transcripts are spliced, translated into amino acid sequence, and post-translationally modified. Each protein can exist as multiple chemical or sequence-specific proteoforms, and each has the potential to be a critical mediator of a physiological or pathophysiological signaling cascade. Here, we provide an overview of how different proteoforms come about in biological systems and how they are most commonly measured using mass spectrometry-based proteomics and bioinformatics. Our goal is to present this information at a level accessible to every scientist interested in mass spectrometry and its application to proteome profiling. We will specifically discuss recent data linking various protein post-translational modifications to cardiovascular disease and conclude with a discussion for enablement and democratization of proteomics across the cardiovascular and scientific community. The aim is to inform and inspire the readership to explore a larger breadth of proteoform, particularity post-translational modifications, related to their particular areas of expertise in cardiovascular physiology.
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Affiliation(s)
- Justyna Fert-Bober
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA
| | - Christopher I Murray
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA
| | - Sarah J Parker
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA.
| | - Jennifer E Van Eyk
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA
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21
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Roberts DS, Chen B, Tiambeng TN, Wu Z, Ge Y, Jin S. Reproducible Large-Scale Synthesis of Surface Silanized Nanoparticles as an Enabling Nanoproteomics Platform: Enrichment of the Human Heart Phosphoproteome. NANO RESEARCH 2019; 12:1473-1481. [PMID: 31341559 PMCID: PMC6656398 DOI: 10.1007/s12274-019-2418-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
A reproducible synthetic strategy was developed for facile large-scale (200 mg) synthesis of surface silanized magnetite (Fe3O4) nanoparticles (NPs) for biological applications. After further coupling a phosphate-specific affinity ligand, these functionalized magnetic NPs were used for the highly specific enrichment of phosphoproteins from a complex biological mixture. Moreover, correlating the surface silane density of the silanized magnetite NPs to their resultant enrichment performance established a simple and reliable quality assurance control to ensure reproducible synthesis of these NPs routinely in large scale and optimal phosphoprotein enrichment performance from batch-to-batch. Furthermore, by successful exploitation of a top-down phosphoproteomics strategy that integrates this high throughput nanoproteomics platform with online liquid chromatography (LC) and tandem mass spectrometry (MS/MS), we were able to specifically enrich, identify, and characterize endogenous phosphoproteins from highly complex human cardiac tissue homogenate. This nanoproteomics platform possesses a unique combination of scalability, specificity, reproducibility, and efficiency for the capture and enrichment of low abundance proteins in general, thereby enabling downstream proteomics applications.
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Affiliation(s)
- David S. Roberts
- Department of Chemistry, University of Wisconsin-Madison, Wisconsin 53706, USA
| | - Bifan Chen
- Department of Chemistry, University of Wisconsin-Madison, Wisconsin 53706, USA
| | - Timothy N. Tiambeng
- Department of Chemistry, University of Wisconsin-Madison, Wisconsin 53706, USA
| | - Zhijie Wu
- Department of Chemistry, University of Wisconsin-Madison, Wisconsin 53706, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Wisconsin 53706, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Wisconsin 53706, USA
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22
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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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23
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Badimon L, Mendieta G, Ben-Aicha S, Vilahur G. Post-Genomic Methodologies and Preclinical Animal Models: Chances for the Translation of Cardioprotection to the Clinic. Int J Mol Sci 2019; 20:ijms20030514. [PMID: 30691061 PMCID: PMC6387468 DOI: 10.3390/ijms20030514] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 01/23/2019] [Indexed: 12/02/2022] Open
Abstract
Although many cardioprotective strategies have demonstrated benefits in animal models of myocardial infarction, they have failed to demonstrate cardioprotection in the clinical setting highlighting that new therapeutic target and treatment strategies aimed at reducing infarct size are urgently needed. Completion of the Human Genome Project in 2001 fostered the post-genomic research era with the consequent development of high-throughput “omics” platforms including transcriptomics, proteomics, and metabolomics. Implementation of these holistic approaches within the field of cardioprotection has enlarged our understanding of ischemia/reperfusion injury with each approach capturing a different angle of the global picture of the disease. It has also contributed to identify potential prognostic/diagnostic biomarkers and discover novel molecular therapeutic targets. In this latter regard, “omic” data analysis in the setting of ischemic conditioning has allowed depicting potential therapeutic candidates, including non-coding RNAs and molecular chaperones, amenable to pharmacological development. Such discoveries must be tested and validated in a relevant and reliable myocardial infarction animal model before moving towards the clinical setting. Moreover, efforts should also focus on integrating all “omic” datasets rather than working exclusively on a single “omic” approach. In the following manuscript, we will discuss the power of implementing “omic” approaches in preclinical animal models to identify novel molecular targets for cardioprotection of interest for drug development.
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Affiliation(s)
- Lina Badimon
- Cardiovascular Program- ICCC, Research Institute-Hospital de la Santa Creu i Sant Pau, IIB-Sant Pau, 08025 Barcelona, Spain. (L.B.).
- Centro de Investigación Biomédica en Red Cardiovascular (CIBERCV) Instituto de Salud Carlos III, 28029 Madrid, Spain..
- Cardiovascular Research Chair, Universidad Autónoma Barcelona (UAB) 08025 Barcelona, Spain.
| | - Guiomar Mendieta
- Cardiovascular Program- ICCC, Research Institute-Hospital de la Santa Creu i Sant Pau, IIB-Sant Pau, 08025 Barcelona, Spain. (L.B.).
- Department of Cardiology, Hospital Clinic, 08036 Brcelona, Spain.
| | - Soumaya Ben-Aicha
- Cardiovascular Program- ICCC, Research Institute-Hospital de la Santa Creu i Sant Pau, IIB-Sant Pau, 08025 Barcelona, Spain. (L.B.).
| | - Gemma Vilahur
- Cardiovascular Program- ICCC, Research Institute-Hospital de la Santa Creu i Sant Pau, IIB-Sant Pau, 08025 Barcelona, Spain. (L.B.).
- Centro de Investigación Biomédica en Red Cardiovascular (CIBERCV) Instituto de Salud Carlos III, 28029 Madrid, Spain..
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24
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Cai W, Hite ZL, Lyu B, Wu Z, Lin Z, Gregorich ZR, Messer AE, McIlwain SJ, Marston SB, Kohmoto T, Ge Y. Temperature-sensitive sarcomeric protein post-translational modifications revealed by top-down proteomics. J Mol Cell Cardiol 2018; 122:11-22. [PMID: 30048711 DOI: 10.1016/j.yjmcc.2018.07.247] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/11/2018] [Accepted: 07/21/2018] [Indexed: 10/28/2022]
Abstract
Despite advancements in symptom management for heart failure (HF), this devastating clinical syndrome remains the leading cause of death in the developed world. Studies using animal models have greatly advanced our understanding of the molecular mechanisms underlying HF; however, differences in cardiac physiology and the manifestation of HF between animals, particularly rodents, and humans necessitates the direct interrogation of human heart tissue samples. Nevertheless, an ever-present concern when examining human heart tissue samples is the potential for artefactual changes related to temperature changes during tissue shipment or sample processing. Herein, we examined the effects of temperature on the post-translational modifications (PTMs) of sarcomeric proteins, the proteins responsible for muscle contraction, under conditions mimicking those that might occur during tissue shipment or sample processing. Using a powerful top-down proteomics method, we found that sarcomeric protein PTMs were differentially affected by temperature. Specifically, cardiac troponin I and enigma homolog isoform 2 showed robust increases in phosphorylation when tissue was incubated at either 4 °C or 22 °C. The observed increase is likely due to increased cyclic AMP levels and activation of protein kinase A in the tissue. On the contrary, cardiac troponin T and myosin regulatory light chain phosphorylation decreased when tissue was incubated at 4 °C or 22 °C. Furthermore, significant protein degradation was also observed after incubation at 4 °C or 22 °C. Overall, these results indicate that temperature exerts various effects on sarcomeric protein PTMs and careful tissue handling is critical for studies involving human heart samples. Moreover, these findings highlight the power of top-down proteomics for examining the integrity of cardiac tissue samples.
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Affiliation(s)
- 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
| | - Zachary L Hite
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Beini Lyu
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Zhijie Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ziqing Lin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA; Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - 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
| | - Andrew E Messer
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Sean J McIlwain
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Steve B Marston
- National Heart and Lung Institute, Imperial College London, London, UK
| | - 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; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.
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25
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Klein BA, Reiz B, Robertson IM, Irving M, Li L, Sun YB, Sykes BD. Reversible Covalent Reaction of Levosimendan with Cardiac Troponin C in Vitro and in Situ. Biochemistry 2018; 57:2256-2265. [DOI: 10.1021/acs.biochem.8b00109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Brittney A. Klein
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Béla Reiz
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton, Alberta T6H 2H7, Canada
| | - Ian M. Robertson
- Pharmaceutical and Health Benefits Branch, Ministry of Health, Government of Alberta, Edmonton, Alberta T5J 3Z5, Canada
| | - Malcolm Irving
- Randall Centre for Cell and Molecular Biophysics and British Heart Foundation Centre of Research Excellence, King’s College London, London SE1 1UL, U.K
| | - Liang Li
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton, Alberta T6H 2H7, Canada
| | - Yin-Biao Sun
- Randall Centre for Cell and Molecular Biophysics and British Heart Foundation Centre of Research Excellence, King’s College London, London SE1 1UL, U.K
| | - Brian D. Sykes
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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26
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27
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Lyon YA, Riggs D, Fornelli L, Compton PD, Julian RR. The Ups and Downs of Repeated Cleavage and Internal Fragment Production in Top-Down Proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:150-157. [PMID: 29038993 PMCID: PMC5786485 DOI: 10.1007/s13361-017-1823-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 09/08/2017] [Accepted: 09/23/2017] [Indexed: 05/10/2023]
Abstract
Analysis of whole proteins by mass spectrometry, or top-down proteomics, has several advantages over methods relying on proteolysis. For example, proteoforms can be unambiguously identified and examined. However, from a gas-phase ion-chemistry perspective, proteins are enormous molecules that present novel challenges relative to peptide analysis. Herein, the statistics of cleaving the peptide backbone multiple times are examined to evaluate the inherent propensity for generating internal versus terminal ions. The raw statistics reveal an inherent bias favoring production of terminal ions, which holds true regardless of protein size. Importantly, even if the full suite of internal ions is generated by statistical dissociation, terminal ions are predicted to account for at least 50% of the total ion current, regardless of protein size, if there are three backbone dissociations or fewer. Top-down analysis should therefore be a viable approach for examining proteins of significant size. Comparison of the purely statistical analysis with actual top-down data derived from ultraviolet photodissociation (UVPD) and higher-energy collisional dissociation (HCD) reveals that terminal ions account for much of the total ion current in both experiments. Terminal ion production is more favored in UVPD relative to HCD, which is likely due to differences in the mechanisms controlling fragmentation. Importantly, internal ions are not found to dominate from either the theoretical or experimental point of view. Graphical abstract ᅟ.
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Affiliation(s)
- Yana A Lyon
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Dylan Riggs
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Luca Fornelli
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, 2145 N. Sheridan Road, Evanston, IL, 60208, USA
| | - Philip D Compton
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, 2145 N. Sheridan Road, Evanston, IL, 60208, USA
| | - Ryan R Julian
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA.
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28
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Plymire DA, Wing CE, Robinson DE, Patrie SM. Continuous Elution Proteoform Identification of Myelin Basic Protein by Superficially Porous Reversed-Phase Liquid Chromatography and Fourier Transform Mass Spectrometry. Anal Chem 2017; 89:12030-12038. [PMID: 29016107 DOI: 10.1021/acs.analchem.7b02426] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Myelin basic protein (MBP) plays an important structural and functional role in the neuronal myelin sheath. Translated MBP exhibits extreme microheterogeneity with numerous alternative splice variants (ASVs) and post-translational modifications (PTMs) reportedly tied to central nervous system maturation, myelin stability, and the pathobiology of various de- and dys-myelinating disorders. Conventional bioanalytical tools cannot efficiently examine ASV and PTM events simultaneously, which limits understanding of the role of MBP microheterogeneity in human physiology and disease. To address this need, we report on a top-down proteomics pipeline that combines superficially porous reversed-phase liquid chromatography (SPLC), Fourier transform mass spectrometry (FTMS), data-independent acquisition (DIA) with nozzle-skimmer dissociation (NSD), and aligned data processing resources to rapidly characterize abundant MBP proteoforms within murine tissue. The three-tier proteoform identification and characterization workflow resolved four known MBP ASVs and hundreds of differentially modified states from a single 90 min SPLC-FTMS run on ∼0.5 μg of material. This included 323 proteoforms for the 14.1 kDa ASV alone. We also identified two novel ASVs from an alternative transcriptional start site (ATSS) of the MBP gene as well as a never before characterized S-acylation event linking palmitic acid, oleic acid, and stearic acid at C78 of the 17.125 kDa ASV.
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Affiliation(s)
- Daniel A Plymire
- Department of Pathology, UT Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Casey E Wing
- Department of Pathology, UT Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, Texas 75390, 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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