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Rossler KJ, de Lange WJ, Mann MW, Aballo TJ, Melby JA, Zhang J, Kim G, Bayne EF, Zhu Y, Farrell ET, Kamp TJ, Ralphe JC, Ge Y. Lactate- and immunomagnetic-purified hiPSC-derived cardiomyocytes generate comparable engineered cardiac tissue constructs. JCI Insight 2024; 9:e172168. [PMID: 37988170 PMCID: PMC10906451 DOI: 10.1172/jci.insight.172168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/17/2023] [Indexed: 11/23/2023] Open
Abstract
Three-dimensional engineered cardiac tissue (ECT) using purified human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) has emerged as an appealing model system for the study of human cardiac biology and disease. A recent study reported widely used metabolic (lactate) purification of monolayer hiPSC-CM cultures results in an ischemic cardiomyopathy-like phenotype compared with magnetic antibody-based cell sorting (MACS) purification, complicating the interpretation of studies using lactate-purified hiPSC-CMs. Herein, our objective was to determine if use of lactate relative to MACS-purified hiPSC-CMs affects the properties of resulting hiPSC-ECTs. Therefore, hiPSC-CMs were differentiated and purified using either lactate-based media or MACS. Global proteomics revealed that lactate-purified hiPSC-CMs displayed a differential phenotype over MACS hiPSC-CMs. hiPSC-CMs were then integrated into 3D hiPSC-ECTs and cultured for 4 weeks. Structurally, there was no significant difference in sarcomere length between lactate and MACS hiPSC-ECTs. Assessment of isometric twitch force and Ca2+ transient measurements revealed similar functional performance between purification methods. High-resolution mass spectrometry-based quantitative proteomics showed no significant difference in protein pathway expression or myofilament proteoforms. Taken together, this study demonstrates that lactate- and MACS-purified hiPSC-CMs generate ECTs with comparable structural, functional, and proteomic features, and it suggests that lactate purification does not result in an irreversible change in a hiPSC-CM phenotype.
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Affiliation(s)
- Kalina J. Rossler
- Molecular and Cellular Pharmacology Training Program
- Department of Cell and Regenerative Biology
| | | | | | - Timothy J. Aballo
- Molecular and Cellular Pharmacology Training Program
- Department of Cell and Regenerative Biology
| | | | | | | | | | - Yanlong Zhu
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Timothy J. Kamp
- Department of Cell and Regenerative Biology
- Department of Medicine
| | | | - Ying Ge
- Department of Cell and Regenerative Biology
- Department of Chemistry, and
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Pergande MR, Osterbauer KJ, Buck KM, Roberts DS, Wood NN, Balasubramanian P, Mann MW, Rossler KJ, Diffee GM, Colman RJ, Anderson RM, Ge Y. Mass Spectrometry-Based Multiomics Identifies Metabolic Signatures of Sarcopenia in Rhesus Monkey Skeletal Muscle. J Proteome Res 2023. [PMID: 37991985 DOI: 10.1021/acs.jproteome.3c00474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Sarcopenia is a progressive disorder characterized by age-related loss of skeletal muscle mass and function. Although significant progress has been made over the years to identify the molecular determinants of sarcopenia, the precise mechanisms underlying the age-related loss of contractile function remains unclear. Advances in "omics" technologies, including mass spectrometry-based proteomic and metabolomic analyses, offer great opportunities to better understand sarcopenia. Herein, we performed mass spectrometry-based analyses of the vastus lateralis from young, middle-aged, and older rhesus monkeys to identify molecular signatures of sarcopenia. In our proteomic analysis, we identified proteins that change with age, including those involved in adenosine triphosphate and adenosine monophosphate metabolism as well as fatty acid beta oxidation. In our untargeted metabolomic analysis, we identified metabolites that changed with age largely related to energy metabolism including fatty acid beta oxidation. Pathway analysis of age-responsive proteins and metabolites revealed changes in muscle structure and contraction as well as lipid, carbohydrate, and purine metabolism. Together, this study discovers new metabolic signatures and offers new insights into the molecular mechanisms underlying sarcopenia for the evaluation and monitoring of a therapeutic treatment of sarcopenia.
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Affiliation(s)
- Melissa R Pergande
- Department of Cell and Regenerative Biology, University of Wisconsin─Madison, Madison, Wisconsin 53705, United States
| | - Katie J Osterbauer
- Department of Medicine, University of Wisconsin─Madison, Madison, Wisconsin 53705, United States
| | - Kevin M Buck
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - David S Roberts
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Nina N Wood
- Department of Medicine, University of Wisconsin─Madison, Madison, Wisconsin 53705, United States
| | - Priya Balasubramanian
- Department of Medicine, University of Wisconsin─Madison, Madison, Wisconsin 53705, United States
| | - Morgan W Mann
- Department of Medicine, University of Wisconsin─Madison, Madison, Wisconsin 53705, United States
| | - Kalina J Rossler
- Department of Cell and Regenerative Biology, University of Wisconsin─Madison, Madison, Wisconsin 53705, United States
| | - Gary M Diffee
- Department of Kinesiology, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Ricki J Colman
- Department of Cell and Regenerative Biology, University of Wisconsin─Madison, Madison, Wisconsin 53705, United States
- Wisconsin National Primate Research Center, University of Wisconsin─Madison, Madison, Wisconsin 53715, United States
| | - Rozalyn M Anderson
- Department of Medicine, University of Wisconsin─Madison, Madison, Wisconsin 53705, United States
- Geriatric Research Education and Clinical Center, William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin 53705, United States
| | - Ying Ge
- 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
- Human Proteomics Program, University of Wisconsin─Madison, Madison, Wisconsin 53705, United States
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Pergande MR, Osterbauer KJ, Buck KM, Roberts DS, Wood NN, Balasubramanian P, Mann MW, Rossler K, Diffee GM, Colman RJ, Anderson RM, Ge Y. Mass spectrometry-based multi-omics identifies metabolic signatures of sarcopenia in rhesus monkey skeletal muscle. bioRxiv 2023:2023.07.31.551315. [PMID: 37577600 PMCID: PMC10418093 DOI: 10.1101/2023.07.31.551315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Sarcopenia is a progressive disorder characterized by age-related loss of skeletal muscle mass and function. Although significant progress has been made over the years to identify the molecular determinants of sarcopenia, the precise mechanisms underlying the age-related loss of contractile function remains unclear. Advances in omics technologies, including mass spectrometry-based proteomic and metabolomic analyses, offer great opportunities to better understand sarcopenia. Herein, we performed mass spectrometry-based analyses of the vastus lateralis from young, middle-aged, and older rhesus monkeys to identify molecular signatures of sarcopenia. In our proteomic analysis, we identified numerous proteins that change with age, including those involved in adenosine triphosphate and adenosine monophosphate metabolism as well as fatty acid beta oxidation. In our untargeted metabolomic analysis, we identified multiple metabolites that changed with age largely related to energy metabolism including fatty acid beta oxidation. Pathway analysis of age-responsive proteins and metabolites revealed changes in muscle structure and contraction as well as lipid, carbohydrate, and purine metabolism. Together, this study discovers new metabolic signatures and offer new insights into the molecular mechanism underlying sarcopenia for the evaluation and monitoring of therapeutic treatment of sarcopenia.
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Mann MW, Fu Y, Gearhart RL, Xu X, Roberts DS, Li Y, Zhou J, Ge Y, Brasier AR. Bromodomain-containing Protein 4 regulates innate inflammation via modulation of alternative splicing. Front Immunol 2023; 14:1212770. [PMID: 37435059 PMCID: PMC10331468 DOI: 10.3389/fimmu.2023.1212770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/05/2023] [Indexed: 07/13/2023] Open
Abstract
Introduction Bromodomain-containing Protein 4 (BRD4) is a transcriptional regulator which coordinates gene expression programs controlling cancer biology, inflammation, and fibrosis. In the context of airway viral infection, BRD4-specific inhibitors (BRD4i) block the release of pro-inflammatory cytokines and prevent downstream epithelial plasticity. Although the chromatin modifying functions of BRD4 in inducible gene expression have been extensively investigated, its roles in post-transcriptional regulation are not well understood. Given BRD4's interaction with the transcriptional elongation complex and spliceosome, we hypothesize that BRD4 is a functional regulator of mRNA processing. Methods To address this question, we combine data-independent analysis - parallel accumulation-serial fragmentation (diaPASEF) with RNA-sequencing to achieve deep and integrated coverage of the proteomic and transcriptomic landscapes of human small airway epithelial cells exposed to viral challenge and treated with BRD4i. Results We discover that BRD4 regulates alternative splicing of key genes, including Interferon-related Developmental Regulator 1 (IFRD1) and X-Box Binding Protein 1 (XBP1), related to the innate immune response and the unfolded protein response (UPR). We identify requirement of BRD4 for expression of serine-arginine splicing factors, splicosome components and the Inositol-Requiring Enzyme 1 IREα affecting immediate early innate response and the UPR. Discussion These findings extend the transcriptional elongation-facilitating actions of BRD4 in control of post-transcriptional RNA processing via modulating splicing factor expression in virus-induced innate signaling.
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Affiliation(s)
- Morgan W. Mann
- Department of Medicine, University of Wisconsin – Madison, Madison, WI, United States
| | - Yao Fu
- Department of Medicine, University of Wisconsin – Madison, Madison, WI, United States
| | - Robert L. Gearhart
- Department of Chemistry, University of Wisconsin – Madison, Madison, WI, United States
| | - Xiaofang Xu
- Department of Medicine, University of Wisconsin – Madison, Madison, WI, United States
| | - David S. Roberts
- Department of Chemistry, University of Wisconsin – Madison, Madison, WI, United States
| | - Yi Li
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, United States
| | - Jia Zhou
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin – Madison, Madison, WI, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, United States
| | - Allan R. Brasier
- Department of Medicine, University of Wisconsin – Madison, Madison, WI, United States
- Institute for Clinical and Translational Research, University of Wisconsin-Madison, Madison, WI, United States
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Rossler KJ, de Lange WJ, Mann MW, Aballo TJ, Melby JA, Zhang J, Kim G, Bayne EF, Zhu Y, Farrell ET, Kamp TJ, Ralphe JC, Ge Y. Lactate and Immunomagnetic-purified iPSC-derived Cardiomyocytes Generate Comparable Engineered Cardiac Tissue Constructs. bioRxiv 2023:2023.05.05.539642. [PMID: 37205556 PMCID: PMC10187273 DOI: 10.1101/2023.05.05.539642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Three-dimensional engineered cardiac tissue (ECT) using purified human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) has emerged as an appealing model system for the study of human cardiac biology and disease. A recent study reported widely-used metabolic (lactate) purification of monolayer hiPSC-CM cultures results in an ischemic cardiomyopathy-like phenotype compared to magnetic antibody-based cell sorting (MACS) purification, complicating the interpretation of studies using lactate-purified hiPSC-CMs. Herein, our objective was to determine if use of lactate relative to MACs-purified hiPSC-CMs impacts the properties of resulting hiPSC-ECTs. Therefore, hiPSC-CMs were differentiated and purified using either lactate-based media or MACS. After purification, hiPSC-CMs were combined with hiPSC-cardiac fibroblasts to create 3D hiPSC-ECT constructs maintained in culture for four weeks. There were no structural differences observed, and there was no significant difference in sarcomere length between lactate and MACS hiPSC-ECTs. Assessment of isometric twitch force, Ca 2+ transients, and β-adrenergic response revealed similar functional performance between purification methods. High-resolution mass spectrometry (MS)-based quantitative proteomics showed no significant difference in any protein pathway expression or myofilament proteoforms. Taken together, this study demonstrates lactate- and MACS-purified hiPSC-CMs generate ECTs with comparable molecular and functional properties, and suggests lactate purification does not result in an irreversible change in hiPSC-CM phenotype.
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Roberts DS, Mann MW, Melby JA, Larson EJ, Zhu Y, Brasier AR, Jin S, Ge Y. Structural O-Glycoform Heterogeneity of the SARS-CoV-2 Spike Protein Receptor-Binding Domain Revealed by Native Top-Down Mass Spectrometry. bioRxiv 2021. [PMID: 33688648 DOI: 10.1101/2021.02.28.433291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes an extensively glycosylated surface spike (S) protein to mediate host cell entry and the S protein glycosylation is strongly implicated in altering viral binding/function and infectivity. However, the structures and relative abundance of the new O-glycans found on the S protein regional-binding domain (S-RBD) remain cryptic because of the challenges in intact glycoform analysis. Here, we report the complete structural characterization of intact O-glycan proteoforms using native top-down mass spectrometry (MS). By combining trapped ion mobility spectrometry (TIMS), which can separate the protein conformers of S-RBD and analyze their gas phase structural variants, with ultrahigh-resolution Fourier transform ion cyclotron resonance (FTICR) MS analysis, the O-glycoforms of the S-RBD are comprehensively characterized, so that seven O-glycoforms and their relative molecular abundance are structurally elucidated for the first time. These findings demonstrate that native top-down MS can provide a high-resolution proteoform-resolved mapping of diverse O-glycoforms of the S glycoprotein, which lays a strong molecular foundation to uncover the functional roles of their O-glycans. This proteoform-resolved approach can be applied to reveal the structural O-glycoform heterogeneity of emergent SARS-CoV-2 S-RBD variants, as well as other O-glycoproteins in general.
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Mann MW, Gueguen B, Guillou S, Debrand E, Soufflet C. Chess-playing epilepsy: a case report with video-EEG and back averaging. Epileptic Disord 2004; 6:293-6. [PMID: 15634627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2004] [Accepted: 09/16/2004] [Indexed: 05/01/2023]
Abstract
A patient suffering from juvenile myoclonic epilepsy experienced myoclonic jerks, fairly regularly, while playing chess. The myoclonus appeared particularly when he had to plan his strategy, to choose between two solutions or while raising the arm to move a chess figure. Video-EEG-polygraphy was performed, with back averaging of the myoclonus registered during a chess match and during neuropsychological testing with Kohs cubes. The EEG spike wave complexes were localised in the fronto-central region. [Published with video sequences].
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Affiliation(s)
- M W Mann
- Neurosurgery Department, Centre hospitalier St Anne, Paris, France.
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