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Lin W, Mousavi F, Blum BC, Heckendorf CF, Lawton M, Lampl N, Hekman R, Guo H, McComb M, Emili A. PANAMA-enabled high-sensitivity dual nanoflow LC-MS metabolomics and proteomics analysis. CELL REPORTS METHODS 2024; 4:100803. [PMID: 38959888 DOI: 10.1016/j.crmeth.2024.100803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 03/16/2024] [Accepted: 06/05/2024] [Indexed: 07/05/2024]
Abstract
High-sensitivity nanoflow liquid chromatography (nLC) is seldom employed in untargeted metabolomics because current sample preparation techniques are inefficient at preventing nanocapillary column performance degradation. Here, we describe an nLC-based tandem mass spectrometry workflow that enables seamless joint analysis and integration of metabolomics (including lipidomics) and proteomics from the same samples without instrument duplication. This workflow is based on a robust solid-phase micro-extraction step for routine sample cleanup and bioactive molecule enrichment. Our method, termed proteomic and nanoflow metabolomic analysis (PANAMA), improves compound resolution and detection sensitivity without compromising the depth of coverage as compared with existing widely used analytical procedures. Notably, PANAMA can be applied to a broad array of specimens, including biofluids, cell lines, and tissue samples. It generates high-quality, information-rich metabolite-protein datasets while bypassing the need for specialized instrumentation.
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Affiliation(s)
- Weiwei Lin
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Department of Pharmacology, Physiology & Biophysics, Boston University School of Medicine, Boston, MA, USA.
| | - Fatemeh Mousavi
- Center for Network Systems Biology, Boston University, Boston, MA, USA
| | - Benjamin C Blum
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Christian F Heckendorf
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Matthew Lawton
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Noah Lampl
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Ryan Hekman
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Hongbo Guo
- Center for Network Systems Biology, Boston University, Boston, MA, USA
| | - Mark McComb
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Department of Biology, Boston University, Boston, MA, USA.
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Menezes Junior ADS, de França-e-Silva ALG, de Oliveira HL, de Lima KBA, Porto IDOP, Pedroso TMA, Silva DDME, Freitas AF. Genetic Mutations and Mitochondrial Redox Signaling as Modulating Factors in Hypertrophic Cardiomyopathy: A Scoping Review. Int J Mol Sci 2024; 25:5855. [PMID: 38892064 PMCID: PMC11173352 DOI: 10.3390/ijms25115855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is a heart condition characterized by cellular and metabolic dysfunction, with mitochondrial dysfunction playing a crucial role. Although the direct relationship between genetic mutations and mitochondrial dysfunction remains unclear, targeting mitochondrial dysfunction presents promising opportunities for treatment, as there are currently no effective treatments available for HCM. This review adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis Extension for Scoping Reviews guidelines. Searches were conducted in databases such as PubMed, Embase, and Scopus up to September 2023 using "MESH terms". Bibliographic references from pertinent articles were also included. Hypertrophic cardiomyopathy (HCM) is influenced by ionic homeostasis, cardiac tissue remodeling, metabolic balance, genetic mutations, reactive oxygen species regulation, and mitochondrial dysfunction. The latter is a common factor regardless of the cause and is linked to intracellular calcium handling, energetic and oxidative stress, and HCM-induced hypertrophy. Hypertrophic cardiomyopathy treatments focus on symptom management and complication prevention. Targeted therapeutic approaches, such as improving mitochondrial bioenergetics, are being explored. This includes coenzyme Q and elamipretide therapies and metabolic strategies like therapeutic ketosis. Understanding the biomolecular, genetic, and mitochondrial mechanisms underlying HCM is crucial for developing new therapeutic modalities.
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Affiliation(s)
- Antonio da Silva Menezes Junior
- Faculdade de Medicina, Departamento de Clínica Médica, Universidade Federal de Goiás (UFG), Goiânia 74020-020, Brazil; (A.L.G.d.F.-e.-S.); (H.L.d.O.); (K.B.A.d.L.); (D.d.M.e.S.); (A.F.F.J.)
| | - Ana Luísa Guedes de França-e-Silva
- Faculdade de Medicina, Departamento de Clínica Médica, Universidade Federal de Goiás (UFG), Goiânia 74020-020, Brazil; (A.L.G.d.F.-e.-S.); (H.L.d.O.); (K.B.A.d.L.); (D.d.M.e.S.); (A.F.F.J.)
| | - Henrique Lima de Oliveira
- Faculdade de Medicina, Departamento de Clínica Médica, Universidade Federal de Goiás (UFG), Goiânia 74020-020, Brazil; (A.L.G.d.F.-e.-S.); (H.L.d.O.); (K.B.A.d.L.); (D.d.M.e.S.); (A.F.F.J.)
| | - Khissya Beatryz Alves de Lima
- Faculdade de Medicina, Departamento de Clínica Médica, Universidade Federal de Goiás (UFG), Goiânia 74020-020, Brazil; (A.L.G.d.F.-e.-S.); (H.L.d.O.); (K.B.A.d.L.); (D.d.M.e.S.); (A.F.F.J.)
| | - Iane de Oliveira Pires Porto
- Faculdade de Medicina, Universidade de Rio Verde (UniRV), Campus Aparecida, Aparecida de Goiânia 74345-030, Brazil; (I.d.O.P.P.); (T.M.A.P.)
| | - Thays Millena Alves Pedroso
- Faculdade de Medicina, Universidade de Rio Verde (UniRV), Campus Aparecida, Aparecida de Goiânia 74345-030, Brazil; (I.d.O.P.P.); (T.M.A.P.)
| | - Daniela de Melo e Silva
- Faculdade de Medicina, Departamento de Clínica Médica, Universidade Federal de Goiás (UFG), Goiânia 74020-020, Brazil; (A.L.G.d.F.-e.-S.); (H.L.d.O.); (K.B.A.d.L.); (D.d.M.e.S.); (A.F.F.J.)
| | - Aguinaldo F. Freitas
- Faculdade de Medicina, Departamento de Clínica Médica, Universidade Federal de Goiás (UFG), Goiânia 74020-020, Brazil; (A.L.G.d.F.-e.-S.); (H.L.d.O.); (K.B.A.d.L.); (D.d.M.e.S.); (A.F.F.J.)
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Dababneh S, Hamledari H, Maaref Y, Jayousi F, Hosseini DB, Khan A, Jannati S, Jabbari K, Arslanova A, Butt M, Roston TM, Sanatani S, Tibbits GF. Advances in Hypertrophic Cardiomyopathy Disease Modelling Using hiPSC-Derived Cardiomyocytes. Can J Cardiol 2024; 40:766-776. [PMID: 37952715 DOI: 10.1016/j.cjca.2023.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/21/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023] Open
Abstract
The advent of human induced pluripotent stem cells (hiPSCs) and their capacity to be differentiated into beating human cardiomyocytes (CMs) in vitro has revolutionized human disease modelling, genotype-phenotype predictions, and therapeutic testing. Hypertrophic cardiomyopathy (HCM) is a common inherited cardiomyopathy and the leading known cause of sudden cardiac arrest in young adults and athletes. On a molecular level, HCM is often driven by single pathogenic genetic variants, usually in sarcomeric proteins, that can alter the mechanical, electrical, signalling, and transcriptional properties of the cell. A deeper knowledge of these alterations is critical to better understanding HCM manifestation, progression, and treatment. Leveraging hiPSC-CMs to investigate the molecular mechanisms driving HCM presents a unique opportunity to dissect the consequences of genetic variants in a sophisticated and controlled manner. In this review, we summarize the molecular underpinnings of HCM and the role of hiPSC-CM studies in advancing our understanding, and we highlight the advances in hiPSC-CM-based modelling of HCM, including maturation, contractility, multiomics, and genome editing, with the notable exception of electrophysiology, which has been previously covered.
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Affiliation(s)
- Saif Dababneh
- Cellular and Regenerative Medicine Centre, BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada; Department of Cellular and Physiological Sciences, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Homa Hamledari
- Cellular and Regenerative Medicine Centre, BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada; Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Yasaman Maaref
- Cellular and Regenerative Medicine Centre, BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada; Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Farah Jayousi
- Cellular and Regenerative Medicine Centre, BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada; Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Dina B Hosseini
- Cellular and Regenerative Medicine Centre, BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada; Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Aasim Khan
- Cellular and Regenerative Medicine Centre, BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada; Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Shayan Jannati
- Faculty of Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kosar Jabbari
- Cellular and Regenerative Medicine Centre, BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada; Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Alia Arslanova
- Cellular and Regenerative Medicine Centre, BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada; Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Mariam Butt
- Cellular and Regenerative Medicine Centre, BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada; Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Thomas M Roston
- Division of Cardiology and Centre for Cardiovascular Innovation, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shubhayan Sanatani
- Cellular and Regenerative Medicine Centre, BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Glen F Tibbits
- Cellular and Regenerative Medicine Centre, BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada; Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada; School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada; Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
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Hovhannisyan Y, Li Z, Callon D, Suspène R, Batoumeni V, Canette A, Blanc J, Hocini H, Lefebvre C, El-Jahrani N, Kitsara M, L'honoré A, Kordeli E, Fornes P, Concordet JP, Tachdjian G, Rodriguez AM, Vartanian JP, Béhin A, Wahbi K, Joanne P, Agbulut O. Critical contribution of mitochondria in the development of cardiomyopathy linked to desmin mutation. Stem Cell Res Ther 2024; 15:10. [PMID: 38167524 PMCID: PMC10763022 DOI: 10.1186/s13287-023-03619-7] [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: 10/03/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Beyond the observed alterations in cellular structure and mitochondria, the mechanisms linking rare genetic mutations to the development of heart failure in patients affected by desmin mutations remain unclear due in part, to the lack of relevant human cardiomyocyte models. METHODS To shed light on the role of mitochondria in these mechanisms, we investigated cardiomyocytes derived from human induced pluripotent stem cells carrying the heterozygous DESE439K mutation that were either isolated from a patient or generated by gene editing. To increase physiological relevance, cardiomyocytes were either cultured on an anisotropic micropatterned surface to obtain elongated and aligned cardiomyocytes, or as a cardiac spheroid to create a micro-tissue. Moreover, when applicable, results from cardiomyocytes were confirmed with heart biopsies of suddenly died patient of the same family harboring DESE439K mutation, and post-mortem heart samples from five control healthy donors. RESULTS The heterozygous DESE439K mutation leads to dramatic changes in the overall cytoarchitecture of cardiomyocytes, including cell size and morphology. Most importantly, mutant cardiomyocytes display altered mitochondrial architecture, mitochondrial respiratory capacity and metabolic activity reminiscent of defects observed in patient's heart tissue. Finally, to challenge the pathological mechanism, we transferred normal mitochondria inside the mutant cardiomyocytes and demonstrated that this treatment was able to restore mitochondrial and contractile functions of cardiomyocytes. CONCLUSIONS This work highlights the deleterious effects of DESE439K mutation, demonstrates the crucial role of mitochondrial abnormalities in the pathophysiology of desmin-related cardiomyopathy, and opens up new potential therapeutic perspectives for this disease.
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Affiliation(s)
- Yeranuhi Hovhannisyan
- UMR CNRS 8256, INSERM U1164, Biological Adaptation and Ageing, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 7, Quai St Bernard (case 256), 75005, Paris, France
| | - Zhenlin Li
- UMR CNRS 8256, INSERM U1164, Biological Adaptation and Ageing, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 7, Quai St Bernard (case 256), 75005, Paris, France
| | - Domitille Callon
- UMR CNRS 8256, INSERM U1164, Biological Adaptation and Ageing, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 7, Quai St Bernard (case 256), 75005, Paris, France
- Department of Pathology, Academic Hospital of Reims, Reims, France
| | - Rodolphe Suspène
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université Paris Cité, Paris, France
| | - Vivien Batoumeni
- UMR CNRS 8256, INSERM U1164, Biological Adaptation and Ageing, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 7, Quai St Bernard (case 256), 75005, Paris, France
- Ksilink, Strasbourg, France
| | - Alexis Canette
- Service de Microscopie Électronique (IBPS-SME), Institut de Biologie Paris-Seine (IBPS), CNRS, Sorbonne Université, Paris, France
| | - Jocelyne Blanc
- UMR CNRS 8256, INSERM U1164, Biological Adaptation and Ageing, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 7, Quai St Bernard (case 256), 75005, Paris, France
| | - Hakim Hocini
- INSERM U955, Equipe 16, Université Paris-Est Créteil, Créteil, France
| | - Cécile Lefebvre
- INSERM U955, Equipe 16, Université Paris-Est Créteil, Créteil, France
| | - Nora El-Jahrani
- INSERM U955, Equipe 16, Université Paris-Est Créteil, Créteil, France
| | - Maria Kitsara
- UMR CNRS 8256, INSERM U1164, Biological Adaptation and Ageing, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 7, Quai St Bernard (case 256), 75005, Paris, France
| | - Aurore L'honoré
- UMR CNRS 8256, INSERM U1164, Biological Adaptation and Ageing, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 7, Quai St Bernard (case 256), 75005, Paris, France
| | - Ekaterini Kordeli
- UMR CNRS 8256, INSERM U1164, Biological Adaptation and Ageing, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 7, Quai St Bernard (case 256), 75005, Paris, France
| | - Paul Fornes
- Department of Pathology, Academic Hospital of Reims, Reims, France
| | - Jean-Paul Concordet
- INSERM U1154, CNRS UMR7196, Museum National d'Histoire Naturelle, Paris, France
| | - Gérard Tachdjian
- Laboratoire de Cytogénétique, Service d'Histologie-Embryologie-Cytogénétique, AP-HP, Hôpital Antoine Béclère, Université Paris Saclay, Clamart, France
| | - Anne-Marie Rodriguez
- UMR CNRS 8256, INSERM U1164, Biological Adaptation and Ageing, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 7, Quai St Bernard (case 256), 75005, Paris, France
| | - Jean-Pierre Vartanian
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université Paris Cité, Paris, France
| | - Anthony Béhin
- Reference Center for Muscle Diseases Paris-Est, Myology Institute, AP-HP, Pitié-Salpêtrière Hospital, Sorbonne Université, Paris, France
| | - Karim Wahbi
- Cardiology Department, AP-HP, Cochin Hospital, Université Paris Cité, Paris, France
| | - Pierre Joanne
- UMR CNRS 8256, INSERM U1164, Biological Adaptation and Ageing, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 7, Quai St Bernard (case 256), 75005, Paris, France.
| | - Onnik Agbulut
- UMR CNRS 8256, INSERM U1164, Biological Adaptation and Ageing, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 7, Quai St Bernard (case 256), 75005, Paris, France.
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