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Dai H, Liu Y, Zhu M, Tao S, Hu C, Luo P, Jiang A, Zhang G. Machine learning and experimental validation of novel biomarkers for hypertrophic cardiomyopathy and cancers. J Cell Mol Med 2024; 28:e70034. [PMID: 39160643 PMCID: PMC11333198 DOI: 10.1111/jcmm.70034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/24/2024] [Accepted: 06/19/2024] [Indexed: 08/21/2024] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is a hereditary cardiac disorder marked by anomalous thickening of the myocardium, representing a significant contributor to mortality. While the involvement of immune inflammation in the development of cardiac ailments is well-documented, its specific impact on HCM pathogenesis remains uncertain. Five distinct machine learning algorithms, namely LASSO, SVM, RF, Boruta and XGBoost, were utilized to discover new biomarkers associated with HCM. A unique nomogram was developed using two newly identified biomarkers and subsequently validated. Furthermore, samples of HCM and normal heart tissues were gathered from our institution to confirm the variance in expression levels and prognostic significance of GATM and MGST1. Five novel biomarkers (DARS2, GATM, MGST1, SDSL and ARG2) associated with HCM were identified. Subsequent validation revealed that GATM and MGST1 exhibited significant diagnostic utility for HCM in both the training and test cohorts, with all AUC values exceeding 0.8. Furthermore, a novel risk assessment model for HCM patients based on the expression levels of GATM and MGST1 demonstrated favourable performance in both the training (AUC = 0.88) and test cohorts (AUC = 0.9). Furthermore, our study revealed that GATM and MGST1 exhibited elevated expression levels in HCM tissues, demonstrating strong discriminatory ability between HCM and normal cardiac tissues (AUC of GATM = 0.79; MGST1 = 0.86). Our findings suggest that two specific cell types, monocytes and multipotent progenitors (MPP), may play crucial roles in the pathogenesis of HCM. Notably, GATM and MGST1 were found to be highly expressed in various tumours and showed significant prognostic implications. Functionally, GATM and MGST1 are likely involved in xenobiotic metabolism and epithelial mesenchymal transition in a wide range of cancer types. GATM and MGST1 have been identified as novel biomarkers implicated in the progression of both HCM and cancer. Additionally, monocytes and MPP may also play a role in facilitating the progression of HCM.
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Affiliation(s)
- Hualei Dai
- Cardiovascular CenterThe Affiliated Hospital of Yunnan University, Yunnan UniversityKunmingYunnanChina
- School of MedicineYunnan UniversityKunmingYunnanChina
| | - Ying Liu
- Department of GynecologyYunnan Cancer Hospital and The Third Affiliated Hospital of Kunming Medical UniversityKunmingYunnanChina
| | - Meng Zhu
- Department of GeriatricsThe Affiliated Huaian Hospital of Xuzhou Medical University, Huaian Second People's HospitalHuaianJiangsuChina
| | - Siming Tao
- Cardiovascular CenterThe Affiliated Hospital of Yunnan University, Yunnan UniversityKunmingYunnanChina
| | - Chengcheng Hu
- Cardiovascular CenterThe Affiliated Hospital of Yunnan University, Yunnan UniversityKunmingYunnanChina
| | - Peng Luo
- Department of OncologyZhujiang Hospital, Southern Medical UniversityGuangzhouChina
| | - Aimin Jiang
- Department of UrologyChangzheng Hospital, Naval Medical UniversityShanghaiChina
| | - Guimin Zhang
- Cardiovascular CenterThe Affiliated Hospital of Yunnan University, Yunnan UniversityKunmingYunnanChina
- School of MedicineYunnan UniversityKunmingYunnanChina
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2
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Jiang J, Wu H, Ji Y, Han K, Tang JM, Hu S, Lei W. Development and disease-specific regulation of RNA splicing in cardiovascular system. Front Cell Dev Biol 2024; 12:1423553. [PMID: 39045460 PMCID: PMC11263117 DOI: 10.3389/fcell.2024.1423553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/17/2024] [Indexed: 07/25/2024] Open
Abstract
Alternative splicing is a complex gene regulatory process that distinguishes itself from canonical splicing by rearranging the introns and exons of an immature pre-mRNA transcript. This process plays a vital role in enhancing transcriptomic and proteomic diversity from the genome. Alternative splicing has emerged as a pivotal mechanism governing complex biological processes during both heart development and the development of cardiovascular diseases. Multiple alternative splicing factors are involved in a synergistic or antagonistic manner in the regulation of important genes in relevant physiological processes. Notably, circular RNAs have only recently garnered attention for their tissue-specific expression patterns and regulatory functions. This resurgence of interest has prompted a reevaluation of the topic. Here, we provide an overview of our current understanding of alternative splicing mechanisms and the regulatory roles of alternative splicing factors in cardiovascular development and pathological process of different cardiovascular diseases, including cardiomyopathy, myocardial infarction, heart failure and atherosclerosis.
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Affiliation(s)
- Jinxiu Jiang
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
| | - Hongchun Wu
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
| | - Yabo Ji
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
| | - Kunjun Han
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
| | - Jun-Ming Tang
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Shijun Hu
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
| | - Wei Lei
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
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3
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Steczina S, Mohran S, Bailey LRJ, McMillen TS, Kooiker KB, Wood NB, Davis J, Previs MJ, Olivotto I, Pioner JM, Geeves MA, Poggesi C, Regnier M. MYBPC3-c.772G>A mutation results in haploinsufficiency and altered myosin cycling kinetics in a patient induced stem cell derived cardiomyocyte model of hypertrophic cardiomyopathy. J Mol Cell Cardiol 2024; 191:27-39. [PMID: 38648963 PMCID: PMC11116032 DOI: 10.1016/j.yjmcc.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 03/13/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
Approximately 40% of hypertrophic cardiomyopathy (HCM) mutations are linked to the sarcomere protein cardiac myosin binding protein-C (cMyBP-C). These mutations are either classified as missense mutations or truncation mutations. One mutation whose nature has been inconsistently reported in the literature is the MYBPC3-c.772G > A mutation. Using patient-derived human induced pluripotent stem cells differentiated to cardiomyocytes (hiPSC-CMs), we have performed a mechanistic study of the structure-function relationship for this MYBPC3-c.772G > A mutation versus a mutation corrected, isogenic cell line. Our results confirm that this mutation leads to exon skipping and mRNA truncation that ultimately suggests ∼20% less cMyBP-C protein (i.e., haploinsufficiency). This, in turn, results in increased myosin recruitment and accelerated myofibril cycling kinetics. Our mechanistic studies suggest that faster ADP release from myosin is a primary cause of accelerated myofibril cross-bridge cycling due to this mutation. Additionally, the reduction in force generating heads expected from faster ADP release during isometric contractions is outweighed by a cMyBP-C phosphorylation mediated increase in myosin recruitment that leads to a net increase of myofibril force, primarily at submaximal calcium activations. These results match well with our previous report on contractile properties from myectomy samples of the patients from whom the hiPSC-CMs were generated, demonstrating that these cell lines are a good model to study this pathological mutation and extends our understanding of the mechanisms of altered contractile properties of this HCM MYBPC3-c.772G > A mutation.
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Affiliation(s)
- Sonette Steczina
- Department of Bioengineering, University of Washington, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Saffie Mohran
- Department of Bioengineering, University of Washington, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Logan R J Bailey
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Molecular and Cellular Biology, University of Washington, Seattle, WA 98109, USA; Department of Lab Medicine and Pathology, University of Washington, Seattle, WA 98109, USA
| | - Timothy S McMillen
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, USA; Center for Translational Muscle Research, University of Washington, Seattle, WA 98109, USA
| | - Kristina B Kooiker
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Neil B Wood
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT 05404, USA
| | - Jennifer Davis
- Department of Bioengineering, University of Washington, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Lab Medicine and Pathology, University of Washington, Seattle, WA 98109, USA
| | - Michael J Previs
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT 05404, USA
| | - Iacopo Olivotto
- Department of Experimental and Clinical Medicine, Division of Physiology, University of Florence, Italy
| | | | | | - Corrado Poggesi
- Department of Experimental and Clinical Medicine, Division of Physiology, University of Florence, Italy
| | - Michael Regnier
- Department of Bioengineering, University of Washington, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Center for Translational Muscle Research, University of Washington, Seattle, WA 98109, USA.
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4
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Glavaški M, Velicki L, Vučinić N. Hypertrophic Cardiomyopathy: Genetic Foundations, Outcomes, Interconnections, and Their Modifiers. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1424. [PMID: 37629714 PMCID: PMC10456451 DOI: 10.3390/medicina59081424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/30/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023]
Abstract
Hypertrophic cardiomyopathy (HCM) is the most prevalent heritable cardiomyopathy. HCM is considered to be caused by mutations in cardiac sarcomeric protein genes. Recent research suggests that the genetic foundation of HCM is much more complex than originally postulated. The clinical presentations of HCM are very variable. Some mutation carriers remain asymptomatic, while others develop severe HCM, terminal heart failure, or sudden cardiac death. Heterogeneity regarding both genetic mutations and the clinical course of HCM hinders the establishment of universal genotype-phenotype correlations. However, some trends have been identified. The presence of a mutation in some genes encoding sarcomeric proteins is associated with earlier HCM onset, more severe left ventricular hypertrophy, and worse clinical outcomes. There is a diversity in the mechanisms implicated in the pathogenesis of HCM. They may be classified into groups, but they are interrelated. The lack of known supplementary elements that control the progression of HCM indicates that molecular mechanisms that exist between genotype and clinical presentations may be crucial. Secondary molecular changes in pathways implicated in HCM pathogenesis, post-translational protein modifications, and epigenetic factors affect HCM phenotypes. Cardiac loading conditions, exercise, hypertension, diet, alcohol consumption, microbial infection, obstructive sleep apnea, obesity, and environmental factors are non-molecular aspects that change the HCM phenotype. Many mechanisms are implicated in the course of HCM. They are mostly interconnected and contribute to some extent to final outcomes.
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Affiliation(s)
- Mila Glavaški
- Faculty of Medicine, University of Novi Sad, Hajduk Veljkova 3, 21000 Novi Sad, Serbia; (L.V.)
| | - Lazar Velicki
- Faculty of Medicine, University of Novi Sad, Hajduk Veljkova 3, 21000 Novi Sad, Serbia; (L.V.)
- Institute of Cardiovascular Diseases Vojvodina, Put Doktora Goldmana 4, 21204 Sremska Kamenica, Serbia
| | - Nataša Vučinić
- Faculty of Medicine, University of Novi Sad, Hajduk Veljkova 3, 21000 Novi Sad, Serbia; (L.V.)
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5
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Molecular Diagnosis of Hypertrophic Cardiomyopathy (HCM): In the Heart of Cardiac Disease. J Clin Med 2022; 12:jcm12010225. [PMID: 36615026 PMCID: PMC9821215 DOI: 10.3390/jcm12010225] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is an inherited myocardial disease with the presence of left ventricular hypertrophy (LVH). The disease is characterized by high locus, allelic and phenotypic heterogeneity, even among members of the same family. The list of confirmed and potentially relevant genes implicating the disease is constantly increasing, with novel genes frequently reported. Heterozygous alterations in the five main sarcomeric genes (MYBPC3, MYH7, TNNT2, TNNI3, and MYL2) are estimated to account for more than half of confirmed cases. The genetic discoveries of recent years have shed more light on the molecular pathogenic mechanisms of HCM, contributing to substantial advances in the diagnosis of the disease. Genetic testing applying next-generation sequencing (NGS) technologies and early diagnosis prior to the clinical manifestation of the disease among family members demonstrate an important improvement in the field.
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Nguyen MB, Mital S, Mertens L, Jeewa A, Friedberg MK, Aguet J, Adler A, Lam CZ, Dragulescu A, Rakowski H, Villemain O. Pediatric Hypertrophic Cardiomyopathy: Exploring the Genotype-Phenotype Association. J Am Heart Assoc 2022; 11:e024220. [PMID: 35179047 PMCID: PMC9075072 DOI: 10.1161/jaha.121.024220] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/11/2022] [Indexed: 11/19/2022]
Abstract
Pediatric hypertrophic cardiomyopathy (HCM) is the most common form of cardiomyopathy in children and a leading cause of sudden cardiac death. Yet, the association between genotype variation, phenotype expression, and adverse events in pediatric HCM has not been fully elucidated. Although the literature on this topic is evolving in adult HCM, the evidence in children is lacking. Solidifying our understanding of this relationship could improve risk stratification as well as improve our comprehension of the underlying pathophysiological characteristics of pediatric HCM. In this state-of-the-art review, we examine the current literature on genetic variations in HCM and their association with outcomes in children, discuss the current approaches to identifying cardiovascular phenotypes in pediatric HCM, and explore possible avenues that could improve sudden cardiac death risk assessment.
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Affiliation(s)
- Minh B. Nguyen
- Division of CardiologyLabatt Family Heart CentreHospital for Sick ChildrenUniversity of TorontoOntarioCanada
| | - Seema Mital
- Division of CardiologyLabatt Family Heart CentreHospital for Sick ChildrenUniversity of TorontoOntarioCanada
| | - Luc Mertens
- Division of CardiologyLabatt Family Heart CentreHospital for Sick ChildrenUniversity of TorontoOntarioCanada
| | - Aamir Jeewa
- Division of CardiologyLabatt Family Heart CentreHospital for Sick ChildrenUniversity of TorontoOntarioCanada
| | - Mark K. Friedberg
- Division of CardiologyLabatt Family Heart CentreHospital for Sick ChildrenUniversity of TorontoOntarioCanada
| | - Julien Aguet
- Department of Diagnostic ImagingHospital for Sick ChildrenUniversity of TorontoOntarioCanada
| | - Arnon Adler
- Division of CardiologyPeter Munk Cardiac CentreToronto General HospitalUniversity of TorontoOntarioCanada
| | - Christopher Z. Lam
- Division of CardiologyLabatt Family Heart CentreHospital for Sick ChildrenUniversity of TorontoOntarioCanada
| | - Andreea Dragulescu
- Division of CardiologyLabatt Family Heart CentreHospital for Sick ChildrenUniversity of TorontoOntarioCanada
| | - Harry Rakowski
- Division of CardiologyPeter Munk Cardiac CentreToronto General HospitalUniversity of TorontoOntarioCanada
| | - Olivier Villemain
- Division of CardiologyLabatt Family Heart CentreHospital for Sick ChildrenUniversity of TorontoOntarioCanada
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7
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Choi S, Cho N, Kim KK. Non-canonical splice junction processing increases the diversity of RBFOX2 splicing isoforms. Int J Biochem Cell Biol 2022; 144:106172. [PMID: 35124219 DOI: 10.1016/j.biocel.2022.106172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 01/23/2022] [Accepted: 02/01/2022] [Indexed: 12/13/2022]
Abstract
The underlying mechanisms of splicing regulation through non-canonical splice junction processing remain largely unknown. Here, we identified two RBFOX2 splicing isoforms by alternative 3' splice site selection of exon 9; the non-canonical splice junction processed RBFOX2 transcript (RBFOX2-N.C.) was expressed by the selection of the 3' splice GG acceptor sequence. The cytoplasmic localization of RBFOX2-C., a canonical splice junction-processed RBFOX2 transcript, was different from that of RBFOX2-N.C., which showed nuclear localization. In addition, we confirmed that RBFOX2-C. showed a significantly stronger localization into stress granules than RBFOX2-N.C. upon sodium arsenite treatment. Next, we investigated the importance of non-canonical 3' splice GG sequence selection of specific cis-regulatory elements using minigene constructs of the RBFOX2 gene. We found that the non-canonical 3' splice GG sequence and suboptimal branch point site adjacent region were critical for RBFOX2-N.C. expression through a non-canonical 3' splice selection. Our results suggest a regulatory mechanism for the non-canonical 3' splice selection in the RBFOX2 gene, providing a basis for studies related to the regulation of alternative pre-mRNA splicing through non-canonical splice junction processing.
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Affiliation(s)
- Sunkyung Choi
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Namjoon Cho
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Kee K Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea.
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8
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Tangye SG, Gray PE, Pillay BA, Yap JY, Figgett WA, Reeves J, Kummerfeld SK, Stoddard J, Uzel G, Jing H, Su HC, Campbell DE, Sullivan A, Burnett L, Peake J, Ma CS. Hyper-IgE Syndrome due to an Elusive Novel Intronic Homozygous Variant in DOCK8. J Clin Immunol 2022; 42:119-129. [PMID: 34657245 PMCID: PMC10461790 DOI: 10.1007/s10875-021-01152-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/27/2021] [Indexed: 11/29/2022]
Abstract
Rare, biallelic loss-of-function mutations in DOCK8 result in a combined immune deficiency characterized by severe and recurrent cutaneous infections, eczema, allergies, and susceptibility to malignancy, as well as impaired humoral and cellular immunity and hyper-IgE. The advent of next-generation sequencing technologies has enabled the rapid molecular diagnosis of rare monogenic diseases, including inborn errors of immunity. These advances have resulted in the implementation of gene-guided treatments, such as hematopoietic stem cell transplant for DOCK8 deficiency. However, putative disease-causing variants revealed by next-generation sequencing need rigorous validation to demonstrate pathogenicity. Here, we report the eventual diagnosis of DOCK8 deficiency in a consanguineous family due to a novel homozygous intronic deletion variant that caused aberrant exon splicing and subsequent loss of expression of DOCK8 protein. Remarkably, the causative variant was not initially detected by clinical whole-genome sequencing but was subsequently identified and validated by combining advanced genomic analysis, RNA-seq, and flow cytometry. This case highlights the need to adopt multipronged confirmatory approaches to definitively solve complex genetic cases that result from variants outside protein-coding exons and conventional splice sites.
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Affiliation(s)
- Stuart G Tangye
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- Clinical Immunogenomics Research Consortium of Australasia (CIRCA), Sydney, New South Wales, Australia
| | - Paul E Gray
- Clinical Immunogenomics Research Consortium of Australasia (CIRCA), Sydney, New South Wales, Australia
- Department of Immunology and Infectious Diseases, Sydney Children's Hospital, Sydney, New South Wales, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Bethany A Pillay
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Jin Yan Yap
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales, 2010, Australia
- Clinical Immunogenomics Research Consortium of Australasia (CIRCA), Sydney, New South Wales, Australia
| | - William A Figgett
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales, 2010, Australia
| | - John Reeves
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Sarah K Kummerfeld
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales, 2010, Australia
| | - Jennifer Stoddard
- Immunology Service, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, MD, USA
| | - Gulbu Uzel
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Huie Jing
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Dianne E Campbell
- Department of Allergy and Immunology, Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Anna Sullivan
- Clinical Immunogenomics Research Consortium of Australasia (CIRCA), Sydney, New South Wales, Australia
- Queensland Children's Hospital and University of Queensland, South Brisbane, Queensland, Australia
| | - Leslie Burnett
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- Clinical Immunogenomics Research Consortium of Australasia (CIRCA), Sydney, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Jane Peake
- Clinical Immunogenomics Research Consortium of Australasia (CIRCA), Sydney, New South Wales, Australia
- Queensland Children's Hospital and University of Queensland, South Brisbane, Queensland, Australia
| | - Cindy S Ma
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales, 2010, Australia.
- St Vincent's Clinical School, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia.
- Clinical Immunogenomics Research Consortium of Australasia (CIRCA), Sydney, New South Wales, Australia.
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9
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James V, Nizamudeen ZA, Lea D, Dottorini T, Holmes TL, Johnson BB, Arkill KP, Denning C, Smith JGW. Transcriptomic Analysis of Cardiomyocyte Extracellular Vesicles in Hypertrophic Cardiomyopathy Reveals Differential snoRNA Cargo. Stem Cells Dev 2021; 30:1215-1227. [PMID: 34806414 PMCID: PMC8742282 DOI: 10.1089/scd.2021.0202] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is characterized by increased left ventricular wall thickness that can lead to devastating conditions such as heart failure and sudden cardiac death. Despite extensive study, the mechanisms mediating many of the associated clinical manifestations remain unknown and human models are required. To address this, human-induced pluripotent stem cell (hiPSC) lines were generated from patients with a HCM-associated mutation (c.ACTC1G301A) and isogenic controls created by correcting the mutation using CRISPR/Cas9 gene editing technology. Cardiomyocytes (hiPSC-CMs) were differentiated from these hiPSCs and analyzed at baseline, and at increased contractile workload (2 Hz electrical stimulation). Released extracellular vesicles (EVs) were isolated and characterized after a 24-h culture period and transcriptomic analysis performed on both hiPSC-CMs and released EVs. Transcriptomic analysis of cellular mRNA showed the HCM mutation caused differential splicing within known HCM pathways, and disrupted metabolic pathways. Analysis at increasing contraction frequency showed further disruption of metabolic gene expression, with an additive effect in the HCM background. Intriguingly, we observed differences in snoRNA cargo within HCM released EVs that specifically altered when HCM hiPSC-CMs were subjected to increased workload. These snoRNAs were predicted to have roles in post-translational modifications and alternative splicing, processes differentially regulated in HCM. As such, the snoRNAs identified in this study may unveil mechanistic insight into unexplained HCM phenotypes and offer potential future use as HCM biomarkers or as targets in future RNA-targeting therapies.
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Affiliation(s)
- Victoria James
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Zubair A Nizamudeen
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Daniel Lea
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Terri L Holmes
- Faculty of Medicine and Health Sciences, Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Benjamin B Johnson
- Faculty of Medicine and Health Sciences, Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Kenton P Arkill
- School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Chris Denning
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - James G W Smith
- Faculty of Medicine and Health Sciences, Norwich Medical School, University of East Anglia, Norwich, United Kingdom
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10
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Stamm P, Kirmes I, Palmer A, Molitor M, Kvandova M, Kalinovic S, Mihalikova D, Reid G, Wenzel P, Münzel T, Daiber A, Jansen T. Doxorubicin induces wide-spread transcriptional changes in the myocardium of hearts distinguishing between mice with preserved and impaired cardiac function. Life Sci 2021; 284:119879. [PMID: 34390723 DOI: 10.1016/j.lfs.2021.119879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 12/12/2022]
Abstract
AIMS Doxorubicin (DOX) is an important drug for the treatment of various tumor entities. However, the occurrence of heart failure limits its application. This study investigated differential gene expression profiles in the left and right ventricles of DOX treated mice with either preserved or impaired myocardial function. We provide new mechanistic insights into the pathophysiology of DOX-induced heart failure and have discovered pathways that counteract DOX-induced cardiotoxicity. MAIN METHODS We used in total 48 male mice and applied a chronic low dose DOX administration (5 mg/kg per injection, in total 20 mg/kg over 4 weeks) to induce heart failure. Echocardiographic parameters were evaluated one week after the final dose and mice were separated according to functional parameters into doxorubicin responding and non-responding animals. Post mortem, measurements of reactive oxygen species (ROS) and gene expression profiling was performed in separated right and left hearts. KEY FINDINGS We detected significant ROS production in the left heart of the mice in response to DOX treatment, although interestingly, not in the right heart. We found that transcriptional changes differ between right and left heart correlating with the occurrence of myocardial dysfunction. SIGNIFICANCE Doxorubicin induces changes in gene expression in the entire heart of animals without necessarily impairing cardiac function. We identified a set of transcripts that are associated with DOX cardiotoxicity. These might represent promising targets to ameliorate DOX-induced heart failure. Moreover, our results emphasize that parameters of left and right heart function should be evaluated during standardized echocardiography in patients undergoing DOX therapy.
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Affiliation(s)
- Paul Stamm
- Department of Cardiology, Cardiology I, University Medical Center Mainz, Mainz, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
| | - Ina Kirmes
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Alexander Palmer
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Michael Molitor
- Department of Cardiology, Cardiology I, University Medical Center Mainz, Mainz, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany; Center for Thrombosis and Hemostasis Mainz, University Medical Center Mainz, Mainz, Germany
| | - Miroslava Kvandova
- Department of Cardiology, Cardiology I, University Medical Center Mainz, Mainz, Germany
| | - Sanela Kalinovic
- Department of Cardiology, Cardiology I, University Medical Center Mainz, Mainz, Germany
| | - Dominika Mihalikova
- Department of Cardiology, Cardiology I, University Medical Center Mainz, Mainz, Germany
| | | | - Philip Wenzel
- Department of Cardiology, Cardiology I, University Medical Center Mainz, Mainz, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany; Center for Thrombosis and Hemostasis Mainz, University Medical Center Mainz, Mainz, Germany
| | - Thomas Münzel
- Department of Cardiology, Cardiology I, University Medical Center Mainz, Mainz, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
| | - Andreas Daiber
- Department of Cardiology, Cardiology I, University Medical Center Mainz, Mainz, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
| | - Thomas Jansen
- Department of Cardiology, Cardiology I, University Medical Center Mainz, Mainz, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany.
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11
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Cheng Z, Qi M, Zhang C, Mao Y. Myocardial Fibrosis in the Pathogenesis, Diagnosis, and Treatment of Hypertrophic Cardiomyopathy. CARDIOVASCULAR INNOVATIONS AND APPLICATIONS 2021. [DOI: 10.15212/cvia.2021.0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is a type of hereditary cardiomyopathy caused by gene mutation. Its histological features include cardiomyocyte hypertrophy and disarray as well as myocardial fibrosis. Gene mutation, abnormal signal transduction, and abnormal energy metabolism are
considered the main mechanisms of myocardial fibrosis. There is a strong correlation between myocardial fibrosis and the occurrence, development, and prognosis of HCM. We review the application of myocardial fibrosis in the diagnosis and treatment of HCM, focusing on research progress and
the application of magnetic resonance imaging on the basis of the characteristics of fibrosis in the diagnosis and prognosis of HCM.
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Affiliation(s)
- Zeyi Cheng
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, No. 37, Guoxue Alley, Chengdu, 610041 Sichuan, China
| | - Miaomiao Qi
- Department of Cardiology, The Second Hospital of Lanzhou University, Lanzhou, 730000 Gansu, China
| | - Chengyuan Zhang
- The Second Medical School of Lanzhou University, Lanzhou, 730000 Gansu, China
| | - Yanxia Mao
- The Second Medical School of Lanzhou University, Lanzhou, 730000 Gansu, China
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12
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Truty R, Ouyang K, Rojahn S, Garcia S, Colavin A, Hamlington B, Freivogel M, Nussbaum RL, Nykamp K, Aradhya S. Spectrum of splicing variants in disease genes and the ability of RNA analysis to reduce uncertainty in clinical interpretation. Am J Hum Genet 2021; 108:696-708. [PMID: 33743207 PMCID: PMC8059334 DOI: 10.1016/j.ajhg.2021.03.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/02/2021] [Indexed: 12/20/2022] Open
Abstract
The complexities of gene expression pose challenges for the clinical interpretation of splicing variants. To better understand splicing variants and their contribution to hereditary disease, we evaluated their prevalence, clinical classifications, and associations with diseases, inheritance, and functional characteristics in a 689,321-person clinical cohort and two large public datasets. In the clinical cohort, splicing variants represented 13% of all variants classified as pathogenic (P), likely pathogenic (LP), or variants of uncertain significance (VUSs). Most splicing variants were outside essential splice sites and were classified as VUSs. Among all individuals tested, 5.4% had a splicing VUS. If RNA analysis were to contribute supporting evidence to variant interpretation, we estimated that splicing VUSs would be reclassified in 1.7% of individuals in our cohort. This would result in a clinically significant result (i.e., P/LP) in 0.1% of individuals overall because most reclassifications would change VUSs to likely benign. In ClinVar, splicing VUSs were 4.8% of reported variants and could benefit from RNA analysis. In the Genome Aggregation Database (gnomAD), splicing variants comprised 9.4% of variants in protein-coding genes; most were rare, precluding unambiguous classification as benign. Splicing variants were depleted in genes associated with dominant inheritance and haploinsufficiency, although some genes had rare variants at essential splice sites or had common splicing variants that were most likely compatible with normal gene function. Overall, we describe the contribution of splicing variants to hereditary disease, the potential utility of RNA analysis for reclassifying splicing VUSs, and how natural variation may confound clinical interpretation of splicing variants.
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Affiliation(s)
| | - Karen Ouyang
- Invitae, 1400 16th St, San Francisco, CA 94103, USA
| | - Susan Rojahn
- Invitae, 1400 16th St, San Francisco, CA 94103, USA
| | - Sarah Garcia
- Invitae, 1400 16th St, San Francisco, CA 94103, USA
| | | | | | | | | | - Keith Nykamp
- Invitae, 1400 16th St, San Francisco, CA 94103, USA
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13
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Clinical relevance of genotype-phenotype correlations beyond vascular events in a cohort study of 1500 Marfan syndrome patients with FBN1 pathogenic variants. Genet Med 2021; 23:1296-1304. [PMID: 33731877 PMCID: PMC8257477 DOI: 10.1038/s41436-021-01132-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/11/2021] [Accepted: 02/16/2021] [Indexed: 11/24/2022] Open
Abstract
Purpose Marfan syndrome (MFS) is a connective tissue disorder in which several systems are affected with great phenotypic variability. Although known to be associated with pathogenic variants in the FBN1 gene, few genotype–phenotype correlations have been found in proband studies only. Methods In 1,575 consecutive MFS probands and relatives from the most comprehensive database worldwide, we established survival curves and sought genotype–phenotype correlations. Results A risk chart could be established with clinical and genetic data. Premature termination codon variants were not only associated with a shorter life expectancy and a high lifelong risk of aortic event, but also with the highest risk of severe scoliosis and a lower risk for ectopia lentis (EL) surgery. In-frame variants could be subdivided according to their impact on the cysteine content of fibrillin-1 with a global higher severity for cysteine loss variants and the highest frequency of EL surgery for cysteine addition variants. Conclusion This study shows that FBN1 genotype–phenotype correlations exist for both aortic and extra-aortic features. It can be used for optimal risk stratification of patients with a great importance for genetic counseling and personalized medicine. This also provides additional data for the overall understanding of the role of fibrillin-1 in various organs.
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14
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Hamzeloo-Moghadam M, Rezaei Tavirani M, Jahani-Sherafat S, Rezaei Tavirani S, Esmaeili S, Ansari M, Ahmadzadeh A. Side effects of omeprazole: a system biology study. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2021; 14:334-341. [PMID: 34659661 PMCID: PMC8514216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 07/29/2021] [Indexed: 11/28/2022]
Abstract
AIM To assess the effects of omeprazole on the human cardiovascular system is the main aim of this study. BACKGROUND Omeprazole as a proton pump inhibitor is widely consumed to inhibit gastric acid secretion. METHODS Gene expression profiles of "human coronary artery endothelial cells" in the absence and presence of omeprazole were downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) interacted as an interactome, and the hub nodes are determined. The DEGs were enriched via gene ontology (GO) analysis. The critical hubs were identified based on the GO findings. RESULTS Among 103 queried DEGs, 61 individuals were included in the main connected component. CTNNB1, HNRNPA1, SRSF4, TRA2A, SFPQ, and RBM5 genes were identified as critical hub genes. Six clusters of biological terms were introduced as deregulated elements in the presence of omeprazole. CONCLUSION In conclusion, long-term consumption of omeprazole may be accompanied with undesirable effects, however more evidence is required.
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Affiliation(s)
- Maryam Hamzeloo-Moghadam
- Traditional Medicine and Materia Medica Research Center and Department of Traditional Pharmacy, School of Traditional Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mostafa Rezaei Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Somayeh Jahani-Sherafat
- Laser Application in Medical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sina Rezaei Tavirani
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Somayeh Esmaeili
- Traditional Medicine and Materia Medica Research Center and Department of Traditional Pharmacy, School of Traditional Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mojtaba Ansari
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Ahmadzadeh
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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15
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Robinson EL, Pedrosa da Costa Gomes C, Potočnjak I, Hellemans J, Betsou F, de Gonzalo-Calvo D, Stoll M, Birhan Yilmaz M, Ágg B, Beis D, Carmo-Fonseca M, Enguita FJ, Dogan S, Tuna BG, Schroen B, Ammerlaan W, Kuster GM, Carpusca I, Pedrazzini T, Emanueli C, Martelli F, Devaux Y. A Year in the Life of the EU-CardioRNA COST Action: CA17129 Catalysing Transcriptomics Research in Cardiovascular Disease. Noncoding RNA 2020; 6:E17. [PMID: 32443579 PMCID: PMC7345156 DOI: 10.3390/ncrna6020017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 05/11/2020] [Indexed: 02/07/2023] Open
Abstract
The EU-CardioRNA Cooperation in Science and Technology (COST) Action is a European-wide consortium established in 2018 with 31 European country members and four associate member countries to build bridges between translational researchers from academia and industry who conduct research on non-coding RNAs, cardiovascular diseases and similar research areas. EU-CardioRNA comprises four core working groups (WG1-4). In the first year since its launch, EU-CardioRNA met biannually to exchange and discuss recent findings in related fields of scientific research, with scientific sessions broadly divided up according to WG. These meetings are also an opportunity to establish interdisciplinary discussion groups, brainstorm ideas and make plans to apply for joint research grants and conduct other scientific activities, including knowledge transfer. Following its launch in Brussels in 2018, three WG meetings have taken place. The first of these in Lisbon, Portugal, the second in Istanbul, Turkey, and the most recent in Maastricht, The Netherlands. Each meeting includes a scientific session from each WG. This meeting report briefly describes the highlights and key take-home messages from each WG session in this first successful year of the EU-CardioRNA COST Action.
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Affiliation(s)
- Emma Louise Robinson
- Department of Cardiology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands;
| | | | - Ines Potočnjak
- Institute for Clinical Medical Research and Education, University Hospital Centre Sisters of Charity, Zagreb 10 000, Croatia;
| | | | - Fay Betsou
- Integrated BioBank of Luxembourg, L-3555 Dudelange, Luxembourg; (F.B.); (W.A.)
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, 25198 Lleida, Spain;
| | - Monika Stoll
- Institute of Human Genetics, Genetic Epidemiology, University of Münster, 48149 Münster, Germany;
| | - Mehmet Birhan Yilmaz
- Department of Cardiology, Faculty of Medicine, Dokuz Eylül University, İzmir 35330, Turkey;
| | - Bence Ágg
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, H-1085 Budapest, Hungary;
- Pharmahungary Group, H-6722 Szeged, Hungary
| | - Dimitris Beis
- Centre for Clinical, Experimental Surgery, & Translational Research, Biomedical Research Foundation, Academy of Athens, 115 27 Athens, Greece;
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (M.C.-F.); (F.J.E.)
| | - Francisco J. Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (M.C.-F.); (F.J.E.)
| | - Soner Dogan
- Department of Medical Biology, School of Medicine, Yeditepe University, Istanbul 34755, Turkey;
| | - Bilge G. Tuna
- Department of Biophysics, School of Medicine, Yeditepe University, Istanbul 34755, Turkey
| | - Blanche Schroen
- Department of Cardiology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands;
| | - Wim Ammerlaan
- Integrated BioBank of Luxembourg, L-3555 Dudelange, Luxembourg; (F.B.); (W.A.)
| | - Gabriela M. Kuster
- Department of Biomedicine, University Hospital Basel and University of Basel, 4031 Basel, Switzerland;
| | - Irina Carpusca
- Cardiovascular Research Unit, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (C.P.d.C.G.); (I.C.)
| | - Thierry Pedrazzini
- Department of Medicine, University of Lausanne Medical School, 1005 Lausanne, Switzerland;
| | - Costanza Emanueli
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK;
| | - Fabio Martelli
- Molecular Cardiology Laboratory, Policlinico San Donato IRCCS, San Donato Milanese, 20097 Milan, Italy;
| | - Yvan Devaux
- Cardiovascular Research Unit, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (C.P.d.C.G.); (I.C.)
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