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Beasley JMT, Korn DR, Tucker NN, Alves ETM, Muratov EN, Bizon C, Tropsha A. ExEmPLAR (Extracting, Exploring, and Embedding Pathways Leading to Actionable Research): a user-friendly interface for knowledge graph mining. Bioinformatics 2024; 40:btad779. [PMID: 38175789 PMCID: PMC10812875 DOI: 10.1093/bioinformatics/btad779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 12/05/2023] [Accepted: 01/02/2024] [Indexed: 01/06/2024] Open
Abstract
SUMMARY Knowledge graphs are being increasingly used in biomedical research to link large amounts of heterogenous data and facilitate reasoning across diverse knowledge sources. Wider adoption and exploration of knowledge graphs in the biomedical research community is limited by requirements to understand the underlying graph structure in terms of entity types and relationships, represented as nodes and edges, respectively, and learn specialized query languages for graph mining and exploration. We have developed a user-friendly interface dubbed ExEmPLAR (Extracting, Exploring, and Embedding Pathways Leading to Actionable Research) to aid reasoning over biomedical knowledge graphs and assist with data-driven research and hypothesis generation. We explain the key functionalities of ExEmPLAR and demonstrate its use with a case study considering the relationship of Trypanosoma cruzi, the etiological agent of Chagas disease, to frequently associated cardiovascular conditions. AVAILABILITY AND IMPLEMENTATION ExEmPLAR is freely accessible at https://www.exemplar.mml.unc.edu/. For code and instructions for the using the application, see: https://github.com/beasleyjonm/AOP-COP-Path-Extractor.
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Affiliation(s)
- Jon-Michael T Beasley
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Daniel R Korn
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nyssa N Tucker
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Erick T M Alves
- Department of Pharmacy, University of São Paulo, São Paulo, SP 05508, Brazil
| | - Eugene N Muratov
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Chris Bizon
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alexander Tropsha
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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2
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Naito S, Higo S, Kameda S, Ogawa S, Tabata T, Akazawa Y, Nakamura D, Nakamoto K, Sera F, Kuramoto Y, Asano Y, Hikoso S, Miyagawa S, Sakata Y. End-stage Hypertrophic Cardiomyopathy with Advanced Heart Failure in Patients Carrying MYH7 R453 Variants: A Case Series. Intern Med 2023; 62:3167-3173. [PMID: 36948619 PMCID: PMC10686745 DOI: 10.2169/internalmedicine.1497-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/12/2023] [Indexed: 03/24/2023] Open
Abstract
The MYH7 R453 variant has been identified in inherited hypertrophic cardiomyopathy (HCM) and is associated with sudden death and a poor prognosis. The detailed clinical course of HCM with the MYH7 R453 variant, from a preserved to a reduced left ventricular ejection fraction, has not been reported. We identified the MYH7 R453C and R453H variants in three patients who progressively developed advanced heart failure requiring circulatory support and summarized the clinical course and echocardiographic parameters of these patients over the years. Because of the rapid disease progression, we consider genetic screening for patients with HCM imperative for future prognosis stratification.
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Affiliation(s)
| | - Shuichiro Higo
- Department of Medical Therapeutics for Heart Failure, Osaka University Graduate School of Medicine, Japan
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Japan
| | - Satoshi Kameda
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Japan
| | - Shou Ogawa
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Japan
| | - Tomoka Tabata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Japan
| | - Yasuhiro Akazawa
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Japan
| | - Daisuke Nakamura
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Japan
| | - Kei Nakamoto
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Japan
| | - Fusako Sera
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Japan
| | - Yuki Kuramoto
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Japan
| | - Yoshihiro Asano
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Japan
- Clinical Genetic Counseling Room, National Cerebral and Cardiovascular Center, Japan
| | - Shungo Hikoso
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Japan
| | - Shigeru Miyagawa
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Japan
| | - Yasushi Sakata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Japan
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3
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Yang C, Chen F, Li S, Zeng X, Wang S, Lan J. Association of rs35006907 Polymorphism with Risk of Dilated Cardiomyopathy in Han Chinese Population. Balkan J Med Genet 2023; 26:27-34. [PMID: 38711908 PMCID: PMC11071056 DOI: 10.2478/bjmg-2023-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024] Open
Abstract
Background Several investigations have demonstrated the association of MTSS1 with left ventricular (LV) structure and function. A recently published study has even revealed that rs35006907 was associated with both MTSS1 expression and the risk of dilated cardiomyopathy (DCM). Objective Our study intended to investigate the relationship between rs35006907 and the risk of DCM in the Han Chinese population. Methods A total of 529 DCM and 600 healthy controls were recruited. We conducted genotyping for rs35006907 in all participants. Gene association studies were performed to assess the association between rs35006907 and the risk of DCM. A series of functional assays including western blot, realtime PCR and firefly luciferase reporter gene assays were conducted to illuminate the underlying mechanism. Results We found that rs35006907-A allele was significantly associated with reduced risk of DCM in additive (p= 0.004; OR=0.78; 95% CI=0.66-0.93) and recessive models (p= 0.0005; OR=0.56; 95%CI=0.41-0.78) when compared with the rs35006907-C allele. There were significant differences in the left ventricular end-diastolic diameter (LVEDD) and left ventricular ejection fraction (LVEF) between rs35006907-CC/AC and AA genotypes. Furthermore, the variant rs35006907-A allele presented lower reporter gene activity, reduced mRNA and protein expression levels when compared with the C allele. Conclusions Our findings demonstrated that rs35006907-C allele increased the risk of DCM in Han Chinese population. Besides, rs35006907-C displayed higher reporter gene activity and increased MTSS1 expression in human samples.
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Affiliation(s)
- C Yang
- Division of Cardiology, Panzhihua Central Hospital, Panzhihua, China
| | - F Chen
- Department of Hematology, Panzhihua Central Hospital, Panzhihua, China
| | - Sh Li
- Division of Cardiology, Panzhihua Central Hospital, Panzhihua, China
| | - X Zeng
- Division of Cardiology, Panzhihua Central Hospital, Panzhihua, China
| | - Sh Wang
- Division of Cardiology, Panzhihua Central Hospital, Panzhihua, China
| | - J Lan
- Division of Cardiology, Panzhihua Central Hospital, Panzhihua, China
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Wolfe JT, He W, Kim MS, Liang HL, Shradhanjali A, Jurkiewicz H, Freudinger BP, Greene AS, LaDisa JF, Tayebi L, Mitchell ME, Tomita-Mitchell A, Tefft BJ. 3D-bioprinting of patient-derived cardiac tissue models for studying congenital heart disease. Front Cardiovasc Med 2023; 10:1162731. [PMID: 37293290 PMCID: PMC10247285 DOI: 10.3389/fcvm.2023.1162731] [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: 02/09/2023] [Accepted: 04/27/2023] [Indexed: 06/10/2023] Open
Abstract
Introduction Congenital heart disease is the leading cause of death related to birth defects and affects 1 out of every 100 live births. Induced pluripotent stem cell technology has allowed for patient-derived cardiomyocytes to be studied in vitro. An approach to bioengineer these cells into a physiologically accurate cardiac tissue model is needed in order to study the disease and evaluate potential treatment strategies. Methods To accomplish this, we have developed a protocol to 3D-bioprint cardiac tissue constructs comprised of patient-derived cardiomyocytes within a hydrogel bioink based on laminin-521. Results Cardiomyocytes remained viable and demonstrated appropriate phenotype and function including spontaneous contraction. Contraction remained consistent during 30 days of culture based on displacement measurements. Furthermore, tissue constructs demonstrated progressive maturation based on sarcomere structure and gene expression analysis. Gene expression analysis also revealed enhanced maturation in 3D constructs compared to 2D cell culture. Discussion This combination of patient-derived cardiomyocytes and 3D-bioprinting represents a promising platform for studying congenital heart disease and evaluating individualized treatment strategies.
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Affiliation(s)
- Jayne T. Wolfe
- Department of Biomedical Engineering, Medical College of Wisconsin & Marquette University, Milwaukee, WI, United States
| | - Wei He
- Department of Biomedical Engineering, Medical College of Wisconsin & Marquette University, Milwaukee, WI, United States
| | - Min-Su Kim
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Huan-Ling Liang
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Akankshya Shradhanjali
- Department of Biomedical Engineering, Medical College of Wisconsin & Marquette University, Milwaukee, WI, United States
| | - Hilda Jurkiewicz
- Department of Biomedical Engineering, Medical College of Wisconsin & Marquette University, Milwaukee, WI, United States
| | | | | | - John F. LaDisa
- Department of Biomedical Engineering, Medical College of Wisconsin & Marquette University, Milwaukee, WI, United States
- Department of Pediatrics - Section of Cardiology, Children’s Wisconsin, Milwaukee, WI, United States
- The Herma Heart Institute, Children’s Wisconsin, Milwaukee, WI, United States
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Lobat Tayebi
- School of Dentistry, Marquette University, Milwaukee, WI, United States
| | - Michael E. Mitchell
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States
- The Herma Heart Institute, Children’s Wisconsin, Milwaukee, WI, United States
| | - Aoy Tomita-Mitchell
- Department of Biomedical Engineering, Medical College of Wisconsin & Marquette University, Milwaukee, WI, United States
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States
- The Herma Heart Institute, Children’s Wisconsin, Milwaukee, WI, United States
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Brandon J. Tefft
- Department of Biomedical Engineering, Medical College of Wisconsin & Marquette University, Milwaukee, WI, United States
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States
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Ding Y, Wang M, Bu H, Li J, Lin X, Xu X. Application of an F0-based genetic assay in adult zebrafish to identify modifier genes of an inherited cardiomyopathy. Dis Model Mech 2023; 16:dmm049427. [PMID: 35481478 PMCID: PMC9239171 DOI: 10.1242/dmm.049427] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/19/2022] [Indexed: 01/08/2023] Open
Abstract
Modifier genes contribute significantly to our understanding of pathophysiology in human diseases; however, effective approaches to identify modifier genes are still lacking. Here, we aim to develop a rapid F0-based genetic assay in adult zebrafish using the bag3 gene knockout (bag3e2/e2) cardiomyopathy model as a paradigm. First, by utilizing a classic genetic breeding approach, we identified dnajb6b as a deleterious modifier gene for bag3 cardiomyopathy. Next, we established an F0-based genetic assay in adult zebrafish through injection of predicted microhomology-mediated end joining (MMEJ)-inducing single guide RNA/Cas9 protein complex. We showed that effective gene knockdown is maintained in F0 adult fish, enabling recapitulation of both salutary modifying effects of the mtor haploinsufficiency and deleterious modifying effects of the dnajb6b gene on bag3 cardiomyopathy. We finally deployed the F0-based genetic assay to screen differentially expressed genes in the bag3 cardiomyopathy model. As a result, myh9b was identified as a novel modifier gene for bag3 cardiomyopathy. Together, these data prove the feasibility of an F0 adult zebrafish-based genetic assay that can be effectively used to discover modifier genes for inherited cardiomyopathy.
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Affiliation(s)
- Yonghe Ding
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Mingmin Wang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Medicine, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Haisong Bu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiothoracic Surgery, Xiangfan Hospital, Central South University, Changsha 410008, China
| | - Jiarong Li
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Surgery, The Second Xiangfan Hospital of Central South University, Changsha 410011, China
| | - Xueying Lin
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaolei Xu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
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Moossavi M, Lu X, Herrmann J, Xu X. Molecular mechanisms of anthracycline induced cardiotoxicity: Zebrafish come into play. Front Cardiovasc Med 2023; 10:1080299. [PMID: 36970353 PMCID: PMC10036604 DOI: 10.3389/fcvm.2023.1080299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/22/2023] [Indexed: 03/12/2023] Open
Abstract
Anthracyclines are among the most potent chemotherapeutics; however, cardiotoxicity significantly restricts their use. Indeed, anthracycline-induced cardiotoxicity (AIC) fares among the worst types of cardiomyopathy, and may only slowly and partially respond to standard heart failure therapies including β-blockers and ACE inhibitors. No therapy specifically designed to treat anthracycline cardiomyopathy at present, and neither is it known if any such strategy could be developed. To address this gap and to elucidate the molecular basis of AIC with a therapeutic goal in mind, zebrafish has been introduced as an in vivo vertebrate model about a decade ago. Here, we first review our current understanding of the basic molecular and biochemical mechanisms of AIC, and then the contribution of zebrafish to the AIC field. We summarize the generation of embryonic zebrafish AIC models (eAIC) and their use for chemical screening and assessment of genetic modifiers, and then the generation of adult zebrafish AIC models (aAIC) and their use for discovering genetic modifiers via forward mutagenesis screening, deciphering spatial-temporal-specific mechanisms of modifier genes, and prioritizing therapeutic compounds via chemical genetic tools. Several therapeutic target genes and related therapies have emerged, including a retinoic acid (RA)-based therapy for the early phase of AIC and an autophagy-based therapy that, for the first time, is able to reverse cardiac dysfunction in the late phase of AIC. We conclude that zebrafish is becoming an important in vivo model that would accelerate both mechanistic studies and therapeutic development of AIC.
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Affiliation(s)
- Maryam Moossavi
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, United States
| | - Xiaoguang Lu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, United States
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Joerg Herrmann
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, United States
| | - Xiaolei Xu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, United States
- Correspondence: Xiaolei Xu
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Modeling Reduced Contractility and Stiffness Using iPSC-Derived Cardiomyocytes Generated From Female Becker Muscular Dystrophy Carrier. JACC Basic Transl Sci 2023. [DOI: 10.1016/j.jacbts.2022.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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8
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Isola G. Prospective Advances in Genome Editing Investigation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1396:301-313. [DOI: 10.1007/978-981-19-5642-3_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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9
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Zhu K, Bao X, Wang Y, Lu T, Zhang L. Human induced pluripotent stem cell (hiPSC)-derived cardiomyocyte modelling of cardiovascular diseases for natural compound discovery. Biomed Pharmacother 2023; 157:113970. [PMID: 36371854 DOI: 10.1016/j.biopha.2022.113970] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/29/2022] [Accepted: 11/01/2022] [Indexed: 11/11/2022] Open
Abstract
Cardiovascular disease (CVD) remains the leading cause of death worldwide. Natural compounds extracted from medicinal plants characterized by diverse biological activities and low toxicity or side effects, are increasingly taking center stage in the search for new drugs. Currently, preclinical evaluation of natural products relies mainly on the use of immortalized cell lines of human origin or animal models. Increasing evidence indicates that cardiomyopathy models based on immortalized cell lines do not recapitulate pathogenic phenotypes accurately and a substantial physiological discrepancy between animals and humans casts doubt on the clinical relevance of animal models for these studies. The newly developed human induced pluripotent stem cell (hiPSC) technology in combination with highly-efficient cardiomyocyte differentiation methods provides an ideal tool for modeling human cardiomyopathies in vitro. Screening of drugs, especially screening of natural products, based on these models has been widely used and has shown that evaluation in such models can recapitulate important aspects of the physiological properties of drugs. The purpose of this review is to provide information on the latest developments in this area of research and to help researchers perform screening of natural products using the hiPSC-CM platform.
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Affiliation(s)
- Keyang Zhu
- Zhejiang Key Laboratory of Pathophysiology, School of Public Health, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, PR China
| | - Xiaoming Bao
- Department of Cardiology, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang, PR China; Department of Global Health, Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, Zhejiang, PR China
| | - Yingchao Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Ting Lu
- Clinical Research Center of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, PR China.
| | - Ling Zhang
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, PR China.
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Titin-truncating variants in hiPSC cardiomyocytes induce pathogenic proteinopathy and sarcomere defects with preserved core contractile machinery. Stem Cell Reports 2022; 18:220-236. [PMID: 36525964 PMCID: PMC9860080 DOI: 10.1016/j.stemcr.2022.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 12/23/2022] Open
Abstract
Titin-truncating variants (TTNtv) are the single largest genetic cause of dilated cardiomyopathy (DCM). In this study we modeled disease phenotypes of A-band TTNtv-induced DCM in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) using genome editing and tissue engineering technologies. Transcriptomic, cellular, and micro-tissue studies revealed that A-band TTNtv hiPSC-CMs exhibit pathogenic proteinopathy, sarcomere defects, aberrant Na+ channel activities, and contractile dysfunction. These phenotypes establish a dual mechanism of poison peptide effect and haploinsufficiency that collectively contribute to DCM pathogenesis. However, TTNtv cellular defects did not interfere with the function of the core contractile machinery, the actin-myosin-troponin-Ca2+ complex, and preserved the therapeutic mechanism of sarcomere modulators. Treatment of TTNtv cardiac micro-tissues with investigational sarcomere modulators augmented contractility and resulted in sustained transcriptomic changes that promote reversal of DCM disease signatures. Together, our findings elucidate the underlying pathogenic mechanisms of A-band TTNtv-induced DCM and demonstrate the validity of sarcomere modulators as potential therapeutics.
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11
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Destici E, Zhu F, Tran S, Preissl S, Farah EN, Zhang Y, Hou X, Poirion OB, Lee AY, Grinstein JD, Bloomekatz J, Kim HS, Hu R, Evans SM, Ren B, Benner C, Chi NC. Human-gained heart enhancers are associated with species-specific cardiac attributes. NATURE CARDIOVASCULAR RESEARCH 2022; 1:830-843. [PMID: 36817700 PMCID: PMC9937543 DOI: 10.1038/s44161-022-00124-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022]
Abstract
The heart, a vital organ which is first to develop, has adapted its size, structure and function in order to accommodate the circulatory demands for a broad range of animals. Although heart development is controlled by a relatively conserved network of transcriptional/chromatin regulators, how the human heart has evolved species-specific features to maintain adequate cardiac output and function remains to be defined. Here, we show through comparative epigenomic analysis the identification of enhancers and promoters that have gained activity in humans during cardiogenesis. These cis-regulatory elements (CREs) are associated with genes involved in heart development and function, and may account for species-specific differences between human and mouse hearts. Supporting these findings, genetic variants that are associated with human cardiac phenotypic/disease traits, particularly those differing between human and mouse, are enriched in human-gained CREs. During early stages of human cardiogenesis, these CREs are also gained within genomic loci of transcriptional regulators, potentially expanding their role in human heart development. In particular, we discovered that gained enhancers in the locus of the early human developmental regulator ZIC3 are selectively accessible within a subpopulation of mesoderm cells which exhibits cardiogenic potential, thus possibly extending the function of ZIC3 beyond its conserved left-right asymmetry role. Genetic deletion of these enhancers identified a human gained enhancer that was required for not only ZIC3 and early cardiac gene expression at the mesoderm stage but also cardiomyocyte differentiation. Overall, our results illuminate how human gained CREs may contribute to human-specific cardiac attributes, and provide insight into how transcriptional regulators may gain cardiac developmental roles through the evolutionary acquisition of enhancers.
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Affiliation(s)
- Eugin Destici
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Fugui Zhu
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Shaina Tran
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Sebastian Preissl
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Elie N. Farah
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
| | - Xiameng Hou
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Olivier B. Poirion
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ah Young Lee
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
| | - Jonathan D. Grinstein
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Hong Sook Kim
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Robert Hu
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Sylvia M. Evans
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, 92093, USA
- Institute of Genomic Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Chris Benner
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Neil C. Chi
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
- Institute of Genomic Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
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12
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Genetic Basis of Dilated Cardiomyopathy in Dogs and Its Potential as a Bidirectional Model. Animals (Basel) 2022; 12:ani12131679. [PMID: 35804579 PMCID: PMC9265105 DOI: 10.3390/ani12131679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/16/2022] [Accepted: 06/25/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Heart disease is a leading cause of death for both humans and dogs. Inherited heart diseases, including dilated cardiomyopathy (DCM), account for a proportion of these cases. Human and canine patients with DCM suffer from an enlarged heart that can no longer pump efficiently, resulting in heart failure. This causes symptoms or clinical signs like difficulty breathing, irregular heartbeat, and eventually death. The symptoms or clinical signs of this disease vary in age of onset at the beginning of symptoms, sex predisposition, and overall disease progression. Despite the many similarities in DCM in both species, only a few candidate genes so far have been linked to this disease in dogs versus tens of genes identified in human DCM. Additionally, the use of induced pluripotent stem cells, or engineered stem cells, has been widely used in the study of human genetic heart disease but has not yet been fully adapted to study heart disease in dogs. This review describes the current knowledge on the genetics and subtypes of naturally occurring DCM in dogs, and how advances in research might benefit the dog but also the human patient. Additionally, a novel method using canine engineered stem cells to uncover unknown contributions of mistakes in DNA to the progression of DCM will be introduced along with its applications for human DCM disease modeling and treatment. Abstract Cardiac disease is a leading cause of death for both humans and dogs. Genetic cardiomyopathies, including dilated cardiomyopathy (DCM), account for a proportion of these cases in both species. Patients may suffer from ventricular enlargement and systolic dysfunction resulting in congestive heart failure and ventricular arrhythmias with high risk for sudden cardiac death. Although canine DCM has similar disease progression and subtypes as in humans, only a few candidate genes have been found to be associated with DCM while the genetic background of human DCM has been more thoroughly studied. Additionally, experimental disease models using induced pluripotent stem cells have been widely adopted in the study of human genetic cardiomyopathy but have not yet been fully adapted for the in-depth study of canine genetic cardiomyopathies. The clinical presentation of DCM is extremely heterogeneous for both species with differences occurring based on sex predisposition, age of onset, and the rate of disease progression. Both genetic predisposition and environmental factors play a role in disease development which are identical in dogs and humans in contrast to other experimental animals. Interestingly, different dog breeds have been shown to develop distinct DCM phenotypes, and this presents a unique opportunity for modeling as there are multiple breed-specific models for DCM with less genetic variance than human DCM. A better understanding of DCM in dogs has the potential for improved selection for breeding and could lead to better overall care and treatment for human and canine DCM patients. At the same time, progress in research made for human DCM can have a positive impact on the care given to dogs affected by DCM. Therefore, this review will analyze the feasibility of canines as a naturally occurring bidirectional disease model for DCM in both species. The histopathology of the myocardium in canine DCM will be evaluated in three different breeds compared to control tissue, and the known genetics that contributes to both canine and human DCM will be summarized. Lastly, the prospect of canine iPSCs as a novel method to uncover the contributions of genetic variants to the pathogenesis of canine DCM will be introduced along with the applications for disease modeling and treatment.
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Abstract
Cardiovascular disease remains the leading cause of morbidity and mortality in the developed world. In recent decades, extraordinary effort has been devoted to defining the molecular and pathophysiological characteristics of the diseased heart and vasculature. Mouse models have been especially powerful in illuminating the complex signaling pathways, genetic and epigenetic regulatory circuits, and multicellular interactions that underlie cardiovascular disease. The advent of CRISPR genome editing has ushered in a new era of cardiovascular research and possibilities for genetic correction of disease. Next-generation sequencing technologies have greatly accelerated the identification of disease-causing mutations, and advances in gene editing have enabled the rapid modeling of these mutations in mice and patient-derived induced pluripotent stem cells. The ability to correct the genetic drivers of cardiovascular disease through delivery of gene editing components in vivo, while still facing challenges, represents an exciting therapeutic frontier. In this review, we provide an overview of cardiovascular disease mechanisms and the potential applications of CRISPR genome editing for disease modeling and correction. We also discuss the extent to which mice can faithfully model cardiovascular disease and the opportunities and challenges that lie ahead.
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Affiliation(s)
- Ning Liu
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas
| | - Eric N Olson
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas
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14
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Liu Y, Li X, Zhao X, Dong J, Zhang C, Lin T. Establishment of a human iPSC (ZZUNEUi026-A) from a dilated cardiomyopathy patient carrying heterozygous Vinculin (c. 625A > T) mutant. Stem Cell Res 2022; 62:102812. [PMID: 35567849 DOI: 10.1016/j.scr.2022.102812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/06/2022] [Accepted: 05/08/2022] [Indexed: 11/29/2022] Open
Abstract
Dilated cardiomyopathy (DCM) is defined by left ventricular (or biventricular dilation) and systolic dysfunction, which eventually develops into congestive heart failure and arrhythmia. Vinculin is a membrane-associated protein, which functions to transmit contractile force. Defects in vinculin have been reported to be associated with DCM and hypertrophic cardiomyopathy. A human induced pluripotent stem cell (iPSC) line (ZZUNEUi026-A) was generated from a DCM patient carrying heterozygous Vinculin mutant (c.A625 > T; p.Met209 > Leu). The cell line was derived from peripheral blood mononuclear cells by nonintegrative Sendai virus. ZZUNEUi026-A showed pluripotency markers and normal karyotype, and it could differentiate into three germ layers in vitro.
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Affiliation(s)
- Yangyang Liu
- Department of Cardiology, Hami Central Hospital, Hami, Xinjiang 839000, China; Henan Key Laboratory of Hereditary Cardiovascular Diseases, Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Xiaowei Li
- Department of Cardiology, Hami Central Hospital, Hami, Xinjiang 839000, China; Henan Key Laboratory of Hereditary Cardiovascular Diseases, Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Xiaoyan Zhao
- Henan Key Laboratory of Hereditary Cardiovascular Diseases, Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Jianzeng Dong
- Henan Key Laboratory of Hereditary Cardiovascular Diseases, Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Chunyang Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
| | - Tao Lin
- Department of Cardiology, Hami Central Hospital, Hami, Xinjiang 839000, China.
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15
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Dou W, Malhi M, Zhao Q, Wang L, Huang Z, Law J, Liu N, Simmons CA, Maynes JT, Sun Y. Microengineered platforms for characterizing the contractile function of in vitro cardiac models. MICROSYSTEMS & NANOENGINEERING 2022; 8:26. [PMID: 35299653 PMCID: PMC8882466 DOI: 10.1038/s41378-021-00344-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 11/12/2021] [Accepted: 12/03/2021] [Indexed: 05/08/2023]
Abstract
Emerging heart-on-a-chip platforms are promising approaches to establish cardiac cell/tissue models in vitro for research on cardiac physiology, disease modeling and drug cardiotoxicity as well as for therapeutic discovery. Challenges still exist in obtaining the complete capability of in situ sensing to fully evaluate the complex functional properties of cardiac cell/tissue models. Changes to contractile strength (contractility) and beating regularity (rhythm) are particularly important to generate accurate, predictive models. Developing new platforms and technologies to assess the contractile functions of in vitro cardiac models is essential to provide information on cell/tissue physiologies, drug-induced inotropic responses, and the mechanisms of cardiac diseases. In this review, we discuss recent advances in biosensing platforms for the measurement of contractile functions of in vitro cardiac models, including single cardiomyocytes, 2D monolayers of cardiomyocytes, and 3D cardiac tissues. The characteristics and performance of current platforms are reviewed in terms of sensing principles, measured parameters, performance, cell sources, cell/tissue model configurations, advantages, and limitations. In addition, we highlight applications of these platforms and relevant discoveries in fundamental investigations, drug testing, and disease modeling. Furthermore, challenges and future outlooks of heart-on-a-chip platforms for in vitro measurement of cardiac functional properties are discussed.
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Affiliation(s)
- Wenkun Dou
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8 Canada
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8 Canada
| | - Manpreet Malhi
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8 Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8 Canada
| | - Qili Zhao
- Institute of Robotics and Automatic Information System and the Tianjin Key Laboratory of Intelligent Robotics, Nankai University, Tianjin, 300350 China
| | - Li Wang
- School of Mechanical & Automotive Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353 China
| | - Zongjie Huang
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8 Canada
| | - Junhui Law
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8 Canada
| | - Na Liu
- School of Mechatronics Engineering and Automation, Shanghai University, Shanghai, 200444 China
| | - Craig A. Simmons
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8 Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9 Canada
- Translational Biology & Engineering Program, Ted Rogers Centre for Heart Research, Toronto, ON M5G 1M1 Canada
| | - Jason T. Maynes
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8 Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8 Canada
- Department of Anesthesiology and Pain Medicine, University of Toronto, Toronto, ON M5S 1A8 Canada
- Department of Anesthesia and Pain Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8 Canada
| | - Yu Sun
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8 Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9 Canada
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, ON M5S 3G4 Canada
- Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1 Canada
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16
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Bang ML, Bogomolovas J, Chen J. Understanding the molecular basis of cardiomyopathy. Am J Physiol Heart Circ Physiol 2022; 322:H181-H233. [PMID: 34797172 PMCID: PMC8759964 DOI: 10.1152/ajpheart.00562.2021] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/16/2021] [Accepted: 11/16/2021] [Indexed: 02/03/2023]
Abstract
Inherited cardiomyopathies are a major cause of mortality and morbidity worldwide and can be caused by mutations in a wide range of proteins located in different cellular compartments. The present review is based on Dr. Ju Chen's 2021 Robert M. Berne Distinguished Lectureship of the American Physiological Society Cardiovascular Section, in which he provided an overview of the current knowledge on the cardiomyopathy-associated proteins that have been studied in his laboratory. The review provides a general summary of the proteins in different compartments of cardiomyocytes associated with cardiomyopathies, with specific focus on the proteins that have been studied in Dr. Chen's laboratory.
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Affiliation(s)
- Marie-Louise Bang
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Milan Unit, Milan, Italy
- IRCCS Humanitas Research Hospital, Rozzano (Milan), Italy
| | - Julius Bogomolovas
- Division of Cardiovascular Medicine, Department of Medicine Cardiology, University of California, San Diego, La Jolla, California
| | - Ju Chen
- Division of Cardiovascular Medicine, Department of Medicine Cardiology, University of California, San Diego, La Jolla, California
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17
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Cheng L, Wang X, Chou H, Liu T, Fu H, Li G. Proteomic Sequencing of Stellate Ganglions in Rabbits With Myocardial Infarction. Front Physiol 2021; 12:687424. [PMID: 34975513 PMCID: PMC8716754 DOI: 10.3389/fphys.2021.687424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 11/17/2021] [Indexed: 11/20/2022] Open
Abstract
The stellate ganglion (SG) of the autonomic nervous system plays important role in cardiovascular diseases (CDs). Myocardial infarction (MI) is associated with sustained increasing cardiac sympathetic nerve activity. Expressions and functions of proteins in SG tissue after MI are remaining unclear. This study is to explore the expression characteristics of proteins in SGs associated with MI. Japanese big-ear white rabbits (n = 22) were randomly assigned to the control group and MI group. The MI model was established by left anterior descending coronary artery ligation and confirmed by serum myocardial enzymes increasing 2,3,5-triphenyltetrazolium (TTC) staining and echocardiography. The expressions of proteins in rabbit SGs after MI were detected using tandem mass tags (TMT) quantitative proteomic sequencing. There were 3,043 credible proteins were predicted in rabbit SG tissues and 383 differentially expressed proteins (DEPs) including 143 upregulated and 240 downregulated proteins. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEPs involved in adrenergic signaling in cardiomyocytes, positive regulation of ERK1 and ERK2 cascade, and other biological processes. Three kinds of proteins directly correlated to CDs were selected to be validated by the subsequent western blot experiment. This study first identified the characterization of proteins in rabbit SG after MI, which laid a solid foundation for revealing the mechanism of roles of SG on the MI process.
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18
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Müller D, Donath S, Brückner EG, Biswanath Devadas S, Daniel F, Gentemann L, Zweigerdt R, Heisterkamp A, Kalies SMK. How Localized Z-Disc Damage Affects Force Generation and Gene Expression in Cardiomyocytes. Bioengineering (Basel) 2021; 8:bioengineering8120213. [PMID: 34940366 PMCID: PMC8698600 DOI: 10.3390/bioengineering8120213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/02/2021] [Accepted: 12/09/2021] [Indexed: 11/24/2022] Open
Abstract
The proper function of cardiomyocytes (CMs) is highly related to the Z-disc, which has a pivotal role in orchestrating the sarcomeric cytoskeletal function. To better understand Z-disc related cardiomyopathies, novel models of Z-disc damage have to be developed. Human pluripotent stem cell (hPSC)-derived CMs can serve as an in vitro model to better understand the sarcomeric cytoskeleton. A femtosecond laser system can be applied for localized and defined damage application within cells as single Z-discs can be removed. We have investigated the changes in force generation via traction force microscopy, and in gene expression after Z-disc manipulation in hPSC-derived CMs. We observed a significant weakening of force generation after removal of a Z-disc. However, no significant changes of the number of contractions after manipulation were detected. The stress related gene NF-kB was significantly upregulated. Additionally, α-actinin (ACTN2) and filamin-C (FLNc) were upregulated, pointing to remodeling of the Z-disc and the sarcomeric cytoskeleton. Ultimately, cardiac troponin I (TNNI3) and cardiac muscle troponin T (TNNT2) were significantly downregulated. Our results allow a better understanding of transcriptional coupling of Z-disc damage and the relation of damage to force generation and can therefore finally pave the way to novel therapies of sarcomeric disorders.
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Affiliation(s)
- Dominik Müller
- Institute of Quantum Optics, Leibniz University Hannover, 30167 Hannover, Germany; (D.M.); (S.D.); (E.G.B.); (F.D.); (L.G.); (A.H.)
- REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; (S.B.D.); (R.Z.)
- Lower Saxony Centre for Biomedical Engineering and Implant Research and Development (NIFE), 30625 Hannover, Germany
| | - Sören Donath
- Institute of Quantum Optics, Leibniz University Hannover, 30167 Hannover, Germany; (D.M.); (S.D.); (E.G.B.); (F.D.); (L.G.); (A.H.)
- Lower Saxony Centre for Biomedical Engineering and Implant Research and Development (NIFE), 30625 Hannover, Germany
| | - Emanuel Georg Brückner
- Institute of Quantum Optics, Leibniz University Hannover, 30167 Hannover, Germany; (D.M.); (S.D.); (E.G.B.); (F.D.); (L.G.); (A.H.)
- Lower Saxony Centre for Biomedical Engineering and Implant Research and Development (NIFE), 30625 Hannover, Germany
| | - Santoshi Biswanath Devadas
- REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; (S.B.D.); (R.Z.)
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic, Transplantation and Vascular Surgery (HTTG), Hannover Medical School, 30625 Hannover, Germany
| | - Fiene Daniel
- Institute of Quantum Optics, Leibniz University Hannover, 30167 Hannover, Germany; (D.M.); (S.D.); (E.G.B.); (F.D.); (L.G.); (A.H.)
- Lower Saxony Centre for Biomedical Engineering and Implant Research and Development (NIFE), 30625 Hannover, Germany
| | - Lara Gentemann
- Institute of Quantum Optics, Leibniz University Hannover, 30167 Hannover, Germany; (D.M.); (S.D.); (E.G.B.); (F.D.); (L.G.); (A.H.)
- REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; (S.B.D.); (R.Z.)
- Lower Saxony Centre for Biomedical Engineering and Implant Research and Development (NIFE), 30625 Hannover, Germany
| | - Robert Zweigerdt
- REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; (S.B.D.); (R.Z.)
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic, Transplantation and Vascular Surgery (HTTG), Hannover Medical School, 30625 Hannover, Germany
| | - Alexander Heisterkamp
- Institute of Quantum Optics, Leibniz University Hannover, 30167 Hannover, Germany; (D.M.); (S.D.); (E.G.B.); (F.D.); (L.G.); (A.H.)
- REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; (S.B.D.); (R.Z.)
- Lower Saxony Centre for Biomedical Engineering and Implant Research and Development (NIFE), 30625 Hannover, Germany
| | - Stefan Michael Klaus Kalies
- Institute of Quantum Optics, Leibniz University Hannover, 30167 Hannover, Germany; (D.M.); (S.D.); (E.G.B.); (F.D.); (L.G.); (A.H.)
- REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; (S.B.D.); (R.Z.)
- Lower Saxony Centre for Biomedical Engineering and Implant Research and Development (NIFE), 30625 Hannover, Germany
- Correspondence:
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19
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Guo H, Liu L, Nishiga M, Cong L, Wu JC. Deciphering pathogenicity of variants of uncertain significance with CRISPR-edited iPSCs. Trends Genet 2021; 37:1109-1123. [PMID: 34509299 DOI: 10.1016/j.tig.2021.08.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 10/20/2022]
Abstract
Genetic variants play an important role in conferring risk for cardiovascular diseases (CVDs). With the rapid development of next-generation sequencing (NGS), thousands of genetic variants associated with CVDs have been identified by genome-wide association studies (GWAS), but the function of more than 40% of genetic variants is still unknown. This gap of knowledge is a barrier to the clinical application of the genetic information. However, determining the pathogenicity of a variant of uncertain significance (VUS) is challenging due to the lack of suitable model systems and accessible technologies. By combining clustered regularly interspaced short palindromic repeats (CRISPR) and human induced pluripotent stem cells (iPSCs), unprecedented advances are now possible in determining the pathogenicity of VUS in CVDs. Here, we summarize recent progress and new strategies in deciphering pathogenic variants for CVDs using CRISPR-edited human iPSCs.
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Affiliation(s)
- Hongchao Guo
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lichao Liu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Masataka Nishiga
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Le Cong
- Department of Pathology and Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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20
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Cho Y, Tachibana S, Lam K, Arita Y, Khosrowjerdi S, Zhang O, Liang A, Li R, Andreyev A, Murphy AN, Ross RS. Perm1 promotes cardiomyocyte mitochondrial biogenesis and protects against hypoxia/reoxygenation-induced damage in mice. J Biol Chem 2021; 297:100825. [PMID: 34029594 PMCID: PMC8214196 DOI: 10.1016/j.jbc.2021.100825] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 04/27/2021] [Accepted: 05/20/2021] [Indexed: 11/25/2022] Open
Abstract
Normal contractile function of the heart depends on a constant and reliable production of ATP by cardiomyocytes. Dysregulation of cardiac energy metabolism can result in immature heart development and disrupt the ability of the adult myocardium to adapt to stress, potentially leading to heart failure. Further, restoration of abnormal mitochondrial function can have beneficial effects on cardiac dysfunction. Previously, we identified a novel protein termed Perm1 (PGC-1 and estrogen-related receptor (ERR)-induced regulator, muscle 1) that is enriched in skeletal and cardiac-muscle mitochondria and transcriptionally regulated by PGC-1 (peroxisome proliferator-activated receptor gamma coactivator 1) and ERR. The role of Perm1 in the heart is poorly understood and is studied here. We utilized cell culture, mouse models, and human tissue, to study its expression and transcriptional control, as well as its role in transcription of other factors. Critically, we tested Perm1's role in cardiomyocyte mitochondrial function and its ability to protect myocytes from stress-induced damage. Our studies show that Perm1 expression increases throughout mouse cardiogenesis, demonstrate that Perm1 interacts with PGC-1α and enhances activation of PGC-1 and ERR, increases mitochondrial DNA copy number, and augments oxidative capacity in cultured neonatal mouse cardiomyocytes. Moreover, we found that Perm1 reduced cellular damage produced as a result of hypoxia and reoxygenation-induced stress and mitigated cell death of cardiomyocytes. Taken together, our results show that Perm1 promotes mitochondrial biogenesis in mouse cardiomyocytes. Future studies can assess the potential of Perm1 to be used as a novel therapeutic to restore cardiac dysfunction induced by ischemic injury.
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Affiliation(s)
- Yoshitake Cho
- Division of Cardiovascular Medicine, Department of Medicine, University of California San Diego, La Jolla, California, USA; Department of Medicine/Cardiology, Veterans Administration Healthcare, San Diego, California, USA.
| | - Shizuko Tachibana
- Division of Cardiovascular Medicine, Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Kayla Lam
- Division of Cardiovascular Medicine, Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Yoh Arita
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Shamim Khosrowjerdi
- Division of Cardiovascular Medicine, Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Oliver Zhang
- Division of Cardiovascular Medicine, Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Alex Liang
- Division of Cardiovascular Medicine, Department of Medicine, University of California San Diego, La Jolla, California, USA; Department of Medicine/Cardiology, Veterans Administration Healthcare, San Diego, California, USA
| | - Ruixia Li
- Division of Cardiovascular Medicine, Department of Medicine, University of California San Diego, La Jolla, California, USA; Department of Medicine/Cardiology, Veterans Administration Healthcare, San Diego, California, USA
| | - Aleksander Andreyev
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Anne N Murphy
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Robert S Ross
- Division of Cardiovascular Medicine, Department of Medicine, University of California San Diego, La Jolla, California, USA; Department of Medicine/Cardiology, Veterans Administration Healthcare, San Diego, California, USA
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21
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Tayal U, Ware JS, Lakdawala NK, Heymans S, Prasad SK. Understanding the genetics of adult-onset dilated cardiomyopathy: what a clinician needs to know. Eur Heart J 2021; 42:2384-2396. [PMID: 34153989 DOI: 10.1093/eurheartj/ehab286] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/10/2021] [Accepted: 05/19/2021] [Indexed: 12/28/2022] Open
Abstract
There is increasing understanding of the genetic basis to dilated cardiomyopathy and in this review, we offer a practical primer for the practising clinician. We aim to help all clinicians involved in the care of patients with dilated cardiomyopathy to understand the clinical relevance of the genetic basis of dilated cardiomyopathy, introduce key genetic concepts, explain which patients and families may benefit from genetic testing, which genetic tests are commonly performed, how to interpret genetic results, and the clinical applications of results. We conclude by reviewing areas for future research in this dynamic field.
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Affiliation(s)
- Upasana Tayal
- National Heart Lung Institute, Imperial College London, UK.,Cardiovascular Research Centre, Royal Brompton & Harefield Hospitals, London, UK
| | - James S Ware
- National Heart Lung Institute, Imperial College London, UK.,Cardiovascular Research Centre, Royal Brompton & Harefield Hospitals, London, UK.,MRC London Institute of Medical Sciences, London, UK
| | - Neal K Lakdawala
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephane Heymans
- Department of Cardiology, CARIM School for Cardiovascular Diseases Faculty of Health, Medicine and Life Sciences, Maastricht University, The Netherlands.,Department of Cardiovascular Sciences, Centre for Molecular and Vascular Biology, Leuven, KU, Belgium.,The Netherlands Heart Institute, Nl-HI, Utrecht, The Netherlands
| | - Sanjay K Prasad
- National Heart Lung Institute, Imperial College London, UK.,Cardiovascular Research Centre, Royal Brompton & Harefield Hospitals, London, UK
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22
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Jiang X, Chen Y, Liu X, Ye L, Yu M, Shen Z, Lei W, Hu S. Uncovering Inherited Cardiomyopathy With Human Induced Pluripotent Stem Cells. Front Cell Dev Biol 2021; 9:672039. [PMID: 34079803 PMCID: PMC8166268 DOI: 10.3389/fcell.2021.672039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
In the past decades, researchers discovered the contribution of genetic defects to the pathogenesis of primary cardiomyopathy and tried to explain the pathogenesis of these diseases by establishing a variety of disease models. Although human heart tissues and primary cardiomyocytes have advantages in modeling human heart diseases, they are difficult to obtain and culture in vitro. Defects developed in genetically modified animal models are notably different from human diseases at the molecular level. The advent of human induced pluripotent stem cells (hiPSCs) provides an unprecedented opportunity to further investigate the pathogenic mechanisms of inherited cardiomyopathies in vitro using patient-specific hiPSC-derived cardiomyocytes. In this review, we will make a summary of recent advances in in vitro inherited cardiomyopathy modeling using hiPSCs.
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Affiliation(s)
- Xue Jiang
- Department of Cardiovascular Surgery of The First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Medical College, Soochow University, Suzhou, China
| | - Yihuan Chen
- Department of Cardiovascular Surgery of The First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Medical College, Soochow University, Suzhou, China
| | - Xiaofeng Liu
- The Affiliated Haian Hospital of Nantong University, Nantong, China
| | - Lingqun Ye
- Department of Cardiovascular Surgery of The First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Medical College, Soochow University, Suzhou, China
| | - Miao Yu
- Department of Cardiovascular Surgery of The First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Medical College, Soochow University, Suzhou, China
| | - Zhenya Shen
- Department of Cardiovascular Surgery of The First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Medical College, Soochow University, Suzhou, China
| | - Wei Lei
- Department of Cardiovascular Surgery of The First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Medical College, Soochow University, Suzhou, China
| | - Shijun Hu
- Department of Cardiovascular Surgery of The First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Medical College, Soochow University, Suzhou, China
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Micheu MM, Rosca AM. Patient-specific induced pluripotent stem cells as “disease-in-a-dish” models for inherited cardiomyopathies and channelopathies – 15 years of research. World J Stem Cells 2021; 13:281-303. [PMID: 33959219 PMCID: PMC8080539 DOI: 10.4252/wjsc.v13.i4.281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/11/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023] Open
Abstract
Among inherited cardiac conditions, a special place is kept by cardiomyopathies (CMPs) and channelopathies (CNPs), which pose a substantial healthcare burden due to the complexity of the therapeutic management and cause early mortality. Like other inherited cardiac conditions, genetic CMPs and CNPs exhibit incomplete penetrance and variable expressivity even within carriers of the same pathogenic deoxyribonucleic acid variant, challenging our understanding of the underlying pathogenic mechanisms. Until recently, the lack of accurate physiological preclinical models hindered the investigation of fundamental cellular and molecular mechanisms. The advent of induced pluripotent stem cell (iPSC) technology, along with advances in gene editing, offered unprecedented opportunities to explore hereditary CMPs and CNPs. Hallmark features of iPSCs include the ability to differentiate into unlimited numbers of cells from any of the three germ layers, genetic identity with the subject from whom they were derived, and ease of gene editing, all of which were used to generate “disease-in-a-dish” models of monogenic cardiac conditions. Functionally, iPSC-derived cardiomyocytes that faithfully recapitulate the patient-specific phenotype, allowed the study of disease mechanisms in an individual-/allele-specific manner, as well as the customization of therapeutic regimen. This review provides a synopsis of the most important iPSC-based models of CMPs and CNPs and the potential use for modeling disease mechanisms, personalized therapy and deoxyribonucleic acid variant functional annotation.
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Affiliation(s)
- Miruna Mihaela Micheu
- Department of Cardiology, Clinical Emergency Hospital of Bucharest, Bucharest 014452, Romania
| | - Ana-Maria Rosca
- Cell and Tissue Engineering Laboratory, Institute of Cellular Biology and Pathology "Nicolae Simionescu", Bucharest 050568, Romania
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Genetic Cardiomyopathies: The Lesson Learned from hiPSCs. J Clin Med 2021; 10:jcm10051149. [PMID: 33803477 PMCID: PMC7967174 DOI: 10.3390/jcm10051149] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 12/17/2022] Open
Abstract
Genetic cardiomyopathies represent a wide spectrum of inherited diseases and constitute an important cause of morbidity and mortality among young people, which can manifest with heart failure, arrhythmias, and/or sudden cardiac death. Multiple underlying genetic variants and molecular pathways have been discovered in recent years; however, assessing the pathogenicity of new variants often needs in-depth characterization in order to ascertain a causal role in the disease. The application of human induced pluripotent stem cells has greatly helped to advance our knowledge in this field and enabled to obtain numerous in vitro patient-specific cellular models useful to study the underlying molecular mechanisms and test new therapeutic strategies. A milestone in the research of genetically determined heart disease was the introduction of genomic technologies that provided unparalleled opportunities to explore the genetic architecture of cardiomyopathies, thanks to the generation of isogenic pairs. The aim of this review is to provide an overview of the main research that helped elucidate the pathophysiology of the most common genetic cardiomyopathies: hypertrophic, dilated, arrhythmogenic, and left ventricular noncompaction cardiomyopathies. A special focus is provided on the application of gene-editing techniques in understanding key disease characteristics and on the therapeutic approaches that have been tested.
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Choi DK, Kim YK, HoonYu J, Min SH, Park SW. Genome editing of hPSCs: Recent progress in hPSC-based disease modeling for understanding disease mechanisms. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 181:271-287. [PMID: 34127196 DOI: 10.1016/bs.pmbts.2021.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Generation of proper models for studying human genetic diseases has been hindered until recently by the scarcity of primary cell samples from genetic disease patients and inefficient genetic modification tools. However, recent advances in clustered, regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology and human induced pluripotent stem cells (hiPSCs) have provided an opportunity to explore the function of pathogenic variants and obtain gene-corrected cells for autologous cell therapy. In this chapter, we address recent applications of CRISPR/Cas9 to hiPSCs in genetic diseases, including neurodegenerative, cardiovascular, and rare diseases.
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Affiliation(s)
- Dong-Kyu Choi
- New Drug Development Center, DGMIF, Daegu, Republic of Korea
| | - Yong-Kyu Kim
- New Drug Development Center, DGMIF, Daegu, Republic of Korea
| | - Ji HoonYu
- New Drug Development Center, DGMIF, Daegu, Republic of Korea
| | - Sang-Hyun Min
- New Drug Development Center, DGMIF, Daegu, Republic of Korea
| | - Sang-Wook Park
- Department of Oral Biochemistry, School of Dentistry, Chonnam National University, Gwangju, Republic of Korea.
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Lin H, McBride KL, Garg V, Zhao MT. Decoding Genetics of Congenital Heart Disease Using Patient-Derived Induced Pluripotent Stem Cells (iPSCs). Front Cell Dev Biol 2021; 9:630069. [PMID: 33585486 PMCID: PMC7873857 DOI: 10.3389/fcell.2021.630069] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/04/2021] [Indexed: 12/20/2022] Open
Abstract
Congenital heart disease (CHD) is the most common cause of infant death associated with birth defects. Recent next-generation genome sequencing has uncovered novel genetic etiologies of CHD, from inherited and de novo variants to non-coding genetic variants. The next phase of understanding the genetic contributors of CHD will be the functional illustration and validation of this genome sequencing data in cellular and animal model systems. Human induced pluripotent stem cells (iPSCs) have opened up new horizons to investigate genetic mechanisms of CHD using clinically relevant and patient-specific cardiac cells such as cardiomyocytes, endothelial/endocardial cells, cardiac fibroblasts and vascular smooth muscle cells. Using cutting-edge CRISPR/Cas9 genome editing tools, a given genetic variant can be corrected in diseased iPSCs and introduced to healthy iPSCs to define the pathogenicity of the variant and molecular basis of CHD. In this review, we discuss the recent progress in genetics of CHD deciphered by large-scale genome sequencing and explore how genome-edited patient iPSCs are poised to decode the genetic etiologies of CHD by coupling with single-cell genomics and organoid technologies.
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Affiliation(s)
- Hui Lin
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States.,The Heart Center, Nationwide Children's Hospital, Columbus, OH, United States.,Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, United States
| | - Kim L McBride
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States.,The Heart Center, Nationwide Children's Hospital, Columbus, OH, United States.,Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Vidu Garg
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States.,The Heart Center, Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States.,Department of Molecular Genetics, The Ohio State University, Columbus, OH, United States
| | - Ming-Tao Zhao
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States.,The Heart Center, Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
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Abstract
PURPOSE OF REVIEW This review highlights recent progress in applying genome editing to the study and treatment of cardiovascular disease (CVD). RECENT FINDINGS Recent work has shown that genome editing can be used to determine the pathogenicity of variants of unknown significance in patient-derived induced pluripotent stem cells. These cells can also be used to test therapeutic genome editing approaches in a personalized manner. Somatic genome editing holds great promise for the treatment of CVD, and important proof of concept experiments have already been performed in animal models. Here we briefly review recent progress in patient-derived cells, as well as the development of somatic genome-editing therapies for CVD, with a particular focus on liver and heart. SUMMARY Translating this technology into the clinic will require precise editing enzymes, efficient delivery systems, and mitigation of off-target events and immune responses. Further development of these technologies will improve diagnostics and enable permanent correction of some of the most severe forms of CVD.
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Hawley MH, Almontashiri N, Biesecker LG, Berger N, Chung WK, Garcia J, Grebe TA, Kelly MA, Lebo MS, Macaya D, Mei H, Platt J, Richard G, Ryan A, Thomson KL, Vatta M, Walsh R, Ware JS, Wheeler M, Zouk H, Mason-Suares H, Funke B. An assessment of the role of vinculin loss of function variants in inherited cardiomyopathy. Hum Mutat 2020; 41:1577-1587. [PMID: 32516855 DOI: 10.1002/humu.24061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/11/2020] [Accepted: 05/24/2020] [Indexed: 11/05/2022]
Abstract
The ACMG/AMP variant classification framework was intended for highly penetrant Mendelian conditions. While it is appreciated that clinically relevant variants exhibit a wide spectrum of penetrance, accurately assessing and expressing the pathogenicity of variants with lower penetrance can be challenging. The vinculin (VCL) gene illustrates these challenges. Model organism data provide evidence that loss of function of VCL may play a role in cardiomyopathy and aggregate case-control studies suggest low penetrance. VCL loss of function variants, however, are rarely identified in affected probands and therefore there is a paucity of family studies clarifying the clinical significance of individual variants. This study, which aggregated data from >18,000 individuals who underwent gene panel or exome testing for inherited cardiomyopathies, identified 32 probands with VCL loss-of-function variants and confirmed enrichment in probands with dilated cardiomyopathy (odds ratio [OR] = 9.01; confidence interval [CI] = 4.93-16.45). Our data revealed that the majority of these individuals (89.5%) had pediatric onset of disease. Family studies demonstrated that heterozygous loss of function of VCL alone is insufficient to cause cardiomyopathy but that these variants do contribute to disease risk. In conclusion, VCL loss-of-function variants should be reported in a diagnostic setting but need to be clearly distinguished as having lower penetrance.
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Affiliation(s)
- Megan H Hawley
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts
| | - Naif Almontashiri
- Faculty of Applied Medical Sciences, Center for Genetics and Inherited Diseases, Taibah University, Almadinah Almunwarah, Saudi Arabia
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Natalie Berger
- Department of Maternal Fetal Medicine, SSM Health St Mary's Hospital, Madison, Wisconsin
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, New York
| | - John Garcia
- Invitae Corporation, San Francisco, California
| | - Theresa A Grebe
- Division of Genetics and Metabolism, Department of Child Health, Phoenix Children's Hospital, University of Arizona College of Medicine, Phoenix, Arizona
| | - Melissa A Kelly
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | - Matthew S Lebo
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts
| | | | - Hui Mei
- GeneDx, Inc, Gaithersburg, Maryland
| | - Julia Platt
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California
| | | | - Ashley Ryan
- Division of Genetics and Metabolism, Department of Child Health, Phoenix Children's Hospital, University of Arizona College of Medicine, Phoenix, Arizona
| | - Kate L Thomson
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Roddy Walsh
- Department of Clinical and Experimental Cardiology, Heart Centre, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherland
| | - James S Ware
- National Heart and Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre, Royal Brompton and Harefield Hospitals NHS Foundation Trust, Harefield, UK
| | - Matthew Wheeler
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California
| | - Hana Zouk
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts
| | - Heather Mason-Suares
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts
| | - Birgit Funke
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts
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Modeling Cardiovascular Diseases with hiPSC-Derived Cardiomyocytes in 2D and 3D Cultures. Int J Mol Sci 2020; 21:ijms21093404. [PMID: 32403456 PMCID: PMC7246991 DOI: 10.3390/ijms21093404] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 12/15/2022] Open
Abstract
In the last decade, the generation of cardiac disease models based on human-induced pluripotent stem cells (hiPSCs) has become of common use, providing new opportunities to overcome the lack of appropriate cardiac models. Although much progress has been made toward the generation of hiPSC-derived cardiomyocytes (hiPS-CMs), several lines of evidence indicate that two-dimensional (2D) cell culturing presents significant limitations, including hiPS-CMs immaturity and the absence of interaction between different cell types and the extracellular matrix. More recently, new advances in bioengineering and co-culture systems have allowed the generation of three-dimensional (3D) constructs based on hiPSC-derived cells. Within these systems, biochemical and physical stimuli influence the maturation of hiPS-CMs, which can show structural and functional properties more similar to those present in adult cardiomyocytes. In this review, we describe the latest advances in 2D- and 3D-hiPSC technology for cardiac disease mechanisms investigation, drug development, and therapeutic studies.
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Shrestha R, Lieberth J, Tillman S, Natalizio J, Bloomekatz J. Using Zebrafish to Analyze the Genetic and Environmental Etiologies of Congenital Heart Defects. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1236:189-223. [PMID: 32304074 DOI: 10.1007/978-981-15-2389-2_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Congenital heart defects (CHDs) are among the most common human birth defects. However, the etiology of a large proportion of CHDs remains undefined. Studies identifying the molecular and cellular mechanisms that underlie cardiac development have been critical to elucidating the origin of CHDs. Building upon this knowledge to understand the pathogenesis of CHDs requires examining how genetic or environmental stress changes normal cardiac development. Due to strong molecular conservation to humans and unique technical advantages, studies using zebrafish have elucidated both fundamental principles of cardiac development and have been used to create cardiac disease models. In this chapter we examine the unique toolset available to zebrafish researchers and how those tools are used to interrogate the genetic and environmental contributions to CHDs.
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Affiliation(s)
- Rabina Shrestha
- Department of Biology, University of Mississippi, Oxford, MS, USA
| | - Jaret Lieberth
- Department of Biology, University of Mississippi, Oxford, MS, USA
| | - Savanna Tillman
- Department of Biology, University of Mississippi, Oxford, MS, USA
| | - Joseph Natalizio
- Department of Biology, University of Mississippi, Oxford, MS, USA
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31
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van den Brink L, Grandela C, Mummery CL, Davis RP. Inherited cardiac diseases, pluripotent stem cells, and genome editing combined-the past, present, and future. Stem Cells 2020; 38:174-186. [PMID: 31664757 PMCID: PMC7027796 DOI: 10.1002/stem.3110] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/09/2019] [Indexed: 12/15/2022]
Abstract
Research on mechanisms underlying monogenic cardiac diseases such as primary arrhythmias and cardiomyopathies has until recently been hampered by inherent limitations of heterologous cell systems, where mutant genes are expressed in noncardiac cells, and physiological differences between humans and experimental animals. Human-induced pluripotent stem cells (hiPSCs) have proven to be a game changer by providing new opportunities for studying the disease in the specific cell type affected, namely the cardiomyocyte. hiPSCs are particularly valuable because not only can they be differentiated into unlimited numbers of these cells, but they also genetically match the individual from whom they were derived. The decade following their discovery showed the potential of hiPSCs for advancing our understanding of cardiovascular diseases, with key pathophysiological features of the patient being reflected in their corresponding hiPSC-derived cardiomyocytes (the past). Now, recent advances in genome editing for repairing or introducing genetic mutations efficiently have enabled the disease etiology and pathogenesis of a particular genotype to be investigated (the present). Finally, we are beginning to witness the promise of hiPSC in personalized therapies for individual patients, as well as their application in identifying genetic variants responsible for or modifying the disease phenotype (the future). In this review, we discuss how hiPSCs could contribute to improving the diagnosis, prognosis, and treatment of an individual with a suspected genetic cardiac disease, thereby developing better risk stratification and clinical management strategies for these potentially lethal but treatable disorders.
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Affiliation(s)
- Lettine van den Brink
- Department of Anatomy and EmbryologyLeiden University Medical CenterRC LeidenThe Netherlands
| | - Catarina Grandela
- Department of Anatomy and EmbryologyLeiden University Medical CenterRC LeidenThe Netherlands
| | - Christine L. Mummery
- Department of Anatomy and EmbryologyLeiden University Medical CenterRC LeidenThe Netherlands
| | - Richard P. Davis
- Department of Anatomy and EmbryologyLeiden University Medical CenterRC LeidenThe Netherlands
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32
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Porrello ER, Delbridge LMD. HFpEF-Time to Explore the Role of Genetic Heterogeneity in Phenotypic Variability: New Mechanistic Insights Offer Promise for Personalized Therapies. Circulation 2019; 140:1607-1609. [PMID: 31710521 DOI: 10.1161/circulationaha.119.042496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Enzo R Porrello
- Department of Physiology, School of Biomedical Science, University of Melbourne, Australia (E.R.P., L.M.D.D.).,Murdoch Children's Research Institute, Melbourne, Australia (E.R.P.)
| | - Lea M D Delbridge
- Department of Physiology, School of Biomedical Science, University of Melbourne, Australia (E.R.P., L.M.D.D.)
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33
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Affiliation(s)
- Ning Ma
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Division of Cardiology, Department of Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Sophia L Zhang
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Division of Cardiology, Department of Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Division of Cardiology, Department of Medicine, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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