1
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Perea-Gil I, Seeger T, Bruyneel AAN, Termglinchan V, Monte E, Lim EW, Vadgama N, Furihata T, Gavidia AA, Arthur Ataam J, Bharucha N, Martinez-Amador N, Ameen M, Nair P, Serrano R, Kaur B, Feyen DAM, Diecke S, Snyder MP, Metallo CM, Mercola M, Karakikes I. Serine biosynthesis as a novel therapeutic target for dilated cardiomyopathy. Eur Heart J 2022; 43:3477-3489. [PMID: 35728000 PMCID: PMC9794189 DOI: 10.1093/eurheartj/ehac305] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 04/14/2022] [Accepted: 05/24/2022] [Indexed: 12/30/2022] Open
Abstract
AIMS Genetic dilated cardiomyopathy (DCM) is a leading cause of heart failure. Despite significant progress in understanding the genetic aetiologies of DCM, the molecular mechanisms underlying the pathogenesis of familial DCM remain unknown, translating to a lack of disease-specific therapies. The discovery of novel targets for the treatment of DCM was sought using phenotypic sceening assays in induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) that recapitulate the disease phenotypes in vitro. METHODS AND RESULTS Using patient-specific iPSCs carrying a pathogenic TNNT2 gene mutation (p.R183W) and CRISPR-based genome editing, a faithful DCM model in vitro was developed. An unbiased phenotypic screening in TNNT2 mutant iPSC-derived cardiomyocytes (iPSC-CMs) with small molecule kinase inhibitors (SMKIs) was performed to identify novel therapeutic targets. Two SMKIs, Gö 6976 and SB 203580, were discovered whose combinatorial treatment rescued contractile dysfunction in DCM iPSC-CMs carrying gene mutations of various ontologies (TNNT2, TTN, LMNA, PLN, TPM1, LAMA2). The combinatorial SMKI treatment upregulated the expression of genes that encode serine, glycine, and one-carbon metabolism enzymes and significantly increased the intracellular levels of glucose-derived serine and glycine in DCM iPSC-CMs. Furthermore, the treatment rescued the mitochondrial respiration defects and increased the levels of the tricarboxylic acid cycle metabolites and ATP in DCM iPSC-CMs. Finally, the rescue of the DCM phenotypes was mediated by the activating transcription factor 4 (ATF4) and its downstream effector genes, phosphoglycerate dehydrogenase (PHGDH), which encodes a critical enzyme of the serine biosynthesis pathway, and Tribbles 3 (TRIB3), a pseudokinase with pleiotropic cellular functions. CONCLUSIONS A phenotypic screening platform using DCM iPSC-CMs was established for therapeutic target discovery. A combination of SMKIs ameliorated contractile and metabolic dysfunction in DCM iPSC-CMs mediated via the ATF4-dependent serine biosynthesis pathway. Together, these findings suggest that modulation of serine biosynthesis signalling may represent a novel genotype-agnostic therapeutic strategy for genetic DCM.
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Affiliation(s)
- Isaac Perea-Gil
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Timon Seeger
- Department of Medicine III, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Arne A N Bruyneel
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Vittavat Termglinchan
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Emma Monte
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Esther W Lim
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Nirmal Vadgama
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
| | - Takaaki Furihata
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Alexandra A Gavidia
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
| | - Jennifer Arthur Ataam
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Nike Bharucha
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Noel Martinez-Amador
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
| | - Mohamed Ameen
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Pooja Nair
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
| | - Ricardo Serrano
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Balpreet Kaur
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
| | - Dries A M Feyen
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Sebastian Diecke
- Max-Delbrueck-Center for Molecular Medicine, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Christian M Metallo
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Mark Mercola
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Ioannis Karakikes
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
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2
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Metzl-Raz E, Bharucha N, Arthur Ataam J, Gavidia AA, Greenleaf WJ, Karakikes I. Generation of a dual edited human induced pluripotent stem cell Myl7-GFP reporter line with inducible CRISPRi/dCas9. Stem Cell Res 2022; 61:102754. [PMID: 35325819 PMCID: PMC9169598 DOI: 10.1016/j.scr.2022.102754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/11/2022] [Accepted: 03/17/2022] [Indexed: 11/19/2022] Open
Abstract
Temporal regulation of CRISPRi activity is critical for genetic screens. Here, we present an inducible CRISPRi platform enabling selection of iPSC-derived cardiomyocytes and reversible gene knockdown. We targeted a doxycycline-inducible dCas9-KRAB-mCherry cassette into the AAVS1 locus in an MYL7-mGFP reporter iPSC line. A clone with bi-allelic integration displayed minimally leaky CRISPRi activity and strong expression upon addition of doxycycline in iPSCs, iPSC-derived cardiomyocytes, and multilineage differentiated cells. The CRISPRi activity was validated by targeting the MYOCD gene in iPSC cardiomyocytes. In summary, we developed a robust inducible CRISPRi platform to interrogate gene function in human iPSC-derived cardiomyocytes and other cells.
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Affiliation(s)
- Eyal Metzl-Raz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Nike Bharucha
- Department Cardiothoracic Surgery and Stanford Cardiovascular Institute, Stanford, CA, USA
| | - Jennifer Arthur Ataam
- Department Cardiothoracic Surgery and Stanford Cardiovascular Institute, Stanford, CA, USA
| | - Alexandra A Gavidia
- Department Cardiothoracic Surgery and Stanford Cardiovascular Institute, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ioannis Karakikes
- Department Cardiothoracic Surgery and Stanford Cardiovascular Institute, Stanford, CA, USA
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3
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Bharucha N, Ataam JA, Gavidia AA, Karakikes I. Generation of AAVS1 integrated doxycycline-inducible CRISPR-Prime Editor human induced pluripotent stem cell line. Stem Cell Res 2021; 57:102610. [PMID: 34875545 PMCID: PMC9126997 DOI: 10.1016/j.scr.2021.102610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/01/2021] [Accepted: 11/23/2021] [Indexed: 10/19/2022] Open
Abstract
Prime editing uses the Cas9 nickase fused to a reverse transcriptase to copy a DNA sequence into a specific locus from a 'prime editing' guide RNA (pegRNA), eliminating the need for double-stranded DNA breaks and donor DNA templates. To facilitate prime editing in human induced pluripotent stem cells (iPSCs), we integrated a doxycycline-inducible Prime Editor protein (PE2) into the AAVS1 genomic safe harbor locus. Prime editing of iPSCs resulted in precise insertion of three nucleotides in HEK3 locus with high efficiency, demonstrating the utility of this approach. This engineered cell line can be used to edit a single or multiple genomic loci by introducing a target-specific pegRNA for precise and effective genome editing to facilitate disease modeling and functional genetics studies.
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Affiliation(s)
- Nike Bharucha
- Department of Cardiothoracic Surgery and Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jennifer Arthur Ataam
- Department of Cardiothoracic Surgery and Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Alexandra A Gavidia
- Department of Cardiothoracic Surgery and Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ioannis Karakikes
- Department of Cardiothoracic Surgery and Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA.
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4
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Feyen DA, Perea-Gil I, Maas RG, Harakalova M, Gavidia AA, Ataam JA, Wu TH, Vink A, Pei J, Vadgama N, Suurmeijer AJ, te Rijdt WP, Vu M, Amatya PL, Prado M, Zhang Y, Dunkenberger L, Sluijter JP, Sallam K, Asselbergs FW, Mercola M, Karakikes I. Unfolded Protein Response as a Compensatory Mechanism and Potential Therapeutic Target in PLN R14del Cardiomyopathy. Circulation 2021; 144:382-392. [PMID: 33928785 PMCID: PMC8667423 DOI: 10.1161/circulationaha.120.049844] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND Phospholamban (PLN) is a critical regulator of calcium cycling and contractility in the heart. The loss of arginine at position 14 in PLN (R14del) is associated with dilated cardiomyopathy with a high prevalence of ventricular arrhythmias. How the R14 deletion causes dilated cardiomyopathy is poorly understood, and there are no disease-specific therapies. METHODS We used single-cell RNA sequencing to uncover PLN R14del disease mechanisms in human induced pluripotent stem cells (hiPSC-CMs). We used both 2-dimensional and 3-dimensional functional contractility assays to evaluate the impact of modulating disease-relevant pathways in PLN R14del hiPSC-CMs. RESULTS Modeling of the PLN R14del cardiomyopathy with isogenic pairs of hiPSC-CMs recapitulated the contractile deficit associated with the disease in vitro. Single-cell RNA sequencing revealed the induction of the unfolded protein response (UPR) pathway in PLN R14del compared with isogenic control hiPSC-CMs. The activation of UPR was also evident in the hearts from PLN R14del patients. Silencing of each of the 3 main UPR signaling branches (IRE1, ATF6, or PERK) by siRNA exacerbated the contractile dysfunction of PLN R14del hiPSC-CMs. We explored the therapeutic potential of activating the UPR with a small molecule activator, BiP (binding immunoglobulin protein) inducer X. PLN R14del hiPSC-CMs treated with BiP protein inducer X showed a dose-dependent amelioration of the contractility deficit in both 2-dimensional cultures and 3-dimensional engineered heart tissues without affecting calcium homeostasis. CONCLUSIONS Together, these findings suggest that the UPR exerts a protective effect in the setting of PLN R14del cardiomyopathy and that modulation of the UPR might be exploited therapeutically.
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Affiliation(s)
- Dries A.M. Feyen
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA,Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Isaac Perea-Gil
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA,Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Renee G.C. Maas
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Magdalena Harakalova
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Alexandra A. Gavidia
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jennifer Arthur Ataam
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA,Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ting-Hsuan Wu
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aryan Vink
- Department of Pathology, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Jiayi Pei
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Nirmal Vadgama
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA,Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Albert J. Suurmeijer
- Deptment of Pathology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Wouter P. te Rijdt
- Netherlands Heart Institute, Utrecht, The Netherlands,Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Michelle Vu
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA,Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Prashila L. Amatya
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA,Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Maricela Prado
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yuan Zhang
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Logan Dunkenberger
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joost P.G. Sluijter
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Karim Sallam
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA,Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Folkert W. Asselbergs
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands,Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, United Kingdom,Health Data Research UK and Institute of Health Informatics, University College London, London, United Kingdom
| | - Mark Mercola
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA,Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ioannis Karakikes
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA,Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA,Address for Correspondence: Ioannis Karakikes, PhD, Stanford University School of Medicine, Department of Cardiothoracic Surgery, 300 Pasteur Dr, Suite 1347, Stanford, California 94305, USA. Telephone: 650-721-0784,
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5
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Zhang Y, Ameen M, Perea Gil I, Arthur J, Gavidia AA, Bharucha N, Wang KC, Karakikes I. Abstract MP175: Disruption of the Genome Architecture at the
PRRX1
Locus is Associated With the Pathogenesis of
LMNA
-related Dilated Cardiomyopathy. Circ Res 2020. [DOI: 10.1161/res.127.suppl_1.mp175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background:
LMNA
, a gene encoding A-type lamin proteins (abbreviated as lamin A), is one of the most frequently mutated genes in dilated cardiomyopathy (DCM). The molecular mechanisms underlying cardiomyocyte dysfunction in
LMNA
-related DCM remain elusive, translating to the lack of disease-specific therapies. Lamin A has been shown to play a critical role in genome organization via interactions with the chromatin at specific regions called lamina-associated domains (LADs). However, little is known about whether DCM-causing
LMNA
mutations rearrange the genome conformation and chromosome accessibility. The overarching goal of this study is to define the role of genome organization in
LMNA
-related DCM.
Methods:
LMNA
-related DCM was modeled
in vitro
using cardiomyocytes derived from induced pluripotent stem cells (iPSC-CMs) from DCM patients carrying a frameshift mutation in the
LMNA
gene (c. 348_349insG; p. K117fs) and isogenic controls. We combined genome-wide single cell functional genomic and epigenomic mapping analyses to define the gene regulation and cis-regulatory interactions in isogenic iPSC-CMs.
Results:
Single-cell RNA-seq revealed global gene dysregulation in
LMNA
mutant compared to isogenic control iPSC-CMs. The homeodomain transcription factor
PRRX1
was significantly upregulated in mutant cells. We showed that LAD integrity is disrupted at the
PRRX1
locus in mutant iPSC-CMs. In agreement, DNA fluorescence
in situ
hybridization (FISH) revealed that the
PRRX1
locus loses peripheral association and relocates towards the transcriptionally active nuclear interior in mutant iPSC-CMs. Correspondingly, single-cell assay for transposase accessible chromatin (ATAC)-seq showed increased chromatin co-accessibility at the
PRRX1
locus, providing a plausible explanation for ectopic activation of
PRRX1
in
LMNA
mutant iPSC-CMs.
Conclusion:
Our data suggest that
LMNA
haploinsufficiency disrupts the structure of LADs, leading to ectopic promoter interactions and altered gene expression in
LMNA
-related DCM iPSC-CMs. We identified
PRRX1
as a promising candidate locus linking changes in LAD organization with gene dysregulation in
LMNA
-related DCM.
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Affiliation(s)
- Yuan Zhang
- Stanford Univ Sch of Medicine, Stanford, CA
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6
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Perea Gil I, Bellbachir N, Gavidia AA, Arthur J, Zhang Y, Vadgama N, Oikonomopoulos A, Roura S, Wu JC, Bayes-Genis A, Karakikes I. Abstract 274: Activation of CaMKII Signaling Pathway Contributes to the Pathogenesis of Genetic Hypertrophic Cardiomyopathy. Circ Res 2020. [DOI: 10.1161/res.127.suppl_1.274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background:
Hypertrophic cardiomyopathy (HCM) is the most prevalent form of genetic cardiomyopathy associated with ventricular arrhythmia and sudden cardiac death. To date, several pathogenic variants of sarcomeric protein genes have been identified in genetic HCM. However, the mechanisms by which specific mutations cause the hallmark phenotypes of HCM remain largely unresolved. There is a major unmet need for a better understanding of disease mechanisms in order to predict individuals at risk for sudden cardiac death and design mechanism-based therapeutics.
Methods:
We modeled HCM
in vitro
using human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) from HCM patients with a history of ventricular arrhythmias and sudden cardiac death harboring a heterozygous mutation in the Tropomyosin 1 gene (TPM1, c.107 A>G). We studied the functional and molecular consequences of the TPM1 mutation in iPSC-CMs to determine the molecular mechanism of HCM pathogenesis.
Results:
In mutant cardiomyocytes we observed impaired mechanical relaxation, aberrant intracellular calcium cycling and increased incidence of delayed after-depolarizations when compared to isogenic controls, recapitulating the HCM phenotype
in vitro
. Genome wide transcriptional profiling revealed a significant enrichment of genes associated with calcium dysregulation and the activation of the Calcium/Calmodulin-Dependent Protein Kinase II (CaMKII) pathway in mutant cardiomyocytes. Conversely, pharmacological inhibition of CaMKII pathway rescued the arrhythmic phenotype of mutant cardiomyocytes
in vitro
.
Conclusions:
Taken together, our data suggest a mechanistic link between the activation of CaMKII signaling pathway and the pathogenesis of sarcomeric HCM. These results provide a better understanding of the arrhythmogenic signaling pathway associated with the HCM phenotype and could potentially lead to mechanism-based targeted therapeutics for genetic HCM patients.
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Affiliation(s)
| | | | | | | | | | | | | | - Santiago Roura
- Germans Trias i Pujol Health Science Rsch Institute, Badalona, Spain
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