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Dondi C, Vogler G, Gupta A, Walls SM, Kervadec A, Romero MR, Diop SB, Goode J, Thomas JB, Colas AR, Bodmer R, Montminy M, Ocorr K. The nutrient sensor CRTC & Sarcalumenin / Thinman represent a new pathway in cardiac hypertrophy. bioRxiv 2023:2023.10.02.560407. [PMID: 37873259 PMCID: PMC10592890 DOI: 10.1101/2023.10.02.560407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Obesity and type 2 diabetes are at epidemic levels and a significant proportion of these patients are diagnosed with left ventricular hypertrophy. CREB R egulated T ranscription C o-activator ( CRTC ) is a key regulator of metabolism in mammalian hepatocytes, where it is activated by calcineurin (CaN) to increase expression of gluconeogenic genes. CaN is known its role in pathological cardiac hypertrophy, however, a role for CRTC in the heart has not been identified. In Drosophila , CRTC null mutants have little body fat and exhibit severe cardiac restriction, myofibrillar disorganization, cardiac fibrosis and tachycardia, all hallmarks of heart disease. Cardiac-specific knockdown of CRTC , or its coactivator CREBb , mimicked the reduced body fat and heart defects of CRTC null mutants. Comparative gene expression in CRTC loss- or gain-of-function fly hearts revealed contra-regulation of genes involved in glucose, fatty acid, and amino acid metabolism, suggesting that CRTC also acts as a metabolic switch in the heart. Among the contra-regulated genes with conserved CREB binding sites, we identified the fly ortholog of Sarcalumenin, which is a Ca 2+ -binding protein in the sarcoplasmic reticulum. Cardiac knockdown recapitulated the loss of CRTC cardiac restriction and fibrotic phenotypes, suggesting it is a downstream effector of CRTC we named thinman ( tmn ). Importantly, cardiac overexpression of either CaN or CRTC in flies caused hypertrophy that was reversed in a CRTC mutant background, suggesting CRTC mediates hypertrophy downstream of CaN, perhaps as an alternative to NFAT. CRTC novel role in the heart is likely conserved in vertebrates as knockdown in zebrafish also caused cardiac restriction, as in fl ies. These data suggest that CRTC is involved in myocardial cell maintenance and that CaN-CRTC- Sarcalumenin/ tmn signaling represents a novel and conserved pathway underlying cardiac hypertrophy.
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Birker K, Ge S, Kirkland NJ, Theis JL, Marchant J, Fogarty ZC, Missinato MA, Kalvakuri S, Grossfeld P, Engler AJ, Ocorr K, Nelson TJ, Colas AR, Olson TM, Vogler G, Bodmer R. Mitochondrial MICOS complex genes, implicated in hypoplastic left heart syndrome, maintain cardiac contractility and actomyosin integrity. eLife 2023; 12:e83385. [PMID: 37404133 PMCID: PMC10361721 DOI: 10.7554/elife.83385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 07/04/2023] [Indexed: 07/06/2023] Open
Abstract
Hypoplastic left heart syndrome (HLHS) is a severe congenital heart disease (CHD) with a likely oligogenic etiology, but our understanding of the genetic complexities and pathogenic mechanisms leading to HLHS is limited. We therefore performed whole genome sequencing (WGS) on a large cohort of HLHS patients and their families to identify candidate genes that were then tested in Drosophila heart model for functional and structural requirements. Bioinformatic analysis of WGS data from an index family comprised of a HLHS proband born to consanguineous parents and postulated to have a homozygous recessive disease etiology, prioritized 9 candidate genes with rare, predicted damaging homozygous variants. Of the candidate HLHS gene homologs tested, cardiac-specific knockdown (KD) of mitochondrial MICOS complex subunit Chchd3/6 resulted in drastically compromised heart contractility, diminished levels of sarcomeric actin and myosin, reduced cardiac ATP levels, and mitochondrial fission-fusion defects. Interestingly, these heart defects were similar to those inflicted by cardiac KD of ATP synthase subunits of the electron transport chain (ETC), consistent with the MICOS complex's role in maintaining cristae morphology and ETC complex assembly. Analysis of 183 genomes of HLHS patient-parent trios revealed five additional HLHS probands with rare, predicted damaging variants in CHCHD3 or CHCHD6. Hypothesizing an oligogenic basis for HLHS, we tested 60 additional prioritized candidate genes in these cases for genetic interactions with Chchd3/6 in sensitized fly hearts. Moderate KD of Chchd3/6 in combination with Cdk12 (activator of RNA polymerase II), RNF149 (goliath, gol, E3 ubiquitin ligase), or SPTBN1 (β Spectrin, β-Spec, scaffolding protein) caused synergistic heart defects, suggesting the potential involvement of a diverse set of pathways in HLHS. Further elucidation of novel candidate genes and genetic interactions of potentially disease-contributing pathways is expected to lead to a better understanding of HLHS and other CHDs.
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Affiliation(s)
- Katja Birker
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Shuchao Ge
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Natalie J Kirkland
- Department of Bioengineering, University of California, San Diego, San Diego, United States
| | - Jeanne L Theis
- Cardiovascular Genetics Research Laboratory, Mayo Clinic, Rochester, United States
| | - James Marchant
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Zachary C Fogarty
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, United States
| | - Maria A Missinato
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Sreehari Kalvakuri
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Paul Grossfeld
- Department of Pediatrics, University of California, San Diego, San Diego, United States
| | - Adam J Engler
- Department of Bioengineering, University of California, San Diego, San Diego, United States
| | - Karen Ocorr
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Timothy J Nelson
- Center for Regenerative Medicine, Mayo Clinic, Rochester, United States
| | - Alexandre R Colas
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Timothy M Olson
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, United States
| | - Georg Vogler
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
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Kervadec A, Kezos J, Ni H, Yu M, Marchant J, Spiering S, Kannan S, Kwon C, Andersen P, Bodmer R, Grandi E, Ocorr K, Colas AR. Multiplatform modeling of atrial fibrillation identifies phospholamban as a central regulator of cardiac rhythm. Dis Model Mech 2023; 16:dmm049962. [PMID: 37293707 PMCID: PMC10387351 DOI: 10.1242/dmm.049962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 05/26/2023] [Indexed: 06/10/2023] Open
Abstract
Atrial fibrillation (AF) is a common and genetically inheritable form of cardiac arrhythmia; however, it is currently not known how these genetic predispositions contribute to the initiation and/or maintenance of AF-associated phenotypes. One major barrier to progress is the lack of experimental systems to investigate the effects of gene function on rhythm parameters in models with human atrial and whole-organ relevance. Here, we assembled a multi-model platform enabling high-throughput characterization of the effects of gene function on action potential duration and rhythm parameters using human induced pluripotent stem cell-derived atrial-like cardiomyocytes and a Drosophila heart model, and validation of the findings using computational models of human adult atrial myocytes and tissue. As proof of concept, we screened 20 AF-associated genes and identified phospholamban loss of function as a top conserved hit that shortens action potential duration and increases the incidence of arrhythmia phenotypes upon stress. Mechanistically, our study reveals that phospholamban regulates rhythm homeostasis by functionally interacting with L-type Ca2+ channels and NCX. In summary, our study illustrates how a multi-model system approach paves the way for the discovery and molecular delineation of gene regulatory networks controlling atrial rhythm with application to AF.
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Affiliation(s)
- Anaïs Kervadec
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - James Kezos
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Haibo Ni
- Department of Pharmacology, UC Davis, Davis, CA 95616, USA
| | - Michael Yu
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - James Marchant
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Sean Spiering
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Suraj Kannan
- Johns Hopkins University, Baltimore, MD 21205, USA
| | - Chulan Kwon
- Johns Hopkins University, Baltimore, MD 21205, USA
| | | | - Rolf Bodmer
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | | | - Karen Ocorr
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Alexandre R. Colas
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
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4
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Kannan S, Miyamoto M, Zhu R, Lynott M, Guo J, Chen EZ, Colas AR, Lin BL, Kwon C. Trajectory reconstruction identifies dysregulation of perinatal maturation programs in pluripotent stem cell-derived cardiomyocytes. Cell Rep 2023; 42:112330. [PMID: 37014753 PMCID: PMC10545814 DOI: 10.1016/j.celrep.2023.112330] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/12/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
A limitation in the application of pluripotent stem cell-derived cardiomyocytes (PSC-CMs) is the failure of these cells to achieve full functional maturity. The mechanisms by which directed differentiation differs from endogenous development, leading to consequent PSC-CM maturation arrest, remain unclear. Here, we generate a single-cell RNA sequencing (scRNA-seq) reference of mouse in vivo CM maturation with extensive sampling of previously difficult-to-isolate perinatal time periods. We subsequently generate isogenic embryonic stem cells to create an in vitro scRNA-seq reference of PSC-CM-directed differentiation. Through trajectory reconstruction, we identify an endogenous perinatal maturation program that is poorly recapitulated in vitro. By comparison with published human datasets, we identify a network of nine transcription factors (TFs) whose targets are consistently dysregulated in PSC-CMs across species. Notably, these TFs are only partially activated in common ex vivo approaches to engineer PSC-CM maturation. Our study can be leveraged toward improving the clinical viability of PSC-CMs.
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Affiliation(s)
- Suraj Kannan
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Matthew Miyamoto
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Renjun Zhu
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Michaela Lynott
- Sanford Burham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Jason Guo
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Elaine Zhelan Chen
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Alexandre R Colas
- Sanford Burham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Brian Leei Lin
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Chulan Kwon
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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5
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Missinato MA, Murphy S, Lynott M, Yu MS, Kervadec A, Chang YL, Kannan S, Loreti M, Lee C, Amatya P, Tanaka H, Huang CT, Puri PL, Kwon C, Adams PD, Qian L, Sacco A, Andersen P, Colas AR. Conserved transcription factors promote cell fate stability and restrict reprogramming potential in differentiated cells. Nat Commun 2023; 14:1709. [PMID: 36973293 PMCID: PMC10043290 DOI: 10.1038/s41467-023-37256-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 03/08/2023] [Indexed: 03/29/2023] Open
Abstract
Defining the mechanisms safeguarding cell fate identity in differentiated cells is crucial to improve 1) - our understanding of how differentiation is maintained in healthy tissues or altered in a disease state, and 2) - our ability to use cell fate reprogramming for regenerative purposes. Here, using a genome-wide transcription factor screen followed by validation steps in a variety of reprogramming assays (cardiac, neural and iPSC in fibroblasts and endothelial cells), we identified a set of four transcription factors (ATF7IP, JUNB, SP7, and ZNF207 [AJSZ]) that robustly opposes cell fate reprogramming in both lineage and cell type independent manners. Mechanistically, our integrated multi-omics approach (ChIP, ATAC and RNA-seq) revealed that AJSZ oppose cell fate reprogramming by 1) - maintaining chromatin enriched for reprogramming TF motifs in a closed state and 2) - downregulating genes required for reprogramming. Finally, KD of AJSZ in combination with MGT overexpression, significantly reduced scar size and improved heart function by 50%, as compared to MGT alone post-myocardial infarction. Collectively, our study suggests that inhibition of barrier to reprogramming mechanisms represents a promising therapeutic avenue to improve adult organ function post-injury.
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Affiliation(s)
- Maria A Missinato
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Sean Murphy
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Michaela Lynott
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Michael S Yu
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Anaïs Kervadec
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Yu-Ling Chang
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Suraj Kannan
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Mafalda Loreti
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Christopher Lee
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Prashila Amatya
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Hiroshi Tanaka
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Chun-Teng Huang
- Viral Vector Core Facility Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Pier Lorenzo Puri
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Chulan Kwon
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Peter D Adams
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Li Qian
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alessandra Sacco
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Peter Andersen
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Alexandre R Colas
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA.
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6
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Saha S, Spinelli L, Castro Mondragon JA, Kervadec A, Lynott M, Kremmer L, Roder L, Krifa S, Torres M, Brun C, Vogler G, Bodmer R, Colas AR, Ocorr K, Perrin L. Genetic architecture of natural variation of cardiac performance from flies to humans. eLife 2022; 11:82459. [DOI: 10.7554/elife.82459] [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] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022] Open
Abstract
Deciphering the genetic architecture of human cardiac disorders is of fundamental importance but their underlying complexity is a major hurdle. We investigated the natural variation of cardiac performance in the sequenced inbred lines of the Drosophila Genetic Reference Panel (DGRP). Genome-wide associations studies (GWAS) identified genetic networks associated with natural variation of cardiac traits which were used to gain insights as to the molecular and cellular processes affected. Non-coding variants that we identified were used to map potential regulatory non-coding regions, which in turn were employed to predict transcription factors (TFs) binding sites. Cognate TFs, many of which themselves bear polymorphisms associated with variations of cardiac performance, were also validated by heart-specific knockdown. Additionally, we showed that the natural variations associated with variability in cardiac performance affect a set of genes overlapping those associated with average traits but through different variants in the same genes. Furthermore, we showed that phenotypic variability was also associated with natural variation of gene regulatory networks. More importantly, we documented correlations between genes associated with cardiac phenotypes in both flies and humans, which supports a conserved genetic architecture regulating adult cardiac function from arthropods to mammals. Specifically, roles for PAX9 and EGR2 in the regulation of the cardiac rhythm were established in both models, illustrating that the characteristics of natural variations in cardiac function identified in Drosophila can accelerate discovery in humans.
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Affiliation(s)
- Saswati Saha
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Lionel Spinelli
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | | | - Anaïs Kervadec
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Michaela Lynott
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Laurent Kremmer
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Laurence Roder
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Sallouha Krifa
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Magali Torres
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Christine Brun
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
- CNRS
| | - Georg Vogler
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Alexandre R Colas
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Karen Ocorr
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Laurent Perrin
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
- CNRS
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7
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Schroeder AM, Nielsen T, Lynott M, Vogler G, Colas AR, Bodmer R. Nascent polypeptide-Associated Complex and Signal Recognition Particle have cardiac-specific roles in heart development and remodeling. PLoS Genet 2022; 18:e1010448. [PMID: 36240221 PMCID: PMC9604979 DOI: 10.1371/journal.pgen.1010448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 10/26/2022] [Accepted: 09/27/2022] [Indexed: 11/25/2022] Open
Abstract
Establishing a catalog of Congenital Heart Disease (CHD) genes and identifying functional networks would improve our understanding of its oligogenic underpinnings. Our studies identified protein biogenesis cofactors Nascent polypeptide-Associated Complex (NAC) and Signal-Recognition-Particle (SRP) as disease candidates and novel regulators of cardiac differentiation and morphogenesis. Knockdown (KD) of the alpha- (Nacα) or beta-subunit (bicaudal, bic) of NAC in the developing Drosophila heart disrupted cardiac developmental remodeling resulting in a fly with no heart. Heart loss was rescued by combined KD of Nacα with the posterior patterning Hox gene Abd-B. Consistent with a central role for this interaction in cardiogenesis, KD of Nacα in cardiac progenitors derived from human iPSCs impaired cardiac differentiation while co-KD with human HOXC12 and HOXD12 rescued this phenotype. Our data suggest that Nacα KD preprograms cardioblasts in the embryo for abortive remodeling later during metamorphosis, as Nacα KD during translation-intensive larval growth or pupal remodeling only causes moderate heart defects. KD of SRP subunits in the developing fly heart produced phenotypes that targeted specific segments and cell types, again suggesting cardiac-specific and spatially regulated activities. Together, we demonstrated directed function for NAC and SRP in heart development, and that regulation of NAC function depends on Hox genes.
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Affiliation(s)
- Analyne M. Schroeder
- Development, Aging and Regeneration Program, Center for Genetic Disorders and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
- * E-mail: (AMS); (RB)
| | - Tanja Nielsen
- Development, Aging and Regeneration Program, Center for Genetic Disorders and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
| | - Michaela Lynott
- Development, Aging and Regeneration Program, Center for Genetic Disorders and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
| | - Georg Vogler
- Development, Aging and Regeneration Program, Center for Genetic Disorders and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
| | - Alexandre R. Colas
- Development, Aging and Regeneration Program, Center for Genetic Disorders and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Center for Genetic Disorders and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
- * E-mail: (AMS); (RB)
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8
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Cheng J, Tsuda M, Okolotowicz K, Dwyer M, Bushway PJ, Colas AR, Lancman JJ, Schade D, Perea-Gil I, Bruyneel AAN, Lee J, Vadgama N, Quach J, McKeithan WL, Biechele TL, Wu JC, Moon RT, Si Dong PD, Karakikes I, Cashman JR, Mercola M. Small-molecule probe reveals a kinase cascade that links stress signaling to TCF/LEF and Wnt responsiveness. Cell Chem Biol 2021; 28:625-635.e5. [PMID: 33503403 PMCID: PMC8140986 DOI: 10.1016/j.chembiol.2021.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 08/02/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
Wnt signaling plays a central role in tissue maintenance and cancer. Wnt activates downstream genes through β-catenin, which interacts with TCF/LEF transcription factors. A major question is how this signaling is coordinated relative to tissue organization and renewal. We used a recently described class of small molecules that binds tubulin to reveal a molecular cascade linking stress signaling through ATM, HIPK2, and p53 to the regulation of TCF/LEF transcriptional activity. These data suggest a mechanism by which mitotic and genotoxic stress can indirectly modulate Wnt responsiveness to exert coherent control over cell shape and renewal. These findings have implications for understanding tissue morphogenesis and small-molecule anticancer therapeutics.
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Affiliation(s)
- Jiongjia Cheng
- Human BioMolecular Research Institute, 5310 Eastgate Mall, San Diego, CA 92121, USA
| | - Masanao Tsuda
- Sanford-Burnham-Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Karl Okolotowicz
- Human BioMolecular Research Institute, 5310 Eastgate Mall, San Diego, CA 92121, USA
| | - Mary Dwyer
- Human BioMolecular Research Institute, 5310 Eastgate Mall, San Diego, CA 92121, USA
| | - Paul J Bushway
- Sanford-Burnham-Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; University of California, San Diego, San Diego, CA 92093, USA
| | - Alexandre R Colas
- Sanford-Burnham-Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Joseph J Lancman
- Sanford-Burnham-Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Dennis Schade
- Human BioMolecular Research Institute, 5310 Eastgate Mall, San Diego, CA 92121, USA; Institute of Pharmacy, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, Kiel, Germany
| | - Isaac Perea-Gil
- Cardiovascular Institute, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94305, USA
| | - Arne A N Bruyneel
- Cardiovascular Institute, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94305, USA
| | - Jaechol Lee
- Cardiovascular Institute, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94305, USA
| | - Nirmal Vadgama
- Cardiovascular Institute, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94305, USA
| | - Justine Quach
- Human BioMolecular Research Institute, 5310 Eastgate Mall, San Diego, CA 92121, USA
| | - Wesley L McKeithan
- Sanford-Burnham-Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; Cardiovascular Institute, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94305, USA
| | - Travis L Biechele
- Department of Pharmacology, University of Washington, Seattle, WA 98105, USA
| | - Joseph C Wu
- Cardiovascular Institute, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94305, USA; Department of Medicine, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94305, USA
| | - Randall T Moon
- Department of Pharmacology, University of Washington, Seattle, WA 98105, USA
| | - P Duc Si Dong
- Sanford-Burnham-Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ioannis Karakikes
- Cardiovascular Institute, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94305, USA; Department of Cardiothoracic Surgery, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94305, USA
| | - John R Cashman
- Sanford-Burnham-Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Mark Mercola
- Sanford-Burnham-Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; University of California, San Diego, San Diego, CA 92093, USA; Cardiovascular Institute, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94305, USA; Department of Medicine, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94305, USA.
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9
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Murphy SA, Miyamoto M, Kervadec A, Kannan S, Tampakakis E, Kambhampati S, Lin BL, Paek S, Andersen P, Lee DI, Zhu R, An SS, Kass DA, Uosaki H, Colas AR, Kwon C. PGC1/PPAR drive cardiomyocyte maturation at single cell level via YAP1 and SF3B2. Nat Commun 2021; 12:1648. [PMID: 33712605 PMCID: PMC7955035 DOI: 10.1038/s41467-021-21957-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 02/22/2021] [Indexed: 02/07/2023] Open
Abstract
Cardiomyocytes undergo significant structural and functional changes after birth, and these fundamental processes are essential for the heart to pump blood to the growing body. However, due to the challenges of isolating single postnatal/adult myocytes, how individual newborn cardiomyocytes acquire multiple aspects of the mature phenotype remains poorly understood. Here we implement large-particle sorting and analyze single myocytes from neonatal to adult hearts. Early myocytes exhibit wide-ranging transcriptomic and size heterogeneity that is maintained until adulthood with a continuous transcriptomic shift. Gene regulatory network analysis followed by mosaic gene deletion reveals that peroxisome proliferator-activated receptor coactivator-1 signaling, which is active in vivo but inactive in pluripotent stem cell-derived cardiomyocytes, mediates the shift. This signaling simultaneously regulates key aspects of cardiomyocyte maturation through previously unrecognized proteins, including YAP1 and SF3B2. Our study provides a single-cell roadmap of heterogeneous transitions coupled to cellular features and identifies a multifaceted regulator controlling cardiomyocyte maturation.
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Affiliation(s)
- Sean A Murphy
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Matthew Miyamoto
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anaïs Kervadec
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Suraj Kannan
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Emmanouil Tampakakis
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sandeep Kambhampati
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Brian Leei Lin
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sam Paek
- Rutgers Institute for Translational Medicine and Science, New Brunswick, NJ, USA
| | - Peter Andersen
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dong-Ik Lee
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Renjun Zhu
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Steven S An
- Rutgers Institute for Translational Medicine and Science, New Brunswick, NJ, USA
| | - David A Kass
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hideki Uosaki
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Alexandre R Colas
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Chulan Kwon
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Biomedical engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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10
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Theis JL, Vogler G, Missinato MA, Li X, Nielsen T, Zeng XXI, Martinez-Fernandez A, Walls SM, Kervadec A, Kezos JN, Birker K, Evans JM, O'Byrne MM, Fogarty ZC, Terzic A, Grossfeld P, Ocorr K, Nelson TJ, Olson TM, Colas AR, Bodmer R. Patient-specific genomics and cross-species functional analysis implicate LRP2 in hypoplastic left heart syndrome. eLife 2020; 9:e59554. [PMID: 33006316 PMCID: PMC7581429 DOI: 10.7554/elife.59554] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/29/2020] [Indexed: 12/12/2022] Open
Abstract
Congenital heart diseases (CHDs), including hypoplastic left heart syndrome (HLHS), are genetically complex and poorly understood. Here, a multidisciplinary platform was established to functionally evaluate novel CHD gene candidates, based on whole-genome and iPSC RNA sequencing of a HLHS family-trio. Filtering for rare variants and altered expression in proband iPSCs prioritized 10 candidates. siRNA/RNAi-mediated knockdown in healthy human iPSC-derived cardiomyocytes (hiPSC-CM) and in developing Drosophila and zebrafish hearts revealed that LDL receptor-related protein LRP2 is required for cardiomyocyte proliferation and differentiation. Consistent with hypoplastic heart defects, compared to patents the proband's iPSC-CMs exhibited reduced proliferation. Interestingly, rare, predicted-damaging LRP2 variants were enriched in a HLHS cohort; however, understanding their contribution to HLHS requires further investigation. Collectively, we have established a multi-species high-throughput platform to rapidly evaluate candidate genes and their interactions during heart development, which are crucial first steps toward deciphering oligogenic underpinnings of CHDs, including hypoplastic left hearts.
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Affiliation(s)
- Jeanne L Theis
- Cardiovascular Genetics Research LaboratoryRochesterUnited States
| | - Georg Vogler
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Maria A Missinato
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Xing Li
- Division of Biomedical Statistics and Informatics, Mayo ClinicRochesterUnited States
| | - Tanja Nielsen
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
- Doctoral Degrees and Habilitations, Department of Biology, Chemistry, and Pharmacy, Freie Universität BerlinBerlinGermany
| | - Xin-Xin I Zeng
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | | | - Stanley M Walls
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Anaïs Kervadec
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - James N Kezos
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Katja Birker
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Jared M Evans
- Division of Biomedical Statistics and Informatics, Mayo ClinicRochesterUnited States
| | - Megan M O'Byrne
- Division of Biomedical Statistics and Informatics, Mayo ClinicRochesterUnited States
| | - Zachary C Fogarty
- Division of Biomedical Statistics and Informatics, Mayo ClinicRochesterUnited States
| | - André Terzic
- Department of Cardiovascular Medicine, Mayo ClinicRochesterUnited States
- Department of Molecular and Pharmacology and Experimental Therapeutics, Mayo ClinicLa JollaUnited States
- Center for Regenerative Medicine, Mayo ClinicRochesterUnited States
- Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo ClinicRochesterUnited States
| | - Paul Grossfeld
- University of California San Diego, Rady’s HospitalSan DiegoUnited States
- Division of General Internal Medicine, Mayo ClinicRochesterUnited States
| | - Karen Ocorr
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Timothy J Nelson
- Department of Molecular and Pharmacology and Experimental Therapeutics, Mayo ClinicLa JollaUnited States
- Center for Regenerative Medicine, Mayo ClinicRochesterUnited States
- Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo ClinicRochesterUnited States
| | - Timothy M Olson
- Department of Cardiovascular Medicine, Mayo ClinicRochesterUnited States
- Department of Molecular and Pharmacology and Experimental Therapeutics, Mayo ClinicLa JollaUnited States
- Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo ClinicRochesterUnited States
| | - Alexandre R Colas
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Rolf Bodmer
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
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11
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Elmén L, Volpato CB, Kervadec A, Pineda S, Kalvakuri S, Alayari NN, Foco L, Pramstaller PP, Ocorr K, Rossini A, Cammarato A, Colas AR, Hicks AA, Bodmer R. Silencing of CCR4-NOT complex subunits affects heart structure and function. Dis Model Mech 2020; 13:dmm044727. [PMID: 32471864 PMCID: PMC7390626 DOI: 10.1242/dmm.044727] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/19/2020] [Indexed: 12/12/2022] Open
Abstract
The identification of genetic variants that predispose individuals to cardiovascular disease and a better understanding of their targets would be highly advantageous. Genome-wide association studies have identified variants that associate with QT-interval length (a measure of myocardial repolarization). Three of the strongest associating variants (single-nucleotide polymorphisms) are located in the putative promotor region of CNOT1, a gene encoding the central CNOT1 subunit of CCR4-NOT: a multifunctional, conserved complex regulating gene expression and mRNA stability and turnover. We isolated the minimum fragment of the CNOT1 promoter containing all three variants from individuals homozygous for the QT risk alleles and demonstrated that the haplotype associating with longer QT interval caused reduced reporter expression in a cardiac cell line, suggesting that reduced CNOT1 expression might contribute to abnormal QT intervals. Systematic siRNA-mediated knockdown of CCR4-NOT components in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) revealed that silencing CNOT1 and other CCR4-NOT genes reduced their proliferative capacity. Silencing CNOT7 also shortened action potential duration. Furthermore, the cardiac-specific knockdown of Drosophila orthologs of CCR4-NOT genes in vivo (CNOT1/Not1 and CNOT7/8/Pop2) was either lethal or resulted in dilated cardiomyopathy, reduced contractility or a propensity for arrhythmia. Silencing CNOT2/Not2, CNOT4/Not4 and CNOT6/6L/twin also affected cardiac chamber size and contractility. Developmental studies suggested that CNOT1/Not1 and CNOT7/8/Pop2 are required during cardiac remodeling from larval to adult stages. To summarize, we have demonstrated how disease-associated genes identified by GWAS can be investigated by combining human cardiomyocyte cell-based and whole-organism in vivo heart models. Our results also suggest a potential link of CNOT1 and CNOT7/8 to QT alterations and further establish a crucial role of the CCR4-NOT complex in heart development and function.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Lisa Elmén
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Claudia B Volpato
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100 Bolzano, Italy
| | - Anaïs Kervadec
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Santiago Pineda
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Sreehari Kalvakuri
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Nakissa N Alayari
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Luisa Foco
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100 Bolzano, Italy
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100 Bolzano, Italy
| | - Karen Ocorr
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Alessandra Rossini
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100 Bolzano, Italy
| | - Anthony Cammarato
- Johns Hopkins University, Division of Cardiology, 720 Rutland Ave., Baltimore, MD 21205, USA
| | - Alexandre R Colas
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100 Bolzano, Italy
| | - Rolf Bodmer
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
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12
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Schroeder AM, Allahyari M, Vogler G, Missinato MA, Nielsen T, Yu MS, Theis JL, Larsen LA, Goyal P, Rosenfeld JA, Nelson TJ, Olson TM, Colas AR, Grossfeld P, Bodmer R. Model system identification of novel congenital heart disease gene candidates: focus on RPL13. Hum Mol Genet 2020; 28:3954-3969. [PMID: 31625562 DOI: 10.1093/hmg/ddz213] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/28/2019] [Accepted: 06/21/2019] [Indexed: 12/12/2022] Open
Abstract
Genetics is a significant factor contributing to congenital heart disease (CHD), but our understanding of the genetic players and networks involved in CHD pathogenesis is limited. Here, we searched for de novo copy number variations (CNVs) in a cohort of 167 CHD patients to identify DNA segments containing potential pathogenic genes. Our search focused on new candidate disease genes within 19 deleted de novo CNVs, which did not cover known CHD genes. For this study, we developed an integrated high-throughput phenotypical platform to probe for defects in cardiogenesis and cardiac output in human induced pluripotent stem cell (iPSC)-derived multipotent cardiac progenitor (MCPs) cells and, in parallel, in the Drosophila in vivo heart model. Notably, knockdown (KD) in MCPs of RPL13, a ribosomal gene and SON, an RNA splicing cofactor, reduced proliferation and differentiation of cardiomyocytes, while increasing fibroblasts. In the fly, heart-specific RpL13 KD, predominantly at embryonic stages, resulted in a striking 'no heart' phenotype. KD of Son and Pdss2, among others, caused structural and functional defects, including reduced or abolished contractility, respectively. In summary, using a combination of human genetics and cardiac model systems, we identified new genes as candidates for causing human CHD, with particular emphasis on ribosomal genes, such as RPL13. This powerful, novel approach of combining cardiac phenotyping in human MCPs and in the in vivo Drosophila heart at high throughput will allow for testing large numbers of CHD candidates, based on patient genomic data, and for building upon existing genetic networks involved in heart development and disease.
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Affiliation(s)
- Analyne M Schroeder
- Development, Aging and Regeneration Program, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Massoud Allahyari
- Department of Pediatrics, UCSD School of Medicine, La Jolla, CA, USA
| | - Georg Vogler
- Development, Aging and Regeneration Program, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Maria A Missinato
- Development, Aging and Regeneration Program, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Tanja Nielsen
- Development, Aging and Regeneration Program, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Michael S Yu
- Development, Aging and Regeneration Program, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Jeanne L Theis
- Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Lars A Larsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Preeya Goyal
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Timothy J Nelson
- Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Timothy M Olson
- Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Alexandre R Colas
- Development, Aging and Regeneration Program, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Paul Grossfeld
- Department of Pediatrics, UCSD School of Medicine, La Jolla, CA, USA
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
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13
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Elmén L, Zlamal JE, Scott DA, Lee RB, Chen DJ, Colas AR, Rodionov DA, Peterson SN. Dietary Emulsifier Sodium Stearoyl Lactylate Alters Gut Microbiota in vitro and Inhibits Bacterial Butyrate Producers. Front Microbiol 2020; 11:892. [PMID: 32499766 PMCID: PMC7243350 DOI: 10.3389/fmicb.2020.00892] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/16/2020] [Indexed: 12/12/2022] Open
Abstract
Dietary emulsifiers are widely used in industrially processed foods, although the effects of these food additives on human gut microbiota are not well studied. Here, we investigated the effects of five different emulsifiers [glycerol monoacetate, glycerol monostearate, glycerol monooleate, propylene glycol monostearate, and sodium stearoyl lactylate (SSL)] on fecal microbiota in vitro. We found that 0.025% (w/v) of SSL reduced the relative abundance of the bacterial class Clostridia and others. The relative abundance of the families Clostridiaceae, Lachnospiraceae, and Ruminococcaceae was substantially reduced whereas that of Bacteroidaceae and Enterobacteriaceae was increased. Given the marked impact of SSL on Clostridia, we used genome reconstruction to predict community-wide production of short-chain fatty acids, which were experimentally assessed by GC-MS analysis. SSL significantly reduced concentrations of butyrate, and increased concentrations of propionate compared to control cultures. The presence of SSL increased lipopolysaccharide, LPS and flagellin in cultured communities, thereby enhancing the proinflammatory potential of SSL-selected bacterial communities.
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Affiliation(s)
- Lisa Elmén
- Tumor Microenvironment and Cancer Immunology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Jaime E Zlamal
- Tumor Microenvironment and Cancer Immunology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - David A Scott
- Tumor Microenvironment and Cancer Immunology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Ryan B Lee
- Tumor Microenvironment and Cancer Immunology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Daniel J Chen
- Tumor Microenvironment and Cancer Immunology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Alexandre R Colas
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Dmitry A Rodionov
- Tumor Microenvironment and Cancer Immunology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States.,A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Scott N Peterson
- Tumor Microenvironment and Cancer Immunology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
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14
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Bruyneel AAN, Colas AR, Karakikes I, Mercola M. AlleleProfileR: A versatile tool to identify and profile sequence variants in edited genomes. PLoS One 2019; 14:e0226694. [PMID: 31877162 PMCID: PMC6932767 DOI: 10.1371/journal.pone.0226694] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 12/02/2019] [Indexed: 12/15/2022] Open
Abstract
Gene editing strategies, such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeat/Cas9 (CRISPR/Cas9), are revolutionizing biology. However, quantitative and sensitive detection of targeted mutations are required to evaluate and quantify the genome editing outcomes. Here we present AlleleProfileR, a new analysis tool, written in a combination of R and C++, with the ability to batch process the sequence analysis of large and complex genome editing experiments, including the recently developed base editing technologies.
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Affiliation(s)
- Arne A. N. Bruyneel
- Stanford Cardiovascular Institute, Stanford School of Medicine, Stanford, CA United States of America
- Department of Medicine, Division of Cardiovascular Medicine, Stanford School of Medicine, Stanford, CA, United States of America
- * E-mail:
| | - Alexandre R. Colas
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States of America
| | - Ioannis Karakikes
- Stanford Cardiovascular Institute, Stanford School of Medicine, Stanford, CA United States of America
- Department of Cardiothoracic Surgery, Stanford School of Medicine, Stanford, CA, United States of America
| | - Mark Mercola
- Stanford Cardiovascular Institute, Stanford School of Medicine, Stanford, CA United States of America
- Department of Medicine, Division of Cardiovascular Medicine, Stanford School of Medicine, Stanford, CA, United States of America
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15
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El Harane N, Kervadec A, Bellamy V, Pidial L, Neametalla HJ, Perier MC, Lima Correa B, Thiébault L, Cagnard N, Duché A, Brunaud C, Lemitre M, Gauthier J, Bourdillon AT, Renault MP, Hovhannisyan Y, Paiva S, Colas AR, Agbulut O, Hagège A, Silvestre JS, Menasché P, Renault NKE. Acellular therapeutic approach for heart failure: in vitro production of extracellular vesicles from human cardiovascular progenitors. Eur Heart J 2019; 39:1835-1847. [PMID: 29420830 DOI: 10.1093/eurheartj/ehy012] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [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] [Received: 01/17/2017] [Accepted: 01/09/2018] [Indexed: 01/15/2023] Open
Abstract
Aims We have shown that extracellular vesicles (EVs) secreted by embryonic stem cell-derived cardiovascular progenitor cells (Pg) recapitulate the therapeutic effects of their parent cells in a mouse model of chronic heart failure (CHF). Our objectives are to investigate whether EV released by more readily available cell sources are therapeutic, whether their effectiveness is influenced by the differentiation state of the secreting cell, and through which mechanisms they act. Methods and results The total EV secreted by human induced pluripotent stem cell-derived cardiovascular progenitors (iPSC-Pg) and human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CM) were isolated by ultracentrifugation and characterized by Nanoparticle Tracking Analysis, western blot, and cryo-electron microscopy. In vitro bioactivity assays were used to evaluate their cellular effects. Cell and EV microRNA (miRNA) content were assessed by miRNA array. Myocardial infarction was induced in 199 nude mice. Three weeks later, mice with left ventricular ejection fraction (LVEF) ≤ 45% received transcutaneous echo-guided injections of iPSC-CM (1.4 × 106, n = 19), iPSC-Pg (1.4 × 106, n = 17), total EV secreted by 1.4 × 106 iPSC-Pg (n = 19), or phosphate-buffered saline (control, n = 17) into the peri-infarct myocardium. Seven weeks later, hearts were evaluated by echocardiography, histology, and gene expression profiling, blinded to treatment group. In vitro, EV were internalized by target cells, increased cell survival, cell proliferation, and endothelial cell migration in a dose-dependent manner and stimulated tube formation. Extracellular vesicles were rich in miRNAs and most of the 16 highly abundant, evolutionarily conserved miRNAs are associated with tissue-repair pathways. In vivo, EV outperformed cell injections, significantly improving cardiac function through decreased left ventricular volumes (left ventricular end systolic volume: -11%, P < 0.001; left ventricular end diastolic volume: -4%, P = 0.002), and increased LVEF (+14%, P < 0.0001) relative to baseline values. Gene profiling revealed that EV-treated hearts were enriched for tissue reparative pathways. Conclusion Extracellular vesicles secreted by iPSC-Pg are effective in the treatment of CHF, possibly, in part, through their specific miRNA signature and the associated stimulation of distinct cardioprotective pathways. The processing and regulatory advantages of EV could make them effective substitutes for cell transplantation.
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Affiliation(s)
- Nadia El Harane
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-970, Paris Centre de Recherche Cardiovasculaire, 56, rue Leblanc, 75015 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Anaïs Kervadec
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-970, Paris Centre de Recherche Cardiovasculaire, 56, rue Leblanc, 75015 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Valérie Bellamy
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-970, Paris Centre de Recherche Cardiovasculaire, 56, rue Leblanc, 75015 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Laetitia Pidial
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-970, Paris Centre de Recherche Cardiovasculaire, 56, rue Leblanc, 75015 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Hany J Neametalla
- Department of Cardiology, Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, 20, rue Leblanc, 75015 Paris, France
| | - Marie-Cécile Perier
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-970, Paris Centre de Recherche Cardiovasculaire, 56, rue Leblanc, 75015 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Bruna Lima Correa
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-970, Paris Centre de Recherche Cardiovasculaire, 56, rue Leblanc, 75015 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Léa Thiébault
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-970, Paris Centre de Recherche Cardiovasculaire, 56, rue Leblanc, 75015 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Nicolas Cagnard
- Université Paris Descartes, US 024 SFR Necker, 24 Boulevard du Montparnasse, 75015 Paris, France
| | - Angéline Duché
- Institut National de la Santé et de la Recherche Médicale (INSERM), U 1016, Institut Cochin, Université Paris Descartes, Sorbonne Paris Cité, 22 rue Mechain, 75014 Paris, France.,CNRS, Université Paris Descartes, UMR-8104, Paris, France
| | - Camille Brunaud
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Mathilde Lemitre
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-970, Paris Centre de Recherche Cardiovasculaire, 56, rue Leblanc, 75015 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Jeanne Gauthier
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-970, Paris Centre de Recherche Cardiovasculaire, 56, rue Leblanc, 75015 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Ecole normale supérieure, PSL Research University Paris, 45 rue d'Ulm, 75005 Paris, France
| | | | - Marc P Renault
- IRIF, Université Paris Diderot-Paris 7, UMR 8243, Bâtiment Sophie Germain, 8 place Aurélie Nemours, 75013 Paris, France
| | - Yeranuhi Hovhannisyan
- Sorbonne Universités, UPMC Université de Paris-6, Institut de Biologie Paris-Seine (IBPS), UMR CNRS 8256, Biological Adaptation and Ageing, 4 Place Jussieu, 75005 Paris, France
| | - Solenne Paiva
- Sorbonne Universités, UPMC Université de Paris-6, Institut de Biologie Paris-Seine (IBPS), UMR CNRS 8256, Biological Adaptation and Ageing, 4 Place Jussieu, 75005 Paris, France
| | - Alexandre R Colas
- Sanford Burnham Prebys Medical Discovery Institute, Development, Aging and Regeneration Program, 10901 N Torrey Pines Rd, La Jolla, 92037 CA, USA
| | - Onnik Agbulut
- Sorbonne Universités, UPMC Université de Paris-6, Institut de Biologie Paris-Seine (IBPS), UMR CNRS 8256, Biological Adaptation and Ageing, 4 Place Jussieu, 75005 Paris, France
| | - Albert Hagège
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-970, Paris Centre de Recherche Cardiovasculaire, 56, rue Leblanc, 75015 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Department of Cardiology, Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, 20, rue Leblanc, 75015 Paris, France
| | - Jean-Sébastien Silvestre
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-970, Paris Centre de Recherche Cardiovasculaire, 56, rue Leblanc, 75015 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Philippe Menasché
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-970, Paris Centre de Recherche Cardiovasculaire, 56, rue Leblanc, 75015 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Department of Cardiovascular Surgery, Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, 20, rue Leblanc, 75015 Paris, France
| | - Nisa K E Renault
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-970, Paris Centre de Recherche Cardiovasculaire, 56, rue Leblanc, 75015 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
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16
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Yu MS, Spiering S, Colas AR. Generation of First Heart Field-like Cardiac Progenitors and Ventricular-like Cardiomyocytes from Human Pluripotent Stem Cells. J Vis Exp 2018:57688. [PMID: 29985326 PMCID: PMC6101765 DOI: 10.3791/57688] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The generation of large amounts of functional human pluripotent stem cells-derived cardiac progenitors and cardiomyocytes of defined heart field origin is a pre-requisite for cell-based cardiac therapies and disease modeling. We have recently shown that Id genes are both necessary and sufficient to specify first heart field progenitors during vertebrate development. This differentiation protocol leverages these findings and uses Id1 overexpression in combination with Activin A as potent specifying cues to produce first heart field-like (FHF-L) progenitors. Importantly, resulting progenitors efficiently differentiate (~70-90%) into ventricular-like cardiomyocytes. Here we describe a detailed method to 1) generate Id1-overexpressing hPSCs and 2) differentiate scalable quantities of cryopreservable FHF-L progenitors and ventricular-like cardiomyocytes.
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Affiliation(s)
- Michael S Yu
- Sanford Burnham Prebys Medical Discovery Institute; Department of Bioengineering, University of California at San Diego
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17
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McKeithan WL, Savchenko A, Yu MS, Cerignoli F, Bruyneel AAN, Price JH, Colas AR, Miller EW, Cashman JR, Mercola M. An Automated Platform for Assessment of Congenital and Drug-Induced Arrhythmia with hiPSC-Derived Cardiomyocytes. Front Physiol 2017; 8:766. [PMID: 29075196 PMCID: PMC5641590 DOI: 10.3389/fphys.2017.00766] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 09/19/2017] [Indexed: 12/12/2022] Open
Abstract
The ability to produce unlimited numbers of human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) harboring disease and patient-specific gene variants creates a new paradigm for modeling congenital heart diseases (CHDs) and predicting proarrhythmic liabilities of drug candidates. However, a major roadblock to implementing hiPSC-CM technology in drug discovery is that conventional methods for monitoring action potential (AP) kinetics and arrhythmia phenotypes in vitro have been too costly or technically challenging to execute in high throughput. Herein, we describe the first large-scale, fully automated and statistically robust analysis of AP kinetics and drug-induced proarrhythmia in hiPSC-CMs. The platform combines the optical recording of a small molecule fluorescent voltage sensing probe (VoltageFluor2.1.Cl), an automated high throughput microscope and automated image analysis to rapidly generate physiological measurements of cardiomyocytes (CMs). The technique can be readily adapted on any high content imager to study hiPSC-CM physiology and predict the proarrhythmic effects of drug candidates.
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Affiliation(s)
- Wesley L McKeithan
- Department of Medicine, Cardiovascular Institute, Stanford University, Stanford, CA, United States.,Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Alex Savchenko
- Department of Medicine, Cardiovascular Institute, Stanford University, Stanford, CA, United States
| | - Michael S Yu
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States.,Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | | | - Arne A N Bruyneel
- Department of Medicine, Cardiovascular Institute, Stanford University, Stanford, CA, United States
| | | | - Alexandre R Colas
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Evan W Miller
- Departments of Chemistry, Molecular and Cell Biology, Helen Wills Neuroscience, University of California, Berkeley, Berkeley, CA, United States
| | - John R Cashman
- Human BioMolecular Research Institute, San Diego, CA, United States
| | - Mark Mercola
- Department of Medicine, Cardiovascular Institute, Stanford University, Stanford, CA, United States
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18
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Cunningham TJ, Yu MS, McKeithan WL, Spiering S, Carrette F, Huang CT, Bushway PJ, Tierney M, Albini S, Giacca M, Mano M, Puri PL, Sacco A, Ruiz-Lozano P, Riou JF, Umbhauer M, Duester G, Mercola M, Colas AR. Id genes are essential for early heart formation. Genes Dev 2017; 31:1325-1338. [PMID: 28794185 PMCID: PMC5580654 DOI: 10.1101/gad.300400.117] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/17/2017] [Indexed: 01/08/2023]
Abstract
Deciphering the fundamental mechanisms controlling cardiac specification is critical for our understanding of how heart formation is initiated during embryonic development and for applying stem cell biology to regenerative medicine and disease modeling. Using systematic and unbiased functional screening approaches, we discovered that the Id family of helix-loop-helix proteins is both necessary and sufficient to direct cardiac mesoderm formation in frog embryos and human embryonic stem cells. Mechanistically, Id proteins specify cardiac cell fate by repressing two inhibitors of cardiogenic mesoderm formation-Tcf3 and Foxa2-and activating inducers Evx1, Grrp1, and Mesp1. Most importantly, CRISPR/Cas9-mediated ablation of the entire Id (Id1-4) family in mouse embryos leads to failure of anterior cardiac progenitor specification and the development of heartless embryos. Thus, Id proteins play a central and evolutionarily conserved role during heart formation and provide a novel means to efficiently produce cardiovascular progenitors for regenerative medicine and drug discovery applications.
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Affiliation(s)
- Thomas J Cunningham
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Michael S Yu
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA.,Department of Bioengineering, University of California at San Diego, La Jolla, California 92037, USA
| | - Wesley L McKeithan
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA.,Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA.,Department of Medicine and Cardiovascular Institute, Stanford University, Palo Alto, California 94305, USA
| | - Sean Spiering
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Florent Carrette
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Chun-Teng Huang
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Paul J Bushway
- Department of Bioengineering, University of California at San Diego, La Jolla, California 92037, USA
| | - Matthew Tierney
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Sonia Albini
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Mauro Giacca
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
| | - Miguel Mano
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Pier Lorenzo Puri
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA.,Istituti di Ricovero e Cura a Carattere Scientifico, Fondazione Santa Lucia, 00179 Rome, Italy
| | - Alessandra Sacco
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Pilar Ruiz-Lozano
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA.,Regencor, Inc., Los Altos, California 94022, USA
| | - Jean-Francois Riou
- UMR 7622 Developmental Biology, Sorbonne Universités, University Pierre and Marie Curie, F- 75005 Paris, France
| | - Muriel Umbhauer
- UMR 7622 Developmental Biology, Sorbonne Universités, University Pierre and Marie Curie, F- 75005 Paris, France
| | - Gregg Duester
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Mark Mercola
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA.,Department of Medicine and Cardiovascular Institute, Stanford University, Palo Alto, California 94305, USA
| | - Alexandre R Colas
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
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19
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McKeithan WL, Colas AR, Bushway PJ, Ray S, Mercola M. Serum-free generation of multipotent mesoderm (Kdr+) progenitor cells in mouse embryonic stem cells for functional genomics screening. ACTA ACUST UNITED AC 2013; Chapter 1:Unit 1F.13. [PMID: 23154934 DOI: 10.1002/9780470151808.sc01f13s23] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This unit describes a robust protocol for producing multipotent Kdr-expressing mesoderm progenitor cells in serum-free conditions, and for functional genomics screening using these cells. Kdr-positive cells are able to differentiate into a wide array of mesodermal derivatives, including vascular endothelial cells, cardiomyocytes, hematopoietic progenitors, and smooth muscle cells. The efficient generation of such progenitor cells is of particular interest because it permits subsequent steps in cardiovascular development to be analyzed in detail, including deciphering the mechanisms that direct differentiation. In addition, the oligonucleotide transfection protocol used to functionally screen siRNA and miRNA libraries is a powerful tool to reveal networks of genes, signaling proteins, and miRNAs that control the diversification of cardiovascular lineages from multipotent progenitors. Technical limitations, troubleshooting, and potential applications of these methods are discussed.
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20
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Colas AR, McKeithan WL, Cunningham TJ, Bushway PJ, Garmire LX, Duester G, Subramaniam S, Mercola M. Whole-genome microRNA screening identifies let-7 and mir-18 as regulators of germ layer formation during early embryogenesis. Genes Dev 2012; 26:2567-79. [PMID: 23152446 DOI: 10.1101/gad.200758.112] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Tight control over the segregation of endoderm, mesoderm, and ectoderm is essential for normal embryonic development of all species, yet how neighboring embryonic blastomeres can contribute to different germ layers has never been fully explained. We postulated that microRNAs, which fine-tune many biological processes, might modulate the response of embryonic blastomeres to growth factors and other signals that govern germ layer fate. A systematic screen of a whole-genome microRNA library revealed that the let-7 and miR-18 families increase mesoderm at the expense of endoderm in mouse embryonic stem cells. Both families are expressed in ectoderm and mesoderm, but not endoderm, as these tissues become distinct during mouse and frog embryogenesis. Blocking let-7 function in vivo dramatically affected cell fate, diverting presumptive mesoderm and ectoderm into endoderm. siRNA knockdown of computationally predicted targets followed by mutational analyses revealed that let-7 and miR-18 down-regulate Acvr1b and Smad2, respectively, to attenuate Nodal responsiveness and bias blastomeres to ectoderm and mesoderm fates. These findings suggest a crucial role for the let-7 and miR-18 families in germ layer specification and reveal a remarkable conservation of function from amphibians to mammals.
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