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Kobeissi H, Gao X, DePalma SJ, Ewoldt JK, Wang MC, Das SL, Jilberto J, Nordsletten D, Baker BM, Chen CS, Lejeune E. MicroBundlePillarTrack: A Python package for automated segmentation, tracking, and analysis of pillar deflection in cardiac microbundles. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001231. [PMID: 39114859 PMCID: PMC11304080 DOI: 10.17912/micropub.biology.001231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/18/2024] [Accepted: 07/10/2024] [Indexed: 08/10/2024]
Abstract
Movies of human induced pluripotent stem cell (hiPSC)-derived engineered cardiac tissue (microbundles) contain abundant information about structural and functional maturity. However, extracting these data in a reproducible and high-throughput manner remains a major challenge. Furthermore, it is not straightforward to make direct quantitative comparisons across the multiple in vitro experimental platforms employed to fabricate these tissues. Here, we present "MicroBundlePillarTrack," an open-source optical flow-based package developed in Python to track the deflection of pillars in cardiac microbundles grown on experimental platforms with two different pillar designs ("Type 1" and "Type 2" design). Our software is able to automatically segment the pillars, track their displacements, and output time-dependent metrics for contractility analysis, including beating amplitude and rate, contractile force, and tissue stress. Because this software is fully automated, it will allow for both faster and more reproducible analyses of larger datasets and it will enable more reliable cross-platform comparisons as compared to existing approaches that require manual steps and are tailored to a specific experimental platform. To complement this open-source software, we share a dataset of 1,540 brightfield example movies on which we have tested our software. Through sharing this data and software, our goal is to directly enable quantitative comparisons across labs, and facilitate future collective progress via the biomedical engineering open-source data and software ecosystem.
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Affiliation(s)
- Hiba Kobeissi
- Department of Mechanical Engineering, Center for Multiscale and Translational Mechanobiology, Boston University, Boston, Massachusetts, United States
| | - Xining Gao
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States
- Institute for Medical Engineering and Science, Harvard–MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, United States
| | - Samuel J. DePalma
- Department of Biomedical Engineering, University of Michigan–Ann Arbor, Ann Arbor, Michigan, United States
| | - Jourdan K. Ewoldt
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States
| | - Miranda C. Wang
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States
- Institute for Medical Engineering and Science, Harvard–MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, United States
| | - Shoshana L. Das
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States
- Institute for Medical Engineering and Science, Harvard–MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, United States
| | - Javiera Jilberto
- Department of Biomedical Engineering, University of Michigan–Ann Arbor, Ann Arbor, Michigan, United States
| | - David Nordsletten
- Department of Biomedical Engineering, University of Michigan–Ann Arbor, Ann Arbor, Michigan, United States
- Department of Cardiac Surgery, University of Michigan–Ann Arbor, Ann Arbor, Michigan, United States
- School of Imaging Sciences and Biomedical Engineering, King’s Health Partners, King's College London, London, England, United Kingdom
| | - Brendon M. Baker
- Department of Biomedical Engineering, University of Michigan–Ann Arbor, Ann Arbor, Michigan, United States
| | - Christopher S. Chen
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, United States
| | - Emma Lejeune
- Department of Mechanical Engineering, Center for Multiscale and Translational Mechanobiology, Boston University, Boston, Massachusetts, United States
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Jilberto J, DePalma SJ, Lo J, Kobeissi H, Quach L, Lejeune E, Baker BM, Nordsletten D. A data-driven computational model for engineered cardiac microtissues. Acta Biomater 2023; 172:123-134. [PMID: 37879587 PMCID: PMC10938557 DOI: 10.1016/j.actbio.2023.10.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 10/27/2023]
Abstract
Engineered heart tissues (EHTs) present a potential solution to some of the current challenges in the treatment of heart disease; however, the development of mature, adult-like cardiac tissues remains elusive. Mechanical stimuli have been observed to improve whole-tissue function and cardiomyocyte (CM) maturation, although our ability to fully utilize these mechanisms is hampered, in part, by our incomplete understanding of the mechanobiology of EHTs. In this work, we leverage experimental data, produced by a mechanically tunable experimental setup, to introduce a tissue-specific computational modeling pipeline of EHTs. Our new modeling pipeline generates simulated, image-based EHTs, capturing ECM and myofibrillar structure as well as functional parameters estimated directly from experimental data. This approach enables the unique estimation of EHT function by data-based estimation of CM active stresses. We use this experimental and modeling pipeline to study different mechanical environments, where we contrast the force output of the tissue with the computed active stress of CMs. We show that the significant differences in measured experimental forces can largely be explained by the levels of myofibril formation achieved by the CMs in the distinct mechanical environments, with active stress showing more muted variations across conditions. The presented model also enables us to dissect the relative contributions of myofibrils and extracellular matrix to tissue force output, a task difficult to address experimentally. These results highlight the importance of tissue-specific modeling to augment EHT experiments, providing deeper insights into the mechanobiology driving EHT function. STATEMENT OF SIGNIFICANCE: Engineered heart tissues (EHTs) have the potential to revolutionize the way heart disease is treated. However, developing mature cardiomyocytes (CM) in these tissues remains a challenge due, in part, to our incomplete understanding of the fundamental biomechanical mechanisms that drive EHT development. This work integrates the experimental data of an EHT platform developed to study the influence of mechanics in CM maturation with computational biomechanical models. This approach is used to augment conclusions obtained in-vitro - by measuring quantities such as cell stress and strain - and to dissect the relevance of each component in the whole tissue performance. Our results show how a combination of specialized in-silico and in-vitro approaches can help us better understand the mechanobiology of EHTs.
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Affiliation(s)
- Javiera Jilberto
- Department of Biomedical Engineering, University of Michigan, MI, USA.
| | - Samuel J DePalma
- Department of Biomedical Engineering, University of Michigan, MI, USA
| | - Jason Lo
- Department of Biomedical Engineering, University of Michigan, MI, USA
| | - Hiba Kobeissi
- Department of Mechanical Engineering, Boston University, MA, USA
| | - Lani Quach
- Department of Biomedical Engineering, University of Michigan, MI, USA
| | - Emma Lejeune
- Department of Mechanical Engineering, Boston University, MA, USA
| | - Brendon M Baker
- Department of Biomedical Engineering, University of Michigan, MI, USA
| | - David Nordsletten
- Department of Biomedical Engineering, University of Michigan, MI, USA; Department of Cardiac Surgery, University of Michigan, MI, USA; Department of Biomedical Engineering, School of Imaging Sciences and Biomedical Engineering, King's College London, London, UK
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Balasubramanian H, Hobson CM, Chew TL, Aaron JS. Imagining the future of optical microscopy: everything, everywhere, all at once. Commun Biol 2023; 6:1096. [PMID: 37898673 PMCID: PMC10613274 DOI: 10.1038/s42003-023-05468-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023] Open
Abstract
The optical microscope has revolutionized biology since at least the 17th Century. Since then, it has progressed from a largely observational tool to a powerful bioanalytical platform. However, realizing its full potential to study live specimens is hindered by a daunting array of technical challenges. Here, we delve into the current state of live imaging to explore the barriers that must be overcome and the possibilities that lie ahead. We venture to envision a future where we can visualize and study everything, everywhere, all at once - from the intricate inner workings of a single cell to the dynamic interplay across entire organisms, and a world where scientists could access the necessary microscopy technologies anywhere.
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Affiliation(s)
| | - Chad M Hobson
- Advanced Imaging Center; Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Teng-Leong Chew
- Advanced Imaging Center; Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Jesse S Aaron
- Advanced Imaging Center; Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, 20147, USA.
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Arzt M, Pohlman S, Mozneb M, Sharma A. Chemically Defined Production of Tri-Lineage Human iPSC-Derived Cardiac Spheroids. Curr Protoc 2023; 3:e767. [PMID: 37154466 PMCID: PMC11215757 DOI: 10.1002/cpz1.767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Cardiac spheroids derived from human induced pluripotent stem cells (hiPSC-cardiac spheroids) represent a powerful three-dimensional (3D) model for examining cardiac physiology and for drug toxicity screening. Recent advances with self-organizing, multicellular cardiac organoids highlight the capability of directed stem cell differentiation approaches to recapitulate the composition of the human heart in vitro. Using hiPSC-derived cardiomyocytes (hiPSC-CMs), hiPSC-derived endothelial cells (hiPSC-ECs), and hiPSC-derived cardiac fibroblasts (hiPSC-CFs) is advantageous for enabling tri-cellular crosstalk within a multilineage system and for generating patient-specific models. Chemically defined medium containing factors needed to simultaneously maintain hiPSC-CMs, hiPSC-ECs, and hiPSC-CFs is used to produce the spheroid system. In this article, we present protocols to illustrate the methods for conducting small-molecule-mediated differentiations of hiPSCs into cardiomyocytes, endothelial cells, and cardiac fibroblasts, as well as to assemble the fully integrated cardiac spheroids. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Maintenance and expansion of hiPSCs Basic Protocol 2: Differentiation of hiPSCs into cardiomyocytes Basic Protocol 3: Differentiation of hiPSCs into vascular endothelial cells Basic Protocol 4: Differentiation of hiPSCs into cardiac fibroblasts Basic Protocol 5: Production of hiPSC-derived cardiac spheroids.
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Affiliation(s)
- Madelyn Arzt
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Stephany Pohlman
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- CIRM Bridges to Stem Cell Research Program, California State University, Channel Islands, CA, USA
| | - Maedeh Mozneb
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Arun Sharma
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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5
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Pintacuda G, Hsu YHH, Tsafou K, Li KW, Martín JM, Riseman J, Biagini JC, Ching JK, Mena D, Gonzalez-Lozano MA, Egri SB, Jaffe J, Smit AB, Fornelos N, Eggan KC, Lage K. Protein interaction studies in human induced neurons indicate convergent biology underlying autism spectrum disorders. CELL GENOMICS 2023; 3:100250. [PMID: 36950384 PMCID: PMC10025425 DOI: 10.1016/j.xgen.2022.100250] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 10/18/2022] [Accepted: 12/28/2022] [Indexed: 01/26/2023]
Abstract
Autism spectrum disorders (ASDs) have been linked to genes with enriched expression in the brain, but it is unclear how these genes converge into cell-type-specific networks. We built a protein-protein interaction network for 13 ASD-associated genes in human excitatory neurons derived from induced pluripotent stem cells (iPSCs). The network contains newly reported interactions and is enriched for genetic and transcriptional perturbations observed in individuals with ASDs. We leveraged the network data to show that the ASD-linked brain-specific isoform of ANK2 is important for its interactions with synaptic proteins and to characterize a PTEN-AKAP8L interaction that influences neuronal growth. The IGF2BP1-3 complex emerged as a convergent point in the network that may regulate a transcriptional circuit of ASD-associated genes. Our findings showcase cell-type-specific interactomes as a framework to complement genetic and transcriptomic data and illustrate how both individual and convergent interactions can lead to biological insights into ASDs.
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Affiliation(s)
- Greta Pintacuda
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yu-Han H. Hsu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kalliopi Tsafou
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ka Wan Li
- Department of Molecular and Cellular Neurobiology, CNCR, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Jacqueline M. Martín
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Jackson Riseman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Julia C. Biagini
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joshua K.T. Ching
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daya Mena
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Miguel A. Gonzalez-Lozano
- Department of Molecular and Cellular Neurobiology, CNCR, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Shawn B. Egri
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jake Jaffe
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology, CNCR, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Nadine Fornelos
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kevin C. Eggan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kasper Lage
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, 4000 Roskilde, Denmark
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Multi-Omics Profiling of Hypertrophic Cardiomyopathy Reveals Altered Mechanisms in Mitochondrial Dynamics and Excitation-Contraction Coupling. Int J Mol Sci 2023; 24:ijms24054724. [PMID: 36902152 PMCID: PMC10002553 DOI: 10.3390/ijms24054724] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Hypertrophic cardiomyopathy is one of the most common inherited cardiomyopathies and a leading cause of sudden cardiac death in young adults. Despite profound insights into the genetics, there is imperfect correlation between mutation and clinical prognosis, suggesting complex molecular cascades driving pathogenesis. To investigate this, we performed an integrated quantitative multi-omics (proteomic, phosphoproteomic, and metabolomic) analysis to illuminate the early and direct consequences of mutations in myosin heavy chain in engineered human induced pluripotent stem-cell-derived cardiomyocytes relative to late-stage disease using patient myectomies. We captured hundreds of differential features, which map to distinct molecular mechanisms modulating mitochondrial homeostasis at the earliest stages of pathobiology, as well as stage-specific metabolic and excitation-coupling maladaptation. Collectively, this study fills in gaps from previous studies by expanding knowledge of the initial responses to mutations that protect cells against the early stress prior to contractile dysfunction and overt disease.
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7
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Romero JC, Berlinicke C, Chow S, Duan Y, Wang Y, Chamling X, Smirnova L. Oligodendrogenesis and myelination tracing in a CRISPR/Cas9-engineered brain microphysiological system. Front Cell Neurosci 2023; 16:1094291. [PMID: 36744062 PMCID: PMC9893511 DOI: 10.3389/fncel.2022.1094291] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/16/2022] [Indexed: 01/20/2023] Open
Abstract
Introduction Oligodendrocytes (OLs) are the myelin-forming cells of the central nervous system (CNS). Although OLs can be differentiated from human-induced pluripotent stem cells (hiPSCs), the in vitro modeling of axon myelination in human cells remains challenging. Brain microphysiological systems (bMPS, e.g. organoids) are complex three-dimensional (3D) cultures that offer an ideal system to study this process as OLs differentiate in a more in vivo-like environment; surrounded by neurons and astrocytes, which support the myelination of axons. Methods Here, we take advantage of CRISPR/Cas9 technology to generate a hiPSC line in which proteolipid protein 1 (PLP1), an OLs marker, is tagged with super-fold GFP (sfGFP). While generating the PLP1-sfGFP reporter, we used reverse transfection and obtained higher Knock-In (KI) efficiency compared to forward transfection (61-72 vs. 46%). Results After validation of the KI and quality control of the PLP1-sfGFP line, selected clones were differentiated into bMPS, and the fidelity, specificity, and function of the tagged PLP protein were verified in this model. We tracked different stages of oligodendrogenesis in the verified lines based on PLP1-sfGFP+ cells' morphology, and the presence of PLP1-sfGFP surrounding axons during bMPS' differentiation. Finally, we challenged the bMPS with cuprizone and quantified changes in both the percentage of PLP1-sfGFP expressing cells and the intensity of GFP expression. Discussion This work demonstrates an efficient method for generating hiPSC KI lines and the description of a new 3D model to study OL differentiation, migration, and maturation both during in vitro neurodevelopment as well as in response to environmental chemicals or disease-associated stressors.
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Affiliation(s)
- July Carolina Romero
- Bloomberg School of Public Health, Center for Alternatives to Animal Testing, Johns Hopkins University, Baltimore, MD, United States
| | - Cynthia Berlinicke
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Sharon Chow
- Bloomberg School of Public Health, Center for Alternatives to Animal Testing, Johns Hopkins University, Baltimore, MD, United States
| | - Yukan Duan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Yifei Wang
- Bloomberg School of Public Health, Center for Alternatives to Animal Testing, Johns Hopkins University, Baltimore, MD, United States
| | - Xitiz Chamling
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Lena Smirnova
- Bloomberg School of Public Health, Center for Alternatives to Animal Testing, Johns Hopkins University, Baltimore, MD, United States
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8
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Mechanism based therapies enable personalised treatment of hypertrophic cardiomyopathy. Sci Rep 2022; 12:22501. [PMID: 36577774 PMCID: PMC9797561 DOI: 10.1038/s41598-022-26889-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 12/21/2022] [Indexed: 12/29/2022] Open
Abstract
Cardiomyopathies have unresolved genotype-phenotype relationships and lack disease-specific treatments. Here we provide a framework to identify genotype-specific pathomechanisms and therapeutic targets to accelerate the development of precision medicine. We use human cardiac electromechanical in-silico modelling and simulation which we validate with experimental hiPSC-CM data and modelling in combination with clinical biomarkers. We select hypertrophic cardiomyopathy as a challenge for this approach and study genetic variations that mutate proteins of the thick (MYH7R403Q/+) and thin filaments (TNNT2R92Q/+, TNNI3R21C/+) of the cardiac sarcomere. Using in-silico techniques we show that the destabilisation of myosin super relaxation observed in hiPSC-CMs drives disease in virtual cells and ventricles carrying the MYH7R403Q/+ variant, and that secondary effects on thin filament activation are necessary to precipitate slowed relaxation of the cell and diastolic insufficiency in the chamber. In-silico modelling shows that Mavacamten corrects the MYH7R403Q/+ phenotype in agreement with hiPSC-CM experiments. Our in-silico model predicts that the thin filament variants TNNT2R92Q/+ and TNNI3R21C/+ display altered calcium regulation as central pathomechanism, for which Mavacamten provides incomplete salvage, which we have corroborated in TNNT2R92Q/+ and TNNI3R21C/+ hiPSC-CMs. We define the ideal characteristics of a novel thin filament-targeting compound and show its efficacy in-silico. We demonstrate that hybrid human-based hiPSC-CM and in-silico studies accelerate pathomechanism discovery and classification testing, improving clinical interpretation of genetic variants, and directing rational therapeutic targeting and design.
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9
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Agarwal R, Wakimoto H, Paulo JA, Zhang Q, Reichart D, Toepfer C, Sharma A, Tai AC, Lun M, Gorham J, DePalma SR, Gygi SP, Seidman J, Seidman CE. Pathogenesis of Cardiomyopathy Caused by Variants in ALPK3, an Essential Pseudokinase in the Cardiomyocyte Nucleus and Sarcomere. Circulation 2022; 146:1674-1693. [PMID: 36321451 PMCID: PMC9698156 DOI: 10.1161/circulationaha.122.059688] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND ALPK3 encodes α-kinase 3, a muscle-specific protein of unknown function. ALPK3 loss-of-function variants cause cardiomyopathy with distinctive clinical manifestations in both children and adults, but the molecular functions of ALPK3 remain poorly understood. METHODS We explored the putative kinase activity of ALPK3 and the consequences of damaging variants using isogenic human induced pluripotent stem cell-derived cardiomyocytes, mice, and human patient tissues. RESULTS Multiple sequence alignment of all human α-kinase domains and their orthologs revealed 4 conserved residues that were variant only in ALPK3, demonstrating evolutionary divergence of the ALPK3 α-kinase domain sequence. Phosphoproteomic evaluation of both ALPK3 kinase domain inhibition and overexpression failed to detect significant changes in catalytic activity, establishing ALPK3 as a pseudokinase. Investigations into alternative functions revealed that ALPK3 colocalized with myomesin proteins (MYOM1, MYOM2) at both the nuclear envelope and the sarcomere M-band. ALPK3 loss-of-function variants caused myomesin proteins to mislocalize and also dysregulated several additional M-band proteins involved in sarcomere protein turnover, which ultimately impaired cardiomyocyte structure and function. CONCLUSIONS ALPK3 is an essential cardiac pseudokinase that inserts in the nuclear envelope and the sarcomere M-band. Loss of ALPK3 causes mislocalization of myomesins, critical force-buffering proteins in cardiomyocytes, and also dysregulates M-band proteins necessary for sarcomere protein turnover. We conclude that ALPK3 cardiomyopathy induces ventricular dilatation caused by insufficient myomesin-mediated force buffering and hypertrophy by impairment of sarcomere proteostasis.
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Affiliation(s)
- Radhika Agarwal
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
| | - Hiroko Wakimoto
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
| | - Joao A. Paulo
- Department of Cell Biology (J.A.P., S.P.G.), Harvard Medical School, Boston, MA
| | - Qi Zhang
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
| | - Daniel Reichart
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
| | - Christopher Toepfer
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA.,Radcliffe Department of Medicine (C.T.), University of Oxford, United Kingdom.,Wellcome Centre for Human Genetics (C.T.), University of Oxford, United Kingdom
| | - Arun Sharma
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA.,Board of Governors Regenerative Medicine Institute (A.S.), Cedars-Sinai Medical Center, Los Angeles, CA.,Smidt Heart Institute (A.S.), Cedars-Sinai Medical Center, Los Angeles, CA.,Department of Biomedical Sciences (A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
| | - Angela C. Tai
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
| | - Mingyue Lun
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
| | - Joshua Gorham
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
| | - Steven R. DePalma
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
| | - Steven P. Gygi
- Department of Cell Biology (J.A.P., S.P.G.), Harvard Medical School, Boston, MA
| | - J.G. Seidman
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
| | - Christine E. Seidman
- Department of Genetics (R.A., H.W., Q.Z., D.R., C.T., A.S., A.C.T., M.L., J.G., S.R.D., J.G.S., C.E.S.), Harvard Medical School, Boston, MA.,Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, MA (C.E.S.).,Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
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10
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Das SL, Sutherland BP, Lejeune E, Eyckmans J, Chen CS. Mechanical response of cardiac microtissues to acute localized injury. Am J Physiol Heart Circ Physiol 2022; 323:H738-H748. [PMID: 36053751 DOI: 10.1152/ajpheart.00305.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
After a myocardial infarction (MI), the heart undergoes changes including local remodeling that can lead to regional abnormalities in mechanical and electrical properties, ultimately increasing the risk of arrythmias and heart failure. While these responses have been successfully recapitulated in animal models of MI, local changes in tissue and cell-level mechanics caused by MI remain difficult to study in vivo. Here, we developed an in vitro cardiac microtissue (CMT) injury system which through acute focal injury recapitulates aspects of the regional responses seen following an MI. Using a pulsed laser, cell death was induced in the center of the microtissue causing a loss of calcium signaling and a complete loss of contractile function in the injured region and resulting in a 39% reduction in the CMT's overall force production. After 7 days, the injured area remained void of CMs and showed increased expression of vimentin and fibronectin, two markers for fibrotic remodeling. Interestingly, while the injured region showed minimal recovery, calcium amplitudes in uninjured regions returned to levels comparable to control. Furthermore, overall force production returned to pre-injury levels despite the lack of contractile function in the injured region. Instead, uninjured regions exhibited elevated contractile function, compensating for the loss of function in the injured region, drawing parallels to changes in tissue-level mechanics seen in vivo. Overall, this work presents a new in vitro model to study cardiac tissue remodeling and electromechanical changes after injury.
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Affiliation(s)
- Shoshana L Das
- Harvard-MIT Program in Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, United States.,Department of Biomedical Engineering, Boston University, Boston, MA, United States.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States
| | - Bryan P Sutherland
- Department of Biomedical Engineering, Boston University, Boston, MA, United States.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States
| | - Emma Lejeune
- Department of Mechanical Engineering, Boston University, Boston, MA, United States
| | - Jeroen Eyckmans
- Department of Biomedical Engineering, Boston University, Boston, MA, United States.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States
| | - Christopher S Chen
- Department of Biomedical Engineering, Boston University, Boston, MA, United States.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States
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11
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Mao Q, Acharya A, Rodríguez-delaRosa A, Marchiano F, Dehapiot B, Al Tanoury Z, Rao J, Díaz-Cuadros M, Mansur A, Wagner E, Chardes C, Gupta V, Lenne PF, Habermann BH, Theodoly O, Pourquié O, Schnorrer F. Tension-driven multi-scale self-organisation in human iPSC-derived muscle fibers. eLife 2022; 11:76649. [PMID: 35920628 PMCID: PMC9377800 DOI: 10.7554/elife.76649] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
Human muscle is a hierarchically organised tissue with its contractile cells called myofibers packed into large myofiber bundles. Each myofiber contains periodic myofibrils built by hundreds of contractile sarcomeres that generate large mechanical forces. To better understand the mechanisms that coordinate human muscle morphogenesis from tissue to molecular scales, we adopted a simple in vitro system using induced pluripotent stem cell-derived human myogenic precursors. When grown on an unrestricted two-dimensional substrate, developing myofibers spontaneously align and self-organise into higher-order myofiber bundles, which grow and consolidate to stable sizes. Following a transcriptional boost of sarcomeric components, myofibrils assemble into chains of periodic sarcomeres that emerge across the entire myofiber. More efficient myofiber bundling accelerates the speed of sarcomerogenesis suggesting that tension generated by bundling promotes sarcomerogenesis. We tested this hypothesis by directly probing tension and found that tension build-up precedes sarcomere assembly and increases within each assembling myofibril. Furthermore, we found that myofiber ends stably attach to other myofibers using integrin-based attachments and thus myofiber bundling coincides with stable myofiber bundle attachment in vitro. A failure in stable myofiber attachment results in a collapse of the myofibrils. Overall, our results strongly suggest that mechanical tension across sarcomeric components as well as between differentiating myofibers is key to coordinate the multi-scale self-organisation of muscle morphogenesis.
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Affiliation(s)
- Qiyan Mao
- Turing Centre for Living Systems, Aix Marseille University, CNRS, IDBM, Marseille, France
| | - Achyuth Acharya
- Turing Centre for Living Systems, Aix Marseille University, CNRS, IDBM, Marseille, France
| | | | - Fabio Marchiano
- Turing Centre for Living Systems, Aix Marseille University, CNRS, IDBM, Marseille, France
| | - Benoit Dehapiot
- Turing Centre for Living Systems, Aix Marseille University, CNRS, IDBM, Marseille, France
| | - Ziad Al Tanoury
- Department of Pathology, Brigham and Women's Hospital, Boston, United States
| | - Jyoti Rao
- Department of Pathology, Brigham and Women's Hospital, Boston, United States
| | | | - Arian Mansur
- Harvard Stem Cell Institute, Boston, United States
| | - Erica Wagner
- Department of Pathology, Brigham and Women's Hospital, Boston, United States
| | - Claire Chardes
- Turing Centre for Living Systems, Aix Marseille University, CNRS, IDBM, Marseille, France
| | - Vandana Gupta
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
| | - Pierre-François Lenne
- Turing Centre for Living Systems, Aix Marseille University, CNRS, IDBM, Marseille, France
| | - Bianca H Habermann
- Turing Centre for Living Systems, Aix Marseille University, CNRS, IDBM, Marseille, France
| | - Olivier Theodoly
- Turing Centre for Living Systems, Aix Marseille University, CNRS, LAI, Marseille, France
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Frank Schnorrer
- Turing Centre for Living Systems, Aix Marseille University, CNRS, IDBM, Marseille, France
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12
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Zhi H, Zhou S, Pan W, Shang Y, Zeng Z, Zhang H. The Promising Nanovectors for Gene Delivery in Plant Genome Engineering. Int J Mol Sci 2022; 23:ijms23158501. [PMID: 35955636 PMCID: PMC9368765 DOI: 10.3390/ijms23158501] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/24/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
Highly efficient gene delivery systems are essential for genetic engineering in plants. Traditional delivery methods have been widely used, such as Agrobacterium-mediated transformation, polyethylene glycol (PEG)-mediated delivery, biolistic particle bombardment, and viral transfection. However, genotype dependence and other drawbacks of these techniques limit the application of genetic engineering, particularly genome editing in many crop plants. There is a great need to develop newer gene delivery vectors or methods. Recently, nanomaterials such as mesoporous silica particles (MSNs), AuNPs, carbon nanotubes (CNTs), and layer double hydroxides (LDHs), have emerged as promising vectors for the delivery of genome engineering tools (DNA, RNA, proteins, and RNPs) to plants in a species-independent manner with high efficiency. Some exciting results have been reported, such as the successful delivery of cargo genes into plants and the generation of genome stable transgenic cotton and maize plants, which have provided some new routines for genome engineering in plants. Thus, in this review, we summarized recent progress in the utilization of nanomaterials for plant genetic transformation and discussed the advantages and limitations of different methods. Furthermore, we emphasized the advantages and potential broad applications of nanomaterials in plant genome editing, which provides guidance for future applications of nanomaterials in plant genetic engineering and crop breeding.
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Affiliation(s)
- Heng Zhi
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China; (H.Z.); (S.Z.); (W.P.)
- Institute of Advanced Agricultural Science, Peking University, Weifang 261000, China;
| | - Shengen Zhou
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China; (H.Z.); (S.Z.); (W.P.)
- Institute of Advanced Agricultural Science, Peking University, Weifang 261000, China;
| | - Wenbo Pan
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China; (H.Z.); (S.Z.); (W.P.)
- Institute of Advanced Agricultural Science, Peking University, Weifang 261000, China;
| | - Yun Shang
- Institute of Advanced Agricultural Science, Peking University, Weifang 261000, China;
| | - Zhanghua Zeng
- Institute of Environment and Sustainable Development in Agriculture, CAAS Chinese Academy of Agricultural Science, Beijing 100081, China;
| | - Huawei Zhang
- Institute of Advanced Agricultural Science, Peking University, Weifang 261000, China;
- Correspondence:
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13
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Maria Cherian R, Prajapati C, Penttinen K, Häkli M, Koivisto JT, Pekkanen-Mattila M, Aalto-Setälä K. Fluorescent hiPSC-derived MYH6-mScarlet cardiomyocytes for real-time tracking, imaging, and cardiotoxicity assays. Cell Biol Toxicol 2022; 39:145-163. [PMID: 35870039 PMCID: PMC10042918 DOI: 10.1007/s10565-022-09742-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/29/2022] [Indexed: 11/02/2022]
Abstract
AbstractHuman induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) hold great potential in the cardiovascular field for human disease modeling, drug development, and regenerative medicine. However, multiple hurdles still exist for the effective utilization of hiPSC-CMs as a human-based experimental platform that can be an alternative to the current animal models. To further expand their potential as a research tool and bridge the translational gap, we have generated a cardiac-specific hiPSC reporter line that differentiates into fluorescent CMs using CRISPR-Cas9 genome editing technology. The CMs illuminated with the mScarlet fluorescence enable their non-invasive continuous tracking and functional cellular phenotyping, offering a real-time 2D/3D imaging platform. Utilizing the reporter CMs, we developed an imaging-based cardiotoxicity screening system that can monitor distinct drug-induced structural toxicity and CM viability in real time. The reporter fluorescence enabled visualization of sarcomeric disarray and displayed a drug dose–dependent decrease in its fluorescence. The study also has demonstrated the reporter CMs as a biomaterial cytocompatibility analysis tool that can monitor dynamic cell behavior and maturity of hiPSC-CMs cultured in various biomaterial scaffolds. This versatile cardiac imaging tool that enables real time tracking and high-resolution imaging of CMs has significant potential in disease modeling, drug screening, and toxicology testing.
Graphical abstract
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14
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Bosáková V, De Zuani M, Sládková L, Garlíková Z, Jose SS, Zelante T, Hortová Kohoutková M, Frič J. Lung Organoids—The Ultimate Tool to Dissect Pulmonary Diseases? Front Cell Dev Biol 2022; 10:899368. [PMID: 35912110 PMCID: PMC9326165 DOI: 10.3389/fcell.2022.899368] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/24/2022] [Indexed: 11/15/2022] Open
Abstract
Organoids are complex multicellular three-dimensional (3D) in vitro models that are designed to allow accurate studies of the molecular processes and pathologies of human organs. Organoids can be derived from a variety of cell types, such as human primary progenitor cells, pluripotent stem cells, or tumor-derived cells and can be co-cultured with immune or microbial cells to further mimic the tissue niche. Here, we focus on the development of 3D lung organoids and their use as disease models and drug screening tools. We introduce the various experimental approaches used to model complex human diseases and analyze their advantages and disadvantages. We also discuss validation of the organoids and their physiological relevance to the study of lung diseases. Furthermore, we summarize the current use of lung organoids as models of host-pathogen interactions and human lung diseases such as cystic fibrosis, chronic obstructive pulmonary disease, or SARS-CoV-2 infection. Moreover, we discuss the use of lung organoids derived from tumor cells as lung cancer models and their application in personalized cancer medicine research. Finally, we outline the future of research in the field of human induced pluripotent stem cell-derived organoids.
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Affiliation(s)
- Veronika Bosáková
- International Clinical Research Center, St. Anne’s University Hospital Brno, Brno, Czechia
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Marco De Zuani
- International Clinical Research Center, St. Anne’s University Hospital Brno, Brno, Czechia
| | - Lucie Sládková
- Institute of Hematology and Blood Transfusion, Prague, Czechia
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czechia
| | - Zuzana Garlíková
- International Clinical Research Center, St. Anne’s University Hospital Brno, Brno, Czechia
| | - Shyam Sushama Jose
- International Clinical Research Center, St. Anne’s University Hospital Brno, Brno, Czechia
| | - Teresa Zelante
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | | | - Jan Frič
- International Clinical Research Center, St. Anne’s University Hospital Brno, Brno, Czechia
- Institute of Hematology and Blood Transfusion, Prague, Czechia
- *Correspondence: Jan Frič,
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15
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Dolgalev G, Poverennaya E. Applications of CRISPR-Cas Technologies to Proteomics. Genes (Basel) 2021; 12:1790. [PMID: 34828396 PMCID: PMC8625504 DOI: 10.3390/genes12111790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/12/2022] Open
Abstract
CRISPR-Cas-based genome editing is a revolutionary approach that has provided an unprecedented investigational power for the life sciences. Rapid and efficient, CRISPR-Cas technologies facilitate the generation of complex biological models and at the same time provide the necessary methods required to study these models in depth. The field of proteomics has already significantly benefited from leveraging the power of CRISPR-Cas technologies, however, many potential applications of these technologies in the context of proteomics remain unexplored. In this review, we intend to provide an introduction to the CRISPR-Cas technologies and demonstrate how they can be applied to solving proteome-centric questions. To achieve this goal, we begin with the description of the modern suite of CRISPR-Cas-based tools, focusing on the more mature CRISPR-Cas9 system. In the second part of this review, we highlight both established and potential applications of the CRISPR-Cas technologies to proteomics.
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16
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Zhang K, Cloonan PE, Sundaram S, Liu F, Das SL, Ewoldt JK, Bays JL, Tomp S, Toepfer CN, Marsiglia JDC, Gorham J, Reichart D, Eyckmans J, Seidman JG, Seidman CE, Chen CS. Plakophilin-2 truncating variants impair cardiac contractility by disrupting sarcomere stability and organization. SCIENCE ADVANCES 2021; 7:eabh3995. [PMID: 34652945 PMCID: PMC8519574 DOI: 10.1126/sciadv.abh3995] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/25/2021] [Indexed: 05/10/2023]
Abstract
Progressive loss of cardiac systolic function in arrhythmogenic cardiomyopathy (ACM) has recently gained attention as an important clinical consideration in managing the disease. However, the mechanisms leading to reduction in cardiac contractility are poorly defined. Here, we use CRISPR gene editing to generate human induced pluripotent stem cells (iPSCs) that harbor plakophilin-2 truncating variants (PKP2tv), the most prevalent ACM-linked mutations. The PKP2tv iPSC–derived cardiomyocytes are shown to have aberrant action potentials and reduced systolic function in cardiac microtissues, recapitulating both the electrical and mechanical pathologies reported in ACM. By combining cell micropatterning with traction force microscopy and live imaging, we found that PKP2tvs impair cardiac tissue contractility by destabilizing cell-cell junctions and in turn disrupting sarcomere stability and organization. These findings highlight the interplay between cell-cell adhesions and sarcomeres required for stabilizing cardiomyocyte structure and function and suggest fundamental pathogenic mechanisms that may be shared among different types of cardiomyopathies.
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Affiliation(s)
- Kehan Zhang
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Paige E. Cloonan
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Subramanian Sundaram
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Feng Liu
- State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China
| | - Shoshana L. Das
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Harvard-MIT Program in Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jourdan K. Ewoldt
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Jennifer L. Bays
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Samuel Tomp
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Christopher N. Toepfer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | | | - Joshua Gorham
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Reichart
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jeroen Eyckmans
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | | | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Christopher S. Chen
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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17
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Zhao B, Zhang K, Chen CS, Lejeune E. Sarc-Graph: Automated segmentation, tracking, and analysis of sarcomeres in hiPSC-derived cardiomyocytes. PLoS Comput Biol 2021; 17:e1009443. [PMID: 34613960 PMCID: PMC8523047 DOI: 10.1371/journal.pcbi.1009443] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 10/18/2021] [Accepted: 09/10/2021] [Indexed: 12/03/2022] Open
Abstract
A better fundamental understanding of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) has the potential to advance applications ranging from drug discovery to cardiac repair. Automated quantitative analysis of beating hiPSC-CMs is an important and fast developing component of the hiPSC-CM research pipeline. Here we introduce “Sarc-Graph,” a computational framework to segment, track, and analyze sarcomeres in fluorescently tagged hiPSC-CMs. Our framework includes functions to segment z-discs and sarcomeres, track z-discs and sarcomeres in beating cells, and perform automated spatiotemporal analysis and data visualization. In addition to reporting good performance for sarcomere segmentation and tracking with little to no parameter tuning and a short runtime, we introduce two novel analysis approaches. First, we construct spatial graphs where z-discs correspond to nodes and sarcomeres correspond to edges. This makes measuring the network distance between each sarcomere (i.e., the number of connecting sarcomeres separating each sarcomere pair) straightforward. Second, we treat tracked and segmented components as fiducial markers and use them to compute the approximate deformation gradient of the entire tracked population. This represents a new quantitative descriptor of hiPSC-CM function. We showcase and validate our approach with both synthetic and experimental movies of beating hiPSC-CMs. By publishing Sarc-Graph, we aim to make automated quantitative analysis of hiPSC-CM behavior more accessible to the broader research community. Heart disease is the leading cause of death worldwide. Because of this, many researchers are studying heart cells in the lab and trying to create artificial heart tissue. Recently, there has been a growing focus on human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). These are cells that are safely sampled from living humans, for example from the blood or skin, that are then transformed into human heart muscle cells. One active research goal is to use these cells to repair the damaged heart. Another active research goal is to test new drugs on these cells before testing them in animals and humans. However, one major challenge is that hiPSC-CMs often have an irregular internal structure that is difficult to analyze. At present, their behavior is far from fully understood. To address this, we have created software to automatically analyze movies of beating hiPSC-CMs. With our software, it is possible to quantify properties such as the amount and direction of beating cell contraction, and the variation in behavior across different parts of each cell. These tools will enable further quantitative analysis of hiPSC-CMs. With these tools, it will be easier to understand, control, and optimize artificial heart tissue created with hiPSC-CMs, and quantify the effects of drugs on hiPSC-CM behavior.
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Affiliation(s)
- Bill Zhao
- Department of Mechanical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Kehan Zhang
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- The Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, United States of America
| | - Christopher S. Chen
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- The Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, United States of America
| | - Emma Lejeune
- Department of Mechanical Engineering, Boston University, Boston, Massachusetts, United States of America
- * E-mail:
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18
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Agarwal R, Paulo JA, Toepfer CN, Ewoldt JK, Sundaram S, Chopra A, Zhang Q, Gorham J, DePalma SR, Chen CS, Gygi SP, Seidman CE, Seidman JG. Filamin C Cardiomyopathy Variants Cause Protein and Lysosome Accumulation. Circ Res 2021; 129:751-766. [PMID: 34405687 PMCID: PMC9053646 DOI: 10.1161/circresaha.120.317076] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Radhika Agarwal
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher N. Toepfer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Radcliffe Department of Medicine, University of Oxford, OX3 9DU, UK
- Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - Jourdan K. Ewoldt
- Department of Biomedical Engineering, Boston University, Boston, MA 02115, USA
| | - Subramanian Sundaram
- Department of Biomedical Engineering, Boston University, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Anant Chopra
- Department of Biomedical Engineering, Boston University, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Qi Zhang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Joshua Gorham
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Steven R. DePalma
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher S. Chen
- Department of Biomedical Engineering, Boston University, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - J. G. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Corresponding Author: Jonathan G Seidman, , 77 Avenue Louis Pasteur, Boston, MA 02115
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19
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Chen DY, Khan N, Close BJ, Goel RK, Blum B, Tavares AH, Kenney D, Conway HL, Ewoldt JK, Chitalia VC, Crossland NA, Chen CS, Kotton DN, Baker SC, Fuchs SY, Connor JH, Douam F, Emili A, Saeed M. SARS-CoV-2 Disrupts Proximal Elements in the JAK-STAT Pathway. J Virol 2021; 95:e0086221. [PMID: 34260266 PMCID: PMC8428404 DOI: 10.1128/jvi.00862-21] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 07/02/2021] [Indexed: 12/26/2022] Open
Abstract
SARS-CoV-2 can infect multiple organs, including lung, intestine, kidney, heart, liver, and brain. The molecular details of how the virus navigates through diverse cellular environments and establishes replication are poorly defined. Here, we generated a panel of phenotypically diverse, SARS-CoV-2-infectible human cell lines representing different body organs and performed longitudinal survey of cellular proteins and pathways broadly affected by the virus. This revealed universal inhibition of interferon signaling across cell types following SARS-CoV-2 infection. We performed systematic analyses of the JAK-STAT pathway in a broad range of cellular systems, including immortalized cells and primary-like cardiomyocytes, and found that SARS-CoV-2 targeted the proximal pathway components, including Janus kinase 1 (JAK1), tyrosine kinase 2 (Tyk2), and the interferon receptor subunit 1 (IFNAR1), resulting in cellular desensitization to type I IFN. Detailed mechanistic investigation of IFNAR1 showed that the protein underwent ubiquitination upon SARS-CoV-2 infection. Furthermore, chemical inhibition of JAK kinases enhanced infection of stem cell-derived cultures, indicating that the virus benefits from inhibiting the JAK-STAT pathway. These findings suggest that the suppression of interferon signaling is a mechanism widely used by the virus to evade antiviral innate immunity, and that targeting the viral mediators of immune evasion may help block virus replication in patients with COVID-19. IMPORTANCE SARS-CoV-2 can infect various organs in the human body, but the molecular interface between the virus and these organs remains unexplored. In this study, we generated a panel of highly infectible human cell lines originating from various body organs and employed these cells to identify cellular processes commonly or distinctly disrupted by SARS-CoV-2 in different cell types. One among the universally impaired processes was interferon signaling. Systematic analysis of this pathway in diverse culture systems showed that SARS-CoV-2 targets the proximal JAK-STAT pathway components, destabilizes the type I interferon receptor though ubiquitination, and consequently renders the infected cells resistant to type I interferon. These findings illuminate how SARS-CoV-2 can continue to propagate in different tissues even in the presence of a disseminated innate immune response.
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Affiliation(s)
- Da-Yuan Chen
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Nazimuddin Khan
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Brianna J. Close
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Raghuveera K. Goel
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA
| | - Benjamin Blum
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA
| | - Alexander H. Tavares
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Devin Kenney
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Hasahn L. Conway
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Jourdan K. Ewoldt
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Vipul C. Chitalia
- Renal Section, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
- Boston Veterans Affairs Healthcare System, Boston, Massachusetts, USA
- Institute of Medical Engineering and Sciences, MA Institute of Technology, Cambridge, Massachusetts, USA
| | - Nicholas A. Crossland
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Christopher S. Chen
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Susan C. Baker
- Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, Maywood, Illinois, USA
| | - Serge Y. Fuchs
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John H. Connor
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Florian Douam
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Andrew Emili
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA
| | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
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20
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Psaras Y, Margara F, Cicconet M, Sparrow AJ, Repetti GG, Schmid M, Steeples V, Wilcox JA, Bueno-Orovio A, Redwood CS, Watkins HC, Robinson P, Rodriguez B, Seidman JG, Seidman CE, Toepfer CN. CalTrack: High-Throughput Automated Calcium Transient Analysis in Cardiomyocytes. Circ Res 2021; 129:326-341. [PMID: 34018815 PMCID: PMC8260473 DOI: 10.1161/circresaha.121.318868] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/06/2021] [Accepted: 05/20/2021] [Indexed: 11/21/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Yiangos Psaras
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine (Y.P., F.M., A.J.S., M.S., V.S., C.S.R., H.C.W., P.R., C.N.T.), University of Oxford, United Kingdom
| | - Francesca Margara
- Computer Science (F.M., A.B.-O., B.R.), University of Oxford, United Kingdom
| | - Marcelo Cicconet
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine (Y.P., F.M., A.J.S., M.S., V.S., C.S.R., H.C.W., P.R., C.N.T.), University of Oxford, United Kingdom
- Computer Science (F.M., A.B.-O., B.R.), University of Oxford, United Kingdom
- Wellcome Centre for Human Genetics (H.C.W., C.N.T.), University of Oxford, United Kingdom
- Image and Data Analysis Core (M.C.), Harvard Medical School, Boston, MA
- Genetics (G.G.R., J.A.L.W., J.G.S., C.E.S., C.N.T.), Harvard Medical School, Boston, MA
- Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Boston, MA (C.E.S.)
- Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Alexander J. Sparrow
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine (Y.P., F.M., A.J.S., M.S., V.S., C.S.R., H.C.W., P.R., C.N.T.), University of Oxford, United Kingdom
- Computer Science (F.M., A.B.-O., B.R.), University of Oxford, United Kingdom
- Wellcome Centre for Human Genetics (H.C.W., C.N.T.), University of Oxford, United Kingdom
- Image and Data Analysis Core (M.C.), Harvard Medical School, Boston, MA
- Genetics (G.G.R., J.A.L.W., J.G.S., C.E.S., C.N.T.), Harvard Medical School, Boston, MA
- Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Boston, MA (C.E.S.)
- Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Giuliana G. Repetti
- Genetics (G.G.R., J.A.L.W., J.G.S., C.E.S., C.N.T.), Harvard Medical School, Boston, MA
| | - Manuel Schmid
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine (Y.P., F.M., A.J.S., M.S., V.S., C.S.R., H.C.W., P.R., C.N.T.), University of Oxford, United Kingdom
- Computer Science (F.M., A.B.-O., B.R.), University of Oxford, United Kingdom
- Wellcome Centre for Human Genetics (H.C.W., C.N.T.), University of Oxford, United Kingdom
- Image and Data Analysis Core (M.C.), Harvard Medical School, Boston, MA
- Genetics (G.G.R., J.A.L.W., J.G.S., C.E.S., C.N.T.), Harvard Medical School, Boston, MA
- Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Boston, MA (C.E.S.)
- Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Violetta Steeples
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine (Y.P., F.M., A.J.S., M.S., V.S., C.S.R., H.C.W., P.R., C.N.T.), University of Oxford, United Kingdom
- Computer Science (F.M., A.B.-O., B.R.), University of Oxford, United Kingdom
- Wellcome Centre for Human Genetics (H.C.W., C.N.T.), University of Oxford, United Kingdom
- Image and Data Analysis Core (M.C.), Harvard Medical School, Boston, MA
- Genetics (G.G.R., J.A.L.W., J.G.S., C.E.S., C.N.T.), Harvard Medical School, Boston, MA
- Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Boston, MA (C.E.S.)
- Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Jonathan A.L. Wilcox
- Genetics (G.G.R., J.A.L.W., J.G.S., C.E.S., C.N.T.), Harvard Medical School, Boston, MA
| | | | - Charles S. Redwood
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine (Y.P., F.M., A.J.S., M.S., V.S., C.S.R., H.C.W., P.R., C.N.T.), University of Oxford, United Kingdom
- Computer Science (F.M., A.B.-O., B.R.), University of Oxford, United Kingdom
- Wellcome Centre for Human Genetics (H.C.W., C.N.T.), University of Oxford, United Kingdom
- Image and Data Analysis Core (M.C.), Harvard Medical School, Boston, MA
- Genetics (G.G.R., J.A.L.W., J.G.S., C.E.S., C.N.T.), Harvard Medical School, Boston, MA
- Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Boston, MA (C.E.S.)
- Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Hugh C. Watkins
- Wellcome Centre for Human Genetics (H.C.W., C.N.T.), University of Oxford, United Kingdom
| | - Paul Robinson
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine (Y.P., F.M., A.J.S., M.S., V.S., C.S.R., H.C.W., P.R., C.N.T.), University of Oxford, United Kingdom
| | - Blanca Rodriguez
- Computer Science (F.M., A.B.-O., B.R.), University of Oxford, United Kingdom
| | - Jonathan G. Seidman
- Genetics (G.G.R., J.A.L.W., J.G.S., C.E.S., C.N.T.), Harvard Medical School, Boston, MA
| | - Christine E. Seidman
- Genetics (G.G.R., J.A.L.W., J.G.S., C.E.S., C.N.T.), Harvard Medical School, Boston, MA
- Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Boston, MA (C.E.S.)
- Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Christopher N. Toepfer
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine (Y.P., F.M., A.J.S., M.S., V.S., C.S.R., H.C.W., P.R., C.N.T.), University of Oxford, United Kingdom
- Wellcome Centre for Human Genetics (H.C.W., C.N.T.), University of Oxford, United Kingdom
- Genetics (G.G.R., J.A.L.W., J.G.S., C.E.S., C.N.T.), Harvard Medical School, Boston, MA
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21
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Abstract
The use of genome editing tools is expanding our understanding of various human diseases by providing insight into gene-disease interactions. Despite the recognized role of toxicants in the development of human health issues and conditions, there is currently limited characterization of their mechanisms of action, and the application of CRISPR-based genome editing to the study of toxicants could help in the identification of novel gene-environment interactions. CRISPR-based functional screens enable identification of cellular mechanisms fundamental for response and susceptibility to a given toxicant. The aim of this review is to inform future directions in the application of CRISPR technologies in toxicological studies. We review and compare different types of CRISPR-based methods including pooled, anchored, combinatorial, and perturb-sequencing screens in vitro, in addition to pooled screenings in model organisms. © 2021 Wiley Periodicals LLC.
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Affiliation(s)
- Amin Sobh
- Department of Medicine, University of Florida Health Cancer Center, University of Florida, Gainesville, Florida
| | - Max Russo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Christopher D Vulpe
- Department of Physiological Sciences, Center for Environmental and Human Toxicology, University of Florida, Gainesville, Florida
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22
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Thompson MK, Sobol RW, Prakash A. Exploiting DNA Endonucleases to Advance Mechanisms of DNA Repair. BIOLOGY 2021; 10:530. [PMID: 34198612 PMCID: PMC8232306 DOI: 10.3390/biology10060530] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 12/17/2022]
Abstract
The earliest methods of genome editing, such as zinc-finger nucleases (ZFN) and transcription activator-like effector nucleases (TALENs), utilize customizable DNA-binding motifs to target the genome at specific loci. While these approaches provided sequence-specific gene-editing capacity, the laborious process of designing and synthesizing recombinant nucleases to recognize a specific target sequence, combined with limited target choices and poor editing efficiency, ultimately minimized the broad utility of these systems. The discovery of clustered regularly interspaced short palindromic repeat sequences (CRISPR) in Escherichia coli dates to 1987, yet it was another 20 years before CRISPR and the CRISPR-associated (Cas) proteins were identified as part of the microbial adaptive immune system, by targeting phage DNA, to fight bacteriophage reinfection. By 2013, CRISPR/Cas9 systems had been engineered to allow gene editing in mammalian cells. The ease of design, low cytotoxicity, and increased efficiency have made CRISPR/Cas9 and its related systems the designer nucleases of choice for many. In this review, we discuss the various CRISPR systems and their broad utility in genome manipulation. We will explore how CRISPR-controlled modifications have advanced our understanding of the mechanisms of genome stability, using the modulation of DNA repair genes as examples.
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Affiliation(s)
- Marlo K. Thompson
- Mitchell Cancer Institute, University of South Alabama Health, Mobile, AL 36604, USA; (M.K.T.); (R.W.S.)
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Robert W. Sobol
- Mitchell Cancer Institute, University of South Alabama Health, Mobile, AL 36604, USA; (M.K.T.); (R.W.S.)
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Aishwarya Prakash
- Mitchell Cancer Institute, University of South Alabama Health, Mobile, AL 36604, USA; (M.K.T.); (R.W.S.)
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
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23
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Leoni C, Bianchi N, Vincenzetti L, Monticelli S. An optimized workflow for CRISPR-Cas9 deletion of surface and intracellular factors in primary human T lymphocytes. PLoS One 2021; 16:e0247232. [PMID: 33600503 PMCID: PMC7891767 DOI: 10.1371/journal.pone.0247232] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/03/2021] [Indexed: 12/27/2022] Open
Abstract
The appropriate regulation of T lymphocyte functions is key to achieve protective immune responses, while at the same time limiting the risks of tissue damage and chronic inflammation. Deciphering the mechanisms underpinning T cell responses in humans may therefore be beneficial for a range of infectious and chronic diseases. Recently, the development of methods based on CRISPR-Cas9 gene-editing has greatly expanded the available tool-box for the mechanistic studies of primary human T cell responses. While the deletion of a surface protein has become a relatively straightforward task, as long as an antibody for detection is available, the identification and selection of cells lacking an intracellular protein, a non-coding RNA or a protein for which no antibody is available, remain more problematic. Here, we discuss the options currently available to scientists interested in performing gene-editing in primary human T lymphocytes and we describe the optimization of a workflow for the screening and analysis of lymphocytes following gene-editing with CRISPR-Cas9 based on T cell cloning and T7 endonuclease I cleavage assay.
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MESH Headings
- CRISPR-Cas Systems/genetics
- Cell Cycle Proteins/deficiency
- Cell Cycle Proteins/genetics
- Cells, Cultured
- Endoribonucleases/deficiency
- Endoribonucleases/genetics
- Gene Editing/methods
- Humans
- Membrane Proteins/deficiency
- Membrane Proteins/genetics
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/deficiency
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- T-Box Domain Proteins/deficiency
- T-Box Domain Proteins/genetics
- T-Lymphocytes/cytology
- T-Lymphocytes/metabolism
- Transcription Factors/deficiency
- Transcription Factors/genetics
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Affiliation(s)
- Cristina Leoni
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Niccolò Bianchi
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Lucia Vincenzetti
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Silvia Monticelli
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
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24
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Future Leaders to Watch – Christopher Toepfer and Manuel Schmid. Biol Open 2021. [PMCID: PMC7903992 DOI: 10.1242/bio.058568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Future Leaders to Watch is a series of interviews with the first authors of a selection of papers published in Biology Open, helping early-career researchers promote themselves alongside their papers. Christopher Toepfer and Manuel Schmid are co-first authors on ‘Myosin super relaxation (SRX) a perspective on fundamental biology, human disease, and cardiac therapeutics’, published in BiO. Christopher is a Sir Henry Wellcome Postdoctoral Fellow and British Heart Foundation Centre of Research Excellence (CRE) Intermediate Transition Fellow in the department of Cardiovascular Medicine at the Radcliffe Department of Medicine, University of Oxford, UK. Manuel is a Research Assistant in the department of Cardiovascular Medicine at the Radcliffe Department of Medicine, University of Oxford, UK. They are investigating the mechanisms that control heart function and impact acquired and inherited cardiovascular conditions.
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25
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Ward T, Tai W, Morton S, Impens F, Van Damme P, Van Haver D, Timmerman E, Venturini G, Zhang K, Jang MY, Willcox JAL, Haghighi A, Gelb BD, Chung WK, Goldmuntz E, Porter GA, Lifton RP, Brueckner M, Yost HJ, Bruneau BG, Gorham J, Kim Y, Pereira A, Homsy J, Benson CC, DePalma SR, Varland S, Chen CS, Arnesen T, Gevaert K, Seidman C, Seidman JG. Mechanisms of Congenital Heart Disease Caused by NAA15 Haploinsufficiency. Circ Res 2021; 128:1156-1169. [PMID: 33557580 PMCID: PMC8048381 DOI: 10.1161/circresaha.120.316966] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Tarsha Ward
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Warren Tai
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Sarah Morton
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School.,Division of Newborn Medicine, Boston Children's Hospital (S.M.)
| | - Francis Impens
- VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium (F.I., D.V.H., E.T., K.G.).,VIB Proteomics Core, B-9000 Ghent, Belgium (F.I., D.V.H., E.T.).,Biomolecular Medicine (F.I., D.V.H., E.T., K.G.), Ghent University, B-9000 Ghent, Belgium
| | - Petra Van Damme
- Biochemistry and Microbiology (P.V.D.), Ghent University, B-9000 Ghent, Belgium
| | - Delphi Van Haver
- VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium (F.I., D.V.H., E.T., K.G.).,VIB Proteomics Core, B-9000 Ghent, Belgium (F.I., D.V.H., E.T.).,Biomolecular Medicine (F.I., D.V.H., E.T., K.G.), Ghent University, B-9000 Ghent, Belgium
| | - Evy Timmerman
- VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium (F.I., D.V.H., E.T., K.G.).,VIB Proteomics Core, B-9000 Ghent, Belgium (F.I., D.V.H., E.T.).,Biomolecular Medicine (F.I., D.V.H., E.T., K.G.), Ghent University, B-9000 Ghent, Belgium
| | - Gabriela Venturini
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School.,University of Sao Paulo (G.V.)
| | - Kehan Zhang
- Biomedical Engineering, Boston University, MA (K.Z., C.S.C.).,The Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA (K.Z., C.S.C.)
| | - Min Young Jang
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Jon A L Willcox
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Alireza Haghighi
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School.,Howard Hughes Medical Institute (A.H., C.S.), Harvard Medical School.,Medicine, Brigham and Women's Hospital (A.H., C.S.)
| | - Bruce D Gelb
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York (B.D.G.)
| | - Wendy K Chung
- Pediatrics and Medicine, Columbia University Medical Center, New York (W.K.C.)
| | - Elizabeth Goldmuntz
- Cardiology, Children's Hospital of Philadelphia, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia (E.G.)
| | | | - Richard P Lifton
- Genetics, Yale University School of Medicine, New Haven (R.P.L., M.B.).,Laboratory of Human Genetics and Genomics, Rockefeller University, New York (R.P.L.)
| | - Martina Brueckner
- Genetics, Yale University School of Medicine, New Haven (R.P.L., M.B.).,Pediatrics, Yale University School of Medicine, New Haven (M.B.)
| | - H Joseph Yost
- Molecular Medicine Program, University of Utah, Salt Lake City (H.J.Y.)
| | | | - Joshua Gorham
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Yuri Kim
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School.,Division of Cardiovascular Medicine, Brigham and Women's Hospital (Y.K.)
| | - Alexandre Pereira
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Jason Homsy
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Craig C Benson
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Steven R DePalma
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Sylvia Varland
- Biomedicine (S.V., T.A.), University of Bergen, N-5020 Bergen, Norway.,Biological Sciences (S.V., T.A.), University of Bergen, N-5020 Bergen, Norway.,Donnelly Centre for Cellular and Biomolecular Research, Toronto, Canada (S.V.)
| | - Christopher S Chen
- Biomedical Engineering, Boston University, MA (K.Z., C.S.C.).,The Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA (K.Z., C.S.C.)
| | - Thomas Arnesen
- Biomedicine (S.V., T.A.), University of Bergen, N-5020 Bergen, Norway.,Biological Sciences (S.V., T.A.), University of Bergen, N-5020 Bergen, Norway.,Surgery, Haukeland University Hospital, N-5021 Bergen, Norway (T.A.)
| | - Kris Gevaert
- Biomolecular Medicine (F.I., D.V.H., E.T., K.G.), Ghent University, B-9000 Ghent, Belgium
| | - Christine Seidman
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School.,Howard Hughes Medical Institute (A.H., C.S.), Harvard Medical School.,Medicine, Brigham and Women's Hospital (A.H., C.S.)
| | - J G Seidman
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
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26
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Nikitaki Z, Pariset E, Sudar D, Costes SV, Georgakilas AG. In Situ Detection of Complex DNA Damage Using Microscopy: A Rough Road Ahead. Cancers (Basel) 2020; 12:E3288. [PMID: 33172046 PMCID: PMC7694657 DOI: 10.3390/cancers12113288] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022] Open
Abstract
Complexity of DNA damage is considered currently one if not the primary instigator of biological responses and determinant of short and long-term effects in organisms and their offspring. In this review, we focus on the detection of complex (clustered) DNA damage (CDD) induced for example by ionizing radiation (IR) and in some cases by high oxidative stress. We perform a short historical perspective in the field, emphasizing the microscopy-based techniques and methodologies for the detection of CDD at the cellular level. We extend this analysis on the pertaining methodology of surrogate protein markers of CDD (foci) colocalization and provide a unique synthesis of imaging parameters, software, and different types of microscopy used. Last but not least, we critically discuss the main advances and necessary future direction for the better detection of CDD, with important outcomes in biological and clinical setups.
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Affiliation(s)
- Zacharenia Nikitaki
- Physics Department, School of Applied Mathematical and Physical Sciences, DNA Damage Laboratory, National Technical University of Athens (NTUA), 15780 Zografou, Athens, Greece
| | - Eloise Pariset
- Space Biosciences Division, Radiation Biophysics Laboratory, NASA Ames Research Center, Moffett Field, CA 94035, USA; (E.P.); (S.V.C.)
- Universities Space Research Association (USRA), Mountain View, CA 94043, USA
| | - Damir Sudar
- Life Sciences Department, Quantitative Imaging Systems LLC, Portland, OR 97209, USA;
| | - Sylvain V. Costes
- Space Biosciences Division, Radiation Biophysics Laboratory, NASA Ames Research Center, Moffett Field, CA 94035, USA; (E.P.); (S.V.C.)
| | - Alexandros G. Georgakilas
- Physics Department, School of Applied Mathematical and Physical Sciences, DNA Damage Laboratory, National Technical University of Athens (NTUA), 15780 Zografou, Athens, Greece
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27
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Chen DY, Khan N, Close BJ, Goel RK, Blum B, Tavares AH, Kenney D, Conway HL, Ewoldt JK, Kapell S, Chitalia VC, Crossland NA, Chen CS, Kotton DN, Baker SC, Connor JH, Douam F, Emili A, Saeed M. SARS-CoV-2 desensitizes host cells to interferon through inhibition of the JAK-STAT pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 33140044 DOI: 10.1101/2020.10.27.358259] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
SARS-CoV-2 can infect multiple organs, including lung, intestine, kidney, heart, liver, and brain. The molecular details of how the virus navigates through diverse cellular environments and establishes replication are poorly defined. Here, we performed global proteomic analysis of the virus-host interface in a newly established panel of phenotypically diverse, SARS-CoV-2-infectable human cell lines representing different body organs. This revealed universal inhibition of interferon signaling across cell types following SARS-CoV-2 infection. We performed systematic analyses of the JAK-STAT pathway in a broad range of cellular systems, including immortalized cell lines and primary-like cardiomyocytes, and found that several pathway components were targeted by SARS-CoV-2 leading to cellular desensitization to interferon. These findings indicate that the suppression of interferon signaling is a mechanism widely used by SARS-CoV-2 in diverse tissues to evade antiviral innate immunity, and that targeting the viral mediators of immune evasion may help block virus replication in patients with COVID-19.
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28
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Sharma A, Wasson LK, Willcox JA, Morton SU, Gorham JM, DeLaughter DM, Neyazi M, Schmid M, Agarwal R, Jang MY, Toepfer CN, Ward T, Kim Y, Pereira AC, DePalma SR, Tai A, Kim S, Conner D, Bernstein D, Gelb BD, Chung WK, Goldmuntz E, Porter G, Tristani-Firouzi M, Srivastava D, Seidman JG, Seidman CE. GATA6 mutations in hiPSCs inform mechanisms for maldevelopment of the heart, pancreas, and diaphragm. eLife 2020; 9:53278. [PMID: 33054971 PMCID: PMC7593088 DOI: 10.7554/elife.53278] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 10/14/2020] [Indexed: 12/18/2022] Open
Abstract
Damaging GATA6 variants cause cardiac outflow tract defects, sometimes with pancreatic and diaphragmic malformations. To define molecular mechanisms for these diverse developmental defects, we studied transcriptional and epigenetic responses to GATA6 loss of function (LoF) and missense variants during cardiomyocyte differentiation of isogenic human induced pluripotent stem cells. We show that GATA6 is a pioneer factor in cardiac development, regulating SMYD1 that activates HAND2, and KDR that with HAND2 orchestrates outflow tract formation. LoF variants perturbed cardiac genes and also endoderm lineage genes that direct PDX1 expression and pancreatic development. Remarkably, an exon 4 GATA6 missense variant, highly associated with extra-cardiac malformations, caused ectopic pioneer activities, profoundly diminishing GATA4, FOXA1/2, and PDX1 expression and increasing normal retinoic acid signaling that promotes diaphragm development. These aberrant epigenetic and transcriptional signatures illuminate the molecular mechanisms for cardiovascular malformations, pancreas and diaphragm dysgenesis that arise in patients with distinct GATA6 variants.
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Affiliation(s)
- Arun Sharma
- Department of Genetics, Harvard Medical School, Boston, United States.,Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, United States.,Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, United States
| | - Lauren K Wasson
- Department of Genetics, Harvard Medical School, Boston, United States.,Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
| | - Jon Al Willcox
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Sarah U Morton
- Department of Genetics, Harvard Medical School, Boston, United States.,Division of Newborn Medicine, Boston Children's Hospital, Boston, United States
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, Boston, United States
| | | | - Meraj Neyazi
- Department of Genetics, Harvard Medical School, Boston, United States.,Hannover Medical School, Hannover, Germany
| | - Manuel Schmid
- Department of Genetics, Harvard Medical School, Boston, United States.,Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
| | - Radhika Agarwal
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Min Young Jang
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Christopher N Toepfer
- Department of Genetics, Harvard Medical School, Boston, United States.,Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom.,Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tarsha Ward
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Yuri Kim
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Alexandre C Pereira
- Department of Genetics, Harvard Medical School, Boston, United States.,Laboratory of Genetics and Molecular Cardiology, Heart Institute, Medical School of University of Sao Paulo, Sao Paulo, Brazil
| | - Steven R DePalma
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Angela Tai
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Seongwon Kim
- Department of Genetics, Harvard Medical School, Boston, United States
| | - David Conner
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Daniel Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, United States
| | - Bruce D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Wendy K Chung
- Department of Medicine, Columbia University Medical Center, New York, United States
| | - Elizabeth Goldmuntz
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - George Porter
- Department of Pediatrics, University of Rochester Medical Center, Rochester, United States
| | - Martin Tristani-Firouzi
- Division of Pediatric Cardiology, University of Utah School of Medicine, Salt Lake City, United States
| | | | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, United States.,Howard Hughes Medical Institute, Harvard Medical School, Boston, United States.,Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Boston, United States
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29
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Sharma A, Garcia G, Wang Y, Plummer JT, Morizono K, Arumugaswami V, Svendsen CN. Human iPSC-Derived Cardiomyocytes Are Susceptible to SARS-CoV-2 Infection. CELL REPORTS MEDICINE 2020; 1:100052. [PMID: 32835305 PMCID: PMC7323681 DOI: 10.1016/j.xcrm.2020.100052] [Citation(s) in RCA: 195] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/27/2020] [Accepted: 06/18/2020] [Indexed: 12/27/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is a pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is defined by respiratory symptoms, but cardiac complications including viral myocarditis are also prevalent. Although ischemic and inflammatory responses caused by COVID-19 can detrimentally affect cardiac function, the direct impact of SARS-CoV-2 infection on human cardiomyocytes is not well understood. Here, we utilize human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) as a model to examine the mechanisms of cardiomyocyte-specific infection by SARS-CoV-2. Microscopy and RNA sequencing demonstrate that SARS-CoV-2 can enter hiPSC-CMs via ACE2. Viral replication and cytopathic effect induce hiPSC-CM apoptosis and cessation of beating after 72 h of infection. SARS-CoV-2 infection activates innate immune response and antiviral clearance gene pathways, while inhibiting metabolic pathways and suppressing ACE2 expression. These studies show that SARS-CoV-2 can infect hiPSC-CMs in vitro, establishing a model for elucidating infection mechanisms and potentially a cardiac-specific antiviral drug screening platform. Human iPSC-derived cardiomyocytes are susceptible to SARS-CoV-2 infection ACE2 antibody blunts SARS-CoV-2 infection in cardiomyocytes Infected human iPSC-derived cardiomyocytes activate viral clearance pathways
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Affiliation(s)
- Arun Sharma
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Gustavo Garcia
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yizhou Wang
- Genomics Core, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jasmine T Plummer
- Genomics Core, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Kouki Morizono
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.,UCLA AIDS Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Vaithilingaraja Arumugaswami
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Clive N Svendsen
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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30
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Toepfer CN, Garfinkel AC, Venturini G, Wakimoto H, Repetti G, Alamo L, Sharma A, Agarwal R, Ewoldt JF, Cloonan P, Letendre J, Lun M, Olivotto I, Colan S, Ashley E, Jacoby D, Michels M, Redwood CS, Watkins HC, Day SM, Staples JF, Padrón R, Chopra A, Ho CY, Chen CS, Pereira AC, Seidman JG, Seidman CE. Myosin Sequestration Regulates Sarcomere Function, Cardiomyocyte Energetics, and Metabolism, Informing the Pathogenesis of Hypertrophic Cardiomyopathy. Circulation 2020; 141:828-842. [PMID: 31983222 PMCID: PMC7077965 DOI: 10.1161/circulationaha.119.042339] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 12/20/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Hypertrophic cardiomyopathy (HCM) is caused by pathogenic variants in sarcomere protein genes that evoke hypercontractility, poor relaxation, and increased energy consumption by the heart and increased patient risks for arrhythmias and heart failure. Recent studies show that pathogenic missense variants in myosin, the molecular motor of the sarcomere, are clustered in residues that participate in dynamic conformational states of sarcomere proteins. We hypothesized that these conformations are essential to adapt contractile output for energy conservation and that pathophysiology of HCM results from destabilization of these conformations. METHODS We assayed myosin ATP binding to define the proportion of myosins in the super relaxed state (SRX) conformation or the disordered relaxed state (DRX) conformation in healthy rodent and human hearts, at baseline and in response to reduced hemodynamic demands of hibernation or pathogenic HCM variants. To determine the relationships between myosin conformations, sarcomere function, and cell biology, we assessed contractility, relaxation, and cardiomyocyte morphology and metabolism, with and without an allosteric modulator of myosin ATPase activity. We then tested whether the positions of myosin variants of unknown clinical significance that were identified in patients with HCM, predicted functional consequences and associations with heart failure and arrhythmias. RESULTS Myosins undergo physiological shifts between the SRX conformation that maximizes energy conservation and the DRX conformation that enables cross-bridge formation with greater ATP consumption. Systemic hemodynamic requirements, pharmacological modulators of myosin, and pathogenic myosin missense mutations influenced the proportions of these conformations. Hibernation increased the proportion of myosins in the SRX conformation, whereas pathogenic variants destabilized these and increased the proportion of myosins in the DRX conformation, which enhanced cardiomyocyte contractility, but impaired relaxation and evoked hypertrophic remodeling with increased energetic stress. Using structural locations to stratify variants of unknown clinical significance, we showed that the variants that destabilized myosin conformations were associated with higher rates of heart failure and arrhythmias in patients with HCM. CONCLUSIONS Myosin conformations establish work-energy equipoise that is essential for life-long cellular homeostasis and heart function. Destabilization of myosin energy-conserving states promotes contractile abnormalities, morphological and metabolic remodeling, and adverse clinical outcomes in patients with HCM. Therapeutic restabilization corrects cellular contractile and metabolic phenotypes and may limit these adverse clinical outcomes in patients with HCM.
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Affiliation(s)
- Christopher N. Toepfer
- Department of Genetics, Harvard Medical School, Boston, MA (C.N.T., A.C.G., G.V., H.W., G.R., A.S., R.A., A.C.P., J.G.S., C.E.S.)
- Cardiovascular Medicine, Radcliffe Department of Medicine (C.N.T., C.S.R., H.C.W.), University of Oxford, UK
- Wellcome Centre for Human Genetics (C.N.T., H.C.W.), University of Oxford, UK
| | - Amanda C. Garfinkel
- Department of Genetics, Harvard Medical School, Boston, MA (C.N.T., A.C.G., G.V., H.W., G.R., A.S., R.A., A.C.P., J.G.S., C.E.S.)
| | - Gabriela Venturini
- Department of Genetics, Harvard Medical School, Boston, MA (C.N.T., A.C.G., G.V., H.W., G.R., A.S., R.A., A.C.P., J.G.S., C.E.S.)
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor)-University of São Paulo Medical School, Brazil (G.V., A.C.P.)
| | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, MA (C.N.T., A.C.G., G.V., H.W., G.R., A.S., R.A., A.C.P., J.G.S., C.E.S.)
| | - Giuliana Repetti
- Department of Genetics, Harvard Medical School, Boston, MA (C.N.T., A.C.G., G.V., H.W., G.R., A.S., R.A., A.C.P., J.G.S., C.E.S.)
| | - Lorenzo Alamo
- Centro de Biología Estructural, Instituto Venezolano de Investigaciones Cientifìcas (IVIC), Caracas (L.A., R.P.)
| | - Arun Sharma
- Department of Genetics, Harvard Medical School, Boston, MA (C.N.T., A.C.G., G.V., H.W., G.R., A.S., R.A., A.C.P., J.G.S., C.E.S.)
| | - Radhika Agarwal
- Department of Genetics, Harvard Medical School, Boston, MA (C.N.T., A.C.G., G.V., H.W., G.R., A.S., R.A., A.C.P., J.G.S., C.E.S.)
| | - Jourdan F. Ewoldt
- Department of Biomedical Engineering, Boston University, MA (J.F.E., P.C., J.L., A.C., C.S.C.)
| | - Paige Cloonan
- Department of Biomedical Engineering, Boston University, MA (J.F.E., P.C., J.L., A.C., C.S.C.)
| | - Justin Letendre
- Department of Biomedical Engineering, Boston University, MA (J.F.E., P.C., J.L., A.C., C.S.C.)
| | - Mingyue Lun
- Department of Medicine, Division of Genetics (M.L.), Brigham and Women’s Hospital, Boston, MA
| | - Iacopo Olivotto
- Cardiomyopathy Unit and Genetic Unit, Careggi University Hospital, Florence, Italy (I.O.)
| | - Steve Colan
- Department of Cardiology, Boston Children’s Hospital, MA (S.C.)
| | - Euan Ashley
- Center for Inherited Cardiovascular Disease, Stanford University, CA (E.A.)
| | - Daniel Jacoby
- Department of Internal Medicine, Section of Cardiovascular Diseases, Yale School of Medicine, New Haven, CT (D.J.)
| | - Michelle Michels
- Department of Cardiology, Thorax Center, Erasmus MC, Rotterdam, The Netherlands (M.M.)
| | - Charles S. Redwood
- Cardiovascular Medicine, Radcliffe Department of Medicine (C.N.T., C.S.R., H.C.W.), University of Oxford, UK
| | - Hugh C. Watkins
- Cardiovascular Medicine, Radcliffe Department of Medicine (C.N.T., C.S.R., H.C.W.), University of Oxford, UK
- Wellcome Centre for Human Genetics (C.N.T., H.C.W.), University of Oxford, UK
| | - Sharlene M. Day
- Department of Internal Medicine, University of Michigan, Ann Arbor (S.M.D.)
| | - James F. Staples
- Department of Biology, University of Western Ontario, London, Canada (J.F.S.)
| | - Raúl Padrón
- Centro de Biología Estructural, Instituto Venezolano de Investigaciones Cientifìcas (IVIC), Caracas (L.A., R.P.)
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester (R.P.)
| | - Anant Chopra
- Department of Biomedical Engineering, Boston University, MA (J.F.E., P.C., J.L., A.C., C.S.C.)
| | - Carolyn Y. Ho
- Cardiovascular Division (C.Y.H., C.E.S.), Brigham and Women’s Hospital, Boston, MA
| | - Christopher S. Chen
- Department of Biomedical Engineering, Boston University, MA (J.F.E., P.C., J.L., A.C., C.S.C.)
| | - Alexandre C. Pereira
- Department of Genetics, Harvard Medical School, Boston, MA (C.N.T., A.C.G., G.V., H.W., G.R., A.S., R.A., A.C.P., J.G.S., C.E.S.)
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor)-University of São Paulo Medical School, Brazil (G.V., A.C.P.)
| | - Jonathan G. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA (C.N.T., A.C.G., G.V., H.W., G.R., A.S., R.A., A.C.P., J.G.S., C.E.S.)
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA (C.N.T., A.C.G., G.V., H.W., G.R., A.S., R.A., A.C.P., J.G.S., C.E.S.)
- Cardiovascular Division (C.Y.H., C.E.S.), Brigham and Women’s Hospital, Boston, MA
- Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
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31
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Sharma A, Sances S, Workman MJ, Svendsen CN. Multi-lineage Human iPSC-Derived Platforms for Disease Modeling and Drug Discovery. Cell Stem Cell 2020; 26:309-329. [PMID: 32142662 PMCID: PMC7159985 DOI: 10.1016/j.stem.2020.02.011] [Citation(s) in RCA: 163] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human induced pluripotent stem cells (hiPSCs) provide a powerful platform for disease modeling and have unlocked new possibilities for understanding the mechanisms governing human biology, physiology, and genetics. However, hiPSC-derivatives have traditionally been utilized in two-dimensional monocultures, in contrast to the multi-systemic interactions that influence cells in the body. We will discuss recent advances in generating more complex hiPSC-based systems using three-dimensional organoids, tissue-engineering, microfluidic organ-chips, and humanized animal systems. While hiPSC differentiation still requires optimization, these next-generation multi-lineage technologies can augment the biomedical researcher's toolkit and enable more realistic models of human tissue function.
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Affiliation(s)
- Arun Sharma
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Samuel Sances
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Michael J Workman
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Clive N Svendsen
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
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32
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Cattoglio C, Darzacq X, Tjian R, Hansen AS. Estimating Cellular Abundances of Halo-tagged Proteins in Live Mammalian Cells by Flow Cytometry. Bio Protoc 2020; 10:e3527. [PMID: 33654751 DOI: 10.21769/bioprotoc.3527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/24/2019] [Accepted: 01/29/2020] [Indexed: 11/02/2022] Open
Abstract
Accurate abundance measurements of cellular proteins are required to achieve a quantitative and predictive understanding of any biological process inside the cell. Existing methods to determine absolute protein abundances are labor-intensive and/or require sophisticated experimental and computational infrastructure (e.g., fluorescence correlation spectroscopy (FCS)-calibrated imaging and quantitative mass spectrometry). Here we detail a straightforward flow cytometry-based method to measure the absolute abundance of any Halo-tagged protein in live cells that uses a standard mammalian cell line with a known number of Halo-CTCF proteins recently characterized in our lab. The protocol only comprises a few steps. First, a cell line expressing the Halo-tagged protein of interest is grown and labeled side-by-side with our standard line. Then, average fluorescence intensities are measured by conventional flow cytometry analysis and finally a simple calculation is applied to estimate the absolute number of the Halo-tagged protein of interest per cell. Once the protein of interest has been endogenously tagged with HaloTag, which we routinely achieve by Cas9-mediated genome editing, the presented protocol is fast, convenient, reproducible, cost-effective and readily accessible.
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Affiliation(s)
- Claudia Cattoglio
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA.,CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA.,CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA.,CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Anders S Hansen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA.,CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
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33
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Cattoglio C, Pustova I, Darzacq X, Tjian R, Hansen AS. Assessing Self-interaction of Mammalian Nuclear Proteins by Co-immunoprecipitation. Bio Protoc 2020; 10:e3526. [PMID: 33654750 PMCID: PMC7842838 DOI: 10.21769/bioprotoc.3526] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/25/2020] [Accepted: 01/13/2020] [Indexed: 11/02/2022] Open
Abstract
Protein-protein interactions constitute the molecular foundations of virtually all biological processes. Co-immunoprecipitation (CoIP) experiments are probably the most widely used method to probe both heterotypic and homotypic protein-protein interactions. Recent advances in super-resolution microscopy have revealed that several nuclear proteins such as transcription factors are spatially distributed into local high-concentration clusters in mammalian cells, suggesting that many nuclear proteins self-interact. These observations have further underscored the need for orthogonal biochemical approaches for testing if self-association occurs, and if so, what the mechanisms are. Here, we describe a CoIP protocol specifically optimized to test self-association of endogenously tagged nuclear proteins (self-CoIP), and to evaluate the role of nucleic acids in such self-interaction. This protocol has proven reliable and robust in our hands, and it can be used to test both homotypic and heterotypic (CoIP) protein-protein interactions.
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Affiliation(s)
- Claudia Cattoglio
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Iryna Pustova
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Anders S. Hansen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
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Effects of Spaceflight on Human Induced Pluripotent Stem Cell-Derived Cardiomyocyte Structure and Function. Stem Cell Reports 2019; 13:960-969. [PMID: 31708475 PMCID: PMC6915842 DOI: 10.1016/j.stemcr.2019.10.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 12/21/2022] Open
Abstract
With extended stays aboard the International Space Station (ISS) becoming commonplace, there is a need to better understand the effects of microgravity on cardiac function. We utilized human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) to study the effects of microgravity on cell-level cardiac function and gene expression. The hiPSC-CMs were cultured aboard the ISS for 5.5 weeks and their gene expression, structure, and functions were compared with ground control hiPSC-CMs. Exposure to microgravity on the ISS caused alterations in hiPSC-CM calcium handling. RNA-sequencing analysis demonstrated that 2,635 genes were differentially expressed among flight, post-flight, and ground control samples, including genes involved in mitochondrial metabolism. This study represents the first use of hiPSC technology to model the effects of spaceflight on human cardiomyocyte structure and function.
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Toepfer CN, Sharma A, Cicconet M, Garfinkel AC, Mücke M, Neyazi M, Willcox JA, Agarwal R, Schmid M, Rao J, Ewoldt J, Pourquié O, Chopra A, Chen CS, Seidman JG, Seidman CE. SarcTrack. Circ Res 2019; 124:1172-1183. [PMID: 30700234 PMCID: PMC6485312 DOI: 10.1161/circresaha.118.314505] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/18/2019] [Accepted: 01/30/2019] [Indexed: 12/18/2022]
Abstract
RATIONALE Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) in combination with CRISPR/Cas9 genome editing provide unparalleled opportunities to study cardiac biology and disease. However, sarcomeres, the fundamental units of myocyte contraction, are immature and nonlinear in hiPSC-CMs, which technically challenge accurate functional interrogation of contractile parameters in beating cells. Furthermore, existing analysis methods are relatively low-throughput, indirectly assess contractility, or only assess well-aligned sarcomeres found in mature cardiac tissues. OBJECTIVE We aimed to develop an analysis platform that directly, rapidly, and automatically tracks sarcomeres in beating cardiomyocytes. The platform should assess sarcomere content, contraction and relaxation parameters, and beat rate. METHODS AND RESULTS We developed SarcTrack, a MatLab software that monitors fluorescently tagged sarcomeres in hiPSC-CMs. The algorithm determines sarcomere content, sarcomere length, and returns rates of sarcomere contraction and relaxation. By rapid measurement of hundreds of sarcomeres in each hiPSC-CM, SarcTrack provides large data sets for robust statistical analyses of multiple contractile parameters. We validated SarcTrack by analyzing drug-treated hiPSC-CMs, confirming the contractility effects of compounds that directly activate (CK-1827452) or inhibit (MYK-461) myosin molecules or indirectly alter contractility (verapamil and propranolol). SarcTrack analysis of hiPSC-CMs carrying a heterozygous truncation variant in the myosin-binding protein C ( MYBPC3) gene, which causes hypertrophic cardiomyopathy, recapitulated seminal disease phenotypes including cardiac hypercontractility and diminished relaxation, abnormalities that normalized with MYK-461 treatment. CONCLUSIONS SarcTrack provides a direct and efficient method to quantitatively assess sarcomere function. By improving existing contractility analysis methods and overcoming technical challenges associated with functional evaluation of hiPSC-CMs, SarcTrack enhances translational prospects for sarcomere-regulating therapeutics and accelerates interrogation of human cardiac genetic variants.
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Affiliation(s)
- Christopher N. Toepfer
- From the Department of Genetics (C.N.T., A.S., A.C.G., M.N., J.A.L.W., R.A., M.S., J.R., O.P., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
- Cardiovascular Medicine, Radcliffe Department of Medicine (C.N.T.), University of Oxford, United Kingdom
- Wellcome Centre for Human Genetics (C.N.T.), University of Oxford, United Kingdom
| | - Arun Sharma
- From the Department of Genetics (C.N.T., A.S., A.C.G., M.N., J.A.L.W., R.A., M.S., J.R., O.P., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
| | - Marcelo Cicconet
- Image and Data Analysis Core (M.C.), Harvard Medical School, Boston, MA
| | - Amanda C. Garfinkel
- From the Department of Genetics (C.N.T., A.S., A.C.G., M.N., J.A.L.W., R.A., M.S., J.R., O.P., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
| | - Michael Mücke
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine, Berlin, Germany (M.M.)
- German Centre for Cardiovascular Research, Berlin, Germany (M.M.)
- Charité-Universitätsmedizin, Berlin, Germany (M.M.)
| | - Meraj Neyazi
- From the Department of Genetics (C.N.T., A.S., A.C.G., M.N., J.A.L.W., R.A., M.S., J.R., O.P., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
- Hannover Medical School, Germany (M.N.)
| | - Jon A.L. Willcox
- From the Department of Genetics (C.N.T., A.S., A.C.G., M.N., J.A.L.W., R.A., M.S., J.R., O.P., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
| | - Radhika Agarwal
- From the Department of Genetics (C.N.T., A.S., A.C.G., M.N., J.A.L.W., R.A., M.S., J.R., O.P., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
| | - Manuel Schmid
- From the Department of Genetics (C.N.T., A.S., A.C.G., M.N., J.A.L.W., R.A., M.S., J.R., O.P., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
- Deutsches Herzzentrum München, Technische Universität München, Germany (M.S.)
| | - Jyoti Rao
- From the Department of Genetics (C.N.T., A.S., A.C.G., M.N., J.A.L.W., R.A., M.S., J.R., O.P., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
- Department of Pathology (J.R., O.P.), Brigham and Women’s Hospital, Boston, MA
- Harvard Stem Cell Institute, Boston, MA (J.R., O.P.)
| | - Jourdan Ewoldt
- Biomedical Engineering, Boston University, MA (J.E., A.C., C.S.C.)
- The Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA (J.E., A.C., C.S.C.)
| | - Olivier Pourquié
- From the Department of Genetics (C.N.T., A.S., A.C.G., M.N., J.A.L.W., R.A., M.S., J.R., O.P., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
- Department of Pathology (J.R., O.P.), Brigham and Women’s Hospital, Boston, MA
- Harvard Stem Cell Institute, Boston, MA (J.R., O.P.)
| | - Anant Chopra
- Biomedical Engineering, Boston University, MA (J.E., A.C., C.S.C.)
- The Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA (J.E., A.C., C.S.C.)
| | - Christopher S. Chen
- Biomedical Engineering, Boston University, MA (J.E., A.C., C.S.C.)
- The Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA (J.E., A.C., C.S.C.)
| | - Jonathan G. Seidman
- From the Department of Genetics (C.N.T., A.S., A.C.G., M.N., J.A.L.W., R.A., M.S., J.R., O.P., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
| | - Christine E. Seidman
- From the Department of Genetics (C.N.T., A.S., A.C.G., M.N., J.A.L.W., R.A., M.S., J.R., O.P., J.G.S., C.E.S.), Harvard Medical School, Boston, MA
- Cardiovascular Division, Department of Medicine (C.E.S.), Brigham and Women’s Hospital, Boston, MA
- Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
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Ford K, McDonald D, Mali P. Functional Genomics via CRISPR-Cas. J Mol Biol 2019; 431:48-65. [PMID: 29959923 PMCID: PMC6309720 DOI: 10.1016/j.jmb.2018.06.034] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/02/2018] [Accepted: 06/14/2018] [Indexed: 12/22/2022]
Abstract
RNA-guided CRISPR (clustered regularly interspaced short palindromic repeat)-associated Cas proteins have recently emerged as versatile tools to investigate and engineer the genome. The programmability of CRISPR-Cas has proven especially useful for probing genomic function in high-throughput. Facile single-guide RNA library synthesis allows CRISPR-Cas screening to rapidly investigate the functional consequences of genomic, transcriptomic, and epigenomic perturbations. Furthermore, by combining CRISPR-Cas perturbations with downstream single-cell analyses (flow cytometry, expression profiling, etc.), forward screens can generate robust data sets linking genotypes to complex cellular phenotypes. In the following review, we highlight recent advances in CRISPR-Cas genomic screening while outlining protocols and pitfalls associated with screen implementation. Finally, we describe current challenges limiting the utility of CRISPR-Cas screening as well as future research needed to resolve these impediments. As CRISPR-Cas technologies develop, so too will their clinical applications. Looking ahead, patient centric functional screening in primary cells will likely play a greater role in disease management and therapeutic development.
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Affiliation(s)
- Kyle Ford
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA
| | - Daniella McDonald
- Biomedical Sciences Graduate Program, University of California, San Diego, San Diego, CA 92093, USA
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA.
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Sharma A, McKeithan WL, Serrano R, Kitani T, Burridge PW, Del Álamo JC, Mercola M, Wu JC. Use of human induced pluripotent stem cell-derived cardiomyocytes to assess drug cardiotoxicity. Nat Protoc 2018; 13:3018-3041. [PMID: 30413796 PMCID: PMC6502639 DOI: 10.1038/s41596-018-0076-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cardiotoxicity has historically been a major cause of drug removal from the pharmaceutical market. Several chemotherapeutic compounds have been noted for their propensities to induce dangerous cardiac-specific side effects such as arrhythmias or cardiomyocyte apoptosis. However, improved preclinical screening methodologies have enabled cardiotoxic compounds to be identified earlier in the drug development pipeline. Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) can be used to screen for drug-induced alterations in cardiac cellular contractility, electrophysiology, and viability. We previously established a novel 'cardiac safety index' (CSI) as a metric that can evaluate potential cardiotoxic drugs via high-throughput screening of hiPSC-CMs. This metric quantitatively examines drug-induced alterations in CM function, using several in vitro readouts, and normalizes the resulting toxicity values to the in vivo maximum drug blood plasma concentration seen in preclinical or clinical pharmacokinetic models. In this ~1-month-long protocol, we describe how to differentiate hiPSCs into hiPSC-CMs and subsequently implement contractility and cytotoxicity assays that can evaluate drug-induced cardiotoxicity in hiPSC-CMs. We also describe how to carry out the calculations needed to generate the CSI metric from these quantitative toxicity measurements.
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Affiliation(s)
- Arun Sharma
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Wesley L McKeithan
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Ricardo Serrano
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, San Diego, CA, USA
| | - Tomoya Kitani
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul W Burridge
- Department of Pharmacology and Center for Pharmacogenomics, Northwestern University School of Medicine, Chicago, IL, USA
| | - Juan C Del Álamo
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, San Diego, CA, USA
| | - Mark Mercola
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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Stage-specific Effects of Bioactive Lipids on Human iPSC Cardiac Differentiation and Cardiomyocyte Proliferation. Sci Rep 2018; 8:6618. [PMID: 29700394 PMCID: PMC5920079 DOI: 10.1038/s41598-018-24954-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/12/2018] [Indexed: 12/21/2022] Open
Abstract
Bioactive lipids such as sphingosine-1-phosphate (S1P) and lysophosphatidic acid (LPA) regulate diverse processes including cell proliferation, differentiation, and migration. However, their roles in cardiac differentiation and cardiomyocyte proliferation have not been explored. Using a 96-well differentiation platform for generating human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) we found that S1P and LPA can independently enhance cardiomyocyte generation when administered at an early stage of differentiation. We showed that the combined S1P and LPA treatment of undifferentiated hiPSCs resulted in increased nuclear accumulation of β-catenin, the canonical Wnt signaling pathway mediator, and synergized with CHIR99021, a glycogen synthase kinase 3 beta inhibitor, to enhance mesodermal induction and subsequent cardiac differentiation. At later stages of cardiac differentiation, the addition of S1P and LPA resulted in cell cycle initiation in hiPSC-CMs, an effect mediated through increased ERK signaling. Although the addition of S1P and LPA alone was insufficient to induce cell division, it was able to enhance β-catenin-mediated hiPSC-CM proliferation. In summary, we demonstrated a developmental stage-specific effect of bioactive lipids to enhance hiPSC-CM differentiation and proliferation via modulating the effect of canonical Wnt/β-catenin and ERK signaling. These findings may improve hiPSC-CM generation for cardiac disease modeling, precision medicine, and regenerative therapies.
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Sharma A, Mücke M, Seidman CE. Human Induced Pluripotent Stem Cell Production and Expansion from Blood using a Non-Integrating Viral Reprogramming Vector. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2018; 122:e58. [PMID: 29851250 PMCID: PMC5986089 DOI: 10.1002/cpmb.58] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We describe a method to transform blood lymphocytes into human-induced pluripotent stem cells by delivering four transcription factors with a non-integrative virus. Using human peripheral blood mononuclear cells (PBMCs) as the source cell type for hiPSC reprogramming is advantageous since blood samples are rapidly and safely obtained from nearly-all subjects. Reprogramming factors needed to make hiPSCs are introduced by infecting the PBMCs with non-integrating Sendai virus vectors. Reprogrammed cells can subsequently be quickly expanded for downstream use. In this unit, we present current protocols for the isolation of PBMCs from a small sample of human blood and subsequent viral reprogramming and expansion of PBMCs into hiPSCs. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Arun Sharma
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Michael Mücke
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
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40
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Sharma A, Toepfer CN, Schmid M, Garfinkel AC, Seidman CE. Differentiation and Contractile Analysis of GFP-Sarcomere Reporter hiPSC-Cardiomyocytes. ACTA ACUST UNITED AC 2018; 96:21.12.1-21.12.12. [PMID: 29364522 DOI: 10.1002/cphg.53] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) represent a powerful cellular platform for illuminating mechanisms of human cardiovascular disease and for pharmacological screening. Recent advances in CRISPR/Cas9-mediated genome editing technology underlie this profound utility. We have generated hiPSC-CMs harboring fluorescently-tagged sarcomeric proteins, which provide a tool to non-invasively study human sarcomere function and dysfunction. In this unit, we illustrate methods for conducting high-efficiency, small molecule-mediated differentiation of hiPSCs into cardiomyocytes, and for performing non-invasive contractile analysis through direct sarcomere tracking of GFP-sarcomere reporter hiPSC-CMs. We believe that this type of analysis can overcome sensitivity problems found in other forms of contractile assays involving hiPSC-CMs by directly measuring contractility at the fundamental contractile unit of the hiPSC-CM, the sarcomere. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Arun Sharma
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Christopher N Toepfer
- Department of Genetics, Harvard Medical School, Boston, Massachusetts.,Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Manuel Schmid
- Department of Genetics, Harvard Medical School, Boston, Massachusetts.,Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
| | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts
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