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Zheng Y, Li Y, Zhou K, Li T, VanDusen NJ, Hua Y. Precise genome-editing in human diseases: mechanisms, strategies and applications. Signal Transduct Target Ther 2024; 9:47. [PMID: 38409199 PMCID: PMC10897424 DOI: 10.1038/s41392-024-01750-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/28/2024] Open
Abstract
Precise genome-editing platforms are versatile tools for generating specific, site-directed DNA insertions, deletions, and substitutions. The continuous enhancement of these tools has led to a revolution in the life sciences, which promises to deliver novel therapies for genetic disease. Precise genome-editing can be traced back to the 1950s with the discovery of DNA's double-helix and, after 70 years of development, has evolved from crude in vitro applications to a wide range of sophisticated capabilities, including in vivo applications. Nonetheless, precise genome-editing faces constraints such as modest efficiency, delivery challenges, and off-target effects. In this review, we explore precise genome-editing, with a focus on introduction of the landmark events in its history, various platforms, delivery systems, and applications. First, we discuss the landmark events in the history of precise genome-editing. Second, we describe the current state of precise genome-editing strategies and explain how these techniques offer unprecedented precision and versatility for modifying the human genome. Third, we introduce the current delivery systems used to deploy precise genome-editing components through DNA, RNA, and RNPs. Finally, we summarize the current applications of precise genome-editing in labeling endogenous genes, screening genetic variants, molecular recording, generating disease models, and gene therapy, including ex vivo therapy and in vivo therapy, and discuss potential future advances.
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Affiliation(s)
- Yanjiang Zheng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yifei Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kaiyu Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Tiange Li
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Nathan J VanDusen
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| | - Yimin Hua
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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Zhou P, VanDusen NJ, Zhang Y, Cao Y, Sethi I, Hu R, Zhang S, Wang G, Ye L, Mazumdar N, Chen J, Zhang X, Guo Y, Li B, Ma Q, Lee JY, Gu W, Yuan GC, Ren B, Chen K, Pu WT. Dynamic changes in P300 enhancers and enhancer-promoter contacts control mouse cardiomyocyte maturation. Dev Cell 2023; 58:898-914.e7. [PMID: 37071996 PMCID: PMC10231645 DOI: 10.1016/j.devcel.2023.03.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 02/16/2023] [Accepted: 03/05/2023] [Indexed: 04/20/2023]
Abstract
Cardiomyocyte differentiation continues throughout murine gestation and into the postnatal period, driven by temporally regulated expression changes in the transcriptome. The mechanisms that regulate these developmental changes remain incompletely defined. Here, we used cardiomyocyte-specific ChIP-seq of the activate enhancer marker P300 to identify 54,920 cardiomyocyte enhancers at seven stages of murine heart development. These data were matched to cardiomyocyte gene expression profiles at the same stages and to Hi-C and H3K27ac HiChIP chromatin conformation data at fetal, neonatal, and adult stages. Regions with dynamic P300 occupancy exhibited developmentally regulated enhancer activity, as measured by massively parallel reporter assays in cardiomyocytes in vivo, and identified key transcription factor-binding motifs. These dynamic enhancers interacted with temporal changes of the 3D genome architecture to specify developmentally regulated cardiomyocyte gene expressions. Our work provides a 3D genome-mediated enhancer activity landscape of murine cardiomyocyte development.
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Affiliation(s)
- Pingzhu Zhou
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Nathan J VanDusen
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yanchun Zhang
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Yangpo Cao
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Isha Sethi
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Rong Hu
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Shuo Zhang
- Houston Methodist Hospital Research Institute, Houston, TX 77030, USA
| | - Guangyu Wang
- Cardiovascular Department, Houston Methodist, Weill Cornell Medical College, Houston, TX, USA
| | - Lincai Ye
- Department of Thoracic and Cardiovascular Surgery, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Neil Mazumdar
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Jian Chen
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Xiaoran Zhang
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Yuxuan Guo
- Peking University Health Science Center, Beijing, China
| | - Bin Li
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Qing Ma
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Julianna Y Lee
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Weiliang Gu
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pharmacology, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kaifu Chen
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA.
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA.
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Zheng Y, VanDusen NJ. Massively Parallel Reporter Assays for High-Throughput In Vivo Analysis of Cis-Regulatory Elements. J Cardiovasc Dev Dis 2023; 10:jcdd10040144. [PMID: 37103023 PMCID: PMC10146671 DOI: 10.3390/jcdd10040144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
The rapid improvement of descriptive genomic technologies has fueled a dramatic increase in hypothesized connections between cardiovascular gene expression and phenotypes. However, in vivo testing of these hypotheses has predominantly been relegated to slow, expensive, and linear generation of genetically modified mice. In the study of genomic cis-regulatory elements, generation of mice featuring transgenic reporters or cis-regulatory element knockout remains the standard approach. While the data obtained is of high quality, the approach is insufficient to keep pace with candidate identification and therefore results in biases introduced during the selection of candidates for validation. However, recent advances across a range of disciplines are converging to enable functional genomic assays that can be conducted in a high-throughput manner. Here, we review one such method, massively parallel reporter assays (MPRAs), in which the activities of thousands of candidate genomic regulatory elements are simultaneously assessed via the next-generation sequencing of a barcoded reporter transcript. We discuss best practices for MPRA design and use, with a focus on practical considerations, and review how this emerging technology has been successfully deployed in vivo. Finally, we discuss how MPRAs are likely to evolve and be used in future cardiovascular research.
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Cao Y, Zhang X, Akerberg BN, Yuan H, Sakamoto T, Xiao F, VanDusen NJ, Zhou P, Sweat ME, Wang Y, Prondzynski M, Chen J, Zhang Y, Wang P, Kelly DP, Pu WT. In Vivo Dissection of Chamber-Selective Enhancers Reveals Estrogen-Related Receptor as a Regulator of Ventricular Cardiomyocyte Identity. Circulation 2023; 147:881-896. [PMID: 36705030 PMCID: PMC10010668 DOI: 10.1161/circulationaha.122.061955] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND Cardiac chamber-selective transcriptional programs underpin the structural and functional differences between atrial and ventricular cardiomyocytes (aCMs and vCMs). The mechanisms responsible for these chamber-selective transcriptional programs remain largely undefined. METHODS We nominated candidate chamber-selective enhancers (CSEs) by determining the genome-wide occupancy of 7 key cardiac transcription factors (GATA4, MEF2A, MEF2C, NKX2-5, SRF, TBX5, TEAD1) and transcriptional coactivator P300 in atria and ventricles. Candidate enhancers were tested using an adeno-associated virus-mediated massively parallel reporter assay. Chromatin features of CSEs were evaluated by performing assay of transposase accessible chromatin sequencing and acetylation of histone H3 at lysine 27-HiChIP on aCMs and vCMs. CSE sequence requirements were determined by systematic tiling mutagenesis of 29 CSEs at 5 bp resolution. Estrogen-related receptor (ERR) function in cardiomyocytes was evaluated by Cre-loxP-mediated inactivation of ERRα and ERRγ in cardiomyocytes. RESULTS We identified 134 066 and 97 506 regions reproducibly occupied by at least 1 transcription factor or P300, in atria or ventricles, respectively. Enhancer activities of 2639 regions bound by transcription factors or P300 were tested in aCMs and vCMs by adeno-associated virus-mediated massively parallel reporter assay. This identified 1092 active enhancers in aCMs or vCMs. Several overlapped loci associated with cardiovascular disease through genome-wide association studies, and 229 exhibited chamber-selective activity in aCMs or vCMs. Many CSEs exhibited differential chromatin accessibility between aCMs and vCMs, and CSEs were enriched for aCM- or vCM-selective acetylation of histone H3 at lysine 27-anchored loops. Tiling mutagenesis of 29 CSEs identified the binding motif of ERRα/γ as important for ventricular enhancer activity. The requirement of ERRα/γ to activate ventricular CSEs and promote vCM identity was confirmed by loss of the vCM gene profile in ERRα/γ knockout vCMs. CONCLUSIONS We identified 229 CSEs that could be useful research tools or direct therapeutic gene expression. We showed that chamber-selective multi-transcription factor, P300 occupancy, open chromatin, and chromatin looping are predictive features of CSEs. We found that ERRα/γ are essential for maintenance of ventricular identity. Finally, our gene expression, epigenetic, 3-dimensional genome, and enhancer activity atlas provide key resources for future studies of chamber-selective gene regulation.
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Affiliation(s)
- Yangpo Cao
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Xiaoran Zhang
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Brynn N Akerberg
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Haiyun Yuan
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangzhou, China (H.Y.)
| | - Tomoya Sakamoto
- Cardiovascular Institute, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia (T.S., D.P.K.)
| | - Feng Xiao
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Nathan J VanDusen
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis (N.J.V.)
| | - Pingzhu Zhou
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Mason E Sweat
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Yi Wang
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Maksymilian Prondzynski
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Jian Chen
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Yan Zhang
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Peizhe Wang
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Daniel P Kelly
- Cardiovascular Institute, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia (T.S., D.P.K.)
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.).,Harvard Stem Cell Institute, Cambridge, MA (W.T.P.)
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Affiliation(s)
- Yanjiang Zheng
- Department of Biochemistry, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Nathan J. VanDusen
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Catalina E. Butler
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Qing Ma
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Justin S. King
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - William T. Pu
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
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VanDusen NJ, Zheng Y, Butler CE, Ma Q, King JS, Pu WT. Abstract 106: Efficient In Vivo Homology-Directed Repair Within Cardiomyocytes. Circ Res 2021. [DOI: 10.1161/res.129.suppl_1.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
CRISPR/Cas9-based genome editing technologies provide powerful tools for genetic manipulation. Delivery of Cas9 and a homology directed repair (HDR) template using adeno-associated virus (AAV; CASAAV-HDR), was recently shown to enable creation of precise genomic edits, even within postmitotic cells. Here we studied CASAAV-HDR in cardiomyocytes. We constructed an AAV9 vector containing a gRNA targeting the ventricle specific Myl2 gene, and a promoterless HDR template that replaces the native Myl2 stop codon with a self-cleaving 2A peptide followed by mScarlet, a red fluorescent protein. When this vector was injected into Cas9 expressing newborn mice, we observed mScarlet expression within a remarkably high fraction of cardiomyocytes, approximately 45%. Expression was ventricle specific, consistent with the Myl2 expression profile. Similarly, when we targeted the atrial specific Myl7 gene, we observed mScarlet expression in ~20% of atrial cardiomyocytes. Amplicon sequencing of Myl2 and Myl7 transcripts showed that the vast majority of transcripts with an insertion were mutation-free, indicating that CASAAV-HDR is precise. Furthermore, CASAAV-HDR efficiency was comparable when AAV was delivered to fetal, neonatal, or mature mice. Next we targeted seven additional loci: Yap1, Tmem43, Nfatc3, Bdh1, Mkl1, Ttn, and Pln, fusing either an HA tag or mScarlet to each. Insertion efficiency varied dramatically between loci, with HDR efficiency generally correlating with target gene expression. TTN-mScarlet and mScarlet-PLN fusion proteins localized to the sarcomere and sarcoplasmic reticulum, respectively, consistent with the localization of the endogenous proteins. Collectively these data indicate that systemic delivery of CASAAV-HDR vectors can achieve efficient, precise, in vivo somatic genome modification that does not require cardiomyocyte proliferation. We successfully used this technology to monitor protein localization and anticipate it will be useful for many other applications, such as precise introduction of mutations to model disease or probe gene function. CASAAV-HDR may also enable efficient, permanent, and precisely targeted delivery of therapeutic transgenes to validated loci.
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Affiliation(s)
| | - Yanjiang Zheng
- Shanghai Univ of Traditional Chinese Medicine, Shanghai, China
| | | | - Qing Ma
- Boston Children's Hosp, Boston, MA
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Akerberg BN, Gu F, VanDusen NJ, Zhang X, Dong R, Li K, Zhang B, Zhou B, Sethi I, Ma Q, Wasson L, Wen T, Liu J, Dong K, Conlon FL, Zhou J, Yuan GC, Zhou P, Pu WT. A reference map of murine cardiac transcription factor chromatin occupancy identifies dynamic and conserved enhancers. Nat Commun 2019; 10:4907. [PMID: 31659164 PMCID: PMC6817842 DOI: 10.1038/s41467-019-12812-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 09/27/2019] [Indexed: 01/09/2023] Open
Abstract
Mapping the chromatin occupancy of transcription factors (TFs) is a key step in deciphering developmental transcriptional programs. Here we use biotinylated knockin alleles of seven key cardiac TFs (GATA4, NKX2-5, MEF2A, MEF2C, SRF, TBX5, TEAD1) to sensitively and reproducibly map their genome-wide occupancy in the fetal and adult mouse heart. These maps show that TF occupancy is dynamic between developmental stages and that multiple TFs often collaboratively occupy the same chromatin region through indirect cooperativity. Multi-TF regions exhibit features of functional regulatory elements, including evolutionary conservation, chromatin accessibility, and activity in transcriptional enhancer assays. H3K27ac, a feature of many enhancers, incompletely overlaps multi-TF regions, and multi-TF regions lacking H3K27ac retain conservation and enhancer activity. TEAD1 is a core component of the cardiac transcriptional network, co-occupying cardiac regulatory regions and controlling cardiomyocyte-specific gene functions. Our study provides a resource for deciphering the cardiac transcriptional regulatory network and gaining insights into the molecular mechanisms governing heart development.
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Affiliation(s)
- Brynn N. Akerberg
- 0000 0004 0378 8438grid.2515.3Department of Cardiology, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115 USA
| | - Fei Gu
- 0000 0004 0378 8438grid.2515.3Department of Cardiology, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115 USA ,grid.481558.5Alibaba Cloud Intelligence Business Group, Alibaba Group, 311121 Hangzhou, China
| | - Nathan J. VanDusen
- 0000 0004 0378 8438grid.2515.3Department of Cardiology, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115 USA
| | - Xiaoran Zhang
- 0000 0004 0378 8438grid.2515.3Department of Cardiology, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115 USA
| | - Rui Dong
- 0000 0001 2106 9910grid.65499.37Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215 USA
| | - Kai Li
- 0000 0004 0378 8438grid.2515.3Department of Cardiology, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115 USA
| | - Bing Zhang
- 0000 0004 0368 8293grid.16821.3cXin Hua Hospital, Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Bin Zhou
- 0000 0004 0467 2285grid.419092.7Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, 200031 Shanghai, China
| | - Isha Sethi
- 0000 0004 0378 8438grid.2515.3Department of Cardiology, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115 USA
| | - Qing Ma
- 0000 0004 0378 8438grid.2515.3Department of Cardiology, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115 USA
| | - Lauren Wasson
- 0000000122483208grid.10698.36Biology Department, University of North Carolina at Chapel Hill, 120 South Road, Chapel Hill, NC 27599 USA
| | - Tong Wen
- 0000 0004 1758 4073grid.412604.5Department of Cardiology, The First Affiliated Hospital of Nanchang University, 330006 Nanchang, China
| | - Jinhua Liu
- 0000 0004 1758 4073grid.412604.5Department of Respiratory Medicine, The First Affiliated Hospital of Nanchang University, 330006 Nanchang, China
| | - Kunzhe Dong
- 0000 0001 2284 9329grid.410427.4Department of Pharmacology & Toxicology, Medical College of Georgia, Augusta University, 1459 Laney Walker Boulevard, Augusta, GA 30912 USA
| | - Frank L. Conlon
- 0000000122483208grid.10698.36Biology Department, University of North Carolina at Chapel Hill, 120 South Road, Chapel Hill, NC 27599 USA
| | - Jiliang Zhou
- 0000 0001 2284 9329grid.410427.4Department of Pharmacology & Toxicology, Medical College of Georgia, Augusta University, 1459 Laney Walker Boulevard, Augusta, GA 30912 USA
| | - Guo-Cheng Yuan
- 0000 0001 2106 9910grid.65499.37Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215 USA ,000000041936754Xgrid.38142.3cDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 USA
| | - Pingzhu Zhou
- 0000 0004 0378 8438grid.2515.3Department of Cardiology, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115 USA
| | - William T. Pu
- 0000 0004 0378 8438grid.2515.3Department of Cardiology, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115 USA ,000000041936754Xgrid.38142.3cHarvard Stem Cell Institute, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138 USA
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Guo Y, Jardin BD, Zhou P, Sethi I, Akerberg BN, Toepfer CN, Ai Y, Li Y, Ma Q, Guatimosim S, Hu Y, Varuzhanyan G, VanDusen NJ, Zhang D, Chan DC, Yuan GC, Seidman CE, Seidman JG, Pu WT. Hierarchical and stage-specific regulation of murine cardiomyocyte maturation by serum response factor. Nat Commun 2018; 9:3837. [PMID: 30242271 PMCID: PMC6155060 DOI: 10.1038/s41467-018-06347-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 08/30/2018] [Indexed: 02/06/2023] Open
Abstract
After birth, cardiomyocytes (CM) acquire numerous adaptations in order to efficiently pump blood throughout an animal's lifespan. How this maturation process is regulated and coordinated is poorly understood. Here, we perform a CRISPR/Cas9 screen in mice and identify serum response factor (SRF) as a key regulator of CM maturation. Mosaic SRF depletion in neonatal CMs disrupts many aspects of their maturation, including sarcomere expansion, mitochondrial biogenesis, transverse-tubule formation, and cellular hypertrophy. Maintenance of maturity in adult CMs is less dependent on SRF. This stage-specific activity is associated with developmentally regulated SRF chromatin occupancy and transcriptional regulation. SRF directly activates genes that regulate sarcomere assembly and mitochondrial dynamics. Perturbation of sarcomere assembly but not mitochondrial dynamics recapitulates SRF knockout phenotypes. SRF overexpression also perturbs CM maturation. Together, these data indicate that carefully balanced SRF activity is essential to promote CM maturation through a hierarchy of cellular processes orchestrated by sarcomere assembly.
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Affiliation(s)
- Yuxuan Guo
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Blake D Jardin
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA
| | - Pingzhu Zhou
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Isha Sethi
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Brynn N Akerberg
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Christopher N Toepfer
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Radcliffe Department of Medicine and Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Yulan Ai
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Yifei Li
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, 610041, Chengdu, Sichuan, China
| | - Qing Ma
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Silvia Guatimosim
- Department of Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, MG, CEP: 31270-901, Brazil
| | - Yongwu Hu
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
- Wenzhou Medical University, School of Life Sciences, Wenzhou, China
| | - Grigor Varuzhanyan
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, MC 114-96, Pasadena, CA, 91125, USA
| | - Nathan J VanDusen
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Donghui Zhang
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, 430062, Wuhan, China
| | - David C Chan
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, MC 114-96, Pasadena, CA, 91125, USA
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, 75 Francis Street, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD, 20815, USA
| | - Jonathan G Seidman
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA.
- Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA, 02138, USA.
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9
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Abstract
In vivo loss-of-function studies are currently limited by the need for appropriate conditional knockout alleles. CRISPR/Cas9 is a powerful tool commonly used to induce loss-of-function mutations in vitro. However, CRISPR components have been difficult to deploy in vivo. To address this problem, we developed the CASAAV (CRISPR/Cas9/AAV-based somatic mutagenesis) platform, in which recombinant adeno-associated virus (AAV) is used to deliver tandem guide RNAs and Cre recombinase to Cre-dependent Cas9-P2A-GFP mice. Because Cre is under the control of a tissue-specific promoter, this system allows temporally controlled, cell type-selective knockout of virtually any gene to be obtained within a month using only one mouse line. Here, we focus on gene disruption in cardiomyocytes, but the system could easily be adapted to inactivate genes in other cell types transduced by AAV. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Nathan J. VanDusen
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115 USA
| | - Yuxuan Guo
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115 USA
| | - Weiliang Gu
- Department of Pharmacology, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - William T. Pu
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115 USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02130, USA
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10
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Guo Y, VanDusen NJ, Zhang L, Gu W, Sethi I, Guatimosim S, Ma Q, Jardin BD, Ai Y, Zhang D, Chen B, Guo A, Yuan GC, Song LS, Pu WT. Analysis of Cardiac Myocyte Maturation Using CASAAV, a Platform for Rapid Dissection of Cardiac Myocyte Gene Function In Vivo. Circ Res 2017; 120:1874-1888. [PMID: 28356340 PMCID: PMC5466492 DOI: 10.1161/circresaha.116.310283] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/22/2017] [Accepted: 03/29/2017] [Indexed: 11/16/2022]
Abstract
RATIONALE Loss-of-function studies in cardiac myocytes (CMs) are currently limited by the need for appropriate conditional knockout alleles. The factors that regulate CM maturation are poorly understood. Previous studies on CM maturation have been confounded by heart dysfunction caused by whole organ gene inactivation. OBJECTIVE To develop a new technical platform to rapidly characterize cell-autonomous gene function in postnatal murine CMs and apply it to identify genes that regulate transverse tubules (T-tubules), a hallmark of mature CMs. METHODS AND RESULTS We developed CRISPR/Cas9/AAV9-based somatic mutagenesis, a platform in which AAV9 delivers tandem guide RNAs targeting a gene of interest and cardiac troponin-T promoter-driven Cre to RosaCas9GFP/Cas9GFP neonatal mice. When directed against junctophilin-2 (Jph2), a gene previously implicated in T-tubule maturation, we achieved efficient, rapid, and CM-specific JPH2 depletion. High-dose AAV9 ablated JPH2 in 64% CMs and caused lethal heart failure, whereas low-dose AAV9 ablated JPH2 in 22% CMs and preserved normal heart function. In the context of preserved heart function, CMs lacking JPH2 developed T-tubules that were nearly morphologically normal, indicating that JPH2 does not have a major, cell-autonomous role in T-tubule maturation. However, in hearts with severe dysfunction, both adeno-associated virus-transduced and nontransduced CMs exhibited T-tubule disruption, which was more severe in the transduced subset. These data indicate that cardiac dysfunction disrupts T-tubule structure and that JPH2 protects T-tubules in this context. We then used CRISPR/Cas9/AAV9-based somatic mutagenesis to screen 8 additional genes for required, cell-autonomous roles in T-tubule formation. We identified RYR2 (Ryanodine Receptor-2) as a novel, cell-autonomously required T-tubule maturation factor. CONCLUSIONS CRISPR/Cas9/AAV9-based somatic mutagenesis is a powerful tool to study cell-autonomous gene functions. Genetic mosaics are invaluable to accurately define cell-autonomous gene function. JPH2 has a minor role in normal T-tubule maturation but is required to stabilize T-tubules in the failing heart. RYR2 is a novel T-tubule maturation factor.
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Affiliation(s)
- Yuxuan Guo
- From the Cardiology, Boston Children's Hospital, MA (Y.G., N.J.V., Q.M., B.D.J., Y.A., D.Z., W.T.P.); Institute of Basic Medicine (L.Z.) and Pharmacology, School of Pharmacy (W.G.), Shanghai University of Traditional Chinese Medicine, China; Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (I.S., G.-C.Y.); Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil (S.G.); Cardiovascular Medicine, Department of Internal Medicine, François M. Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City (B.C., A.G., L.-S.S.); Veterans Affairs Medical Center, Iowa City (L.-S.S.); and Harvard Stem Cell Institute, Cambridge, MA (W.T.P.)
| | - Nathan J VanDusen
- From the Cardiology, Boston Children's Hospital, MA (Y.G., N.J.V., Q.M., B.D.J., Y.A., D.Z., W.T.P.); Institute of Basic Medicine (L.Z.) and Pharmacology, School of Pharmacy (W.G.), Shanghai University of Traditional Chinese Medicine, China; Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (I.S., G.-C.Y.); Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil (S.G.); Cardiovascular Medicine, Department of Internal Medicine, François M. Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City (B.C., A.G., L.-S.S.); Veterans Affairs Medical Center, Iowa City (L.-S.S.); and Harvard Stem Cell Institute, Cambridge, MA (W.T.P.)
| | - Lina Zhang
- From the Cardiology, Boston Children's Hospital, MA (Y.G., N.J.V., Q.M., B.D.J., Y.A., D.Z., W.T.P.); Institute of Basic Medicine (L.Z.) and Pharmacology, School of Pharmacy (W.G.), Shanghai University of Traditional Chinese Medicine, China; Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (I.S., G.-C.Y.); Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil (S.G.); Cardiovascular Medicine, Department of Internal Medicine, François M. Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City (B.C., A.G., L.-S.S.); Veterans Affairs Medical Center, Iowa City (L.-S.S.); and Harvard Stem Cell Institute, Cambridge, MA (W.T.P.)
| | - Weiliang Gu
- From the Cardiology, Boston Children's Hospital, MA (Y.G., N.J.V., Q.M., B.D.J., Y.A., D.Z., W.T.P.); Institute of Basic Medicine (L.Z.) and Pharmacology, School of Pharmacy (W.G.), Shanghai University of Traditional Chinese Medicine, China; Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (I.S., G.-C.Y.); Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil (S.G.); Cardiovascular Medicine, Department of Internal Medicine, François M. Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City (B.C., A.G., L.-S.S.); Veterans Affairs Medical Center, Iowa City (L.-S.S.); and Harvard Stem Cell Institute, Cambridge, MA (W.T.P.)
| | - Isha Sethi
- From the Cardiology, Boston Children's Hospital, MA (Y.G., N.J.V., Q.M., B.D.J., Y.A., D.Z., W.T.P.); Institute of Basic Medicine (L.Z.) and Pharmacology, School of Pharmacy (W.G.), Shanghai University of Traditional Chinese Medicine, China; Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (I.S., G.-C.Y.); Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil (S.G.); Cardiovascular Medicine, Department of Internal Medicine, François M. Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City (B.C., A.G., L.-S.S.); Veterans Affairs Medical Center, Iowa City (L.-S.S.); and Harvard Stem Cell Institute, Cambridge, MA (W.T.P.)
| | - Silvia Guatimosim
- From the Cardiology, Boston Children's Hospital, MA (Y.G., N.J.V., Q.M., B.D.J., Y.A., D.Z., W.T.P.); Institute of Basic Medicine (L.Z.) and Pharmacology, School of Pharmacy (W.G.), Shanghai University of Traditional Chinese Medicine, China; Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (I.S., G.-C.Y.); Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil (S.G.); Cardiovascular Medicine, Department of Internal Medicine, François M. Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City (B.C., A.G., L.-S.S.); Veterans Affairs Medical Center, Iowa City (L.-S.S.); and Harvard Stem Cell Institute, Cambridge, MA (W.T.P.)
| | - Qing Ma
- From the Cardiology, Boston Children's Hospital, MA (Y.G., N.J.V., Q.M., B.D.J., Y.A., D.Z., W.T.P.); Institute of Basic Medicine (L.Z.) and Pharmacology, School of Pharmacy (W.G.), Shanghai University of Traditional Chinese Medicine, China; Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (I.S., G.-C.Y.); Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil (S.G.); Cardiovascular Medicine, Department of Internal Medicine, François M. Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City (B.C., A.G., L.-S.S.); Veterans Affairs Medical Center, Iowa City (L.-S.S.); and Harvard Stem Cell Institute, Cambridge, MA (W.T.P.)
| | - Blake D Jardin
- From the Cardiology, Boston Children's Hospital, MA (Y.G., N.J.V., Q.M., B.D.J., Y.A., D.Z., W.T.P.); Institute of Basic Medicine (L.Z.) and Pharmacology, School of Pharmacy (W.G.), Shanghai University of Traditional Chinese Medicine, China; Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (I.S., G.-C.Y.); Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil (S.G.); Cardiovascular Medicine, Department of Internal Medicine, François M. Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City (B.C., A.G., L.-S.S.); Veterans Affairs Medical Center, Iowa City (L.-S.S.); and Harvard Stem Cell Institute, Cambridge, MA (W.T.P.)
| | - Yulan Ai
- From the Cardiology, Boston Children's Hospital, MA (Y.G., N.J.V., Q.M., B.D.J., Y.A., D.Z., W.T.P.); Institute of Basic Medicine (L.Z.) and Pharmacology, School of Pharmacy (W.G.), Shanghai University of Traditional Chinese Medicine, China; Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (I.S., G.-C.Y.); Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil (S.G.); Cardiovascular Medicine, Department of Internal Medicine, François M. Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City (B.C., A.G., L.-S.S.); Veterans Affairs Medical Center, Iowa City (L.-S.S.); and Harvard Stem Cell Institute, Cambridge, MA (W.T.P.)
| | - Donghui Zhang
- From the Cardiology, Boston Children's Hospital, MA (Y.G., N.J.V., Q.M., B.D.J., Y.A., D.Z., W.T.P.); Institute of Basic Medicine (L.Z.) and Pharmacology, School of Pharmacy (W.G.), Shanghai University of Traditional Chinese Medicine, China; Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (I.S., G.-C.Y.); Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil (S.G.); Cardiovascular Medicine, Department of Internal Medicine, François M. Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City (B.C., A.G., L.-S.S.); Veterans Affairs Medical Center, Iowa City (L.-S.S.); and Harvard Stem Cell Institute, Cambridge, MA (W.T.P.)
| | - Biyi Chen
- From the Cardiology, Boston Children's Hospital, MA (Y.G., N.J.V., Q.M., B.D.J., Y.A., D.Z., W.T.P.); Institute of Basic Medicine (L.Z.) and Pharmacology, School of Pharmacy (W.G.), Shanghai University of Traditional Chinese Medicine, China; Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (I.S., G.-C.Y.); Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil (S.G.); Cardiovascular Medicine, Department of Internal Medicine, François M. Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City (B.C., A.G., L.-S.S.); Veterans Affairs Medical Center, Iowa City (L.-S.S.); and Harvard Stem Cell Institute, Cambridge, MA (W.T.P.)
| | - Ang Guo
- From the Cardiology, Boston Children's Hospital, MA (Y.G., N.J.V., Q.M., B.D.J., Y.A., D.Z., W.T.P.); Institute of Basic Medicine (L.Z.) and Pharmacology, School of Pharmacy (W.G.), Shanghai University of Traditional Chinese Medicine, China; Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (I.S., G.-C.Y.); Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil (S.G.); Cardiovascular Medicine, Department of Internal Medicine, François M. Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City (B.C., A.G., L.-S.S.); Veterans Affairs Medical Center, Iowa City (L.-S.S.); and Harvard Stem Cell Institute, Cambridge, MA (W.T.P.)
| | - Guo-Cheng Yuan
- From the Cardiology, Boston Children's Hospital, MA (Y.G., N.J.V., Q.M., B.D.J., Y.A., D.Z., W.T.P.); Institute of Basic Medicine (L.Z.) and Pharmacology, School of Pharmacy (W.G.), Shanghai University of Traditional Chinese Medicine, China; Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (I.S., G.-C.Y.); Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil (S.G.); Cardiovascular Medicine, Department of Internal Medicine, François M. Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City (B.C., A.G., L.-S.S.); Veterans Affairs Medical Center, Iowa City (L.-S.S.); and Harvard Stem Cell Institute, Cambridge, MA (W.T.P.)
| | - Long-Sheng Song
- From the Cardiology, Boston Children's Hospital, MA (Y.G., N.J.V., Q.M., B.D.J., Y.A., D.Z., W.T.P.); Institute of Basic Medicine (L.Z.) and Pharmacology, School of Pharmacy (W.G.), Shanghai University of Traditional Chinese Medicine, China; Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (I.S., G.-C.Y.); Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil (S.G.); Cardiovascular Medicine, Department of Internal Medicine, François M. Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City (B.C., A.G., L.-S.S.); Veterans Affairs Medical Center, Iowa City (L.-S.S.); and Harvard Stem Cell Institute, Cambridge, MA (W.T.P.)
| | - William T Pu
- From the Cardiology, Boston Children's Hospital, MA (Y.G., N.J.V., Q.M., B.D.J., Y.A., D.Z., W.T.P.); Institute of Basic Medicine (L.Z.) and Pharmacology, School of Pharmacy (W.G.), Shanghai University of Traditional Chinese Medicine, China; Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (I.S., G.-C.Y.); Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil (S.G.); Cardiovascular Medicine, Department of Internal Medicine, François M. Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City (B.C., A.G., L.-S.S.); Veterans Affairs Medical Center, Iowa City (L.-S.S.); and Harvard Stem Cell Institute, Cambridge, MA (W.T.P.).
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11
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Galdos FX, Guo Y, Paige SL, VanDusen NJ, Wu SM, Pu WT. Cardiac Regeneration: Lessons From Development. Circ Res 2017; 120:941-959. [PMID: 28302741 DOI: 10.1161/circresaha.116.309040] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/14/2016] [Accepted: 12/15/2016] [Indexed: 02/06/2023]
Abstract
Palliative surgery for congenital heart disease has allowed patients with previously lethal heart malformations to survive and, in most cases, to thrive. However, these procedures often place pressure and volume loads on the heart, and over time, these chronic loads can cause heart failure. Current therapeutic options for initial surgery and chronic heart failure that results from failed palliation are limited, in part, by the mammalian heart's low inherent capacity to form new cardiomyocytes. Surmounting the heart regeneration barrier would transform the treatment of congenital, as well as acquired, heart disease and likewise would enable development of personalized, in vitro cardiac disease models. Although these remain distant goals, studies of heart development are illuminating the path forward and suggest unique opportunities for heart regeneration, particularly in fetal and neonatal periods. Here, we review major lessons from heart development that inform current and future studies directed at enhancing cardiac regeneration.
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Affiliation(s)
- Francisco X Galdos
- From the Cardiovascular Institute, School of Medicine, Stanford University, CA (F.X.G., S.L.P., S.M.W.); Department of Cardiology, Boston Children's Hospital, MA (Y.G., N.J.V., W.T.P.); Division of Pediatric Cardiology, Department of Pediatrics (S.L.P.), Division of Cardiovascular Medicine, Department of Medicine (S.M.W.), and Institute of Stem Cell and Regenerative Biology, School of Medicine, Stanford, CA (F.X.G., S.L.P., S.M.W.); and Harvard Stem Cell Institute, Harvard University, Cambridge, MA (W.T.P.)
| | - Yuxuan Guo
- From the Cardiovascular Institute, School of Medicine, Stanford University, CA (F.X.G., S.L.P., S.M.W.); Department of Cardiology, Boston Children's Hospital, MA (Y.G., N.J.V., W.T.P.); Division of Pediatric Cardiology, Department of Pediatrics (S.L.P.), Division of Cardiovascular Medicine, Department of Medicine (S.M.W.), and Institute of Stem Cell and Regenerative Biology, School of Medicine, Stanford, CA (F.X.G., S.L.P., S.M.W.); and Harvard Stem Cell Institute, Harvard University, Cambridge, MA (W.T.P.)
| | - Sharon L Paige
- From the Cardiovascular Institute, School of Medicine, Stanford University, CA (F.X.G., S.L.P., S.M.W.); Department of Cardiology, Boston Children's Hospital, MA (Y.G., N.J.V., W.T.P.); Division of Pediatric Cardiology, Department of Pediatrics (S.L.P.), Division of Cardiovascular Medicine, Department of Medicine (S.M.W.), and Institute of Stem Cell and Regenerative Biology, School of Medicine, Stanford, CA (F.X.G., S.L.P., S.M.W.); and Harvard Stem Cell Institute, Harvard University, Cambridge, MA (W.T.P.)
| | - Nathan J VanDusen
- From the Cardiovascular Institute, School of Medicine, Stanford University, CA (F.X.G., S.L.P., S.M.W.); Department of Cardiology, Boston Children's Hospital, MA (Y.G., N.J.V., W.T.P.); Division of Pediatric Cardiology, Department of Pediatrics (S.L.P.), Division of Cardiovascular Medicine, Department of Medicine (S.M.W.), and Institute of Stem Cell and Regenerative Biology, School of Medicine, Stanford, CA (F.X.G., S.L.P., S.M.W.); and Harvard Stem Cell Institute, Harvard University, Cambridge, MA (W.T.P.)
| | - Sean M Wu
- From the Cardiovascular Institute, School of Medicine, Stanford University, CA (F.X.G., S.L.P., S.M.W.); Department of Cardiology, Boston Children's Hospital, MA (Y.G., N.J.V., W.T.P.); Division of Pediatric Cardiology, Department of Pediatrics (S.L.P.), Division of Cardiovascular Medicine, Department of Medicine (S.M.W.), and Institute of Stem Cell and Regenerative Biology, School of Medicine, Stanford, CA (F.X.G., S.L.P., S.M.W.); and Harvard Stem Cell Institute, Harvard University, Cambridge, MA (W.T.P.).
| | - William T Pu
- From the Cardiovascular Institute, School of Medicine, Stanford University, CA (F.X.G., S.L.P., S.M.W.); Department of Cardiology, Boston Children's Hospital, MA (Y.G., N.J.V., W.T.P.); Division of Pediatric Cardiology, Department of Pediatrics (S.L.P.), Division of Cardiovascular Medicine, Department of Medicine (S.M.W.), and Institute of Stem Cell and Regenerative Biology, School of Medicine, Stanford, CA (F.X.G., S.L.P., S.M.W.); and Harvard Stem Cell Institute, Harvard University, Cambridge, MA (W.T.P.).
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12
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VanDusen NJ, Casanovas J, Vincentz JW, Firulli BA, Osterwalder M, Lopez-Rios J, Zeller R, Zhou B, Grego-Bessa J, De La Pompa JL, Shou W, Firulli AB. Hand2 is an essential regulator for two Notch-dependent functions within the embryonic endocardium. Cell Rep 2014; 9:2071-83. [PMID: 25497097 DOI: 10.1016/j.celrep.2014.11.021] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 10/24/2014] [Accepted: 11/13/2014] [Indexed: 12/12/2022] Open
Abstract
The basic-helix-loop-helix (bHLH) transcription factor Hand2 plays critical roles during cardiac morphogenesis via expression and function within myocardial, neural crest, and epicardial cell populations. Here, we show that Hand2 plays two essential Notch-dependent roles within the endocardium. Endocardial ablation of Hand2 results in failure to develop a patent tricuspid valve, intraventricular septum defects, and hypotrabeculated ventricles, which collectively resemble the human congenital defect tricuspid atresia. We show endocardial Hand2 to be an integral downstream component of a Notch endocardium-to-myocardium signaling pathway and a direct transcriptional regulator of Neuregulin1. Additionally, Hand2 participates in endocardium-to-endocardium-based cell signaling, with Hand2 mutant hearts displaying an increased density of coronary lumens. Molecular analyses further reveal dysregulation of several crucial components of Vegf signaling, including VegfA, VegfR2, Nrp1, and VegfR3. Thus, Hand2 functions as a crucial downstream transcriptional effector of endocardial Notch signaling during both cardiogenesis and coronary vasculogenesis.
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Affiliation(s)
- Nathan J VanDusen
- Riley Heart Research Center, Wells Center for Pediatric Research, Departments of Pediatrics and Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Jose Casanovas
- Riley Heart Research Center, Wells Center for Pediatric Research, Departments of Pediatrics and Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Joshua W Vincentz
- Riley Heart Research Center, Wells Center for Pediatric Research, Departments of Pediatrics and Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Beth A Firulli
- Riley Heart Research Center, Wells Center for Pediatric Research, Departments of Pediatrics and Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Marco Osterwalder
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Javier Lopez-Rios
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Rolf Zeller
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Bin Zhou
- Department of Genetics, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Joaquim Grego-Bessa
- Department of Developmental Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - José Luis De La Pompa
- Cardiovascular Developmental Biology Program, Cardiovascular Development and Repair Department, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Weinian Shou
- Riley Heart Research Center, Wells Center for Pediatric Research, Departments of Pediatrics and Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Anthony B Firulli
- Riley Heart Research Center, Wells Center for Pediatric Research, Departments of Pediatrics and Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA.
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13
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Chen H, Zhang W, Sun X, Yoshimoto M, Chen Z, Zhu W, Liu J, Shen Y, Yong W, Li D, Zhang J, Lin Y, Li B, VanDusen NJ, Snider P, Schwartz RJ, Conway SJ, Field LJ, Yoder MC, Firulli AB, Carlesso N, Towbin JA, Shou W. Fkbp1a controls ventricular myocardium trabeculation and compaction by regulating endocardial Notch1 activity. Development 2013; 140:1946-57. [PMID: 23571217 DOI: 10.1242/dev.089920] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Trabeculation and compaction of the embryonic myocardium are morphogenetic events crucial for the formation and function of the ventricular walls. Fkbp1a (FKBP12) is a ubiquitously expressed cis-trans peptidyl-prolyl isomerase. Fkbp1a-deficient mice develop ventricular hypertrabeculation and noncompaction. To determine the physiological function of Fkbp1a in regulating the intercellular and intracellular signaling pathways involved in ventricular trabeculation and compaction, we generated a series of Fkbp1a conditional knockouts. Surprisingly, cardiomyocyte-restricted ablation of Fkbp1a did not give rise to the ventricular developmental defect, whereas endothelial cell-restricted ablation of Fkbp1a recapitulated the ventricular hypertrabeculation and noncompaction observed in Fkbp1a systemically deficient mice, suggesting an important contribution of Fkbp1a within the developing endocardia in regulating the morphogenesis of ventricular trabeculation and compaction. Further analysis demonstrated that Fkbp1a is a novel negative modulator of activated Notch1. Activated Notch1 (N1ICD) was significantly upregulated in Fkbp1a-ablated endothelial cells in vivo and in vitro. Overexpression of Fkbp1a significantly reduced the stability of N1ICD and direct inhibition of Notch signaling significantly reduced hypertrabeculation in Fkbp1a-deficient mice. Our findings suggest that Fkbp1a-mediated regulation of Notch1 plays an important role in intercellular communication between endocardium and myocardium, which is crucial in controlling the formation of the ventricular walls.
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Affiliation(s)
- Hanying Chen
- Riley Heart Research Center, Division of Pediatric Cardiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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14
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VanDusen NJ, Firulli AB. Twist factor regulation of non-cardiomyocyte cell lineages in the developing heart. Differentiation 2012; 84:79-88. [PMID: 22516205 DOI: 10.1016/j.diff.2012.03.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 02/14/2012] [Accepted: 03/07/2012] [Indexed: 12/31/2022]
Abstract
The heart is a complex organ that is composed of numerous cell types, which must integrate their programs for proper specification, differentiation and cardiac morphogenesis. During cardiogenesis members of the Twist-family of basic helix-loop-helix (bHLH) transcription factors play distinct roles within cardiac lineages such as the endocardium and extra-cardiac lineages such as the cardiac neural crest (cNCC) and epicardium. While the study of these cell populations is often eclipsed by that of cardiomyocytes, the contributions of non-cardiomyocytes to development and disease are increasingly being appreciated as both dynamic and essential. This review summarizes what is known regarding Twist-family bHLH function in extra-cardiac cell populations and the endocardium, with a focus on regulatory mechanisms, downstream targets, and expression profiles. Improving our understanding of the molecular pathways that Twist-family bHLH factors mediate in these lineages will be necessary to ascertain how their dysfunction leads to congenital disease and adult pathologies such as myocardial infarctions and cardiac fibroblast induced fibrosis. Indeed, this knowledge will prove to be critical to clinicians seeking to improve current treatments.
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Affiliation(s)
- Nathan J VanDusen
- Riley Heart Research Center, Wells Center for Pediatric Research, Division of Pediatric Cardiology, Department of Medical and Molecular Genetics, Indiana Medical School, 1044 W. Walnut St., Indianapolis, IN 46202-5225, USA
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Barnes RM, Firulli BA, VanDusen NJ, Morikawa Y, Conway SJ, Cserjesi P, Vincentz JW, Firulli AB. Hand2 loss-of-function in Hand1-expressing cells reveals distinct roles in epicardial and coronary vessel development. Circ Res 2011; 108:940-9. [PMID: 21350214 DOI: 10.1161/circresaha.110.233171] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
RATIONALE The basic helix-loop-helix (bHLH) transcription factors Hand1 and Hand2 are essential for embryonic development. Given their requirement for cardiogenesis, it is imperative to determine their impact on cardiovascular function. OBJECTIVE To deduce the role of Hand2 within the epicardium. METHOD AND RESULTS We engineered a Hand1 allele expressing Cre recombinase. Cardiac Hand1 expression is largely limited to cells of the primary heart field, overlapping little with Hand2 expression. Hand1 is expressed within the septum transversum, and the Hand1 lineage marks the proepicardial organ and epicardium. To examine Hand factor functional overlap, we conditionally deleted Hand2 from Hand1-expressing cells. Hand2 mutants display defective epicardialization and fail to form coronary arteries, coincident with altered extracellular matrix deposition and Pdgfr expression. CONCLUSIONS These data demonstrate a hierarchal relationship whereby transient Hand1 septum transversum expression defines epicardial precursors that are subsequently dependent on Hand2 function.
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Affiliation(s)
- Ralston M Barnes
- Riley Heart Research Center, Wells Center for Pediatric Research, Division of Pediatric Cardiology, Departments of Anatomy and Medical and Molecular Genetics, Indiana Medical School, Indianapolis, 46202-5225, USA
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