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Jia X, Wu J, Chen X, Hou S, Li Y, Zhao L, Zhu Y, Li Z, Deng C, Su W, Zhuo Y. Cell atlas of trabecular meshwork in glaucomatous non-human primates and DEGs related to tissue contract based on single-cell transcriptomics. iScience 2023; 26:108024. [PMID: 37867950 PMCID: PMC10589847 DOI: 10.1016/j.isci.2023.108024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 05/22/2023] [Accepted: 09/19/2023] [Indexed: 10/24/2023] Open
Abstract
As the major channel of aqueous humor outflow, dysfunction of trabecular meshwork (TM) can lead to intraocular pressure elevating, which can trigger primary open-angle glaucoma (POAG). In this study, we use single-cell RNA sequencing (scRNA-seq) technique to build an atlas and further explore the spontaneous POAG and healthy macaques cellular heterogeneity associated with the dysfunction of TM contraction. We built the TM atlas, which identified 14 different cell types. In Beam A, Beam B, Beam C, and smooth muscle cell (SMC) cell types, we first found multiple genes associated with TM contraction (e.g., TPM1, ACTC1, TNNT1), determining their differential expression in the POAG and healthy groups. In addition, the microstructural alterations in TM of POAG non-human primates were observed, which was compact and collapsed. Thus, our study indicated that TPM1 may be a key target for regulating TM structure, contraction function, and resistance of aqueous humor outflow.
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Affiliation(s)
- Xu Jia
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, Guangdong, China
- The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Jian Wu
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
- Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China
| | - Xiaohong Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, Guangdong, China
| | - Simeng Hou
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
- Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China
| | - Yangyang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, Guangdong, China
| | - Ling Zhao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, Guangdong, China
| | - Yingting Zhu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, Guangdong, China
| | - Zhidong Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, Guangdong, China
| | - Caibin Deng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, Guangdong, China
| | - Wenru Su
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, Guangdong, China
| | - Yehong Zhuo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, Guangdong, China
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Cao J, Routh AL, Kuyumcu-Martinez MN. Nanopore sequencing reveals full-length Tropomyosin 1 isoforms and their regulation by RNA-binding proteins during rat heart development. J Cell Mol Med 2021; 25:8352-8362. [PMID: 34302435 PMCID: PMC8419188 DOI: 10.1111/jcmm.16795] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 12/11/2022] Open
Abstract
Alternative splicing (AS) contributes to the diversity of the proteome by producing multiple isoforms from a single gene. Although short‐read RNA‐sequencing methods have been the gold standard for determining AS patterns of genes, they have a difficulty in defining full‐length mRNA isoforms assembled using different exon combinations. Tropomyosin 1 (TPM1) is an actin‐binding protein required for cytoskeletal functions in non‐muscle cells and for contraction in muscle cells. Tpm1 undergoes AS regulation to generate muscle versus non‐muscle TPM1 protein isoforms with distinct physiological functions. It is unclear which full‐length Tpm1 isoforms are produced via AS and how they are regulated during heart development. To address these, we utilized nanopore long‐read cDNA sequencing without gene‐specific PCR amplification. In rat hearts, we identified full‐length Tpm1 isoforms composed of distinct exons with specific exon linkages. We showed that Tpm1 undergoes AS transitions during embryonic heart development such that muscle‐specific exons are connected generating predominantly muscle‐specific Tpm1 isoforms in adult hearts. We found that the RNA‐binding protein RBFOX2 controls AS of rat Tpm1 exon 6a, which is important for cooperative actin binding. Furthermore, RBFOX2 regulates Tpm1 AS of exon 6a antagonistically to the RNA‐binding protein PTBP1. In sum, we defined full‐length Tpm1 isoforms with different exon combinations that are tightly regulated during cardiac development and provided insights into the regulation of Tpm1 AS by RNA‐binding proteins. Our results demonstrate that nanopore sequencing is an excellent tool to determine full‐length AS variants of muscle‐enriched genes.
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Affiliation(s)
- Jun Cao
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Andrew L Routh
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA.,Sealy Centre for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas, USA
| | - Muge N Kuyumcu-Martinez
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA.,Institute for Translational Sciences, University of Texas Medical Branch, Galveston, Texas, USA.,Department of Neuroscience, Cell Biology, and Anatomy, University of Texas Medical Branch, Galveston, Texas, USA
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3
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Camps J, Breuls N, Sifrim A, Giarratana N, Corvelyn M, Danti L, Grosemans H, Vanuytven S, Thiry I, Belicchi M, Meregalli M, Platko K, MacDonald ME, Austin RC, Gijsbers R, Cossu G, Torrente Y, Voet T, Sampaolesi M. Interstitial Cell Remodeling Promotes Aberrant Adipogenesis in Dystrophic Muscles. Cell Rep 2021; 31:107597. [PMID: 32375047 DOI: 10.1016/j.celrep.2020.107597] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 03/06/2020] [Accepted: 04/10/2020] [Indexed: 12/26/2022] Open
Abstract
Fibrosis and fat replacement in skeletal muscle are major complications that lead to a loss of mobility in chronic muscle disorders, such as muscular dystrophy. However, the in vivo properties of adipogenic stem and precursor cells remain unclear, mainly due to the high cell heterogeneity in skeletal muscles. Here, we use single-cell RNA sequencing to decomplexify interstitial cell populations in healthy and dystrophic skeletal muscles. We identify an interstitial CD142-positive cell population in mice and humans that is responsible for the inhibition of adipogenesis through GDF10 secretion. Furthermore, we show that the interstitial cell composition is completely altered in muscular dystrophy, with a near absence of CD142-positive cells. The identification of these adipo-regulatory cells in the skeletal muscle aids our understanding of the aberrant fat deposition in muscular dystrophy, paving the way for treatments that could counteract degeneration in patients with muscular dystrophy.
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Affiliation(s)
- Jordi Camps
- Laboratory of Translational Cardiomyology, Department of Development and Regeneration, Stem Cell Research Institute, KU Leuven, 3000 Leuven, Belgium; Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Natacha Breuls
- Laboratory of Translational Cardiomyology, Department of Development and Regeneration, Stem Cell Research Institute, KU Leuven, 3000 Leuven, Belgium
| | - Alejandro Sifrim
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium; Wellcome Genome Campus, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Nefele Giarratana
- Laboratory of Translational Cardiomyology, Department of Development and Regeneration, Stem Cell Research Institute, KU Leuven, 3000 Leuven, Belgium
| | - Marlies Corvelyn
- Laboratory of Translational Cardiomyology, Department of Development and Regeneration, Stem Cell Research Institute, KU Leuven, 3000 Leuven, Belgium
| | - Laura Danti
- Laboratory of Translational Cardiomyology, Department of Development and Regeneration, Stem Cell Research Institute, KU Leuven, 3000 Leuven, Belgium
| | - Hanne Grosemans
- Laboratory of Translational Cardiomyology, Department of Development and Regeneration, Stem Cell Research Institute, KU Leuven, 3000 Leuven, Belgium
| | - Sebastiaan Vanuytven
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Irina Thiry
- Laboratory for Molecular Virology and Gene Therapy, and Leuven Viral Vector Core, KU Leuven, 3000 Leuven, Belgium
| | - Marzia Belicchi
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Centro Dino Ferrari, 20122 Milan, Italy
| | - Mirella Meregalli
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Centro Dino Ferrari, 20122 Milan, Italy
| | - Khrystyna Platko
- Department of Medicine, The Research Institute of St. Joe's Hamilton, Hamilton Centre for Kidney Research, McMaster University, Hamilton, ON L8N 4A6, Canada
| | - Melissa E MacDonald
- Department of Medicine, The Research Institute of St. Joe's Hamilton, Hamilton Centre for Kidney Research, McMaster University, Hamilton, ON L8N 4A6, Canada
| | - Richard C Austin
- Department of Medicine, The Research Institute of St. Joe's Hamilton, Hamilton Centre for Kidney Research, McMaster University, Hamilton, ON L8N 4A6, Canada
| | - Rik Gijsbers
- Laboratory for Molecular Virology and Gene Therapy, and Leuven Viral Vector Core, KU Leuven, 3000 Leuven, Belgium
| | - Giulio Cossu
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Yvan Torrente
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Centro Dino Ferrari, 20122 Milan, Italy
| | - Thierry Voet
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium; Wellcome Genome Campus, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Maurilio Sampaolesi
- Laboratory of Translational Cardiomyology, Department of Development and Regeneration, Stem Cell Research Institute, KU Leuven, 3000 Leuven, Belgium; Human Anatomy Unit, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy.
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Fochi S, Lorenzi P, Galasso M, Stefani C, Trabetti E, Zipeto D, Romanelli MG. The Emerging Role of the RBM20 and PTBP1 Ribonucleoproteins in Heart Development and Cardiovascular Diseases. Genes (Basel) 2020; 11:genes11040402. [PMID: 32276354 PMCID: PMC7230170 DOI: 10.3390/genes11040402] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/04/2020] [Accepted: 04/06/2020] [Indexed: 12/17/2022] Open
Abstract
Alternative splicing is a regulatory mechanism essential for cell differentiation and tissue organization. More than 90% of human genes are regulated by alternative splicing events, which participate in cell fate determination. The general mechanisms of splicing events are well known, whereas only recently have deep-sequencing, high throughput analyses and animal models provided novel information on the network of functionally coordinated, tissue-specific, alternatively spliced exons. Heart development and cardiac tissue differentiation require thoroughly regulated splicing events. The ribonucleoprotein RBM20 is a key regulator of the alternative splicing events required for functional and structural heart properties, such as the expression of TTN isoforms. Recently, the polypyrimidine tract-binding protein PTBP1 has been demonstrated to participate with RBM20 in regulating splicing events. In this review, we summarize the updated knowledge relative to RBM20 and PTBP1 structure and molecular function; their role in alternative splicing mechanisms involved in the heart development and function; RBM20 mutations associated with idiopathic dilated cardiovascular disease (DCM); and the consequences of RBM20-altered expression or dysfunction. Furthermore, we discuss the possible application of targeting RBM20 in new approaches in heart therapies.
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5
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Dube DK, Dube S, Shrestha R, Abbott L, Randhawa S, Muthu V, Fan Y, Wang J, Sanger JM, Sanger JW, Poiesz BJ. Qualitative and quantitative evaluation of TPM transcripts and proteins in developing striated chicken muscles indicate TPM4α is the major sarcomeric cardiac tropomyosin from early embryonic life to adulthood. Cytoskeleton (Hoboken) 2018; 75:437-449. [PMID: 30255988 PMCID: PMC6279486 DOI: 10.1002/cm.21495] [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: 06/11/2018] [Revised: 07/13/2018] [Accepted: 07/30/2018] [Indexed: 11/09/2022]
Abstract
The chicken has been used since the 1980s as an animal model for developmental studies regarding tropomyosin isoform diversity in striated muscles, however, the pattern of expression of transcripts as well as the corresponding TPM proteins of various tropomyosin isoforms in avian hearts are not well documented. In this study, using conventional and qRT-PCR, we report the expression of transcripts for various sarcomeric TPM isoforms in striated muscles through development. Transcripts of both TPM1α and TPM1κ, the two sarcomeric isoforms of the TPM1 gene, are expressed in embryonic chicken hearts but disappear in post hatch stages. TPM1α transcripts are expressed in embryonic and adult skeletal muscle. The sarcomeric isoform of the TPM2 gene is expressed mostly in embryonic skeletal muscles. As reported earlier, TPM3α is expressed in embryonic heart and skeletal muscle but significantly lower in adult striated muscle. TPM4α transcripts are expressed from embryonic to adult chicken hearts but not in skeletal muscle. Our 2D Western blot analyses using CH1 monoclonal antibody followed by mass spectra evaluations found TPM4α protein is the major sarcomeric tropomysin expressed in embryonic chicken hearts. However, in 7-day-old embryonic hearts, a minute quantity of TPM1α or TPM1κ is also expressed. This finding suggests that sarcomeric TPM1 protein may play some important role in cardiac contractility and/or cardiac morphogenesis during embryogenesis. Since only the transcripts of TPM4α are expressed in adult chicken hearts, it is logical to presume that TPM4α is the only sarcomeric TPM protein produced in adult cardiac tissues.
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Affiliation(s)
- Dipak K Dube
- Department of Medicine, Upatate Medical University, Syracuse, New York
| | - Syamalima Dube
- Department of Medicine, Upatate Medical University, Syracuse, New York
| | - Runa Shrestha
- Department of Medicine, Upatate Medical University, Syracuse, New York
| | - Lynn Abbott
- Department of Medicine, Upatate Medical University, Syracuse, New York
| | - Samender Randhawa
- Department of Medicine, Upatate Medical University, Syracuse, New York
| | - Vasundhara Muthu
- Department of Medicine, Upatate Medical University, Syracuse, New York
| | - Yingli Fan
- Department of Cell and Developmental Biology, Upatate Medical University, Syracuse, New York
| | - Jushuo Wang
- Department of Cell and Developmental Biology, Upatate Medical University, Syracuse, New York
| | - Jean M Sanger
- Department of Cell and Developmental Biology, Upatate Medical University, Syracuse, New York
| | - Joseph W Sanger
- Department of Cell and Developmental Biology, Upatate Medical University, Syracuse, New York
| | - Bernard J Poiesz
- Department of Medicine, Upatate Medical University, Syracuse, New York
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6
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Dube S, Abbott L, Randhawa S, Fan Y, Wang J, Sanger JM, Sanger JW, Poiesz BJ, Dube DK. Sarcomeric TPM3α in developing chicken. Cytoskeleton (Hoboken) 2018; 75:174-182. [PMID: 29220867 PMCID: PMC5899948 DOI: 10.1002/cm.21426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/27/2017] [Accepted: 11/30/2017] [Indexed: 01/11/2023]
Abstract
Cloning and sequencing of various tropomyosin isoforms expressed in chickens have been described since the early 1980s. However, to the best of our knowledge, this is the first report on the molecular characterization and the expression of the sarcomeric isoform of the TPM3 gene in cardiac and skeletal muscles from developing as well as adult chickens. Expression of TPM3α was performed by conventional RT-PCR as well as qRT-PCR using relative expression (by ΔCT as well as ΔΔCT methods) and by determining absolute copy number. The results employing all these methods show that the expression level of TPM3α is maximum in embryonic (10-day/15-day old) skeletal muscle and can barely be detected in both cardiac and skeletal muscles from the adult chicken. Our various RT-PCR analyses suggest that the expression of high molecular weight TPM3 isoforms are regulated at the transcription level from the proximal promoter at the 5'-end of the TPM3 gene.
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Affiliation(s)
- Syamalima Dube
- Department of Medicine, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York 13210
| | - Lynn Abbott
- Department of Medicine, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York 13210
| | - Samender Randhawa
- Department of Medicine, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York 13210
| | - Yingli Fan
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York 13210
| | - Jushuo Wang
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York 13210
| | - Jean M Sanger
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York 13210
| | - Joseph W. Sanger
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York 13210
| | - Bernard J. Poiesz
- Department of Medicine, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York 13210
| | - Dipak K. Dube
- Department of Medicine, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York 13210
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York 13210
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Liu Z, Wang L, Welch JD, Ma H, Zhou Y, Vaseghi HR, Yu S, Wall JB, Alimohamadi S, Zheng M, Yin C, Shen W, Prins JF, Liu J, Qian L. Single-cell transcriptomics reconstructs fate conversion from fibroblast to cardiomyocyte. Nature 2017; 551:100-104. [PMID: 29072293 PMCID: PMC5954984 DOI: 10.1038/nature24454] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 09/22/2017] [Indexed: 12/18/2022]
Abstract
Direct lineage conversion offers a new strategy for tissue regeneration and disease modelling. Despite recent success in directly reprogramming fibroblasts into various cell types, the precise changes that occur as fibroblasts progressively convert to the target cell fates remain unclear. The inherent heterogeneity and asynchronous nature of the reprogramming process renders it difficult to study this process using bulk genomic techniques. Here we used single-cell RNA sequencing to overcome this limitation and analysed global transcriptome changes at early stages during the reprogramming of mouse fibroblasts into induced cardiomyocytes (iCMs). Using unsupervised dimensionality reduction and clustering algorithms, we identified molecularly distinct subpopulations of cells during reprogramming. We also constructed routes of iCM formation, and delineated the relationship between cell proliferation and iCM induction. Further analysis of global gene expression changes during reprogramming revealed unexpected downregulation of factors involved in mRNA processing and splicing. Detailed functional analysis of the top candidate splicing factor, Ptbp1, revealed that it is a critical barrier for the acquisition of cardiomyocyte-specific splicing patterns in fibroblasts. Concomitantly, Ptbp1 depletion promoted cardiac transcriptome acquisition and increased iCM reprogramming efficiency. Additional quantitative analysis of our dataset revealed a strong correlation between the expression of each reprogramming factor and the progress of individual cells through the reprogramming process, and led to the discovery of new surface markers for the enrichment of iCMs. In summary, our single-cell transcriptomics approaches enabled us to reconstruct the reprogramming trajectory and to uncover intermediate cell populations, gene pathways and regulators involved in iCM induction.
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Affiliation(s)
- Ziqing Liu
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
| | - Li Wang
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
| | - Joshua D. Welch
- Department of Computer Science, University of North Carolina at Chapel Hill
| | - Hong Ma
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
| | - Yang Zhou
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
| | - Haley Ruth Vaseghi
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
| | - Shuo Yu
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
| | - Joseph Blake Wall
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
| | - Sahar Alimohamadi
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
| | - Michael Zheng
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
| | - Chaoying Yin
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
| | - Weining Shen
- Department of Statistics, University of California at Irvine
| | - Jan F. Prins
- Department of Computer Science, University of North Carolina at Chapel Hill
| | - Jiandong Liu
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
| | - Li Qian
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
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Thomas DR, Chadwell BA, Walker GR, Budde JE, VandeBerg JL, Butcher MT. Ontogeny of myosin isoform expression and prehensile function in the tail of the gray short-tailed opossum ( Monodelphis domestica). J Appl Physiol (1985) 2017; 123:513-525. [PMID: 28522766 DOI: 10.1152/japplphysiol.00651.2016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 04/18/2017] [Accepted: 05/15/2017] [Indexed: 11/22/2022] Open
Abstract
Terrestrial opossums use their semiprehensile tail for grasping nesting materials as opposed to arboreal maneuvering. We relate the development of this adaptive behavior with ontogenetic changes in myosin heavy chain (MHC) isoform expression from 21 days to adulthood. Monodelphis domestica is expected to demonstrate a progressive ability to flex the distal tail up to age 7 mo, when it should exhibit routine nest construction. We hypothesize that juvenile stages (3-7 mo) will be characterized by retention of the neonatal isoform (MHC-Neo), along with predominant expression of fast MHC-2X and -2B, which will transition into greater MHC-1β and -2A isoform content as development progresses. This hypothesis was tested using Q-PCR to quantify and compare gene expression of each isoform with its protein content determined by gel electrophoresis and densitometry. These data were correlated with nesting activity in an age-matched sample of each age group studied. Shifts in regulation of MHC gene transcripts matched well with isoform expression. Notably, mRNA for MHC-Neo and -2B decrease, resulting in little-to-no isoform translation after age 7 mo, whereas mRNA for MHC-1β and -2A increase, and this corresponds with subtle increases in content for these isoforms into late adulthood. Despite the tail remaining intrinsically fast-contracting, a critical growth period for isoform transition is observed between 7 and 13 mo, correlating primarily with use of the tail during nesting activities. Functional transitions in MHC isoforms and fiber type properties may be associated with muscle "tuning" repetitive nest remodeling tasks requiring sustained contractions of the caudal flexors.NEW & NOTEWORTHY Little is understood about skeletal muscle development as it pertains to tail prehensility in mammals. This study uses an integrative approach of relating both MHC gene and protein expression with behavioral and morphometric changes to reveal a predominant fast MHC expression with subtle isoform transitions in caudal muscle across ontogeny. The functional shifts observed are most notably correlated with increased tail grasping for nesting activities.
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Affiliation(s)
- Dylan R Thomas
- Department of Biological Sciences, Youngstown State University, Youngstown, Ohio
| | - Brad A Chadwell
- Department of Biomedical Sciences, Ohio University Heritage College of Osteopathic Medicine, Athens, Ohio; and
| | - Gary R Walker
- Department of Biological Sciences, Youngstown State University, Youngstown, Ohio
| | - Julio E Budde
- Department of Biological Sciences, Youngstown State University, Youngstown, Ohio
| | - John L VandeBerg
- South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville/Edinburg, Harlingen, Texas
| | - Michael T Butcher
- Department of Biological Sciences, Youngstown State University, Youngstown, Ohio;
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9
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Dube DK, Dube S, Abbott L, Wang J, Fan Y, Alshiekh-Nasany R, Shah KK, Rudloff AP, Poiesz BJ, Sanger JM, Sanger JW. Identification, characterization, and expression of sarcomeric tropomyosin isoforms in zebrafish. Cytoskeleton (Hoboken) 2017; 74:125-142. [PMID: 27998020 PMCID: PMC5352492 DOI: 10.1002/cm.21352] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 11/22/2016] [Accepted: 12/13/2016] [Indexed: 01/14/2023]
Abstract
Tropomyosin is a component of thin filaments that constitute myofibrils, the contractile apparatus of striated muscles. In vertebrates, except for fish, four TPM genes TPM1, TPM2, TPM3, and TPM4 are known. In zebrafish, there are six TPM genes that include the paralogs of the TPM1 (TPM1-1 and TPM1-2), the paralogs of the TPM4 gene (TPM4-1 and TPM4-2), and the two single copy genes TPM2 and TPM3. In this study, we have identified, cloned, and sequenced the TPM1-1κ isoform of the TPM1-1 gene and also discovered a new isoform TPM1-2ν of the TPM1-2. Further, we have cloned and sequenced the sarcomeric isoform of the TPM4-2 gene designated as TPM4-2α. Using conventional RT-PCR, we have shown the expression of the sarcomeric isoforms of TPM1-1, TPM1-2, TPM2, TPM3, TPM4-1, and TPM4-2 in heart and skeletal muscles. By qRT-PCR using both relative expression as well as the absolute copy number, we have shown that TPM1-1α, TPM1-2α, and TPM1-2ν are expressed mostly in skeletal muscle; the level of expression of TPM1-1κ is significantly lower compared to TPM1-1α in skeletal muscle. In addition, both TPM4-1α and TPM4-2α are predominantly expressed in heart. 2D Western blot analyses using anti-TPM antibody followed by Mass Spectrometry of the proteins from the antibody-stained spots show that TPM1-1α and TPM3α are expressed in skeletal muscle whereas TPM4-1α and TPM3α are expressed in zebrafish heart. To the best of our knowledge, this is by far the most comprehensive analysis of tropomyosin expression in zebrafish, one of the most popular animal models for gene expression study.
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Affiliation(s)
- Dipak K Dube
- Department of Medicine, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York, 13210
| | - Syamalima Dube
- Department of Medicine, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York, 13210
| | - Lynn Abbott
- Department of Medicine, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York, 13210
| | - Jushuo Wang
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York, 13210
| | - Yingli Fan
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York, 13210
| | - Ruham Alshiekh-Nasany
- Department of Medicine, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York, 13210
| | - Kalpesh K Shah
- Department of Medicine, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York, 13210
| | - Alexander P Rudloff
- Department of Medicine, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York, 13210
| | - Bernard J Poiesz
- Department of Medicine, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York, 13210
| | - Jean M Sanger
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York, 13210
| | - Joseph W Sanger
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York, 13210
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10
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Dube S, Thomas A, Abbott L, Benz P, Mitschow C, Dube DK, Poiesz BJ. Expression of tropomyosin 2 gene isoforms in human breast cancer cell lines. Oncol Rep 2016; 35:3143-50. [PMID: 27108600 PMCID: PMC4869935 DOI: 10.3892/or.2016.4732] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/12/2015] [Indexed: 01/14/2023] Open
Abstract
In humans, four tropomyosin genes (TPM1, TPM2, TPM3, and TPM4) are known to produce a multitude of isoforms via alternate splicing and/or using alternate promoters. Expression of tropomyosin has been shown to be modulated at both the transcription and the translational levels. Tropomyosins are known to make up some of the stress fibers of human epithelial cells and differences in their expression has been demonstrated in malignant breast epithelial cell lines compared to 'normal' breast cell lines. We have recently reported the expression of four novel TPM1 isoforms (TPM1λ, TPM1µ, TPM1ν, and TPM1ξ) from human malignant tumor breast cell lines that are not expressed in adult and fetal cardiac tissue. Also, we evaluated their expression in relation to the stress fiber formation. In this study, nine malignant breast epithelial cell lines and three 'normal' breast cell lines were examined for stress fiber formation and expression of tropomyosin 2 (TPM2) isoform-specific RNAs and proteins. Stress fiber formation was assessed by immunofluorescence using Leica AF6000 Deconvolution microscope. Stress fiber formation was strong (++++) in the 'normal' cell lines and varied among the malignant cell lines (negative to +++). No new TPM2 gene RNA isoforms were identified, and TPM2β was the most frequently expressed TPM2 RNA and protein isoform. Stress fiber formation positively correlated with TPM2β RNA or protein expression at high, statistically significant degrees. Previously, we had shown that TPM1δ and TPM1λ positively and inversely, respectively, correlated with stress fiber formation. The most powerful predictor of stress fiber formation was the combination of TPM2β RNA, TPM1δ RNA, and the inverse of TPM1λ RNA expression. Our results suggest that the increased expression of TPM1λ and the decreased expression of TPM1δ RNA and TPM2β may lead to decreased stress fiber formation and malignant transformation in human breast epithelial cells.
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Affiliation(s)
- Syamalima Dube
- Division of Hematology/Oncology, Department of Medicine, Upstate Medical University, Syracuse, NY 13210, USA
| | - Anish Thomas
- Division of Hematology/Oncology, Department of Medicine, Upstate Medical University, Syracuse, NY 13210, USA
| | - Lynn Abbott
- Division of Hematology/Oncology, Department of Medicine, Upstate Medical University, Syracuse, NY 13210, USA
| | - Patricia Benz
- Division of Hematology/Oncology, Department of Medicine, Upstate Medical University, Syracuse, NY 13210, USA
| | - Charles Mitschow
- Division of Hematology/Oncology, Department of Medicine, Upstate Medical University, Syracuse, NY 13210, USA
| | - Dipak K Dube
- Division of Hematology/Oncology, Department of Medicine, Upstate Medical University, Syracuse, NY 13210, USA
| | - Bernard J Poiesz
- Division of Hematology/Oncology, Department of Medicine, Upstate Medical University, Syracuse, NY 13210, USA
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11
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Zhang T, Lin Y, Liu J, Zhang ZG, Fu W, Guo LY, Pan L, Kong X, Zhang MK, Lu YH, Huang ZR, Xie Q, Li WH, Xu XQ. Rbm24 Regulates Alternative Splicing Switch in Embryonic Stem Cell Cardiac Lineage Differentiation. Stem Cells 2016; 34:1776-89. [PMID: 26990106 DOI: 10.1002/stem.2366] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 02/23/2016] [Indexed: 11/06/2022]
Abstract
The transition of embryonic stem cell (ESC) pluripotency to differentiation is accompanied by an expansion of mRNA and proteomic diversity. Post-transcriptional regulation of ESCs is critically governed by cell type-specific splicing. However, little is known about the splicing factors and the molecular mechanisms directing ESC early lineage differentiation. Our study identifies RNA binding motif protein 24 (Rbm24) as a key splicing regulator that plays an essential role in controlling post-transcriptional networks during ESC transition into cardiac differentiation. Using an inducible mouse ESC line in which gene expression could be temporally regulated, we demonstrated that forced expression of Rbm24 in ESCs dramatically induced a switch to cardiac specification. Genome-wide RNA sequencing analysis identified more than 200 Rbm24-regulated alternative splicing events (AS) which occurred in genes essential for the ESC pluripotency or differentiation. Remarkably, AS genes regulated by Rbm24 composed of transcriptional factors, cytoskeleton proteins, and ATPase gene family members which are critical components required for cardiac development and functionality. Furthermore, we show that Rbm24 regulates ESC differentiation by promoting alternative splicing of pluripotency genes. Among the Rbm24-regulated events, Tpm1, an actin filament family gene, was identified to possess ESC/tissue specific isoforms. We demonstrated that these isoforms were functionally distinct and that their exon AS switch was essential for ESC differentiation. Our results suggest that ESC's switching into the differentiation state can be initiated by a tissue-specific splicing regulator, Rbm24. This finding offers a global view on how an RNA binding protein influences ESC lineage differentiation by a splicing-mediated regulatory mechanism. Stem Cells 2016;34:1776-1789.
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Affiliation(s)
- Tao Zhang
- Institute of Stem Cell and Regenerative Medicine, Medical College, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Yu Lin
- Institute of Stem Cell and Regenerative Medicine, Medical College, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Jing Liu
- Institute of Stem Cell and Regenerative Medicine, Medical College, Xiamen University, Xiamen, Fujian, People's Republic of China.,ShenZhen Research Institute, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Zi Guan Zhang
- Institute of Stem Cell and Regenerative Medicine, Medical College, Xiamen University, Xiamen, Fujian, People's Republic of China.,Department of Cardiology, The First Affiliated Hospital, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Wei Fu
- Institute of Stem Cell and Regenerative Medicine, Medical College, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Li Yan Guo
- Institute of Stem Cell and Regenerative Medicine, Medical College, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Lei Pan
- Institute of Stem Cell and Regenerative Medicine, Medical College, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Xu Kong
- Institute of Stem Cell and Regenerative Medicine, Medical College, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Meng Kai Zhang
- Institute of Stem Cell and Regenerative Medicine, Medical College, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Ying Hua Lu
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Zheng Rong Huang
- Department of Cardiology, The First Affiliated Hospital, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Qiang Xie
- Department of Cardiology, The First Affiliated Hospital, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Wei Hua Li
- Department of Cardiology, The First Affiliated Hospital, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Xiu Qin Xu
- Institute of Stem Cell and Regenerative Medicine, Medical College, Xiamen University, Xiamen, Fujian, People's Republic of China
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12
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Expression of Tropomyosin 1 Gene Isoforms in Human Breast Cancer Cell Lines. Int J Breast Cancer 2015; 2015:859427. [PMID: 26171250 PMCID: PMC4480939 DOI: 10.1155/2015/859427] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 04/17/2015] [Accepted: 04/28/2015] [Indexed: 01/14/2023] Open
Abstract
Nine malignant breast epithelial cell lines and 3 normal breast cell lines were examined for stress fiber formation and expression of TPM1 isoform-specific RNAs and proteins. Stress fiber formation was strong (++++) in the normal cell lines and varied among the malignant cell lines (negative to +++). Although TPM1γ and TPM1δ were the dominant transcripts of TPM1, there was no clear evidence for TPM1δ protein expression. Four novel human TPM1 gene RNA isoforms were discovered (λ, μ, ν, and ξ), which were not identified in adult and fetal human cardiac tissues. TPM1λ was the most frequent isoform expressed in the malignant breast cell lines, and it was absent in normal breast epithelial cell lines. By western blotting, we were unable to distinguish between TPM1γ, λ, and ν protein expression, which were the only TPM1 gene protein isoforms potentially expressed. Some malignant cell lines demonstrated increased or decreased expression of these isoforms relative to the normal breast cell lines. Stress fiber formation did not correlate with TPM1γ RNA expression but significantly and inversely correlated with TPM1δ and TPM1λ expression, respectively. The exact differences in expression of these novel isoforms and their functional properties in breast epithelial cells will require further study.
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13
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Sanger JM, Sanger JW. Recent advances in muscle research. Anat Rec (Hoboken) 2015; 297:1539-42. [PMID: 25125167 DOI: 10.1002/ar.22986] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 06/16/2014] [Indexed: 12/26/2022]
Affiliation(s)
- Jean M Sanger
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, New York
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14
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Wang J, Fan Y, Dube DK, Sanger JM, Sanger JW. Jasplakinolide reduces actin and tropomyosin dynamics during myofibrillogenesis. Cytoskeleton (Hoboken) 2014; 71:513-29. [PMID: 25145272 DOI: 10.1002/cm.21189] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 08/12/2014] [Indexed: 12/20/2022]
Abstract
The premyofibril model proposes a three-stage process for the de novo assembly of myofibrils in cardiac and skeletal muscles: premyofibrils to nascent myofibrils to mature myofibrils. FRAP experiments and jasplakinolide, a drug that stabilizes F-actin, permitted us to determine how decreasing the dynamics of actin filaments affected the dynamics of tropomyosin, troponin-T, troponin-C, and two Z-Band proteins (alpha-actinin, FATZ) in premyofibrils versus mature myofibrils. Jasplakinolide reduced markedly the dynamics of actin in premyofibrils and in mature myofibrils in skeletal muscles. Two isoforms of tropomyosin-1 (TPM1α, TPM1κ) are more dynamic in premyofibrils than in mature myofibrils in control skeletal muscles. Jasplakinolide reduced the exchange rates of tropomyosins in premyofibrils but not in mature myofibrils. The reduced tropomyosin recoveries did not match the YFP-actin recoveries in premyofibrils in jasplakinolide. There were no significant differences in the effects of jasplakinolide on the dynamics of troponins in the thin filaments or of two Z-band proteins in premyofibrils or skeletal mature myofibrils. Cardiac control mature myofibrils lack nebulin, and small decreases in actin (∼5%) and two tropomyosin isoforms (∼10-15%) dynamics are detected in premyofibril to mature myofibril transformations compared with skeletal muscle. In contrast to skeletal muscle, jasplakinolide lowered the dynamics of actin and tropomyosin isoforms in the cardiac mature myofibrils. These results suggest that the dynamics of tropomyosins in control muscle cells are related to actin exchange. These results also suggest a stabilizing role for nebulin, an actin and tropomyosin-binding protein, present in mature myofibrils but not in premyofibrils of skeletal muscles.
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Affiliation(s)
- Jushuo Wang
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, New York
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