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Kaplan MM, Zeidler M, Knapp A, Hölzl M, Kress M, Fritsch H, Krogsdam A, Flucher BE. Spatial transcriptomics in embryonic mouse diaphragm muscle reveals regional gradients and subdomains of developmental gene expression. iScience 2024; 27:110018. [PMID: 38883818 PMCID: PMC11177202 DOI: 10.1016/j.isci.2024.110018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/22/2024] [Accepted: 05/14/2024] [Indexed: 06/18/2024] Open
Abstract
The murine embryonic diaphragm is a primary model for studying myogenesis and neuro-muscular synaptogenesis, both representing processes regulated by spatially organized genetic programs of myonuclei located in distinct myodomains. However, a spatial gene expression pattern of embryonic mouse diaphragm has not been reported. Here, we provide spatially resolved gene expression data for horizontally sectioned embryonic mouse diaphragms at embryonic days E14.5 and E18.5. These data reveal gene signatures for specific muscle regions with distinct maturity and fiber type composition, as well as for a central neuromuscular junction (NMJ) and a peripheral myotendinous junction (MTJ) compartment. Comparing spatial expression patterns of wild-type mice with those of transgenic mice lacking either the skeletal muscle calcium channel CaV1.1 or β-catenin, reveals curtailed muscle development and dysregulated expression of genes potentially involved in NMJ formation. Altogether, these datasets provide a powerful resource for further studies of muscle development and NMJ formation in the mouse.
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Affiliation(s)
| | - Maximilian Zeidler
- Institute of Physiology, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Annabella Knapp
- Institute of Clinical and Functional Anatomy, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Martina Hölzl
- Deep Sequencing Core and Institute for Bioinformatics Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Michaela Kress
- Institute of Physiology, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Helga Fritsch
- Institute of Clinical and Functional Anatomy, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Anne Krogsdam
- Deep Sequencing Core and Institute for Bioinformatics Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Bernhard E Flucher
- Institute of Physiology, Medical University Innsbruck, 6020 Innsbruck, Austria
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2
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Gomatam CK, Ingale P, Rodriguez G, Munger S, Pomeranets R, Krishna S, Lowe J, Howard ZM, Rafael-Fortney JA. Cell-type specific effects of mineralocorticoid receptor gene expression suggest intercellular communication regulating fibrosis in skeletal muscle disease. Front Physiol 2024; 15:1322729. [PMID: 38737833 PMCID: PMC11082420 DOI: 10.3389/fphys.2024.1322729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/28/2024] [Indexed: 05/14/2024] Open
Abstract
Introduction: Duchenne muscular dystrophy (DMD) is a fatal striated muscle degenerative disease. DMD is caused by loss of dystrophin protein, which results in sarcolemmal instability and cycles of myofiber degeneration and regeneration. Pathology is exacerbated by overactivation of infiltrating immune cells and fibroblasts, which leads to chronic inflammation and fibrosis. Mineralocorticoid receptors (MR), a type of nuclear steroid hormone receptors, are potential therapeutic targets for DMD. MR antagonists show clinical efficacy on DMD cardiomyopathy and preclinical efficacy on skeletal muscle in DMD models. Methods: We have previously generated myofiber and myeloid MR knockout mouse models to dissect cell-specific functions of MR within dystrophic muscles. Here, we compared skeletal muscle gene expression from both knockouts to further define cell-type specific signaling downstream from MR. Results: Myeloid MR knockout increased proinflammatory and profibrotic signaling, including numerous myofibroblast signature genes. Tenascin C was the most highly upregulated fibrotic gene in myeloid MR-knockout skeletal muscle and is a component of fibrosis in dystrophic skeletal muscle. Surprisingly, lysyl oxidase (Lox), canonically a collagen crosslinker, was increased in both MR knockouts, but did not localize to fibrotic regions of skeletal muscle. Lox localized within myofibers, including only a region of quadriceps muscles. Lysyl oxidase like 1 (Loxl1), another Lox family member, was increased only in myeloid MR knockout muscle and localized specifically to fibrotic regions. Discussion: This study suggests that MR signaling in the dystrophic muscle microenvironment involves communication between contributing cell types and modulates inflammatory and fibrotic pathways in muscle disease.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jill A. Rafael-Fortney
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, OH, United States
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4
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Chen Q, Zhang W, Cai J, Ni Y, Xiao L, Zhang J. Transcriptome analysis in comparing carcass and meat quality traits of Jiaxing Black Pig and Duroc × Duroc × Berkshire × Jiaxing Black Pig crosses. Gene 2022; 808:145978. [PMID: 34592352 DOI: 10.1016/j.gene.2021.145978] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/31/2021] [Accepted: 09/24/2021] [Indexed: 01/17/2023]
Abstract
This study compares two typical strains: Chinese local excellent meat quality of Jiaxing Black (JXB) Pig and quadratic crossbred pig strain Duroc × Duroc × Berkshire × Jiaxing Black (DDBJ). It was found that between the two pig strains, carcass traits and meat quality traits differed significantly. This is exemplified by the leanness and dressing out percent of DDBJ that were significantly higher than JXB pigs of the same age (P < 0.05) and the better growth rate of DDBJ pigs as to JXB pigs was shown by quantifying muscle proliferation and differentiation of longissimus dorsi muscle employing Hematoxylin and Eosin staining of longissimus dorsi muscle. Nutrients such as inosinic acid, intramuscular fat, and free amino acids in the longissimus dorsi muscle were significantly higher in JXB pigs than DDBJ pigs (p < 0.0001); saturated fatty acids were higher in JXB than in DDBJ pigs (p = 0.0097); essential amino acids and fresh taste amino acids (serine, glutamic acid, proline, glycine, alanine) of JXB pigs was higher than that of DDBJ pigs (p < 0.0001) and amino acids in longissimus dorsi muscle of JXB pigs surpasses the amino acid concentration of DDBJ pigs (p < 0.0001), thus showing the superiority of JXB in terms of meat quality. However, the content of polyunsaturated fatty acids, which is responsible for poor meat quality, was significantly higher in the longissimus dorsi muscle of DDBJ pig than JXB pigs (p < 0.0001); RNA-seq analysis of 5 biological replicates from two of the strains was performed. The screening of 164 up-regulated genes and 183 down-regulated genes found in longissimus dorsi muscle of DDBJ was done and the results identified differentially expressed genes related to muscle development, adipogenesis, amino acid metabolism, fatty acid metabolism and inosine synthesis. In conclusion, the study identified functional genes, elucidated the mechanisms associated with carcass quality traits, meat quality traits and other related traits, and provided means of genetic enhancement to improve meat quality traits and carcass traits in Chinese commercial pigs.
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Affiliation(s)
- Qiangqiang Chen
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Wei Zhang
- Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Jianfeng Cai
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Yifan Ni
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lixia Xiao
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Jinzhi Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
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5
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Wang R, Chen F, Chen Q, Wan X, Shi M, Chen AK, Ma Z, Li G, Wang M, Ying Y, Liu Q, Li H, Zhang X, Ma J, Zhong J, Chen M, Zhang MQ, Zhang Y, Chen Y, Zhu D. MyoD is a 3D genome structure organizer for muscle cell identity. Nat Commun 2022; 13:205. [PMID: 35017543 PMCID: PMC8752600 DOI: 10.1038/s41467-021-27865-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 12/15/2021] [Indexed: 12/15/2022] Open
Abstract
The genome exists as an organized, three-dimensional (3D) dynamic architecture, and each cell type has a unique 3D genome organization that determines its cell identity. An unresolved question is how cell type-specific 3D genome structures are established during development. Here, we analyzed 3D genome structures in muscle cells from mice lacking the muscle lineage transcription factor (TF), MyoD, versus wild-type mice. We show that MyoD functions as a “genome organizer” that specifies 3D genome architecture unique to muscle cell development, and that H3K27ac is insufficient for the establishment of MyoD-induced chromatin loops in muscle cells. Moreover, we present evidence that other cell lineage-specific TFs might also exert functional roles in orchestrating lineage-specific 3D genome organization during development. Pioneer transcription factors (TFs) have been proposed to act as protein anchors to orchestrate cell type-specific 3D genome architecture. MyoD is a pioneer TF for myogenic lineage specification. Here the authors provide further support for the role of MyoD in 3D genome architecture in muscle stem cells by comparing MyoD knockout and wild-type mice.
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Affiliation(s)
- Ruiting Wang
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, 100005, Beijing, China
| | - Fengling Chen
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, BNRist, Department of Automation, Tsinghua University, 100084, Beijing, China
| | - Qian Chen
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, 100005, Beijing, China
| | - Xin Wan
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, 100005, Beijing, China
| | - Minglei Shi
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Antony K Chen
- Department of Biomedical Engineering, College of Future Technology, Peking University, 100871, Beijing, China
| | - Zhao Ma
- Department of Biomedical Engineering, College of Future Technology, Peking University, 100871, Beijing, China.,Department of Biomedical Engineering, College of Engineering, Peking University, 100871, Beijing, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellent in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Science, 100049, Beijing, China
| | - Min Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellent in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Science, 100049, Beijing, China
| | - Yachen Ying
- Department of Biomedical Engineering, College of Future Technology, Peking University, 100871, Beijing, China.,Department of Biomedical Engineering, College of Engineering, Peking University, 100871, Beijing, China
| | - Qinyao Liu
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, 100005, Beijing, China
| | - Hu Li
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, 100005, Beijing, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), 510320, Guangzhou, China
| | - Xu Zhang
- Beijing institute of collaborative innovation, 100094, Beijing, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Jiayun Zhong
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Meihong Chen
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, 100005, Beijing, China
| | - Michael Q Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, BNRist, Department of Automation, Tsinghua University, 100084, Beijing, China. .,MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Medicine, Tsinghua University, 100084, Beijing, China. .,Department of Biological Sciences, Center for Systems Biology, The University of Texas, Dallas 800 West Campbell Road, RL11, Richardson, TX, 75080-3021, USA.
| | - Yong Zhang
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, 100005, Beijing, China.
| | - Yang Chen
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, 100005, Beijing, China. .,MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, BNRist, Department of Automation, Tsinghua University, 100084, Beijing, China. .,MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Medicine, Tsinghua University, 100084, Beijing, China.
| | - Dahai Zhu
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, 100005, Beijing, China. .,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), 510320, Guangzhou, China.
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Coudert L, Osseni A, Gangloff YG, Schaeffer L, Leblanc P. The ESCRT-0 subcomplex component Hrs/Hgs is a master regulator of myogenesis via modulation of signaling and degradation pathways. BMC Biol 2021; 19:153. [PMID: 34330273 PMCID: PMC8323235 DOI: 10.1186/s12915-021-01091-4] [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: 02/09/2021] [Accepted: 07/09/2021] [Indexed: 11/30/2022] Open
Abstract
Background Myogenesis is a highly regulated process ending with the formation of myotubes, the precursors of skeletal muscle fibers. Differentiation of myoblasts into myotubes is controlled by myogenic regulatory factors (MRFs) that act as terminal effectors of signaling cascades involved in the temporal and spatial regulation of muscle development. Such signaling cascades converge and are controlled at the level of intracellular trafficking, but the mechanisms by which myogenesis is regulated by the endosomal machinery and trafficking is largely unexplored. The Endosomal Sorting Complex Required for Transport (ESCRT) machinery composed of four complexes ESCRT-0 to ESCRT-III regulates the biogenesis and trafficking of endosomes as well as the associated signaling and degradation pathways. Here, we investigate its role in regulating myogenesis. Results We uncovered a new function of the ESCRT-0 hepatocyte growth factor-regulated tyrosine kinase substrate Hrs/Hgs component in the regulation of myogenesis. Hrs depletion strongly impairs the differentiation of murine and human myoblasts. In the C2C12 murine myogenic cell line, inhibition of differentiation was attributed to impaired MRF in the early steps of differentiation. This alteration is associated with an upregulation of the MEK/ERK signaling pathway and a downregulation of the Akt2 signaling both leading to the inhibition of differentiation. The myogenic repressors FOXO1 as well as GSK3β were also found to be both activated when Hrs was absent. Inhibition of the MEK/ERK pathway or of GSK3β by the U0126 or azakenpaullone compounds respectively significantly restores the impaired differentiation observed in Hrs-depleted cells. In addition, functional autophagy that is required for myogenesis was also found to be strongly inhibited. Conclusions We show for the first time that Hrs/Hgs is a master regulator that modulates myogenesis at different levels through the control of trafficking, signaling, and degradation pathways. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01091-4.
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Affiliation(s)
- L Coudert
- Institut NeuroMyoGène, CNRS UMR5310, INSERM U1217, Faculté de Médecine Rockefeller, Université Claude Bernard Lyon, 8 avenue Rockefeller, 69373, 09, Lyon, Cedex, France
| | - A Osseni
- Institut NeuroMyoGène, CNRS UMR5310, INSERM U1217, Faculté de Médecine Rockefeller, Université Claude Bernard Lyon, 8 avenue Rockefeller, 69373, 09, Lyon, Cedex, France
| | - Y G Gangloff
- Institut NeuroMyoGène, CNRS UMR5310, INSERM U1217, Faculté de Médecine Rockefeller, Université Claude Bernard Lyon, 8 avenue Rockefeller, 69373, 09, Lyon, Cedex, France
| | - L Schaeffer
- Institut NeuroMyoGène, CNRS UMR5310, INSERM U1217, Faculté de Médecine Rockefeller, Université Claude Bernard Lyon, 8 avenue Rockefeller, 69373, 09, Lyon, Cedex, France
| | - P Leblanc
- Institut NeuroMyoGène, CNRS UMR5310, INSERM U1217, Faculté de Médecine Rockefeller, Université Claude Bernard Lyon, 8 avenue Rockefeller, 69373, 09, Lyon, Cedex, France.
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