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| SCSMRD: A database for single-cell skeletal muscle regeneration |
FENG Xi-kang1, XIE Chun-di2, LI Yong-yao3, WANG Zi-shuai3#, BAI Li-jing3#
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1 School of Software, Northwestern Polytechnical University, Xi’an 710072, P.R.China
2 Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
3 Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, P.R.China
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摘要
产肉量是家畜（包括猪、牛和羊等）重要生产力指标和经济性状之一。产肉量是典型的数量性状，受多基因调控。影响产肉性状形成的基础是骨骼肌组织的生长和发育。骨骼肌生长发育是一个复杂的生物学过程，包括成肌细胞的形成、增殖、凋亡、迁移、融合和分化。骨骼肌损伤修复过程中基因表达变化与初始胚胎发育过程类似，完美的重现了上述骨骼肌生长发育过程。因此，骨骼肌损伤修复被认为是研究骨骼肌生长发育的理想模型。鉴定骨骼肌损伤修复过程中调节肌生成相关重要基因和特定调控网络，能够为家畜产肉量等重要经济生产性状形成的分子机制提供理论支持。已有研究表明，骨骼肌功能障碍与肌营养不良、萎缩，2型糖尿病和衰老相关的肌肉减少症等500多种人类疾病密切相关。因此，深入了解骨骼肌损伤修复过程中基因表达差异以及调控网络，也能为再生医学提供新的药物靶点，这些靶点可以增强或诱导功能性骨骼肌从头生成，以治疗先天性缺失或创伤性组织损失。
近些年针对小鼠骨骼肌损伤修复的单细胞RNA 测序(scRNA-seq)陆续产出了大量数据，但是，从单细胞水平研究骨骼肌再生过程中基因表达变化的数据库尚未构建。本研究汇集了七个关键再生时间点和正常骨骼肌单细胞RNA-seq数据（共计超过 105,000 个细胞）开展一系列生物信息分析，包括细胞聚类、细胞类型注释、细胞周期识别、骨骼肌卫星细胞发育状态转换轨迹和调节单元动态表达图谱构建等。开发构建了SCSMRD （https://scsmrd.fengs-lab.com）数据库，界面友好，操作简单，提供了多种搜索功能，包括，用户感兴趣基因在不同细胞类型和损伤修复不同时间点的动态表达图谱，不同细胞类型中特异调节单元网络动态变化和用户感兴趣基因基因在骨骼肌卫星细胞发育状态转变过程中的表达模式等。SCSMRD数据库为研究人员在单细胞层面研究骨骼肌损伤修复的转录组动态变化提供了可靠的生信技术支撑和数据支持。
Abstract
Skeletal muscle regeneration is a complex process where various cell types and cytokines are involved. Single-cell RNA-sequencing (scRNA-seq) provides the opportunity to deconvolute heterogeneous tissue into individual cells based on their transcriptomic profiles. Recent scRNA-seq studies on mouse muscle regeneration have provided insights to understand the transcriptional dynamics that underpin muscle regeneration. However, a database to investigate gene expression profiling during skeletal muscle regeneration at the single-cell level is lacking. Here, we collected over 105 000 cells at 7 key regenerative time-points and non-injured muscles and developed a database, the Single-cell Skeletal Muscle Regeneration Database (SCSMRD). SCSMRD allows users to search the dynamic expression profiles of genes of interest across different cell types during the skeletal muscle regeneration process. It also provides a network to show the activity of regulons in different cell types at different time points. Pesudotime analysis showed the state changes trajectory of muscle stem cells (MuSCs) during skeletal muscle regeneration. This database is freely available at https://scsmrd.fengs-lab.com.
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Received: 07 December 2021
Accepted: 27 February 2022
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This research was supported by the National Natural Science Foundation of China (31972539 and 32102513), the Science, Technology, and Innovation Commission of Shenzhen Municipality, China (JCYJ20180306173644635), the Fundamental Research Funds for the Central Universities, China (G2020KY05109), the Natural Science Basic Research Program of Shaanxi Province, China (2022JQ-644), and the Basic Research Programs of Taicang, China (TC2021JC14).
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| About author: #Correspondence WANG Zi-shuai, E-mail: wangzishuai@caas.cn; BAI Li-jing, E-mail: bailijing@caas.cn |
Cite this article:
FENG Xi-kang, XIE Chun-di, LI Yong-yao, WANG Zi-shuai, BAI Li-jing.
2023.
SCSMRD: A database for single-cell skeletal muscle regeneration. Journal of Integrative Agriculture, 22(3): 864-871.
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Argiles J M, Campos N, Lopez-Pedrosa J M, Rueda R, Rodriguez-Manas L. 2016. Skeletal muscle regulates metabolism via interorgan crosstalk: Roles in health and disease. Journal of the American Medical Directors Association, 17, 789–796.
Arnold L, Henry A, Poron F, Baba-Amer Y, Van Rooijen N, Plonquet A, Gherardi R K, Chazaud B. 2007. Inflammatory monocytes recruited after skeletal muscle injury switch into antiinflammatory macrophages to support myogenesis. Journal of Experimental Medicine, 204, 1057–1069.
Baghdadi M B, Tajbakhsh S. 2018. Regulation and phylogeny of skeletal muscle regeneration. Developmental Biology, 433, 200–209.
Beiner J M, Jokl P. 2001. Muscle contusion injuries: Current treatment options. Journal of the American Academy of Orthopaedic Surgeons, 9, 227–237.
Brass E P. 1996. Skeletal muscle metabolism as a target for drug therapy in peripheral arterial disease. Vascular Medicine, 1, 55–59.
Brawand D, Soumillon M, Necsulea A, Julien P, Csardi G, Harrigan P, Weier M, Liechti A, Aximu-Petri A, Kircher M, Albert F W, Zeller U, Khaitovich P, Grutzner F, Bergmann S, Nielsen R, Paabo S, Kaessmann H. 2011. The evolution of gene expression levels in mammalian organs. Nature, 478, 343–351.
Chal J, Pourquie O. 2017. Making muscle: Skeletal myogenesis in vivo and in vitro. Development, 144, 2104–2122.
Chen J, Swofford R, Johnson J, Cummings B B, Rogel N, Lindblad-Toh K, Haerty W, Palma F D, Regev A. 2019. A quantitative framework for characterizing the evolutionary history of mammalian gene expression. Genome Research, 29, 53–63.
Dell’Orso S, Juan A H, Ko K D, Naz F, Perovanovic J, Gutierrez-Cruz G, Feng X, Sartorelli V. 2019. Single cell analysis of adult mouse skeletal muscle stem cells in homeostatic and regenerative conditions. Development, 146, dev174177.
Gan Z, Fu T, Kelly D P, Vega R B. 2018. Skeletal muscle mitochondrial remodeling in exercise and diseases. Cell Research, 28, 969–980.
Ghaleb A M, Yang V W. 2017. Krüppel-like factor 4 (KLF4): What we currently know. Gene, 611, 27–37.
Giordani L,He G J, Negroni E,Sakai H,Law J Y C, Siu M M, Wan R, Corneau A, Tajbakhsh S,Cheung T H, Grand F. 2019. High-dimensional single-cell cartography reveals novel skeletal muscle-resident cell populations. Molecular Cell, 74, 609–621.
Goldman J A, Poss K D. 2020. Gene regulatory programmes of tissue regeneration. Nature Reviews Genetics, 21, 511–525.
Guschanski K, Warnefors M, Kaessmann H. 2017. The evolution of duplicate gene expression in mammalian organs. Genome Research, 27, 1461–1474.
Han X, Wang R, Zhou Y, Fei L, Sun H, Lai S, Saadatpour A, Zhou Z, Chen H, Ye F, Huang D, Xu Y, Huang W, Jiang M, Jiang X, Mao J, Chen Y, Lu C, Xie J, Fang Q, et al. 2018. Mapping the mouse cell atlas by microwell-seq. Cell, 172, 1091–1107.
Huard J, Li Y, Fu F H. 2002. Muscle injuries and repair: Current trends in research. Journal of Bone and Joint Surgery American Volume, 84, 822–832.
Janky R S, Verfaillie A, Imrichová H, Van de Sande B, Standaert L, Christiaens V, Hulselmans G, Herten K, Naval Sanchez M, Potier D, Svetlichnyy D, Kalender Atak Z, Fiers M, Marine J C, Aerts S. 2014. iRegulon: From a gene list to a gene regulatory network using large motif and track collections. PLoS Computational Biology, 10, e1003731.
Jrvinen T A H, Kriinen M, Jrvinen M, Kalimo H. 2000. Muscle strain injuries. Current Opinion in Rheumatology, 12, 155–161.
Kent-Braun J A, Miller R G, Weiner M W. 1995. Human skeletal muscle metabolism in health and disease: Utility of magnetic resonance spectroscopy. Exercise and Sport Sciences Reviews, 23, 305–348.
Ma A, Wang C, Chang Y, Brennan F H, McDermaid A, Liu B, Zhang C, Popovich P G, Ma Q. 2020. IRIS3: Integrated cell-type-specific regulon inference server from single-cell RNA-Seq. Nucleic Acids Research, 48, W275–W286.
Merkin J, Russell C, Chen P, Burge C B. 2012. Evolutionary dynamics of gene and isoform regulation in Mammalian tissues. Science, 338, 1593–1602.
Meunier J, Lemoine F, Soumillon M, Liechti A, Weier M, Guschanski K, Hu H, Khaitovich P, Kaessmann H. 2013. Birth and expression evolution of mammalian microRNA genes. Genome Reseach, 23, 34–45.
De Micheli A J, Laurilliard E J, Heinke C L, Ravichandran H, Fraczek P, Soueid-Baumgarten S, De Vlaminck I, Elemento O, Cosgrove B D. 2020. Single-cell analysis of the muscle stem cell hierarchy identifies heterotypic communication signals involved in skeletal muscle regeneration. Cell Reports, 30, 3583–3595.
Necsulea A, Kaessmann H. 2014. Evolutionary dynamics of coding and non-coding transcriptomes. Nature Reviews Genetics, 15, 734–748.
Oprescu S N, Yue F, Qiu J, Brito L F, Kuang S. 2020. Temporal dynamics and heterogeneity of cell populations during skeletal muscle regeneration. Iscience, 23, 100993.
Paylor B, Natarajan A, Zhang R H, Rossi F. 2011. Nonmyogenic cells in skeletal muscle regeneration. Current Topics in Developmental Biology, 96, 139–165.
St Pierre B A, Tidball J G. 1994. Differential response of macrophage subpopulations to soleus muscle reloading after rat hindlimb suspension. Journal of Applied Physiology, 77, 290–297.
Rai M, Coleman Z, Curley M, Nityanandam A, Robles-Murguia M, Jiao J, Finkelstein D, Wang T D, Xu B, Fan Y P, Demontis F. 2021. Proteasome stress in skeletal muscle mounts a long-range protective response that delays retinal and brain aging. Cell Metabolism, 33, 1137–1154.
Relaix F, Zammit P S. 2012. Satellite cells are essential for skeletal muscle regeneration: The cell on the edge returns centre stage. Development, 139, 2845–2856.
Schmalbruch H, Lewis D M. 2000. Dynamics of nuclei of muscle fibers and connective tissue cells in normal and denervated rat muscles. Muscle & Nerve, 23, 617–626.
Stump C S, Henriksen E J, Wei Y, Sowers J R. 2006. The metabolic syndrome: Role of skeletal muscle metabolism. Annals of Medicine, 38, 389–402.
Turner N J, Badylak S F. 2012. Regeneration of skeletal muscle. Cell and Tissue Research, 347, 759–774.
Villalta S A, Rinaldi C, Deng B, Liu G, Fedor B, Tidball J G. 2011. Interleukin-10 reduces the pathology of mdx muscular dystrophy by deactivating M1 macrophages and modulating macrophage phenotype. Human Molecular Genetics, 20, 790–805.
Welch J D, Kozareva V, Ferreira A, Vanderburg C, Martin C, Macosko E Z. 2019. Single-cell multi-omic integration compares and contrasts features of brain cell identity. Cell, 177, 1873–1887.
Wolf F A, Angerer P, Theis F J. 2018. SCANPY: large-scale single-cell gene expression data analysis. Genome Biology, 19, 1–5.
Wosczyna M N, Rando T A. 2018. A muscle stem cell support group: Coordinated cellular responses in muscle regeneration. Developmental Cell, 46, 135–143.
Yang W, Hu P. 2018. Skeletal muscle regeneration is modulated by inflammation. Journal of Orthopaedic Translation, 13, 25–32.
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