1
|
Korb A, Tajbakhsh S, Comai GE. Functional specialisation and coordination of myonuclei. Biol Rev Camb Philos Soc 2024; 99:1164-1195. [PMID: 38477382 DOI: 10.1111/brv.13063] [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: 04/10/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 03/14/2024]
Abstract
Myofibres serve as the functional unit for locomotion, with the sarcomere as fundamental subunit. Running the entire length of this structure are hundreds of myonuclei, located at the periphery of the myofibre, juxtaposed to the plasma membrane. Myonuclear specialisation and clustering at the centre and ends of the fibre are known to be essential for muscle contraction, yet the molecular basis of this regionalisation has remained unclear. While the 'myonuclear domain hypothesis' helped explain how myonuclei can independently govern large cytoplasmic territories, novel technologies have provided granularity on the diverse transcriptional programs running simultaneously within the syncytia and added a new perspective on how myonuclei communicate. Building upon this, we explore the critical cellular and molecular sources of transcriptional and functional heterogeneity within myofibres, discussing the impact of intrinsic and extrinsic factors on myonuclear programs. This knowledge provides new insights for understanding muscle development, repair, and disease, but also opens avenues for the development of novel and precise therapeutic approaches.
Collapse
Affiliation(s)
- Amaury Korb
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Stem Cells & Development Unit, 25 rue du Dr. Roux, Institut Pasteur, Paris, F-75015, France
| | - Shahragim Tajbakhsh
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Stem Cells & Development Unit, 25 rue du Dr. Roux, Institut Pasteur, Paris, F-75015, France
| | - Glenda E Comai
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Stem Cells & Development Unit, 25 rue du Dr. Roux, Institut Pasteur, Paris, F-75015, France
| |
Collapse
|
2
|
Ogbe SE, Wang J, Shi Y, Wang Y, Xu Z, Abankwa JK, Dal Pozzo L, Zhao S, Zhou H, Peng Y, Chu X, Wang X, Bian Y. Insights into the epitranscriptomic role of N 6-methyladenosine on aging skeletal muscle. Biomed Pharmacother 2024; 177:117041. [PMID: 38964182 DOI: 10.1016/j.biopha.2024.117041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/18/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
The modification of RNA through the N6-methyladenosine (m6A) has emerged as a growing area of research due to its regulatory role in gene expression and various biological processes regulating the expression of genes. m6A RNA methylation is a post-transcriptional modification that is dynamic and reversible and found in mRNA, tRNA, rRNA, and other non-coding RNA of most eukaryotic cells. It is executed by special proteins known as "writers," which initiate methylation; "erasers," which remove methylation; and "readers," which recognize it and regulate the expression of the gene. Modification by m6A regulates gene expression by affecting the splicing, translation, stability, and localization of mRNA. Aging causes molecular and cellular damage, which forms the basis of most age-related diseases. The decline in skeletal muscle mass and functionality because of aging leads to metabolic disorders and morbidities. The inability of aged muscles to regenerate and repair after injury poses a great challenge to the geriatric populace. This review seeks to explore the m6A epigenetic regulation in the myogenesis and regeneration processes in skeletal muscle as well as the progress made on the m6A epigenetic regulation of aging skeletal muscles.
Collapse
Affiliation(s)
- Susan Enechojo Ogbe
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Department of Physiology, Federal University, Wukari, Taraba 670101, Nigeria
| | - JiDa Wang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - YueXuan Shi
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Ying Wang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Zhe Xu
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Joseph Kofi Abankwa
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Lisa Dal Pozzo
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - ShuWu Zhao
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - HuiFang Zhou
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - YanFei Peng
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - XiaoQian Chu
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - XiangLing Wang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - YuHong Bian
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| |
Collapse
|
3
|
Espino-Gonzalez E, Dalbram E, Mounier R, Gondin J, Farup J, Jessen N, Treebak JT. Impaired skeletal muscle regeneration in diabetes: From cellular and molecular mechanisms to novel treatments. Cell Metab 2024; 36:1204-1236. [PMID: 38490209 DOI: 10.1016/j.cmet.2024.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/10/2024] [Accepted: 02/22/2024] [Indexed: 03/17/2024]
Abstract
Diabetes represents a major public health concern with a considerable impact on human life and healthcare expenditures. It is now well established that diabetes is characterized by a severe skeletal muscle pathology that limits functional capacity and quality of life. Increasing evidence indicates that diabetes is also one of the most prevalent disorders characterized by impaired skeletal muscle regeneration, yet underlying mechanisms and therapeutic treatments remain poorly established. In this review, we describe the cellular and molecular alterations currently known to occur during skeletal muscle regeneration in people with diabetes and animal models of diabetes, including its associated comorbidities, e.g., obesity, hyperinsulinemia, and insulin resistance. We describe the role of myogenic and non-myogenic cell types on muscle regeneration in conditions with or without diabetes. Therapies for skeletal muscle regeneration and gaps in our knowledge are also discussed, while proposing future directions for the field.
Collapse
Affiliation(s)
- Ever Espino-Gonzalez
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Emilie Dalbram
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Rémi Mounier
- Institut NeuroMyoGène, Unité Physiopathologie et Génétique du Neurone et du Muscle, Université Claude Bernard Lyon 1, CNRS UMR 5261, Inserm U1315, Univ Lyon, Lyon, France
| | - Julien Gondin
- Institut NeuroMyoGène, Unité Physiopathologie et Génétique du Neurone et du Muscle, Université Claude Bernard Lyon 1, CNRS UMR 5261, Inserm U1315, Univ Lyon, Lyon, France
| | - Jean Farup
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark; Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Niels Jessen
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark; Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus 8200, Denmark; Department of Clinical Pharmacology, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Jonas T Treebak
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark.
| |
Collapse
|
4
|
Kedlian VR, Wang Y, Liu T, Chen X, Bolt L, Tudor C, Shen Z, Fasouli ES, Prigmore E, Kleshchevnikov V, Pett JP, Li T, Lawrence JEG, Perera S, Prete M, Huang N, Guo Q, Zeng X, Yang L, Polański K, Chipampe NJ, Dabrowska M, Li X, Bayraktar OA, Patel M, Kumasaka N, Mahbubani KT, Xiang AP, Meyer KB, Saeb-Parsy K, Teichmann SA, Zhang H. Human skeletal muscle aging atlas. NATURE AGING 2024; 4:727-744. [PMID: 38622407 PMCID: PMC11108788 DOI: 10.1038/s43587-024-00613-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/19/2024] [Indexed: 04/17/2024]
Abstract
Skeletal muscle aging is a key contributor to age-related frailty and sarcopenia with substantial implications for global health. Here we profiled 90,902 single cells and 92,259 single nuclei from 17 donors to map the aging process in the adult human intercostal muscle, identifying cellular changes in each muscle compartment. We found that distinct subsets of muscle stem cells exhibit decreased ribosome biogenesis genes and increased CCL2 expression, causing different aging phenotypes. Our atlas also highlights an expansion of nuclei associated with the neuromuscular junction, which may reflect re-innervation, and outlines how the loss of fast-twitch myofibers is mitigated through regeneration and upregulation of fast-type markers in slow-twitch myofibers with age. Furthermore, we document the function of aging muscle microenvironment in immune cell attraction. Overall, we present a comprehensive human skeletal muscle aging resource ( https://www.muscleageingcellatlas.org/ ) together with an in-house mouse muscle atlas to study common features of muscle aging across species.
Collapse
Affiliation(s)
- Veronika R Kedlian
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yaning Wang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Tianliang Liu
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiaoping Chen
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Catherine Tudor
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Zhuojian Shen
- Department of Thoracic Surgery, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Eirini S Fasouli
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Jan Patrick Pett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tong Li
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - John E G Lawrence
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Shani Perera
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Qin Guo
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xinrui Zeng
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Lu Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Krzysztof Polański
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nana-Jane Chipampe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Monika Dabrowska
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Xiaobo Li
- Core Facilities for Medical Science, Sun Yat-sen University, Guangzhou, China
| | - Omer Ali Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Minal Patel
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Natsuhiko Kumasaka
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, Cambridge, UK
- Collaborative Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Andy Peng Xiang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK.
- Collaborative Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
| | - Hongbo Zhang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
| |
Collapse
|
5
|
Yin Y, He GJ, Hu S, Tse EHY, Cheung TH. Muscle stem cell niche dynamics during muscle homeostasis and regeneration. Curr Top Dev Biol 2024; 158:151-177. [PMID: 38670704 DOI: 10.1016/bs.ctdb.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
The process of skeletal muscle regeneration involves a coordinated interplay of specific cellular and molecular interactions within the injury site. This review provides an overview of the cellular and molecular components in regenerating skeletal muscle, focusing on how these cells or molecules in the niche regulate muscle stem cell functions. Dysfunctions of muscle stem cell-to-niche cell communications during aging and disease will also be discussed. A better understanding of how niche cells coordinate with muscle stem cells for muscle repair will greatly aid the development of therapeutic strategies for treating muscle-related disorders.
Collapse
Affiliation(s)
- Yishu Yin
- Division of Life Science, Center for Stem Cell Research, HKUST-Nan Fung Life Sciences Joint Laboratory, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, P.R. China
| | - Gary J He
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong, P.R. China
| | - Shenyuan Hu
- Division of Life Science, Center for Stem Cell Research, HKUST-Nan Fung Life Sciences Joint Laboratory, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, P.R. China
| | - Erin H Y Tse
- Division of Life Science, Center for Stem Cell Research, HKUST-Nan Fung Life Sciences Joint Laboratory, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, P.R. China; Hong Kong Center for Neurodegenerative Diseases, Hong Kong, P.R. China
| | - Tom H Cheung
- Division of Life Science, Center for Stem Cell Research, HKUST-Nan Fung Life Sciences Joint Laboratory, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, P.R. China; Hong Kong Center for Neurodegenerative Diseases, Hong Kong, P.R. China; Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, Shenzhen-Hong Kong Institute of Brain Science, HKUST Shenzhen Research Institute, Shenzhen, P.R. China.
| |
Collapse
|
6
|
Hsu JE, Ruiz L, Hwang Y, Guzman S, Cho CS, Cheng W, Si Y, Macpherson P, Schrank M, Jun G, Kang HM, Kim M, Brooks S, Lee JH. High-Resolution Spatial Transcriptomic Atlas of Mouse Soleus Muscle: Unveiling Single Cell and Subcellular Heterogeneity in Health and Denervation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582103. [PMID: 38464282 PMCID: PMC10925160 DOI: 10.1101/2024.02.26.582103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Skeletal muscle is essential for both movement and metabolic processes, characterized by a complex and ordered structure. Despite its importance, a detailed spatial map of gene expression within muscle tissue has been challenging to achieve due to the limitations of existing technologies, which struggle to provide high-resolution views. In this study, we leverage the Seq-Scope technique, an innovative method that allows for the observation of the entire transcriptome at an unprecedented submicron spatial resolution. By applying this technique to the mouse soleus muscle, we analyze and compare the gene expression profiles in both healthy conditions and following denervation, a process that mimics aspects of muscle aging. Our approach reveals detailed characteristics of muscle fibers, other cell types present within the muscle, and specific subcellular structures such as the postsynaptic nuclei at neuromuscular junctions, hybrid muscle fibers, and areas of localized expression of genes responsive to muscle injury, along with their histological context. The findings of this research significantly enhance our understanding of the diversity within the muscle cell transcriptome and its variation in response to denervation, a key factor in the decline of muscle function with age. This breakthrough in spatial transcriptomics not only deepens our knowledge of muscle biology but also sets the stage for the development of new therapeutic strategies aimed at mitigating the effects of aging on muscle health, thereby offering a more comprehensive insight into the mechanisms of muscle maintenance and degeneration in the context of aging and disease.
Collapse
Affiliation(s)
- Jer-En Hsu
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Lloyd Ruiz
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Yongha Hwang
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Space Planning and Analysis, University of Michigan, Ann Arbor, MI, USA
| | - Steve Guzman
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Chun-Seok Cho
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Weiqiu Cheng
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Yichen Si
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Peter Macpherson
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Mitchell Schrank
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Goo Jun
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Hyun-Min Kang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Myungjin Kim
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Susan Brooks
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Jun Hee Lee
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
7
|
Santarelli P, Rosti V, Vivo M, Lanzuolo C. Chromatin organization of muscle stem cell. Curr Top Dev Biol 2024; 158:375-406. [PMID: 38670713 DOI: 10.1016/bs.ctdb.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
The proper functioning of skeletal muscles is essential throughout life. A crucial crosstalk between the environment and several cellular mechanisms allows striated muscles to perform successfully. Notably, the skeletal muscle tissue reacts to an injury producing a completely functioning tissue. The muscle's robust regenerative capacity relies on the fine coordination between muscle stem cells (MuSCs or "satellite cells") and their specific microenvironment that dictates stem cells' activation, differentiation, and self-renewal. Critical for the muscle stem cell pool is a fine regulation of chromatin organization and gene expression. Acquiring a lineage-specific 3D genome architecture constitutes a crucial modulator of muscle stem cell function during development, in the adult stage, in physiological and pathological conditions. The context-dependent relationship between genome structure, such as accessibility and chromatin compartmentalization, and their functional effects will be analysed considering the improved 3D epigenome knowledge, underlining the intimate liaison between environmental encounters and epigenetics.
Collapse
Affiliation(s)
- Philina Santarelli
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Valentina Rosti
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy; CNR Institute of Biomedical Technologies, Milan, Italy
| | - Maria Vivo
- Università degli studi di Salerno, Fisciano, Italy.
| | - Chiara Lanzuolo
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy; CNR Institute of Biomedical Technologies, Milan, Italy.
| |
Collapse
|
8
|
Varshney A, Manickam N, Orchard P, Tovar A, Zhang Z, Feng F, Erdos MR, Narisu N, Ventresca C, Nishino K, Rai V, Stringham HM, Jackson AU, Tamsen T, Gao C, Yang M, Koues OI, Welch JD, Burant CF, Williams LK, Jenkinson C, DeFronzo RA, Norton L, Saramies J, Lakka TA, Laakso M, Tuomilehto J, Mohlke KL, Kitzman JO, Koistinen HA, Liu J, Boehnke M, Collins FS, Scott LJ, Parker SCJ. Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571696. [PMID: 38168419 PMCID: PMC10760134 DOI: 10.1101/2023.12.15.571696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Skeletal muscle, the largest human organ by weight, is relevant to several polygenic metabolic traits and diseases including type 2 diabetes (T2D). Identifying genetic mechanisms underlying these traits requires pinpointing the relevant cell types, regulatory elements, target genes, and causal variants. Here, we used genetic multiplexing to generate population-scale single nucleus (sn) chromatin accessibility (snATAC-seq) and transcriptome (snRNA-seq) maps across 287 frozen human skeletal muscle biopsies representing 456,880 nuclei. We identified 13 cell types that collectively represented 983,155 ATAC summits. We integrated genetic variation to discover 6,866 expression quantitative trait loci (eQTL) and 100,928 chromatin accessibility QTL (caQTL) (5% FDR) across the five most abundant cell types, cataloging caQTL peaks that atlas-level snATAC maps often miss. We identified 1,973 eGenes colocalized with caQTL and used mediation analyses to construct causal directional maps for chromatin accessibility and gene expression. 3,378 genome-wide association study (GWAS) signals across 43 relevant traits colocalized with sn-e/caQTL, 52% in a cell-specific manner. 77% of GWAS signals colocalized with caQTL and not eQTL, highlighting the critical importance of population-scale chromatin profiling for GWAS functional studies. GWAS-caQTL colocalization showed distinct cell-specific regulatory paradigms. For example, a C2CD4A/B T2D GWAS signal colocalized with caQTL in muscle fibers and multiple chromatin loop models nominated VPS13C, a glucose uptake gene. Sequence of the caQTL peak overlapping caSNP rs7163757 showed allelic regulatory activity differences in a human myocyte cell line massively parallel reporter assay. These results illuminate the genetic regulatory architecture of human skeletal muscle at high-resolution epigenomic, transcriptomic, and cell state scales and serve as a template for population-scale multi-omic mapping in complex tissues and traits.
Collapse
Affiliation(s)
- Arushi Varshney
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Nandini Manickam
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Peter Orchard
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Adelaide Tovar
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Zhenhao Zhang
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Fan Feng
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Michael R Erdos
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Narisu Narisu
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Christa Ventresca
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Dept. of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Kirsten Nishino
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Vivek Rai
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Heather M Stringham
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Anne U Jackson
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Tricia Tamsen
- Biomedical Research Core Facilities Advanced Genomics Core, University of Michigan, Ann Arbor, MI, USA
| | - Chao Gao
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Mao Yang
- Department of Internal Medicine, Center for Individualized and Genomic Medicine Research, Henry Ford Hospital, Detroit, MI, USA
| | - Olivia I Koues
- Biomedical Research Core Facilities Advanced Genomics Core, University of Michigan, Ann Arbor, MI, USA
| | - Joshua D Welch
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Charles F Burant
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - L Keoki Williams
- Department of Internal Medicine, Center for Individualized and Genomic Medicine Research, Henry Ford Hospital, Detroit, MI, USA
| | - Chris Jenkinson
- South Texas Diabetes and Obesity Research Institute, School of Medicine, University of Texas, Rio Grande Valley, TX, USA
| | - Ralph A DeFronzo
- Department of Medicine/Diabetes Division, University of Texas Health, San Antonio, TX, USA
| | - Luke Norton
- Department of Medicine/Diabetes Division, University of Texas Health, San Antonio, TX, USA
| | - Jouko Saramies
- Savitaipale Health Center, South Karelia Central Hospital, Lappeenranta, Finland
| | - Timo A Lakka
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Markku Laakso
- Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Jaakko Tuomilehto
- Dept. of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Dept. of Public Health, University of Helsinki, Helsinki, Finland
- Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Karen L Mohlke
- Dept. of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Jacob O Kitzman
- Dept. of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Heikki A Koistinen
- Dept. of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Medicine, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Jie Liu
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Michael Boehnke
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Francis S Collins
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Laura J Scott
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Stephen C J Parker
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Dept. of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
9
|
O'Reilly CL, Bodine SC, Miller BF. Current limitations and future opportunities of tracer studies of muscle ageing. J Physiol 2023:10.1113/JP285616. [PMID: 38051758 PMCID: PMC11150331 DOI: 10.1113/jp285616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/22/2023] [Indexed: 12/07/2023] Open
Affiliation(s)
- Colleen L O'Reilly
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Sue C Bodine
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Oklahoma City Veterans Association, Oklahoma City, OK, USA
| | - Benjamin F Miller
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Oklahoma City Veterans Association, Oklahoma City, OK, USA
| |
Collapse
|
10
|
Baldwin M, Buckley CD, Guilak F, Hulley P, Cribbs AP, Snelling S. A roadmap for delivering a human musculoskeletal cell atlas. Nat Rev Rheumatol 2023; 19:738-752. [PMID: 37798481 DOI: 10.1038/s41584-023-01031-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2023] [Indexed: 10/07/2023]
Abstract
Advances in single-cell technologies have transformed the ability to identify the individual cell types present within tissues and organs. The musculoskeletal bionetwork, part of the wider Human Cell Atlas project, aims to create a detailed map of the healthy musculoskeletal system at a single-cell resolution throughout tissue development and across the human lifespan, with complementary generation of data from diseased tissues. Given the prevalence of musculoskeletal disorders, this detailed reference dataset will be critical to understanding normal musculoskeletal function in growth, homeostasis and ageing. The endeavour will also help to identify the cellular basis for disease and lay the foundations for novel therapeutic approaches to treating diseases of the joints, soft tissues and bone. Here, we present a Roadmap delineating the critical steps required to construct the first draft of a human musculoskeletal cell atlas. We describe the key challenges involved in mapping the extracellular matrix-rich, but cell-poor, tissues of the musculoskeletal system, outline early milestones that have been achieved and describe the vision and directions for a comprehensive musculoskeletal cell atlas. By embracing cutting-edge technologies, integrating diverse datasets and fostering international collaborations, this endeavour has the potential to drive transformative changes in musculoskeletal medicine.
Collapse
Affiliation(s)
- Mathew Baldwin
- The Botnar Institute for Musculoskeletal Sciences, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford, UK
| | - Christopher D Buckley
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford, UK
| | - Farshid Guilak
- Department of Orthopaedic Surgery, Washington University in St. Louis, St. Louis, MO, USA
- Shriners Hospitals for Children, St. Louis, MO, USA
| | - Philippa Hulley
- The Botnar Institute for Musculoskeletal Sciences, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford, UK
| | - Adam P Cribbs
- The Botnar Institute for Musculoskeletal Sciences, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford, UK
| | - Sarah Snelling
- The Botnar Institute for Musculoskeletal Sciences, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford, UK.
| |
Collapse
|
11
|
Cao Y, Ai Y, Zhang X, Zhang J, Long X, Zhu Y, Wang L, Gu Q, Han H. Genome-wide epigenetic dynamics during postnatal skeletal muscle growth in Hu sheep. Commun Biol 2023; 6:1077. [PMID: 37872364 PMCID: PMC10593826 DOI: 10.1038/s42003-023-05439-0] [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: 08/07/2022] [Accepted: 10/10/2023] [Indexed: 10/25/2023] Open
Abstract
Hypertrophy and fiber transformation are two prominent features of postnatal skeletal muscle development. However, the role of epigenetic modifications is less understood. ATAC-seq, whole genome bisulfite sequencing, and RNA-seq were applied to investigate the epigenetic dynamics of muscle in Hu sheep at 3 days, 3 months, 6 months, and 12 months after birth. All 6865 differentially expressed genes were assigned into three distinct tendencies, highlighting the balanced protein synthesis, accumulated immune activities, and restrained cell division in postnatal development. We identified 3742 differentially accessible regions and 11799 differentially methylated regions that were associated with muscle-development-related pathways in certain stages, like D3-M6. Transcription factor network analysis, based on genomic loci with high chromatin accessibility and low methylation, showed that ARID5B, MYOG, and ENO1 were associated with muscle hypertrophy, while NR1D1, FADS1, ZFP36L2, and SLC25A1 were associated with muscle fiber transformation. Taken together, these results suggest that DNA methylation and chromatin accessibility contributed toward regulating the growth and fiber transformation of postnatal skeletal muscle in Hu sheep.
Collapse
Affiliation(s)
- Yutao Cao
- Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yue Ai
- Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiaosheng Zhang
- Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Tianjin, China
| | - Jinlong Zhang
- Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Tianjin, China
| | - Xianlei Long
- Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Yaning Zhu
- Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Linli Wang
- Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qingyi Gu
- Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Hongbing Han
- Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China.
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China.
- Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China.
| |
Collapse
|
12
|
Lin H, Peng H, Sun Y, Si M, Wu J, Wang Y, Thomas SS, Sun Z, Hu Z. Reprogramming of cis-regulatory networks during skeletal muscle atrophy in male mice. Nat Commun 2023; 14:6581. [PMID: 37853001 PMCID: PMC10584982 DOI: 10.1038/s41467-023-42313-3] [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: 03/28/2023] [Accepted: 10/05/2023] [Indexed: 10/20/2023] Open
Abstract
A comprehensive atlas of cis-regulatory elements and their dynamic activity is necessary to understand the transcriptional basis of cellular structure maintenance, metabolism, and responses to the environment. Here we show, using matched single-nucleus chromatin accessibility and RNA-sequencing from juvenile male C57BL6 mice, an atlas of accessible chromatin regions in both normal and denervated skeletal muscles. We identified cell-type-specific cis-regulatory networks, highlighting the dynamic regulatory circuits mediating transitions between myonuclear types. Through comparison of normal and perturbed muscle, we delineated the reprogramming of cis-regulatory networks in response to denervation, described the interplay of promoters/enhancers and target genes. We further unveil a hierarchical structure of transcription factors that delineate a regulatory network in atrophic muscle, identifying ELK4 as a key atrophy-related transcription factor that instigates muscle atrophy through TGF-β1 regulation. This study furnishes a rich genomic resource, essential for decoding the regulatory dynamics of skeletal muscle in both physiological and pathological states.
Collapse
Affiliation(s)
- Hongchun Lin
- Nephrology Division, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
- Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hui Peng
- Nephrology Division, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China.
- Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Yuxiang Sun
- Nephrology Division, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Meijun Si
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangzhou, 510080, China
| | - Jiao Wu
- Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yanlin Wang
- Division of Nephrology, Department of Medicine, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Sandhya S Thomas
- Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zheng Sun
- Endocrinology Division, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhaoyong Hu
- Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.
| |
Collapse
|
13
|
Rubenstein AB, Smith GR, Zhang Z, Chen X, Chambers TL, Ruf-Zamojski F, Mendelev N, Cheng WS, Zamojski M, Amper MAS, Nair VD, Marderstein AR, Montgomery SB, Troyanskaya OG, Zaslavsky E, Trappe T, Trappe S, Sealfon SC. Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.558914. [PMID: 37808658 PMCID: PMC10557702 DOI: 10.1101/2023.09.26.558914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Endurance exercise is an important health modifier. We studied cell-type specific adaptations of human skeletal muscle to acute endurance exercise using single-nucleus (sn) multiome sequencing in human vastus lateralis samples collected before and 3.5 hours after 40 min exercise at 70% VO2max in four subjects, as well as in matched time of day samples from two supine resting circadian controls. High quality same-cell RNA-seq and ATAC-seq data were obtained from 37,154 nuclei comprising 14 cell types. Among muscle fiber types, both shared and fiber-type specific regulatory programs were identified. Single-cell circuit analysis identified distinct adaptations in fast, slow and intermediate fibers as well as LUM-expressing FAP cells, involving a total of 328 transcription factors (TFs) acting at altered accessibility sites regulating 2,025 genes. These data and circuit mapping provide single-cell insight into the processes underlying tissue and metabolic remodeling responses to exercise.
Collapse
Affiliation(s)
- Aliza B. Rubenstein
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Gregory R. Smith
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Zidong Zhang
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Xi Chen
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA
| | - Toby L. Chambers
- Human Performance Laboratory, Ball State University, Muncie, IN 47306, USA
| | - Frederique Ruf-Zamojski
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Natalia Mendelev
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Wan Sze Cheng
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Michel Zamojski
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mary Anne S. Amper
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Venugopalan D. Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Andrew R. Marderstein
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Stephen B. Montgomery
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Olga G. Troyanskaya
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Todd Trappe
- Human Performance Laboratory, Ball State University, Muncie, IN 47306, USA
| | - Scott Trappe
- Human Performance Laboratory, Ball State University, Muncie, IN 47306, USA
- Senior author
| | - Stuart C. Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA
| |
Collapse
|
14
|
Gaulton KJ, Preissl S, Ren B. Interpreting non-coding disease-associated human variants using single-cell epigenomics. Nat Rev Genet 2023; 24:516-534. [PMID: 37161089 PMCID: PMC10629587 DOI: 10.1038/s41576-023-00598-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2023] [Indexed: 05/11/2023]
Abstract
Genome-wide association studies (GWAS) have linked hundreds of thousands of sequence variants in the human genome to common traits and diseases. However, translating this knowledge into a mechanistic understanding of disease-relevant biology remains challenging, largely because such variants are predominantly in non-protein-coding sequences that still lack functional annotation at cell-type resolution. Recent advances in single-cell epigenomics assays have enabled the generation of cell type-, subtype- and state-resolved maps of the epigenome in heterogeneous human tissues. These maps have facilitated cell type-specific annotation of candidate cis-regulatory elements and their gene targets in the human genome, enhancing our ability to interpret the genetic basis of common traits and diseases.
Collapse
Affiliation(s)
- Kyle J Gaulton
- Department of Paediatrics, Paediatric Diabetes Research Center, University of California San Diego School of Medicine, La Jolla, CA, USA.
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Bing Ren
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
| |
Collapse
|
15
|
Cai C, Yue Y, Yue B. Single-cell RNA sequencing in skeletal muscle developmental biology. Biomed Pharmacother 2023; 162:114631. [PMID: 37003036 DOI: 10.1016/j.biopha.2023.114631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/29/2023] [Accepted: 03/29/2023] [Indexed: 04/01/2023] Open
Abstract
Skeletal muscle is the most extensive tissue in mammals, and they perform several functions; it is derived from paraxial mesodermal somites and undergoes hyperplasia and hypertrophy to form multinucleated, contractile, and functional muscle fibers. Skeletal muscle is a complex heterogeneous tissue composed of various cell types that establish communication strategies to exchange biological information; therefore, characterizing the cellular heterogeneity and transcriptional signatures of skeletal muscle is central to understanding its ontogeny's details. Studies of skeletal myogenesis have focused primarily on myogenic cells' proliferation, differentiation, migration, and fusion and ignored the intricate network of cells with specific biological functions. The rapid development of single-cell sequencing technology has recently enabled the exploration of skeletal muscle cell types and molecular events during development. This review summarizes the progress in single-cell RNA sequencing and its applications in skeletal myogenesis, which will provide insights into skeletal muscle pathophysiology.
Collapse
Affiliation(s)
- Cuicui Cai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu 610225, China; Guyuan Branch, Ningxia Academy of Agriculture and Forestry Sciences, Guyuan 7560000, China
| | - Yuan Yue
- Department of Pathobiology and Immunology, Hebei University of Chinese Medicine, Shijiazhuang 050200, China
| | - Binglin Yue
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu 610225, China.
| |
Collapse
|
16
|
Soule TG, Pontifex CS, Rosin N, Joel MM, Lee S, Nguyen MD, Chhibber S, Pfeffer G. A protocol for single nucleus RNA-seq from frozen skeletal muscle. Life Sci Alliance 2023; 6:e202201806. [PMID: 36914268 PMCID: PMC10011611 DOI: 10.26508/lsa.202201806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/14/2023] Open
Abstract
Single-cell technologies are a method of choice to obtain vast amounts of cell-specific transcriptional information under physiological and diseased states. Myogenic cells are resistant to single-cell RNA sequencing because of their large, multinucleated nature. Here, we report a novel, reliable, and cost-effective method to analyze frozen human skeletal muscle by single-nucleus RNA sequencing. This method yields all expected cell types for human skeletal muscle and works on tissue frozen for long periods of time and with significant pathological changes. Our method is ideal for studying banked samples with the intention of studying human muscle disease.
Collapse
Affiliation(s)
- Tyler Gb Soule
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
| | - Carly S Pontifex
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
| | - Nicole Rosin
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
| | - Matthew M Joel
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
| | - Sukyoung Lee
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
| | - Minh Dang Nguyen
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Sameer Chhibber
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Gerald Pfeffer
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
| |
Collapse
|
17
|
Butto T, Mungikar K, Baumann P, Winter J, Lutz B, Gerber S. Nuclei on the Rise: When Nuclei-Based Methods Meet Next-Generation Sequencing. Cells 2023; 12:cells12071051. [PMID: 37048124 PMCID: PMC10093037 DOI: 10.3390/cells12071051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
In the last decade, we have witnessed an upsurge in nuclei-based studies, particularly coupled with next-generation sequencing. Such studies aim at understanding the molecular states that exist in heterogeneous cell populations by applying increasingly more affordable sequencing approaches, in addition to optimized methodologies developed to isolate and select nuclei. Although these powerful new methods promise unprecedented insights, it is important to understand and critically consider the associated challenges. Here, we provide a comprehensive overview of the rise of nuclei-based studies and elaborate on their advantages and disadvantages, with a specific focus on their utility for transcriptomic sequencing analyses. Improved designs and appropriate use of the various experimental strategies will result in acquiring biologically accurate and meaningful information.
Collapse
Affiliation(s)
- Tamer Butto
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, 55128 Mainz, Germany
- Correspondence: (T.B.); (S.G.); Tel.: +49-(0)6131-39-27331 (S.G.)
| | - Kanak Mungikar
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
| | - Peter Baumann
- Faculty of Biology, Johannes Gutenberg-University, 55128 Mainz, Germany
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Jennifer Winter
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
- Leibniz Institute for Resilience Research (LIR), 55122 Mainz, Germany
| | - Beat Lutz
- Leibniz Institute for Resilience Research (LIR), 55122 Mainz, Germany
- Institute of Physiological Chemistry, University Medical Center Mainz, 55128 Mainz, Germany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
- Correspondence: (T.B.); (S.G.); Tel.: +49-(0)6131-39-27331 (S.G.)
| |
Collapse
|
18
|
Abbassi-Daloii T, el Abdellaoui S, Voortman LM, Veeger TTJ, Cats D, Mei H, Meuffels DE, van Arkel E, 't Hoen PAC, Kan HE, Raz V. A transcriptome atlas of leg muscles from healthy human volunteers reveals molecular and cellular signatures associated with muscle location. eLife 2023; 12:80500. [PMID: 36744868 PMCID: PMC9988256 DOI: 10.7554/elife.80500] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 02/03/2023] [Indexed: 02/07/2023] Open
Abstract
Skeletal muscles support the stability and mobility of the skeleton but differ in biomechanical properties and physiological functions. The intrinsic factors that regulate muscle-specific characteristics are poorly understood. To study these, we constructed a large atlas of RNA-seq profiles from six leg muscles and two locations from one muscle, using biopsies from 20 healthy young males. We identified differential expression patterns and cellular composition across the seven tissues using three bioinformatics approaches confirmed by large-scale newly developed quantitative immune-histology procedures. With all three procedures, the muscle samples clustered into three groups congruent with their anatomical location. Concomitant with genes marking oxidative metabolism, genes marking fast- or slow-twitch myofibers differed between the three groups. The groups of muscles with higher expression of slow-twitch genes were enriched in endothelial cells and showed higher capillary content. In addition, expression profiles of Homeobox (HOX) transcription factors differed between the three groups and were confirmed by spatial RNA hybridization. We created an open-source graphical interface to explore and visualize the leg muscle atlas (https://tabbassidaloii.shinyapps.io/muscleAtlasShinyApp/). Our study reveals the molecular specialization of human leg muscles, and provides a novel resource to study muscle-specific molecular features, which could be linked with (patho)physiological processes.
Collapse
Affiliation(s)
| | - Salma el Abdellaoui
- Department of Human Genetics, Leiden University Medical CenterLeidenNetherlands
| | - Lenard M Voortman
- Division of Cell and Chemical Biology, Leiden University Medical CenterLeidenNetherlands
| | - Thom TJ Veeger
- C.J. Gorter MRI Center, Department of Radiology, Leiden University Medical CenterLeidenNetherlands
| | - Davy Cats
- Sequencing Analysis Support Core, Leiden University Medical CenterLeidenNetherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical CenterLeidenNetherlands
| | - Duncan E Meuffels
- Orthopedic and Sport Medicine Department, Erasmus MC, University Medical Center RotterdamRotterdamNetherlands
| | | | - Peter AC 't Hoen
- Department of Human Genetics, Leiden University Medical CenterLeidenNetherlands
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical CenterRadboudNetherlands
| | - Hermien E Kan
- C.J. Gorter MRI Center, Department of Radiology, Leiden University Medical CenterLeidenNetherlands
- Duchenne Center NetherlandsLeidenNetherlands
| | - Vered Raz
- Department of Human Genetics, Leiden University Medical CenterLeidenNetherlands
| |
Collapse
|
19
|
Bagley JR, Denes LT, McCarthy JJ, Wang ET, Murach KA. The myonuclear domain in adult skeletal muscle fibres: past, present and future. J Physiol 2023; 601:723-741. [PMID: 36629254 PMCID: PMC9931674 DOI: 10.1113/jp283658] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
Most cells in the body are mononuclear whereas skeletal muscle fibres are uniquely multinuclear. The nuclei of muscle fibres (myonuclei) are usually situated peripherally which complicates the equitable distribution of gene products. Myonuclear abundance can also change under conditions such as hypertrophy and atrophy. Specialised zones in muscle fibres have different functions and thus distinct synthetic demands from myonuclei. The complex structure and regulatory requirements of multinuclear muscle cells understandably led to the hypothesis that myonuclei govern defined 'domains' to maintain homeostasis and facilitate adaptation. The purpose of this review is to provide historical context for the myonuclear domain and evaluate its veracity with respect to mRNA and protein distribution resulting from myonuclear transcription. We synthesise insights from past and current in vitro and in vivo genetically modified models for studying the myonuclear domain under dynamic conditions. We also cover the most contemporary knowledge on mRNA and protein transport in muscle cells. Insights from emerging technologies such as single myonuclear RNA-sequencing further inform our discussion of the myonuclear domain. We broadly conclude: (1) the myonuclear domain can be flexible during muscle fibre growth and atrophy, (2) the mechanisms and role of myonuclear loss and motility deserve further consideration, (3) mRNA in muscle is actively transported via microtubules and locally restricted, but proteins may travel far from a myonucleus of origin and (4) myonuclear transcriptional specialisation extends beyond the classic neuromuscular and myotendinous populations. A deeper understanding of the myonuclear domain in muscle may promote effective therapies for ageing and disease.
Collapse
Affiliation(s)
- James R. Bagley
- Muscle Physiology Laboratory, Department of Kinesiology, San Francisco State University, San Francisco, California
| | | | - John J. McCarthy
- The Center for Muscle Biology, University of Kentucky, Lexington, Kentucky
- Department of Physiology, College of Medicine, University of Kentucky
| | - Eric T. Wang
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, University of Florida, Gainesville, Florida
- Myology Institute, University of Florida
- Genetics Institute, University of Florida
| | - Kevin A. Murach
- Exercise Science Research Center, Department of Health, Human Performance, and Recreation, University of Arkansas, Fayetteville, Arkansas
- Cell and Molecular Biology Graduate Program, University of Arkansas
| |
Collapse
|
20
|
Preissl S, Gaulton KJ, Ren B. Characterizing cis-regulatory elements using single-cell epigenomics. Nat Rev Genet 2023; 24:21-43. [PMID: 35840754 PMCID: PMC9771884 DOI: 10.1038/s41576-022-00509-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2022] [Indexed: 12/24/2022]
Abstract
Cell type-specific gene expression patterns and dynamics during development or in disease are controlled by cis-regulatory elements (CREs), such as promoters and enhancers. Distinct classes of CREs can be characterized by their epigenomic features, including DNA methylation, chromatin accessibility, combinations of histone modifications and conformation of local chromatin. Tremendous progress has been made in cataloguing CREs in the human genome using bulk transcriptomic and epigenomic methods. However, single-cell epigenomic and multi-omic technologies have the potential to provide deeper insight into cell type-specific gene regulatory programmes as well as into how they change during development, in response to environmental cues and through disease pathogenesis. Here, we highlight recent advances in single-cell epigenomic methods and analytical tools and discuss their readiness for human tissue profiling.
Collapse
Affiliation(s)
- Sebastian Preissl
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA.
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Kyle J Gaulton
- Department of Paediatrics, Paediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA.
| | - Bing Ren
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA.
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
| |
Collapse
|
21
|
Han S, Kim K, Park S, Lee AJ, Chun H, Jung I. scAVENGERS: a genotype-based deconvolution of individuals in multiplexed single-cell ATAC-seq data without reference genotypes. NAR Genom Bioinform 2022; 4:lqac095. [PMID: 36601579 PMCID: PMC9803874 DOI: 10.1093/nargab/lqac095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 11/09/2022] [Accepted: 12/11/2022] [Indexed: 01/01/2023] Open
Abstract
Genetic differences inferred from sequencing reads can be used for demultiplexing of pooled single-cell RNA-seq (scRNA-seq) data across multiple donors without WGS-based reference genotypes. However, such methods could not be directly applied to single-cell ATAC-seq (scATAC-seq) data owing to the lower read coverage for each variant compared to scRNA-seq. We propose a new software, scATAC-seq Variant-based EstimatioN for GEnotype ReSolving (scAVENGERS), which resolves this issue by calling more individual-specific germline variants and using an optimized mixture model for the scATAC-seq. The benchmark conducted with three synthetic multiplexed scATAC-seq datasets of peripheral blood mononuclear cells and prefrontal cortex tissues showed outstanding performance compared to existing methods in terms of accuracy, doublet detection, and a portion of donor-assigned cells. Furthermore, analyzing the effect of the improved sections provided insight into handling pooled single-cell data in the future. Our source code of the devised software is available at GitHub: https://github.com/kaistcbfg/scAVENGERS.
Collapse
Affiliation(s)
- Seungbeom Han
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Kyukwang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Seongwan Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Andrew J Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hyonho Chun
- Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Inkyung Jung
- To whom correspondence should be addressed. Tel: +82 42 350 7315; Fax: +82 42 350 2610;
| |
Collapse
|
22
|
Perez K, Ciotlos S, McGirr J, Limbad C, Doi R, Nederveen JP, Nilsson MI, Winer DA, Evans W, Tarnopolsky M, Campisi J, Melov S. Single nuclei profiling identifies cell specific markers of skeletal muscle aging, frailty, and senescence. Aging (Albany NY) 2022; 14:9393-9422. [PMID: 36516485 PMCID: PMC9792217 DOI: 10.18632/aging.204435] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
Aging is accompanied by a loss of muscle mass and function, termed sarcopenia, which causes numerous morbidities and economic burdens in human populations. Mechanisms implicated in age-related sarcopenia or frailty include inflammation, muscle stem cell depletion, mitochondrial dysfunction, and loss of motor neurons, but whether there are key drivers of sarcopenia are not yet known. To gain deeper insights into age-related muscle loss, we performed transcriptome profiling on lower limb muscle biopsies from 72 young, elderly, and frail human subjects using bulk RNA-seq (N = 72) and single-nuclei RNA-seq (N = 17). This combined approach revealed changes in gene expression that occur with age and frailty in multiple cell types comprising mature skeletal muscle. Notably, we found increased expression of the genes MYH8 and PDK4, and decreased expression of the gene IGFN1, in aged muscle. We validated several key genes changes in fixed human muscle tissue using digital spatial profiling. We also identified a small population of nuclei that express CDKN1A, present only in aged samples, consistent with p21cip1-driven senescence in this subpopulation. Overall, our findings identify unique cellular subpopulations in aged and sarcopenic skeletal muscle, which will facilitate the development of new therapeutic strategies to combat age-related frailty.
Collapse
Affiliation(s)
- Kevin Perez
- Buck Institute for Research on Aging, Novato, CA 94952, USA
| | - Serban Ciotlos
- Buck Institute for Research on Aging, Novato, CA 94952, USA
| | - Julia McGirr
- Buck Institute for Research on Aging, Novato, CA 94952, USA
| | | | - Ryosuke Doi
- Buck Institute for Research on Aging, Novato, CA 94952, USA
- Drug Discovery Research, Astellas Pharma, Tsukuba, Ibaraki, Japan
| | | | | | | | - William Evans
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA
| | | | - Judith Campisi
- Buck Institute for Research on Aging, Novato, CA 94952, USA
| | - Simon Melov
- Buck Institute for Research on Aging, Novato, CA 94952, USA
| |
Collapse
|
23
|
Cervantes-Pérez SA, Thibivillliers S, Tennant S, Libault M. Review: Challenges and perspectives in applying single nuclei RNA-seq technology in plant biology. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111486. [PMID: 36202294 DOI: 10.1016/j.plantsci.2022.111486] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/12/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Plant single-cell RNA-seq technology quantifies the abundance of plant transcripts at a single-cell resolution. Deciphering the transcriptomes of each plant cell, their regulation during plant cell development, and their response to environmental stresses will support the functional study of genes, the establishment of precise transcriptional programs, the prediction of more accurate gene regulatory networks, and, in the long term, the design of de novo gene pathways to enhance selected crop traits. In this review, we will discuss the opportunities, challenges, and problems, and share tentative solutions associated with the generation and analysis of plant single-cell transcriptomes. We will discuss the benefit and limitations of using plant protoplasts vs. nuclei to conduct single-cell RNA-seq experiments on various plant species and organs, the functional annotation of plant cell types based on their transcriptomic profile, the characterization of the dynamic regulation of the plant genes during cell development or in response to environmental stress, the need to characterize and integrate additional layers of -omics datasets to capture new molecular modalities at the single-cell level and reveal their causalities, the deposition and access to single-cell datasets, and the accessibility of this technology to plant scientists.
Collapse
Affiliation(s)
- Sergio Alan Cervantes-Pérez
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68503, USA
| | - Sandra Thibivillliers
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68503, USA; Center for Biotechnology, University of Nebraska, Lincoln, NE 68588, USA; Single Cell Genomics Core Facility, University of Nebraska-Lincoln, NE 68588, USA
| | - Sutton Tennant
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68503, USA
| | - Marc Libault
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68503, USA; Center for Biotechnology, University of Nebraska, Lincoln, NE 68588, USA; Single Cell Genomics Core Facility, University of Nebraska-Lincoln, NE 68588, USA.
| |
Collapse
|
24
|
Ruoss S, Esparza MC, Vasquez-Bolanos LS, Nasamran CA, Fisch KM, Engler AJ, Ward SR. Spatial transcriptomics tools allow for regional exploration of heterogeneous muscle pathology in the pre-clinical rabbit model of rotator cuff tear. J Orthop Surg Res 2022; 17:440. [PMID: 36195913 PMCID: PMC9531386 DOI: 10.1186/s13018-022-03326-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/18/2022] [Indexed: 11/21/2022] Open
Abstract
Background Conditions affecting skeletal muscle, such as chronic rotator cuff tears, low back pain, dystrophies, and many others, often share changes in muscle phenotype: intramuscular adipose and fibrotic tissue increase while contractile tissue is lost. The underlying changes in cell populations and cell ratios observed with these phenotypic changes complicate the interpretation of tissue-level transcriptional data. Novel single-cell transcriptomics has limited capacity to address this problem because muscle fibers are too long to be engulfed in single-cell droplets and single nuclei transcriptomics are complicated by muscle fibers’ multinucleation. Therefore, the goal of this project was to evaluate the potential and challenges of a spatial transcriptomics technology to add dimensionality to transcriptional data in an attempt to better understand regional cellular activity in heterogeneous skeletal muscle tissue. Methods The 3′ Visium spatial transcriptomics technology was applied to muscle tissue of a rabbit model of rotator cuff tear. Healthy control and tissue collected at 2 and 16 weeks after tenotomy was utilized and freshly snap frozen tissue was compared with tissue stored for over 6 years to evaluate whether this technology is retrospectively useful in previously acquired tissues. Transcriptional information was overlayed with standard hematoxylin and eosin (H&E) stains of the exact same histological sections. Results Sequencing saturation and number of genes detected was not affected by sample storage duration. Unbiased clustering matched the underlying tissue type-based on H&E assessment. Connective-tissue-rich areas presented with lower unique molecular identifier counts are compared with muscle fibers even though tissue permeabilization was standardized across the section. A qualitative analysis of resulting datasets revealed heterogeneous fiber degeneration–regeneration after tenotomy based on (neonatal) myosin heavy chain 8 detection and associated differentially expressed gene analysis. Conclusions This protocol can be used in skeletal muscle to explore spatial transcriptional patterns and confidently relate them to the underlying histology, even for tissues that have been stored for up to 6 years. Using this protocol, there is potential for novel transcriptional pathway discovery in longitudinal studies since the transcriptional information is unbiased by muscle composition and cell type changes.
Collapse
Affiliation(s)
- Severin Ruoss
- Department of Orthopaedic Surgery, UC San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0863, USA
| | - Mary C Esparza
- Department of Orthopaedic Surgery, UC San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0863, USA
| | - Laura S Vasquez-Bolanos
- Department of Orthopaedic Surgery, UC San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0863, USA.,Department of Bioengineering, UC San Diego, La Jolla, CA, USA
| | - Chanond A Nasamran
- Center for Computational Biology and Bioinformatics, UC San Diego, La Jolla, CA, USA
| | - Kathleen M Fisch
- Center for Computational Biology and Bioinformatics, UC San Diego, La Jolla, CA, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, UC San Diego, La Jolla, CA, USA
| | - Adam J Engler
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
| | - Samuel R Ward
- Department of Orthopaedic Surgery, UC San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0863, USA. .,Department of Bioengineering, UC San Diego, La Jolla, CA, USA. .,Department of Radiology, UC San Diego, La Jolla, CA, USA.
| |
Collapse
|
25
|
Scripture-Adams DD, Chesmore KN, Barthélémy F, Wang RT, Nieves-Rodriguez S, Wang DW, Mokhonova EI, Douine ED, Wan J, Little I, Rabichow LN, Nelson SF, Miceli MC. Single nuclei transcriptomics of muscle reveals intra-muscular cell dynamics linked to dystrophin loss and rescue. Commun Biol 2022; 5:989. [PMID: 36123393 PMCID: PMC9485160 DOI: 10.1038/s42003-022-03938-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/01/2022] [Indexed: 02/05/2023] Open
Abstract
In Duchenne muscular dystrophy, dystrophin loss leads to chronic muscle damage, dysregulation of repair, fibro-fatty replacement, and weakness. We develop methodology to efficiently isolate individual nuclei from minute quantities of frozen skeletal muscle, allowing single nuclei sequencing of irreplaceable archival samples and from very small samples. We apply this method to identify cell and gene expression dynamics within human DMD and mdx mouse muscle, characterizing effects of dystrophin rescue by exon skipping therapy at single nuclei resolution. DMD exon 23 skipping events are directly observed and increased in myonuclei from treated mice. We describe partial rescue of type IIa and IIx myofibers, expansion of an MDSC-like myeloid population, recovery of repair/remodeling M2-macrophage, and repression of inflammatory POSTN1 + fibroblasts in response to exon skipping and partial dystrophin restoration. Use of this method enables exploration of cellular and transcriptomic mechanisms of dystrophin loss and repair within an intact muscle environment. Our initial findings will scaffold our future work to more directly examine muscular dystrophies and putative recovery pathways.
Collapse
Affiliation(s)
- Deirdre D Scripture-Adams
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kevin N Chesmore
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Florian Barthélémy
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Richard T Wang
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shirley Nieves-Rodriguez
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Derek W Wang
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Amgen, Thousand Oaks, CA, USA
| | - Ekaterina I Mokhonova
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Emilie D Douine
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jijun Wan
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Isaiah Little
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Laura N Rabichow
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Stanley F Nelson
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| | - M Carrie Miceli
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA.
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
26
|
LIM CHANGHYUN, NUNES EVERSONA, CURRIER BRADS, MCLEOD JONATHANC, THOMAS AARONCQ, PHILLIPS STUARTM. An Evidence-Based Narrative Review of Mechanisms of Resistance Exercise-Induced Human Skeletal Muscle Hypertrophy. Med Sci Sports Exerc 2022; 54:1546-1559. [PMID: 35389932 PMCID: PMC9390238 DOI: 10.1249/mss.0000000000002929] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Skeletal muscle plays a critical role in physical function and metabolic health. Muscle is a highly adaptable tissue that responds to resistance exercise (RE; loading) by hypertrophying, or during muscle disuse, RE mitigates muscle loss. Resistance exercise training (RET)-induced skeletal muscle hypertrophy is a product of external (e.g., RE programming, diet, some supplements) and internal variables (e.g., mechanotransduction, ribosomes, gene expression, satellite cells activity). RE is undeniably the most potent nonpharmacological external variable to stimulate the activation/suppression of internal variables linked to muscular hypertrophy or countering disuse-induced muscle loss. Here, we posit that despite considerable research on the impact of external variables on RET and hypertrophy, internal variables (i.e., inherent skeletal muscle biology) are dominant in regulating the extent of hypertrophy in response to external stimuli. Thus, identifying the key internal skeletal muscle-derived variables that mediate the translation of external RE variables will be pivotal to determining the most effective strategies for skeletal muscle hypertrophy in healthy persons. Such work will aid in enhancing function in clinical populations, slowing functional decline, and promoting physical mobility. We provide up-to-date, evidence-based perspectives of the mechanisms regulating RET-induced skeletal muscle hypertrophy.
Collapse
Affiliation(s)
- CHANGHYUN LIM
- Department of Kinesiology, McMaster University, Hamilton, Ontario, CANADA
| | - EVERSON A. NUNES
- Department of Kinesiology, McMaster University, Hamilton, Ontario, CANADA
- Department of Physiological Science, Federal University of Santa Catarina, Florianópolis, Santa-Catarina, BRAZIL
| | - BRAD S. CURRIER
- Department of Kinesiology, McMaster University, Hamilton, Ontario, CANADA
| | - JONATHAN C. MCLEOD
- Department of Kinesiology, McMaster University, Hamilton, Ontario, CANADA
| | - AARON C. Q. THOMAS
- Department of Kinesiology, McMaster University, Hamilton, Ontario, CANADA
| | - STUART M. PHILLIPS
- Department of Kinesiology, McMaster University, Hamilton, Ontario, CANADA
| |
Collapse
|
27
|
Williams K, Yokomori K, Mortazavi A. Heterogeneous Skeletal Muscle Cell and Nucleus Populations Identified by Single-Cell and Single-Nucleus Resolution Transcriptome Assays. Front Genet 2022; 13:835099. [PMID: 35646075 PMCID: PMC9136090 DOI: 10.3389/fgene.2022.835099] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Single-cell RNA-seq (scRNA-seq) has revolutionized modern genomics, but the large size of myotubes and myofibers has restricted use of scRNA-seq in skeletal muscle. For the study of muscle, single-nucleus RNA-seq (snRNA-seq) has emerged not only as an alternative to scRNA-seq, but as a novel method providing valuable insights into multinucleated cells such as myofibers. Nuclei within myofibers specialize at junctions with other cell types such as motor neurons. Nuclear heterogeneity plays important roles in certain diseases such as muscular dystrophies. We survey current methods of high-throughput single cell and subcellular resolution transcriptomics, including single-cell and single-nucleus RNA-seq and spatial transcriptomics, applied to satellite cells, myoblasts, myotubes and myofibers. We summarize the major myonuclei subtypes identified in homeostatic and regenerating tissue including those specific to fiber type or at junctions with other cell types. Disease-specific nucleus populations were found in two muscular dystrophies, FSHD and Duchenne muscular dystrophy, demonstrating the importance of performing transcriptome studies at the single nucleus level in muscle.
Collapse
Affiliation(s)
- Katherine Williams
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, United States
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, United States
| | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, United States
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, United States
| |
Collapse
|