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Chen L, Kong X, Johnston KG, Mortazavi A, Holmes TC, Tan Z, Yokomori K, Xu X. Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy. Genome Res 2024; 34:665-679. [PMID: 38777608 PMCID: PMC11216401 DOI: 10.1101/gr.278717.123] [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: 11/09/2023] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is linked to abnormal derepression of the transcription activator DUX4. This effect is localized to a low percentage of cells, requiring single-cell analysis. However, single-cell/nucleus RNA-seq cannot fully capture the transcriptome of multinucleated large myotubes. To circumvent these issues, we use multiplexed error-robust fluorescent in situ hybridization (MERFISH) spatial transcriptomics that allows profiling of RNA transcripts at a subcellular resolution. We simultaneously examined spatial distributions of 140 genes, including 24 direct DUX4 targets, in in vitro differentiated myotubes and unfused mononuclear cells (MNCs) of control, isogenic D4Z4 contraction mutant and FSHD patient samples, as well as the individual nuclei within them. We find myocyte nuclei segregate into two clusters defined by the expression of DUX4 target genes, which is exclusively found in patient/mutant nuclei, whereas MNCs cluster based on developmental states. Patient/mutant myotubes are found in "FSHD-hi" and "FSHD-lo" states with the former signified by high DUX4 target expression and decreased muscle gene expression. Pseudotime analyses reveal a clear bifurcation of myoblast differentiation into control and FSHD-hi myotube branches, with variable numbers of DUX4 target-expressing nuclei found in multinucleated FSHD-hi myotubes. Gene coexpression modules related to extracellular matrix and stress gene ontologies are significantly altered in patient/mutant myotubes compared with the control. We also identify distinct subpathways within the DUX4 gene network that may differentially contribute to the disease transcriptomic phenotype. Taken together, our MERFISH-based study provides effective gene network profiling of multinucleated cells and identifies FSHD-induced transcriptomic alterations during myoblast differentiation.
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Affiliation(s)
- Lujia Chen
- Department of Biomedical Engineering, University of California, Irvine, California 92697, USA
- Center for Neural Circuit Mapping, University of California, Irvine, California 92697, USA
| | - Xiangduo Kong
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California 92697, USA
| | - Kevin G Johnston
- Department of Anatomy and Neurobiology, School of Medicine, University of California Irvine, Irvine, California 92697, USA
| | - Ali Mortazavi
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California 92697, USA
| | - Todd C Holmes
- Center for Neural Circuit Mapping, University of California, Irvine, California 92697, USA
- Department of Physiology and Biophysics, School of Medicine, University of California Irvine, Irvine, California 92697, USA
| | - Zhiqun Tan
- Center for Neural Circuit Mapping, University of California, Irvine, California 92697, USA;
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California 92697, USA
- Department of Anatomy and Neurobiology, School of Medicine, University of California Irvine, Irvine, California 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, California 92697, USA
| | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California 92697, USA;
| | - Xiangmin Xu
- Department of Biomedical Engineering, University of California, Irvine, California 92697, USA;
- Center for Neural Circuit Mapping, University of California, Irvine, California 92697, USA
- Department of Anatomy and Neurobiology, School of Medicine, University of California Irvine, Irvine, California 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, California 92697, USA
- Department of Computer Science, University of California, Irvine, California 92697, USA
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Vincenten SCC, Voermans NC, Cameron D, van Engelen BGM, van Alfen N, Mul K. The complementary use of muscle ultrasound and MRI in FSHD: Early versus later disease stage follow-up. Clin Neurophysiol 2024:S1388-2457(24)00064-6. [PMID: 38521678 DOI: 10.1016/j.clinph.2024.02.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/09/2024] [Accepted: 02/28/2024] [Indexed: 03/25/2024]
Abstract
OBJECTIVES Muscle MRI and ultrasound provide complementary techniques for characterizing muscle changes and tracking disease progression in facioscapulohumeral muscular dystrophy (FSHD). In this cohort study, we provide longitudinal data that compares both imaging modalities head-to-head. METHODS FSHD patients were assessed at baseline and after five years. Standardized muscle MRI and ultrasound images of five leg muscles were assessed bilaterally. Fat replacement was quantified using MRI fat-fraction (FF) and ultrasound Heckmatt and echogenicity z-scores (EZ-score). Muscle edema was evaluated using T2-weighted turbo inversion recovery magnitude (TIRM) MRI. RESULTS Twenty FSHD patients were included. Muscles with normal baseline imaging showed increases in ultrasound EZ-scores (≥1; in 17%) more often than MRI FF increases (≥10%; in 7%) over time. Muscles with only baseline ultrasound abnormalities often showed considerable FF increases (in 22%), and TIRM positivity at follow-up (44%). Muscles with increased FF at baseline showed stable (80%) or increasing FF (20%) over time. EZ-scores of those muscles either increased (23%), decreased (33%) or remained stable (44%). CONCLUSIONS Muscle ultrasound may capture accelerated pathological muscle changes in FSHD in early disease, while muscle MRI appears better-suited to detecting and monitoring pathology in later stages. SIGNIFICANCE Our results help establish each techniques' optimal use as imaging biomarker.
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Affiliation(s)
- Sanne C C Vincenten
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands; Clinical Neuromuscular Imaging Group, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Nicol C Voermans
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Donnie Cameron
- Clinical Neuromuscular Imaging Group, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Medical Imaging, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Baziel G M van Engelen
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nens van Alfen
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands; Clinical Neuromuscular Imaging Group, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Karlien Mul
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
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Parker E, Hamrick MW. Role of fibro-adipogenic progenitor cells in muscle atrophy and musculoskeletal diseases. Curr Opin Pharmacol 2021; 58:1-7. [PMID: 33839480 DOI: 10.1016/j.coph.2021.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/16/2021] [Accepted: 03/06/2021] [Indexed: 01/01/2023]
Abstract
Maintaining muscle mass is clinically important as muscle helps to regulate metabolic systems of the body as well as support activities of daily living that require mobility, strength, and power. Losing muscle mass decreases an individual's independence and quality of life, and at the same time increases the risk of disease burden. Fibro-adipogenic progenitor (FAP) cells are a group of muscle progenitor cells that play an important role in muscle regeneration and maintenance of skeletal muscle fiber size. These important functions of FAPs are mediated by a complex secretome that interacts in a paracrine manner to stimulate muscle satellite cells to divide and differentiate. Dysregulation of FAP differentiation leads to fibrosis, fatty infiltration, muscle atrophy, and impaired muscle regeneration. Functional deficits in skeletal muscle resulting from atrophy, fibrosis, or fatty infiltration will reduce biomechanical stresses on the skeleton, and both FAP-derived adipocytes and FAPs themselves are likely to secrete factors that can induce bone loss. These findings suggest that FAPs represent a cell population to be targeted therapeutically to improve both muscle and bone health in settings of aging, injury, and disease.
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Affiliation(s)
- Emily Parker
- Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Mark W Hamrick
- Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.
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Bittel AJ, Sreetama SC, Bittel DC, Horn A, Novak JS, Yokota T, Zhang A, Maruyama R, Rowel Q. Lim K, Jaiswal JK, Chen YW. Membrane Repair Deficit in Facioscapulohumeral Muscular Dystrophy. Int J Mol Sci 2020; 21:E5575. [PMID: 32759720 PMCID: PMC7432481 DOI: 10.3390/ijms21155575] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/28/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022] Open
Abstract
Deficits in plasma membrane repair have been identified in dysferlinopathy and Duchenne Muscular Dystrophy, and contribute to progressive myopathy. Although Facioscapulohumeral Muscular Dystrophy (FSHD) shares clinicopathological features with these muscular dystrophies, it is unknown if FSHD is characterized by plasma membrane repair deficits. Therefore, we exposed immortalized human FSHD myoblasts, immortalized myoblasts from unaffected siblings, and myofibers from a murine model of FSHD (FLExDUX4) to focal, pulsed laser ablation of the sarcolemma. Repair kinetics and success were determined from the accumulation of intracellular FM1-43 dye post-injury. We subsequently treated FSHD myoblasts with a DUX4-targeting antisense oligonucleotide (AON) to reduce DUX4 expression, and with the antioxidant Trolox to determine the role of DUX4 expression and oxidative stress in membrane repair. Compared to unaffected myoblasts, FSHD myoblasts demonstrate poor repair and a greater percentage of cells that failed to repair, which was mitigated by AON and Trolox treatments. Similar repair deficits were identified in FLExDUX4 myofibers. This is the first study to identify plasma membrane repair deficits in myoblasts from individuals with FSHD, and in myofibers from a murine model of FSHD. Our results suggest that DUX4 expression and oxidative stress may be important targets for future membrane-repair therapies.
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Affiliation(s)
- Adam J. Bittel
- Research Center for Genetic Medicine, Children’s National Hospital, 111 Michigan Ave NW, Washington, DC 20010, USA; (A.J.B.); (S.C.S.); (D.C.B.); (A.H.); (J.S.N.); (A.Z.)
| | - Sen Chandra Sreetama
- Research Center for Genetic Medicine, Children’s National Hospital, 111 Michigan Ave NW, Washington, DC 20010, USA; (A.J.B.); (S.C.S.); (D.C.B.); (A.H.); (J.S.N.); (A.Z.)
| | - Daniel C. Bittel
- Research Center for Genetic Medicine, Children’s National Hospital, 111 Michigan Ave NW, Washington, DC 20010, USA; (A.J.B.); (S.C.S.); (D.C.B.); (A.H.); (J.S.N.); (A.Z.)
| | - Adam Horn
- Research Center for Genetic Medicine, Children’s National Hospital, 111 Michigan Ave NW, Washington, DC 20010, USA; (A.J.B.); (S.C.S.); (D.C.B.); (A.H.); (J.S.N.); (A.Z.)
| | - James S. Novak
- Research Center for Genetic Medicine, Children’s National Hospital, 111 Michigan Ave NW, Washington, DC 20010, USA; (A.J.B.); (S.C.S.); (D.C.B.); (A.H.); (J.S.N.); (A.Z.)
- Department of Genomics and Precision Medicine, The George Washington University School of Medicine and Health Science, 111 Michigan Ave NW, Washington, DC 20010, USA
| | - Toshifumi Yokota
- Department of Medical Genetics, University of Alberta, 116 St. & 85 Ave., Edmonton, AB T6G 2R3, Canada; (T.Y.); (R.M.); (K.R.Q.L.)
| | - Aiping Zhang
- Research Center for Genetic Medicine, Children’s National Hospital, 111 Michigan Ave NW, Washington, DC 20010, USA; (A.J.B.); (S.C.S.); (D.C.B.); (A.H.); (J.S.N.); (A.Z.)
| | - Rika Maruyama
- Department of Medical Genetics, University of Alberta, 116 St. & 85 Ave., Edmonton, AB T6G 2R3, Canada; (T.Y.); (R.M.); (K.R.Q.L.)
| | - Kenji Rowel Q. Lim
- Department of Medical Genetics, University of Alberta, 116 St. & 85 Ave., Edmonton, AB T6G 2R3, Canada; (T.Y.); (R.M.); (K.R.Q.L.)
| | - Jyoti K. Jaiswal
- Research Center for Genetic Medicine, Children’s National Hospital, 111 Michigan Ave NW, Washington, DC 20010, USA; (A.J.B.); (S.C.S.); (D.C.B.); (A.H.); (J.S.N.); (A.Z.)
- Department of Integrative Systems Biology, Institute for Biomedical Sciences, The George Washington University, 2121 I St. NW, Washington, DC 20052, USA
| | - Yi-Wen Chen
- Research Center for Genetic Medicine, Children’s National Hospital, 111 Michigan Ave NW, Washington, DC 20010, USA; (A.J.B.); (S.C.S.); (D.C.B.); (A.H.); (J.S.N.); (A.Z.)
- Department of Integrative Systems Biology, Institute for Biomedical Sciences, The George Washington University, 2121 I St. NW, Washington, DC 20052, USA
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