1
|
Danckaert A, Trignol A, Le Loher G, Loubens S, Staels B, Duez H, Shorte SL, Mayeuf-Louchart A. MuscleJ2: a rebuilding of MuscleJ with new features for high-content analysis of skeletal muscle immunofluorescence slides. Skelet Muscle 2023; 13:14. [PMID: 37612778 PMCID: PMC10463807 DOI: 10.1186/s13395-023-00323-1] [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: 02/10/2023] [Accepted: 07/25/2023] [Indexed: 08/25/2023] Open
Abstract
Histological analysis of skeletal muscle is of major interest for understanding its behavior in different pathophysiological conditions, such as the response to different environments or myopathies. In this context, many software programs have been developed to perform automated high-content analysis. We created MuscleJ, a macro that runs in ImageJ/Fiji on batches of images. MuscleJ is a multianalysis tool that initially allows the analysis of muscle fibers, capillaries, and satellite cells. Since its creation, it has been used in many studies, and we have further developed the software and added new features, which are presented in this article. We converted the macro into a Java-language plugin with an improved user interface. MuscleJ2 provides quantitative analysis of fibrosis, vascularization, and cell phenotype in whole muscle sections. It also performs analysis of the peri-myonuclei, the individual capillaries, and any staining in the muscle fibers, providing accurate quantification within regional sublocalizations of the fiber. A multicartography option allows users to visualize multiple results simultaneously. The plugin is freely available to the muscle science community.
Collapse
Affiliation(s)
- Anne Danckaert
- UTechS Photonic BioImaging/C2RT, Institut Pasteur, Université Paris Cité, 75015, Paris, France.
| | - Aurélie Trignol
- French Armed Forces Biomedical Research Institute - IRBA, Brétigny-sur-Orge, France
| | - Guillaume Le Loher
- UTechS Photonic BioImaging/C2RT, Institut Pasteur, Université Paris Cité, 75015, Paris, France
- École Centrale d'Electronique (ECE), Paris, France
| | - Sébastien Loubens
- CHU Lille, INSERM, Institut Pasteur de Lille, Univ. Lille, U1011-EGID, Lille, 59000, France
- Service Neuropédiatrie, CHU Lille, 59000, Lille, France
| | - Bart Staels
- CHU Lille, INSERM, Institut Pasteur de Lille, Univ. Lille, U1011-EGID, Lille, 59000, France
| | - Hélène Duez
- CHU Lille, INSERM, Institut Pasteur de Lille, Univ. Lille, U1011-EGID, Lille, 59000, France
| | - Spencer L Shorte
- UTechS Photonic BioImaging/C2RT, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Alicia Mayeuf-Louchart
- CHU Lille, INSERM, Institut Pasteur de Lille, Univ. Lille, U1011-EGID, Lille, 59000, France.
| |
Collapse
|
2
|
Abbassi-Daloii T, El Abdellaoui S, Kan HE, van den Akker E, 't Hoen PAC, Raz V, Voortman LM. Quantitative analysis of myofiber type composition in human and mouse skeletal muscles. STAR Protoc 2023; 4:102075. [PMID: 36853713 PMCID: PMC9898062 DOI: 10.1016/j.xpro.2023.102075] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/28/2022] [Accepted: 01/09/2023] [Indexed: 01/30/2023] Open
Abstract
Skeletal muscles are composed of different myofiber types characterized by the expression of myosin heavy chain isoforms, which can be affected by physical activity, aging, and pathological conditions. Here, we present a step-by-step high-throughput semi-automated approach for performing myofiber type quantification of entire human or mouse muscle tissue sections, including immunofluorescence staining, image acquisition, processing, and quantification. For complete details on the use and execution of this protocol, please refer to Abbassi-Daloii et al. (2022).1.
Collapse
Affiliation(s)
- Tooba Abbassi-Daloii
- Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Salma El Abdellaoui
- Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Hermien E Kan
- C.J. Gorter MRI Center, Department of Radiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Duchenne Center Netherlands, the Netherlands
| | - Erik van den Akker
- Molecular Epidemiology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands; Leiden Computational Biology Center, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands; Delft Bioinformatics Lab, TU Delft, 2628 XE Delft, the Netherlands
| | - Peter A C 't Hoen
- Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Vered Raz
- Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands.
| | - Lenard M Voortman
- Cell and Chemical Biology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands.
| |
Collapse
|
3
|
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:e80500. [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] [Grants] [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
|