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Xin J, Liu S. Identifying hub genes and dysregulated pathways in Duchenne muscular dystrophy. Int J Neurosci 2024:1-13. [PMID: 38179963 DOI: 10.1080/00207454.2024.2302551] [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: 05/31/2022] [Accepted: 01/02/2024] [Indexed: 01/06/2024]
Abstract
PURPOSE The aim of this study was to identify the hub genes and dysregulated pathways in the progression of duchenne muscular dystrophy (DMD) and to unveil detailedly the cellular and molecular mechanisms associated with DMD for developing efficacious treatments in the future. MATERIAL AND METHODS Three mRNA microarray datasets (GSE13608, GSE38417 and GSE109178) were downloaded from Gene Expression Omnibus (GEO). The differentially expressed genes (DEGs) between DMD and normal tissues were obtained via R package. Function enrichment analyses were implemented respectively using DAVID online database. The network analysis of protein-protein interaction network (PPI) was conducted using String. Cytoscape and String were used to analyse modules and screen hub genes. The expression of the identified hub genes was confirmed in mdx mice through using qRT-PCR. RESULTS In total, 519 DEGs were identified, consisting of 393 upregulated genes and 126 downregulated genes. The enriched functions and pathways of the DEGs mainly involve extracellular matrix organization, collagen fibril organization, interferon-gamma-mediated signaling pathway, muscle contraction, endoplasmic reticulum lumen, MHC class II receptor activity, phagosome, graft-versus-host disease, cardiomyocytes, calcium signaling pathway. Twelve hub genes were discovered and biological process analysis proved that these genes were mainly enriched cell cycle, cell division. The result of qRT-PCR suggested that increase in expression of CD44, ECT2, TYMS, MAGEL2, HLA-DMA, SERPINH1, TNNT2 was confirmed in mdx mice and the downregulation of ASB2 and LEPREL1 was also observed. CONCLUSION In conclusion, DEGs and hub genes identified in the current research help us probe the molecular mechanisms underlying the pathogenesis and progression of DMD, and provide candidate targets for diagnosis and treatment of DMD.
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Affiliation(s)
- Jianzeng Xin
- College of life sciences, Yantai University, Yantai, P. R. China
| | - Sheng Liu
- School of Pharmacy, Yantai University, Yantai, P. R. China
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Heezen LGM, Abdelaal T, van Putten M, Aartsma-Rus A, Mahfouz A, Spitali P. Spatial transcriptomics reveal markers of histopathological changes in Duchenne muscular dystrophy mouse models. Nat Commun 2023; 14:4909. [PMID: 37582915 PMCID: PMC10427630 DOI: 10.1038/s41467-023-40555-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/02/2023] [Indexed: 08/17/2023] Open
Abstract
Duchenne muscular dystrophy is caused by mutations in the DMD gene, leading to lack of dystrophin. Chronic muscle damage eventually leads to histological alterations in skeletal muscles. The identification of genes and cell types driving tissue remodeling is a key step to developing effective therapies. Here we use spatial transcriptomics in two Duchenne muscular dystrophy mouse models differing in disease severity to identify gene expression signatures underlying skeletal muscle pathology and to directly link gene expression to muscle histology. We perform deconvolution analysis to identify cell types contributing to histological alterations. We show increased expression of specific genes in areas of muscle regeneration (Myl4, Sparc, Hspg2), fibrosis (Vim, Fn1, Thbs4) and calcification (Bgn, Ctsk, Spp1). These findings are confirmed by smFISH. Finally, we use differentiation dynamic analysis in the D2-mdx muscle to identify muscle fibers in the present state that are predicted to become affected in the future state.
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Affiliation(s)
- L G M Heezen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - T Abdelaal
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
- Systems and Biomedical Engineering Department, Faculty of Engineering Cairo University, Giza, Egypt
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - M van Putten
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - A Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - A Mahfouz
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - P Spitali
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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Sinha S, Elbaz‐Alon Y, Avinoam O. Ca 2+ as a coordinator of skeletal muscle differentiation, fusion and contraction. FEBS J 2022; 289:6531-6542. [PMID: 35689496 PMCID: PMC9795905 DOI: 10.1111/febs.16552] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/05/2022] [Accepted: 06/09/2022] [Indexed: 12/30/2022]
Abstract
Muscle regeneration is essential for vertebrate muscle homeostasis and recovery after injury. During regeneration, muscle stem cells differentiate into myocytes, which then fuse with pre-existing muscle fibres. Hence, differentiation, fusion and contraction must be tightly regulated during regeneration to avoid the disastrous consequences of premature fusion of myocytes to actively contracting fibres. Cytosolic calcium (Ca2+ ), which is coupled to both induction of myogenic differentiation and contraction, has more recently been implicated in the regulation of myocyte-to-myotube fusion. In this viewpoint, we propose that Ca2+ -mediated coordination of differentiation, fusion and contraction is a feature selected in the amniotes to facilitate muscle regeneration.
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Affiliation(s)
- Sansrity Sinha
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Yael Elbaz‐Alon
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Ori Avinoam
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
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Lambrescu I, Popa A, Manole E, Ceafalan LC, Gaina G. Application of Droplet Digital PCR Technology in Muscular Dystrophies Research. Int J Mol Sci 2022; 23:ijms23094802. [PMID: 35563191 PMCID: PMC9099497 DOI: 10.3390/ijms23094802] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 11/25/2022] Open
Abstract
Although they are considered rare disorders, muscular dystrophies have a strong impact on people’s health. Increased disease severity with age, frequently accompanied by the loss of ability to walk in some people, and the lack of treatment, have directed the researchers towards the development of more effective therapeutic strategies aimed to improve the quality of life and life expectancy, slow down the progression, and delay the onset or convert a severe phenotype into a milder one. Improved understanding of the complex pathology of these diseases together with the tremendous advances in molecular biology technologies has led to personalized therapeutic procedures. Different approaches that are currently under extensive investigation require more efficient, sensitive, and less invasive methods. Due to its remarkable analytical sensitivity, droplet digital PCR has become a promising tool for accurate measurement of biomarkers that monitor disease progression and quantification of various therapeutic efficiency and can be considered a tool for non-invasive prenatal diagnosis and newborn screening. Here, we summarize the recent applications of droplet digital PCR in muscular dystrophy research and discuss the factors that should be considered to get the best performance with this technology.
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Affiliation(s)
- Ioana Lambrescu
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Department of Cell Biology and Histology, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Alexandra Popa
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Department of Animal Production and Public Health, University of Agronomic Sciences and Veterinary Medicine of Bucharest, 050097 Bucharest, Romania
| | - Emilia Manole
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Pathology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
| | - Laura Cristina Ceafalan
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Department of Cell Biology and Histology, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Gisela Gaina
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Correspondence: ; Tel.: +40-21-319-2732
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Mulè MP, Martins AJ, Tsang JS. Normalizing and denoising protein expression data from droplet-based single cell profiling. Nat Commun 2022; 13:2099. [PMID: 35440536 PMCID: PMC9018908 DOI: 10.1038/s41467-022-29356-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 03/01/2022] [Indexed: 12/02/2022] Open
Abstract
Multimodal single-cell profiling methods that measure protein expression with oligo-conjugated antibodies hold promise for comprehensive dissection of cellular heterogeneity, yet the resulting protein counts have substantial technical noise that can mask biological variations. Here we integrate experiments and computational analyses to reveal two major noise sources and develop a method called "dsb" (denoised and scaled by background) to normalize and denoise droplet-based protein expression data. We discover that protein-specific noise originates from unbound antibodies encapsulated during droplet generation; this noise can thus be accurately estimated and corrected by utilizing protein levels in empty droplets. We also find that isotype control antibodies and the background protein population average in each cell exhibit significant correlations across single cells, we thus use their shared variance to correct for cell-to-cell technical noise in each cell. We validate these findings by analyzing the performance of dsb in eight independent datasets spanning multiple technologies, including CITE-seq, ASAP-seq, and TEA-seq. Compared to existing normalization methods, our approach improves downstream analyses by better unmasking biologically meaningful cell populations. Our method is available as an open-source R package that interfaces easily with existing single cell software platforms such as Seurat, Bioconductor, and Scanpy and can be accessed at "dsb [ https://cran.r-project.org/package=dsb ]".
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Affiliation(s)
- Matthew P Mulè
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
- NIH-Oxford-Cambridge Scholars Program, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Andrew J Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - John S Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA.
- NIH Center for Human Immunology (CHI), National Institutes of Health (NIH), Bethesda, MD, USA.
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Xu X, Hao Y, Wu J, Zhao J, Xiong S. Assessment of Weighted Gene Co-Expression Network Analysis to Explore Key Pathways and Novel Biomarkers in Muscular Dystrophy. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2021; 14:431-444. [PMID: 33883925 PMCID: PMC8053709 DOI: 10.2147/pgpm.s301098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022]
Abstract
Purpose This study aimed to explore the key molecular pathways involved in Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) and thereby identify hub genes to be potentially used as novel biomarkers using a bioinformatics approach. Methods Raw GSE109178 data were collected from the Gene Expression Omnibus (GEO) database. Weighted gene co-expression network analysis (WGCNA) was conducted on the top 50% of altered genes. The key modules associated with the clinical features of DMD and BMD were identified. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed using the DAVID website. A protein-protein interaction (PPI) network was constructed using the STRING website. MCODE, together with the Cytohubba plug-ins of Cytoscape, screened out the potential hub genes, which were subsequently verified via receiver operating characteristic (ROC) curves in other datasets. Results Among the 11 modules obtained, the black module was predominantly associated with pathology and DMD, whereas the light-green module was primarily related to age and BMD. Functional enrichment assessments indicated that the genes in the black module were primarily clustered in “immune response” and “phagosome,” whereas the ones in the light-green module were chiefly enriched in “protein polyubiquitination”. Eleven essential genes were eventually identified, including VCAM1, TYROBP, CD44, ITGB2, CSF1R, LCP2, C3AR1, CCL2, and ITGAM for DMD, along with UBA5 and UBR2 for BMD. Conclusion Overall, our findings may be useful for investigating the mechanisms underlying DMD and BMD. In addition, the hub genes discovered might serve as novel molecular markers correlated with dystrophinopathies.
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Affiliation(s)
- Xiaoxue Xu
- Department of Neurology, The First Hospital of China Medical University, Shenyang, People's Republic of China
| | - Yuehan Hao
- Department of Neurology, The First Hospital of China Medical University, Shenyang, People's Republic of China
| | - Jiao Wu
- Department of Neurology, The People's Hospital of Liaoning Province, Shenyang, People's Republic of China
| | - Jing Zhao
- Department of Neurology, The First Hospital of China Medical University, Shenyang, People's Republic of China
| | - Shuang Xiong
- Liaoning Academy of Analytic Science, Construction Engineering Center of Important Technology Innovation and Research and Development Base in Liaoning Province, Shenyang, People's Republic of China
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