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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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Poleboyina PK, Alagumuthu M, Pasha A, Ravinder D, Pasumarthi D, Pawar SC. Entrectinib a Plausible Inhibitor for Osteopontin (SPP1) in Cervical Cancer-Integrated Bioinformatic Approach. Appl Biochem Biotechnol 2023; 195:7766-7795. [PMID: 37086377 DOI: 10.1007/s12010-023-04541-7] [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] [Accepted: 04/11/2023] [Indexed: 04/23/2023]
Abstract
Cervical cancer is one of the major causes of death in women, especially in developing countries bearing more than a quarter of the global burden. Secreted phosphoprotein-1, also known as OPN (osteopontin), is an integrin-binding glycophosphoprotein that is overexpressed in a variety of tumors. OPN is a chemokine-like calcified ECM-associated protein that plays a crucial role in evaluating the metastatic potential of various cancers. However, the role of SPP1 in the tumor microenvironment and associated signaling pathways in CC is still unclear. In our study, three CC microarray datasets (GSE9750, GSE46857, and GSE67522) were obtained from the GEO database to identify the differentially expressed genes. Enrichment analysis was carried out by Enrichr and ShinyGO and the PPI interaction network was created by using String and Cytoscape. GEPIA datasets were used to validate the top 10 hub genes, and virtual screening, docking, and dynamic simulation studies were used to identify a suitable inhibitor against the OPN protein using MVD, PyRx, and GROMACS respectively. Our results show that a total of 11 DEGs were common for three datasets and gene ontology pathway enrichment analysis revealed that 2 biological processes i.e. programmed cell death and animal organ development commonly affected mechanisms in all three datasets. Docking and dynamic studies revealed that Entrectinib showed excellent binding affinity against OPN protein. Based on the results, we conclude that OPN is one of the most upregulated genes in cervical cancer and Entrectinib emerges to be a promising potential OPN inhibitor to curtail cervical cancer progression. Schematic representation: The schematic representation of methodology steps is illustrated in the graphical abstract. Schematic representation of methodology.
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Affiliation(s)
- Pavan Kumar Poleboyina
- Department of Genetics & Biotechnology, University College of Science, Osmania University, -500007, Hyderabad, Telangana, India
| | - Manikandan Alagumuthu
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, -632014, Vellore, India
| | - Akbar Pasha
- Department of Genetics & Biotechnology, University College of Science, Osmania University, -500007, Hyderabad, Telangana, India
| | - Doneti Ravinder
- Department of Genetics & Biotechnology, University College of Science, Osmania University, -500007, Hyderabad, Telangana, India
| | - Deepthi Pasumarthi
- Department of Genetics & Biotechnology, University College of Science, Osmania University, -500007, Hyderabad, Telangana, India
| | - Smita C Pawar
- Department of Genetics & Biotechnology, University College of Science, Osmania University, -500007, Hyderabad, Telangana, India.
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Wang R, Kumar B, Bhat-Nakshatri P, Khatpe AS, Murphy MP, Wanczyk KE, Simpson E, Chen D, Gao H, Liu Y, Doud EH, Mosley AL, Nakshatri H. A human skeletal muscle stem/myotube model reveals multiple signaling targets of cancer secretome in skeletal muscle. iScience 2023; 26:106541. [PMID: 37102148 PMCID: PMC10123345 DOI: 10.1016/j.isci.2023.106541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/16/2022] [Accepted: 03/24/2023] [Indexed: 04/03/2023] Open
Abstract
Skeletal muscle dysfunction or reprogramming due to the effects of the cancer secretome is observed in multiple malignancies. Although mouse models are routinely used to study skeletal muscle defects in cancer, because of species specificity of certain cytokines/chemokines in the secretome, a human model system is required. Here, we establish simplified multiple skeletal muscle stem cell lines (hMuSCs), which can be differentiated into myotubes. Using single nuclei ATAC-seq (snATAC-seq) and RNA-seq (snRNA-seq), we document chromatin accessibility and transcriptomic changes associated with the transition of hMuSCs to myotubes. Cancer secretome accelerated stem to myotube differentiation, altered the alternative splicing machinery and increased inflammatory, glucocorticoid receptor, and wound healing pathways in hMuSCs. Additionally, cancer secretome reduced metabolic and survival pathway associated miR-486, AKT, and p53 signaling in hMuSCs. hMuSCs underwent myotube differentiation when engrafted into NSG mice and thus providing a humanized in vivo skeletal muscle model system to study cancer cachexia.
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Affiliation(s)
- Ruizhong Wang
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Brijesh Kumar
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | - Aditi S. Khatpe
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Michael P. Murphy
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- VA Roudebush Medical Center, Indianapolis, IN 46202, USA
| | - Kristen E. Wanczyk
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- VA Roudebush Medical Center, Indianapolis, IN 46202, USA
| | - Edward Simpson
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Duojiao Chen
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Hongyu Gao
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yunlong Liu
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Emma H. Doud
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Amber L. Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Harikrishna Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- VA Roudebush Medical Center, Indianapolis, IN 46202, USA
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Han X, Han J, Wang N, Ji G, Guo R, Li J, Wu H, Ma S, Fang P, Song X. Identification of Auxiliary Biomarkers and Description of the Immune Microenvironmental Characteristics in Duchenne Muscular Dystrophy by Bioinformatical Analysis and Experiment. Front Neurosci 2022; 16:891670. [PMID: 35720684 PMCID: PMC9204148 DOI: 10.3389/fnins.2022.891670] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
Background Duchenne muscular dystrophy (DMD) is a genetic muscle disorder characterized by progressive muscle wasting associated with persistent inflammation. In this study, we aimed to identify auxiliary biomarkers and further characterize the immune microenvironment in DMD. Methods Differentially expressed genes (DEGs) were identified between DMD and normal muscle tissues based on Gene Expression Omnibus (GEO) datasets. Bioinformatical analysis was used to screen and identify potential diagnostic signatures of DMD which were further validated by real-time quantitative reverse transcription PCR (RT-qPCR). We also performed single-sample gene-set enrichment analysis (ssGSEA) to characterize the proportion of tissue-infiltrating immune cells to determine the inflammatory state of DMD. Results In total, 182 downregulated genes and 263 upregulated genes were identified in DMD. C3, SPP1, TMSB10, TYROBP were regarded as adjunct biomarkers and successfully validated by RT-qPCR. The infiltration of macrophages, CD4+, and CD8+ T cells was significantly higher (p < 0.05) in DMD compared with normal muscle tissues, while the infiltration of activated B cells, CD56dim natural killer cells, and type 17 T helper (Th17) cells was lower. In addition, the four biomarkers (C3, SPP1, TMSB10, TYROBP) were strongly associated with immune cells and immune-related pathways in DMD muscle tissues. Conclusion Analyses demonstrated C3, SPP1, TMSB10, and TYROBP may serve as biomarkers and enhance our understanding of immune responses in DMD. The infiltration of immune cells into the muscle microenvironment might exert a critical impact on the development and occurrence of DMD.
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Affiliation(s)
- Xu Han
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
| | - Jingzhe Han
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
| | - Ning Wang
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
| | - Guang Ji
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
| | - Ruoyi Guo
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
| | - Jing Li
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
| | - Hongran Wu
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
| | - Shaojuan Ma
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
| | - Pingping Fang
- Department of Neurology, Handan Central Hospital, Handan, China
| | - Xueqin Song
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
- *Correspondence: Xueqin Song,
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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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Molendijk J, Blazev R, Mills RJ, Ng YK, Watt KI, Chau D, Gregorevic P, Crouch PJ, Hilton JBW, Lisowski L, Zhang P, Reue K, Lusis AJ, Hudson JE, James DE, Seldin MM, Parker BL. Proteome-wide systems genetics identifies UFMylation as a regulator of skeletal muscle function. eLife 2022; 11:82951. [PMID: 36472367 PMCID: PMC9833826 DOI: 10.7554/elife.82951] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Improving muscle function has great potential to improve the quality of life. To identify novel regulators of skeletal muscle metabolism and function, we performed a proteomic analysis of gastrocnemius muscle from 73 genetically distinct inbred mouse strains, and integrated the data with previously acquired genomics and >300 molecular/phenotypic traits via quantitative trait loci mapping and correlation network analysis. These data identified thousands of associations between protein abundance and phenotypes and can be accessed online (https://muscle.coffeeprot.com/) to identify regulators of muscle function. We used this resource to prioritize targets for a functional genomic screen in human bioengineered skeletal muscle. This identified several negative regulators of muscle function including UFC1, an E2 ligase for protein UFMylation. We show UFMylation is up-regulated in a mouse model of amyotrophic lateral sclerosis, a disease that involves muscle atrophy. Furthermore, in vivo knockdown of UFMylation increased contraction force, implicating its role as a negative regulator of skeletal muscle function.
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Affiliation(s)
- Jeffrey Molendijk
- Department of Anatomy and Physiology, University of MelbourneMelbourneAustralia,Centre for Muscle Research, University of MelbourneMelbourneAustralia
| | - Ronnie Blazev
- Department of Anatomy and Physiology, University of MelbourneMelbourneAustralia,Centre for Muscle Research, University of MelbourneMelbourneAustralia
| | | | - Yaan-Kit Ng
- Department of Anatomy and Physiology, University of MelbourneMelbourneAustralia,Centre for Muscle Research, University of MelbourneMelbourneAustralia
| | - Kevin I Watt
- Department of Anatomy and Physiology, University of MelbourneMelbourneAustralia,Centre for Muscle Research, University of MelbourneMelbourneAustralia
| | - Daryn Chau
- Department of Biological Chemistry and Center for Epigenetics and Metabolism, University of California, IrvineIrvineUnited States
| | - Paul Gregorevic
- Department of Anatomy and Physiology, University of MelbourneMelbourneAustralia,Centre for Muscle Research, University of MelbourneMelbourneAustralia
| | - Peter J Crouch
- Department of Biochemistry and Pharmacology, University of MelbourneMelbourneAustralia
| | - James BW Hilton
- Department of Biochemistry and Pharmacology, University of MelbourneMelbourneAustralia
| | - Leszek Lisowski
- Children's Medical Research Institute, University of SydneySydneyAustralia,Military Institute of MedicineWarszawaPoland
| | - Peixiang Zhang
- Department of Human Genetics/Medicine, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Karen Reue
- Department of Human Genetics/Medicine, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Aldons J Lusis
- Department of Human Genetics/Medicine, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los AngelesLos AngelesUnited States
| | - James E Hudson
- QIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - David E James
- Charles Perkins Centre, School of Life and Environmental Science, School of Medical Science, University of SydneySydneyAustralia
| | - Marcus M Seldin
- Department of Biological Chemistry and Center for Epigenetics and Metabolism, University of California, IrvineIrvineUnited States
| | - Benjamin L Parker
- Department of Anatomy and Physiology, University of MelbourneMelbourneAustralia,Centre for Muscle Research, University of MelbourneMelbourneAustralia
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