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Klimenko ES, Sukhareva KS, Vlasova YA, Smolina NA, Fomicheva YV, Knyazeva A, Muravyev AS, Sorokina MY, Gavrilova LS, Boldyreva LV, Medvedeva SS, Sejersen T, Kostareva AA. Flnc expression impacts mitochondrial function, autophagy, and calcium handling in C2C12 cells. Exp Cell Res 2024:114174. [PMID: 39089502 DOI: 10.1016/j.yexcr.2024.114174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/12/2024] [Accepted: 07/21/2024] [Indexed: 08/04/2024]
Affiliation(s)
- E S Klimenko
- Almazov National Medical Research Centre, Saint-Petersburg, Russia
| | - K S Sukhareva
- Almazov National Medical Research Centre, Saint-Petersburg, Russia
| | - Yu A Vlasova
- Almazov National Medical Research Centre, Saint-Petersburg, Russia
| | - N A Smolina
- Almazov National Medical Research Centre, Saint-Petersburg, Russia
| | - Yu V Fomicheva
- Almazov National Medical Research Centre, Saint-Petersburg, Russia
| | - A Knyazeva
- Almazov National Medical Research Centre, Saint-Petersburg, Russia
| | - A S Muravyev
- Almazov National Medical Research Centre, Saint-Petersburg, Russia
| | - M Yu Sorokina
- Almazov National Medical Research Centre, Saint-Petersburg, Russia
| | - L S Gavrilova
- Almazov National Medical Research Centre, Saint-Petersburg, Russia
| | - L V Boldyreva
- Scientific-Research Institute of Neurosciences and Medicine, Novosibirsk, Russia; Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S S Medvedeva
- Scientific-Research Institute of Neurosciences and Medicine, Novosibirsk, Russia; Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - T Sejersen
- Department of Women´s and Children´s Health, Karolinska Institutet, Department of Child Neurology, Karolinska University Hospital, Astrid Lindgren Children's Hospital, Stockholm, Sweden,; Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, Shatin, New Territories, Hong Kong
| | - A A Kostareva
- Almazov National Medical Research Centre, Saint-Petersburg, Russia; Department of Women´s and Children´s Health, Karolinska Institutet, Department of Child Neurology, Karolinska University Hospital, Astrid Lindgren Children's Hospital, Stockholm, Sweden,; Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, Shatin, New Territories, Hong Kong
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Wan H, Teh MT, Mastroianni G, Ahmad US. Comparative Transcriptome Analysis Identifies Desmoglein-3 as a Potential Oncogene in Oral Cancer Cells. Cells 2023; 12:2710. [PMID: 38067138 PMCID: PMC10705960 DOI: 10.3390/cells12232710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/14/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
The role of desmoglein-3 (DSG3) in oncogenesis is unclear. This study aimed to uncover molecular mechanisms through comparative transcriptome analysis in oral cancer cells, defining potential key genes and associated biological processes related to DSG3 expression. Four mRNA libraries of oral squamous carcinoma H413 cell lines were sequenced, and 599 candidate genes exhibited differential expression between DSG3-overexpressing and matched control lines, with 12 genes highly significantly differentially expressed, including 9 upregulated and 3 downregulated. Genes with known implications in cancer, such as MMP-13, KRT84, OLFM4, GJA1, AMOT and ADAMTS1, were strongly linked to DSG3 overexpression. Gene ontology analysis indicated that the DSG3-associated candidate gene products participate in crucial cellular processes such as junction assembly, focal adhesion, extracellular matrix formation, intermediate filament organisation and keratinocyte differentiation. Validation of RNA-Seq was performed through RT-qPCR, Western blotting and immunofluorescence analyses. Furthermore, using transmission electron microscopy, we meticulously examined desmosome morphology and revealed a slightly immature desmosome structure in DSG3-overexpressing cells compared to controls. No changes in desmosome frequency and diameter were observed between the two conditions. This study underscores intricate and multifaceted alterations associated with DSG3 in oral squamous carcinoma cells, implying a potential oncogenic role of this gene in biological processes that enable cell communication, motility and survival.
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Affiliation(s)
- Hong Wan
- Center for Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Muy-Teck Teh
- Center for Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Giulia Mastroianni
- School of Biological and Behavioural Sciences, Faculty of Science and Engineering, Queen Mary University of London, London E1 4NS, UK
| | - Usama Sharif Ahmad
- Center for Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
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Ji H, Yuan L, Jiang W, Jiang Y, Jiang M, Sun X, Chen J. Bioinformatics analysis of immune cell infiltration patterns and potential diagnostic markers in atherosclerosis. Sci Rep 2023; 13:19821. [PMID: 37963970 PMCID: PMC10645850 DOI: 10.1038/s41598-023-47257-8] [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: 09/11/2023] [Accepted: 11/10/2023] [Indexed: 11/16/2023] Open
Abstract
This study aimed to investigate efficient diagnostic markers and molecular mechanisms of atherosclerosis and to analyze the role of immune infiltration through bioinformatics analysis. Expression profile datasets (GSE28829 and GSE43292) of patients with atherosclerosis and healthy controls were downloaded from the GEO database. Glutamine (GLN) metabolism-associated genes were obtained from the Molecular Signatures Database (MSigDB). The limma package in R was used to identify differentially expressed genes (DEGs). Significant modules were filtered using Weighted Gene Co-expression Network Analysis (WGCNA). MSigDB sets were subjected to Gene Set Enrichment Analysis and Gene Set Variation Analysis. The biological functions of DEGs were examined using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. STRING and Cytoscape software were used to identify hub genes and functional modules through protein-protein interaction (PPI) network analysis. The xCell software was adopted to assess the composition patterns of immune and stromal cells. Correlation analyses were performed for key genes and immune cell subtypes. We identified 308 DEGs and GLN-associated genes. Functional enrichment analysis showed that these genes were strongly enriched in muscle contract, muscle tissue development, cutile fiber, mycobacterial, and actin binding. Enriched KEGG pathways comprised dilated cardiomyopathy, hypertrophic cardiomyopathy, and the cAMP signaling pathway. In the PPI network analysis, 27 genes were identified as hub genes. The area under the curve (AUC) values of 27 biomarkers were relatively high, indicating high diagnostic values. The atherosclerosis group exhibited a markedly higher degree of infiltration than the control group. This study identified 27 GLN-associated genes as potential biomarkers for the diagnosis of atherosclerosis. It provides a new perspective on immune responses that facilitates exploration of the molecular mechanisms of atherosclerosis.
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Affiliation(s)
- Haigang Ji
- Department of Cardiovascular Medicine, Changzhou Hospital Affiliated to Nanjing University of Chinese Medicine, Changzhou, 213003, China
| | - Ling Yuan
- Department of Cardiovascular Medicine, Changzhou Hospital Affiliated to Nanjing University of Chinese Medicine, Changzhou, 213003, China
| | - Wenbo Jiang
- Department of Cardiovascular Medicine, Suqian Hospital Affiliated to Nanjing University of Chinese Medicine, Suqian, 223800, China
| | - Yinke Jiang
- Department of Cardiovascular Medicine, Changzhou Hospital Affiliated to Nanjing University of Chinese Medicine, Changzhou, 213003, China
| | - Mengke Jiang
- Department of Cardiovascular Medicine, Changzhou Hospital Affiliated to Nanjing University of Chinese Medicine, Changzhou, 213003, China
| | - Xuemei Sun
- Department of Cardiovascular Medicine, Changzhou Hospital Affiliated to Nanjing University of Chinese Medicine, Changzhou, 213003, China
| | - Jing Chen
- Department of Gastroenterology, Tongde Hospital of Zhejiang Province, Hangzhou, 310012, China.
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Liang Y, Pan JM, Zhu KC, Xian L, Guo HY, Liu BS, Zhang N, Yang JW, Zhang DC. Genome-Wide Identification of Trachinotus ovatus Antimicrobial Peptides and Their Immune Response against Two Pathogen Challenges. Mar Drugs 2023; 21:505. [PMID: 37888440 PMCID: PMC10608450 DOI: 10.3390/md21100505] [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: 08/15/2023] [Revised: 09/13/2023] [Accepted: 09/17/2023] [Indexed: 10/28/2023] Open
Abstract
Golden pompano, Trachinotus ovatus, as a highly nutritious commercially valuable marine fish, has become one of the preferred species for many fish farmers due to its rapid growth, wide adaptability, and ease of feeding and management. However, with the expansion of aquaculture scale, bacterial and parasitic diseases have also become major threats to the golden pompano industry. This study, based on comparative genomics, shows the possibility of preferential evolution of freshwater fish over marine fish by analyzing the phylogenetic relationships and divergence times of 14 marine fish and freshwater fish. Furthermore, we identified antimicrobial peptide genes from 14 species at the genomic level and found that the number of putative antimicrobial peptides may be related to species evolution. Subsequently, we classified the 341 identified AMPs from golden pompano into 38 categories based on the classification provided by the APD3. Among them, TCP represented the highest proportion, accounting for 23.2% of the total, followed by scolopendin, lectin, chemokine, BPTI, and histone-derived peptides. At the same time, the distribution of AMPs in chromosomes varied with type, and covariance analysis showed the frequency of its repeat events. Enrichment analysis and PPI indicated that AMP was mainly concentrated in pathways associated with disease immunity. In addition, our transcriptomic data measured the expression of putative AMPs of golden pompano in 12 normal tissues, as well as in the liver, spleen, and kidney infected with Streptococcus agalactiae and skin infected with Cryptocaryon irritans. As the infection with S. agalactiae and C. irritans progressed, we observed tissue specificity in the number and types of responsive AMPs. Positive selection of AMP genes may participate in the immune response through the MAPK signaling pathway. The genome-wide identification of antimicrobial peptides in the golden pompano provided a complete database of potential AMPs that can contribute to further understanding the immune mechanisms in pathogens. AMPs were expected to replace traditional antibiotics and be developed into targeted drugs against specific bacterial and parasitic pathogens for more precise and effective treatment to improve aquaculture production.
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Affiliation(s)
- Yu Liang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.L.); (J.-M.P.); (K.-C.Z.); (L.X.); (H.-Y.G.); (B.-S.L.); (N.Z.); (J.-W.Y.)
- Guangxi Marine Microbial Resources Industrialization Engineering Technology Research Center, Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning 530008, China
| | - Jin-Min Pan
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.L.); (J.-M.P.); (K.-C.Z.); (L.X.); (H.-Y.G.); (B.-S.L.); (N.Z.); (J.-W.Y.)
| | - Ke-Cheng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.L.); (J.-M.P.); (K.-C.Z.); (L.X.); (H.-Y.G.); (B.-S.L.); (N.Z.); (J.-W.Y.)
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Lin Xian
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.L.); (J.-M.P.); (K.-C.Z.); (L.X.); (H.-Y.G.); (B.-S.L.); (N.Z.); (J.-W.Y.)
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Hua-Yang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.L.); (J.-M.P.); (K.-C.Z.); (L.X.); (H.-Y.G.); (B.-S.L.); (N.Z.); (J.-W.Y.)
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Bao-Suo Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.L.); (J.-M.P.); (K.-C.Z.); (L.X.); (H.-Y.G.); (B.-S.L.); (N.Z.); (J.-W.Y.)
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Nan Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.L.); (J.-M.P.); (K.-C.Z.); (L.X.); (H.-Y.G.); (B.-S.L.); (N.Z.); (J.-W.Y.)
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Jing-Wen Yang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.L.); (J.-M.P.); (K.-C.Z.); (L.X.); (H.-Y.G.); (B.-S.L.); (N.Z.); (J.-W.Y.)
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Dian-Chang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.L.); (J.-M.P.); (K.-C.Z.); (L.X.); (H.-Y.G.); (B.-S.L.); (N.Z.); (J.-W.Y.)
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
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The Hippo Pathway: A Master Regulatory Network Important in Cancer. Cells 2021; 10:cells10061416. [PMID: 34200285 PMCID: PMC8226666 DOI: 10.3390/cells10061416] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 12/11/2022] Open
Abstract
The Hippo pathway is pervasively activated and has been well recognized to play critical roles in human cancer. The deregulation of Hippo signaling involved in cancer development, progression, and resistance to cancer treatment have been confirmed in several human cancers. Its biological significance and deregulation in cancer have drawn increasing interest in the past few years. A fundamental understanding of the complexity of the Hippo pathway in cancer is crucial for improving future clinical interventions and therapy for cancers. In this review, we try to clarify the complex regulation and function of the Hippo signaling network in cancer development, including its role in signal transduction, metabolic regulation, and tumor development, as well as tumor therapies targeting the Hippo pathway.
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Wu J, Xu C, Guan X, Ni D, Yang X, Yang Z, Wang M. Comprehensive analysis of tumor microenvironment and identification of an immune signature to predict the prognosis and immunotherapeutic response in lung squamous cell carcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:569. [PMID: 33987267 DOI: 10.21037/atm-21-463] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background Tumor mutation burden (TMB) and immune microenvironment are important determinants of prognosis and immunotherapeutic efficacy for cancer patients. The aim of the present study was to develop an immune signature to effectively predict prognosis and immunotherapeutic response in patients with lung squamous cell carcinoma (LUSC). Methods TMB and immune microenvironment characteristics were comprehensively analyzed by multi-omics data in LUSC. The immune signature was further constructed and validated in multiple independent datasets by LASSO Cox regression analysis. Next, the value of immune signature in predicting the response of immunotherapy was evaluated. Finally, the possible mechanism of immune signature was also investigated. Results A novel immune signature based on 5 genes was constructed and validated to predict the prognosis of LUSC patients. These genes were filamin-C, Rho family GTPase 1, interleukin 4-induced gene-1, transglutaminase 2, and prostaglandin I2 synthase. High-risk patients had significantly poorer survival than low-risk patients. A nomogram was also developed based on the immune signature and tumor stage, which showed good application. Furthermore, we found that the immune signature had a significant correlation with immune checkpoint, microsatellite instability, tumor infiltrating lymphocytes, cytotoxic activity scores, and T-cell-inflamed score, suggesting low-risk patients are more likely to benefit from immunotherapy. Finally, functional enrichment and pathway analyses revealed several significantly enriched immune-related biological processes and metabolic pathways. Conclusions In the present study, we developed a novel immune signature that could predict prognosis and immunotherapeutic response in LUSC patients. The results not only help identify LUSC patients with poor survival, but also increase our understanding of the immune microenvironment and immunotherapy in LUSC.
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Affiliation(s)
- Jinlong Wu
- Department of Thoracic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Chengfeng Xu
- Department of Pharmacy, Shidong Hospital of Shanghai Yangpu District, Shanghai, China
| | - Xin Guan
- Department of Thoracic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Da Ni
- Department of Thoracic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xuhui Yang
- Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhiyin Yang
- Department of Thoracic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Mingsong Wang
- Department of Thoracic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Special Issue "Genetic Advances in Neuromuscular Disorders: From Gene Identification to Gene Therapy". Genes (Basel) 2021; 12:genes12020242. [PMID: 33567614 PMCID: PMC7915748 DOI: 10.3390/genes12020242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 11/17/2022] Open
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