1
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Yang Y, Zou GM, Wei XS, Zhang Z, Zhuo L, Xu QQ, Li WG. Identification and validation of biomarkers in membranous nephropathy and pan-cancer analysis. Front Immunol 2024; 15:1302909. [PMID: 38846934 PMCID: PMC11153720 DOI: 10.3389/fimmu.2024.1302909] [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: 09/27/2023] [Accepted: 05/10/2024] [Indexed: 06/09/2024] Open
Abstract
Background Membranous nephropathy (MN) is an autoimmune disease and represents the most prevalent type of renal pathology in adult patients afflicted with nephrotic syndrome. Despite substantial evidence suggesting a possible link between MN and cancer, the precise underlying mechanisms remain elusive. Methods In this study, we acquired and integrated two MN datasets (comprising a single-cell dataset and a bulk RNA-seq dataset) from the Gene Expression Omnibus database for differential expression gene (DEG) analysis, hub genes were obtained by LASSO and random forest algorithms, the diagnostic ability of hub genes was assessed using ROC curves, and the degree of immune cell infiltration was evaluated using the ssGSEA function. Concurrently, we gathered pan-cancer-related genes from the TCGA and GTEx databases, to analyze the expression, mutation status, drug sensitivity and prognosis of hub genes in pan-cancer. Results We conducted intersections between the set of 318 senescence-related genes and the 366 DEGs, resulting in the identification of 13 senescence-related DEGs. Afterwards, we meticulously analyzed these genes using the LASSO and random forest algorithms, which ultimately led to the discovery of six hub genes through intersection (PIK3R1, CCND1, TERF2IP, SLC25A4, CAPN2, and TXN). ROC curves suggest that these hub genes have good recognition of MN. After performing correlation analysis, examining immune infiltration, and conducting a comprehensive pan-cancer investigation, we validated these six hub genes through immunohistochemical analysis using human renal biopsy tissues. The pan-cancer analysis notably accentuates the robust association between these hub genes and the prognoses of individuals afflicted by diverse cancer types, further underscoring the importance of mutations within these hub genes across various cancers. Conclusion This evidence indicates that these genes could potentially play a pivotal role as a critical link connecting MN and cancer. As a result, they may hold promise as valuable targets for intervention in cases of both MN and cancer.
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Affiliation(s)
| | | | | | | | | | | | - Wen-ge Li
- *Correspondence: Qian-qian Xu, ; Wen-ge Li,
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2
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Xu F, Xie L, He J, Huang Q, Shen Y, Chen L, Zeng X. Detection of common pathogenesis of rheumatoid arthritis and atherosclerosis via microarray data analysis. Heliyon 2024; 10:e28029. [PMID: 38628735 PMCID: PMC11019104 DOI: 10.1016/j.heliyon.2024.e28029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/28/2024] [Accepted: 03/11/2024] [Indexed: 04/19/2024] Open
Abstract
Despite extensive research reveal rheumatoid arthritis (RA) is related to atherosclerosis (AS), common pathogenesis between these two diseases still needs to be explored. In current study, we explored the common pathogenesis between rheumatoid arthritis (RA) and atherosclerosis (AS) by identifying 297 Differentially Expressed Genes (DEGs) associated with both diseases. Through KEGG and GO functional analysis, we highlighted the correlation of these DEGs with crucial biological processes such as the vesicle transport, immune system process, signaling receptor binding, chemokine signaling and many others. Employing Protein-Protein Interaction (PPI) network analysis, we elucidated the associations between DEGs, revealing three gene modules enriched in immune system process, vesicle, signaling receptor binding, Pertussis, and among others. Additionally, through CytoHubba analysis, we pinpointed 11 hub genes integral to intergrin-mediated signaling pathway, plasma membrane, phosphotyrosine binding, chemokine signaling pathway and so on. Further investigation via the TRRUST database identified two key Transcription Factors (TFs), SPI1 and RELA, closely linked with these hub genes, shedding light on their regulatory roles. Finally, leveraging the collective insights from hub genes and TFs, we proposed 10 potential drug candidates targeting the molecular mechanisms underlying RA and AS pathogenesis. Further investigation on xCell revealed that 14 types of cells were all different in both AS and RA. This study underscores the shared pathogenic mechanisms, pivotal genes, and potential therapeutic interventions bridging RA and AS, offering valuable insights for future research and clinical management strategies.
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Affiliation(s)
- Fan Xu
- Department of Cardiovascular Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, China
- Key Laboratory of Cardio-Thoracic Surgery (Fujian Medical University), Fujian Province University, Fuzhou, Fujian Province, China
| | - Linfeng Xie
- Department of Cardiovascular Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, China
- Fujian Medical University, Fuzhou, Fujian Province, China
| | - Jian He
- Department of Cardiovascular Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, China
- Fujian Medical University, Fuzhou, Fujian Province, China
| | - Qiuyu Huang
- Department of Cardiovascular Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, China
- Key Laboratory of Cardio-Thoracic Surgery (Fujian Medical University), Fujian Province University, Fuzhou, Fujian Province, China
| | - Yanming Shen
- Department of Cardiovascular Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, China
- Fujian Medical University, Fuzhou, Fujian Province, China
| | - Liangwan Chen
- Department of Cardiovascular Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, China
- Key Laboratory of Cardio-Thoracic Surgery (Fujian Medical University), Fujian Province University, Fuzhou, Fujian Province, China
| | - Xiaohong Zeng
- Department of Rheumatology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian Province, China
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3
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Tan L, Li X, Qin H, Zhang Q, Wang J, Chen T, Zhang C, Zhang X, Tan Y. Identified S100A9 as a target for diagnosis and treatment of ulcerative colitis by bioinformatics analysis. Sci Rep 2024; 14:5517. [PMID: 38448514 PMCID: PMC10917761 DOI: 10.1038/s41598-024-55944-3] [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: 10/23/2023] [Accepted: 02/29/2024] [Indexed: 03/08/2024] Open
Abstract
Ulcerative colitis (UC) is a chronic, recurrent inflammatory bowel disease. UC confronts with severe challenges including the unclear pathogenesis and lack of specific diagnostic markers, demanding for identifying predictive biomarkers for UC diagnosis and treatment. We perform immune infiltration and weighted gene co-expression network analysis on gene expression profiles of active UC, inactive UC, and normal controls to identify UC related immune cell and hub genes. Neutrophils, M1 macrophages, activated dendritic cells, and activated mast cells are significantly enriched in active UC. MMP-9, CHI3L1, CXCL9, CXCL10, CXCR2 and S100A9 are identified as hub genes in active UC. Specifically, S100A9 is significantly overexpressed in mice with colitis. The receiver operating characteristic curve demonstrates the excellent performance of S100A9 expression in diagnosing active UC. Inhibition of S100A9 expression reduces DSS-induced colonic inflammation. These identified biomarkers associated with activity in UC patients enlighten the new insights of UC diagnosis and treatment.
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Affiliation(s)
- Lulu Tan
- The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People' Hospital, Yichang, 443000, China
| | - Xin Li
- Wuhan Asia Heart Hospital, Wuhan, 430022, China
| | - Hong Qin
- The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People' Hospital, Yichang, 443000, China
| | - Qingqing Zhang
- Haiyan County Hospital of Traditional Chinese Medicine, Jiaxing, 314399, China
| | - Jinfeng Wang
- The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People' Hospital, Yichang, 443000, China
| | - Tao Chen
- The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People' Hospital, Yichang, 443000, China
| | - Chengwu Zhang
- The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People' Hospital, Yichang, 443000, China
| | - Xiaoying Zhang
- The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People' Hospital, Yichang, 443000, China.
| | - Yuyan Tan
- The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People' Hospital, Yichang, 443000, China.
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4
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Luan Z, Zhang J, Wang Y. Identification of marker genes for spinal cord injury. Front Med (Lausanne) 2024; 11:1364380. [PMID: 38463490 PMCID: PMC10921937 DOI: 10.3389/fmed.2024.1364380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 02/07/2024] [Indexed: 03/12/2024] Open
Abstract
Introduction Spinal cord injury (SCI) is a profoundly disabling and devastating neurological condition, significantly impacting patients' quality of life. It imposes unbearable psychological and economic pressure on both patients and their families, as well as placing a heavy burden on society. Methods In this study, we integrated datasets GSE5296 and GSE47681 as training groups, analyzed gene variances between sham group and SCI group mice, and conducted Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis based on the differentially expressed genes. Subsequently, we performed Weighted Gene Correlation Network Analysis (WGCNA) and Lasso regression analyses. Results We identified four characteristic disease genes: Icam1, Ch25h, Plaur and Tm4sf1. We examined the relationship between SCI and immune cells, and validated the expression of the identified disease-related genes in SCI rats using PCR and immunohistochemistry experiments. Discussion In conclusion, we have identified and verified four genes related to SCI: Icam1, Ch25h, Plaur and Tm4sf1, which could offer insights for SCI treatment.
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Affiliation(s)
- Zhiwei Luan
- Department of Orthopedic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China
| | - Jiayu Zhang
- Department of Hygienic Toxicology, College of Public Health, Harbin Medical University, Harbin, China
| | - Yansong Wang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- NHC Key Laboratory of Cell Transplantation, Harbin Medical University, Harbin, China
- Heilongjiang Provincial Key Laboratory of Hard Tissue Development and Regeneration, Harbin Medical University, Harbin, China
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Kreissner KO, Faller B, Talucci I, Maric HM. MARTin-an open-source platform for microarray analysis. FRONTIERS IN BIOINFORMATICS 2024; 4:1329062. [PMID: 38405547 PMCID: PMC10885354 DOI: 10.3389/fbinf.2024.1329062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/15/2024] [Indexed: 02/27/2024] Open
Abstract
Background: Microarray technology has brought significant advancements to high-throughput analysis, particularly in the comprehensive study of biomolecular interactions involving proteins, peptides, and antibodies, as well as in the fields of gene expression and genotyping. With the ever-increasing volume and intricacy of microarray data, an accurate, reliable and reproducible analysis is essential. Furthermore, there is a high level of variation in the format of microarrays. This not only holds true between different sample types but is also due to differences in the hardware used during the production of the arrays, as well as the personal preferences of the individual users. Therefore, there is a need for transparent, broadly applicable and user-friendly image quantification techniques to extract meaningful information from these complex datasets, while also addressing the challenges posed by specific microarray and imager formats, which can flaw analysis and interpretation. Results: Here we introduce MicroArray Rastering Tool (MARTin), as a versatile tool developed primarily for the analysis of protein and peptide microarrays. Our software provides state-of-the-art methodologies, offering researchers a comprehensive tool for microarray image quantification. MARTin is independent of the microarray platform used and supports various configurations including high-density formats and printed arrays with significant x and y offsets. This is made possible by granting the user the ability to freely customize parts of the application to their specific microarray format. Thanks to built-in features like adaptive filtering and autofit, measurements can be done very efficiently and are highly reproducible. Furthermore, our tool integrates metadata management and integrity check features, providing a straightforward quality control method, along with a ready-to-use interface for in-depth data analysis. This not only promotes good scientific practice in the field of microarray analysis but also enhances the ability to explore and examine the generated data. Conclusion: MARTin has been developed to empower its users with a reliable, efficient, and intuitive tool for peptidomic and proteomic array analysis, thereby facilitating data-driven discovery across disciplines. Our software is an open-source project freely available via the GNU Affero General Public License licence on GitHub.
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Affiliation(s)
- Kai O. Kreissner
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | | | - Ivan Talucci
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
- Department of Neurology, University Hospital Würzburg, Würzburg, Bavaria, Germany
| | - Hans M. Maric
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
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6
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Hu F, Zhu Y, Tian J, Xu H, Xue Q. Single-Cell Sequencing Combined with Transcriptome Sequencing Constructs a Predictive Model of Key Genes in Multiple Sclerosis and Explores Molecular Mechanisms Related to Cellular Communication. J Inflamm Res 2024; 17:191-210. [PMID: 38226354 PMCID: PMC10788626 DOI: 10.2147/jir.s442684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/28/2023] [Indexed: 01/17/2024] Open
Abstract
Background Multiple sclerosis (MS) causes chronic inflammation and demyelination of the central nervous system and comprises a class of neurodegenerative diseases in which interactions between multiple immune cell types mediate the involvement of MS development. However, the early diagnosis and treatment of MS remain challenging. Methods Gene expression profiles of MS patients were obtained from the Gene Expression Omnibus (GEO) database. Single-cell and intercellular communication analyses were performed to identify candidate gene sets. Predictive models were constructed using LASSO regression. Relationships between genes and immune cells were analyzed by single sample gene set enrichment analysis (ssGSEA). The molecular mechanisms of key genes were explored using gene enrichment analysis. An miRNA network was constructed to search for target miRNAs related to key genes, and related transcription factors were searched by transcriptional regulation analysis. We utilized the GeneCard database to detect the correlations between disease-regulated genes and key genes. We verified the mRNA expression of 4 key genes by reverse transcription-quantitative PCR (RT‒qPCR). Results Monocyte marker genes were selected as candidate gene sets. CD3D, IL2RG, MS4A6A, and NCF2 were found to be the key genes by LASSO regression. We constructed a prediction model with AUC values of 0.7569 and 0.719. The key genes were closely related to immune factors and immune cells. We explored the signaling pathways and molecular mechanisms involving the key genes by gene enrichment analysis. We obtained and visualized the miRNAs associated with the key genes using the miRcode database. We also predicted the transcription factors involved. We used validated key genes in MS patients, several of which were confirmed by RT‒qPCR. Conclusion The prediction model constructed with the CD3D, IL2RG, MS4A6A, and NCF2 genes has good diagnostic efficacy and provides new ideas for the diagnosis and treatment of MS.
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Affiliation(s)
- Fangzhou Hu
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215000, People’s Republic of China
| | - Yunfei Zhu
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215000, People’s Republic of China
| | - Jingluan Tian
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215000, People’s Republic of China
| | - Hua Xu
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215000, People’s Republic of China
- Department of Neurology, Affiliated Jintan Hospital of Jiangsu University, Changzhou Jintan First People’s Hospital, Changzhou, Jiangsu, 215006, People’s Republic of China
| | - Qun Xue
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215000, People’s Republic of China
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7
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Liu R, Wang Q, Zhang X. Identification of prognostic coagulation-related signatures in clear cell renal cell carcinoma through integrated multi-omics analysis and machine learning. Comput Biol Med 2024; 168:107779. [PMID: 38061153 DOI: 10.1016/j.compbiomed.2023.107779] [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] [Received: 07/27/2023] [Revised: 10/30/2023] [Accepted: 11/28/2023] [Indexed: 01/10/2024]
Abstract
Clear cell renal cell carcinoma is a threat to public health with high morbidity and mortality. Clinical evidence has shown that cancer-associated thrombosis poses significant challenges to treatments, including drug resistance and difficulties in surgical decision-making in ccRCC. However, the coagulation pathway, one of the core mechanisms of cancer-associated thrombosis, recently found closely related to the tumor microenvironment and immune-related pathway, is rarely researched in ccRCC. Therefore, we integrated bulk RNA-seq data, DNA mutation and methylation data, single-cell data, and proteomic data to perform a comprehensive analysis of coagulation-related genes in ccRCC. First, we demonstrated the importance of the coagulation-related gene set by consensus clustering. Based on machine learning, we identified 5 coagulation signature genes and verified their clinical value in TCGA, ICGC, and E-MTAB-1980 databases. It's also demonstrated that the specific expression patterns of coagulation signature genes driven by CNV and methylation were closely correlated with pathways including apoptosis, immune infiltration, angiogenesis, and the construction of extracellular matrix. Moreover, we identified two types of tumor cells in single-cell data by machine learning, and the coagulation signature genes were differentially expressed in two types of tumor cells. Besides, the signature genes were proven to influence immune cells especially the differentiation of T cells. And their protein level was also validated.
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Affiliation(s)
- Ruijie Liu
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, China.
| | - Qi Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, China.
| | - Xiaoping Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, China.
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8
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Wang SH, Xia YJ, Yu J, He CY, Han JR, Bai JX. S100 Calcium-Binding Protein A8 Functions as a Tumor-Promoting Factor in Renal Cell Carcinoma via Activating NF-κB Signaling Pathway. J INVEST SURG 2023; 36:2241081. [PMID: 37527815 DOI: 10.1080/08941939.2023.2241081] [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: 02/08/2023] [Revised: 06/10/2023] [Accepted: 07/21/2023] [Indexed: 08/03/2023]
Abstract
BACKGROUND Renal cell carcinoma (RCC), arising from the renal tubular epithelium, is one of the most common types of genitourinary malignancies. Based on the Gene Expression Omnibus (GEO) database (GSE100666), S100 calcium-binding protein A8 (S100A8) was highly expressed in RCC tissues. S100A8, an inflammatory regulatory factor, has emerged as an important mediator associated with the occurrence and development of cancer. MATERIALS AND METHODS The Gene Expression Omnibus (GEO) database was used to identify the key genes and investigate the main signaling pathways in RCC. Human RCC samples and corresponding adjacent normal tissues were collected in our hospital. The expression of S100A8 in human RCC samples was detected using western blotting and immunohistochemical analysis. S100A8 overexpression or knockdown was mediated by using Lipofectamine 3000 in human renal cell carcinoma cell line 786-O and ACHN cells. Basic experiments, including MTT and cell apoptosis assays, were utilized for investigating the function of S100A8 in RCC. Furthermore, the levels of inflammation were also evaluated in 786-O and ACHN cells. RESULTS In the current study, we found that downregulation of S100A8 inhibited proliferation and promoted apoptosis in 786-O and ACHN RCC cells. Of note, S100A8 silencing downregulated the phosphorylation of NF-κB p65, thereby decreasing the levels of TNF-α, cleaved caspase1, and MMP9. By contrast, S100A8 upregulation could increase these expressions. CONCLUSION Overall, S100A8 knockdown restrained RCC malignant biological properties, which was associated with the deactivation of the NF-κB signaling pathway. This present study demonstrates new insights that S100A8 may be a potential therapeutic target in RCC.
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Affiliation(s)
- Shu-Hui Wang
- Department of Integrated Traditional Chinese and Western Medicine and Geriatrics, Hongqi Hospital Affiliated to Mudanjiang Medical University, Mudanjiang, Heilongjiang, China
| | - Yan-Jie Xia
- Department of Laboratory Medicine, Hongqi Hospital Affiliated to Mudanjiang Medical University, Mudanjiang, Heilongjiang, China
| | - Jing Yu
- Department of Endocrinology, Hongqi Hospital Affiliated to Mudanjiang Medical University, Mudanjiang, Heilongjiang, China
| | - Chun-Yan He
- Department of Urology, Hongqi Hospital Affiliated to Mudanjiang Medical University, Mudanjiang, Heilongjiang, China
| | - Jie-Ru Han
- School of Basic Medical Sciences, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China
| | - Ji-Xiang Bai
- Department of Urology, Hongqi Hospital Affiliated to Mudanjiang Medical University, Mudanjiang, Heilongjiang, China
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9
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Zhang Q, Hu W, Xiong L, Wen J, Wei T, Yan L, Liu Q, Zhu S, Bai Y, Zeng Y, Yin Z, Yang J, Zhang W, Wu M, Zhang Y, Peng G, Bao S, Liu L. IHGA: An interactive web server for large-scale and comprehensive discovery of genes of interest in hepatocellular carcinoma. Comput Struct Biotechnol J 2023; 21:3987-3998. [PMID: 37635767 PMCID: PMC10457689 DOI: 10.1016/j.csbj.2023.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/04/2023] [Accepted: 08/04/2023] [Indexed: 08/29/2023] Open
Abstract
Mining gene expression data is valuable for discovering novel biomarkers and therapeutic targets in hepatocellular carcinoma (HCC). Although emerging data mining tools are available for pan-cancer-related gene data analysis, few tools are dedicated to HCC. Moreover, tools specifically designed for HCC have restrictions such as small data scale and limited functionality. Therefore, we developed IHGA, a new interactive web server for discovering genes of interest in HCC on a large-scale and comprehensive basis. Integrative HCC Gene Analysis (IHGA) contains over 100 independent HCC patient-derived datasets (with over 10,000 tissue samples) and more than 90 cell models. IHGA allows users to conduct a series of large-scale and comprehensive analyses and data visualizations based on gene mRNA levels, including expression comparison, correlation analysis, clinical characteristics analysis, survival analysis, immune system interaction analysis, and drug sensitivity analysis. This method notably enhanced the richness of clinical data in IHGA. Additionally, IHGA integrates artificial intelligence (AI)-assisted gene screening based on natural language models. IHGA is free, user-friendly, and can effectively reduce time spent during data collection, organization, and analysis. In conclusion, IHGA is competitive in terms of data scale, data diversity, and functionality. It effectively alleviates the obstacles caused by HCC heterogeneity to data mining work and helps advance research on the molecular mechanisms of HCC.
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Affiliation(s)
- Qiangnu Zhang
- Division of Hepatobiliary and Pancreas Surgery, Department of General Surgery, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020 Shenzhen, China
- Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, 510632 Guangzhou, China
| | - Weibin Hu
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, Institute for Brain Research and Rehabilitation, South China Normal University, 510631 Guangzhou, China
| | - Lingfeng Xiong
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangdong Pharmaceutical University, 510632 Guangzhou, China
| | - Jin Wen
- Department of Neurology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), 518020 Shenzhen, China
| | - Teng Wei
- Cytotherapy Laboratory, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), 518020 Shenzhen, China
| | - Lesen Yan
- Division of Hepatobiliary and Pancreas Surgery, Department of General Surgery, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020 Shenzhen, China
| | - Quan Liu
- Laboratory Medicine Center, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), 518000 Shenzhen, China
| | - Siqi Zhu
- Laboratory Medicine Center, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), 518000 Shenzhen, China
| | - Yu Bai
- Division of Hepatobiliary and Pancreas Surgery, Department of General Surgery, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020 Shenzhen, China
| | - Yuandi Zeng
- Division of Hepatobiliary and Pancreas Surgery, Department of General Surgery, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020 Shenzhen, China
| | - Zexin Yin
- Division of Hepatobiliary and Pancreas Surgery, Department of General Surgery, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020 Shenzhen, China
| | - Jilin Yang
- Division of Hepatobiliary and Pancreas Surgery, Department of General Surgery, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020 Shenzhen, China
| | - Wenjian Zhang
- Division of Hepatobiliary and Pancreas Surgery, Department of General Surgery, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020 Shenzhen, China
| | - Meilong Wu
- Division of Hepatobiliary and Pancreas Surgery, Department of General Surgery, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020 Shenzhen, China
| | - Yusen Zhang
- Division of Hepatobiliary and Pancreas Surgery, Department of General Surgery, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020 Shenzhen, China
| | - Gongze Peng
- Division of Hepatobiliary and Pancreas Surgery, Department of General Surgery, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020 Shenzhen, China
| | - Shiyun Bao
- Division of Hepatobiliary and Pancreas Surgery, Department of General Surgery, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020 Shenzhen, China
| | - Liping Liu
- Division of Hepatobiliary and Pancreas Surgery, Department of General Surgery, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020 Shenzhen, China
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10
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Liu M, Wang Y, Shi W, Yang C, Wang Q, Chen J, Li J, Chen B, Sun G. PCDH7 as the key gene related to the co-occurrence of sarcopenia and osteoporosis. Front Genet 2023; 14:1163162. [PMID: 37476411 PMCID: PMC10354703 DOI: 10.3389/fgene.2023.1163162] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/06/2023] [Indexed: 07/22/2023] Open
Abstract
Sarcopenia and osteoporosis, two degenerative diseases in older patients, have become severe health problems in aging societies. Muscles and bones, the most important components of the motor system, are derived from mesodermal and ectodermal mesenchymal stem cells. The adjacent anatomical relationship between them provides the basic conditions for mechanical and chemical signals, which may contribute to the co-occurrence of sarcopenia and osteoporosis. Identifying the potential common crosstalk genes between them may provide new insights for preventing and treating their development. In this study, DEG analysis, WGCNA, and machine learning algorithms were used to identify the key crosstalk genes of sarcopenia and osteoporosis; this was then validated using independent datasets and clinical samples. Finally, four crosstalk genes (ARHGEF10, PCDH7, CST6, and ROBO3) were identified, and mRNA expression and protein levels of PCDH7 in clinical samples from patients with sarcopenia, with osteoporosis, and with both sarcopenia and osteoporosis were found to be significantly higher than those from patients without sarcopenia or osteoporosis. PCDH7 seems to be a key gene related to the development of both sarcopenia and osteoporosis.
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Affiliation(s)
- Mingchong Liu
- Department of Traumatic Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yongheng Wang
- Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Wentao Shi
- Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Chensong Yang
- Department of Traumatic Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qidong Wang
- Department of Traumatic Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jingyao Chen
- Institute for Regenerative Medicine, Shanghai East Hospital, The Institute for Biomedical Engineering and Nano Science, Tongji University School of Medicine, Shanghai, China
| | - Jun Li
- Institute for Regenerative Medicine, Shanghai East Hospital, The Institute for Biomedical Engineering and Nano Science, Tongji University School of Medicine, Shanghai, China
| | - Bingdi Chen
- Institute for Regenerative Medicine, Shanghai East Hospital, The Institute for Biomedical Engineering and Nano Science, Tongji University School of Medicine, Shanghai, China
| | - Guixin Sun
- Department of Traumatic Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
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11
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Liu T, Liu Y, Su X, Peng L, Chen J, Xing P, Qiao X, Wang Z, Di J, Zhao M, Jiang B, Qu H. Genome-wide transcriptomics and copy number profiling identify patient-specific CNV-lncRNA-mRNA regulatory triplets in colorectal cancer. Comput Biol Med 2023; 153:106545. [PMID: 36646024 DOI: 10.1016/j.compbiomed.2023.106545] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/19/2022] [Accepted: 01/10/2023] [Indexed: 01/13/2023]
Abstract
Screening cancer genomes has provided an in-depth characterization of genetic variants such as copy number variations (CNVs) and gene expression changes of non-coding transcripts. Single-dimensional experiments are often designed to differentiate a patient cohort into various sets with the aim of identifying molecular changes among groups; however, this may be inadequate to decipher the causal relationship between molecular signatures in individual patients. To overcome this challenge with respect to personalized medicine, we implemented a patient-specific multi-dimensional integrative approach to uncover coherent signals from multiple independent platforms. In particular, we focused on the consistent gene dosage effects of CNVs for both mRNA and long non-coding RNA (lncRNA) expression in nine colorectal cancer patients. We identified 511 CNV-lncRNA-mRNA regulatory triplets associated with CNVs and aberrant expression of both mRNAs and lncRNAs. By filtering out inconsistent changes among CNVs, mRNAs, and lncRNAs, we further characterized 165 coherent motifs associated with 56 genes. In total, 108 motifs were linked with 31 copy number gains, 44 upregulated lncRNAs, and 45 upregulated mRNAs. Another 57 coherent downregulated motifs were also collected. We discuss how for many of these CNV-lncRNA-mRNA regulatory triplets, their clinical impact remains to be explored, including survival time, microsatellite instability, tumor stage, and primary tumor sites. By validating two example CNV-lncRNA-mRNA triplets with up- and down-regulation, we confirmed that individual variations in multiple dimensions are a robust tool to identify reliable molecular signals for personalized medicine. In summary, we utilized a patient-specific computational pipeline to explore the consistent CNV-driven motifs consisting of lncRNAs and mRNAs. We also identified LSM14B as a potential promoter in colorectal cancer progression, suggesting that it may serve as a target for colorectal cancer treatment.
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Affiliation(s)
- Tianqi Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Yining Liu
- The School of Public Health, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China
| | - Xiangqian Su
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Lin Peng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Jiangbo Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Pu Xing
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Xiaowen Qiao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Zaozao Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Jiabo Di
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Min Zhao
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia.
| | - Beihai Jiang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
| | - Hong Qu
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, PR China.
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12
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In silico analysis revealed the potential circRNA-miRNA-mRNA regulative network of non-small cell lung cancer (NSCLC). Comput Biol Med 2023; 152:106315. [PMID: 36495751 DOI: 10.1016/j.compbiomed.2022.106315] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 10/31/2022] [Accepted: 11/13/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND The primary source of death in the world is non-small cell lung cancer (NSCLC). However, NSCLCs pathophysiology is still not completely understood. The current work sought to study the differential expression of mRNAs involved in NSCLC and their interactions with miRNAs and circRNAs. METHODS We utilized three microarray datasets (GSE21933, GSE27262, and GSE33532) from the GEO NCBI database to identify the differentially expressed genes (DEGs) in NSCLC. We employed DAVID Functional annotation tool to investigate the underlying GO biological process, molecular functions, and KEGG pathways involved in NSCLC. We performed the Protein-protein interaction (PPI) network, MCODE, and CytoHubba analysis from Cytoscape software to identify the significant DEGs in NSCLC. We utilized miRnet to anticipate and build interaction between miRNAs and mRNAs in NSCLC and ENCORI to predict the miRNA-circRNA relationships and build the ceRNA regulatory network. Finally, we executed the gene expression and Kaplan-Meier survival analysis to validate the significant DEGs in the ceRNA network utilizing TCGA NSCLC and GEPIA data. RESULTS We revealed a total of 156 overlapped DEGs (47 upregulated and 109 downregulated genes) in NSCLC. The PPI network, MCODE, and CytoHubba analysis revealed 12 hub genes (cdkn3, rrm2, ccnb1, aurka, nuf2, tyms, kif11, hmmr, ccnb2, nek2, anln, and birc5) that are associated with NSCLC. We identified that these 12 genes encode 12 mRNAs that are strongly linked with 8 miRNAs, and further, we revealed that 1 circRNA was associated with this 5 miRNA. We constructed the ceRNAs network that contained 1circRNA-5miRNAs-7mRNAs. The expression of these seven significant genes in LUAD & LUSC (NSCLC) was considerably higher in the TCGA database than in normal tissues. Kaplan-Meier survival plot reveals that increased expression of these hub genes was related to a poor survival rate in LUAD. CONCLUSION Overall, we developed a circRNA-miRNA-mRNA regulation network to study the probable mechanism of NSCLC.
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13
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Chen H, Shi X, Ren L, Zhuo H, Zeng L, Qin Q, Wan Y, Sangdan W, Zhou L. Identification of the miRNA-mRNA regulatory network associated with radiosensitivity in esophageal cancer based on integrative analysis of the TCGA and GEO data. BMC Med Genomics 2022; 15:249. [PMID: 36456979 PMCID: PMC9714096 DOI: 10.1186/s12920-022-01392-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The current study set out to identify the miRNA-mRNA regulatory networks that influence the radiosensitivity in esophageal cancer based on the The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. METHODS Firstly, esophageal cancer-related miRNA-seq and mRNA-seq data were retrieved from the TCGA database, and the mRNA dataset of esophageal cancer radiotherapy was downloaded from the GEO database to analyze the differential expressed miRNAs (DEmiRNAs) and mRNAs (DEmRNAs) in radiosensitive and radioresistant samples, followed by the construction of the miRNA-mRNA regulatory network and Gene Ontology and KEGG enrichment analysis. Additionally, a prognostic risk model was constructed, and its accuracy was evaluated by means of receiver operating characteristic analysis. RESULTS A total of 125 DEmiRNAs and 42 DEmRNAs were closely related to the radiosensitivity in patients with esophageal cancer. Based on 47 miRNA-mRNA interactions, including 21 miRNAs and 21 mRNAs, the miRNA-mRNA regulatory network was constructed. The prognostic risk model based on 2 miRNAs (miR-132-3p and miR-576-5p) and 4 mRNAs (CAND1, ZDHHC23, AHR, and MTMR4) could accurately predict the prognosis of esophageal cancer patients. Finally, it was verified that miR-132-3p/CAND1/ZDHHC23 and miR-576-5p/AHR could affect the radiosensitivity in esophageal cancer. CONCLUSION Our study demonstrated that miR-132-3p/CAND1/ZDHHC23 and miR-576-5p/AHR were critical molecular pathways related to the radiosensitivity of esophageal cancer.
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Affiliation(s)
- Hongmin Chen
- grid.412901.f0000 0004 1770 1022Cancer Center, West China Hospital of Sichuan University, No. 37 Guoxue Lane, Wuhou District, Chengdu, 610041 People’s Republic of China
| | - Xiaoxiao Shi
- grid.13291.380000 0001 0807 1581Department of Medical Oncology, Chengdu Shang Jin Nan Fu Hospital (West China Hospital, S.C.U.), Chengdu, 611730 People’s Republic of China
| | - Li Ren
- grid.412901.f0000 0004 1770 1022Cancer Center, West China Hospital of Sichuan University, No. 37 Guoxue Lane, Wuhou District, Chengdu, 610041 People’s Republic of China
| | - Hongyu Zhuo
- grid.412901.f0000 0004 1770 1022Cancer Center, West China Hospital of Sichuan University, No. 37 Guoxue Lane, Wuhou District, Chengdu, 610041 People’s Republic of China
| | - Li Zeng
- grid.412901.f0000 0004 1770 1022Cancer Center, West China Hospital of Sichuan University, No. 37 Guoxue Lane, Wuhou District, Chengdu, 610041 People’s Republic of China
| | - Qing Qin
- grid.412901.f0000 0004 1770 1022Cancer Center, West China Hospital of Sichuan University, No. 37 Guoxue Lane, Wuhou District, Chengdu, 610041 People’s Republic of China
| | - Yuming Wan
- grid.412901.f0000 0004 1770 1022Cancer Center, West China Hospital of Sichuan University, No. 37 Guoxue Lane, Wuhou District, Chengdu, 610041 People’s Republic of China
| | - Wangmu Sangdan
- Department of Oncology, People’s Hospital of Tibet Autonomous Region, Lhasa, 850000 People’s Republic of China
| | - Lin Zhou
- grid.412901.f0000 0004 1770 1022Cancer Center, West China Hospital of Sichuan University, No. 37 Guoxue Lane, Wuhou District, Chengdu, 610041 People’s Republic of China ,grid.13291.380000 0001 0807 1581Department of Thoracic Oncology, State Key Laboratory of Biotherapy, Sichuan University, No. 1, Keyuan 4th Road, Gaopeng Avenue, Chengdu, 610041 People’s Republic of China
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14
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Shih ML, Lee JC, Cheng SY, Lawal B, Ho CL, Wu CC, Tzeng DTW, Chen JH, Wu ATH. Transcriptomic discovery of a theranostic signature (SERPINE1/MMP3/COL1A1/SPP1) for head and neck squamous cell carcinomas and identification of antrocinol as a candidate drug. Comput Biol Med 2022; 150:106185. [PMID: 37859283 DOI: 10.1016/j.compbiomed.2022.106185] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/04/2022] [Accepted: 10/08/2022] [Indexed: 11/03/2022]
Abstract
Head and neck squamous cell carcinomas (HNSCC) are prevalent malignancies with a disappointing prognosis, necessitating the search for theranostic biomarkers for better management. Based on a meta-analysis of transcriptomic data containing ten clinical datasets of HNSCC and matched nonmalignant samples, we identified SERPINE1/MMP3/COL1A1/SPP1 as essential hub genes as the potential theranostic biomarkers. Our analysis suggests these hub genes are associated with the extracellular matrix, peptidoglycans, cell migration, wound-healing processes, complement and coagulation cascades, and the AGE-RAGE signaling pathway within the tumor microenvironment. Also, these hub genes were associated with tumor-immune infiltrating cells and immunosuppressive phenotypes of HNSCC. Further investigation of The Cancer Genome Atlas (TCGA) cohorts revealed that these hub genes were associated with staging, metastasis, and poor survival in HNSCC patients. Molecular docking simulations were performed to evaluate binding activities between the hub genes and antrocinol, a novel small-molecule derivative of an anticancer phytochemical antrocin previously discovered by our group. Antrocinol showed high affinities to MMP3 and COL1A1. Notably, antrocinol presented satisfactory drug-like and ADMET properties for therapeutic applications. These results hinted at the potential of antrocinol as an anti-HNSCC candidate via targeting MMP3 and COL1A1. In conclusion, we identified hub genes: SERPINE1/MMP3/COL1A1/SPP1 as potential diagnostic biomarkers and antrocinol as a potential new drug for HNSCC.
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Affiliation(s)
- Ming-Lang Shih
- Division of General Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, 11490, Taiwan
| | - Jih-Chin Lee
- Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, National Defense Medical Center, 325, Section 2, Chenggong Road, Taipei, 114, Taiwan
| | - Sheng-Yao Cheng
- Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, National Defense Medical Center, 325, Section 2, Chenggong Road, Taipei, 114, Taiwan
| | - Bashir Lawal
- UPMC Hillman Cancer Center, Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15213, USA; Graduate Institute for Cancer Biology & Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan.
| | - Ching-Liang Ho
- Division of Hematology and Oncology Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, 114, Taiwan
| | - Cheng-Chia Wu
- Department of Radiation Oncology, Columbia Irving University Medical Center, Manhattan, NY, USA
| | - David T W Tzeng
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Jia-Hong Chen
- Division of Hematology and Oncology Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, 114, Taiwan
| | - Alexander T H Wu
- The PhD Program of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, 110, Taiwan; TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, 110, Taiwan; Clinical Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei, 110, Taiwan; Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, 110, Taiwan.
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15
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Wang Z, Xia Q, Su W, Zhang M, Gu Y, Xu J, Chen W, Jiang T. The commonness in immune infiltration of rheumatoid arthritis and atherosclerosis: Screening for central targets via microarray data analysis. Front Immunol 2022; 13:1013531. [PMID: 36311761 PMCID: PMC9606677 DOI: 10.3389/fimmu.2022.1013531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 09/30/2022] [Indexed: 11/13/2022] Open
Abstract
Background Although increasing evidence has reported an increased risk of atherosclerosis (AS) in rheumatoid arthritis (RA), the communal molecular mechanism of this phenomenon is still far from being fully elucidated. Hence, this article aimed to explore the pathogenesis of RA complicated with AS. Methods Based on the strict inclusion/exclusion criteria, four gene datasets were downloaded from the Gene Expression Omnibus (GEO) database. After identifying the communal differentially expressed genes (DEGs) and hub genes, comprehensive bioinformatics analysis, including functional annotation, co-expression analysis, expression validation, drug-gene prediction, and TF-mRNA-miRNA regulatory network construction, was conducted. Moreover, the immune infiltration of RA and AS was analyzed and compared based on the CIBERSORT algorithm, and the correlation between hub genes and infiltrating immune cells was evaluated in RA and AS respectively. Results A total of 54 upregulated and 12 downregulated communal DEGs were screened between GSE100927 and GSE55457, and functional analysis of these genes indicated that the potential pathogenesis lies in immune terms. After the protein-protein interaction (PPI) network construction, a total of six hub genes (CCR5, CCR7, IL7R, PTPRC, CD2, and CD3D) were determined as hub genes, and the subsequent comprehensive bioinformatics analysis of the hub genes re-emphasized the importance of the immune system in RA and AS. Additionally, three overlapping infiltrating immune cells were found between RA and AS based on the CIBERSORT algorithm, including upregulated memory B cells, follicular helper T cells and γδT cells. Conclusions Our study uncover the communal central genes and commonness in immune infiltration between RA and AS, and the analysis of six hub genes and three immune cells profile might provide new insights into potential pathogenesis therapeutic direction of RA complicated with AS.
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Affiliation(s)
- Zuoxiang Wang
- Department of Cardiology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Qingyue Xia
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wenxing Su
- Department of Plastic and Burn Surgery, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Mingyang Zhang
- Department of Cardiology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yiyu Gu
- Department of Cardiology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jialiang Xu
- Department of Cardiology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Weixiang Chen
- Department of Cardiology, The First Affiliated Hospital of Soochow University, Suzhou, China
- *Correspondence: Weixiang Chen, ; Tingbo Jiang,
| | - Tingbo Jiang
- Department of Cardiology, The First Affiliated Hospital of Soochow University, Suzhou, China
- *Correspondence: Weixiang Chen, ; Tingbo Jiang,
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