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Xiao X, Cheng W, Zhang G, Wang C, Sun B, Zha C, Kong F, Jia Y. Long Noncoding RNA: Shining Stars in the Immune Microenvironment of Gastric Cancer. Front Oncol 2022; 12:862337. [PMID: 35402261 PMCID: PMC8989925 DOI: 10.3389/fonc.2022.862337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/03/2022] [Indexed: 12/24/2022] Open
Abstract
Gastric cancer (GC) is a kind of malignant tumor disease that poses a serious threat to human health. The GC immune microenvironment (TIME) is a very complex tumor microenvironment, mainly composed of infiltrating immune cells, extracellular matrix, tumor-associated fibroblasts, cytokines and chemokines, all of which play a key role in inhibiting or promoting tumor development and affecting tumor prognosis. Long non-coding RNA (lncRNA) is a non-coding RNA with a transcript length is more than 200 nucleotides. LncRNAs are expressed in various infiltrating immune cells in TIME and are involved in innate and adaptive immune regulation, which is closely related to immune escape, migration and invasion of tumor cells. LncRNA-targeted therapeutic effect prediction for GC immunotherapy provides a new approach for clinical research on the disease.
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Affiliation(s)
- Xian Xiao
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.,National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China.,Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Wen Cheng
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.,National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China.,Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Guixing Zhang
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.,National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China.,Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Chaoran Wang
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.,National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China.,Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Binxu Sun
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.,National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Chunyuan Zha
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.,National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China.,Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Fanming Kong
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.,National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Yingjie Jia
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.,National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
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2
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The Hypoxia-Related Gene COL5A1 Is a Prognostic and Immunological Biomarker for Multiple Human Tumors. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:6419695. [PMID: 35082969 PMCID: PMC8786464 DOI: 10.1155/2022/6419695] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/15/2021] [Accepted: 12/14/2021] [Indexed: 01/19/2023]
Abstract
Background Collagen type V alpha 1 chain (COL5A1) is a hypoxia-related gene (a collagen family protein) and participates in the formation of the extracellular matrix. Although some evidence supports a significant role for COL5A1 in the progression of several cancers, a pan-cancer analysis of COL5A1 is not currently available. Herein, we aimed to assess the prognostic value of COL5A1 in 33 human cancers and to investigate its underlying immunological function. Methods Through multiple bioinformatics methods, we analyzed the data from Oncomine, TCGA, CCLE, HPA, DNMIVD, and cBioPortal database to explore the potential underlying carcinogenic effect of COL5A1, including the relevance of COL5A1 to the outcome, DNA methylation, tumor microenvironment, immune cells infiltration, and drug sensitivity in 33 human cancers. The effects of COL5A1 on glioma cell proliferation, migration, and invasion were verified in cellular experiments. Results Our findings indicated that COL5A1 was expressed at high levels in 13 cancers and was negatively related to the prognosis of 11 cancers. Additionally, COL5A1 was coexpressed with genes encoding the major histocompatibility complex, immune activators, immune suppressors, chemokines, chemokine receptors, mismatch repair genes, and immune checkpoints. We also identified different roles for COL5A1 in the immunocyte infiltration in different cancers. The correlation between COL5A1 and drug sensitivity was found in several cancers. COL5A1 potentially influenced the tumor progression through immune-related pathways, negative regulation of immune system processes, chemokine signaling pathways, JAK-STAT pathways, T cell receptor pathways, lymphocyte migration, and antigen processing and presentation, among other processes. Conclusions Based on our study, COL5A1 may be employed as a prognostic marker in different malignancies because of its impact on tumorigenesis and immune cell infiltration and have implications for cancer immune checkpoint inhibitors and chemotherapy.
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Zhang S, Xiang X, Liu L, Yang H, Cen D, Tang G. Bioinformatics Analysis of Hub Genes and Potential Therapeutic Agents Associated with Gastric Cancer. Cancer Manag Res 2021; 13:8929-8951. [PMID: 34876855 PMCID: PMC8643151 DOI: 10.2147/cmar.s341485] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/16/2021] [Indexed: 12/31/2022] Open
Abstract
Purpose The current treatment methods available for advanced gastric cancer are not very promising. Hence, it is important to explore novel biomarkers and potential therapeutic agents to treat gastric cancer (GC). This study aimed to identify hub genes associated with GC prognosis and explore potential drugs for its treatment. Materials and Methods Three gene expression data of GC and normal tissues were downloaded from the Gene Expression Omnibus (GEO) and processed to identify the differentially expressed genes (DEGs). We conducted a comprehensive analysis of DEGs, including functional enrichment analysis, construction of protein-protein interaction (PPI) network, identification of hub genes, survival analysis and expression verification of hub genes. Finally, we constructed the network of miRNA-mRNA, and predicted the drugs that might be effective for GC treatment. Results A total of 340 DEGs, including 94 up-regulated and 246 down-regulated genes, were identified. Among the up-regulated DEGs, the enrichment terms were primarily related to tumorigenesis and tumor progression, extracellular matrix organization, and collagen catabolic process. Additionally, 10 hub genes (FN1, COL3A1, COL1A2, BGN, THBS2, COL5A2, THBS1, COL5A1, SPARC, and COL4A1) were identified, out of which 7 genes were significantly associated with poor overall survival (OS) in GC. The expression levels of these 7 hub genes were verified using real-time PCR, immunohistochemistry, and the GEPIA2 (Gene Expression Profiling Interactive Analysis) server. A regulatory network of miRNA-mRNA was also constructed, and the top 4 interactive miRNAs (hsa-miR-29b-3p, hsa-miR-140-3p, hsa-miR-29a-3p, and hsa-miR-29c-3p) that targeted the most hub genes were identified. Finally, fourteen small molecules were predicted to be effective in treating GC. Conclusion The identification of the hub genes, miRNA-mRNA network, and potential candidate drugs associated with GC provides new insights into the molecular mechanisms and treatment of GC.
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Affiliation(s)
- Shiyu Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning City, Guangxi Province, People's Republic of China
| | - Xuelian Xiang
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning City, Guangxi Province, People's Republic of China
| | - Li Liu
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning City, Guangxi Province, People's Republic of China
| | - Huiying Yang
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning City, Guangxi Province, People's Republic of China
| | - Dongliang Cen
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning City, Guangxi Province, People's Republic of China
| | - Guodu Tang
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning City, Guangxi Province, People's Republic of China
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Liu L, Cai L, Liu C, Yu S, Li B, Pan L, Zhao J, Zhao Y, Li W, Yan X. Construction and Validation of a Novel Glycometabolism-Related Gene Signature Predicting Survival in Patients With Ovarian Cancer. Front Genet 2020; 11:585259. [PMID: 33281878 PMCID: PMC7689371 DOI: 10.3389/fgene.2020.585259] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/19/2020] [Indexed: 12/22/2022] Open
Abstract
Among all fatal gynecological malignant tumors, ovarian cancer has the highest mortality rate. The purpose of this study was to develop a stable and personalized glycometabolism-related prognostic signature to predict the overall survival of ovarian cancer patients. The gene expression profiles and clinical information of ovarian cancer patients were derived from four public GEO datasets, which were divided into training and testing cohorts. Glycometabolism-related genes significantly associated with prognosis were selected. A risk score model was established and validated to evaluate its predictive value. We found 5 genes significantly related to prognosis and established a five-mRNA signature. The five-mRNA signature significantly divided patients into a low-risk group and a high-risk group in the training set and validation set. Survival analysis showed that high risk scores obtained by the model were significantly correlated with adverse survival outcomes and could be regarded as an independent predictor for patients with ovarian cancer. In addition, the five-mRNA signature can predict the overall survival of ovarian cancer patients in different subgroups. In summary, we successfully constructed a model that can predict the prognosis of patients with ovarian cancer, which provides new insights into postoperative treatment strategies, promotes individualized therapy, and provides potential new targets for immunotherapy.
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Affiliation(s)
- Lixiao Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Luya Cai
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Chuan Liu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China
| | - Shanshan Yu
- Department of Chemoradiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Bingxin Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Luyao Pan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jinduo Zhao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ye Zhao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wenfeng Li
- Department of Chemoradiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiaojian Yan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Lu Y, Fang Z, Li M, Chen Q, Zeng T, Lu L, Chen Q, Zhang H, Zhou Q, Sun Y, Xue X, Hu Y, Chen L, Su S. Dynamic edge-based biomarker non-invasively predicts hepatocellular carcinoma with hepatitis B virus infection for individual patients based on blood testing. J Mol Cell Biol 2020; 11:665-677. [PMID: 30925583 PMCID: PMC6788726 DOI: 10.1093/jmcb/mjz025] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/27/2019] [Accepted: 03/20/2019] [Indexed: 02/07/2023] Open
Abstract
Hepatitis B virus (HBV)-induced hepatocellular carcinoma (HCC) is a major cause of cancer-related deaths in Asia and Africa. Developing effective and non-invasive biomarkers of HCC for individual patients remains an urgent task for early diagnosis and convenient monitoring. Analyzing the transcriptomic profiles of peripheral blood mononuclear cells from both healthy donors and patients with chronic HBV infection in different states (i.e. HBV carrier, chronic hepatitis B, cirrhosis, and HCC), we identified a set of 19 candidate genes according to our algorithm of dynamic network biomarkers. These genes can both characterize different stages during HCC progression and identify cirrhosis as the critical transition stage before carcinogenesis. The interaction effects (i.e. co-expressions) of candidate genes were used to build an accurate prediction model: the so-called edge-based biomarker. Considering the convenience and robustness of biomarkers in clinical applications, we performed functional analysis, validated candidate genes in other independent samples of our collected cohort, and finally selected COL5A1, HLA-DQB1, MMP2, and CDK4 to build edge panel as prediction models. We demonstrated that the edge panel had great performance in both diagnosis and prognosis in terms of precision and specificity for HCC, especially for patients with alpha-fetoprotein-negative HCC. Our study not only provides a novel edge-based biomarker for non-invasive and effective diagnosis of HBV-associated HCC to each individual patient but also introduces a new way to integrate the interaction terms of individual molecules for clinical diagnosis and prognosis from the network and dynamics perspectives.
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Affiliation(s)
- Yiyu Lu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhaoyuan Fang
- Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Meiyi Li
- Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Minhang Branch, Zhongshan Hospital/Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai, China
| | - Qian Chen
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Tao Zeng
- Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lina Lu
- Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qilong Chen
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hui Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qianmei Zhou
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yan Sun
- Qidong Liver Cancer Institute, Qidong People's Hospital, Qidong, China
| | - Xuefeng Xue
- Qidong Liver Cancer Institute, Qidong People's Hospital, Qidong, China
| | - Yiyang Hu
- Institute of Liver Disease, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Luonan Chen
- Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China.,Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai, China
| | - Shibing Su
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Amjad E, Asnaashari S, Sokouti B, Dastmalchi S. Systems biology comprehensive analysis on breast cancer for identification of key gene modules and genes associated with TNM-based clinical stages. Sci Rep 2020; 10:10816. [PMID: 32616754 PMCID: PMC7331704 DOI: 10.1038/s41598-020-67643-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 06/12/2020] [Indexed: 12/11/2022] Open
Abstract
Breast cancer (BC), as one of the leading causes of death among women, comprises several subtypes with controversial and poor prognosis. Considering the TNM (tumor, lymph node, metastasis) based classification for staging of breast cancer, it is essential to diagnose the disease at early stages. The present study aims to take advantage of the systems biology approach on genome wide gene expression profiling datasets to identify the potential biomarkers involved at stage I, stage II, stage III, and stage IV as well as in the integrated group. Three HER2-negative breast cancer microarray datasets were retrieved from the GEO database, including normal, stage I, stage II, stage III, and stage IV samples. Additionally, one dataset was also extracted to test the developed predictive models trained on the three datasets. The analysis of gene expression profiles to identify differentially expressed genes (DEGs) was performed after preprocessing and normalization of data. Then, statistically significant prioritized DEGs were used to construct protein-protein interaction networks for the stages for module analysis and biomarker identification. Furthermore, the prioritized DEGs were used to determine the involved GO enrichment and KEGG signaling pathways at various stages of the breast cancer. The recurrence survival rate analysis of the identified gene biomarkers was conducted based on Kaplan-Meier methodology. Furthermore, the identified genes were validated not only by using several classification models but also through screening the experimental literature reports on the target genes. Fourteen (21 genes), nine (17 genes), eight (10 genes), four (7 genes), and six (8 genes) gene modules (total of 53 unique genes out of 63 genes with involving those with the same connectivity degree) were identified for stage I, stage II, stage III, stage IV, and the integrated group. Moreover, SMC4, FN1, FOS, JUN, and KIF11 and RACGAP1 genes with the highest connectivity degrees were in module 1 for abovementioned stages, respectively. The biological processes, cellular components, and molecular functions were demonstrated for outcomes of GO analysis and KEGG pathway assessment. Additionally, the Kaplan-Meier analysis revealed that 33 genes were found to be significant while considering the recurrence-free survival rate as an alternative to overall survival rate. Furthermore, the machine learning calcification models show good performance on the determined biomarkers. Moreover, the literature reports have confirmed all of the identified gene biomarkers for breast cancer. According to the literature evidence, the identified hub genes are highly correlated with HER2-negative breast cancer. The 53-mRNA signature might be a potential gene set for TNM based stages as well as possible therapeutics with potentially good performance in predicting and managing recurrence-free survival rates at stages I, II, III, and IV as well as in the integrated group. Moreover, the identified genes for the TNM-based stages can also be used as mRNA profile signatures to determine the current stage of the breast cancer.
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Affiliation(s)
- Elham Amjad
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Solmaz Asnaashari
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Babak Sokouti
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Siavoush Dastmalchi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
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Wu J, Lv Q, Huang H, Zhu M, Meng D. Screening and Identification of Key Biomarkers in Inflammatory Breast Cancer Through Integrated Bioinformatic Analyses. Genet Test Mol Biomarkers 2020; 24:484-491. [PMID: 32598242 DOI: 10.1089/gtmb.2020.0047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background: Inflammatory breast cancer (IBC) is a rare type of breast cancer with poor prognoses, moreover its pathogenesis is not entirely clear. The aim of this study was to identify key genes of IBC, which might serve as diagnostic biomarkers and/or therapeutic targets. Methods: Two microarray datasets, GSE23720 and GSE45581, were obtained from the Gene Expression Omnibus database, and a differential expression analysis was performed. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to understand the potential biological functions of the differentially expressed genes (DEGs). Next, a protein-protein interaction (PPI) network was constructed and visualized by Cytoscape. Functional modules and hub genes were screened using MCODE and cytohubba plug-ins, and the Cancer Genome Atlas survival analysis along with quantitative reverse transcriptional polymerase chain reactions of clinical samples was used to validate the effect that the hub genes have on IBC. Results: A total of 215 DEGs were identified, consisting of 105 upregulated and 110 downregulated genes. GO and KEGG analyses showed that the enriched terms and pathways were mainly associated with cell cycle, proliferation, drug metabolism, and oncogenesis. From the PPI network, we identified six hub genes, including Cell Division Cycle 45 (CDC45), Polo Like Kinase 1 (PLK1), BUB1 Mitotic Checkpoint Serine/Threonine Kinase B (BUB1B), Cell Division Cycle 20 (CDC20), Aurora Kinase A (AURKA), and Mitotic Arrest Deficient 2 Like 1 (MAD2L1). The survival analyses and expression validation studies verified the robustness of these hub genes. Conclusion: This study provides new insights into the understanding of the molecular mechanisms of IBC; in addition, the identified hub genes may serve as potential targets for diagnosis and treatment.
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Affiliation(s)
- Junqiang Wu
- Department of Breast Surgery, The Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Qing Lv
- Department of Breast Surgery, The Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Hu Huang
- Department of Breast Surgery, The Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Mingjie Zhu
- Department of Breast Surgery, The Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Dong Meng
- Department of Breast Surgery, The Affiliated Hospital of Jiangnan University, Wuxi, China
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Lv Q, Liu Y, Huang H, Zhu M, Wu J, Meng D. Identification of Potential Key Genes and Pathways for Inflammatory Breast Cancer Based on GEO and TCGA Databases. Onco Targets Ther 2020; 13:5541-5550. [PMID: 32606769 PMCID: PMC7305851 DOI: 10.2147/ott.s255300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/18/2020] [Indexed: 11/23/2022] Open
Abstract
Introduction Inflammatory breast cancer (IBC) is a rare type of breast cancer with poor prognosis, and the pathogenesis of this life-threatening disease is yet to be fully elucidated. This study aims to identify key genes of IBC, which could be potential diagnostic or therapeutic targets. Methods Four datasets GSE5847, GSE22597, GSE23720, and GSE45581 were downloaded from the Gene Expression Omnibus (GEO) and differential expression analysis was performed. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to understand the potential bio-functions of the differentially expressed genes (DEGs). Protein-protein interaction (PPI) network was constructed for functional modules analysis and hub genes identification, and TCGA survival analysis and qRT-PCR of clinical samples were used to further explore and validate the effect of hub genes on IBC. Results A total of 114 DEGs were identified from the GEO datasets. GO and KEGG analyses showed that the DEGs were mainly enriched in oncogenesis and cell adhesion. From the PPI network, we screened out five hub genes, including PTPRC, IL6, SELL, CD40, and SPN. Survival analysis and expression validation verified the robustness of the hub genes. Discussion The present study provides new insight into the understanding of IBC pathogenesis and the identified hub genes may serve as potential targets for diagnosis and treatment.
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Affiliation(s)
- Qing Lv
- Department of Breast Surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, People's Republic of China
| | - Yansong Liu
- Department of Breast Surgery, Tumor Hospital of Mudanjiang City, Mudanjiang, Heilongjiang, People's Republic of China
| | - Hu Huang
- Department of Breast Surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, People's Republic of China
| | - Mingjie Zhu
- Department of Breast Surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, People's Republic of China
| | - Junqiang Wu
- Department of Breast Surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, People's Republic of China
| | - Dong Meng
- Department of Breast Surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, People's Republic of China
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Shi Y, Duan Z, Zhang X, Zhang X, Wang G, Li F. Down-regulation of the let-7i facilitates gastric cancer invasion and metastasis by targeting COL1A1. Protein Cell 2020; 10:143-148. [PMID: 29858755 PMCID: PMC6340894 DOI: 10.1007/s13238-018-0550-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Yue Shi
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, 130021, China
| | - Zipeng Duan
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, 130021, China
| | - Xun Zhang
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, 130021, China
| | - Xiaotian Zhang
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, 130021, China
| | - Guoqing Wang
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, 130021, China.
- The Key Laboratory for Bionics Engineering, Ministry of Education, Jilin University, Changchun, 130021, China.
| | - Fan Li
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, 130021, China.
- The Key Laboratory for Bionics Engineering, Ministry of Education, Jilin University, Changchun, 130021, China.
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Liu T, Ye P, Ye Y, Lu S, Han B. Circular RNA hsa_circRNA_002178 silencing retards breast cancer progression via microRNA-328-3p-mediated inhibition of COL1A1. J Cell Mol Med 2020; 24:2189-2201. [PMID: 31957232 PMCID: PMC7011152 DOI: 10.1111/jcmm.14875] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 09/12/2019] [Accepted: 11/12/2019] [Indexed: 01/06/2023] Open
Abstract
Circular RNAs (circRNAs) are a group of non-coding RNAs implicated in the pathogenesis of cancer progression, which exert their functions via regulation of microRNAs (miRNAs) and genes. The present study uses gain- and loss-of-function approaches to evaluate the functions of hsa_circRNA_002178 in angiogenesis along with energy metabolism and underlying downstream signals. The expression pattern of hsa_circRNA_002178 in clinical breast cancer tissues and its association with prognosis were characterized at first. Next, the energy metabolism and angiogenesis as well as cell viability were evaluated when the expression of hsa_circRNA_002178 in breast cancer cells was knocked down by siRNA. The interaction between hsa_circRNA_002178 and its downstream miR-328-3p was identified, followed by the analysis of their functions in regulation of breast cancer cellular behaviours. The target gene of miR-328-3p was predicted and verified, followed by identifying its role in the breast cancer progression. Higher expression of hsa_circRNA_002178 shared an association with worse prognosis in breast cancer. The inhibition of hsa_circRNA_002178 resulted in reductions in cell viability, energy metabolism and tube formation ability. Hsa_circRNA_002178 could competitively bind to miR-328-3p and down-regulated its expression. Restoration of miR-328-3p eliminated the tumour-promoting effects of hsa_circRNA_002178. COL1A1, as a target of miR-328-3p, could be up-regulated by overexpression of hsa_circRNA_002178. In vivo experiments further confirmed the inhibition of tumour growth and inflammation by silencing hsa_circRNA_002178 or up-regulating miR-328-3p. Taken together, hsa_circRNA_002178 is highlighted as a promising target for breast cancer due to the anti-tumour effects achieved by silencing hsa_circRNA_002178.
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Affiliation(s)
- Ting Liu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
| | - Ping Ye
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Yuanyuan Ye
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
| | - Sen Lu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
| | - Baosan Han
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
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11
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Yang CW, Cao HH, Guo Y, Feng YM, Zhang N. Identification of Novel Breast Cancer Genes based on Gene Expression Profiles and PPI Data. CURR PROTEOMICS 2019. [DOI: 10.2174/1570164616666190126111354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:Breast cancer is one of the most common malignancies, and a threat to female health all over the world. However, the molecular mechanism of breast cancer has not been fully discovered yet.Objective:It is crucial to identify breast cancer-related genes, which could provide new biomarker for breast cancer diagnosis as well as potential treatment targets.Methods:Here we used the minimum redundancy-maximum relevance (mRMR) method to select significant genes, then mapped the transcripts of the genes on the Protein-Protein Interaction (PPI) network and traced the shortest path between each pair of two proteins.Results:As a result, we identified 24 breast cancer-related genes whose betweenness were over 700. The GO enrichment analysis indicated that the transcription and oxygen level are very important in breast cancer. And the pathway analysis indicated that most of these 24 genes are enriched in prostate cancer, endocrine resistance, and pathways in cancer.Conclusion:We hope these 24 genes might be useful for diagnosis, prognosis and treatment for breast cancer.
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Affiliation(s)
- Cheng-Wen Yang
- Tianjin Key Lab of BME Measurement, Department of Biomedical Engineering, Tianjin University, Tianjin, China
| | - Huan-Huan Cao
- Tianjin Key Lab of BME Measurement, Department of Biomedical Engineering, Tianjin University, Tianjin, China
| | - Yu Guo
- Tianjin Key Lab of BME Measurement, Department of Biomedical Engineering, Tianjin University, Tianjin, China
| | - Yuan-Ming Feng
- Tianjin Key Lab of BME Measurement, Department of Biomedical Engineering, Tianjin University, Tianjin, China
| | - Ning Zhang
- Tianjin Key Lab of BME Measurement, Department of Biomedical Engineering, Tianjin University, Tianjin, China
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12
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Prospective molecular mechanism of COL5A1 in breast cancer based on a microarray, RNA sequencing and immunohistochemistry. Oncol Rep 2019; 42:151-175. [PMID: 31059074 PMCID: PMC6549075 DOI: 10.3892/or.2019.7147] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 04/16/2019] [Indexed: 12/11/2022] Open
Abstract
Breast cancer (BC) has a complex etiology and pathogenesis, and is the most common malignant tumor type in females, in USA in 2018, yet its relevant molecular mechanisms remain largely unknown. The collagen type V α-1 chain (COL5A1) gene is differentially expressed in renal and ovarian cancer. Using bioinformatics methods, COL5A1 was determined to also be a significant gene in BC, but its association with BC has not been sufficiently reported. COL5A1 microarray and relevant clinical data were collected from the Gene Expression Omnibus, The Cancer Genome Atlas and other databases to summarize COL5A1 expression in BC and its subtypes at the mRNA and protein levels. All associated information was comprehensively analyzed by various software. The clinical significance of the mutation was obtained via the cBioPortal. Furthermore, Gene Ontology functional annotation and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were also performed to investigate the mechanism of COL5A1 in BC. Immunohistochemistry was also conducted to detect and confirm COL5A1 expression. It was determined that COL5A1 was highly expressed in BC tissues, compared with normal tissues at the mRNA level [standard mean difference, 0.84; 95% confidence interval (CI), 0.60-1.07; P=0.108]. The area under the summary receiver operator characteristic curve for COL5A1 was 0.87 (95% CI, 0.84-0.90). COL5A1 expression was altered in 32/817 (4%) sequenced samples. KEGG analysis confirmed the most notable pathways, including focal adhesion, extracellular matrix-receptor interaction and regulation of the actin cytoskeleton. Immunohistochemical detection was used to verify the expression of COL5A1 in 136 selected cases of invasive BC tissues and 55 cases of adjacent normal tissues, while the rate of high expression of COL5A1 in BC was up to 90.4%. These results indicated that COL5A1 is highly expressed at the mRNA and protein levels in BC, and the prognosis of patients with BC with high COL5A1 expression may be reduced; therefore, COL5A1 may be used independently or combined with other detection factors in BC diagnosis.
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13
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Chen HC, Tseng YK, Shu CW, Weng TJ, Liou HH, Yen LM, Hsieh IC, Wang CC, Wu PC, Shiue YL, Fu TY, Tsai KW, Ger LP, Liu PF. Differential clinical significance of COL5A1 and COL5A2 in tongue squamous cell carcinoma. J Oral Pathol Med 2019; 48:468-476. [PMID: 30972812 DOI: 10.1111/jop.12861] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/26/2019] [Accepted: 04/04/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Type V collagen (COL5), in the functional heterotrimer [α1(V)2 α2(V)] isoform, participates in the malignancies of various cancers. However, its role in tongue squamous cell carcinoma (TSCC) remains unclear. MATERIALS AND METHODS The expression levels of COL5A1 and COL5A2 polypeptide chains were examined using the tissue microarray from 245 TSCC patients with immunohistochemistry. Paired t test and Wilcoxon signed-rank test were performed for comparisons among the groups. Survival rates were estimated by using the Kaplan-Meier method and compared with log-rank tests. A Cox proportional hazards model was used to evaluate the impact of protein expression level on survival rate. RESULTS Expression level of COL5A1 was significantly increased in tumor tissues (P < 0.001) compared to that in corresponding adjacent normal tissues. High expression level of COL5A1 was associated with advanced pathological stage (III, IV, P = 0.015) and lymph node metastasis (P = 0.005) of TSCC patients. High expression level of COL5A1 was also correlated with poor disease-specific survival (DSS, P = 0.001) and disease-free survival (DFS, P = 0.003) in TSCC patients. However, high expression level of COL5A2 was correlated with better DFS in TSCC patients (P = 0.043). Moreover, co-expression level of high (COL5A1)2 /low (COL5A2) heterotrimer was correlated with worse DSS (P = 0.004) and DFS (P = 0.004). CONCLUSION COL5A1 is an unfavorable factor for tumorigenesis, clinicopathological outcomes, and prognosis, whereas COL5A2 is only a favorable factor for prognosis in TSCC. The co-expression of high (COL5A1)2/low (COL5A2) heterotrimer is a more potential unfavorable factor for prognosis in TSCC.
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Affiliation(s)
- Hung-Chih Chen
- Division of Oral & Maxillary Surgery, Department of Stomatology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Dental Laboratory Technology, Shu Zen College of Medicine and Management, Kaohsiung, Taiwan
| | - Yu-Kai Tseng
- Department of Orthopedics, Show Chwan Memorial Hospital, Changhua, Taiwan.,Department of Orthopedics, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Chih-Wen Shu
- School of Medicine for International Students, I-Shou University, Kaohsiung, Taiwan.,Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Ta-Jung Weng
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan.,Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Huei-Han Liou
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Liang-Ming Yen
- Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - I-Chien Hsieh
- Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Cheng-Ching Wang
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Pi-Chuan Wu
- Department of Nutrition and Food Service, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Yow-Ling Shiue
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Ting-Ying Fu
- Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Kuo-Wang Tsai
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan.,Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Chemical Biology, National Pingtung University of Education, Pingtung, Taiwan
| | - Luo-Ping Ger
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan.,Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Pei-Feng Liu
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Oral Hygiene, Shu-Zen Junior College of Medicine and Management, Kaohsiung, Taiwan
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14
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Hao S, Lv J, Yang Q, Wang A, Li Z, Guo Y, Zhang G. Identification of Key Genes and Circular RNAs in Human Gastric Cancer. Med Sci Monit 2019; 25:2488-2504. [PMID: 30948703 PMCID: PMC6463957 DOI: 10.12659/msm.915382] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Globally, gastric cancer (GC) is the third most common source of cancer-associated mortality. The aim of this study was to identify key genes and circular RNAs (circRNAs) in GC diagnosis, prognosis, and therapy and to further explore the potential molecular mechanisms of GC. Material/Methods Differentially expressed genes (DEGs) and circRNAs (DE circRNAs) between GC tissues and adjacent non-tumor tissues were identified from 3 mRNA and 3 circRNA expression profiles. Functional analyses were performed, and protein–protein interaction (PPI) networks were constructed. The significant modules and key genes in the PPI networks were identified. Kaplan-Meier analysis was performed to evaluate the prognostic value of these key genes. Potential miRNA-binding sites of the DE circRNAs and target genes of these miRNAs were predicted and used to construct DE circRNA–miRNA–mRNA networks. Results A total of 196 upregulated and 311 downregulated genes were identified in GC. The results of functional analysis showed that these DEGs were significantly enriched in a variety of functions and pathways, including extracellular matrix-related pathways. Ten hub genes (COL1A1, COL3A1, COL1A2, COL5A2, FN1, THBS1, COL5A1, SPARC, COL18A1, and COL11A1) were identified via PPI network analysis. Kaplan-Meier analysis revealed that 7 of these were associated with a poor overall survival in GC patients. Furthermore, we identified 2 DE circRNAs, hsa_circ_0000332 and hsa_circ_0021087. To reveal the potential molecular mechanisms of circRNAs in GC, DE circRNA–microRNA–mRNA networks were constructed. Conclusions Key candidate genes and circRNAs were identified, and novel PPI and circRNA–microRNA–mRNA networks in GC were constructed. These may provide useful information for the exploration of potential biomarkers and targets for the diagnosis, prognosis, and therapy of GC.
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Affiliation(s)
- Shuhong Hao
- Department of Hematology and Oncology, The Second Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Junfeng Lv
- Department of Radiology, The Second Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Qiwei Yang
- Medical Research Center, The Second Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Ao Wang
- Department of Orthopedics, The Second Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Zhaoyan Li
- Department of Orthopedics, The Second Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Yuchen Guo
- Department of Gastrointestinal Surgery, The First Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Guizhen Zhang
- Medical Research Center, The Second Hospital of Jilin University, Changchun, Jilin, China (mainland).,Department of Orthopedics, The Second Hospital of Jilin University, Changchun, Jilin, China (mainland)
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15
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Van Berckelaer C, Rypens C, van Dam P, Pouillon L, Parizel M, Schats KA, Kockx M, Tjalma WAA, Vermeulen P, van Laere S, Bertucci F, Colpaert C, Dirix L. Infiltrating stromal immune cells in inflammatory breast cancer are associated with an improved outcome and increased PD-L1 expression. Breast Cancer Res 2019; 21:28. [PMID: 30777104 PMCID: PMC6380068 DOI: 10.1186/s13058-019-1108-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 01/25/2019] [Indexed: 11/10/2022] Open
Abstract
Background Inflammatory breast cancer (IBC) is a rare and rapidly progressive form of invasive breast cancer. The aim of this study was to explore the clinical evolution, stromal tumour-infiltrating lymphocytes (sTIL) infiltration and programmed death-ligand 1 (PD-L1) expression in a large IBC cohort. Patients and methods Data were collected prospectively from patients with IBC as part of an international collaborative effort since 1996. In total, 143 patients with IBC starting treatment between June 1996 and December 2016 were included. Clinicopathological variables were collected, and sTIL were scored by two pathologists on standard H&E stained sections. PD-L1 expression was assessed using a validated PD-L1 (SP142) assay. A validation cohort of 64 patients with IBC was used to test our findings. Results Survival outcomes of IBC remained poor with a 5-year overall survival (OS) of 45.6%. OS was significantly better in patients with primary non-metastatic disease who received taxane-containing (neo)adjuvant therapy (P = 0.01), had a hormone receptor-positive tumour (P = 0.001) and had lower cN stage at diagnosis (P = 0.001). PD-L1 positivity on immune cells (42.9%) was higher in IBC than in non-IBC in both our patient samples and the validation cohort. Furthermore, PD-L1 expression predicted pCR (P = 0.002) and correlated with sTIL infiltration (P < 0.001). sTIL infiltration of more than 10% of the stroma was a significant predictor of improved OS (HR 0.47, 95% CI 0.27–0.81, P = 0.006) in a multivariate model. Conclusions IBC is characterised by poor survival and high PD-L1 immunoreactivity on sTIL. This suggests a role for PD1/PD-L1 inhibitors in the treatment of IBC. Furthermore, we showed that PD-L1 expression predicts response to neo-adjuvant therapy and that sTIL have prognostic significance in IBC. Electronic supplementary material The online version of this article (10.1186/s13058-019-1108-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- C Van Berckelaer
- Translational Cancer Research Unit, GZA Hospitals & CORE, MIPRO, University of Antwerp, Antwerp, Belgium. .,Multidisciplinary Breast Clinic, Unit Gynaecologic Oncology, Antwerp University Hospital (UZA), Edegem, Belgium.
| | - C Rypens
- Translational Cancer Research Unit, GZA Hospitals & CORE, MIPRO, University of Antwerp, Antwerp, Belgium
| | - P van Dam
- Multidisciplinary Breast Clinic, Unit Gynaecologic Oncology, Antwerp University Hospital (UZA), Edegem, Belgium
| | - L Pouillon
- Department of Medical Oncology, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
| | - M Parizel
- Department of Pathology, Antwerp University Hospital (UZA), Edegem, Belgium
| | | | - M Kockx
- HistoGeneX, Antwerp, Belgium
| | - W A A Tjalma
- Multidisciplinary Breast Clinic, Unit Gynaecologic Oncology, Antwerp University Hospital (UZA), Edegem, Belgium
| | - P Vermeulen
- Translational Cancer Research Unit, GZA Hospitals & CORE, MIPRO, University of Antwerp, Antwerp, Belgium.,Department of Medical Oncology, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
| | - S van Laere
- Translational Cancer Research Unit, GZA Hospitals & CORE, MIPRO, University of Antwerp, Antwerp, Belgium
| | - F Bertucci
- Predictive Oncology team, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Marseille, France
| | - C Colpaert
- Department of Pathology, Antwerp University Hospital (UZA), Edegem, Belgium.,Department of Pathology, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
| | - L Dirix
- Translational Cancer Research Unit, GZA Hospitals & CORE, MIPRO, University of Antwerp, Antwerp, Belgium.,Department of Medical Oncology, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
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16
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Feng G, Ma HM, Huang HB, Li YW, Zhang P, Huang JJ, Cheng L, Li GR. Overexpression of COL5A1 promotes tumor progression and metastasis and correlates with poor survival of patients with clear cell renal cell carcinoma. Cancer Manag Res 2019; 11:1263-1274. [PMID: 30799953 PMCID: PMC6369854 DOI: 10.2147/cmar.s188216] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background and aims COL5A1 has been identified to be involved in metastasis of clear cell renal cell carcinoma (ccRCC) by bioinformatic analysis. This study aimed to investigate COL5A1 expression and its clinical significance in ccRCC. The function of COL5A1 in ccRCC was further investigated. Methods COL5A1 expression was examined in 256 ccRCC tissues and paired adjacent normal renal tissues by immunohistochemistry and real-time quantitative PCR. The clinical significance of COL5A1 expression was evaluated. Downregulation of COL5A1 was achieved using siRNA. The effects of COL5A1 silencing on cell proliferation, apoptosis, migration, invasion in vitro, and tumor growth in vivo were investigated. Results COL5A1 expression was upregulated in the majority of the ccRCC tissues at both protein and mRNA levels. COL5A1 expression was significantly correlated with tumor diameter, tumor stage, tumor grade, distant metastasis, recurrence, necrosis, and sarcomatoid (all P<0.05). COL5A1 expression was also significantly associated with overall survival of ccRCC patients (HR 1.876; P=0.027) and recurrence-free survival of localized ccRCC patients (HR 4.751; P<0.001). The accuracy of TNM, University of California Los Angeles Integrated Staging System, and Mayo clinic stage, size, grade, and necrosis prognostic models was improved when COL5A1 expression was added. Conclusion COL5A1 knockdown significantly inhibited cell proliferation, induced cell apoptosis, inhibited cell migration and invasion in vitro, and inhibited tumor growth in vivo. Therefore, COL5A1 may be a novel prognostic biomarker and a promising therapeutic target for ccRCC.
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Affiliation(s)
- Gang Feng
- Clinical Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu 241001, Anhui, China, .,Anhui Province Key Laboratory of Active Biological Macro-molecules Research, Wannan Medical College, Wuhu 241002, Anhui, China,
| | - Hui-Min Ma
- Clinical Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu 241001, Anhui, China,
| | - Hou-Bao Huang
- Department of Urology, The First Affiliated Hospital of Wannan Medical College, Wuhu 241001, Anhui, China
| | - Ya-Wei Li
- Department of Urology, The First Affiliated Hospital of Wannan Medical College, Wuhu 241001, Anhui, China
| | - Peng Zhang
- Clinical Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu 241001, Anhui, China,
| | - Jian-Jun Huang
- Clinical Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu 241001, Anhui, China,
| | - Long Cheng
- Clinical Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu 241001, Anhui, China, .,Anhui Province Key Laboratory of Active Biological Macro-molecules Research, Wannan Medical College, Wuhu 241002, Anhui, China,
| | - Guo-Rong Li
- Department of Urology, North Hospital, CHU of Saint-Etienne, Saint-Etienne 42055, France
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17
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Wang L, Hu X, Wang P, Shao ZM. Integrative 3' Untranslated Region-Based Model to Identify Patients with Low Risk of Axillary Lymph Node Metastasis in Operable Triple-Negative Breast Cancer. Oncologist 2018; 24:22-30. [PMID: 30082491 DOI: 10.1634/theoncologist.2017-0609] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 04/09/2018] [Accepted: 05/16/2018] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Sentinel lymph node biopsy is the standard surgical staging approach for operable triple-negative breast cancer (TNBC) with clinically negative axillae. In this study, we sought to develop a model to predict TNBC patients with negative nodal involvement, who would benefit from the exemption of the axillary staging surgery. MATERIALS AND METHODS We evaluated 3' untranslated region (3'UTR) profiles using microarray data of TNBC from two Gene Expression Omnibus datasets. Samples from GSE31519 were divided into training set (n = 164) and validation set (n = 163), and GSE76275 was used to construct testing set (n = 164). We built a six-member 3'UTR panel (ADD2, COL1A1, APOL2, IL21R, PKP2, and EIF4G3) using an elastic net model to estimate the risk of lymph node metastasis (LNM). Receiver operating characteristic and logistic analyses were used to assess the association between the panel and LNM status. RESULTS The six-member 3'UTR-panel showed a high distinguishing power with an area under the curve of 0.712, 0.729, and 0.708 in the training, validation, and testing sets, respectively. After adjustment by tumor size, the 3'UTR panel retained significant predictive power in the training, validation, and testing sets (odds ratio = 4.93, 4.58, and 3.59, respectively; p < .05 for all). A combinatorial analysis of the 3'UTR panel and tumor size yielded an accuracy of 97.2%, 100%, and 100% in training, validation, and testing set, respectively. CONCLUSION This study established an integrative 3'UTR-based model as a promising predictor for nodal negativity in operable TNBC. Although a prospective study is needed to validate the model, our results may permit a no axillary surgery option for selected patients. IMPLICATIONS FOR PRACTICE Currently, sentinel lymph node biopsy is the standard approach for surgical staging in breast cancer patients with negative axillae. Prediction estimation for lymph node metastasis of breast cancer relies on clinicopathological characteristics, which is unreliable, especially in triple-negative breast cancer (TNBC)-a highly heterogeneous disease. The authors developed and validated an effective prediction model for the lymph node status of patients with TNBC, which integrates 3'UTR markers and tumor size. This is the first 3'UTR-based model that will help identify TNBC patients with low risk of nodal involvement who are most likely to benefit from exemption axillary surgery.
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Affiliation(s)
- Lei Wang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Xin Hu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Peng Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Zhi-Ming Shao
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
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18
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Liu W, Wei H, Gao Z, Chen G, Liu Y, Gao X, Bai G, He S, Liu T, Xu W, Yang X, Jiao J, Xiao J. COL5A1 may contribute the metastasis of lung adenocarcinoma. Gene 2018; 665:57-66. [PMID: 29702185 DOI: 10.1016/j.gene.2018.04.066] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/09/2018] [Accepted: 04/23/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Lung cancer leads to the largest number of cancer-related deaths worldwide and is usually accompanied with metastasis which is the primary cause of those death and correlated with poor prognosis. However, the mechanism of lung cancer metastasis is still lack of definition. METHODS We compared the primary lung adenocarcinoma (AD) and its metastasis tissues induced by overexpression of KrasG12D and inactivation of P53 in mouse lungs by analyzing GSE40222 about the differentially expressed genes (DEGs), pathways and hub genes. And human lung AD databases are used to verify the conversed changes of identified key gene and then followed functional studies are performed to explore the functions of key gene. RESULTS We identified 165 genes differentially expressed in lung AD metastasis compared to primary AD. Pathway analysis identified 649 GO biological processes and 8 KEGG pathways, such as ECM-receptor interaction. Biological network interaction identified the hub genes during lung adenocarcinoma metastasis, such as the up-regulated COL5A1, a novel gene in AD metastasis. We found it's also increased in human AD and advanced stage. Knockdown of COL5A1 in human AD metastatic cells inhibited cell growth and invasion, and induced cell apoptosis. Notably, higher expression of COL5A1 was observed in the lung AD patients with recurrence and short survive. CONCLUSION By analyzing mouse lung AD and its metastases, we identified the potential key genes and pathways regulating lung AD metastasis, such as COL5A1. The following analysis of COL5A1 in human AD database and cells explores its functions, holding the implications of target therapy in AD metastasis and also providing more clues for future studies.
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Affiliation(s)
- Weibo Liu
- Department of Orthopedic Oncology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Haifeng Wei
- Department of Orthopedic Oncology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Zhengyu Gao
- Department of Rehabilitation, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
| | - Guanghui Chen
- Department of Orthopedic Oncology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Yujie Liu
- Department of Orthopedic Oncology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Xin Gao
- Department of Orthopedic Oncology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Guangjian Bai
- Department of Orthopedic Oncology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Shaohui He
- Department of Orthopedic Oncology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Tielong Liu
- Department of Orthopedic Oncology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Wei Xu
- Department of Orthopedic Oncology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China.
| | - Xinghai Yang
- Department of Orthopedic Oncology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China.
| | - Jian Jiao
- Department of Orthopedic Oncology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Jianru Xiao
- Department of Orthopedic Oncology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China.
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19
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Ren W, Zhang Y, Zhang L, Lin Q, Zhang J, Xu G. Overexpression of collagen type V α1 chain in human breast invasive ductal carcinoma is mediated by TGF-β1. Int J Oncol 2018; 52:1694-1704. [PMID: 29568948 DOI: 10.3892/ijo.2018.4317] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 03/13/2018] [Indexed: 11/06/2022] Open
Abstract
Collagen type V α1 chain (COL5A1) is a minor fibrillar collagen in mammals that co-polymerizes with type I collagen to adjust the diameter of collagen molecules. However, the function of COL5A1 in invasive ductal carcinoma (IDC) of the human breast remains unknown. In the present study, our group examined the expression of COL5A1 in IDC compared with its adjacent normal tissue and fibroadenoma of the breast. COL5A1 was revealed to be overexpressed in IDC compared with benign tumor and adjacent normal control tissues, and was associated with the expression of estrogen receptor and progesterone receptor. No association between COL5A1 expression and tumor size, lymph node metastasis, clinical stage, age, or Her2 expression was identified. High expression of COL5A1 mRNA was associated with distant metastasis free survival in patients with breast cancer. Knockdown of COL5A1 led to a decrease of cell viability, as detected by the WST-1 assay, and an inhibition of migration and invasion, as detected by wound healing and Transwell assays, respectively, in the breast cancer cell line MCF-7. The expression of COL5A1 in MCF-7 cells was downregulated by transforming growth factor (TGF)‑β1, which was abolished in the presence of SB-431542, an inhibitor of TGF-β type I receptor. In conclusion, these data indicated that COL5A1 is overexpressed in IDC and regulated by TGF-β1, suggesting that an increase of COL5A1 reflects tumor progression and may serve as a novel biomarker and therapeutic target for the treatment of breast IDC.
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Affiliation(s)
- Weimin Ren
- Center Laboratory, Jinshan Hospital, Fudan University, Shanghai 201508, P.R. China
| | - Youyuan Zhang
- Department of Pathology, Jinshan Hospital, Fudan University, Shanghai 201508, P.R. China
| | - Lingyun Zhang
- Center Laboratory, Jinshan Hospital, Fudan University, Shanghai 201508, P.R. China
| | - Qunbo Lin
- Center Laboratory, Jinshan Hospital, Fudan University, Shanghai 201508, P.R. China
| | - Jinguo Zhang
- Center Laboratory, Jinshan Hospital, Fudan University, Shanghai 201508, P.R. China
| | - Guoxiong Xu
- Center Laboratory, Jinshan Hospital, Fudan University, Shanghai 201508, P.R. China
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Doebar SC, Sieuwerts AM, de Weerd V, Stoop H, Martens JW, van Deurzen CH. Gene Expression Differences between Ductal Carcinoma in Situ with and without Progression to Invasive Breast Cancer. THE AMERICAN JOURNAL OF PATHOLOGY 2017. [DOI: 10.1016/j.ajpath.2017.03.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Elucidation of the Anti-Inflammatory Mechanisms of Bupleuri and Scutellariae Radix Using System Pharmacological Analyses. Mediators Inflamm 2017; 2017:3709874. [PMID: 28190938 PMCID: PMC5278517 DOI: 10.1155/2017/3709874] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/13/2016] [Accepted: 12/22/2016] [Indexed: 12/14/2022] Open
Abstract
Objective. This study was aimed at elucidating the molecular mechanisms underlying the anti-inflammatory effect of the combined application of Bupleuri Radix and Scutellariae Radix and explored the potential therapeutic efficacy of these two drugs on inflammation-related diseases. Methods. After searching the databases, we collected the active ingredients of Bupleuri Radix and Scutellariae Radix and calculated their oral bioavailability (OB) and drug-likeness (DL) based on the absorption-distribution-metabolism-elimination (ADME) model. In addition, we predicted the drug targets of the selected active components based on weighted ensemble similarity (WES) and used them to construct a drug-target network. Gene ontology (GO) analysis and KEGG mapper tools were performed on these predicted target genes. Results. We obtained 30 compounds from Bupleuri Radix and Scutellariae Radix of good quality as indicated by ADME assays, which possess potential pharmacological activity. These 30 ingredients have a total of 121 potential target genes, which are involved in 24 biological processes related to inflammation. Conclusions. Combined application of Bupleuri Radix and Scutellariae Radix was found not only to directly inhibit the synthesis and release of inflammatory cytokines, but also to have potential therapeutic effects against inflammation-induced pain. In addition, a combination therapy of these two drugs exhibited systemic treatment efficacy and provided a theoretical basis for the development of drugs against inflammatory diseases.
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Wang D, Wang J, Jiang Y, Liang Y, Xu D. BFDCA: A Comprehensive Tool of Using Bayes Factor for Differential Co-Expression Analysis. J Mol Biol 2016; 429:446-453. [PMID: 27984044 DOI: 10.1016/j.jmb.2016.10.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/22/2016] [Accepted: 10/23/2016] [Indexed: 10/20/2022]
Abstract
Comparing the gene-expression profiles between biological conditions is useful for understanding gene regulation underlying complex phenotypes. Along this line, analysis of differential co-expression (DC) has gained attention in the recent years, where genes under one condition have different co-expression patterns compared with another. We developed an R package Bayes Factor approach for Differential Co-expression Analysis (BFDCA) for DC analysis. BFDCA is unique in integrating various aspects of DC patterns (including Shift, Cross, and Re-wiring) into one uniform Bayes factor. We tested BFDCA using simulation data and experimental data. Simulation results indicate that BFDCA outperforms existing methods in accuracy and robustness of detecting DC pairs and DC modules. Results of using experimental data suggest that BFDCA can cluster disease-related genes into functional DC subunits and estimate the regulatory impact of disease-related genes well. BFDCA also achieves high accuracy in predicting case-control phenotypes by using significant DC gene pairs as markers. BFDCA is publicly available at http://dx.doi.org/10.17632/jdz4vtvnm3.1.
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Affiliation(s)
- Duolin Wang
- College of Computer Science and Technology, Jilin University, Changchun, China 130012; Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Juexin Wang
- Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Yuexu Jiang
- College of Computer Science and Technology, Jilin University, Changchun, China 130012; Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Yanchun Liang
- College of Computer Science and Technology, Jilin University, Changchun, China 130012; Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Dong Xu
- College of Computer Science and Technology, Jilin University, Changchun, China 130012; Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
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