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Wang T, Chen X, Jing F, Li Z, Tan H, Luo Y, Shi H. Identifying the hub genes in non-small cell lung cancer by integrated bioinformatics methods and analyzing the prognostic values. Pathol Res Pract 2021; 228:153654. [PMID: 34749208 DOI: 10.1016/j.prp.2021.153654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 10/07/2021] [Accepted: 10/09/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Lung cancer, a malignant tumor, has the highest mortality and second most common morbidity worldwide. Non-small cell lung cancer (NSCLC) is the most common pathological subtype of lung cancer. This study aimed to identify the gene signature associated with the NSCLC prognosis using bioinformatics analysis. MATERIALS AND METHODS The dataset GSE103512 was utilized to construct co-expression networks using weighted gene co-expression network analysis (WGCNA). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed using Database for Annotation, Visualization, and Integrated Discovery. Gene set enrichment analysis was conducted to ascertain the function of the hub genes more accurately. The relationship between the hub genes and immune infiltration was investigated using a single sample gene set enrichment analysis. Hub genes were screened and validated by other datasets and online websites. RESULTS The results of WGCNA demonstrated that the blue module was most significantly related to tumor progression in NSCLC. Functional enrichment analysis showed that the blue module was associated with DNA replication, cell division, mitotic nuclear division, and cell cycle. A total of five hub genes (RFC5, UBE2S, CHAF1A, FANCI, and TMEM194A) were chosen to be identified and validated at transcriptional and translational levels. Receiver operating characteristic curve verified that the mRNA levels of these five genes can excellently discriminate between normal and tumor tissues. Survival analysis was also performed. Additionally, the protein levels of these five genes were also significantly different between tumor and normal tissues. Immune infiltration analysis showed that the expression levels of the hub genes had a negative correlation with the infiltration levels of many cells related to innate immune response, antigen-presenting process, humoral immune response, or T cell-mediated immune responses. CONCLUSIONS We identified five hub genes associated with the NSCLC tumorigenesis. NSCLC patients with higher expressions of each hub gene had a worse prognosis than those with lower expressions. Moreover, the hub genes might serve as biomarkers and therapeutic targets for precise diagnosis, target therapy, and immunotherapy of NSCLC in the future.
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Affiliation(s)
- Tengyong Wang
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Xiaoxuan Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
| | - Fangqi Jing
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zehua Li
- West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Huaicheng Tan
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yiqiao Luo
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Huashan Shi
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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De Rienzo A, Coleman MH, Yeap BY, Severson DT, Wadowski B, Gustafson CE, Jensen RV, Chirieac LR, Richards WG, Bueno R. Association of RERG Expression with Female Survival Advantage in Malignant Pleural Mesothelioma. Cancers (Basel) 2021; 13:cancers13030565. [PMID: 33540554 PMCID: PMC7867122 DOI: 10.3390/cancers13030565] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 12/12/2022] Open
Abstract
Sex differences in incidence, prognosis, and treatment response have been described for many cancers. In malignant pleural mesothelioma (MPM), a lethal disease associated with asbestos exposure, men outnumber women 4 to 1, but women consistently live longer than men following surgery-based therapy. This study investigated whether tumor expression of genes associated with estrogen signaling could potentially explain observed survival differences. Two microarray datasets of MPM tumors were analyzed to discover estrogen-related genes associated with survival. A validation cohort of MPM tumors was selected to balance the numbers of men and women and control for competing prognostic influences. The RAS like estrogen regulated growth inhibitor (RERG) gene was identified as the most differentially-expressed estrogen-related gene in these tumors and predicted prognosis in discovery datasets. In the sex-matched validation cohort, low RERG expression was significantly associated with increased risk of death among women. No association between RERG expression and survival was found among men, and no relationship between estrogen receptor protein or gene expression and survival was found for either sex. Additional investigations are needed to elucidate the molecular mechanisms underlying this association and its sex specificity.
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Affiliation(s)
- Assunta De Rienzo
- Thoracic Surgery Oncology Laboratory and The International Mesothelioma Program, Division of Thoracic Surgery, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA; (M.H.C.); (D.T.S.); (B.W.); (C.E.G.); (W.G.R.); (R.B.)
- Correspondence: ; Tel.: +1-(617)-732-6526
| | - Melissa H. Coleman
- Thoracic Surgery Oncology Laboratory and The International Mesothelioma Program, Division of Thoracic Surgery, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA; (M.H.C.); (D.T.S.); (B.W.); (C.E.G.); (W.G.R.); (R.B.)
- Department of Surgery, University of California San Francisco, 500 Parnassus Ave, MUW 405, Box 0118, San Francisco, CA 94143, USA
| | - Beow Y. Yeap
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02114, USA;
| | - David T. Severson
- Thoracic Surgery Oncology Laboratory and The International Mesothelioma Program, Division of Thoracic Surgery, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA; (M.H.C.); (D.T.S.); (B.W.); (C.E.G.); (W.G.R.); (R.B.)
| | - Benjamin Wadowski
- Thoracic Surgery Oncology Laboratory and The International Mesothelioma Program, Division of Thoracic Surgery, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA; (M.H.C.); (D.T.S.); (B.W.); (C.E.G.); (W.G.R.); (R.B.)
| | - Corinne E. Gustafson
- Thoracic Surgery Oncology Laboratory and The International Mesothelioma Program, Division of Thoracic Surgery, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA; (M.H.C.); (D.T.S.); (B.W.); (C.E.G.); (W.G.R.); (R.B.)
| | - Roderick V. Jensen
- Department of Biological Sciences, Virginia Tech, 970 Washington Street SW, Blacksburg, VA 24061, USA;
| | - Lucian R. Chirieac
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA;
| | - William G. Richards
- Thoracic Surgery Oncology Laboratory and The International Mesothelioma Program, Division of Thoracic Surgery, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA; (M.H.C.); (D.T.S.); (B.W.); (C.E.G.); (W.G.R.); (R.B.)
| | - Raphael Bueno
- Thoracic Surgery Oncology Laboratory and The International Mesothelioma Program, Division of Thoracic Surgery, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA; (M.H.C.); (D.T.S.); (B.W.); (C.E.G.); (W.G.R.); (R.B.)
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Liu C, Chen Y, Deng Y, Dong Y, Jiang J, Chen S, Kang W, Deng J, Sun H. Survival-based bioinformatics analysis to identify hub genes and key pathways in non-small cell lung cancer. Transl Cancer Res 2019; 8:1188-1198. [PMID: 35116861 PMCID: PMC8797769 DOI: 10.21037/tcr.2019.06.35] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/21/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND Lung cancer is one of the leading causes of cancer mortality worldwide. Here, we performed an integrative bioinformatics analysis to screen hub genes and critical pathways in non-small cell lung cancer (NSCLC) based on the overall survival rate of differentially expressed genes (DEGs). METHODS Four datasets from the gene expression omnibus (GEO) were used to identify the DEGs. To obtain robust DEGs in NSCLC, only the DEGs that co-existed in the four datasets were selected for subsequent analysis. To identify the genes correlated with overall survival, the overall survival of these genes was then analyzed using the Kaplan-Meier plotter database. The genes significantly correlated with survival were used to perform gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analysis; next, these genes were used to construct a protein-protein interaction network. MCODE and CytoHubba were used to identify the clusters and hub genes. Finally, the hub genes were validated in the Cancer Genome Atlas (TCGA) and the Human Protein Atlas (HPA). RESULTS We found 522 up-regulated DEGs, and 989 down-regulated DEGs between the NSCLC and normal lung tissue, and 895 of them were correlated with a higher overall survival. GO analysis showed that the DEGs that were associated with a higher overall survival were enriched in cell division, cell cycle, DNA replication, angiogenesis, and cell migration. KEGG analysis was consistent with GO analysis and showed that p53 signaling pathway, pyrimidine metabolism, cGMP-PKG signaling pathway and renin secretion pathway were associated with overall survival in NSCLC. In the protein-protein analysis, we identified seven clusters and six hub genes which were BUB1B, CCNB1, CENPE, KIF18A, NDC10, and MAD2L1. Of these genes, CENPE and KIF18A had not been reported until now. Finally, the dysregulated expression of the six hub genes was validated by the data from the TCGA and HPA. CONCLUSIONS We identified the hub genes and potential mechanisms of NSCLC based on multiple-microarray analysis and overall survival; then, validated the hub genes in the TCGA and HPA database. These hub genes may serve as potential therapeutic targets.
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Affiliation(s)
- Chunliang Liu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu Chen
- Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yuqi Deng
- Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu Dong
- Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jixuan Jiang
- Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Si Chen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Wenfeng Kang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jiong Deng
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Haipeng Sun
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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Jasmine R, Manikandan K, Karthikeyan. Evaluating the antioxidant and anticancer property of Ficus carica fruits. ACTA ACUST UNITED AC 2015. [DOI: 10.5897/ajb2014.13742] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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De Rienzo A, Richards WG, Yeap BY, Coleman MH, Sugarbaker PE, Chirieac LR, Wang YE, Quackenbush J, Jensen RV, Bueno R. Sequential binary gene ratio tests define a novel molecular diagnostic strategy for malignant pleural mesothelioma. Clin Cancer Res 2013; 19:2493-502. [PMID: 23493352 DOI: 10.1158/1078-0432.ccr-12-2117] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE To develop a standardized approach for molecular diagnostics, we used the gene expression ratio bioinformatic technique to design a molecular signature to diagnose malignant pleural mesothelioma (MPM) from among other potentially confounding diagnoses and differentiate the epithelioid from the sarcomatoid histologic subtype of MPM. In addition, we searched for pathways relevant in MPM in comparison with other related cancers to identify unique molecular features in MPM. EXPERIMENTAL DESIGN We conducted microarray analysis on 113 specimens including MPMs and a spectrum of tumors and benign tissues comprising the differential diagnosis of MPM. We generated a sequential combination of binary gene expression ratio tests able to discriminate MPM from other thoracic malignancies. We compared this method with other bioinformatic tools and validated this signature in an independent set of 170 samples. Functional enrichment analysis was conducted to identify differentially expressed probes. RESULTS A sequential combination of gene expression ratio tests was the best molecular approach to distinguish MPM from all the other samples. Bioinformatic and molecular validations showed that the sequential gene ratio tests were able to identify the MPM samples with high sensitivity and specificity. In addition, the gene ratio technique was able to differentiate the epithelioid from the sarcomatoid type of MPM. Novel genes and pathways specifically activated in MPM were identified. CONCLUSIONS New clinically relevant molecular tests have been generated using a small number of genes to accurately distinguish MPMs from other thoracic samples, supporting our hypothesis that the gene expression ratio approach could be a useful tool in the differential diagnosis of cancers.
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Affiliation(s)
- Assunta De Rienzo
- The Thoracic Surgery Oncology Laboratory, and International Mesothelioma Program, Division of Thoracic Surgery, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts 02115, USA
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Hashemi SA, Abediankenari S, Ghasemi M, Azadbakht M, Yousefzadeh Y, Dehpour AA. The Effect of Fig Tree Latex (Ficus carica) on Stomach Cancer Line. IRANIAN RED CRESCENT MEDICAL JOURNAL 2011; 13:272-5. [PMID: 22737478 PMCID: PMC3371962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Revised: 01/02/2011] [Accepted: 01/10/2011] [Indexed: 12/03/2022]
Abstract
BACKGROUND The therapeutic effect of herbal materials in inhibition of cancer cell growth was shown. This study investigates the effect of fig tree latex (Ficus carica) on stomach cancer line. METHODS The in vitro effect of different doses of fig tree latex on stomach cancer cell line and the peripheral blood mononuclear cells was evaluated after 72 hours. RESULTS Fig tree latex could inhibit the proliferation of cancer cell line without any cytotoxic effect on human normal cells. Five mg/ml was the optimum concentration in inhibition of cell line growth. CONCLUSION Cancer cell line was more sensitive to Ficus carica latex than normal cells. This anticancer activity might be due to presence of its proteolytic enzymes.
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Affiliation(s)
- S A Hashemi
- Department of Microbiology and Immunology, Mazandaran University of Medical Sciences, Sari, Iran
| | - S Abediankenari
- Department of Microbiology and Immunology, Mazandaran University of Medical Sciences, Sari, Iran,Correspondence: Saeid Abediankenari, PhD Assistant Professor of Immunology, Department of Microbiology and Immunology, Mazandaran University of Medical Sciences, Sari, Iran, Tel: +98-912-1985667, E-mail:
| | - M Ghasemi
- Department of Pathology, Mazandaran University of Medical Sciences, Sari, Iran
| | - M Azadbakht
- Department of Pharmacogenosy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Y Yousefzadeh
- Department of Microbiology and Immunology, Mazandaran University of Medical Sciences, Sari, Iran
| | - A A Dehpour
- Department of Biology, Islamic Azad University, Ghaemshahr Branch, Ghaemshahr, Iran
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