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Jin YB, Liang XC, Cai JH, Wang K, Wang CY, Wang WH, Chen XL, Bao S. Mechanism of action of icaritin on uterine corpus endometrial carcinoma based on network pharmacology and experimental evaluation. Front Oncol 2023; 13:1205604. [PMID: 37538114 PMCID: PMC10394632 DOI: 10.3389/fonc.2023.1205604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/28/2023] [Indexed: 08/05/2023] Open
Abstract
Background Uterine corpus endometrial carcinoma (UCEC) belongs to a group of epithelial malignant tumors. Icaritin is the main active compound of Epimedii Folium. Icaritin has been utilized to induce UCEC cells to death. Methods We wished to identify potential targets for icaritin in the treatment of UCEC, as well as to provide a groundwork for future studies into its pharmacologic mechanism of action. Network pharmacology was employed to conduct investigations on icaritin. Target proteins were chosen from the components of icaritin for UCEC treatment. A protein-protein interaction (PPI) network was established using overlapping genes. Analyses of enrichment of function and signaling pathways were undertaken using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively, to select "hub genes". Finally, experiments were carried out to ascertain the effect of icaritin on endometrial cancer (HEC-1-A) cells. Results We demonstrated that icaritin has bioactive components and putative targets that are therapeutically important. Icaritin treatment induced sustained activation of the phosphoinositide 3-kinase/protein kinase B (PI3K/Akt pathway) and inhibited growth of HEC-1-A cells. Conclusion Our data provide a rationale for preclinical and clinical evaluations of icaritin for UCEC therapy.
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Affiliation(s)
- Yan-Bin Jin
- Department of Gynecology and Obstetrics, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
- Key Laboratory of Reproductive Health Diseases Research and Translation (Hainan Medical University), Ministry of Education, Haikou, Hainan, China
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China
- Medical Laboratory Center, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
| | - Xiao-Chen Liang
- Department of Gynecology and Obstetrics, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
- Key Laboratory of Reproductive Health Diseases Research and Translation (Hainan Medical University), Ministry of Education, Haikou, Hainan, China
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China
- Medical Laboratory Center, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
| | - Jun-Hong Cai
- Medical Laboratory Center, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
| | - Kang Wang
- Department of Gynecology and Obstetrics, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
| | - Chen-Yang Wang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Wen-Hua Wang
- Department of Obstetrics and Gynecology, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Xiu-Li Chen
- Department of Gynecology and Obstetrics, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
- Key Laboratory of Reproductive Health Diseases Research and Translation (Hainan Medical University), Ministry of Education, Haikou, Hainan, China
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China
- Medical Laboratory Center, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
| | - Shan Bao
- Department of Gynecology and Obstetrics, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
- Key Laboratory of Reproductive Health Diseases Research and Translation (Hainan Medical University), Ministry of Education, Haikou, Hainan, China
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China
- Medical Laboratory Center, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
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Ding Y, Li X, Li J. COVID-19–associated lncRNAs as predictors of survival in uterine corpus endometrial carcinoma: A prognostic model. Front Genet 2022; 13:986453. [PMID: 36147497 PMCID: PMC9486303 DOI: 10.3389/fgene.2022.986453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/08/2022] [Indexed: 12/05/2022] Open
Abstract
Background: Patients with uterine corpus endometrial carcinoma (UCEC) may be susceptible to the coronavirus disease-2019 (COVID-19). Long non–coding RNAs take on a critical significance in UCEC occurrence, development, and prognosis. Accordingly, this study aimed to develop a novel model related to COVID-19–related lncRNAs for optimizing the prognosis of endometrial carcinoma. Methods: The samples of endometrial carcinoma patients and the relevant clinical data were acquired in the Carcinoma Genome Atlas (TCGA) database. COVID-19–related lncRNAs were analyzed and obtained by coexpression. Univariate, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analyses were performed to establish a COVID-19–related lncRNA risk model. Kaplan–Meier analysis, principal component analysis (PCA), and functional enrichment annotation were used to analyze the risk model. Finally, the potential immunotherapeutic signatures and drug sensitivity prediction targeting this model were also discussed. Results: The risk model comprising 10 COVID-19–associated lncRNAs was identified as a predictive ability for overall survival (OS) in UCEC patients. PCA analysis confirmed a reliable clustering ability of the risk model. By regrouping the patients with this model, different clinic-pathological characteristics, immunotherapeutic response, and chemotherapeutics sensitivity were also observed in different groups. Conclusion: This risk model was developed based on COVID-19–associated lncRNAs which would be conducive to the precise treatment of patients with UCEC.
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Affiliation(s)
- Yang Ding
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shatin, HongKong, China
| | - Xia Li
- Department of Obstetrics and Gynaecology, Heze Municipal Hospital, Heze, Shandong, China
| | - Jiena Li
- Department of Obstetrics and Gynaecology, Heze Municipal Hospital, Heze, Shandong, China
- *Correspondence: Jiena Li, ; Liqun Zhu,
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Novel DNA Damage-Related Subtypes Characterization Identifies Uterine Corpus Endometrial Carcinoma (UCEC) Based on Machine Learning. JOURNAL OF ONCOLOGY 2022; 2022:3588117. [PMID: 36072975 PMCID: PMC9441400 DOI: 10.1155/2022/3588117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/14/2022] [Accepted: 07/18/2022] [Indexed: 11/17/2022]
Abstract
Objective. Accumulating evidence suggests that DNA damage is associated with numerous gynecological illnesses, particularly advanced uterine corpus endometrial carcinoma (UCEC), illustrating the involvement of the DNA damage pathway in the advancement of UCEC. This research aimed to discover a robust subtype with the potential to contribute to the scientific treatment of UCEC. Methods. In this work, the expression patterns of prognostic DNA damage-related genes were curated, and consensus clustering analyses were undertaken to determine DNA damage subtypes in patients with UCEC in the TCGA cohort. Two DNA damage-related subtypes were identified for further investigation. Differentially expressed genes (DEGs) analysis, gene ontology analysis, mutation analysis, and immune cell infraction analysis were performed to find the molecular mechanism behind it. Finally, the polymerase chain reaction (PCR) was conducted to verify the correlation of the hub genes. Results. In total, 545 patients with UCEC were tested for two distinct DNA damage subtypes. The clinical prognosis was poorer among patients with DNA damage subtype 2 than those in subtype 1. The DEGs analysis and PPI analysis showed that ASMP, BUB1, CENPF, MAD2L1, NCAPG, SGO2, and TOP2A were expressed higher in UCEC tissues than in the normal tissues. Immune cell infraction analysis showed that hub genes were associated with the tumor microenvironment (TME). Conclusion. Altogether, our research identified two distinct DNA damage subtypes that are complicated and heterogeneous. A better knowledge of the characteristics of the TME may be gained by quantitative measurement of DNA damage subtypes in individual patients, which can also lead to the development of more successful treatment regimens.
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Dong Y, Zhang T, Li X, Yu F, Yu H, Shao S. Identification of Key Prognostic-Related miRNA-mRNA Pairs in the Progression of Endometrial Carcinoma. Gynecol Obstet Invest 2022; 87:12-21. [PMID: 35081534 DOI: 10.1159/000520339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 10/19/2021] [Indexed: 11/19/2022]
Abstract
OBJECTIVES Endometrial carcinoma (EC) is one of the leading causes of death from gynecological cancer due to the high recurrence rate. However, the molecular mechanisms of EC progression are not well understood. This study aimed to identify critical genes and miRNAs associated with the progression and prognosis of EC and find the potential mRNA-miRNA regulatory relationship. DESIGN The mRNA and miRNA data were downloaded from The Cancer Genome Atlas (TCGA) database. Next, differentially expressed genes (DEGs) were identified. Subsequently, prognosis-related genes and miRNAs were identified, followed by co-expression analysis of these mRNAs and miRNAs. Materials, Setting, and Methods: Samples in the mRNA microarray were divided into normal (n = 35), early stage (n = 385), and advanced stage (n = 153). Next, DEGs in normal versus early stage and early stage versus advanced stage were, respectively, identified, followed by Venn analysis to screen overlapping DEGs in 2 comparison groups. Based on the expression level of these DEGs, univariate Cox regression analysis and Kaplan-Meier method were performed to obtain prognosis-related genes. Moreover, genes-related miRNAs were predicted, and miRNA-mRNA co-expressed pairs were identified. Then, survival analysis of co-expressed miRNA was performed. Finally, co-expressed genes of key genes were identified, and then functional enrichment analysis was conducted. RESULTS After integrating analysis, 326 overlapping (309 upregulated and 17 downregulated) DEGs were obtained. Univariate Cox regression analysis showed that 44 mRNAs and 8 miRNAs were associated with the prognosis of EC. Combined with the co-expressed analysis, only one prognosis-related hsa-miR-326/ELFN2 axis was obtained. In addition, functional enrichment analysis showed that co-expressed genes of ELFN2 were mainly involved in the PI3K-Akt signaling pathway. LIMITATIONS These findings were obtained via bioinformatics analysis, and thus further experimental studies are urgently demanded to validate our results. CONCLUSIONS One key miRNA-mRNA regulatory pair (hsa-miR-326-ELFN2) was screened. This study provided a bioinformatics basis for the molecular mechanism of EC progression and might contribute to the identification of novel therapeutic targets.
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Affiliation(s)
- Ying Dong
- Schools of Medicine and Nursing Sciences, Huzhou University, Huzhou Central Hospital, Huzhou, China
| | - Ting Zhang
- Schools of Medicine and Nursing Sciences, Huzhou University, Huzhou, China
| | - Xining Li
- Schools of Medicine and Nursing Sciences, Huzhou University, Huzhou, China
| | - Feng Yu
- Schools of Medicine and Nursing Sciences, Huzhou University, Huzhou, China
| | - Hongwei Yu
- Schools of Medicine and Nursing Sciences, Huzhou University, Huzhou, China
| | - Shengwen Shao
- Schools of Medicine and Nursing Sciences, Huzhou University, Huzhou, China
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Coll-de la Rubia E, Martinez-Garcia E, Dittmar G, Nazarov PV, Bebia V, Cabrera S, Gil-Moreno A, Colás E. In silico Approach for Validating and Unveiling New Applications for Prognostic Biomarkers of Endometrial Cancer. Cancers (Basel) 2021; 13:5052. [PMID: 34680205 PMCID: PMC8534093 DOI: 10.3390/cancers13205052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/29/2021] [Accepted: 10/02/2021] [Indexed: 12/20/2022] Open
Abstract
Endometrial cancer (EC) mortality is directly associated with the presence of prognostic factors. Current stratification systems are not accurate enough to predict the outcome of patients. Therefore, identifying more accurate prognostic EC biomarkers is crucial. We aimed to validate 255 prognostic biomarkers identified in multiple studies and explore their prognostic application by analyzing them in TCGA and CPTAC datasets. We analyzed the mRNA and proteomic expression data to assess the statistical prognostic performance of the 255 proteins. Significant biomarkers related to overall survival (OS) and recurrence-free survival (RFS) were combined and signatures generated. A total of 30 biomarkers were associated either to one or more of the following prognostic factors: histological type (n = 15), histological grade (n = 6), FIGO stage (n = 1), molecular classification (n = 16), or they were associated to OS (n = 11), and RFS (n = 5). A prognostic signature composed of 11 proteins increased the accuracy to predict OS (AUC = 0.827). The study validates and identifies new potential applications of 30 proteins as prognostic biomarkers and suggests to further study under-studied biomarkers such as TPX2, and confirms already used biomarkers such as MSH6, MSH2, or L1CAM. These results are expected to advance the quest for biomarkers to accurately assess the risk of EC patients.
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Affiliation(s)
- Eva Coll-de la Rubia
- Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona, CIBERONC, 08035 Barcelona, Spain; (S.C.); (A.G.-M.)
| | - Elena Martinez-Garcia
- Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (E.M.-G.); (G.D.); (P.V.N.)
| | - Gunnar Dittmar
- Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (E.M.-G.); (G.D.); (P.V.N.)
| | - Petr V. Nazarov
- Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (E.M.-G.); (G.D.); (P.V.N.)
| | - Vicente Bebia
- Gynaecological Department, Vall Hebron University Hospital, CIBERONC, 08035 Barcelona, Spain;
| | - Silvia Cabrera
- Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona, CIBERONC, 08035 Barcelona, Spain; (S.C.); (A.G.-M.)
- Gynaecological Department, Vall Hebron University Hospital, CIBERONC, 08035 Barcelona, Spain;
| | - Antonio Gil-Moreno
- Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona, CIBERONC, 08035 Barcelona, Spain; (S.C.); (A.G.-M.)
- Gynaecological Department, Vall Hebron University Hospital, CIBERONC, 08035 Barcelona, Spain;
| | - Eva Colás
- Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona, CIBERONC, 08035 Barcelona, Spain; (S.C.); (A.G.-M.)
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Li R, Liao B, Wang B, Dai C, Liang X, Tian G, Wu F. Identification of Tumor Tissue of Origin with RNA-Seq Data and Using Gradient Boosting Strategy. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6653793. [PMID: 33681364 PMCID: PMC7904362 DOI: 10.1155/2021/6653793] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/19/2021] [Accepted: 02/06/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND Cancer of unknown primary (CUP) is a type of malignant tumor, which is histologically diagnosed as a metastatic carcinoma while the tissue-of-origin cannot be identified. CUP accounts for roughly 5% of all cancers. Traditional treatment for CUP is primarily broad-spectrum chemotherapy; however, the prognosis is relatively poor. Thus, it is of clinical importance to accurately infer the tissue-of-origin of CUP. METHODS We developed a gradient boosting framework to trace tissue-of-origin of 20 types of solid tumors. Specifically, we downloaded the expression profiles of 20,501 genes for 7713 samples from The Cancer Genome Atlas (TCGA), which were used as the training data set. The RNA-seq data of 79 tumor samples from 6 cancer types with known origins were also downloaded from the Gene Expression Omnibus (GEO) for an independent data set. RESULTS 400 genes were selected to train a gradient boosting model for identification of the primary site of the tumor. The overall 10-fold cross-validation accuracy of our method was 96.1% across 20 types of cancer, while the accuracy for the independent data set reached 83.5%. CONCLUSION Our gradient boosting framework was proven to be accurate in identifying tumor tissue-of-origin on both training data and independent testing data, which might be of practical usage.
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Affiliation(s)
- Ruixi Li
- School of Mathematics and Statistics, Hainan Normal University, Haikou 570100, China
- Key Laboratory of Computational Science and Application of Hainan Province, Haikou 571158, China
- Key Laboratory of Data Science and Intelligence Education (Hainan Normal University), Ministry of Education, Haikou 571158, China
| | - Bo Liao
- School of Mathematics and Statistics, Hainan Normal University, Haikou 570100, China
- Key Laboratory of Computational Science and Application of Hainan Province, Haikou 571158, China
- Key Laboratory of Data Science and Intelligence Education (Hainan Normal University), Ministry of Education, Haikou 571158, China
| | - Bo Wang
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao 266000, China
- Geneis (Beijing) Co., Ltd., Beijing 100102, China
| | - Chan Dai
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao 266000, China
- Geneis (Beijing) Co., Ltd., Beijing 100102, China
| | - Xin Liang
- School of Mathematics and Statistics, Hainan Normal University, Haikou 570100, China
- Key Laboratory of Computational Science and Application of Hainan Province, Haikou 571158, China
- Key Laboratory of Data Science and Intelligence Education (Hainan Normal University), Ministry of Education, Haikou 571158, China
| | - Geng Tian
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao 266000, China
- Geneis (Beijing) Co., Ltd., Beijing 100102, China
| | - Fangxiang Wu
- School of Mathematics and Statistics, Hainan Normal University, Haikou 570100, China
- Key Laboratory of Computational Science and Application of Hainan Province, Haikou 571158, China
- Key Laboratory of Data Science and Intelligence Education (Hainan Normal University), Ministry of Education, Haikou 571158, China
- Division of Biomedical Engineering, Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, SK, S7N5A9, Canada
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Wang Y, Liang N, Xue Z, Xue X. Identifying an Eight-Gene Signature to Optimize Overall Survival Prediction of Esophageal Adenocarcinoma Using Bioinformatics Analysis of ceRNA Network. Onco Targets Ther 2020; 13:13041-13054. [PMID: 33376353 PMCID: PMC7764560 DOI: 10.2147/ott.s287084] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 11/29/2020] [Indexed: 12/31/2022] Open
Abstract
Background and Aims Esophageal adenocarcinoma (EAC) patients usually have a poor prognosis without early diagnosis. In this study, we aimed to identify a novel signature to improve the prediction of overall survival (OS) in EAC. Methods Eighty-one and 68 samples from The Cancer Genome Atlas (TCGA) and GSE19417 dataset were included for discovery and survival validation, respectively. In the TCGA cohort, a total of 1,811 DEmRNAs, 1,096 DElncRNAs, and 31 DEmiRNAs were identified between EAC and normal esophagus tissues. A mRNA–miRNA–lncRNA ceRNA network of EAC was established, which consisted of 94 DEmRNAs, 13 DEmiRNAs, and 46 DElncRNAs. Results In this study, we identified eight genes (UBE2B, LAMP2, B3GNT2, TAF9B, EFNA1, PHF8, PIGA, and NEURL1) which were related to survival in EAC. The independent external microarray data from the Gene Expression Omnibus (GEO) was used to validate these candidate genes. The prognostic ability of the signature was also validated in EAC patients in our hospital. Patients assigned to the high-risk group had a poor overall survival rate compared with the low-risk. Conclusion The current study provides novel insights into the mRNA-related ceRNA network in EAC and the eight mRNA biomarkers may be independent prognostic signatures in predicting the survival of EAC patients.
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Affiliation(s)
- Yuanyong Wang
- Department of Thoracic Surgery, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Naixin Liang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Zhiqiang Xue
- Department of Thoracic Surgery, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Xinying Xue
- Department of Respiratory Disease, Beijing Shijitan Hospital, Capital Medical University, Beijing, People's Republic of China.,Department of Respiratory Disease, School of Clinical Medicine, Weifang Medical University, Weifang, Shandong, People's Republic of China
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Kołat D, Kałuzińska Ż, Orzechowska M, Bednarek AK, Płuciennik E. Functional genomics of AP-2α and AP-2γ in cancers: in silico study. BMC Med Genomics 2020; 13:174. [PMID: 33213447 PMCID: PMC7678100 DOI: 10.1186/s12920-020-00823-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/12/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Among all causes of death, cancer is the most prevalent and is only outpaced by cardiovascular diseases. Molecular theory of carcinogenesis states that apoptosis and proliferation are regulated by groups of tumor suppressors or oncogenes. Transcription factors are example of proteins comprising representatives of both cancer-related groups. Exemplary family of transcription factors which exhibits dualism of function is Activating enhancer-binding Protein 2 (AP-2). Scientific reports concerning their function in carcinogenesis depend on particular family member and/or tumor type which proves the issue to be unsolved. Therefore, the present study examines role of the best-described AP-2 representatives, AP-2α and AP-2γ, through ontological analysis of their target genes and investigation what processes are differentially regulated in 21 cancers using samples deposited in Genomic Data Analysis Center (GDAC) Firehose. METHODS Expression data with clinical annotation was collected from TCGA-dedicated repository GDAC Firehose. Transcription factor targets were obtained from Gene Transcription Regulation Database (GTRD), TRANScription FACtor database (TRANSFAC) and Transcriptional Regulatory Relationships Unraveled by Sentence-based Text mining (TRRUST). Monocle3 R package was used for global samples profiling while Protein ANalysis THrough Evolutionary Relationships (PANTHER) tool was used to perform gene ontology analysis. RESULTS With RNA-seq data and Monocle3 or PANTHER tools we outlined differences in many processes and signaling pathways, separating tumor from normal tissues or tumors from each other. Unexpectedly, a number of alterations in basal-like breast cancer were identified that distinguished it from other subtypes, which could bring future clinical benefits. CONCLUSIONS Our findings indicate that while the AP-2α/γ role remains ambiguous, their activity is based on processes that underlie the cancer hallmarks and their expression could have potential in diagnosis of selected tumors.
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Affiliation(s)
- Damian Kołat
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752, Lodz, Poland.
| | - Żaneta Kałuzińska
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752, Lodz, Poland
| | - Magdalena Orzechowska
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752, Lodz, Poland
| | - Andrzej K Bednarek
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752, Lodz, Poland
| | - Elżbieta Płuciennik
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752, Lodz, Poland
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Zeng H, Ji J, Song X, Huang Y, Li H, Huang J, Ma X. Stemness Related Genes Revealed by Network Analysis Associated With Tumor Immune Microenvironment and the Clinical Outcome in Lung Adenocarcinoma. Front Genet 2020; 11:549213. [PMID: 33193623 PMCID: PMC7525184 DOI: 10.3389/fgene.2020.549213] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/24/2020] [Indexed: 02/05/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is one of the leading fatal malignancy with high morbidity and mortality worldwide. However, due to its complicated mechanism and lack of effective clinical therapeutics, early diagnosis and prognosis are still unsatisfactory. Most of the previous studies focused on cancer stem cells (CSCs), the relationship between cancer stemness (stem-like characteristics) and anti-tumor immunity has not been clearly revealed. Therefore, this study aimed to comprehensively analyze the role of cancer stemness and tumor microenvironment (TME) in LUAD using weighted gene co-expression network analysis (WGCNA). We constructed a gene co-expression network, identified key modules, and hub genes, and further explored the relationship between hub gene expression and cancer immunological characteristics through a variety of algorithms, including Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE) and Gene Set Enrichment Analysis (GSEA). The hub genes were renamed stemness related genes (SRGs), whose functions were examined at the transcription and protein levels through survival analysis with additional samples, Oncomine database, immunohistochemistry, single cell RNA sequencing (scRNA-seq) and single-sample Gene Set Enrichment Analysis (ssGSEA). Subsequently, Tumor Immune Dysfunction and Exclusion (TIDE) and Connectivity Map (CMap) were implemented for treatment and prognosis analyses. As a result, 15 co-expressed SRGs (CCNA2, CCNB1, CDC20, CDCA5, CDCA8, FEN1, KIF2C, KPNA2, MCM6, NUSAP1, RACGAP1, RRM2, SPAG5, TOP2A, and TPX2) were identified. The overexpression of which was discovered to be associated with reduced immune infiltration in LUAD. It was discovered that there was a general negative correlation between cancer stemness and immunity. The expression of SRGs could probably affect our tumor occurrence, progression, the efficacy of chemotherapy and immunotherapy, and clinical outcomes. In conclusion, the 15 SRGs reported in our study may be used as potential candidate biomarkers for prognostic indicators and therapeutic targets after further validation.
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Affiliation(s)
- Hao Zeng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center for Biotherapy, Chengdu, China.,West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Jianrui Ji
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center for Biotherapy, Chengdu, China.,West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Xindi Song
- West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yeqian Huang
- West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Hui Li
- West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Juan Huang
- Department of Hematology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Xuelei Ma
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center for Biotherapy, Chengdu, China.,West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
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Li X, He J, Yu M, Zhang W, Sun J. [BUB1 gene is highly expressed in gastric cancer:analysis based on Oncomine database and bioinformatics]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2020; 40:683-692. [PMID: 32897212 DOI: 10.12122/j.issn.1673-4254.2020.05.11] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To investigate the expression of BUB1 gene in gastric cancer. METHODS Oncomine, GEPIA, BioGPS and Kaplan-Meier Plotter databases were used to analyze the difference of BUB1 gene expression between gastric cancer tissue and normal gastric tissue. The association of BUB1 expression level with the prognosis of gastric cancer patients was also analyzed. The Cancer Cell Line Encyclopedia (CCLE) was explored to analyze the expression of BUB1 in T cells and B cells in gastric cancer patients, and the String database was used to generate the network map of BUB1-related proteins and functional annotation of gene ontology (GO). The related pathways of KEGG were analyzed. Tumor immune assessment resource (TIMER) database was used to analyze the expression of BUB1 in immune infiltration and its effect on prognosis of gastric cancer patients. To further verify the results of gene chip analysis in Oncomine database, we collected 30 pairs of surgical specimens of gastric adenocarcinoma and adjacent tissues from patients admitted to the First Affiliated Hospital of Chengdu Medical College from March, 2018 to July, 2019. The results of BUB1 gene expression in Oncomine database were verified by PCR and immunohistochemistry. RESULTS Oncomine, GEPIA and BioGPS analyses showed that BUB1 was highly expressed in gastric cancer compared with normal gastric tissue. Kaplan-Meier survival analysis showed that the progression-free survival time (HR=0.52, 95% CI:0.41-0.67, P < 0.05) and the overall survival time (HR=0.67, 95% CI:0.55-0.82, P < 0.05) were prolonged in gastric cancer patients with a high expression of BUB1. Through String data collection, BUB1-related proteins were mainly enriched in 13 cellular components, 4 molecular functions and 12 biological processes, involving 4 signal pathways. TIMER database analysis showed that CD4+ T cells and macrophages with high expressions of BUB1 mRNA in the immune microenvironment were associated with a favorable 5-year survival outcome of patients with gastric cancer. In the surgical specimens, real-time quantitative PCR showed that the expression level of BUB1 mRNA was significantly higher in gastric cancer tissues than in the adjacent gastric mucosa tissues, and immunohistochemical results demonstrated positive BUB1 staining in the gastric cancer tissues. CONCLUSIONS BUB1 gene is highly expressed in gastric cancer. BUB1 may reduce tumor immunosuppression and helps to evaluate the prognosis of patients with gastric cancer.
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Affiliation(s)
- Xiaoyan Li
- Department of endocrinology, First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, China
| | - Jie He
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, China
| | - Mi Yu
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, China
| | - Wei Zhang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, China
| | - Jian Sun
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, China
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11
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Besso MJ, Montivero L, Lacunza E, Argibay MC, Abba M, Furlong LI, Colas E, Gil-Moreno A, Reventos J, Bello R, Vazquez-Levin MH. Identification of early stage recurrence endometrial cancer biomarkers using bioinformatics tools. Oncol Rep 2020; 44:873-886. [PMID: 32705231 PMCID: PMC7388212 DOI: 10.3892/or.2020.7648] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 04/22/2020] [Indexed: 01/08/2023] Open
Abstract
Endometrial cancer (EC) is the sixth most common cancer in women worldwide. Early diagnosis is critical in recurrent EC management. The present study aimed to identify biomarkers of EC early recurrence using a workflow that combined text and data mining databases (DisGeNET, Gene Expression Omnibus), a prioritization algorithm to select a set of putative candidates (ToppGene), protein-protein interaction network analyses (Search Tool for the Retrieval of Interacting Genes, cytoHubba), association analysis of selected genes with clinicopathological parameters, and survival analysis (Kaplan-Meier and Cox proportional hazard ratio analyses) using a The Cancer Genome Atlas cohort. A total of 10 genes were identified, among which the targeting protein for Xklp2 (TPX2) was the most promising independent prognostic biomarker in stage I EC. TPX2 expression (mRNA and protein) was higher (P<0.0001 and P<0.001, respectively) in ETS variant transcription factor 5-overexpressing Hec1a and Ishikawa cells, a previously reported cell model of aggressive stage I EC. In EC biopsies, TPX2 mRNA expression levels were higher (P<0.05) in high grade tumors (grade 3) compared with grade 1–2 tumors (P<0.05), in tumors with deep myometrial invasion (>50% compared with <50%; P<0.01), and in intermediate-high recurrence risk tumors compared with low-risk tumors (P<0.05). Further validation studies in larger and independent EC cohorts will contribute to confirm the prognostic value of TPX2.
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Affiliation(s)
- María José Besso
- Laboratorio de Estudios de Interacción Celular en Reproducción y Cáncer, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina (CONICET)‑Fundación IBYME (FIBYME), Ciudad Autónoma de Buenos Aires 1428ADN, Argentina
| | - Luciana Montivero
- Laboratorio de Estudios de Interacción Celular en Reproducción y Cáncer, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina (CONICET)‑Fundación IBYME (FIBYME), Ciudad Autónoma de Buenos Aires 1428ADN, Argentina
| | - Ezequiel Lacunza
- Centro de Investigaciones Inmunológicas, Básicas y Aplicadas, Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Buenos Aires 1900, Argentina
| | - María Cecilia Argibay
- Laboratorio de Estudios de Interacción Celular en Reproducción y Cáncer, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina (CONICET)‑Fundación IBYME (FIBYME), Ciudad Autónoma de Buenos Aires 1428ADN, Argentina
| | - Martín Abba
- Centro de Investigaciones Inmunológicas, Básicas y Aplicadas, Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Buenos Aires 1900, Argentina
| | - Laura Inés Furlong
- Integrative Biomedical Informatics Group, Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08002 Barcelona, Spain
| | - Eva Colas
- Biomedical Research Group in Gynecology, Vall d´Hebron Research Institute (VHIR), Universitat Autónoma de Barcelona, CIBERONC, 08035 Barcelona, Spain
| | - Antonio Gil-Moreno
- Biomedical Research Group in Gynecology, Vall d´Hebron Research Institute (VHIR), Universitat Autónoma de Barcelona, CIBERONC, 08035 Barcelona, Spain
| | - Jaume Reventos
- Biomedical Research Group in Gynecology, Vall d´Hebron Research Institute (VHIR), Universitat Autónoma de Barcelona, CIBERONC, 08035 Barcelona, Spain
| | - Ricardo Bello
- Departamento de Metodología, Estadística y Matemática, Universidad de Tres de Febrero, Sáenz Peña, Buenos Aires B1674AHF, Argentina
| | - Mónica Hebe Vazquez-Levin
- Laboratorio de Estudios de Interacción Celular en Reproducción y Cáncer, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina (CONICET)‑Fundación IBYME (FIBYME), Ciudad Autónoma de Buenos Aires 1428ADN, Argentina
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Chen F, Wu P, Shen M, He M, Chen L, Qiu C, Shi H, Zhang T, Wang J, Xie K, Dai G, Wang J, Zhang G. Transcriptome Analysis of Differentially Expressed Genes Related to the Growth and Development of the Jinghai Yellow Chicken. Genes (Basel) 2019; 10:genes10070539. [PMID: 31319533 PMCID: PMC6678745 DOI: 10.3390/genes10070539] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 12/18/2022] Open
Abstract
The growth traits are important traits in chickens. Compared to white feather broiler breeds, Chinese local broiler breeds have a slow growth rate. The main genes affecting the growth traits of local chickens in China are still unclear and need to be further explored. This experiment used fast-growth and slow-growth groups of the Jinghai Yellow chicken as the research objects. Three males and three females with similar body weights were selected from the two groups at four weeks old and eight weeks old, respectively, with a total of 24 individuals selected. After slaughter, their chest muscles were taken for transcriptome sequencing. In the differentially expressed genes screening, all of the genes obtained were screened by fold change ≥ 2 and false discovery rate (FDR) < 0.05. For four-week-old chickens, a total of 172 differentially expressed genes were screened in males, where there were 68 upregulated genes and 104 downregulated genes in the fast-growth group when compared with the slow-growth group. A total of 31 differentially expressed genes were screened in females, where there were 11 upregulated genes and 20 downregulated genes in the fast-growth group when compared with the slow-growth group. For eight-week-old chickens, a total of 37 differentially expressed genes were screened in males. The fast-growth group had 28 upregulated genes and 9 downregulated genes when compared with the slow-growth group. A total of 44 differentially expressed genes were screened in females. The fast-growth group had 13 upregulated genes and 31 downregulated genes when compared with the slow-growth group. Through gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, many genes were found to be related to cell proliferation and differentiation, muscle growth, and cell division such as SNCG, MCL1, ARNTL, PLPPR4, VAMP1, etc. Real-time PCR results were consistent with the RNA-Seq data and validated the findings. The results of this study will help to understand the regulation mechanism of the growth and development of Jinghai Yellow chicken and provide a theoretical basis for improving the growth rate of Chinese local chicken breeds.
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Affiliation(s)
- Fuxiang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Pengfei Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Manman Shen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Mingliang He
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Lan Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Cong Qiu
- Jiangsu Jinghai Poultry Group Co., Ltd., Nantong 226100, China
| | - Huiqiang Shi
- Jiangsu Jinghai Poultry Group Co., Ltd., Nantong 226100, China
| | - Tao Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Jiahong Wang
- Upper School, Rutgers Preparatory School, NJ 08873, USA
| | - Kaizhou Xie
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Guojun Dai
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Jinyu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Genxi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
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Bang LG, Dasari VR, Kim D, Gogoi RP. Differential gene expression induced by Verteporfin in endometrial cancer cells. Sci Rep 2019; 9:3839. [PMID: 30846786 PMCID: PMC6405995 DOI: 10.1038/s41598-019-40495-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 02/07/2019] [Indexed: 12/12/2022] Open
Abstract
Endometrial cancer (EMCA) is a clinically heterogeneous disease. Previously, we tested the efficacy of Verteporfin (VP) in EMCA cells and observed cytotoxic and anti-proliferative effects. In this study, we analyzed RNA sequencing data to investigate the comprehensive transcriptomic landscape of VP treated Type 1 EMCA cell lines, including HEC-1-A and HEC-1-B. There were 549 genes with differential expression of two-fold or greater and P < 0.05 after false discovery rate correction for the HEC-1-B cell line. Positive regulation of TGFβ1 production, regulation of lipoprotein metabolic process, cell adhesion, endodermal cell differentiation, formation and development, and integrin mediated signaling pathway were among the significantly associated terms. A functional enrichment analysis of differentially expressed genes after VP treatment revealed extracellular matrix organization Gene Ontology as the most significant. CDC23 and BUB1B, two genes crucially involved in mitotic checkpoint progression, were found to be the pair with the best association from STRING among differentially expressed genes in VP treated HEC-1-B cells. Our in vivo results indicate that subcutaneous tumors in mice were regressed after VP treatment by inhibiting cell cycle pathway proteins. The present study revealed multiple key genes of pathological significance in EMCA, thereby improving our understanding of molecular profiles of EMCA cells.
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Affiliation(s)
- Lisa Gahyun Bang
- Biomedical and Translational Informatics Institute, Geisinger, Danville, PA, USA
| | | | - Dokyoon Kim
- Biomedical and Translational Informatics Institute, Geisinger, Danville, PA, USA
- Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Radhika P Gogoi
- Weis Center for Research, Geisinger Clinic, Danville, PA, USA.
- Geisinger Medical Center, Danville, PA, USA.
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Wang Y, Ren F, Chen P, Liu S, Song Z, Ma X. Identification of a six-gene signature with prognostic value for patients with endometrial carcinoma. Cancer Med 2018; 7:5632-5642. [PMID: 30306731 PMCID: PMC6247034 DOI: 10.1002/cam4.1806] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 09/09/2018] [Accepted: 09/10/2018] [Indexed: 12/13/2022] Open
Abstract
Uterine corpus endometrial carcinoma (UCEC) is frequently diagnosed among women worldwide. However, there are different prognostic outcomes because of heterogeneity. Thus, the aim of the current study was to identify a gene signature that can predict the prognosis of patients with UCEC. UCEC gene expression profiles were first downloaded from the The Cancer Genome Atlas (TCGA) database. After data processing and forward screening, 11 390 key genes were selected. The UCEC samples were randomly divided into training and testing sets. In total, 996 genes with prognostic value were then examined by univariate Cox survival analysis with a P-value <0.01 in the training set. Next, using robust likelihood-based survival modeling, we developed a six-gene signature (CTSW, PCSK4, LRRC8D, TNFRSF18, IHH, and CDKN2A) with a prognostic function in UCEC. A prognostic risk score system was developed by multivariate Cox proportional hazard regression based on this six-gene signature. According to the Kaplan-Meier curve, patients in the high-risk group had significantly poorer overall survival (OS) outcomes than those in the low-risk group (log-rank test P-value <0.0001). This signature was further validated in the testing dataset and the entire TCGA dataset. In conclusion, we conducted an integrated study to develop a six-gene signature for the prognostic prediction of patients with UCEC. Our findings may provide novel biomarkers for prognosis and have significant implications in the understanding of therapeutic targets for UCEC.
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Affiliation(s)
- Yizi Wang
- Department of Obstetrics and GynecologyShengjing Hospital of China Medical UniversityShenyangChina
| | - Fang Ren
- Department of Obstetrics and GynecologyShengjing Hospital of China Medical UniversityShenyangChina
| | - Peng Chen
- Department of Obstetrics and GynecologyShengjing Hospital of China Medical UniversityShenyangChina
| | - Shuang Liu
- Department of Obstetrics and GynecologyShengjing Hospital of China Medical UniversityShenyangChina
| | - Zixuan Song
- Department of Obstetrics and GynecologyShengjing Hospital of China Medical UniversityShenyangChina
| | - Xiaoxin Ma
- Department of Obstetrics and GynecologyShengjing Hospital of China Medical UniversityShenyangChina
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Tang J, Kong D, Cui Q, Wang K, Zhang D, Gong Y, Wu G. Prognostic Genes of Breast Cancer Identified by Gene Co-expression Network Analysis. Front Oncol 2018; 8:374. [PMID: 30254986 PMCID: PMC6141856 DOI: 10.3389/fonc.2018.00374] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 08/21/2018] [Indexed: 12/11/2022] Open
Abstract
Breast cancer is one of the most common malignancies. The molecular mechanisms of its pathogenesis are still to be investigated. The aim of this study was to identify the potential genes associated with the progression of breast cancer. Weighted gene co-expression network analysis (WGCNA) was used to construct free-scale gene co-expression networks to explore the associations between gene sets and clinical features, and to identify candidate biomarkers. The gene expression profiles of GSE1561 were selected from the Gene Expression Omnibus (GEO) database. RNA-seq data and clinical information of breast cancer from TCGA were used for validation. A total of 18 modules were identified via the average linkage hierarchical clustering. In the significant module (R2 = 0.48), 42 network hub genes were identified. Based on the Cancer Genome Atlas (TCGA) data, 5 hub genes (CCNB2, FBXO5, KIF4A, MCM10, and TPX2) were correlated with poor prognosis. Receiver operating characteristic (ROC) curve validated that the mRNA levels of these 5 genes exhibited excellent diagnostic efficiency for normal and tumor tissues. In addition, the protein levels of these 5 genes were also significantly higher in tumor tissues compared with normal tissues. Among them, CCNB2, KIF4A, and TPX2 were further upregulated in advanced tumor stage. In conclusion, 5 candidate biomarkers were identified for further basic and clinical research on breast cancer with co-expression network analysis.
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Affiliation(s)
- Jianing Tang
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Deguang Kong
- Department of General Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qiuxia Cui
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kun Wang
- Department of Thyroid and Breast Surgery, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Dan Zhang
- Department of Thyroid and Breast Surgery, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Gong
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Gaosong Wu
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
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