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Pharmacogenetics of the Primary and Metastatic Osteosarcoma: Gene Expression Profile Associated with Outcome. Int J Mol Sci 2023; 24:ijms24065607. [PMID: 36982681 PMCID: PMC10059037 DOI: 10.3390/ijms24065607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 03/17/2023] Open
Abstract
Osteosarcoma (OS) is the most common malignant bone tumor in children and adolescents. In recent decades, OS treatment has reached a plateau and drug resistance is still a major challenge. Therefore, the present study aimed to analyze the expression of the genes related to pharmacogenetics in OS. The expression of 32 target genes in 80 paired specimens (pre-chemotherapeutic primary tumor, post-chemotherapeutic primary tumor and pulmonary metastasis) obtained from 33 patients diagnosed with OS were analyzed by the real-time PCR methodology. As the calibrators (control), five normal bone specimens were used. The present study identified associations between the OS outcome and the expression of the genes TOP2A, DHFR, MTHFR, BCL2L1, CASP3, FASLG, GSTM3, SOD1, ABCC1, ABCC2, ABCC3, ABCC5, ABCC6, ABCC10, ABCC11, ABCG2, RALBP1, SLC19A1, SLC22A1, ERCC1 and MSH2. In addition, the expression of the ABCC10, GGH, GSTM3 and SLC22A1 genes were associated with the disease event, and the metastasis specimens showed a high expression profile of ABCC1, ABCC3 and ABCC4 genes and a low expression of SLC22A1 and ABCC10 genes, which is possibly an important factor for resistance in OS metastasis. Therefore, our findings may, in the future, contribute to clinical management as prognostic factors as well as possible therapeutic targets.
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Uusküla-Reimand L, Wilson MD. Untangling the roles of TOP2A and TOP2B in transcription and cancer. SCIENCE ADVANCES 2022; 8:eadd4920. [PMID: 36322662 PMCID: PMC9629710 DOI: 10.1126/sciadv.add4920] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/12/2022] [Indexed: 06/09/2023]
Abstract
Type II topoisomerases (TOP2) are conserved regulators of chromatin topology that catalyze reversible DNA double-strand breaks (DSBs) and are essential for maintaining genomic integrity in diverse dynamic processes such as transcription, replication, and cell division. While controlled TOP2-mediated DSBs are an elegant solution to topological constraints of DNA, DSBs also contribute to the emergence of chromosomal translocations and mutations that drive cancer. The central importance of TOP2 enzymes as frontline chemotherapeutic targets is well known; however, their precise biological functions and impact in cancer development are still poorly understood. In this review, we provide an updated overview of TOP2A and TOP2B in the regulation of chromatin topology and transcription, and discuss the recent discoveries linking TOP2 activities with cancer pathogenesis.
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Affiliation(s)
- Liis Uusküla-Reimand
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Michael D. Wilson
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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Zhao H, Chen C, Song H, Qin R, Wang X, He Q, Li F, Zhao H, Li Y. DNA Topoisomerase II-α Regulated by miR-22-5p Promotes Hepatocellular Carcinoma Invasion and Migration through the Hippo Pathway. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:4277254. [PMID: 36299605 PMCID: PMC9592219 DOI: 10.1155/2022/4277254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/27/2022] [Indexed: 10/10/2023]
Abstract
DNA topoisomerases (TOPs) are dysregulated in various types of cancer. However, how TOP II-alpha (TOP2A) contributes to hepatocellular carcinoma (HCC) progression remains elusive. Cohort analysis revealed that the increased expression of TOP2A was associated with poor clinical outcomes and TOP2A was significantly upregulated in HCC tissues and cell lines. In vitro, TOP2A expression level is related to cell invasion and migration, which may be due to the alteration of epithelial-mesenchymal transition by the TOP2A. Moreover, we used verteporfin (a Hippo inhibitor) to test how the Hippo pathway promotes the effect of TOP2A on the HCC phenotype and found that TOP2A induces tumor progression through the Hippo pathway. Finally, miR-22-5p inhibited tumor progression by sponging TOP2A.
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Affiliation(s)
- Haichao Zhao
- Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan 030032, China
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 300032, China
| | - Changzhou Chen
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 300032, China
| | - Huangqin Song
- Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan 030032, China
| | - Rongyi Qin
- Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan 030032, China
| | - Xiaoxiao Wang
- Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan 030032, China
| | - Qizu He
- Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan 030032, China
| | - Feng Li
- Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan 030032, China
| | - Haoliang Zhao
- Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan 030032, China
| | - Yanjun Li
- Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan 030032, China
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Liu Z, Xing L, Zhu Y, Shi P, Deng G. Association between TOP2A, RRM1, HER2, ERCC1 expression and response to chemotherapy in patients with non-muscle invasive bladder cancer. Heliyon 2022; 8:e09643. [PMID: 35711974 PMCID: PMC9194599 DOI: 10.1016/j.heliyon.2022.e09643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/22/2022] [Accepted: 05/30/2022] [Indexed: 11/30/2022] Open
Abstract
Purpose This study aimed to detect the expression levels of topoisomerase IIα (TOP2A), ribonucleotide reductase catalytic subunit M1 (RRM1),c-erbB-2 (HER2) and excision repair cross complementing group 1 (ERCC1) in non-muscular invasive bladder cancer (NMIBC) and explore the correlation between the expression of these genes and NMBIC sensitivity to pirarubicin or gemcitabine treatment. Materials and methods NMIBC patient tissues and the bladder cancer cell lines BIU-87 and KK47 were selected for the exploration of drug sensitivity in vitro. Immunohistochemistry was used to examine protein expression in tissues. Reverse transcription-polymerase chain reaction (RT-qPCR) and a Western blot assay were used to detect the mRNA and protein levels in cells. The cell IC50 value was evaluated by an MTT assay. Flow cytometry was used to sort the cell subpopulations. Results In the pirarubicin-treated group, the patients with high TOP2A expression experienced lower recurrence rates than those with low TOP2A expression, whereas TOP2A and HER2 co-expression resulted in higher recurrence rates. The patients with low RRM1 expression, especially those with low ERCC1 expression, experienced lower recurrence rates than the patients with high RRM1 expression in the gemcitabine-treated group. Tumour cells with high TOP2A expression were highly sensitive to pirarubicin, and TOP2A+ HER2- cells were more sensitive to pirarubicin than TOP2A+ HER2+ cells. Cells with low RRM1 expression levels were sensitive to gemcitabine, and RRM1−ERCC1- cells were more sensitive to gemcitabine than RRM1−ERCC1+ cells. Conclusion High TOP2A expression or low RRM1 expression could predict the sensitivity of NMIBC to pirarubicin or gemcitabine treatment. HER2 and ERCC1 expression may affect the effect of TOP2A and RRM1, thus affecting the efficacy of chemotherapeutic drugs.
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Affiliation(s)
- Zhifei Liu
- Department of Urology, Tangshan People's Hospital, Hebei 063001, China
| | - Liyong Xing
- Department of Urology, Tangshan People's Hospital, Hebei 063001, China
| | - Yanfeng Zhu
- Department of Urology, Tangshan People's Hospital, Hebei 063001, China
| | - Peng Shi
- Department of Urology, Tangshan People's Hospital, Hebei 063001, China
| | - Gang Deng
- Department of Urology, Tangshan People's Hospital, Hebei 063001, China
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Boot A, Liu M, Stantial N, Shah V, Yu W, Nitiss KC, Nitiss JL, Jinks-Robertson S, Rozen SG. Recurrent mutations in topoisomerase IIα cause a previously undescribed mutator phenotype in human cancers. Proc Natl Acad Sci U S A 2022; 119:e2114024119. [PMID: 35058360 PMCID: PMC8795545 DOI: 10.1073/pnas.2114024119] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/13/2021] [Indexed: 01/01/2023] Open
Abstract
Topoisomerases nick and reseal DNA to relieve torsional stress associated with transcription and replication and to resolve structures such as knots and catenanes. Stabilization of the yeast Top2 cleavage intermediates is mutagenic in yeast, but whether this extends to higher eukaryotes is less clear. Chemotherapeutic topoisomerase poisons also elevate cleavage, resulting in mutagenesis. Here, we describe p.K743N mutations in human topoisomerase hTOP2α and link them to a previously undescribed mutator phenotype in cancer. Overexpression of the orthologous mutant protein in yeast generated a characteristic pattern of 2- to 4-base pair (bp) duplications resembling those in tumors with p.K743N. Using mutant strains and biochemical analysis, we determined the genetic requirements of this mutagenic process and showed that it results from trapping of the mutant yeast yTop2 cleavage complex. In addition to 2- to 4-bp duplications, hTOP2α p.K743N is also associated with deletions that are absent in yeast. We call the combined pattern of duplications and deletions ID_TOP2α. All seven tumors carrying the hTOP2α p.K743N mutation showed ID_TOP2α, while it was absent from all other tumors examined (n = 12,269). Each tumor with the ID_TOP2α signature had indels in several known cancer genes, which included frameshift mutations in tumor suppressors PTEN and TP53 and an activating insertion in BRAF. Sequence motifs found at ID_TOP2α mutations were present at 80% of indels in cancer-driver genes, suggesting that ID_TOP2α mutagenesis may contribute to tumorigenesis. The results reported here shed further light on the role of topoisomerase II in genome instability.
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Affiliation(s)
- Arnoud Boot
- Programme in Cancer and Stem Cell Biology, Duke University-National University of Singapore Medical School (Duke-NUS Medical School), 169857 Singapore;
- Centre for Computational Biology, Duke-NUS Medical School, 169857 Singapore
| | - Mo Liu
- Programme in Cancer and Stem Cell Biology, Duke University-National University of Singapore Medical School (Duke-NUS Medical School), 169857 Singapore
- Centre for Computational Biology, Duke-NUS Medical School, 169857 Singapore
| | - Nicole Stantial
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Viraj Shah
- Pharmaceutical Sciences Department, University of Illinois at Chicago, Rockford, IL 61107
| | - Willie Yu
- Programme in Cancer and Stem Cell Biology, Duke University-National University of Singapore Medical School (Duke-NUS Medical School), 169857 Singapore
- Centre for Computational Biology, Duke-NUS Medical School, 169857 Singapore
| | - Karin C Nitiss
- Pharmaceutical Sciences Department, University of Illinois at Chicago, Rockford, IL 61107
| | - John L Nitiss
- Pharmaceutical Sciences Department, University of Illinois at Chicago, Rockford, IL 61107
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710;
| | - Steven G Rozen
- Programme in Cancer and Stem Cell Biology, Duke University-National University of Singapore Medical School (Duke-NUS Medical School), 169857 Singapore;
- Centre for Computational Biology, Duke-NUS Medical School, 169857 Singapore
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Du X, Xue Z, Lv J, Wang H. Expression of the Topoisomerase II Alpha (TOP2A) Gene in Lung Adenocarcinoma Cells and the Association with Patient Outcomes. Med Sci Monit 2020; 26:e929120. [PMID: 33361736 PMCID: PMC7774312 DOI: 10.12659/msm.929120] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background This study was carried out to analyze TOP2A expression in lung adenocarcinoma (LUAD) and to assess its value in clinical diagnosis and prognosis. Material/Methods The Cancer Genome Atlas (TCGA) database was used to study the relationship of TOP2A expression with the progression and prognosis of LUAD. For a further elucidation of the value of TOP2A in LUAD, the effect of TOP2A knockout on cell viability and related protein expression of LUAD cell line A549 in vitro was investigated by using RNA interference, MTT, flow cytometry, RT-PCR, and western blot analysis. Results According to the results of database analysis, TOP2A expression in LUAD was higher than that in normal lung tissues. There was a strong correlation of TOP2A expression with clinicopathological and epidemiological parameters of LUAD. The survival rate of LUAD patients with high TOP2A expression was lower than that of patients with low expression (P<0.001). The expression of TOP2A in A549 cells was higher than that in Beas-2B cells. After decreased expression of TOP2A in A549 cells, the proliferation of A549 cells was downregulated and the apoptosis rate was increased. It was further verified that TOP2A low expression exerts a role in LUAD through activation of the ERK/JNK/p-P38/CHOP signaling pathway. Conclusions The findings from this study showed that TOP2A expression was upregulated in a human lung adenocarcinoma cell line, and this finding was supported by bioinformatics analysis. Further studies are required to determine whether TOP2A expression is a prognostic biomarker and potential therapeutic target in patients with lung adenocarcinoma.
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Affiliation(s)
- Xiaomei Du
- Respiratory and Critical Care Department, Xi'an XD Group Hospital, Xi'an, Shanxi, China (mainland)
| | - Zhiwen Xue
- Respiratory and Critical Care Department, Xi'an XD Group Hospital, Xi'an, Shanxi, China (mainland)
| | - Jianning Lv
- Respiratory and Critical Care Department, Xi'an XD Group Hospital, Xi'an, Shanxi, China (mainland)
| | - Heidou Wang
- Infectious Diseases Department, The Eighth Hospital of Xi'an, Xi'an, Shanxi, China (mainland)
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Williams SG, Aw Yeang HX, Mitchell C, Caramia F, Byrne DJ, Fox SB, Haupt S, Schittenhelm RB, Neeson PJ, Haupt Y, Keam SP. Immune molecular profiling of a multiresistant primary prostate cancer with a neuroendocrine-like phenotype: a case report. BMC Urol 2020; 20:171. [PMID: 33115461 PMCID: PMC7592533 DOI: 10.1186/s12894-020-00738-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/06/2020] [Indexed: 02/06/2023] Open
Abstract
Background Understanding the drivers of recurrence in aggressive prostate cancer requires detailed molecular and genomic understanding in order to aid therapeutic interventions.
We provide here a case report of histological, transcriptional, proteomic, immunological, and genomic features in a longitudinal study of multiple biopsies from diagnosis, through treatment, and subsequent recurrence.
Case presentation Here we present a case study of a male in 70 s with high-grade clinically-localised acinar adenocarcinoma treated with definitive hormone therapy and radiotherapy. The patient progressed rapidly with rising PSA and succumbed without metastasis 52 months after diagnosis.
We identified the expression of canonical histological markers of neuroendocrine PC (NEPC) including synaptophysin, neuron-specific enolase and thyroid transcription factor 1, as well as intact AR expression, in the recurrent disease only.
The resistant disease was also marked by an extremely low immune infiltrate, extensive genomic chromosomal aberrations, and overactivity in molecular hallmarks of NEPC disease including Aurora kinase and E2F, as well as novel alterations in the cMYB pathway. We also observed that responses to both primary treatments (high dose-rate brachytherapy and androgen deprivation therapies) were consistent with known optimal responses—ruling out treatment inefficacy as a factor in relapse.
Conclusions These data provide novel insights into a case of locally recurrent aggressive prostate cancer harbouring NEPC pathology, in the absence of detected metastasis.
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Affiliation(s)
- Scott G Williams
- Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Australia.,Tumor Suppression Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia.,Pathology Department, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Han Xian Aw Yeang
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Catherine Mitchell
- Pathology Department, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Franco Caramia
- Tumor Suppression Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - David J Byrne
- Pathology Department, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Stephen B Fox
- Pathology Department, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Sue Haupt
- Tumor Suppression Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics & Metabolomics Facility, Monash University, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Paul J Neeson
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Ygal Haupt
- Tumor Suppression Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Simon P Keam
- Tumor Suppression Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia. .,Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.
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A review of clinical and emerging biomarkers for breast cancers: towards precision medicine for patients. JOURNAL OF RADIOTHERAPY IN PRACTICE 2020. [DOI: 10.1017/s1460396920000746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractBackground:Breast cancer is the most commonly diagnosed malignancy among women and accounts for about 25% of all new cancer cases and 13% of all cancer deaths in Canadian women. It is a highly heterogeneous disease, encompassing multiple tumour entities, each characterised by distinct morphology, behaviour and clinical implications. Moreover, different breast tumour subtypes have different risk factors, clinical presentation, histopathological features, outcome and response to systemic therapies. Therefore, any strategies capable of the stratification of breast cancer by clinically relevant subtypes are an important requirement for personalised and targeted treatment. Therefore, in the advancement towards the concept of precision medicine that takes individual patient variability into account, several investigators have focused on the identification of effective clinical breast cancer biomarkers that interrogate key aberrant pathways potentially targetable with molecular targeted or immunological therapies.Methods and materials:This paper reports on a review of 11 current clinical and emerging biomarkers used in screening for early detection and diagnosis, to stratify patients by disease subtype, to identify patients’ risk for metastatic disease and subsequent relapse, to monitor patient response to specific treatment and to provide clinicians the possibility of prospectively identifying groups of patients who will benefit from a particular treatment.Conclusion:The future holds promising for the use of effective clinical breast cancer biomarkers for early detection and personalised patient-specific targeted treatment and increased patient survival. Breast cancer biomarkers can potentially assist in early-staged, non-invasive, sensitive and specific breast cancer detection and screening, provide clinically useful information for identification of patients with a greater likelihood of benefiting from the specific treatment, offer a better understanding of the metastatic process in cancer patients, predict disease and for patients with the established disease can assist define the nature of the disease, monitor the success of treatment and guide the clinical management of the disease.
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Identification of common candidate genes and pathways for progression of ovarian, cervical and endometrial cancers. Meta Gene 2020. [DOI: 10.1016/j.mgene.2019.100634] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Qiu HZ, Huang J, Xiang CC, Li R, Zuo ED, Zhang Y, Shan L, Cheng X. Screening and Discovery of New Potential Biomarkers and Small Molecule Drugs for Cervical Cancer: A Bioinformatics Analysis. Technol Cancer Res Treat 2020; 19:1533033820980112. [PMID: 33302814 PMCID: PMC7734488 DOI: 10.1177/1533033820980112] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/09/2020] [Accepted: 11/04/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Cervical cancer (CC) is the second most common type of malignant tumor survival rate is low in advanced stage, metastatic, and recurrent CC patients. This study aimed at identifying potential genes and drugs for CC diagnosis and targeting therapies. METHODS Three GEO mRNA microarray datasets of CC tissues and non-cancerous tissues were analyzed for differentially expressed genes (DEGs) by limma package. GO (Gene Ontologies) and KEGG (Kyoto Encyclopedia of Genes and Genomes) were used to explore the relationships between the DEGs. Protein-protein interaction (PPI) of these genes was established by the STRING database. MCODE was used for screening significant modules in the PPI networks to select hub genes. Biochemical mechanisms of the hub genes were investigated with Metascape. GEPIA database was used for validating the core genes. According to these DEGs, molecular candidates for CC were recognized from the CMAP database. RESULTS We identified 309 overlapping DEGs in the 2 tissue-types. Pathway analysis revealed that the DEGs were involved in cell cycle, DNA replication, and p53 signaling. PPI networks between overlapping DEGs showed 68 high-connectivity DEGs that were chosen as hub genes. The GEPIA database showed that the expression levels of RRM2, CDC45, GINS2, HELLS, KNTC1, MCM2, MYBL2, PCNA, RAD54 L, RFC4, RFC5, TK1, TOP2A, and TYMS in CC tissues were significantly different from those in the healthy tissues and were significantly relevant to the OS of CC. We found 10 small molecules from the CMAP database that could change the trend of gene expression in CC tissues, including piperlongumine and chrysin. CONCLUSIONS The 14 DEGs identified in this study could serve as novel prognosis biomarkers for the detection and forecasting of CC. Small molecule drugs like piperlongumine and chrysin could be potential therapeutic drugs for CC treatment.
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Affiliation(s)
- Hui-Zhu Qiu
- Department of Hematology and Oncology, Soochow University Affiliated Taicang Hospital (The First People’s Hospital of Taicang), Jiangsu, China
| | - Ji Huang
- Department of Pharmacy, Soochow University Affiliated Taicang Hospital (The First People’s Hospital of Taicang), Jiangsu, China
| | - Cheng-Cheng Xiang
- Department of Hematology and Oncology, Soochow University Affiliated Taicang Hospital (The First People’s Hospital of Taicang), Jiangsu, China
| | - Rong Li
- Department of Hematology and Oncology, Soochow University Affiliated Taicang Hospital (The First People’s Hospital of Taicang), Jiangsu, China
| | - Er-Dong Zuo
- Department of Hematology and Oncology, Soochow University Affiliated Taicang Hospital (The First People’s Hospital of Taicang), Jiangsu, China
| | - Yuan Zhang
- Department of Hematology and Oncology, Soochow University Affiliated Taicang Hospital (The First People’s Hospital of Taicang), Jiangsu, China
| | - Li Shan
- Department of Hematology and Oncology, Soochow University Affiliated Taicang Hospital (The First People’s Hospital of Taicang), Jiangsu, China
| | - Xu Cheng
- Department of Hematology and Oncology, Soochow University Affiliated Taicang Hospital (The First People’s Hospital of Taicang), Jiangsu, China
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Abstract
Adenoid cystic carcinoma (ACC) is one of the most frequent malignancies of salivary glands. The objective of this study was to identify key genes and potential mechanisms during ACC samples.The gene expression profiles of GSE88804 data set were downloaded from Gene Expression Omnibus. The GSE88804 data set contained 22 samples, including 15 ACC samples and 7 normal salivary gland tissues. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were constructed, and protein-protein interaction network of differentially expressed genes (DEGs) was performed by Cytoscape. The top 10 hub genes were analyzed based on Gene Expression Profiling Interactive Analysis. Then, DEGs between ACC samples and normal salivary gland samples were analyzed by gene set enrichment analysis. Furthermore, miRTarBase and Cytoscape were used for visualization of miRNA-mRNA regulatory network. KEGG pathway analysis was undertaken using DIANA-miRPath v3.0.In total, 382 DEGs were identified, including 119 upregulated genes and 263 downregulated genes. GO analysis showed that DEGs were mainly enriched in extracellular matrix organization, extracellular matrix, and calcium ion binding. KEGG pathway analysis showed that DEGs were mainly enriched in p53 signaling pathway and salivary secretion. Expression analysis and survival analysis showed that ANLN, CCNB2, CDK1, CENPF, DTL, KIF11, and TOP2A are all highly expressed, which all may be related to poor overall survival. Predicted miRNAs of 7 hub DEGs mainly enriched in proteoglycans in cancer and pathways in cancer.This study indicated that identified DEGs and hub genes might promote our understanding of molecular mechanisms, which might be used as molecular targets or diagnostic biomarkers for ACC.
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Affiliation(s)
- Hong-Bing Liu
- Department of Otolaryngology-Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi
| | - Guan-Jiang Huang
- Department of Otorhinolaryngology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province
| | - Meng-Si Luo
- Department of Anesthesiology, Zhongshan Hospital of Traditional Chinese Medicine, Affiliated to Guangzhou University of Chinese Medicine, Zhongshan, Guangdong Province, China
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Chen J, Chen Y, Zheng D, Pang P, Lu J, Zheng X. Pretreatment MR-Based Radiomics Signature as Potential Imaging Biomarker for Assessing the Expression of Topoisomerase II alpha (TOPO-IIα) in Rectal Cancer. J Magn Reson Imaging 2019; 51:1881-1889. [PMID: 31675149 DOI: 10.1002/jmri.26972] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/26/2019] [Accepted: 09/26/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Rectal cancer (RC) is one of the most common cancers throughout the world. Chemotherapy or neoadjuvant chemotherapy play an important role in the treatment of advanced RC. Whether to add topoisomerase inhibitor to individualized chemotherapy is a puzzling question for clinicians. PURPOSE To investigate whether pretreatment MR-based radiomics signature can assess the expression of topoisomerase II alpha (TOPO-IIα) in RC. STUDY TYPE Retrospective. POPULATION In all, 122 patients with RC. Field Strength/Sequence: Pretreatment 3.0T; T2 WI turbo spin echo (TSE) sequence. ASSESSMENT A training group (n = 85) and a test group (n = 37) with pathologically confirmed RC. Patients underwent TOPO-IIα expression. A total of 180 radiomics features were extracted from oblique axial T2 WI TSE images of the entire primary tumor. The least absolute shrinkage and selection operator (LASSO) regression model was used to reduce the dimension of the data and select the features. STATISTICAL TESTS The assessment models were established by multivariable logistic regression analysis. The performance of the model was assessed by the receiver operating characteristic (ROC) curve, nomogram, and calibration. RESULTS The radiomics signature, which consisted of 10 selected optimal features, was significantly associated with TOPO-IIα expression (P < 0.01 for both training and test groups). The area under the curve (AUC), the sensitivity, and the specificity for assessing TOPO-IIα expression, were 0.859, 0.872, and 0.739, respectively, in the training group, while they were 0.762, 0.941, and 0.600 in the test group. The nomogram model of the radiomics signature (Rad-score) had good calibration. Calibration curves were plotted to assess the calibration of the radiomics nomogram that was accompanied with the Hosmer-Lemeshow test (P = 0.52). DATA CONCLUSION The proposed pretreatment MR-based radiomics signature was associated with TOPO-IIα expression. A radiomics nomogram might be helpful in the individualized assessment of TOPO-IIα expression in patients with RC. LEVEL OF EVIDENCE 2 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2020;51:1881-1889.
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Affiliation(s)
- Jiayou Chen
- Department of Radiology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, Fujian, China
| | - Ying Chen
- Department of Radiology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, Fujian, China
| | - Dechun Zheng
- Department of Radiology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, Fujian, China
| | | | - Jianping Lu
- Department of Pathology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, Fujian, China
| | - Xiang Zheng
- Department of Radiology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, Fujian, China
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Amirfallah A, Arason A, Einarsson H, Gudmundsdottir ET, Freysteinsdottir ES, Olafsdottir KA, Johannsson OT, Agnarsson BA, Barkardottir RB, Reynisdottir I. High expression of the vacuole membrane protein 1 (VMP1) is a potential marker of poor prognosis in HER2 positive breast cancer. PLoS One 2019; 14:e0221413. [PMID: 31442252 PMCID: PMC6707546 DOI: 10.1371/journal.pone.0221413] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 08/06/2019] [Indexed: 02/07/2023] Open
Abstract
Background Fusion genes result from genomic structural changes, which can lead to alterations in gene expression that supports tumor development. The aim of the study was to use fusion genes as a tool to identify new breast cancer (BC) genes with a role in BC progression. Methods Fusion genes from breast tumors and BC cell lines were collected from publications. RNA-Seq data from tumors and cell lines were retrieved from databanks and analyzed for fusions with SOAPfuse or the analysis was purchased. Fusion genes identified in both tumors (n = 1724) and cell lines (n = 45) were confirmed by qRT-PCR and sequencing. Their individual genes were ranked by selection criteria that included correlation of their mRNA level with copy number. The expression of the top ranked gene was measured by qRT-PCR in normal tissue and in breast tumors from an exploratory cohort (n = 141) and a validation cohort (n = 277). Expression levels were correlated with clinical and pathological factors as well as the patients’ survival. The results were followed up in BC cohorts from TCGA (n = 818) and METABRIC (n = 2509). Results Vacuole membrane protein 1 (VMP1) was the most promising candidate based on specific selection criteria. Its expression was higher in breast tumor tissue than normal tissue (p = 1x10-4), and its expression was significantly higher in HER2 positive than HER2 negative breast tumors in all four cohorts analyzed. High expression of VMP1 associated with breast cancer specific survival (BCSS) in cohort 1 (hazard ratio (HR) = 2.31, CI 1.27–4.18) and METABRIC (HR = 1.26, CI 1.02–1.57), and also after adjusting for HER2 expression in cohort 1 (HR = 2.03, CI 1.10–3.72). BCSS was not significant in cohort 2 or TCGA cohort, which may be due to differences in treatment regimens. Conclusions The results suggest that high VMP1 expression is a potential marker of poor prognosis in HER2 positive BC. Further studies are needed to elucidate how VMP1 could affect pathways supportive of tumorigenesis.
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Affiliation(s)
- Arsalan Amirfallah
- Cell Biology Unit at the Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
- The Biomedical Center, University of Iceland, Reykjavik, Iceland
| | - Adalgeir Arason
- The Biomedical Center, University of Iceland, Reykjavik, Iceland
- Molecular Pathology Unit at the Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
| | - Hjorleifur Einarsson
- Cell Biology Unit at the Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
| | - Eydis Thorunn Gudmundsdottir
- Cell Biology Unit at the Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
| | - Edda Sigridur Freysteinsdottir
- Molecular Pathology Unit at the Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
| | | | - Oskar Thor Johannsson
- Department of Oncology, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
| | - Bjarni Agnar Agnarsson
- Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Rosa Bjork Barkardottir
- The Biomedical Center, University of Iceland, Reykjavik, Iceland
- Molecular Pathology Unit at the Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
| | - Inga Reynisdottir
- Cell Biology Unit at the Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
- The Biomedical Center, University of Iceland, Reykjavik, Iceland
- * E-mail:
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Zeng S, Liu A, Dai L, Yu X, Zhang Z, Xiong Q, Yang J, Liu F, Xu J, Xue Y, Sun Y, Xu C. Prognostic value of TOP2A in bladder urothelial carcinoma and potential molecular mechanisms. BMC Cancer 2019; 19:604. [PMID: 31216997 PMCID: PMC6582551 DOI: 10.1186/s12885-019-5814-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 06/10/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The prognosis of bladder urothelial carcinoma (BLCA) varies greatly among patients, and conventional pathological predictors are generally inadequate and often inaccurate to predict the heterogeneous behavior of BLCA. This study aims to investigate the prognostic value and function of TOP2A in BLCA. METHODS TOP2A expression level was examined by RNA-sequencing, quantitative real time polymerase chain reaction and immunohistochemistry from 10, 40 and 209 BLCA samples, respectively. Public databases were analyzed for validation. Cell proliferation, migration, invasion assays were performed to explore potential functions of TOP2A in BLCA. Flow cytometry was performed for cell cycle and apoptosis analysis. Univariable and multivariable Cox regression models were performed to identify independent risk factors for the prognosis of BLCA. RESULTS We found TOP2A was significantly upregulated in BLCA samples, especially for high-grade and advanced stage tumors, compared with matched normal epithelial tissue. Univariable COX regression analysis revealed high TOP2A expression was significantly associated with poorer cancer-specific, progression-free and recurrence-free survival, but not independently of clinical characteristics in the multivariable models. Knockdown of TOP2A remarkably inhibited the proliferation of BLCA cells and non-cancerous urothelial cells. Furthermore, migration and invasion capacity of BLCA cells were strongly suppressed after TOP2A knockdown. Moreover, flow cytometry suggested TOP2A had anti-apoptotic function, and knockdown of TOP2A could induce resistance to doxorubicin in J82 cells. CONCLUSIONS In our study, TOP2A was overexpressed in BLCA and could serve as a prognostic biomarker for BLCA. Moreover, TOP2A is functionally important for the proliferation, invasion and survival of BLCA cells.
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Affiliation(s)
- Shuxiong Zeng
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Anwei Liu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Lihe Dai
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Xiaowen Yu
- Department of Geriatrics, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Zhensheng Zhang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Qiao Xiong
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Jun Yang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Fei Liu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Jinshan Xu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Yongping Xue
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Yinghao Sun
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China.
| | - Chuanliang Xu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China.
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Yao Y, Su J, Zhao L, Luo N, Long L, Zhu X. NIMA-related kinase 2 overexpression is associated with poor survival in cancer patients: a systematic review and meta-analysis. Cancer Manag Res 2019; 11:455-465. [PMID: 30655697 PMCID: PMC6322518 DOI: 10.2147/cmar.s188347] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Objective NIMA-related kinase 2 (NEK2) has been reported to be overexpressed in various types of cancer and correlated with poor prognosis. The role(s) of NEK2 in cancer, however, is still uncertain. The aim of this study was to evaluate the prognostic value of NEK2 in human tumors. Methods A comprehensive literature search was performed for PubMed, Embase, Web of Science, and CNKI databases, and eligible studies were included based on the inclusion and exclusion criteria. A meta-analysis of the included studies was then carried out. Results Fifteen studies with 3,280 cancer patients were included in the present meta-analysis. All publications were of moderate to high quality, and had no significant heterogeneity (I2=46%, P=0.03) or publication bias was discovered. The results showed that a high NEK2 level was associated with shorter overall survival (OS) in patients with various types of cancers (pooled HR=1.72, 95% CI 1.49–2.00, P<0.00001). However, the disease-free survival (DFS) had no significant association with NEK2 level (HR=1.13, 95% CI: 0.29–4.38, P=0.85). In the subgroup analyses, high NEK2 level was correlated with an increased risk of poor OS in patients with hepatocellular carcinoma (HR=1.62, 95% CI: 1.25–2.10, P=0.02) and lung cancer (HR=2.18, 95% CI: 1.40–3.38, P=0.0005). However, other factors, including sample size, follow-up period, HR estimation method, and country, also affect the association between NEK2 expression and OS. Analysis of clinicopathological parameters further showed that increased NEK2 level was correlated with younger age, male gender, better tumor differentiation, and lower number of tumor nodules. Conclusion The results of this study indicated that increased expression of NEK2 was associated with unfavorable survival of cancer patients and that NEK2 could be used as a prognostic predictor for cancers.
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Affiliation(s)
- Yang Yao
- Department of Central Laboratory, The First Affiliated Hospital, Xi'an Medical University, Xi'an, Shaanxi 710077, PR China,
| | - Jie Su
- Department of Central Laboratory, The First Affiliated Hospital, Xi'an Medical University, Xi'an, Shaanxi 710077, PR China,
| | - Lei Zhao
- Department of Molecular Physiology and Biophysics, Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Na Luo
- Department of Clinical Medicine (Four-Year Program) of Grade 2014, Xi'an Medical University, Xi'an, Shaanxi 710021, PR China
| | - Lihui Long
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Medical University, Xi'an, Shaanxi 710077, PR China
| | - Xingmei Zhu
- Department of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi 712046, PR China
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Rahman MF, Rahman MR, Islam T, Zaman T, Shuvo MAH, Hossain MT, Islam MR, Karim MR, Moni MA. A bioinformatics approach to decode core genes and molecular pathways shared by breast cancer and endometrial cancer. INFORMATICS IN MEDICINE UNLOCKED 2019. [DOI: 10.1016/j.imu.2019.100274] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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17
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Gao X, Chen Y, Chen M, Wang S, Wen X, Zhang S. Identification of key candidate genes and biological pathways in bladder cancer. PeerJ 2018; 6:e6036. [PMID: 30533316 PMCID: PMC6284430 DOI: 10.7717/peerj.6036] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/29/2018] [Indexed: 12/14/2022] Open
Abstract
Background Bladder cancer is a malignant tumor in the urinary system with high mortality and recurrence rates. However, the causes and recurrence mechanism of bladder cancer are not fully understood. In this study, we used integrated bioinformatics to screen for key genes associated with the development of bladder cancer and reveal their potential molecular mechanisms. Methods The GSE7476, GSE13507, GSE37815 and GSE65635 expression profiles were downloaded from the Gene Expression Omnibus database, and these datasets contain 304 tissue samples, including 81 normal bladder tissue samples and 223 bladder cancer samples. The RobustRankAggreg (RRA) method was utilized to integrate and analyze the four datasets to obtain integrated differentially expressed genes (DEGs), and the gene ontology (GO) functional annotation and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis were performed. Protein-protein interaction (PPI) network and module analyses were performed using Cytoscape software. The OncoLnc online tool was utilized to analyze the relationship between the expression of hub genes and the prognosis of bladder cancer. Results In total, 343 DEGs, including 111 upregulated and 232 downregulated genes, were identified from the four datasets. GO analysis showed that the upregulated genes were mainly involved in mitotic nuclear division, the spindle and protein binding. The downregulated genes were mainly involved in cell adhesion, extracellular exosomes and calcium ion binding. The top five enriched pathways obtained in the KEGG pathway analysis were focal adhesion (FA), PI3K-Akt signaling pathway, proteoglycans in cancer, extracellular matrix (ECM)-receptor interaction and vascular smooth muscle contraction. The top 10 hub genes identified from the PPI network were vascular endothelial growth factor A (VEGFA), TOP2A, CCNB1, Cell division cycle 20 (CDC20), aurora kinase B, ACTA2, Aurora kinase A, UBE2C, CEP55 and CCNB2. Survival analysis revealed that the expression levels of ACTA2, CCNB1, CDC20 and VEGFA were related to the prognosis of patients with bladder cancer. In addition, a KEGG pathway analysis of the top 2 modules identified from the PPI network revealed that Module 1 mainly involved the cell cycle and oocyte meiosis, while the analysis in Module 2 mainly involved the complement and coagulation cascades, vascular smooth muscle contraction and FA. Conclusions This study identified key genes and pathways in bladder cancer, which will improve our understanding of the molecular mechanisms underlying the development and progression of bladder cancer. These key genes might be potential therapeutic targets and biomarkers for the treatment of bladder cancer.
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Affiliation(s)
- Xin Gao
- Central Laboratory, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, China
| | - Yinyi Chen
- Central Laboratory, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, China
| | - Mei Chen
- Central Laboratory, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, China
| | - Shunlan Wang
- Central Laboratory, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, China
| | - Xiaohong Wen
- Central Laboratory, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, China
| | - Shufang Zhang
- Central Laboratory, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, China
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