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Priyamvada P, Ramaiah S. Potential Signature Therapeutic Biomarkers TOP2A, MAD2L1, and CDK1 in Colorectal Cancer: A Systems Biomedicine-Based Approach. Biochem Genet 2024; 62:2166-2194. [PMID: 37884851 DOI: 10.1007/s10528-023-10544-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
Abstract
Colorectal cancer is the third deadliest and fourth most diagnosed cancer. It is heterogeneously driven by varied mutations and mutagens, and thus, it is challenging for targeted therapy. The rapid advancement of high-throughput technology presents considerable opportunities for discovering new colon cancer biomarkers. In the present study, we have explored and identified the biomarkers based on molecular interactions. We curated cancer datasets that were not micro-dissected and performed gene expression analysis. The protein-protein interactions were curated, and a network was constructed for the up-regulated genes. The hub genes were analyzed using 12 different topological parameters. The correlation analysis selected TOP2A, CDK1, CCNB1, AURKA, and MAD2L1 as hub genes. Further, survival analysis was performed to determine the effectiveness of the hub gene on the patient's survival rate. Our findings explore various transcription factors such as E2F4, FOXM1, E2F6, MAX, and SIN3A, along with kinases CSNK2A1, MAPK14, CDK1, CDK4, and CDK2, as potential molecular signatures and aid researchers in understanding the pathophysiological mechanisms underlying CRC development and thus providing novel therapeutic and diagnostic recourse. Furthermore, investigating miRNAs, we focused on hsa-miR-215-5p, hsa-miR-192-5p, and hsa-miR-193b-3p due to their observed impact on a diverse set of colorectal cancer genes. Thereby, the current approach brings into light CRC- related genes at the RNA and protein levels that can potentially act as novel biomarkers opening doors to diagnostic and treatment purposes.
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Affiliation(s)
- P Priyamvada
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
- Department of Bio Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India.
- Department of Bio Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India.
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2
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Çoban V, Çankaya N, Azarkan SY. New oxomethacrylate and acetamide: synthesis, characterization, and their computational approaches: molecular docking, molecular dynamics, and ADME analyses. Drug Chem Toxicol 2024:1-10. [PMID: 38745411 DOI: 10.1080/01480545.2024.2349651] [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: 01/16/2024] [Accepted: 04/25/2024] [Indexed: 05/16/2024]
Abstract
The compounds 2-chloro-N-(3-methoxyphenyl)acetamide (m-acetamide) and 2-(3-methoxyphenylamino)-2-oxoethyl methacrylate (3MPAEMA) were synthesized in this study for the first time in the literature. FTIR, 1H, and 13C NMR spectroscopic techniques were used to characterize it. Subsequently, computational techniques were used to assess various ADME factors, such as drug-likeness properties, bioavailability score, and adherence to Lipinski's rule. Finally, molecular docking experiments were conducted with the human topoisomerase α2 (TOP2A) protein to verify and validate the reliability and stability of the docking procedure. The results of the docking scores, which quantify binding affinity, indicated that these derivatives exhibited a stronger affinity for TOP2A.
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Affiliation(s)
- Verda Çoban
- Graduate Education Institute, Uşak University, Uşak, Turkey
| | - Nevin Çankaya
- Vocational School of Health Services, Uşak University, Uşak, Turkey
| | - Serap Yalçın Azarkan
- Department of Medical Pharmacology, Faculty of Medicine, Kırsehir Ahi Evran University, Kırşehir, Turkey
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3
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Lenin B, Ramasubramanyan S, Vetrivel U, Chitipothu S. Virtual screening and multilevel precision-based prioritisation of natural inhibitors targeting the ATPase domain of human DNA topoisomerase II alpha. J Biomol Struct Dyn 2023; 41:15177-15195. [PMID: 36898858 DOI: 10.1080/07391102.2023.2187234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 02/25/2023] [Indexed: 03/12/2023]
Abstract
Human DNA topoisomerase II alpha (hTopIIα) is a classic chemotherapeutic drug target. The existing hTopIIα poisons cause numerous side effects such as the development of cardiotoxicity, secondary malignancies, and multidrug resistance. The use of catalytic inhibitors targeting the ATP-binding cavity of the enzyme is considered a safer alternative due to the less deleterious mechanism of action. Hence, in this study, we carried out high throughput structure-based virtual screening of the NPASS natural product database against the ATPase domain of hTopIIα and identified the five best ligand hits. This was followed by comprehensive validation through molecular dynamics simulations, binding free energy calculation and ADMET analysis. On stringent multilevel prioritization, we identified promising natural product catalytic inhibitors that showed high binding affinity and stability within the ligand-binding cavity and may serve as ideal hits for anticancer drug development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Barathi Lenin
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India
| | - Sharada Ramasubramanyan
- RS Mehta Jain Department of Biochemistry and Cell Biology, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India
| | - Umashankar Vetrivel
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India
- National Institute of Traditional Medicine, Indian Council of Medical Research, Belagavi, Karnataka, India
| | - Srujana Chitipothu
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India
- Central Research Instrumentation Facility, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India
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4
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Exploring Core Genes by Comparative Transcriptomics Analysis for Early Diagnosis, Prognosis, and Therapies of Colorectal Cancer. Cancers (Basel) 2023; 15:cancers15051369. [PMID: 36900162 PMCID: PMC10000172 DOI: 10.3390/cancers15051369] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers with a high mortality rate. Early diagnosis and therapies for CRC may reduce the mortality rate. However, so far, no researchers have yet investigated core genes (CGs) rigorously for early diagnosis, prognosis, and therapies of CRC. Therefore, an attempt was made in this study to explore CRC-related CGs for early diagnosis, prognosis, and therapies. At first, we identified 252 common differentially expressed genes (cDEGs) between CRC and control samples based on three gene-expression datasets. Then, we identified ten cDEGs (AURKA, TOP2A, CDK1, PTTG1, CDKN3, CDC20, MAD2L1, CKS2, MELK, and TPX2) as the CGs, highlighting their mechanisms in CRC progression. The enrichment analysis of CGs with GO terms and KEGG pathways revealed some crucial biological processes, molecular functions, and signaling pathways that are associated with CRC progression. The survival probability curves and box-plot analyses with the expressions of CGs in different stages of CRC indicated their strong prognostic performance from the earlier stage of the disease. Then, we detected CGs-guided seven candidate drugs (Manzamine A, Cardidigin, Staurosporine, Sitosterol, Benzo[a]pyrene, Nocardiopsis sp., and Riccardin D) by molecular docking. Finally, the binding stability of four top-ranked complexes (TPX2 vs. Manzamine A, CDC20 vs. Cardidigin, MELK vs. Staurosporine, and CDK1 vs. Riccardin D) was investigated by using 100 ns molecular dynamics simulation studies, and their stable performance was observed. Therefore, the output of this study may play a vital role in developing a proper treatment plan at the earlier stages of CRC.
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Synthesis and Evaluation of Antiproliferative Activity, Topoisomerase IIα Inhibition, DNA Binding and Non-Clinical Toxicity of New Acridine-Thiosemicarbazone Derivatives. Pharmaceuticals (Basel) 2022; 15:ph15091098. [PMID: 36145320 PMCID: PMC9506480 DOI: 10.3390/ph15091098] [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: 07/06/2022] [Revised: 08/16/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
In this study, we report the synthesis of twenty new acridine–thiosemicarbazone derivatives and their antiproliferative activities. Mechanisms of action such as the inhibition of topoisomerase IIα and the interaction with DNA have been studied for some of the most active derivatives by means of both in silico and in vitro methods, and evaluations of the non-clinical toxicities (in vivo) in mice. In general, the compounds showed greater cytotoxicity against B16-F10 cells, with the highest potency for DL-08 (IC50 = 14.79 µM). Derivatives DL-01 (77%), DL-07 (74%) and DL-08 (79%) showed interesting inhibition of topoisomerase IIα when compared to amsacrine, at 100 µM. In silico studies proposed the way of bonding of these compounds and a possible stereoelectronic reason for the absence of enzymatic activity for CL-07 and DL-06. Interactions with DNA presented different spectroscopic effects and indicate that the compound CL-07 has higher affinity for DNA (Kb = 4.75 × 104 M−1; Ksv = 2.6 × 103 M−1). In addition, compounds selected for non-clinical toxicity testing did not show serious signs of toxicity at the dose of 2000 mg/kg in mice; cytotoxic tests performed on leukemic cells (K-562) and its resistant form (K-562 Lucena 1) identified moderate potency for DL-01 and DL-08, with IC50 between 11.45 and 17.32 µM.
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Game-theoretic link relevance indexing on genome-wide expression dataset identifies putative salient genes with potential etiological and diapeutics role in colorectal cancer. Sci Rep 2022; 12:13409. [PMID: 35927308 PMCID: PMC9352798 DOI: 10.1038/s41598-022-17266-0] [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: 10/01/2021] [Accepted: 07/22/2022] [Indexed: 11/08/2022] Open
Abstract
Diapeutics gene markers in colorectal cancer (CRC) can help manage mortality caused by the disease. We applied a game-theoretic link relevance Index (LRI) scoring on the high-throughput whole-genome transcriptome dataset to identify salient genes in CRC and obtained 126 salient genes with LRI score greater than zero. The biomarkers database lacks preliminary information on the salient genes as biomarkers for all the available cancer cell types. The salient genes revealed eleven, one and six overrepresentations for major Biological Processes, Molecular Function, and Cellular components. However, no enrichment with respect to chromosome location was found for the salient genes. Significantly high enrichments were observed for several KEGG, Reactome and PPI terms. The survival analysis of top protein-coding salient genes exhibited superior prognostic characteristics for CRC. MIR143HG, AMOTL1, ACTG2 and other salient genes lack sufficient information regarding their etiological role in CRC. Further investigation in LRI methodology and salient genes to augment the existing knowledge base may create new milestones in CRC diapeutics.
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Colorectal Cancer Diagnosis: The Obstacles We Face in Determining a Non-Invasive Test and Current Advances in Biomarker Detection. Cancers (Basel) 2022; 14:cancers14081889. [PMID: 35454792 PMCID: PMC9029324 DOI: 10.3390/cancers14081889] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Colorectal cancer (CRC) is one of the most common cancers in the western world. CRC originates from precursor adenomatous polyps, which may over time develop into cancer. Endoscopic evaluation remains the gold-standard investigation for the disease. In the absence of molecular tools for early detection, the removal of neoplastic adenomas via polypectomy remains an important measure to prevent dysplastic adenomas from evolving into invasive carcinoma. Colonoscopy is an intrusive procedure that provides an uncomfortable experience for patients. Kits for testing for the presence of blood hemoglobin in the stool are now widely used, and DNA methylation-based detection kits have been approved in the USA for testing the stool and plasma, but few other molecular biomarkers have found their way into medical practice. This review summarizes current trends in the detection and screening of CRC and provides a definitive review of emerging molecular biomarkers for CRC. Abstract Globally, colorectal cancer (CRC) is the third most common cancer, with 1.4 million new cases and over 700,000 deaths per annum. Despite being one of the most common cancers, few molecular approaches to detect CRC exist. Carcinoembryonic antigen (CEA) is a known serum biomarker that is used in CRC for monitoring disease recurrence or response to treatment. However, it can also be raised in multiple benign conditions, thus having no value in early detection or screening for CRC. Molecular biomarkers play an ever-increasing role in the diagnosis, prognosis, and outcome prediction of disease, however, only a limited number of biomarkers are available and none are suitable for early detection and screening of CRC. A PCR-based Epi proColon® blood plasma test for the detection of methylated SEPT9 has been approved by the USFDA for CRC screening in the USA, alongside a stool test for methylated DNA from CRC cells. However, these are reserved for patients who decline traditional screening methods. There remains an urgent need for the development of non-invasive molecular biomarkers that are highly specific and sensitive to CRC and that can be used routinely for early detection and screening. A molecular approach to the discovery of CRC biomarkers focuses on the analysis of the transcriptome of cancer cells to identify differentially expressed genes and proteins. A systematic search of the literature yielded over 100 differentially expressed CRC molecular markers, of which the vast majority are overexpressed in CRC. In terms of function, they largely belong to biological pathways involved in cell division, regulation of gene expression, or cell proliferation, to name a few. This review evaluates the current methods used for CRC screening, current availability of biomarkers, and new advances within the field of biomarker detection for screening and early diagnosis of CRC.
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Molinaro C, Wambang N, Bousquet T, Vercoutter-Edouart AS, Pélinski L, Cailliau K, Martoriati A. A Novel Copper(II) Indenoisoquinoline Complex Inhibits Topoisomerase I, Induces G2 Phase Arrest, and Autophagy in Three Adenocarcinomas. Front Oncol 2022; 12:837373. [PMID: 35280788 PMCID: PMC8908320 DOI: 10.3389/fonc.2022.837373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/26/2022] [Indexed: 12/30/2022] Open
Abstract
Topoisomerases, targets of inhibitors used in chemotherapy, induce DNA breaks accumulation leading to cancer cell death. A newly synthesized copper(II) indenoisoquinoline complex WN197 exhibits a cytotoxic effect below 0.5 µM, on MDA-MB-231, HeLa, and HT-29 cells. At low doses, WN197 inhibits topoisomerase I. At higher doses, it inhibits topoisomerase IIα and IIβ, and displays DNA intercalation properties. DNA damage is detected by the presence of γH2AX. The activation of the DNA Damage Response (DDR) occurs through the phosphorylation of ATM/ATR, Chk1/2 kinases, and the increase of p21, a p53 target. WN197 induces a G2 phase arrest characterized by the unphosphorylated form of histone H3, the accumulation of phosphorylated Cdk1, and an association of Cdc25C with 14.3.3. Cancer cells die by autophagy with Beclin-1 accumulation, LC3-II formation, p62 degradation, and RAPTOR phosphorylation in the mTOR complex. Finally, WN197 by inhibiting topoisomerase I at low concentration with high efficiency is a promising agent for the development of future DNA damaging chemotherapies.
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Affiliation(s)
- Caroline Molinaro
- Univ. Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | | | - Till Bousquet
- Univ. Lille, CNRS, Centrale Lille, Univ. Artois, UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide, Lille, France
| | | | - Lydie Pélinski
- Univ. Lille, CNRS, Centrale Lille, Univ. Artois, UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide, Lille, France
| | - Katia Cailliau
- Univ. Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Alain Martoriati
- Univ. Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
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Identification of a novel catalytic inhibitor of topoisomerase II alpha that engages distinct mechanisms in p53 wt or p53 -/- cells to trigger G2/M arrest and senescence. Cancer Lett 2022; 526:284-303. [PMID: 34843865 DOI: 10.1016/j.canlet.2021.11.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/10/2021] [Accepted: 11/19/2021] [Indexed: 12/18/2022]
Abstract
We report a novel topoisomerase IIα inhibitor, mercaptopyridine oxide (MPO), which induces G2/M arrest and senescence with distinctly different cell cycle regulators (p21 or p14ARF) in HCT116p 53WT and HCT116 p53-/- cells, respectively. MPO treatment induced defective topoisomerase IIα-mediated decatenation process and inhibition of the enzyme's catalytic activity that stalled entry into mitosis. Topoisomerase IIα inhibition was associated with ROS-mediated activation of ATM-Chk2 kinase axis in HCT116 p53WT cells, but not in HCT116 p53-/- cells displaying early Chk1 activation. Results suggest that E2F1 stabilization might link MPO-induced p53 phospho-activation in HCT116 p53WT cells or p14ARF induction in HCT116 p53-/- cells. Also, interaction between topoisomerase IIα and Chk1 was induced in both cell lines, which could be important for decatenation checkpoint activation, even upon p53 ablation. Notably, TCGA dataset analyses revealed topoisomerase IIα upregulation across a wide array of cancers, which was associated with lower overall survival. Corroborating that increased topoisomerase IIα expression might offer susceptibility to the novel inhibitor, MPO (5 μM) induced strong inhibition in colony forming ability of pancreatic and hepatocellular cancer cell lines. These data highlight a novel topoisomerase IIα inhibitor and provide proof-of-concept for its therapeutic potential against cancers even with loss-of-function of p53.
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Carvalho RF, do Canto LM, Cury SS, Frøstrup Hansen T, Jensen LH, Rogatto SR. Drug Repositioning Based on the Reversal of Gene Expression Signatures Identifies TOP2A as a Therapeutic Target for Rectal Cancer. Cancers (Basel) 2021; 13:5492. [PMID: 34771654 PMCID: PMC8583090 DOI: 10.3390/cancers13215492] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/21/2021] [Accepted: 10/28/2021] [Indexed: 12/12/2022] Open
Abstract
Rectal cancer is a common disease with high mortality rates and limited therapeutic options. Here we combined the gene expression signatures of rectal cancer patients with the reverse drug-induced gene-expression profiles to identify drug repositioning candidates for cancer therapy. Among the predicted repurposable drugs, topoisomerase II inhibitors (doxorubicin, teniposide, idarubicin, mitoxantrone, and epirubicin) presented a high potential to reverse rectal cancer gene expression signatures. We showed that these drugs effectively reduced the growth of colorectal cancer cell lines closely representing rectal cancer signatures. We also found a clear correlation between topoisomerase 2A (TOP2A) gene copy number or expression levels with the sensitivity to topoisomerase II inhibitors. Furthermore, CRISPR-Cas9 and shRNA screenings confirmed that loss-of-function of the TOP2A has the highest efficacy in reducing cellular proliferation. Finally, we observed significant TOP2A copy number gains and increased expression in independent cohorts of rectal cancer patients. These findings can be translated into clinical practice to evaluate TOP2A status for targeted and personalized therapies based on topoisomerase II inhibitors in rectal cancer patients.
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Affiliation(s)
- Robson Francisco Carvalho
- Department of Clinical Genetics, University Hospital of Southern Denmark, 7100 Vejle, Denmark;
- Institute of Regional Health Research, University of Southern Denmark, 5230 Odense, Denmark
- Department of Functional and Structural Biology—Institute of Bioscience, São Paulo State University (UNESP), Botucatu 18618-689, Brazil;
| | - Luisa Matos do Canto
- Department of Clinical Genetics, University Hospital of Southern Denmark, 7100 Vejle, Denmark;
- Institute of Regional Health Research, University of Southern Denmark, 5230 Odense, Denmark
| | - Sarah Santiloni Cury
- Department of Functional and Structural Biology—Institute of Bioscience, São Paulo State University (UNESP), Botucatu 18618-689, Brazil;
| | - Torben Frøstrup Hansen
- Department of Oncology, University Hospital of Southern Denmark, 7100 Vejle, Denmark; (T.F.H.); (L.H.J.)
- Danish Colorectal Cancer Center South, 7100 Vejle, Denmark
| | - Lars Henrik Jensen
- Department of Oncology, University Hospital of Southern Denmark, 7100 Vejle, Denmark; (T.F.H.); (L.H.J.)
- Danish Colorectal Cancer Center South, 7100 Vejle, Denmark
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, University Hospital of Southern Denmark, 7100 Vejle, Denmark;
- Institute of Regional Health Research, University of Southern Denmark, 5230 Odense, Denmark
- Danish Colorectal Cancer Center South, 7100 Vejle, Denmark
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11
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Lucchetta M, Pellegrini M. Drug repositioning by merging active subnetworks validated in cancer and COVID-19. Sci Rep 2021; 11:19839. [PMID: 34615934 PMCID: PMC8494853 DOI: 10.1038/s41598-021-99399-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 09/23/2021] [Indexed: 02/08/2023] Open
Abstract
Computational drug repositioning aims at ranking and selecting existing drugs for novel diseases or novel use in old diseases. In silico drug screening has the potential for speeding up considerably the shortlisting of promising candidates in response to outbreaks of diseases such as COVID-19 for which no satisfactory cure has yet been found. We describe DrugMerge as a methodology for preclinical computational drug repositioning based on merging multiple drug rankings obtained with an ensemble of disease active subnetworks. DrugMerge uses differential transcriptomic data on drugs and diseases in the context of a large gene co-expression network. Experiments with four benchmark diseases demonstrate that our method detects in first position drugs in clinical use for the specified disease, in all four cases. Application of DrugMerge to COVID-19 found rankings with many drugs currently in clinical trials for COVID-19 in top positions, thus showing that DrugMerge can mimic human expert judgment.
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Affiliation(s)
- Marta Lucchetta
- Institute of Informatics and Telematics (IIT), CNR, Pisa, 56124, Italy
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, 53100, Italy
| | - Marco Pellegrini
- Institute of Informatics and Telematics (IIT), CNR, Pisa, 56124, Italy.
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van Breda SG, Mathijs K, Pieters H, Sági‐Kiss V, Kuhnle GG, Georgiadis P, Saccani G, Parolari G, Virgili R, Sinha R, Hemke G, Hung Y, Verbeke W, Masclee AA, Vleugels‐Simon CB, van Bodegraven AA, de Kok TM. Replacement of Nitrite in Meat Products by Natural Bioactive Compounds Results in Reduced Exposure to N-Nitroso Compounds: The PHYTOME Project. Mol Nutr Food Res 2021; 65:e2001214. [PMID: 34382747 PMCID: PMC8530897 DOI: 10.1002/mnfr.202001214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 07/16/2021] [Indexed: 11/07/2022]
Abstract
SCOPE It has been proposed that endogenously form N-nitroso compounds (NOCs) are partly responsible for the link between red meat consumption and colorectal cancer (CRC) risk. As nitrite has been indicated as critical factor in the formation of NOCs, the impact of replacing the additive sodium nitrite (E250) by botanical extracts in the PHYTOME project is evaluated. METHOD AND RESULTS A human dietary intervention study is conducted in which healthy subjects consume 300 g of meat for 2 weeks, in subsequent order: conventional processed red meat, white meat, and processed red meat with standard or reduced levels of nitrite and added phytochemicals. Consumption of red meat products enriched with phytochemicals leads to a significant reduction in the faecal excretion of NOCs, as compared to traditionally processed red meat products. Gene expression changes identify cell proliferation as main affects molecular mechanism. High nitrate levels in drinking water in combination with processed red meat intake further stimulates NOC formation, an effect that could be mitigated by replacement of E250 by natural plant extracts. CONCLUSION These findings suggest that addition of natural extracts to conventionally processed red meat products may help to reduce CRC risk, which is mechanistically support by gene expression analyses.
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Affiliation(s)
- Simone G. van Breda
- Department of ToxicogenomicsGROW‐school for Oncology and Developmental BiologyMaastricht University Medical CenterP.O. Box 616, 6200 MD Maastrichtthe Netherlands
| | - Karen Mathijs
- Department of ToxicogenomicsGROW‐school for Oncology and Developmental BiologyMaastricht University Medical CenterP.O. Box 616, 6200 MD Maastrichtthe Netherlands
| | - Harm‐Jan Pieters
- Department of ToxicogenomicsGROW‐school for Oncology and Developmental BiologyMaastricht University Medical CenterP.O. Box 616, 6200 MD Maastrichtthe Netherlands
| | - Virág Sági‐Kiss
- Department of Food & Nutritional SciencesUniversity of ReadingReadingUK
| | - Gunter G. Kuhnle
- Department of Food & Nutritional SciencesUniversity of ReadingReadingUK
| | - Panagiotis Georgiadis
- National Hellenic Research FoundationInstitute of BiologyMedicinal Chemistry and BiotechnologyAthensGreece
| | - Giovanna Saccani
- SSICA‐Experimental Station for the Food Preserving IndustryParmaItaly
| | - Giovanni Parolari
- SSICA‐Experimental Station for the Food Preserving IndustryParmaItaly
| | - Roberta Virgili
- SSICA‐Experimental Station for the Food Preserving IndustryParmaItaly
| | - Rashmi Sinha
- Division of Cancer Epidemiology & GeneticsNational Cancer InstituteNational Institutes of HealthBethesdaMDUSA
| | - Gert Hemke
- Hemke NutriconsultPrins Clauslaan 70, 5684 GB BestThe Netherlands
| | - Yung Hung
- Department of Agricultural EconomicsGhent UniversityCoupure links 653Gent9000Belgium
| | - Wim Verbeke
- Department of Agricultural EconomicsGhent UniversityCoupure links 653Gent9000Belgium
| | - Ad A. Masclee
- Division of Gastroenterology‐HepatologyDepartment of Internal MedicineMaastricht University Medical CenterMaastrichtThe Netherlands
| | | | | | - Theo M. de Kok
- Department of ToxicogenomicsGROW‐school for Oncology and Developmental BiologyMaastricht University Medical CenterP.O. Box 616, 6200 MD Maastrichtthe Netherlands
| | - the PHYTOME consortium
- Department of ToxicogenomicsGROW‐school for Oncology and Developmental BiologyMaastricht University Medical CenterP.O. Box 616, 6200 MD Maastrichtthe Netherlands
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13
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Tarpgaard LS, Qvortrup C, Nielsen SL, Stenvang J, Detlefsen S, Brünner N, Pfeiffer P. New use for old drugs: Epirubicin in colorectal cancer. Acta Oncol 2021; 60:954-956. [PMID: 33783307 DOI: 10.1080/0284186x.2021.1904519] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
| | - Camilla Qvortrup
- Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Signe L. Nielsen
- Faculty of Health and Medical Sciences, Institute of Drug Design and Pharmacology, University of Copenhagen, Frederiksberg, Denmark
| | - Jan Stenvang
- Faculty of Health and Medical Sciences, Institute of Drug Design and Pharmacology, University of Copenhagen, Frederiksberg, Denmark
| | - Sönke Detlefsen
- Department of Pathology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Nils Brünner
- Faculty of Health and Medical Sciences, Institute of Drug Design and Pharmacology, University of Copenhagen, Frederiksberg, Denmark
| | - Per Pfeiffer
- Department of Oncology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
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14
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Patil AR, Leung MY, Roy S. Identification of Hub Genes in Different Stages of Colorectal Cancer through an Integrated Bioinformatics Approach. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:5564. [PMID: 34070979 PMCID: PMC8197092 DOI: 10.3390/ijerph18115564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022]
Abstract
Colorectal cancer (CRC) is the third most common cancer that contributes to cancer-related morbidity. However, the differential expression of genes in different phases of CRC is largely unknown. Moreover, very little is known about the role of stress-survival pathways in CRC. We sought to discover the hub genes and identify their roles in several key pathways, including oxidative stress and apoptosis in the different stages of CRC. To identify the hub genes that may be involved in the different stages of CRC, gene expression datasets were obtained from the gene expression omnibus (GEO) database. The differentially expressed genes (DEGs) common among the different datasets for each group were obtained using the robust rank aggregation method. Then, gene enrichment analysis was carried out with Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases. Finally, the protein-protein interaction networks were constructed using the Cytoscape software. We identified 40 hub genes and performed enrichment analysis for each group. We also used the Oncomine database to identify the DEGs related to stress-survival and apoptosis pathways involved in different stages of CRC. In conclusion, the hub genes were found to be enriched in several key pathways, including the cell cycle and p53 signaling pathway. Some of the hub genes were also reported in the stress-survival and apoptosis pathways. The hub DEGs revealed from our study may be used as biomarkers and may explain CRC development and progression mechanisms.
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Affiliation(s)
- Abhijeet R. Patil
- Computational Science Program, The University of Texas at El Paso, El Paso, TX 79968, USA; (A.R.P.); (M.-Y.L.)
| | - Ming-Ying Leung
- Computational Science Program, The University of Texas at El Paso, El Paso, TX 79968, USA; (A.R.P.); (M.-Y.L.)
- Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968, USA
- Department of Mathematical Sciences, The University of Texas at El Paso, El Paso, TX 79968, USA
| | - Sourav Roy
- Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968, USA
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX 79968, USA
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15
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Basnet U, Patil AR, Kulkarni A, Roy S. Role of Stress-Survival Pathways and Transcriptomic Alterations in Progression of Colorectal Cancer: A Health Disparities Perspective. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:5525. [PMID: 34063993 PMCID: PMC8196775 DOI: 10.3390/ijerph18115525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/07/2021] [Accepted: 05/19/2021] [Indexed: 12/09/2022]
Abstract
Every year, more than a million individuals are diagnosed with colorectal cancer (CRC) across the world. Certain lifestyle and genetic factors are known to drive the high incidence and mortality rates in some groups of individuals. The presence of enormous amounts of reactive oxygen species is implicated for the on-set and carcinogenesis, and oxidant scavengers are thought to be important in CRC therapy. In this review, we focus on the ethnicity-based CRC disparities in the U.S., the negative effects of oxidative stress and apoptosis, and gene regulation in CRC carcinogenesis. We also highlight the use of antioxidants for CRC treatment, along with screening for certain regulatory genetic elements and oxidative stress indicators as potential biomarkers to determine the CRC risk and progression.
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Affiliation(s)
- Urbashi Basnet
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA; (U.B.); (A.K.)
| | - Abhijeet R. Patil
- Computational Science Program, University of Texas at El Paso, El Paso, TX 79968, USA;
| | - Aditi Kulkarni
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA; (U.B.); (A.K.)
| | - Sourav Roy
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA; (U.B.); (A.K.)
- The Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX 79968, USA
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16
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Wang J, Wang F, Li Q, Wang Q, Li J, Wang Y, Sun J, Lu D, Zhou H, Li S, Ma S, Xie J, Wen T. Proteomics and molecular network analyses reveal that the interaction between the TAT-DCF1 peptide and TAF6 induces an antitumor effect in glioma cells. Mol Omics 2021; 16:73-82. [PMID: 31899468 DOI: 10.1039/c9mo00068b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Glioblastoma is the most lethal brain cancer in adults. Despite advances in surgical techniques, radiotherapy, and chemotherapy, their therapeutic effect is far from significant, since the detailed underlying pathological mechanism of this cancer is unclear. The establishment of molecular interaction networks has laid the foundation for the exploration of these mechanisms with a view to improving therapy for glioblastoma. In the present study, to further explore the cellular role of DCF1 (dendritic cell-derived factor 1), the proteins bound to TAT-DCF1 (transactivator of transcription-dendritic cell-derived factor 1) were identified, and biosystem analysis was employed. Functional enrichment analyses indicate that TAT-DCF1 induced important biological changes in U251 cells. Furthermore, the established molecular interaction networks indicated that TAT-DCF1 directly interacted with TAF6 in glioma cells and with UBC in HEK293T (human embryonic kidney 293T) cells. In addition, further biological experiments demonstrate that TAT-DCF1 induced the activation of the RPS27A/TOP2A/HMGB2/BCL-2 signaling pathway via interaction with TAF6 in U251 cells. Taken together, these findings suggest that the TAT-DCF1 peptide possesses great potential for the development of glioblastoma therapy through the interaction with TAF6-related pathways and provides further theoretic evidence for the mechanisms underlying the antitumor effects of TAT-DCF1.
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Affiliation(s)
- Jiao Wang
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, 99 Shang Da Road, Shanghai 200444, China.
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17
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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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18
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Chen X, Wang L, Su X, Luo SY, Tang X, Huang Y. Identification of potential target genes and crucial pathways in small cell lung cancer based on bioinformatic strategy and human samples. PLoS One 2020; 15:e0242194. [PMID: 33186389 PMCID: PMC7665632 DOI: 10.1371/journal.pone.0242194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
Small cell lung cancer (SCLC) is a carcinoma of the lungs with strong invasion, poor prognosis and resistant to multiple chemotherapeutic drugs. It has posed severe challenges for the effective treatment of lung cancer. Therefore, searching for genes related to the development and prognosis of SCLC and uncovering their underlying molecular mechanisms are urgent problems to be resolved. This study is aimed at exploring the potential pathogenic and prognostic crucial genes and key pathways of SCLC via bioinformatic analysis of public datasets. Firstly, 117 SCLC samples and 51 normal lung samples were collected and analyzed from three gene expression datasets. Then, 102 up-regulated and 106 down-regulated differentially expressed genes (DEGs) were observed. And then, functional annotation and pathway enrichment analyzes of DEGs was performed utilizing the FunRich. The protein-protein interaction (PPI) network of the DEGs was constructed through the STRING website, visualized by Cytoscape. Finally, the expression levels of eight hub genes were confirmed in Oncomine database and human samples from SCLC patients. It showed that CDC20, BUB1, TOP2A, RRM2, CCNA2, UBE2C, MAD2L1, and BUB1B were upregulated in SCLC tissues compared to paired adjacent non-cancerous tissues. These suggested that eight hub genes might be viewed as new biomarkers for prognosis of SCLC or to guide individualized medication for the therapy of SCLC.
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Affiliation(s)
- Xiuwen Chen
- Department of Pathology, Taihe Hospital, Hubei University of Medicine, Hubei, China
| | - Li Wang
- Department of Pathology, Taihe Hospital, Hubei University of Medicine, Hubei, China
| | - Xiaomin Su
- Department of Immunology, Nankai University School of Medicine, Tianjin, China
| | - Sen-yuan Luo
- Department of Pathology, Taihe Hospital, Hubei University of Medicine, Hubei, China
| | - Xianbin Tang
- Department of Pathology, Taihe Hospital, Hubei University of Medicine, Hubei, China
| | - Yugang Huang
- Department of Pathology, Taihe Hospital, Hubei University of Medicine, Hubei, China
- * E-mail:
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Wang YQ, Yang YS, Chen J, Liu MH, Chen GQ, Huang Y. FAM122A maintains DNA stability possibly through the regulation of topoisomerase IIα expression. Exp Cell Res 2020; 396:112242. [PMID: 32866497 DOI: 10.1016/j.yexcr.2020.112242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/31/2020] [Accepted: 08/19/2020] [Indexed: 12/22/2022]
Abstract
FAM122A is a housekeeping gene and highly conserved in mammals. More recently, we have demonstrated that FAM122A is essential for maintaining the growth of hepatocellular carcinoma cells, in which we unexpectedly found that FAM122A deletion increases γH2AX protein level, suggesting that FAM122A may participate in the regulation of DNA homeostasis or stability. In this study, we continued to investigate the potential role of FAM122A in DNA damage and/or repair. We found that CRISPR/Cas9-mediated FAM122A deletion enhances endogenous DNA damages in cancer cells but not in normal cells, demonstrating a significant increase in γH2AX protein and foci formation of γH2AX and 53BP1, as well as DNA breaks by comet assay. Further, we found that FAM122A deletion greatly increases TOP2α protein level, and significantly and specifically enhances TOP2 poisons (etoposide and doxorubicin)-induced DNA damage effects in cancer cells. Moreover, FAM122A is found to be interacted with TOP2α, instead of TOP2β. However, FAM122A knockout doesn't affect the intracellular ROS levels and the process of DNA repair after removal of etoposide with short-term stimulation, suggesting that FAM122A deletion-enhanced DNA damage does not result from endogenous overproduction of ROS and/or impairment of DNA repair ability. Collectively, our study provides the first demonstration that FAM122A is critical for maintaining DNA stability probably by modulating TOP2α protein, and FAM122A deletion combined with TOP2-targeted drugs may represent a potential novel chemotherapeutic strategy for cancer patients.
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Affiliation(s)
- Yin-Qi Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, and Chinese Academy of Medical Sciences Research Unit, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yun-Sheng Yang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, and Chinese Academy of Medical Sciences Research Unit, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Chen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, and Chinese Academy of Medical Sciences Research Unit, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Man-Hua Liu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, and Chinese Academy of Medical Sciences Research Unit, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guo-Qiang Chen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, and Chinese Academy of Medical Sciences Research Unit, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Huang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, and Chinese Academy of Medical Sciences Research Unit, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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20
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Vennou KE, Piovani D, Kontou PI, Bonovas S, Bagos PG. Multiple outcome meta-analysis of gene-expression data in inflammatory bowel disease. Genomics 2020; 112:1761-1767. [DOI: 10.1016/j.ygeno.2019.09.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 01/02/2023]
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21
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Ding X, Duan H, Luo H. Identification of Core Gene Expression Signature and Key Pathways in Colorectal Cancer. Front Genet 2020; 11:45. [PMID: 32153633 PMCID: PMC7046836 DOI: 10.3389/fgene.2020.00045] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/15/2020] [Indexed: 12/17/2022] Open
Abstract
Objective Colorectal cancer (CRC) is considered the most prevalent malignant tumor that contributes to high cancer-related mortality. However, the signaling pathways involved in CRC and CRC-driven genes are largely unknown. We sought to discover a novel biomarker in CRC. Materials and Methods All clinical CRC samples (n = 20) were from Renmin Hospital of Wuhan University. We first selected MAD2L1 by integrated bioinformatics analysis of a GSE dataset. Next, the expression of MAD2L1 in tissues and cell lines was verified by quantitative real-time PCR. The effects of MAD2L1 on cell growth, proliferation, the cell cycle, and apoptosis were examined by in vitro assays. Results We identified 683 shared DEGs (420 upregulated and 263 downregulated), and the top twenty genes (CDK1, CCNA2, TOP2A, PLK1, MAD2L1, AURKA, BUB1B, UBE2C, TPX2, RRM2, KIF11, NCAPG, MELK, NUSAP1, MCM4, RFC4, PTTG1, CHEK1, CEP55, DTL) were selected by integrated analysis. These hub genes were significantly overexpressed in CRC samples and were positively correlated. Our data revealed that the expression of MAD2L1 in CRC tissues is higher than that in normal tissues. MAD2L1 knockdown significantly suppressed CRC cell growth by impairing cell cycle progression and inducing cell apoptosis. Conclusion MAD2L1, as a novel oncogenic gene, plays a role in regulating cancer cell growth and apoptosis and could be used as a new biomarker for diagnosis and therapy in CRC.
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Affiliation(s)
- Xiang Ding
- Department of Gastroenterology, Renmin Hospital, Wuhan University, Wuhan, China
| | - Houyu Duan
- Department of Gastroenterology, Renmin Hospital, Wuhan University, Wuhan, China
| | - Hesheng Luo
- Department of Gastroenterology, Renmin Hospital, Wuhan University, Wuhan, China
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22
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Chen Z, Lin Y, Gao J, Lin S, Zheng Y, Liu Y, Chen SQ. Identification of key candidate genes for colorectal cancer by bioinformatics analysis. Oncol Lett 2019; 18:6583-6593. [PMID: 31788116 PMCID: PMC6865583 DOI: 10.3892/ol.2019.10996] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 08/16/2019] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers of the digestive tract. Although numerous studies have been conducted to elucidate the cause of CRC, the exact mechanism of CRC development remains to be determined. To identify candidate genes that may be involved in CRC development and progression, the microarray datasets GSE41657, GSE77953 and GSE113513 were downloaded from the Gene Expression Omnibus database. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes were used for functional enrichment analysis of differentially expressed genes (DEGs). A protein-protein interaction network was constructed, and the hub genes were subjected to module analysis and identification using Search Tool for the Retrieval of Interacting Genes/Proteins and Cytoscape. A total of 142 DEGs were identified, with enriched functions and pathways in the ‘cell cycle’, ‘cell proliferation’, ‘the mitotic cell cycle’ and ‘one-carbon metabolic process’. In addition, 10 hub genes were identified, and functional analysis indicated that these genes are mainly enriched in ‘cell division’, ‘cell cycle’ and functions associated with nucleotide binding processes. Survival analysis demonstrated that DNA topoisomerase II α, cyclin-dependent kinase 1 and CDC28 protein kinase regulatory subunit 2 may be involved in cancer invasion or recurrence. The DEGs identified in the present study may help explain the molecular mechanisms of CRC development and progression.
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Affiliation(s)
- Zhihua Chen
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350004, P.R. China
| | - Yilin Lin
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350004, P.R. China
| | - Ji Gao
- School of Nursing, Fujian Medical University, Fuzhou, Fujian 350004, P.R. China
| | - Suyong Lin
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350004, P.R. China
| | - Yan Zheng
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350004, P.R. China
| | - Yisu Liu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350004, P.R. China
| | - Shao Qin Chen
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350004, P.R. China
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23
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Fang Y, Yang C, Zhang L, Wei L, Lin J, Zhao J, Peng J. Spica Prunellae Extract Enhances Fluorouracil Sensitivity of 5-Fluorouracil-Resistant Human Colon Carcinoma HCT-8/5-FU Cells via TOP2 α and miR-494. BIOMED RESEARCH INTERNATIONAL 2019; 2019:5953619. [PMID: 31662984 PMCID: PMC6791265 DOI: 10.1155/2019/5953619] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/12/2019] [Accepted: 08/09/2019] [Indexed: 02/07/2023]
Abstract
The use of 5-fluorouracil (5-FU) has been proven benefits, but it also has adverse events in colorectal cancer (CRC) chemotherapy. In this study, we explored the mechanism of 5-FU resistance by bioinformatics analysis of the NCBI public dataset series GSE81005. Fifteen hub genes were screened out of 582 different expressed genes. Modules of the hub genes in protein-protein interaction networks gathered to TOP2α showed a decrease in HCT-8 cells but an increase in 5-FU-resistant HCT-8/5-FU cells with 5-FU exposure. Downregulation of TOP2α with siRNA or miR-494 transfection resulted in an increase of cytotoxicity and decrease of cell colonies to 5-FU for HCT-8/5-FU cells. Moreover, we found that an ethanol extract of Spica Prunellae (EESP), which is a traditional Chinese medicine with clinically beneficial effects in various cancers, was able to enhance the sensitivity of 5-FU in HCT-8/5-FU cells and partly reverse the 5-FU resistance effect. It significantly helped suppress cell growth and induced cell apoptosis in HCT-8/5-FU cells with the expression of TOP2α being significantly suppressed, which increased by 5-FU. Consistently, miR-494, which reportedly regulates TOP2α, exhibited reverse trends in EESP/5-FU combination treatment. These results suggested that Spica Prunellae may be beneficial in the treatment of 5-FU-resistant CRC patients.
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Affiliation(s)
- Yi Fang
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
- Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - Chi Yang
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Ling Zhang
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
- Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - Lihui Wei
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
- Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - Jiumao Lin
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
- Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - Jinyan Zhao
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
- Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - Jun Peng
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
- Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
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Yu C, Chen F, Jiang J, Zhang H, Zhou M. Screening key genes and signaling pathways in colorectal cancer by integrated bioinformatics analysis. Mol Med Rep 2019; 20:1259-1269. [PMID: 31173250 PMCID: PMC6625394 DOI: 10.3892/mmr.2019.10336] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 04/24/2019] [Indexed: 01/14/2023] Open
Abstract
The aim of the present study was to identify potential key genes associated with the progression and prognosis of colorectal cancer (CRC). Differentially expressed genes (DEGs) between CRC and normal samples were screened by integrated analysis of gene expression profile datasets, including the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was conducted to identify the biological role of DEGs. In addition, a protein‑protein interaction network and survival analysis were used to identify the key genes. The profiles of GSE9348, GSE22598 and GSE113513 were downloaded from the GEO database. A total of 405 common DEGs were identified, including 236 down‑ and 169 upregulated. GO analysis revealed that the downregulated DEGs were mainly enriched in 'detoxification of copper ion' [biological process, (BP)], 'oxidoreductase activity, acting on CH‑OH group of donors, NAD or NADP as acceptor' [molecular function, (MF)] and 'brush border' [cellular component, (CC)]. Upregulated DEGs were mainly involved in 'nuclear division' (BP), 'snoRNA binding' (MF) and 'nucleolar part' (CC). KEGG pathway analysis revealed that DEGs were mainly involved in 'mineral absorption', 'nitrogen metabolism', 'cell cycle' and 'caffeine metabolism'. A PPI network was constructed with 268 nodes and 1,027 edges. The top one module was selected, and it was revealed that module‑related genes were mainly enriched in the GO terms 'sister chromatid segregation' (BP), 'chemokine activity' (MF), and 'condensed chromosome (CC)'. The KEGG pathway was mainly enriched in 'cell cycle', 'progesterone‑mediated oocyte maturation', 'chemokine signaling pathway', 'IL‑17 signaling pathway', 'legionellosis', and 'rheumatoid arthritis'. DNA topoisomerase II‑α (TOP2A), mitotic arrest deficient 2 like 1 (MAD2L1), cyclin B1 (CCNB1), checkpoint kinase 1 (CHEK1), cell division cycle 6 (CDC6) and ubiquitin conjugating enzyme E2 C (UBE2C) were indicated as hub genes. Furthermore, survival analysis revealed that TOP2A, MAD2L1, CDC6 and CHEK1 may serve as prognostic biomarkers in CRC. The present study provided insights into the molecular mechanism of CRC that may be useful in further investigations.
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Affiliation(s)
- Chang Yu
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Fuqiang Chen
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Jianjun Jiang
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Hong Zhang
- The First Affiliated Hospital, University of Science and Technology of China, Hefei, Anhui 230026, P.R. China
| | - Meijuan Zhou
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
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25
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Qi Y, Qi H, Liu Z, He P, Li B. Bioinformatics Analysis of Key Genes and Pathways in Colorectal Cancer. J Comput Biol 2019; 26:364-375. [PMID: 30810359 DOI: 10.1089/cmb.2018.0237] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is the third most prevalent cancer in the world. Although great progress has been made, the specific molecular mechanism remains unclear. This study aimed to explore the differentially expressed genes (DEGs) and underlying mechanisms of CRC using bioinformatics analysis. In this study, we identified a total of 1353 DEGs in the database of GSE113513, including 715 up- and 638 downregulated genes. Gene ontology analysis results showed that upregulated DEGs were significantly enriched in cell division, cell proliferation, and DNA replication. The downregulated DEGs were enriched in immune response, relation of cell growth and inflammatory response. The Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that upregulated DEGs were enriched in cell cycle and p53 signaling pathway, whereas the downregulated DEGs were enriched in drug metabolism, metabolism of xenobiotics by cytochrome P450, and nitrogen metabolism. A total of 124 up-key genes and 35 down-key genes were identified from the protein-protein interaction networks. Furthermore, we identified five up-modules (up-A, up-B, up-C, up-D, and up-E) and three down-modules (d-A, d-B, and d-C) by module analysis. The module up-A was enriched in sister chromatid cohesion, cell division, and mitotic nuclear division. Pathways associated with cell cycle, progesterone-mediated oocyte maturation, oocyte meiosis, and p53 signaling pathway. Whereas the d-A was mainly enriched in G-protein coupled receptor signaling pathway, cell chemotaxis, and chemokine-mediated signaling pathway. The pathways enriched in chemokine signaling pathway, cytokine-cytokine receptor interaction, and alcoholism. These key genes and pathways might be used as molecular targets and diagnostic biomarkers for the treatment of CRC.
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Affiliation(s)
- Yuewen Qi
- 1 Department of Gastroenterology, Affiliated Hospital of Chengde Medical College, Chengde, P.R. China
| | - Haowen Qi
- 2 Department of Acupuncture and Massage, Chengde Hospital of Traditional Chinese Medicine, Chengde, P.R. China
| | - Zeyuan Liu
- 3 Department of Special Medicine, Qingdao University Medical College, Qingdao, P.R. China
| | - Peiyuan He
- 1 Department of Gastroenterology, Affiliated Hospital of Chengde Medical College, Chengde, P.R. China
| | - Bingqing Li
- 1 Department of Gastroenterology, Affiliated Hospital of Chengde Medical College, Chengde, P.R. China
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Gan Y, Li Y, Li T, Shu G, Yin G. CCNA2 acts as a novel biomarker in regulating the growth and apoptosis of colorectal cancer. Cancer Manag Res 2018; 10:5113-5124. [PMID: 30464611 PMCID: PMC6217169 DOI: 10.2147/cmar.s176833] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE Colorectal cancer (CRC) is considered to be the most prevalent malignant tumors that contribute to high cancer-related mortality. However, the signaling pathways involved in CRC and CRC-driven genes are largely unknown. We seek to discover a novel biomarker in CRC. MATERIALS AND METHODS All clinical CRC samples (n=33) were from Xiangya Hospital. We first selected CCNA2 by integrated bioinformatics analysis of four GSE databases. Next, the expression of CCNA2 in tissues and cell lines was verified by quantitative real-time PCR. The effects of CCNA2 on cell growth, proliferation, cell cycle, and apoptosis were examined by in vitro assays. RESULTS We identified 498 shared DEGs (294 upregulated and 204 downregulated), and the top ten hub genes were selected by integrated analysis. These hub genes were significantly overexpressed in CRC samples and were positively correlated. Our data revealed that the expression of CCNA2 in CRC tissues is higher than that in normal tissues. The CCNA2 knockdown could significantly suppress CRC cell growth by impairing cell cycle progression and inducing cell apoptosis. CONCLUSION CCNA2, as a novel oncogenic gene, plays a role in regulating cancer cell growth and apoptosis. It could be used as a new biomarker for diagnosis and therapy in CRC.
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Affiliation(s)
- Yaqi Gan
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan Province, China,
- Department of Pathology, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China,
| | - Yimin Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan Province, China,
- Department of Pathology, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China,
| | - Tong Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan Province, China,
- Department of Pathology, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China,
| | - Guang Shu
- Department of Pathology, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China,
| | - Gang Yin
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan Province, China,
- Department of Pathology, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China,
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27
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Xiong Y, Yuan L, Chen L, Zhu Y, Zhang S, Liu X, Xiao Y, Wang X. Identifying a Novel Biomarker TOP2A of Clear Cell Renal Cell Carcinoma (ccRCC) Associated with Smoking by Co-Expression Network Analysis. J Cancer 2018; 9:3912-3922. [PMID: 30410595 PMCID: PMC6218786 DOI: 10.7150/jca.25900] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/26/2018] [Indexed: 12/16/2022] Open
Abstract
Although it is well known that smoking is one of pathogenesis of clear cell renal cell carcinoma (ccRCC), the underlying molecular mechanism is still unclear. In our study, the microarray dataset GSE46699 is analyzed by weighted gene co-expression network analysis (WGCNA). Then we identify 15 co-expressed gene modules in which the lightcyan module (R2 = 0.30) is the most significant. Combined with the protein-protein interaction (PPI) network and WGCNA, two hub genes are identified. Meanwhile, linear regression analyses indicate that TOP2A has a higher connection with smoking in ccRCC, survival analysis proved that overexpression of TOP2A in ccRCC could lead to shorter survival time. Furthermore, bioinformatical analyses based on GSE46699 and GSE2109 as well as qRT-PCR experiment show similar results that TOP2A is significantly up-regulated in smoking ccRCC compared to non-smoking ccRCC samples. In addition, Functional analysis, pathway enrichment analysis and gene set enrichment analysis (GSEA) indicate that high expression of TOP2A is related to cell cycle and p53 signaling pathway in ccRCC samples. Moreover, in vitro experiments revealed that TOP2A induced cell cycle arrest at G2 phase and proliferation inhibition via p53 phosphorylation. Taken together, by using WGCNA, we have identified a novel biomarker named TOP2A, which could affect the development of smoking-related ccRCC by regulating cell cycle and p53 signaling pathway.
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Affiliation(s)
- Yaoyi Xiong
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Lushun Yuan
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Liang Chen
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yuan Zhu
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan, China
| | - Shanshan Zhang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan, China
| | - Xuefeng Liu
- Department of Pathology, Lombardi Comprehensive Cancer Center, Georgetown University Medical School, Washington DC, USA
| | - Yu Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan, China
| | - Xinghuan Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
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Ren L, Liu J, Gou K, Xing C. Copy number variation and high expression of DNA topoisomerase II alpha predict worse prognosis of cancer: a meta-analysis. J Cancer 2018; 9:2082-2092. [PMID: 29937926 PMCID: PMC6010676 DOI: 10.7150/jca.23681] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/26/2018] [Indexed: 12/20/2022] Open
Abstract
Background: Increasing numbers of literatures have investigated the association between TOP2A and cancer prognosis. But the results of the relationship between the two were inconclusive. The aim of this meta-analysis was to elucidate whether TOP2A could predict prognosis of cancer. Materials and Methods: A systematically searching for potentially valuable literature was conducted through electronic databases containing PubMed and Web of Science. Hazard Ratio (HR) and their 95% confidence interval (CI) were used to assess the strength of association between TOP2A and cancer prognosis. Results: Finally twenty-five studies were included in this meta-analysis. High expression of TOP2A was associated with shorter disease free survival (DFS) of cancer prognosis compared with low expression of TOP2A (HR= 1.36, 95% CI= 1.18-1.57, P<0.001). Amplification of TOP2A gene showed no significant association with overall survival (OS), disease free survival (DFS) or relapse free survival (RFS) compared with non-amplification of TOP2A (OS: HR= 0.96, 95%CI= 0.75-1.22, P= 0.735; DFS: HR= 0.93, 95%CI= 0.70-1.23, P= 0.621; RFS: HR= 0.97, 95%CI= 0.71-1.34, P= 0.867). In the subgroup of regions, TOP2A amplification was associated with longer overall survival (HR= 0.66, 95%CI= 0.46-0.96, P= 0.029) in Australia. Alteration (amplification or deletion) of TOP2A gene demonstrated shorter survival according to OS and RFS compared with those with normal TOP2A status (OS: HR= 1.37, 95%CI= 1.22-1.55, P<0.001; RFS: HR= 1.26, 95%CI= 1.12-1.41, P<0.001). Conclusion: High TOP2A expression suggested significant relationship with worse cancer prognosis. Alteration (amplification or deletion) of TOP2A gene was also significantly related to shorter survival of cancer patients. Therefore, TOP2A might be used as an indicator for poor prognosis of cancer in the future.
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Affiliation(s)
| | | | | | - Chengzhong Xing
- Department of anorectal surgery, the First Affiliated Hospital of China Medical University
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29
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Identification of Common Genes Refers to Colorectal Carcinogenesis with Paired Cancer and Noncancer Samples. DISEASE MARKERS 2018; 2018:3452739. [PMID: 29651323 PMCID: PMC5830953 DOI: 10.1155/2018/3452739] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/16/2017] [Indexed: 12/13/2022]
Abstract
Colorectal cancer is a malignant tumor which harmed human beings' health. The aim of this study was to explore common biomarkers associated with colorectal carcinogenesis in paired cancer and noncancer samples. At first, fifty-nine pairs of colorectal cancer and noncancer samples from three gene expression datasets were collected and analyzed. Then, 181 upregulation and 282 downregulation common differential expression genes (DEGs) were found. Next, functional annotation was performed in the DAVID database with the DEGs. Finally, real-time polymerase chain reaction (PCR) assay was conducted to verify the analyses in sixteen colorectal cancer and individual-matched adjacent mucosa samples. Real-time PCR showed that MCM2, RNASEH2A, and TOP2A were upregulated in colorectal cancer compared with adjacent mucosa samples (MCM2, P < 0.001; RNASEH2A, P < 0.001; TOP2A, P = 0.001). These suggested that 463 DEGs might contribute to colorectal carcinogenesis.
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30
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Shvero A, Hilly O, Bubis G, Hamzany Y, Koren R, Rath-Wolfson L. Expression of Topoisomerase II-α protein in salivary gland tumors. Mol Clin Oncol 2017; 7:1064-1068. [PMID: 29285375 DOI: 10.3892/mco.2017.1463] [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: 05/24/2017] [Accepted: 10/18/2017] [Indexed: 11/05/2022] Open
Abstract
Salivary glands give rise to approximately 30 histological distinct tumor types, which results in a diagnostic challenge for the pathologist. The present retrospective, immunohistochemical study aimed to evaluate the expression of Topoisomerase II-α, a nuclear enzyme, as a diagnostic and prognostic marker in benign and malignant salivary gland tumors, including leomorphic adenoma, mucoepidermoid carcinoma, acinic cell carcinoma and carcinoma ex-pleomorphic adenoma. A total of 59 cases of benign and malignant salivary gland tumors were included in the present study. Representative paraffin-embedded sections were immunostained for Topoisomerase II-α (Topo II-α). The expression level was semi-quantified for each case and then correlated with the histological diagnosis using hematoxylin and eosin-stained slides, grade of tumor and total survival. Significant differences were revealed between the expression level of Topo II-α in pleomorphic adenoma and mucoepidermoid carcinoma (P<0.001), carcinoma ex-pleomorphic adenoma (P<0.001), acinic cell carcinoma (P=0.005) and a group composed of all the malignant tumors (P<0.001). Cancer-specific survival rates were insignificantly increased in tumors expressing low levels of Topo II-α (P=0.464). Thus, the present study demonstrated different expression levels of Topo II-α in benign and malignant salivary gland tumors. These differing expression levels may act as valuable biomarkers for the correct histological diagnosis. Further studies conducted on a larger scale may lead to even more conclusive results.
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Affiliation(s)
- Asaf Shvero
- Department of Urology, Sheba Medical Center, Tel Hashomer, Israel.,Sackler School of Medicine Tel Aviv University, Tel Aviv, Israel
| | - Ohad Hilly
- Sackler School of Medicine Tel Aviv University, Tel Aviv, Israel.,Otolaryngology-Head and Neck Surgery, Rabin Medical Center, Petah Tikva, Israel
| | - Golan Bubis
- St. George's University of London, University of Nicosia, Nicosia, Cyprus
| | - Yaniv Hamzany
- Sackler School of Medicine Tel Aviv University, Tel Aviv, Israel.,Otolaryngology-Head and Neck Surgery, Rabin Medical Center, Petah Tikva, Israel
| | - Rumelia Koren
- Sackler School of Medicine Tel Aviv University, Tel Aviv, Israel.,Department of Pathology, Hasharon Hospital, Rabin Medical Center, Petah Tikva, Israel
| | - Lea Rath-Wolfson
- Sackler School of Medicine Tel Aviv University, Tel Aviv, Israel.,Department of Pathology, Hasharon Hospital, Rabin Medical Center, Petah Tikva, Israel
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31
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Wang L, Tan RZ, Zhang ZX, Yin R, Zhang YL, Cui WJ, He T. Association between Twist and multidrug resistance gene-associated proteins in Taxol ®-resistant MCF-7 cells and a 293 cell model of Twist overexpression. Oncol Lett 2017; 15:1058-1066. [PMID: 29399166 PMCID: PMC5772891 DOI: 10.3892/ol.2017.7438] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 10/18/2017] [Indexed: 12/13/2022] Open
Abstract
Multidrug resistance (MDR) severely limits the effectiveness of chemotherapy. Previous studies have identified Twist as a key factor of acquired MDR in breast, gastric and prostate cancer. However, the underlying mechanisms of action of Twist in MDR remain unclear. In the present study, the expression levels of MDR-associated proteins, including lung resistance-related protein (LRP), topoisomerase IIα (TOPO IIα), MDR-associated protein (MRP) and P-glycoprotein (P-gp), and the expression of Twist in cancerous tissues and pericancerous tissues of human breast cancer, were examined. In order to simulate Taxol® resistance in cells, a Taxol®-resistant human mammary adenocarcinoma cell subline (MCF-7/Taxol®) was established by repeatedly exposing MCF-7 cells to high concentrations of Taxol® (up to 15 µg/ml). Twist was also overexpressed in 293 cells by transfecting this cell line with pcDNA5/FRT/TO vector containing full-length hTwist cDNA to explore the dynamic association between Twist and MDR gene-associated proteins. It was identified that the expression levels of Twist, TOPO IIα, MRP and P-gp were upregulated and LRP was downregulated in human breast cancer tissues, which was consistent with the expression of these proteins in the Taxol®-resistant MCF-7 cell model. Notably, the overexpression of Twist in 293 cells increased the resistance to Taxol®, Trichostatin A and 5-fluorouracil, and also upregulated the expression of MRP and P-gp. Taken together, these data demonstrated that Twist may promote drug resistance in cells and cancer tissues through regulating the expression of MDR gene-associated proteins, which may assist in understanding the mechanisms of action of Twist in drug resistance.
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Affiliation(s)
- Li Wang
- Research Center of Combined Traditional Chinese and Western Medicine, Affiliated Traditional Medicine Hospital, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Rui-Zhi Tan
- Research Center of Combined Traditional Chinese and Western Medicine, Affiliated Traditional Medicine Hospital, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Zhi-Xia Zhang
- Department of Medicine, Zaozhuang Vocational College, Zaozhuang, Shandong 277800, P.R. China
| | - Rui Yin
- Institute for Cancer Medicine, Research Center for Preclinical Medicine and College of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Yong-Liang Zhang
- Institute for Cancer Medicine, Research Center for Preclinical Medicine and College of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Wei-Jia Cui
- Institute for Cancer Medicine, Research Center for Preclinical Medicine and College of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Tao He
- Institute for Cancer Medicine, Research Center for Preclinical Medicine and College of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
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32
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Zhou Z, Liu S, Zhang M, Zhou R, Liu J, Chang Y, Zhao Q. Overexpression of Topoisomerase 2-Alpha Confers a Poor Prognosis in Pancreatic Adenocarcinoma Identified by Co-Expression Analysis. Dig Dis Sci 2017; 62:2790-2800. [PMID: 28815403 DOI: 10.1007/s10620-017-4718-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 08/08/2017] [Indexed: 01/16/2023]
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is the fourth most common cause of human cancer-related death in the developed countries. Its progression and prognosis are influenced by a complex network of gene interactions. AIMS The purpose of this study is to explore key genes associated with pancreatic ductal adenocarcinoma and to predict the possible mechanisms. METHODS A weighted gene co-expression network was constructed to identify gene modules associated with the progression of PDAC. RESULTS In the significant module (R 2 = 0.30), a total of 20 network hub genes were identified, 6 of which were also hub nodes in the protein-protein interaction network of the module genes. In validation, TOP2A has a higher correlation than other hub genes. Also, in the test set (n = 118), TOP2A was more highly expressed in PDAC than normal pancreas samples (P < 0.001). What is more, gene set enrichment analysis demonstrated that eight gene sets (n = 118), "nucleotide excision repair," "P53 signaling pathway," "proteasome," "mismatch repair," "homologous recombination," "DNA replication," "cell cycle," and "base excision repair," were enriched (FDR < 0.05). In gene ontology analysis, TOP2A in the enriched set was associated with cell cycle and cell division. Furthermore, survival analysis indicated that higher expression of TOP2A resulted in the lower overall survival time as well as disease-free survival time. CONCLUSION TOP2A was identified in association with the progression and prognosis of PDAC probably by regulating cell cycle and p53 signaling pathway.
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MESH Headings
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/metabolism
- Carcinoma, Pancreatic Ductal/enzymology
- Carcinoma, Pancreatic Ductal/genetics
- Carcinoma, Pancreatic Ductal/pathology
- Cell Cycle/genetics
- Computational Biology
- DNA Topoisomerases, Type II/genetics
- DNA Topoisomerases, Type II/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Databases, Genetic
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Neoplastic
- Gene Regulatory Networks
- Humans
- Pancreatic Neoplasms/enzymology
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/pathology
- Poly-ADP-Ribose Binding Proteins
- Prognosis
- Protein Interaction Maps
- Signal Transduction
- Systems Biology
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
- Up-Regulation
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Affiliation(s)
- Zhou Zhou
- Department of Gastroenterology, Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Shi Liu
- Department of Gastroenterology, Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Meng Zhang
- Department of Gastroenterology, Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Rui Zhou
- Department of Gastroenterology, Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Jing Liu
- Department of Gastroenterology, Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Ying Chang
- Department of Gastroenterology, Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Qiu Zhao
- Department of Gastroenterology, Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, Hubei Province, People's Republic of China.
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Differences of protein expression profiles, KRAS and BRAF mutation, and prognosis in right-sided colon, left-sided colon and rectal cancer. Sci Rep 2017; 7:7882. [PMID: 28801584 PMCID: PMC5554205 DOI: 10.1038/s41598-017-08413-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 07/10/2017] [Indexed: 01/05/2023] Open
Abstract
To compare protein expression levels, gene mutation and survival among Right-Sided Colon Cancer (RSCC), Left-Sided Colon Cancer (LSCC) and rectal cancer patients, 57 cases of RSCC, 87 LSCC and 145 rectal cancer patients were included retrospectively. Our results demonstrated significant differences existed among RSCC, LSCC and rectal cancer regarding tumor diameter, differentiation, invasion depth and TNM stage. No significant difference was identified in expression levels of MLH1, MSH2, MSH6, PMS2, β-Tubulin III, P53, Ki67 and TOPIIα, and gene mutation of KRAS and BRAF among three groups. Progression Free Survival (PFS) of RSCC was significantly lower than that of LRCC and rectal cancer. In univariate analyses, RSCC, preoperative chemoradiotherapy, poor differentiation, advanced TNM stage, elevated serum CEA and CA19-9 level, tumor deposit, perineural and vascular invasion were found to be predictive factors of shorter PFS. In multivariate analyses, only differentiation and TNM stages were found to be independent predictors of PFS. In conclusion, compared with LSCC and rectal cancer, RSCC has larger tumor size, poor differentiation, advanced TNM stage and shorter survival. The shorter survival in RSCC might be attributed to the advanced tumor stage caused by its inherent position feature of proximal colon rather than genetic difference.
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Cao Y, Ke R, Wang S, Zhu X, Chen J, Huang C, Jiang Y, Lv L. DNA topoisomerase IIα and Ki67 are prognostic factors in patients with hepatocellular carcinoma. Oncol Lett 2017; 13:4109-4116. [PMID: 28599412 PMCID: PMC5453054 DOI: 10.3892/ol.2017.5999] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 02/07/2017] [Indexed: 01/23/2023] Open
Abstract
The present study was designed to determine the significance of DNA topoisomerase IIa (TopoIIα) and Ki67 in hepatocellular carcinoma cells (HCCs). The present study included 353 patients with HCC. The association of clinicopathological data with the expression of TopoIIα and Ki67 by immunohistochemistry was analyzed by χ2 test. Cox multivariate proportional hazards regression analysis and Kaplan-Meier analysis were performed with all the variables to derive risk estimates associated with overall survival (OS)/recurrence-free survival (RFS) and to control for confounders. TopoIIα and Ki67 were detected in the nuclei of the tumor cells. With TopoIIα, 35.7% of cells exhibited high expression, which was associated with tumor-node-metastasis stage, tumor size and α-fetoprotein level. With Ki67, 37.1% of cells exhibited high expression, which was associated with tumor-node-metastasis stage, tumor size and α-fetoprotein level. Correlation was identified between the expression level of TopoIIα and Ki67 in HCCs (r=0.444). Multivariate analysis revealed that high TopoIIα expression is a prognostic indicator for RFS [hazard ratio (HR), 2.002; 95% confidence interval (CI), 1.429–2.806] and OS (HR, 2.749; 95% CI, 1.919–3.939), and high Ki67 expression is a prognostic indicator for OS (HR, 1.816; 95% CI, 1.273–2.589). The TopoIIα-low group had a significantly increased RFS rate (55.6 vs. 31.7%) and OS rate (66.5 vs. 23.8%) compared with the TopoIIα-high group. The OS rate was increased in the Ki67-low group compared with the Ki67-high group (67.0 vs. 26.5%). Expression of TopoIIα and Ki67 are independent prognostic factors for survival in HCCs. TopoIIα was positively associated with Ki67 expression.
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Affiliation(s)
- Yi Cao
- Department of Hepatobiliary Surgery, Fuzhou General Hospital, Fuzhou, Fujian 350025, P.R. China
| | - Ruisheng Ke
- Department of Hepatobiliary Surgery, Fuzhou General Hospital, Fuzhou, Fujian 350025, P.R. China
| | - Shaohu Wang
- Department of Hepatobiliary Surgery, Fuzhou General Hospital, Fuzhou, Fujian 350025, P.R. China
| | - Xu Zhu
- Department of Hepatobiliary Surgery, Fuzhou General Hospital, Fuzhou, Fujian 350025, P.R. China
| | - Jianwei Chen
- Department of Hepatobiliary Surgery, Fuzhou General Hospital, Fuzhou, Fujian 350025, P.R. China
| | - Chao Huang
- Department of Hepatobiliary Surgery, Fuzhou General Hospital, Fuzhou, Fujian 350025, P.R. China
| | - Yi Jiang
- Department of Hepatobiliary Surgery, Fuzhou General Hospital, Fuzhou, Fujian 350025, P.R. China
| | - Lizhi Lv
- Department of Hepatobiliary Surgery, Fuzhou General Hospital, Fuzhou, Fujian 350025, P.R. China
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35
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Chen D, Maruschke M, Hakenberg O, Zimmermann W, Stief CG, Buchner A. TOP2A, HELLS, ATAD2, and TET3 Are Novel Prognostic Markers in Renal Cell Carcinoma. Urology 2017; 102:265.e1-265.e7. [PMID: 28069330 DOI: 10.1016/j.urology.2016.12.050] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 12/21/2016] [Accepted: 12/27/2016] [Indexed: 01/02/2023]
Abstract
OBJECTIVE To identify and validate novel prognostic marker genes in clear cell renal cell carcinoma (RCC) that are increasingly expressed during tumor progression. METHODS Total RNA was isolated from normal renal tissue, primary G1 and G3 tumors, 14 samples each, and 32 metastases from RCC patients. Expression profiles were created using oligonucleotide microarrays. Significant gene expression differences (P < .05) were identified among normal kidney, primary tumor, and metastases. For all filtered genes, univariate survival analysis was carried out. Genes for which lower expression was significantly associated with longer survival were further analyzed using multivariate analysis. Expression of the best candidate markers was further validated in an independent cohort of 55 primary tumors using quantitative real-time polymerase chain reaction. RESULTS Fifty-nine genes exhibited increased expression in primary RCC compared with normal kidney, and in metastases compared with primary tumors. In univariate or multivariate survival analysis, upregulation of 15 genes was significant. Expression of 8 genes was validated by quantitative real-time polymerase chain reaction. Survival analysis in an independent cohort of 55 RCC patients based on expression in primary RCC showed that TOP2A (hazard ratio [HR] = 4.3, P = .005), HELLS (HR = 3.7, P = .007), ATAD2 (HR = 3.7, P = .019), and TET3 (HR = 2.8, P = .035) represent independent predictors for cancer-specific survival. The proteins encoded by these genes function as topoisomerase, helicase, chromatin modifier, and methyl cytosine dioxygenase, respectively. They are involved in proliferation, transcription, and epigenetic modification. CONCLUSION High mRNA levels of TOP2A, HELLS, ATAD2, and TET3 are independent predictors of poor outcome in RCC patients and may be used for individual risk-adapted therapy in the future.
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Affiliation(s)
- Dong Chen
- Department of Urology, Campus Grosshadern, Ludwig-Maximilians-University, Munich, Germany; Department of Urology, Sun-Yat-sen University Cancer Center, Guangzhou, China
| | - Matthias Maruschke
- Department of Urology, University of Rostock, Rostock, Germany; Department of Urology, HELIOS Hanseklinikum Stralsund, Stralsund, Germany
| | | | - Wolfgang Zimmermann
- Tumor Immunology Laboratory, LIFE Center, Ludwig-Maximilians-University, Munich, Germany
| | - Christian G Stief
- Department of Urology, Campus Grosshadern, Ludwig-Maximilians-University, Munich, Germany
| | - Alexander Buchner
- Department of Urology, Campus Grosshadern, Ludwig-Maximilians-University, Munich, Germany.
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Tarpgaard LS, Qvortrup C, Nygård SB, Nielsen SL, Andersen DR, Jensen NF, Stenvang J, Detlefsen S, Brünner N, Pfeiffer P. A phase II study of Epirubicin in oxaliplatin-resistant patients with metastatic colorectal cancer and TOP2A gene amplification. BMC Cancer 2016; 16:91. [PMID: 26867764 PMCID: PMC4750171 DOI: 10.1186/s12885-016-2124-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/03/2016] [Indexed: 12/28/2022] Open
Abstract
ᅟ The overall purpose of this study is to provide proof of concept for introducing the anthracycline epirubicin as an effective, biomarker-guided treatment for metastatic colorectal cancer (mCRC) patients who are refractory to treatment with oxaliplatin-based chemotherapy and have TOP2A gene amplification in their tumor cells. Background Epirubicin is an anthracycline that targets DNA topoisomerase 2-α enzyme encoded by the TOP2A gene. It is used for treatment of several malignancies, but currently not in CRC. TOP2A gene amplifications predict improved efficacy of epirubicin in patients with breast cancer and thus could be an alternative option for patients with CRC and amplified TOP2A gene. We have previously analysed the frequency of TOP2A gene aberrations in CRC and found that 46.6 % of these tumors had TOP2A copy gain and 2.0 % had loss of TOP2A when compared to adjacent normal tissue. The TOP2A gene is located on chromosome 17 and when the TOP2A/CEN-17 ratio was applied to identify tumors with gene loss or amplifications, 10.5 % had a ratio ≥ 1.5 consistent with gene amplification and 2.6 % had a ratio ≤ 0.8 suggesting gene deletions. Based on these observations and the knowledge gained from treatment of breast cancer patients, we have initiated a prospective clinical, phase II protocol using epirubicin (90 mg/m2 iv q 3 weeks) in mCRC patients, who are refractory to treatment with oxaliplatin. Methods/Design The study is an open label, single arm, phase II study, investigating the efficacy of epirubicin in patients with oxaliplatin refractory mCRC and with a cancer cell TOP2A/CEN-17 ratio ≥ 1.5. TOP2A gene amplification measured by fluorescence in situ hybridization. A total of 25 evaluable patients (15 + 10 in two steps) will be included (Simon’s two-stage minimax design). Every nine weeks, response is measured by computed tomography imaging and evaluated according to RECIST 1.1. The primary end-point of the study is progression-free survival. Trial registration Eudract no. 2013-001648-79.
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Affiliation(s)
- Line S Tarpgaard
- Department of Oncology, Odense University Hospital, Odense, Denmark.
| | - Camilla Qvortrup
- Department of Oncology, Odense University Hospital, Odense, Denmark.
| | - Sune B Nygård
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, University of Copenhagen, Frederiksberg, Denmark. .,Department of Pathology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.
| | - Signe L Nielsen
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, University of Copenhagen, Frederiksberg, Denmark.
| | - Diana R Andersen
- Department of Oncology, Odense University Hospital, Odense, Denmark.
| | - Niels Frank Jensen
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, University of Copenhagen, Frederiksberg, Denmark.
| | - Jan Stenvang
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, University of Copenhagen, Frederiksberg, Denmark.
| | - Sönke Detlefsen
- Department of Pathology, Odense University Hospital, Odense, Denmark.
| | - Nils Brünner
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, University of Copenhagen, Frederiksberg, Denmark.
| | - Per Pfeiffer
- Department of Oncology, Odense University Hospital, Odense, Denmark.
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Ip JCY, Pang TCY, Glover AR, Soon P, Zhao JT, Clarke S, Robinson BG, Gill AJ, Sidhu SB. Immunohistochemical validation of overexpressed genes identified by global expression microarrays in adrenocortical carcinoma reveals potential predictive and prognostic biomarkers. Oncologist 2015; 20:247-56. [PMID: 25657202 PMCID: PMC4350804 DOI: 10.1634/theoncologist.2014-0392] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 01/02/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Adrenocortical carcinoma (ACC) is a rare malignancy with a poor prognosis. The aim of this study was to identify novel protein signatures that would predict clinical outcomes in a large cohort of patients with ACC based on data from previous gene expression microarray studies. MATERIALS AND METHODS A tissue microarray was generated from the paraffin tissue blocks of 61 patients with clinical outcomes data. Selected protein biomarkers based on previous gene expression microarray profiling studies were selected, and immunohistochemistry staining was performed. Staining patterns were correlated with clinical outcomes, and a multivariate analysis was undertaken to identify potential biomarkers of prognosis. RESULTS Median overall survival was 45 months, with a 5-year overall survival rate of 44%. Median disease-free survival was 58 months, with a 5-year disease-free survival rate of 44%. The proliferation marker Ki-67 and DNA topoisomerase TOP2A were associated with significantly poorer overall and disease-free survival. The results also showed strong correlation between the transcriptional repressor EZH2 and TOP2A expression, suggesting a novel role for EZH2 as an additional marker of prognosis. In contrast, increased expression of the BARD1 protein, with its ubiquitin ligase function, was associated with significantly improved overall and disease-free survival, which has yet to be documented for ACC. CONCLUSION We present novel biomarkers that assist in determining prognosis for patients with ACC. Ki-67, TOP2A, and EZH2 were all significantly associated with poorer outcomes, whereas BARD1 was associated with improved overall survival. It is hoped that these biomarkers may help tailor additional therapy and be potential targets for directed therapy.
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Affiliation(s)
- Julian C Y Ip
- Kolling Institute of Medical Research, Endocrine and Oncology Surgical Unit, and Department of Anatomical Pathology, Royal North Shore Hospital, Faculty of Medicine, Northern Clinical School, and Department of Surgery, Westmead Hospital, University of Sydney, New South Wales, Australia; South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Tony C Y Pang
- Kolling Institute of Medical Research, Endocrine and Oncology Surgical Unit, and Department of Anatomical Pathology, Royal North Shore Hospital, Faculty of Medicine, Northern Clinical School, and Department of Surgery, Westmead Hospital, University of Sydney, New South Wales, Australia; South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Anthony R Glover
- Kolling Institute of Medical Research, Endocrine and Oncology Surgical Unit, and Department of Anatomical Pathology, Royal North Shore Hospital, Faculty of Medicine, Northern Clinical School, and Department of Surgery, Westmead Hospital, University of Sydney, New South Wales, Australia; South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Patsy Soon
- Kolling Institute of Medical Research, Endocrine and Oncology Surgical Unit, and Department of Anatomical Pathology, Royal North Shore Hospital, Faculty of Medicine, Northern Clinical School, and Department of Surgery, Westmead Hospital, University of Sydney, New South Wales, Australia; South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Jing Ting Zhao
- Kolling Institute of Medical Research, Endocrine and Oncology Surgical Unit, and Department of Anatomical Pathology, Royal North Shore Hospital, Faculty of Medicine, Northern Clinical School, and Department of Surgery, Westmead Hospital, University of Sydney, New South Wales, Australia; South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Stephen Clarke
- Kolling Institute of Medical Research, Endocrine and Oncology Surgical Unit, and Department of Anatomical Pathology, Royal North Shore Hospital, Faculty of Medicine, Northern Clinical School, and Department of Surgery, Westmead Hospital, University of Sydney, New South Wales, Australia; South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Bruce G Robinson
- Kolling Institute of Medical Research, Endocrine and Oncology Surgical Unit, and Department of Anatomical Pathology, Royal North Shore Hospital, Faculty of Medicine, Northern Clinical School, and Department of Surgery, Westmead Hospital, University of Sydney, New South Wales, Australia; South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Anthony J Gill
- Kolling Institute of Medical Research, Endocrine and Oncology Surgical Unit, and Department of Anatomical Pathology, Royal North Shore Hospital, Faculty of Medicine, Northern Clinical School, and Department of Surgery, Westmead Hospital, University of Sydney, New South Wales, Australia; South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Stan B Sidhu
- Kolling Institute of Medical Research, Endocrine and Oncology Surgical Unit, and Department of Anatomical Pathology, Royal North Shore Hospital, Faculty of Medicine, Northern Clinical School, and Department of Surgery, Westmead Hospital, University of Sydney, New South Wales, Australia; South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales, Australia
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Sudan S, Rupasinghe HV. Antiproliferative activity of long chain acylated esters of quercetin-3-O-glucoside in hepatocellular carcinoma HepG2 cells. Exp Biol Med (Maywood) 2015; 240:1452-64. [PMID: 25681471 DOI: 10.1177/1535370215570828] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 12/16/2014] [Indexed: 01/27/2023] Open
Abstract
Despite their strong role in human health, poor bioavailability of flavonoids limits their biological effects in vivo. Enzymatically catalyzed acylation of fatty acids to flavonoids is one of the approaches of increasing cellular permeability and hence, biological activities. In this study, six long chain fatty acid esters of quercetin-3-O-glucoside (Q3G) acylated enzymatically and were used for determining their antiproliferative action in hepatocellular carcinoma cells (HepG2) in comparison to precursor compounds and two chemotherapy drugs (Sorafenib and Cisplatin). Fatty acid esters of Q3G showed significant inhibition of HepG2 cell proliferation by 85 to 90% after 6 h and 24 h of treatment, respectively. The cell death due to these novel compounds was associated with cell-cycle arrest in S-phase and apoptosis observed by DNA fragmentation, fluorescent microscopy and elevated caspase-3 activity and strong DNA topoisomerase II inhibition. Interestingly, Q3G esters showed significantly low toxicity to normal liver cells than Sorafenib (P < 0.05), a chemotherapy drug for hepatocellular carcinoma. Among all, oleic acid ester of Q3G displayed the greatest antiproliferation action and a high potential as an anti-cancer therapeutic. Overall, the results of the study suggest strong antiproliferative action of these novel food-derived compounds in treatment of cancer.
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Affiliation(s)
- Sudhanshu Sudan
- Department of Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada
| | - Hp Vasantha Rupasinghe
- Department of Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4RN, Canada
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Methods of overcoming treatment resistance in colorectal cancer. Crit Rev Oncol Hematol 2013; 89:217-30. [PMID: 24075059 DOI: 10.1016/j.critrevonc.2013.08.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 07/28/2013] [Accepted: 08/30/2013] [Indexed: 12/25/2022] Open
Abstract
Metastatic colorectal cancer remains a lethal disease with a poor prognosis in the majority of patients. Multiple drug combinations have been developed in recent years that have significantly improved response rates and overall survival however resistance to these drugs is inevitable. Novel agents are currently being developed and participation in clinical trials should be encouraged. In the absence of other treatment options in a patient with good performance status, there is compelling evidence for re-challenging with previously administered agents in different combinations. The aim of this review is to discuss mechanisms of resistance and methods to overcome treatment resistance in patients with metastatic colorectal cancer who are refractory to 5-FU, irinotecan, oxaliplatin, cetuximab and bevacizumab therapy.
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Jain M, Zhang L, He M, Zhang YQ, Patterson EE, Nilubol N, Shen M, Kebebew E. TOP2A is overexpressed and is a therapeutic target for adrenocortical carcinoma. Endocr Relat Cancer 2013; 20:361-70. [PMID: 23533247 PMCID: PMC4990817 DOI: 10.1530/erc-12-0403] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Adrenocortical carcinoma (ACC) is a rare but aggressive malignancy with no effective therapy for patients with unresectable disease. The aim of the current study was i) to evaluate TOP2A expression and function in human adrenocortical neoplasm and ACC cells and ii) to determine the anticancer activity of agents that target TOP2A. TOP2A mRNA and protein expression levels were evaluated in 112 adrenocortical tissue samples (21 normal adrenal cortex, 80 benign adrenocortical tumors, and 11 ACCs). In vitro siRNA knockdown of TOP2A in ACC cell lines (NCI-H295R and SW13) was used to determine its effect on cellular proliferation, cell cycle, anchorage-independent growth, and cellular invasion. We screened 14 TOP2A inhibitors for their anticancer activity in ACC cells. TOP2A mRNA and protein expression was significantly higher in ACC than in benign and normal adrenocortical tissue samples (P<0.05). Knockdown of TOP2A gene expression in ACC cell lines significantly decreased cell proliferation, anchorage-independent growth, and invasion (P<0.05). A screening assay in NCI-H295R cells showed that 11 of 14 TOP2A inhibitors had antiproliferative activity, 5 of the 14 TOP2A inhibitors had a higher antiproliferative activity than mitotane, and aclarubicin was the agent with the highest activity. Aclarubicin was validated to significantly decrease proliferation and tumor spheroid size in both NCI-H295R and SW13 ACC cell lines (P<0.05). Our results suggest that TOP2A is overexpressed in ACC, regulates cellular proliferation and invasion in ACC cells, and is an attractive target for ACC therapy. Of the TOP2A inhibitors screened, aclarubicin is a good candidate agent to test in future clinical trials for patients with locally advanced and metastatic ACC.
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Affiliation(s)
- Meenu Jain
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Lisa Zhang
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Mei He
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Ya-Qin Zhang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
| | - Erin E. Patterson
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Naris Nilubol
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
| | - Electron Kebebew
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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Song L, Robson T, Doig T, Brenn T, Mathers M, Brown ER, Doherty V, Bartlett JMS, Anderson N, Melton DW. DNA repair and replication proteins as prognostic markers in melanoma. Histopathology 2012; 62:343-50. [PMID: 23020778 DOI: 10.1111/j.1365-2559.2012.04362.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AIMS Elevated expression of DNA repair and replication genes has been reported in thick, non-fixed primary melanomas that subsequently went on to metastasize, when compared to non-recurrent primary tumours. This increased expression could contribute to the extreme resistance shown by melanoma to DNA-damaging chemotherapeutics. We have investigated the hypothesis that levels of key DNA repair and replication proteins are prognostic biomarkers in melanoma. METHODS AND RESULTS We used a tissue microarray containing samples from all stages of melanomagenesis to investigate the hypothesis that levels of key DNA repair and replication proteins are prognostic biomarkers in a larger, more representative and readily available set of fixed primary melanomas. High expression of topoisomerase IIα (TOP2A), that relieves torsional stress during DNA replication, and XRCC5 (Ku80), required for DNA double-strand break repair, were associated with significantly worse survival. CONCLUSIONS Two (XRCC5 and TOP2A) of seven DNA repair and replication proteins studied were prognostic for melanoma.
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Affiliation(s)
- Liang Song
- Edinburgh Cancer Research Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
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High TOP2B/TOP2A expression ratio at diagnosis correlates with favourable outcome for standard chemotherapy in acute myeloid leukaemia. Br J Cancer 2012; 107:108-15. [PMID: 22627319 PMCID: PMC3389410 DOI: 10.1038/bjc.2012.206] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Background: Cytosine arabinoside-based chemotherapy coupled with anthracycline is currently the first-line treatment for acute myeloid leukaemia (AML), but diverse responses to the regimen constitute obstacles to successful treatment. Therefore, outcome prediction to chemotherapy at diagnosis is believed to be a critical consideration. Methods: The mRNA expression of 12 genes closely involved in the actions of cytosine arabinoside and anthracycline was evaluated by real-time reverse transcriptase PCR (RT–PCR), in 54 diagnostic bone marrow specimens of M2-subtype AML. Results: Low expression levels of ribonucleotide reductase M2 (RRM2) and high expression levels of topoisomerase 2 beta (TOP2B) were correlated with longer survival in a univariate analysis. Another interesting finding is that high ratios of TOP2B/RRM2 and TOP2B/TOP2 alpha (TOP2A) in a combined analysis were also shown to have a prognostic impact for longer survival with improved accuracy. Among the four markers, when adjusted for the influence of other clinical factors in multivariate analysis, the TOP2B/TOP2A ratio was significantly correlated with treatment outcomes; patients with high ratios trended toward longer disease-free survival (HR, 0.24; P=0.002) and overall survival (HR, 0.29; P=0.005). Conclusion: Genes with distinct expression profiles such as TOP2B/TOP2A expression ratio at diagnosis can be employed for outcome prediction after the treatment with standard regimens in AML patients with M2 subtype.
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Gao XH, Yu ZQ, Zhang C, Bai CG, Zheng JM, Fu CG. DNA topoisomerase II alpha: a favorable prognostic factor in colorectal caner. Int J Colorectal Dis 2012; 27:429-35. [PMID: 22076611 DOI: 10.1007/s00384-011-1346-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/20/2011] [Indexed: 02/04/2023]
Abstract
PURPOSE There is a lack of study concerning expression of Topoisomerase IIα (Topo IIα) and long-term results in colorectal cancer patients. We aimed to investigate the relationship between expression of Topo IIα and clinicopathological parameters including overall survival in colorectal cancer. METHODS Paraffin-fixed specimens from a large prospective cohort of colorectal cancer patients who had been followed up for 4 years were assayed immunohistochemically. RESULTS Of 490 colorectal cancer patients accessible for Topo IIα expression, expression of Topo IIα was scored as (-) in 4 (0.8%) patients, (+) in 41 (8.4%) patients, (++) in 396 (80.8%) patients, and (+++) in 49 (10.0%) patients. Overexpression of Topo IIα was found to be related with lower T stage (p = 0.042), lower N stage (p = 0.038), and a lower incidence of recurrence with nearly significance (p = 0.053). Kaplan-Meier analyses showed that overexpression of Topo IIα was related with prolonged overall survival (p = 0.022) and disease-free survival (p = 0.036). Multivariate analyses showed that elevated serum CEA (p < 0.001), elevated serum CA199 (p = 0.002), poor differentiation (p = 0.001), advanced Dukes stage (p < 0.001), and lower expression of Topo IIα (p = 0.017) were independent predictive factors for poor prognosis. CONCLUSIONS Topo IIα expression is a valuable prognostic indicator for colorectal cancer and would be useful in treatment selection for early colorectal cancer and malignant colorectal polyps resected under endoscopy, especially when it is used in combination with serum CEA, CA199, and differentiation.
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Affiliation(s)
- Xian Hua Gao
- Department of Colorectal Surgery of Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
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Linnebacher M, Lorenz P, Koy C, Jahnke A, Born N, Steinbeck F, Wollbold J, Latzkow T, Thiesen HJ, Glocker MO. Clonality characterization of natural epitope-specific antibodies against the tumor-related antigen topoisomerase IIa by peptide chip and proteome analysis: a pilot study with colorectal carcinoma patient samples. Anal Bioanal Chem 2012; 403:227-38. [PMID: 22349330 DOI: 10.1007/s00216-012-5781-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 01/16/2012] [Accepted: 01/23/2012] [Indexed: 01/03/2023]
Affiliation(s)
- Michael Linnebacher
- Department of General Surgery, Molecular Oncology and Immunotherapy, Medical Faculty, University of Rostock, Rostock, Germany
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Fenouille N, Grosso S, Yunchao S, Mary D, Pontier-Bres R, Imbert V, Czerucka D, Caroli-Bosc FX, Peyron JF, Lagadec P. Calpain 2-dependent IκBα degradation mediates CPT-11 secondary resistance in colorectal cancer xenografts. J Pathol 2012; 227:118-29. [PMID: 22069124 DOI: 10.1002/path.3034] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 09/20/2011] [Accepted: 10/21/2011] [Indexed: 12/12/2022]
Abstract
CPT-11 (irinotecan), the first-line chemotherapy for advanced stage colorectal cancer, remains inactive in about half of patients (primary chemoresistance) and almost all initial responders develop secondary resistance after several courses of treatment (8 months on average). Nude mice bearing HT-29 colon cancer xenografts were treated with CPT-11 and/or an NF-κB inhibitor for two courses. We confirm that NF-κB inhibition potentiated CPT-11 anti-tumoural effect after the first course of treatment. However, tumours grew again at the end of the second course of treatment, generating resistant tumours. We observed an increase in the basal NF-κB activation in resistant tumours and in two resistant sublines, either obtained from resistant HT-29 tumours (HT-29R cells) or generated in vitro (RSN cells). The decrease of NF-κB activation in HT-29R and RSN cells by stable transfections with the super-repressor form of IκBα augmented their sensitivity to CPT-11. Comparing gene expression profiles of HT-29 and HT-29R cells, we identified the S100A10/Annexin A2 complex and calpain 2 as over-expressed potential NF-κB inducers. SiRNA silencing of calpain 2 but not of S100A10 and/or annexin A2, resulted in a decrease in NF-κB activation, an increase in cellular levels of IκBα and a partial restoration of the CPT-11 sensitivity in both HT-29R and RSN cells, suggesting that calpain 2-dependent IκBα degradation mediates CPT-11 secondary resistance. Thus, targeted therapies directed against calpain 2 may represent a novel strategy to enhance the anti-cancer efficacy of CPT-11.
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Affiliation(s)
- Nina Fenouille
- INSERM, U895, Centre Méditerranéen de Médecine Moléculaire (C3M), Equipe Inflammation, Cancer, Cellules Souches Cancéreuses, Nice, France
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de Mejía EG, Ramírez-Mares MV. Ardisia: health-promoting properties and toxicity of phytochemicals and extracts. Toxicol Mech Methods 2012; 21:667-74. [PMID: 22003924 DOI: 10.3109/15376516.2011.601355] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ardisia species (Myrsinaceae) are found throughout tropical and subtropical regions of the world. Traditional medicinal uses attributed to Ardisia include alleviation of liver cancer, swelling, rheumatism, earache, cough, fever, diarrhea, broken bones, dysmenorrhea, respiratory tract infections, traumatic injuries, inflammation, pain, snake and insect bites, birth complications and to improve general blood circulation, among others. Ardisia species are rich in polyphenols, triterpenoid saponins, isocoumarins, quinones and alkylphenols. A summary of the uses, potential health benefits, adverse reactions and important bioactive phytochemicals isolated from the Ardisia species is presented. Future research needs to include more toxicological studies, more comprehensive chemical characterization of extracts, bioavailability, extract standardization, investigation of possible herb-drug interactions, plant improvement with regards to bioactivity and composition, and additional human and animal studies to confirm the health-promoting properties claimed for Ardisia species. The information presented here exemplifies the potential of Ardisia species as a source of chemotherapeutic, chemo-modulating and/or chemopreventive agents.
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Affiliation(s)
- Elvira González de Mejía
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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da Cunha IW, De Brot L, Carvalho KC, Rocha RM, Fregnani JH, Falzoni R, de Oliveira Ferreira F, Júnior SA, Lopes A, Muto NH, Reis LFL, Soares FA, Vassallo J. Prognostication of Soft Tissue Sarcomas Based on Chromosome 17q Gene and Protein Status: Evaluation of TOP2A, HER-2/neu, and Survivin. Ann Surg Oncol 2011; 19:1790-9. [DOI: 10.1245/s10434-011-2184-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Indexed: 01/11/2023]
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Etoposide-mediated glioblastoma cell death: dependent or independent on the expression of its target, topoisomerase II alpha? J Cancer Res Clin Oncol 2011; 137:1705-12. [DOI: 10.1007/s00432-011-1046-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2011] [Accepted: 08/15/2011] [Indexed: 11/26/2022]
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Gobble RM, Qin LX, Brill ER, Angeles CV, Ugras S, O'Connor RB, Moraco NH, Decarolis PL, Antonescu C, Singer S. Expression profiling of liposarcoma yields a multigene predictor of patient outcome and identifies genes that contribute to liposarcomagenesis. Cancer Res 2011; 71:2697-705. [PMID: 21335544 DOI: 10.1158/0008-5472.can-10-3588] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Liposarcomas are the most common type of soft tissue sarcoma but their genetics are poorly defined. To identify genes that contribute to liposarcomagenesis and serve as prognostic candidates, we undertook expression profiling of 140 primary liposarcoma samples, which were randomly split into training set (n = 95) and test set (n = 45). A multigene predictor for distant recurrence-free survival (DRFS) was developed by the supervised principal component method. Expression levels of the 588 genes in the predictor were used to calculate a risk score for each patient. In validation of the predictor in the test set, patients with low risk score had a 3-year DRFS of 83% versus 45% for high risk score patients (P = 0.001). The HR for high versus low score, adjusted for histologic subtype, was 4.42 (95% CI, 1.26-15.55; P = 0.021). The concordance probability for risk score was 0.732. In contrast, the concordance probability for histologic subtype, which had been considered the best predictor of outcome in liposarcoma, was 0.669. Genes related to adipogenesis, DNA replication, mitosis, and spindle assembly checkpoint control were all highly represented in the multigene predictor. Three genes from the predictor, TOP2A, PTK7, and CHEK1, were found to be overexpressed in liposarcoma samples of all five subtypes and in liposarcoma cell lines. RNAi-mediated knockdown of these genes in liposarcoma cell lines reduced proliferation and invasiveness and increased apoptosis. Taken together, our findings identify genes that seem to be involved in liposarcomagenesis and have promise as therapeutic targets, and support the use of this multigene predictor to improve risk stratification for individual patients with liposarcoma.
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Affiliation(s)
- Ryan M Gobble
- Department of Surgery, Sarcoma Disease Management Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
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Immunotherapy for treating metastatic colorectal cancer. Surg Oncol 2011; 21:67-77. [PMID: 21292476 DOI: 10.1016/j.suronc.2010.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2010] [Revised: 10/10/2010] [Accepted: 10/14/2010] [Indexed: 01/17/2023]
Abstract
BACKGROUND Colorectal cancer remains one of the leading causes of death in the world. Surgery still remains the mainstay of treatment for primary and metastatic colorectal cancer. Immunotherapy used as an adjunct to surgery can play an important role in controlling the spread of tumour. METHODS The online databases PubMed, Medline, Scirus and Medscape Oncology were used to identify articles of relevance. Keywords included; "Immunotherapy", "Cellular Immunotherapy", "Metastatic Colorectal Cancer", "Monoclonal Antibody" "Tumour Vaccines" and "Adoptive Cell Therapy". The databases search was from the period of June 1995 until May 2010 inclusive. RESULTS Our understanding of tumour immunology has allowed the development of some successful therapies. Immunotherapy through the use of monoclonal antibodies is an effective adjunct to chemotherapy for metastatic colorectal cancer. Other modalities that are in the stages of development are cellular and conjugated vaccines. However, these vaccines are being experimented in advanced stages of colorectal tumours. CONCLUSION Colorectal cancer vaccines are being developed for advanced stages of colorectal tumour. However, their use as an early adjunct could potentially limit the spread of tumour or even result in cure. Further trials are required to ensure the safety and efficacy of cellular vaccines against colorectal tumours to allow their use on patients early in their disease presentation.
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