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Sun C, Huang S, Wang H, Xie R, Zhang L, Zhou Q, He X, Ju W. Non-SMC condensin I complex subunit H enhances proliferation, migration, and invasion of hepatocellular carcinoma. Mol Carcinog 2019; 58:2266-2275. [PMID: 31523845 PMCID: PMC6899668 DOI: 10.1002/mc.23114] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/26/2019] [Accepted: 08/30/2019] [Indexed: 12/16/2022]
Abstract
Non‐SMC condensing I complex subunit H (NCAPH) is a member of the Barr protein family and part of the condensin I complex. The upregulation of NCAPH is associated with poor prognosis in patients with colon cancer. However, the relationship between NCAPH and hepatocellular carcinoma (HCC) remains unclear. This study aimed to explore NCAPH expression in HCC tissues and to investigate NCAPH functions in HCC cells. In this study, we found that high expression of NCAPH in HCC indicated worse prognosis via bioinformatics analysis. Consistently, quantitative real‐time polymerase chain reaction assays in 20 pairs of HCC specimens and the immunohistochemical analysis of 100 HCC tissues showed the upregulation of NCAPH. We established stable NCAPH‐overexpressing and NCAPH knockdown cell lines. Cell Counting Kit‐8 assays and colony formation assay were performed to analyze cell proliferation. Migration and invasion were analyzed by Transwell assays. Subcutaneous xenograft models were used to explore the role of NCAPH in tumor formation in vivo. Our results showed that NCAPH promoted tumor proliferation, migration, and invasion in vitro and in vivo. In conclusion, our findings indicate that NCAPH could serve as a novel prognostic biomarker and a potential therapeutic target for patients with HCC.
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Affiliation(s)
- Chengjun Sun
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shanzhou Huang
- Department of General Surgery, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
| | - Hanyu Wang
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Rongxing Xie
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lishan Zhang
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qi Zhou
- Department of Liver Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.,Department of General Surgery, Hui Ya Hospital of The First Affiliated Hospital, Sun Yat-sen University, Huizhou, Guangdong, China
| | - Xiaoshun He
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Weiqiang Ju
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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Classification of early and late stage liver hepatocellular carcinoma patients from their genomics and epigenomics profiles. PLoS One 2019; 14:e0221476. [PMID: 31490960 PMCID: PMC6730898 DOI: 10.1371/journal.pone.0221476] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/07/2019] [Indexed: 02/07/2023] Open
Abstract
Background Liver Hepatocellular Carcinoma (LIHC) is one of the major cancers worldwide, responsible for millions of premature deaths every year. Prediction of clinical staging is vital to implement optimal therapeutic strategy and prognostic prediction in cancer patients. However, to date, no method has been developed for predicting the stage of LIHC from the genomic profile of samples. Methods The Cancer Genome Atlas (TCGA) dataset of 173 early stage (stage-I), 177 late stage (stage-II, Stage-III and stage-IV) and 50 adjacent normal tissue samples for 60,483 RNA transcripts and 485,577 methylation CpG sites, was extensively analyzed to identify the key transcriptomic expression and methylation-based features using different feature selection techniques. Further, different classification models were developed based on selected key features to categorize different classes of samples implementing different machine learning algorithms. Results In the current study, in silico models have been developed for classifying LIHC patients in the early vs. late stage and cancerous vs. normal samples using RNA expression and DNA methylation data. TCGA datasets were extensively analyzed to identify differentially expressed RNA transcripts and methylated CpG sites that can discriminate early vs. late stages and cancer vs. normal samples of LIHC with high precision. Naive Bayes model developed using 51 features that combine 21 CpG methylation sites and 30 RNA transcripts achieved maximum MCC (Matthew’s correlation coefficient) 0.58 with an accuracy of 78.87% on the validation dataset in discrimination of early and late stage. Additionally, the prediction models developed based on 5 RNA transcripts and 5 CpG sites classify LIHC and normal samples with an accuracy of 96–98% and AUC (Area Under the Receiver Operating Characteristic curve) 0.99. Besides, multiclass models also developed for classifying samples in the normal, early and late stage of cancer and achieved an accuracy of 76.54% and AUC of 0.86. Conclusion Our study reveals stage prediction of LIHC samples with high accuracy based on the genomics and epigenomics profiling is a challenging task in comparison to the classification of cancerous and normal samples. Comprehensive analysis, differentially expressed RNA transcripts, methylated CpG sites in LIHC samples and prediction models are available from CancerLSP (http://webs.iiitd.edu.in/raghava/cancerlsp/).
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53
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Ma Q, Xu Y, Liao H, Cai Y, Xu L, Xiao D, Liu C, Pu W, Zhong X, Guo X. Identification and validation of key genes associated with non-small-cell lung cancer. J Cell Physiol 2019; 234:22742-22752. [PMID: 31127628 DOI: 10.1002/jcp.28839] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 12/24/2022]
Abstract
Non-small-cell lung cancer (NSCLC) is one of the main causes of death induced by cancer globally. However, the molecular aberrations in NSCLC patients remain unclearly. In the present study, four messenger RNA microarray datasets (GSE18842, GSE40275, GSE43458, and GSE102287) were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between NSCLC tissues and adjacent lung tissues were obtained from GEO2R and the overlapping DEGs were identified. Moreover, functional and pathway enrichment were performed by Funrich, while the protein-protein interaction (PPI) network construction were obtained from STRING and hub genes were visualized and identified by Cytoscape software. Furthermore, validation, overall survival (OS) and tumor staging analysis of selected hub genes were performed by GEPIA. A total of 367 DEGs (95 upregulated and 272 downregulated) were obtained through gene integration analysis. The PPI network consisted of 94 nodes and 1036 edges in the upregulated DEGs and 272 nodes and 464 edges in the downregulated DEGs, respectively. The PPI network identified 46 upregulated and 27 downregulated hub genes among the DEGs, and six (such as CENPE, NCAPH, MYH11, LRRK2, HSD17B6, and A2M) of that have not been identified to be associated with NSCLC so far. Moreover, the expression differences of the mentioned hub genes were consistent with that in lung adenocarcinoma and lung squamous cell carcinoma in the TCGA database. Further analysis showed that all the six hub genes were associated with tumor staging except MYH11, while only the upregulated DEG CENPE was associated with the worse OS of patients with NSCLC. In conclusion, the current study showed that CENPE, NCAPH, MYH11, LRRK2, HSD17B6, and A2M might be the key genes contributed to tumorigenesis or tumor progression in NSCLC, further functional study is needed to explore the involved mechanisms.
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Affiliation(s)
- Qiang Ma
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Yuan Xu
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Hebin Liao
- Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China
| | - Yan Cai
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Lei Xu
- Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China
| | - Dan Xiao
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Chang Liu
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Wenjie Pu
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Xiaowu Zhong
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Xiaolan Guo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
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Liu J, Zhou S, Li S, Jiang Y, Wan Y, Ma X, Cheng W. Eleven genes associated with progression and prognosis of endometrial cancer (EC) identified by comprehensive bioinformatics analysis. Cancer Cell Int 2019; 19:136. [PMID: 31139013 PMCID: PMC6528324 DOI: 10.1186/s12935-019-0859-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/13/2019] [Indexed: 12/25/2022] Open
Abstract
Background Endometrial cancer (EC) is one of the female malignant tumors. Endometrial cancer predominately affects post-menopausal women. Bioinformatics analysis has been widely applied to screen and analyze genes in linkage to various types of cancer progression. Methods Download the gene expression profile from Gene Expression Omnibus (GEO). Calculate raw expression data according to pre-processing procedures. We performed the “limma” R language package to screen DEGs between Endometrial cancer tissue samples and normal uterus tissue samples. Enrichment of the functions and pathways was analyzed by using clusterprofiler. We utilized Search Tool for the Retrieval of Interacting Genes Database (STRING) to assess protein–protein interaction (PPI) information, and then we used plug-in Molecular Complex Detection (MCODE) to screen hub modules of PPI network in Cytoscape. We also performed functional analysis on the genes in the hub module by using clusterprofiler. Next, we utilized the “WGCNA” package in R to establish co-expression network for the DEGs. The Venn diagram was performed to overlap the gene in key module and hub PPI cluster. We validated the key genes in TCGA, GEPIA, UALCAN and Immunohistochemistry staining obtained from The Human Protein Atlas database. And then we did ROC curve analysis by SPSS. Gene set enrichment analysis (GSEA) and mutation analysis were also performed for hub genes. Results Functional and pathway enrichment analysis demonstrated that the upregulated differentially expressed genes (DEGs) were significantly enriched in CXCR chemokine receptor binding, chemokine activity, chemokine receptor binding, G-protein coupled receptor binding, RAGE receptor binding, cytokine activity, microtubule binding, receptor regulator activity and microtubule motor activity, and the down-regulated genes were highly enriched in collagen binding. After using STRING software to construct PPI network, 30 prominent proteins were identified and the first two significant modules were selected. In co-expression network, 5 EC-related modules were identified. Among them, the turquoise module has the highest correlation with the EC. We further analyzed the genes in the PPI and turquoise module, and selected eleven key genes related to EC after validation of TCGA database, GEPIA, UALCAN and immunohistochemistry. Six of them had mutation significance. Conclusions In summary, these 11 genes may become new therapy targets for EC treatment. Electronic supplementary material The online version of this article (10.1186/s12935-019-0859-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- JinHui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029 Jiangsu China
| | - ShuLin Zhou
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029 Jiangsu China
| | - SiYue Li
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029 Jiangsu China
| | - Yi Jiang
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029 Jiangsu China
| | - YiCong Wan
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029 Jiangsu China
| | - XiaoLing Ma
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029 Jiangsu China
| | - WenJun Cheng
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029 Jiangsu China
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Cui F, Hu J, Xu Z, Tan J, Tang H. Overexpression of NCAPH is upregulated and predicts a poor prognosis in prostate cancer. Oncol Lett 2019; 17:5768-5776. [PMID: 31186803 DOI: 10.3892/ol.2019.10260] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 03/18/2019] [Indexed: 01/07/2023] Open
Abstract
Prostate cancer (PCa) is one of the most frequently diagnosed types of cancer worldwide. However, there remains a lack of accurate biomarkers to predict the outcome of PCa. Non-SMC condensin I complex subunit H (NCAPH) encodes a regulatory subunit of the non-structural maintenance of chromosomes condensin I complex. The present study aimed to investigate whether NCAPH may be a novel diagnostic marker for PCa by analyzing public datasets, including GSE17951, GSE55945 and a dataset from The Cancer Genome Atlas. The current results, to the best of our knowledge, demonstrated for the first time that NCAPH is significantly upregulated in PCa. Furthermore, it was identified that NCAPH expression is higher in stage T3/T4 and N1 PCa samples compared with stage T2 and N0 PCa samples, respectively. Kaplan-Meier analysis demonstrated that overexpression of NCAPH is associated with poor survival of patients with PCa. Bioinformatics analysis revealed that NCAPH is involved in regulating the PCa cell cycle by interacting with a number of proteins, including non-SMC condensin I complex subunit D2, non-SMC condensin I complex subunit G, structural maintenance of chromosomes 4, structural maintenance of chromosomes 2, Aurora kinase A, Aurora kinase B, cyclin-dependent kinase 1, H2A histone family member Z, POC1 centriolar protein A and histone cluster 2 H2A family member C. In summary, the present results suggest NCAPH may be a novel and beneficial diagnostic and therapeutic target in PCa.
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Affiliation(s)
- Feilun Cui
- Department of Urology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, P.R. China
| | - Jianpeng Hu
- Department of Urology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, P.R. China
| | - Zhipeng Xu
- Department of Urology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, P.R. China
| | - Jian Tan
- Department of Urology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, P.R. China
| | - Huaming Tang
- Department of Urology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, P.R. China
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Arai T, Kojima S, Yamada Y, Sugawara S, Kato M, Yamazaki K, Naya Y, Ichikawa T, Seki N. Micro-ribonucleic acid expression signature of metastatic castration-resistant prostate cancer: Regulation of NCAPH by antitumor miR-199a/b-3p. Int J Urol 2019; 26:506-520. [PMID: 30818424 DOI: 10.1111/iju.13911] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/20/2018] [Indexed: 12/21/2022]
Abstract
OBJECTIVES To identify oncogenes regulated by micro-ribonucleic acid, miR-199a/b-3p, in metastatic castration-resistant prostate cancer. METHODS Advanced ribonucleic acid sequencing technologies were applied to construct a micro-ribonucleic acid expression signature using metastatic castration-resistant prostate cancer autopsy specimens. Ectopic expression of mature micro-ribonucleic acids or small-interfering ribonucleic acids were applied to functional assays for cancer cell lines. Genome-wide gene expression and in silico database analyses were carried out to predict micro-ribonucleic acid targets. RESULTS Ectopic expression of miR-199a/b inhibited cancer cell aggressiveness. The gene coding for non-structural maintenance of chromosomes condensin I complex subunit H was directly regulated by miR-199a/b-3p. High expression of condensin I complex subunit H was significantly associated with poor disease-free survival by The Cancer Genome Atlas database analysis (P < 0.0001). Overexpression of condensin I complex subunit H was detected in hormone-sensitive prostate cancer and castration-resistant prostate cancer specimens, and knockdown assays showed that its expression enhanced cancer cell migration and invasive abilities. CONCLUSIONS Small ribonucleic acid sequencing of metastatic castration-resistant prostate cancer specimens showed the presence of several antitumor micro-ribonucleic acids whose targets are involved in hormone-sensitive prostate cancer and metastatic castration-resistant prostate cancer pathogenesis. Condensin I complex subunit H seems to be a promising diagnostic marker and therapeutic target for this disease. Our approach, based on the roles of anti-tumor micro-ribonucleic acids and their targets, will contribute to an improved understanding of the molecular pathogenesis of hormone-sensitive prostate cancer and metastatic castration-resistant prostate cancer.
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Affiliation(s)
- Takayuki Arai
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba, Japan.,Department of Urology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Satoko Kojima
- Department of Urology, Teikyo University Chiba Medical Center, Ichihara, Japan
| | - Yasutaka Yamada
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba, Japan.,Department of Urology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Sho Sugawara
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba, Japan.,Department of Urology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Mayuko Kato
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba, Japan.,Department of Urology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Kazuto Yamazaki
- Department of Pathology, Teikyo University Chiba Medical Center, Ichihara, Japan
| | - Yukio Naya
- Department of Urology, Teikyo University Chiba Medical Center, Ichihara, Japan
| | - Tomohiko Ichikawa
- Department of Urology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Naohiko Seki
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba, Japan
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Roy S, Hooiveld GJ, Seehawer M, Caruso S, Heinzmann F, Schneider AT, Frank AK, Cardenas DV, Sonntag R, Luedde M, Trautwein C, Stein I, Pikarsky E, Loosen S, Tacke F, Ringelhan M, Avsaroglu SK, Goga A, Buendia MA, Vucur M, Heikenwalder M, Zucman-Rossi J, Zender L, Roderburg C, Luedde T. microRNA 193a-5p Regulates Levels of Nucleolar- and Spindle-Associated Protein 1 to Suppress Hepatocarcinogenesis. Gastroenterology 2018; 155:1951-1966.e26. [PMID: 30165047 PMCID: PMC6279541 DOI: 10.1053/j.gastro.2018.08.032] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 08/15/2018] [Accepted: 08/18/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS We performed an integrated analysis to identify microRNAs (miRNAs) and messenger RNAs (mRNAs) with altered expression in liver tumors from 3 mouse models of hepatocellular carcinoma (HCC) and human tumor tissues. METHODS We analyzed miRNA and mRNA expression profiles of liver tissues from mice with diethylnitrosamine-induced hepatocarcinogenesis, conditional expression of lymphotoxin alpha and lymphotoxin beta, or inducible expression of a Myc transgene (Tet-O-Myc mice), as well as male C57BL/6 mice (controls). miRNA mimics were expressed and miRNAs and mRNAs were knocked down in human (Huh7, Hep3B, JHH2) hepatoma cell lines; cells were analyzed for viability, proliferation, apoptosis, migration, and invasion. Cells were grown as xenograft tumors in nude mice and analyzed. We combined in silico target gene prediction with mRNA profiles from all 3 mouse models. We quantified miRNA levels in 146 fresh-frozen tissues from patients (125 HCCs, 17 matched nontumor tissues, and 4 liver samples from patients without cancer) and published human data sets and tested correlations with patient survival times using Kaplan-Meier curves and the log-rank test. Levels of NUSAP1 mRNA were quantified in 237 HCCs and 5 nontumor liver samples using the TaqMan assay. RESULTS Levels of the miRNA 193a-5p (MIR193A-5p) were reduced in liver tumors from all 3 mouse tumor models and in human HCC samples, compared with nontumor liver tissues. Expression of a MIR193A-5p mimic in hepatoma cells reduced proliferation, survival, migration, and invasion and their growth as xenograft tumors in nude mice. We found nucleolar and spindle-associated protein 1 (NUSAP1) to be a target of MIR193A-5p; HCC cells and tissues with low levels of MIR193A-5p had increased expression of NUSAP1. Increased levels of NUSAP1 in HCC samples correlated with shorter survival times of patients. Knockdown of NUSAP1 in Huh7 cells reduced proliferation, survival, migration, and growth as xenograft tumors in nude mice. Hydrodynamic tail-vein injections of a small hairpin RNA against NUSAP1 reduced growth of Akt1-Myc-induced tumors in mice. CONCLUSIONS MIR193A-5p appears to prevent liver tumorigenesis by reducing levels of NUSAP1. Levels of MIR193A-5p are reduced in mouse and human HCC cells and tissues, leading to increased levels of NUSAP1, associated with shorter survival times of patients. Integrated analyses of miRNAs and mRNAs in tumors from mouse models can lead to identification of therapeutic targets in humans. The currently reported miRNA and mRNA profiling data have been submitted to the Gene Expression Omnibus (super-series accession number GSE102418).
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Affiliation(s)
- Sanchari Roy
- Division of Gastroenterology, Hepatology and Hepatobiliary Oncology,Department of Medicine III, University Hospital RWTH Aachen, Aachen Germany
| | - Guido J. Hooiveld
- Nutrition, Metabolism & Genomics Group, Division of Human Nutrition, Wageningen University, Wageningen, Netherlands
| | - Marco Seehawer
- Department of Internal Medicine VIII, University Hospital Tübingen, 72076 Tübingen, Germany,Department of Physiology I, Institute of Physiology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Stefano Caruso
- Inserm UMR-1162, Functional Genomics of Solid Tumors, University Paris Descartes, University University Paris Diderot, University Paris 13, Labex Immuno-Oncology, Paris, France
| | - Florian Heinzmann
- Department of Internal Medicine VIII, University Hospital Tübingen, 72076 Tübingen, Germany,Department of Physiology I, Institute of Physiology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | | | - Anna K. Frank
- Department of Medicine III, University Hospital RWTH Aachen, Aachen Germany
| | | | - Roland Sonntag
- Department of Medicine III, University Hospital RWTH Aachen, Aachen Germany
| | - Mark Luedde
- Department of Cardiology, University Hospital Kiel, 25105 Kiel, Germany
| | | | - Ilan Stein
- Department of Pathology, Hadassah–Hebrew University Medical Center, Jerusalem, Israel
| | - Eli Pikarsky
- Department of Pathology, Hadassah–Hebrew University Medical Center, Jerusalem, Israel
| | - Sven Loosen
- Department of Medicine III, University Hospital RWTH Aachen, Aachen Germany
| | - Frank Tacke
- Department of Medicine III, University Hospital RWTH Aachen, Aachen Germany
| | - Marc Ringelhan
- Technische Universität München, Ismaningerstr. 22, 81675 München
| | - Seda Kilinc Avsaroglu
- Department of Cell and Tissue Biology, University of California, San Francisco, CA 94143-0452
| | - Andrei Goga
- Department of Cell and Tissue Biology, University of California, San Francisco, CA 94143-0452
| | - Marie-Annick Buendia
- Inserm Unit U1193, University Paris-Sud, Paul Brousse Hospital, Villejuif, France
| | - Mihael Vucur
- Division of Gastroenterology, Hepatology and Hepatobiliary Oncology
| | - Mathias Heikenwalder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Germany
| | - Jessica Zucman-Rossi
- Inserm UMR-1162, Functional Genomics of Solid Tumors, University Paris Descartes, University University Paris Diderot, University Paris 13, Labex Immuno-Oncology, Paris, France
| | - Lars Zender
- Department of Internal Medicine VIII, University Hospital Tübingen, 72076 Tübingen, Germany,Department of Physiology I, Institute of Physiology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany,Translational Gastrointestinal Oncology Group, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | | | - Tom Luedde
- Division of Gastroenterology, Hepatology and Hepatobiliary Oncology, Aachen Germany; Department of Medicine III, University Hospital RWTH Aachen, Aachen Germany.
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Liu K, Li Y, Yu B, Wang F, Mi T, Zhao Y. Silencing non-SMC chromosome-associated polypeptide G inhibits proliferation and induces apoptosis in hepatocellular carcinoma cells. Can J Physiol Pharmacol 2018; 96:1246-1254. [PMID: 30089216 DOI: 10.1139/cjpp-2018-0195] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The present study was designed to investigate the significance of non-structural maintenance of chromosomes (non-SMC) chromosome-associated polypeptide G (NCAPG), a subunit of condensin complex I, in the development of hepatocellular carcinoma (HCC). NCAPG protein expression in human HCC and paracancerous hepatic tissues were examined using immunohistochemistry, and NCAPG mRNA expression in HCC cell lines were quantified using quantitative RT-PCR. Lentivirus-mediated RNA interference was used to silence NCAPG in HCC cells. Cell proliferation was monitored by MTT assay. Cell colony-forming capacity was measured by colony formation assay. Apoptosis was determined by flow cytometry. The results showed that increased protein expression of NCAPG was found in HCC tissues compared with the matched paracancerous hepatic tissues. At the mRNA level, increased expression of NCAPG was found in HCC cells as opposed to the normal hepatocytes. Silencing of NCAPG in BEL-7404 and SMMC-7721 cells led to decreased cell proliferation and increased apoptosis. These changes were associated with increased mRNA expressions of P53, P27, and Bad, but decreased mRNA expression of EGFR, Akt, survivin, and JNK. NCAPG might play an oncogenic role in the development of liver cancer. Further studies to clarify its role and underlying mechanisms in the development of liver cancer are warranted.
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Affiliation(s)
- Kaikun Liu
- a The Second Clinical Medical School of Lanzhou University, Lanzhou, Gansu Province, 730030; China.,b Department of Surgical Oncology, The Second Hospital of Lanzhou, Lanzhou, Gansu Province, 730000; China
| | - Yumin Li
- a The Second Clinical Medical School of Lanzhou University, Lanzhou, Gansu Province, 730030; China.,c Department of General Surgery, The Second Hospital of Lanzhou University, Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu Province, 730030, China
| | - Bo Yu
- b Department of Surgical Oncology, The Second Hospital of Lanzhou, Lanzhou, Gansu Province, 730000; China
| | - Furong Wang
- a The Second Clinical Medical School of Lanzhou University, Lanzhou, Gansu Province, 730030; China
| | - Taiyu Mi
- b Department of Surgical Oncology, The Second Hospital of Lanzhou, Lanzhou, Gansu Province, 730000; China
| | - Yongxun Zhao
- d The First Clinical Medical School of Lanzhou University, Lanzhou, Gansu Province, 730030; China
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Nash AJ, Mandaviya PR, Dib MJ, Uitterlinden AG, van Meurs J, Heil SG, Andrew T, Ahmadi KR. Interaction between plasma homocysteine and the MTHFR c.677C > T polymorphism is associated with site-specific changes in DNA methylation in humans. FASEB J 2018; 33:833-843. [PMID: 30080444 DOI: 10.1096/fj.201800400r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
One-carbon metabolism provides a direct link among dietary folate/vitamin B12 exposure, the activity of the enzyme methylenetetrahydrofolate reductase (MTHFR), and epigenetic regulation of the genome via DNA methylation. Previously, it has been shown that the common c.677C > T polymorphism in MTHFR influences global DNA methylation status through a direct interaction with folate status and (indirectly) with total homocysteine (tHcy) levels. To build on that and other more recent observations that have further highlighted associations among MTHFR c.677C > T, tHcy, and aberrations in DNA methylation, we investigated whether the interaction between mildly elevated plasma tHcy and the c.677C > T polymorphism is associated with site-specific changes in DNA methylation in humans. We used data on plasma tHcy levels, c.677C > T polymorphism, and site-specific DNA methylation levels for a total of 915 white women and 335 men from the TwinsUK registry ( n = 610) and the Rotterdam study ( n = 670). We performed methylome-wide association analyses in each cohort to model the interaction between levels of tHcy and c.677C > T genotypes on DNA methylation β values. Our meta-analysis identified 13 probes significantly associated with rs1801133 × tHcy levels [false-discovery rate (FDR) < 0.05]. The most significant associations were with a cluster of probes at the AGTRAP-MTHFR-NPPA/B gene locus on chromosome 1 (FDR = 1.3E-04), with additional probes on chromosomes 2, 3, 4, 7, 12, 16, and 19. Our top 2 hits on chromosome 1 were functionally associated with variability in expression of the TNF receptor superfamily member 8 ( TNFRSF8) gene/locus on that chromosome. This is the first study, to our knowledge, to provide a direct link between perturbations in 1-carbon metabolism, through an interaction of tHcy and the activity of MTHFR enzyme on epigenetic regulation of the genome via DNA methylation.-Nash, A. J., Mandaviya, P. R., Dib, M.-J., Uitterlinden, A. G., van Meurs, J., Heil, S. G., Andrew, T., Ahmadi, K. R. Interaction between plasma homocysteine and the MTHFR c.677C>T polymorphism is associated with site-specific changes in DNA methylation in humans.
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Affiliation(s)
- Alexander J Nash
- Institute of Clinical Sciences and Medical Research Council (MRC) London Institute of Medical Sciences, Imperial College, London, United Kingdom
| | - Pooja R Mandaviya
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marie-Joe Dib
- Department of Genomics of Common Disease, Imperial College, London, United Kingdom; and
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joyce van Meurs
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sandra G Heil
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Toby Andrew
- Department of Genomics of Common Disease, Imperial College, London, United Kingdom; and
| | - Kourosh R Ahmadi
- Department of Nutritional Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
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Wang HZ, Yang SH, Li GY, Cao X. Subunits of human condensins are potential therapeutic targets for cancers. Cell Div 2018; 13:2. [PMID: 29467813 PMCID: PMC5819170 DOI: 10.1186/s13008-018-0035-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/05/2018] [Indexed: 11/16/2022] Open
Abstract
The main role of condensins is to regulate chromosome condensation and segregation during cell cycles. Recently, it has been suggested in the literatures that subunits of condensin I and condensin II are involved in some human cancers. This paper will first briefly discuss discoveries of human condensins, their components and structures, and their multiple cellular functions. This will be followed by reviews of most recent studies on subunits of human condensins and their dysregulations or mutations in human cancers. It can be concluded that many of these subunits have potentials to be novel targets for cancer therapies. However, hCAP-D2, a subunit of human condensin I, has not been directly documented to be associated with any human cancers to date. This review hypothesizes that hCAP-D2 can also be a potential therapeutic target for human cancers, and therefore that all subunits of human condensins are potential therapeutic targets for human cancers.
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Affiliation(s)
- Hong-Zhen Wang
- 1School of Life Sciences, Jilin Normal University, Siping, 136000 P. R. China.,2Key Laboratory for Molecular Enzymology and Engineering of The Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012 P. R. China.,3Department of Chemical and Biological Engineering, University of Ottawa, Ottawa, K1N 6N5 Canada
| | - Si-Han Yang
- 1School of Life Sciences, Jilin Normal University, Siping, 136000 P. R. China
| | - Gui-Ying Li
- 2Key Laboratory for Molecular Enzymology and Engineering of The Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012 P. R. China
| | - Xudong Cao
- 3Department of Chemical and Biological Engineering, University of Ottawa, Ottawa, K1N 6N5 Canada
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Shen D, Skibbens RV. Chl1 DNA helicase and Scc2 function in chromosome condensation through cohesin deposition. PLoS One 2017; 12:e0188739. [PMID: 29186203 PMCID: PMC5706694 DOI: 10.1371/journal.pone.0188739] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 11/13/2017] [Indexed: 02/02/2023] Open
Abstract
Chl1 DNA helicase promotes sister chromatid cohesion and associates with both the cohesion establishment acetyltransferase Eco1/Ctf7 and the DNA polymerase processivity factor PCNA that supports Eco1/Ctf7 function. Mutation in CHL1 results in precocious sister chromatid separation and cell aneuploidy, defects that arise through reduced levels of chromatin-bound cohesins which normally tether together sister chromatids (trans tethering). Mutation of Chl1 family members (BACH1/BRIP/FANCJ and DDX11/ChlR1) also exhibit genotoxic sensitivities, consistent with a role for Chl1 in trans tethering which is required for efficient DNA repair. Chl1 promotes the recruitment of Scc2 to DNA which is required for cohesin deposition onto DNA. There is limited evidence, however, that Scc2 also directs the deposition onto DNA of condensins which promote tethering in cis (intramolecular DNA links). Here, we test the ability of Chl1 to promote cis tethering and the role of both Chl1 and Scc2 to promote condensin recruitment to DNA. The results reveal that chl1 mutant cells exhibit significant condensation defects both within the rDNA locus and genome-wide. Importantly, chl1 mutant cell condensation defects do not result from reduced chromatin binding of condensin, but instead through reduced chromatin binding of cohesin. We tested scc2-4 mutant cells and similarly found no evidence of reduced condensin recruitment to chromatin. Consistent with a role for Scc2 specifically in cohesin deposition, scc2-4 mutant cell condensation defects are irreversible. We thus term Chl1 a novel regulator of both chromatin condensation and sister chromatid cohesion through cohesin-based mechanisms. These results reveal an exciting interface between DNA structure and the highly conserved cohesin complex.
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Affiliation(s)
- Donglai Shen
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Robert V. Skibbens
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
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