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Guo Z, Guo L. YAP/TEAD-induced PRIM1 contributes to the progression and poor prognosis of gastric carcinoma. Transl Oncol 2023; 38:101791. [PMID: 37741096 PMCID: PMC10541473 DOI: 10.1016/j.tranon.2023.101791] [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: 01/17/2023] [Revised: 09/06/2023] [Accepted: 09/15/2023] [Indexed: 09/25/2023] Open
Abstract
Gastric carcinoma has a poor prognosis and low survival rate. PRIM1 is closely associated with the origin of DNA replication and serves as a carcinogenic factor in multiple tumors. This study aimed to explore the functions of PRIM1 in the progression of gastric carcinoma. The luciferase reporter assay examined the regulatory effect of YAP1/TEAD4 on PRIM1. A xenograft tumor mouse model was constructed to observe cancer cell proliferation in vivo. The upregulation of PRIM1 was found in gastric carcinoma cells and tissues, and it was associated with poor prognosis. Silencing PRIM1 inhibited cell proliferation, arrested the cell cycle, and upregulated Cdc25, Cyclin B, and Cdc2 expression. In addition, apoptosis was increased upon PRIM1 knockdown, accompanied by increased protein levels of cleaved caspase-3 and caspase-8. In vivo, knockdown of PRIM1 suppressed the growth of xenograft tumors formed by gastric carcinoma cells. Moreover, PRIM1 silencing elevated the chemosensitivity of gastric carcinoma cells. By investigating molecular events downstream of the Hippo signaling pathway, we found that PRIM1 was a target gene of the YAP1/TEAD4 transcriptional regulatory complex. PRIM1 represents a novel target for gastric carcinoma therapeutic approaches.
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Affiliation(s)
- Zijun Guo
- Department of Operating Room, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning, China
| | - Lin Guo
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning, China.
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2
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Wang X, Wu Y, Liu J, Xu X, Sheng Z, Liu W, Chen M, Ma Y, Zhao D, Li D, Zheng X. Identification of target and pathway of aspirin combined with Lipitor treatment in prostate cancer through integrated bioinformatics analysis. Toxicol Appl Pharmacol 2022; 452:116169. [PMID: 35926565 DOI: 10.1016/j.taap.2022.116169] [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: 02/17/2022] [Revised: 06/27/2022] [Accepted: 07/12/2022] [Indexed: 12/24/2022]
Abstract
PURPOSE Our previous studies have confirmed that aspirin combined with Lipitor inhibited the development of prostate cancer (PCa), but the mechanisms need to be comprehensively expounded. The study aims to screen out the hub genes of combination therapy and to explore their association with the pathogenesis and prognosis of PCa. METHODS Gene expressions were quantified by RNA sequencing (RNA-seq). Altered biological function, pathways of differentially expressed genes (DEGs), protein-protein interaction network, the filtering of hub genes, gene co-expression and the pathogenesis and prognosis were revealed by bioinformatics analysis. The correlation between hub gene expression and patient survival was validated by Kaplan-Meier. The effects of silent DNA replication and sister chromatid cohesion 1 (siDSCC1) combined with Lipitor and aspirin on DSCC1 expression, viability, invasion and migration of PCa cells were detected by qRT-PCR, Wound healing and transwell assays. RESULTS 157 overlapped DEGs involved in FoxO, PI3K-Akt and p53 signaling pathways were identified. Ten hub genes (NEIL3, CDC7, DSCC1, CDC25C, PRIM1, MCM10, FBXO5, DTL, SERPINE1, EXO1) were verified to be correlated with the pathology and prognosis of PCa. DSCC1 silencing not only inhibited the viability, migration and invasion of PCa cells, but also strengthened the suppressing effects of Lipitor and aspirin alone or in combination on PCa cells. CONCLUSION The enrichment pathways and targets of Lipitor combined with aspirin in PCa are discovered, and DSCC1 silencing can potentiate the effect of Lipitor combined with aspirin in the treatment of PCa.
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Affiliation(s)
- Xiao Wang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen City 529020, China
| | - Yi Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Junlei Liu
- Allan H. Conney Laboratory for Anticancer Research, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Xuetao Xu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen City 529020, China
| | - Zhaojun Sheng
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen City 529020, China
| | - Wenfeng Liu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen City 529020, China
| | - Min Chen
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen City 529020, China
| | - Yanyan Ma
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen City 529020, China
| | - Denggao Zhao
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen City 529020, China
| | - Dongli Li
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen City 529020, China
| | - Xi Zheng
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Ruters University, Piscataway NJ08854, USA.
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3
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Qin R, Cao L, Ye C, Wang J, Sun Z. Screening of genes related to survival prognosis of cervical squamous cell carcinoma and construction of prognosis prediction model. J Obstet Gynaecol Res 2021; 47:3310-3321. [PMID: 34219322 DOI: 10.1111/jog.14827] [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: 08/05/2020] [Revised: 04/01/2021] [Accepted: 04/30/2021] [Indexed: 12/09/2022]
Abstract
AIM We aimed to screen for the genes related to survival prognosis of cervical squamous cell carcinoma (CSCC) and then constructed a prognosis prediction model. METHODS The GSE63514 dataset was obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO). The CSCC gene dataset and the GSE44001 dataset were obtained from The Cancer Genome Atlas and NCBI GEO, respectively. The Kaplan-Meier (KM) curve was used to evaluate the association between high and low prognosis that was with the actual survival prognosis information. The Cox proportional hazards model was used to screen out the optimized prognostic-related signature differentially expressed gene (DEG) combinations. Gene set enrichment analysis was used to perform pathway enrichment annotation analysis for DEGs that were related to risk grouping. RESULTS In total, 16 399 DEGs were obtained and 23 gene ontology biological processes and 8 Kyoto Encyclopedia of Genes and Genomes pathways were screened. Nine optimized DEG groups related to independent prognosis were selected. The KM curves of pathologic N0 and N1 showed that low-risk group were associated with a better overall survival (p = 1.518e; p = 1.704e-01). The pathways related to risk grouping were cytokine-cytokine receptor interaction, JAK stat signaling pathway, and glycolysis-gluconeogenesis. CONCLUSION On the basis of this study, we established a prognostic risk model, which provided a reliable prognostic tool and was of great significance for locating the biomarkers related to survival prognosis in CSCC.
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Affiliation(s)
- Rui Qin
- Department of Obstetrics and Gynecology, The Third Hospital of Jilin University, Changchun, Jilin, P.R. China
| | - Lu Cao
- Department of Obstetrics and Gynecology, The Third Hospital of Jilin University, Changchun, Jilin, P.R. China
| | - Cong Ye
- Department of Obstetrics and Gynecology, The Third Hospital of Jilin University, Changchun, Jilin, P.R. China
| | - Junrong Wang
- Department of Obstetrics and Gynecology, The Third Hospital of Jilin University, Changchun, Jilin, P.R. China
| | - Ziqian Sun
- Department of Obstetrics and Gynecology, The Third Hospital of Jilin University, Changchun, Jilin, P.R. China
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4
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Zhu M, Wu M, Bian S, Song Q, Xiao M, Huang H, You L, Zhang J, Zhang J, Cheng C, Ni W, Zheng W. DNA primase subunit 1 deteriorated progression of hepatocellular carcinoma by activating AKT/mTOR signaling and UBE2C-mediated P53 ubiquitination. Cell Biosci 2021; 11:42. [PMID: 33622397 PMCID: PMC7903777 DOI: 10.1186/s13578-021-00555-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/11/2021] [Indexed: 12/13/2022] Open
Abstract
Background DNA primase subunit 1 (PRIM1) has been reported as a novel oncogene in several cancer types. However, its roles in hepatocellular carcinoma (HCC) remain unclear. This study aimed to investigate underlying mechanisms of PRIM1 and identify it as a potential molecular target for HCC. Methods Hub genes were screened between HCC tissues and normal liver tissues in 3 gene expression omnibus (GEO) datasets and the cancer genome atlas (TCGA). The expression features and prognostic value of one of the hub genes PRIM1 were analyzed by bioinformatic analyses and immunohistochemistry. Loss-of-function and gain-of-function studies were used to investigate the regulatory role of PRIM1 in HCC cells. Real-time (RT)-qPCR, western blotting, and ubiquitin immunoprecipitation assays were performed to explore the underlying mechanisms. The xenograft model was employed to detect the roles of PRIM1 in tumor growth in vivo. Finally, the 3D spheroid model was conducted to validate the role of PRIM1 in tumor growth and sorafenib resistance. Results The hub genes of HCC were screened in multiple bioinformatic datasets. PRIM1, as one of the hub genes, was significantly overexpressed in HCC tissues in mRNA and protein levels. In addition, high expression of PRIM1 indicated poor prognosis of HCC patients in TCGA, ICGC, and Nantong cohorts. Overexpression of PRIM1 promoted the proliferation, migration/invasion, and sorafenib resistance of HCC cells, with the decrease in apoptosis and cell cycle arrest. Mechanically, PRIM1 facilitated epithelial-mesenchymal transition (EMT) process and the activity of PI3K/AKT/mTOR signaling of HCC cells. Additionally, PRIM1 could cause the ubiquitination and degradation of P53 by upregulating Ubiquitin Conjugating Enzyme E2 C (UBE2C). Furthermore, knockdown of PRIM1 significantly inhibited the growth of xenograft tumors and HCC cells-derived spheroids with enhanced sorafenib resistance. Conclusion This study implies that PRIM1 may play a key role in the progression of HCC and may serve as a potential target for HCC treatment.
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Affiliation(s)
- Mengqi Zhu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China.,School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, China.,Department of Oncology, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China
| | - Mengna Wu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China
| | - Saiyan Bian
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China.,School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, China
| | - Qianqian Song
- Department of Radiology, Wake Forest School of Medicine, One Medical Center Boulevard, Winston-Salem, 27157 NC, USA
| | - Mingbing Xiao
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China
| | - Hua Huang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China
| | - Li You
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China
| | - Jianping Zhang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China
| | - Jie Zhang
- Department of Oncology, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China
| | - Chun Cheng
- School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, China
| | - Wenkai Ni
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China.
| | - Wenjie Zheng
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China. .,Department of Oncology, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China.
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Jiang J, Zhang Y, Xu R, Ren L, Chen J, Lu H. PRIM1 promotes the proliferation of hepatocellular carcinoma cells in vitro and in vivo. J Cancer 2020; 11:6601-6611. [PMID: 33046981 PMCID: PMC7545666 DOI: 10.7150/jca.47870] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/06/2020] [Indexed: 12/15/2022] Open
Abstract
PRIM1 plays an important role during oncogenesis, however it has never been reported in liver cancer, and thus our objective is to explore the role of PRIM1 in liver cancer. We selected RNAseq data of 50 paired liver cancer samples from the Cancer Gene Atlas (TCGA), and then bioinformatics methods and Mann-Whitney U test were used to analyze the correlation between PRIM1 and the clinical pathological stage of liver cancer. Quantitative polymerase chain reaction (QPCR) was used to detect mRNA expression of PRIM1 in BEL-7404, BCL-7402, HepG2 and SMMC-7721 cell lines. LV-PRIM1-RNAi was transfected into BEL-7404 and SMMC-7721 cells by lentivirus, and then Celigo imaging cytometer, Caspase3/7 Assay, flow cytometry and MTT assay were used to detect the proliferation and apoptosis of BEL-7404 and SMMC-7721 cells with ≥50% gene reduction rate after lentivirus transfection detected by QPCR. BEL-7404 and SMMC-7721 carrying PRIM1 gene were used for oncogenesis in vitro to observe the weight and fluorescence intensity of the tumor. Bioinformatics method was used to obtain the information about PRIM1 gene, and the correlation between PRIM1 and clinical pathological stage of liver cancer was analyzed by Mann-Whitney U test. QPCR results showed that PRIM1 was expressed in BEL-7404, BCL-7402, HepG2 and SMMC-7721 cell lines, which was highest in BCL-7404 cell line. Celigo imaging cytometer, Caspase3/7 Assay, flow cytometry and MTT assay showed that the proliferative ability of BEL-7404 and SMMC-7721 were decreased after LV-PRIM1-RNAi transfection. Furthermore, the weight and the fluorescence intensity of the tumors in vitro formed by LV-PRIM1-RNAi cells on SCID mice were decreased. So, interference of PRIM1 expression can inhibit the proliferation of BEL-7404 and SMMC-7721 cells, as well as induce the apoptosis of liver cancer cells.
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Affiliation(s)
- Jinqun Jiang
- Department of Clinical Laboratory, Yuebei People's Hospital, Shaoguan, Guangdong Province 512026 P.R. China
| | - YuZhu Zhang
- Department of Breast Disease, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province 510282 P.R. China
| | - Rui Xu
- Department of Breast Disease, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province 510282 P.R. China
| | - Liping Ren
- Department of Breast Disease, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province 510282 P.R. China
| | - Junqian Chen
- Department of Breast Disease, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province 510282 P.R. China
| | - Hai Lu
- The Second Affiliated Hospital of GuangZhou University of Chinese Medicine , Guangzhou, Guangdong Province 510282 P.R. China.,The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province 510282 P.R. China
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Systems Biology Approach Identifies Prognostic Signatures of Poor Overall Survival and Guides the Prioritization of Novel BET-CHK1 Combination Therapy for Osteosarcoma. Cancers (Basel) 2020; 12:cancers12092426. [PMID: 32859084 PMCID: PMC7564419 DOI: 10.3390/cancers12092426] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 08/01/2020] [Accepted: 08/14/2020] [Indexed: 12/12/2022] Open
Abstract
Osteosarcoma (OS) patients exhibit poor overall survival, partly due to copy number variations (CNVs) resulting in dysregulated gene expression and therapeutic resistance. To identify actionable prognostic signatures of poor overall survival, we employed a systems biology approach using public databases to integrate CNVs, gene expression, and survival outcomes in pediatric, adolescent, and young adult OS patients. Chromosome 8 was a hotspot for poor prognostic signatures. The MYC-RAD21 copy number gain (8q24) correlated with increased gene expression and poor overall survival in 90% of the patients (n = 85). MYC and RAD21 play a role in replication-stress, which is a therapeutically actionable network. We prioritized replication-stress regulators, bromodomain and extra-terminal proteins (BETs), and CHK1, in order to test the hypothesis that the inhibition of BET + CHK1 in MYC-RAD21+ pediatric OS models would be efficacious and safe. We demonstrate that MYC-RAD21+ pediatric OS cell lines were sensitive to the inhibition of BET (BETi) and CHK1 (CHK1i) at clinically achievable concentrations. While the potentiation of CHK1i-mediated effects by BETi was BET-BRD4-dependent, MYC expression was BET-BRD4-independent. In MYC-RAD21+ pediatric OS xenografts, BETi + CHK1i significantly decreased tumor growth, increased survival, and was well tolerated. Therefore, targeting replication stress is a promising strategy to pursue as a therapeutic option for this devastating disease.
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7
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DNA Primase Subunit 1 Expression in Hepatocellular Carcinoma and Its Clinical Implication. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9689312. [PMID: 32908930 PMCID: PMC7463366 DOI: 10.1155/2020/9689312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/10/2020] [Indexed: 11/22/2022]
Abstract
DNA Primase Subunit 1 (PRIM1) is crucial for cancer development and progression. However, there remains a lack of comprehension concerning the clinical implication of PRIM1 in HCC. Here, aberrant expression of PRIM1 was identified in HCC according to available databases. The prognostic value of PRIM1 in patients presenting with HCC was further assessed based on TCGA data. Gene set enrichment analysis (GSEA) was subsequently conducted to investigate the potential function of PRIM1. Additionally, the correlations between tumor-infiltrating immune cells (TIICs) and PRIM1 expression were evaluated. The data from TCGA, GEO, ONCOMINE, and HCCDB databases illustrated that PRIM1 was overexpressed in HCC tissues, compared to normal liver tissues (all p < 0.05). Kaplan-Meier analysis revealed that high PRIM1 expression in HCC was closely correlated with worse overall survival (p < 0.05). The univariate and multivariate analyses illustrated that PRIM1 expression was an independent novel prognostic indicator in HCC. Additionally, the area under the receiver operating characteristic (AUROC) curve for PRIM1 reached 0.8651, indicating the diagnostic significance of PRIM1 in patients with HCC. GSEA showed that PRIM1 overexpression was significantly enriched in several tumor-related signaling pathways. Besides, TIIC analysis clarified the association between PRIM1 expression and TIICs in HCC. The findings disclose that PRIM1 profoundly implicated in promoting tumorigenesis might work as a desirable biomarker for HCC.
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8
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Zhu Z, Li L, Xu J, Ye W, Chen B, Zeng J, Huang Z. Comprehensive analysis reveals a metabolic ten-gene signature in hepatocellular carcinoma. PeerJ 2020; 8:e9201. [PMID: 32518728 PMCID: PMC7258935 DOI: 10.7717/peerj.9201] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/24/2020] [Indexed: 12/17/2022] Open
Abstract
Background Due to the complicated molecular and cellular heterogeneity in hepatocellular carcinoma (HCC), the morbidity and mortality still remains high level in the world. However, the number of novel metabolic biomarkers and prognostic models could be applied to predict the survival of HCC patients is still small. In this study, we constructed a metabolic gene signature by systematically analyzing the data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and International Cancer Genome Consortium (ICGC). Methods Differentially expressed genes (DEGs) between tumors and paired non-tumor samples of 50 patients from TCGA dataset were calculated for subsequent analysis. Univariate cox proportional hazard regression and LASSO analysis were performed to construct a gene signature. The Kaplan–Meier analysis, time-dependent receiver operating characteristic (ROC), Univariate and Multivariate Cox regression analysis, stratification analysis were used to assess the prognostic value of the gene signature. Furthermore, the reliability and validity were validated in four types of testing cohorts. Moreover, the diagnostic capability of the gene signature was investigated to further explore the clinical significance. Finally, Go enrichment analysis and Gene Set Enrichment Analysis (GSEA) have been performed to reveal the different biological processes and signaling pathways which were active in high risk or low risk group. Results Ten prognostic genes were identified and a gene signature were constructed to predict overall survival (OS). The gene signature has demonstrated an excellent ability for predicting survival prognosis. Univariate and Multivariate analysis revealed the gene signature was an independent prognostic factor. Furthermore, stratification analysis indicated the model was a clinically and statistically significant for all subgroups. Moreover, the gene signature demonstrated a high diagnostic capability in differentiating normal tissue and HCC. Finally, several significant biological processes and pathways have been identified to provide new insights into the development of HCC. Conclusion The study have identified ten metabolic prognostic genes and developed a prognostic gene signature to provide more powerful prognostic information and improve the survival prediction for HCC.
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Affiliation(s)
- Zhipeng Zhu
- Department of Gastrointestinal Surgery, Xiamen Cancer Center, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
| | - Lulu Li
- Department of Gastrointestinal Surgery, Xiamen Cancer Center, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
| | - Jiuhua Xu
- Department of Clinical Medicine, Fujian Medical University, Xiamen, Fujian, China
| | - Weipeng Ye
- Department of Clinical Medicine, Fujian Medical University, Xiamen, Fujian, China
| | - Borong Chen
- Department of Gastrointestinal Surgery, Xiamen Cancer Center, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
| | - Junjie Zeng
- Department of Gastrointestinal Surgery, Xiamen Cancer Center, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
| | - Zhengjie Huang
- Department of Gastrointestinal Surgery, Xiamen Cancer Center, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China.,Department of Clinical Medicine, Fujian Medical University, Xiamen, Fujian, China
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9
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Jiang S, Zhou F, Zhang Y, Zhou W, Zhu L, Zhang M, Luo J, Ma R, Xu X, Zhu J, Dong X, Zhang S, Fang J, Sun J, Yang X. Identification of tumorigenicity-associated genes in osteosarcoma cell lines based on bioinformatic analysis and experimental validation. J Cancer 2020; 11:3623-3633. [PMID: 32284759 PMCID: PMC7150450 DOI: 10.7150/jca.37393] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 03/03/2020] [Indexed: 12/12/2022] Open
Abstract
Osteosarcoma is the most common primary malignant tumor of bone. Tumorigenic investigation of osteosarcoma cell lines may facilitate preclinical studies of targeted therapy. Therefore, the aim of this study was to explore the tumorigenicity-associated genes in osteosarcoma cells. We found that 138 genes were highly expressed and 86 genes were lowly expressed in highly tumorigenic osteosarcoma cell lines (143B, MNNG/HOS, and SJSA-1) compared with poorly tumorigenic osteosarcoma cell lines (MG-63, Saos-2, and U-2 OS). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that highly expressed genes were associated with amino acids and energy metabolism, while lowly expressed genes were associated with cell cycle and DNA replication. Gene Ontology (GO) analysis showed that highly expressed genes were associated with endoplasmic reticulum stress response and aggrephagy, whereas lowly expressed genes were correlated with extracellular matrix assembly and DNA damage response. Further analysis identified six highly expressed genes and six lowly expressed genes. Three of highly expressed genes (DDX10, FOXA2, and HEY1) were correlated with poor prognosis, while three of lowly expressed genes (CYP26B1, GP1BB, and IFI44) showed the opposite trend in patients with osteosarcoma. Knockdown of HEY1 significantly inhibited the tumorigenicity of 143B cells in BALB/c nude mice.
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Affiliation(s)
- Shaojie Jiang
- Department of Radiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China.,School of Medical Imaging, Hangzhou Medical College, Hangzhou, Zhejiang, 310013, China
| | - Fei Zhou
- Department of Radiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China
| | - Yanhua Zhang
- Department of Pathology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China
| | - Weiping Zhou
- Department of Diagnostic Ultrasound and Echocardiography, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China
| | - Linghua Zhu
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China
| | - Miaofeng Zhang
- Department of Orthopedic Surgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China
| | - Jingfeng Luo
- Department of Radiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China
| | - Rui Ma
- Department of Surgery, Zhejiang University Hospital, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Xiufang Xu
- School of Medical Imaging, Hangzhou Medical College, Hangzhou, Zhejiang, 310013, China
| | - Jiying Zhu
- School of Medical Imaging, Hangzhou Medical College, Hangzhou, Zhejiang, 310013, China
| | - Xue Dong
- Department of Radiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China
| | - Shuangling Zhang
- Department of Radiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China
| | - Jie Fang
- Key Laboratory of Experimental Animal and Safety Research, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang 310013, China
| | - Jihong Sun
- Department of Radiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China
| | - Xiaoming Yang
- Department of Radiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China.,Image-Guided Bio-Molecular Intervention Research, Department of Radiology, University of Washington School of Medicine, Seattle, Washington, 98109, USA
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10
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Holzer S, Rzechorzek NJ, Short IR, Jenkyn-Bedford M, Pellegrini L, Kilkenny ML. Structural Basis for Inhibition of Human Primase by Arabinofuranosyl Nucleoside Analogues Fludarabine and Vidarabine. ACS Chem Biol 2019; 14:1904-1912. [PMID: 31479243 PMCID: PMC6757278 DOI: 10.1021/acschembio.9b00367] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/03/2019] [Indexed: 12/17/2022]
Abstract
Nucleoside analogues are widely used in clinical practice as chemotherapy drugs. Arabinose nucleoside derivatives such as fludarabine are effective in the treatment of patients with acute and chronic leukemias and non-Hodgkin's lymphomas. Although nucleoside analogues are generally known to function by inhibiting DNA synthesis in rapidly proliferating cells, the identity of their in vivo targets and mechanism of action are often not known in molecular detail. Here we provide a structural basis for arabinose nucleotide-mediated inhibition of human primase, the DNA-dependent RNA polymerase responsible for initiation of DNA synthesis in DNA replication. Our data suggest ways in which the chemical structure of fludarabine could be modified to improve its specificity and affinity toward primase, possibly leading to less toxic and more effective therapeutic agents.
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Affiliation(s)
- Sandro Holzer
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.
| | - Neil J. Rzechorzek
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.
| | - Isobel R. Short
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.
| | - Michael Jenkyn-Bedford
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.
| | - Luca Pellegrini
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.
| | - Mairi L. Kilkenny
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.
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Job A, Schmitt LM, von Wenserski L, Lankat-Buttgereit B, Gress TM, Buchholz M, Gallmeier E. Inactivation of PRIM1 Function Sensitizes Cancer Cells to ATR and CHK1 Inhibitors. Neoplasia 2018; 20:1135-1143. [PMID: 30257222 PMCID: PMC6154763 DOI: 10.1016/j.neo.2018.08.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/29/2018] [Accepted: 08/31/2018] [Indexed: 12/14/2022] Open
Abstract
The phosphoinositide 3-kinase-related kinase ATR is a central regulator of the DNA damage response. Its chemical inhibition eliminates subsets of cancer cells in various tumor types. This effect is caused at least partly by the synthetically lethal relationship between ATR and certain DNA repair genes. In a previous screen using an siRNA library against DNA repair genes, we identified PRIM1, a part of the polymerase α-primase complex, as acting synthetically lethal with ATR. Applying a genetic ATR knock-in model of colorectal cancer cells, we confirmed that PRIM1 depletion inhibited proliferation of ATR-deficient cells and excluded artifacts due to clonal variation using an ATR reexpressing cell clone. We expanded these data by demonstrating in different cell lines that also chemical inhibition of ATR or its main effector kinase CHK1 reduces proliferation upon depletion of PRIM1. Mechanistically, PRIM1 depletion in ATR-deficient cells caused S-phase stasis in the absence of increased DNA damage followed by Wee1-mediated activation of caspase 8 and apoptosis. As PRIM1 inactivation sensitizes cancer cells to ATR and CHK1 inhibitors, mutations in PRIM1 or other components of the polymerase α-primase complex could represent novel targets for individualized tumor therapeutic approaches using ATR/CHK1 inhibitors, as has been previously demonstrated for POLD1, the catalytic subunit of polymerase δ.
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Affiliation(s)
- Albert Job
- Center for Tumor Biology and Immunology, Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University Marburg, Marburg, Germany
| | - Lisa-Maria Schmitt
- Center for Tumor Biology and Immunology, Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University Marburg, Marburg, Germany
| | - Lisa von Wenserski
- Center for Tumor Biology and Immunology, Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University Marburg, Marburg, Germany
| | - Brigitte Lankat-Buttgereit
- Center for Tumor Biology and Immunology, Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University Marburg, Marburg, Germany
| | - Thomas M Gress
- Center for Tumor Biology and Immunology, Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University Marburg, Marburg, Germany
| | - Malte Buchholz
- Center for Tumor Biology and Immunology, Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University Marburg, Marburg, Germany
| | - Eike Gallmeier
- Center for Tumor Biology and Immunology, Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University Marburg, Marburg, Germany.
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12
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Zhang Y, Yang F. Analyzing the disease module associated with osteosarcoma via a network- and pathway-based approach. Exp Ther Med 2018; 16:2584-2592. [PMID: 30210606 PMCID: PMC6122582 DOI: 10.3892/etm.2018.6506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/13/2018] [Indexed: 12/18/2022] Open
Abstract
Osteosarcoma is the most common type of primary malignant bone tumor observed in children and adolescents. The aim of the present study was to identify an osteosarcoma-related gene module (OSM) by looking for a dense module following the integration of signals from genome-wide association studies (GWAS) into the human protein-protein interaction (PPI) network. A dataset of somatic mutations in osteosarcoma was obtained from the dbGaP database and their testing P-values were incorporated into the PPI network from a recent study using the dmGWAS bioconductor package. An OSM containing 201 genes (OS genes) and 268 interactions, which were closely associated with immune response, intracellular signal transduction and cell activity was identified. Topological analysis of the OSM identified 11 genes, including APP, APPBP2, ATXN1, HSP90B1, IKZF1, KRTAP10-1, PAK1, PDPK1, SMAD4, SUZ12 and TP53 as potential diagnostic biomarkers for osteosarcoma. The overall survival analysis of osteosarcoma for those 11 genes based on a dataset from the Cancer Genome Atlas, identified APP, HSP90B1, SUZ12 and IKZF1 as osteosarcoma survival-related genes. The results of the present study should be helpful in understanding the diagnosis and treatment of osteosarcoma and its underlying mechanisms. In addition, the methodology used in the present study may be suitable for the analysis of other types of disease.
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Affiliation(s)
- Yi Zhang
- Department of Orthopaedic Microsurgery, Central Hospital of Zibo, Zibo, Shandong 255000, P.R. China
| | - Fei Yang
- Department of Orthopedic Joint Surgery, Central Hospital of Zibo, Zibo, Shandong 255000, P.R. China
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13
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Ren YM, Duan YH, Sun YB, Yang T, Zhao WJ, Zhang DL, Tian ZW, Tian MQ. Exploring the key genes and pathways of side population cells in human osteosarcoma using gene expression array analysis. J Orthop Surg Res 2018; 13:153. [PMID: 29921292 PMCID: PMC6006685 DOI: 10.1186/s13018-018-0860-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/08/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Human osteosarcoma (OS) is one of the most common primary bone sarcoma, because of early metastasis and few treatment strategies. It has been reported that the tumorigenicity and self-renewal capacity of side population (SP) cells play roles in human OS via regulating of target genes. This study aims to complement the differentially expressed genes (DEGs) that regulated between the SP cells and the non-SP cells from primary human OS and identify their functions and molecular pathways associated with OS. METHODS The gene expression profile GSE63390 was downloaded, and bioinformatics analysis was made. RESULTS One hundred forty-one DEGs totally were identified. Among them, 72 DEGs (51.06%) were overexpressed, and the remaining 69 DEGs (48.94%) were underexpressed. Gene ontology (GO) and pathway enrichment analysis of target genes were performed. We furthermore identified some relevant core genes using gene-gene interaction network analysis such as EIF4E, FAU, HSPD1, IL-6, and KISS1, which may have a relationship with the development process of OS. We also discovered that EIF4E/mTOR signaling pathway could be a potential research target for therapy and tumorigenesis of OS. CONCLUSION This analysis provides a comprehensive understanding of the roles of DEGs coming from SP cells in the development of OS. However, these predictions need further experimental validation in future studies.
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Affiliation(s)
- Yi-Ming Ren
- Department of Joint and Sport Medicine, Tianjin Union Medical Center, Jieyuan Road 190, Hongqiao District, Tianjin, 300121 People’s Republic of China
| | - Yuan-Hui Duan
- Department of Joint and Sport Medicine, Tianjin Union Medical Center, Jieyuan Road 190, Hongqiao District, Tianjin, 300121 People’s Republic of China
| | - Yun-Bo Sun
- Department of Joint and Sport Medicine, Tianjin Union Medical Center, Jieyuan Road 190, Hongqiao District, Tianjin, 300121 People’s Republic of China
| | - Tao Yang
- Department of Joint and Sport Medicine, Tianjin Union Medical Center, Jieyuan Road 190, Hongqiao District, Tianjin, 300121 People’s Republic of China
| | - Wen-Jun Zhao
- Department of Joint and Sport Medicine, Tianjin Union Medical Center, Jieyuan Road 190, Hongqiao District, Tianjin, 300121 People’s Republic of China
| | - Dong-Liang Zhang
- Department of Joint and Sport Medicine, Tianjin Union Medical Center, Jieyuan Road 190, Hongqiao District, Tianjin, 300121 People’s Republic of China
| | - Zheng-Wei Tian
- Department of Joint and Sport Medicine, Tianjin Union Medical Center, Jieyuan Road 190, Hongqiao District, Tianjin, 300121 People’s Republic of China
| | - Meng-Qiang Tian
- Department of Joint and Sport Medicine, Tianjin Union Medical Center, Jieyuan Road 190, Hongqiao District, Tianjin, 300121 People’s Republic of China
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14
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Yoon DS, Cha DS, Alfhili MA, Keiper BD, Lee MH. Subunits of the DNA polymerase alpha-primase complex promote Notch-mediated proliferation with discrete and shared functions in C. elegans germline. FEBS J 2018; 285:2590-2604. [PMID: 29775245 DOI: 10.1111/febs.14512] [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] [Received: 12/12/2017] [Revised: 05/04/2018] [Accepted: 05/15/2018] [Indexed: 11/27/2022]
Abstract
Notch receptor signaling is a highly conserved cell communication system in most multicellular organisms and plays a critical role at several junctures in animal development. In Caenorhabditis elegans,GLP-1/Notch signaling is essential for both germline stem cell maintenance and germ cell proliferation during gonad development. Here, we show that subunits (POLA-1, DIV-1, PRI-1, and PRI-2) of the DNA polymerase alpha-primase complex are required for germ cell proliferation in response to GLP-1/Notch signaling in different tissues at different developmental stages. Specifically, genetic and functional analyses demonstrated that (a) maternally contributed DIV-1 (regulatory subunit) is indispensable non-cell autonomously for GLP-1/Notch-mediated germ cell proliferation during early larval development, whereas POLA-1 (catalytic subunit) and two primase subunits, PRI-1 and PRI-2, do not appear to be essential; (b) germline POLA-1, PRI-1, and PRI-2 play a crucial role in GLP-1/Notch-mediated maintenance of proliferative cell fate during adulthood, while DIV-1 is dispensable; and (c) germline POLA-1, DIV-1, PRI-1, and PRI-2 function in tandem with PUF (Pumilio/FBF) RNA-binding proteins to maintain germline stem cells in the adult gonad. These findings suggest that the subunits of the DNA polymerase alpha-primase complex exhibit both discrete and shared functions in GLP-1/Notch or PUF-mediated germ cell dynamics in C. elegans. These findings link the biological functions of DNA replication machineries to signals that maintain a stem cell population, and may have further implications for Notch-dependent tumors.
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Affiliation(s)
- Dong Suk Yoon
- Department of Medicine (Hematology/Oncology), Brody School of Medicine at East Carolina University, Greenville, NC, USA
| | - Dong Seok Cha
- Department of Medicine (Hematology/Oncology), Brody School of Medicine at East Carolina University, Greenville, NC, USA.,Department of Oriental Pharmacy, College of Pharmacy, Woosuk University, Jeonbuk, Korea
| | - Mohammad A Alfhili
- Department of Medicine (Hematology/Oncology), Brody School of Medicine at East Carolina University, Greenville, NC, USA.,Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Brett D Keiper
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, NC, USA
| | - Myon-Hee Lee
- Department of Medicine (Hematology/Oncology), Brody School of Medicine at East Carolina University, Greenville, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, NC, USA
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15
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Hocke S, Guo Y, Job A, Orth M, Ziesch A, Lauber K, De Toni EN, Gress TM, Herbst A, Göke B, Gallmeier E. A synthetic lethal screen identifies ATR-inhibition as a novel therapeutic approach for POLD1-deficient cancers. Oncotarget 2016; 7:7080-95. [PMID: 26755646 PMCID: PMC4872770 DOI: 10.18632/oncotarget.6857] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 01/01/2016] [Indexed: 12/22/2022] Open
Abstract
The phosphoinositide 3-kinase-related kinase ATR represents a central checkpoint regulator and mediator of DNA-repair. Its inhibition selectively eliminates certain subsets of cancer cells in various tumor types, but the underlying genetic determinants remain enigmatic. Here, we applied a synthetic lethal screen directed against 288 DNA-repair genes using the well-defined ATR knock-in model of DLD1 colorectal cancer cells to identify potential DNA-repair defects mediating these effects. We identified a set of DNA-repair proteins, whose knockdown selectively killed ATR-deficient cancer cells. From this set, we further investigated the profound synthetic lethal interaction between ATR and POLD1. ATR-dependent POLD1 knockdown-induced cell killing was reproducible pharmacologically in POLD1-depleted DLD1 cells and a panel of other colorectal cancer cell lines by using chemical inhibitors of ATR or its major effector kinase CHK1. Mechanistically, POLD1 depletion in ATR-deficient cells caused caspase-dependent apoptosis without preceding cell cycle arrest and increased DNA-damage along with impaired DNA-repair. Our data could have clinical implications regarding tumor genotype-based cancer therapy, as inactivating POLD1 mutations have recently been identified in small subsets of colorectal and endometrial cancers. POLD1 deficiency might thus represent a predictive marker for treatment response towards ATR- or CHK1-inhibitors that are currently tested in clinical trials.
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Affiliation(s)
- Sandra Hocke
- Department of Medicine II, Ludwig-Maximilians-University of Munich, 81377 Munich, Germany
| | - Yang Guo
- Department of Medicine II, Ludwig-Maximilians-University of Munich, 81377 Munich, Germany
| | - Albert Job
- Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University of Marburg, 35043 Marburg, Germany
| | - Michael Orth
- Department of Radiotherapy and Radiation Oncology, Ludwig-Maximilians-University of Munich, 81377 Munich, Germany
| | - Andreas Ziesch
- Department of Medicine II, Ludwig-Maximilians-University of Munich, 81377 Munich, Germany
| | - Kirsten Lauber
- Department of Radiotherapy and Radiation Oncology, Ludwig-Maximilians-University of Munich, 81377 Munich, Germany
| | - Enrico N De Toni
- Department of Medicine II, Ludwig-Maximilians-University of Munich, 81377 Munich, Germany
| | - Thomas M Gress
- Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University of Marburg, 35043 Marburg, Germany
| | - Andreas Herbst
- Department of Medicine II, Ludwig-Maximilians-University of Munich, 81377 Munich, Germany
| | - Burkhard Göke
- Department of Medicine II, Ludwig-Maximilians-University of Munich, 81377 Munich, Germany
| | - Eike Gallmeier
- Department of Medicine II, Ludwig-Maximilians-University of Munich, 81377 Munich, Germany.,Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University of Marburg, 35043 Marburg, Germany
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16
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Boudet J, Devillier JC, Allain FHT, Lipps G. Structures to complement the archaeo-eukaryotic primases catalytic cycle description: What's next? Comput Struct Biotechnol J 2015; 13:339-51. [PMID: 25987967 PMCID: PMC4434180 DOI: 10.1016/j.csbj.2015.04.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/20/2015] [Accepted: 04/24/2015] [Indexed: 12/25/2022] Open
Abstract
DNA replication is a crucial stage in the transfer of genetic information from parent to daughter cells. This mechanism involves multiple proteins with one key player being the primase. Primases are single-stranded DNA dependent RNA polymerases. On the leading strand, they synthesize the primer once allowing DNA elongation while on the lagging strand primers are generated repeatedly (Okazaki fragments). Primases have the unique ability to create the first phosphodiester bond yielding a dinucleotide which is initially elongated by primases and then by DNA polymerases. Primase activity has been studied in the last decades but the detailed molecular steps explaining some unique features remain unclear. High-resolution structures of free and bound primases domains have brought significant insights in the understanding of the primase reaction cycle. Here, we give a short review of the structural work conducted in the field of archaeo-eukaryotic primases and we underline the missing “pictures” of the active forms of the enzyme which are of major interest. We organized our analysis with respect to the progression through the catalytic pathway.
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Affiliation(s)
- Julien Boudet
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
- Corresponding author. Tel.: + 41 446330723; fax: + 41 446331294.
| | - Jean-Christophe Devillier
- University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, 4132 Muttenz, Switzerland
| | - Frédéric H.-T. Allain
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Georg Lipps
- University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, 4132 Muttenz, Switzerland
- Corresponding author. Tel.: + 41 614674301; fax: + 41 614674701.
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17
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Abstract
For the past 30 years, improvements in the survival of patients with osteosarcoma have been mostly incremental. Despite evidence of genomic instability and a high frequency of chromothripsis and kataegis, osteosarcomas carry few recurrent targetable mutations, and trials of targeted agents have been generally disappointing. Bone has a highly specialized immune environment and many immune signalling pathways are important in bone homeostasis. The success of the innate immune stimulant mifamurtide in the adjuvant treatment of non-metastatic osteosarcoma suggests that newer immune-based treatments, such as immune checkpoint inhibitors, may substantially improve disease outcome.
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Affiliation(s)
- Maya Kansara
- 1] Research Division, Peter MacCallum Cancer Centre, Melbourne, 3002, Victoria, Australia. [2] Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, 3010, Victoria, Australia
| | - Michele W Teng
- 1] Immunology in Cancer and Infection Laboratory and Cancer Immunoregulation and Immunotherapy Laboratory, QIMR Berghofer Medical Research Institute, Herston, 4006, Queensland, Australia. [2] School of Medicine, University of Queensland, Herston, 4006, Queensland, Australia
| | - Mark J Smyth
- 1] Immunology in Cancer and Infection Laboratory and Cancer Immunoregulation and Immunotherapy Laboratory, QIMR Berghofer Medical Research Institute, Herston, 4006, Queensland, Australia. [2] School of Medicine, University of Queensland, Herston, 4006, Queensland, Australia
| | - David M Thomas
- 1] Research Division, Peter MacCallum Cancer Centre, Melbourne, 3002, Victoria, Australia. [2] Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, 3010, Victoria, Australia. [3] The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, 2010, New South Wales, Australia
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18
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Islam AKMT, Jeong BS, Bari ATMG, Lim CG, Jeon SH. MapReduce based parallel gene selection method. APPL INTELL 2014. [DOI: 10.1007/s10489-014-0561-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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19
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Srinivasan H, Allory Y, Sill M, Vordos D, Alhamdani MSS, Radvanyi F, Hoheisel JD, Schröder C. Prediction of recurrence of non muscle-invasive bladder cancer by means of a protein signature identified by antibody microarray analyses. Proteomics 2014; 14:1333-42. [DOI: 10.1002/pmic.201300320] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 02/05/2014] [Accepted: 02/28/2014] [Indexed: 12/27/2022]
Affiliation(s)
- Harish Srinivasan
- Division of Functional Genome Analysis; Deutsches Krebsforschungszentrum (DKFZ); Heidelberg Germany
| | - Yves Allory
- Département de Pathologie et Plateforme de Ressources Biologiques, AP-HP Hôpitaux Universitaires Henri Mondor; Créteil France
| | - Martin Sill
- Division of Biostatistics; Deutsches Krebsforschungszentrum (DKFZ); Heidelberg Germany
| | - Dimitri Vordos
- AP-HP Hôpitaux Universitaires Henri Mondor; Service d´Urologie; Créteil France
| | | | | | - Jörg D. Hoheisel
- Division of Functional Genome Analysis; Deutsches Krebsforschungszentrum (DKFZ); Heidelberg Germany
| | - Christoph Schröder
- Division of Functional Genome Analysis; Deutsches Krebsforschungszentrum (DKFZ); Heidelberg Germany
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20
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Abstract
Osteosarcoma is a primary bone malignancy with a particularly high incidence rate in children and adolescents relative to other age groups. The etiology of this often aggressive cancer is currently unknown, because complicated structural and numeric genomic rearrangements in cancer cells preclude understanding of tumour development. In addition, few consistent genetic changes that may indicate effective molecular therapeutic targets have been reported. However, high-resolution techniques continue to improve knowledge of distinct areas of the genome that are more commonly associated with osteosarcomas. Copy number gains at chromosomes 1p, 1q, 6p, 8q, and 17p as well as copy number losses at chromosomes 3q, 6q, 9, 10, 13, 17p, and 18q have been detected by numerous groups, but definitive oncogenes or tumour suppressor genes remain elusive with respect to many loci. In this paper, we examine studies of the genetics of osteosarcoma to comprehensively describe the heterogeneity and complexity of this cancer.
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21
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Ladanyi M, Gorlick R. Molecular Pathology and Molecular Pharmacology of Osteosarcoma. ACTA ACUST UNITED AC 2010. [DOI: 10.1080/15513810009168647] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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22
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Osteosarcoma development and stem cell differentiation. Clin Orthop Relat Res 2008; 466:2114-30. [PMID: 18563507 PMCID: PMC2492997 DOI: 10.1007/s11999-008-0335-z] [Citation(s) in RCA: 270] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Accepted: 05/20/2008] [Indexed: 01/31/2023]
Abstract
Osteosarcoma is the most common nonhematologic malignancy of bone in children and adults. The peak incidence occurs in the second decade of life, with a smaller peak after age 50. Osteosarcoma typically arises around the growth plate of long bones. Most osteosarcoma tumors are of high grade and tend to develop pulmonary metastases. Despite clinical improvements, patients with metastatic or recurrent diseases have a poor prognosis. Here, we reviewed the current understanding of human osteosarcoma, with an emphasis on potential links between defective osteogenic differentiation and bone tumorigenesis. Existing data indicate osteosarcoma tumors display a broad range of genetic and molecular alterations, including the gains, losses, or arrangements of chromosomal regions, inactivation of tumor suppressor genes, and the deregulation of major signaling pathways. However, except for p53 and/or RB mutations, most alterations are not constantly detected in the majority of osteosarcoma tumors. With a rapid expansion of our knowledge about stem cell biology, emerging evidence suggests osteosarcoma should be regarded as a differentiation disease caused by genetic and epigenetic changes that interrupt osteoblast differentiation from mesenchymal stem cells. Understanding the molecular pathogenesis of human osteosarcoma could ultimately lead to the development of diagnostic and prognostic markers, as well as targeted therapeutics for osteosarcoma patients.
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23
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Wurmbach E, Chen YB, Khitrov G, Zhang W, Roayaie S, Schwartz M, Fiel I, Thung S, Mazzaferro V, Bruix J, Bottinger E, Friedman S, Waxman S, Llovet JM. Genome-wide molecular profiles of HCV-induced dysplasia and hepatocellular carcinoma. Hepatology 2007; 45:938-47. [PMID: 17393520 DOI: 10.1002/hep.21622] [Citation(s) in RCA: 537] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
UNLABELLED Although HCC is the third-leading cause of cancer-related deaths worldwide, there is only an elemental understanding of its molecular pathogenesis. In western countries, HCV infection is the main etiology underlying this cancer's accelerating incidence. To characterize the molecular events of the hepatocarcinogenic process, and to identify new biomarkers for early HCC, the gene expression profiles of 75 tissue samples were analyzed representing the stepwise carcinogenic process from preneoplastic lesions (cirrhosis and dysplasia) to HCC, including 4 neoplastic stages (very early HCC to metastatic tumors) from patients with HCV infection. We identified gene signatures that accurately reflect the pathological progression of disease at each stage. Eight genes distinguish between control and cirrhosis, 24 between cirrhosis and dysplasia, 93 between dysplasia and early HCC, and 9 between early and advanced HCC. Using quantitative real-time reverse-transcription PCR, we validated several novel molecular tissue markers for early HCC diagnosis, specifically induction of abnormal spindle-like, microcephaly-associated protein, hyaluronan-mediated motility receptor, primase 1, erythropoietin, and neuregulin 1. In addition, pathway analysis revealed dysregulation of the Notch and Toll-like receptor pathways in cirrhosis, followed by deregulation of several components of the Jak/STAT pathway in early carcinogenesis, then upregulation of genes involved in DNA replication and repair and cell cycle in late cancerous stages. CONCLUSION These findings provide a comprehensive molecular portrait of genomic changes in progressive HCV-related HCC.
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Affiliation(s)
- Elisa Wurmbach
- Mount Sinai Liver Cancer Program, Division of Hematology/Oncology, Department of Medicine, Mount Sinai School of Medicine, New York, NY 10029, USA.
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24
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Abstract
Osteosarcoma is a devastating but rare disease, whose study has illuminated both the basic biology and clinical management of cancer over the past 30 years. These contributions have included insight into the roles of key cancer genes such as the retinoblastoma tumor suppressor gene and TP53, the identification of familial cancer syndromes implicating DNA helicases, and dramatic improvements in survival by the use of adjuvant chemotherapy. This review provides a synoptic overview of our current understanding of the molecular causes of osteosarcoma, and suggests future directions for study.
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Affiliation(s)
- Maya Kansara
- Ian Potter Foundation Centre for Cancer Genomics and Predictive Medicine and Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
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25
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Bransfield KL, Askham JM, Leek JP, Robinson PA, Mighell AJ. Phenotypic changes associated with DYNACTIN-2 (DCTN2) over expression characterise SJSA-1 osteosarcoma cells. Mol Carcinog 2006; 45:157-63. [PMID: 16369996 DOI: 10.1002/mc.20151] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DYNACTIN-2 (DCTN2) localises to chromosome 12q13-q15, a region prone to stable amplification in several cancers. Transient DCTN2 overexpression has a significant impact on cellular phenotype primarily due to disruption of the DYNEIN-dynactin motor. Changes reported include alterations of microtubule-directed movement of molecular (e.g. TP53) and organelle (e.g. Golgi) cargoes towards the nucleus, centrosome biology, cellular movement and mitosis with a potential predisposition to mitotic block and polyploidy. These changes would be expected to be of relevance to carcinogenesis. To investigate this, we report the first study of DCTN2 genomic amplification and sustained DCTN2 overexpression in cancer cells. QFMPCR was employed to characterise the extent of chromosome 12q13-q15 amplicons in SJSA-1, SJRH30, U373MG and CCF-STTG1 cancer cells. DCTN2 amplification was present in SJSA-1, U373MG and SJRH30 cells, yet was incomplete at the 5'-end in SJRH30 cells. Only SJSA-1 cells were characterised by DCTN2 overexpression on Western blot analyses. Microscopy studies distinguished SJSA-1 cells by greater DCTN2 immunofluorescence and diminished centrosome and 58K protein Golgi-marker focus compared to SJRH30 cells. Indirect evidence derived from the published work of others indicated that TP53 transport into the nucleus was unimpaired. Furthermore, we observed that SJSA-1 cells were easy to propagate. In conclusion, persistent DCTN2 overexpression can be tolerated in SJSA-1 cancer cells despite phenotypic abnormalities predicted from transient overexpression studies. This preliminary study does not support a major role for DCTN2 overexpression in carcinogenesis, although further studies would be necessary to confirm this.
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Affiliation(s)
- Kieran L Bransfield
- Molecular Medicine Unit, The University of Leeds, St. James's University Hospital, Leeds, United Kingdom
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Nishio J, Gentry JD, Neff JR, Nelson M, Daniels W, Perry D, Gatalica Z, Bridge JA. Monoallelic deletion of the p53 gene through chromosomal translocation in a small cell osteosarcoma. Virchows Arch 2006; 448:852-6. [PMID: 16596382 DOI: 10.1007/s00428-006-0181-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Accepted: 02/21/2006] [Indexed: 10/24/2022]
Abstract
Small cell osteosarcoma is a rare bone tumor of high-grade malignancy that most often arises in the metaphysis of long bones in the second decade of life. Cytogenetic and molecular genetic findings in small cell osteosarcoma are poorly defined. Conventional cytogenetic analysis of a small cell osteosarcoma arising in the proximal tibia of a 9-year-old male revealed a diploid chromosomal complement with complex structural rearrangements involving chromosomes 6, 16, and 17. Immunohistochemical assessment of p53 protein expression revealed nuclear p53 immunoreactivity in approximately 15% of the neoplastic cells. Subsequent fluorescence in situ hybridization (FISH) analyses confirmed loss of the p53 gene locus on the derivative chromosome 17 homolog and were negative for amplification of the MDM2, CDK4, c-MYC, HER-2/neu, CCND1, and COPS3 gene loci. To the best of our knowledge, this represents the first demonstration of monoallelic deletion of p53 in small cell osteosarcoma, suggesting that p53 alterations may play an important role in the development of small cell osteosarcoma as well as conventional osteosarcoma.
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Affiliation(s)
- Jun Nishio
- Department of Pathology and Microbiology, University of Nebraska Medical Center, 983135 Nebraska Medical Center, Omaha, NE 68198-3135, USA
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Fan L, Yotov WV, Zhu T, Esmailzadeh L, Joyal JS, Sennlaub F, Heveker N, Chemtob S, Rivard GE. Tissue factor enhances protease-activated receptor-2-mediated factor VIIa cell proliferative properties. J Thromb Haemost 2005; 3:1056-63. [PMID: 15869604 DOI: 10.1111/j.1538-7836.2005.01250.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
In addition to its hemostatic functions, factor (F)VIIa exhibits cell proliferative properties as seen in angiogenesis and tumor growth. A role for tissue factor (TF) and protease-activated receptors (PAR)-1 and -2 in cell proliferation remain to be clarified. We tested the hypothesis that FVIIa induces cell proliferation by a mechanism involving TF and PAR-2. Human recombinant FVIIa induced cell proliferation of human BOSC23 cells transfected with plasmid containing human TF DNA sequence. Because DNA primase 1 (PRIM1) plays an essential role in cell proliferation, we used the cloned PRIM1 promoter upstream of the reporter gene chloramphenicol acetyl transferase (CAT) to elucidate the mode of action of FVIIa. FVIIa evoked a dose-dependent increase in cell proliferation and PRIM1 induction, which were markedly potentiated (4-5-fold) by the presence of TF and abrogated by TF antisense oligonucleotide. PRIM1 induction by FVIIa was also abolished by PAR-2 but not by PAR-1 antisense. In contrast, thrombin induced a small increase in CAT activity which was unaffected by TF, but was prevented only by PAR-1 antisense as well as the thrombin inhibitor hirudin. Proliferative properties of FVIIa were associated with a TF-dependent increase in intracellular calcium and were mediated by a concordant phosphorylation of p44/42 MAP kinase. In conclusion, data reveal that FVIIa induces PRIM1 and ensuing cellular proliferation via a TF- and of the PARs entirely PAR-2-dependent pathway, in distinction to that of thrombin which is PAR-1-dependent and TF-independent. We speculate that FVIIa-TF-PAR-2 inhibitors may be effective in suppressing cell proliferation.
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Affiliation(s)
- L Fan
- Center de Recherche, Hôpital Sainte-Justine, Université de Montréal Montréal, Québec, Canada
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Eppert K, Wunder JS, Aneliunas V, Tsui LC, Scherer SW, Andrulis IL. Altered expression and deletion of RMO1 in osteosarcoma. Int J Cancer 2004; 114:738-46. [PMID: 15609301 DOI: 10.1002/ijc.20786] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In order to increase our understanding of the molecular events underlying osteosarcoma progression, the expression of approximately 950 genes was examined in 24 primary and metastatic osteosarcoma tumor specimens. A gene, RMO1, was isolated with decreased expression in metastatic samples. Real-Time PCR corroborated this pattern, revealing lower expression in the primary sample in 6 of 7 cases for which both primary and metastatic osteosarcoma samples were available from the same patient (p = 0.034). RMO1 is located at 2q33, a region of frequent loss of heterozygosity in cancer, and exhibited loss of heterozygosity in 6 out of 9 primary osteosarcoma tumor samples (67%). Loss of heterozygosity is evident in primary tumors while the decrease in gene expression is seen in the metastatic samples, indicating that these 2 events are separately implicated in cancer progression. Cloning of RMO1 revealed an open reading frame with multiple splice forms with significant homology to GRB7, 10 and 14 and MIG10 in the region containing a Pleckstrin homology domain and a Ras association domain, suggestive of a role in cell signaling and migration. Northern blot analysis indicated that RMO1 mRNA is ubiquitously expressed in tissues except for peripheral blood leukocytes. These data suggest that RMO1 may be a candidate for a protein involved in inhibiting tumor progression.
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Affiliation(s)
- Kolja Eppert
- Fred A. Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
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Man TK, Lu XY, Jaeweon K, Perlaky L, Harris CP, Shah S, Ladanyi M, Gorlick R, Lau CC, Rao PH. Genome-wide array comparative genomic hybridization analysis reveals distinct amplifications in osteosarcoma. BMC Cancer 2004; 4:45. [PMID: 15298715 PMCID: PMC514550 DOI: 10.1186/1471-2407-4-45] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2004] [Accepted: 08/07/2004] [Indexed: 12/23/2022] Open
Abstract
Background Osteosarcoma is a highly malignant bone neoplasm of children and young adults. It is characterized by extremely complex karyotypes and high frequency of chromosomal amplifications. Currently, only the histological response (degree of necrosis) to therapy represent gold standard for predicting the outcome in a patient with non-metastatic osteosarcoma at the time of definitive surgery. Patients with lower degree of necrosis have a higher risk of relapse and poor outcome even after chemotherapy and complete resection of the primary tumor. Therefore, a better understanding of the underlying molecular genetic events leading to tumor initiation and progression could result in the identification of potential diagnostic and therapeutic targets. Methods We used a genome-wide screening method – array based comparative genomic hybridization (array-CGH) to identify DNA copy number changes in 48 patients with osteosarcoma. We applied fluorescence in situ hybridization (FISH) to validate some of amplified clones in this study. Results Clones showing gains (79%) were more frequent than losses (66%). High-level amplifications and homozygous deletions constitute 28.6% and 3.8% of tumor genome respectively. High-level amplifications were present in 238 clones, of which about 37% of them showed recurrent amplification. Most frequently amplified clones were mapped to 1p36.32 (PRDM16), 6p21.1 (CDC5L, HSPCB, NFKBIE), 8q24, 12q14.3 (IFNG), 16p13 (MGRN1), and 17p11.2 (PMP22 MYCD, SOX1,ELAC27). We validated some of the amplified clones by FISH from 6p12-p21, 8q23-q24, and 17p11.2 amplicons. Homozygous deletions were noted for 32 clones and only 7 clones showed in more than one case. These 7 clones were mapped to 1q25.1 (4 cases), 3p14.1 (4 cases), 13q12.2 (2 cases), 4p15.1 (2 cases), 6q12 (2 cases), 6q12 (2 cases) and 6q16.3 (2 cases). Conclusions This study clearly demonstrates the utility of array CGH in defining high-resolution DNA copy number changes and refining amplifications. The resolution of array CGH technology combined with human genome database suggested the possible target genes present in the gained or lost clones.
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Affiliation(s)
- Tsz-Kwong Man
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Xin-Yan Lu
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Laszlo Perlaky
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Charles P Harris
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Richard Gorlick
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ching C Lau
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Pulivarthi H Rao
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
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Sandberg AA, Bridge JA. Updates on the cytogenetics and molecular genetics of bone and soft tissue tumors: osteosarcoma and related tumors. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0165-4608(03)00105-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Lau CC, Harris CP, Lu XY, Perlaky L, Gogineni S, Chintagumpala M, Hicks J, Johnson ME, Davino NA, Huvos AG, Meyers PA, Healy JH, Gorlick R, Rao PH. Frequent amplification and rearrangement of chromosomal bands 6p12-p21 and 17p11.2 in osteosarcoma. Genes Chromosomes Cancer 2003; 39:11-21. [PMID: 14603437 DOI: 10.1002/gcc.10291] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Osteosarcoma (OS) is a highly malignant bone neoplasm of children and young adults. It is characterized by chaotic karyotypes with complex marker chromosomes. We applied a combination of molecular cytogenetic techniques including comparative genomic hybridization (CGH), spectral karyotyping (SKY), and fluorescence in situ hybridization (FISH) to decipher the chromosomal complexity in a panel of 25 tumors. Combined SKY and G-banding analysis identified several novel recurrent breakpoint clusters and 9 nonrecurrent reciprocal translocations. CGH identified several recurrent chromosomal losses including 2q, 3p, 9, 10p, 12q, 13q, 14q, 15q, 16, 17p, and 18q, gains including Xp, Xq, 5q, 6p, 8q, 17p, and 20q, and high-level chromosomal amplifications at Xp11.2, 1q21-q22, 4p11, 4q12, 5p15, 6p12.1, 8q13, 8q23, 10q11, 10q22, 11q13, 11q23, 12q13-q14, 13q21-q34, 16q22, 17p11.2, 17q21-q22, 18q22, 20p11.2, and 20q12. Frequent amplification and rearrangement involving chromosomal bands at 6p12-p21 and 17p11.2 were found in 28% and 32% of cases, respectively. In an attempt to identify the genes involved in these amplicons, we used three nonoverlapping BAC clones contained within each amplicon as probes for FISH analysis, leading to a more detailed characterization and quantification of the 6p and 17p amplicons.
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Affiliation(s)
- Ching C Lau
- Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA.
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Abstract
DNA primases are enzymes whose continual activity is required at the DNA replication fork. They catalyze the synthesis of short RNA molecules used as primers for DNA polymerases. Primers are synthesized from ribonucleoside triphosphates and are four to fifteen nucleotides long. Most DNA primases can be divided into two classes. The first class contains bacterial and bacteriophage enzymes found associated with replicative DNA helicases. These prokaryotic primases contain three distinct domains: an amino terminal domain with a zinc ribbon motif involved in binding template DNA, a middle RNA polymerase domain, and a carboxyl-terminal region that either is itself a DNA helicase or interacts with a DNA helicase. The second major primase class comprises heterodimeric eukaryotic primases that form a complex with DNA polymerase alpha and its accessory B subunit. The small eukaryotic primase subunit contains the active site for RNA synthesis, and its activity correlates with DNA replication during the cell cycle.
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Affiliation(s)
- D N Frick
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, USA.
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Abstract
In this past year, a large number of reports have described cytogenetic and biologic studies of sarcomas. The cytogenetic studies provide further evidence that a growing number of sarcomas seem to be defined by consistent chromosomal abnormalities that can be detected using a variety of molecular genetic tests. However, in addition to these specific abnormalities, many sarcomas have other extremely complex genetic changes. This complexity has made it quite difficult to understand the importance of any single abnormality. Laboratory studies complementing these genetic studies have provided further understanding of sarcoma cellular and molecular biology. Importantly, both types of studies have had significant impact in the clinic in the form of more objective diagnostic tests, potential novel prognostic markers, and even new therapeutic strategies. Together, these papers highlight how genetic studies may offer tremendous insight into sarcoma biology. However, they also highlight some limitations of these approaches as well. Novel experimental approaches may be required to facilitate the continued progress in this field toward the development of better therapeutic strategies.
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Affiliation(s)
- S X Skapek
- Department of Hematology/Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.
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Nath J, Johnson KL. A review of fluorescence in situ hybridization (FISH): current status and future prospects. Biotech Histochem 2000; 75:54-78. [PMID: 10941509 DOI: 10.3109/10520290009064150] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) is a powerful technique for detecting DNA or RNA sequences in cells, tissues and tumors. This molecular cytogenetic technique enables the localization of specific DNA sequences within interphase chromatin and metaphase chromosomes and the identification of both structural and numerical chromosome changes. FISH is quickly becoming one of the most extensively used cytochemical staining techniques owing to its sensitivity and versatility, and with the improvement of current technology and cost effectiveness, its use will surely continue to expand. Here we review the wide variety of current applications and future prospects of FISH technology.
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Affiliation(s)
- J Nath
- Genetics and Developmental Biology Program, West Virginia University, Morgantown 26506-6108, USA.
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