1
|
He X, Chen X, Yang C, Wang W, Sun H, Wang J, Fu J, Dong H. Prognostic value of RNA methylation-related genes in gastric adenocarcinoma based on bioinformatics. PeerJ 2024; 12:e16951. [PMID: 38436027 PMCID: PMC10909369 DOI: 10.7717/peerj.16951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/24/2024] [Indexed: 03/05/2024] Open
Abstract
Background Gastric cancer (GC) is a malignant tumor that originates from the epithelium of the gastric mucosa and has a poor prognosis. Stomach adenocarcinoma (STAD) covers 95% of total gastric cancer. This study aimed to identify the prognostic value of RNA methylation-related genes in gastric cancer. Methods In this study, The Cancer Genome Atlas (TCGA)-STAD and GSE84426 cohorts were downloaded from public databases. Patients were classified by consistent cluster analysis based on prognosis-related differentially expressed RNA methylation genes Prognostic genes were obtained by differential expression, univariate Cox and least absolute shrinkage and selection operator (LASSO) analyses. The prognostic model was established and validated in the training set, test set and validation set respectively. Independent prognostic analysis was implemented. Finally, the expression of prognostic genes was affirmed by reverse transcription quantitative PCR (RT-qPCR). Results In total, four prognostic genes (ACTA2, SAPCD2, PDK4 and APOD) related to RNA methylation were identified and enrolled into the risk signature. The STAD patients were divided into high- and low-risk groups based on the medium value of the risk score, and patients in the high-risk group had a poor prognosis. In addition, the RNA methylation-relevant risk signature was validated in the test and validation sets, and was authenticated as a reliable independent prognostic predictor. The nomogram was constructed based on the independent predictors to predict the 1/3/5-year survival probability of STAD patients. The gene set enrichment analysis (GSEA) result suggested that the poor prognosis in the high-risk subgroup may be related to immune-related pathways. Finally, the experimental results indicated that the expression trends of RNA methylation-relevant prognostic genes in gastric cancer cells were in agreement with the result of bioinformatics. Conclusion Our study established a novel RNA methylation-related risk signature for STAD, which was of considerable significance for improving prognosis of STAD patients and offering theoretical support for clinical therapy.
Collapse
Affiliation(s)
- Xionghui He
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Xiang Chen
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Changcheng Yang
- Department of Medical Oncology, The First Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Wei Wang
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Hening Sun
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Junjie Wang
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Jincheng Fu
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Huaying Dong
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| |
Collapse
|
2
|
Xu H, Jiang C, Yao F, Liang H, Yan H, Chen D, Wu Y, Zhong L. Pan-Cancer Analysis Reveals the Relation between TRMT112 and Tumor Microenvironment. JOURNAL OF ONCOLOGY 2022; 2022:1445932. [PMID: 36081672 PMCID: PMC9448524 DOI: 10.1155/2022/1445932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/29/2022] [Accepted: 08/09/2022] [Indexed: 11/17/2022]
Abstract
Dysregulated epigenetic modifications play a critical role in cancer development where TRMT112 is a member of the transfer RNA (tRNA) methyltransferase family. Till now, no studies have revealed the linkage between TRMT112 expression and diverse types of tumors. Based on TCGA data, we first probed into the relation between TRMT112 and prognosis and the potential role of TRMT112 in tumor microenvironment across 33 types of tumor. TRMT112 presented with increased expression in most cancers, which was significantly prognostic. Furthermore, TRMT112 was associated with tumor-associated fibroblasts in a variety of cancers. Additionally, a positive relationship was identified between TRMT112 expression and multiple tumor-related immune infiltrations, such as dendritic cells, CD8+ T cells, macrophages, CD4+ T cells, neutrophils, and B cells in lung adenocarcinoma and breast invasive carcinoma. In summary, our results suggest that TRMT112 might be a potential prognostic predictor of cancers and involved in regulating multiple cancer-related immune responses to some extent.
Collapse
Affiliation(s)
- Haitao Xu
- Department of Hematology, Anqing Municipal Hospital, Anqing Medical Center Affiliated to Anhui Medical University, Anqing, China
| | - Caihong Jiang
- Department of Pediatric Surgery, Anqing Municipal Hospital, Anqing Medical Center Affiliated to Anhui Medical University, Anqing, China
| | - Fusheng Yao
- Department of Hematology, Anqing Municipal Hospital, Anqing Medical Center Affiliated to Anhui Medical University, Anqing, China
| | - Hong Liang
- Department of Hematology, Anqing Municipal Hospital, Anqing Medical Center Affiliated to Anhui Medical University, Anqing, China
| | - Hong Yan
- Department of Hematology, Anqing Municipal Hospital, Anqing Medical Center Affiliated to Anhui Medical University, Anqing, China
| | - Dangui Chen
- Department of Hematology, Anqing Municipal Hospital, Anqing Medical Center Affiliated to Anhui Medical University, Anqing, China
| | - Youzhi Wu
- Department of Hematology, Anqing Municipal Hospital, Anqing Medical Center Affiliated to Anhui Medical University, Anqing, China
| | - Long Zhong
- Department of Hematology, Anqing Municipal Hospital, Anqing Medical Center Affiliated to Anhui Medical University, Anqing, China
| |
Collapse
|
3
|
Zheng F, Du F, Zhao J, Wang X, Si Y, Jin P, Qian H, Xu B, Yuan P. The emerging role of RNA N6-methyladenosine methylation in breast cancer. Biomark Res 2021; 9:39. [PMID: 34044876 PMCID: PMC8161983 DOI: 10.1186/s40364-021-00295-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 05/18/2021] [Indexed: 02/07/2023] Open
Abstract
N6-methyladenosine (m6A) modification is the most prevalent internal mRNA modification and is involved in many biological processes in eukaryotes. Accumulating evidence has demonstrated that m6A may play either a promoting or suppressing role in breast cancer, including in tumorigenesis, metastasis and angiogenesis. In this review, we summarize the latest research progress on the biological function and prognostic value of m6A modification in breast cancer, as well as potential related therapeutic strategies.
Collapse
Affiliation(s)
- Fangchao Zheng
- Department of Medical Oncology, National Cancer Centre/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, Beijing, 100021, China
| | - Feng Du
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), The VIPII Gastrointestinal Cancer Division of Medical Department, Peking University Cancer Hospital and Institute, Beijing, 100021, China
| | - Jiuda Zhao
- Breast Disease Diagnosis and Treatment Center, Affiliated Hospital of Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Xue Wang
- Department of VIP Medical Services, National Cancer Centre/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yiran Si
- Department of Medical Oncology, National Cancer Centre/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, Beijing, 100021, China
| | - Peng Jin
- Department of Surgery, National Cancer Centre/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, Cancer Hospital/Institute, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Centre/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, Beijing, 100021, China
| | - Peng Yuan
- Department of Medical Oncology, National Cancer Centre/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, Beijing, 100021, China. .,Department of VIP Medical Services, National Cancer Centre/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| |
Collapse
|
4
|
Single nucleotide polymorphisms in piRNA-pathway genes: an insight into genetic determinants of human diseases. Mol Genet Genomics 2019; 295:1-12. [DOI: 10.1007/s00438-019-01612-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/22/2019] [Indexed: 12/23/2022]
|
5
|
Huang MS, Yuan FQ, Gao Y, Liu JY, Chen YX, Wang CJ, He BM, Zhou HH, Liu ZQ. Circular RNA screening from EIF3a in lung cancer. Cancer Med 2019; 8:4159-4168. [PMID: 31197975 PMCID: PMC6675731 DOI: 10.1002/cam4.2338] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/24/2019] [Accepted: 05/26/2019] [Indexed: 12/21/2022] Open
Abstract
Eukaryotic initiation factor 3 (EIF3) is one of the largest and most complex translation initiation factors, which consists of 13 subunits named eukaryotic translation initiation factor 3 subunit A (EIF3a) to EIF3m. EIF3a is the largest subunit of EIF3. Previous studies suggested that EIF3a is a housekeeping gene, recent results have found that EIF3a is closely related to the tumorigenesis and drug resistance. Circular RNAs (circRNAs) derived from biologically important gene can play an important role in gene regulation. However, the mechanism underlying circRNAs’ biological functions is not well understood yet. In this work, we screened 31 EIF3a‐derived circRNAs, in which two circEIF3as were identified to be correlated with cisplatin drug sensitivity in lung cancer. Two circEIF3as were found involved in RNA‐binding proteins‐mediated biological processes and may be related to translational regulation according to bioinformatics analyses. CircEIF3as, the transcriptional initiation factor EIF3a transcribed circRNAs, are associated with both drug sensitivity and translation regulation. These findings mean that they may have a functional synergy effect with EIF3a or be valuable therapeutic targets for treatment like EIF3a. This is the first study that exploits circRNAs screening from EIF3a in lung cancer, our findings provide a novel perspective on the function of EIF3a and circEIF3as in lung cancer.
Collapse
Affiliation(s)
- Ma-Sha Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Fu-Qiang Yuan
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Yang Gao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Jun-Yan Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Yi-Xin Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Chen-Jing Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Bai-Mei He
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Hong-Hao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China.,Xiangya Hospital, Central South University, Changsha, P. R. China
| | - Zhao-Qian Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China.,Xiangya Hospital, Central South University, Changsha, P. R. China
| |
Collapse
|
6
|
Yu G, Liao J, Wu J, Ding J, Zhang L. The proliferation of colorectal cancer cells is suppressed by silencing of EIF3H. Biosci Biotechnol Biochem 2018; 82:1694-1701. [PMID: 30022709 DOI: 10.1080/09168451.2018.1484271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
ABSTRACT
Colorectal cancer is one of the most common causes of cancer-related deaths worldwide. Eukaryotic translation initiation factor 3, subunit H (EIF3H) is a subunit of EIF3, which is involved in mRNA recruitment and ribosomal complex disassembly and is known to be a driver of cell proliferation and survival in cancer. To investigate its function in colorectal cancer, the Oncomine database was used to evaluate the expression of EIF3H in human colorectal cancer and normal tissues. Then, we constructed a Lentivirus shorthair EIF3H vector (Lv-shEIF3H) to silence EIF3H expression in the colorectal cancer cell lines HCT116 and SW1116. We observed impaired cell growth and colony formation in these silenced cell lines. In addition, we showed that EIF3H knock-down led to cell apoptosis. In conclusion, EIF3H plays key roles in the apoptosis in colorectal cancer cells, which suggests EIF3H as a potential diagnostic biomarker in colorectal cancer.
Collapse
Affiliation(s)
- Genhua Yu
- Department of Radiotherapy, Huzhou Central Hospital, Zhejiang, China
| | - Jiaqun Liao
- Department of Oncology, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Junlan Wu
- Department of Oncology, Shanghai Armed Police Corps Hospital, Shanghai, China
| | - Jun Ding
- Department of colorectal surgery, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lin Zhang
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
7
|
Yin JY, Zhang JT, Zhang W, Zhou HH, Liu ZQ. eIF3a: A new anticancer drug target in the eIF family. Cancer Lett 2017; 412:81-87. [PMID: 29031564 DOI: 10.1016/j.canlet.2017.09.055] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 09/12/2017] [Accepted: 09/25/2017] [Indexed: 02/04/2023]
Abstract
eIF3a is the largest subunit of eIF3, which is a key player in all steps of translation initiation. During the past years, eIF3a is recognized as a proto-oncogene, which is an important discovery in this field. It is widely reported to be correlated with cancer occurrence, metastasis, prognosis, and therapeutic response. Recently, the mechanisms of eIF3a action in the carcinogenesis are unveiled gradually. A number of cellular, physiological, and pathological processes involving eIF3a are identified. Most importantly, it is emerging as a new potential drug target in the eIF family, and some small molecule inhibitors are being developed. Thus, we perform a critical review of recent advances in understanding eIF3a physiological and pathological functions, with specific focus on its role in cancer and anticancer drug targets.
Collapse
Affiliation(s)
- Ji-Ye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, PR China.
| | - Jian-Ting Zhang
- Department of Pharmacology & Toxicology and IU Cancer Center, Indiana University School of Medicine, Indianapolis IN 46202, USA
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, PR China
| | - Hong-Hao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, PR China
| | - Zhao-Qian Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, PR China.
| |
Collapse
|
8
|
Bondy-Chorney E, Baldwin RM, Didillon A, Chabot B, Jasmin BJ, Côté J. RNA binding protein RALY promotes Protein Arginine Methyltransferase 1 alternatively spliced isoform v2 relative expression and metastatic potential in breast cancer cells. Int J Biochem Cell Biol 2017; 91:124-135. [PMID: 28733251 DOI: 10.1016/j.biocel.2017.07.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 07/09/2017] [Accepted: 07/15/2017] [Indexed: 01/24/2023]
Abstract
Aberrant expression of Protein Arginine Methyltransferases (PRMTs) has been observed in several cancer types, including breast cancer. We previously reported that the PRMT1v2 isoform, which is generated through inclusion of alternative exon 2, is overexpressed in breast cancer cells and promotes their invasiveness. However, the precise mechanism by which expression of this isoform is controlled and how it is dysregulated in breast cancer remains unknown. Using a custom RNA interference-based screen, we identified several RNA binding proteins (RBP) which, when knocked down, altered the relative abundance of the alternatively spliced PRMT1v2 isoform. Amongst the top hits were SNW Domain containing 1 (SNW1) and RBP-associated with lethal yellow mutation (RALY), which both associated with the PRMT1 pre-mRNA and upon depletion caused an increase or decrease in the relative abundance of PRMT1v2 isoform mRNA and protein. Most importantly, a significant decrease in invasion was observed upon RALY knockdown in aggressive breast cancer cells, consistent with targeting PRMT1v2 directly, and this effect was rescued by the exogenous re-expression of PRMT1v2. We show that SNW1 expression is decreased, while RALY expression is increased in breast cancer cells and tumours, which correlates with decreased patient survival. This work revealed crucial insight into the mechanisms regulating the expression of the PRMT1 alternatively spliced isoform v2 and its dysregulation in breast cancer. It also provides proof-of-concept support for the development of therapeutic strategies where regulators of PRMT1 exon 2 alternative splicing are targeted as an approach to selectively reduce PRMT1v2 levels and metastasis in breast cancer.
Collapse
Affiliation(s)
- Emma Bondy-Chorney
- Department of Cellular and Molecular Medicine, University of Ottawa, Centre for Neuromuscular Disease, Ottawa, Ontario, K1H 8L1, Canada
| | - R Mitchell Baldwin
- Department of Cellular and Molecular Medicine, University of Ottawa, Centre for Neuromuscular Disease, Ottawa, Ontario, K1H 8L1, Canada
| | - Andréanne Didillon
- Department of Cellular and Molecular Medicine, University of Ottawa, Centre for Neuromuscular Disease, Ottawa, Ontario, K1H 8L1, Canada
| | - Benoît Chabot
- Département de microbiologie et d'infectiologie, Faculté de Médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1 K 2R1, Canada
| | - Bernard J Jasmin
- Department of Cellular and Molecular Medicine, University of Ottawa, Centre for Neuromuscular Disease, Ottawa, Ontario, K1H 8L1, Canada
| | - Jocelyn Côté
- Department of Cellular and Molecular Medicine, University of Ottawa, Centre for Neuromuscular Disease, Ottawa, Ontario, K1H 8L1, Canada.
| |
Collapse
|
9
|
Xu JZ, Wen F, Wang XR. The eIF3a Arg803Lys genetic polymorphism is associated with susceptibility to and chemoradiotherapy efficacy in cervical carcinoma. Kaohsiung J Med Sci 2017; 33:187-194. [DOI: 10.1016/j.kjms.2017.01.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/20/2016] [Accepted: 12/26/2016] [Indexed: 10/20/2022] Open
|
10
|
Wang SQ, Liu Y, Yao MY, Jin J. Eukaryotic Translation Initiation Factor 3a (eIF3a) Promotes Cell Proliferation and Motility in Pancreatic Cancer. J Korean Med Sci 2016; 31:1586-94. [PMID: 27550487 PMCID: PMC4999401 DOI: 10.3346/jkms.2016.31.10.1586] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 06/27/2016] [Indexed: 12/13/2022] Open
Abstract
Identifying a target molecule that is crucially involved in pancreatic tumor growth and metastasis is necessary in developing an effective treatment. The study aimed to investigate the role of the eukaryotic translation initiation factor 3a (eIF3a) in the cell proliferation and motility in pancreatic cancer. Our data showed that the expression of eIF3a was upregulated in pancreatic ductal adenocarcinoma as compared with its expression in normal pancreatic tissues. Knockdown of eIF3a by a specific shRNA caused significant decreases in cell proliferation and clonogenic abilities in pancreatic cancer SW1990 and Capan-1 cells. Consistently, the pancreatic cancer cell growth rates were also impaired in xenotransplanted mice. Moreover, wound-healing assay showed that depletion of eIF3a significantly slowed down the wound recovery processes in SW1990 and Capan-1 cells. Transwell migration and invasion assays further showed that cell migration and invasion abilities were significantly inhibited by knockdown of eIF3a in SW1990 and Capan-1 cells. Statistical analysis of eIF3a expression in 140 cases of pancreatic ductal adenocarcinoma samples revealed that eIF3a expression was significantly associated with tumor metastasis and TNM staging. These analyses suggest that eIF3a contributes to cell proliferation and motility in pancreatic ductal adenocarcinoma.
Collapse
Affiliation(s)
- Shu Qian Wang
- General Surgery Department, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yu Liu
- General Surgery Department, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Min Ya Yao
- General Surgery Department, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jing Jin
- Department of Neurosurgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
| |
Collapse
|
11
|
Abstract
The eukaryotic translation initiation factor 3a (eIF3a) is one of the core subunits of the translation initiation complex eIF3, responsible for ribosomal subunit joining and mRNA recruitment to the ribosome. Our previous study identified that it was correlated with platinum response in lung cancer. The current study aims to test the hypothesis that eIF3a may affect the drug response and prognosis of ovarian cancer patients receiving platinum-based chemotherapy by regulating xeroderma pigmentosum complementation group C (XPC) and p27Kip1. Immunohistochemistry and western blot was used to determine the expression of eIF3a in 126 human ovarian cancer tissues followed by association analysis of eIF3a expression with patient's response and survival. Ectopic over-expression and RNA interference knockdown of eIF3a were carried out in A2780/cisplatin (DDP) and its parental A2780 cells, respectively, to determine the effect of altered eIF3a expression on cellular response to cisplatin by employing MTT assay. Western Blot analyses were also carried out to determine the regulation of eIF3a on XPC and p27Kip1. eIF3a expression was associated with response of ovarian cancer patients to DDP-based chemotherapy and their survival. Overexpression and knockdown of eIF3a increased and decreased the cellular response to cisplatin in A2780/DDP and A2780 cells, respectively. In addition, XPC and p27Kip1 were down regulated by eIF3a. eIF3a improves ovarian cancer patients' response to DDP-based chemotherapy via down regulating XPC and p27Kip1.
Collapse
|
12
|
Liu K, Lei Z, Yao H, Lei S, Zhao H. Impact of a Eukaryotic Translation Initiation Factor 3a Polymorphism on Susceptibility to Gastric Cancer. Med Princ Pract 2016; 25:461-5. [PMID: 27333287 PMCID: PMC5588499 DOI: 10.1159/000447741] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 06/21/2016] [Indexed: 01/17/2023] Open
Abstract
OBJECTIVE To investigate single nucleotide polymorphisms in the eukaryotic translation initiation factor 3a (eIF3a) gene and the risk for gastric cancer within the Chinese population. SUBJECTS AND METHODS A total of 322 patients with gastric cancer were selected as the patient group and 340 non-gastric cancer patients were selected as the control group using the case-control method. Polymerase chain reaction-sequence-specific primer technology was leveraged to genotype the rs77382849 single nucleotide polymorphism in the eIF3a gene. The demographic characteristics of the study population and other exposures to risk factors were collected. Unconditional logistic regression analysis was performed to determine the association between the risk factors and gastric cancer. RESULTS A higher frequency of the eIF3a rs77382849 GG homozygote genotype was observed in the gastric cancer patients compared with the controls (63.98 vs. 54.41%, p < 0.05). After adjustment of exposure risks, such as age, gender, smoking, and drinking, the rs77382849 single nucleotide polymorphism was still associated with susceptibility to gastric cancer. When the eIF3a rs77382849 GG homozygote genotype was used as the reference group, the GA genotype (GA vs. GG: OR = 0.545, 95% CI: 0.386-0.769, p = 0.001) and AA genotype (AA vs. GG: OR = 0.245, 95% CI: 0.072-0.836, p = 0.025) were both correlated with a significantly decreased risk for gastric cancer development. CONCLUSION An association between eIF3a rs77382849 polymorphism and susceptibility to gastric cancer was observed in these Chinese patients.
Collapse
Affiliation(s)
| | | | | | | | - Hua Zhao
- *Dr. Hua Zhao, Department of General Surgery, The Second Xiangya Hospital, Central South University, 139, Middle Renmin road, Changsha, Hunan 410000 (PR China), E-Mail
| |
Collapse
|
13
|
Yin JY, Meng XG, Qian CY, Li XP, Chen J, Zheng Y, Liu R, Zhou HH, Liu ZQ. Association of positively selected eIF3a polymorphisms with toxicity of platinum-based chemotherapy in NSCLC patients. Acta Pharmacol Sin 2015; 36:375-84. [PMID: 25732572 DOI: 10.1038/aps.2014.160] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 11/13/2014] [Indexed: 01/06/2023] Open
Abstract
AIM Eukaryotic translation initiation factor 3 subunit A (eIF3a) plays critical roles in regulating the initiation of protein translation, and eIF3a is highly expressed in lung cancer. In this study, we investigated the association of the positively selected SNPs of eIF3a with the response to and toxicity of platinum-based chemotherapy in Chinese patients with non-small cell lung cancer (NSCLC). METHODS SNP data for eIF3a locus were downloaded from HapMap database. For each SNP, haplotype, LD profile and population differentiation were analyzed. The long-range haplotype (LRH) test was employed to identify positively selected SNPs of eIF3a. A total of 325 NSCLC patients were enrolled and genotyped for these SNPs. RESULTS Five positively selected (rs1409314, rs4752219, rs4752220, rs7091672 and rs10510050) and 5 non-positively selected SNPs (rs10886342, rs11198804, rs2275112, rs10787899 and rs4752269) were identified in the LRH test. However, none of them was correlated with the platinum-based chemotherapy response. In contrast, 4 of the positively selected SNPs (rs1409314, rs4752219, rs4752220 and rs7091672) were significantly correlated with the toxicities tested (neutropenia, anemia, thrombocytopenia, emesis and hepatotoxicity). In addition, rs10510050 was significantly correlated with thrombocytopenia, emesis and hepatotoxicity. None of the 5 non-positively selected SNPs was correlated with the 5 toxicities. CONCLUSION The positively selected SNPs of eIF3a are significantly correlated with platinum-based chemotherapy toxicities in Chinese NSCLC patients.
Collapse
|
14
|
Purrington KS, Slettedahl S, Bolla MK, Michailidou K, Czene K, Nevanlinna H, Bojesen SE, Andrulis IL, Cox A, Hall P, Carpenter J, Yannoukakos D, Haiman CA, Fasching PA, Mannermaa A, Winqvist R, Brenner H, Lindblom A, Chenevix-Trench G, Benitez J, Swerdlow A, Kristensen V, Guénel P, Meindl A, Darabi H, Eriksson M, Fagerholm R, Aittomäki K, Blomqvist C, Nordestgaard BG, Nielsen SF, Flyger H, Wang X, Olswold C, Olson JE, Mulligan AM, Knight JA, Tchatchou S, Reed MWR, Cross SS, Liu J, Li J, Humphreys K, Clarke C, Scott R, Fostira F, Fountzilas G, Konstantopoulou I, Henderson BE, Schumacher F, Le Marchand L, Ekici AB, Hartmann A, Beckmann MW, Hartikainen JM, Kosma VM, Kataja V, Jukkola-Vuorinen A, Pylkäs K, Kauppila S, Dieffenbach AK, Stegmaier C, Arndt V, Margolin S, Balleine R, Arias Perez JI, Pilar Zamora M, Menéndez P, Ashworth A, Jones M, Orr N, Arveux P, Kerbrat P, Truong T, Bugert P, Toland AE, Ambrosone CB, Labrèche F, Goldberg MS, Dumont M, Ziogas A, Lee E, Dite GS, Apicella C, Southey MC, Long J, Shrubsole M, Deming-Halverson S, Ficarazzi F, Barile M, Peterlongo P, Durda K, Jaworska-Bieniek K, Tollenaar RAEM, Seynaeve C, Brüning T, Ko YD, Van Deurzen CHM, Martens JWM, Kriege M, Figueroa JD, Chanock SJ, Lissowska J, Tomlinson I, Kerin MJ, Miller N, Schneeweiss A, Tapper WJ, Gerty SM, Durcan L, Mclean C, Milne RL, Baglietto L, dos Santos Silva I, Fletcher O, Johnson N, Van'T Veer LJ, Cornelissen S, Försti A, Torres D, Rüdiger T, Rudolph A, Flesch-Janys D, Nickels S, Weltens C, Floris G, Moisse M, Dennis J, Wang Q, Dunning AM, Shah M, Brown J, Simard J, Anton-Culver H, Neuhausen SL, Hopper JL, Bogdanova N, Dörk T, Zheng W, Radice P, Jakubowska A, Lubinski J, Devillee P, Brauch H, Hooning M, García-Closas M, Sawyer E, Burwinkel B, Marmee F, Eccles DM, Giles GG, Peto J, Schmidt M, Broeks A, Hamann U, Chang-Claude J, Lambrechts D, Pharoah PDP, Easton D, Pankratz VS, Slager S, Vachon CM, Couch FJ. Genetic variation in mitotic regulatory pathway genes is associated with breast tumor grade. Hum Mol Genet 2014; 23:6034-46. [PMID: 24927736 PMCID: PMC4204763 DOI: 10.1093/hmg/ddu300] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 05/20/2014] [Accepted: 06/10/2014] [Indexed: 01/01/2023] Open
Abstract
Mitotic index is an important component of histologic grade and has an etiologic role in breast tumorigenesis. Several small candidate gene studies have reported associations between variation in mitotic genes and breast cancer risk. We measured associations between 2156 single nucleotide polymorphisms (SNPs) from 194 mitotic genes and breast cancer risk, overall and by histologic grade, in the Breast Cancer Association Consortium (BCAC) iCOGS study (n = 39 067 cases; n = 42 106 controls). SNPs in TACC2 [rs17550038: odds ratio (OR) = 1.24, 95% confidence interval (CI) 1.16-1.33, P = 4.2 × 10(-10)) and EIF3H (rs799890: OR = 1.07, 95% CI 1.04-1.11, P = 8.7 × 10(-6)) were significantly associated with risk of low-grade breast cancer. The TACC2 signal was retained (rs17550038: OR = 1.15, 95% CI 1.07-1.23, P = 7.9 × 10(-5)) after adjustment for breast cancer risk SNPs in the nearby FGFR2 gene, suggesting that TACC2 is a novel, independent genome-wide significant genetic risk locus for low-grade breast cancer. While no SNPs were individually associated with high-grade disease, a pathway-level gene set analysis showed that variation across the 194 mitotic genes was associated with high-grade breast cancer risk (P = 2.1 × 10(-3)). These observations will provide insight into the contribution of mitotic defects to histological grade and the etiology of breast cancer.
Collapse
Affiliation(s)
- Kristen S Purrington
- Department of Health Sciences Research, Department of Oncology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, USA
| | | | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics
| | | | - Stig E Bojesen
- Copenhagen General Population Study, Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Irene L Andrulis
- Ontario Cancer Genetics Network, Department of Molecular Genetics
| | - Angela Cox
- CRUK/YCR Sheffield Cancer Research Centre, Department of Oncology
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics
| | | | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory INRASTES, National Centre for Scientific Research 'Demokritos', Athens, Greece
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Peter A Fasching
- University Breast Center Franconia, Department of Gynecology and Obstetrics, David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, USA
| | - Arto Mannermaa
- School of Medicine, Institute of Clinical Medicine, Oncology, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland, Imaging Center, Department of Clinical Pathology
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Chemistry and Biocenter Oulu, University of Oulu, Oulu University Hospital/NordLab Oulu, Oulu, Finland
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Consortium (DKTK), Heidelberg, Germany
| | | | | | - Javier Benitez
- Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain, Centro de Investigación en Red de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, Division of Breast Cancer Research, Institute of Cancer Research, Sutton, UK
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway, Faculty of Medicine (Faculty Division Ahus), University of Oslo (UiO), Oslo, Norway
| | - Pascal Guénel
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, Villejuif, France, University Paris-Sud, UMRS 1018, Villejuif, France
| | - Alfons Meindl
- Division of Gynaecology and Obstetrics, Technische Universität München, Munich, Germany
| | - Hatef Darabi
- Department of Medical Epidemiology and Biostatistics
| | | | - Rainer Fagerholm
- Department of Obstetrics and Gynecology, Oncology and Clinical Genetics
| | | | - Carl Blomqvist
- Department of Oncology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Børge G Nordestgaard
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | | | - Henrik Flyger
- Department of Breast Surgery, Herlev Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Xianshu Wang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, USA
| | | | | | - Anna Marie Mulligan
- Department of Laboratory Medicine and Pathobiology, Laboratory Medicine Program, University Health Network, Toronto, Canada
| | - Julia A Knight
- Prosserman Centre for Health Research, Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Sandrine Tchatchou
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Canada
| | - Malcolm W R Reed
- CRUK/YCR Sheffield Cancer Research Centre, Department of Oncology
| | - Simon S Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Jianjun Liu
- Human Genetics Division, Genome Institute of Singapore, Singapore, Singapore
| | - Jingmei Li
- Human Genetics Division, Genome Institute of Singapore, Singapore, Singapore
| | | | - Christine Clarke
- Westmead Institute for Cancer Research, Sydney Medical School Westmead, University of Sydney at the Westmead Millennium Institute, Westmead, Australia
| | - Rodney Scott
- Division of Genetics, Hunter Area Pathology Service and University of Newcastle, Newcastle, Australia
| | - Florentia Fostira
- Molecular Diagnostics Laboratory INRASTES, National Centre for Scientific Research 'Demokritos', Athens, Greece
| | - George Fountzilas
- Department of Medical Oncology, "Papageorgiou" Hospital, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory INRASTES, National Centre for Scientific Research 'Demokritos', Athens, Greece
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Fredrick Schumacher
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Loic Le Marchand
- Epidemiology Program, Cancer Research Center, University of Hawaii, Honolulu, USA
| | | | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | | | - Jaana M Hartikainen
- School of Medicine, Institute of Clinical Medicine, Oncology, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland, Imaging Center, Department of Clinical Pathology
| | - Veli-Matti Kosma
- School of Medicine, Institute of Clinical Medicine, Oncology, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland, Imaging Center, Department of Clinical Pathology
| | - Vesa Kataja
- School of Medicine, Institute of Clinical Medicine, Oncology, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland, Cancer Center, Kuopio University Hospital, Kuopio, Finland
| | | | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Chemistry and Biocenter Oulu, University of Oulu, Oulu University Hospital/NordLab Oulu, Oulu, Finland
| | - Saila Kauppila
- Department of Pathology, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Aida Karina Dieffenbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Consortium (DKTK), Heidelberg, Germany
| | | | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research
| | - Sara Margolin
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Rosemary Balleine
- Westmead Millenium Institute for Medical Research, Sydney, Australia
| | | | - M Pilar Zamora
- Servicio de Oncología Médica, Hospital Universitario La Paz, Madrid, Spain
| | | | - Alan Ashworth
- Breakthrough Breast Cancer Research Centre and Division of Breast Cancer Research
| | | | - Nick Orr
- Breakthrough Breast Cancer Research Centre and Division of Breast Cancer Research
| | - Patrick Arveux
- Center Georges-Francois Leclerc, Registry of Gynecologic Tumors, Dijon, France
| | - Pierre Kerbrat
- Centre Eugène Marquis, Department of Medical Oncology, Rennes, France
| | - Thérèse Truong
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, Villejuif, France, University Paris-Sud, UMRS 1018, Villejuif, France
| | - Peter Bugert
- German Red Cross Blood Service of Baden-Württemberg-Hessen, Mannheim, Germany, Medical Faculty Mannheim, Institute of Transfusion Medicine and Immunology, Heidelberg University, Heidelberg, Germany
| | - Amanda E Toland
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, USA
| | | | - France Labrèche
- Department of Environmental & Occupational Health and of Social & Preventive Medicine, School of Public Health, Université de Montréal, Montreal, Canada
| | - Mark S Goldberg
- Department of Medicine, McGill University, Montreal, Canada, Division of Clinical Epidemiology, McGill University Health Centre, Royal Victoria Hospital, Montreal, Canada
| | - Martine Dumont
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec Research Center and Laval University, Quebec City, Canada
| | - Argyrios Ziogas
- Department of Epidemiology, University of California Irvine, Irvine, USA
| | - Eunjung Lee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Gillian S Dite
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, Melbourne School of Population Health
| | - Carmel Apicella
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, Melbourne School of Population Health
| | | | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, USA
| | - Martha Shrubsole
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, USA
| | - Sandra Deming-Halverson
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, USA
| | - Filomena Ficarazzi
- Cogentech Cancer Genetic Test Laboratory, Milan, Italy, IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Monica Barile
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia (IEO), Milan, Italy
| | - Paolo Peterlongo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Katarzyna Durda
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | | | | | - Caroline Seynaeve
- Family Cancer Clinic, Department of Medical Oncology, Erasmus MC-Daniel den Hoed Cancer Centrer, Rotterdam, The Netherlands
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance (IPA), Bochum, Germany
| | - Yon-Dschun Ko
- Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, Germany
| | | | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Mieke Kriege
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Jonine D Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, USA
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Memorial Cancer Center & Institute of Oncology, Warsaw, Poland
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics and Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Michael J Kerin
- Clinical Science Institute, University Hospital Galway, Galway, Ireland
| | - Nicola Miller
- Clinical Science Institute, University Hospital Galway, Galway, Ireland
| | - Andreas Schneeweiss
- Department of Obstetrics and Gynecology, National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | | | - Susan M Gerty
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Lorraine Durcan
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Catriona Mclean
- Anatomical Pathology, The Alfred Hospital, Melbourne, Australia
| | - Roger L Milne
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, The University of Melbourne, Melbourne, Australia, Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Australia
| | - Laura Baglietto
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, The University of Melbourne, Melbourne, Australia, Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Australia
| | - Isabel dos Santos Silva
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Olivia Fletcher
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Nichola Johnson
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Laura J Van'T Veer
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Sten Cornelissen
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, Center for Primary Health Care Research, University of Lund, Malmö, Sweden
| | - Diana Torres
- Molecular Genetics of Breast Cancer, Institute of Human Genetics, Pontificia University Javeriana, Bogota, Colombia
| | - Thomas Rüdiger
- Institute of Pathology, Städtisches Klinikum Karlsruhe, Karlsruhe, Germany
| | | | - Dieter Flesch-Janys
- Department of Cancer Epidemiology/Clinical Cancer Registry and Institute for Medical Biometrics and Epidemiology, University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | | | | | | | - Matthieu Moisse
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium, Vesalius Research Center (VRC), VIB, Leuven, Belgium
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Judith Brown
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care
| | - Jacques Simard
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec Research Center and Laval University, Quebec City, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California Irvine, Irvine, USA
| | | | - John L Hopper
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, Melbourne School of Population Health
| | | | - Thilo Dörk
- Department of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, USA
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy and
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Peter Devillee
- Department of Human Genetics & Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany, University of Tübingen, Tübingen, Germany
| | - Maartje Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | | | - Elinor Sawyer
- Division of Cancer Studies, Kings College London, Guy's Hospital, London, UK
| | - Barbara Burwinkel
- Department of Obstetrics and Gynecology, Molecular Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frederick Marmee
- Department of Obstetrics and Gynecology, National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | - Diana M Eccles
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Graham G Giles
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, The University of Melbourne, Melbourne, Australia, Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Australia
| | - Julian Peto
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Marjanka Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Annegien Broeks
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | | | | | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium, Vesalius Research Center (VRC), VIB, Leuven, Belgium
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | | | | | | | - Fergus J Couch
- Department of Health Sciences Research, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, USA,
| |
Collapse
|
15
|
Lin VCH, Kuo PT, Lin YC, Chen Y, Hseu YC, Yang HL, Kao JY, Ho CT, Way TD. Penta-O-galloyl-β-D-glucose suppresses EGF-induced eIF3i expression through inhibition of the PI3K/AKT/mTOR pathway in prostate cancer cells. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:8990-8996. [PMID: 25123845 DOI: 10.1021/jf502447e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Approximately 70% of prostate cancer patients will develop bone metastasis in axial and other regions of the skeleton. Epidermal growth factor (EGF) generated from bone tissue contributes to prostate cancer metastasis. In a previous study, penta-O-galloyl-β-D-glucose (PGG) suppressed androgen-independent prostate cancer bone metastasis by transcriptionally repressing EGF-induced MMP-9 expression. This study utilized proteomics to analyze the effects of PGG in EGF-induced prostate cancer bone metastasis. This study showed that PGG suppressed EGF-induced eIF3i expression in PC-3 cells. By transfection of eIF3i shRNA, it was observed that reduced eIF3i expression suppressed the invasion of PC-3 cells in vitro. PGG reduced EGF-induced eIF3i expression through inhibition of the PI3K/AKT/mTOR pathway. Therefore, PGG may be able to be used as a potential new therapeutic drug for prostate cancer bone metastasis.
Collapse
|
16
|
Rawlings-Goss RA, Campbell MC, Tishkoff SA. Global population-specific variation in miRNA associated with cancer risk and clinical biomarkers. BMC Med Genomics 2014; 7:53. [PMID: 25169894 PMCID: PMC4159108 DOI: 10.1186/1755-8794-7-53] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 08/12/2014] [Indexed: 12/30/2022] Open
Abstract
Background MiRNA expression profiling is being actively investigated as a clinical biomarker and diagnostic tool to detect multiple cancer types and stages as well as other complex diseases. Initial investigations, however, have not comprehensively taken into account genetic variability affecting miRNA expression and/or function in populations of different ethnic backgrounds. Therefore, more complete surveys of miRNA genetic variability are needed to assess global patterns of miRNA variation within and between diverse human populations and their effect on clinically relevant miRNA genes. Methods Genetic variation in 1524 miRNA genes was examined using whole genome sequencing (60x coverage) in a panel of 69 unrelated individuals from 14 global populations, including European, Asian and African populations. Results We identified 33 previously undescribed miRNA variants, and 31 miRNA containing variants that are globally population-differentiated in frequency between African and non-African populations (PD-miRNA). The top 1% of PD-miRNA were significantly enriched for regulation of genes involved in glucose/insulin metabolism and cell division (p < 10−7), most significantly the mitosis pathway, which is strongly linked to cancer onset. Overall, we identify 7 PD-miRNAs that are currently implicated as cancer biomarkers or diagnostics: hsa-mir-202, hsa-mir-423, hsa-mir-196a-2, hsa-mir-520h, hsa-mir-647, hsa-mir-943, and hsa-mir-1908. Notably, hsa-mir-202, a potential breast cancer biomarker, was found to show significantly high allele frequency differentiation at SNP rs12355840, which is known to affect miRNA expression levels in vivo and subsequently breast cancer mortality. Conclusion MiRNA expression profiles represent a promising new category of disease biomarkers. However, population specific genetic variation can affect the prevalence and baseline expression of these miRNAs in diverse populations. Consequently, miRNA genetic and expression level variation among ethnic groups may be contributing in part to health disparities observed in multiple forms of cancer, specifically breast cancer, and will be an essential consideration when assessing the utility of miRNA biomarkers for the clinic.
Collapse
|
17
|
Newton R, Wernisch L. A meta-analysis of multiple matched copy number and transcriptomics data sets for inferring gene regulatory relationships. PLoS One 2014; 9:e105522. [PMID: 25148247 PMCID: PMC4141782 DOI: 10.1371/journal.pone.0105522] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/21/2014] [Indexed: 12/25/2022] Open
Abstract
Inferring gene regulatory relationships from observational data is challenging. Manipulation and intervention is often required to unravel causal relationships unambiguously. However, gene copy number changes, as they frequently occur in cancer cells, might be considered natural manipulation experiments on gene expression. An increasing number of data sets on matched array comparative genomic hybridisation and transcriptomics experiments from a variety of cancer pathologies are becoming publicly available. Here we explore the potential of a meta-analysis of thirty such data sets. The aim of our analysis was to assess the potential of in silico inference of trans-acting gene regulatory relationships from this type of data. We found sufficient correlation signal in the data to infer gene regulatory relationships, with interesting similarities between data sets. A number of genes had highly correlated copy number and expression changes in many of the data sets and we present predicted potential trans-acted regulatory relationships for each of these genes. The study also investigates to what extent heterogeneity between cell types and between pathologies determines the number of statistically significant predictions available from a meta-analysis of experiments.
Collapse
Affiliation(s)
- Richard Newton
- Biostatistics Unit, Medical Research Council, Cambridge, United Kingdom
- * E-mail:
| | - Lorenz Wernisch
- Biostatistics Unit, Medical Research Council, Cambridge, United Kingdom
| |
Collapse
|
18
|
Xu X, Han L, Duan L, Zhao Y, Yang H, Zhou B, Ma R, Yuan R, Zhou H, Liu Z. Association between eIF3α polymorphism and severe toxicity caused by platinum-based chemotherapy in non-small cell lung cancer patients. Br J Clin Pharmacol 2013; 75:516-23. [PMID: 22804784 DOI: 10.1111/j.1365-2125.2012.04379.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 07/03/2012] [Indexed: 01/05/2023] Open
Abstract
AIM Platinum-induced toxicity severely impedes successful chemotherapy in lung cancer patients. The nucleotide excision repair (NER) pathway is considered as one of the major factors contributing to platinum effects. Furthermore, genetic variances of the NER pathway influence platinum toxicity. eIF3α, over expressed in many malignancies, is an up-stream gene of NER and could regulate its activity. The purpose of this study was to investigate whether eIF3α polymorphism is associated with severe platinum toxicity in patients with non-small cell lung cancer (NSCLC). METHODS Two hundred and eighty-two incident NSCLC patients, from three different institutions, were enrolled and followed up. These patients were diagnosed and histologically confirmed with non-small cell lung cancer. All patients accepted platinum based chemotherapy for at least two cycles. Twenty-two SNPs of eIF3α were detected in these patients. RESULTS eIF3α Arg803Lys C > T polymorphism was associated with cisplatin-induced toxicity in NSCLC patients (P = 0.02, OR = 0.54, 95% CI 0.32, 93). T-carrier subjects presented better tolerance to platinum nephrotoxicity, but poorer tolerance to ototoxicity. CONCLUSION eIF3α Arg803Lys was associated with platinum toxicity in NSCLC patients and could be considered as a predictor for pretreatment evaluation in lung cancer patients.
Collapse
Affiliation(s)
- Xiaojing Xu
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Age-specific gene expression signatures for breast tumors and cross-species conserved potential cancer progression markers in young women. PLoS One 2013; 8:e63204. [PMID: 23704896 PMCID: PMC3660335 DOI: 10.1371/journal.pone.0063204] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 04/02/2013] [Indexed: 12/21/2022] Open
Abstract
Breast cancer in young women is more aggressive with a poorer prognosis and overall survival compared to older women diagnosed with the disease. Despite recent research, the underlying biology and molecular alterations that drive the aggressive nature of breast tumors associated with breast cancer in young women have yet to be elucidated. In this study, we performed transcriptomic profile and network analyses of breast tumors arising in Middle Eastern women to identify age-specific gene signatures. Moreover, we studied molecular alterations associated with cancer progression in young women using cross-species comparative genomics approach coupled with copy number alterations (CNA) associated with breast cancers from independent studies. We identified 63 genes specific to tumors in young women that showed alterations distinct from two age cohorts of older women. The network analyses revealed potential critical regulatory roles for Myc, PI3K/Akt, NF-κB, and IL-1 in disease characteristics of breast tumors arising in young women. Cross-species comparative genomics analysis of progression from pre-invasive ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC) revealed 16 genes with concomitant genomic alterations, CCNB2, UBE2C, TOP2A, CEP55, TPX2, BIRC5, KIAA0101, SHCBP1, UBE2T, PTTG1, NUSAP1, DEPDC1, HELLS, CCNB1, KIF4A, and RRM2, that may be involved in tumorigenesis and in the processes of invasion and progression of disease. Array findings were validated using qRT-PCR, immunohistochemistry, and extensive in silico analyses of independently performed microarray datasets. To our knowledge, this study provides the first comprehensive genomic analysis of breast cancer in Middle Eastern women in age-specific cohorts and potential markers for cancer progression in young women. Our data demonstrate that cancer appearing in young women contain distinct biological characteristics and deregulated signaling pathways. Moreover, our integrative genomic and cross-species analysis may provide robust biomarkers for the detection of disease progression in young women, and lead to more effective treatment strategies.
Collapse
|
20
|
Yamaga R, Ikeda K, Horie-Inoue K, Ouchi Y, Suzuki Y, Inoue S. RNA sequencing of MCF-7 breast cancer cells identifies novel estrogen-responsive genes with functional estrogen receptor-binding sites in the vicinity of their transcription start sites. Discov Oncol 2013; 4:222-32. [PMID: 23526455 DOI: 10.1007/s12672-013-0140-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 03/09/2013] [Indexed: 12/25/2022] Open
Abstract
Estrogen receptor α (ERα) is a key transcription factor in breast cancer, which plays an essential role in the pathophysiology of the disease by regulating the expression of various target genes. In the present study, we performed deep RNA sequencing (RNA-seq) as an unbiased high-throughput technique for comprehensive transcriptome analysis in ERα-positive human breast cancer MCF-7 cells, to facilitate the elucidation of ERα regulatory gene networks. From the 17,336 mapped RefSeq genes from the sequenced fragments of the cell samples treated with estrogen time dependently, substantial numbers of sequence reads were observed in 3,386 genes (>100 tags per million reads per sample at any of the six time points studied). ERα occupancy within and in the proximal regions of the genes (<10-kb upstream and downstream regions) was significantly enriched in the subgroup of the 3,386 genes compared to the whole 17,336 RefSeq genes. Of the 3,386 genes, we focused on 29 genes, which included ERα occupancy adjacent to their transcription start sites and whose expression was estrogen dependently altered by >3-fold. Knockdown studies using siRNAs specific to the 29 genes validated that prototypic ERα targets V-myc myelocytomatosis viral oncogene homolog and cyclin D1 promote both proliferation and migration of MCF-7 cells and further identified novel candidate ERα targets EIF3A and tumor protein D52-like 1, which will also facilitate the proliferation or migration of MCF-7 cells. Taken together, the present findings provide a valuable dataset that will elucidate ERα regulatory mechanisms in breast cancer biology, based on the integrative analysis of RNA-seq combined with the genome-wide information for ERα occupancy.
Collapse
Affiliation(s)
- Ryonosuke Yamaga
- Department of Geriatric Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bumkyo-ku, Tokyo, 113-8655, Japan
| | | | | | | | | | | |
Collapse
|
21
|
Allen WL, Stevenson L, Coyle VM, Jithesh PV, Proutski I, Carson G, Gordon MA, Lenz HJD, Van Schaeybroeck S, Longley DB, Johnston PG. A systems biology approach identifies SART1 as a novel determinant of both 5-fluorouracil and SN38 drug resistance in colorectal cancer. Mol Cancer Ther 2012; 11:119-31. [PMID: 22027693 PMCID: PMC3272421 DOI: 10.1158/1535-7163.mct-11-0510] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Chemotherapy response rates for advanced colorectal cancer remain disappointingly low, primarily because of drug resistance, so there is an urgent need to improve current treatment strategies. To identify novel determinants of resistance to the clinically relevant drugs 5-fluorouracil (5-FU) and SN38 (the active metabolite of irinotecan), transcriptional profiling experiments were carried out on pretreatment metastatic colorectal cancer biopsies and HCT116 parental and chemotherapy-resistant cell line models using a disease-specific DNA microarray. To enrich for potential chemoresistance-determining genes, an unsupervised bioinformatics approach was used, and 50 genes were selected and then functionally assessed using custom-designed short interfering RNA (siRNA) screens. In the primary siRNA screen, silencing of 21 genes sensitized HCT116 cells to either 5-FU or SN38 treatment. Three genes (RAPGEF2, PTRF, and SART1) were selected for further analysis in a panel of 5 colorectal cancer cell lines. Silencing SART1 sensitized all 5 cell lines to 5-FU treatment and 4/5 cell lines to SN38 treatment. However, silencing of RAPGEF2 or PTRF had no significant effect on 5-FU or SN38 sensitivity in the wider cell line panel. Further functional analysis of SART1 showed that its silencing induced apoptosis that was caspase-8 dependent. Furthermore, silencing of SART1 led to a downregulation of the caspase-8 inhibitor, c-FLIP, which we have previously shown is a key determinant of drug resistance in colorectal cancer. This study shows the power of systems biology approaches for identifying novel genes that regulate drug resistance and identifies SART1 as a previously unidentified regulator of c-FLIP and drug-induced activation of caspase-8.
Collapse
Affiliation(s)
- Wendy L. Allen
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland
| | - Leanne Stevenson
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland
| | - Vicky M. Coyle
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland
| | - Puthen V. Jithesh
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland
| | - Irina Proutski
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland
| | - Gail Carson
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland
| | - Michael A Gordon
- Division of Medical Oncology, University of Southern California/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90033, USA
| | - Heinz-Josef D Lenz
- Division of Medical Oncology, University of Southern California/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90033, USA
| | - Sandra Van Schaeybroeck
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland
| | - Daniel B. Longley
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland
| | - Patrick G. Johnston
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland
| |
Collapse
|
22
|
Translational control gone awry: a new mechanism of tumorigenesis and novel targets of cancer treatments. Biosci Rep 2011; 31:1-15. [PMID: 20964625 DOI: 10.1042/bsr20100077] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Translational control is one of primary regulation mechanisms of gene expression. Eukaryotic translational control mainly occurs at the initiation step, the speed-limiting step, which involves more than ten translation initiation factors [eIFs (eukaryotic initiation factors)]. Changing the level or function of these eIFs results in abnormal translation of specific mRNAs and consequently abnormal growth of cells that leads to human diseases, including cancer. Accumulating evidence from recent studies showed that the expression of many eIFs was associated with malignant transformation, cancer prognosis, as well as gene expression regulation. In the present paper, we perform a critical review of recent advances in understanding the role and mechanism of eIF action in translational control and cancer as well as the possibility of targeting eIFs for therapeutic development.
Collapse
|
23
|
Keller A, Harz C, Matzas M, Meder B, Katus HA, Ludwig N, Fischer U, Meese E. Identification of novel SNPs in glioblastoma using targeted resequencing. PLoS One 2011; 6:e18158. [PMID: 21695249 PMCID: PMC3112142 DOI: 10.1371/journal.pone.0018158] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Accepted: 02/21/2011] [Indexed: 01/06/2023] Open
Abstract
High-throughput sequencing opens avenues to find genetic variations that may be indicative of an increased risk for certain diseases. Linking these genomic data to other “omics” approaches bears the potential to deepen our understanding of pathogenic processes at the molecular level. To detect novel single nucleotide polymorphisms (SNPs) for glioblastoma multiforme (GBM), we used a combination of specific target selection and next generation sequencing (NGS). We generated a microarray covering the exonic regions of 132 GBM associated genes to enrich target sequences in two GBM tissues and corresponding leukocytes of the patients. Enriched target genes were sequenced with Illumina and the resulting reads were mapped to the human genome. With this approach we identified over 6000 SNPs, including over 1300 SNPs located in the targeted genes. Integrating the genome-wide association study (GWAS) catalog and known disease associated SNPs, we found that several of the detected SNPs were previously associated with smoking behavior, body mass index, breast cancer and high-grade glioma. Particularly, the breast cancer associated allele of rs660118 SNP in the gene SART1 showed a near doubled frequency in glioblastoma patients, as verified in an independent control cohort by Sanger sequencing. In addition, we identified SNPs in 20 of 21 GBM associated antigens providing further evidence that genetic variations are significantly associated with the immunogenicity of antigens.
Collapse
Affiliation(s)
- Andreas Keller
- Biomarker Discovery Center Heidelberg, Heidelberg, Germany
| | - Christian Harz
- Department of Human Genetics, Medical School, Saarland University, Homburg, Germany
| | - Mark Matzas
- Biomarker Discovery Center Heidelberg, Heidelberg, Germany
| | - Benjamin Meder
- Department of Internal Medicine, University of Heidelberg, Heidelberg, Germany
| | - Hugo A. Katus
- Department of Internal Medicine, University of Heidelberg, Heidelberg, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Medical School, Saarland University, Homburg, Germany
| | - Ulrike Fischer
- Department of Human Genetics, Medical School, Saarland University, Homburg, Germany
| | - Eckart Meese
- Department of Human Genetics, Medical School, Saarland University, Homburg, Germany
- * E-mail:
| |
Collapse
|
24
|
Evaluation of associations between common variation in mitotic regulatory pathways and risk of overall and high grade breast cancer. Breast Cancer Res Treat 2011; 129:617-22. [PMID: 21607584 DOI: 10.1007/s10549-011-1587-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2011] [Accepted: 05/10/2011] [Indexed: 02/08/2023]
Abstract
Mitotic regulatory pathways insure proper timing of mitotic entry, sister chromatid cohesion and separation, and cytokinesis. Disruption of this process results in inappropriate chromosome segregation and aneuploidy, and appears to contribute to cancer. Specifically, disregulation and somatic mutation of mitotic regulators has been observed in human cancers, and overexpression of mitotic regulators is common in aggressive and late stage tumors. However, the role of germline variation in mitotic pathways and risk of cancer is not well understood. We tested 1,084 haplotype-tagging and functional variants from 164 genes in mitotic regulatory pathways in 791 Caucasian women with breast cancer and 843 healthy controls for association with risk of overall and high grade breast cancer. Sixty-one single nucleotide polymorphisms (SNPs) from 40 genes were associated (P < 0.05) with risk of breast cancer in a log-additive model. In addition, 60 SNPs were associated (P < 0.05) with risk of high grade breast cancer. However, none of these associations were significant after Bonferroni correction for multiple testing. In gene-level analyses, CDC25C, SCC1/RAD21, TLK2, and SMC6L1 were associated (P < 0.05) with overall breast cancer risk, CDC6, CDC27, SUMO3, RASSF1, KIF2, and CDC14A were associated with high grade breast cancer risk, and EIF3S10 and CDC25A were associated with both. Further investigation in breast and other cancers are needed to understand the influence of inherited variation in mitotic genes on tumor grade and cancer risk.
Collapse
|
25
|
Saletta F, Suryo Rahmanto Y, Richardson DR. The translational regulator eIF3a: the tricky eIF3 subunit! Biochim Biophys Acta Rev Cancer 2010; 1806:275-86. [PMID: 20647036 DOI: 10.1016/j.bbcan.2010.07.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 07/07/2010] [Accepted: 07/11/2010] [Indexed: 01/10/2023]
Abstract
Regulation of gene expression is a fundamental step in cellular physiology as abnormalities in this process may lead to de-regulated growth and cancer. Translation of mRNA is mainly regulated at the rate-limiting initiation step, where many eukaryotic initiation factors (eIFs) are involved. The largest and most complex initiation factor is eIF3 which plays a role in translational regulation, cell growth and cancer. The largest subunit of eIF3 is eIF3a, although it is not required for the general function of eIF3 in translation initiation. However, eIF3a may play a role as a regulator of a subset of mRNAs and has been demonstrated to regulate the expression of p27(kip1), tyrosinated α-tubulin and ribonucleotide reductase M2 subunit. These molecules have a pivotal role in the regulation of the cell cycle. Moreover, the eIF3a mRNA is ubiquitously expressed in all tissues at different levels and is found elevated in a number of cancer types. eIF3a can modulate the cell cycle and may be a translational regulator for proteins important for entrance into S phase. The expression of eIF3a is decreased in differentiated cells in culture and the suppression of eIF3a expression can reverse the malignant phenotype and change the sensitivity of cells to cell cycle modulators. However, the role of eIF3a in cancer is still unclear. In fact, some studies have identified eIF3a to be involved in cancer development, while other results indicate that it could provide protection against evolution into higher malignancy. Together, these findings highlight the "tricky" and interesting nature of eIF3a.
Collapse
Affiliation(s)
- Federica Saletta
- Iron Metabolism and Chelation Program, Department of Pathology and Bosch Institute, Blackburn Building (D06), University of Sydney, Sydney, New South Wales, 2006 Australia
| | | | | |
Collapse
|
26
|
Wang X, Pankratz VS, Fredericksen Z, Tarrell R, Karaus M, McGuffog L, Pharaoh PD, Ponder BA, Dunning AM, Peock S, Cook M, Oliver C, Frost D, Sinilnikova OM, Stoppa-Lyonnet D, Mazoyer S, Houdayer C, Hogervorst FB, Hooning MJ, Ligtenberg MJ, Spurdle A, Chenevix-Trench G, Schmutzler RK, Wappenschmidt B, Engel C, Meindl A, Domchek SM, Nathanson KL, Rebbeck TR, Singer CF, Gschwantler-Kaulich D, Dressler C, Fink A, Szabo CI, Zikan M, Foretova L, Claes K, Thomas G, Hoover RN, Hunter DJ, Chanock SJ, Easton DF, Antoniou AC, Couch FJ. Common variants associated with breast cancer in genome-wide association studies are modifiers of breast cancer risk in BRCA1 and BRCA2 mutation carriers. Hum Mol Genet 2010; 19:2886-97. [PMID: 20418484 PMCID: PMC2893806 DOI: 10.1093/hmg/ddq174] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Accepted: 04/21/2010] [Indexed: 12/19/2022] Open
Abstract
Recent studies have identified single nucleotide polymorphisms (SNPs) that significantly modify breast cancer risk in BRCA1 and BRCA2 mutation carriers. Since these risk modifiers were originally identified as genetic risk factors for breast cancer in genome-wide association studies (GWASs), additional risk modifiers for BRCA1 and BRCA2 may be identified from promising signals discovered in breast cancer GWAS. A total of 350 SNPs identified as candidate breast cancer risk factors (P < 1 x 10(-3)) in two breast cancer GWAS studies were genotyped in 3451 BRCA1 and 2006 BRCA2 mutation carriers from nine centers. Associations with breast cancer risk were assessed using Cox models weighted for penetrance. Eight SNPs in BRCA1 carriers and 12 SNPs in BRCA2 carriers, representing an enrichment over the number expected, were significantly associated with breast cancer risk (P(trend) < 0.01). The minor alleles of rs6138178 in SNRPB and rs6602595 in CAMK1D displayed the strongest associations in BRCA1 carriers (HR = 0.78, 95% CI: 0.69-0.90, P(trend) = 3.6 x 10(-4) and HR = 1.25, 95% CI: 1.10-1.41, P(trend) = 4.2 x 10(-4)), whereas rs9393597 in LOC134997 and rs12652447 in FBXL7 showed the strongest associations in BRCA2 carriers (HR = 1.55, 95% CI: 1.25-1.92, P(trend) = 6 x 10(-5) and HR = 1.37, 95% CI: 1.16-1.62, P(trend) = 1.7 x 10(-4)). The magnitude and direction of the associations were consistent with the original GWAS. In subsequent risk assessment studies, the loci appeared to interact multiplicatively for breast cancer risk in BRCA1 and BRCA2 carriers. Promising candidate SNPs from GWAS were identified as modifiers of breast cancer risk in BRCA1 and BRCA2 carriers. Upon further validation, these SNPs together with other genetic and environmental factors may improve breast cancer risk assessment in these populations.
Collapse
Affiliation(s)
- Xianshu Wang
- Department of Laboratory Medicine and Pathology and
| | | | | | - Robert Tarrell
- Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Mary Karaus
- Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Lesley McGuffog
- Department of Public Health and Primary Care, Cancer Research UK Genetic Epidemiology Unit and
| | | | | | | | - Susan Peock
- Department of Public Health and Primary Care, Cancer Research UK Genetic Epidemiology Unit and
| | - Margaret Cook
- Department of Public Health and Primary Care, Cancer Research UK Genetic Epidemiology Unit and
| | - Clare Oliver
- Department of Public Health and Primary Care, Cancer Research UK Genetic Epidemiology Unit and
| | - Debra Frost
- Department of Public Health and Primary Care, Cancer Research UK Genetic Epidemiology Unit and
| | - EMBRACE
- Department of Public Health and Primary Care, Cancer Research UK Genetic Epidemiology Unit and
| | - Olga M. Sinilnikova
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon/Centre Léon Bérard, Lyon, France
| | - Dominique Stoppa-Lyonnet
- INSERM U509, Service de Génétique Oncologique, Institut Curie, Université Paris-Descartes, Paris, France
| | - Sylvie Mazoyer
- Equipe labellisée LIGUE 2008, UMR5201 CNRS, Centre Léon Bérard, Université de Lyon, Lyon, France
| | - Claude Houdayer
- INSERM U509, Service de Génétique Oncologique, Institut Curie, Université Paris-Descartes, Paris, France
| | - GEMO
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon/Centre Léon Bérard, Lyon, France
- INSERM U509, Service de Génétique Oncologique, Institut Curie, Université Paris-Descartes, Paris, France
| | - Frans B.L. Hogervorst
- Department of Pathology, Family Cancer Clinic, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maartje J. Hooning
- Department of Medical Oncology, Rotterdam Family Cancer Clinic, Erasmus, The Netherlands
| | | | - HEBON
- Department of Pathology, Family Cancer Clinic, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Amanda Spurdle
- Queensland Institute of Medical Research, Brisbane, QLD 4029, Australia
| | | | - kConFab
- kConFab (Kathleen Cunningham Foundation Consortium for Research into Familial Breast Cancer), Peter MacCallum Cancer Institute, Melbourne, VIC 3002, Australia
| | - Rita K. Schmutzler
- Center of Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
| | - Barbara Wappenschmidt
- Center of Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
| | - Christoph Engel
- Institute of Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Alfons Meindl
- Department of Obstetrics and Gynaecology, Klinikum rechts der Isar, Technical University, Munich, Germany
| | | | | | | | | | | | | | | | | | - Michal Zikan
- Department of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Kathleen Claes
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Gilles Thomas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Robert N. Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David J. Hunter
- Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, MA, USA
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA and
| | - Stephen J. Chanock
- Advanced Technology Center, National Cancer Institute, Gaithersburg, MD, USA
| | - Douglas F. Easton
- Department of Public Health and Primary Care, Cancer Research UK Genetic Epidemiology Unit and
| | - Antonis C. Antoniou
- Department of Public Health and Primary Care, Cancer Research UK Genetic Epidemiology Unit and
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology and
- Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| |
Collapse
|
27
|
Couch FJ, Wang X, Bamlet WR, de Andrade M, Petersen GM, McWilliams RR. Association of mitotic regulation pathway polymorphisms with pancreatic cancer risk and outcome. Cancer Epidemiol Biomarkers Prev 2010; 19:251-7. [PMID: 20056645 DOI: 10.1158/1055-9965.epi-09-0629] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Mitosis is a highly regulated process that serves to ensure the fidelity of cell division. The disruption of mitotic regulators leading to aneuploidy and polyploidy is commonly observed in cancer cells. Single nucleotide polymorphisms (SNP) in regulators of mitosis may promote chromosome missegregation and influence pancreatic cancer and/or survival. METHODS Thirty-four SNPs, previously associated with breast cancer risk, from 33 genes involved in the regulation of mitosis, were investigated for associations with pancreatic cancer risk in 1,143 Caucasian patients with pancreatic adenocarcinoma and 1,097 unaffected controls from the Mayo Clinic. Associations with survival from pancreatic cancer were also assessed using 1,030 pancreatic cancer cases with known outcome. RESULTS Two SNPs in the APC (rs2431238) and NIN (rs10145182) loci, of 34 examined, were significantly associated with pancreatic cancer risk (P = 0.035 and P = 0.038, respectively). Further analyses of individuals categorized by smoking and body mass index identified several SNPs displaying significant associations (P < 0.05) with pancreatic cancer risk, including APC rs2431238 in individuals with high body mass index (>/=30; P = 0.031) and NIN rs10145182 in ever smokers (P = 0.01). In addition, survival analyses detected significant associations between SNPs in EIF3S10 and overall survival (P = 0.009), SNPs from five genes and survival in resected cancer cases (P < 0.05), and SNPs from two other genes (P < 0.05) and survival of locally advanced cancer cases. CONCLUSION Common variation in genes encoding regulators of mitosis may independently influence pancreatic cancer susceptibility and survival.
Collapse
Affiliation(s)
- Fergus J Couch
- Department of Laboratory Medicine and Pathology, Stabile 2-42, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA.
| | | | | | | | | | | |
Collapse
|