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Zhang Y, Wu Y, Jia Z, Cao D, Yang N, Wang Y, Cao X, Jiang J. Long non-coding RNA polymorphisms on 8q24 are associated with the prognosis of gastric cancer in a Chinese population. PeerJ 2020; 8:e8600. [PMID: 32117633 PMCID: PMC7039120 DOI: 10.7717/peerj.8600] [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: 10/11/2019] [Accepted: 01/19/2020] [Indexed: 12/24/2022] Open
Abstract
Background Gastric cancer (GC) remains the third leading cause of cancer death in China. Although genome-wide association studies have identified the association between several single nucleotide polymorphisms (SNPs) on 8q24 and the risk of GC, the role of these SNPs in the prognosis of GC in Chinese populations has not yet been fully evaluated. Therefore, this study was conducted to explore the association between long non-coding RNA (lncRNA) polymorphisms on 8q24 and the prognosis of GC. Methods We genotyped 726 surgically resected GC patients to explore the association between eight SNPs in the lncRNAs CCAT1 (rs10087719, rs7816475), PCAT1 (rs1026411), PRNCR1 (rs12682421, rs13252298), and CASC8 (rs1562430, rs4871789, rs6983267) transcribed from the 8q24 locus and the prognosis of GC in a Chinese population. Results We found that the patients carrying rs12682421 AA genotypes survived for a shorter time than those with the GG/GA genotype (HR = 1.39, 95% confidence interval (CI) [1.09-1.78]). Compared with the CC/CT genotype, the TT genotype of rs1562430 was associated with an increased risk of death (HR = 1.38, 95% CI [1.06-1.80]). Furthermore, the results also identified the rs1026411 SNP as an independent prognostic factor for poor survival in GC patients. Patients carrying AA/AG variant genotypes had a 36% increased risk of death compared to those carrying the GG genotype (HR = 1.36, 95% CI [1.06-1.74]). These findings suggested that the rs12682421, rs1026411 and rs1562430 SNPs may contribute to the survival of GC and be prognostic markers for GC.
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Affiliation(s)
- Yangyu Zhang
- Division of Clinical Research, First Hospital of Jilin University, Changchun, Jilin, China
| | - Yanhua Wu
- Division of Clinical Research, First Hospital of Jilin University, Changchun, Jilin, China
| | - Zhifang Jia
- Division of Clinical Research, First Hospital of Jilin University, Changchun, Jilin, China
| | - Donghui Cao
- Division of Clinical Research, First Hospital of Jilin University, Changchun, Jilin, China
| | - Na Yang
- Division of Clinical Research, First Hospital of Jilin University, Changchun, Jilin, China
| | - Yueqi Wang
- Division of Clinical Research, First Hospital of Jilin University, Changchun, Jilin, China
| | - Xueyuan Cao
- Department of Gastric and Colorectal Surgery, First Hospital of Jilin University, Changchun, Jilin, China
| | - Jing Jiang
- Division of Clinical Research, First Hospital of Jilin University, Changchun, Jilin, China
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Guan Q, Zeng Q, Yan H, Xie J, Cheng J, Ao L, He J, Zhao W, Chen K, Guo Y, Guan G, Guo Z. A qualitative transcriptional signature for the early diagnosis of colorectal cancer. Cancer Sci 2019; 110:3225-3234. [PMID: 31335996 PMCID: PMC6778657 DOI: 10.1111/cas.14137] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 06/26/2019] [Accepted: 06/26/2019] [Indexed: 12/12/2022] Open
Abstract
Currently, using biopsy specimens for the early diagnosis of colorectal cancer (CRC) is not entirely reliable due to insufficient sampling amount and inaccurate sampling location. Thus, it is necessary to develop a signature that can accurately identify patients with CRC under these clinical scenarios. Based on the relative expression orderings of genes within individual samples, we developed a qualitative transcriptional signature to discriminate CRC tissues, including CRC adjacent normal tissues from non-CRC individuals. The signature was validated using multiple microarray and RNA sequencing data from different sources. In the training data, a signature consisting of 7 gene pairs was identified. It was well validated in both biopsy and surgical resection specimens from multiple datasets measured by different platforms. For biopsy specimens, 97.6% of 42 CRC tissues and 94.5% of 163 non-CRC (normal or inflammatory bowel disease) tissues were correctly classified. For surgically resected specimens, 99.5% of 854 CRC tissues and 96.3% of 81 CRC adjacent normal tissues were correctly identified as CRC. Notably, we additionally measured 33 CRC biopsy specimens by the Affymetrix platform and 13 CRC surgical resection specimens, with different proportions of tumor epithelial cells, ranging from 40% to 100%, by the RNA sequencing platform, and all these samples were correctly identified as CRC. The signature can be used for the early diagnosis of CRC, which is also suitable for minimum biopsy specimens and inaccurately sampled specimens, and thus has potential value for clinical application.
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Affiliation(s)
- Qingzhou Guan
- Department of Bioinformatics, School of Basic Medical Sciences, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China.,Key Laboratory of Medical Bioinformatics, Fuzhou, China
| | - Qiuhong Zeng
- Department of Bioinformatics, School of Basic Medical Sciences, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China.,Key Laboratory of Medical Bioinformatics, Fuzhou, China
| | - Haidan Yan
- Department of Bioinformatics, School of Basic Medical Sciences, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China.,Key Laboratory of Medical Bioinformatics, Fuzhou, China
| | - Jiajing Xie
- Department of Bioinformatics, School of Basic Medical Sciences, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China.,Key Laboratory of Medical Bioinformatics, Fuzhou, China
| | - Jun Cheng
- Department of Bioinformatics, School of Basic Medical Sciences, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China.,Key Laboratory of Medical Bioinformatics, Fuzhou, China
| | - Lu Ao
- Department of Bioinformatics, School of Basic Medical Sciences, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China.,Key Laboratory of Medical Bioinformatics, Fuzhou, China
| | - Jun He
- Department of Bioinformatics, School of Basic Medical Sciences, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China.,Key Laboratory of Medical Bioinformatics, Fuzhou, China
| | - Wenyuan Zhao
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Kui Chen
- Department of General Surgery, Affiliated Fuzhou First Hospital of Fujian Medical University, Fuzhou, China
| | - You Guo
- Department of Bioinformatics, School of Basic Medical Sciences, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China.,Key Laboratory of Medical Bioinformatics, Fuzhou, China
| | - Guoxian Guan
- Department of Colorectal Surgery, The Affiliated Union Hospital of Fujian Medical University, Fuzhou, China
| | - Zheng Guo
- Department of Bioinformatics, School of Basic Medical Sciences, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China.,Key Laboratory of Medical Bioinformatics, Fuzhou, China
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Li YQ, Chen J, Yin JY, Liu ZQ, Li XP. Gene expression and single nucleotide polymorphism of ATP7B are associated with platinum-based chemotherapy response in non-small cell lung cancer patients. J Cancer 2018; 9:3532-3539. [PMID: 30310510 PMCID: PMC6171024 DOI: 10.7150/jca.26286] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 07/26/2018] [Indexed: 02/06/2023] Open
Abstract
Objectives: Platinum-based chemotherapy is first-line treatment for non-small cell lung cancer (NSCLC) patients. The efficacy is limited by drug resistance. Recent studies suggest that ATP7B, a copper efflux transporter, may be involved in platinum resistance. However, the clinical significance of ATP7B expression in NSCLC is controversial. Moreover, the effects of single nucleotide polymorphisms (SNPs) in ATP7B gene on the response to platinum-based chemotherapy are scarcely understood. The aim of our study is to evaluate the clinical value of ATP7B in NSCLC patients and explore the interrelationships between ATP7B SNPs and protein expression, and their association with chemotherapy response. Materials and Methods: A total of 247 NSCLC patients were recruited in this study. Among them, 158 patients who received platinum-based chemotherapy were used to explore the interrelationships between ATP7B SNPs, protein expression and chemotherapy response, while 89 patients who underwent surgical resection were used to further investigate the association between ATP7B SNPs and expression level. We genotyped 15 SNPs of ATP7B by Sequenom MassARRAY and determined ATP7B protein levels by immunohistochemistry. Results: Patients with ATP7B-negative tumors had improved chemotherapeutic response (p=0.025) and better overall survival (p=0.044) compared with the patients with ATP7B-positive tumors. The multivariate Cox regression analysis revealed that ATP7B expression was an independent prognostic factor (HR=0.639, 95%CI=0.424-0.962, p=0.032). Moreover, we found that the rs9526814 GG genotype was significantly associated with favorable response to platinum-based chemotherapy when compared with TT+TG genotypes (OR=0.362, 95CI%=0.140-0.935, p=0.036). Mechanistically, rs9526814 GG genotype showed a strong trend towards reduced expression level of ATP7B compared with the TT+TG genotypes (p= 0.048). Conclusion: Our findings indicate that ATP7B rs9526814 may contribute to platinum resistance by influencing ATP7B gene expression and can be used as a potential biomarker to predict the sensitivity of platinum-based chemotherapy in NSCLC patients.
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Affiliation(s)
- Yue-Qin Li
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, P.R. China.,Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P.R. China
| | - Juan Chen
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, P.R. China.,Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P.R. China
| | - Ji-Ye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P.R. China
| | - Zhao-Qian Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P.R. China
| | - Xiang-Ping Li
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, P.R. China.,Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P.R. China
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