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Zhong G, Lin Y, Huang Z. Identification of a novel circRNA-miRNA-mRNA regulatory axis in hepatocellular carcinoma based on bioinformatics analysis. Sci Rep 2023; 13:3728. [PMID: 36878930 PMCID: PMC9988886 DOI: 10.1038/s41598-023-30567-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 02/25/2023] [Indexed: 03/08/2023] Open
Abstract
In recent years, circular RNAs (circRNAs) have been found to play an essential regulatory role in hepatocellular carcinoma (HCC) through various mechanisms, particularly the endogenous competitive RNA (ceRNA) mechanism. Therefore, it is significant to explore the circRNAs in hepatoma. In this study, we constructed the ceRNA and survival network using Cytoscape. We also used R, Perl software, and multiple online databases and platforms, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), to perform overall survival, immune cell infiltration, immune checkpoints, pathway activity, and anticancer drug sensitivity analysis of the genes. Finally, the receiver operator characteristic curve (ROC) analysis was performed to identify the diagnosis value of the genes. KEGG analysis revealed the T cell receptor signaling pathway as the main enrichment pathway. A total of 29 genes related to survival and prognosis were screened out. The findings suggest that ZNF544, WDR76, ACTG1, RASSF3, E2F3, ASRGL1, and POGK are associated with multilevel immune cell infiltration. Additionally, immune checkpoint analysis screened out the ACTG1, E2F3, RASSF3, and WDR76. It was also revealed that the WDR76, E2F3, ASRGL1, and POGK mainly activated the cell cycle and DNA damage response (DDR) pathway. The results suggest that the sensitivity toward trametinib, refametinib (RDEA119), and selumetinib correlates to the expression of WDR76. ROC analysis showed that the area under the curve (AUC) of all genes in the regulatory axis was greater than 0.7. The identified hsa_circ_0000417/hsa_circ_0002688/hsa_circ_0001387--hsa-miR-199a-5p--WDR76 regulatory axis may provide new insights into the progression, clinical diagnosis, and treatment of HCC.
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Affiliation(s)
- Guoqiang Zhong
- Department of Gastroenterology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China.,The Graduate School, Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Yan Lin
- Department of Gastroenterology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China.,The Graduate School, Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Zansong Huang
- Department of Gastroenterology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China. .,The Graduate School, Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China.
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A review of radiation genomics: integrating patient radiation response with genomics for personalised and targeted radiation therapy. JOURNAL OF RADIOTHERAPY IN PRACTICE 2018. [DOI: 10.1017/s1460396918000547] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
AbstractBackgroundThe success of radiation therapy for cancer patients is dependent on the ability to deliver a total tumouricidal radiation dose capable of eradicating all cancer cells within the clinical target volume, however, the radiation dose tolerance of the surrounding healthy tissues becomes the main dose-limiting factor. The normal tissue adverse effects following radiotherapy are common and significantly impact the quality of life of patients. The likelihood of developing these adverse effects following radiotherapy cannot be predicted based only on the radiation treatment parameters. However, there is evidence to suggest that some common genetic variants are associated with radiotherapy response and the risk of developing adverse effects. Radiation genomics is a field that has evolved in recent years investigating the association between patient genomic data and the response to radiation therapy. This field aims to identify genetic markers that are linked to individual radiosensitivity with the potential to predict the risk of developing adverse effects due to radiotherapy using patient genomic information. It also aims to determine the relative radioresponse of patients using their genetic information for the potential prediction of patient radiation treatment response.Methods and materialsThis paper reports on a review of recent studies in the field of radiation genomics investigating the association between genomic data and patients response to radiation therapy, including the investigation of the role of genetic variants on an individual’s predisposition to enhanced radiotherapy radiosensitivity or radioresponse.ConclusionThe potential for early prediction of treatment response and patient outcome is critical in cancer patients to make decisions regarding continuation, escalation, discontinuation, and/or change in treatment options to maximise patient survival while minimising adverse effects and maintaining patients’ quality of life.
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Liu S, Yang TB, Nan YL, Li AH, Pan DX, Xu Y, Li S, Li T, Zeng XY, Qiu XQ. Genetic variants of cell cycle pathway genes predict disease-free survival of hepatocellular carcinoma. Cancer Med 2017. [PMID: 28639733 PMCID: PMC5504311 DOI: 10.1002/cam4.1067] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Disruption of the cell cycle pathway has previously been related to development of human cancers. However, associations between genetic variants of cell cycle pathway genes and prognosis of hepatocellular carcinoma (HCC) remain largely unknown. In this study, we evaluated the associations between 24 potential functional single nucleotide polymorphisms (SNPs) of 16 main cell cycle pathway genes and disease‐free survival (DFS) of 271 HCC patients who had undergone radical surgery resection. We identified two SNPs, i.e., SMAD3 rs11556090 A>G and RBL2 rs3929G>C, that were independently predictive of DFS in an additive genetic model with false‐positive report probability (FPRP) <0.2. The SMAD3 rs11556090G allele was associated with a poorer DFS, compared with the A allele [hazard ratio (HR) = 1.46, 95% confidential interval (95% CI) = 1.13–1.89, P = 0.004]; while the RBL2 rs3929 C allele was associated with a superior DFS, compared with the G allele (HR = 0.74, 95% CI = 0.57–0.96, P = 0.023). Additionally, patients with an increasing number of unfavorable genotypes (NUGs) of these loci had a significant shorter DFS (Ptrend = 0.0001). Further analysis using receiver operating characteristic (ROC) curves showed that the model including the NUGs and known prognostic clinical variables demonstrated a significant improvement in predicting the 1‐year DFS (P = 0.011). Moreover, the RBL2 rs3929 C allele was significantly associated with increased mRNA expression levels of RBL2 in liver tissue (P = 1.8 × 10−7) and the whole blood (P = 3.9 × 10−14). Our data demonstrated an independent or a joint effect of SMAD3 rs11556090 and RBL2 rs3929 in the cell cycle pathway on DFS of HCC, which need to be validated by large cohort and biological studies.
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Affiliation(s)
- Shun Liu
- Department of Epidemiology, School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, Guangxi, 530021, China
| | - Tian-Bo Yang
- Affiliated Tumor Hospital of Guangxi Medical University, 71 Hedi Road, Nanning, Guangxi, 530021, China
| | - Yue-Li Nan
- Shenzhen Longhua Center for Chronic Diseases Prevention and Control, 118 Guanlan Road, Shenzhen, Guangdong, 518110, China
| | - An-Hua Li
- GuangXi Center for Disease Prevention and Control, 18 Jinzhou Road, Nanning, Guangxi, 530021, China
| | - Dong-Xiang Pan
- GuangXi Center for Disease Prevention and Control, 18 Jinzhou Road, Nanning, Guangxi, 530021, China
| | - Yang Xu
- Department of Epidemiology, School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, Guangxi, 530021, China
| | - Shu Li
- Department of Epidemiology, School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, Guangxi, 530021, China
| | - Ting Li
- Medical Scientific Research Centre, Guangxi Medical University, 22 Shuangyong Road, Nanning, Guangxi, 530021, China
| | - Xiao-Yun Zeng
- Department of Epidemiology, School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, Guangxi, 530021, China
| | - Xiao-Qiang Qiu
- Department of Epidemiology, School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, Guangxi, 530021, China
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Guo X, Li D, Chen Y, An J, Wang K, Xu Z, Chen Z, Xing J. SNP rs2057482 in HIF1A gene predicts clinical outcome of aggressive hepatocellular carcinoma patients after surgery. Sci Rep 2015; 5:11846. [PMID: 26115041 PMCID: PMC4481773 DOI: 10.1038/srep11846] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 06/08/2015] [Indexed: 01/30/2023] Open
Abstract
Hypoxia-inducible factor 1α (HIF-1α) plays an important role in tumor growth and metastasis. Genetic variations of HIF1A gene have been shown to influence the developing risk and prognosis in many types of human malignancies. However, their association with clinical outcomes of hepatocellular carcinoma (HCC) patients remains unclear. To investigate the predictive role of single nucleotide polymorphisms (SNPs) in HIF1A gene in HCC patients’ outcomes, we genotyped three functional SNPs (rs2057482, rs1957757 and rs2301113) in HIF1A gene and assessed their associations with clinicopathological parameters and prognosis of 492 surgical HCC patients. The patients with variant alleles (CT+TT) of SNP rs2057482 had a significantly lower recurrence risk when compared with patients with the CC genotype. In stratified analysis, the protective effect of rs2057482 CT+TT genotype was more evident in patients with adverse strata, compared with patients with favorable strata. Additionally, strong joint predictive effect between rs2057482 genotypes and AFP level, stage or differentiation were observed. Functional assay also indicated the significant effect of rs2057482 on gene expression. In conclusion, SNP rs2057482 in HIF1A gene is significantly associated with clinical outcomes of Chinese HCC patients after surgery, especially in those with aggressive status, which warrants further validation in other patient populations.
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Affiliation(s)
- Xu Guo
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center &Department of Cell Biology, Fourth Military Medical University, Xi'an, China
| | - Deyang Li
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center &Department of Cell Biology, Fourth Military Medical University, Xi'an, China
| | - Yibing Chen
- Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, Xi'an, China
| | - Jiaze An
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Kan Wang
- Department of Pain treatment, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
| | - Zhuding Xu
- Department of liver Surgery, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, Shanghai, China
| | - Zhinan Chen
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center &Department of Cell Biology, Fourth Military Medical University, Xi'an, China
| | - Jinliang Xing
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center &Department of Cell Biology, Fourth Military Medical University, Xi'an, China.,Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, Xi'an, China
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Guo Z, Shu Y, Zhou H, Zhang W, Wang H. Radiogenomics helps to achieve personalized therapy by evaluating patient responses to radiation treatment. Carcinogenesis 2015; 36:307-17. [PMID: 25604391 DOI: 10.1093/carcin/bgv007] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Radiogenomics is the whole genome application of radiogenetics, which focuses on uncovering the underlying genetic causes of individual variation in sensitivity to radiation. There is a growing consensus that radiosensitivity is a complex, inherited polygenic trait, dependent on the interaction of many genes involved in multiple cell processes. An understanding of the genes involved in processes such as DNA damage response and oxidative stress response, has evolved toward examination of how genetic variants, most often, single nucleotide polymorphisms (SNPs), may influence interindividual radioresponse. Many experimental approaches, such as candidate SNP association studies, genome-wide association studies and massively parallel sequencing are being proposed to address these questions. We present a review focusing on recent advances in association studies of SNPs to radiotherapy response and discuss challenges and opportunities for further studies. We also highlight the clinical perspective of radiogenomics in the future of personalized treatment in radiation oncology.
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Affiliation(s)
- Zhen Guo
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University and Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha 410008, P.R. China
| | - Yan Shu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA and
| | - Honghao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University and Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha 410008, P.R. China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University and Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha 410008, P.R. China;
| | - Hui Wang
- Department of Radiation Oncology, Hunan Provincial Tumor Hospital & Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha 410013, P.R. China
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Guo X, Li D, Wu Y, Chen Y, Zhou X, Wang X, Huang X, Li X, Yang H, Xing J. Genetic variants in genes of tricarboxylic acid cycle key enzymes are associated with prognosis of patients with non-small cell lung cancer. Lung Cancer 2014; 87:162-8. [PMID: 25576295 DOI: 10.1016/j.lungcan.2014.12.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 11/27/2014] [Accepted: 12/13/2014] [Indexed: 12/01/2022]
Abstract
INTRODUCTION Non-small cell lung cancer (NSCLC) is characterized by poor prognosis and only a few molecular markers may be potentially used to predict the outcome. Metabolic reprogramming is a hallmark of cancer, including the alterations of tricarboxylic acid (TCA) cycle key enzymes. However, the significance of single nucleotide polymorphisms (SNPs) in genes encoding these key enzymes has not been investigated in NSCLC. PATIENTS AND METHODS In this study, we genotyped 18 potentially functional SNPs in 7 genes belonging to 3 TCA cycle enzyme families (SDH, FH and IDH) using Sequenom iPLEX genotyping system in a cohort of 500 NSCLC patients. Multivariate Cox proportional hazards model and Kaplan-Meier curve were used for the survival analysis. RESULTS Our results showed that SDHC gene: SNP rs12064957, IDH2 gene: SNP rs11540478 and FH gene: SNP rs1414493 were associated with overall survival (OS) and SDHA gene: SNP rs13173911, IDH2 gene: SNP rs4932158 were associated with recurrence-free survival (RFS) of NSCLC patients. Unfavorable genotypes of these SNPs showed a significant cumulative effect on OS and RFS of NSCLC patients (both P<0.001). Furthermore, survival tree analysis indicated that FH: rs1414493 was the primary risk factor contributing to OS of NSCLC patients and the IDH2: rs4932158 was the primary risk factor contributing to RFS of NSCLC patients. CONCLUSION Our data suggest that SNPs in TCA cycle key enzyme genes may serve as potential biomarkers to predict the outcomes of NSCLC. Further studies with different ethnicities are needed to validate our findings and generalize their clinical utility.
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Affiliation(s)
- Xu Guo
- State Key Laboratory of Cancer Biologyand Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, Xi'an710032, China
| | - Deyang Li
- State Key Laboratory of Cancer Biologyand Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, Xi'an710032, China
| | - Yousheng Wu
- State Key Laboratory of Cancer Biologyand Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, Xi'an710032, China
| | - Yibing Chen
- State Key Laboratory of Cancer Biologyand Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, Xi'an710032, China
| | - Xingchun Zhou
- State Key Laboratory of Cancer Biologyand Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, Xi'an710032, China
| | - Xiaoyan Wang
- Department of Breast Center, Tumor Hospital of Shaanxi Province, Xi'an 710061, China
| | - Xiaojun Huang
- State Key Laboratory of Cancer Biologyand Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, Xi'an710032, China
| | - Xiaofei Li
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an 710038, China
| | - Hushan Yang
- Division of Population Science, Department of Medical Oncology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
| | - Jinliang Xing
- State Key Laboratory of Cancer Biologyand Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, Xi'an710032, China.
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Tang S, Pan Y, Wang Y, Hu L, Cao S, Chu M, Dai J, Shu Y, Xu L, Chen J, Jin G, Hu Z, Ma H, Shen H. Genome-wide association study of survival in early-stage non-small cell lung cancer. Ann Surg Oncol 2014; 22:630-5. [PMID: 25145502 DOI: 10.1245/s10434-014-3983-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Indexed: 11/18/2022]
Abstract
BACKGROUND Lung cancer, especially non-small cell lung cancer (NSCLC), is the leading cause of cancer-related deaths all over the world. Studies have indicated that molecular biomarkers, including genetic variants, may provide additional values for the targeted treatments and clinical outcomes of NSCLC patients. To better understand the effects of molecular biomarkers on the treatment of NSCLC, we conducted a genome-wide analysis to investigate the prognostic implications of genetic variants in early-stage NSCLC patients with surgery. METHODS A genome wide scan of 906,703 single-nucleotide polymorphisms (SNPs) was conducted in a cohort with 365 early-stage NSCLC patients with surgery, followed by a fast-track replication in another independent cohort of 327 NSCLC patients from Nanjing, China. Cox models were used to screen and validate significant SNPs associated with the overall survival of early-stage NSCLC patients. RESULTS We found that rs10023113 in calcium/calmodulin-dependent protein kinase II delta (CAMK2D) was consistently associated with survival of early-stage NSCLC in the GWAS scan and the replication cohort [GWAS scan: hazard ratio (HR) 2.84; 95 % confidence interval (CI) 1.90-4.23, P = 1.29 × 10(-6); replication cohort: HR 2.19, 95 % CI 1.15-4.21, P = 1.80 × 10(-2)]. When combining all the patients, the results showed that the variant allele of rs10023113 was significantly associated with poor prognosis of early-stage NSCLC with P value of 3.40 × 10(-7) (HR 2.30, 95 % CI 1.67-3.17). CONCLUSIONS These findings suggest that CAMK2D rs10023113 may be a potentially prognostic marker for overall survival of early-stage NSCLC patients in Chinese population.
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Affiliation(s)
- Shaowen Tang
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
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Li X, Shao M, Wang S, Zhao X, Chen H, Qian J, Song X, Wang J, Jin L, Wu J, Li Q, Bai C, Han B, Gao Z, Lu D. Heterozygote advantage of methylenetetrahydrofolate reductase polymorphisms on clinical outcomes in advanced non-small cell lung cancer (NSCLC) patients treated with platinum-based chemotherapy. Tumour Biol 2014; 35:11159-70. [PMID: 25104092 DOI: 10.1007/s13277-014-2427-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 07/31/2014] [Indexed: 10/24/2022] Open
Abstract
Methylenetetrahydrofolate reductase (MTHFR) enzyme is essential for transmethylation reactions including DNA methylation and DNA synthesis and thereby may contribute to cancer prognosis. In our study, a total of 1,004 advanced non-small cell lung cancer (NSCLC) patients receiving first-line, platinum-based chemotherapy regimens were used for genotyping 10 tag single nucleotide polymorphisms (SNPs) of MTHFR. Association was assessed between the SNPs and treatment outcomes. We found that polymorphism of rs1537514 showed the most significant effect: heterozygote associated with better clinical benefit (P = 0.002) and decreased risk of grade 3 or 4 gastrointestinal toxicity (P = 0.027), while the mutant homozygote associated with increased risk of severe gastrointestinal toxicity (P = 0.031) and thrombocytopenia (P = 009). The heterozygotes of exon polymorphisms (rs1801131, rs1801133) also yielded better clinical benefit (P = 0.030 for rs1801131) and decreased risk of severe gastrointestinal toxicity (P = 0.004 for rs1801131) or thrombocytopenia (P = 0.016 for 1801133). However, overall survival (OS) and progression-free survival (PFS) did not differ for the MTHFR polymorphisms, except for heterozygote of rs1537514 showing significant effects with better PFS (P = 0.022). Clinical factors as age, gender, and smoking status had significant effects for the OS (P = 0.003, 0.002, and 0.012, respectively) while performance status and chemotherapy regimens for PFS (P = 0.001 and 3.9 × 10(-6), respectively). The results indicate that a heterozygous advantage may exist in certain MTHFR variants, and the polymorphisms (especially rs1537514) may play a predictive role of treatment efficacy and adverse effects in NSCLC patients treated with platinum-based chemotherapy.
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Affiliation(s)
- Xiaoying Li
- State Key Laboratory of Genetic Engineering, Fudan-VARI Genetic Epidemiology Center and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, 200433, Shanghai, China
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Guo X, Li H, Fei F, Liu B, Li X, Yang H, Chen Z, Xing J. Genetic variations in SLC3A2/CD98 gene as prognosis predictors in non-small cell lung cancer. Mol Carcinog 2014; 54 Suppl 1:E52-60. [PMID: 24782339 DOI: 10.1002/mc.22167] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 03/21/2014] [Accepted: 03/31/2014] [Indexed: 12/22/2022]
Abstract
Non-small cell lung cancer (NSCLC) is characterized by poor prognosis and only a few molecular markers may be potentially used to predict the risk of progression. This study aims to assess the effects of single nucleotide polymorphisms (SNPs) in the CD98 gene on prognosis of NSCLC patients. We genotyped three potential functional SNPs in CD98 gene using Sequenom iPLEX genotyping system in a cohort of 482 NSCLC patients. Multivariate cox proportional hazards model and Kaplan-Meier curve were used for the survival analysis. The variant-containing genotypes of rs1059292 in 5'-flanking region of CD98 gene were significantly associated with an increased risk of death in the multivariate analysis (Hazard ratio [HR], 1.49; 95% confidence interval [95% CI]: 1.04-2.14 in a dominant model). In stratified analysis, the association remained significant in patients with poor differentiation (HR=1.81, 95% CI=1.01-3.25). In addition, rs1059292 also showed a borderline significant association with T stage (OR=1.49; 95% CI: 0.96-2.35) and N stage (OR=1.53; 95% CI: 0.98-2.39). Functional analysis demonstrated that variant genotype of SNP rs1059292 significantly enhanced the transcription activity of CD98 gene promoter. Our data suggest that genetic variation of rs1059292 in CD98 gene may affect clinical outcome of NSCLC in Chinese population.
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Affiliation(s)
- Xu Guo
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center & Department of Cell Biology, The Fourth Military Medical University, Xi'an, P. R., China
| | - Hongwei Li
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center & Department of Cell Biology, The Fourth Military Medical University, Xi'an, P. R., China
| | - Fei Fei
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center & Department of Cell Biology, The Fourth Military Medical University, Xi'an, P. R., China
| | - Boya Liu
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, P. R., China
| | - Xiaofei Li
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, P. R., China
| | - Hushan Yang
- Division of Population Science, Department of Medical Oncology, Kimmel Cancer, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Zhinan Chen
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center & Department of Cell Biology, The Fourth Military Medical University, Xi'an, P. R., China
| | - Jinliang Xing
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center & Department of Cell Biology, The Fourth Military Medical University, Xi'an, P. R., China
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Han JY, Wang H, Xie YT, Li Y, Zheng LY, Ruan Y, Song AP, Tian XX, Fang WG. Association of germline variation in CCNE1 and CDK2 with breast cancer risk, progression and survival among Chinese Han women. PLoS One 2012; 7:e49296. [PMID: 23185313 PMCID: PMC3504019 DOI: 10.1371/journal.pone.0049296] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Accepted: 10/04/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Somatic alterations of cyclin-dependent kinase 2 (CDK2)-cyclin E complex have been shown to contribute to breast cancer (BC) development and progression. This study aimed to explore the effects of single nucleotide polymorphisms (SNPs) in CDK2 and CCNE1 (a gene encoding G1/S specific cyclin E1 protein, formerly called cyclin E) on BC risk, progression and survival in a Chinese Han population. METHODOLOGY/PRINCIPAL FINDINGS We herein genotyped 6 haplotype-tagging SNPs (htSNPs) of CCNE1 and 2 htSNPs of CDK2 in 1207 BC cases and 1207 age-matched controls among Chinese Han women, and then reconstructed haplotype blocks according to our genotyping data and linkage disequilibrium status of these htSNPs. For CCNE1, the minor allele homozygotes of three htSNPs were associated with BC risk (rs3218035: adjusted odds ratio [aOR] = 3.35, 95% confidence interval [CI] = 1.69-6.67; rs3218038: aOR = 1.81, 95% CI = 1.22-2.70; rs3218042: aOR = 2.64, 95% CI = 1.31-5.34), and these three loci showed a dose-dependent manner in increasing BC risk (P(trend) = 0.0001). Moreover, the 5-SNP haplotype CCGTC, which carried none of minor alleles of the 3 at-risk SNPs, was associated with a favorable event-free survival (hazard ratio [HR] = 0.53, 95% CI = 0.32-0.90). Stratified analysis suggested that the minor-allele homozygote carriers of rs3218038 had a worse event-free survival among patients with aggressive tumours (in tumour size>2 cm group: HR = 2.06, 95% CI = 1.06-3.99; in positive lymph node metastasis group: HR = 2.41, 95% CI = 1.15-5.03; in stage II-IV group: HR = 2.03, 95% CI = 1.09-3.79). For CDK2, no significant association was found. CONCLUSIONS/SIGNIFICANCE This study indicates that genetic variants in CCNE1 may contribute to BC risk and survival in Chinese Han population. They may become molecular markers for individual evaluation of BC susceptibility and prognosis. Nevertheless, further validation studies are needed.
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Affiliation(s)
- Ji-Yuan Han
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
| | - Hui Wang
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
| | - Yun-Tao Xie
- Breast Center, Peking University School of Oncology, Beijing Cancer Hospital & Institute, Beijing, People' Republic of China
| | - Yan Li
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
| | - Li-Yuan Zheng
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
| | - Yuan Ruan
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
| | - Ai-Ping Song
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
| | - Xin-Xia Tian
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
| | - Wei-Gang Fang
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
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Lee Y, Yoon KA, Joo J, Lee D, Bae K, Han JY, Lee JS. Prognostic implications of genetic variants in advanced non-small cell lung cancer: a genome-wide association study. Carcinogenesis 2012; 34:307-13. [PMID: 23144319 DOI: 10.1093/carcin/bgs356] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The prognostic significance of inherited genetic variants in advanced-stage non-small cell lung cancer (NSCLC) patients remains unknown. In this study, we genotyped 271 817 single-nucleotide polymorphisms in 348 advanced NSCLC patients who received chemotherapy and analyzed their association with prognosis by using Cox proportional hazard regression model adjusted for known prognostic factors. Top candidate single-nucleotide polymorphisms (SNPs) were selected using the bootstrap re-sampling procedure. Median age of patient population was 56 years. Proportions of female, never smokers and adenocarcinoma were 64.9, 67.5 and 80.4%, respectively. We identified 17 top candidate SNPs related to prognosis using cut-off minimum P value of <5.0 × 10(-5) in at least 70% of 1000 bootstrap samples. These SNPs were located in the genomic regions of the FAM154A, ANKS1A, DLST, THSD7B, NCOA2, CDH8, SLC35D2, NALCN and EGF genes. The most significant SNP, rs1571228 (9p22.1:FAM154A), was significantly associated with overall survival in dominant model [AG+GG to AA, hazard ratio (HR) of death (95% CI) = 0.53 (0.42-0.67); P = 2.025 × 10(-7)]. The SNP at 4q25:EGF, rs11098063, for which some genetic variations was previously reported to be associated with prognosis, also showed significant association with overall survival in additive model [CC versus CT versus TT, HR (95% CI) = 1.00 versus 0.61 (0.47-0.78) versus 0.39 (0.19-0.79); P = 9.582 × 10(-6)]. Survival differences according to the genotype of these SNPs were independent of sex, smoking, histology and chemotherapy regimens. These results suggested the variants at multiple genetic loci might contribute to the risk of death in advanced NSCLC patients receiving chemotherapy.
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Affiliation(s)
- Youngjoo Lee
- Center for Lung Cancer, National Cancer Center, Goyang, Gyeonggi, Republic of Korea
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