1
|
Long E, Patel H, Byun J, Amos CI, Choi J. Functional studies of lung cancer GWAS beyond association. Hum Mol Genet 2022; 31:R22-R36. [PMID: 35776125 DOI: 10.1093/hmg/ddac140] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/01/2022] [Accepted: 06/16/2022] [Indexed: 11/14/2022] Open
Abstract
Fourteen years after the first genome-wide association study (GWAS) of lung cancer was published, approximately forty-five genomic loci have now been significantly associated with lung cancer risk. While functional characterization was performed for several of these loci, a comprehensive summary of current molecular understanding of lung cancer risk has been lacking. Further, many novel computational and experimental tools now became available to accelerate the functional assessment of disease-associated variants, moving beyond locus-by-locus approaches. In this review, we first highlight the heterogeneity of lung cancer GWAS findings across histological subtypes, ancestries, and smoking status, which poses unique challenges to follow-up studies. We then summarize the published lung cancer post-GWAS studies for each risk-associated locus to assess the current understanding of biological mechanisms beyond the initial statistical association. We further summarize strategies for GWAS functional follow-up studies considering cutting-edge functional genomics tools and providing a catalog of available resources relevant to lung cancer. Overall, we aim to highlight the importance of integrating computational and experimental approaches to draw biological insights from the lung cancer GWAS results beyond association.
Collapse
Affiliation(s)
- Erping Long
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Harsh Patel
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, 77030, USA.,Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, 77030, USA.,Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
2
|
Lebrett MB, Crosbie EJ, Smith MJ, Woodward ER, Evans DG, Crosbie PAJ. Targeting lung cancer screening to individuals at greatest risk: the role of genetic factors. J Med Genet 2021; 58:217-226. [PMID: 33514608 PMCID: PMC8005792 DOI: 10.1136/jmedgenet-2020-107399] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 12/06/2020] [Accepted: 12/08/2020] [Indexed: 12/24/2022]
Abstract
Lung cancer (LC) is the most common global cancer. An individual’s risk of developing LC is mediated by an array of factors, including family history of the disease. Considerable research into genetic risk factors for LC has taken place in recent years, with both low-penetrance and high-penetrance variants implicated in increasing or decreasing a person’s risk of the disease. LC is the leading cause of cancer death worldwide; poor survival is driven by late onset of non-specific symptoms, resulting in late-stage diagnoses. Evidence for the efficacy of screening in detecting cancer earlier, thereby reducing lung-cancer specific mortality, is now well established. To ensure the cost-effectiveness of a screening programme and to limit the potential harms to participants, a risk threshold for screening eligibility is required. Risk prediction models (RPMs), which provide an individual’s personal risk of LC over a particular period based on a large number of risk factors, may improve the selection of high-risk individuals for LC screening when compared with generalised eligibility criteria that only consider smoking history and age. No currently used RPM integrates genetic risk factors into its calculation of risk. This review provides an overview of the evidence for LC screening, screening related harms and the use of RPMs in screening cohort selection. It gives a synopsis of the known genetic risk factors for lung cancer and discusses the evidence for including them in RPMs, focusing in particular on the use of polygenic risk scores to increase the accuracy of targeted lung cancer screening.
Collapse
Affiliation(s)
- Mikey B Lebrett
- Division of Infection, Immunity and Respiratory Medicine, The University of Manchester Faculty of Biology Medicine and Health, Manchester, UK.,Prevention and Early Detection Theme, NIHR Manchester Biomedical Research Centre, Manchester, UK
| | - Emma J Crosbie
- Prevention and Early Detection Theme, NIHR Manchester Biomedical Research Centre, Manchester, UK.,Division of Cancer Sciences, The University of Manchester Faculty of Biology Medicine and Health, Manchester, UK
| | - Miriam J Smith
- Prevention and Early Detection Theme, NIHR Manchester Biomedical Research Centre, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Emma R Woodward
- Prevention and Early Detection Theme, NIHR Manchester Biomedical Research Centre, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - D Gareth Evans
- Prevention and Early Detection Theme, NIHR Manchester Biomedical Research Centre, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Philip A J Crosbie
- Division of Infection, Immunity and Respiratory Medicine, The University of Manchester Faculty of Biology Medicine and Health, Manchester, UK .,Prevention and Early Detection Theme, NIHR Manchester Biomedical Research Centre, Manchester, UK.,Manchester Thoracic Oncology Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| |
Collapse
|
3
|
Hypothalamic expression of the atypical chemokine receptor ACKR2 is involved in the systemic regulation of glucose tolerance. Biochim Biophys Acta Mol Basis Dis 2019; 1865:1126-1137. [PMID: 30738810 DOI: 10.1016/j.bbadis.2019.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 12/06/2018] [Accepted: 01/02/2019] [Indexed: 02/02/2023]
Abstract
In experimental obesity, the hypothalamus is affected by an inflammatory response activated by dietary saturated fats. This inflammation is triggered as early as one day after exposure to a high-fat diet, and during its progression, there is recruitment of inflammatory cells from the systemic circulation. The objective of the present study was identifying chemokines potentially involved in the development of hypothalamic diet-induced inflammation. In order to identify chemokines potentially involved in this process, we performed a real-time PCR array that determined Ackr2 as one of the transcripts undergoing differential regulation in obese-prone as compared to obese-resistant mice fed a high-fat diet for three days. ACKR2 is a decoy receptor that acts as an inhibitor of the signals generated by several CC inflammatory chemokines. Our results show that Ackr2 expression is rapidly induced after exposure to dietary fats both in obese-prone and obese-resistant mice. In immunofluorescence studies, ACKR2 was detected in hypothalamic neurons expressing POMC and NPY and also in microglia and astrocytes. The lentiviral overexpression of ACKR2 in the hypothalamus reduced diet-induced hypothalamic inflammation; however, there was no change in spontaneous caloric intake and body mass. Nevertheless, the overexpression of ACKR2 resulted in improvement of glucose tolerance, which was accompanied by reduced insulin secretion and increased whole body insulin sensitivity. Thus, ACKR2 is a decoy chemokine receptor expressed in most hypothalamic cells that is modulated by dietary intervention and acts to reduce diet-induced inflammation, leading to improved glucose tolerance due to improved insulin action.
Collapse
|
4
|
Bach DH, Kim D, Bae SY, Kim WK, Hong JY, Lee HJ, Rajasekaran N, Kwon S, Fan Y, Luu TTT, Shin YK, Lee J, Lee SK. Targeting Nicotinamide N-Methyltransferase and miR-449a in EGFR-TKI-Resistant Non-Small-Cell Lung Cancer Cells. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 11:455-467. [PMID: 29858080 PMCID: PMC5992482 DOI: 10.1016/j.omtn.2018.03.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/05/2018] [Accepted: 03/26/2018] [Indexed: 12/29/2022]
Abstract
Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) are used clinically as target therapies for lung cancer patients, but the occurrence of acquired drug resistance limits their efficacy. Nicotinamide N-methyltransferase (NNMT), a cancer-associated metabolic enzyme, is commonly overexpressed in various human tumors. Emerging evidence also suggests a crucial loss of function of microRNAs (miRNAs) in modulating tumor progression in response to standard therapies. However, their precise roles in regulating the development of drug-resistant tumorigenesis are still poorly understood. Herein, we established EGFR-TKI-resistant non-small-cell lung cancer (NSCLC) models and observed a negative correlation between the expression levels of NNMT and miR-449a in tumor cells. Additionally, knockdown of NNMT suppressed p-Akt and tumorigenesis, while re-expression of miR-449a induced phosphatase and tensin homolog (PTEN), and inhibited tumor growth. Furthermore, yuanhuadine, an antitumor agent, significantly upregulated miR-449a levels while critically suppressing NNMT expression. These findings suggest a novel therapeutic approach for overcoming EGFR-TKI resistance to NSCLC treatment.
Collapse
Affiliation(s)
- Duc-Hiep Bach
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, Korea
| | - Donghwa Kim
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, Korea
| | - Song Yi Bae
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, Korea
| | - Won Kyung Kim
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, Korea
| | - Ji-Young Hong
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, Korea
| | - Hye-Jung Lee
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, Korea
| | - Nirmal Rajasekaran
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Korea
| | - Soonbum Kwon
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Korea
| | - Yanhua Fan
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, Korea
| | - Thi-Thu-Trang Luu
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, Korea
| | - Young Kee Shin
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Pharmacy, Seoul National University, Seoul, Korea
| | - Jeeyeon Lee
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Korea
| | - Sang Kook Lee
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, Korea.
| |
Collapse
|
5
|
Yadav S, Chandra A, Kumar A, Mittal B. Association of TERT-CLPTM1L and 8q24 Common Genetic Variants with Gallbladder Cancer Susceptibility and Prognosis in North Indian Population. Biochem Genet 2018; 56:267-282. [PMID: 29450669 DOI: 10.1007/s10528-018-9843-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 01/27/2018] [Indexed: 12/21/2022]
Abstract
Gallbladder carcinoma (GBC) is one of the common malignancy of the biliary tract. Several genome wide and candidate gene studies have reported associations between multiple cancer types and single-nucleotide polymorphisms on 5p15.33 and 8q24.21 loci. However, predisposition potential of these genetic variants has not been assessed in GBC. We performed the present study to assess the potential of five polymorphisms on 5p15.33 and one on 8q24.21 locus in GBC risk and treatment response in patients undergoing chemoradiotherapy. We extracted genomic DNA from peripheral blood and genotyped selected SNPs using TaqMan allelic discrimination assays in 523 GBC cases and 274 controls from the north-Indian population. Statistical tests were performed to assess the association of selected common genetic variants with gallbladder cancer susceptibility and prognosis. Binary logistic regression analysis showed significant association of TERT rs2736100C > A [OR(CI) = 0.690(0.515-0.924), p value = 0.013], CLPTM1L rs401681C > T [OR(CI) = 0.586(0.405-0.847), p value = 0.004], and CASC8 rs6983267G > T [OR(CI) = 1.629(1.215-2.186), p value = 0.001] with GBC risk. Further, using multivariate logistic regression, we observed that haplotype CLPTM1L Crs401681Crs31489 TERT Trs2853676Ars2736100 MIR4457 Grs4635969 [OR(CI) = 7.52 (1.79-31.52), p value = 0.0064] is significantly associated with poor treatment response. In survival analysis, Kaplan-Meier survival curves showed significantly poor survival and COX regression suggested significantly higher hazard ratio in TT genotype carriers of CASC8 rs6983267 [OR(CI) = 4.28(1. 07-17.10), p value = 0.040] as compared to major allele and heterozygous (GG+GT) genotypes in metastatic GBC cases. The study revealed that 5p15.33 and 8q24.21 genetic variants significantly influence GBC risk and treatment response in north-Indian population.
Collapse
Affiliation(s)
- Saurabh Yadav
- Department of Surgical Gastroenterology, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS), Lucknow, Uttar Pradesh, 226014, India
| | - Abhijit Chandra
- Department of Surgical Gastroenterology, King George's Medical University, Lucknow, Uttar Pradesh, 226003, India
| | - Ashok Kumar
- Department of Surgical Gastroenterology, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS), Lucknow, Uttar Pradesh, 226014, India
| | - Balraj Mittal
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, 226025, India.
| |
Collapse
|
6
|
Tang J, Hu C, Mei H, Peng L, Li H. CLPTM1L gene rs402710 (C > T) and rs401681 (C > T) polymorphisms associate with decreased cancer risk: a meta-analysis. Oncotarget 2017; 8:102446-102457. [PMID: 29254260 PMCID: PMC5731970 DOI: 10.18632/oncotarget.22268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 09/20/2017] [Indexed: 12/15/2022] Open
Abstract
Cleft lip and palate transmembrane 1-like (CLPTM1L) gene rs402710 (C > T) and rs401681 (C > T) polymorphisms have been widely studied for their potential relation to cancer risk, but studies have produced conflicting results. To systematically evaluate the association between these two polymorphisms and overall cancer risk, we conducted a comprehensive meta-analysis on all relevant articles found in the PubMed and EMBASE databases published prior to May 1, 2017. There were 26 articles with 28 studies, including 30,770 cases and 34,089 controls, for the rs402710 polymorphism and 38 articles with 48 studies, including 67,849 cases and 328,226 controls, for the rs401681 polymorphism. The pooled results indicated that both rs402710 and rs401681 polymorphisms are significantly associated with decreased overall cancer risk. In our stratification analysis, a significant association of the rs402710 polymorphism with lung and bladder cancers was identified among Asian and Caucasian populations in both hospital-based and population-based studies. The rs401681 polymorphism was significantly associated with a decreased risk of lung cancer, bladder cancer, and basal cell carcinoma in Asians and in hospital-based studies. CLPTM1L gene rs402710 and rs401681 polymorphisms thus have a protective association with various types of cancer, especially lung cancer among Asians.
Collapse
Affiliation(s)
- Jianzhou Tang
- Department of Biological and Environmental Engineering, Changsha University, Changsha 410003, Hunan, China
| | - Changming Hu
- Department of Molecular Pathology, Guangzhou Kingmed Center for Clinical Laboratory, Guangzhou 510000, Guangdong, China
| | - Hua Mei
- Department of Somatic Stem Cell, Hunan Guangxiu Hospital, Changsha 410002, Hunan, China
| | - Liang Peng
- Department of Biological and Environmental Engineering, Changsha University, Changsha 410003, Hunan, China
| | - Hui Li
- Department of Microbiology and Immunology, Medical School of Jishou University, Jishou 416000, Hunan, China
| |
Collapse
|
7
|
Lee DH, Heo YR, Park WJ, Lee JH. A TERT-CLPTM1 locus polymorphism (rs401681) is associated with EGFR mutation in non-small cell lung cancer. Pathol Res Pract 2017; 213:1340-1343. [PMID: 29033187 DOI: 10.1016/j.prp.2017.09.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 09/23/2017] [Accepted: 09/29/2017] [Indexed: 02/06/2023]
Abstract
Telomere length is associated with lung carcinogenesis, and recent studies have focused on telomere-maintaining genes and their polymorphisms. Cancer susceptibility of the rs401681 polymorphism, located in the TERT-CLPTM1L locus, has been studied in many cancers. We examined the clinicopathological and prognostic value of rs401681 variants in lung cancer. The relationship between rs401681 variants and telomere length was analyzed in 134 non-small cell lung cancers (NSCLCs). The rs401681 polymorphism had the following genotype frequencies: C/C in 52.2% of the samples, C/T in 30.6%, and T/T in 17.2%. The T allele showed a strong correlation with EGFR mutation (p=0.037). Telomeres in the tumor samples were 3.26-fold longer, on average, than telomeres in matched normal samples (SD=0.48), and there were no differences in telomere length according to rs401681 polymorphism. Smoking was associated with telomere shortening (p=0.01). Survival analysis showed no prognostic value for rs401681 polymorphisms or telomere length in NSCLC. These results suggested that the rs401681 polymorphism contributes to lung carcinogenesis only in patients harboring an EGFR mutation. However, the polymorphism was not associated with survival; therefore, further comprehensive analysis should be performed.
Collapse
Affiliation(s)
- Deok Heon Lee
- Department of Thoracic and Cardiovascular Surgery, Kyungpook National University Hospital, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Yu-Ran Heo
- Department of Anatomy, Keimyung University School of Medicine, Dongsan Medical Center, Daegu, Republic of Korea
| | - Won-Jin Park
- Department of Anatomy, Keimyung University School of Medicine, Dongsan Medical Center, Daegu, Republic of Korea
| | - Jae-Ho Lee
- Department of Anatomy, Keimyung University School of Medicine, Dongsan Medical Center, Daegu, Republic of Korea.
| |
Collapse
|
8
|
Liu C, Cui H, Gu D, Zhang M, Fang Y, Chen S, Tang M, Zhang B, Chen H. Genetic polymorphisms and lung cancer risk: Evidence from meta-analyses and genome-wide association studies. Lung Cancer 2017; 113:18-29. [PMID: 29110844 DOI: 10.1016/j.lungcan.2017.08.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/18/2017] [Accepted: 08/25/2017] [Indexed: 01/30/2023]
Abstract
A growing number of studies investigating the association between Single Nucleotide Polymorphisms (SNPs) and lung cancer risk have been published since over a decade ago. An updated integrative assessment on the credibility and strength of the associations is required. We searched PubMed, Medline, and Web of Science on or before August 29th, 2016. A total of 198 articles were deemed eligible for inclusion, which addressed the associations between 108 variants and lung cancer. Among the 108 variants, 63 were reported to be significantly associated with lung cancer while the remaining 45 were reported non-significant. Further evaluation integrating the Venice Criteria and false-positive report probability (FPRP) was performed to determine the strength of cumulative epidemiological evidence for the 63 significant associations. As a result, 15 SNPs on or near 12 genes and one miRNA with strong evidence of association with lung cancer risk were identified, including TERT (rs2736098), CHRNA3 (rs1051730), AGPHD1 (rs8034191), CLPTM1L (rs401681 and rs402710), BAT3 (rs3117582), TRNAA (rs4324798), ERCC2 (Lys751Gln), miR-146a2 (rs2910164), CYP1B1 (Arg48Gly), GSTM1 (null/present), SOD2 (C47T), IL-10 (-592C/A and -819C/T), and TP53 (intron 6). 19 SNPs were given moderate rating and 17 SNPs were rated as having weak evidence. In addition, all of the 29 SNPs identified in 12 genome-wide association studies (GWAS) were proved to be noteworthy based on FPRP value. This review summarizes and evaluates the cumulative evidence of genetic polymorphisms and lung cancer risk, which can serve as a general and useful reference for further genetic studies.
Collapse
Affiliation(s)
- Caiyang Liu
- Department of Cardiothoracic Surgery, First Affiliated Hospital of Chongqing Medical University, No.1, Youyi Road, Yuzhong District, Chongqing 400010, China
| | - Huijie Cui
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Dongqing Gu
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Min Zhang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Yanfei Fang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Siyu Chen
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Mingshuang Tang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Ben Zhang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Huanwen Chen
- Department of Cardiothoracic Surgery, First Affiliated Hospital of Chongqing Medical University, No.1, Youyi Road, Yuzhong District, Chongqing 400010, China.
| |
Collapse
|
9
|
Genetic susceptibility variants for lung cancer: replication study and assessment as expression quantitative trait loci. Sci Rep 2017; 7:42185. [PMID: 28181565 PMCID: PMC5299838 DOI: 10.1038/srep42185] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/06/2017] [Indexed: 12/13/2022] Open
Abstract
Many single nucleotide polymorphisms (SNPs) have been associated with lung cancer but lack confirmation and functional characterization. We retested the association of 56 candidate SNPs with lung adenocarcinoma risk and overall survival in a cohort of 823 Italian patients and 779 healthy controls, and assessed their function as expression quantitative trait loci (eQTLs). In the replication study, eight SNPs (rs401681, rs3019885, rs732765, rs2568494, rs16969968, rs6495309, rs11634351, and rs4105144) associated with lung adenocarcinoma risk and three (rs9557635, rs4105144, and rs735482) associated with survival. Five of these SNPs acted as cis-eQTLs, being associated with the transcription of IREB2 (rs2568494, rs16969968, rs11634351, rs6495309), PSMA4 (rs6495309) and ERCC1 (rs735482), out of 10,821 genes analyzed in lung. For these three genes, we obtained experimental evidence of differential allelic expression in lung tissue, pointing to the existence of in-cis genomic variants that regulate their transcription. These results suggest that these SNPs exert their effects on cancer risk/outcome through the modulation of mRNA levels of their target genes.
Collapse
|
10
|
Carkic J, Nikolic N, Radojevic-Skodric S, Kuzmanovic-Pficer J, Brajovic G, Antunovic M, Milasin J, Popovic B. The role of TERT-CLPTM1L SNPs, hTERT expression and telomere length in the pathogenesis of oral squamous cell carcinoma. J Oral Sci 2016; 58:449-458. [DOI: 10.2334/josnusd.16-0108] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Jelena Carkic
- Institute of Human Genetics, School of Dental Medicine, University of Belgrade
| | - Nadja Nikolic
- Institute of Human Genetics, School of Dental Medicine, University of Belgrade
| | | | - Jovana Kuzmanovic-Pficer
- Department for Medical Statistics and Informatics, School of Dental Medicine, University of Belgrade
| | - Gavrilo Brajovic
- Department of Physiology, School of Dental Medicine, University of Belgrade
| | - Marija Antunovic
- Clinic of Oral Surgery, School of Medicine, University of Montenegro
| | - Jelena Milasin
- Institute of Human Genetics, School of Dental Medicine, University of Belgrade
| | - Branka Popovic
- Institute of Human Genetics, School of Dental Medicine, University of Belgrade
| |
Collapse
|
11
|
Wei R, DeVilbiss FT, Liu W. Genetic Polymorphism, Telomere Biology and Non-Small Lung Cancer Risk. J Genet Genomics 2015; 42:549-561. [PMID: 26554909 DOI: 10.1016/j.jgg.2015.08.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 08/03/2015] [Accepted: 08/10/2015] [Indexed: 02/06/2023]
Abstract
Recent genome-wide association studies (GWAS) have identified a number of chromosomal regions associated with the risk of lung cancer. Of these regions, single-nucleotide polymorphisms (SNPs), especially rs2736100 located in the telomerase reverse transcriptase (TERT) gene show unique and significant association with non-small cell lung cancer (NSCLC) in a few subpopulations including women, nonsmokers, East Asians and those with adenocarcinoma. Recent studies have also linked rs2736100 with a longer telomere length and lung cancer risk. In this review, we seek to summarize the relationship between these factors and to further link the underlying telomere biology to lung cancer etiology. We conclude that genetic alleles combined with environmental (e.g., less-smoking) and physiological factors (gender and age) that confer longer telomere length are strong risk factors for NSCLC. This linkage may be particularly relevant in lung adenocarcinoma driven by epidermal growth factor receptor (EGFR) mutations, as these mutations have also been strongly linked to female gender, less-smoking history, adenocarcinoma histology and East Asian ethnicity. By establishing this connection, a strong argument is made for further investigating of the involvement of these entities during the tumorigenesis of NSCLC.
Collapse
Affiliation(s)
- Rongrong Wei
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, USA
| | - Frank T DeVilbiss
- School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Wanqing Liu
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, USA.
| |
Collapse
|
12
|
Wang J, Zhang B, Yang Z, Zhou L, Geng T, Li H, Fu X, Xue X, Liu M, Tong R, Jin T, Zhang Y. Association of gastrointestinal gland cancer susceptibility loci with esophageal carcinoma among the Chinese Han population: a case-control study. Tumour Biol 2015; 37:1627-33. [PMID: 26304507 DOI: 10.1007/s13277-015-3945-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 08/17/2015] [Indexed: 12/20/2022] Open
Abstract
Esophageal carcinoma (EC) is a common malignancy worldwide. Previous studies indicated that gastrointestinal gland cancer and EC share some susceptibility loci. Our aim was to identify new single nucleotide polymorphisms (SNPs) associated with EC by investigating whether known gastrointestinal cancers susceptibility loci are found in EC patients. A Chinese Han population case-control study was conducted to assess SNP associations with EC risk. Twenty-six SNPs were selected from gastrointestinal cancer susceptibility loci, and 360 EC patients and 310 controls were genotyped for these SNPs using Sequenom MassARRAY technology. The association of SNP frequencies with EC was analyzed by chi-square tests, and genetic model analysis. After Hardy-Weinberg equilibrium (HWE) p value screening, we excluded two SNPs. Based on chi-square tests, the minor alleles of rs13294589 (p = 0.046) and rs4924935 (p = 0.046) were correlated with reduced EC risk and rs4269383 (p = 0.010) and rs10953615 (p = 0.036) were correlated with increased EC risk. In the genetic model analyses, we found that the minor alleles "T" of rs401681, "A" of rs10088262, and "C" of rs4924935 may reduce the risk of EC. rs401681 has previously been reported to be associated with EC. To the best of our knowledge, we are the first to report an association of the other five SNPs with EC. Our findings provide evidence for the genetic variants associated with susceptibility to EC in the Chinese Han population, which might be used as potential molecular markers for detecting susceptibility to EC in Chinese Han people.
Collapse
Affiliation(s)
- Junqi Wang
- Department of Chest Surgery, Baoji Central Hospital, Baoji, 721000, China
| | - Baoping Zhang
- Department of Chest Surgery, Baoji Central Hospital, Baoji, 721000, China
| | - Zhi Yang
- Department of Chest Surgery, Baoji Central Hospital, Baoji, 721000, China
| | - Long Zhou
- National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Tingting Geng
- National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi'an, 710069, China.,School of Medicine, Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Haipeng Li
- Department of Chest Surgery, Baoji Central Hospital, Baoji, 721000, China
| | - Xiaowei Fu
- Department of Chest Surgery, Baoji Central Hospital, Baoji, 721000, China
| | - Xiaolei Xue
- Department of Chest Surgery, Baoji Central Hospital, Baoji, 721000, China
| | - Mingwei Liu
- Department of Chest Surgery, Baoji Central Hospital, Baoji, 721000, China
| | - Ruifeng Tong
- Department of Chest Surgery, Baoji Central Hospital, Baoji, 721000, China
| | - Tianbo Jin
- National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi'an, 710069, China. .,, Mailbox 386, #229 North Taibai Road, Xi'an, 710069, Shaanxi, China.
| | - Yong Zhang
- School of Medicine, Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China. .,Department of Chest Surgery, First Affiliated Hospital of the Medical College, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
| |
Collapse
|
13
|
Abstract
The knowledge of molecular mechanism that underlies the genetic predisposition to lung cancer is yet limited. Results from previous studies addressing the association of AGPHD1 variant rs8034191 with lung carcinogenesis remain inconclusive. Herein, we combined these data and re-examined the association. We performed a meta-analysis of Asian studies identified through various ways. Using the data collected from each eligible study, we combined the effect estimates (ORs and its 95 % CIs) with the fixed effects model (Mantel-Haenszel method). Statistical analyses were done using STATA software. Data from nine studies (29,290 subjects) carried out in Asian populations were analyzed in this work. There was no overall association between variant rs8034191 and lung cancer risk under the allele frequency model (OR = 1.03, 95 % CI = 0.93-1.13, P heterogeneity = 0.522). We observed the same associations under other genetic models and in the subgroup analyses by ethnicity and smoking status. Our results indicate that variant rs8034191 in the AGPHD1 gene may not modify the genetic risk of lung cancer in Asian populations.
Collapse
Affiliation(s)
- Hong Wang
- Department of Lung Cancer, Affiliated Hospital of Academy of Military Medical Sciences (307 Hospital of PLA), No. 8 DongDa Road, FengTai Area, Beijing, People's Republic of China,
| | | |
Collapse
|
14
|
Zhou L, Xie J, Gu EL, Huang Y, Qu Y, Xu AP, Zhu Y, Wang H. Common genetic variant on BMP4 contributes to colorectal adenoma and cancer: A meta-analysis based on 15 studies. Cytokine 2015; 72:154-9. [PMID: 25647270 DOI: 10.1016/j.cyto.2014.12.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 12/05/2014] [Accepted: 12/25/2014] [Indexed: 12/21/2022]
Abstract
Epidemiological studies indicate a genetic contribution to colorectal cancer (CRC), but specific genetic variants remain unknown. Genome-wide association studies have identified rs4444235 at BMP4 as a new colorectal cancer (CRC) and colorectal adenoma (CRA) susceptibility locus in populations of European descent. After that, several validation studies have been conducted among various ethnic populations to investigate if the SNP was associated with CRC/CRA, but the results have been inconsistent. To investigate this inconsistency and derive a more precise estimation of the relationship, a meta-analysis involving 54,631 CRC cases, 3995 CRA cases and 88,098 controls from 15 studies was performed. Potential sources of heterogeneity including ethnicity, sample size, study design and endpoint were also assessed. Overall, the summary OR of CRC was 1.06 (95% CI: 1.04-1.08, P<10(-5)). In the subgroup analysis by ethnicity, significantly increased risks were found in East Asians (OR=1.07, 95% CI: 1.01-1.12, P=0.01) and Caucasians (OR=1.07, 95% CI: 1.05-1.10, P<10(-5)); while no significant associations were found among African Americans and other ethnic populations in all genetic models. In addition, significant associations were also detected for CRA with per-allele OR of 1.09 (95% CI: 1.03-1.14, P=0.001). Our findings demonstrated that BMP4-rs4444235 is a risk factor associated with increased CRC and CRA susceptibility, but these associations vary in different ethnic populations.
Collapse
Affiliation(s)
- Lei Zhou
- Department of Gastroenterology, Jing'an District Centre Hospital of Shanghai (Huashan Hospital Fudan University Jing'an Branch), 200040, PR China
| | - Jun Xie
- Department of Gastroenterology, Jing'an District Centre Hospital of Shanghai (Huashan Hospital Fudan University Jing'an Branch), 200040, PR China
| | - Er-li Gu
- Department of Gastroenterology, Jing'an District Centre Hospital of Shanghai (Huashan Hospital Fudan University Jing'an Branch), 200040, PR China
| | - Yao Huang
- Department of Gastroenterology, Jing'an District Centre Hospital of Shanghai (Huashan Hospital Fudan University Jing'an Branch), 200040, PR China
| | - Yan Qu
- Department of Gastroenterology, Jing'an District Centre Hospital of Shanghai (Huashan Hospital Fudan University Jing'an Branch), 200040, PR China
| | - Ai-Ping Xu
- Department of Gastroenterology, Jing'an District Centre Hospital of Shanghai (Huashan Hospital Fudan University Jing'an Branch), 200040, PR China
| | - Yin Zhu
- Department of Gastroenterology, Jing'an District Centre Hospital of Shanghai (Huashan Hospital Fudan University Jing'an Branch), 200040, PR China
| | - Hong Wang
- Department of Gastroenterology, Jing'an District Centre Hospital of Shanghai (Huashan Hospital Fudan University Jing'an Branch), 200040, PR China.
| |
Collapse
|
15
|
Common genetic variants (rs4779584 and rs10318) at 15q13.3 contributes to colorectal adenoma and colorectal cancer susceptibility: evidence based on 22 studies. Mol Genet Genomics 2014; 290:901-12. [PMID: 25475391 DOI: 10.1007/s00438-014-0970-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 11/25/2014] [Indexed: 01/20/2023]
Abstract
Several genome-wide association studies on colorectal cancer (CRC) have reported similar findings of a new susceptibility locus, 15q13.3. After that, a number of studies have reported that the rs4779584 and rs10318 polymorphisms at chromosome 15q13.3 have been implicated in CRC and colorectal adenoma (CRA) risk; however, these studies have yielded inconsistent results. To investigate this inconsistency, we performed a meta-analysis of 22 studies involving a total of 48,468 CRC cases, 4,189 CRA cases, and 85,105 controls for the two polymorphisms to evaluate its effect on genetic susceptibility for CRC/CRA. Potential sources of heterogeneity and publication bias were also systematically explored. Overall, the summary odds ratio (OR) of rs4779584-T variant for CRC was 1.13 (95 % CI 1.09-1.16, P < 10(-5)) and 1.15 (95 % CI 1.04-1.28, P = 0.006) for CRA. After stratified by ethnicity, significantly increased CRC risks were found for rs4779584 polymorphism among East Asians and Caucasians, while no significant associations were detected among African American and other ethnic populations. A meta-analysis of studies on the rs10318 polymorphism also showed significant overall association with CRC, yielding a per-allele OR of 1.13 (95 % CI 1.02-1.24, P = 0.02). In the subgroup analysis by ethnicity, significantly increased CRC risks were found in Caucasians; whereas no significant associations were found among East Asians and African Americans. This meta-analysis demonstrated that the rs4779584 and rs10318 polymorphism at 15q13.3 is a risk factor associated with increased CRC/CRA susceptibility, but these associations vary in different ethnic populations.
Collapse
|
16
|
Quantitative assessment of the influence of common variation rs16892766 at 8q23.3 with colorectal adenoma and cancer susceptibility. Mol Genet Genomics 2014; 290:461-9. [DOI: 10.1007/s00438-014-0928-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 09/19/2014] [Indexed: 01/04/2023]
|
17
|
Bielecka ZF, Czarnecka AM, Szczylik C. Genomic Analysis as the First Step toward Personalized Treatment in Renal Cell Carcinoma. Front Oncol 2014; 4:194. [PMID: 25120953 PMCID: PMC4110478 DOI: 10.3389/fonc.2014.00194] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 07/09/2014] [Indexed: 12/13/2022] Open
Abstract
Drug resistance mechanisms in renal cell carcinoma (RCC) still remain elusive. Although most patients initially respond to targeted therapy, acquired resistance can still develop eventually. Most of the patients suffer from intrinsic (genetic) resistance as well, suggesting that there is substantial need to broaden our knowledge in the field of RCC genetics. As molecular abnormalities occur for various reasons, ranging from single nucleotide polymorphisms to large chromosomal defects, conducting whole-genome association studies using high-throughput techniques seems inevitable. In principle, data obtained via genome-wide research should be continued and performed on a large scale for the purposes of drug development and identification of biological pathways underlying cancerogenesis. Genetic alterations are mostly unique for each histological RCC subtype. According to recently published data, RCC is a highly heterogeneous tumor. In this paper, the authors discuss the following: (1) current state-of-the-art knowledge on the potential biomarkers of RCC subtypes; (2) significant obstacles encountered in the translational research on RCC; and (3) recent molecular findings that may have a crucial impact on future therapeutic approaches.
Collapse
Affiliation(s)
- Zofia Felicja Bielecka
- Department of Oncology with the Laboratory of Molecular Oncology, Military Institute of Medicine , Warsaw , Poland ; Postgraduate School of Molecular Medicine, Medical University of Warsaw , Warsaw , Poland
| | - Anna Małgorzata Czarnecka
- Department of Oncology with the Laboratory of Molecular Oncology, Military Institute of Medicine , Warsaw , Poland
| | - Cezary Szczylik
- Department of Oncology with the Laboratory of Molecular Oncology, Military Institute of Medicine , Warsaw , Poland
| |
Collapse
|