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Clayton EA, Khalid S, Ban D, Wang L, Jordan IK, McDonald JF. Tumor suppressor genes and allele-specific expression: mechanisms and significance. Oncotarget 2020; 11:462-479. [PMID: 32064050 PMCID: PMC6996918 DOI: 10.18632/oncotarget.27468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/13/2020] [Indexed: 12/12/2022] Open
Abstract
Recent findings indicate that allele-specific expression (ASE) at specific cancer driver gene loci may be of importance in onset/progression of the disease. Of particular interest are loss-of-function (LOF) of tumor suppressor gene (TSGs) alleles. While LOF tumor suppressor mutations are typically considered to be recessive, if these mutant alleles can be significantly differentially expressed relative to wild-type alleles in heterozygotes, the clinical consequences could be significant. LOF TSG alleles are shown to be segregating at high frequencies in world-wide populations of normal/healthy individuals. Matched sets of normal and tumor tissues isolated from 233 cancer patients representing four diverse tumor types demonstrate functionally important changes in patterns of ASE in individuals heterozygous for LOF TSG alleles associated with cancer onset/progression. While a variety of molecular mechanisms were identified as potentially contributing to changes in ASE patterns in cancer, changes in DNA copy number and allele-specific alternative splicing possibly mediated by antisense RNA emerged as predominant factors. In conclusion, LOF TSGs are segregating in human populations at significant frequencies indicating that many otherwise healthy individuals are at elevated risk of developing cancer. Changes in ASE between normal and cancer tissues indicates that LOF TSG alleles may contribute to cancer onset/progression even when heterozygous with wild-type functional alleles.
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Affiliation(s)
- Evan A. Clayton
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shareef Khalid
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Dongjo Ban
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Lu Wang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- PanAmerican Bioinformatics Institute, Cali, Colombia
| | - I. King Jordan
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- PanAmerican Bioinformatics Institute, Cali, Colombia
- Applied Bioinformatics Laboratory, Atlanta, GA, USA
| | - John F. McDonald
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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Cheng B, Zhang H, Liu C, Chen X, Chen Y, Sun Y, Leng L, Li Y, Luan P, Li H. Functional Intronic Variant in the Retinoblastoma 1 Gene Underlies Broiler Chicken Adiposity by Altering Nuclear Factor-kB and SRY-Related HMG Box Protein 2 Binding Sites. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:9727-9737. [PMID: 31398034 DOI: 10.1021/acs.jafc.9b01719] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The present study aimed to search for chicken abdominal fat deposition-related polymorphisms within RB1 and to provide functional evidence for significantly associated genetic variants. Association analyses showed that 11 single nucleotide polymorphisms (SNPs) in intron 17 of RB1, were significantly associated with both abdominal fat weight (P < 0.05) and abdominal fat percentage (P < 0.05). Functional analysis revealed that the A allele of g.32828A>G repressed the transcriptional efficiency of RB1 in vitro, through binding nuclear factor-kappa B (NF-KB) and SRY-related HMG box protein 2 (SOX2). Furthermore, RB1 mRNA expression levels in the abdominal fat tissue of individuals with the A/A genotype of g.32828A>G were lower than those of individuals with the G/G genotype. Collectively, we propose that the intronic SNP g.32828A>G of RB1 is an obesity-associated variant that directly affects binding with NF-KB and SOX2, leading to changes in RB1 expression which in turn may influence chicken abdominal fat deposition.
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Affiliation(s)
- Bohan Cheng
- Key Laboratory of Chicken Genetics and Breeding , Ministry of Agriculture and Rural Affairs , Harbin 150030 , Heilongjiang , China
- Key Laboratory of Animal Genetics, Breeding and Reproduction , Education Department of Heilongjiang Province , Harbin 150030 , Heilongjiang , China
- College of Animal Science and Technology , Northeast Agricultural University , Harbin 150030 , Heilongjiang , China
| | - Hui Zhang
- Key Laboratory of Chicken Genetics and Breeding , Ministry of Agriculture and Rural Affairs , Harbin 150030 , Heilongjiang , China
- Key Laboratory of Animal Genetics, Breeding and Reproduction , Education Department of Heilongjiang Province , Harbin 150030 , Heilongjiang , China
- College of Animal Science and Technology , Northeast Agricultural University , Harbin 150030 , Heilongjiang , China
| | - Chang Liu
- Key Laboratory of Chicken Genetics and Breeding , Ministry of Agriculture and Rural Affairs , Harbin 150030 , Heilongjiang , China
- Key Laboratory of Animal Genetics, Breeding and Reproduction , Education Department of Heilongjiang Province , Harbin 150030 , Heilongjiang , China
- College of Animal Science and Technology , Northeast Agricultural University , Harbin 150030 , Heilongjiang , China
| | - Xi Chen
- Key Laboratory of Chicken Genetics and Breeding , Ministry of Agriculture and Rural Affairs , Harbin 150030 , Heilongjiang , China
- Key Laboratory of Animal Genetics, Breeding and Reproduction , Education Department of Heilongjiang Province , Harbin 150030 , Heilongjiang , China
- College of Animal Science and Technology , Northeast Agricultural University , Harbin 150030 , Heilongjiang , China
| | - Yaofeng Chen
- Key Laboratory of Chicken Genetics and Breeding , Ministry of Agriculture and Rural Affairs , Harbin 150030 , Heilongjiang , China
- Key Laboratory of Animal Genetics, Breeding and Reproduction , Education Department of Heilongjiang Province , Harbin 150030 , Heilongjiang , China
- College of Animal Science and Technology , Northeast Agricultural University , Harbin 150030 , Heilongjiang , China
| | - Yuhang Sun
- Key Laboratory of Chicken Genetics and Breeding , Ministry of Agriculture and Rural Affairs , Harbin 150030 , Heilongjiang , China
- Key Laboratory of Animal Genetics, Breeding and Reproduction , Education Department of Heilongjiang Province , Harbin 150030 , Heilongjiang , China
- College of Animal Science and Technology , Northeast Agricultural University , Harbin 150030 , Heilongjiang , China
| | - Li Leng
- Key Laboratory of Chicken Genetics and Breeding , Ministry of Agriculture and Rural Affairs , Harbin 150030 , Heilongjiang , China
- Key Laboratory of Animal Genetics, Breeding and Reproduction , Education Department of Heilongjiang Province , Harbin 150030 , Heilongjiang , China
- College of Animal Science and Technology , Northeast Agricultural University , Harbin 150030 , Heilongjiang , China
| | - Yumao Li
- Key Laboratory of Chicken Genetics and Breeding , Ministry of Agriculture and Rural Affairs , Harbin 150030 , Heilongjiang , China
- Key Laboratory of Animal Genetics, Breeding and Reproduction , Education Department of Heilongjiang Province , Harbin 150030 , Heilongjiang , China
- College of Animal Science and Technology , Northeast Agricultural University , Harbin 150030 , Heilongjiang , China
| | - Peng Luan
- Key Laboratory of Chicken Genetics and Breeding , Ministry of Agriculture and Rural Affairs , Harbin 150030 , Heilongjiang , China
- Key Laboratory of Animal Genetics, Breeding and Reproduction , Education Department of Heilongjiang Province , Harbin 150030 , Heilongjiang , China
- College of Animal Science and Technology , Northeast Agricultural University , Harbin 150030 , Heilongjiang , China
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding , Ministry of Agriculture and Rural Affairs , Harbin 150030 , Heilongjiang , China
- Key Laboratory of Animal Genetics, Breeding and Reproduction , Education Department of Heilongjiang Province , Harbin 150030 , Heilongjiang , China
- College of Animal Science and Technology , Northeast Agricultural University , Harbin 150030 , Heilongjiang , China
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Tsakogiannis D, Moschonas GD, Daskou M, Stylianidou Z, Kyriakopoulou Z, Kottaridi C, Dimitriou TG, Gartzonika C, Markoulatos P. Polymorphic variability in the exon 19 of the RB1 gene and its flanking intronic sequences in HPV16-associated precancerous lesions in the Greek population. J Med Microbiol 2018; 67:1638-1644. [PMID: 30303478 DOI: 10.1099/jmm.0.000843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
PURPOSE The tumour suppressor protein RB plays a decisive role in negative control of the cell cycle, inhibiting tumour development. The present analysis investigated the prevalence of the nucleotide polymorphism A153104G, which is located at intron 18 of the RB1 gene, and investigated the impact of the polymorphic variability in the exon 19 and its flanking intronic sequences on the severity of cervical disease in HPV16-positive Greek women. METHODOLOGY The nucleotide polymorphism A153104G was detected by PCR-RFLP assay, while the amplicons were further subjected to cloning and sequencing. Moreover, molecular evolutionary analysis was performed using the maximum-likelihood (ML) and empirical Bayesian (EB) methods in order to evaluate the selective pressure acting on exon 19 of the RB1 gene.Results/Key findings. The A153104G nucleotide polymorphism was only detected in one control case. Moreover, sequence analysis of the amplicons revealed that the polymorphic variability in the RB1 gene increased with the severity of the cervical dysplasia. The link between the observed polymorphic variability and the progress of cervical disease was reflected in the molecular evolutionary analysis that was performed on the exon 19 of the RB1 gene, since negative selective pressure was acting upon exon 19 in the control and low-grade squamous intraepithelial lesion (LSIL) cervical samples, while positive selective pressure was acting upon exon 19 in the high-grade squamous intraepithelial lesion (HSIL) specimens. CONCLUSIONS The A153104G nucleotide polymorphism did not emerge as a potential biomarker for the development of precancerous lesions in the Greek patients, while the accumulation of sequence variations in RB1 gene might influence patients' susceptibility towards the progression of cervical neoplasia.
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Affiliation(s)
- D Tsakogiannis
- 1Microbiology-Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - G D Moschonas
- 1Microbiology-Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - M Daskou
- 1Microbiology-Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Z Stylianidou
- 1Microbiology-Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Z Kyriakopoulou
- 1Microbiology-Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - C Kottaridi
- 2Department of Cytopathology, National and Kapodistrian University of Athens, Medical School, 'ATTIKON' University Hospital, 1 Rimini, Haidari, 12462, Athens, Greece
| | - T G Dimitriou
- 1Microbiology-Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - C Gartzonika
- 3Department of Microbiology, University of Ioannina, Medical School, Ioannina, Greece
| | - P Markoulatos
- 1Microbiology-Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Biopolis, 41500 Larissa, Greece
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4
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Combination of genetic variants in cyclin D1 and retinoblastoma genes predict clinical outcome in oral cancer patients. Tumour Biol 2015; 37:3609-17. [DOI: 10.1007/s13277-015-4179-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/01/2015] [Indexed: 12/30/2022] Open
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5
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Association analysis of p16 (CDKN2A) and RB1 polymorphisms with susceptibility to cervical cancer in Indian population. Mol Biol Rep 2011; 39:407-14. [DOI: 10.1007/s11033-011-0752-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 04/27/2011] [Indexed: 10/18/2022]
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Henley SA, Francis SM, Demone J, Ainsworth P, Dick FA. A cancer derived mutation in the retinoblastoma gene with a distinct defect for LXCXE dependent interactions. Cancer Cell Int 2010; 10:8. [PMID: 20298605 PMCID: PMC2859746 DOI: 10.1186/1475-2867-10-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Accepted: 03/18/2010] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The interaction between viral oncoproteins such as Simian virus 40 TAg, adenovirus E1A, and human papilloma virus E7, and the retinoblastoma protein (pRB) occurs through a well characterized peptide sequence, LXCXE, on the viral protein and a well conserved groove in the pocket domain of pRB. Cellular proteins, such as histone deacetylases, also use this mechanism to interact with the retinoblastoma protein to repress transcription at cell cycle regulated genes. For these reasons this region of the pRB pocket domain is thought to play a critical role in growth suppression. RESULTS In this study, we identify and characterize a tumor derived allele of the retinoblastoma gene (RB1) that possesses a discrete defect in its ability to interact with LXCXE motif containing proteins that compromises proliferative control. To assess the frequency of similar mutations in the RB1 gene in human cancer, we screened blood and tumor samples for similar alleles. We screened almost 700 samples and did not detect additional mutations, indicating that this class of mutation is rare. CONCLUSIONS Our work provides proof of principal that alleles encoding distinct, partial loss of function mutations in the retinoblastoma gene that specifically lose LXCXE dependent interactions, are found in human cancer.
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Ramus SJ, Vierkant RA, Johnatty SE, Pike MC, Van Den Berg DJ, Wu AH, Pearce CL, Menon U, Gentry-Maharaj A, Gayther SA, DiCioccio RA, McGuire V, Whittemore AS, Song H, Easton DF, Pharoah PDP, Garcia-Closas M, Chanock S, Lissowska J, Brinton L, Terry KL, Cramer DW, Tworoger SS, Hankinson SE, Berchuck A, Moorman PG, Schildkraut JM, Cunningham JM, Liebow M, Kjaer SK, Hogdall E, Hogdall C, Blaakaer J, Ness RB, Moysich KB, Edwards RP, Carney ME, Lurie G, Goodman MT, Wang-Gohrke S, Kropp S, Chang-Claude J, Webb PM, Chen X, Beesley J, Chenevix-Trench G, Goode EL. Consortium analysis of 7 candidate SNPs for ovarian cancer. Int J Cancer 2008; 123:380-388. [PMID: 18431743 DOI: 10.1002/ijc.23448] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The Ovarian Cancer Association Consortium selected 7 candidate single nucleotide polymorphisms (SNPs), for which there is evidence from previous studies of an association with variation in ovarian cancer or breast cancer risks. The SNPs selected for analysis were F31I (rs2273535) in AURKA, N372H (rs144848) in BRCA2, rs2854344 in intron 17 of RB1, rs2811712 5' flanking CDKN2A, rs523349 in the 3' UTR of SRD5A2, D302H (rs1045485) in CASP8 and L10P (rs1982073) in TGFB1. Fourteen studies genotyped 4,624 invasive epithelial ovarian cancer cases and 8,113 controls of white non-Hispanic origin. A marginally significant association was found for RB1 when all studies were included [ordinal odds ratio (OR) 0.88 (95% confidence interval (CI) 0.79-1.00) p = 0.041 and dominant OR 0.87 (95% CI 0.76-0.98) p = 0.025]; when the studies that originally suggested an association were excluded, the result was suggestive although no longer statistically significant (ordinal OR 0.92, 95% CI 0.79-1.06). This SNP has also been shown to have an association with decreased risk in breast cancer. There was a suggestion of an association for AURKA, when one study that caused significant study heterogeneity was excluded [ordinal OR 1.10 (95% CI 1.01-1.20) p = 0.027; dominant OR 1.12 (95% CI 1.01-1.24) p = 0.03]. The other 5 SNPs in BRCA2, CDKN2A, SRD5A2, CASP8 and TGFB1 showed no association with ovarian cancer risk; given the large sample size, these results can also be considered to be informative. These null results for SNPs identified from relatively large initial studies shows the importance of replicating associations by a consortium approach.
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Affiliation(s)
- Susan J Ramus
- Translational Research Laboratory, University College London EGA Institute for Women's Health, London, United Kingdom
| | | | - Sharon E Johnatty
- The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | - Malcolm C Pike
- University of Southern California, Keck School of Medicine, Los Angeles, CA
| | | | - Anna H Wu
- University of Southern California, Keck School of Medicine, Los Angeles, CA
| | | | - Usha Menon
- Gynaecological Cancer Research Centre, University College London, EGA Institute for Women's Health, London, United Kingdom
| | - Aleksandra Gentry-Maharaj
- Gynaecological Cancer Research Centre, University College London, EGA Institute for Women's Health, London, United Kingdom
| | - Simon A Gayther
- Translational Research Laboratory, University College London EGA Institute for Women's Health, London, United Kingdom
| | | | | | | | - Honglin Song
- Cancer Research United Kingdom Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Douglas F Easton
- Cancer Research United Kingdom Genetic Epidemiology Unit, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Paul D P Pharoah
- Cancer Research United Kingdom Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | | | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, Cancer Center and M. Sklodowska-Curie Institute of Oncology, Warsaw, Poland
| | - Louise Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Kathryn L Terry
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital, Boston, MA
| | - Daniel W Cramer
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital, Boston, MA
| | - Shelley S Tworoger
- Channing Laboratory, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Susan E Hankinson
- Channing Laboratory, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC
| | - Patricia G Moorman
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC
| | - Joellen M Schildkraut
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC
| | | | - Mark Liebow
- College of Medicine, Mayo Clinic, Rochester, MN
| | | | | | - Claus Hogdall
- Rigshospitalet, The Juliane Marie Centre, University of Copenhagen, Copenhagen, Denmark
| | | | - Roberta B Ness
- Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | | | | | | | - Galina Lurie
- Cancer Research Center, University of Hawaii, Honolulu, Hawaii
| | - Marc T Goodman
- Cancer Research Center, University of Hawaii, Honolulu, Hawaii
| | | | - Silke Kropp
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Penelope M Webb
- The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | - Xiaoqing Chen
- The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | - Jonathan Beesley
- The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | - Georgia Chenevix-Trench
- The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
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Driver KE, Song H, Lesueur F, Ahmed S, Barbosa-Morais NL, Tyrer JP, Ponder BAJ, Easton DF, Pharoah PDP, Dunning AM. Association of single-nucleotide polymorphisms in the cell cycle genes with breast cancer in the British population. Carcinogenesis 2008; 29:333-41. [PMID: 18174243 DOI: 10.1093/carcin/bgm284] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Using a large-scale case-control study, we examined whether common single-nucleotide polymorphisms (SNPs) within 13 genes involved in the cell cycle pathway are associated with breast cancer risk. Seventy-nine tag SNPs were used to evaluate 240 common SNPs found in the genes: CCND1, CCND2, CCND3, CCNE1, CDK2, CDK4, CDK6, CDKN1A, CDKNIB, CDKN2A/CDKN2B, CDKN2C and CDKN2D. These were genotyped in 2270 cases and 2280 controls from the Studies in Epidemiology and Risks of Cancer Heredity (SEARCH) study. Tag SNPs showing evidence of statistically significant differences between cases and controls (P < 0.1) were genotyped in a further 2200 cases and 2280 controls from the same population. This approach found evidence for breast cancer-associated SNPs in four of the cell cycle genes: the cyclin CCNE1 rs997669 had an odds ratio (OR) (GG/AA) of 1.18 [95% confidence interval (95% CI) 1.04-1.34] P = 0.003 and the cyclin-dependent kinase inhibitors-CDKN1A rs3176336: OR (TT/AA) = 1.25 (95% CI 1.11-1.42) P = 0.0026; CDKN1B rs34330: OR (TT/CC) = 1.22 (95% CI 1.02-1.47) P = 0.013 and the region of CDKN2A/2B rs3731239: OR (CC/TT) = 0.90 (95% CI 0.79-1.03) P = 0.013 and rs3218005 OR (GG/AA) = 1.55 (95% CI 1.02-2.37) P = 0.013 (P-values unadjusted for multiple testing). We were able to exclude the D-type cyclins, cyclin-dependent kinases, CDKN2C and CDKN2D from having any significantly associated risk with breast cancer in our study population. The combined effects of the cell cycle genes considered here provide evidence for a significant association with breast cancer risk in a global test (P-heterogeneity = 0.010, P-trend = 0.048). Further large-scale studies are needed to confirm these results.
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Affiliation(s)
- Kristy E Driver
- Cancer Research UK Department of Oncology, Strangeways Research Laboratory, University of Cambridge, Cambridge CB1 8RN, UK
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9
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Pharoah PDP, Tyrer J, Dunning AM, Easton DF, Ponder BAJ. Association between common variation in 120 candidate genes and breast cancer risk. PLoS Genet 2007; 3:e42. [PMID: 17367212 PMCID: PMC1828694 DOI: 10.1371/journal.pgen.0030042] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2006] [Accepted: 02/02/2007] [Indexed: 01/20/2023] Open
Abstract
Association studies in candidate genes have been widely used to search for common low penetrance susceptibility alleles, but few definite associations have been established. We have conducted association studies in breast cancer using an empirical single nucleotide polymorphism (SNP) tagging approach to capture common genetic variation in genes that are candidates for breast cancer based on their known function. We genotyped 710 SNPs in 120 candidate genes in up to 4,400 breast cancer cases and 4,400 controls using a staged design. Correction for population stratification was done using the genomic control method, on the basis of data from 280 genomic control SNPs. Evidence for association with each SNP was assessed using a Cochran–Armitage trend test (p-trend) and a two-degrees of freedom χ2 test for heterogeneity (p-het). The most significant single SNP (p-trend = 8 × 10−5) was not significant at a nominal 5% level after adjusting for population stratification and multiple testing. To evaluate the overall evidence for an excess of positive associations over the proportion expected by chance, we applied two global tests: the admixture maximum likelihood (AML) test and the rank truncated product (RTP) test corrected for population stratification. The admixture maximum likelihood experiment-wise test for association was significant for both the heterogeneity test (p = 0.0031) and the trend test (p = 0.017), but no association was observed using the rank truncated product method for either the heterogeneity test or the trend test (p = 0.12 and p = 0.24, respectively). Genes in the cell-cycle control pathway and genes involved in steroid hormone metabolism and signalling were the main contributors to the association. These results suggest that a proportion of SNPs in these candidate genes are associated with breast cancer risk, but that the effects of individual SNPs is likely to be small. Large sample sizes from multicentre collaboration will be needed to identify associated SNPs with certainty. The polygenic model of cancer susceptibility suggests that multiple alleles contribute to the excess familial risk of most common cancers. Candidate gene association studies have been a commonly used approach in the search for such alleles. We have investigated over 700 common variants in genes that are candidates for breast cancer susceptibility in a large case-control study of breast cancer, but no single variant was identified at an appropriate level of statistical significance. The purpose of this study was to consider these data as a whole, using a novel method, the admixture maximum likelihood test, to test the hypothesis that a proportion (unknown) of the variants we investigated are associated with breast cancer. After adjusting for population substructure, we found evidence for association that was robust to all but the most extreme assumptions about the degree of population stratification. Genes in the cell-cycle control and steroid hormone metabolism and signalling pathways were the main contributors. These results suggest that a proportion of single nucleotide polymorphisms (SNPs) in these candidate genes are associated with breast cancer risk, but that the effects of individual SNPs are likely to be small. Large sample sizes from multicentre collaboration will be needed to identify associated SNPs with certainty.
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Affiliation(s)
- Paul D P Pharoah
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom.
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10
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Song H, Ramus SJ, Shadforth D, Quaye L, Kjaer SK, Dicioccio RA, Dunning AM, Hogdall E, Hogdall C, Whittemore AS, McGuire V, Lesueur F, Easton DF, Jacobs IJ, Ponder BAJ, Gayther SA, Pharoah PDP. Common Variants in RB1 Gene and Risk of Invasive Ovarian Cancer. Cancer Res 2006; 66:10220-6. [PMID: 17047088 DOI: 10.1158/0008-5472.can-06-2222] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Somatic alteration of the RB1 gene is common in several types of cancer, and germ-line variants are implicated in others. We have used a single nucleotide polymorphism (SNP) tagging approach to evaluate the association between common variants (SNP) in RB1 and risks of invasive ovarian cancer. We genotyped 11 tagging SNPs in three ovarian case-control studies from the United Kingdom, United States, and Denmark, comprising >1500 cases and 4,800 controls. Two SNPs showed significant association with ovarian cancer risk: carriers of the minor allele of rs2854344 were at reduced risk compared with the common homozygotes [odds ratio (OR), 0.73; 95% confidence interval (95% CI), 0.61-0.89; P = 0.0009 dominant model]. Similarly, the minor allele of rs4151620 was found to be associated with reduced risk (rare versus common homozygote; OR, 0.19; 95% CI, 0.07-0.53; P = 0.00005 recessive model). After adjusting for multiple testing, the most significant association (rs4151620) was P = 0.001. A global test comparing common haplotype frequencies in cases and controls was of borderline significance (P(8df) = 0.04). There are no common coding SNPs in the RB1 gene. However, intron 17 of RB1 contains the open reading frame for the P2RY5 gene, and rs4151620 is perfectly correlated with rs2227311, which is located in the 5'-untranslated region of P2RY5 and is predicted to affect P2RY5 transcription. rs2854344 has been reported previously to be associated with breast cancer risk. The possible associations of rs2854344 and rs4151620 with ovarian cancer risk warrant confirmation in independent case-control studies before studies on their biological mode of action.
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Affiliation(s)
- Honglin Song
- Cancer Research UK Department of Oncology, Strangeways Research Laboratory, University of Cambridge, Cambridge, United Kingdom.
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