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Sargazi S, Heidari Nia M, Mirinejad S, Moudi M, Jafari Shahroudi M, Saravani R, Valian-Borojeni S. Association of a Novel KIF26B Gene Polymorphism with Susceptibility to Schizophrenia and Breast Cancer: A Case-Control Study. IRANIAN JOURNAL OF PUBLIC HEALTH 2021; 50:397-406. [PMID: 33748005 PMCID: PMC7956084 DOI: 10.18502/ijph.v50i2.5359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Background KIF26B gene is found to play essential roles in regulating different aspects of cell proliferation and development of the nervous system. We aimed to determine if rs12407427 T/C polymorphism could affect susceptibility to schizophrenia (SZN) and breast cancer (BC), the two genetically correlated diseases. Methods The current case-control study was performed from Aug 2018 to Dec 2018. Briefly, 159 female pathologically confirmed BC cases referring to Alzahra Hospital, Isfahan, Iran, and 102 psychologically confirmed SZN patients (60 males and 42 females) admitted to Baharan Hospital, Zahedan, Iran, were enrolled. Using the salting-out method, genomic DNA was extracted, and variants were genotyped using allele-specific amplification refractory mutation system polymerase chain reaction (ARMS-PCR) method. Results The results revealed a significant association between the KIF26B rs12407427 codominant CT (P=0.001), CC (P=0.0001), dominant CT+CC, and recessive CC (P=0.001) genotypes with the risk of developing SZN. Significant correlations were also found regarding rs12407427 and BC susceptibility in different inheritance models, including over-dominant CT (P=0.026), dominant CT+CC (P=0.001), recessive CC (P=0.009), and codominant CT and CC (P=0.001) genotypes. The over-presence of the C allele was also correlated with an increased risk for SZN (P=0.0001) and BC (P=0.0001). Finally, computational analysis predicted that T/C variation in this polymorphism could change the binding sites in proteins involved in splicing. Conclusion rs12407427 T/C as a de novo KIF26B variant might be a novel genetic biomarker for SZN and/or BC susceptibility in a sample of the Iranian population.
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Affiliation(s)
- Saman Sargazi
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Milad Heidari Nia
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Biology, Faculty of Science, Isfahan University, Isfahan, Iran
| | - Shekoufeh Mirinejad
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mahdiyeh Moudi
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mahdiyeh Jafari Shahroudi
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Ramin Saravani
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
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Winter JM, Curry NL, Gildea DM, Williams KA, Lee M, Hu Y, Crawford NPS. Modifier locus mapping of a transgenic F2 mouse population identifies CCDC115 as a novel aggressive prostate cancer modifier gene in humans. BMC Genomics 2018; 19:450. [PMID: 29890952 PMCID: PMC5996485 DOI: 10.1186/s12864-018-4827-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 05/25/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND It is well known that development of prostate cancer (PC) can be attributed to somatic mutations of the genome, acquired within proto-oncogenes or tumor-suppressor genes. What is less well understood is how germline variation contributes to disease aggressiveness in PC patients. To map germline modifiers of aggressive neuroendocrine PC, we generated a genetically diverse F2 intercross population using the transgenic TRAMP mouse model and the wild-derived WSB/EiJ (WSB) strain. The relevance of germline modifiers of aggressive PC identified in these mice was extensively correlated in human PC datasets and functionally validated in cell lines. RESULTS Aggressive PC traits were quantified in a population of 30 week old (TRAMP x WSB) F2 mice (n = 307). Correlation of germline genotype with aggressive disease phenotype revealed seven modifier loci that were significantly associated with aggressive disease. RNA-seq were analyzed using cis-eQTL and trait correlation analyses to identify candidate genes within each of these loci. Analysis of 92 (TRAMP x WSB) F2 prostates revealed 25 candidate genes that harbored both a significant cis-eQTL and mRNA expression correlations with an aggressive PC trait. We further delineated these candidate genes based on their clinical relevance, by interrogating human PC GWAS and PC tumor gene expression datasets. We identified four genes (CCDC115, DNAJC10, RNF149, and STYXL1), which encompassed all of the following characteristics: 1) one or more germline variants associated with aggressive PC traits; 2) differential mRNA levels associated with aggressive PC traits; and 3) differential mRNA expression between normal and tumor tissue. Functional validation studies of these four genes using the human LNCaP prostate adenocarcinoma cell line revealed ectopic overexpression of CCDC115 can significantly impede cell growth in vitro and tumor growth in vivo. Furthermore, CCDC115 human prostate tumor expression was associated with better survival outcomes. CONCLUSION We have demonstrated how modifier locus mapping in mouse models of PC, coupled with in silico analyses of human PC datasets, can reveal novel germline modifier genes of aggressive PC. We have also characterized CCDC115 as being associated with less aggressive PC in humans, placing it as a potential prognostic marker of aggressive PC.
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Affiliation(s)
- Jean M Winter
- Metastasis Genetics Section, Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA.,Present address: Dame Roma Mitchell Cancer Research Laboratories, Adelaide Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, 5000, Australia
| | - Natasha L Curry
- Metastasis Genetics Section, Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Derek M Gildea
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Kendra A Williams
- Metastasis Genetics Section, Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Minnkyong Lee
- Metastasis Genetics Section, Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Ying Hu
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, NIH, Rockville, MD, 20892, USA
| | - Nigel P S Crawford
- Metastasis Genetics Section, Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA. .,, Present address: Sanofi, 55 Corporate Dr., Bridgewater, NJ, 08897, USA.
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3
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Netto GJ, Eich ML, Varambally S. Prostate Cancer: An Update on Molecular Pathology with Clinical Implications. EUR UROL SUPPL 2017. [DOI: 10.1016/j.eursup.2017.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Abstract
A wide array of molecular markers and genomic signatures, reviewed in this article, may soon be used as adjuncts to currently established screening strategies, prognostic parameters, and early detection markers. Markers of genetic susceptibility to PCA, recurrent epigenetic and genetic alterations, including ETS gene fusions, PTEN alterations, and urine-based early detection marker PCA3, are discussed. Impact of recent genome-wide assessment on our understanding of key pathways of PCA development and progression and their potential clinical implications are highlighted.
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5
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Hurley PJ, Sundi D, Shinder B, Simons BW, Hughes RM, Miller RM, Benzon B, Faraj SF, Netto GJ, Vergara IA, Erho N, Davicioni E, Karnes RJ, Yan G, Ewing C, Isaacs SD, Berman DM, Rider JR, Jordahl KM, Mucci LA, Huang J, An SS, Park BH, Isaacs WB, Marchionni L, Ross AE, Schaeffer EM. Germline Variants in Asporin Vary by Race, Modulate the Tumor Microenvironment, and Are Differentially Associated with Metastatic Prostate Cancer. Clin Cancer Res 2015; 22:448-58. [PMID: 26446945 DOI: 10.1158/1078-0432.ccr-15-0256] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 09/10/2015] [Indexed: 12/20/2022]
Abstract
PURPOSE Prostate cancers incite tremendous morbidity upon metastatic growth. We previously identified Asporin (ASPN) as a potential mediator of metastatic progression found within the tumor microenvironment. ASPN contains an aspartic acid (D)-repeat domain and germline polymorphisms in D-repeat-length have been associated with degenerative diseases. Associations of germline ASPN D polymorphisms with risk of prostate cancer progression to metastatic disease have not been assessed. EXPERIMENTAL DESIGN Germline ASPN D-repeat-length was retrospectively analyzed in 1,600 men who underwent radical prostatectomy for clinically localized prostate cancer and in 548 noncancer controls. Multivariable Cox proportional hazards models were used to test the associations of ASPN variations with risk of subsequent oncologic outcomes, including metastasis. Orthotopic xenografts were used to establish allele- and stroma-specific roles for ASPN D variants in metastatic prostate cancer. RESULTS Variation at the ASPN D locus was differentially associated with poorer oncologic outcomes. ASPN D14 [HR, 1.72; 95% confidence interval (CI), 1.05-2.81, P = 0.032] and heterozygosity for ASPN D13/14 (HR, 1.86; 95% CI, 1.03-3.35, P = 0.040) were significantly associated with metastatic recurrence, while homozygosity for the ASPN D13 variant was significantly associated with a reduced risk of metastatic recurrence (HR, 0.44; 95% CI, 0.21-0.94, P = 0.035) in multivariable analyses. Orthotopic xenografts established biologic roles for ASPN D14 and ASPN D13 variants in metastatic prostate cancer progression that were consistent with patient-based data. CONCLUSIONS We observed associations between ASPN D variants and oncologic outcomes, including metastasis. Our data suggest that ASPN expressed in the tumor microenvironment is a heritable modulator of metastatic progression.
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Affiliation(s)
- Paula J Hurley
- Brady Urological Institute, Department of Urology, Johns Hopkins University, Baltimore, Maryland. Department of Oncology, Johns Hopkins University, Baltimore, Maryland. Sidney Kimmel Comprehensive Cancer Institute, Johns Hopkins University, Baltimore, Maryland.
| | - Debasish Sundi
- Brady Urological Institute, Department of Urology, Johns Hopkins University, Baltimore, Maryland
| | - Brian Shinder
- Brady Urological Institute, Department of Urology, Johns Hopkins University, Baltimore, Maryland
| | - Brian W Simons
- Brady Urological Institute, Department of Urology, Johns Hopkins University, Baltimore, Maryland. Department of Molecular and Comparative Pathobiology, Johns Hopkins University, Baltimore, Maryland
| | - Robert M Hughes
- Brady Urological Institute, Department of Urology, Johns Hopkins University, Baltimore, Maryland
| | - Rebecca M Miller
- Brady Urological Institute, Department of Urology, Johns Hopkins University, Baltimore, Maryland
| | - Benjamin Benzon
- Brady Urological Institute, Department of Urology, Johns Hopkins University, Baltimore, Maryland
| | - Sheila F Faraj
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | - George J Netto
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | | | - Nicholas Erho
- Genome Dx Biosciences Inc., Vancouver, British Columbia, Canada
| | - Elai Davicioni
- Genome Dx Biosciences Inc., Vancouver, British Columbia, Canada
| | | | - Guifang Yan
- Brady Urological Institute, Department of Urology, Johns Hopkins University, Baltimore, Maryland
| | - Charles Ewing
- Brady Urological Institute, Department of Urology, Johns Hopkins University, Baltimore, Maryland
| | - Sarah D Isaacs
- Brady Urological Institute, Department of Urology, Johns Hopkins University, Baltimore, Maryland
| | - David M Berman
- Department of Pathology and Molecular Medicine and Cancer Research Institute, Queens University, Kingston, Ontario, Canada
| | - Jennifer R Rider
- Department of Epidemiology, Harvard University, T.H. Chan School of Public Health, Boston, Massachusetts
| | - Kristina M Jordahl
- Department of Epidemiology, Harvard University, T.H. Chan School of Public Health, Boston, Massachusetts
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard University, T.H. Chan School of Public Health, Boston, Massachusetts
| | - Jessie Huang
- The Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Steven S An
- The Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland. The Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland. Physical Sciences-Oncology Center, Johns Hopkins University, Baltimore, Maryland
| | - Ben H Park
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland. Sidney Kimmel Comprehensive Cancer Institute, Johns Hopkins University, Baltimore, Maryland
| | - William B Isaacs
- Brady Urological Institute, Department of Urology, Johns Hopkins University, Baltimore, Maryland
| | - Luigi Marchionni
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland
| | - Ashley E Ross
- Brady Urological Institute, Department of Urology, Johns Hopkins University, Baltimore, Maryland. Department of Oncology, Johns Hopkins University, Baltimore, Maryland. Sidney Kimmel Comprehensive Cancer Institute, Johns Hopkins University, Baltimore, Maryland. Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | - Edward M Schaeffer
- Brady Urological Institute, Department of Urology, Johns Hopkins University, Baltimore, Maryland. Department of Oncology, Johns Hopkins University, Baltimore, Maryland. Sidney Kimmel Comprehensive Cancer Institute, Johns Hopkins University, Baltimore, Maryland
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Decker B, Ostrander EA. Dysregulation of the homeobox transcription factor gene HOXB13: role in prostate cancer. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2014; 7:193-201. [PMID: 25206306 PMCID: PMC4157396 DOI: 10.2147/pgpm.s38117] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Prostate cancer (PC) is the most common noncutaneous cancer in men, and epidemiological studies suggest that about 40% of PC risk is heritable. Linkage analyses in hereditary PC families have identified multiple putative loci. However, until recently, identification of specific risk alleles has proven elusive. Cooney et al used linkage mapping and segregation analysis to identify a putative risk locus on chromosome 17q21-22. In search of causative variant(s) in genes from the candidate region, a novel, potentially deleterious G84E substitution in homeobox transcription factor gene HOXB13 was observed in multiple hereditary PC families. In follow-up testing, the G84E allele was enriched in cases, especially those with an early diagnosis or positive family history of disease. This finding was replicated by others, confirming HOXB13 as a PC risk gene. The HOXB13 protein plays diverse biological roles in embryonic development and terminally differentiated tissue. In tumor cell lines, HOXB13 participates in a number of biological functions, including coactivation and localization of the androgen receptor and FOXA1. However, no consensus role has emerged and many questions remain. All HOXB13 variants with a proposed role in PC risk are predicted to damage the protein and lie in domains that are highly conserved across species. The G84E variant has the strongest epidemiological support and lies in a highly conserved MEIS protein-binding domain, which binds cofactors required for activation. On the basis of epidemiological and biological data, the G84E variant likely modulates the interaction between the HOXB13 protein and the androgen receptor, as well as affecting FOXA1-mediated transcriptional programming. However, further studies of the mutated protein are required to clarify the mechanisms by which this translates into PC risk.
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Affiliation(s)
- Brennan Decker
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA ; Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Helfand BT, Catalona WJ. The Epidemiology and Clinical Implications of Genetic Variation in Prostate Cancer. Urol Clin North Am 2014; 41:277-97. [DOI: 10.1016/j.ucl.2014.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Eeles R, Goh C, Castro E, Bancroft E, Guy M, Al Olama AA, Easton D, Kote-Jarai Z. The genetic epidemiology of prostate cancer and its clinical implications. Nat Rev Urol 2014; 11:18-31. [PMID: 24296704 DOI: 10.1038/nrurol.2013.266] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Worldwide, familial and epidemiological studies have generated considerable evidence of an inherited component to prostate cancer. Indeed, rare highly penetrant genetic mutations have been implicated. Genome-wide association studies (GWAS) have also identified 76 susceptibility loci associated with prostate cancer risk, which occur commonly but are of low penetrance. However, these mutations interact multiplicatively, which can result in substantially increased risk. Currently, approximately 30% of the familial risk is due to such variants. Evaluating the functional aspects of these variants would contribute to our understanding of prostate cancer aetiology and would enable population risk stratification for screening. Furthermore, understanding the genetic risks of prostate cancer might inform predictions of treatment responses and toxicities, with the goal of personalized therapy. However, risk modelling and clinical translational research are needed before we can translate risk profiles generated from these variants into use in the clinical setting for targeted screening and treatment.
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Affiliation(s)
- Rosalind Eeles
- Oncogenetics Team, Division of Cancer Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Chee Goh
- Oncogenetics Team, Division of Cancer Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Elena Castro
- Oncogenetics Team, Division of Cancer Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Elizabeth Bancroft
- Clinical Academic Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5PT, UK
| | - Michelle Guy
- Oncogenetics Team, Division of Cancer Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Ali Amin Al Olama
- Cancer Research UK Centre for Cancer Genetic Epidemiology, Strangeways Laboratory, University of Cambridge, Cambridge CB1 8RN, UK
| | - Douglas Easton
- Departments of Public Health & Primary Care and Oncology, Strangeways Laboratory, University of Cambridge, Cambridge CB1 8RN, UK
| | - Zsofia Kote-Jarai
- Oncogenetics Team, Division of Cancer Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
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Xu J, Sun J, Zheng SL. Prostate cancer risk-associated genetic markers and their potential clinical utility. Asian J Androl 2013; 15:314-22. [PMID: 23564047 PMCID: PMC3739659 DOI: 10.1038/aja.2013.42] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 03/16/2013] [Accepted: 03/18/2013] [Indexed: 02/02/2023] Open
Abstract
Prostate cancer (PCa) is one of the most common cancers among men in Western developed countries and its incidence has increased considerably in many other parts of the world, including China. The etiology of PCa is largely unknown but is thought to be multifactorial, where inherited genetics plays an important role. In this article, we first briefly review results from studies of familial aggregation and genetic susceptibility to PCa. We then recap key findings of rare and high-penetrance PCa susceptibility genes from linkage studies in PCa families. We devote a significant portion of this article to summarizing discoveries of common and low-penetrance PCa risk-associated single-nucleotide polymorphisms (SNPs) from genetic association studies in PCa cases and controls, especially those from genome-wide association studies (GWASs). A strong focus of this article is to review the literature on the potential clinical utility of these implicated genetic markers. Most of these published studies described PCa risk estimation using a genetic score derived from multiple risk-associated SNPs and its utility in determining the need for prostate biopsy. Finally, we comment on the newly proposed concept of genetic score; the notion is to treat it as a marker for genetic predisposition, similar to family history, rather than a diagnostic marker to discriminate PCa patients from non-cancer patients. Available evidence to date suggests that genetic score is an objective and better measurement of inherited risk of PCa than family history. Another unique feature of this article is the inclusion of genetic association studies of PCa in Chinese and Japanese populations.
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Affiliation(s)
- Jianfeng Xu
- Fudan Institute of Urology, Huashan Hospital, Fudan UniversityFudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai 200040, China.
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The 2013 Genetics Society of America Medal. Genetics 2013; 194:5-7. [DOI: 10.1534/genetics.113.150672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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11
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Ledet EM, Hu X, Sartor O, Rayford W, Li M, Mandal D. Characterization of germline copy number variation in high-risk African American families with prostate cancer. Prostate 2013; 73:614-23. [PMID: 23060098 DOI: 10.1002/pros.22602] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 09/10/2012] [Indexed: 01/24/2023]
Abstract
BACKGROUND Prostate cancer is a complex multi-allelic disease and the most common malignancy in men. The incidence of prostate cancer in African American men is more than twice as high as that of any other race. Despite the high prevalence of prostate cancer amongst African American men, this population has been under represented in genetic studies of prostate cancer. Although genomic copy number variations (CNVs) have been detected in prostate tumors, this is the first study describing germline CNVs in African American hereditary prostate cancer families. METHODS Ten high-risk African American families with three or more affected individuals and with an early age of onset were recruited. From these families, 37 individuals, including 23 affected males, and 14 unaffected males, were selected for CNV analysis. Array comparative genomic hybridization was used to characterize germline CNVs unique to African American men with hereditary prostate cancer. RESULTS Through common aberration analysis in affected family members; novel CNVs were identified at chromosomes 1p36.13 and 16q23.3. Differential analysis comparing affected and unaffected family members identified 9.4 kb duplication on chromosome 14q32.33 which segregate with prostate cancer patients in these high-risk families. CONCLUSIONS The duplication at 14q32.33 encompasses IGHG3 gene which has been shown to have both significant gains in copy number as well as overexpression in prostate tumors in African Americans. These CNVs may represent a component of genetic predisposition which contributes to the high prevalence and mortality of prostate cancer in African American men.
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Affiliation(s)
- Elisa M Ledet
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, Louisiana 70112, USA
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Genetic heterogeneity in Finnish hereditary prostate cancer using ordered subset analysis. Eur J Hum Genet 2012; 21:437-43. [PMID: 22948022 DOI: 10.1038/ejhg.2012.185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Prostate cancer (PrCa) is the most common male cancer in developed countries and the second most common cause of cancer death after lung cancer. We recently reported a genome-wide linkage scan in 69 Finnish hereditary PrCa (HPC) families, which replicated the HPC9 locus on 17q21-q22 and identified a locus on 2q37. The aim of this study was to identify and to detect other loci linked to HPC. Here we used ordered subset analysis (OSA), conditioned on nonparametric linkage to these loci to detect other loci linked to HPC in subsets of families, but not the overall sample. We analyzed the families based on their evidence for linkage to chromosome 2, chromosome 17 and a maximum score using the strongest evidence of linkage from either of the two loci. Significant linkage to a 5-cM linkage interval with a peak OSA nonparametric allele-sharing LOD score of 4.876 on Xq26.3-q27 (ΔLOD=3.193, empirical P=0.009) was observed in a subset of 41 families weakly linked to 2q37, overlapping the HPCX1 locus. Two peaks that were novel to the analysis combining linkage evidence from both primary loci were identified; 18q12.1-q12.2 (OSA LOD=2.541, ΔLOD=1.651, P=0.03) and 22q11.1-q11.21 (OSA LOD=2.395, ΔLOD=2.36, P=0.006), which is close to HPC6. Using OSA allows us to find additional loci linked to HPC in subsets of families, and underlines the complex genetic heterogeneity of HPC even in highly aggregated families.
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Cicek MS, Cunningham JM, Fridley BL, Serie DJ, Bamlet WR, Diergaarde B, Haile RW, Le Marchand L, Krontiris TG, Younghusband HB, Gallinger S, Newcomb PA, Hopper JL, Jenkins MA, Casey G, Schumacher F, Chen Z, DeRycke MS, Templeton AS, Winship I, Green RC, Green JS, Macrae FA, Parry S, Young GP, Young JP, Buchanan D, Thomas DC, Bishop DT, Lindor NM, Thibodeau SN, Potter JD, Goode EL. Colorectal cancer linkage on chromosomes 4q21, 8q13, 12q24, and 15q22. PLoS One 2012; 7:e38175. [PMID: 22675446 PMCID: PMC3364975 DOI: 10.1371/journal.pone.0038175] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 05/01/2012] [Indexed: 12/19/2022] Open
Abstract
A substantial proportion of familial colorectal cancer (CRC) is not a consequence of known susceptibility loci, such as mismatch repair (MMR) genes, supporting the existence of additional loci. To identify novel CRC loci, we conducted a genome-wide linkage scan in 356 white families with no evidence of defective MMR (i.e., no loss of tumor expression of MMR proteins, no microsatellite instability (MSI)-high tumors, or no evidence of linkage to MMR genes). Families were ascertained via the Colon Cancer Family Registry multi-site NCI-supported consortium (Colon CFR), the City of Hope Comprehensive Cancer Center, and Memorial University of Newfoundland. A total of 1,612 individuals (average 5.0 per family including 2.2 affected) were genotyped using genome-wide single nucleotide polymorphism linkage arrays; parametric and non-parametric linkage analysis used MERLIN in a priori-defined family groups. Five lod scores greater than 3.0 were observed assuming heterogeneity. The greatest were among families with mean age of diagnosis less than 50 years at 4q21.1 (dominant HLOD = 4.51, α = 0.84, 145.40 cM, rs10518142) and among all families at 12q24.32 (dominant HLOD = 3.60, α = 0.48, 285.15 cM, rs952093). Among families with four or more affected individuals and among clinic-based families, a common peak was observed at 15q22.31 (101.40 cM, rs1477798; dominant HLOD = 3.07, α = 0.29; dominant HLOD = 3.03, α = 0.32, respectively). Analysis of families with only two affected individuals yielded a peak at 8q13.2 (recessive HLOD = 3.02, α = 0.51, 132.52 cM, rs1319036). These previously unreported linkage peaks demonstrate the continued utility of family-based data in complex traits and suggest that new CRC risk alleles remain to be elucidated.
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Affiliation(s)
- Mine S. Cicek
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Medical Genetics, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Julie M. Cunningham
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Medical Genetics, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Brooke L. Fridley
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Medical Genetics, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Daniel J. Serie
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Medical Genetics, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - William R. Bamlet
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Medical Genetics, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Brenda Diergaarde
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Robert W. Haile
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Loic Le Marchand
- University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Theodore G. Krontiris
- Department of Molecular Medicine, Beckman Research Institute of the City of Hope, Duarte, California, United States of America
| | | | - Steven Gallinger
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Polly A. Newcomb
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - John L. Hopper
- Departments of Public Health and Medicine, University of Melbourne, Victoria, Australia
| | - Mark A. Jenkins
- Departments of Public Health and Medicine, University of Melbourne, Victoria, Australia
| | - Graham Casey
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Fredrick Schumacher
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Zhu Chen
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Melissa S. DeRycke
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Medical Genetics, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Allyson S. Templeton
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Ingrid Winship
- Departments of Public Health and Medicine, University of Melbourne, Victoria, Australia
| | - Roger C. Green
- Faculty of Medicine, Memorial University of Newfoundland, St. Johns, Newfoundland, Canada
| | - Jane S. Green
- Faculty of Medicine, Memorial University of Newfoundland, St. Johns, Newfoundland, Canada
| | - Finlay A. Macrae
- Colorectal Medicine and Genetics and Department of Medicine, University of Melbourne, The Royal Melbourne Hospital, Victoria, Australia
| | - Susan Parry
- New Zealand Familial GI Cancer Registry, Auckland City Hospital, Auckland, New Zealand
- Department of Gastroenterology, Middlemore Hospital, Auckland, New Zealand
| | - Graeme P. Young
- Flinders Centre for Cancer Prevention and Control, Flinders University, Adelaide, Australia
| | - Joanne P. Young
- Familial Cancer Laboratory, Queensland Institute of Medical Research, Queensland, Australia
| | - Daniel Buchanan
- Familial Cancer Laboratory, Queensland Institute of Medical Research, Queensland, Australia
| | - Duncan C. Thomas
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, United States of America
| | - D. Timothy Bishop
- University of Leeds, Leeds Institute of Molecular Medicine, Leeds, United Kingdom
| | - Noralane M. Lindor
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Medical Genetics, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Stephen N. Thibodeau
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Medical Genetics, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - John D. Potter
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Centre for Public Health Research, Massey University, Wellington, New Zealand
| | - Ellen L. Goode
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Medical Genetics, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
- * E-mail:
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