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Gong J, Kim DM, Freeman MR, Kim H, Ellis L, Smith B, Theodorescu D, Posadas E, Figlin R, Bhowmick N, Freedland SJ. Genetic and biological drivers of prostate cancer disparities in Black men. Nat Rev Urol 2024; 21:274-289. [PMID: 37964070 DOI: 10.1038/s41585-023-00828-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2023] [Indexed: 11/16/2023]
Abstract
Black men with prostate cancer have historically had worse outcomes than white men with prostate cancer. The causes of this disparity in outcomes are multi-factorial, but a potential basis is that prostate cancers in Black men are biologically distinct from prostate cancers in white men. Evidence suggests that genetic and ancestral factors, molecular pathways involving androgen and non-androgen receptor signalling, inflammation, epigenetics, the tumour microenvironment and tumour metabolism are contributing factors to the racial disparities observed. Key genetic and molecular pathways linked to prostate cancer risk and aggressiveness have potential clinical relevance. Describing biological drivers of prostate cancer disparities could inform efforts to improve outcomes for Black men with prostate cancer.
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Affiliation(s)
- Jun Gong
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - Daniel M Kim
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Michael R Freeman
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Hyung Kim
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Leigh Ellis
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bethany Smith
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Dan Theodorescu
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Edwin Posadas
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Robert Figlin
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Neil Bhowmick
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Stephen J Freedland
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Section of Urology, Durham VA Medical Center, Durham, NC, USA
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Samtal C, El Jaddaoui I, Hamdi S, Bouguenouch L, Ouldim K, Nejjari C, Ghazal H, Bekkari H. Review of prostate cancer genomic studies in Africa. Front Genet 2022; 13:911101. [DOI: 10.3389/fgene.2022.911101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022] Open
Abstract
Prostate cancer (PCa) is the second most commonly diagnosed in men worldwide and one of the most frequent cancers in men in Africa. The heterogeneity of this cancer fosters the need to identify potential genetic risk factors/biomarkers. Omics variations may significantly contribute to early diagnosis and personalized treatment. However, there are few genomic studies of this disease in African populations. This review sheds light on the status of genomics research on PCa in Africa and outlines the common variants identified thus far. The allele frequencies of the most significant SNPs in Afro-native, Afro-descendants, and European populations were compared. We advocate how these few but promising data will aid in understanding, better diagnosing, and precisely treating this cancer and the need for further collaborative research on the genomics of PCa in the African continent.
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Romero J, Costa GMF, Rocha LPC, Siqueira S, Moreira PR, Almeida-Leite CM. Polymorphisms of Nav1.6 sodium channel, Brain-derived Neurotrophic Factor, Catechol-O-methyltransferase and Guanosine Triphosphate Cyclohydrolase 1 genes in trigeminal neuralgia. Clin Neurol Neurosurg 2021; 208:106880. [PMID: 34418703 DOI: 10.1016/j.clineuro.2021.106880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 12/18/2022]
Abstract
SUBJECTS Trigeminal neuralgia is a neuropathic pain characterized by episodes of severe shock-like pain within the distribution of one or more divisions of the trigeminal nerve. Pain can be influenced by ethnicity, environment, gender, psychological traits, and genetics. Molecules Nav1.6 sodium channel, Brain-derived Neurotrophic Factor, Catechol-O-methyltransferase and Guanosine Triphosphate Cyclohydrolase 1 have been involved in mechanisms that underlie pain and neurological conditions. OBJECTIVE The aim of this case-control study was to investigate the occurrence of genetic polymorphisms in Nav1.6 sodium channel (SCN8A/rs303810), Brain-derived Neurotrophic Factor (BDNF/rs6265/Val66Met), Catechol-O-methyltransferase (COMT/rs4680/Val158Met), and Guanosine Triphosphate Cyclohydrolase 1 (GCH1/rs8007267) genes in trigeminal neuralgia patients. METHODS Ninety-six subjects were divided into two groups: 48 with trigeminal neuralgia diagnosis and 48 controls. Pain was evaluated by visual analog scale and genomic DNA was obtained from oral swabs and analyzed by real-time polymerase chain reaction. RESULTS No association was observed among SCN8A, BDNF, COMT or GCH1 polymorphisms and the presence of trigeminal neuralgia. Genotype distribution and allele frequencies did not correlate to pain severity. CONCLUSIONS Although no association of evaluated polymorphisms and trigeminal neuralgia or pain was observed, our data contributes to the knowledge of genetic susceptibility to trigeminal neuralgia, which is very scarce. Further studies may focus on other polymorphisms and mutations, as well as on epigenetics and transcriptional regulation of these genes, in order to clarify or definitively exclude the role of Nav1.6, BDNF, COMT or GCH1 in trigeminal neuralgia susceptibility and pathophysiology.
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Affiliation(s)
- Jgaj Romero
- Programa de Pós-Graduação em Patologia, Faculdade de Medicina, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil.
| | - Grazielle Mara Ferreira Costa
- Programa de Pós-Graduação em Patologia, Faculdade de Medicina, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil.
| | - Luiz Paulo Carvalho Rocha
- Programa de Pós-Graduação em Biologia Celular, Instituto de Ciências Biológicas (ICB), UFMG, Belo Horizonte, MG, Brazil.
| | - Srdt Siqueira
- Hospital das Clínicas, Universidade de São Paulo, São Paulo, SP, Brazil.
| | | | - Camila Megale Almeida-Leite
- Programa de Pós-Graduação em Patologia, Faculdade de Medicina, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil; Departamento de Morfologia, ICB, UFMG, Belo Horizonte, MG, Brazil.
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4
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Bree KK, Henley PJ, Pettaway CA. Germline Predisposition to Prostate Cancer in Diverse Populations. Urol Clin North Am 2021; 48:411-423. [PMID: 34210495 DOI: 10.1016/j.ucl.2021.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
There remains a paucity of data related to germline genetic alterations predisposing patients to prostate cancer. Recent data suggest that African American, Hispanic, and Asian and Pacific Islander men exhibit genetic alterations in both highly penetrant germline genes, including BRCA1/2, ATM, and CHEK2, and the mismatch repair genes associated with Lynch syndrome, as well as low-penetrant single-nucleotide polymorphisms. However, cohort sizes remain small in many studies limiting the ability to determine clinical significance, appropriate risk stratification, and treatment implications in these diverse populations.
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Affiliation(s)
- Kelly K Bree
- The University of Texas MD Anderson Cancer Center, Department of Urology, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Patrick J Henley
- The University of Texas MD Anderson Cancer Center, Department of Urology, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Curtis A Pettaway
- The University of Texas MD Anderson Cancer Center, Department of Urology, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
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Batai K, Cui Z, Arora A, Shah-Williams E, Hernandez W, Ruden M, Hollowell CMP, Hooker SE, Bathina M, Murphy AB, Bonilla C, Kittles RA. Genetic loci associated with skin pigmentation in African Americans and their effects on vitamin D deficiency. PLoS Genet 2021; 17:e1009319. [PMID: 33600456 PMCID: PMC7891745 DOI: 10.1371/journal.pgen.1009319] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 12/21/2020] [Indexed: 01/08/2023] Open
Abstract
A recent genome-wide association study (GWAS) in African descent populations identified novel loci associated with skin pigmentation. However, how genomic variations affect skin pigmentation and how these skin pigmentation gene variants affect serum 25(OH) vitamin D variation has not been explored in African Americans (AAs). In order to further understand genetic factors that affect human skin pigmentation and serum 25(OH)D variation, we performed a GWAS for skin pigmentation with 395 AAs and a replication study with 681 AAs. Then, we tested if the identified variants are associated with serum 25(OH) D concentrations in a subset of AAs (n = 591). Skin pigmentation, Melanin Index (M-Index), was measured using a narrow-band reflectometer. Multiple regression analysis was performed to identify variants associated with M-Index and to assess their role in serum 25(OH)D variation adjusting for population stratification and relevant confounding variables. A variant near the SLC24A5 gene (rs2675345) showed the strongest signal of association with M-Index (P = 4.0 x 10-30 in the pooled dataset). Variants in SLC24A5, SLC45A2 and OCA2 together account for a large proportion of skin pigmentation variance (11%). The effects of these variants on M-Index was modified by sex (P for interaction = 0.009). However, West African Ancestry (WAA) also accounts for a large proportion of M-Index variance (23%). M-Index also varies among AAs with high WAA and high Genetic Score calculated from top variants associated with M-Index, suggesting that other unknown genomic factors related to WAA are likely contributing to skin pigmentation variation. M-Index was not associated with serum 25(OH)D concentrations, but the Genetic Score was significantly associated with vitamin D deficiency (serum 25(OH)D levels less than 12 ng/mL) (OR, 1.30; 95% CI, 1.04-1.64). The findings support the hypothesis suggesting that skin pigmentation evolved responding to increased demand for subcutaneous vitamin D synthesis in high latitude environments.
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Affiliation(s)
- Ken Batai
- Department of Urology, University of Arizona, Tucson, Arizona, United States of America
| | - Zuxi Cui
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Amit Arora
- Department of Epidemiology and Biostatistics, University of Arizona, Tucson, Arizona, United States of America
| | - Ebony Shah-Williams
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, Indiana United States of America
| | - Wenndy Hernandez
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Maria Ruden
- Department of Surgery, Cook County Health and Hospitals System, Chicago, Illinois, United States of America
| | - Courtney M. P. Hollowell
- Department of Surgery, Cook County Health and Hospitals System, Chicago, Illinois, United States of America
| | - Stanley E. Hooker
- Division of Health Equities, Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California, United States of America
| | - Madhavi Bathina
- Division of Health Equities, Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California, United States of America
| | - Adam B. Murphy
- Department of Urology, Northwestern University, Chicago, Illinois, United States of America
| | - Carolina Bonilla
- Departamento de Medicina Preventiva, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Rick A. Kittles
- Division of Health Equities, Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California, United States of America
- * E-mail:
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6
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Harris AM, DeGiorgio M. Identifying and Classifying Shared Selective Sweeps from Multilocus Data. Genetics 2020; 215:143-171. [PMID: 32152048 PMCID: PMC7198270 DOI: 10.1534/genetics.120.303137] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/29/2020] [Indexed: 11/18/2022] Open
Abstract
Positive selection causes beneficial alleles to rise to high frequency, resulting in a selective sweep of the diversity surrounding the selected sites. Accordingly, the signature of a selective sweep in an ancestral population may still remain in its descendants. Identifying signatures of selection in the ancestor that are shared among its descendants is important to contextualize the timing of a sweep, but few methods exist for this purpose. We introduce the statistic SS-H12, which can identify genomic regions under shared positive selection across populations and is based on the theory of the expected haplotype homozygosity statistic H12, which detects recent hard and soft sweeps from the presence of high-frequency haplotypes. SS-H12 is distinct from comparable statistics because it requires a minimum of only two populations, and properly identifies and differentiates between independent convergent sweeps and true ancestral sweeps, with high power and robustness to a variety of demographic models. Furthermore, we can apply SS-H12 in conjunction with the ratio of statistics we term [Formula: see text] and [Formula: see text] to further classify identified shared sweeps as hard or soft. Finally, we identified both previously reported and novel shared sweep candidates from human whole-genome sequences. Previously reported candidates include the well-characterized ancestral sweeps at LCT and SLC24A5 in Indo-Europeans, as well as GPHN worldwide. Novel candidates include an ancestral sweep at RGS18 in sub-Saharan Africans involved in regulating the platelet response and implicated in sudden cardiac death, and a convergent sweep at C2CD5 between European and East Asian populations that may explain their different insulin responses.
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Affiliation(s)
- Alexandre M Harris
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802
- Molecular, Cellular, and Integrative Biosciences at the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida 33431
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Martinelli RP, Rodriguez JM, Daurelio LD, Esteban L. In silico identification of novel transcription factors associated with CYP27B1 transcriptional regulation in LPS-challenged mononuclear phagocytes. J Steroid Biochem Mol Biol 2020; 199:105590. [PMID: 32001361 DOI: 10.1016/j.jsbmb.2020.105590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 12/13/2019] [Accepted: 01/13/2020] [Indexed: 01/08/2023]
Abstract
Renal and extrarenal production of the active form of vitamin D, 1,25-dihydroxyvitamin D (1,25(OH)2D), is catalyzed by CYP27B1, an enzyme also called 1-α-hydroxylase. The overproduction of 1,25(OH)2D has been described in granulomatous diseases. High circulating concentrations of 1,25(OH)2D can lead to hypercalcemia. The aim of this work was to characterize the transcriptional regulation of CYP27B1 in human mononuclear phagocytes exposed to LPS due to its relevance to understanding the hypercalcemia and ectopic calcifications associated with chronic inflammatory diseases such as tuberculosis and other granulomatous diseases. The human CYP27B1 promoter analysis identified binding sites for published TF, SNPs, novel putative TFBS and conserved sites compared to mice. Then, using microarray data, a meta-analysis was performed to obtain a global view of the gene expression in LPS-challenged dendritic cells, monocytes and macrophages. Finally, two experiments, GSE40885 and time series GSE19765, were analyzed in-depth using differential expression analysis which permitted the identification of TF co-expressed with CYP27B1. This work allowed us to formulate a CYP27B1 transcriptional regulation model for LPS-challenged monocytes/macrophages. The importance of two TF families, NFKB and CEBPB, was confirmed. Data also suggests that PLAGL2 and STAT4 which are novel TF could participate in the CYP27B1 transcriptional regulation in cells exposed to LPS. These TF, in turn, would be interacting with regions that present polymorphisms in the general population which might explain the pathological phenotypes associated with altered vitamin D metabolism.
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Affiliation(s)
- Romina P Martinelli
- Departamento de Química Biológica, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina; Cátedra de Genética Humana, Facultad de Medicina, Universidad Abierta Interamericana, Rosario, Santa Fe, Argentina.
| | - Julia M Rodriguez
- Departamento de Química Biológica, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Lucas D Daurelio
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina; Laboratorio de Investigaciones en Fisiología y Biología Molecular Vegetal (LIFiBVe), Cátedra de Fisiología Vegetal, Facultad de Ciencias Agrarias, Universidad Nacional del Litoral, Esperanza, Santa Fe, Argentina.
| | - Luis Esteban
- Departamento de Química Biológica, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina.
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8
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Bhargava HK, Leo P, Elliott R, Janowczyk A, Whitney J, Gupta S, Fu P, Yamoah K, Khani F, Robinson BD, Rebbeck TR, Feldman M, Lal P, Madabhushi A. Computationally Derived Image Signature of Stromal Morphology Is Prognostic of Prostate Cancer Recurrence Following Prostatectomy in African American Patients. Clin Cancer Res 2020; 26:1915-1923. [PMID: 32139401 PMCID: PMC7165025 DOI: 10.1158/1078-0432.ccr-19-2659] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/17/2019] [Accepted: 01/30/2020] [Indexed: 12/24/2022]
Abstract
PURPOSE Between 30%-40% of patients with prostate cancer experience disease recurrence following radical prostatectomy. Existing clinical models for recurrence risk prediction do not account for population-based variation in the tumor phenotype, despite recent evidence suggesting the presence of a unique, more aggressive prostate cancer phenotype in African American (AA) patients. We investigated the capacity of digitally measured, population-specific phenotypes of the intratumoral stroma to create improved models for prediction of recurrence following radical prostatectomy. EXPERIMENTAL DESIGN This study included 334 radical prostatectomy patients subdivided into training (VT, n = 127), validation 1 (V1, n = 62), and validation 2 (V2, n = 145). Hematoxylin and eosin-stained slides from resected prostates were digitized, and 242 quantitative descriptors of the intratumoral stroma were calculated using a computational algorithm. Machine learning and elastic net Cox regression models were constructed using VT to predict biochemical recurrence-free survival based on these features. Performance of these models was assessed using V1 and V2, both overall and in population-specific cohorts. RESULTS An AA-specific, automated stromal signature, AAstro, was prognostic of recurrence risk in both independent validation datasets [V1,AA: AUC = 0.87, HR = 4.71 (95% confidence interval (CI), 1.65-13.4), P = 0.003; V2,AA: AUC = 0.77, HR = 5.7 (95% CI, 1.48-21.90), P = 0.01]. AAstro outperformed clinical standard Kattan and CAPRA-S nomograms, and the underlying stromal descriptors were strongly associated with IHC measurements of specific tumor biomarker expression levels. CONCLUSIONS Our results suggest that considering population-specific information and stromal morphology has the potential to substantially improve accuracy of prognosis and risk stratification in AA patients with prostate cancer.
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Affiliation(s)
- Hersh K Bhargava
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California
| | - Patrick Leo
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio
| | - Robin Elliott
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio
| | - Andrew Janowczyk
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio
| | - Jon Whitney
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio
| | - Sanjay Gupta
- Department of Urology, Case Western Reserve University, Cleveland, Ohio
- Louis Stokes Cleveland Veterans Administration Medical Center, Cleveland, Ohio
| | - Pingfu Fu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Kosj Yamoah
- Moffitt Cancer Center & Research Institute and Department of Radiation Oncology, University of South Florida, Tampa, Florida
| | - Francesca Khani
- Departments of Pathology and Laboratory Medicine and Urology, Weill Cornell Medicine, New York, New York
| | - Brian D Robinson
- Departments of Pathology and Laboratory Medicine and Urology, Weill Cornell Medicine, New York, New York
| | - Timothy R Rebbeck
- T.H. Chan School of Public Health and Dana Farber Cancer Institute, Harvard University, Boston, Massachusetts
| | - Michael Feldman
- Department of Pathology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Priti Lal
- Department of Pathology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anant Madabhushi
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio.
- Louis Stokes Cleveland Veterans Administration Medical Center, Cleveland, Ohio
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Single Nucleotide Polymorphisms in 25-Hydroxyvitamin D3 1-Alpha-Hydroxylase ( CYP27B1) Gene: The Risk of Malignant Tumors and Other Chronic Diseases. Nutrients 2020; 12:nu12030801. [PMID: 32197412 PMCID: PMC7146376 DOI: 10.3390/nu12030801] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/13/2020] [Accepted: 03/16/2020] [Indexed: 12/31/2022] Open
Abstract
: Vitamin D is widely known for its roles in the promotion of apoptosis and differentiation, with simultaneous inhibition of proliferation, inflammation, angiogenesis, invasion, and metastasis. Modern literature lacks complete information on polymorphisms in CYP27B1, the only enzyme capable of vitamin D activation. This review presents gathered data that relate to genetic variants in CYP27B1 gene in correlation to multiple diseases, mostly concerning colorectal, prostate, breast, lung, and pancreatic cancers, as well as on other pathologies, such as non-Hodgkin's lymphoma, oral lichen planus, or multiple sclerosis.
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10
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Wilson BD, Ricks-Santi LJ, Mason TE, Abbas M, Kittles RA, Dunston GM, Kanaan YM. Admixture Mapping Links RACGAP1 Regulation to Prostate Cancer in African Americans. Cancer Genomics Proteomics 2018; 15:185-191. [PMID: 29695400 DOI: 10.21873/cgp.20076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 11/16/2017] [Accepted: 11/20/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND/AIM Prostate cancer is the most common malignancy in US males. African American men have higher incidence and mortality rates than European Americans. Five single nucleotide polymorphisms are associated with PCa. We hypothesized haplotypes inferred from these SNPs are also associated with PCa. PATIENTS AND METHODS We genotyped SNPs in a case-control admixture mapping study. SNP haplotypes inferred for 157 PCa cases and 150 controls were used in the regression analysis. RESULTS We found an association between "GTCCC", "ATTCT", and "ACCCC" haplotypes and PCa after ancestry adjustment (OR=3.62, 95%CI=1.42-9.21, p=0.0070; OR=7.89, 95%CI=2.36-26.31, p=0.0008; OR=4.34, 95%CI=1.75-10.78, p=0.0016). The rs615382 variant disrupts the recombination signal binding protein with immunoglobulin kappa J binding site in Rac GTPase activating protein 1 (RACGAP1). CONCLUSION Disruption of notch 1 mediated-repression of RACGAP1 may contribute to PCa in African Americans.
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Affiliation(s)
- Bradford D Wilson
- National Human Genome Center, Howard University, Washington, DC, U.S.A.
| | | | - Tshela E Mason
- National Human Genome Center, Howard University, Washington, DC, U.S.A
| | - Muneer Abbas
- National Human Genome Center, Howard University, Washington, DC, U.S.A.,Department of Microbiology, Howard University, Washington, DC, U.S.A
| | - Rick A Kittles
- City of Hope Comprehensive Cancer Center, Duarte, CA, U.S.A
| | - Georgia M Dunston
- National Human Genome Center, Howard University, Washington, DC, U.S.A.,Department of Microbiology, Howard University, Washington, DC, U.S.A
| | - Yasmine M Kanaan
- Department of Microbiology, Howard University, Washington, DC, U.S.A
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11
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Chen L, Wei J, Zhang S, Lou Z, Wang X, Ren Y, Qi H, Xie Z, Chen Y, Chen F, Wu Q, Fan X, Xu H, Huang S, Weng G. Association of VDR gene TaqI polymorphism with the susceptibility to prostate cancer in Asian population evaluated by an updated systematic meta-analysis. Onco Targets Ther 2018; 11:3267-3280. [PMID: 29910622 PMCID: PMC5987782 DOI: 10.2147/ott.s151002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Background The vitamin D receptor (VDR) plays a key role in vitamin-mediated signaling pathway. Emerging evidence has suggested that the VDR polymorphism may contribute to the risk of prostate cancer (PCa). However, the existing results are not conclusive in Asian population. Methods We aim to evaluate the potential role of VDR polymorphisms on PCa of Asian population. PubMed, Scopus, Embase, Web of Science, Chinese National Knowledge Infrastructure, Wang Fang Data, and VIP Periodical were retrieved, and eligible studies (case–control or cohort study) meeting the inclusion criteria were evaluated through an updated meta-analysis using Stata13.0 software. Results A total of 1,363 cases and 2,101 controls obtained from 13 eligible publications were eventually included in this meta-analysis. Our results show that a significant association of VDR taq1 polymorphism with PCa risk, especially in the Japanese population. In the clinical stage-stratified analysis, the pooled results revealed no significant difference in genetic polymorphisms between the local stage and control groups, whereas there was increased frequency of T allele and TT genotype in the advanced tumor stage group compared with local tumor stage or control groups. Similarly, no significant difference was seen in Gleason <7 and control groups, but the T allele and TT genotype were significantly higher in the Gleason ≥7 group compared with Gleason <7 or control groups. Conclusion The VDR TaqI polymorphism might be associated with PCa risk in Asian population, especially in the Japanese population. Also, PCa patients carrying the T allele or TT genotype were more likely to progress to advanced stage. These results suggest that VDR TaqI polymorphisms may be potential diagnostic biomarkers for PCa susceptibility.
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Affiliation(s)
- Liangliang Chen
- Department of Urologic Surgery, Ningbo Urology and Nephrology Hospital, Urology and Nephrology Institute of Ningbo University, Ningbo, China
| | - Junjun Wei
- Department of Urologic Surgery, Ningbo Urology and Nephrology Hospital, Urology and Nephrology Institute of Ningbo University, Ningbo, China
| | - Shuwei Zhang
- Department of Urologic Surgery, Ningbo Urology and Nephrology Hospital, Urology and Nephrology Institute of Ningbo University, Ningbo, China
| | - Zhongguan Lou
- Department of Urologic Surgery, Ningbo Urology and Nephrology Hospital, Urology and Nephrology Institute of Ningbo University, Ningbo, China
| | - Xue Wang
- Department of Urologic Surgery, Ningbo Urology and Nephrology Hospital, Urology and Nephrology Institute of Ningbo University, Ningbo, China
| | - Yu Ren
- Department of Urologic Surgery, Ningbo Urology and Nephrology Hospital, Urology and Nephrology Institute of Ningbo University, Ningbo, China
| | - Honggang Qi
- Department of Urologic Surgery, Ningbo Urology and Nephrology Hospital, Urology and Nephrology Institute of Ningbo University, Ningbo, China
| | - Zhenhua Xie
- Department of Urologic Surgery, Ningbo Urology and Nephrology Hospital, Urology and Nephrology Institute of Ningbo University, Ningbo, China
| | - Yirun Chen
- Department of Urologic Surgery, Ningbo Urology and Nephrology Hospital, Urology and Nephrology Institute of Ningbo University, Ningbo, China
| | - Feng Chen
- Department of Urologic Surgery, Ningbo Urology and Nephrology Hospital, Urology and Nephrology Institute of Ningbo University, Ningbo, China
| | - Qihang Wu
- Department of Urologic Surgery, Ningbo Urology and Nephrology Hospital, Urology and Nephrology Institute of Ningbo University, Ningbo, China
| | - Xiaoxiao Fan
- Department of Urologic Surgery, Ningbo Urology and Nephrology Hospital, Urology and Nephrology Institute of Ningbo University, Ningbo, China
| | - Honglei Xu
- Department of Urologic Surgery, Ningbo Urology and Nephrology Hospital, Urology and Nephrology Institute of Ningbo University, Ningbo, China
| | - Shuaishuai Huang
- Department of Urologic Surgery, Ningbo Urology and Nephrology Hospital, Urology and Nephrology Institute of Ningbo University, Ningbo, China
| | - Guobin Weng
- Department of Urologic Surgery, Ningbo Urology and Nephrology Hospital, Urology and Nephrology Institute of Ningbo University, Ningbo, China
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Mahmoud AM, Al-Alem U, Dabbous F, Ali MM, Batai K, Shah E, Kittles RA. Zinc Intake and Risk of Prostate Cancer: Case-Control Study and Meta-Analysis. PLoS One 2016; 11:e0165956. [PMID: 27824905 PMCID: PMC5100936 DOI: 10.1371/journal.pone.0165956] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/20/2016] [Indexed: 01/21/2023] Open
Abstract
Zinc is an essential dietary element that has been implicated in the pathogenesis of prostate cancer, a cancer that disproportionately affects men of African descent. Studies assessing the association of zinc intake and prostate cancer have yielded inconsistent results. Furthermore, very little is known about the relationship between zinc intake and prostate cancer among African Americans. We examined the association between self-reported zinc intake and prostate cancer in a hospital-based case-control study of African Americans. We then compared our results with previous studies by performing a meta-analysis to summarize the evidence regarding the association between zinc and prostate cancer. Newly diagnosed African American men with histologically confirmed prostate cancer (n = 127) and controls (n = 81) were recruited from an urban academic urology clinic in Washington, DC. Controls had higher zinc intake, with a mean of 14 mg/day versus 11 mg/day for cases. We observed a non-significant, non-linear increase in prostate cancer when comparing tertiles of zinc intake (OR <6.5 vs 6.5-12.5mg/day 1.8, 95% CI: 0.6,5.6; OR <6.5 vs >12.5mg/day 1.3, 95% CI: 0.2,6.5). The pooled estimate from 17 studies (including 3 cohorts, 2 nested case-control, 11 case-control studies, and 1 randomized clinical trial, with a total of 111,199 participants and 11,689 cases of prostate cancer) was 1.07hi vs lo 95% CI: 0.98-1.16. Using a dose-response meta-analysis, we observed a non-linear trend in the relationship between zinc intake and prostate cancer (p for nonlinearity = 0.0022). This is the first study to examine the relationship between zinc intake in black men and risk of prostate cancer and systematically evaluate available epidemiologic evidence about the magnitude of the relationship between zinc intake and prostate cancer. Despite of the lower intake of zinc by prostate cancer patients, our meta-analysis indicated that there is no evidence for an association between zinc intake and prostate cancer.
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Affiliation(s)
- Abeer M. Mahmoud
- Department of Kinesiology and Nutrition and Department of Physical Therapy, School of Applied Health Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Pathology, South Egypt Cancer Institute, Assiut University, Assiut, Egypt
- * E-mail:
| | - Umaima Al-Alem
- Division of Epidemiology and Biostatistics, School of Public Health, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Firas Dabbous
- James R. & Helen D. Russell Institute for Research & Innovation, Advocate Lutheran General Hospital, Park Ridge, Illinois, United States of America
| | - Mohamed M. Ali
- Department of Kinesiology and Nutrition and Department of Physical Therapy, School of Applied Health Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Ken Batai
- Department of Surgery, College of Medicine, University of Arizona, Tucson, Arizona, United States of America
| | - Ebony Shah
- Department of Surgery, College of Medicine, University of Arizona, Tucson, Arizona, United States of America
| | - Rick A. Kittles
- Department of Surgery, College of Medicine, University of Arizona, Tucson, Arizona, United States of America
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Lynch HT, Kosoko‐Lasaki O, Leslie SW, Rendell M, Shaw T, Snyder C, D'Amico AV, Buxbaum S, Isaacs WB, Loeb S, Moul JW, Powell I. Screening for familial and hereditary prostate cancer. Int J Cancer 2016; 138:2579-91. [DOI: 10.1002/ijc.29949] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 10/30/2015] [Accepted: 11/03/2015] [Indexed: 12/28/2022]
Affiliation(s)
- Henry T. Lynch
- Hereditary Cancer Center and Department of Preventive MedicineCreighton University2500 California PlazaOmaha NE
| | - Omofolasade Kosoko‐Lasaki
- Departments of Surgery, Preventive Medicine & Public HealthCreighton University2500 California PlazaOmaha NE
| | - Stephen W. Leslie
- Department of Surgery (Urology)Creighton University Medical Center601 North 30th Street, Suite 3700Omaha NE
| | - Marc Rendell
- Department of Internal MedicineCreighton University Medical Center601 North 30th Street, Suite 3700Omaha NE
| | - Trudy Shaw
- Hereditary Cancer Center and Department of Preventive MedicineCreighton University2500 California PlazaOmaha NE
| | - Carrie Snyder
- Hereditary Cancer Center and Department of Preventive MedicineCreighton University2500 California PlazaOmaha NE
| | - Anthony V. D'Amico
- Department of Radiation OncologyBrigham and Women's Hospital and Dana Farber Cancer Institute, Harvard Medical SchoolBoston MA
| | - Sarah Buxbaum
- Jackson State University School of Health Sciences350 W. Woodrow Wilson DriveJackson MS
| | - William B. Isaacs
- Departments of Urology and OncologyJohns Hopkins University School of Medicine, Marburg 115, Johns Hopkins Hospital600 N. Wolfe StBaltimore MD
| | - Stacy Loeb
- Department of Urology and Population HealthNew York University550 1st Ave VZ30 (#612)New York NY
| | - Judd W. Moul
- Duke Prostate Center, Division of Urologic Surgery, DUMC 3707‐Room 1562 Duke SouthDuke University Medical CenterDurham NC
| | - Isaac Powell
- Department of UrologyWayne State University, Karmanos Cancer Institute, University Health Center 7‐CDetroit MI
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14
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Almesri N, Das NS, Ali ME, Gumaa K, Giha HA. Independent associations of polymorphisms in vitamin D binding protein (GC) and vitamin D receptor (VDR) genes with obesity and plasma 25OHD3 levels demonstrate sex dimorphism. Appl Physiol Nutr Metab 2015; 41:345-53. [PMID: 26881316 DOI: 10.1139/apnm-2015-0284] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We investigated a possible association between polymorphisms in vitamin D binding protein (GC) and vitamin D receptor (VDR) genes and obesity in Bahraini adults. For this purpose, 406 subjects with varying body mass indexes (BMIs) were selected. Plasma levels of 25-hydroxyvitamin D3 (25OHD3) were measured by chemiluminescence immunoassay. Six single nucleotide polymorphisms, 2 in the VDR gene (rs731236 TC and rs12721377 AG) and 4 in the GC gene (rs2282679 AC, rs4588 CA, rs7041 GT, and rs2298849 TC), were genotyped by real-time polymerase chain reaction. We found that the rs7041 minor allele (G) and rare genotype (GG) were associated with higher BMI (p = 0.007 and p = 0.012, respectively), but they did not influence 25OHD3 levels. However, the minor alleles of rs2282679 (A) and rs4588 (C) were associated with low 25OHD3 plasma levels (p = 0.039 and p = 0.021, respectively), but not with BMI. Having categorized the subjects based on their sex, we found that (i) rs7041 GG associated with high BMI in females (p = 0.003), (ii) rs4588 CC associated with high BMI in females (p = 0.034) and low 25OHD3 levels in males (p = 0.009), and (iii) rs12721377 AA associated with low 25OHD3 levels in females (p = 0.039). Notably, none of the common haplotypes (6 in the GC gene and 3 in the VDR gene) were associated with BMI. Therefore, polymorphisms in the GC (rs2282679, rs4588, rs7041) and VDR (rs12721377) genes were independently associated with obesity and 25OHD3 levels with a clear sex dimorphism.
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Affiliation(s)
- Norah Almesri
- a Department of Biochemistry, College of Medicine and Medical Sciences (CMMS), Arabian Gulf University (AGU), PO Box 26671, Manama, Bahrain
| | - Nagalla S Das
- b Clinical Chemistry Laboratory, Salmaniya Medical Complex (SMC), Manama, Kingdom of Bahrain
| | - Muhallab E Ali
- a Department of Biochemistry, College of Medicine and Medical Sciences (CMMS), Arabian Gulf University (AGU), PO Box 26671, Manama, Bahrain
| | - Khalid Gumaa
- c Division of Biosciences - Cell and Developmental Biology, University College London (UCL), London, UK
| | - Hayder Ahmed Giha
- a Department of Biochemistry, College of Medicine and Medical Sciences (CMMS), Arabian Gulf University (AGU), PO Box 26671, Manama, Bahrain
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Analysis of Prostate Cancer Susceptibility Variants in South African Men: Replicating Associations on Chromosomes 8q24 and 10q11. Prostate Cancer 2015; 2015:465184. [PMID: 26347821 PMCID: PMC4549549 DOI: 10.1155/2015/465184] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 08/02/2015] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association studies (GWAS) have implicated single nucleotide polymorphisms (SNPs) on chromosomes 2p15, 6q25, 7p15.2, 7q21, 8q24, 10q11, 10q26, 11q13, 17q12, 17q24, 19q13, and Xp11, with prostate cancer (PCa) susceptibility and/or tumour aggressiveness, in populations of African, European, and Asian ancestry. The objective of this study was to confirm these associations in South African Mixed Ancestry and White men. We evaluated 17 prioritised GWAS SNPs in South African cases (331 Mixed Ancestry and 155 White) and controls (178 Mixed Ancestry and 145 White). The replicated SNP associations for the different South African ethnic groups were rs7008482 (8q24) (p = 2.45 × 10−5), rs6983267 (8q24) (p = 4.48 × 10−7), and rs10993994 (10q11) (p = 1.40 × 10−3) in Mixed Ancestry men and rs10993994 (p = 1.56 × 10−9) in White men. No significant associations were observed for the analyses stratified by disease aggressiveness in the individual and the combined population group analysis. The present study demonstrates that a number of known PCa susceptibility variants may contribute to disease susceptibility in South African men. Larger genetic investigations extended to other South African population groups are warranted to confirm the role of these and other SNPs in disease susceptibility.
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Common vitamin D pathway gene variants reveal contrasting effects on serum vitamin D levels in African Americans and European Americans. Hum Genet 2014; 133:1395-405. [PMID: 25085266 PMCID: PMC4185105 DOI: 10.1007/s00439-014-1472-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 07/18/2014] [Indexed: 01/06/2023]
Abstract
Vitamin D deficiency is more common among African Americans (AAs) than among European Americans (EAs), and epidemiologic evidence links vitamin D status to many health outcomes. Two genome-wide association studies (GWAS) in European populations identified vitamin D pathway gene single-nucleotide polymorphisms (SNPs) associated with serum vitamin D [25(OH)D] levels, but a few of these SNPs have been replicated in AAs. Here, we investigated the associations of 39 SNPs in vitamin D pathway genes, including 19 GWAS-identified SNPs, with serum 25(OH)D concentrations in 652 AAs and 405 EAs. Linear and logistic regression analyses were performed adjusting for relevant environmental and biological factors. The pattern of SNP associations was distinct between AAs and EAs. In AAs, six GWAS-identified SNPs in GC, CYP2R1, and DHCR7/NADSYN1 were replicated, while nine GWAS SNPs in GC and CYP2R1 were replicated in EAs. A CYP2R1 SNP, rs12794714, exhibited the strongest signal of association in AAs. In EAs, however, a different CYP2R1 SNP, rs1993116, was the most strongly associated. Our models, which take into account genetic and environmental variables, accounted for 20 and 28 % of the variance in serum vitamin D levels in AAs and EAs, respectively.
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Solomon JD, Heitzer MD, Liu TT, Beumer JH, Parise RA, Normolle DP, Leach DA, Buchanan G, DeFranco DB. VDR activity is differentially affected by Hic-5 in prostate cancer and stromal cells. Mol Cancer Res 2014; 12:1166-80. [PMID: 24825850 DOI: 10.1158/1541-7786.mcr-13-0395] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
UNLABELLED Patients with prostate cancer treated with androgen deprivation therapy (ADT) eventually develop castrate-resistant prostate cancer (CRPC). 1,25-Dihydroxyvitamin D3 (1,25D3/calcitriol) is a potential adjuvant therapy that confers antiproliferative and pro-differentiation effects in vitro, but has had mixed results in clinical trials. The impact of the tumor microenvironment on 1,25D3 therapy in patients with CRPC has not been assessed. Transforming growth factor β (TGFβ), which is associated with the development of tumorigenic "reactive stroma" in prostate cancer, induced vitamin D3 receptor (VDR) expression in the human WPMY-1 prostate stromal cell line. Similarly, TGFβ enhanced 1,25D3-induced upregulation of CYP24A1, which metabolizes 1,25D3 and thereby limits VDR activity. Ablation of Hic-5, a TGFβ-inducible nuclear receptor coregulator, inhibited basal VDR expression, 1,25D3-induced CYP24A1 expression and metabolism of 1,25D3 and TGFβ-enhanced CYP24A1 expression. A Hic-5-responsive sequence was identified upstream (392-451 bp) of the CYP24A1 transcription start site that is occupied by VDR only in the presence of Hic-5. Ectopic expression of Hic-5 sensitized LNCaP prostate tumor cells to growth-inhibitory effects of 1,25D3 independent of CYP24A1. The sensitivity of Hic-5-expressing LNCaP cells to 1,25D3-induced growth inhibition was accentuated in coculture with Hic-5-ablated WPMY-1 cells. Therefore, these findings indicate that the search for mechanisms to sensitize prostate cancer cells to the antiproliferative effects of VDR ligands needs to account for the impact of VDR activity in the tumor microenvironment. IMPLICATIONS Hic-5 acts as a coregulator with distinct effects on VDR transactivation, in prostate cancer and stromal cells, and may exert diverse effects on adjuvant therapy designed to exploit VDR activity in prostate cancer.
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Affiliation(s)
| | | | | | | | | | - Daniel P Normolle
- Biostatistics Facility, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, Pennsylvania; and
| | - Damien A Leach
- The Basil Hetzel Institute for Translational Health Research, University of Adelaide, South Australia, Australia
| | - Grant Buchanan
- The Basil Hetzel Institute for Translational Health Research, University of Adelaide, South Australia, Australia
| | - Donald B DeFranco
- Departments of Molecular Genetics and Developmental Biology and Pharmacology and Chemical Biology;
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18
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Hazelett DJ, Rhie SK, Gaddis M, Yan C, Lakeland DL, Coetzee SG, Henderson BE, Noushmehr H, Cozen W, Kote-Jarai Z, Eeles RA, Easton DF, Haiman CA, Lu W, Farnham PJ, Coetzee GA. Comprehensive functional annotation of 77 prostate cancer risk loci. PLoS Genet 2014; 10:e1004102. [PMID: 24497837 PMCID: PMC3907334 DOI: 10.1371/journal.pgen.1004102] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 11/14/2013] [Indexed: 11/19/2022] Open
Abstract
Genome-wide association studies (GWAS) have revolutionized the field of cancer genetics, but the causal links between increased genetic risk and onset/progression of disease processes remain to be identified. Here we report the first step in such an endeavor for prostate cancer. We provide a comprehensive annotation of the 77 known risk loci, based upon highly correlated variants in biologically relevant chromatin annotations--we identified 727 such potentially functional SNPs. We also provide a detailed account of possible protein disruption, microRNA target sequence disruption and regulatory response element disruption of all correlated SNPs at r(2) ≥ 0.88%. 88% of the 727 SNPs fall within putative enhancers, and many alter critical residues in the response elements of transcription factors known to be involved in prostate biology. We define as risk enhancers those regions with enhancer chromatin biofeatures in prostate-derived cell lines with prostate-cancer correlated SNPs. To aid the identification of these enhancers, we performed genomewide ChIP-seq for H3K27-acetylation, a mark of actively engaged enhancers, as well as the transcription factor TCF7L2. We analyzed in depth three variants in risk enhancers, two of which show significantly altered androgen sensitivity in LNCaP cells. This includes rs4907792, that is in linkage disequilibrium (r(2) = 0.91) with an eQTL for NUDT11 (on the X chromosome) in prostate tissue, and rs10486567, the index SNP in intron 3 of the JAZF1 gene on chromosome 7. Rs4907792 is within a critical residue of a strong consensus androgen response element that is interrupted in the protective allele, resulting in a 56% decrease in its androgen sensitivity, whereas rs10486567 affects both NKX3-1 and FOXA-AR motifs where the risk allele results in a 39% increase in basal activity and a 28% fold-increase in androgen stimulated enhancer activity. Identification of such enhancer variants and their potential target genes represents a preliminary step in connecting risk to disease process.
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Affiliation(s)
- Dennis J. Hazelett
- Departments of Urology and Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Suhn Kyong Rhie
- Departments of Urology and Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Malaina Gaddis
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Chunli Yan
- Departments of Urology and Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Daniel L. Lakeland
- Sonny Astani Department of Civil and Environmental Engineering, University of Southern California, Los Angeles, California, United States of America
| | - Simon G. Coetzee
- Department of Genetics, University of São Paulo, Ribeirão Preto, Brazil
| | - Ellipse/GAME-ON consortium
- Department of Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | | | - Brian E. Henderson
- Department of Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Houtan Noushmehr
- Department of Genetics, University of São Paulo, Ribeirão Preto, Brazil
| | - Wendy Cozen
- USC Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | | | - Rosalind A. Eeles
- The Institute of Cancer Research, Sutton, United Kingdom
- Royal Marsden National Health Service (NHS) Foundation Trust, London and Sutton, United Kingdom
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Christopher A. Haiman
- Department of Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Wange Lu
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Peggy J. Farnham
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Gerhard A. Coetzee
- Departments of Urology and Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
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Karami S, Andreotti G, Koutros S, Barry KH, Moore LE, Han S, Hoppin JA, Sandler DP, Lubin JH, Burdette LA, Yuenger J, Yeager M, Freeman LEB, Blair A, Alavanja MCR. Pesticide exposure and inherited variants in vitamin d pathway genes in relation to prostate cancer. Cancer Epidemiol Biomarkers Prev 2013; 22:1557-66. [PMID: 23833127 PMCID: PMC3773544 DOI: 10.1158/1055-9965.epi-12-1454] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Vitamin D and its metabolites are believed to impede carcinogenesis by stimulating cell differentiation, inhibiting cell proliferation, and inducing apoptosis. Certain pesticides have been shown to deregulate vitamin D's anticarcinogenic properties. We hypothesize that certain pesticides may be linked to prostate cancer via an interaction with vitamin D genetic variants. METHODS We evaluated interactions between 41 pesticides and 152 single-nucleotide polymorphisms (SNP) in nine vitamin D pathway genes among 776 prostate cancer cases and 1,444 male controls in a nested case-control study of Caucasian pesticide applicators within the Agricultural Health Study. We assessed Pinteraction values using likelihood ratio tests from unconditional logistic regression and a false discovery rate (FDR) to account for multiple comparisons. RESULTS Five significant interactions (P < 0.01) displayed a monotonic increase in prostate cancer risk with individual pesticide use in one genotype and no association in the other. These interactions involved parathion and terbufos use and three vitamin D genes (VDR, RXRB, and GC). The exposure-response pattern among participants with increasing parathion use with the homozygous CC genotype for GC rs7041 compared with unexposed participants was noteworthy [low vs. no exposure: OR, 2.58, 95% confidence interval (CI), 1.07-6.25; high vs. no exposure: OR, 3.09, 95% CI, 1.10-8.68; Pinteraction = 3.8 × 10(-3)]. CONCLUSIONS In this study, genetic variations in vitamin D pathway genes, particularly GC rs7041, an SNP previously linked to lower circulating vitamin D levels, modified pesticide associations with prostate cancer risk. IMPACT Because our study is the first to examine this relationship, additional studies are needed to rule out chance findings.
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Affiliation(s)
- Sara Karami
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD 20852, USA.
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20
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Kinseth MA, Jia Z, Rahmatpanah F, Sawyers A, Sutton M, Wang-Rodriguez J, Mercola D, McGuire KL. Expression differences between African American and Caucasian prostate cancer tissue reveals that stroma is the site of aggressive changes. Int J Cancer 2013; 134:81-91. [PMID: 23754304 DOI: 10.1002/ijc.28326] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 05/22/2013] [Indexed: 12/21/2022]
Abstract
In prostate cancer, race/ethnicity is the highest risk factor after adjusting for age. African Americans have more aggressive tumors at every clinical stage of the disease, resulting in poorer prognosis and increased mortality. A major barrier to identifying crucial gene activity differences is heterogeneity, including tissue composition variation intrinsic to the histology of prostate cancer. We hypothesized that differences in gene expression in specific tissue types would reveal mechanisms involved in the racial disparities of prostate cancer. We examined 17 pairs of arrays for AAs and Caucasians that were formed by closely matching the samples based on the known tissue type composition of the tumors. Using pair-wise t-test we found significantly altered gene expression between AAs and CAs. Independently, we performed multiple linear regression analyses to associate gene expression with race considering variation in percent tumor and stroma tissue. The majority of differentially expressed genes were associated with tumor-adjacent stroma rather than tumor tissue. Extracellular matrix, integrin family and signaling mediators of the epithelial-to-mesenchymal transition (EMT) pathways were all downregulated in stroma of AAs. Using MetaCore (GeneGo) analysis, we observed that 35% of significant (p < 10(-3)) pathways identified EMT and 25% identified immune response pathways especially for interleukins-2, -4, -5, -6, -7, -10, -13, -15 and -22 as the major changes. Our studies reveal that altered immune and EMT processes in tumor-adjacent stroma may be responsible for the aggressive nature of prostate cancer in AAs.
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Ogbah Z, Visa L, Badenas C, Ríos J, Puig-Butille JA, Bonifaci N, Guino E, Augé JM, Kolm I, Carrera C, Pujana MÁ, Malvehy J, Puig S. Serum 25-hydroxyvitamin D3 levels and vitamin D receptor variants in melanoma patients from the Mediterranean area of Barcelona. BMC MEDICAL GENETICS 2013; 14:26. [PMID: 23413917 PMCID: PMC3648347 DOI: 10.1186/1471-2350-14-26] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 02/12/2013] [Indexed: 02/04/2023]
Abstract
BACKGROUND Serum 25-hydroxyvitamin D3 (Vitamin D) insufficiency and single-nucleotide polymorphisms (SNPs) on its receptor, Vitamin D receptor (VDR), have been reported to be involved in melanoma susceptibility in populations mostly from northern countries. OBJECTIVE To investigate 25-hydroxyvitamin D3 levels and VDR SNPs in melanoma patients from sunny area of Barcelona, two studies were carried out. The first study evaluated the levels of Vitamin D at time of melanoma diagnosis and the second one analyzed the association between VDR genetic variants and risk of having a high nevus number, the strongest phenotypic risk factor for melanoma. METHODS The levels of 25-hydroxyvitamin D3 in 81 melanoma patients at diagnosis were measured. In a second group of melanoma patients, including 150 with low and 113 with high nevus number, 11 VDR SNPs were analyzed for their association with nevus number. RESULTS In the first study, 68% of patients had insufficient levels of 25-hydroxyvitamin D3 (<25 ng/ml). Autumn-winter months and fair phototype were associated with 25-hydroxyvitamin D3 insufficiency; after multivariate analysis, season of sampling remained the only independent predictor of 25-hydroxyvitamin D3 levels. In the second study, VDR variant rs2189480 (P = 0.006) was associated with risk of high nevus number whereas rs2239179 (P = 0.044) and rs7975128 (P = 0.0005) were protective against high nevus number. After Bonferroni adjustment only rs7975128 remained significant. In stratified analysis, SNP rs7975128 was found protective against multiple melanomas (P = 0.021). CONCLUSION This study showed that even in Barcelona, a sunny Mediterranean area, 25-hydroxyvitamin D3 levels were sub-optimal in the majority of melanoma patients at diagnosis. The involvement of VDR in nevi and, in turn, in melanoma susceptibility has also been suggested. Larger studies are needed to confirm our findings.
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Höbaus J, Thiem U, Hummel DM, Kallay E. Role of calcium, vitamin D, and the extrarenal vitamin D hydroxylases in carcinogenesis. Anticancer Agents Med Chem 2013; 13:20-35. [PMID: 23094918 PMCID: PMC3826118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Revised: 05/05/2012] [Accepted: 05/16/2012] [Indexed: 06/01/2023]
Abstract
Vitamin D deficiency and low calcium intake are considered risk factors for several cancers. Vitamin D, synthesized in the skin or ingested through the diet, is transformed through two hydroxylation steps to the active metabolite, 1α,25-dihydroxyvitamin D3 (1,25-D3). 25-hydroxylases in the liver are responsible for the first hydroxylation step. The ultimate activation is performed by the renal 25-hydroxyvitamin D 1α-hydroxylase (CYP27B1), while the 1,25-dihydroxyvitamin D 24-hydroxylase (CYP24A1) in the kidneys degrades the active metabolite. These two renal vitamin D hydroxylases control the endocrine serum 1,25-D3 levels, and are responsible for maintaining mineral homeostasis. In addition, the active vitamin D hormone 1,25-D3 regulates cellular proliferation, differentiation, and apoptosis in multiple tissues in a paracrine/autocrine manner. Interestingly, it is the low serum level of the precursor 25- hydroxyvitamin D3 (25-D3) that predisposes to numerous cancers and other chronic diseases, and not the serum concentration of the active vitamin D hormone. The extra-renal autocrine/paracrine vitamin D system is able to synthesize and degrade locally the active 1,25- D3 necessary to maintain normal cell growth and to counteract mitogenic stimuli. Thus, vitamin D hydroxylases play a prominent role in this process. The present review describes the role of the vitamin D hydroxylases in cancer pathogenesis and the cross-talk between the extra-renal autocrine/paracrine vitamin D system and calcium in cancer prevention.
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Affiliation(s)
- Julia Höbaus
- Department of Pathophysiology and Allergy Research
| | - Ursula Thiem
- Department of Pathophysiology and Allergy Research
- Division of Nephrology and Dialysis, Medical University of Vienna
| | | | - Enikö Kallay
- Department of Pathophysiology and Allergy Research
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Grant DJ, Hoyo C, Akushevich L, Iversen ES, Whitaker R, Marks J, Berchuck A, Schildkraut JM. Vitamin D receptor (VDR) polymorphisms and risk of ovarian cancer in Caucasian and African American women. Gynecol Oncol 2012; 129:173-8. [PMID: 23262379 DOI: 10.1016/j.ygyno.2012.12.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 12/12/2012] [Accepted: 12/13/2012] [Indexed: 10/27/2022]
Abstract
OBJECTIVE Polymorphisms in the vitamin D receptor (VDR) gene have been shown in some studies to be associated with the risk of epithelial ovarian cancer (EOC) in Caucasian women. There are no published reports among African Americans. METHODS Case-control data from the North Carolina Ovarian Cancer Study were analyzed using logistic regression to determine the association between seven VDR polymorphisms and EOC in both Caucasians (513 cases, 532 controls) and African Americans (74 cases, 79 controls). In a larger sample of African-Americans (125 cases, 155 controls), we assessed associations between six SNPs in proximity of rs7975232. RESULTS African American women who carried at least one minor allele of rs7975232 were at higher risk for invasive EOC controlling for age and admixture with an odds ratio (OR) for association under the log-additive model of 2.08 (95% confidence interval (CI)=1.19, 3.63, p=0.010). No association was observed between any of the VDR variants and EOC among Caucasians. A larger sample of African Americans revealed a nearly two-fold increased risk of invasive EOC associated with rs7305032, a SNP in proximity to rs7975232 (R(2)=0.369) with a log-additive OR of 1.87 (95% CI=1.20, 2.93, p=0.006). CONCLUSIONS This is the first report showing VDR variants associated with ovarian cancer risk in African American women. A larger study of African American women is needed to confirm these findings. These results imply that vitamin D exposure is a possible modifiable risk factor of ovarian cancer among African Americans.
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Affiliation(s)
- Delores J Grant
- Department of Biology and Cancer Research Program, JLC-Biomedical/Biotechnology Research Institute, North Carolina Central University, Durham, NC, USA
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Ricks-Santi LJ, Apprey V, Mason T, Wilson B, Abbas M, Hernandez W, Hooker S, Doura M, Bonney G, Dunston G, Kittles R, Ahaghotu C. Identification of genetic risk associated with prostate cancer using ancestry informative markers. Prostate Cancer Prostatic Dis 2012; 15:359-64. [PMID: 22801071 PMCID: PMC4291058 DOI: 10.1038/pcan.2012.19] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 04/13/2012] [Accepted: 04/19/2012] [Indexed: 12/18/2022]
Abstract
BACKGROUND Prostate cancer (PCa) is a common malignancy and a leading cause of cancer death among men in the United States with African-American (AA) men having the highest incidence and mortality rates. Given recent results from admixture mapping and genome-wide association studies for PCa in AA men, it is clear that many risk alleles are enriched in men with West African genetic ancestry. METHODS A total of 77 ancestry informative markers (AIMs) within surrounding candidate gene regions were genotyped and haplotyped using Pyrosequencing in 358 unrelated men enrolled in a PCa genetic association study at the Howard University Hospital between 2000 and 2004. Sequence analysis of promoter region single-nucleotide polymorphisms (SNPs) to evaluate disruption of transcription factor-binding sites was conducted using in silico methods. RESULTS Eight AIMs were significantly associated with PCa risk after adjusting for age and West African ancestry. SNP rs1993973 (intervening sequences) had the strongest association with PCa using the log-additive genetic model (P=0.002). SNPs rs1561131 (genotypic, P=0.007), rs1963562 (dominant, P=0.01) and rs615382 (recessive, P=0.009) remained highly significant after adjusting for both age and ancestry. We also tested the independent effect of each significantly associated SNP and rs1561131 (P=0.04) and rs1963562 (P=0.04) remained significantly associated with PCa development. After multiple comparisons testing using the false discovery rate, rs1993973 remained significant. Analysis of the rs156113-, rs1963562-rs615382l and rs1993973-rs585224 haplotypes revealed that the least frequently found haplotypes in this population were significantly associated with a decreased risk of PCa (P=0.032 and 0.0017, respectively). CONCLUSIONS The approach for SNP selection utilized herein showed that AIMs may not only leverage increased linkage disequilibrium in populations to identify risk and protective alleles, but may also be informative in dissecting the biology of PCa and other health disparities.
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Affiliation(s)
- L J Ricks-Santi
- Division of Genetics, Department of Pediatrics and Child Health, Howard University College of Medicine, Washington, DC 20060, 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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Batai K, Shah E, Murphy AB, Newsome J, Ruden M, Ahaghotu C, Kittles RA. Fine-mapping of IL16 gene and prostate cancer risk in African Americans. Cancer Epidemiol Biomarkers Prev 2012; 21:2059-68. [PMID: 22923025 DOI: 10.1158/1055-9965.epi-12-0707] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Prostate cancer is the most common type of cancer among men in the United States, and its incidence and mortality rates are disproportionate among ethnic groups. Although genome-wide association studies of European descents have identified candidate loci associated with prostate cancer risk, including a variant in IL16, replication studies in African Americans (AA) have been inconsistent. Here we explore single-nucleotide polymorphism (SNP) variation in IL16 in AAs and test for association with prostate cancer. METHODS Association tests were conducted for 2,257 genotyped and imputed SNPs spanning IL16 in 605 AA prostate cancer cases and controls from Washington, D.C. Eleven of them were also genotyped in a replication population of 1,093 AAs from Chicago. We tested for allelic association adjusting for age, global and local West African ancestry. RESULTS Analyses of genotyped and imputed SNPs revealed that a cluster of IL16 SNPs were significantly associated with prostate cancer risk. The strongest association was found at rs7175701 (P = 9.8 × 10(-8)). In the Chicago population, another SNP (rs11556218) was associated with prostate cancer risk (P = 0.01). In the pooled analysis, we identified three independent loci within IL16 that were associated with prostate cancer risk. SNP expression quantitative trait loci analyses revealed that rs7175701 is predicted to influence the expression of IL16 and other cancer-related genes. CONCLUSION Our study provides evidence that IL16 polymorphisms play a role in prostate cancer susceptibility among AAs. IMPACT Our findings are significant given that there has been limited focus on the role of IL16 genetic polymorphisms on prostate cancer risk in AAs.
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Affiliation(s)
- Ken Batai
- Institute of Human Genetics, College of Medicine, School of Public Health, University of Illinois at Chicago, Chicago, IL 60607-4067, USA
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Wheeler HE, Gorsic LK, Welsh M, Stark AL, Gamazon ER, Cox NJ, Dolan ME. Genome-wide local ancestry approach identifies genes and variants associated with chemotherapeutic susceptibility in African Americans. PLoS One 2011; 6:e21920. [PMID: 21755009 PMCID: PMC3130766 DOI: 10.1371/journal.pone.0021920] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 06/08/2011] [Indexed: 12/31/2022] Open
Abstract
Chemotherapeutic agents are used in the treatment of many cancers, yet variable resistance and toxicities among individuals limit successful outcomes. Several studies have indicated outcome differences associated with ancestry among patients with various cancer types. Using both traditional SNP-based and newly developed gene-based genome-wide approaches, we investigated the genetics of chemotherapeutic susceptibility in lymphoblastoid cell lines derived from 83 African Americans, a population for which there is a disparity in the number of genome-wide studies performed. To account for population structure in this admixed population, we incorporated local ancestry information into our association model. We tested over 2 million SNPs and identified 325, 176, 240, and 190 SNPs that were suggestively associated with cytarabine-, 5'-deoxyfluorouridine (5'-DFUR)-, carboplatin-, and cisplatin-induced cytotoxicity, respectively (p≤10(-4)). Importantly, some of these variants are found only in populations of African descent. We also show that cisplatin-susceptibility SNPs are enriched for carboplatin-susceptibility SNPs. Using a gene-based genome-wide association approach, we identified 26, 11, 20, and 41 suggestive candidate genes for association with cytarabine-, 5'-DFUR-, carboplatin-, and cisplatin-induced cytotoxicity, respectively (p≤10(-3)). Fourteen of these genes showed evidence of association with their respective chemotherapeutic phenotypes in the Yoruba from Ibadan, Nigeria (p<0.05), including TP53I11, COPS5 and GAS8, which are known to be involved in tumorigenesis. Although our results require further study, we have identified variants and genes associated with chemotherapeutic susceptibility in African Americans by using an approach that incorporates local ancestry information.
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Affiliation(s)
- Heather E. Wheeler
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Lidija K. Gorsic
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Marleen Welsh
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Amy L. Stark
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Eric R. Gamazon
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Nancy J. Cox
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - M. Eileen Dolan
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
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