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Song X, Ru M, Steinsnyder Z, Tkachuk K, Kopp RP, Sullivan J, Gümüş ZH, Offit K, Joseph V, Klein RJ. SNPs at SMG7 Associated with Time from Biochemical Recurrence to Prostate Cancer Death. Cancer Epidemiol Biomarkers Prev 2022; 31:1466-1472. [PMID: 35511739 PMCID: PMC9250608 DOI: 10.1158/1055-9965.epi-22-0053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/25/2022] [Accepted: 05/02/2022] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND A previous genome-wide association study identified several loci with genetic variants associated with prostate cancer survival time in two cohorts from Sweden. Whether these variants have an effect in other populations or if their effect is homogenous across the course of disease is unknown. METHODS These variants were genotyped in a cohort of 1,298 patients. Samples were linked with age, PSA level, Gleason score, cancer stage at surgery, and times from surgery to biochemical recurrence to death from prostate cancer. SNPs rs2702185 and rs73055188 were tested for association with prostate cancer-specific survival time using a multivariate Cox proportional hazard model. SNP rs2702185 was further tested for association with time to biochemical recurrence and time from biochemical recurrence to death with a multi-state model. RESULTS SNP rs2702185 at SMG7 was associated with prostate cancer-specific survival time, specifically the time from biochemical recurrence to prostate cancer death (HR, 2.5; 95% confidence interval, 1.4-4.5; P = 0.0014). Nine variants were in linkage disequilibrium (LD) with rs2702185; one, rs10737246, was found to be most likely to be functional based on LD patterns and overlap with open chromatin. Patterns of open chromatin and correlation with gene expression suggest that this SNP may affect expression of SMG7 in T cells. CONCLUSIONS The SNP rs2702185 at the SMG7 locus is associated with time from biochemical recurrence to prostate cancer death, and its LD partner rs10737246 is predicted to be functional. IMPACT These results suggest that future association studies of prostate cancer survival should consider various intervals over the course of disease.
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Affiliation(s)
- Xiaoyu Song
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
| | - Meng Ru
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
| | - Zoe Steinsnyder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Kaitlyn Tkachuk
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Ryan P. Kopp
- Department of Urology, Oregon Health and Science University, Portland, OR, 97239 USA
| | - John Sullivan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Zeynep H. Gümüş
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Vijai Joseph
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Robert J. Klein
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
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2
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Chen D, Zhang R, Xie A, Yuan J, Zhang J, Huang Y, Zhang H, Zhang F. Clinical correlations and prognostic value of Nudix hydroxylase 10 in patients with gastric cancer. Bioengineered 2021; 12:9779-9789. [PMID: 34696672 PMCID: PMC8809933 DOI: 10.1080/21655979.2021.1995104] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 02/05/2023] Open
Abstract
Gastric cancer (GC) is one of the most common and lethal cancers worldwide. The Nudix hydroxylase (NUDT) genes have been reported to play notable roles in tumor progression. However, the role of NUDT10 in GC has not been reported. In this study, we investigated the expression of NUDT10 in GC and its association with clinicopathological characteristics. Quantitative real-time polymerase chain reaction and analyses of The Cancer Genome Atlas and Human Protein Atlas databases were performed to determine NUDT10 mRNA and protein expression. Receiver operating characteristic curve analysis was used to assess the diagnostic value of NUDT10 in patients with GC. We used Cox regression and the Kaplan-Meier method to assess the correlations between clinicopathological factors and survival outcomes of patients with GC. Gene set enrichment analysis (GSEA) was performed to identify the underlying signaling pathways. NUDT10 mRNA and protein expression was significantly lower in GC tissues compared to normal tissues. Interestingly, higher NUDT10 expression was correlated with advanced tumor stage, deeper local invasion, and worse survival outcomes. Patients with higher NUDT10 expression had a significantly worse prognosis than those with lower NUDT10 expression. Multivariate analysis showed that high NUDT10 expression was an independent predictor of survival outcome. Several pathways, including mismatch repair, nucleotide excision repair, extracellular matrix receptor interaction, and cancer signaling, were identified as enriched pathways in GC through GSEA. To our knowledge, this study is the first to characterize NUDT10 expression in GC. Our study demonstrates that NUDT10 is a promising independent biomarker for GC prognosis.
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Affiliation(s)
- Diqun Chen
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Rouxin Zhang
- College of Science and Technology, China Three Gorges University, Yichang, China
| | - Aosi Xie
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Jinpeng Yuan
- Department of Abdominal Surgery, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Jinhai Zhang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Yongjian Huang
- Department of Gastrointestinal Surgery, Shantou Guorui Hospital, Shantou, China
| | - Hongxia Zhang
- Health Care Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- CONTACT Hongxia Zhang Health Care Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, China; Feiran Zhang Department of Gastrointestinal Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Feiran Zhang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
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3
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Bardhan A, Banerjee A, Basu K, Pal DK, Ghosh A. PRNCR1: a long non-coding RNA with a pivotal oncogenic role in cancer. Hum Genet 2021; 141:15-29. [PMID: 34727260 PMCID: PMC8561087 DOI: 10.1007/s00439-021-02396-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/26/2021] [Indexed: 02/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been gaining importance in the field of cancer research in recent years. PRNCR1 (prostate cancer-associated non-coding RNA1) is a 12.7 kb, intron-less lncRNA found to play an oncogenic role in malignancy of diverse organs including prostate, breast, lung, oral cavity, colon and rectum. Single-nucleotide polymorphisms (SNPs) of PRNCR1 locus have been found to be associated with cancer susceptibility in different populations. In this review, an attempt has been made for the first time to summarize all sorts of available data on PRNCR1 to date from relevant databases (GeneCard, LncExpDB, Ensembl genome browser, and PubMed). As functional roles of PRNCR1, miRNA (microRNA) sponging was mostly highlighted in the pathogenesis of different cancer; in addition, an association of the lncRNA with chromatin-modifying complex to enhance androgen receptor-mediated gene transcription was reported in prostate cancer. Diagnostic and prognostic importance of PRNCR1 was found in some malignancies suggesting potency of the lncRNA to serve as a clinical biomarker. For PRNCR1 SNPs, although cancer susceptibility of the risk alleles/genotypes was reported in different populations, majorities of the findings were not replicated and underlying molecular mechanisms remained unexplored. Therapeutic implication of PRNCR1 was not studied well and future research may come up in this direction for intervening novel strategies to fight against cancer.
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Affiliation(s)
- Abhishek Bardhan
- Genetics of Non-Communicable Diseases, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal, 700073, India
| | - Anwesha Banerjee
- Genetics of Non-Communicable Diseases, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal, 700073, India
| | - Keya Basu
- Department of Pathology, IPGME&R, Kolkata, West Bengal, India
| | | | - Amlan Ghosh
- Genetics of Non-Communicable Diseases, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal, 700073, India.
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4
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Wang X, Hayes JE, Xu X, Gao X, Mehta D, Lilja HG, Klein RJ. Validation of prostate cancer risk variants rs10993994 and rs7098889 by CRISPR/Cas9 mediated genome editing. Gene 2020; 768:145265. [PMID: 33122083 DOI: 10.1016/j.gene.2020.145265] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/10/2020] [Accepted: 10/20/2020] [Indexed: 12/20/2022]
Abstract
GWAS have identified numerous SNPs associated with prostate cancer risk. One such SNP is rs10993994. It is located in the β-microseminoprotein (MSMB) promoter region, mediates MSMB prostate secretion levels, and is linked to mRNA expression changes in both MSMB and the adjacent gene NCOA4. In addition, our previous work showed a second SNP, rs7098889, is in positive linkage disequilibrium with rs10993994 and associated with MSMB expression independent of rs10993994. Here, we generate a series of clones with single alleles removed by double guide RNA (gRNA) mediated CRISPR/Cas9 deletions, through which we demonstrate that each of these SNPs independently and greatly alters MSMB expression in an allele-specific manner. We further show that these SNPs have no substantial effect on the expression of NCOA4. These data demonstrate that a single SNP can have a large effect on gene expression and illustrate the importance of functional validation studies to deconvolute observed correlations. The method we have developed is generally applicable to test any SNP for which a relevant heterozygous cell line is available. AUTHOR SUMMARY: In pursuing the underlying biological mechanism of prostate cancer pathogenesis, scientists utilized the existence of common single nucleotide polymorphisms (SNPs) in the human genome as genetic markers to perform large scale genome wide association studies (GWAS) and have so far identified more than a hundred prostate cancer risk variants. Such variants provide an unbiased and systematic new venue to study the disease mechanism, and the next big challenge is to translate these genetic associations to the causal role of altered gene function in oncogenesis. The majority of these variants are waiting to be studied and lots of them may act in oncogenesis through gene expression regulation. To prove the concept, we took rs10993994 and its linked rs7098889 as an example and engineered single cell clones by allelic-specific CRISPR/Cas9 deletion to separate the effect of each allele. We observed that a single nucleotide difference would lead to surprisingly high level of MSMB gene expression change in a gene specific and cell-type specific manner. Our study strongly supports the notion that differential level of gene expression caused by risk variants and their associated genetic locus play a major role in oncogenesis and also highlights the importance of studying the function of MSMB encoded β-MSP in prostate cancer pathogenesis.
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Affiliation(s)
- Xing Wang
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - James E Hayes
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Program in Cancer Biology and Genetics and Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, United States; Graduate School of Biomedical Sciences, Weill Cornell Medical College, New York, NY, United States
| | - Xing Xu
- Program in Cancer Biology and Genetics and Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, United States; Graduate School of Biomedical Sciences, Weill Cornell Medical College, New York, NY, United States
| | - Xiaoni Gao
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Program in Cancer Biology and Genetics and Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, United States
| | - Dipti Mehta
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Hans G Lilja
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, United States; Departments of Laboratory Medicine and Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States; Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK and Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Robert J Klein
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Program in Cancer Biology and Genetics and Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, United States.
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5
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Zhang L, Walsh MF, Jairam S, Mandelker D, Zhong Y, Kemel Y, Chen YB, Musheyev D, Zehir A, Jayakumaran G, Brzostowski E, Birsoy O, Yang C, Li Y, Somar J, DeLair D, Pradhan N, Berger MF, Cadoo K, Carlo MI, Robson ME, Stadler ZK, Iacobuzio-Donahue CA, Joseph V, Offit K. Fumarate hydratase FH c.1431_1433dupAAA (p.Lys477dup) variant is not associated with cancer including renal cell carcinoma. Hum Mutat 2019; 41:103-109. [PMID: 31444830 DOI: 10.1002/humu.23900] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 08/13/2019] [Accepted: 08/19/2019] [Indexed: 01/25/2023]
Abstract
Fumarate hydratase (FH) mutations underpin the autosomal recessive syndrome. FH deficiency and the autosomal dominant syndrome hereditary leiomyomatosis and renal cell carcinoma (HLRCC). The FH c.1431_1433dupAAA (p.Lys477dup) genomic alteration has been conclusively shown to contribute to FH deficiency when occurring with another FH germline alteration. However, a sufficiently large dataset has been lacking to conclusively determine its clinical significance to cancer predisposition in the heterozygous state. We reviewed a series of 7,571 patients with cancer who received germline results through MSK-IMPACT testing at the Memorial Sloan Kettering Cancer Center. The FH c.1431_1433dupAAA (p.Lys477dup) variant was detected in 24 individuals, none of whom was affected with renal cancer. Eleven of the 372 patients with renal cancer were identified to carried pathogenic FH variants associated with HLRCC. None of these 372 patients with renal cancer carried the FH c.1431_1433dupAAA variant. Our data indicate the FH c.1431_1433dupAAA is not associated with cancer including renal cell carcinoma.
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Affiliation(s)
- Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Michael F Walsh
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York City, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Sowmya Jairam
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Yi Zhong
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York.,Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Yelena Kemel
- Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Ying-Bei Chen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | | | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Edyta Brzostowski
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Ozge Birsoy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Ciyu Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Yirong Li
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Joshua Somar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Deborah DeLair
- Department of Pathology, New York University Medical Center, New York City, New York
| | - Nisha Pradhan
- University of Colorado School of Medicine, Aurora, Colorado
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Karen Cadoo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York.,Department of Medicine, Weill Cornell Medical College, New York City, New York
| | - Maria I Carlo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York.,Department of Medicine, Weill Cornell Medical College, New York City, New York
| | - Mark E Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York.,Department of Medicine, Weill Cornell Medical College, New York City, New York
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York.,Department of Medicine, Weill Cornell Medical College, New York City, New York
| | - Christine A Iacobuzio-Donahue
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Vijai Joseph
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York.,Department of Medicine, Weill Cornell Medical College, New York City, New York
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York.,Department of Medicine, Weill Cornell Medical College, New York City, New York
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6
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The relationship between KLK3 rs17632542 and PRNCR1 rs16901979 polymorphisms with susceptibility to prostate cancer. Meta Gene 2019. [DOI: 10.1016/j.mgene.2019.100595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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7
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Li W, Gu M. NUDT11 rs5945572 polymorphism and prostate cancer risk: a meta-analysis. Int J Clin Exp Med 2015; 8:3474-3481. [PMID: 26064238 PMCID: PMC4443072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 02/03/2015] [Indexed: 06/04/2023]
Abstract
The association between the NUDT10 rs5945572 polymorphism and prostate cancer (PCa) was not clear. We thus conducted a meta-analysis to assess the association between NUDT10 rs5945572 polymorphism and PCa risk. A literature search was carried out using PUBMED, EMBASE, and Cochrane Library Central database before Dec 2014. The strength of the associations between the NUDT10 rs5945572 polymorphism and PCa risk was measured by odds ratios (OR) with 95% confidence intervals (CI). The random-effects model was used. NUDT10 rs5945572 polymorphism was significantly associated with PCa risk (OR = 1.22, 95% CI 1.19-1.26, P < 0.001, I(2) = 0%, Figure 2). In the subgroup analysis by ethnicity, a significant association was found among Caucasians (OR = 1.25, 95% CI 1.00-1.57, P = 0.05, I(2) = 0%), and Asians (OR = 1.23, 95% CI 1.19-1.28, P < 0.001, I(2) = 0%), and Africans (OR = 1.22, 95% CI 1.03-1.45, P = 0.02, I(2) = 48%). In conclusion, this meta-analysis found a significant association between NUDT10 rs5945572 polymorphism and prostate cancer.
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Affiliation(s)
- Wencheng Li
- Department of Urology, Nanjing First Hospital, Nanjing Medical UniversityNanjing 210006, Jiangsu, China
| | - Min Gu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing 210029, Jiangsu, China
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8
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Cook MB, Wang Z, Yeboah ED, Tettey Y, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Chung CC, Chokkalingam AP, Chu LW, Yeager M, Hutchinson A, Yu K, Rand KA, Haiman CA, Hoover RN, Hsing AW, Chanock SJ. A genome-wide association study of prostate cancer in West African men. Hum Genet 2014; 133:509-21. [PMID: 24185611 PMCID: PMC3988225 DOI: 10.1007/s00439-013-1387-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 10/19/2013] [Indexed: 01/24/2023]
Abstract
Age-adjusted mortality rates for prostate cancer are higher for African-American men compared with those of European ancestry. Recent data suggest that West African men also have elevated risk for prostate cancer relative to European men. Genetic susceptibility to prostate cancer could account for part of this difference. We conducted a genome-wide association study (GWAS) of prostate cancer in West African men in the Ghana Prostate Study. Association testing was performed using multivariable logistic regression adjusted for age and genetic ancestry for 474 prostate cancer cases and 458 population-based controls on the Illumina HumanOmni-5 Quad BeadChip. The most promising association was at 10p14 within an intron of a long non-coding RNA (lncRNA RP11-543F8.2) 360 kb centromeric of GATA3 (p = 1.29E-7). In sub-analyses, SNPs at 5q31.3 were associated with high Gleason score (≥7) cancers, the strongest of which was a missense SNP in PCDHA1 (rs34575154, p = 3.66E-8), and SNPs at Xq28 (rs985081, p = 8.66E-9) and 6q21 (rs2185710, p = 5.95E-8) were associated with low Gleason score (<7) cancers. We sought to validate our findings in silico in the African Ancestry Prostate Cancer GWAS Consortium, but only one SNP, at 10p14, replicated at p < 0.05. Of the 90 prostate cancer loci reported from studies of men of European, Asian or African-American ancestry, we were able to test 81 in the Ghana Prostate Study, and 10 of these replicated at p < 0.05. Further genetic studies of prostate cancer in West African men are needed to confirm our promising susceptibility loci.
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Affiliation(s)
- Michael Blaise Cook
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, 9609 Medical Center Drive, Rm 7-E106, MSC 9774, Bethesda, MD, 20892-9774, USA,
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9
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Variants at IRX4 as prostate cancer expression quantitative trait loci. Eur J Hum Genet 2013; 22:558-63. [PMID: 24022300 DOI: 10.1038/ejhg.2013.195] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 08/06/2013] [Accepted: 08/09/2013] [Indexed: 11/08/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified numerous prostate cancer-associated risk loci. Some variants at these loci may be regulatory and influence expression of nearby genes. Such loci are known as cis-expression quantitative trait loci (cis-eQTL). As cis-eQTLs are highly tissue-specific, we asked if GWAS-identified prostate cancer risk loci are cis-eQTLs in human prostate tumor tissues. We investigated 50 prostate cancer samples for their genotype at 59 prostate cancer risk-associated single-nucleotide polymorphisms (SNPs) and performed cis-eQTL analysis of transcripts from paired primary tumors within two megabase windows. We tested 586 transcript-genotype associations, of which 27 were significant (false discovery rate ≤10%). An equivalent eQTL analysis of the same prostate cancer risk loci in lymphoblastoid cell lines did not result in any significant associations. The top-ranked cis-eQTL involved the IRX4 (Iroquois homeobox protein 4) transcript and rs12653946, tagged by rs10866528 in our study (P=4.91 × 10(-5)). Replication studies, linkage disequilibrium, and imputation analyses highlight population specificity at this locus. We independently validated IRX4 as a potential prostate cancer risk gene through cis-eQTL analysis of prostate cancer risk variants. Cis-eQTL analysis in relevant tissues, even with a small sample size, can be a powerful method to expedite functional follow-up of GWAS.
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10
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Agalliu I, Wang Z, Wang T, Dunn A, Parikh H, Myers T, Burk RD, Amundadottir L. Characterization of SNPs associated with prostate cancer in men of Ashkenazic descent from the set of GWAS identified SNPs: impact of cancer family history and cumulative SNP risk prediction. PLoS One 2013; 8:e60083. [PMID: 23573233 PMCID: PMC3616024 DOI: 10.1371/journal.pone.0060083] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 02/24/2013] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified multiple SNPs associated with prostate cancer (PrCa). Population isolates may have different sets of risk alleles for PrCa constituting unique population and individual risk profiles. METHODS To test this hypothesis, associations between 31 GWAS SNPs of PrCa were examined among 979 PrCa cases and 1,251 controls of Ashkenazic descent using logistic regression. We also investigated risks by age at diagnosis, pathological features of PrCa, and family history of cancer. Moreover, we examined associations between cumulative number of risk alleles and PrCa and assessed the utility of risk alleles in PrCa risk prediction by comparing the area under the curve (AUC) for different logistic models. RESULTS Of the 31 genotyped SNPs, 8 were associated with PrCa at p ≤ 0.002 (corrected p-value threshold) with odds ratios (ORs) ranging from 1.22 to 1.42 per risk allele. Four SNPs were associated with aggressive PrCa, while three other SNPs showed potential interactions for PrCa by family history of PrCa (rs8102476; 19q13), lung cancer (rs17021918; 4q22), and breast cancer (rs10896449; 11q13). Men in the highest vs. lowest quartile of cumulative number of risk alleles had ORs of 3.70 (95% CI 2.76-4.97); 3.76 (95% CI 2.57-5.50), and 5.20 (95% CI 2.94-9.19) for overall PrCa, aggressive cancer and younger age at diagnosis, respectively. The addition of cumulative risk alleles to the model containing age at diagnosis and family history of PrCa yielded a slightly higher AUC (0.69 vs. 0.64). CONCLUSION These data define a set of risk alleles associated with PrCa in men of Ashkenazic descent and indicate possible genetic differences for PrCa between populations of European and Ashkenazic ancestry. Use of genetic markers might provide an opportunity to identify men at highest risk for younger age of onset PrCa; however, their clinical utility in identifying men at highest risk for aggressive cancer remains limited.
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Affiliation(s)
- Ilir Agalliu
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, United States of America.
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