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Risk Allele Frequency Analysis and Risk Prediction of Single-Nucleotide Polymorphisms for Prostate Cancer. Genes (Basel) 2022; 13:genes13112039. [DOI: 10.3390/genes13112039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/29/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
The incidence of prostate cancer (PCa) varies by ethnicity. This study aimed to provide insights into the genetic cause of PCa, which can result in differences in incidence among individuals of diverse ancestry. We collected data on PCa-associated single-nucleotide polymorphisms (SNPs) from a genome-wide association study catalog. Fisher’s exact tests were used to analyze the significance of enrichment or depletion of the effect on the allele at a given SNP. A network analysis was performed based on PCa-related SNPs that showed significant differences among ethnicities. The SNP-based polygenic risk score (PRS) was calculated, and its correlation with PCa incidence was evaluated. European, African, and East Asian populations had different heatmap patterns. Calculated PRS from the allele frequencies of PCa was the highest among Africans, followed by Europeans, and was the lowest among East Asians. PRS was positively correlated with the incidence and mortality of PCa. Network analysis revealed that AR, CDKN1B, and MAD1L1 are genes related to ethnic differences in PCa. The incidence and mortality of PCa showed a strong correlation with PRS according to ethnicity, which may suggest the effect of genetic factors, such as the AR gene, on PCa pathogenesis.
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Chen Z, Ge M. Discovering pathways in benign prostate hyperplasia: A functional genomics pilot study. Exp Ther Med 2021; 21:242. [PMID: 33603850 PMCID: PMC7851599 DOI: 10.3892/etm.2021.9673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 10/13/2020] [Indexed: 11/06/2022] Open
Abstract
Benign prostate hyperplasia (BPH) is one of the well-known urological neoplasms common in males with an increasing number of associated deaths in aging males. It causes uncomfortable urinary symptoms, including urine flow blockage, and may cause bladder, urinary tract or kidney problems. The histopathological and clinical knowledge regarding BPH is limited. In the present study, an in silico approach was applied that uses genome-scale microarray expression data to discover a wide range of protein-protein interactions in addition to focusing on specific genes responsible for BPH to develop prognostic biomarkers. Various genes that were differentially expressed in BPH were identified. Gene and functional annotation clusters were determined and an interaction analysis with disease phenotypes of BPH was performed, as well as an RNA tissue specificity analysis. Furthermore, a molecular docking study of certain short-listed gene biomarkers, namely anterior gradient 2 (AGR2; PDB ID: 2LNT), steroid 5α-reductase 2 (PDB ID: 6OQX), zinc finger protein 3 (PDB ID: 5T00) and collagen type XII α1 chain (PDB ID: 1U5M), was performed in order to identify alternative Chinese herbal agents for the treatment of BPH. Data from the present study revealed that AGR2 receptor (PDB ID: 2LNT) and berberine (Huang Bo) form the most stable complex and therefore may be assessed in further pharmacological studies for the treatment of BPH.
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Affiliation(s)
- Zheling Chen
- Department of Traditional Chinese Medicine, Zhenxin Community Health Service Center, Shanghai 201824, P.R. China
| | - Minyao Ge
- Department of Urology Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, P.R. China
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Hellwege JN, Stallings S, Torstenson ES, Carroll R, Borthwick KM, Brilliant MH, Crosslin D, Gordon A, Hripcsak G, Jarvik GP, Linneman JG, Devi P, Peissig PL, Sleiman PAM, Hakonarson H, Ritchie MD, Verma SS, Shang N, Denny JC, Roden DM, Velez Edwards DR, Edwards TL. Heritability and genome-wide association study of benign prostatic hyperplasia (BPH) in the eMERGE network. Sci Rep 2019; 9:6077. [PMID: 30988330 PMCID: PMC6465359 DOI: 10.1038/s41598-019-42427-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 03/27/2019] [Indexed: 02/07/2023] Open
Abstract
Benign prostatic hyperplasia (BPH) results in a significant public health burden due to the morbidity caused by the disease and many of the available remedies. As much as 70% of men over 70 will develop BPH. Few studies have been conducted to discover the genetic determinants of BPH risk. Understanding the biological basis for this condition may provide necessary insight for development of novel pharmaceutical therapies or risk prediction. We have evaluated SNP-based heritability of BPH in two cohorts and conducted a genome-wide association study (GWAS) of BPH risk using 2,656 cases and 7,763 controls identified from the Electronic Medical Records and Genomics (eMERGE) network. SNP-based heritability estimates suggest that roughly 60% of the phenotypic variation in BPH is accounted for by genetic factors. We used logistic regression to model BPH risk as a function of principal components of ancestry, age, and imputed genotype data, with meta-analysis performed using METAL. The top result was on chromosome 22 in SYN3 at rs2710383 (p-value = 4.6 × 10-7; Odds Ratio = 0.69, 95% confidence interval = 0.55-0.83). Other suggestive signals were near genes GLGC, UNCA13, SORCS1 and between BTBD3 and SPTLC3. We also evaluated genetically-predicted gene expression in prostate tissue. The most significant result was with increasing predicted expression of ETV4 (chr17; p-value = 0.0015). Overexpression of this gene has been associated with poor prognosis in prostate cancer. In conclusion, although there were no genome-wide significant variants identified for BPH susceptibility, we present evidence supporting the heritability of this phenotype, have identified suggestive signals, and evaluated the association between BPH and genetically-predicted gene expression in prostate.
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Affiliation(s)
- Jacklyn N Hellwege
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sarah Stallings
- Division of Geriatric Medicine, Meharry-Vanderbilt Alliance, Nashville, TN, USA
| | - Eric S Torstenson
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Robert Carroll
- Department of Biomedical Informatics Vanderbilt University, Nashville, TN, USA
| | | | - Murray H Brilliant
- Center for Human Genetics, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - David Crosslin
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA, USA
| | - Adam Gordon
- Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
- Medical Informatics Services, New York-Presbyterian Hospital, New York, NY, USA
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA, USA
| | - James G Linneman
- Office of Research Computing and Analytics/Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Parimala Devi
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA, USA
| | - Peggy L Peissig
- Center for Computational and Biomedical Informatics, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Patrick A M Sleiman
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Ning Shang
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Josh C Denny
- Department of Biomedical Informatics Vanderbilt University, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M Roden
- Department of Biomedical Informatics Vanderbilt University, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Digna R Velez Edwards
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Biomedical Informatics Vanderbilt University, Nashville, TN, USA.
- Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt Epidemiology Center, Institute for Medicine and Public Health, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Todd L Edwards
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.
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Zeng XT, Su XJ, Li S, Weng H, Liu TZ, Wang XH. Association between SRD5A2 rs523349 and rs9282858 Polymorphisms and Risk of Benign Prostatic Hyperplasia: A Meta-Analysis. Front Physiol 2017; 8:688. [PMID: 28955247 PMCID: PMC5600931 DOI: 10.3389/fphys.2017.00688] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 08/28/2017] [Indexed: 01/25/2023] Open
Abstract
Objective: Previous studies have reported that rs523349 (V89L) and rs9282858 (A49T) polymorphisms in the gene 5α-reductase II (SRD5A2) are associated with the risk of benign prostatic hyperplasia (BPH), but different opinions have emerged. In view of distinct discrepancies among those findings, we performed this meta-analysis to ascertain a more accurate association between SRD5A2 rs523349 and rs9282858 polymorphisms and the risk of BPH. Methods: Studies investigating the association between SRD5A2 rs523349 and rs9282858 polymorphisms and susceptibility to BPH were searched from the databases of PubMed, Embase, Wanfang, and Chinese National Knowledge Infrastructure (CNKI).The strength of correlation was assessed by crude odds ratios (ORs) with their corresponding 95% confidence intervals (95% CIs). Moreover, subgroup analysis was conducted to further ascertain such relationship and investigate sources of heterogeneity. Results:SRD5A2 rs9282858 (A49T) polymorphism showed a significant correlation with increased BPH susceptibility under allele T vs.allele A genetic model (OR = 2.51, 95% CI = 1.29-4.88) in total analysis, and stratification analysis by ethnicity also revealed a similar association in Caucasian group under the same contrast. SRD5A2 rs523349 (V89L) polymorphism showed no significant role in BPH occurrence in total analysis, but its reducing and increasing effects on the disease risk were reflected in Caucasian and other-ethnicity subgroups, respectively, after stratification analysis by ethnicity. Conclusion: In conclusion, SRD5A2 rs9282858 polymorphism may elevate the susceptibility to BPH, while the polymorphism rs523349 may exert different influences on the disease in people of different ethnic lines.
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Affiliation(s)
- Xian-Tao Zeng
- Department of Urology, Zhongnan Hospital of Wuhan UniversityWuhan, China.,Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan UniversityWuhan, China
| | - Xin-Jun Su
- Department of Urology, Zhongnan Hospital of Wuhan UniversityWuhan, China
| | - Sheng Li
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan UniversityWuhan, China
| | - Hong Weng
- Department of Urology, Zhongnan Hospital of Wuhan UniversityWuhan, China.,Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan UniversityWuhan, China
| | - Tong-Zu Liu
- Department of Urology, Zhongnan Hospital of Wuhan UniversityWuhan, China
| | - Xing-Huan Wang
- Department of Urology, Zhongnan Hospital of Wuhan UniversityWuhan, China.,Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan UniversityWuhan, China
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Bachour DM, Chahin E, Al-Fahoum S. Human Kallikrein-2, Prostate Specific Antigen and Free- Prostate Specific Antigen in Combination to Discriminate Prostate Cancer from Benign Diseases in Syrian Patients. Asian Pac J Cancer Prev 2016; 16:7085-8. [PMID: 26514494 DOI: 10.7314/apjcp.2015.16.16.7085] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The high incidence of prostate cancer as the most common malignancy in males in many countries raises the question of developing reliable detection tests. The prostate specific antigen (PSA) test is the most widely used for screening for prostate cancer; however, its low specificity elevates the number of unnecessarily biopsies. Serum human kallikrein-2 (hK2) is considered as a promising marker, and especially its ratio to fPSA, for predicting the presence of malignancy to select the best choice referring to biopsy or surveillance. In this study, we investigated the role of hK2 and its combinations with other markers to discriminate prostate cancer from benign diseases in Syrian patients. MATERIALS AND METHODS In this prospective oriented cross-sectional cohort study, serum samples were collected from patients referred to many Hospitals in Damascus, Syria, between May 2011 and March 2012, and diagnosed with biopsy proven benign prostate hyperplasia (BPH) or prostate cancer (PCa). Serum was analyzed for hK2, PSA and fPSA, and the ratios of fPSA/PSA and hK2/fPSA were calculated. RESULTS We found that mean hK2/fPSA ratios were significantly higher (P=0.01) in prostate cancer patients than in the BPH or control groups. Also the ratio hk2/fPSA gave the largest area under the curve (AUC:0.96) which was significantly larger than for fPSA/PSA (AUC:0.41) indicative of higher specificity. CONCLUSIONS Our results demonstrate that the ratio of hK2/fPSA might be superior to the use of fPSA/PSA alone. The hK2 could be shown to enhance the early detection of prostate cancer; especially the ratio hK2/fPSA improves specificity and hence may reduce the number of negative biopsies.
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Affiliation(s)
- Dala-Maria Bachour
- Master Student, Faculty of Pharmacy, Damascus University, Syria E-mail :
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