1
|
Chen WC, Chen YC, Chen YH, Liu TY, Tsai CH, Tsai FJ. Identification of novel genetic susceptibility loci for calcium-containing kidney stone disease by genome-wide association study and polygenic risk score in a Taiwanese population. Urolithiasis 2024; 52:94. [PMID: 38896256 DOI: 10.1007/s00240-024-01577-0] [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: 01/23/2024] [Accepted: 05/04/2024] [Indexed: 06/21/2024]
Abstract
Approximately 80% of kidney stone diseases contain calcium. Inherited genetic factors are among the variables that influence the development of calcium-containing kidney stone diseases (CKSD). Previous genome-wide association studies (GWAS) on stone diseases have been reported worldwide; however, these are not focused on calcium-containing stones. We conducted a GWAS to identify germline genetic polymorphisms associated with CKSD in a Medical Center in Taiwan; hence, this study was based primarily on a hospital-based database. CKSD was diagnosed using the chart records. Patients infected with urea-splitting-microorganisms and those with at least two urinary pH value below 5.5 were excluded. None of the patients had cystic stones based on stone analysis. Those over 40 years of age with no history of CKSD and no microscopic hematuria on urinalysis were considered as controls. The DNA isolated from the blood of 14,934 patients (63.7% male and 36.3% female) with CKSD and 29,868 controls (10,830 men and 19,038 women) at a medical center was genotyped for approximately 714,457 single nucleotide polymorphisms (SNPs) with minor allele frequency of ≥ 0.05. We used PLINK 1.9 to calculate the polygenic risk score (PRS) to investigate the association between CKSD and controls. The accuracy of the PRS was verified by dividing it into the training and testing groups. The statistical analyses were calculated with the area under the curve (AUC) using IBM SPSS version 22. We identified 432 susceptibility loci that reached a genome-wide threshold of P < 1.0 × 10- 5. A total of 132 SNPs reached a threshold of P < 5 × 10- 8 using a stricter definition of significance on chromosomes 4, 13, 16, 17, and 18. At the top locus of our study, SNPs in DGKH, PDILT, BCAS3, and ABCG2 have been previously reported. RN7SKP27, HDAC4, PCDH15, AP003068.2, and NFATC1 were novel findings in this study. PRS was adjusted for sex and age, resulting in an AUC of 0.65. The number of patients in the top quartile of PRS was 1.39 folds in the risk of CKSD than patients in the bottom quartile. Our data identified the significance of GWAS for patients with CKSD in a hospital-based study. The PRS also had a high AUC for discriminating patients with CKSD from controls. A total of 132 SNP loci of SNPs significantly associated with the development of CKSD. This first survey, which focused on patients with CKSD, will provide novel insights specific to CKSD and its potential clinical biomarkers.
Collapse
Affiliation(s)
- Wen-Chi Chen
- Department of Urology, Department of Medical Research, Department of Medical Genetics, Million-Person Precision Medicine Initiative, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Integrated Medicine, School of Chinese Medicine, College of Chinese Medicine, School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan
| | - Yu-Chia Chen
- Department of Urology, Department of Medical Research, Department of Medical Genetics, Million-Person Precision Medicine Initiative, China Medical University Hospital, Taichung, Taiwan
| | - Yung-Hsiang Chen
- Department of Urology, Department of Medical Research, Department of Medical Genetics, Million-Person Precision Medicine Initiative, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Integrated Medicine, School of Chinese Medicine, College of Chinese Medicine, School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan
- Department of Psychology, College of Medical and Health Science, Asia University, Taichung, Taiwan
| | - Ting-Yuan Liu
- Department of Urology, Department of Medical Research, Department of Medical Genetics, Million-Person Precision Medicine Initiative, China Medical University Hospital, Taichung, Taiwan
| | - Chang-Hai Tsai
- Department of Urology, Department of Medical Research, Department of Medical Genetics, Million-Person Precision Medicine Initiative, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Integrated Medicine, School of Chinese Medicine, College of Chinese Medicine, School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan
| | - Fuu-Jen Tsai
- Department of Urology, Department of Medical Research, Department of Medical Genetics, Million-Person Precision Medicine Initiative, China Medical University Hospital, Taichung, Taiwan.
- Graduate Institute of Integrated Medicine, School of Chinese Medicine, College of Chinese Medicine, School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan.
- Division of Medical Genetics, China Medical University Children's Hospital, Taichung, Taiwan.
| |
Collapse
|
2
|
Atmoko W, Raharja PAR, Birowo P, Hamid ARAH, Taher A, Rasyid N. Genetic polymorphisms as prognostic factors for recurrent kidney stones: A systematic review and meta-analysis. PLoS One 2021; 16:e0251235. [PMID: 33956883 PMCID: PMC8101940 DOI: 10.1371/journal.pone.0251235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 04/22/2021] [Indexed: 11/25/2022] Open
Abstract
Genetic polymorphisms have been suggested as risk factors affecting the occurrence and recurrence of kidney stones, although findings regarding the latter remain inconclusive. We performed this systematic review and meta-analysis to clarify the associations between genetic polymorphisms and recurrent kidney stones. PubMed, SCOPUS, EMBASE, and Cochrane Library databases were searched through May 28th, 2020 to identify eligible studies. The Quality in prognostic studies (QUIPS) tool was used to evaluate bias risk. Allelic frequencies and different inheritance models were assessed. All analyses were performed using Review manager 5.4. A total of 14 studies were included for meta-analysis, assessing urokinase (ApaL1) and vitamin D receptor (VDR) (ApaI, BsmI, FokI, and TaqI) gene polymorphisms. The ApaLI polymorphism demonstrated protective association in the recessive model [odds ratio (OR) 0.45, P < 0.01] albeit higher risk among Caucasians in the heterozygous model (OR 16.03, P < 0.01). The VDR-ApaI polymorphism showed protective association in the dominant model (OR 0.60, P < 0.01). Among Asians, the VDR-FokI polymorphism recessive model showed significant positive association (OR 1.70, P < 0.01) and the VDR-TaqI polymorphism heterozygous model exhibited protective association (OR 0.72, P < 0.01). The VDR-BsmI polymorphism was not significantly associated with recurrent kidney stones in any model. Urokinase-ApaLI (recessive model), VDR-ApaI (dominant model), and VDR-TaqI (heterozygous model) polymorphisms were associated with decreased recurrent kidney stone risk whereas urokinase-ApaLI (heterozygous model) and VDR-FokI polymorphisms were associated with increased risk among Caucasians and Asians, respectively. These findings will assist in identifying individuals at risk of kidney stone recurrence.
Collapse
Affiliation(s)
- Widi Atmoko
- Department of Urology, Faculty of Medicine, Universitas Indonesia, Cipto Mangunkusumo Hospital, Jakarta, Indonesia
| | - Putu Angga Risky Raharja
- Department of Urology, Faculty of Medicine, Universitas Indonesia, Cipto Mangunkusumo Hospital, Jakarta, Indonesia
| | - Ponco Birowo
- Department of Urology, Faculty of Medicine, Universitas Indonesia, Cipto Mangunkusumo Hospital, Jakarta, Indonesia
| | | | - Akmal Taher
- Department of Urology, Faculty of Medicine, Universitas Indonesia, Cipto Mangunkusumo Hospital, Jakarta, Indonesia
| | - Nur Rasyid
- Department of Urology, Faculty of Medicine, Universitas Indonesia, Cipto Mangunkusumo Hospital, Jakarta, Indonesia
- * E-mail:
| |
Collapse
|
3
|
Donmez C, Konac E, Aydogan BT, Bilen CY. Might E-cadherin promoter polymorphisms of rs16260 and rs5030625 associate with the risk of nephrolithiasis? SPRINGERPLUS 2016; 5:1673. [PMID: 27733975 PMCID: PMC5040654 DOI: 10.1186/s40064-016-3363-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 09/22/2016] [Indexed: 12/30/2022]
Abstract
Purpose To study whether −160 C > A (rs16260) and −347 G > GA (rs5030625) single nucleotide polymorphisms of the regulatory region (rSNPs) of CDH1 gene modulate the risk of nephrolithiasis. Methods Genomic DNA of 101 patients with calcium oxalate nephrolithiasis and 114 healthy controls were screened for both polymorphisms, using polymerase chain reaction-restriction fragments length polymorphism method (PCR-RLFP). Haplotype frequencies were also analyzed. To determine the association of rSNPs of CDH1 gene with the clinicopathological features of nephrolithiasis, nearly all possible etiological factors were documented. These factors were family history, gender, age, body mass index, liquid consumption, eating habits, tea–coffee and meat (oxalate rich) consumption, adequate physical activity, and all serum and urine levels—the serum levels of Na, K, Cl, phosphate, Ca, Mg, uric acid, albumin, blood urea nitrogen (BUN), creatinine and serum parathyroid hormone (PTH) as well as 24 h urine excretions of creatinine, Na, K, Cl, phosphate, Ca, Mg, citrate, oxalate, uric acid, albumin and BUN. Results Significant differences were found between rs16260 and the risk of nephrolithiasis. Patients having CA genotype of rs16260 CDH1 polymorphism were associated with an almost trifold increased risk for developing kidney stone than those with the AA genotype (95 % CI 1.08–7.28, OR 2.8, P = 0.033). We also found that non-A allele carriers (CC) had significantly higher nephrolithiasis risk associated with the clinicopathological characteristics including serum calcium (P = 0.027) and 24 h urinary magnesium level (P = 0.042). Moreover, we did find a directly proportional relationship between the CA genotype and serum calcium levels (P = 0.041). There was no significant difference between patients and controls in terms of the distribution of rs5030625 genotypes and alleles (P > 0.05). Likewise, no associations between the rs16260 and rs5030625 haplotypes and susceptibility to kidney stone were observed (P > 0.05). Conclusion Regulatory variants of rs16260 of the CDH1 gene may confer susceptibility to nephrolithiasis. This may have important implications for understanding the pathophysiological mechanisms of the disease and suggesting novel targets for drug treatment.
Collapse
Affiliation(s)
- Cigdem Donmez
- Department of Medical Biology and Genetics, Faculty of Medicine, Gazi University, Besevler, 06510 Ankara, Turkey
| | - Ece Konac
- Department of Medical Biology and Genetics, Faculty of Medicine, Gazi University, Besevler, 06510 Ankara, Turkey
| | - Batuhan T Aydogan
- Department of Urology, Faculty of Medicine, Hacettepe University, Sıhhiye, 06100 Ankara, Turkey
| | - Cenk Y Bilen
- Department of Urology, Faculty of Medicine, Hacettepe University, Sıhhiye, 06100 Ankara, Turkey
| |
Collapse
|
4
|
Rungroj N, Nettuwakul C, Sudtachat N, Praditsap O, Sawasdee N, Sritippayawan S, Chuawattana D, Yenchitsomanus PT. A whole genome SNP genotyping by DNA microarray and candidate gene association study for kidney stone disease. BMC MEDICAL GENETICS 2014; 15:50. [PMID: 24886237 PMCID: PMC4031563 DOI: 10.1186/1471-2350-15-50] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 04/28/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND Kidney stone disease (KSD) is a complex disorder with unknown etiology in majority of the patients. Genetic and environmental factors may cause the disease. In the present study, we used DNA microarray to genotype single nucleotide polymorphisms (SNP) and performed candidate gene association analysis to determine genetic variations associated with the disease. METHODS A whole genome SNP genotyping by DNA microarray was initially conducted in 101 patients and 105 control subjects. A set of 104 candidate genes reported to be involved in KSD, gathered from public databases and candidate gene association study databases, were evaluated for their variations associated with KSD. RESULTS Altogether 82 SNPs distributed within 22 candidate gene regions showed significant differences in SNP allele frequencies between the patient and control groups (P < 0.05). Of these, 4 genes including BGLAP, AHSG, CD44, and HAO1, encoding osteocalcin, fetuin-A, CD44-molecule and glycolate oxidase 1, respectively, were further assessed for their associations with the disease because they carried high proportion of SNPs with statistical differences of allele frequencies between the patient and control groups within the gene. The total of 26 SNPs showed significant differences of allele frequencies between the patient and control groups and haplotypes associated with disease risk were identified. The SNP rs759330 located 144 bp downstream of BGLAP where it is a predicted microRNA binding site at 3'UTR of PAQR6 - a gene encoding progestin and adipoQ receptor family member VI, was genotyped in 216 patients and 216 control subjects and found to have significant differences in its genotype and allele frequencies (P = 0.0007, OR 2.02 and P = 0.0001, OR 2.02, respectively). CONCLUSIONS Our results suggest that these candidate genes are associated with KSD and PAQR6 comes into our view as the most potent candidate since associated SNP rs759330 is located in the miRNA binding site and may affect mRNA expression level.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Pa-Thai Yenchitsomanus
- Division of Molecular Medicine, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
| |
Collapse
|
5
|
Tan M, Xia S, Zhang Q, Zhu J, Bao E. The -160C>a polymorphism in E-cadherin is associated with the risk of nephrolithiasis. PLoS One 2013; 8:e73109. [PMID: 24023817 PMCID: PMC3759430 DOI: 10.1371/journal.pone.0073109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 07/24/2013] [Indexed: 11/22/2022] Open
Abstract
Nephrolithiasis is a common disorder worldwide. E-cadherin (CDH1) is involved in epithelial cell-cell interactions and plays important roles in the etiology of nephrolithiasis. We hypothesized that variants in the CDH1 gene are associated with risk of nephrolithiasis. In a hospital-based case-control study of 127 nephrolithiasis patients and 152 controls frequency matched by age and sex, we genotyped the functional -160C>A (rs16260) polymorphism and assessed its associations with risk of nephrolithiasis in a Chinese population. We found that the CA/AA genotypes were associated with a significantly decreased risk of nephrolithiasis (OR = 0.53, 95%CI = 0.32-0.87), compared with the CC genotype, particularly among subgroups of BMI > 24 kg/m2 (OR = 0.38, 95%CI = 0.17-0.85), age ≤ 57 years (OR = 0.47, 95%CI = 0.24-0.93), and men (OR = 0.56, 95%CI = 0.29-0.99). Our results suggest that the CDH1 polymorphism is involved in the etiology of nephrolithiasis and thus may be a marker for genetic susceptibility to nephrolithiasis.
Collapse
Affiliation(s)
- Mingyue Tan
- Department of Urology, Shanghai First People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Shengqiang Xia
- Department of Urology, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, China
| | - Qi Zhang
- Department of Urology, Shanghai First People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jiang Zhu
- Department of Urology, Shanghai First People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
- * E-mail: (SX); (EB)
| | - Erdun Bao
- Department of Urology, Shanghai First People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
- * E-mail: (SX); (EB)
| |
Collapse
|
6
|
Tugcu V, Simsek A, Tarhan T, Atalar F, Bitkin A, Tasci AI, Kural AR, Altug T. OPN gene polymorphism (Ala250) and lower serum OPN levels are associated with urolithiasis. Ren Fail 2013; 35:825-9. [DOI: 10.3109/0886022x.2013.794431] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
7
|
Li Y, Tang Y, Zhou R, Sun D, Duan Y, Wang N, Chen Z, Shen N. Genetic polymorphism in the 3′-untranslated region of the E-cadherin gene is associated with risk of different cancers. Mol Carcinog 2011; 50:857-62. [DOI: 10.1002/mc.20765] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 02/09/2011] [Accepted: 02/10/2011] [Indexed: 01/21/2023]
|
8
|
E-cadherin gene 3'-UTR C/T polymorphism in Turkish patients with nephrolithiasis. Mol Biol Rep 2010; 38:4931-4. [PMID: 21161401 DOI: 10.1007/s11033-010-0635-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 12/03/2010] [Indexed: 10/18/2022]
Abstract
Nephrolithiasis is a complex disease and many gene polymorphisms have been associated with stone formation. In this study we aimed to investigate another possible relationship between E-cadherin gene (CHD1) 3'-UTR C/T polymorphism and calcium oxalate nephrolithiasis in the Turkish population. Study population was composed of 143 patients with nephrolithiasis and 158 control subjects. CHD1 3'-UTR C/T polymorphism was analysed using polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) technique. Genotype distribution of the investigated polymorphism was not deviated from Hardy-Weinberg equilibrium (HWE) in patients and control subjects (P > 0.05). C allele frequency was 85.7 and 85.1% in patients and controls, respectively (P = 0.836). Genotype distributions of the CHD1 3'-UTR C/T polymorphism among patients were also not significantly different from those among control subjects (P = 0.636). Our results showed that there is no association between the CHD1 gene 3'-UTR C/T polymorphism and nephrolithiasis in our population.
Collapse
|
9
|
Vezzoli G, Terranegra A, Arcidiacono T, Soldati L. Genetics and calcium nephrolithiasis. Kidney Int 2010; 80:587-93. [PMID: 20962745 DOI: 10.1038/ki.2010.430] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Calcium nephrolithiasis is one of the most prevalent uronephrologic disorders in the western countries. Studies in families and twins evidenced a genetic predisposition to calcium nephrolithiasis. Family-based or case-control studies of single-candidate genes evidenced the possible involvement of calcium-sensing receptor (CASR), vitamin D receptor (VDR), and osteopontin (OPN) gene polymorphisms in stone formation. The only high-throughput genome-wide association study identified claudin 14 (CLDN14) gene as a possible major gene of nephrolithiasis. Specific phenotypes were related with these genes: CASR gene in normocitraturic patients, VDR gene in hypocitraturic patients with severe clinical course, and CLDN14 gene in hypercalciuric patients. The pathogenetic weight of these genes remains unclear, but an alteration of their expression may occur in stone formers. Technological skills, accurate clinical examination, and a detailed phenotype description are the basis to get new insight about the genetic basis of nephrolithiasis.
Collapse
Affiliation(s)
- Giuseppe Vezzoli
- Nephrology and Dialysis Unit, San Raffaele Scientific Institute, via Olgettina 60, Milan, Italy.
| | | | | | | |
Collapse
|
10
|
Lai KC, Lin WY, Man KM, Tsai CH, Chen HY, Tsai FJ, Chen FJ, Chen HY, Liu HP, Ho TJ, Huang PH, Liu PL, Lin FY, Shen JL, Liu JT, Chen YH, Chen WC. Association of interleukin-18 gene polymorphisms with calcium oxalate kidney stone disease. ACTA ACUST UNITED AC 2009; 44:20-6. [DOI: 10.3109/00365590903449332] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Kuang-Chi Lai
- Department of Surgery, China Medical University Beigang Hospital, Yunlin, Taiwan
- Department of Anesthesiology, Tungs' MetroHarbor Hospital, Taichung, Taiwan
| | - Wei-Yong Lin
- Graduate Institute of Integrated Medicine, Graduate Institute of Chinese Medical Science, Graduate Institute of Acupuncture Science, School of Chinese Medicine, and School of Medicine, College of Chinese Medicine, Department of Ophthalmology, Department of Obstetric and Gynecology, Department of Medical Genetics and Pediatrics, and Department of Urology, China Medical University and Hospital, Taichung, Taiwan
| | - Kee-Ming Man
- Graduate Institute of Integrated Medicine, Graduate Institute of Chinese Medical Science, Graduate Institute of Acupuncture Science, School of Chinese Medicine, and School of Medicine, College of Chinese Medicine, Department of Ophthalmology, Department of Obstetric and Gynecology, Department of Medical Genetics and Pediatrics, and Department of Urology, China Medical University and Hospital, Taichung, Taiwan
- Department of Anesthesiology, Tungs' MetroHarbor Hospital, Taichung, Taiwan
| | - Chou-Haung Tsai
- Graduate Institute of Integrated Medicine, Graduate Institute of Chinese Medical Science, Graduate Institute of Acupuncture Science, School of Chinese Medicine, and School of Medicine, College of Chinese Medicine, Department of Ophthalmology, Department of Obstetric and Gynecology, Department of Medical Genetics and Pediatrics, and Department of Urology, China Medical University and Hospital, Taichung, Taiwan
| | - Huey-Yi Chen
- Graduate Institute of Integrated Medicine, Graduate Institute of Chinese Medical Science, Graduate Institute of Acupuncture Science, School of Chinese Medicine, and School of Medicine, College of Chinese Medicine, Department of Ophthalmology, Department of Obstetric and Gynecology, Department of Medical Genetics and Pediatrics, and Department of Urology, China Medical University and Hospital, Taichung, Taiwan
- Department of Anesthesiology, Tungs' MetroHarbor Hospital, Taichung, Taiwan
| | - Fuu-Jen Tsai
- Graduate Institute of Integrated Medicine, Graduate Institute of Chinese Medical Science, Graduate Institute of Acupuncture Science, School of Chinese Medicine, and School of Medicine, College of Chinese Medicine, Department of Ophthalmology, Department of Obstetric and Gynecology, Department of Medical Genetics and Pediatrics, and Department of Urology, China Medical University and Hospital, Taichung, Taiwan
- Department of Anesthesiology, Tungs' MetroHarbor Hospital, Taichung, Taiwan
| | - Fun-Jou Chen
- Graduate Institute of Integrated Medicine, Graduate Institute of Chinese Medical Science, Graduate Institute of Acupuncture Science, School of Chinese Medicine, and School of Medicine, College of Chinese Medicine, Department of Ophthalmology, Department of Obstetric and Gynecology, Department of Medical Genetics and Pediatrics, and Department of Urology, China Medical University and Hospital, Taichung, Taiwan
| | - Hsin-Yi Chen
- Graduate Institute of Integrated Medicine, Graduate Institute of Chinese Medical Science, Graduate Institute of Acupuncture Science, School of Chinese Medicine, and School of Medicine, College of Chinese Medicine, Department of Ophthalmology, Department of Obstetric and Gynecology, Department of Medical Genetics and Pediatrics, and Department of Urology, China Medical University and Hospital, Taichung, Taiwan
- Department of Anesthesiology, Tungs' MetroHarbor Hospital, Taichung, Taiwan
| | - Hsin-Ping Liu
- Graduate Institute of Integrated Medicine, Graduate Institute of Chinese Medical Science, Graduate Institute of Acupuncture Science, School of Chinese Medicine, and School of Medicine, College of Chinese Medicine, Department of Ophthalmology, Department of Obstetric and Gynecology, Department of Medical Genetics and Pediatrics, and Department of Urology, China Medical University and Hospital, Taichung, Taiwan
| | - Tsung-Jung Ho
- Department of Surgery, China Medical University Beigang Hospital, Yunlin, Taiwan
- Graduate Institute of Integrated Medicine, Graduate Institute of Chinese Medical Science, Graduate Institute of Acupuncture Science, School of Chinese Medicine, and School of Medicine, College of Chinese Medicine, Department of Ophthalmology, Department of Obstetric and Gynecology, Department of Medical Genetics and Pediatrics, and Department of Urology, China Medical University and Hospital, Taichung, Taiwan
| | - Po-Hsun Huang
- Division of Cardiology, Department of Internal Medicine, Taipei Veterans General Hospital; Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Po-Len Liu
- Department of Respiratory Therapy, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Feng-Yen Lin
- Division of Anesthesiology, Department of Anesthesiology, School of Medicine, Taipei Medical University and Hospital, Taipei, Taiwan
| | - Jui-Lung Shen
- Graduate Institute of Integrated Medicine, Graduate Institute of Chinese Medical Science, Graduate Institute of Acupuncture Science, School of Chinese Medicine, and School of Medicine, College of Chinese Medicine, Department of Ophthalmology, Department of Obstetric and Gynecology, Department of Medical Genetics and Pediatrics, and Department of Urology, China Medical University and Hospital, Taichung, Taiwan
- Department of Dermatology, Taichung Veterans General Hospital, Taichung, Taiwan,
| | - Jung-Tung Liu
- School of Medicine, Department of Neurosurgery, Chung-Shan Medical University and Hospital, Taichung, Taiwan
| | - Yung-Hsiang Chen
- Graduate Institute of Integrated Medicine, Graduate Institute of Chinese Medical Science, Graduate Institute of Acupuncture Science, School of Chinese Medicine, and School of Medicine, College of Chinese Medicine, Department of Ophthalmology, Department of Obstetric and Gynecology, Department of Medical Genetics and Pediatrics, and Department of Urology, China Medical University and Hospital, Taichung, Taiwan
| | - Wen-Chi Chen
- Graduate Institute of Integrated Medicine, Graduate Institute of Chinese Medical Science, Graduate Institute of Acupuncture Science, School of Chinese Medicine, and School of Medicine, College of Chinese Medicine, Department of Ophthalmology, Department of Obstetric and Gynecology, Department of Medical Genetics and Pediatrics, and Department of Urology, China Medical University and Hospital, Taichung, Taiwan
- Department of Anesthesiology, Tungs' MetroHarbor Hospital, Taichung, Taiwan
| |
Collapse
|
11
|
Beeghly-Fadiel A, Lu W, Gao YT, Long J, Deming SL, Cai Q, Zheng Y, Shu XO, Zheng W. E-cadherin polymorphisms and breast cancer susceptibility: a report from the Shanghai Breast Cancer Study. Breast Cancer Res Treat 2009; 121:445-52. [PMID: 19834798 DOI: 10.1007/s10549-009-0579-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Accepted: 10/05/2009] [Indexed: 01/27/2023]
Abstract
The epithelial transmembrane glycoprotein E-cadherin (CDH1) is necessary for intercellular adhesion, cell signaling, and maintenance of cellular differentiation; reduced expression contributes to cell proliferation, invasion, and cancer progression. Functional or potentially functional single nucleotide polymorphisms (SNPs) in E-cadherin have been previously identified and evaluated in relation to cancer risk; however, studies on breast cancer have been sparse. Forty-six SNPs were genotyped to capture genetic variation of the CDH1 gene among 2,290 Phase 1 and 1,944 Phase 2 participants of the Shanghai Breast Cancer Study (SBCS), a large, population-based, case-control study. No overall associations between E-cadherin SNPs and breast cancer risk were observed. When stratified by menopausal status, associations that were consistent between Phases 1 and 2 and significant when data from both phases were combined were observed for several SNPs. Although none of these associations retained statistical significance after correcting for the total number of polymorphisms evaluated, this study suggests that genetic variation in CDH1 may be associated with breast cancer risk, and that this relationship may vary by menopausal status.
Collapse
Affiliation(s)
- Alicia Beeghly-Fadiel
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Institute of Medicine and Public Health, Vanderbilt University Medical Center, Vanderbilt University School of Medicine, 2525 West End Avenue, 8th Floor, Nashville, TN 37203-1738, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Abstract
Urolithiasis is a relevant clinical problem with a subsequent burden for health system. The aim of this review is to provide recent progress made using genetic polymorphisms to define pathophysiology, to identify persons at risk for kidney stone disease and to predict treatment response. Population case-control studies are useful both as an alternative and an adjunct as compared to family studies. These involve either whole genome scanning or candidate gene approaches. While whole genome scanning is likely to be widely used in future, at present, candidate gene studies are more feasible. When performing candidate gene case-control studies factors such as study design, methods for recruitment of case and controls, selection of candidate genes, functional significance of polymorphisms chosen for study and statistical analysis require close attention to ensure that only genuine associations are detected. Some of the significant genes that play role in stone formation include calcitonin receptor gene (CTR), vitamin D receptor (VDR), Urokinase, Interleukin, (IL-1β, IL-Ra), E-Cadherin, Androgen & oestrogen receptor gene, vascular endothelial growth factor (VEGF) and Arginine p21. In our case-control study we studied CTR, VDR, Urokinase, IL-1β(-511 and +3954), IL-Ra from north India and predict that VDR, IL-β (-511) and IL-1Ra gene may be used as a possible genetic marker for earlier detection in patients who are at risk for calcium oxalate stone disease. Further, linkage disequilibrium and haplotype structure of a certain candidate gene is important for association analysis. When a certain polymorphic allele has been found to be associated with disease, it is further explained on basis of LD and haplotype structure by one or more other alleles. Once it is determined which haplotype carries the risk allele, by means of molecular biological functional analyses, the variants on that haplotype allele truly causing the effect can be determined.
Collapse
|
13
|
Mittal RD, Bid HK, Manchanda PK, Kapoor R. Association of Interleukin-1β Gene and Receptor Antagonist Polymorphisms with Calcium Oxalate Urolithiasis. J Endourol 2007; 21:1565-70. [DOI: 10.1089/end.2007.0071] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Rama D. Mittal
- Department of Urology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Hemant K. Bid
- Department of Urology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Parmeet K. Manchanda
- Department of Urology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Rakesh Kapoor
- Department of Urology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| |
Collapse
|
14
|
Shan K, Xiao-Wei M, Na W, Xiu-Feng Z, Deng-Gui W, Wei G, Zheng-Mao Z, Yan L. Association of three single nucleotide polymorphisms of the E-cadherin gene with endometriosis in a Chinese population. Reproduction 2007; 134:373-8. [PMID: 17660246 DOI: 10.1530/rep-07-0104] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Endometriosis, one of the most frequent diseases in gynecology, is a benign but invasive and metastatic disease. The altered expression of E-cadherin may play an important role in developing endometriosis. In this paper, we discuss the association of three single nucleotide polymorphisms (SNPs) on the E-cadherin gene and risk of endometriosis. We examined the genotype frequency of three polymorphisms in 152 endometriosis patients and 189 control women. There was a significant difference in the frequency of the E-cadherin 3'-UTR C --> T genotypes between endometriosis and controls (P = 0.01). The frequency of the C allele in patients (71.1%) was significantly higher than in the controls (63.8%; P = 0.04). When compared with the T/T + T/C genotypes, the C/C genotype had a significantly increased susceptibility to endometriosis, with an adjusted odds ratio of 1.79 (95% confidence interval = 1.17-2.76). No significant difference was found between endometriosis and control women on two polymorphisms (-160 C --> A, -347 G --> GA) at the gene promoter region of E-cadherin. The -160 C --> A and -347 G --> GA polymorphisms displayed linkage disequilibrium (D' = 0.999). The -160 A/-347 GA haplotype was only detected in endometriosis patients (2%). These data show a relation between the E-cadherin 3'-UTR C --> T polymorphism, the -160 A/-347 GA haplotype of two promoter polymorphisms and risk of endometriosis, suggesting a potential role in endometriosis development, at least in North Chinese women.
Collapse
Affiliation(s)
- Kang Shan
- Department of Obstetrics and Gynecology, Fourth Hospital, Hebei Medical University, Shijiazhuang 050011, China
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Chen JM, Férec C, Cooper DN. A systematic analysis of disease-associated variants in the 3' regulatory regions of human protein-coding genes II: the importance of mRNA secondary structure in assessing the functionality of 3' UTR variants. Hum Genet 2006; 120:301-33. [PMID: 16807757 DOI: 10.1007/s00439-006-0218-x] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Accepted: 05/29/2006] [Indexed: 12/13/2022]
Abstract
In an attempt both to catalogue 3' regulatory region (3' RR)-mediated disease and to improve our understanding of the structure and function of the 3' RR, we have performed a systematic analysis of disease-associated variants in the 3' RRs of human protein-coding genes. We have previously analysed the variants that have occurred in two specific domains/motifs of the 3' untranslated region (3' UTR) as well as in the 3' flanking region. Here we have focused upon 83 known variants within the upstream sequence (USS; between the translational termination codon and the upstream core polyadenylation signal sequence) of the 3' UTR. To place these variants in their proper context, we first performed a comprehensive survey of known cis-regulatory elements within the USS and the mechanisms by which they effect post-transcriptional gene regulation. Although this survey supports the view that RNA regulatory elements function within the context of specific secondary structures, there are no general rules governing how secondary structure might exert its influence. We have therefore addressed this question by systematically evaluating both functional and non-functional (based upon in vitro reporter gene and/or electrophoretic mobility shift assay data) USS variant-containing sequences against known cis-regulatory motifs within the context of predicted RNA secondary structures. This has allowed us not only to establish a reliable and objective means to perform secondary structure prediction but also to identify consistent patterns of secondary structural change that could potentiate the discrimination of functional USS variants from their non-functional counterparts. The resulting rules were then used to infer potential functionality in the case of some of the remaining functionally uncharacterized USS variants, from their predicted secondary structures. This not only led us to identify further patterns of secondary structural change but also several potential novel cis-regulatory motifs within the 3' UTRs studied.
Collapse
|
16
|
Wu HC, Lai MT, Wu CI, Chen HY, Wan L, Tsai FJ, Chen WC. E-cadherin gene 3'-UTR C/T polymorphism is associated with prostate cancer. Urol Int 2006; 75:350-3. [PMID: 16327305 DOI: 10.1159/000089173] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2005] [Accepted: 07/15/2005] [Indexed: 11/19/2022]
Abstract
INTRODUCTION E-cadherin (CDH-1) is a cell-cell adhesive molecule which maintains cell integrity and communication between the intracellular and extracellular world. CDH-1 may therefore be related to carcinogenesis. A polymorphism located at the 3'-UTR of the CDH-1 gene is associated with stone disease; however, its relationship to prostate cancer has not been reported. We aimed to study whether there is an association between the 3'-UTR polymorphism and prostate cancer. MATERIALS AND METHODS We collected 96 patients with prostate cancer and 114 normal controls for this study. The polymorphism of the CDH-1 gene was studied by polymerase chain reaction-based restriction analysis. RESULTS There was a significant difference in genotype distribution of the CDH-1 gene polymorphism between cancer patients and normal controls (p < 0.001). The distribution of the CDH-1 gene CC genotype in prostate cancer patients (51.0%) was higher than in the controls (10.5%). The odds ratio for the CDH-1 'C' allele was 2.896 (95% CI = 1.908-4.396). There was no significant difference according to age, pathological grading, clinical staging, and responsiveness to hormonal therapy among patients. Only 3 patients (3.1%) had a history of urolithiasis. CONCLUSIONS The CDH-1 gene 3'-UTR C/T polymorphism is associated with prostate cancer. The 'CC' homozygote indicates a relatively higher risk for developing prostate cancer than other genotypes.
Collapse
Affiliation(s)
- Hsi-Chin Wu
- Department of Urology, China Medical University Hospital, Taichung, Taiwan
| | | | | | | | | | | | | |
Collapse
|
17
|
Gambaro G, Vezzoli G, Casari G, Rampoldi L, D'Angelo A, Borghi L. Genetics of hypercalciuria and calcium nephrolithiasis: from the rare monogenic to the common polygenic forms. Am J Kidney Dis 2005; 44:963-86. [PMID: 15558518 DOI: 10.1053/j.ajkd.2004.06.030] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Idiopathic calcium nephrolithiasis is a multifactorial disease with a pathogenesis that involves a complex interaction of environmental and individual factors. This review discusses what is known about monogenic renal calcium stone-related disorders, provides an update on genetic research in calcium nephrolithiasis and such intermediate phenotypes as idiopathic hypercalciuria, discusses the problems that these conditions pose to clinicians and geneticists interested in their pathogenesis, and proposes some method tools potentially useful in this research frame of reference.
Collapse
Affiliation(s)
- Giovanni Gambaro
- Department of Biomedical and Surgical Sciences, Division of Nephrology, University of Verona, Verona, Italy.
| | | | | | | | | | | |
Collapse
|
18
|
Schwonbeck S, Krause-Griep A, Gajovic-Eichelmann N, Ehrentreich-Förster E, Meinl W, Glatt H, Bier FF. Cohort analysis of a single nucleotide polymorphism on DNA chips. Biosens Bioelectron 2005; 20:956-66. [PMID: 15530792 DOI: 10.1016/j.bios.2004.06.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A method has been developed to determine SNPs on DNA chips by applying a flow-through bioscanner. As a practical application we demonstrated the fast and simple SNP analysis of 24 genotypes in an array of 96 spots with a single hybridisation and dissociation experiment. The main advantage of this methodical concept is the parallel and fast analysis without any need of enzymatic digestion. Additionally, the DNA chip format used is appropriate for parallel analysis up to 400 spots. The polymorphism in the gene of the human phenol sulfotransferase SULT1A1 was studied as a model SNP. Biotinylated PCR products containing the SNP (The SNP summary web site: ) (mutant) and those containing no mutation (wild-type) were brought onto the chips coated with NeutrAvidin using non-contact spotting. This was followed by an analysis which was carried out in a flow-through biochip scanner while constantly rinsing with buffer. After removing the non-biotinylated strand a fluorescent probe was hybridised, which is complementary to the wild-type sequence. If this probe binds to a mutant sequence, then one single base is not fully matching. Thereby, the mismatched hybrid (mutant) is less stable than the full-matched hybrid (wild-type). The final step after hybridisation on the chip involves rinsing with a buffer to start dissociation of the fluorescent probe from the immobilised DNA strand. The online measurement of the fluorescence intensity by the biochip scanner provides the possibility to follow the kinetics of the hybridisation and dissociation processes. According to the different stability of the full-match and the mismatch, either visual discrimination or kinetic analysis is possible to distinguish SNP-containing sequence from the wild-type sequence.
Collapse
Affiliation(s)
- Susanne Schwonbeck
- Department of Molecular Bioanalytics and Bioelectronics, Fraunhofer Institute for Biomedical Engineering, Arthur-Scheunert-Allee 114-116, D-14558 Nuthetal, Germany
| | | | | | | | | | | | | |
Collapse
|
19
|
Shastry BS. Role of SNP/haplotype map in gene discovery and drug development: An overview. Drug Dev Res 2004. [DOI: 10.1002/ddr.10377] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|