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Chang LW, Hung SC, Chou YE, Chen CS, Li JR, Lin CY, Wang SS, Yang SF. The impacts of MACC1 gene polymorphisms on urothelial cell carcinoma susceptibility and clinicopathologic characteristics in Taiwan. J Cancer 2023; 14:3532-3538. [PMID: 38021160 PMCID: PMC10647202 DOI: 10.7150/jca.90130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 10/14/2023] [Indexed: 12/01/2023] Open
Abstract
Urothelial cell carcinoma (UCC) is a common malignancy of the urinary tract in Taiwan. Metastasis-Associated in Colon Cancer 1 (MACC1), a newly identified oncogene and regulator of the HGF/Met signaling pathway, has been shown to play a critical role in the development and progression of several types of cancer. Our study aims to investigate the impact of MACC1 gene polymorphisms on the clinicopathological features of patients with UCC. In this study, we included a total of 719 patients with UCC and 719 healthy controls. The genotyping of five MACC1 gene polymorphisms (rs1990172, rs975263, rs3095007, rs4721888, and rs3735615) was performed using real-time PCR with TaqMan assays. Our findings indicate that urothelial cancer patients with MACC1 rs3095007 A allele had a decreased risk of >T2 stage [Odds ratio (OR)=0.619, 95% CI=0.394-0.971, p=0.036] and lymph node invasion (OR=0.448, 95% CI=0.201-0.998, p=0.044). Additionally, these individuals were associated with longer relapse-free survival (p=0.007) and overall survival (p=0.028). In conclusion, our findings demonstrate that urothelial cancer patients with MACC1 (rs3095007) CA and AA genotypes have a lower risk of advanced T stage and lymph node metastasis. Additionally, these genotypes were associated with longer relapse-free survival and overall survival, highlighting the potential of these biomarkers as predictors of UCC prognosis.
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Affiliation(s)
- Li-Wen Chang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Sheng-Chun Hung
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Ying-Erh Chou
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Chuan-Shu Chen
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Jian-Ri Li
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
- Department of Medicine and Nursing, Hungkuang University, Taichung, Taiwan
| | - Chia-Yen Lin
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, National Yang Ming University, Taipei, Taiwan
| | - Shian-Shiang Wang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Applied Chemistry, National Chi Nan University, Nantou, Taiwan
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
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2
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Huang HC, Shiu BH, Nassef Y, Huang CC, Chou YE, Ting WC, Chang LC, Lin JC, Hsiao LK, Yang SF, Su SC. Impact of carbonic anhydrase 9 gene polymorphism on the progression of colorectal cancer. J Cancer 2022; 13:2775-2780. [PMID: 35812185 PMCID: PMC9254877 DOI: 10.7150/jca.73898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/02/2022] [Indexed: 11/20/2022] Open
Abstract
Colorectal cancer (CRC) is a commonly occurring tumor type worldwide, and its development is governed by a connection between genetic variations and acquired factors. Carbonic anhydrase 9 (CA9) is a cell-surface pH modulator that has been demonstrated to contribute to key steps of cancer progression. Here, we attempted to interrogate the effect of CA9 gene polymorphisms on the development of CRC in 470 cases and 470 gender- and age-matched non-cancer controls. We found that none of three CA9 single-nucleotide polymorphisms (SNPs) tested, including rs2071676, rs3829078, and rs1048638, was significantly associated with the occurrence of CRC. Yet, while evaluating the clinicopathological variables, cases carrying at least one reference allele (G allele) of rs2071676 tended to develop poorly differentiated tumors less frequently than those who are homozygous for the alternative allele (A allele) of rs2071676 (GA+GG vs AA; OR, 0.483; 95% CI, 0.242-0.963; p=0.036). Further stratification revealed that as compared to homozygous carriers of the alternative allele (AA), cases of colon cancer bearing at least one reference allele of rs2071676 (GA+GG) less frequently developed poorly differentiated tumors (OR, 0.449; 95% CI, 0.221-0.911; p=0.024) and lymphovascular invasion (OR, 0.570; 95% CI, 0.361-0.900; p=0.015). Such genetic effect was exclusively observed in colon cancer but not in rectal cancer. Our results indicate an anatomical site-specific impact of CA9 gene polymorphisms on modulating the progression of colorectal malignancies.
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Affiliation(s)
- Hsien-Cheng Huang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Emergency Medicine, Kuang Tien General Hospital, Taichung, Taiwan
| | - Bei-Hao Shiu
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Surgery, Chung Shan Medical University Hospital, Taichung, Taiwan.,School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Yasser Nassef
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Chi-Chou Huang
- Department of Surgery, Chung Shan Medical University Hospital, Taichung, Taiwan.,School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Ying-Erh Chou
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Wen-Chien Ting
- Department of Surgery, Chung Shan Medical University Hospital, Taichung, Taiwan.,School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Lun-Ching Chang
- Department of Mathematical Sciences, Florida Atlantic University, Florida, USA
| | - Jian-Cheng Lin
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | | | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Shih-Chi Su
- Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan.,Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
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3
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Saleem S, Khan R, Haider G, Hasan S, Fatima F, Zehra S, Azhar A. Association of genetic polymorphism rs2071676 in carbonic anhydrase gene (CA9) with the risk of squamous cell carcinoma of lungs and esophagus. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00812-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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4
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Yu YY, Chiou HL, Tsao SM, Huang CC, Lin CY, Lee CY, Tsao TCY, Yang SF, Huang YW. Association of Carbonic Anhydrase 9 Polymorphism and the Epithelial Growth Factor Receptor Mutations in Lung Adenocarcinoma Patients. Diagnostics (Basel) 2020; 10:diagnostics10050266. [PMID: 32365566 PMCID: PMC7277165 DOI: 10.3390/diagnostics10050266] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/21/2020] [Accepted: 04/28/2020] [Indexed: 12/11/2022] Open
Abstract
Carbonic anhydrase 9 (CA9) plays a vital role in lung cancer progression. The current study explored the effect of CA9 gene polymorphisms and the epidermal growth factor receptor (EGFR) mutations on the clinicopathological characters of lung adenocarcinoma. In this study, three loci of CA9 single nucleotide polymorphism (SNP) (rs2071676 A>G, rs3829078 A>G, and rs1048638 C>A) were genotyped using the TaqMan allelic discrimination method in 193 EGFR wild type individuals and 281 EGFR mutation subjects. After adjusting for age, gender, and cigarette smoking status in logistic regression, all three CA9 SNPs illustrated a non-significant difference for the distribution between the EGFR wild type group and EGFR mutation group. Nevertheless, a significantly lower rate of CA9 SNP rs2071676 AG (adjusted odds ratio (AOR): 0.40, 95% confidence interval (CI): 0.16-0.95, p = 0.039) and AG+GG (AOR: 0.43, 95% CI: 0.18-0.98, p = 0.046) were found in the male population with L858R EGFR mutation compared to men with EGFR wild type. In addition, the CA9 SNP rs2071676 AG+GG genotype were significantly correlated to the lower tumor stage of lung adenocarcinoma in the whole study population (p = 0.044) and EGFR wild type individuals (p = 0.033). For the male population, the presence of CA9 SNP rs2071676 AG+GG genotype was also correlated to a lower tumor stage (p = 0.037) and fewer lymph node invasion (p = 0.003) in those with EGFR wild type. In conclusion, the existence of CA9 SNP rs2071676 is associated with the rate of EGFR L858R mutation in males. Furthermore, the CA9 SNP rs2071676 is correlated to lower tumor stage and lower risk for developing lymph node metastasis in lung adenocarcinoma, mainly in the EGFR wild type.
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Affiliation(s)
- Ya-Yen Yu
- Institute of Medicine, Chung Shan Medical University, Taichung 402, Taiwan;
- Department of Clinical Laboratory, Changhua Hospital, Changhua 513, Taiwan
| | - Hui-Ling Chiou
- School of Medical Laboratory and Biotechnology, Chung Shan Medical University, Taichung 402, Taiwan;
- Department of Clinical Laboratory, Chung Shan Medical University Hospital, Taichung 402, Taiwan
| | - Shih-Ming Tsao
- Division of Chest, Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung 402, Taiwan; (S.-M.T.); (T.C.-Y.T.)
- School of Medicine, Chung Shan Medical University, Taichung 402, Taiwan
- Institute of Biochemistry, Microbiology and Immunology, Chung Shan Medical University, Taichung 402, Taiwan
| | - Chen-Cheng Huang
- Division of Chest Medicine, Department of Internal Medicine, Taichung Hospital, Ministry of Health and Welfare, Taichung 403, Taiwan;
| | - Chih-Yun Lin
- Department of Health, Pulmonary and Critical Care Unit, Changhua Hospital, Changhua 500, Taiwan;
| | - Chia-Yi Lee
- Department of Ophthalmology, Show Chwan Memorial Hospital, Changhua 500, Taiwan;
| | - Thomas Chang-Yao Tsao
- Division of Chest, Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung 402, Taiwan; (S.-M.T.); (T.C.-Y.T.)
- School of Medicine, Chung Shan Medical University, Taichung 402, Taiwan
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung 402, Taiwan;
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung 402, Taiwan
- Correspondence: (S.-F.Y.); (Y.-W.H.)
| | - Yi-Wen Huang
- Institute of Medicine, Chung Shan Medical University, Taichung 402, Taiwan;
- Department of Health, Pulmonary and Critical Care Unit, Changhua Hospital, Changhua 500, Taiwan;
- Correspondence: (S.-F.Y.); (Y.-W.H.)
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5
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Fan M, Wang J, Wang S, Li T, Pan H, Liu H, Xu H, Zhernakova DV, O'Brien SJ, Feng Z, Chang L, Dai E, Lu J, Xi H, Yu Y, Zhang J, Wang B, Zeng Z. New Gene Variants Associated with the Risk of Chronic HBV Infection. Virol Sin 2020; 35:378-387. [PMID: 32297155 DOI: 10.1007/s12250-020-00200-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 01/16/2020] [Indexed: 12/16/2022] Open
Abstract
Some patients with chronic hepatitis B virus (HBV) infection failed to clear HBV, even persistently continue to produce antibodies to HBV. Here we performed a two stage genome wide association study in a cohort of Chinese patients designed to discover single nucleotide variants that associate with HBV infection and clearance of HBV. The first stage involved genome wide exome sequencing of 101 cases (HBsAg plus anti-HBs positive) compared with 102 control patients (anti-HBs positive, HBsAg negative). Over 80% of individual sequences displayed 20 × sequence coverage. Adapters, uncertain bases > 10% or low-quality base calls (> 50%) were filtered and compared to the human reference genome hg19. In the second stage, 579 chronic HBV infected cases and 439 HBV clearance controls were sequenced with selected genes from the first stage. Although there were no significant associated gene variants in the first stage, two significant gene associations were discovered when the two stages were assessed in a combined analysis. One association showed rs506121-"T" allele [within the dedicator of cytokinesis 8 (DOCK8) gene] was higher in chronic HBV infection group than that in clearance group (P = 0.002, OR = 0.77, 95% CI [0.65, 0.91]). The second association involved rs2071676-A allele within the Carbonic anhydrase (CA9) gene that was significantly elevated in chronic HBV infection group compared to the clearance group (P = 0.0003, OR = 1.35, 95% CI [1.15, 1.58]). Upon replication these gene associations would suggest the influence of DOCK8 and CA9 as potential risk genetic factors in the persistence of HBV infection.
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Affiliation(s)
- Mengjie Fan
- Department of Infectious Diseases, Peking University First Hospital, Beijing, 100034, China
| | - Jing Wang
- Department of Medical Genetics and Development Biology, School of Medical Basic, Capital Medical University, Beijing, 100069, China.,Center for Genetics, National Research Institute for Family Planning, Beijing, 100081, China
| | - Sa Wang
- Department of Infectious Diseases, Peking University First Hospital, Beijing, 100034, China
| | - Tengyan Li
- Center for Genetics, National Research Institute for Family Planning, Beijing, 100081, China
| | - Hong Pan
- Center for Genetics, National Research Institute for Family Planning, Beijing, 100081, China
| | - Hankui Liu
- BGI-Shenzhen, Shenzhen, 518083, China.,BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Huifang Xu
- BGI-Shenzhen, Shenzhen, 518083, China.,BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Daria V Zhernakova
- Laboratory of Genomic Diversity, Center for Computer Technologies, ITMO University, St. Petersburg, Russia, 197101
| | - Stephen J O'Brien
- Laboratory of Genomic Diversity, Center for Computer Technologies, ITMO University, St. Petersburg, Russia, 197101.,Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Ft Lauderdale, FL, 33004, USA
| | - Zhenru Feng
- Department of Laboratory Medicine, Peking University First Hospital, Beijing, 100034, China
| | - Le Chang
- Department of Laboratory Medicine, Peking University First Hospital, Beijing, 100034, China
| | - Erhei Dai
- The Fifth Hospital of Shijiazhuang, Shijiazhuang, 050024, China
| | - Jianhua Lu
- The Fifth Hospital of Shijiazhuang, Shijiazhuang, 050024, China
| | - Hongli Xi
- Department of Infectious Diseases, Peking University First Hospital, Beijing, 100034, China
| | - Yanyan Yu
- Department of Infectious Diseases, Peking University First Hospital, Beijing, 100034, China
| | - Jianguo Zhang
- BGI-Shenzhen, Shenzhen, 518083, China. .,BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Binbin Wang
- Center for Genetics, National Research Institute for Family Planning, Beijing, 100081, China.
| | - Zheng Zeng
- Department of Infectious Diseases, Peking University First Hospital, Beijing, 100034, China.
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6
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Hung SC, Wang SS, Li JR, Chen CS, Lin CY, Chang LW, Chiu KY, Cheng CL, Ou YC, Yang SF. Impact of RAGE polymorphisms on urothelial cell carcinoma clinicopathologic characteristics and long-term survival. Urol Oncol 2019; 37:573.e9-573.e17. [DOI: 10.1016/j.urolonc.2019.02.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/12/2019] [Accepted: 02/18/2019] [Indexed: 12/15/2022]
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7
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Lin CY, Wang SS, Yang CK, Li JR, Chen CS, Hung SC, Chiu KY, Cheng CL, Ou YC, Yang SF. Genetic polymorphism and carbonic anhydrase 9 expression can predict nodal metastatic prostate cancer risk in patients with prostate-specific antigen levels ≤10 ng/ml at initial biopsy. Urol Oncol 2019; 37:814.e9-814.e16. [PMID: 31155437 DOI: 10.1016/j.urolonc.2019.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/01/2019] [Accepted: 05/13/2019] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Active surveillance is a common management method for low-risk prostate cancer (CaP). However, devising a method to prevent disease progression is crucial. Carbon anhydrase 9 (CA9) plays a vital role in cell adhesion and intercellular communication correlated to tumor metastasis. Our study explored the impact of CA9 genetic polymorphism on the clinicopathological features and prognosis of CaP. MATERIALS AND METHODS In total, 579 patients with CaP who underwent robot-assisted radical prostatectomy were enrolled, 270 of whom had an initial prostate-specific antigen (PSA) level ≤10 ng/ml and 309 had initial one >10 ng/ml. Three single-nucleotide polymorphisms of CA9 gene were examined using real-time polymerase chain reaction assay. RESULTS After adjusting the confounding factors, participants carrying at least one G allele at CA9 rs3829078 had a 2.241-fold change in PSA compared with the wild-type carrier (AA), leading to an initial PSA level of ≤10 ng/ml. Furthermore, patients with CaP with an initial PSA level ≤10 ng/ml who carried at least one G allele at CA9 rs3829078 had a 4.532-fold and 3.484-fold risk of lymph node metastasis and lymphovascular invasion, respectively. Moreover, The Cancer Genome Atlas database showed that the CA9 mRNA expression significantly increased N1 disease risk and worsened overall survival trends. CONCLUSION The rs3829078 polymorphic genotype of CA9 can predict the risk of lymph node metastasis of CaP with an initial PSA level ≤10 ng/ml. This is the first study to report a correlation between CA9 gene polymorphisms/CA9 mRNA expression and early detection of CaP.
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Affiliation(s)
- Chia-Yen Lin
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan; Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan; Division of Surgical Critical Care, Department of Critical Care Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Shian-Shiang Wang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan; Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan; Department of Applied Chemistry, National Chi Nan University, Nantou, Taiwan
| | - Cheng-Kuang Yang
- Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Jian-Ri Li
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan; Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan; Department of Medicine and Nursing, Hungkuang University, Taichung, Taiwan
| | - Chuan-Shu Chen
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan; Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Sheng-Chun Hung
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan; Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Kun-Yuan Chiu
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan; Department of Applied Chemistry, National Chi Nan University, Nantou, Taiwan
| | - Chen-Li Cheng
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan; Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yen-Chuan Ou
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan; Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan; Department of Urology, Tung's Taichung MetroHarbor Hospital, Taichung, Taiwan
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan.
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Garcia A, Lopez F, Garcia L, Giraldo O, Bucheli V, Dumontier M. Biotea: semantics for Pubmed Central. PeerJ 2018; 6:e4201. [PMID: 29312824 PMCID: PMC5755483 DOI: 10.7717/peerj.4201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/07/2017] [Indexed: 01/26/2023] Open
Abstract
A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies. In this paper we present the second version of Biotea, a semantic, linked data version of the open-access subset of PubMed Central that has been enhanced with specialized annotation pipelines that uses existing infrastructure from the National Center for Biomedical Ontology. We expose our models, services, software and datasets. Our infrastructure enables manual and semi-automatic annotation, resulting data are represented as RDF-based linked data and can be readily queried using the SPARQL query language. We illustrate the utility of our system with several use cases. Our datasets, methods and techniques are available at http://biotea.github.io.
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Affiliation(s)
- Alexander Garcia
- Ontology Engineering Group, Universidad Politécnica de Madrid, Madrid, Spain
| | - Federico Lopez
- Escuela de Ingeniería de Sistemas y Computación, Universidad del Valle, Cali, Colombia
| | - Leyla Garcia
- Temporal Knowledge Bases Group, Department of Computer Languages and Systems, Universitat Jaume I, Castelló de la Plana, Spain
| | - Olga Giraldo
- Ontology Engineering Group, Universidad Politécnica de Madrid, Madrid, Spain
| | - Victor Bucheli
- Escuela de Ingeniería de Sistemas y Computación, Universidad del Valle, Cali, Colombia
| | - Michel Dumontier
- Maastricht University, Institute of Data Science, Maastricht, The Netherlands
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Shen HP, Hsiao YH, Yang SF, Liu YF, Ko JL, Wang PH. Single nucleotide polymorphisms and haplotypes of carbonic anhydrase 9 can predict invasive squamous cell carcinoma of uterine cervix. Int J Med Sci 2018; 15:587-594. [PMID: 29725249 PMCID: PMC5930460 DOI: 10.7150/ijms.23359] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 03/02/2018] [Indexed: 12/27/2022] Open
Abstract
This study aimed to explore the involvement of carbonic anhydrase 9 (CA9) single nucleotide polymorphisms (SNPs) in the development of invasive cancer of uterine cervix for Taiwanese women. Ninety-seven patients with cervical invasive squamous cell carcinoma and 88 with preinvasive squamous cell lesions as well as 324 control women were recruited. Two CA9 SNPs in exons, including rs2071676 (+201, G/A) in exon 1 and rs3829078 (+1081, A/G) in exon 7, rs1048638 (+1584, C/A) in 3'-untranslated region of exon 11, as well as an 18-base pair deletion/insertion (376deltion393) in exon 1 were selected and their genotypic distributions were determined by real-time polymerase chain reaction. Haplotype was then constructed with rs2071676, 376del393, rs3829078 and rs1048638 in order. The results revealed that Taiwanese women with genotypes CA or CA/AA in CA9 SNP rs1048638 displayed a more risk in developing cervical invasive cancer, assigning wild genotype CC as a reference. AA in SNP rs2071676 tended to increase the risk of developing cervical invasive cancer, using GG/GA as a reference. When women had the diplotypes, carrying at least one haplotype A1AA (one mutant allele A in rs2071676, no deletion in 376del393, no mutant allele A in rs3829078 and one mutant allele A in rs1048638), they were significantly susceptible to cervical invasive cancer. In conclusion, CA9 SNP rs1048638 and haplotype A1AA are associated with the susceptibility of cervical invasive squamous cell carcinoma for Taiwanese women.
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Affiliation(s)
- Huang-Pin Shen
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Obstetrics and Gynecology, Chung Shan Medical University Hospital, Taichung, Taiwan.,School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Yi-Hsuan Hsiao
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Obstetrics and Gynecology, Changhua Christian Hospital, Changhua, Taiwan
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Yu-Fan Liu
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Jiunn-Liang Ko
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Po-Hui Wang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Obstetrics and Gynecology, Chung Shan Medical University Hospital, Taichung, Taiwan.,School of Medicine, Chung Shan Medical University, Taichung, Taiwan
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10
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Hung SC, Wang SS, Li JR, Chen CS, Yang CK, Chiu KY, Cheng CL, Ou YC, Ho HC, Yang SF. Effect of HMGB1 Polymorphisms on Urothelial Cell Carcinoma Susceptibility and Clinicopathological Characteristics. Int J Med Sci 2018; 15:1731-1736. [PMID: 30588197 PMCID: PMC6299401 DOI: 10.7150/ijms.27901] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/18/2018] [Indexed: 12/29/2022] Open
Abstract
The high mobility group box 1 gene (HMGB1) plays a prominent role in cancer progression, angiogenesis, invasion, and metastasis. This study explored the effect of HMGB1 polymorphisms on clinicopathological characteristics of urothelial cell carcinoma (UCC). In total, 1293 participants (431 patients with UCC and 862 healthy controls) were recruited. Four single-nucleotide polymorphisms (SNPs) of HMGB1 (rs1412125, rs1360485, rs1045411, and rs2249825) were assessed using TaqMan real-time polymerase chain reaction assay. The results indicated that individuals carrying at least one T allele at rs1045411 had a lower risk of UCC than those with the wild-type allele [adjusted odds ratio = 0.722, 95% confidence interval (CI) = 0.565-0.924]. Furthermore, female patients with UCC carrying at least one T allele at rs1045411 were at a lower invasive tumor stage than those with the wild-type allele [odds ratio (OR) = 0.396, 95% CI = 0.169-0.929], similar to nonsmoking patients (OR = 0.607, 95% CI = 0.374-0.985). In conclusion, this is the first report on correlation between HMGB1 polymorphisms and UCC risk. Individuals carrying at least one T allele at rs1045411 are associated with a lower risk of UCC and a less invasive disease in women and nonsmokers.
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Affiliation(s)
- Sheng-Chun Hung
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Shian-Shiang Wang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan.,Department of Applied Chemistry, National Chi Nan University, Nantou, Taiwan
| | - Jian-Ri Li
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan.,Department of Medicine and Nursing, Hungkuang University, Taichung, Taiwan Taiwan
| | - Chuan-Shu Chen
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chun-Kuang Yang
- Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Kun-Yuan Chiu
- Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan.,Department of Applied Chemistry, National Chi Nan University, Nantou, Taiwan
| | - Chen-Li Cheng
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yen-Chuan Ou
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan.,Department of Urology, Tung's Taichung MetroHarbor Hospital, Taichung, Taiwan
| | - Hao-Chung Ho
- Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
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11
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Yang SF, Liu YF, Cheng CW, Yang WE, Lin WL, Ko JL, Wang PH. Impact of microRNA-34a and polymorphism of its target gene CA9 on susceptibility to uterine cervical cancer. Oncotarget 2017; 8:77860-77871. [PMID: 29100431 PMCID: PMC5652820 DOI: 10.18632/oncotarget.20842] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 08/17/2017] [Indexed: 01/18/2023] Open
Abstract
The purposes of this study were to associate the genetic polymorphisms in carbonic anhydrase (CA) 9 with uterine cervical cancer and identify the clinical implications. Three single-nucleotide polymorphisms (SNPs), rs2071676 (+201, G/A), rs3829078 (+1081, A/G), and rs1048638 (+1584, C/A), and an 18-base-pair deletion/insertion (376del393) in CA9 were examined. We used the Boyden chamber assay to evaluate the influence of CA9 on the migration of cervical cancers. Tissue microarrays were used to evaluate CAIX immunoreactivity and determine its clinical significance. The results revealed that the CA9 SNP rs1048638 is the only significant polymorphism that increases the risk of cervical cancer in Taiwanese women. We discovered that the CA9 SNP rs1048638 influences the expression of CA9 through the interaction between the 3′-untranslated region (UTR) of exon 11, where the SNP is located, and miR-34a, and influences the migration of cervical cancer cells. Moreover, we demonstrated that CAIX immunoreactivity is related to the occurrence of cervical cancer, and elevated CAIX immunoreactivity is associated with a more advanced stage. In conclusion, the finding that the CA9 SNP rs1048638 exerts its action through duplexes of the miR-34a and CA9 3′-UTRs and plays a vital role in cervical cancer in Taiwanese women may be applicable to translational medicine.
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Affiliation(s)
- Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Yu-Fan Liu
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Chao-Wen Cheng
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Wei-En Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Wea-Lung Lin
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Pathology, Chung Shan Medical University and Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Jiunn-Liang Ko
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Po-Hui Wang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,School of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Obstetrics and Gynecology, Chung Shan Medical University Hospital, Taichung, Taiwan
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12
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3'UTR polymorphisms of carbonic anhydrase IX determine the miR-34a targeting efficiency and prognosis of hepatocellular carcinoma. Sci Rep 2017; 7:4466. [PMID: 28667334 PMCID: PMC5493636 DOI: 10.1038/s41598-017-04732-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 05/19/2017] [Indexed: 12/26/2022] Open
Abstract
Carbonic anhydrase IX (CA9) expression level has been considered as a poor prognostic factor in hepatocellular carcinoma (HCC) patients. However, the judging criteria of CA9 level is hard to define for potential clinical applications. Unlike CA9 expression level, CA9 polymorphism is poorly documented in HCC. Here, we found that people carry A allele at CA9 rs1048638, a 3′UTR SNP, has higher risk of HCC. rs1048638-CA correlates with advanced stages, larger tumor sizes, more vascular invasion, and shorter survival of HCC patients. A allele at CA9 rs1048638 impairs miR-34a, a tumor suppressor miRNA in HCC, binding to CA9 3′UTR and desensitizes CA9 mRNA to miR-34a-dependent RNA degradation. CA9 expression levels were also correlated with miR-34a levels and rs1048638 genotypes in HCC patients. rs1048638 influences HCC risk and progression through effects on miR-34a-targeted CA9 expression in HCC. In conclusion, genetic variations of the CA9 3′UTR play important roles in regulating CA9 expression and cancer progression, which is a novel determinant and target for HCC metastasis and prognosis.
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13
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Pastorek J, Pastorekova S. Hypoxia-induced carbonic anhydrase IX as a target for cancer therapy: from biology to clinical use. Semin Cancer Biol 2014; 31:52-64. [PMID: 25117006 DOI: 10.1016/j.semcancer.2014.08.002] [Citation(s) in RCA: 225] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 07/30/2014] [Accepted: 08/04/2014] [Indexed: 12/12/2022]
Abstract
The tumor microenvironment includes a complicated network of physiological gradients contributing to plasticity of tumor cells and heterogeneity of tumor tissue. Hypoxia is a key component generating intratumoral oxygen gradients, which affect the cellular expression program and lead to therapy resistance and increased metastatic propensity of weakly oxygenated cell subpopulations. One of the adaptive responses of tumor cells to hypoxia involves the increased expression and functional activation of carbonic anhydrase IX (CA IX), a cancer-related cell surface enzyme catalyzing the reversible conversion of carbon dioxide to bicarbonate ion and proton. Via its catalytic activity, CA IX participates in regulation of intracellular and extracellular pH perturbations that result from hypoxia-induced changes in cellular metabolism producing excess of acid. Through the ability to regulate pH, CA IX also facilitates cell migration and invasion. In addition, CA IX has non-catalytic function in cell adhesion and spreading. Thus, CA IX endows tumor cells with survival advantages in hypoxia/acidosis and confers an increased ability to migrate, invade and metastasize. Accordingly, CA IX is expressed in a broad range of tumors, where it is associated with prognosis and therapy outcome. Its expression pattern and functional implications in tumor biology make CA IX a promising therapeutic target, which can be hit either by immunotherapy with monoclonal antibodies or with compounds inhibiting its enzyme activity. The first strategy has already reached the clinical trials, whereas the second one is still in preclinical testing. Both strategies indicate that CA IX can become a clinically useful anticancer target, but urge further efforts toward better selection of patients for immunotherapy and deeper understanding of tumor types, clinical situations and synthetic lethality interactions with other treatment approaches.
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Affiliation(s)
- Jaromir Pastorek
- Department of Molecular Medicine, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Silvia Pastorekova
- Department of Molecular Medicine, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia; Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic.
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14
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Wang SS, Hsieh MJ, Ou YC, Chen CS, Li JR, Hsiao PC, Yang SF. Impacts of ICAM-1 gene polymorphisms on urothelial cell carcinoma susceptibility and clinicopathologic characteristics in Taiwan. Tumour Biol 2014; 35:7483-90. [PMID: 24789429 DOI: 10.1007/s13277-014-1934-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 04/03/2014] [Indexed: 01/13/2023] Open
Abstract
Intercellular adhesion molecule (ICAM)-1, a cell adhesion molecule, is reportedly overexpressed in several cancers and may contribute to tumorgenesis and metastasis. The current study explored the effect of ICAM-1 gene polymorphisms on the susceptibility of developing urothelial cell carcinoma (UCC) and the clinicopathological status. A total of 558 participants, including 279 healthy people and 279 patients with UCC, were recruited for this study. Four single-nucleotide polymorphisms of the ICAM-1 gene were assessed by a real-time polymerase chain reaction with the TaqMan assay. After adjusting for other covariants, the individuals carrying at least one G allele at ICAM-1 rs5498 had a 1.603-fold risk of developing UCC than did wild-type (AA) carriers. Furthermore, UCC patients who carried at least one G allele at rs5498 had a higher invasive stage risk (p < 0.05) than did patients carrying the wild-type allele. In conclusion, the rs5498 polymorphic genotypes of ICAM-1 might contribute to the prediction of susceptibility to and pathological development of UCC. This is the first study to provide insight into risk factors associated with ICAM-1 variants in carcinogenesis of UCC in Taiwan.
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Affiliation(s)
- Shian-Shiang Wang
- Institute of Medicine, Chung Shan Medical University, Taichung, 402, Taiwan
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