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Niu S, Ma J, Li Y, Yue X, Shi K, Pan M, Song L, Tan Y, Gu L, Liu S, Chang J. PTPN23[Thr] variant reduces susceptibility and tumorigenesis in esophageal squamous cell carcinoma through dephosphorylation of EGFR. Cancer Lett 2024; 592:216936. [PMID: 38704135 DOI: 10.1016/j.canlet.2024.216936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
Post-translational modifications (PTMs) have emerged as pivotal regulators of the development of cancers, including esophageal squamous cell carcinoma (ESCC). Here, we conducted a comprehensive analysis of PTM-related genetic variants associated with ESCC risk using large-scale genome-wide and exome-wide association datasets. We observed significant enrichment of PTM-related variants in the ESCC risk loci and identified five variants that were significantly associated with ESCC risk. Among them, rs6780013 in PTPN23 exhibited the highest level of significance in ESCC susceptibility in 9,728 ESCC cases and 10,977 controls (odds ratio [OR] = 0.85, 95 % confidence interval [CI] = 0.81- 0.89, P = 9.77 × 10-14). Further functional investigations revealed that PTPN23[Thr] variant binds to EGFR and modulates its phosphorylation at Thr699. PTPN23[Thr] variant substantially inhibited ESCC cell proliferation both in vitro and in vivo. Our findings underscore the critical role of PTPN23[Thr]-EGFR interaction in ESCC development, providing more insights into the pathogenesis of this cancer.
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Affiliation(s)
- Siyuan Niu
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Jialing Ma
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Yueping Li
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Xinying Yue
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Ke Shi
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Miaoxin Pan
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Lina Song
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Yuqian Tan
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Linglong Gu
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Shasha Liu
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Jiang Chang
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
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Gu L, Yue X, Niu S, Ma J, Liu S, Pan M, Song L, Su Q, Tan Y, Li Y, Chang J. Systematical identification of key genes and regulatory genetic variants associated with prognosis of esophageal squamous cell carcinoma. Mol Carcinog 2024; 63:1013-1023. [PMID: 38380955 DOI: 10.1002/mc.23704] [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: 12/20/2023] [Revised: 01/26/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024]
Abstract
Esophageal squamous cell carcinoma (ESCC) stands as a highly lethal malignancy characterized by pronounced recurrence and metastasis, resulting in a bleak 5-year survival rate. Despite extensive investigations, encompassing genome-wide association studies, the identification of robust prognostic markers has remained elusive. In this study, leveraging four independent data sets comprising 404 ESCC patients, we conducted a systematic analysis to unveil pivotal genes influencing overall survival. our meta-analysis identified 278 genes significantly associated with ESCC prognosis. Further exploration of the prognostic landscape involved an examination of expression quantitative trait loci for these genes, leading to the identification of six tag single nucleotide polymorphisms predictive of overall survival in a cohort of 904 ESCC patients. Notably, functional annotation spotlighted rs11227223, residing in the enhancer region of nuclear paraspeckle assembly transcript 1 (NEAT1), as a crucial variant likely exerting a substantive biological role. Through a series of biochemistry experiments, we conclusively demonstrated that the rs11227223-T allele, indicative of a poorer prognosis, augmented NEAT1 expression. Our results underscore the substantive role of NEAT1 and its regulatory variant in prognostic predictions for ESCC. This comprehensive analysis not only advances our comprehension of ESCC prognosis but also unveils a potential avenue for targeted interventions, offering promise for enhanced clinical outcomes.
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Affiliation(s)
- Linglong Gu
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xinying Yue
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Siyuan Niu
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jialing Ma
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shasha Liu
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Miaoxin Pan
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lina Song
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qianqian Su
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuqian Tan
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yueping Li
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiang Chang
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Li S, Che J, Gu B, Li Y, Han X, Sun T, Pan K, Lv J, Zhang S, Wang C, Zhang T, Wang J, Xue F. Metabolites, Healthy Lifestyle, and Polygenic Risk Score Associated with Upper Gastrointestinal Cancer: Findings from the UK Biobank Study. J Proteome Res 2024; 23:1679-1688. [PMID: 38546438 DOI: 10.1021/acs.jproteome.3c00827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
Previous metabolomics studies have highlighted the predictive value of metabolites on upper gastrointestinal (UGI) cancer, while most of them ignored the potential effects of lifestyle and genetic risk on plasma metabolites. This study aimed to evaluate the role of lifestyle and genetic risk in the metabolic mechanism of UGI cancer. Differential metabolites of UGI cancer were identified using partial least-squares discriminant analysis and the Wilcoxon test. Then, we calculated the healthy lifestyle index (HLI) score and polygenic risk score (PRS) and divided them into three groups, respectively. A total of 15 metabolites were identified as UGI-cancer-related differential metabolites. The metabolite model (AUC = 0.699) exhibited superior discrimination ability compared to those of the HLI model (AUC = 0.615) and the PRS model (AUC = 0.593). Moreover, subgroup analysis revealed that the metabolite model showed higher discrimination ability for individuals with unhealthy lifestyles compared to that with healthy individuals (AUC = 0.783 vs 0.684). Furthermore, in the genetic risk subgroup analysis, individuals with a genetic predisposition to UGI cancer exhibited the best discriminative performance in the metabolite model (AUC = 0.770). These findings demonstrated the clinical significance of metabolic biomarkers in UGI cancer discrimination, especially in individuals with unhealthy lifestyles and a high genetic risk.
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Affiliation(s)
- Shuting Li
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Jiajing Che
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Bingbing Gu
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Yunfei Li
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Xinyue Han
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Tiantian Sun
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Keyu Pan
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Jiali Lv
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Shuai Zhang
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Cheng Wang
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Tao Zhang
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Jialin Wang
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, China
| | - Fuzhong Xue
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
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Tan Y, Song L, Ma J, Pan M, Niu S, Yue X, Li Y, Gu L, Liu S, Chang J. Single-cell analysis identified POSTN + cells associated with the aggressive phenotype and risk of esophageal squamous cell carcinoma. HGG ADVANCES 2024; 5:100278. [PMID: 38369754 PMCID: PMC10924139 DOI: 10.1016/j.xhgg.2024.100278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 02/20/2024] Open
Abstract
Tumors are intricate and heterogeneous systems characterized by mosaic cancer cell populations with diverse expression profiles. Leveraging single-cell technologies, we employed the Scissor algorithm to delineate an epithelial subpopulation associated with the aggressive phenotype in esophageal squamous cell carcinoma (ESCC). This identified subpopulation exhibited elevated expression of genes involved in critical pathways, such as epithelial-mesenchymal transition and PI3K-Akt. Key signature genes within this subpopulation, namely CAV1, COL3A1, COL6A1, POSTN, and TAGLN, demonstrated significant upregulation concomitant with both tumorigenesis and tumor progression across independent single-cell datasets. Furthermore, we selected 1,450 expression quantitative trait loci of the top 62 signature genes of this cell subpopulation to investigate their potential in predicting ESCC risk. The results showed that the POSTN loci were predominantly associated with ESCC susceptibility. Through functional annotation and replication analyses, we identified that the rs1028728 in the POSTN promoter was significantly associated with increased ESCC risk in 7,049 ESCC cases and 8,063 controls (odds ratio = 1.29, 95% confidence interval: 1.18-1.42, p = 4.03 × 10-8). Subsequent biochemical experiments showed that the rs1028728[T] allele enhanced POSTN expression by affecting the binding of PRRX1 in the POSTN promoter. In summary, our meticulous single-cell analysis delineates an invasive epithelial subpopulation in ESCC, with POSTN emerging as an important marker for the aggressive phenotype. These findings offer more insights into potential strategies for the prevention and intervention of ESCC, enriching our understanding of this complex cancer landscape.
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Affiliation(s)
- Yuqian Tan
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Lina Song
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jialing Ma
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Miaoxin Pan
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Siyuan Niu
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xinying Yue
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yueping Li
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Linglong Gu
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shasha Liu
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jiang Chang
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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Turkarslan S, He Y, Hothi P, Murie C, Nicolas A, Kannan K, Park JH, Pan M, Awawda A, Cole ZD, Shapiro MA, Stuhlmiller TJ, Lee H, Patel AP, Cobbs C, Baliga NS. An atlas of causal and mechanistic drivers of interpatient heterogeneity in glioma. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.05.24305380. [PMID: 38633778 PMCID: PMC11023657 DOI: 10.1101/2024.04.05.24305380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Grade IV glioma, formerly known as glioblastoma multiforme (GBM) is the most aggressive and lethal type of brain tumor, and its treatment remains challenging in part due to extensive interpatient heterogeneity in disease driving mechanisms and lack of prognostic and predictive biomarkers. Using mechanistic inference of node-edge relationship (MINER), we have analyzed multiomics profiles from 516 patients and constructed an atlas of causal and mechanistic drivers of interpatient heterogeneity in GBM (gbmMINER). The atlas has delineated how 30 driver mutations act in a combinatorial scheme to causally influence a network of regulators (306 transcription factors and 73 miRNAs) of 179 transcriptional "programs", influencing disease progression in patients across 23 disease states. Through extensive testing on independent patient cohorts, we share evidence that a machine learning model trained on activity profiles of programs within gbmMINER significantly augments risk stratification, identifying patients who are super-responders to standard of care and those that would benefit from 2 nd line treatments. In addition to providing mechanistic hypotheses regarding disease prognosis, the activity of programs containing targets of 2 nd line treatments accurately predicted efficacy of 28 drugs in killing glioma stem-like cells from 43 patients. Our findings demonstrate that interpatient heterogeneity manifests from differential activities of transcriptional programs, providing actionable strategies for mechanistically characterizing GBM from a systems perspective and developing better prognostic and predictive biomarkers for personalized medicine.
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Pérez-Sayáns M, Chamorro-Petronacci CM, Bravo SB, Padín-Iruegas ME, Guitián-Fernández E, Barros-Angueira F, Quintas-Rey R, García-García A. Genetic linkage analysis of head and neck cancer in a Spanish family. Oral Dis 2024; 30:1032-1039. [PMID: 37026679 DOI: 10.1111/odi.14572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 04/08/2023]
Abstract
OBJECTIVES To describe the genetic variants that may be associated with the development of head and neck cancer (HNC) and functionally validating the molecular implications. MATERIALS AND METHODS A prospective observational study was carried out on a family of 3 generations in which 3 members had developed HNC. Peripheral blood sample was taken in a routine procedure for exome sequencing in one relative and genotyping in the remaining twelve relatives. For the functional analysis all-trans retinoic acid (atRA) was extracted from saliva and serum and measured using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The presence of HPV-DNA. RESULTS None of the patients smoked or consumed alcohol. The presence of HPV DNA was not detected in any of the biopsied samples. A total amount of 6 members out of 13 (46.15%) carried out the same mutation of CYP26B1 (2p13.2; G>T). The mean plasma concentration of atRA was 3.3109 ± 1.4791 pg/mL for the study family and 4.7370 ± 1.5992 pg/mL for the controls (p = 0.042). CONCLUSION Lower levels of atRA were confirmed in the study family, which may open the way to the possible relationship between the polymorphism CYP26B1 (2p13.2; G>T) and HNC.
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Affiliation(s)
- Mario Pérez-Sayáns
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Dentistry, Santiago de Compostela University, Santiago de Compostela, Spain
- Institute of Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - Cintia M Chamorro-Petronacci
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Dentistry, Santiago de Compostela University, Santiago de Compostela, Spain
- Institute of Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - Susana B Bravo
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, Santiago de Compostela, Spain
| | - María E Padín-Iruegas
- Department of Functional Biology and Health Sciences, Faculty of Physiotherapy, Human Anatomy and Embryology Area, Vigo University, Pontevedra, Spain
| | - Esteban Guitián-Fernández
- Mass Spectrometry and Proteomics Unit, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Francisco Barros-Angueira
- Molecular Medicine Unit - Galician Public Foundation of Genomic Medicine, Consultation Building, Floor -2, University Hospital Complex of Santiago, Santiago de Compostela, Spain
| | - Rita Quintas-Rey
- Molecular Medicine Unit - Galician Public Foundation of Genomic Medicine, Consultation Building, Floor -2, University Hospital Complex of Santiago, Santiago de Compostela, Spain
| | - Abel García-García
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Dentistry, Santiago de Compostela University, Santiago de Compostela, Spain
- Institute of Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
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Xu X, Qiu L, Zhang M, Wu G. Segregation of nascent GPCRs in the ER-to-Golgi transport by CCHCR1 via direct interaction. J Cell Sci 2024; 137:jcs261685. [PMID: 38230433 PMCID: PMC10912811 DOI: 10.1242/jcs.261685] [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: 09/27/2023] [Accepted: 01/03/2024] [Indexed: 01/18/2024] Open
Abstract
G protein-coupled receptors (GPCRs) constitute the largest superfamily of cell surface signaling proteins that share a common structural topology. When compared with agonist-induced internalization, how GPCRs are sorted and delivered to functional destinations after synthesis in the endoplasmic reticulum (ER) is much less well understood. Here, we demonstrate that depletion of coiled-coil α-helical rod protein 1 (CCHCR1) by siRNA and CRISPR-Cas9 significantly inhibits surface expression and signaling of α2A-adrenergic receptor (α2A-AR; also known as ADRA2A), without affecting α2B-AR. Further studies show that CCHCR1 depletion specifically impedes α2A-AR export from the ER to the Golgi, but not from the Golgi to the surface. We also demonstrate that CCHCR1 selectively interacts with α2A-AR. The interaction is mediated through multiple domains of both proteins and is ionic in nature. Moreover, mutating CCHCR1-binding motifs significantly attenuates ER-to-Golgi export, surface expression and signaling of α2A-AR. Collectively, these data reveal a novel function for CCHCR1 in intracellular protein trafficking, indicate that closely related GPCRs can be sorted into distinct ER-to-Golgi transport routes by CCHCR1 via direct interaction, and provide important insights into segregation and anterograde delivery of nascent GPCR members.
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Affiliation(s)
- Xin Xu
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Lifen Qiu
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Maoxiang Zhang
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Guangyu Wu
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
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Chen WC, Brandenburg JT, Choudhury A, Hayat M, Sengupta D, Swiel Y, Babb de Villiers C, Ferndale L, Aldous C, Soo CC, Lee S, Curtis C, Newton R, Waterboer T, Sitas F, Bradshaw D, Abnet CC, Ramsay M, Parker MI, Singh E, Lewis CM, Mathew CG. Genome-wide association study of esophageal squamous cell cancer identifies shared and distinct risk variants in African and Chinese populations. Am J Hum Genet 2023; 110:1690-1703. [PMID: 37673066 PMCID: PMC10577073 DOI: 10.1016/j.ajhg.2023.08.007] [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: 12/14/2022] [Revised: 08/11/2023] [Accepted: 08/11/2023] [Indexed: 09/08/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) has a high disease burden in sub-Saharan Africa and has a very poor prognosis. Genome-wide association studies (GWASs) of ESCC in predominantly East Asian populations indicate a substantial genetic contribution to its etiology, but no genome-wide studies have been done in populations of African ancestry. Here, we report a GWAS in 1,686 African individuals with ESCC and 3,217 population-matched control individuals to investigate its genetic etiology. We identified a genome-wide-significant risk locus on chromosome 9 upstream of FAM120A (rs12379660, p = 4.58 × 10-8, odds ratio = 1.28, 95% confidence interval = 1.22-1.34), as well as a potential African-specific risk locus on chromosome 2 (rs142741123, p = 5.49 × 10-8) within MYO1B. FAM120A is a component of oxidative stress-induced survival signals, and the associated variants at the FAM120A locus co-localized with highly significant cis-eQTLs in FAM120AOS in both esophageal mucosa and esophageal muscularis tissue. A trans-ethnic meta-analysis was then performed with the African ESCC study and a Chinese ESCC study in a combined total of 3,699 ESCC-affected individuals and 5,918 control individuals, which identified three genome-wide-significant loci on chromosome 9 at FAM120A (rs12379660, pmeta = 9.36 × 10-10), chromosome 10 at PLCE1 (rs7099485, pmeta = 1.48 × 10-8), and chromosome 22 at CHEK2 (rs1033667, pmeta = 1.47 × 10-9). This indicates the existence of both shared and distinct genetic risk loci for ESCC in African and Asian populations. Our GWAS of ESCC conducted in a population of African ancestry indicates a substantial genetic contribution to ESCC risk in Africa.
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Affiliation(s)
- Wenlong Carl Chen
- National Cancer Registry, National Health Laboratory Service, Johannesburg 2131, South Africa; Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa; Strengthening Oncology Services Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa; Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Jean-Tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Mahtaab Hayat
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa; Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Yaniv Swiel
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa; School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Chantal Babb de Villiers
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Lucien Ferndale
- Department of Surgery, Grey's Hospital, Pietermaritzburg 3200, South Africa; College of Health Sciences, School of Clinical Medicine, University of KwaZulu-Natal, Durban 4013, South Africa
| | - Colleen Aldous
- College of Health Sciences, School of Clinical Medicine, University of KwaZulu-Natal, Durban 4013, South Africa
| | - Cassandra C Soo
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Sang Lee
- Social, Genetic and Development Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, SE5 8AF London, UK; NIHR BioResource Centre Maudsley, South London and Maudsley NHS Foundation Trust, King's College London, SE5 8AF London, UK
| | - Charles Curtis
- Social, Genetic and Development Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, SE5 8AF London, UK; NIHR BioResource Centre Maudsley, South London and Maudsley NHS Foundation Trust, King's College London, SE5 8AF London, UK
| | - Rob Newton
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda; University of York, YO10 5DD York, UK
| | - Tim Waterboer
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Freddy Sitas
- Burden of Disease Research Unit, South African Medical Research Council, Cape Town 7505, South Africa; Centre for Primary Health Care and Equity, School of Population, University of New South Wales, Sydney, NSW 2052, Australia; Menzies Centre of Health Policy, School of Public Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Debbie Bradshaw
- Burden of Disease Research Unit, South African Medical Research Council, Cape Town 7505, South Africa
| | - Christian C Abnet
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA
| | - Michele Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - M Iqbal Parker
- Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7700, South Africa
| | - Elvira Singh
- National Cancer Registry, National Health Laboratory Service, Johannesburg 2131, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Cathryn M Lewis
- Social, Genetic and Development Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, SE5 8AF London, UK; Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, SE1 9RT London, UK
| | - Christopher G Mathew
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa; Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa; Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, SE1 9RT London, UK.
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9
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Ying P, Chen C, Lu Z, Chen S, Zhang M, Cai Y, Zhang F, Huang J, Fan L, Ning C, Li Y, Wang W, Geng H, Liu Y, Tian W, Yang Z, Liu J, Huang C, Yang X, Xu B, Li H, Zhu X, Li N, Li B, Wei Y, Zhu Y, Tian J, Miao X. Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human cancer risk. Nat Commun 2023; 14:5958. [PMID: 37749132 PMCID: PMC10520073 DOI: 10.1038/s41467-023-41690-z] [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: 12/20/2022] [Accepted: 09/14/2023] [Indexed: 09/27/2023] Open
Abstract
Genome-wide association studies have identified numerous variants associated with human complex traits, most of which reside in the non-coding regions, but biological mechanisms remain unclear. However, assigning function to the non-coding elements is still challenging. Here we apply Activity-by-Contact (ABC) model to evaluate enhancer-gene regulation effect by integrating multi-omics data and identified 544,849 connections across 20 cancer types. ABC model outperforms previous approaches in linking regulatory variants to target genes. Furthermore, we identify over 30,000 enhancer-gene connections in colorectal cancer (CRC) tissues. By integrating large-scale population cohorts (23,813 cases and 29,973 controls) and multipronged functional assays, we demonstrate an ABC regulatory variant rs4810856 associated with CRC risk (Odds Ratio = 1.11, 95%CI = 1.05-1.16, P = 4.02 × 10-5) by acting as an allele-specific enhancer to distally facilitate PREX1, CSE1L and STAU1 expression, which synergistically activate p-AKT signaling. Our study provides comprehensive regulation maps and illuminates a single variant regulating multiple genes, providing insights into cancer etiology.
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Grants
- Distinguished Young Scholars of China (NSFC-81925032), Key Program of National Natural Science Foundation of China (NSFC-82130098), the Fundamental Research Funds for the Central Universities (2042022rc0026, 2042023kf1005),Knowledge Innovation Program of Wuhan (2023020201010060).
- Youth Program of National Natural Science Foundation of China (NSFC-82003547), Program of Health Commission of Hubei Province (WJ2023M045) and Fundamental Research Funds for the Central Universities (WHU: 2042022kf1031).
- The National Science Fund for Excellent Young Scholars (NSFC-82322058), Program of National Natural Science Foundation of China (NSFC-82103929, NSFC-82273713), Young Elite Scientists Sponsorship Program by cst(2022QNRC001), National Science Fund for Distinguished Young Scholars of Hubei Province of China (2023AFA046), Fundamental Research Funds for the Central Universities (WHU:2042022kf1205) and Knowledge Innovation Program of Wuhan (whkxjsj011, 2023020201010073).
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Affiliation(s)
- Pingting Ying
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan, 430071, China
| | - Can Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan, 430071, China
| | - Zequn Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan, 430071, China
| | - Shuoni Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Ming Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Yimin Cai
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Fuwei Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Jinyu Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Linyun Fan
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Caibo Ning
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Yanmin Li
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Wenzhuo Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Hui Geng
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Yizhuo Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Wen Tian
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Zhiyong Yang
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Jiuyang Liu
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Chaoqun Huang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Xiaojun Yang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Bin Xu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, 430060, China
| | - Heng Li
- Department of Urology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xu Zhu
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, 430071, China
| | - Ni Li
- Office of Cancer Screening, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Bin Li
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Yongchang Wei
- Department of Gastrointestinal Oncology, Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Ying Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China.
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan, 430071, China.
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China.
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan, 430071, China.
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, China.
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10
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Yao XT, Li PP, Liu J, Yang YY, Luo ZL, Jiang HT, He WG, Luo HH, Deng YX, He BC. Wnt/β-Catenin Promotes the Osteoblastic Potential of BMP9 Through Down-Regulating Cyp26b1 in Mesenchymal Stem Cells. Tissue Eng Regen Med 2023; 20:705-723. [PMID: 37010733 PMCID: PMC10352185 DOI: 10.1007/s13770-023-00526-z] [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: 09/29/2022] [Revised: 01/21/2023] [Accepted: 02/09/2023] [Indexed: 04/04/2023] Open
Abstract
BACKGROUND All-trans retinoic acid (ATRA) promotes the osteogenic differentiation induced by bone morphogenetic protein 9 (BMP9), but the intrinsic relationship between BMP9 and ATRA keeps unknown. Herein, we investigated the effect of Cyp26b1, a critical enzyme of ATRA degradation, on the BMP9-induced osteogenic differentiation in mesenchymal stem cells (MSCs), and unveiled possible mechanism through which BMP9 regulates the expression of Cyp26b1. METHODS ATRA content was detected with ELISA and HPLC-MS/MS. PCR, Western blot, and histochemical staining were used to assay the osteogenic markers. Fetal limbs culture, cranial defect repair model, and micro-computed tomographic were used to evaluate the quality of bone formation. IP and ChIP assay were used to explore possible mechanism. RESULTS We found that the protein level of Cyp26b1 was increased with age, whereas the ATRA content decreased. The osteogenic markers induced by BMP9 were increased by inhibiting or silencing Cyp26b1 but reduced by exogenous Cyp26b1. The BMP9-induced bone formation was enhanced by inhibiting Cyp26b1. The cranial defect repair was promoted by BMP9, which was strengthened by silencing Cyp26b1 and reduced by exogenous Cyp26b1. Mechanically, Cyp26b1 was reduced by BMP9, which was enhanced by activating Wnt/β-catenin, and reduced by inhibiting this pathway. β-catenin interacts with Smad1/5/9, and both were recruited at the promoter of Cyp26b1. CONCLUSIONS Our findings suggested the BMP9-induced osteoblastic differentiation was mediated by activating retinoic acid signalling, viadown-regulating Cyp26b1. Meanwhile, Cyp26b1 may be a novel potential therapeutic target for the treatment of bone-related diseases or accelerating bone-tissue engineering.
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Affiliation(s)
- Xin-Tong Yao
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, No. 1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People's Republic of China
- Chongqing Key Laboratory for Biochemistry and Molecular Pharmacology, Chongqing, 400016, People's Republic of China
| | - Pei-Pei Li
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, No. 1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People's Republic of China
- Chongqing Key Laboratory for Biochemistry and Molecular Pharmacology, Chongqing, 400016, People's Republic of China
| | - Jiang Liu
- Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
- Department of Orthopedics, The 960th Hospital of the PLA Joint Logistics Support Force, Ji'nan, 250013, Shandong, People's Republic of China
| | - Yuan-Yuan Yang
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, No. 1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People's Republic of China
- Chongqing Key Laboratory for Biochemistry and Molecular Pharmacology, Chongqing, 400016, People's Republic of China
| | - Zhen-Ling Luo
- Taizhou Food Inspection Centre, Taizhou, 318000, Zhejiang, People's Republic of China
| | - Hai-Tao Jiang
- Department of Orthopaedics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, People's Republic of China
| | - Wen-Ge He
- Department of Orthopaedics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, People's Republic of China
| | - Hong-Hong Luo
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, No. 1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People's Republic of China
- Chongqing Key Laboratory for Biochemistry and Molecular Pharmacology, Chongqing, 400016, People's Republic of China
| | - Yi-Xuan Deng
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, No. 1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People's Republic of China
- Chongqing Key Laboratory for Biochemistry and Molecular Pharmacology, Chongqing, 400016, People's Republic of China
| | - Bai-Cheng He
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, No. 1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People's Republic of China.
- Chongqing Key Laboratory for Biochemistry and Molecular Pharmacology, Chongqing, 400016, People's Republic of China.
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11
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Li S, Guo Y, Liu X, Chen Y. Helicobacter pylori plus N-Methyl-N’-nitro-N-nitrosoguanidine: DNA damage and repair; malignant transformation of human esophageal epithelial cells. MUTATION RESEARCH/GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2023; 888:503636. [PMID: 37188438 DOI: 10.1016/j.mrgentox.2023.503636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/08/2023]
Abstract
N-Methyl-N'-nitro-N-nitrosoguanidine (MNNG), found in pickled foods and in chlorinated water, has been used to induce malignant transformation and gastrointestinal cancer in rats. Helicobacter pylori (HP) is implicated in human gastric cancer and possibly also in esophageal cancer. These two agents - one chemical and the other biological - might act together to induce esophageal cancer. In this study, human esophageal epithelial cells (HEECs) were divided into four groups: HP, MNNG, HP + MNNG, and control. The HP-to-HEEC ratio was 100:1. Cells were exposed for 6 h and then passaged until malignant transformation. HEEC at early, intermediate, and late stages of malignant transformation were used for proliferation, cell-cycle, and invasion assays. The alkaline comet assay was performed and expression of proteins, including γ-H2AX and PAXX, was studied by western blotting, to explore DNA damage and repair processes. Measurements of cell morphology, soft-agar clone formation, and invasiveness, and a nude mouse xenograft model, were used to examine malignancy. The effect of HP was stronger than that of MNNG. The combination HP + MNNG exerted a stronger malignant transformation effect than either HP or MNNG alone. Mechanisms of this combined carcinogenesis may include promotion of cell proliferation, perturbation of the cell cycle, promotion of invasiveness, DNA double-strand break induction, or PAXX inhibition.
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12
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Okuda-Ashitaka E, Matsumoto KI. Tenascin-X as a causal gene for classical-like Ehlers-Danlos syndrome. Front Genet 2023; 14:1107787. [PMID: 37007968 PMCID: PMC10050494 DOI: 10.3389/fgene.2023.1107787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/06/2023] [Indexed: 03/17/2023] Open
Abstract
Tenascin-X (TNX) is an extracellular matrix glycoprotein for which a deficiency results in a recessive form of classical-like Ehlers-Danlos syndrome (clEDS), a heritable connective tissue disorder with hyperextensible skin without atrophic scarring, joint hypermobility, and easy bruising. Notably, patients with clEDS also suffer from not only chronic joint pain and chronic myalgia but also neurological abnormalities such as peripheral paresthesia and axonal polyneuropathy with high frequency. By using TNX-deficient (Tnxb−/−) mice, well-known as a model animal of clEDS, we recently showed that Tnxb−/− mice exhibit hypersensitivity to chemical stimuli and the development of mechanical allodynia due to the hypersensitization of myelinated A-fibers and activation of the spinal dorsal horn. Pain also occurs in other types of EDS. First, we review the underlying molecular mechanisms of pain in EDS, especially that in clEDS. In addition, the roles of TNX as a tumor suppressor protein in cancer progression have been reported. Recent in silico large-scale database analyses have shown that TNX is downregulated in various tumor tissues and that high expression of TNX in tumor cells has a good prognosis. We describe what is so far known about TNX as a tumor suppressor protein. Furthermore, some patients with clEDS show delayed wound healing. Tnxb−/− mice also exhibit impairment of epithelial wound healing in corneas. TNX is also involved in liver fibrosis. We address the molecular mechanism for the induction of COL1A1 by the expression of both a peptide derived from the fibrinogen-related domain of TNX and integrin α11.
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Affiliation(s)
- Emiko Okuda-Ashitaka
- Department of Biomedical Engineering, Osaka Institute of Technology, Osaka, Japan
- *Correspondence: Emiko Okuda-Ashitaka, ; Ken-ichi Matsumoto,
| | - Ken-ichi Matsumoto
- Department of Biosignaling and Radioisotope Experiment, Interdisciplinary Center for Science Research, Head Office for Research and Academic Information, Shimane University, Izumo, Japan
- *Correspondence: Emiko Okuda-Ashitaka, ; Ken-ichi Matsumoto,
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13
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García-Sancha N, Corchado-Cobos R, Gómez-Vecino A, Jiménez-Navas A, Pérez-Baena MJ, Blanco-Gómez A, Holgado-Madruga M, Mao JH, Cañueto J, Castillo-Lluva S, Mendiburu-Eliçabe M, Pérez-Losada J. Evolutionary Origins of Metabolic Reprogramming in Cancer. Int J Mol Sci 2022; 23:ijms232012063. [PMID: 36292921 PMCID: PMC9603151 DOI: 10.3390/ijms232012063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/29/2022] [Accepted: 10/06/2022] [Indexed: 11/23/2022] Open
Abstract
Metabolic changes that facilitate tumor growth are one of the hallmarks of cancer. These changes are not specific to tumors but also take place during the physiological growth of tissues. Indeed, the cellular and tissue mechanisms present in the tumor have their physiological counterpart in the repair of tissue lesions and wound healing. These molecular mechanisms have been acquired during metazoan evolution, first to eliminate the infection of the tissue injury, then to enter an effective regenerative phase. Cancer itself could be considered a phenomenon of antagonistic pleiotropy of the genes involved in effective tissue repair. Cancer and tissue repair are complex traits that share many intermediate phenotypes at the molecular, cellular, and tissue levels, and all of these are integrated within a Systems Biology structure. Complex traits are influenced by a multitude of common genes, each with a weak effect. This polygenic component of complex traits is mainly unknown and so makes up part of the missing heritability. Here, we try to integrate these different perspectives from the point of view of the metabolic changes observed in cancer.
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Affiliation(s)
- Natalia García-Sancha
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Roberto Corchado-Cobos
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Aurora Gómez-Vecino
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Alejandro Jiménez-Navas
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Manuel Jesús Pérez-Baena
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Adrián Blanco-Gómez
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Marina Holgado-Madruga
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
- Departamento de Fisiología y Farmacología, Universidad de Salamanca, 37007 Salamanca, Spain
- Instituto de Neurociencias de Castilla y León (INCyL), 37007 Salamanca, Spain
| | - Jian-Hua Mao
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA 94720, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Javier Cañueto
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
- Departamento de Dermatología, Hospital Universitario de Salamanca, Paseo de San Vicente 58-182, 37007 Salamanca, Spain
| | - Sonia Castillo-Lluva
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC), 28040 Madrid, Spain
| | - Marina Mendiburu-Eliçabe
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
- Correspondence: (M.M.-E.); (J.P.-L.)
| | - Jesús Pérez-Losada
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
- Correspondence: (M.M.-E.); (J.P.-L.)
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14
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Triple chemical derivatization strategy assisted liquid chromatography-mass spectrometry for determination of retinoic acids in human serum. Talanta 2022; 245:123474. [DOI: 10.1016/j.talanta.2022.123474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/06/2022] [Accepted: 04/09/2022] [Indexed: 11/18/2022]
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15
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Wu H, Zhao D, Wang C, Zhang D, Tang M, Qian S, Xu L, Xia T, Zhou J, Wang G, He Y, Gao L, Chen W, Li L, Yang W, Zhao Q, Hu C, Hu A. All-Trans Retinoic Acid Prevents the Progression of Gastric Precancerous Lesions by Regulating Disordered Retinoic Acid Metabolism. Nutr Cancer 2022; 74:3351-3362. [PMID: 35225106 DOI: 10.1080/01635581.2022.2044062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Hanhan Wu
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Didi Zhao
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Chen Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Daoming Zhang
- Department of Gastroenterology, Lujiang County People’s Hospital, Hefei, Anhui, PR China
| | - Min Tang
- Department of Gastroenterology and Hepatology, the Fourth Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
| | - Shiqing Qian
- Department of Pathology, Lujiang County People’s Hospital, Hefei, Anhui, PR China
| | - Lina Xu
- Department of Gastroenterology, Lujiang County People’s Hospital, Hefei, Anhui, PR China
| | - Tao Xia
- Department of Gastroenterology, Lujiang County People’s Hospital, Hefei, Anhui, PR China
| | - Juanyan Zhou
- Department of Gastroenterology and Hepatology, the Fourth Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
| | - Guangjun Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Yue He
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Lei Gao
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Wenjun Chen
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Li Li
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Wanshui Yang
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Qihong Zhao
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Chuanlai Hu
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Anla Hu
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
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Li M, Li C, Lu P, Wang B, Gao Y, Liu W, Shi Y, Ma Y. Expression and function analysis of CRABP2 and FABP5, and their ratio in esophageal squamous cell carcinoma. Open Med (Wars) 2021; 16:1444-1458. [PMID: 34632074 PMCID: PMC8477672 DOI: 10.1515/med-2021-0350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/26/2021] [Accepted: 08/09/2021] [Indexed: 12/29/2022] Open
Abstract
Objective The purpose of this study was to explore the effect of CRABP2 and FABP5, and their ratio on prognosis in esophageal squamous cell carcinoma. Methods The expression data of CRABP2 in esophageal cancer in TCGA and GEO were collected by the public database GEPIA. The expression levels of CRABP2 and FABP5 were examined using immunohistochemistry. The relationship between the two proteins and related clinicopathological parameters were analyzed by χ2 test. Survival analysis was used to investigate the effect of CRABP2 and FABP5, and their ratio on prognosis. Results Compared with normal esophageal mucosal epithelium, there was lower CRABP2 gene mRNA in the esophageal cancer tissue, and the difference was statistically significant (p < 0.01). For the expression level, no significant difference was observed in patients with stages I–IV in esophageal cancer. Immunohistochemistry showed that CRABP2 and FABP5 were both highly expressed in normal esophageal squamous epithelial cells at 100 and 94.1%, while lower in ESCC (75.6 and 58.7%). There was a significant difference in the expression between cancer and adjacent tissues (p < 0.001). No inherent relationship was manifested between the CRABP2 expression and the clinical parameters of the ESCC. The expression of FABP5 was related to lymph node metastasis (p = 0.032), the depth of invasion (p = 0.041), and the AJCC stage (p = 0.013). The ratio of CRABP2 and FABP5 was related to ethnicity (p = 0.001), nerve invasion (p = 0.031), and postoperative treatment (p = 0.038). CRABP2 is positively associated with FABP5 (r = 0.156, p = 0.041) and the ratio (r = 0.334, p = 0.000), while there was a negative correlation between FABP5 and the ratio (r = −0.269, p = 0.000). Patients with CRABP2-positive expression had a significantly longer overall survival than patients with CRABP2-negative expression (p = 0.025). Conclusion CRABP2 as a suppressor factor is expected to be a potential prognosis marker for esophageal squamous cell carcinoma.
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Affiliation(s)
- Mengyan Li
- Departments of Pathology, The First Affiliated Hospital, Xinjiang Medical University, Urumqi, Xinjiang 830011, People's Republic of China
| | - Chao Li
- Departments of Pathology, The First Affiliated Hospital, Xinjiang Medical University, Urumqi, Xinjiang 830011, People's Republic of China
| | - Pengfei Lu
- Departments of Oncology, The First Affiliated Hospital, Xinjiang Medical University, Urumqi, Xinjiang 830011, People's Republic of China
| | - Bo Wang
- Departments of Pathology, The First Affiliated Hospital, Xinjiang Medical University, Urumqi, Xinjiang 830011, People's Republic of China
| | - Yongmei Gao
- Departments of Pathology, The First Affiliated Hospital, Xinjiang Medical University, Urumqi, Xinjiang 830011, People's Republic of China
| | - Wengying Liu
- Departments of Pathology, The First Affiliated Hospital, Xinjiang Medical University, Urumqi, Xinjiang 830011, People's Republic of China
| | - Yan Shi
- Departments of Pathology, The First Affiliated Hospital, Xinjiang Medical University, Urumqi, Xinjiang 830011, People's Republic of China
| | - Yuqing Ma
- Departments of Pathology, The First Affiliated Hospital, Xinjiang Medical University, 393 Liyushan Road, Urumqi, Xinjiang 830011, People's Republic of China
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17
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Yang CS, Chen XL. Research on esophageal cancer: With personal perspectives from studies in China and Kenya. Int J Cancer 2021; 149:264-276. [PMID: 33270917 PMCID: PMC8141013 DOI: 10.1002/ijc.33421] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/11/2022]
Abstract
The most common form of esophageal cancer (EC), esophageal squamous cell carcinoma (ESCC), is prevalent in many unindustrialized societies, among people with lower socioeconomic status and those who frequently use tobacco and alcohol. In some areas, ESCC mortality ranked top among all cancer. In this review, we begin with discussions of the extensive research on EC in Linxian in northern China that started 60 years ago and the recent studies in Kenya from our personal perspectives. Based on the results obtained from these studies and information from the literature, we summarize our current understanding about the risk factors for ESCC including lifestyle factors (smoking, alcohol, consumption of food and beverages at high temperature and other unhealthy habits), poor diet and nutritional insufficiencies and genetic susceptibility. Elimination or minimization of these environmental risk factors, as well as early detection and treatment of precancerous lesions, would be effective means for the prevention of ESCC. Current knowledge of molecular alterations in ESCC (gene mutations, hypermethylation and amplification or overexpression), as well as treatment of ESCC and the potential of targeted therapy, are also discussed. Finally, we propose effective approaches for the prevention of ESCC by adapting a healthy lifestyle, including a healthy diet that would also prevent other diseases. Community outreach, public education and international collaboration are important for achieving this public health goal.
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Affiliation(s)
- Chung S. Yang
- Department of Chemical BiologyErnest Mario School of Pharmacy, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Xiaoxin Luke Chen
- Cancer Research Program, Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central UniversityDurhamNorth CarolinaUSA
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18
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Chong CS, Limviphuvadh V, Maurer-Stroh S. Global spectrum of population-specific common missense variation in cytochrome P450 pharmacogenes. Hum Mutat 2021; 42:1107-1123. [PMID: 34153149 DOI: 10.1002/humu.24243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 04/12/2021] [Accepted: 06/08/2021] [Indexed: 11/06/2022]
Abstract
Next-generation sequencing technology has afforded the discovery of many novel variants that are of significance to inheritable pharmacogenomics (PGx) traits but a large proportion of them have unknown consequences. These include missense variants resulting in single amino acid substitutions in cytochrome P450 (CYP) proteins that can impair enzyme function, leading to altered drug efficacy and toxicity. While most unknown variants are rare, an overlooked minority are variants that are collectively rare but enriched in specific populations. Here, we analyzed sequence variation data in 141,456 individuals from across eight study populations in gnomAD for 38 CYP genes to identify such variants in addition to common variants. By further comparison with data from two PGx-specific databases (PharmVar and PharmGKB) and ClinVar, we identified 234 missense variants in 35 CYP genes, of which 107 were unknown to these databases. Most unknown variants (n = 83) were population-specific common variants and several (n = 7) were found in important CYP pharmacogenes (CYP2D6, CYP4F2, and CYP2C19). Overall, 29% (n = 31) of 107 unknown variants were predicted to affect CYP enzyme function although further biochemical characterization is necessary. These variants may elucidate part of the unexplained interpopulation differences observed in drug response.
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Affiliation(s)
- Cheng-Shoong Chong
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Innovations in Food and Chemical Safety Programme (IFCS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,National University of Singapore Graduate School for Integrative Sciences and Engineering (NGS), National University of Singapore, Singapore, Singapore
| | - Vachiranee Limviphuvadh
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Innovations in Food and Chemical Safety Programme (IFCS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Innovations in Food and Chemical Safety Programme (IFCS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,National University of Singapore Graduate School for Integrative Sciences and Engineering (NGS), National University of Singapore, Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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Tian J, Lu Z, Niu S, Zhang S, Ying P, Wang L, Zhang M, Cai Y, Dong T, Zhu Y, Zhong R, Wang Z, Chang J, Miao X. Aberrant MCM10 SUMOylation induces genomic instability mediated by a genetic variant associated with survival of esophageal squamous cell carcinoma. Clin Transl Med 2021; 11:e485. [PMID: 34185429 PMCID: PMC8236122 DOI: 10.1002/ctm2.485] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 06/13/2021] [Accepted: 06/16/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is one of the common gastrointestinal malignancy with an inferior prognosis outcome. DNA replication licensing aberration induced by dysregulation of minichromosome maintenance proteins (MCMs) causes genomic instability and cancer metastasis. SUMOylation modification plays a pivotal role in regulation of genomic integrity, while its dysregulation fueled by preexisting germline variants in cancers remains poorly understood. METHODS Firstly, we conducted two-stage survival analysis consisting of an exome-wide association study in 904 ESCC samples and another independent 503 ESCC samples. Then, multipronged functional experiments were performed to illuminate the potential biological mechanisms underlying the promising variants, and MCM10 influences the ESCC progression. Finally, we tested the effects of MCM10 inhibitors on ESCC cells. RESULTS A germline variant rs2274110 located at the exon 15 of MCM10 was identified to be significantly associated with the prognosis of ESCC patients. Individuals carrying rs2274110-AA genotypes confer a poor survival (hazard ratio = 1.61, 95% confidence interval = 1.35-1.93, p = 1.35 × 10-7 ), compared with subjects carrying rs2274110-AG/GG genotypes. Furthermore, we interestingly found that the variant can increase SUMOylation levels at K669 site (Lys[K]699Arg[R]) of MCM10 protein mediated by SUMO2/3 enzymes, which resulted in an aberrant overexpression of MCM10. Mechanistically, aberrant overexpression of MCM10 facilitated the proliferation and metastasis abilities of ESCC cells in vitro and in vivo by inducing DNA over-replication and genomic instability, providing functional evidence to support our population finding that high expression of MCM10 is extensively presented in tumor tissues of ESCC and correlated with inferior survival outcomes of multiple cancer types, including ESCC. Finally, MCM10 inhibitors Suramin and its analogues were revealed to effectively block the metastasis of ESCC cells. CONCLUSIONS These findings not only demonstrate a potential biological mechanism between aberrant SUMOylation, genomic instability and cancer metastasis, but also provide a promising biomarker aiding in stratifying ESCC individuals with different prognosis, as well as a potential therapeutic target MCM10.
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Affiliation(s)
- Jianbo Tian
- Department of Epidemiology and BiostatisticsKey Laboratory for Environment and HealthSchool of Public HealthTongji Medical CollegeHuazhong University of Sciences and TechnologyWuhanChina
| | - Zequn Lu
- Department of Epidemiology and BiostatisticsKey Laboratory for Environment and HealthSchool of Public HealthTongji Medical CollegeHuazhong University of Sciences and TechnologyWuhanChina
| | - Siyuan Niu
- Department of Epidemiology and BiostatisticsKey Laboratory for Environment and HealthSchool of Public HealthTongji Medical CollegeHuazhong University of Sciences and TechnologyWuhanChina
| | - Shanshan Zhang
- Department of Epidemiology and BiostatisticsKey Laboratory for Environment and HealthSchool of Public HealthTongji Medical CollegeHuazhong University of Sciences and TechnologyWuhanChina
| | - Pingting Ying
- Department of Epidemiology and BiostatisticsKey Laboratory for Environment and HealthSchool of Public HealthTongji Medical CollegeHuazhong University of Sciences and TechnologyWuhanChina
| | - Lu Wang
- Department of Epidemiology and BiostatisticsKey Laboratory for Environment and HealthSchool of Public HealthTongji Medical CollegeHuazhong University of Sciences and TechnologyWuhanChina
| | - Ming Zhang
- Department of Epidemiology and BiostatisticsKey Laboratory for Environment and HealthSchool of Public HealthTongji Medical CollegeHuazhong University of Sciences and TechnologyWuhanChina
| | - Yimin Cai
- Department of Epidemiology and BiostatisticsKey Laboratory for Environment and HealthSchool of Public HealthTongji Medical CollegeHuazhong University of Sciences and TechnologyWuhanChina
| | - Tianyi Dong
- Department of Epidemiology and BiostatisticsKey Laboratory for Environment and HealthSchool of Public HealthTongji Medical CollegeHuazhong University of Sciences and TechnologyWuhanChina
| | - Ying Zhu
- Department of Epidemiology and BiostatisticsKey Laboratory for Environment and HealthSchool of Public HealthTongji Medical CollegeHuazhong University of Sciences and TechnologyWuhanChina
| | - Rong Zhong
- Department of Epidemiology and BiostatisticsKey Laboratory for Environment and HealthSchool of Public HealthTongji Medical CollegeHuazhong University of Sciences and TechnologyWuhanChina
| | - Zhihua Wang
- Department of UrologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Jiang Chang
- Department of Epidemiology and BiostatisticsKey Laboratory for Environment and HealthSchool of Public HealthTongji Medical CollegeHuazhong University of Sciences and TechnologyWuhanChina
| | - Xiaoping Miao
- Department of Epidemiology and BiostatisticsKey Laboratory for Environment and HealthSchool of Public HealthTongji Medical CollegeHuazhong University of Sciences and TechnologyWuhanChina
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20
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Oncogenic SNORD12B activates the AKT-mTOR-4EBP1 signaling in esophageal squamous cell carcinoma via nucleus partitioning of PP-1α. Oncogene 2021; 40:3734-3747. [PMID: 33941854 DOI: 10.1038/s41388-021-01809-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 04/06/2021] [Accepted: 04/20/2021] [Indexed: 02/03/2023]
Abstract
Esophageal cancer is a complex malignancy and the sixth leading cause of cancer death worldwide. In Eastern Asia including China, about 90% of all incident cases have esophageal squamous cell carcinoma (ESCC). Mounting evidence elucidates that aberrant expression of various non-coding RNAs (ncRNAs) contributes to ESCC progression, but it remains unclear how small nucleolar RNAs (snoRNAs) are involved in ESCC development. We systemically screened clinically relevant snoRNAs in ESCC via integrative analyses of The Cancer Genome Atlas (TCGA) data and validation in ESCC tissues. We found that snoRNA SNORD12B was one of the most evidently upregulated snoRNAs in ESCC specimens and its high expression was significantly associated with poor prognosis of patients. SNORD12B profoundly promoted proliferation, migration, invasion, and metastasis of ESCC cells in vitro and in vivo, indicating its oncogene nature. In particular, SNORD12B could interact with PP-1α, one of the three catalytic subunits of serine/threonine protein phosphatase 1, which is a major phosphatase that directly dephosphorylates AKT to suppress its activation. Interestingly, high levels of SNORD12B in ESCC cells could break interactions between 14-3-3ζ and PP-1α, abolish the retention of PP-1α in the cytosol by 14-3-3ζ and relocate PP-1α from the cytosol to the nucleus. This led to sequestered PP-1α in the nucleus, enhanced phosphorylation of AKT in the cytosol, activated AKT-mTOR-4EBP1 signaling, and, thus, ESCC progression. These insights would improve our understanding of how snoRNAs contribute to tumorigenesis and highlight the potential of snoRNAs as future therapeutic targets against cancers.
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21
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Zeng B, Huang P, Du P, Sun X, Huang X, Fang X, Li L. Comprehensive Study of Germline Mutations and Double-Hit Events in Esophageal Squamous Cell Cancer. Front Oncol 2021; 11:637431. [PMID: 33889545 PMCID: PMC8056176 DOI: 10.3389/fonc.2021.637431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/10/2021] [Indexed: 01/12/2023] Open
Abstract
Esophageal squamous cell cancer (ESCC) is the eighth most common cancer around the world. Several reports have focused on somatic mutations and common germline mutations in ESCC. However, the contributions of pathogenic germline alterations in cancer susceptibility genes (CSGs), highly frequently mutated CSGs, and pathogenically mutated CSG-related pathways in ESCC remain unclear. We obtained data on 571 ESCC cases from public databases and East Asian from the 1000 Genomes Project database and the China Metabolic Analytics Project database to characterize pathogenic mutations. We detected 157 mutations in 75 CSGs, accounting for 25.0% (143/571) of ESCC cases. Six genes had more than five mutations: TP53 (n = 15 mutations), GJB2 (n = 8), BRCA2 (n = 6), RECQL4 (n = 6), MUTYH (n = 6), and PMS2 (n = 5). Our results identified significant differences in pathogenic germline mutations of TP53, BRCA2, and RECQL4 between the ESCC and control cohorts. Moreover, we identified 84 double-hit events (16 germline/somatic double-hit events and 68 somatic/somatic double-hit events) occurring in 18 tumor suppressor genes from 83 patients. Patients who had ESCC with germline/somatic double-hit events were diagnosed at younger ages than patients with the somatic/somatic double-hit events, though the correlation was not significant. Fanconi anemia was the most enriched pathway of pathogenically mutated CSGs, and it appeared to be a primary pathway for ESCC predisposition. The results of this study identified the underlying roles that pathogenic germline mutations in CSGs play in ESCC pathogenesis, increased our awareness about the genetic basis of ESCC, and provided suggestions for using highly mutated CSGs and double-hit features in the early discovery, prevention, and genetic counseling of ESCC.
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Affiliation(s)
- Bing Zeng
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
| | | | - Peina Du
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | | | - Xiaodong Fang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Lin Li
- BGI-Shenzhen, Shenzhen, China
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22
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Wang W, Xu Q, Li B, Li H, Shen S, Wu J, Ge H, Zhang H, Chen S, Chen W, Gao J, Tang H, Liang B, Zheng X, Sun L. Proteomic analysis of psoriatic skin lesions in a Chinese population. J Proteomics 2021; 240:104207. [PMID: 33798793 DOI: 10.1016/j.jprot.2021.104207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 03/18/2021] [Accepted: 03/20/2021] [Indexed: 02/07/2023]
Abstract
Psoriasis is a chronic skin disorder with undefined pathogenesis. Several biomarkers for this disease have been identified by proteomic analysis. We explored the whole-proteomic changes in 45 pairs of psoriatic and adjacent noninvolved skin tissues in a Chinese population. A total of 3686 proteins were identified, of which 3008 were quantified. A total of 102 and 124 proteins were upregulated and downregulated in lesional skin, respectively. SART1 (P = 3.55 × 10-5) and GLTP (P = 1.54 × 10-3) were the most significantly down- and upregulated proteins. Nearly 90% of these differentially regulated proteins exhibited the same expression trends as those in an online RNA sequencing dataset for psoriasis; 19 differentially regulated proteins exhibited a negative relationship with DNA methylation data for psoriatic lesions. The differentially expressed proteins were enriched in ribosomes, antigen processing and presentation, immune response, and IL-17 signalling pathways. This study identified multiple differentially regulated proteins in psoriatic lesions, which suggested that changes in the proteome play important regulatory roles in psoriasis-associated processes. SIGNIFICANCE: Proteomic analysis was performed in 45 pairs of psoriatic and adjacent noninvolved skin tissues in a Chinese population. More than 3000 proteins were quantified, of which 226 were differentially expressed in psoriatic skin tissues. These proteins were mainly enriched in the immune response, antigen processing and presentation and IL-17 signalling pathways, which have been reported to be associated with the pathogenesis of psoriasis.
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Affiliation(s)
- Wenjun Wang
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei 230022, China; Institute of Dermatology, Anhui Medical University, Hefei 230032, China; Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei 230032, China; Anhui Provincial Institute of Translational Medicine, Hefei 230032, China
| | - Qiongqiong Xu
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei 230022, China; Institute of Dermatology, Anhui Medical University, Hefei 230032, China; Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei 230032, China
| | - Bao Li
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei 230022, China; Institute of Dermatology, Anhui Medical University, Hefei 230032, China; Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei 230032, China
| | - Hui Li
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei 230022, China; Institute of Dermatology, Anhui Medical University, Hefei 230032, China; Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei 230032, China
| | - Songke Shen
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei 230022, China; Institute of Dermatology, Anhui Medical University, Hefei 230032, China; Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei 230032, China
| | - Jing Wu
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei 230022, China; Institute of Dermatology, Anhui Medical University, Hefei 230032, China; Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei 230032, China
| | - Huiyao Ge
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei 230022, China; Institute of Dermatology, Anhui Medical University, Hefei 230032, China; Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei 230032, China
| | - Hui Zhang
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei 230022, China; Institute of Dermatology, Anhui Medical University, Hefei 230032, China; Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei 230032, China
| | - Shirui Chen
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei 230022, China; Institute of Dermatology, Anhui Medical University, Hefei 230032, China; Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei 230032, China
| | - Weiwei Chen
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei 230022, China; Institute of Dermatology, Anhui Medical University, Hefei 230032, China; Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei 230032, China
| | - Jinping Gao
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei 230022, China; Institute of Dermatology, Anhui Medical University, Hefei 230032, China; Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei 230032, China
| | - Huayang Tang
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei 230022, China; Institute of Dermatology, Anhui Medical University, Hefei 230032, China; Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei 230032, China
| | - Bo Liang
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei 230022, China; Institute of Dermatology, Anhui Medical University, Hefei 230032, China; Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei 230032, China
| | - Xiaodong Zheng
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei 230022, China; Institute of Dermatology, Anhui Medical University, Hefei 230032, China; Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei 230032, China
| | - Liangdan Sun
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei 230022, China; Institute of Dermatology, Anhui Medical University, Hefei 230032, China; Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei 230032, China; Anhui Provincial Institute of Translational Medicine, Hefei 230032, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei 230032, China.
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Role of Genetic Variation in Cytochromes P450 in Breast Cancer Prognosis and Therapy Response. Int J Mol Sci 2021; 22:ijms22062826. [PMID: 33802237 PMCID: PMC8001203 DOI: 10.3390/ijms22062826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 12/16/2022] Open
Abstract
Breast cancer is the most frequent cancer in the female population worldwide. The role of germline genetic variability in cytochromes P450 (CYP) in breast cancer prognosis and individualized therapy awaits detailed elucidation. In the present study, we used the next-generation sequencing to assess associations of germline variants in the coding and regulatory sequences of all human CYP genes with response of the patients to the neoadjuvant cytotoxic chemotherapy and disease-free survival (n = 105). A total of 22 prioritized variants associating with a response or survival in the above evaluation phase were then analyzed by allelic discrimination in the large confirmation set (n = 802). Associations of variants in CYP1B1, CYP4F12, CYP4X1, and TBXAS1 with the response to the neoadjuvant cytotoxic chemotherapy were replicated by the confirmation phase. However, just association of variant rs17102977 in CYP4X1 passed the correction for multiple testing and can be considered clinically and statistically validated. Replicated associations for variants in CYP4X1, CYP24A1, and CYP26B1 with disease-free survival of all patients or patients stratified to subgroups according to therapy type have not passed a false discovery rate test. Although statistically not confirmed by the present study, the role of CYP genes in breast cancer prognosis should not be ruled out. In conclusion, the present study brings replicated association of variant rs17102977 in CYP4X1 with the response of patients to the neoadjuvant cytotoxic chemotherapy and warrants further research of genetic variation CYPs in breast cancer.
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Guo X, Lin W, Wen W, Huyghe J, Bien S, Cai Q, Harrison T, Chen Z, Qu C, Bao J, Long J, Yuan Y, Wang F, Bai M, Abecasis GR, Albanes D, Berndt SI, Bézieau S, Bishop DT, Brenner H, Buch S, Burnett-Hartman A, Campbell PT, Castellví-Bel S, Chan AT, Chang-Claude J, Chanock SJ, Cho SH, Conti DV, Chapelle ADL, Feskens EJM, Gallinger SJ, Giles GG, Goodman PJ, Gsur A, Guinter M, Gunter MJ, Hampe J, Hampel H, Hayes RB, Hoffmeister M, Kampman E, Kang HM, Keku TO, Kim HR, Le Marchand L, Lee SC, Li CI, Li L, Lindblom A, Lindor N, Milne RL, Moreno V, Murphy N, Newcomb PA, Nickerson DA, Offit K, Pearlman R, Pharoah PDP, Platz EA, Potter JD, Rennert G, Sakoda LC, Schafmayer C, Schmit SL, Schoen RE, Schumacher FR, Slattery ML, Su YR, Tangen CM, Ulrich CM, van Duijnhoven FJB, Van Guelpen B, Visvanathan K, Vodicka P, Vodickova L, Vymetalkova V, Wang X, White E, Wolk A, Woods MO, Casey G, Hsu L, Jenkins MA, Gruber SB, Peters U, Zheng W. Identifying Novel Susceptibility Genes for Colorectal Cancer Risk From a Transcriptome-Wide Association Study of 125,478 Subjects. Gastroenterology 2021; 160:1164-1178.e6. [PMID: 33058866 PMCID: PMC7956223 DOI: 10.1053/j.gastro.2020.08.062] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 08/20/2020] [Accepted: 08/28/2020] [Indexed: 01/07/2023]
Abstract
BACKGROUND AND AIMS Susceptibility genes and the underlying mechanisms for the majority of risk loci identified by genome-wide association studies (GWAS) for colorectal cancer (CRC) risk remain largely unknown. We conducted a transcriptome-wide association study (TWAS) to identify putative susceptibility genes. METHODS Gene-expression prediction models were built using transcriptome and genetic data from the 284 normal transverse colon tissues of European descendants from the Genotype-Tissue Expression (GTEx), and model performance was evaluated using data from The Cancer Genome Atlas (n = 355). We applied the gene-expression prediction models and GWAS data to evaluate associations of genetically predicted gene-expression with CRC risk in 58,131 CRC cases and 67,347 controls of European ancestry. Dual-luciferase reporter assays and knockdown experiments in CRC cells and tumor xenografts were conducted. RESULTS We identified 25 genes associated with CRC risk at a Bonferroni-corrected threshold of P < 9.1 × 10-6, including genes in 4 novel loci, PYGL (14q22.1), RPL28 (19q13.42), CAPN12 (19q13.2), MYH7B (20q11.22), and MAP1L3CA (20q11.22). In 9 known GWAS-identified loci, we uncovered 9 genes that have not been reported previously, whereas 4 genes remained statistically significant after adjusting for the lead risk variant of the locus. Through colocalization analysis in GWAS loci, we additionally identified 12 putative susceptibility genes that were supported by TWAS analysis at P < .01. We showed that risk allele of the lead risk variant rs1741640 affected the promoter activity of CABLES2. Knockdown experiments confirmed that CABLES2 plays a vital role in colorectal carcinogenesis. CONCLUSIONS Our study reveals new putative susceptibility genes and provides new insight into the biological mechanisms underlying CRC development.
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Affiliation(s)
- Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee.
| | - Weiqiang Lin
- The Kidney Disease Center, the First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jeroen Huyghe
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Stephanie Bien
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Tabitha Harrison
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Zhishan Chen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Conghui Qu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jiandong Bao
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Yuan Yuan
- The Kidney Disease Center, the First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Fangqin Wang
- The Kidney Disease Center, the First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengqiu Bai
- The Kidney Disease Center, the First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Goncalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire, Nantes, France
| | - D Timothy Bishop
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany; Division of Preventive Oncology, German Cancer Research Center and National Center for Tumor Diseases, Heidelberg, Germany
| | - Stephan Buch
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden, Dresden, Germany
| | | | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, University of Barcelona, Barcelona, Spain
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany; University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg, Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sang Hee Cho
- Department of Hematology-Oncology, Chonnam National University Hospital, Hwasun, South Korea
| | - David V Conti
- Department of Preventive Medicine and University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Albert de la Chapelle
- Department of Cancer Biology and Genetics and the Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Edith J M Feskens
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, the Netherlands
| | - Steven J Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Mark Guinter
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Marc J Gunter
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden, Dresden, Germany
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, New York
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Ellen Kampman
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, the Netherlands
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina
| | - Hyeong Rok Kim
- Department of Surgery, Chonnam National University Hwasun Hospital and Medical School, Hwasun, Korea
| | | | - Soo Chin Lee
- National University Cancer Institute, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Christopher I Li
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, Virginia
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Victor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Neil Murphy
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Polly A Newcomb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington; School of Public Health, University of Washington, Seattle, Washington
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Rachel Pearlman
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - John D Potter
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel; Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Lori C Sakoda
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Clemens Schafmayer
- Department of General Surgery, University Hospital Rostock, Rostock, Germany
| | - Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - Yu-Ru Su
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, Utah
| | | | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Xiaoliang Wang
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Emily White
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Michael O Woods
- Memorial University of Newfoundland, Discipline of Genetics, St John's, Newfoundland and Labrador, Canada
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Li Hsu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Stephen B Gruber
- Department of Preventive Medicine and University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
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Momozawa Y, Mizukami K. Unique roles of rare variants in the genetics of complex diseases in humans. J Hum Genet 2021; 66:11-23. [PMID: 32948841 PMCID: PMC7728599 DOI: 10.1038/s10038-020-00845-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/06/2020] [Indexed: 12/19/2022]
Abstract
Genome-wide association studies have identified >10,000 genetic variants associated with various phenotypes and diseases. Although the majority are common variants, rare variants with >0.1% of minor allele frequency have been investigated by imputation and using disease-specific custom SNP arrays. Rare variants sequencing analysis mainly revealed have played unique roles in the genetics of complex diseases in humans due to their distinctive features, in contrast to common variants. Unique roles are hypothesis-free evidence for gene causality, a precise target of functional analysis for understanding disease mechanisms, a new favorable target for drug development, and a genetic marker with high disease risk for personalized medicine. As whole-genome sequencing continues to identify more rare variants, the roles associated with rare variants will also increase. However, a better estimation of the functional impact of rare variants across whole genome is needed to enhance their contribution to improvements in human health.
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Affiliation(s)
- Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan.
- Laboratory for Molecular Science for Drug Discovery, Graduate School of Medical Life Science, Yokohama City University, Kanagawa, Japan.
| | - Keijiro Mizukami
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
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26
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Cheng J, Zhuo Z, Yang L, Zhao P, Zhang J, Zhou H, He J, Li P. HMGA2 gene polymorphisms and Wilms tumor susceptibility in Chinese children: a four-center case-control study. Biotechnol Appl Biochem 2020; 67:939-945. [PMID: 31746066 DOI: 10.1002/bab.1857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 11/14/2019] [Indexed: 02/05/2023]
Abstract
Wilms tumor is a kidney malignancy that typically occurs in children. Aberrant expression of HMGA2 gene is commonly seen in many malignant tumors. Yet, HMGA2 gene polymorphisms on Wilms tumor risk are not established. We carried out the first four-center case-control study with 355 patients and 1,070 controls to assess the association of HMGA2 polymorphisms (rs6581658 A>G, rs8756 A>C, and rs968697 T>C) with Wilms tumor risk. All of these three polymorphisms in single could not impact Wilms tumor risk. Stratified analysis revealed a contributing Wilms tumor risk role of rs968697 TC/CC in subgroup of male (TC/CC vs. TT: adjusted odds ratio [OR] = 1.46, 95% confidence interval [CI] = 1.03-2.08, P = 0.035). However, we found that presence of 1-3 protective genotypes were less likely to develop tumor in subgroup of female (adjusted OR = 0.69, 95% CI = 0.48-0.99, P = 0.045). Our findings suggest that HMGA2 gene polymorphisms might influence Wilms tumor predisposition in a weak manner, under certain circumstances.
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Affiliation(s)
- Jiwen Cheng
- Department of Pediatric Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Zhenjian Zhuo
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Liu Yang
- Clinical Laboratory Medicine Center of PLA, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi, China
| | - Pu Zhao
- Department of Neonatology, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, China
| | - Jiao Zhang
- Department of Pediatric Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Haixia Zhou
- Department of Hematology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Peng Li
- Department of Pediatric Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
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27
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Yang N, Ying P, Tian J, Wang X, Mei S, Zou D, Peng X, Gong Y, Yang Y, Zhu Y, Ke J, Zhong R, Chang J, Miao X. Genetic variants in m6A modification genes are associated with esophageal squamous-cell carcinoma in the Chinese population. Carcinogenesis 2020; 41:761-768. [PMID: 32047883 DOI: 10.1093/carcin/bgaa012] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 01/12/2020] [Accepted: 02/08/2020] [Indexed: 12/22/2022] Open
Abstract
N 6-methyladenosine (m6A) is an abundant modification in RNAs that affects RNA metabolism, and it is reported to be closely related to cancer occurrence and metastasis. In this study, we focused on evaluating the associations between genetic variants in m6A modification genes and the risk of esophageal squamous-cell carcinoma (ESCC). By integrating data of our previous genome-wide association studies and the predictions of several annotation tools, we identified a single nucleotide polymorphism, rs2416282 in the promoter of YTHDC2, that was significantly associated with the susceptibility of ESCC (odds ratio = 0.84, 95% CI: 0.77-0.92, P = 2.81 × 10-4). Through further functional experiments in vitro, we demonstrated that rs2416282 regulated YTHDC2 expression. Knockdown of YTHDC2 substantially promoted the proliferation rate of ESCC cells by affecting several cancer-related signaling pathways. Our results suggested that rs2416282 contributed to ESCC risk by regulating YTHDC2 expression. This study provided us a valuable insight into the roles of genetic variants in m6A modification genes for ESCC susceptibility and may contribute to the prevention of this disease in the future.
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Affiliation(s)
- Nan Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Pingting Ying
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyang Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shufang Mei
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Danyi Zou
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiating Peng
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yajie Gong
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Juntao Ke
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rong Zhong
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiang Chang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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28
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Chen Z, Wang Y, Wang J, Kang M, Tang W, Chen S. Assessment of PPARGC1A, PPARGC1B, and PON1 Genetic Polymorphisms in Esophageal Squamous Cell Carcinoma Susceptibility in the Eastern Chinese Han Population: A Case-Control Study Involving 2351 Subjects. DNA Cell Biol 2020; 39:1521-1531. [PMID: 32721231 DOI: 10.1089/dna.2020.5416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Previous studies suggested that alterations in the energy metabolism might be underlying cancer initiation and progression. Polymorphisms of genes involved in energy metabolism regulation, such as peroxisome proliferator-activated receptor gamma coactivator 1α (PPARGC1A), -β (PPARGC1B), and paraoxonase 1 (PON1), might confer susceptibility to esophageal squamous cell carcinoma (ESCC) and partially explain its pathogenesis. We investigated the effects of several single nucleotide polymorphisms (SNPs) in three metabolic-related genes (e.g., PPARGC1A, PPARGC1B, and PON1) on ESCC susceptibility. In total, 829 patients with sporadic ESCC and 1522 nontumor controls were enrolled in the study. SNPs were genotyped using PCR-ligase detection reaction. Our study revealed that the PPARGC1A rs3736265 G/A SNP significantly increased the risk for ESCC (GA vs. GG: adjusted odds ratio [OR] = 1.25, 95% confidence interval [95% CI] = 1.02-1.54, p = 0.034; GA+AA vs. GG: adjusted OR = 1.25, 95% CI = 1.03-1.52, p = 0.027]. In addition, a stratified analysis revealed that the PPARGC1A rs3736265 SNP was correlated with the development of ESCC in male and nondrinking subgroups. We also confirmed that the PPARGC1B rs17572019 G/A SNP promoted the risk of ESCC in subgroup with high alcohol intake. The PPARGC1A rs8192678 C/T polymorphism decreased the susceptibility of ESCC in men. These findings highlight that polymorphisms in PPARGC1A and PPARGC1B may contribute to ESCC susceptibility. In the future, further well-designed epidemiological studies are needed to confirm our findings.
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Affiliation(s)
- Zhan Chen
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Yafeng Wang
- Department of Cardiology, The People's Hospital of Xishuangbanna Dai Autonomous Prefecture, Jinghong, China
| | - Jusi Wang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Mingqiang Kang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Weifeng Tang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Shuchen Chen
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
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29
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Li Z, Song Y, Xu Y, Shen Y, Zhang N, Yang M, Yu D. Identification of Leukocyte telomere length-related genetic variants contributing to predisposition of Esophageal Squamous Cell Carcinoma. J Cancer 2020; 11:5025-5031. [PMID: 32742450 PMCID: PMC7378929 DOI: 10.7150/jca.45165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/04/2020] [Indexed: 12/18/2022] Open
Abstract
Background: Cancers may arise from cells with dysregulated telomeric functions due to shorten telomere length. We and others previously found that short leukocyte telomere length was associated with markedly evaluated risk of esophageal squamous cell carcinoma (ESCC). Hence, we hypothesized that single nucleotide polymorphisms (SNPs) associated with shorter telomere length may contribute to ESCC predisposition. Methods: We systematically evaluated association between seven candidate seven SNPs (CXCR4 rs6430612, TERT rs13172201, TERT rs10069690, TERT rs2853676, TERT rs451360, OBFC1 rs4387287, and VPS34 rs2162440) and ESCC risk in two case-control sets consisting of 1588 ESCC cases and 1600 controls. Logistic regression models were utilized to estimate associations between SNPs and ESCC susceptibility and odds ratios (ORs) and their 95% confidence intervals (95% CIs) were computed. Results: We firstly identified three SNPs (rs6430612, rs13172201 and rs4387287) which are significantly associated with telomere length in Chinese populations (all P<0.05). Importantly, CXCR4 rs6430612 and OBFC1 rs4387287 polymorphisms significantly confer reduced risk of ESCC (P=1.7×10-7 and P=3.9×10-5). On the contrary, we observed an evidently increased risk for ESCC development associated with TERT rs13172201 genetic variant (P=2.2×10-4). Conclusions: In summary, rs6430612, rs13172201 and rs4387287 might be key genetic components in complicated regulation of telomere length and contributing to ESCC predisposition. Our results elucidate the prevalent involvement of genetic variants in telomere biology and further provide pathogenic insights into the role of telomeres in cancer development.
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Affiliation(s)
- Ziqiang Li
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong Province, China
| | - Yemei Song
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Yeyang Xu
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Yue Shen
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Nasha Zhang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Ming Yang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Dianke Yu
- School of Public Health, Qingdao University, Qingdao, Shandong Province, China
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Qin Z, Zhang X, Chen Z, Liu N. Establishment and validation of an immune-based prognostic score model in glioblastoma. Int Immunopharmacol 2020; 85:106636. [PMID: 32534425 DOI: 10.1016/j.intimp.2020.106636] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND Immune escape is one of the landmark features of glioblastoma (GBM). Immunotherapy is undoubtedly a revolution in the field of tumor treatment, especially the application of immune checkpoint inhibitors and CAR-T cells, which have achieved amazing results in fighting against cancer. This study aimed to establish a TP53-related immune-based score model to improve the prognostic of GBM by investigating the gene mutations and the immune landscape of GBM. METHODS Data were obtained from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA) databases. Differentially expressed genes (DEGs) analysis between the TP53 mutated (TP53MUT) and wild-type (TP53WT) GBM patients was conducted. The CIBERSORT algorithm was applied to evaluate the proportion of immune cell types and RNA sequencing (RNA-seq) data from the TCGA and CGGA were used as discovery and validation cohorts, respectively, to build and validate an immune-related prognostic model (IPM). Genes in the IPM model were first screened by univariate Cox analysis, then filtered by the least absolute shrinkage and selection operator (LASSO) Cox regression method to eliminate collinearity among DEGs. A nomogram was finally established and evaluated by combining both the IPM and other clinical factors. RESULTS PTEN was the top most mutated gene in GBM patients (118/393), followed by TP53 (116/393). 332 immune-related genes were identified and the immune response in the TP53WT group was remarkably greater than in the TP53MUT group. The final IPM model composed three immune-related genes: IPM risk score = (0.392 × S100A8 expression) + (0.174 × CXCL1 expression) + (0.368 × IGLL5 expression), significantly correlated with the overall survival (OS) of GBM in the stratified TP53 status subgroups and was an independent prognostic variate for GBM. By integrating the IPM and clinical characteristics, a nomogram was generated to facilitate clinical utilization, with the results suggesting that it has better predictive performance for GBM prognosis than the IPM. CONCLUSIONS The IPM model can identify patients at high-risk and can be combined with other clinical factors to estimate the OS of GBM patients, demonstrating that it is a promising biomarker to optimize the prognosis of GBM.
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Affiliation(s)
- Zhigang Qin
- Department of Neurosurgery, The Third Hospital of Jilin University, China
| | - Xiuli Zhang
- Department of Neurosurgery, The Third Hospital of Jilin University, China; Department of Thoracic Surgery, The Third Hospital of Jilin University, China
| | - Zhuo Chen
- Department of Neurosurgery, The Third Hospital of Jilin University, China
| | - Naijie Liu
- Department of Neurosurgery, The Third Hospital of Jilin University, China.
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Yang Y, Peng X, Ying P, Tian J, Li J, Ke J, Zhu Y, Gong Y, Zou D, Yang N, Wang X, Mei S, Zhong R, Gong J, Chang J, Miao X. AWESOME: a database of SNPs that affect protein post-translational modifications. Nucleic Acids Res 2020; 47:D874-D880. [PMID: 30215764 PMCID: PMC6324025 DOI: 10.1093/nar/gky821] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/04/2018] [Indexed: 12/19/2022] Open
Abstract
Protein post-translational modifications (PTMs), including phosphorylation, ubiquitination, methylation, acetylation, glycosylation et al, are very important biological processes. PTM changes in some critical genes, which may be induced by base-pair substitution, are shown to affect the risk of diseases. Recently, large-scale exome-wide association studies found that missense single nucleotide polymorphisms (SNPs) play an important role in the susceptibility for complex diseases or traits. One of the functional mechanisms of missense SNPs is that they may affect PTMs and leads to a protein dysfunction and its downstream signaling pathway disorder. Here, we constructed a database named AWESOME (A Website Exhibits SNP On Modification Event, http://www.awesome-hust.com), which is an interactive web-based analysis tool that systematically evaluates the role of SNPs on nearly all kinds of PTMs based on 20 available tools. We also provided a well-designed scoring system to compare the performance of different PTM prediction tools and help users to get a better interpretation of results. Users can search SNPs, genes or position of interest, filter with specific modifications or prediction methods, to get a comprehensive PTM change induced by SNPs. In summary, our database provides a convenient way to detect PTM-related SNPs, which may potentially be pathogenic factors or therapeutic targets.
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Affiliation(s)
- Yang Yang
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, China
| | - Xiating Peng
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, China
| | - Pingting Ying
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, China
| | - Jianbo Tian
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, China
| | - Jiaoyuan Li
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, China
| | - Juntao Ke
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, China
| | - Ying Zhu
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, China
| | - Yajie Gong
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, China
| | - Danyi Zou
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, China
| | - Nan Yang
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, China
| | - Xiaoyang Wang
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, China
| | - Shufang Mei
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, China
| | - Rong Zhong
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, China
| | - Jing Gong
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, China
| | - Jiang Chang
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, China
| | - Xiaoping Miao
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, China
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Wang X, Tian J, Zhao Q, Yang N, Ying P, Peng X, Zou D, Zhu Y, Zhong R, Gao Y, Chang J, Miao X. Functional characterization of a low-frequency V1937I variant in FASN associated with susceptibility to esophageal squamous cell carcinoma. Arch Toxicol 2020; 94:2039-2046. [PMID: 32388819 DOI: 10.1007/s00204-020-02738-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/06/2020] [Indexed: 12/31/2022]
Abstract
Metabolic reprogramming has been regarded as one of the core hallmarks of cancer and increased de novo fatty acid synthesis has been documented in multiple tumors including esophageal squamous cell carcinoma (ESCC). Our previous exome-wide analyses found a Val1937Ile variant (rs17848945) in the 34th exon of fatty acid synthase (FASN) that showed a strong association with the risk of ESCC. In this study, we performed a series of functional assays to investigate the biological functions underlying this variant in the development of ESCC. We demonstrated that FASN was upregulated in ESCC and both knockdown and knockout of FASN significantly inhibited ESCC cell proliferation, suggesting a tumor promoter role for this gene in ESCC. Furthermore, the results showed that overexpression of FASN[I] in the ESCC cells substantially enhanced cell proliferation, compared with overexpression of FASN[V], or the control vector. Intriguingly, we found that the FASN[I] variant can enhance the enzyme activity of FASN, and, thus, increase the amount of the FASN end-product, palmitate in the ESCC cells. We also observed elevated palmitate levels in the plasma of the FASN[I] genotype carriers among a total of 632 healthy Chinese adults. In conclusion, our results suggested that the FASN V1937I variant influenced ESCC cell proliferation and susceptibility by altering the catabolic activity of FASN on palmitate. These findings may highlight an important role of palmitate metabolism in the development of ESCC and may contribute to the personalized medicine of this disease.
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Affiliation(s)
- Xiaoyang Wang
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qianyu Zhao
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Nan Yang
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Pingting Ying
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiating Peng
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Danyi Zou
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Zhu
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rong Zhong
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Gao
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jiang Chang
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Ji Z, Li Y, Xiang C, Luo X, Yuan P, Long J, Shen N, Shen Y, Deng L, Li J, Cheng L. TERT-rs33963617 and CLPTM1L-rs77518573 reduce the risk of non-small cell lung cancer in Chinese population. Gene 2020; 731:144357. [PMID: 31935503 DOI: 10.1016/j.gene.2020.144357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 10/25/2022]
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified 5p15.33 as a susceptible locus for lung cancer. However, for non-small cell lung cancer (NSCLC), low-frequency risk variants in this region have not been systematically studied. We intended to explore the associations between low-frequency variants on 5p15.33 and NSCLC using a next-generation sequencing based approach in this study. METHODS We have acquisited the variation spectrum of 400 NSCLC patients on 5p15.33 by sequencing the targeted region before. Candidate variants were primarily selected by restricting the minor allele frequency (MAF 1-5%) and then by comparing their frequency in 400 NSCLC patients with 1008 East Asians from The genome Aggregation Database (gnomAD). The associations between candidate variants and NSCLC were discovered and replicated in two case-control sets: discovery stage with 960 cases and 916 controls, and replication stage with 1596 cases and 1614 controls in total. RESULTS Five low-frequency variants were selected as our candidates and subsequent association analyses showed that 2 polymorphisms were significantly associated with risk of NSCLC, including rs33963617 (OR = 0.63, 95% CI: 0.53-0.76, P = 3.80 × 10-7) in TERT and rs77518573 (OR = 0.73, 95% CI: 0.63-0.84, P = 2.00 × 10-5) in upstream of CLPTM1L. When stratified by histologic subtype, a significant association was only investigated in adenocarcinoma for rs77518573. We also observed an obvious cumulative effect of the two significant variants. CONCLUSIONS We newly identified two NSCLC related variants on chromosome 5p15.33. Both TERT-rs33963617 and CLPTM1L-rs77518573 conferred reduced risk for NSCLC in Chinese Han population.
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Affiliation(s)
- Zhi Ji
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ying Li
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Cheng Xiang
- Department of Endocrinology, Xiaogan Central Hospital, Xiaogan 432000, China
| | - Xia Luo
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Peihong Yuan
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jieyi Long
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Na Shen
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ying Shen
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Lingyan Deng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jiaoyuan Li
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Liming Cheng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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Roberts C. Regulating Retinoic Acid Availability during Development and Regeneration: The Role of the CYP26 Enzymes. J Dev Biol 2020; 8:jdb8010006. [PMID: 32151018 PMCID: PMC7151129 DOI: 10.3390/jdb8010006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 02/17/2020] [Accepted: 02/17/2020] [Indexed: 12/16/2022] Open
Abstract
This review focuses on the role of the Cytochrome p450 subfamily 26 (CYP26) retinoic acid (RA) degrading enzymes during development and regeneration. Cyp26 enzymes, along with retinoic acid synthesising enzymes, are absolutely required for RA homeostasis in these processes by regulating availability of RA for receptor binding and signalling. Cyp26 enzymes are necessary to generate RA gradients and to protect specific tissues from RA signalling. Disruption of RA homeostasis leads to a wide variety of embryonic defects affecting many tissues. Here, the function of CYP26 enzymes is discussed in the context of the RA signalling pathway, enzymatic structure and biochemistry, human genetic disease, and function in development and regeneration as elucidated from animal model studies.
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Affiliation(s)
- Catherine Roberts
- Developmental Biology of Birth Defects, UCL-GOS Institute of Child Health, 30 Guilford St, London WC1N 1EH, UK;
- Institute of Medical and Biomedical Education St George’s, University of London, Cranmer Terrace, Tooting, London SW17 0RE, UK
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Wang J, Lou S, Huang X, Mo Y, Wang Z, Zhu J, Tian X, Shi J, Zhou H, He J, Ruan J. The association of miR34b/c and TP53 gene polymorphisms with Wilms tumor risk in Chinese children. Biosci Rep 2020; 40:222181. [PMID: 32083300 PMCID: PMC7048686 DOI: 10.1042/bsr20194202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 02/07/2023] Open
Abstract
Wilms tumor is the most common pediatric malignancy in the kidney. The miR34b/c is a downstream target gene of the transcription factor p53. The important role of TP53 mutations, the methylation of miR34b/c, and the interaction between these two molecules in tumorigenesis have been well documented. Due to the biological connection between p53 and miR34b/c, in the present study, we investigated the association between polymorphisms in these two molecules and Wilms tumor susceptibility through genotyping two important functional polymorphisms (miR34b/c rs4938723 T>C and TP53 rs1042522 C>G) in 183 cases and 603 controls. Adjusted odds ratios (ORs) and 95% confidence intervals (CIs) derived from the logistic regression analysis were used to assess the correlation of miR34b/c rs4938723 and TP53 rs1042522 polymorphisms with Wilms tumor risk. Our results indicated that the association of miR34b/c rs4938723 and TP53 rs1042522 polymorphisms with Wilms tumor susceptibility was not statistically significant. Stratified analysis by age, gender, and clinical stage, as well as combined effect analysis were also performed, yet, no significant association was found. In conclusion, our study indicated a lack of association between the two selected polymorphisms and Wilms tumor susceptibility. Our findings need to be verified in studies with larger sample size in the future.
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Affiliation(s)
- Juxiang Wang
- Department of Hematology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Susu Lou
- Department of Hematology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Xiaokai Huang
- Department of Hematology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Yixiao Mo
- Department of Hematology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Zhen Wang
- Department of Hematology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Jinhong Zhu
- Department of Clinical Laboratory, Biobank, Harbin Medical University Cancer Hospital, Harbin 150040, Heilongjiang, China
| | - Xiaoqian Tian
- Department of Hematology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Jiandong Shi
- Department of Hematology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Haixia Zhou
- Department of Hematology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Jing He
- Department of Hematology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
- Correspondence: Jichen Ruan () or Jing He ()
| | - Jichen Ruan
- Department of Hematology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
- Correspondence: Jichen Ruan () or Jing He ()
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Li S, Zhuo Z, Chang X, Ma Y, Zhou H, Zhang J, Cheng J, He J, Li Y. NRAS rs2273267 A>T polymorphism reduces neuroblastoma risk in Chinese children. Gene 2020; 727:144262. [PMID: 31759987 DOI: 10.1016/j.gene.2019.144262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 10/21/2019] [Accepted: 11/07/2019] [Indexed: 02/07/2023]
Abstract
Neuroblastoma is an extracranial solid tumor that mainly occurs in childhood. Mutations of NRAS gene have been described in several cancers. However, whether NRAS gene polymorphisms can predict the risk of neuroblastoma have not been investigated. We hypothesized that variations of NRAS gene contribute to neuroblastoma predisposition. Therefore, we conducted a multi-center case-control study using 263 cases and 715 controls to examine the association of NRAS gene rs2273267 A>T polymorphism and neuroblastoma risk. We calculated odds ratios (ORs) and corresponding 95% confidence intervals (CIs) to assess the strength of the associations. Relative to those with AA genotype, subjects with AT/TT genotype had reduced neuroblastoma risk (adjusted OR = 0.72, 95% CI = 0.54-0.96, P = 0.024). Stratified analysis revealed that rs2273267 AT/TT carriers were less likely to develop neuroblastoma for patients with tumor originating from the adrenal gland (adjusted OR = 0.67, 95% CI = 0.45-0.99, P = 0.047) and clinical stages III + IV (adjusted OR = 0.57, 95% CI = 0.36-0.90, P = 0.015). Our findings underline the likely importance of NRAS gene rs2273267 A>T in the risk of neuroblastoma. Further independent case-control studies with functional analysis are needed to verify the role of NRAS gene rs2273267 A>T polymorphism in the risk of neuroblastoma.
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Affiliation(s)
- Suhong Li
- Department of Pathology, Children Hospital and Women Health Center of Shanxi, Taiyuan, 030013 Shannxi, China.
| | - Zhenjian Zhuo
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong 510623, Guangzhou, China
| | - Xinghong Chang
- Department of Clinical Laboratory, Children Hospital and Women Health Center of Shanxi, Taiyuan 030013, Shannxi, China
| | - Yan Ma
- Department of Pathology, Children Hospital and Women Health Center of Shanxi, Taiyuan, 030013 Shannxi, China
| | - Haixia Zhou
- Department of Hematology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Jiao Zhang
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Jiwen Cheng
- Department of Pediatric Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, Shaanxi, China
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong 510623, Guangzhou, China.
| | - Yangyang Li
- Department of Pathology, Children Hospital and Women Health Center of Shanxi, Taiyuan, 030013 Shannxi, China
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Yang N, Tian J, Wang X, Mei S, Zou D, Peng X, Zhu Y, Yang Y, Gong Y, Ke J, Zhong R, Chang J, Miao X. A functional variant in TNXB promoter associates with the risk of esophageal squamous-cell carcinoma. Mol Carcinog 2020; 59:439-446. [PMID: 32056283 DOI: 10.1002/mc.23166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/23/2019] [Accepted: 02/04/2020] [Indexed: 11/11/2022]
Abstract
Our previous study identified a tag single-nucleotide polymorphism (SNP) rs204900 in TNXB associated with risk of esophageal squamous-cell carcinoma (ESCC) in the Chinese population. However, the functional role of TNXB and causal variants had not been interrogated in that study. In the present study, we explored the effects of TNXB expression in the development of ESCC and searched for functional variants in this gene. We found TNXB was downregulated in ESCC tumors. Using small interfering RNAs and CRISPR-Cas9 methods, we identified that both knockdown and knockout of TNXB significantly promoted ESCC cell growth in vitro, suggesting a tumor suppressor role of this gene in ESCC. Through further fine-mapping analysis, we identified that a noncoding variant in the promoter of TNXB, rs411337, predisposed to ESCC risk (odds ratio = 1.36, 95% confidence interval: 1.22-1.51, P = 9.10 × 10-9 ). These findings revealed the functional mechanism of TNXB in the development of ESCC and may contribute to the prevention and treatment of this disease in the future.
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Affiliation(s)
- Nan Yang
- Department of Epidemiology and Biostatistics, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyang Wang
- Department of Epidemiology and Biostatistics, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shufang Mei
- Department of Epidemiology and Biostatistics, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Danyi Zou
- Department of Epidemiology and Biostatistics, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiating Peng
- Department of Epidemiology and Biostatistics, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Zhu
- Department of Epidemiology and Biostatistics, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Yang
- Department of Epidemiology and Biostatistics, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yajie Gong
- Department of Epidemiology and Biostatistics, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Juntao Ke
- Department of Epidemiology and Biostatistics, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rong Zhong
- Department of Epidemiology and Biostatistics, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiang Chang
- Department of Epidemiology and Biostatistics, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Liang B, Ding H, Huang L, Luo H, Zhu X. GWAS in cancer: progress and challenges. Mol Genet Genomics 2020; 295:537-561. [PMID: 32048005 DOI: 10.1007/s00438-020-01647-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/11/2020] [Indexed: 12/31/2022]
Abstract
The genome-wide association study (GWAS) is an effective method to detect single-nucleotide polymorphisms (SNPs) of multiple individual genes based on linkage disequilibrium (LD). GWAS examines genotypes and distinguishing gene characteristics that are exhibited in diseases. In the past few decades, more and more literature has reported the results of applying GWAS to study tumors. Although many pleiotropic loci associated with complex phenotypes have been identified by GWAS, the biological functions of many genetic variation loci remain unclear, and the genetic mechanisms of most complex phenotypes cannot be systematically explained. In this article, we will review the new findings of several tumor types, and categorize the new sites and mechanisms that have recently been discovered. We linked the mechanisms of action of various tumors and searched for links to related gene expression pathways. We found that susceptible sites can be divided into hub genes and peripheral genes; the two interact to link gene expression in a variety of diseases.
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Affiliation(s)
- Baiqiang Liang
- Guangdong Key Laboratory for Research and Development of Natural Drugs, Guangdong Medical University, Zhanjiang, 524023, China.,The Marine Biomedical Research Institute, Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang, 524023, China.,Cancer Center, The Affiliated Hospital, Guangdong Medical University, Zhanjiang, 524023, China
| | - Hongrong Ding
- The Marine Biomedical Research Institute, Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang, 524023, China.,Key Laboratory of Guangdong Provincial Medical Molecular Diagnosis, Dongguan, 523808, China
| | - Lianfang Huang
- Guangdong Key Laboratory for Research and Development of Natural Drugs, Guangdong Medical University, Zhanjiang, 524023, China.,The Marine Biomedical Research Institute, Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang, 524023, China
| | - Haiqing Luo
- Cancer Center, The Affiliated Hospital, Guangdong Medical University, Zhanjiang, 524023, China.
| | - Xiao Zhu
- Guangdong Key Laboratory for Research and Development of Natural Drugs, Guangdong Medical University, Zhanjiang, 524023, China. .,The Marine Biomedical Research Institute, Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang, 524023, China. .,Key Laboratory of Guangdong Provincial Medical Molecular Diagnosis, Dongguan, 523808, China.
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Teng H, Xue M, Liang J, Wang X, Wang L, Wei W, Li C, Zhang Z, Li Q, Ran X, Shi X, Cai W, Wang W, Gao H, Sun Z. Inter- and intratumor DNA methylation heterogeneity associated with lymph node metastasis and prognosis of esophageal squamous cell carcinoma. Am J Cancer Res 2020; 10:3035-3048. [PMID: 32194853 PMCID: PMC7053185 DOI: 10.7150/thno.42559] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 01/22/2020] [Indexed: 12/24/2022] Open
Abstract
Background: Esophageal squamous cell carcinoma (ESCC), one of the leading causes of cancer mortality worldwide, is a heterogeneous cancer with diverse clinical manifestations. However, little is known about the epigenetic heterogeneity and its clinical relevance for this prevalent cancer. Methods: We generated 7.56 Tb single-base resolution whole-genome bisulfite sequencing data for 84 ESCC and paired paraneoplastic tissues. The analysis identified inter- and intratumor DNA methylation (DNAm) heterogeneity, epigenome-wide DNAm alterations together with the functional regulators involved in the hyper- or hypomethylated regions, and their association with clinical features. We then validated the correlation between the methylation level of specific regions and clinical outcomes of 96 ESCC patients in an independent cohort. Results: ESCC manifested substantial inter- and intratumor DNAm heterogeneity. The high intratumor DNAm heterogeneity was associated with lymph node metastasis and worse overall survival. Interestingly, hypermethylated regions in ESCC were enriched in promoters of numerous transcription factors, and demethylated noncoding regions related to RXR transcription factor binding appeared to contribute to the development of ESCC. Furthermore, we identified numerous DNAm alterations associated with carcinogenesis and lymph node metastasis of ESCC. We also validated three novel prognostic markers for ESCC, including one each in the promoter of CLK1, the 3' untranslated region of ZEB2, and the intergenic locus surrounded by several lncRNAs. Conclusions: This study presents the first population-level resource for dissecting base-resolution DNAm variation in ESCC and provides novel insights into the ESCC pathogenesis and progression, which might facilitate diagnosis and prognosis for this prevalent malignancy.
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Yang T, Wen Y, Li J, Tan T, Yang J, Pan J, Hu C, Yao Y, Zhang J, Li S, Xia H, He J, Zou Y. Association of CMYC polymorphisms with hepatoblastoma risk. Transl Cancer Res 2020; 9:849-855. [PMID: 35117430 PMCID: PMC8798278 DOI: 10.21037/tcr.2019.12.19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/26/2019] [Indexed: 02/05/2023]
Abstract
BACKGROUND Single-nucleotide polymorphisms (SNPs) in genes may affect gene expression and contribute to cancer susceptibility. This study aimed to explore the association between CMYC gene polymorphisms and hepatoblastoma risk. METHODS Hepatoblastoma patients and cancer-free controls were recruited and matched by age and sex. Genotypes were determined by TaqMan, and the strength of the association of interest was determined by calculating odds ratios (ORs) and 95% confidence intervals (CIs). The distributions of various CMYC genotypes among subjects were recorded, followed by analyses of associations between CMYC polymorphisms and hepatoblastoma risk. RESULTS A total of 213 hepatoblastoma patients and 958 cancer-free controls were enrolled. No significant associations between the CMYC rs4645943 and rs2070583 polymorphisms and hepatoblastoma risk were found (all P>0.05). In stratification analysis based on age, sex, and clinical stage, the CMYC rs4645943 and rs2070583 polymorphisms were not associated with hepatoblastoma susceptibility (all P>0.05). CONCLUSIONS Thus, the CMYC rs4645943 and rs2070583 polymorphisms were not associated with hepatoblastoma risk in the study cohort.
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Affiliation(s)
- Tianyou Yang
- Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Yang Wen
- First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, China
| | - Jiahao Li
- Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Tianbao Tan
- Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Jiliang Yang
- Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Jing Pan
- Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Chao Hu
- Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Yuxiao Yao
- Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Jiao Zhang
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Suhong Li
- Department of Pathology, Children Hospital and Women Health Center of Shanxi, Taiyuan 030002, China
| | - Huimin Xia
- Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Yan Zou
- Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
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Ke J, Tian J, Mei S, Ying P, Yang N, Wang X, Zou D, Peng X, Yang Y, Zhu Y, Gong Y, Wang Z, Gong J, Zhong R, Chang J, Miao X. Genetic Predisposition to Colon and Rectal Adenocarcinoma Is Mediated by a Super-enhancer Polymorphism Coactivating CD9 and PLEKHG6. Cancer Epidemiol Biomarkers Prev 2020; 29:850-859. [PMID: 31988071 DOI: 10.1158/1055-9965.epi-19-1116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/22/2019] [Accepted: 01/21/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified dozens of loci associated with colon and rectal adenocarcinoma risk. As tissue-specific super-enhancers (SE) play important roles in tumorigenesis, we systematically investigate SEs and inner variants in established GWAS loci to decipher the underlying biological mechanisms. METHODS Through a comprehensive bioinformatics analysis on multi-omics data, we screen potential single-nucleotide polymorphisms (SNP) in cancer-specific SEs, and then subject them to a two-stage case-control study containing 4,929 cases and 7,083 controls from the Chinese population. A series of functional assays, including reporter gene assays, electrophoretic mobility shift assays (EMSA), CRISPR-Cas9 genome editing, chromosome conformation capture (3C) assays, and cell proliferation experiments, are performed to characterize the variant's molecular consequence and target genes. RESULTS The SNP rs11064124 in 12p13.31 is found significantly associated with the risk of colon and rectal adenocarcinoma with an odds ratio (OR) of 0.87 [95% confidence interval (CI), 0.82-0.92, P = 8.67E-06]. The protective rs11064124-G weakens the binding affinity with vitamin D receptor (VDR) and increases the enhancer's activity and interactions with two target genes' promoters, thus coactivating the transcription of CD9 and PLEKHG6, which are both putative tumor suppressor genes for colon and rectal adenocarcinoma. CONCLUSIONS Our integrative study highlights an SE polymorphism rs11064124 and two susceptibility genes CD9 and PLEKHG6 in 12p13.31 for colon and rectal adenocarcinoma. IMPACT These findings suggest a novel insight for genetic pathogenesis of colon and rectal adenocarcinoma, involving transcriptional coactivation of diverse susceptibility genes via the SE element as a gene regulation hub.
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Affiliation(s)
- Juntao Ke
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianbo Tian
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shufang Mei
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Pingting Ying
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Nan Yang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyang Wang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Danyi Zou
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiating Peng
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Yang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Zhu
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yajie Gong
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhihua Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Gong
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Rong Zhong
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiang Chang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoping Miao
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Li G, Song Q, Jiang Y, Cai A, Tang Y, Tang N, Yi D, Zhang R, Wei Z, Liu D, Chen J, Zhang Y, Liu L, Wu Y, Zhang B, Yi D. Cumulative Evidence for Associations between Genetic Variants and Risk of Esophageal Cancer. Cancer Epidemiol Biomarkers Prev 2020; 29:838-849. [PMID: 31969372 DOI: 10.1158/1055-9965.epi-19-1281] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/06/2019] [Accepted: 01/17/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND A large number of studies have been conducted to investigate associations between genetic variants and esophageal cancer risk in the past several decades. However, findings from these studies have been generally inconsistent. We aimed to provide a summary of the current understanding of the genetic architecture of esophageal cancer susceptibility. METHODS We performed a comprehensive field synopsis and meta-analysis to evaluate associations between 95 variants in 70 genes or loci and esophageal cancer risk using data from 304 eligible publications, including 104,904 cases and 159,797 controls, through screening a total of 21,328 citations. We graded levels of cumulative epidemiologic evidence of a significant association with esophageal cancer using the Venice criteria and false-positive report probability tests. We constructed functional annotations for these variants using data from the Encyclopedia of DNA Elements Project and other databases. RESULTS Thirty variants were nominally significantly associated with esophageal cancer risk. Cumulative epidemiologic evidence of a significant association with overall esophageal cancer, esophageal squamous cell carcinoma, or esophageal adenocarcinoma was strong for 13 variants in or near 13 genes (ADH1B, BARX1, CDKN1A, CHEK2, CLPTM1L, CRTC1, CYP1A1, EGF, LTA, MIR34BC, PLCE1, PTEN, and PTGS2). Bioinformatics analysis suggested that these variants and others correlated with them might fall in putative functional regions. CONCLUSIONS Our study summarizes the current literature on the genetic architecture of esophageal cancer susceptibility and identifies several potential polymorphisms that could be involved in esophageal cancer susceptibility. IMPACT These findings provide direction for future studies to identify new genetic factors for esophageal cancer.
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Affiliation(s)
- Gaoming Li
- Department of Health Statistics, Army Medical University, Chongqing, China
| | - Qiuyue Song
- Department of Health Statistics, Army Medical University, Chongqing, China
| | - Yuxing Jiang
- Medical Department, The 305 Hospital of Chinese People's Liberation Army, Beijing, China
| | - Angsong Cai
- Department of Health Statistics, Army Medical University, Chongqing, China
| | - Yong Tang
- Department of Health Statistics, Army Medical University, Chongqing, China
| | - Ning Tang
- Department of Health Statistics, Army Medical University, Chongqing, China
| | - Dali Yi
- Department of Health Statistics, Army Medical University, Chongqing, China
| | - Rui Zhang
- Department of Health Statistics, Army Medical University, Chongqing, China
| | - Zeliang Wei
- Department of Health Statistics, Army Medical University, Chongqing, China
| | - Dingxin Liu
- Department of Statistics, Chongqing Technology and Business University, Chongqing, China
| | - Jia Chen
- Department of Health Statistics, Army Medical University, Chongqing, China
| | - Yanqi Zhang
- Department of Health Statistics, Army Medical University, Chongqing, China
| | - Ling Liu
- Department of Health Statistics, Army Medical University, Chongqing, China
| | - Yazhou Wu
- Department of Health Statistics, Army Medical University, Chongqing, China.
| | - Ben Zhang
- Department of Epidemiology and Biostatistics, First Affiliated Hospital, Army Medical University, Chongqing, China.
| | - Dong Yi
- Department of Health Statistics, Army Medical University, Chongqing, China.
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ALDH3B2 Polymorphism Is Associated with Colorectal Cancer Susceptibility. JOURNAL OF ONCOLOGY 2020; 2020:5179635. [PMID: 32377192 PMCID: PMC7199530 DOI: 10.1155/2020/5179635] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 11/21/2019] [Accepted: 12/03/2019] [Indexed: 12/27/2022]
Abstract
Colorectal cancer (CRC) is the 5th leading cancer in China. Alcohol consumption has been reported to be one of the risk factors of CRC. However, it remains unclear whether genetic variants of alcohol metabolic genes are associated with CRC risk. In this study, we tested the coding variants in the alcohol metabolic genes and the risk of CRC, by using 485 cases and 516 controls. A total of 16 germline coding variants in 10 alcohol metabolic genes were genotyped. We identified that rs3741178 in ALDH3B2 was significantly associated with CRC risk with odds ratio being 2.13 (95% CI: 1.24–3.68, P=0.0064). Further functional annotation suggested that this variant may damage the protein function of ALDH3B2. Our results suggested that ALDH3B2 in the alcohol metabolism pathway contributed to the development of CRC, which may contribute to the prevention of this disease in the future.
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Hua R, Zhuo Z, Ge L, Zhu J, Yuan L, Chen C, Liu J, Cheng J, Zhou H, Zhang J, Xia H, Zhang X, He J. LIN28A gene polymorphisms modify neuroblastoma susceptibility: A four-centre case-control study. J Cell Mol Med 2020; 24:1059-1066. [PMID: 31747721 PMCID: PMC6933387 DOI: 10.1111/jcmm.14827] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/15/2019] [Accepted: 10/28/2019] [Indexed: 02/05/2023] Open
Abstract
Neuroblastoma ranks the most common seen solid tumour in childhood. Overexpression of LIN28A gene has been linked to the development of multiple human malignancies, but the relationship between LIN28A single nucleotide polymorphisms (SNPs) and neuroblastoma susceptibility is still under debate. Herein, we evaluated the correlation of four potentially functional LIN28A SNPs (rs3811464 G>A, rs3811463 T>C, rs34787247 G>A, and rs11247957 G>A) and neuroblastoma susceptibility in 505 neuroblastoma patients and 1070 controls from four independent hospitals in China. The correlation strengths were determined by using odds ratios (ORs) and corresponding 95% confidence intervals (CIs). Among these SNPs, rs34787247 G>A exhibited a significant association with increased susceptibility in neuroblastoma (GA vs GG: adjusted OR = 1.30, 95% CI = 1.03-1.64; AA vs GG: adjusted OR = 2.51, 95% CI = 1.36-4.64, AA/GA vs GG: adjusted OR = 1.42, 95% CI = 1.12-1.80, AA vs GG/GA: adjusted OR = 2.39, 95% CI = 1.29-4.42). Furthermore, the combined analysis of risk genotypes revealed that subjects carrying three risk genotypes (adjusted OR = 1.64, 95% CI = 1.02-2.63) are more inclined to develop neuroblastoma than those without risk genotype, and so do carriers of 1-4 risk genotypes (adjusted OR = 1.26, 95% CI = 1.01-1.56). Stratification analysis further revealed risk effect of rs3811464 G>A, rs34787247 G>A and 1-4 risk genotypes in some subgroups. Haplotype analysis of these four SNPs yields two haplotypes significantly correlated with increased neuroblastoma susceptibility. Overall, our finding indicated that LIN28A SNPs, especially rs34787247 G>A, may increase neuroblastoma risk.
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Affiliation(s)
- Rui‐Xi Hua
- Department of Pediatric SurgeryGuangzhou Institute of PediatricsGuangdong Provincial Key Laboratory of Research in Structural Birth Defect DiseaseGuangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouChina
- Department of OncologyThe First Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouChina
| | - Zhenjian Zhuo
- Department of Pediatric SurgeryGuangzhou Institute of PediatricsGuangdong Provincial Key Laboratory of Research in Structural Birth Defect DiseaseGuangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouChina
| | - Lili Ge
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic DiseasesChildren's Hospital Affiliated to Zhengzhou UniversityHenan Children's HospitalZhengzhou Children's HospitalZhengzhouChina
| | - Jinhong Zhu
- Department of Pediatric SurgeryGuangzhou Institute of PediatricsGuangdong Provincial Key Laboratory of Research in Structural Birth Defect DiseaseGuangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouChina
- Department of Clinical LaboratoryBiobankHarbin Medical University Cancer HospitalHarbinChina
| | - Li Yuan
- Department of Pediatric SurgeryGuangzhou Institute of PediatricsGuangdong Provincial Key Laboratory of Research in Structural Birth Defect DiseaseGuangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouChina
| | - Chongfen Chen
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic DiseasesChildren's Hospital Affiliated to Zhengzhou UniversityHenan Children's HospitalZhengzhou Children's HospitalZhengzhouChina
| | - Jing Liu
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic DiseasesChildren's Hospital Affiliated to Zhengzhou UniversityHenan Children's HospitalZhengzhou Children's HospitalZhengzhouChina
| | - Jiwen Cheng
- Department of Pediatric SurgeryThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Haixia Zhou
- Department of HematologyThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityWenzhouChina
| | - Jiao Zhang
- Department of Pediatric SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Huimin Xia
- Department of Pediatric SurgeryGuangzhou Institute of PediatricsGuangdong Provincial Key Laboratory of Research in Structural Birth Defect DiseaseGuangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouChina
| | - Xianwei Zhang
- Department of Pediatric Oncologic SurgeryChildren's Hospital Affiliated to Zhengzhou UniversityHenan Children's HospitalZhengzhou Children's HospitalZhengzhouChina
| | - Jing He
- Department of Pediatric SurgeryGuangzhou Institute of PediatricsGuangdong Provincial Key Laboratory of Research in Structural Birth Defect DiseaseGuangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouChina
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45
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Liu J, Hua RX, Cheng Y, Zhu J, Zhang J, Cheng J, Zhou H, Xia H, Bian J, He J. HMGA2 Gene rs8756 A>C Polymorphism Reduces Neuroblastoma Risk in Chinese Children: A Four-Center Case-Control Study. Onco Targets Ther 2020; 13:465-472. [PMID: 32021290 PMCID: PMC6970238 DOI: 10.2147/ott.s229975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 01/06/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Neuroblastoma, mainly affecting children, is a lethal malignancy arising from the developing sympathetic nervous system. The genetic etiology of neuroblastoma remains mostly obscure. High mobility group AT-hook 2 (HMGA2), an oncogenic gene, is up-regulated in many tumors. Single nucleotide polymorphisms (SNPs) often modify cancer susceptibility. However, no studies are investigating the association between HMGA2 SNPs and neuroblastoma susceptibility. METHODS We conducted a four-center case-control study to evaluate the association between three HMGA2 polymorphisms (rs6581658 A>G, rs8756 A>C and rs968697 T>C) and neuroblastoma susceptibility in a Chinese population with 505 cases and 1070 controls. Logistic regression was performed to evaluate the strength of the association. RESULTS We found that the rs8756 AC/CC genotypes were associated with a reduced neuroblastoma risk when compared to rs8756 AA genotype [Adjusted odds ratio (OR)=0.74, 95% confidence interval (CI)=0.56-0.99, P=0.039]. Carriers with 3 protective genotypes have lower neuroblastoma susceptibility than those without or with 0-2 protective genotypes. The stratified analysis revealed that the protective effects of rs8756 AC/CC genotypes were more predominant among children of age > 18 months, males, and subgroups with the tumor in the mediastinum. Furthermore, haplotype analysis uncovered that haplotype ACC significantly reduced neuroblastoma risk. CONCLUSION Our study indicated HMGA2 rs8756 A>C polymorphism is significantly associated with decreased neuroblastoma risk.
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Affiliation(s)
- Jiabin Liu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou510623, Guangdong, People’s Republic of China
| | - Rui-Xi Hua
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou510623, Guangdong, People’s Republic of China
- Department of Oncology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou510080, Guangdong, People’s Republic of China
| | - Yun Cheng
- Department of Gynecology, Nanjing First Hospital Affiliated to Nanjing Medical University, Nanjing210006, Jiangsu, People’s Republic of China
| | - Jinhong Zhu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou510623, Guangdong, People’s Republic of China
- Department of Clinical Laboratory, Biobank, Harbin Medical University Cancer Hospital, Harbin150040, Heilongjiang, People’s Republic of China
| | - Jiao Zhang
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou450052, Henan, People’s Republic of China
| | - Jiwen Cheng
- Department of Pediatric Surgery, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an710004, Shaanxi, People’s Republic of China
| | - Haixia Zhou
- Department of Hematology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou325027, Zhejiang, People’s Republic of China
| | - Huimin Xia
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou510623, Guangdong, People’s Republic of China
| | - Jun Bian
- Department of General Surgery, Xi’an Children’s Hospital, Xi’an Jiaotong University Affiliated Children’s Hospital, Xi’an710003, Shaanxi, People’s Republic of China
- Jun Bian Department of General Surgery, Xi’an Children’s Hospital, Xi’an Jiaotong University Affiliated Children’s Hospital, 69 Xiju Court Lane, Xi’an710003, Shaanxi, People’s Republic of ChinaTel/Fax +86-2987692108 Email
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou510623, Guangdong, People’s Republic of China
- Correspondence: Jing He Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, 9 Jinsui Road, Guangzhou510623, Guangdong, People’s Republic of ChinaTel/Fax +86-2038076560 Email
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Ke J, Peng X, Mei S, Tian J, Ying P, Yang N, Wang X, Zou D, Yang Y, Zhu Y, Gong Y, Gong J, Zhong R, Chang J, Fang Z, Miao X. Evaluation of polymorphisms in microRNA-binding sites and pancreatic cancer risk in Chinese population. J Cell Mol Med 2019; 24:2252-2259. [PMID: 31880394 PMCID: PMC7011162 DOI: 10.1111/jcmm.14906] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/12/2019] [Accepted: 12/03/2019] [Indexed: 12/20/2022] Open
Abstract
As promising biomarkers and therapy targets, microRNAs (miRNAs) are involved in various physiological and tumorigenic processes. Genetic variants in miRNA‐binding sites can lead to dysfunction of miRNAs and contribute to disease. However, systematic investigation of the miRNA‐related single nucleotide polymorphisms (SNPs) for pancreatic cancer (PC) risk remains elusive. We performed integrative bioinformatics analyses to select 31 SNPs located in miRNA‐target binding sites using the miRNASNP v2.0, a solid database providing miRNA‐related SNPs for genetic research, and investigated their associations with risk of PC in two large case‐control studies totally including 1847 cases and 5713 controls. We observed that the SNP rs3802266 is significantly associated with increased risk of PC (odds ratio (OR) = 1.21, 95% confidence intervals (CI) = 1.11‐1.31, P = 1.29E‐05). Following luciferase reporter gene assays show that rs3802266‐G creates a stronger binding site for miR‐181a‐2‐3p in 3′ untranslated region (3′UTR) of the gene ZHX2. Expression quantitative trait loci (eQTL) analysis suggests that ZHX2 expression is lower in individuals carrying rs3802266‐G with increased PC risk. In conclusion, our findings highlight the involvement of miRNA‐binding SNPs in PC susceptibility and provide new clues for PC carcinogenesis.
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Affiliation(s)
- Juntao Ke
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiating Peng
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shufang Mei
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianbo Tian
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Pingting Ying
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Nan Yang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyang Wang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Danyi Zou
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Yang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Zhu
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yajie Gong
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Gong
- College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Rong Zhong
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiang Chang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zemin Fang
- Division of Cardiothoracic and Vascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoping Miao
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Isoherranen N, Zhong G. Biochemical and physiological importance of the CYP26 retinoic acid hydroxylases. Pharmacol Ther 2019; 204:107400. [PMID: 31419517 PMCID: PMC6881548 DOI: 10.1016/j.pharmthera.2019.107400] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 08/06/2019] [Indexed: 12/19/2022]
Abstract
The Cytochrome P450 (CYP) family 26 enzymes contribute to retinoic acid (RA) metabolism and homeostasis in humans, mammals and other chordates. The three CYP26 family enzymes, CYP26A1, CYP26B1 and CYP26C1 have all been shown to metabolize all-trans-retinoic acid (atRA) it's 9-cisRA and 13-cisRA isomers and primary metabolites 4-OH-RA and 4-oxo-RA with high efficiency. While no crystal structures of CYP26 enzymes are available, the binding of various ligands has been extensively explored via homology modeling. All three CYP26 enzymes are inducible by treatment with atRA in various prenatal and postnatal tissues and cell types. However, current literature shows that in addition to regulation by atRA, CYP26 enzyme expression is also regulated by other endogenous processes and inflammatory cytokines. In humans and in animal models the expression patterns of CYP26 enzymes have been shown to be tissue and cell type specific, and the expression of the CYP26 enzymes is believed to regulate the formation of critical atRA concentration gradients in various tissue types. Yet, very little data exists on direct disease associations of altered CYP26 expression or activity. Nevertheless, data is emerging describing a variety of human genetic variations in the CYP26 enzymes that are associated with different pathologies. Interestingly, some of these genetic variants result in increased activity of the CYP26 enzymes potentially leading to complex gene-environment interactions due to variability in dietary intake of retinoids. This review highlights the current knowledge of structure-function of CYP26 enzymes and focuses on their role in human retinoid metabolism in different tissues.
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Affiliation(s)
- Nina Isoherranen
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA, USA.
| | - Guo Zhong
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA, USA
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48
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Cai M, Ran D, Zhang X. Advances in identifying coding variants of common complex diseases. JOURNAL OF BIO-X RESEARCH 2019. [DOI: 10.1097/jbr.0000000000000046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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49
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Tang L, Liou YL, Wan ZR, Tang J, Zhou Y, Zhuang W, Wang G. Aberrant DNA methylation of PAX1, SOX1 and ZNF582 genes as potential biomarkers for esophageal squamous cell carcinoma. Biomed Pharmacother 2019; 120:109488. [DOI: 10.1016/j.biopha.2019.109488] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 09/08/2019] [Accepted: 09/22/2019] [Indexed: 12/23/2022] Open
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van 't Hof FNG, Lai D, van Setten J, Bots ML, Vaartjes I, Broderick J, Woo D, Foroud T, Rinkel GJE, de Bakker PIW, Ruigrok YM. Exome-chip association analysis of intracranial aneurysms. Neurology 2019; 94:e481-e488. [PMID: 31732565 DOI: 10.1212/wnl.0000000000008665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 08/01/2019] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To investigate to what extent low-frequency genetic variants (with minor allele frequencies <5%) affect the risk of intracranial aneurysms (IAs). METHODS One thousand fifty-six patients with IA and 2,097 population-based controls from the Netherlands were genotyped with the Illumina HumanExome BeadChip. After quality control (QC) of samples and single nucleotide variants (SNVs), we conducted a single variant analysis using the Fisher exact test. We also performed the variable threshold (VT) test and the sequence kernel association test (SKAT) at different minor allele count (MAC) thresholds of >5 and >0 to test the hypothesis that multiple variants within the same gene are associated with IA risk. Significant results were tested in a replication cohort of 425 patients with IA and 311 controls, and results of the 2 cohorts were combined in a meta-analysis. RESULTS After QC, 995 patients with IA and 2,080 controls remained for further analysis. The single variant analysis comprising 46,534 SNVs did not identify significant loci at the genome-wide level. The gene-based tests showed a statistically significant association for fibulin 2 (FBLN2) (best p = 1 × 10-6 for the VT test, MAC >5). Associations were not statistically significant in the independent but smaller replication cohort (p > 0.57) but became slightly stronger in a meta-analysis of the 2 cohorts (best p = 4.8 × 10-7 for the SKAT, MAC ≥1). CONCLUSION Gene-based tests indicated an association for FBLN2, a gene encoding an extracellular matrix protein implicated in vascular wall remodeling, but independent validation in larger cohorts is warranted. We did not identify any significant associations for single low-frequency genetic variants.
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Affiliation(s)
- Femke N G van 't Hof
- From the Department of Neurology and Neurosurgery (F.N.G.v.H., G.J.E.R., Y.M.R.), Brain Center Rudolf Magnus, Department of Cardiology (J.v.S.), Department of Medical Genetics (P.I.W.d.B.), Centre for Molecular Medicine, and Department of Epidemiology (M.L.B., I.V., P.I.W.d.B.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, the Netherlands; Department of Medical and Molecular Genetics (D.L., T.F.), Indiana University School of Medicine, Indianapolis; and Department of Neurology and Rehabilitation Medicine (J.B., D.W.), University of Cincinnati School of Medicine, OH.
| | - Dongbing Lai
- From the Department of Neurology and Neurosurgery (F.N.G.v.H., G.J.E.R., Y.M.R.), Brain Center Rudolf Magnus, Department of Cardiology (J.v.S.), Department of Medical Genetics (P.I.W.d.B.), Centre for Molecular Medicine, and Department of Epidemiology (M.L.B., I.V., P.I.W.d.B.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, the Netherlands; Department of Medical and Molecular Genetics (D.L., T.F.), Indiana University School of Medicine, Indianapolis; and Department of Neurology and Rehabilitation Medicine (J.B., D.W.), University of Cincinnati School of Medicine, OH
| | - Jessica van Setten
- From the Department of Neurology and Neurosurgery (F.N.G.v.H., G.J.E.R., Y.M.R.), Brain Center Rudolf Magnus, Department of Cardiology (J.v.S.), Department of Medical Genetics (P.I.W.d.B.), Centre for Molecular Medicine, and Department of Epidemiology (M.L.B., I.V., P.I.W.d.B.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, the Netherlands; Department of Medical and Molecular Genetics (D.L., T.F.), Indiana University School of Medicine, Indianapolis; and Department of Neurology and Rehabilitation Medicine (J.B., D.W.), University of Cincinnati School of Medicine, OH
| | - Michiel L Bots
- From the Department of Neurology and Neurosurgery (F.N.G.v.H., G.J.E.R., Y.M.R.), Brain Center Rudolf Magnus, Department of Cardiology (J.v.S.), Department of Medical Genetics (P.I.W.d.B.), Centre for Molecular Medicine, and Department of Epidemiology (M.L.B., I.V., P.I.W.d.B.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, the Netherlands; Department of Medical and Molecular Genetics (D.L., T.F.), Indiana University School of Medicine, Indianapolis; and Department of Neurology and Rehabilitation Medicine (J.B., D.W.), University of Cincinnati School of Medicine, OH
| | - Ilonca Vaartjes
- From the Department of Neurology and Neurosurgery (F.N.G.v.H., G.J.E.R., Y.M.R.), Brain Center Rudolf Magnus, Department of Cardiology (J.v.S.), Department of Medical Genetics (P.I.W.d.B.), Centre for Molecular Medicine, and Department of Epidemiology (M.L.B., I.V., P.I.W.d.B.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, the Netherlands; Department of Medical and Molecular Genetics (D.L., T.F.), Indiana University School of Medicine, Indianapolis; and Department of Neurology and Rehabilitation Medicine (J.B., D.W.), University of Cincinnati School of Medicine, OH
| | - Joseph Broderick
- From the Department of Neurology and Neurosurgery (F.N.G.v.H., G.J.E.R., Y.M.R.), Brain Center Rudolf Magnus, Department of Cardiology (J.v.S.), Department of Medical Genetics (P.I.W.d.B.), Centre for Molecular Medicine, and Department of Epidemiology (M.L.B., I.V., P.I.W.d.B.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, the Netherlands; Department of Medical and Molecular Genetics (D.L., T.F.), Indiana University School of Medicine, Indianapolis; and Department of Neurology and Rehabilitation Medicine (J.B., D.W.), University of Cincinnati School of Medicine, OH
| | - Daniel Woo
- From the Department of Neurology and Neurosurgery (F.N.G.v.H., G.J.E.R., Y.M.R.), Brain Center Rudolf Magnus, Department of Cardiology (J.v.S.), Department of Medical Genetics (P.I.W.d.B.), Centre for Molecular Medicine, and Department of Epidemiology (M.L.B., I.V., P.I.W.d.B.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, the Netherlands; Department of Medical and Molecular Genetics (D.L., T.F.), Indiana University School of Medicine, Indianapolis; and Department of Neurology and Rehabilitation Medicine (J.B., D.W.), University of Cincinnati School of Medicine, OH
| | - Tatiana Foroud
- From the Department of Neurology and Neurosurgery (F.N.G.v.H., G.J.E.R., Y.M.R.), Brain Center Rudolf Magnus, Department of Cardiology (J.v.S.), Department of Medical Genetics (P.I.W.d.B.), Centre for Molecular Medicine, and Department of Epidemiology (M.L.B., I.V., P.I.W.d.B.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, the Netherlands; Department of Medical and Molecular Genetics (D.L., T.F.), Indiana University School of Medicine, Indianapolis; and Department of Neurology and Rehabilitation Medicine (J.B., D.W.), University of Cincinnati School of Medicine, OH
| | - Gabriel J E Rinkel
- From the Department of Neurology and Neurosurgery (F.N.G.v.H., G.J.E.R., Y.M.R.), Brain Center Rudolf Magnus, Department of Cardiology (J.v.S.), Department of Medical Genetics (P.I.W.d.B.), Centre for Molecular Medicine, and Department of Epidemiology (M.L.B., I.V., P.I.W.d.B.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, the Netherlands; Department of Medical and Molecular Genetics (D.L., T.F.), Indiana University School of Medicine, Indianapolis; and Department of Neurology and Rehabilitation Medicine (J.B., D.W.), University of Cincinnati School of Medicine, OH
| | - Paul I W de Bakker
- From the Department of Neurology and Neurosurgery (F.N.G.v.H., G.J.E.R., Y.M.R.), Brain Center Rudolf Magnus, Department of Cardiology (J.v.S.), Department of Medical Genetics (P.I.W.d.B.), Centre for Molecular Medicine, and Department of Epidemiology (M.L.B., I.V., P.I.W.d.B.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, the Netherlands; Department of Medical and Molecular Genetics (D.L., T.F.), Indiana University School of Medicine, Indianapolis; and Department of Neurology and Rehabilitation Medicine (J.B., D.W.), University of Cincinnati School of Medicine, OH
| | - Ynte M Ruigrok
- From the Department of Neurology and Neurosurgery (F.N.G.v.H., G.J.E.R., Y.M.R.), Brain Center Rudolf Magnus, Department of Cardiology (J.v.S.), Department of Medical Genetics (P.I.W.d.B.), Centre for Molecular Medicine, and Department of Epidemiology (M.L.B., I.V., P.I.W.d.B.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, the Netherlands; Department of Medical and Molecular Genetics (D.L., T.F.), Indiana University School of Medicine, Indianapolis; and Department of Neurology and Rehabilitation Medicine (J.B., D.W.), University of Cincinnati School of Medicine, OH
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