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Schmit SL, Tsai YY, Bonner JD, Sanz-Pamplona R, Joshi AD, Ugai T, Lindsey SS, Melas M, McDonnell KJ, Idos GE, Walker CP, Qu C, Kast WM, Da Silva DM, Glickman JN, Chan AT, Giannakis M, Nowak JA, Rennert HS, Robins HS, Ogino S, Greenson JK, Moreno V, Rennert G, Gruber SB. Germline genetic regulation of the colorectal tumor immune microenvironment. BMC Genomics 2024; 25:409. [PMID: 38664626 PMCID: PMC11046907 DOI: 10.1186/s12864-024-10295-1] [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: 05/01/2023] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
OBJECTIVE To evaluate the contribution of germline genetics to regulating the briskness and diversity of T cell responses in CRC, we conducted a genome-wide association study to examine the associations between germline genetic variation and quantitative measures of T cell landscapes in 2,876 colorectal tumors from participants in the Molecular Epidemiology of Colorectal Cancer Study (MECC). METHODS Germline DNA samples were genotyped and imputed using genome-wide arrays. Tumor DNA samples were extracted from paraffin blocks, and T cell receptor clonality and abundance were quantified by immunoSEQ (Adaptive Biotechnologies, Seattle, WA). Tumor infiltrating lymphocytes per high powered field (TILs/hpf) were scored by a gastrointestinal pathologist. Regression models were used to evaluate the associations between each variant and the three T-cell features, adjusting for sex, age, genotyping platform, and global ancestry. Three independent datasets were used for replication. RESULTS We identified a SNP (rs4918567) near RBM20 associated with clonality at a genome-wide significant threshold of 5 × 10- 8, with a consistent direction of association in both discovery and replication datasets. Expression quantitative trait (eQTL) analyses and in silico functional annotation for these loci provided insights into potential functional roles, including a statistically significant eQTL between the T allele at rs4918567 and higher expression of ADRA2A (P = 0.012) in healthy colon mucosa. CONCLUSIONS Our study suggests that germline genetic variation is associated with the quantity and diversity of adaptive immune responses in CRC. Further studies are warranted to replicate these findings in additional samples and to investigate functional genomic mechanisms.
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Affiliation(s)
- Stephanie L Schmit
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA.
- Population and Cancer Prevention Program, Case Comprehensive Cancer Center, Cleveland, OH, USA.
| | - Ya-Yu Tsai
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Joseph D Bonner
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Rebeca Sanz-Pamplona
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Barcelona, Spain
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Tomotaka Ugai
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Sidney S Lindsey
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Marilena Melas
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Kevin J McDonnell
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Gregory E Idos
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Christopher P Walker
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Chenxu Qu
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - W Martin Kast
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Diane M Da Silva
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | | | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Marios Giannakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jonathan A Nowak
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hedy S Rennert
- B. Rappaport Faculty of Medicine, Technion and the Association for Promotion of Research in Precision Medicine (APRPM), Haifa, Israel
| | | | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Tokyo Medical and Dental University (Institute of Science Tokyo), Tokyo, Japan
| | - Joel K Greenson
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Victor Moreno
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Gad Rennert
- B. Rappaport Faculty of Medicine, Technion and the Association for Promotion of Research in Precision Medicine (APRPM), Haifa, Israel
| | - Stephen B Gruber
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA.
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Chen Y, Yu XY, Xu SJ, Shi XQ, Zhang XX, Sun C. An indel introduced by Neanderthal introgression, rs3835124:ATTTATT > ATT, might contribute to prostate cancer risk by regulating PDK1 expression. Ann Hum Genet 2024; 88:126-137. [PMID: 37846608 DOI: 10.1111/ahg.12533] [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: 02/28/2023] [Revised: 07/25/2023] [Accepted: 08/04/2023] [Indexed: 10/18/2023]
Abstract
INTRODUCTION Prostate cancer is one of the most common cancer types in males and rs12621278:A > G has been suggested to be associated with this disease by previous genome-wide association studies. One thousand genomes project data analysis indicated that rs12621278:A > G is within two long-core haplotypes. However, the origin, causal variant(s), and molecular function of these haplotypes were remaining unclear. MATERIALS AND METHODS Population genetics analysis and functional genomics work was performed for this locus. RESULTS Phylogeny analysis verified that the rare haplotype is derived from Neanderthal introgression. Genome annotation suggested that three genetic variants in the core haplotypes, rs116108611:G > A, rs139972066:AAAAAAAA > AAAAAAAAA, and rs3835124:ATTTATT > ATT, are located in functional regions. Luciferase assay indicated that rs139972066:AAAAAAAA > AAAAAAAAA and rs116108611:G > A are not able to alter ITGA6 (integrin alpha 6) and ITGA6 antisense RNA 1 expression, respectively. In contrast, rs3835124:ATTTATT > ATT can significantly influence PDK1 (pyruvate dehydrogenase kinase 1) expression, which was verified by expression quantitative trait locus analysis. This genetic variant can alter transcription factor cut like homeobox 1 interaction efficiency. The introgressed haplotype was observed to be subject to positive selection in East Asian populations. The molecular function of the haplotype suggested that Neanderthal should be with lower PDK1 expression and further different energy homeostasis from modern human. CONCLUSION This study provided new insight into the contribution of Neanderthal introgression to human phenotypes.
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Affiliation(s)
- Ying Chen
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, P. R. China
| | - Xin-Yi Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, P. R. China
| | - Shuang-Jia Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, P. R. China
| | - Xiao-Qian Shi
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, P. R. China
| | - Xin-Xin Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, P. R. China
| | - Chang Sun
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, P. R. China
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Altuna-Coy A, Ruiz-Plazas X, Arreaza-Gil V, Segarra-Tomás J, Chacón MR. In silico analysis of prognostic and diagnostic significance of target genes from prostate cancer cell lines derived exomicroRNAs. Cancer Cell Int 2023; 23:275. [PMID: 37978493 PMCID: PMC10655318 DOI: 10.1186/s12935-023-03123-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Cancer-secreted exovesicles are important for cell-to-cell communication by altering cancer-related signalling pathways. Exovesicles-derived miRNAs (exomiRNAs)-target genes can be useful for diagnostic and prognostic purposes. METHODS ExomiRNA from prostate cancer (PCa) cells (PC-3 and LNCaP) were quantified by qRT-PCR and compared to the healthy cell line RWPE-1 by using miRNome PCR 752 miRNAs Panel. MiRNet database was used to predict exomiRNA-target genes. ExomiRNA-target genes pathway functional enrichment was performed by using Reactome database and Enrichr platform. Protein-protein interaction analysis was carried out by using the STRING database. RNA target-gene sequencing data from The Cancer Genome Atlas Prostate Adenocarcinoma (TCGA-PRAD) database was screened out in 465 PCa patients for candidate gene expression in prostate tumour (PT) tissue and non-pathologic prostate (N-PP) tissue. Signature gene candidates were statistically analysed for diagnosis and prognosis usefulness. RESULTS A total of 36 exomiRNAs were found downregulated when comparing PCa cells vs a healthy cell line; and when comparing PC-3 vs LNCaP, 14 miRNAs were found downregulated and 52 upregulated. Reactome pathway database revealed altered pathways and genes related to miRNA biosynthesis, miRNA-mediated gene silencing (TNRC6B and AGO1), and cell proliferation (CDK6), among others. Results showed that TNRC6B gene expression was up-regulated in PT tissue compared to N-PP (n = 52 paired samples) and could be useful for diagnostic purposes. Likewise, gene expression levels of CDK6, TNRC6B, and AGO1 were down-regulated in high-risk PT (n = 293) compared to low-risk PCa tissue counterparts (n = 172). When gene expression levels of CDK6, TNRC6B, and AGO1 were tested as a prognostic panel, the results showed that these improve the prognostic power of classical biomarkers. CONCLUSION ExomiRNAs-targets genes, TNRC6B, CDK6, and AGO1, showed a deregulated expression profile in PCa tissue and could be useful for PCa diagnosis and prognosis.
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Affiliation(s)
- Antonio Altuna-Coy
- Disease Biomarkers and Molecular Mechanisms Group, IISPV, Joan XXIII University Hospital, Universitat Rovira I Virgili, C/Dr. Mallafré Guasch, 4,, 43007, Tarragona, Spain
| | - Xavier Ruiz-Plazas
- Disease Biomarkers and Molecular Mechanisms Group, IISPV, Joan XXIII University Hospital, Universitat Rovira I Virgili, C/Dr. Mallafré Guasch, 4,, 43007, Tarragona, Spain
- Urology Unit, Joan XXIII University Hospital, Tarragona, Spain
| | - Verónica Arreaza-Gil
- Disease Biomarkers and Molecular Mechanisms Group, IISPV, Joan XXIII University Hospital, Universitat Rovira I Virgili, C/Dr. Mallafré Guasch, 4,, 43007, Tarragona, Spain
| | - José Segarra-Tomás
- Disease Biomarkers and Molecular Mechanisms Group, IISPV, Joan XXIII University Hospital, Universitat Rovira I Virgili, C/Dr. Mallafré Guasch, 4,, 43007, Tarragona, Spain
- Urology Unit, Joan XXIII University Hospital, Tarragona, Spain
| | - Matilde R Chacón
- Disease Biomarkers and Molecular Mechanisms Group, IISPV, Joan XXIII University Hospital, Universitat Rovira I Virgili, C/Dr. Mallafré Guasch, 4,, 43007, Tarragona, Spain.
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Akkaliyev M, Aukenov N, Massabayeva M, Apsalikov B, Rakhyzhanova S, Kuderbaev M. Genetic regulation of testosterone level in overweight males from the Kazakh population and its association with hypogonadism. J Med Life 2023; 16:1343-1349. [PMID: 38107722 PMCID: PMC10719783 DOI: 10.25122/jml-2022-0203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 04/18/2023] [Indexed: 12/19/2023] Open
Abstract
Male hypogonadism and erectile dysfunction in different populations are associated with excess body weight. A key aspect in most studies is the metabolism of sexual hormones, primarily testosterone. At the same time, the binding protein sex hormone binding globulin (SHBG) can play a large role, as it determines the ratio of total and bioavailable testosterone in blood, i.e. both the hormone content and level of its production. Recent research has identified common mutations that affect SHBG levels, such as the rs727428 polymorphic locus, which is associated with alterations in histone protein function, affecting the regulation of ribonucleic acid (RNA) protein SHBG synthesis. Similar relationships have been observed for prevalent mutations, including rs5934505 and rs10822184, in diverse populations. This study involved 300 individuals of Kazakh nationality from the Eastern Kazakhstan region, examining three polymorphic variants of the SHBG gene (rs727428, rs5934505, and rs10822184). The participants were categorized into three groups: individuals with hypogonadism and obesity (group 1, n=85), those with excess body weight but no hypogonadism (group 2, n=70), and individuals with neither excess body weight nor hypogonadism (group 3, n=145). The frequency of mutant gene alleles impacting GPS (SHBG) synthesis in the Kazakh population was notably high, comparable to European and South-East Asian populations. However, the association between excess body weight and these mutations exhibited varying patterns. Hypogonadism was linked to decreased GPS levels, strongly correlating with total testosterone but not bioavailable testosterone. The retention of sexual functions in overweight men was not always directly related to BMI levels and GPS concentrations.
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Affiliation(s)
- Merkhat Akkaliyev
- Department of Surgical Disciplines, Semey Medical University, Semey, Kazakhstan
| | - Nurlan Aukenov
- Department of Health and Human Resources, Ministry of Health, Nur-Sultan, Kazakhstan
| | - Meruyert Massabayeva
- Center of Scientific Research Laboratory, Semey Medical University, Semey, Kazakhstan
| | - Bakytbek Apsalikov
- Department of Family Medicine, Semey Medical University, Semey, Kazakhstan
| | - Saule Rakhyzhanova
- Department of Normal Physiology, Semey Medical University, Semey, Kazakhstan
| | - Muratkhan Kuderbaev
- Department of Surgical Disciplines, Semey Medical University, Semey, Kazakhstan
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Akkaliyev M, Aukenov N, Massabayeva M, Apsalikov B, Rakhyzhanova S, Kuderbaev M, Sadykov N. Effect of SHBG Polymorphism on the Levels of Bioavailable Testosterone and Lipid Metabolism in Older Men of the Kazakh Population. Open Access Maced J Med Sci 2022. [DOI: 10.3889/oamjms.2022.8145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
This study is aimed at investigating the effect of SHBG (rs727428; rs10822184) and LPL (rs754493647) single nucleotide polymorphisms on the concentration of the bioavailable fraction of testosterone in older men.
Materials and methods To study gene mutations, 417 residents of the East Kazakhstan region of Kazakh nationality were examined. The main group included 135 men with signs of hypogonadism (AMS 37-49), and the control group consisted of 282 healthy men (AMS 17-26) of the corresponding age (p = 0.5). Single nucleotide polymorphisms rs 727428 [C / T]; rs10822184 [T / C]; rs754493647 [T / C], was determined by the TaqMan method.
Results Analysis of the rs727428 polymorphism has revealed that the TT allele (rs727428) has a lower level of albumin (p = 0.03), bioavailable testosterone (p = 0.04), and free testosterone (p = 0.6) than in carriers of the CC and CT genotypes. Also, it has shown a decrease in total testosterone (p = 0.001) and an increase in SHBG levels (p = 0.07) in men with the TT genotype of the rs727428 gene polymorphism. The rs10822184 polymorphism demonstrated an increase in triglyceride and LDL levels in TT genotype (p ≤ 0.04), in comparison with CC and CT genotypes.
Conclusion It has been proven that rs727428 (p = 0.001) is associated with testosterone levels and therefore can determine the concentration of bioavailable testosterone. Decreased levels of bioavailable testosterone are a sign of male hypogonadism. This study confirms the effect of rs10822184 on LDL (p = 0.01) and triglyceride (p = 0.04) levels, but its association with androgen levels has not been proven. Our results may be of interest for understanding the etiology of early development of hypogonadism and lipid metabolism disorders in men. To confirm the conclusions, a more detailed study with a large sample of men from the Kazakh population may be required.
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Chien HT, Yeh CC, Young CK, Chen TP, Liao CT, Wang HM, Cho KL, Huang SF. Polygenic Panels Predicting the Susceptibility of Multiple Upper Aerodigestive Tract Cancer in Oral Cancer Patients. J Pers Med 2021; 11:jpm11050425. [PMID: 34070222 PMCID: PMC8158753 DOI: 10.3390/jpm11050425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/08/2021] [Accepted: 05/14/2021] [Indexed: 11/16/2022] Open
Abstract
Head and neck cancer was closely related with habitual use of cigarette and alcohol. Those cancer patients are susceptible to develop multiple primary tumors (MPTs). In this study, we utilized the single nucleotide polymorphisms (SNPs) array (Affymetrix Axion Genome-Wide TWB 2.0 Array Plate) to investigate patients' risks of developing multiple primary cancers. We recruited 712 male head and neck cancer patients between Mar 1996 and Feb 2017. Two hundred and eighty-six patients (40.2%) had MPTs and 426 (59.8%) had single cancer. Four hundred and twelve normal controls were also recruited. A list of seventeen factors was extracted and ten factors were demonstrated to increase the risks of multiple primary cancers (alcohol drinking, rs118169127, rs149089400, rs76367287, rs61401220, rs141057871, rs7129229, older age, rs3760265, rs9554264; all were p value < 0.05). Polygenic scoring model was built and the area under curve to predict the risk developing MPTs is 0.906. Alcohol drinking, among the seventeen factors, was the most important risk factor to develop MPT in upper aerodigestive tract (OR: 7.071, 95% C.I.: 2.134-23.434). For those with high score in polygenic model, routine screening of upper digestive tract including laryngoscope and esophagoscope is suggested to detect new primaries early.
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Affiliation(s)
- Huei-Tzu Chien
- Department of Nutrition and Health Sciences, Chang Gung University of Science and Technology, Tao-Yuan 33302, Taiwan;
- Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Tao-Yuan 33302, Taiwan
| | - Chi-Chin Yeh
- Master Program in Applied Molecular Epidemiology, College of Public Health, Taipei Medical University, Taipei 11031, Taiwan;
- Department of Public Health, College of Public Health, China Medical University, Taichung 40402, Taiwan
- Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei 11696, Taiwan
| | - Chi-Kuang Young
- Department of Otolaryngology, Chang Gung Memorial Hospital, Keelung 20401, Taiwan;
| | - Tzu-Ping Chen
- Department of Thoracic Surgery, Chang Gung Memorial Hospital, Keelung 20401, Taiwan;
| | - Chun-Ta Liao
- Department of Otolaryngology, Head and Neck Surgery, Chang Gung Memorial Hospital, Linkou 33342, Taiwan; (C.-T.L.); (K.-L.C.)
- Medical College, Chang Gung University, Tao-Yuan 33302, Taiwan;
| | - Hung-Ming Wang
- Medical College, Chang Gung University, Tao-Yuan 33302, Taiwan;
- Division of Hematology/Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Tao-Yuan 33342, Taiwan
| | - Kai-Lun Cho
- Department of Otolaryngology, Head and Neck Surgery, Chang Gung Memorial Hospital, Linkou 33342, Taiwan; (C.-T.L.); (K.-L.C.)
| | - Shiang-Fu Huang
- Department of Otolaryngology, Head and Neck Surgery, Chang Gung Memorial Hospital, Linkou 33342, Taiwan; (C.-T.L.); (K.-L.C.)
- Medical College, Chang Gung University, Tao-Yuan 33302, Taiwan;
- Graduate Institute of Clinical Medical Science, Chang Gung University, Tao-Yuan 33302, Taiwan
- Correspondence: ; Tel.: +88-633-281-200 (ext. 3968); Fax: +88-633-979-361
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Simpson BS, Pye H, Whitaker HC. The oncological relevance of fragile sites in cancer. Commun Biol 2021; 4:567. [PMID: 33980983 PMCID: PMC8115686 DOI: 10.1038/s42003-021-02020-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 03/12/2021] [Indexed: 01/15/2023] Open
Abstract
Recent developments in sequencing the cancer genome have provided the first in-depth mapping of structural variants (SV) across 38 tumour types. Sixteen signatures of structural variants have been proposed which broadly characterise the variation seen across cancer types. One signature shows increased duplications and deletions at fragile sites, with little association with the typical DNA repair defects. We discuss how, for many of these fragile sites, the clinical impacts are yet to be explored. One example is NAALADL2, one of the most frequently altered fragile sites in the cancer genome. The copy-number variations (CNVs) which occur at fragile sites, such as NAALADL2, may span many genes without typical DNA repair defects and could have a large impact on cell signalling. In this Perspective, Simpson, Pye, and Whitaker discuss recent research identifying structural genomic variants in human cancers with a particular focus on deletions and duplications at genomic fragile sites. They argue that tumours with predominantly fragile site structural variants represent a distinct mutational signature that warrants further research.
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Affiliation(s)
- Benjamin S Simpson
- Molecular Diagnostics and Therapeutics Group, Research Department of Targeted Intervention, Division of Surgery & Interventional Science, University College London, London, UK
| | - Hayley Pye
- Molecular Diagnostics and Therapeutics Group, Research Department of Targeted Intervention, Division of Surgery & Interventional Science, University College London, London, UK
| | - Hayley C Whitaker
- Molecular Diagnostics and Therapeutics Group, Research Department of Targeted Intervention, Division of Surgery & Interventional Science, University College London, London, UK.
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Mathkar PP, Chen X, Sulovari A, Li D. Characterization of Hepatitis B Virus Integrations Identified in Hepatocellular Carcinoma Genomes. Viruses 2021; 13:v13020245. [PMID: 33557409 PMCID: PMC7915589 DOI: 10.3390/v13020245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 12/19/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality. Almost half of HCC cases are associated with hepatitis B virus (HBV) infections, which often lead to HBV sequence integrations in the human genome. Accurate identification of HBV integration sites at a single nucleotide resolution is critical for developing a better understanding of the cancer genome landscape and of the disease itself. Here, we performed further analyses and characterization of HBV integrations identified by our recently reported VIcaller platform in recurrent or known HCC genes (such as TERT, MLL4, and CCNE1) as well as non-recurrent cancer-related genes (such as CSMD2, NKD2, and RHOU). Our pathway enrichment analysis revealed multiple pathways involving the alcohol dehydrogenase 4 gene, such as the metabolism pathways of retinol, tyrosine, and fatty acid. Further analysis of the HBV integration sites revealed distinct patterns involving the integration upper breakpoints, integrated genome lengths, and integration allele fractions between tumor and normal tissues. Our analysis also implies that the VIcaller method has diagnostic potential through discovering novel clonal integrations in cancer-related genes. In conclusion, although VIcaller is a hypothesis free virome-wide approach, it can still be applied to accurately identify genome-wide integration events of a specific candidate virus and their integration allele fractions.
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Affiliation(s)
- Pranav P. Mathkar
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; (P.P.M.); (A.S.)
| | - Xun Chen
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; (P.P.M.); (A.S.)
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto 606-8501, Japan
- Correspondence: (X.C.); (D.L.)
| | - Arvis Sulovari
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; (P.P.M.); (A.S.)
- Cajal Neuroscience Inc., Seattle, WA 98102, USA
| | - Dawei Li
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; (P.P.M.); (A.S.)
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA
- Correspondence: (X.C.); (D.L.)
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Fiorica PN, Schubert R, Morris JD, Abdul Sami M, Wheeler HE. Multi-ethnic transcriptome-wide association study of prostate cancer. PLoS One 2020; 15:e0236209. [PMID: 32986714 PMCID: PMC7521738 DOI: 10.1371/journal.pone.0236209] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/11/2020] [Indexed: 12/13/2022] Open
Abstract
The genetic risk for prostate cancer has been governed by a few rare variants with high penetrance and over 150 commonly occurring variants with lower impact on risk; however, most of these variants have been identified in studies containing exclusively European individuals. People of non-European ancestries make up less than 15% of prostate cancer GWAS subjects. Across the globe, incidence of prostate cancer varies with population due to environmental and genetic factors. The discrepancy between disease incidence and representation in genetics highlights the need for more studies of the genetic risk for prostate cancer across diverse populations. To better understand the genetic risk for prostate cancer across diverse populations, we performed PrediXcan and GWAS in a case-control study of 4,769 self-identified African American (2,463 cases and 2,306 controls), 2,199 Japanese American (1,106 cases and 1,093 controls), and 2,147 Latin American (1,081 cases and 1,066 controls) individuals from the Multiethnic Genome-wide Scan of Prostate Cancer. We used prediction models from 46 tissues in GTEx version 8 and five models from monocyte transcriptomes in the Multi-Ethnic Study of Atherosclerosis. Across the three populations, we predicted 19 gene-tissue pairs, including five unique genes, to be significantly (lfsr < 0.05) associated with prostate cancer. One of these genes, NKX3-1, replicated in a larger European study. At the SNP level, 110 SNPs met genome-wide significance in the African American study while 123 SNPs met significance in the Japanese American study. Fine mapping revealed three significant independent loci in the African American study and two significant independent loci in the Japanese American study. These identified loci confirm findings from previous GWAS of prostate cancer in diverse populations while PrediXcan-identified genes suggest potential new directions for prostate cancer research in populations across the globe.
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Affiliation(s)
- Peter N. Fiorica
- Department of Chemistry & Biochemistry, Loyola University Chicago, Chicago, IL, United States of America
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
| | - Ryan Schubert
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, United States of America
- Department of Statistics, Loyola University Chicago, Chicago, IL, United States of America
| | - John D. Morris
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, United States of America
| | - Mohammed Abdul Sami
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
| | - Heather E. Wheeler
- Department of Chemistry & Biochemistry, Loyola University Chicago, Chicago, IL, United States of America
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, United States of America
- Department of Public Health, Loyola University Chicago, Chicago, IL, United States of America
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10
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Shen Z, Li Y, Fang Y, Lin M, Feng X, Li Z, Zhan Y, Liu Y, Mou T, Lan X, Wang Y, Li G, Wang J, Deng H. SNX16 activates c-Myc signaling by inhibiting ubiquitin-mediated proteasomal degradation of eEF1A2 in colorectal cancer development. Mol Oncol 2020; 14:387-406. [PMID: 31876369 PMCID: PMC6998659 DOI: 10.1002/1878-0261.12626] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 12/01/2019] [Accepted: 12/02/2019] [Indexed: 01/11/2023] Open
Abstract
Sorting nexin 16 (SNX16), a member of the sorting nexin family, has been implicated in tumor development. However, the function of SNX16 has not yet been investigated in colorectal cancer (CRC). Here, we showed that SNX16 expression was significantly upregulated in CRC tissues compared with normal counterparts. Upregulated mRNA levels of SNX16 predicted poor survival of CRC patients. Functional experiments showed that SNX16 could promote CRC cells growth both in vitro and in vivo. Knockdown of SNX16 induced cell cycle arrest and apoptosis, whereas ectopic overexpression of SNX16 had the opposite effects. Mechanistically, SNX16‐eukaryotic translation elongation factor 1A2 (eEF1A2) interaction could inhibit the degradation and ubiquitination of eEF1A2, followed by activation of downstream c‐Myc signaling. Our study unveiled that the SNX16/eEF1A2/c‐Myc signaling axis could promote colorectal tumorigenesis and SNX16 might potentially serve as a novel biomarker for the diagnosis and an intervention of CRC.
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Affiliation(s)
- Zhiyong Shen
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yongsheng Li
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yuan Fang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Mingdao Lin
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaochuang Feng
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhenkang Li
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yizhi Zhan
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yuechen Liu
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Tingyu Mou
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaoliang Lan
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yanan Wang
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Guoxin Li
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jiping Wang
- Division of Surgical Oncology, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Haijun Deng
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
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11
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Ahmed M, Goh C, Saunders E, Cieza-Borrella C, Kote-Jarai Z, Schumacher FR, Eeles R. Germline genetic variation in prostate susceptibility does not predict outcomes in the chemoprevention trials PCPT and SELECT. Prostate Cancer Prostatic Dis 2019; 23:333-342. [PMID: 31776447 PMCID: PMC7237354 DOI: 10.1038/s41391-019-0181-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 06/02/2019] [Accepted: 06/24/2019] [Indexed: 12/11/2022]
Abstract
Background The development of prostate cancer can be influenced by genetic and environmental factors. Numerous germline SNPs influence prostate cancer susceptibility. The functional pathways in which these SNPs increase prostate cancer susceptibility are unknown. Finasteride is currently not being used routinely as a chemoprevention agent but the long term outcomes of the PCPT trial are awaited. The outcomes of the SELECT trial have not recommended the use of chemoprevention in preventing prostate cancer. This study investigated whether germline risk SNPs could be used to predict outcomes in the PCPT and SELECT trial. Methods Genotyping was performed in European men entered into the PCPT trial (n = 2434) and SELECT (n = 4885). Next generation genotyping was performed using Affymetrix® Eureka™ Genotyping protocols. Logistic regression models were used to test the association of risk scores and the outcomes in the PCPT and SELECT trials. Results Of the 100 SNPs, 98 designed successfully and genotyping was validated for samples genotyped on other platforms. A number of SNPs predicted for aggressive disease in both trials. Men with a higher polygenic score are more likely to develop prostate cancer in both trials, but the score did not predict for other outcomes in the trial. Conclusion Men with a higher polygenic risk score are more likely to develop prostate cancer. There were no interactions of these germline risk SNPs and the chemoprevention agents in the SELECT and PCPT trials.
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Affiliation(s)
- Mahbubl Ahmed
- The Institute of Cancer Research, Royal Marsden Hospital, NHS Foundation Trust, 123 Old Brompton Road, London, SW7 3RP, UK.
| | - Chee Goh
- The Institute of Cancer Research, Royal Marsden Hospital, NHS Foundation Trust, 123 Old Brompton Road, London, SW7 3RP, UK
| | - Edward Saunders
- The Institute of Cancer Research, Royal Marsden Hospital, NHS Foundation Trust, 123 Old Brompton Road, London, SW7 3RP, UK
| | - Clara Cieza-Borrella
- The Institute of Cancer Research, Royal Marsden Hospital, NHS Foundation Trust, 123 Old Brompton Road, London, SW7 3RP, UK
| | | | - Zsofia Kote-Jarai
- The Institute of Cancer Research, Royal Marsden Hospital, NHS Foundation Trust, 123 Old Brompton Road, London, SW7 3RP, UK
| | - Fredrick R Schumacher
- Department of Epidemiology and Biostatistics, Case Western Reserve University; Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
| | - Ros Eeles
- The Institute of Cancer Research, Royal Marsden Hospital, NHS Foundation Trust, 123 Old Brompton Road, London, SW7 3RP, UK
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12
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Huang S, Lv Z, Wen Y, Wei Y, Zhou L, Ke Y, Zhang Y, Xu Q, Li L, Guo Y, Li D, Xie C, Guo Y, Cheng J. miR-129-2-3p directly targets SYK gene and associates with the risk of ischaemic stroke in a Chinese population. J Cell Mol Med 2019; 23:167-176. [PMID: 30499219 PMCID: PMC6307781 DOI: 10.1111/jcmm.13901] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 08/16/2018] [Indexed: 02/05/2023] Open
Abstract
Spleen tyrosine kinase (SYK) gene has been identified as novel susceptibility locus for ischaemic stroke (IS) previously. However, regulation of SYK gene remains unknown in IS. In this study, we aimed to identify miRNAs that might be involved in the development of IS by targeting SYK gene. miRNAs were firstly screened by bioinformatics predicting tool. The expression levels of SYK gene were detected by qRT-PCR and western blotting, respectively, after miRNA transfection. Luciferase reporter assay was applied to investigate the direct binding between miRNAs and target gene. miRNA levels were detected by miRNA TaqMan assays in the blood cells of 270 IS patients and 270 control volunteers. Results suggest that SYK gene might be a direct target of miR-129-2-3p. The blood level of miR-129-2-3p was significantly lower in IS patients (P < 0.05), and negatively associated with the risk of IS (adjusted OR: 0.88; 95% CI: 0.80-0.98; P = 0.021) by multivariable logistic regression analysis. The blood levels of SYK gene were significantly higher in IS patients, and miR-129-2-3p expression was negatively correlated with mean platelet volume. In summary, our study suggests that miR-129-2-3p might be involved in the pathogenesis of IS through interrupting SYK expression and the platelet function, and further investigation is needed to explore the underlying mechanism.
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Affiliation(s)
- Suli Huang
- Department of Molecular EpidemiologyShenzhen Center for Disease Control and PreventionShenzhenGuangdongChina
| | - Ziquan Lv
- Department of Molecular EpidemiologyShenzhen Center for Disease Control and PreventionShenzhenGuangdongChina
| | - Ying Wen
- Department of Molecular EpidemiologyShenzhen Center for Disease Control and PreventionShenzhenGuangdongChina
| | - Yazhen Wei
- Department of Molecular EpidemiologyShenzhen Center for Disease Control and PreventionShenzhenGuangdongChina
| | - Li Zhou
- Department of School HygieneShenzhen Center for Disease Control and PreventionShenzhenGuangdongChina
| | - Yuebin Ke
- Department of Molecular EpidemiologyShenzhen Center for Disease Control and PreventionShenzhenGuangdongChina
| | - Yanwei Zhang
- Department of Molecular EpidemiologyShenzhen Center for Disease Control and PreventionShenzhenGuangdongChina
| | - Qianhui Xu
- Department of NeurologyPeople's Hospital of ShenzhenGuangdongChina
| | - Lu Li
- Research Center of Translational MedicineThe Second Affiliated Hospital of Shantou University Medical CollegeShantouGuangdongChina
| | - Yinsheng Guo
- Department of Molecular EpidemiologyShenzhen Center for Disease Control and PreventionShenzhenGuangdongChina
| | - Di Li
- Department of NeurologyPeople's Hospital of ShenzhenGuangdongChina
| | - Changhui Xie
- Department of Molecular EpidemiologyShenzhen Center for Disease Control and PreventionShenzhenGuangdongChina
| | - Yi Guo
- Department of NeurologyPeople's Hospital of ShenzhenGuangdongChina
| | - Jinquan Cheng
- Department of Molecular EpidemiologyShenzhen Center for Disease Control and PreventionShenzhenGuangdongChina
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13
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Rajendran BK, Deng CX. Characterization of potential driver mutations involved in human breast cancer by computational approaches. Oncotarget 2018; 8:50252-50272. [PMID: 28477017 PMCID: PMC5564847 DOI: 10.18632/oncotarget.17225] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 03/26/2017] [Indexed: 02/06/2023] Open
Abstract
Breast cancer is the second most frequently occurring form of cancer and is also the second most lethal cancer in women worldwide. A genetic mutation is one of the key factors that alter multiple cellular regulatory pathways and drive breast cancer initiation and progression yet nature of these cancer drivers remains elusive. In this article, we have reviewed various computational perspectives and algorithms for exploring breast cancer driver mutation genes. Using both frequency based and mutational exclusivity based approaches, we identified 195 driver genes and shortlisted 63 of them as candidate drivers for breast cancer using various computational approaches. Finally, we conducted network and pathway analysis to explore their functions in breast tumorigenesis including tumor initiation, progression, and metastasis.
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Affiliation(s)
- Barani Kumar Rajendran
- Cancer Research Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Chu-Xia Deng
- Cancer Research Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China
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14
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Kou CTJ, Kandpal RP. Differential Expression Patterns of Eph Receptors and Ephrin Ligands in Human Cancers. BIOMED RESEARCH INTERNATIONAL 2018; 2018:7390104. [PMID: 29682554 PMCID: PMC5851329 DOI: 10.1155/2018/7390104] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/11/2018] [Accepted: 01/22/2018] [Indexed: 12/20/2022]
Abstract
Eph receptors constitute the largest family of receptor tyrosine kinases, which are activated by ephrin ligands that either are anchored to the membrane or contain a transmembrane domain. These molecules play important roles in the development of multicellular organisms, and the physiological functions of these receptor-ligand pairs have been extensively documented in axon guidance, neuronal development, vascular patterning, and inflammation during tissue injury. The recognition that aberrant regulation and expression of these molecules lead to alterations in proliferative, migratory, and invasive potential of a variety of human cancers has made them potential targets for cancer therapeutics. We present here the involvement of Eph receptors and ephrin ligands in lung carcinoma, breast carcinoma, prostate carcinoma, colorectal carcinoma, glioblastoma, and medulloblastoma. The aberrations in their abundances are described in the context of multiple signaling pathways, and differential expression is suggested as the mechanism underlying tumorigenesis.
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Affiliation(s)
- Chung-Ting Jimmy Kou
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Raj P. Kandpal
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA 91766, USA
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15
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Joyce BT, Zheng Y, Zhang Z, Liu L, Kocherginsky M, Murphy R, Achenbach CJ, Musa J, Wehbe F, Just A, Shen J, Vokonas P, Schwartz J, Baccarelli AA, Hou L. miRNA-Processing Gene Methylation and Cancer Risk. Cancer Epidemiol Biomarkers Prev 2018; 27:550-557. [PMID: 29475968 DOI: 10.1158/1055-9965.epi-17-0849] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 12/06/2017] [Accepted: 02/02/2018] [Indexed: 12/20/2022] Open
Abstract
Background: Dysregulation of miRNA and methylation levels are epigenetic hallmarks of cancer, potentially linked via miRNA-processing genes. Studies have found genetic alterations to miRNA-processing genes in cancer cells and human population studies. Our objective was to prospectively examine changes in DNA methylation of miRNA-processing genes and their associations with cancer risk.Methods: We examined cohort data from the Department of Veterans' Affairs Normative Aging Study. Participants were assessed every 3 to 5 years starting in 1999 through 2013 including questionnaires, medical record review, and blood collection. Blood from 686 consenting participants was analyzed using the Illumina 450K BeadChip array to measure methylation at CpG sites throughout the genome. We selected 19 genes based on a literature review, with 519 corresponding CpG sites. We then used Cox proportional hazards models to examine associations with cancer incidence, and generalized estimating equations to examine associations with cancer prevalence. Associations at false discovery rate < 0.05 were considered statistically significant.Results: Methylation of three CpGs (DROSHA: cg23230564, TNRC6B: cg06751583, and TNRC6B: cg21034183) was prospectively associated with time to cancer development (positively for cg06751583, inversely for cg23230564 and cg21034183), whereas methylation of one CpG site (DROSHA: cg16131300) was positively associated with cancer prevalence.Conclusions: DNA methylation of DROSHA, a key miRNA-processing gene, and TNRC6B may play a role in early carcinogenesis.Impact: Changes in miRNA processing may exert multiple effects on cancer development, including protecting against it via altered global miRNAs, and may be a useful early detection biomarker of cancer. Cancer Epidemiol Biomarkers Prev; 27(5); 550-7. ©2018 AACR.
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Affiliation(s)
- Brian T Joyce
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.
| | - Yinan Zheng
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Zhou Zhang
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Lei Liu
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Masha Kocherginsky
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Robert Murphy
- Center for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Chad J Achenbach
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Jonah Musa
- Center for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Health Sciences Integrated Program, Center for Healthcare Studies, Institute of Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Department of Obstetrics and Gynecology, Faculty of Medical Sciences, University of Jos, Plateau State, Nigeria
| | - Firas Wehbe
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Allan Just
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jincheng Shen
- Department of Population Health Sciences, University of Utah School of Medicine, Salt Lake City, Utah
| | - Pantel Vokonas
- VA Normative Aging Study, Veterans Affairs Boston Healthcare System and the Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Joel Schwartz
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Andrea A Baccarelli
- Departments of Epidemiology and Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, New York
| | - Lifang Hou
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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16
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Nowinski S, Santaolalla A, O'Leary B, Loda M, Mirchandani A, Emberton M, Van Hemelrijck M, Grigoriadis A. Systematic identification of functionally relevant risk alleles to stratify aggressive versus indolent prostate cancer. Oncotarget 2018; 9:12812-12824. [PMID: 29560112 PMCID: PMC5849176 DOI: 10.18632/oncotarget.24400] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/25/2018] [Indexed: 12/20/2022] Open
Abstract
Novel approaches for classification, including molecular features, are needed to direct therapy for men with low-grade prostate cancer (PCa), especially men on active surveillance. Risk alleles identified from genome-wide association studies (GWAS) could improve prognostication. Those risk alleles that coincided with genes and somatic copy number aberrations associated with progression of PCa were selected as the most relevant for prognostication. In a systematic literature review, a total of 698 studies were collated. Fifty-three unique SNPs residing in 29 genomic regions, including 8q24, 10q11 and 19q13, were associated with PCa progression. Functional studies implicated 21 of these single nucleotide polymorphisms (SNPs) as modulating the expression of genes in the androgen receptor pathway and several other oncogenes. In particular, 8q24, encompassing MYC, harbours a high density of SNPs conferring unfavourable pathological characteristics in low-grade PCa, while a copy number gain of MYC in low-grade PCa was associated with prostate-specific antigen recurrence after radical prostatectomy. By combining GWAS data with gene expression and structural rearrangements, risk alleles were identified that could provide a new basis for developing a prognostication tool to guide therapy for men with early prostate cancer.
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Affiliation(s)
- Salpie Nowinski
- Cancer Bioinformatics, Innovation Hub, Guy's Cancer Centre, King's College London, London, UK
| | - Aida Santaolalla
- Translational Oncology & Urology Research, King's College London, London, UK
| | - Ben O'Leary
- Breast Cancer NOW Centre, The Institute of Cancer Research, The Royal Marsden Hospital, London, UK
| | - Massimo Loda
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ayesha Mirchandani
- Cancer Bioinformatics, Innovation Hub, Guy's Cancer Centre, King's College London, London, UK
| | - Mark Emberton
- Division of Surgery and Interventional Science, University College London, London, UK
| | | | - Anita Grigoriadis
- Cancer Bioinformatics, Innovation Hub, Guy's Cancer Centre, King's College London, London, UK
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17
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Iordache PD, Mates D, Gunnarsson B, Eggertsson HP, Sulem P, Guðmundsson J, Benónísdóttir S, Csiki IE, Rascu S, Radavoi D, Ursu R, Staicu C, Calota V, Voinoiu A, Jinga M, Rosoga G, Danau R, Sima SC, Badescu D, Suciu N, Radoi V, Manolescu A, Rafnar T, Halldórsson BV, Jinga V, Stefánsson K. Profile of common prostate cancer risk variants in an unscreened Romanian population. J Cell Mol Med 2017; 22:1574-1582. [PMID: 29266682 PMCID: PMC5824401 DOI: 10.1111/jcmm.13433] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/22/2017] [Indexed: 01/08/2023] Open
Abstract
To find sequence variants affecting prostate cancer (PCA) susceptibility in an unscreened Romanian population we use a genome‐wide association study (GWAS). The study population included 990 unrelated pathologically confirmed PCA cases and 1034 male controls. DNA was genotyped using Illumina SNP arrays, and 24.295.558 variants were imputed using the 1000 Genomes data set. An association test was performed between the imputed markers and PCA. A systematic literature review for variants associated with PCA risk identified 115 unique variants that were tested in the Romanian sample set. Thirty of the previously reported SNPs replicated (P‐value < 0.05), with the strongest associations observed at: 8q24.21, 11q13.3, 6q25.3, 5p15.33, 22q13.2, 17q12 and 3q13.2. The replicated variants showing the most significant association in Romania are rs1016343 at 8q24.21 (P = 2.2 × 10−4), rs7929962 at 11q13.3 (P = 2.7 × 10−4) and rs9364554 at 6q25.2 (P = 4.7 × 10−4). None of the variants tested in the Romanian GWAS reached genome‐wide significance (P‐value <5 × 10−8) but 807 markers had P‐values <1 × 10−4. Here, we report the results of the first GWAS of PCA performed in a Romanian population. Our study provides evidence that a substantial fraction of previously validated PCA variants associate with risk in this unscreened Romanian population.
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Affiliation(s)
- Paul D Iordache
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
| | - Dana Mates
- National Institute of Public Health, Bucharest, Romania
| | | | | | | | | | | | | | - Stefan Rascu
- Urology Department, 'Prof. Dr. Th. Burghele' Clinical Hospital, University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
| | - Daniel Radavoi
- Urology Department, 'Prof. Dr. Th. Burghele' Clinical Hospital, University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
| | - Radu Ursu
- Department of Medical Genetics, Faculty of Medicine, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
| | | | | | | | - Mariana Jinga
- Carol Davila University of Medicine and Pharmacy, Dr. Carol Davila Central University Emergency Military Hospital, Bucharest, Romania
| | - Gabriel Rosoga
- Urology Department, 'Prof. Dr. Th. Burghele' Clinical Hospital, University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
| | - Razvan Danau
- Urology Department, 'Prof. Dr. Th. Burghele' Clinical Hospital, University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
| | - Sorin Cristian Sima
- Urology Department, 'Prof. Dr. Th. Burghele' Clinical Hospital, University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
| | - Daniel Badescu
- Urology Department, 'Prof. Dr. Th. Burghele' Clinical Hospital, University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
| | | | - Viorica Radoi
- Department of Medical Genetics, Faculty of Medicine, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
| | - Andrei Manolescu
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
| | | | - Bjarni V Halldórsson
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland.,deCODE genetics/AMGEN, Reykjavik, Iceland
| | - Viorel Jinga
- Urology Department, 'Prof. Dr. Th. Burghele' Clinical Hospital, University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
| | - Kári Stefánsson
- deCODE genetics/AMGEN, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
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18
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Vaidyanathan V, Naidu V, Karunasinghe N, Kao CHJ, Pallati R, Jabed A, Marlow G, Kallingappa P, Ferguson LR. Effect of ageing and single nucleotide polymorphisms associated with the risk of aggressive prostate cancer in a New Zealand population. MOLECULAR BIOSYSTEMS 2017; 13:1967-1980. [PMID: 28783191 DOI: 10.1039/c7mb00203c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Prostate cancer is one of the most significant male health concerns worldwide, and various researchers carrying out molecular diagnostics have indicated that genetic interactions with biological and behavioral factors play an important role in the overall risk and prognosis of this disease. Single nucleotide polymorphisms are increasingly becoming strong biomarker candidates to identify the susceptibility of individuals to prostate cancer. We carried out risk association of different stages of prostate cancer to a number of single nucleotide polymorphisms to identify the susceptible alleles in a New Zealand population and checked the interaction with environmental factors as well. We identified a number of single nucleotide polymorphisms to have associations specifically to the risk of prostate cancer and aggressiveness of the disease, and also certain single nucleotide polymorphisms to be vulnerable to the reported behavioral factors. We have addressed "special" environmental conditions prevalent in New Zealand, which can be used as a model for a bigger worldwide study.
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Affiliation(s)
- Venkatesh Vaidyanathan
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand.
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19
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Qin N, Wang C, Lu Q, Huang T, Zhu M, Wang L, Yu F, Huang M, Jiang Y, Dai J, Ma H, Jin G, Wu C, Lin D, Shen H, Hu Z. A cis-eQTL genetic variant of the cancer-testis gene CCDC116 is associated with risk of multiple cancers. Hum Genet 2017; 136:987-997. [PMID: 28653172 DOI: 10.1007/s00439-017-1827-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 06/19/2017] [Indexed: 11/29/2022]
Abstract
Recent studies have found that cancer-testis (CT) genes, which are expressed predominantly in germ and cancer cells, may be candidate cancer drivers. Because of their crucial roles, genetic variants in these genes may contribute to the development of cancer. Here, we systematically evaluated associations of common variants in CT genes and their promoters for the risk of lung cancer in our initial GWAS (2331 cases and 3077 controls), followed by in silico replication using additional 10,512 lung cancer cases and 9562 controls. We found a significant association between rs3747093 located in the CCDC116 promoter and lung cancer risk (OR = 0.91, P meta = 7.81 × 10-6). Although CCDC116 was expressed at lower levels in somatic tissues compared to the testis, the protective allele A of rs3747093 was associated with decreased CCDC116 expression in many normal tissues, including the lung (P = 8.1 × 10-13). We subsequently genotyped this variant in another four commonly diagnosed cancers (gastric, esophageal, colorectal, and breast cancers), as we found expression quantitative trait locus (eQTL) signals for rs3747093 and CCDC116 in their corresponding normal tissues. Interestingly, we observed consistent associations between rs3747093 and multiple cancers (gastric cancer: OR = 0.85, P = 2.21 × 10-4; esophageal cancer: OR = 0.91, P = 2.57 × 10-2; colorectal cancer: OR = 0.80, P = 1.85 × 10-6; and breast cancer: OR = 0.87, P = 1.55 × 10-3). Taken together, the A allele of rs3747093 showed significant protective effects on cancer risk (OR = 0.88, P pool = 6.52 × 10-13) in an Asian population. Moreover, our findings suggest that low abundance expression of CT genes in normal tissues may also contribute to tumorigenesis, providing a new mechanism of CT genes in the development of cancer.
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Affiliation(s)
- Na Qin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 210029, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Cheng Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 210029, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Qun Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Tongtong Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Meng Zhu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 210029, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Lihua Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Fei Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Mingtao Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Yue Jiang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 210029, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Juncheng Dai
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 210029, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Hongxia Ma
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 210029, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Guangfu Jin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 210029, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Chen Wu
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Dongxin Lin
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Hongbing Shen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 210029, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 210029, China. .,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China. .,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China.
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20
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Vaidyanathan V, Naidu V, Kao CHJ, Karunasinghe N, Bishop KS, Wang A, Pallati R, Shepherd P, Masters J, Zhu S, Goudie M, Krishnan M, Jabed A, Marlow G, Narayanan A, Ferguson LR. Environmental factors and risk of aggressive prostate cancer among a population of New Zealand men - a genotypic approach. MOLECULAR BIOSYSTEMS 2017; 13:681-698. [PMID: 28252132 DOI: 10.1039/c6mb00873a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Prostate cancer is one of the most significant health concerns for men worldwide. Numerous researchers carrying out molecular diagnostics have indicated that genetic interactions with biological and behavioral factors play an important role in the overall risk and prognosis of this disease. Single nucleotide polymorphisms (SNPs) are increasingly becoming strong biomarker candidates to identify susceptibility to prostate cancer. We carried out a gene × environment interaction analysis linked to aggressive and non-aggressive prostate cancer (PCa) with a number of SNPs. By using this method, we identified the susceptible alleles in a New Zealand population, and examined the interaction with environmental factors. We have identified a number of SNPs that have risk associations both with and without environmental interaction. The results indicate that certain SNPs are associated with disease vulnerability based on behavioral factors. The list of genes with SNPs identified as being associated with the risk of PCa in a New Zealand population is provided in the graphical abstract.
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Affiliation(s)
- Venkatesh Vaidyanathan
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | - Vijay Naidu
- School of Engineering, Computer and Mathematical Sciences, Auckland University of Technology, Auckland 1010, New Zealand.
| | - Chi Hsiu-Juei Kao
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | | | - Karen S Bishop
- Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | - Alice Wang
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | - Radha Pallati
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand.
| | - Phillip Shepherd
- Sequenom Facility, Liggins Institute, University of Auckland, Auckland 1023, New Zealand.
| | - Jonathan Masters
- Urology Department, Auckland District Health Board, Auckland, New Zealand.
| | - Shuotun Zhu
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | - Megan Goudie
- Urology Department, Auckland District Health Board, Auckland, New Zealand.
| | - Mohanraj Krishnan
- Department of Obstetrics and Gynaecology, FMHS, University of Auckland, Auckland 1023, New Zealand.
| | - Anower Jabed
- Department of Molecular Medicine and Pathology, FM & HS, University of Auckland, Auckland 1023, New Zealand.
| | - Gareth Marlow
- Experimental Cancer Medicine Centre, Cardiff University, Cardiff, CF14 4XN, UK.
| | - Ajit Narayanan
- School of Engineering, Computer and Mathematical Sciences, Auckland University of Technology, Auckland 1010, New Zealand.
| | - Lynnette R Ferguson
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
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21
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Bondagji NS, Morad FA, Al-Nefaei AAA, Khan IA, Elango R, Abdullah LS, M.Al-Mansouri N, Sabir J, Banaganapalli B, Edris S, Shaik NA. Replication of GWAS loci revealed the moderate effect of TNRC6B
locus on susceptibility of Saudi women to develop uterine leiomyomas. J Obstet Gynaecol Res 2016; 43:330-338. [DOI: 10.1111/jog.13217] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/23/2016] [Indexed: 01/31/2023]
Affiliation(s)
- Nabeel Saleem Bondagji
- Department of Obstetrics and Gynecology; King Abdulaziz University Hospital; Jeddah Saudi Arabia
- Department of Pathology; King Abdulaziz University Hospital; Jeddah Saudi Arabia
| | - Fatima Amanullah Morad
- Princess Al-Jawahara Al-Brahim Center of Excellence in Research of Hereditary Disorders; King Abdulaziz University; Jeddah Saudi Arabia
- Genomics and Biotechnology Section, Department of Biological Sciences, Faculty of Science; King Abdulaziz University; Jeddah Saudi Arabia
| | - Afnan Abed Abdullah Al-Nefaei
- Princess Al-Jawahara Al-Brahim Center of Excellence in Research of Hereditary Disorders; King Abdulaziz University; Jeddah Saudi Arabia
- Genomics and Biotechnology Section, Department of Biological Sciences, Faculty of Science; King Abdulaziz University; Jeddah Saudi Arabia
| | - Imran Ali Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences; King Saud University; Riyadh Saudi Arabia
| | - Ramu Elango
- Department of Genetic Medicine; King Abdulaziz University; Jeddah Saudi Arabia
- Princess Al-Jawahara Al-Brahim Center of Excellence in Research of Hereditary Disorders; King Abdulaziz University; Jeddah Saudi Arabia
| | - Layla Saleh Abdullah
- Department of Pathology; King Abdulaziz University Hospital; Jeddah Saudi Arabia
| | - Nisma M.Al-Mansouri
- Department of Obstetrics and Gynecology; King Abdulaziz University Hospital; Jeddah Saudi Arabia
| | - Jamal Sabir
- Genomics and Biotechnology Section, Department of Biological Sciences, Faculty of Science; King Abdulaziz University; Jeddah Saudi Arabia
| | - Babajan Banaganapalli
- Department of Genetic Medicine; King Abdulaziz University; Jeddah Saudi Arabia
- Princess Al-Jawahara Al-Brahim Center of Excellence in Research of Hereditary Disorders; King Abdulaziz University; Jeddah Saudi Arabia
| | - Sherif Edris
- Genomics and Biotechnology Section, Department of Biological Sciences, Faculty of Science; King Abdulaziz University; Jeddah Saudi Arabia
| | - Noor Ahmad Shaik
- Department of Genetic Medicine; King Abdulaziz University; Jeddah Saudi Arabia
- Princess Al-Jawahara Al-Brahim Center of Excellence in Research of Hereditary Disorders; King Abdulaziz University; Jeddah Saudi Arabia
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22
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Abstract
Adhesion G protein-coupled receptors (aGPCRs) have a long evolutionary history dating back to very basal unicellular eukaryotes. Almost every vertebrate is equipped with a set of different aGPCRs. Genomic sequence data of several hundred extinct and extant species allows for reconstruction of aGPCR phylogeny in vertebrates and non-vertebrates in general but also provides a detailed view into the recent evolutionary history of human aGPCRs. Mining these sequence sources with bioinformatic tools can unveil many facets of formerly unappreciated aGPCR functions. In this review, we extracted such information from the literature and open public sources and provide insights into the history of aGPCR in humans. This includes comprehensive analyses of signatures of selection, variability of human aGPCR genes, and quantitative traits at human aGPCR loci. As indicated by a large number of genome-wide genotype-phenotype association studies, variations in aGPCR contribute to specific human phenotypes. Our survey demonstrates that aGPCRs are significantly involved in adaptation processes, phenotype variations, and diseases in humans.
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Affiliation(s)
- Peter Kovacs
- Integrated Research and Treatment Center (IFB) AdiposityDiseases, Medical Faculty, University of Leipzig, Liebigstr. 21, Leipzig, 04103, Germany.
| | - Torsten Schöneberg
- Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, Leipzig, 04103, Germany.
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23
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Turay D, Khan S, Diaz Osterman CJ, Curtis MP, Khaira B, Neidigh JW, Mirshahidi S, Casiano CA, Wall NR. Proteomic Profiling of Serum-Derived Exosomes from Ethnically Diverse Prostate Cancer Patients. Cancer Invest 2015; 34:1-11. [PMID: 26536157 DOI: 10.3109/07357907.2015.1081921] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Prostate cancer (PCa) remains the most frequently diagnosed male malignancy in Western countries and the second most common cause of male cancer death in the United States. The relatively elevated PCa incidence and mortality among African American men makes this cancer type a challenging health disparity disease. To increase the chance for successful trea tment, earlier detection and prediction of tumor aggress iveness will be important and need to be resolved. This study demonstrates that small membrane-bound vesicles shed from the tumor called exosomes contain ethnically and tumor-specific biomarkers, and could be exploited for their diagnostic and therapeutic potential.
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Affiliation(s)
- David Turay
- a Center for Health Disparities & Molecular Medicine , Loma Linda University School of Medicine , Loma Linda , California , USA.,b Department of Basic Science and Division of Biochemistry , Loma Linda University School of Medicine , Loma Linda , California , USA
| | - Salma Khan
- a Center for Health Disparities & Molecular Medicine , Loma Linda University School of Medicine , Loma Linda , California , USA.,b Department of Basic Science and Division of Biochemistry , Loma Linda University School of Medicine , Loma Linda , California , USA
| | - Carlos J Diaz Osterman
- a Center for Health Disparities & Molecular Medicine , Loma Linda University School of Medicine , Loma Linda , California , USA.,b Department of Basic Science and Division of Biochemistry , Loma Linda University School of Medicine , Loma Linda , California , USA
| | - Matthew P Curtis
- b Department of Basic Science and Division of Biochemistry , Loma Linda University School of Medicine , Loma Linda , California , USA
| | - Balreet Khaira
- b Department of Basic Science and Division of Biochemistry , Loma Linda University School of Medicine , Loma Linda , California , USA
| | - Jonathan W Neidigh
- b Department of Basic Science and Division of Biochemistry , Loma Linda University School of Medicine , Loma Linda , California , USA
| | - Saied Mirshahidi
- c Department of Basic Science and Division of Microbiology and Molecular Genetics , Loma Linda University School of Medicine , Loma Linda , California , USA.,d Cancer Center & Biospecimen Laboratory , Loma Linda University School of Medicine , Loma Linda , California , USA
| | - Carlos A Casiano
- a Center for Health Disparities & Molecular Medicine , Loma Linda University School of Medicine , Loma Linda , California , USA.,c Department of Basic Science and Division of Microbiology and Molecular Genetics , Loma Linda University School of Medicine , Loma Linda , California , USA.,e Department of Medicine, Division of Rheumatology , Loma Linda University School of Medicine , Loma Linda , California , USA
| | - Nathan R Wall
- a Center for Health Disparities & Molecular Medicine , Loma Linda University School of Medicine , Loma Linda , California , USA.,b Department of Basic Science and Division of Biochemistry , Loma Linda University School of Medicine , Loma Linda , California , USA
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24
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Kocarnik JM, Park SL, Han J, Dumitrescu L, Cheng I, Wilkens LR, Schumacher FR, Kolonel L, Carlson CS, Crawford DC, Goodloe RJ, Dilks HH, Baker P, Richardson D, Matise TC, Ambite JL, Song F, Qureshi AA, Zhang M, Duggan D, Hutter C, Hindorff L, Bush WS, Kooperberg C, Le Marchand L, Peters U. Pleiotropic and sex-specific effects of cancer GWAS SNPs on melanoma risk in the population architecture using genomics and epidemiology (PAGE) study. PLoS One 2015; 10:e0120491. [PMID: 25789475 PMCID: PMC4366224 DOI: 10.1371/journal.pone.0120491] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 01/22/2015] [Indexed: 11/19/2022] Open
Abstract
Background Several regions of the genome show pleiotropic associations with multiple cancers. We sought to evaluate whether 181 single-nucleotide polymorphisms previously associated with various cancers in genome-wide association studies were also associated with melanoma risk. Methods We evaluated 2,131 melanoma cases and 20,353 controls from three studies in the Population Architecture using Genomics and Epidemiology (PAGE) study (EAGLE-BioVU, MEC, WHI) and two collaborating studies (HPFS, NHS). Overall and sex-stratified analyses were performed across studies. Results We observed statistically significant associations with melanoma for two lung cancer SNPs in the TERT-CLPTM1L locus (Bonferroni-corrected p<2.8x10-4), replicating known pleiotropic effects at this locus. In sex-stratified analyses, we also observed a potential male-specific association between prostate cancer risk variant rs12418451 and melanoma risk (OR=1.22, p=8.0x10-4). No other variants in our study were associated with melanoma after multiple comparisons adjustment (p>2.8e-4). Conclusions We provide confirmatory evidence of pleiotropic associations with melanoma for two SNPs previously associated with lung cancer, and provide suggestive evidence for a male-specific association with melanoma for prostate cancer variant rs12418451. This SNP is located near TPCN2, an ion transport gene containing SNPs which have been previously associated with hair pigmentation but not melanoma risk. Previous evidence provides biological plausibility for this association, and suggests a complex interplay between ion transport, pigmentation, and melanoma risk that may vary by sex. If confirmed, these pleiotropic relationships may help elucidate shared molecular pathways between cancers and related phenotypes.
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Affiliation(s)
- Jonathan M. Kocarnik
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
| | - S. Lani Park
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Jiali Han
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, Indiana, United States of America
| | - Logan Dumitrescu
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Iona Cheng
- Cancer Prevention Institute of California, Fremont, California, United States of America
| | - Lynne R. Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Fredrick R. Schumacher
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Laurence Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Chris S. Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Dana C. Crawford
- Department of Epidemiology, Case Western Reserve University, Cleveland, Ohio, United States of America
- Biostatistics Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Robert J. Goodloe
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Holli H. Dilks
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Paxton Baker
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Danielle Richardson
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Tara C. Matise
- Department of Genetics, Rutgers University, Piscataway, New Jersey, United States of America
| | - José Luis Ambite
- Information Sciences Institute, University of Southern California, Marina del Rey, California, United States of America
| | - Fengju Song
- Department of Epidemiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People’s Republic of China
- Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Abrar A. Qureshi
- Department of Dermatology, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Mingfeng Zhang
- Department of Dermatology, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - David Duggan
- Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Carolyn Hutter
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, NCI, NIH, Bethesda, Maryland, United States of America
| | - Lucia Hindorff
- Division of Genomic Medicine, NHGRI, NIH, Bethesda, Maryland, Untied States of America
| | - William S. Bush
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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25
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Noncoding RNA-related polymorphisms in pediatric acute lymphoblastic leukemia susceptibility. Pediatr Res 2014; 75:767-73. [PMID: 24618566 DOI: 10.1038/pr.2014.43] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 01/01/2014] [Indexed: 01/16/2023]
Abstract
BACKGROUND Evidence for an inherited genetic risk for pediatric acute lymphoblastic leukemia has been provided in several studies. Most of them focused on coding regions. However, those regions represent only 1.5% of the entire genome. In acute lymphoblastic leukemia (ALL), it has been suggested that the expression of microRNAs (miRNAs) is dysregulated, which suggests that they may have a role in ALL risk. Changes in miRNA function may occur through single-nucleotide polymorphisms (SNPs). Therefore, the aim of this study was to evaluate whether polymorphisms in pre-miRNAs, and/or miRNA-processing genes, contribute to a predisposition for childhood ALL. METHODS In this study, we analyzed 118 SNPs in pre-miRNAs and miRNA-processing genes in 213 B-cell ALL patients and 387 controls. RESULTS We found 11 SNPs significantly associated with ALL susceptibility. These included three SNPs present in miRNA genes (miR-612, miR-499, and miR-449b) and eight SNPs present in six miRNA biogenesis pathway genes (TNRC6B, DROSHA, DGCR8, EIF2C1, CNOT1, and CNOT6). Among the 118 SNPs analyzed, rs12803915 in mir-612 and rs3746444 in mir-499 exhibited a more significant association, with a P value <0.01. CONCLUSION The results of this study indicate that SNP rs12803915 located in pre-mir-612, and SNP rs3746444 located in pre-mir-499, may represent novel markers of B-cell ALL susceptibility.
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26
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Pothlichet J, Quintana-Murci L. The genetics of innate immunity sensors and human disease. Int Rev Immunol 2013; 32:157-208. [PMID: 23570315 DOI: 10.3109/08830185.2013.777064] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Since their discovery, innate immunity microbial sensors have been increasingly studied and shown to play a critical role in innate responses to microbes in several experimental in vitro, ex vivo, and animal models. However, their role in the human response to infection in natural conditions has just started to be deciphered, by means of clinical studies of primary immunodeficiencies and epidemiological genetic studies. Here, we summarize the major findings concerning the genetic diversity of the various families of microbial sensors in humans, and of other molecules involved in the signaling pathways they trigger. Specifically, we review the genetic associations, revealed by both clinical and epidemiological genetics studies, of microbial sensors from five different families: Toll-like receptors, C-type lectin receptors, NOD-like receptors, RIG-I-like receptors, and cytosolic DNA sensors. In particular, we consider the relationships between variation at the genes encoding these molecules and susceptibility to and the severity of infectious diseases and other clinical conditions associated with immune dysfunction, including autoimmunity, inflammation, allergy, and cancer. Despite the fact that the genetic links between innate immunity sensors and human disorders remain still limited, human genetics studies are increasingly improving our understanding of the genuine functions of microbial sensors and downstream signaling molecules in the natural setting.
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Affiliation(s)
- Julien Pothlichet
- Institut Pasteur, Unit of Human Evolutionary Genetics, Paris, France
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27
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Kumar A, Rajendran V, Sethumadhavan R, Purohit R. CEP proteins: the knights of centrosome dynasty. PROTOPLASMA 2013; 250:965-983. [PMID: 23456457 DOI: 10.1007/s00709-013-0488-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 02/12/2013] [Indexed: 06/01/2023]
Abstract
Centrosome forms the backbone of cell cycle progression mechanism. Recent debates have occurred regarding the essentiality of centrosome in cell cycle regulation. CEP family protein is the active component of centrosome and plays a vital role in centriole biogenesis and cell cycle progression control. A total of 31 proteins have been categorized into CEP family protein category and many more are under candidate evaluation. Furthermore, by the recent advancements in genomics and proteomics researches, several new CEP proteins have also been characterized. Here we have summarized the importance of CEP family proteins and their regulation mechanism involved in proper cell cycle progression. Further, we have reviewed the detailed molecular mechanism behind the associated pathological phenotypes and the possible therapeutic approaches. Proteins such as CEP57, CEP63, CEP152, CEP164, and CEP215 have been extensively studied with a detailed description of their molecular mechanisms, which are among the primary targets for drug discovery. Moreover, CEP27, CEP55, CEP70, CEP110, CEP120, CEP135, CEP192, CEP250, CEP290, and CEP350 also seem promising for future drug discovery approaches. Since the overview implicates that the overall researches on CEP proteins are not yet able to present significant details required for effective therapeutics development, thus, it is timely to discuss the importance of future investigations in this field.
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Affiliation(s)
- Ambuj Kumar
- Bioinformatics Division, School of Bio Sciences and Technology, Vellore Institute of Technology University, Vellore, 632014, Tamil Nadu, India
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28
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Edwards TL, Michels KA, Hartmann KE, Edwards DRV. BET1L and TNRC6B associate with uterine fibroid risk among European Americans. Hum Genet 2013; 132:943-53. [PMID: 23604678 PMCID: PMC3715562 DOI: 10.1007/s00439-013-1306-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/10/2013] [Indexed: 01/19/2023]
Abstract
Uterine fibroid (UFs) affect 77 % of women by menopause and account for $9.4 billion in healthcare costs each year. Although UFs are heritable, genetic risk is poorly understood. The first genome-wide association study (GWAS) of UFs was recently performed in a Japanese population, with reported genome-wide significance for single nucleotide polymorphisms (SNPs) across three chromosomal regions. We tested these SNPs for association with UFs in US cohorts. Women were enrolled in the Right from the Start (RFTS) cohort and the BioVU DNA repository. UF status in both cohorts was determined by pelvic imaging. We tested 65 candidate and haplotype-tagging SNPs for association with UFs presence using logistic regression in RFTS and the top three GWAS-associated SNPs in BioVU. We also combined association results from both cohorts using meta-analysis. 1,086 European American (EA) cases and 1,549 controls were examined. Two SNP associations replicated [blocked early in transport 1 homolog (BET1L) rs2280543, RFTS-BioVU meta-odds ratio (OR) = 0.67 95 % confidence interval (CI) 0.38-0.96, Q = 0.70, I = 0, p = 6.9 × 10⁻³; trinucleotide repeat containing 6B (TNRC6B) rs12484776, RFTS-BioVU meta-OR = 1.21, 95 % CI 1.07-1.35, Q = 0.24, I = 28.37, p = 8.7 × 10⁻³). Meta-analyses combining evidence from RFTS, BioVU, and prior GWAS showed little heterogeneity in effect sizes across studies, with meta-p values between 7.45 × 10⁻⁸ and 3.89 × 10⁻⁹, which were stronger than prior GWAS and supported associations observed for all previously identified loci. These data suggest common variants increase risk for UF in both EA and Japanese populations. However, further research is needed to assess the role of these genes across other racial groups.
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Affiliation(s)
- Todd L. Edwards
- Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, Tennessee
- Institute for Medicine and Public Health, Vanderbilt University, Nashville, Tennessee
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee
- Division of Epidemiology, Department of Medicine, Vanderbilt University, Nashville, TN
| | - Kara A. Michels
- Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, Tennessee
- Institute for Medicine and Public Health, Vanderbilt University, Nashville, Tennessee
- Department of Obstetrics and Gynecology, Vanderbilt University, Nashville, TN
| | - Katherine E. Hartmann
- Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, Tennessee
- Institute for Medicine and Public Health, Vanderbilt University, Nashville, Tennessee
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee
- Department of Obstetrics and Gynecology, Vanderbilt University, Nashville, TN
| | - Digna R. Velez Edwards
- Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, Tennessee
- Institute for Medicine and Public Health, Vanderbilt University, Nashville, Tennessee
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee
- Department of Obstetrics and Gynecology, Vanderbilt University, Nashville, TN
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29
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Eph receptors and their ligands: promising molecular biomarkers and therapeutic targets in prostate cancer. Biochim Biophys Acta Rev Cancer 2013; 1835:243-57. [PMID: 23396052 DOI: 10.1016/j.bbcan.2013.01.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 01/21/2013] [Accepted: 01/25/2013] [Indexed: 01/01/2023]
Abstract
Although at present, there is a high incidence of prostate cancer, particularly in the Western world, mortality from this disease is declining and occurs primarily only from clinically significant late stage tumors with a poor prognosis. A major current focus of this field is the identification of new biomarkers which can detect earlier, and more effectively, clinically significant tumors from those deemed "low risk", as well as predict the prognostic course of a particular cancer. This strategy can in turn offer novel avenues for targeted therapies. The large family of Receptor Tyrosine Kinases, the Ephs, and their binding partners, the ephrins, has been implicated in many cancers of epithelial origin through stimulation of oncogenic transformation, tumor angiogenesis, and promotion of increased cell survival, invasion and migration. They also show promise as both biomarkers of diagnostic and prognostic value and as targeted therapies in cancer. This review will briefly discuss the complex roles and biological mechanisms of action of these receptors and ligands and, with regard to prostate cancer, highlight their potential as biomarkers for both diagnosis and prognosis, their application as imaging agents, and current approaches to assessing them as therapeutic targets. This review demonstrates the need for future studies into those particular family members that will prove helpful in understanding the biology and potential as targets for treatment of prostate cancer.
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30
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Garnier S, Truong V, Brocheton J, Zeller T, Rovital M, Wild PS, Ziegler A, Munzel T, Tiret L, Blankenberg S, Deloukas P, Erdmann J, Hengstenberg C, Samani NJ, Schunkert H, Ouwehand WH, Goodall AH, Cambien F, Trégouët DA. Genome-wide haplotype analysis of cis expression quantitative trait loci in monocytes. PLoS Genet 2013; 9:e1003240. [PMID: 23382694 PMCID: PMC3561129 DOI: 10.1371/journal.pgen.1003240] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2012] [Accepted: 11/27/2012] [Indexed: 11/19/2022] Open
Abstract
In order to assess whether gene expression variability could be influenced by several SNPs acting in cis, either through additive or more complex haplotype effects, a systematic genome-wide search for cis haplotype expression quantitative trait loci (eQTL) was conducted in a sample of 758 individuals, part of the Cardiogenics Transcriptomic Study, for which genome-wide monocyte expression and GWAS data were available. 19,805 RNA probes were assessed for cis haplotypic regulation through investigation of ~2,1 × 10(9) haplotypic combinations. 2,650 probes demonstrated haplotypic p-values >10(4)-fold smaller than the best single SNP p-value. Replication of significant haplotype effects were tested for 412 probes for which SNPs (or proxies) that defined the detected haplotypes were available in the Gutenberg Health Study composed of 1,374 individuals. At the Bonferroni correction level of 1.2 × 10(-4) (~0.05/412), 193 haplotypic signals replicated. 1000 G imputation was then conducted, and 105 haplotypic signals still remained more informative than imputed SNPs. In-depth analysis of these 105 cis eQTL revealed that at 76 loci genetic associations were compatible with additive effects of several SNPs, while for the 29 remaining regions data could be compatible with a more complex haplotypic pattern. As 24 of the 105 cis eQTL have previously been reported to be disease-associated loci, this work highlights the need for conducting haplotype-based and 1000 G imputed cis eQTL analysis before commencing functional studies at disease-associated loci.
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Affiliation(s)
- Sophie Garnier
- INSERM, UMR_S 937, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
- ICAN Institute for Cardiometabolism and Nutrition, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
| | - Vinh Truong
- INSERM, UMR_S 937, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
- ICAN Institute for Cardiometabolism and Nutrition, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
| | - Jessy Brocheton
- INSERM, UMR_S 937, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
| | - Tanja Zeller
- Department of General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, Germany
| | - Maxime Rovital
- INSERM, UMR_S 937, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
| | - Philipp S. Wild
- Department of Medicine II, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Andreas Ziegler
- Institut für Medizinische Biometrie und Statistik, Universität Lübeck, Lübeck, Germany
| | | | - Thomas Munzel
- Department of Medicine II, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Laurence Tiret
- INSERM, UMR_S 937, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
- ICAN Institute for Cardiometabolism and Nutrition, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
| | - Stefan Blankenberg
- Department of General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, Germany
| | - Panos Deloukas
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Christian Hengstenberg
- Klinik und Poliklinik für Innere Medizin II, Universität Regensburg, Regensburg, Germany
| | - Nilesh J. Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, United Kingdom
| | | | - Willem H. Ouwehand
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Haematology, University of Cambridge and National Health Service Blood and Transplant, Cambridge, United Kingdom
| | - Alison H. Goodall
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, United Kingdom
| | - François Cambien
- INSERM, UMR_S 937, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
- ICAN Institute for Cardiometabolism and Nutrition, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
| | - David-Alexandre Trégouët
- INSERM, UMR_S 937, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
- ICAN Institute for Cardiometabolism and Nutrition, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
- * E-mail:
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31
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Computational centrosomics: An approach to understand the dynamic behaviour of centrosome. Gene 2012; 511:125-6. [DOI: 10.1016/j.gene.2012.09.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Revised: 08/10/2012] [Accepted: 09/12/2012] [Indexed: 12/30/2022]
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32
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Marthick JR, Dickinson JL. Emerging putative biomarkers: the role of alpha 2 and 6 integrins in susceptibility, treatment, and prognosis. Prostate Cancer 2012; 2012:298732. [PMID: 22900191 PMCID: PMC3415072 DOI: 10.1155/2012/298732] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 05/17/2012] [Indexed: 11/22/2022] Open
Abstract
The genetic architecture underpinning prostate cancer is complex, polygenic and despite recent significant advances many questions remain. Advances in genetic technologies have greatly improved our ability to identify genetic variants associated with complex disease including prostate cancer. Genome-wide association studies (GWASs) and microarray gene expression studies have identified genetic associations with prostate cancer susceptibility and tumour development. The integrins feature prominently in both studies examining the underlying genetic susceptibility and mechanisms driving prostate tumour development. Integrins are cell adhesion molecules involved in extracellular and intracellular signalling and are imperative for tumour development, migration, and angiogenesis. Although several integrins have been implicated in tumour development, the roles of integrin α(2) and integrin α(6) are the focus of this paper as evidence is now emerging that these integrins are implicit in prostate cancer susceptibility, cancer stem cell biology, angiogenesis, cell migration, and metastases to bone and represent potential biomarkers and therapeutic targets. There currently exists an urgent need to develop tools that differentiate indolent from aggressive prostate cancers and predict how patients will respond to treatment. This paper outlines the evidence supporting the use of α(2) and α(6) integrins in clinical applications for tailored patient treatment.
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Affiliation(s)
- James R. Marthick
- Menzies Research Institute Tasmania, University of Tasmania, 17 Liverpool Street Hobart, TAS 7000, Australia
| | - Joanne L. Dickinson
- Menzies Research Institute Tasmania, University of Tasmania, 17 Liverpool Street Hobart, TAS 7000, Australia
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