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Barker R, Biernacka K, Kingshott G, Sewell A, Gwiti P, Martin RM, Lane JA, McGeagh L, Koupparis A, Rowe E, Oxley J, Perks CM, Holly JMP. Associations of CTCF and FOXA1 with androgen and IGF pathways in men with localized prostate cancer. Growth Horm IGF Res 2023; 69-70:101533. [PMID: 37086646 DOI: 10.1016/j.ghir.2023.101533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/30/2023] [Accepted: 04/07/2023] [Indexed: 04/24/2023]
Abstract
AIMS To examine associations between the transcription factors CCCTC-binding factor (CTCF) and forkhead box protein A1 (FOXA1) and the androgen receptor (AR) and their association with components of the insulin-like growth factor (IGF)-pathway in a cohort of men with localized prostate cancer. METHODS Using prostate tissue samples collected during the Prostate cancer: Evidence of Exercise and Nutrition Trial (PrEvENT) trial (N = 70 to 92, depending on section availability), we assessed the abundance of CTCF, FOXA1, AR, IGFIR, p-mTOR, PTEN and IGFBP-2 proteins using a modified version of the Allred scoring system. Validation studies were performed using large, publicly available datasets (TCGA) (N = 489). RESULTS We identified a strong correlation between CTCF and AR staining with benign prostate tissue. CTCF also strongly associated with the IGFIR, with PTEN and with phospho-mTOR. FOXA1 was also correlated with staining for the IGF-IR, with IGFBP-2 and with staining for activated phosphor-mTOR. The staining for the IGF-IR was strongly correlated with the AR. CONCLUSION Our findings emphasise the close and complex links between the endocrine controls, well known to play an important role in prostate cancer, and the transcription factors implicated by the recent genetic evidence.
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Affiliation(s)
- Rachel Barker
- IGF & Metabolic Endocrinology Group, Translational Health Sciences, Bristol Medical School, Learning & Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - Kalina Biernacka
- IGF & Metabolic Endocrinology Group, Translational Health Sciences, Bristol Medical School, Learning & Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - Georgina Kingshott
- IGF & Metabolic Endocrinology Group, Translational Health Sciences, Bristol Medical School, Learning & Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - Alex Sewell
- Department of Cellular Pathology, North Bristol NHS Trust, Southmead Hospital, Bristol BS10 5NB, UK
| | - Paida Gwiti
- Department of Cellular Pathology, North Bristol NHS Trust, Southmead Hospital, Bristol BS10 5NB, UK; Department of Pathology, North West Anglia NHS Foundation Trust, Peterborough PE3 9GZ, UK
| | - Richard M Martin
- Population Health Sciences, Bristol Medical School, University of Bristol, Canynge Hall, 39 Whatley Road, Bristol BS8 2PS, UK; National Institute for Health Research, Biomedical Research Centre at University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Biomedical Research Unit Offices, University Hospitals Bristol Education Centre, Dental Hospital, Lower Maudlin Street, Bristol BS1 2LY, UK
| | - J Athene Lane
- Bristol Trials Centre, Population Health Sciences, Bristol Medical School, University of Bristol, Canynge Hall, 39 Whatley Road, Bristol BS8 2PS, UK
| | - Lucy McGeagh
- Supportive Cancer Care Research Group, Faculty of Health and Life Sciences, Oxford Institute of Nursing, Midwifery and Allied Health Research, Oxford Brookes University, Jack Straws Lane, Marston, Oxford OX3 0FL, UK
| | - Anthony Koupparis
- Department of Urology, Bristol Urological Institute, Southmead Hospital, Bristol BS10 5NB, UK
| | - Edward Rowe
- Department of Urology, Bristol Urological Institute, Southmead Hospital, Bristol BS10 5NB, UK
| | - Jon Oxley
- Department of Cellular Pathology, North Bristol NHS Trust, Southmead Hospital, Bristol BS10 5NB, UK
| | - Claire M Perks
- IGF & Metabolic Endocrinology Group, Translational Health Sciences, Bristol Medical School, Learning & Research Building, Southmead Hospital, Bristol BS10 5NB, UK.
| | - Jeff M P Holly
- IGF & Metabolic Endocrinology Group, Translational Health Sciences, Bristol Medical School, Learning & Research Building, Southmead Hospital, Bristol BS10 5NB, UK
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2
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Labani M, Beheshti A, Argha A, Alinejad-Rokny H. A Comprehensive Investigation of Genomic Variants in Prostate Cancer Reveals 30 Putative Regulatory Variants. Int J Mol Sci 2023; 24:ijms24032472. [PMID: 36768794 PMCID: PMC9916892 DOI: 10.3390/ijms24032472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
Prostate cancer (PC) is the most frequently diagnosed non-skin cancer in the world. Previous studies have shown that genomic alterations represent the most common mechanism for molecular alterations responsible for the development and progression of PC. This highlights the importance of identifying functional genomic variants for early detection in high-risk PC individuals. Great efforts have been made to identify common protein-coding genetic variations; however, the impact of non-coding variations, including regulatory genetic variants, is not well understood. Identification of these variants and the underlying target genes will be a key step in improving the detection and treatment of PC. To gain an understanding of the functional impact of genetic variants, and in particular, regulatory variants in PC, we developed an integrative pipeline (AGV) that uses whole genome/exome sequences, GWAS SNPs, chromosome conformation capture data, and ChIP-Seq signals to investigate the potential impact of genomic variants on the underlying target genes in PC. We identified 646 putative regulatory variants, of which 30 significantly altered the expression of at least one protein-coding gene. Our analysis of chromatin interactions data (Hi-C) revealed that the 30 putative regulatory variants could affect 131 coding and non-coding genes. Interestingly, our study identified the 131 protein-coding genes that are involved in disease-related pathways, including Reactome and MSigDB, for most of which targeted treatment options are currently available. Notably, our analysis revealed several non-coding RNAs, including RP11-136K7.2 and RAMP2-AS1, as potential enhancer elements of the protein-coding genes CDH12 and EZH1, respectively. Our results provide a comprehensive map of genomic variants in PC and reveal their potential contribution to prostate cancer progression and development.
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Affiliation(s)
- Mahdieh Labani
- BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
- Data Analytic Lab, Department of Computing, Macquarie University, Sydney, NSW 2109, Australia
| | - Amin Beheshti
- Data Analytic Lab, Department of Computing, Macquarie University, Sydney, NSW 2109, Australia
| | - Ahmadreza Argha
- The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Hamid Alinejad-Rokny
- BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
- UNSW Data Science Hub, The University of New South Wales, Sydney, NSW 2052, Australia
- Health Data Analytics Program, Centre for Applied AI, Macquarie University, Sydney, NSW 2109, Australia
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Kneppers J, Severson TM, Siefert JC, Schol P, Joosten SEP, Yu IPL, Huang CCF, Morova T, Altıntaş UB, Giambartolomei C, Seo JH, Baca SC, Carneiro I, Emberly E, Pasaniuc B, Jerónimo C, Henrique R, Freedman ML, Wessels LFA, Lack NA, Bergman AM, Zwart W. Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential. Nat Commun 2022; 13:7367. [PMID: 36450752 PMCID: PMC9712620 DOI: 10.1038/s41467-022-35135-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022] Open
Abstract
Androgen receptor (AR) drives prostate cancer (PCa) development and progression. AR chromatin binding profiles are highly plastic and form recurrent programmatic changes that differentiate disease stages, subtypes and patient outcomes. While prior studies focused on concordance between patient subgroups, inter-tumor heterogeneity of AR enhancer selectivity remains unexplored. Here we report high levels of AR chromatin binding heterogeneity in human primary prostate tumors, that overlap with heterogeneity observed in healthy prostate epithelium. Such heterogeneity has functional consequences, as somatic mutations converge on commonly-shared AR sites in primary over metastatic tissues. In contrast, less-frequently shared AR sites associate strongly with AR-driven gene expression, while such heterogeneous AR enhancer usage also distinguishes patients' outcome. These findings indicate that epigenetic heterogeneity in primary disease is directly informative for risk of biochemical relapse. Cumulatively, our results illustrate a high level of AR enhancer heterogeneity in primary PCa driving differential expression and clinical impact.
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Affiliation(s)
- Jeroen Kneppers
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tesa M Severson
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Joseph C Siefert
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Pieter Schol
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Stacey E P Joosten
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ivan Pak Lok Yu
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Chia-Chi Flora Huang
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Tunç Morova
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | | | - Claudia Giambartolomei
- Central RNA Lab, Istituto Italiano di Tecnologia, Genova, Italy
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, USA
| | - Ji-Heui Seo
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, USA
- The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, USA
| | - Sylvan C Baca
- The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, USA
| | - Isa Carneiro
- Department of Pathology, Cancer Biology and Epigenetics Group, Portuguese Oncology Institute of Porto and Porto Comprehensive Cancer Center, Porto, Portugal
| | - Eldon Emberly
- Department of Physics, Simon Fraser University, Burnaby, Canada
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, USA
| | - Carmen Jerónimo
- Department of Pathology, Cancer Biology and Epigenetics Group, Portuguese Oncology Institute of Porto and Porto Comprehensive Cancer Center, Porto, Portugal
| | - Rui Henrique
- Department of Pathology, Cancer Biology and Epigenetics Group, Portuguese Oncology Institute of Porto and Porto Comprehensive Cancer Center, Porto, Portugal
| | - Matthew L Freedman
- The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, USA
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, USA
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Nathan A Lack
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
- School of Medicine, Koç University, Istanbul, Turkey
- Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Istanbul, Turkey
| | - Andries M Bergman
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
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4
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Kneppers J, Bergman AM, Zwart W. Prostate Cancer Epigenetic Plasticity and Enhancer Heterogeneity: Molecular Causes, Consequences and Clinical Implications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1390:255-275. [DOI: 10.1007/978-3-031-11836-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
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Zhang W, Nicholson T, Zhang K. Deciphering the polygenic basis of racial disparities in prostate cancer by an integrative analysis of genomic and transcriptomic data. Cancer Prev Res (Phila) 2021; 15:161-171. [PMID: 34965922 DOI: 10.1158/1940-6207.capr-21-0406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/22/2021] [Accepted: 12/22/2021] [Indexed: 11/16/2022]
Abstract
Prostate cancer (PCa) prevalence in African Americans (AAs) is over 1.5 times the prevalence in European Americans (EAs). Among over a hundred index risk SNPs for PCa, only a few can be verified using the available AAs' data. Their relevance to the prevalence inequality and other racial disparities has not been fully determined. We investigated this issue by an integrative analysis of five public datasets. We categorized the datasets into two classes. The training class consisted of the datasets generated by three genome-wide association studies. The test class contained the TCGA prostate carcinoma data and the data of African and European super-populations in the 1000-Genome project. The polygenic risk scores (PRS) of test samples for cancer occurrence were calculated according to the effects of genetic variants estimated from the training samples. We obtained the following findings. Africans' PRSs are higher than Europeans' scores (p << 0.01); AA patients' PRSs are higher than EA patients' scores (p<3×10-9); the patients with tumors presenting fusion or abnormal expression in ERG and other ETS family genes have lower PRSs than the patients without such aberrations (p < 7×10-5); five tumor progression-related genes have the expression levels being significantly correlated with PRS (FDR<0.01). Additional simulation analysis shows that the high PCa prevalence in African populations makes it challenging to identify individual risk variants using African men's data. The index risk SNPs-based PRS is compatible with the observed racial disparity in PCa prevalence and ETS abnormal cancers may be less heritable compared to other subtypes.
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Affiliation(s)
- Wensheng Zhang
- Xavier NIH RCMI Center of Cancer Research, Xavier Univ. of Louisana
| | | | - Kun Zhang
- Xavier NIH RCMI Center of Cancer Research, Xavier University of Louisiana
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Tian P, Zhong M, Wei GH. Mechanistic insights into genetic susceptibility to prostate cancer. Cancer Lett 2021; 522:155-163. [PMID: 34560228 DOI: 10.1016/j.canlet.2021.09.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022]
Abstract
Prostate cancer (PCa) is the second most common cancer in men and is a highly heritable disease that affects millions of individuals worldwide. Genome-wide association studies have to date discovered nearly 270 genetic loci harboring hundreds of single nucleotide polymorphisms (SNPs) that are associated with PCa susceptibility. In contrast, the functional characterization of the mechanisms underlying PCa risk association is still growing. Given that PCa risk-associated SNPs are highly enriched in noncoding cis-regulatory genomic regions, accumulating evidence suggests a widespread modulation of transcription factor chromatin binding and allelic enhancer activity by these noncoding SNPs, thereby dysregulating gene expression. Emerging studies have shown that a proportion of noncoding variants can modulate the formation of transcription factor complexes at enhancers and CTCF-mediated 3D genome architecture. Interestingly, DNA methylation-regulated CTCF binding could orchestrate a long-range chromatin interaction between PCa risk enhancer and causative genes. Additionally, one-causal-variant-two-risk genes or multiple-risk-variant-multiple-genes are prevalent in some PCa risk-associated loci. In this review, we will discuss the current understanding of the general principles of SNP-mediated gene regulation, experimental advances, and functional evidence supporting the mechanistic roles of several PCa genetic loci with potential clinical impact on disease prevention and treatment.
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Affiliation(s)
- Pan Tian
- Fudan University Shanghai Cancer Center; Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Mengjie Zhong
- Fudan University Shanghai Cancer Center; Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Gong-Hong Wei
- Fudan University Shanghai Cancer Center; Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
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7
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Tian Y, Soupir A, Liu Q, Wu L, Huang CC, Park JY, Wang L. Novel role of prostate cancer risk variant rs7247241 on PPP1R14A isoform transition through allelic TF binding and CpG methylation. Hum Mol Genet 2021; 31:1610-1621. [PMID: 34849858 DOI: 10.1093/hmg/ddab347] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/21/2022] Open
Abstract
Although previous studies identified numerous single nucleotide polymorphisms (SNPs) and their target genes predisposed to prostate cancer (PrCa) risks, SNP-related splicing associations are rarely reported. In this study, we applied distance-based sQTL analysis (sQTLseekeR) using RNA-seq and SNP genotype data from benign prostate tissue (n = 467), and identified significant associations in 3344 SNP-transcript pairs (P ≤ 0.05) at PrCa risk loci. We characterized a common SNP (rs7247241) and its target gene (PPP1R14A) located in chr19q13, a sQTL with risk allele T associated with upregulation of long isoform (P = 9.99E-7). We confirmed the associations in both TCGA (P = 2.42E-24) and GTEX prostate cohorts (P = 9.08E-78). To functionally characterize this SNP, we performed chromatin Immunoprecipitation qPCR and confirmed stronger CTCF and PLAGL2 binding in rs7247241 C than T allele. We found that CTCF binding enrichment was negatively associated with methylation level at the SNP site in human cell lines (r = -0.58). Bisulfite sequencing showed consistent association of rs7247241-T allele with nearby sequence CpG hypermethylation in prostate cell lines and tissues. Importantly, the methylation level at CpG sites nearest to the CTCF binding and first exon splice-in (ψ) of PPP1R14A were significantly associated with aggressive phenotype in the TCGA PrCa cohort. Meanwhile, the long isoform of the gene also promoted cell proliferation. Taken together, with the most updated gene annotations, we reported a set of sQTL associated with multiple traits related to human prostate diseases, and revealed a unique role of PrCa risk SNP rs7247241 on PPP1R14A isoform transition.
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Affiliation(s)
- Yijun Tian
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, United States
| | - Alex Soupir
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, United States
| | - Qian Liu
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, United States
| | - Lang Wu
- Division of Cancer Epidemiology, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii, HI, 96822, United States
| | - Chiang-Ching Huang
- Joseph J. Zilber School of Public Health, University of Wisconsin, Milwaukee, WI, 53226, United States
| | - Jong Y Park
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, United States
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, United States
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8
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Ren N, Liu Q, Yan L, Huang Q. Parallel Reporter Assays Identify Altered Regulatory Role of rs684232 in Leading to Prostate Cancer Predisposition. Int J Mol Sci 2021; 22:8792. [PMID: 34445492 PMCID: PMC8395720 DOI: 10.3390/ijms22168792] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/07/2021] [Accepted: 08/13/2021] [Indexed: 02/06/2023] Open
Abstract
Functional characterization of cancer risk-associated single nucleotide polymorphism (SNP) identified by genome-wide association studies (GWAS) has become a big challenge. To identify the regulatory risk SNPs that can lead to transcriptional misregulation, we performed parallel reporter gene assays with both alleles of 213 prostate cancer risk-associated GWAS SNPs in 22Rv1 cells. We disclosed 32 regulatory SNPs that exhibited different regulatory activities with two alleles. For one of the regulatory SNPs, rs684232, we found that the variation altered chromatin binding of transcription factor FOXA1 on the DNA region and led to aberrant gene expression of VPS53, FAM57A, and GEMIN4, which play vital roles in prostate cancer malignancy. Our findings reveal the roles and underlying mechanism of rs684232 in prostate cancer progression and hold great promise in benefiting prostate cancer patients with prognostic prediction and target therapies.
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Affiliation(s)
| | | | | | - Qilai Huang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao 266237, China; (N.R.); (Q.L.); (L.Y.)
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Zhang W, Dong Y, Sartor O, Zhang K. Comprehensive Analysis of Multiple Cohort Datasets Deciphers the Utility of Germline Single-Nucleotide Polymorphisms in Prostate Cancer Diagnosis. Cancer Prev Res (Phila) 2021; 14:741-752. [PMID: 33866309 DOI: 10.1158/1940-6207.capr-20-0534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 02/09/2021] [Accepted: 04/14/2021] [Indexed: 11/16/2022]
Abstract
Prostate cancer susceptibility is a polygenic trait. We aimed to examine the controversial diagnostic utility of single-nucleotide polymorphisms (SNP) for prostate cancer. We analyzed two datasets collected from Europeans and one from Africans. These datasets were generated by the genome-wide association studies, that is, CGEMS, BPC3, and MEC-Africans, respectively. About 540,000 SNPs, including 61 risk markers that constitute a panel termed MK-61, were commonly genotyped. For each dataset, we augmented the MK-61 panel to generate an MK-61+ one by adding several thousands of SNPs that were moderately associated with prostate cancer occurrence in external dataset(s). We assessed the diagnostic utility of both panels by measuring their predictive strength for prostate cancer occurrence with AUC statistics. We calculated the theoretical AUCs using quantitative genetics model-based formulae and obtained the empirical estimates via 10-fold cross-validation using statistical and machine learning techniques. For the MK-61 panel, the 95% confidence intervals of the theoretical AUCs (AUC-CI.95) were 0.578-0.655, 0.596-0.656, and 0.539-0.596 in the CGEMS, BPC3, and MEC-Africans cohorts, respectively. For the MK-61+ panels, the corresponding AUC-CI.95 were 0.617-0.663, 0.527-0.736, and 0.547-0.565. The empirical AUCs largely fell within the theoretical interval. A promising result (AUC = 0.703, FNR = 0.354, FPR = 0.353) was obtained in the BPC3 cohort when the MK-61+ panel was used. In the CGEMS cohort, the MK-61+ panel complemented PSA in predicting the disease status of PSA ≥ 2.0 ng/mL samples. This study demonstrates that augmented risk SNP panels can enhance prostate cancer prediction for males of European ancestry, especially those with [Formula: see text]ng/mL. PREVENTION RELEVANCE: This study demonstrates that augmented risk SNP panels can enhance prostate cancer prediction for males of European ancestry, especially those with PSA ≥ 2 ng/mL.
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Affiliation(s)
- Wensheng Zhang
- Bioinformatics Core of Xavier NIH RCMI Center of Cancer Research, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Yan Dong
- Department of Structural and Cellular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Oliver Sartor
- Department of Medicine, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Kun Zhang
- Bioinformatics Core of Xavier NIH RCMI Center of Cancer Research, Xavier University of Louisiana, New Orleans, LA 70125, USA. .,Department of Computer Science, Xavier University of Louisiana, New Orleans, LA 70125, USA
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Lozano-Lorca M, Olmedo-Requena R, Vega-Galindo MV, Vázquez-Alonso F, Jiménez-Pacheco A, Salcedo-Bellido I, Sánchez MJ, Jiménez-Moleón JJ. Night Shift Work, Chronotype, Sleep Duration, and Prostate Cancer Risk: CAPLIFE Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E6300. [PMID: 32872503 PMCID: PMC7503878 DOI: 10.3390/ijerph17176300] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 12/25/2022]
Abstract
To analyze the association between prostate cancer (PCa) risk and night shift work, chronotype, and sleep duration in the context of a population-based case-control study of incident prostate cancer in Spain, a total of 465 PCa cases and 410 controls were analyzed. Selection criteria were: (i) age 40-80 years, and (ii) residence in the coverage area of the reference hospitals for ≥6 months before recruitment. Exposure variables were: (i) night shift work (permanent or rotating); (ii) chronotype: morning, neither, or evening (Munich ChronoType Questionnaire) and (iii) sleep duration according to the recommendations of the American National Sleep Foundation. PCa aggressiveness was determined according to the International Society of Urology Pathology classification. Adjusted odds ratios (aOR) and 95% confidence intervals (95% CI) were estimated using logistic regression models. Night shift work was associated with PCa, aOR = 1.47 (95% CI 1.02-2.11), especially for rotating night shifts, aOR = 1.73 (95% CI 1.09-2.75). The magnitude of the association between ever night work and PCa was higher in evening subjects with aOR = 3.14 (95% CI 0.91-10.76) than in morning chronotypes with an aOR = 1.25 (95% CI 0.78-2.00). Working night shifts, especially rotating night shifts, could increase PCa risk. This risk may be higher in people with an evening chronotype.
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Affiliation(s)
- Macarena Lozano-Lorca
- Universidad de Granada, Departamento de Medicina Preventiva y Salud Pública, 18016 Granada, Spain; (M.L.-L.); (I.S.-B.); (M.-J.S.); (J.-J.J.-M.)
- Instituto de Investigación Biosanitaria (ibs.GRANADA), 18014 Granada, Spain
| | - Rocío Olmedo-Requena
- Universidad de Granada, Departamento de Medicina Preventiva y Salud Pública, 18016 Granada, Spain; (M.L.-L.); (I.S.-B.); (M.-J.S.); (J.-J.J.-M.)
- Instituto de Investigación Biosanitaria (ibs.GRANADA), 18014 Granada, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | | | | | | | - Inmaculada Salcedo-Bellido
- Universidad de Granada, Departamento de Medicina Preventiva y Salud Pública, 18016 Granada, Spain; (M.L.-L.); (I.S.-B.); (M.-J.S.); (J.-J.J.-M.)
- Instituto de Investigación Biosanitaria (ibs.GRANADA), 18014 Granada, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - María-José Sánchez
- Universidad de Granada, Departamento de Medicina Preventiva y Salud Pública, 18016 Granada, Spain; (M.L.-L.); (I.S.-B.); (M.-J.S.); (J.-J.J.-M.)
- Instituto de Investigación Biosanitaria (ibs.GRANADA), 18014 Granada, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Andalusian School of Public Health (EASP), 18011 Granada, Spain
| | - José-Juan Jiménez-Moleón
- Universidad de Granada, Departamento de Medicina Preventiva y Salud Pública, 18016 Granada, Spain; (M.L.-L.); (I.S.-B.); (M.-J.S.); (J.-J.J.-M.)
- Instituto de Investigación Biosanitaria (ibs.GRANADA), 18014 Granada, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
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11
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Rocío OR, Macarena LL, Inmaculada SB, Antonio JP, Fernando VA, Marta GC, María-José S, José-Juan JM. Compliance with the 2018 World Cancer Research Fund/American Institute for Cancer Research Cancer Prevention Recommendations and Prostate Cancer. Nutrients 2020; 12:nu12030768. [PMID: 32183345 PMCID: PMC7146507 DOI: 10.3390/nu12030768] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/01/2020] [Accepted: 03/11/2020] [Indexed: 12/16/2022] Open
Abstract
The etiology of prostate cancer (PCa) remains largely unknown. Compliance with the 2018 World Cancer Research Fund/American Institute for Cancer Research (WCRC/AICR) cancer prevention recommendations and its relationship to PCa was evaluated. A total of 398 incident PCa cases and 302 controls were included. The selection criteria for both cases and controls were: (i) age between 40-80 years; and (ii) residence in the coverage area of the reference hospitals for 6 months or more prior to recruitment. A score to measure the compliance with the recommendations of 2018 WCRC/AICR criteria was built. The level of compliance was used as a continuous variable and categorized in terciles. The aggressiveness of PCa was determined according to the ISUP classification. Adjusted odds ratios (aOR) and their 95% confidence intervals (95% CI) were estimated using multivariable logistic regression models. A slight protective tendency was observed between the level of compliance with the preventive recommendations and PCa risk, aOR = 0.81 (95% CI 0.69-0.96) for the total cases of PCa. This association also was observed when the aggressiveness was considered. In addition, limiting consumption of "fast foods", sugar-sweetened drinks, and alcohol were independently associated with lower risk of PCa.
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Affiliation(s)
- Olmedo-Requena Rocío
- Department of Preventive Medicine and Public Health, University of Granada, 18016 Granada, Spain; (L.-L.M.); (S.-B.I.); (S.M.-J.); (J.-M.J.-J.)
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Instituto de Investigación Biosanitaria (ibs.GRANADA), 18014 Granada, Spain
- Correspondence: ; Tel.: +34-958243543
| | - Lozano-Lorca Macarena
- Department of Preventive Medicine and Public Health, University of Granada, 18016 Granada, Spain; (L.-L.M.); (S.-B.I.); (S.M.-J.); (J.-M.J.-J.)
- Instituto de Investigación Biosanitaria (ibs.GRANADA), 18014 Granada, Spain
| | - Salcedo-Bellido Inmaculada
- Department of Preventive Medicine and Public Health, University of Granada, 18016 Granada, Spain; (L.-L.M.); (S.-B.I.); (S.M.-J.); (J.-M.J.-J.)
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Instituto de Investigación Biosanitaria (ibs.GRANADA), 18014 Granada, Spain
| | | | | | - García-Caballos Marta
- Cartuja Primary Health Care Centre, Distrito Sanitario Granada-Metropolitano, 18013 Granada, Spain;
| | - Sánchez María-José
- Department of Preventive Medicine and Public Health, University of Granada, 18016 Granada, Spain; (L.-L.M.); (S.-B.I.); (S.M.-J.); (J.-M.J.-J.)
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Instituto de Investigación Biosanitaria (ibs.GRANADA), 18014 Granada, Spain
- Andalusian School of Public Health (EASP), 18011 Granada, Spain
| | - Jiménez-Moleón José-Juan
- Department of Preventive Medicine and Public Health, University of Granada, 18016 Granada, Spain; (L.-L.M.); (S.-B.I.); (S.M.-J.); (J.-M.J.-J.)
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Instituto de Investigación Biosanitaria (ibs.GRANADA), 18014 Granada, Spain
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12
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Mazrooei P, Kron KJ, Zhu Y, Zhou S, Grillo G, Mehdi T, Ahmed M, Severson TM, Guilhamon P, Armstrong NS, Huang V, Yamaguchi TN, Fraser M, van der Kwast T, Boutros PC, He HH, Bergman AM, Bristow RG, Zwart W, Lupien M. Cistrome Partitioning Reveals Convergence of Somatic Mutations and Risk Variants on Master Transcription Regulators in Primary Prostate Tumors. Cancer Cell 2019; 36:674-689.e6. [PMID: 31735626 DOI: 10.1016/j.ccell.2019.10.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 08/02/2019] [Accepted: 10/17/2019] [Indexed: 12/26/2022]
Abstract
Thousands of noncoding somatic single-nucleotide variants (SNVs) of unknown function are reported in tumors. Partitioning the genome according to cistromes reveals the enrichment of somatic SNVs in prostate tumors as opposed to adjacent normal tissue cistromes of master transcription regulators, including AR, FOXA1, and HOXB13. This parallels enrichment of prostate cancer genetic predispositions over these transcription regulators' tumor cistromes, exemplified at the 8q24 locus harboring both risk variants and somatic SNVs in cis-regulatory elements upregulating MYC expression. However, Massively Parallel Reporter Assays reveal that few SNVs can alter the transactivation potential of individual cis-regulatory elements. Instead, similar to inherited risk variants, SNVs accumulate in cistromes of master transcription regulators required for prostate cancer development.
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Affiliation(s)
- Parisa Mazrooei
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Ken J Kron
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Yanyun Zhu
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Stanley Zhou
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Giacomo Grillo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Tahmid Mehdi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Musaddeque Ahmed
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Tesa M Severson
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Paul Guilhamon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | | | - Vincent Huang
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | | | - Michael Fraser
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Theodorus van der Kwast
- Department of Pathology and Laboratory Medicine, Toronto General Hospital, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Housheng Hansen He
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Andries M Bergman
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Robert G Bristow
- CRUK Manchester Institute and Manchester Cancer Research Centre, University of Manchester, Manchester M20 4GJ, UK
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, The Netherlands; Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands.
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
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13
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Höflmayer D, Steinhoff A, Hube-Magg C, Kluth M, Simon R, Burandt E, Tsourlakis MC, Minner S, Sauter G, Büscheck F, Wilczak W, Steurer S, Huland H, Graefen M, Haese A, Heinzer H, Schlomm T, Jacobsen F, Hinsch A, Poos AM, Oswald M, Rippe K, König R, Schroeder C. Expression of CCCTC-binding factor (CTCF) is linked to poor prognosis in prostate cancer. Mol Oncol 2019; 14:129-138. [PMID: 31736271 DOI: 10.1002/1878-0261.12597] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 10/22/2019] [Accepted: 11/12/2019] [Indexed: 01/06/2023] Open
Abstract
The chromatin-organizing factor CCCTC-binding factor (CTCF) is involved in transcriptional regulation, DNA-loop formation, and telomere maintenance. To evaluate the clinical impact of CTCF in prostate cancer, we analyzed CTCF expression by immunohistochemistry on a tissue microarray containing 17 747 prostate cancers. Normal prostate tissue showed negative to low CTCF expression, while in prostate cancers, CTCF expression was seen in 7726 of our 12 555 (61.5%) tumors and was considered low in 44.6% and high in 17% of cancers. Particularly, high CTCF expression was significantly associated with the presence of the transmembrane protease, serine 2:ETS-related gene fusion: Only 10% of ERG-negative cancers, but 30% of ERG-positive cancers had high-level CTCF expression (P < 0.0001). CTCF expression was significantly associated with advanced pathological tumor stage, high Gleason grade (P < 0.0001 each), nodal metastasis (P = 0.0122), and early biochemical recurrence (P < 0.0001). Multivariable modeling revealed that the prognostic impact of CTCF was independent from established presurgical parameters such as clinical stage and Gleason grade of the biopsy. Comparison with key molecular alterations showed strong associations with the expression of the Ki-67 proliferation marker and presence of phosphatase and tensin homolog deletions (P < 0.0001 each). The results of our study identify CTCF expression as a candidate biomarker for prognosis assessment in prostate cancer.
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Affiliation(s)
- Doris Höflmayer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Amélie Steinhoff
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Claudia Hube-Magg
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Martina Kluth
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Eike Burandt
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | | | - Sarah Minner
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Franziska Büscheck
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Waldemar Wilczak
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Stefan Steurer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Hartwig Huland
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Markus Graefen
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Alexander Haese
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Hans Heinzer
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Thorsten Schlomm
- Department of Urology, Charité - Universitätsmedizin Berlin, Germany
| | - Frank Jacobsen
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Andrea Hinsch
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Alexandra M Poos
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Germany.,Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Faculty of Biosciences, Heidelberg University, Germany.,Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Marcus Oswald
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Germany.,Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Rainer König
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Germany.,Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Cornelia Schroeder
- General, Visceral and Thoracic Surgery Department and Clinic, University Medical Center Hamburg-Eppendorf, Germany
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14
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Xiao F, Zhang P, Wang Y, Tian Y, James M, Huang CC, Wang L, Wang L. Single-nucleotide polymorphism rs13426236 contributes to an increased prostate cancer risk via regulating MLPH splicing variant 4. Mol Carcinog 2019; 59:45-55. [PMID: 31659808 DOI: 10.1002/mc.23127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 10/07/2019] [Accepted: 10/09/2019] [Indexed: 12/20/2022]
Abstract
A prostate cancer risk single-nucleotide polymorphism (SNP), rs13426236, is significantly associated with melanophilin (MLPH) expression. To functionally characterize role of the rs13426236 in prostate cancer, we first performed splicing-specific expression quantitative trait loci analysis and refined the significant association of rs13426236 allele G with an increased expression of MLPH splicing transcript variant 4 (V4) (P = 7.61E-5) but not other protein-coding variants (V1-V3) (P > .05). We then performed an allele-specific reporter assay to determine if SNP-containing sequences functioned as an active enhancer. Compared to allele A, allele G of rs13426236 showed significantly higher luciferase activity on the promoter of the splicing transcript V4 (P < .03) but not on the promoter of transcript V1 (P > .05) in two prostate cancer cell lines (DU145 and 22Rv1). Cell transfection assays showed stronger effect of transcript V4 than V1 on promoting cell proliferation, invasion, and antiapoptotic activities. RNA profiling analysis demonstrated that transcript V4 overexpression caused significant expression changes in glycosylation/glycoprotein and metal-binding gene ontology pathways (FDR < 0.01). We also found that both transcripts V4 and V1 were significantly upregulated in prostate adenocarcinoma (P ≤ 2.49E-6) but only transcript V4 upregulation was associated with poor recurrence-free survival (P = .028, hazard ratio = 1.63, 95% confidence interval = 1.05-2.42) in The Cancer Genome Atlas data. This study provides strong evidence showing that prostate cancer risk SNP rs13426236 upregulates expression of MLPH transcript V4, which may function as a candidate oncogene in prostate cancer.
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Affiliation(s)
- Fankai Xiao
- Henan Key Laboratory for Cancer Research, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.,Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Peng Zhang
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Yuan Wang
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Yijun Tian
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Michael James
- Department of Surgery, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Chiang-Ching Huang
- Department of Biostatistics, University of Wisconsin, Milwaukee, Wisconsin
| | - Lidong Wang
- Henan Key Laboratory for Cancer Research, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Liang Wang
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin.,Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
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15
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Zhang P, Tillmans LS, Thibodeau SN, Wang L. Single-Nucleotide Polymorphisms Sequencing Identifies Candidate Functional Variants at Prostate Cancer Risk Loci. Genes (Basel) 2019; 10:genes10070547. [PMID: 31323811 PMCID: PMC6678189 DOI: 10.3390/genes10070547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/10/2019] [Accepted: 07/16/2019] [Indexed: 01/22/2023] Open
Abstract
Genome-wide association studies have identified over 150 risk loci that increase prostate cancer risk. However, few causal variants and their regulatory mechanisms have been characterized. In this study, we utilized our previously developed single-nucleotide polymorphisms sequencing (SNPs-seq) technology to test allele-dependent protein binding at 903 SNP sites covering 28 genomic regions. All selected SNPs have shown significant cis-association with at least one nearby gene. After preparing nuclear extract using LNCaP cell line, we first mixed the extract with dsDNA oligo pool for protein–DNA binding incubation. We then performed sequencing analysis on protein-bound oligos. SNPs-seq analysis showed protein-binding differences (>1.5-fold) between reference and variant alleles in 380 (42%) of 903 SNPs with androgen treatment and 403 (45%) of 903 SNPs without treatment. From these significant SNPs, we performed a database search and further narrowed down to 74 promising SNPs. To validate this initial finding, we performed electrophoretic mobility shift assay in two SNPs (rs12246440 and rs7077275) at CTBP2 locus and one SNP (rs113082846) at NCOA4 locus. This analysis showed that all three SNPs demonstrated allele-dependent protein-binding differences that were consistent with the SNPs-seq. Finally, clinical association analysis of the two candidate genes showed that CTBP2 was upregulated, while NCOA4 was downregulated in prostate cancer (p < 0.02). Lower expression of CTBP2 was associated with poor recurrence-free survival in prostate cancer. Utilizing our experimental data along with bioinformatic tools provides a strategy for identifying candidate functional elements at prostate cancer susceptibility loci to help guide subsequent laboratory studies.
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Affiliation(s)
- Peng Zhang
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Lori S Tillmans
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | - Stephen N Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | - Liang Wang
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
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16
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Sattarifard H, Hashemi M, Hassanzarei S, Basiri A, Narouie B, Ghavami S. Long non-coding RNA POLR2E gene polymorphisms increased the risk of prostate cancer in a sample of the Iranian population. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2018; 38:1-11. [PMID: 30587086 DOI: 10.1080/15257770.2017.1391394] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The current study aimed to examine the impact of POLR2E rs1046040 and rs3787016 polymorphisms on prostate cancer (PCa) risk in a sample of southeast Iranian population. The present case-control study was performed on 178 patients with PCa and 180 benign prostatic hyperplasia (BPH). Genotyping of the variants was done by mismatch PCR-RFLP. The findings showed that the rs3787016 C > T variant significantly increased the risk of PCa in codominant (OR = 1.84, 95% CI = 1.12-3.03, P = 0.018, CT vs CC), dominant (OR = 1.88, 95% CI = 1.63-3.05, P = 0.011, CT + TT vas CC) and allele (OR = 1.77, 95% CI = 1.52-2.72, P = 0.010, T vs C) inheritance model. Regarding rs1046040 C > T polymorphism, the findings revealed that the CT genotype significantly increased the risk of PCa compared to the CC genotype (OR = 1.60, 95% CI = 1.03-2.49, P = 0.043). Furthermore, rs3787016 CT/rs1046040 CC as well as rs3787016 CT/rs1046040 CT increased the risk of PCa compared to the CC/CC genotype (p = 0.029 and p = 0.014, respectively). Haplotype analysis proposed that rs3787016 T/rs1046040 C significantly increased the risk of PCa compared to C/C (p = 0.037). No significant association was observed between POLR2E variants and clinicopathological characteristics of PCa patients. In conclusion, the findings propose that POLR2E variants may be a risk factor for susceptibility to PCa in a sample of Iranian population.
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Affiliation(s)
- Hedieh Sattarifard
- a Cellular and Molecular Research Center , Zahedan University of Medical Sciences , Zahedan , Iran.,b Department of Clinical Biochemistry, School of Medicine , Zahedan University of Medical Sciences , Zahedan , Iran
| | - Mohammad Hashemi
- a Cellular and Molecular Research Center , Zahedan University of Medical Sciences , Zahedan , Iran.,b Department of Clinical Biochemistry, School of Medicine , Zahedan University of Medical Sciences , Zahedan , Iran
| | - Shekoufeh Hassanzarei
- b Department of Clinical Biochemistry, School of Medicine , Zahedan University of Medical Sciences , Zahedan , Iran
| | - Abbas Basiri
- c Department of Urology, Urology and Nephrology Research Center, Shahid Labbafinejad Medical Center , Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Behzad Narouie
- c Department of Urology, Urology and Nephrology Research Center, Shahid Labbafinejad Medical Center , Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Saeid Ghavami
- d Department of Human Anatomy and Cell Science, Faculty of Health Sciences, College of Medicine , University of Manitoba , Winnipeg , Canada.,e Health Policy Research Center , Shiraz University of Medical Sciences , Shiraz , Iran
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17
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Association between three genetic variants in kallikrein 3 and prostate cancer risk. Biosci Rep 2018; 38:BSR20181151. [PMID: 30413614 PMCID: PMC6265624 DOI: 10.1042/bsr20181151] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 10/24/2018] [Accepted: 11/07/2018] [Indexed: 11/17/2022] Open
Abstract
Background: Epidemiological studies have assessed the association between kallikrein 3 (KLK3) polymorphisms and prostate cancer (PCa) susceptibility. However, published data on this association are somewhat inconclusive. Methods: Articles investigating the association between three KLK3 (rs1058205, rs2735839, and rs266882) variants and PCa susceptibility were searched from online databases, which included 35,838 patients and 36,369 control participants. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to demonstrate the strength of the association. We also utilized ELISA to detect serum expression of KLK3. In addition, in silico tools were adopted to evaluate the relationship of KLK3 expression and PCa survival time. Results: The overall results indicated that polymorphism T>C of rs1058205 was associated with decreased risk of PCa (allele contrast: OR = 0.75, 95% CI = 0.64–0.88, Pheterogeneity < 0.001; homozygote comparison: OR = 0.58, 95% CI = 0.42–0.81, Pheterogeneity < 0.001), particularly in Caucasian population (allele contrast: OR = 0.77, 95% CI = 0.65–0.91, Pheterogeneity < 0.001; homozygote comparison: OR = 0.58, 95% CI = 0.41–0.82, Pheterogeneity < 0.001). No association was observed between the polymorphism A>G of rs2735839 and risk of PCa. In addition, no association was observed between polymorphism A>G of rs266882 and risk of PCa. Serum KLK3 levels in PCa patients carrying CC/CT genotypes were statistically lower than those carrying TT genotypes. Conclusion: This meta-analysis suggests that rs1058205 polymorphism of KLK3 is a risk factor for PCa development, polymorphism T>C of rs1058205 is associated with decreased susceptibility to PCa particularly in Caucasian population.
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18
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DiStefano JK, Kingsley CB. Identification of Disease Susceptibility Alleles in the Next Generation Sequencing Era. Methods Mol Biol 2018; 1706:3-16. [PMID: 29423790 DOI: 10.1007/978-1-4939-7471-9_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The development of next generation sequencing (NGS) technologies has transformed the study of human genetic variation. In less than a decade, NGS has facilitated the discovery of causal mutations in both rare, monogenic diseases and common, heterogeneous disorders, leading to unprecedented improvements in disease diagnosis and treatment strategies. Given the rapid evolution of NGS platforms, it is now possible to analyze whole genomes and exomes quickly and affordably. Further, emerging NGS applications, such as single-cell sequencing, have the power to address specific issues like somatic variation, which is yielding new insights into the role of somatic mutations in cancer and late-onset diseases. Despite limitations associated with current iterations of NGS technologies, the impact of this approach on identifying disease-causing variants has been significant. This chapter provides an overview of several NGS platforms and applications and discusses how these technologies can be used in concert with experimental and computational strategies to identify variants with a causative effect on disease development and progression.
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Affiliation(s)
- Johanna K DiStefano
- Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, 85004, USA.
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19
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Benafif S, Kote-Jarai Z, Eeles RA. A Review of Prostate Cancer Genome-Wide Association Studies (GWAS). Cancer Epidemiol Biomarkers Prev 2018; 27:845-857. [PMID: 29348298 PMCID: PMC6051932 DOI: 10.1158/1055-9965.epi-16-1046] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 10/09/2017] [Accepted: 10/27/2017] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer is the most common cancer in men in Europe and the United States. The genetic heritability of prostate cancer is contributed to by both rarely occurring genetic variants with higher penetrance and moderate to commonly occurring variants conferring lower risks. The number of identified variants belonging to the latter category has increased dramatically in the last 10 years with the development of the genome-wide association study (GWAS) and the collaboration of international consortia that have led to the sharing of large-scale genotyping data. Over 40 prostate cancer GWAS have been reported, with approximately 170 common variants now identified. Clinical utility of these variants could include strategies for population-based risk stratification to target prostate cancer screening to men with an increased genetic risk of disease development, while for those who develop prostate cancer, identifying genetic variants could allow treatment to be tailored based on a genetic profile in the early disease setting. Functional studies of identified variants are needed to fully understand underlying mechanisms of disease and identify novel targets for treatment. This review will outline the GWAS carried out in prostate cancer and the common variants identified so far, and how these may be utilized clinically in the screening for and management of prostate cancer. Cancer Epidemiol Biomarkers Prev; 27(8); 845-57. ©2018 AACR.
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Affiliation(s)
- Sarah Benafif
- The Institute of Cancer Research, Sutton, United Kingdom.
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20
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Polo A, Marchese S, De Petro G, Montella M, Ciliberto G, Budillon A, Costantini S. Identifying a panel of genes/proteins/miRNAs modulated by arsenicals in bladder, prostate, kidney cancers. Sci Rep 2018; 8:10395. [PMID: 29991691 PMCID: PMC6039466 DOI: 10.1038/s41598-018-28739-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/28/2018] [Indexed: 02/07/2023] Open
Abstract
Arsenic and arsenic-derivative compounds, named as arsenicals, represent a worldwide problem for their effect on the human health and, in particular, for their capability to increase the risk of developing cancer such as kidney, bladder and prostate cancer. The main source of arsenical exposure is drinking water. Nowadays, it is well known that the chronic exposure to arsenicals leads to a series of epigenetic alterations that have a role in arsenic-induced effects on human health including cancer. Based on these observations, the aim of our study was to select by network analysis the genes/proteins/miRNAs implicated in kidney, bladder and prostate cancer development upon arsenical exposure. From this analysis we identified: (i) the nodes linking the three molecular networks specific for kidney, bladder and prostate cancer; (ii) the relative HUB nodes (RXRA, MAP3K7, NR3C1, PABPC1, NDRG1, RELA and CTNNB1) that link the three cancer networks; (iii) the miRNAs able to target these HUB nodes. In conclusion, we highlighted a panel of potential molecules related to the molecular mechanisms of arsenical-induced cancerogenesis and suggest their utility as biomarkers or therapeutic targets.
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Affiliation(s)
- Andrea Polo
- Experimental Pharmacology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Silvia Marchese
- Experimental Pharmacology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Giuseppina De Petro
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Brescia, Italy
| | - Maurizio Montella
- Epidemiology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Gennaro Ciliberto
- Scientific Directorate, IRCCS Istituto Nazionale Tumori "Regina Elena", Roma, Italy
| | - Alfredo Budillon
- Experimental Pharmacology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy.
| | - Susan Costantini
- Experimental Pharmacology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy.
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21
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Zhang Y, Zhang D, Lv J, Wang S, Zhang Q. miR-410-3p promotes prostate cancer progression via regulating PTEN/AKT/mTOR signaling pathway. Biochem Biophys Res Commun 2018; 503:2459-2465. [PMID: 29969630 DOI: 10.1016/j.bbrc.2018.06.176] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 06/30/2018] [Indexed: 01/30/2023]
Abstract
Prostate cancer has become one of commonest urologic tumors in male. In recent years, miRNAs are continually attracting attentions of researchers for their special regulatory function in human cancers. Previous study has revealed that miR-410 acts as a biomarker for the diagnosis of prostate cancer. Whereas, the specific biological function of miR-410-3p in prostate cancer remains unknown. The aim of this study is to explore the function and molecular mechanism of miR-410-3p in prostate cancer. The high expression of miR-410-3p was examined in prostate cancer tissues and cell lines by qRT-PCR. Next, the prognostic value was identified by Kaplan Meier method. High expression of miR-410-3p indicated poor prognosis of prostate cancer patients. To investigate the biological function of miR-410-3p in prostate cancer, loss-of function assays were designed and performed in two prostate cancer cell lines (PC3 and DU145). As a result, downregulated miR-410-3p suppressed cell proliferation, migration and EMT progress. Moreover, flow cytometry analysis was performed to determine that the acceleration effects of miR-410-3p on cell apoptosis. Mechanistically, further analysis demonstrated that the effects of miR-410-3p exert oncogenic functions through downregulating PTEN. All findings in this study revealed that miR-410-3p inhibits prostate cancer progression via downregulating PTEN/AKT/mTOR signaling pathway.
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Affiliation(s)
- Yuelong Zhang
- Department of Urology, Zhejiang Provincial People's Hospital, Hangzhou Medical College, 158 Shangtang Road, Hangzhou City, Zhejiang province, 310014, China
| | - Dahong Zhang
- Department of Urology, Zhejiang Provincial People's Hospital, Hangzhou Medical College, 158 Shangtang Road, Hangzhou City, Zhejiang province, 310014, China
| | - Jia Lv
- Department of Urology, Zhejiang Provincial People's Hospital, Hangzhou Medical College, 158 Shangtang Road, Hangzhou City, Zhejiang province, 310014, China
| | - Shuai Wang
- Department of Urology, Zhejiang Provincial People's Hospital, Hangzhou Medical College, 158 Shangtang Road, Hangzhou City, Zhejiang province, 310014, China
| | - Qi Zhang
- Department of Urology, Zhejiang Provincial People's Hospital, Hangzhou Medical College, 158 Shangtang Road, Hangzhou City, Zhejiang province, 310014, China.
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22
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Zhang P, Xia JH, Zhu J, Gao P, Tian YJ, Du M, Guo YC, Suleman S, Zhang Q, Kohli M, Tillmans LS, Thibodeau SN, French AJ, Cerhan JR, Wang LD, Wei GH, Wang L. High-throughput screening of prostate cancer risk loci by single nucleotide polymorphisms sequencing. Nat Commun 2018; 9:2022. [PMID: 29789573 PMCID: PMC5964124 DOI: 10.1038/s41467-018-04451-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 05/02/2018] [Indexed: 12/18/2022] Open
Abstract
Functional characterization of disease-causing variants at risk loci has been a significant challenge. Here we report a high-throughput single-nucleotide polymorphisms sequencing (SNPs-seq) technology to simultaneously screen hundreds to thousands of SNPs for their allele-dependent protein-binding differences. This technology takes advantage of higher retention rate of protein-bound DNA oligos in protein purification column to quantitatively sequence these SNP-containing oligos. We apply this technology to test prostate cancer-risk loci and observe differential allelic protein binding in a significant number of selected SNPs. We also test a unique application of self-transcribing active regulatory region sequencing (STARR-seq) in characterizing allele-dependent transcriptional regulation and provide detailed functional analysis at two risk loci (RGS17 and ASCL2). Together, we introduce a powerful high-throughput pipeline for large-scale screening of functional SNPs at disease risk loci. Functional characterization of disease-causing variants at risk loci in cancer is challenging. Here, in prostate cancer the authors report a pipeline for high-throughput single-nucleotide polymorphisms sequencing (SNPs-seq) for large scale screening of functional SNPs at disease risk loci.
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Affiliation(s)
- Peng Zhang
- Henan Key Laboratory for Esophageal Cancer Research, The First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, 450052, Zhengzhou, Henan, China.,Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Ji-Han Xia
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 5 A, 90220, Oulu, Finland
| | - Jing Zhu
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Ping Gao
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 5 A, 90220, Oulu, Finland
| | - Yi-Jun Tian
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Meijun Du
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Yong-Chen Guo
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Sufyan Suleman
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 5 A, 90220, Oulu, Finland
| | - Qin Zhang
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 5 A, 90220, Oulu, Finland
| | - Manish Kohli
- Department of Oncology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Lori S Tillmans
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Stephen N Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Amy J French
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Li-Dong Wang
- Henan Key Laboratory for Esophageal Cancer Research, The First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, 450052, Zhengzhou, Henan, China.
| | - Gong-Hong Wei
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 5 A, 90220, Oulu, Finland.
| | - Liang Wang
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
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23
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Sattarifard H, Hashemi M, Hassanzarei S, Narouie B, Bahari G. Association between genetic polymorphisms of long non-coding RNA PRNCR1 and prostate cancer risk in a sample of the Iranian population. Mol Clin Oncol 2017; 7:1152-1158. [PMID: 29285392 DOI: 10.3892/mco.2017.1462] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/18/2017] [Indexed: 12/19/2022] Open
Abstract
The aim of the present study was to determine whether there is an association between the long non-coding RNA (lncRNA) prostate cancer-associated non-coding RNA 1 (PRNCR1) polymorphisms and prostate cancer (PCa) risk in a sample of the Iranian population. This case-control study was performed on 178 patients with PCa and 180 subjects with benign prostatic hyperplasia (BPH). Genotyping assay was performed by polymerase chain reaction-restriction fragment length polymorphism. The findings indicated that the GG genotype of the rs13252298 A>G variant significantly increased the risk of PCa (odds ratio=3.49, 95% confidence interval: 1.79-6.81, P=0.0001) compared with AA+AG. As regards the rs1456315 G>A polymorphism, the AG genotype and G allele significantly increased the risk of PCa. As regards the rs7841060 T>G variant, the findings demonstrated that this TG genotype and the G allele significantly increased the risk of PCa. The rs7007694 T>C variant was not found to be associated with the risk of PCa. Haplotype analysis indicated that GTGA and GTGG significantly increased the risk of PCa compared with rs1456315A/rs7007694T/rs7841060T/rs13252298G (ATTG). The PRNCR1 variants were not found to be significantly associated with the clinicopathological characteristics of PCa patients. In conclusion, our findings support an association between PRNCR1 variants and the risk of PCa in a sample of the Iranian population.
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Affiliation(s)
- Hedieh Sattarifard
- Cellular and Molecular Research Center, School of Medicine, Zahedan University of Medical Sciences, Zahedan 98167-43181, Iran.,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 98167-43181, Iran
| | - Mohammad Hashemi
- Cellular and Molecular Research Center, School of Medicine, Zahedan University of Medical Sciences, Zahedan 98167-43181, Iran.,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 98167-43181, Iran
| | - Shekoofeh Hassanzarei
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 98167-43181, Iran
| | - Behzad Narouie
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran 198396-3113, Iran
| | - Gholamreza Bahari
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 98167-43181, Iran
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24
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Genetic association analysis of the RTK/ERK pathway with aggressive prostate cancer highlights the potential role of CCND2 in disease progression. Sci Rep 2017; 7:4538. [PMID: 28674394 PMCID: PMC5495790 DOI: 10.1038/s41598-017-04731-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 05/19/2017] [Indexed: 12/02/2022] Open
Abstract
The RTK/ERK signaling pathway has been implicated in prostate cancer progression. However, the genetic relevance of this pathway to aggressive prostate cancer at the SNP level remains undefined. Here we performed a SNP and gene-based association analysis of the RTK/ERK pathway with aggressive prostate cancer in a cohort comprising 956 aggressive and 347 non-aggressive cases. We identified several loci including rs3217869/CCND2 within the pathway shown to be significantly associated with aggressive prostate cancer. Our functional analysis revealed a statistically significant relationship between rs3217869 risk genotype and decreased CCND2 expression levels in a collection of 119 prostate cancer patient samples. Reduced expression of CCND2 promoted cell proliferation and its overexpression inhibited cell growth of prostate cancer. Strikingly, CCND2 downregulation was consistently observed in the advanced prostate cancer in 18 available clinical data sets with a total amount of 1,095 prostate samples. Furthermore, the lower expression levels of CCND2 markedly correlated with prostate tumor progression to high Gleason score and elevated PSA levels, and served as an independent predictor of biochemical relapse and overall survival in a large cohort of prostate cancer patients. Together, we have identified an association of genetic variants and genes in the RTK/ERK pathway with prostate cancer aggressiveness, and highlighted the potential importance of CCND2 in prostate cancer susceptibility and tumor progression to metastasis.
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25
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Fritz AJ, Ghule PN, Boyd JR, Tye CE, Page NA, Hong D, Shirley DJ, Weinheimer AS, Barutcu AR, Gerrard DL, Frietze S, van Wijnen AJ, Zaidi SK, Imbalzano AN, Lian JB, Stein JL, Stein GS. Intranuclear and higher-order chromatin organization of the major histone gene cluster in breast cancer. J Cell Physiol 2017; 233:1278-1290. [PMID: 28504305 DOI: 10.1002/jcp.25996] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/09/2017] [Indexed: 12/20/2022]
Abstract
Alterations in nuclear morphology are common in cancer progression. However, the degree to which gross morphological abnormalities translate into compromised higher-order chromatin organization is poorly understood. To explore the functional links between gene expression and chromatin structure in breast cancer, we performed RNA-seq gene expression analysis on the basal breast cancer progression model based on human MCF10A cells. Positional gene enrichment identified the major histone gene cluster at chromosome 6p22 as one of the most significantly upregulated (and not amplified) clusters of genes from the normal-like MCF10A to premalignant MCF10AT1 and metastatic MCF10CA1a cells. This cluster is subdivided into three sub-clusters of histone genes that are organized into hierarchical topologically associating domains (TADs). Interestingly, the sub-clusters of histone genes are located at TAD boundaries and interact more frequently with each other than the regions in-between them, suggesting that the histone sub-clusters form an active chromatin hub. The anchor sites of loops within this hub are occupied by CTCF, a known chromatin organizer. These histone genes are transcribed and processed at a specific sub-nuclear microenvironment termed the major histone locus body (HLB). While the overall chromatin structure of the major HLB is maintained across breast cancer progression, we detected alterations in its structure that may relate to gene expression. Importantly, breast tumor specimens also exhibit a coordinate pattern of upregulation across the major histone gene cluster. Our results provide a novel insight into the connection between the higher-order chromatin organization of the major HLB and its regulation during breast cancer progression.
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Affiliation(s)
- Andrew J Fritz
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Prachi N Ghule
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Joseph R Boyd
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Coralee E Tye
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Natalie A Page
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Deli Hong
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont.,Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - David J Shirley
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont
| | - Adam S Weinheimer
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Ahmet R Barutcu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Diana L Gerrard
- Medical Laboratory and Radiation Sciences, University of Vermont College of Nursing and Health Sciences, Burlington, Vermont
| | - Seth Frietze
- Medical Laboratory and Radiation Sciences, University of Vermont College of Nursing and Health Sciences, Burlington, Vermont
| | - Andre J van Wijnen
- Department of Orthopedic Surgery and Biochemistry & Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Sayyed K Zaidi
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Anthony N Imbalzano
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jane B Lian
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Janet L Stein
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Gary S Stein
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
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26
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Hashemi M, Danesh H, Bizhani F, Narouie B, Sotoudeh M, Nouralizadeh A, Sharifiaghdas F, Bahari G, Taheri M. Pri-miR-34b/c rs4938723 polymorphism increased the risk of prostate cancer. Cancer Biomark 2017; 18:155-159. [DOI: 10.3233/cbm-160058] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Mohammad Hashemi
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Hiva Danesh
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Fatemeh Bizhani
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Behzad Narouie
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Sotoudeh
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Akbar Nouralizadeh
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farzaneh Sharifiaghdas
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Gholamreza Bahari
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mohsen Taheri
- Genetics of Non Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
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27
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Kar SP, Adler E, Tyrer J, Hazelett D, Anton-Culver H, Bandera EV, Beckmann MW, Berchuck A, Bogdanova N, Brinton L, Butzow R, Campbell I, Carty K, Chang-Claude J, Cook LS, Cramer DW, Cunningham JM, Dansonka-Mieszkowska A, Doherty JA, Dörk T, Dürst M, Eccles D, Fasching PA, Flanagan J, Gentry-Maharaj A, Glasspool R, Goode EL, Goodman MT, Gronwald J, Heitz F, Hildebrandt MAT, Høgdall E, Høgdall CK, Huntsman DG, Jensen A, Karlan BY, Kelemen LE, Kiemeney LA, Kjaer SK, Kupryjanczyk J, Lambrechts D, Levine DA, Li Q, Lissowska J, Lu KH, Lubiński J, Massuger LFAG, McGuire V, McNeish I, Menon U, Modugno F, Monteiro AN, Moysich KB, Ness RB, Nevanlinna H, Paul J, Pearce CL, Pejovic T, Permuth JB, Phelan C, Pike MC, Poole EM, Ramus SJ, Risch HA, Rossing MA, Salvesen HB, Schildkraut JM, Sellers TA, Sherman M, Siddiqui N, Sieh W, Song H, Southey M, Terry KL, Tworoger SS, Walsh C, Wentzensen N, Whittemore AS, Wu AH, Yang H, Zheng W, Ziogas A, Freedman ML, Gayther SA, Pharoah PDP, Lawrenson K. Enrichment of putative PAX8 target genes at serous epithelial ovarian cancer susceptibility loci. Br J Cancer 2017; 116:524-535. [PMID: 28103614 PMCID: PMC5318969 DOI: 10.1038/bjc.2016.426] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 11/23/2016] [Accepted: 11/29/2016] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified 18 loci associated with serous ovarian cancer (SOC) susceptibility but the biological mechanisms driving these findings remain poorly characterised. Germline cancer risk loci may be enriched for target genes of transcription factors (TFs) critical to somatic tumorigenesis. METHODS All 615 TF-target sets from the Molecular Signatures Database were evaluated using gene set enrichment analysis (GSEA) and three GWAS for SOC risk: discovery (2196 cases/4396 controls), replication (7035 cases/21 693 controls; independent from discovery), and combined (9627 cases/30 845 controls; including additional individuals). RESULTS The PAX8-target gene set was ranked 1/615 in the discovery (PGSEA<0.001; FDR=0.21), 7/615 in the replication (PGSEA=0.004; FDR=0.37), and 1/615 in the combined (PGSEA<0.001; FDR=0.21) studies. Adding other genes reported to interact with PAX8 in the literature to the PAX8-target set and applying an alternative to GSEA, interval enrichment, further confirmed this association (P=0.006). Fifteen of the 157 genes from this expanded PAX8 pathway were near eight loci associated with SOC risk at P<10-5 (including six with P<5 × 10-8). The pathway was also associated with differential gene expression after shRNA-mediated silencing of PAX8 in HeyA8 (PGSEA=0.025) and IGROV1 (PGSEA=0.004) SOC cells and several PAX8 targets near SOC risk loci demonstrated in vitro transcriptomic perturbation. CONCLUSIONS Putative PAX8 target genes are enriched for common SOC risk variants. This finding from our agnostic evaluation is of particular interest given that PAX8 is well-established as a specific marker for the cell of origin of SOC.
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Affiliation(s)
- Siddhartha P Kar
- Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Emily Adler
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Jonathan Tyrer
- Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Dennis Hazelett
- Bioinformatics and Computational Biology Research Center, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Hoda Anton-Culver
- Department of Epidemiology, Director of Genetic Epidemiology Research Institute, UCI Center for Cancer Genetics Research & Prevention, School of Medicine, University of California Irvine, Irvine, CA 92697, USA
| | - Elisa V Bandera
- Cancer Prevention and Control Program, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Matthias W Beckmann
- University Hospital Erlangen, Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen Nuremberg, Universitaetsstrasse 21-23, Erlangen 91054, Germany
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC 27710, USA
| | - Natalia Bogdanova
- Radiation Oncology Research Unit, Hannover Medical School, Hannover 30625, Germany
| | - Louise Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ralf Butzow
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki 00100, Finland
| | - Ian Campbell
- Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC 3002, Australia
- Department of Pathology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Karen Carty
- The Beatson West of Scotland Cancer Centre, Glasgow G12 0YN, UK
| | - Jenny Chang-Claude
- German Cancer Research Center, Division of Cancer Epidemiology, Heidelberg 69120, Germany
- University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Linda S Cook
- Division of Epidemiology and Biostatistics, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA
| | - Daniel W Cramer
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Agnieszka Dansonka-Mieszkowska
- Department of Pathology, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02-781, Poland
| | - Jennifer Anne Doherty
- Department of Epidemiology, The Geisel School of Medicine—at Dartmouth, Hanover, NH 03756, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover 30625, Germany
| | - Matthias Dürst
- Department of Gynecology, Jena-University Hospital-Friedrich Schiller University, Jena 07737, Germany
| | - Diana Eccles
- Faculty of Medicine, University of Southampton, Southampton SO16 5YA, UK
| | - Peter A Fasching
- University Hospital Erlangen, Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen Nuremberg, Universitaetsstrasse 21-23, Erlangen 91054, Germany
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - James Flanagan
- Department of Surgery & Cancer, Imperial College London, London SW7 2AZ, UK
| | - Aleksandra Gentry-Maharaj
- Department of Women's Cancer, Institute for Women's Health, University College London, London W1T 7DN, UK
| | | | - Ellen L Goode
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, MI 55905, USA
| | - Marc T Goodman
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Community and Population Health Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jacek Gronwald
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin 70-001, Poland
| | - Florian Heitz
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte/ Evang. Huyssens-Stiftung/ Knappschaft GmbH, Essen 45136, Germany
- Department of Gynecology and Gynecologic Oncology, Dr Horst Schmidt Kliniken Wiesbaden, Wiesbaden 65199, Germany
| | - Michelle A T Hildebrandt
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Estrid Høgdall
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen 2100, Denmark
- Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, Copenhagen 1165, Denmark
| | - Claus K Høgdall
- The Juliane Marie Centre, Department of Gynecology, Rigshospitalet, University of Copenhagen, Copenhagen 2100, Denmark
| | - David G Huntsman
- British Columbia's Ovarian Cancer Research (OVCARE) Program, Vancouver General Hospital, BC Cancer Agency and University of British Columbia, Vancouver, BC V5Z 1L3, Canada
- Departments of Pathology and Laboratory Medicine and Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC V5Z 1L3, Canada
- Department of Molecular Oncology, BC Cancer Agency Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Allan Jensen
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen 2100, Denmark
| | - Beth Y Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Linda E Kelemen
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29435, USA
| | - Lambertus A Kiemeney
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen 6500 HB, The Netherlands
| | - Susanne K Kjaer
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen 2100, Denmark
- Department of Gynaecology, Rigshospitalet, University of Copenhagen, Copenhagen 2100, Denmark
| | - Jolanta Kupryjanczyk
- Department of Pathology, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02-781, Poland
| | - Diether Lambrechts
- Vesalius Research Center, VIB, Leuven 3000, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven 3000, Belgium
| | - Douglas A Levine
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Qiyuan Li
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Medical College of Xiamen University, Xiamen 361102, China
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02-781, Poland
| | - Karen H Lu
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jan Lubiński
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin 70-001, Poland
| | - Leon F A G Massuger
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Department of Gynaecology, Nijmegen 6500 HB, The Netherlands
| | - Valerie McGuire
- Department of Health Research and Policy—Epidemiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Iain McNeish
- Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Beatson Institute for Cancer Research, Glasgow G12 0YN, UK
| | - Usha Menon
- Department of Women's Cancer, Institute for Women's Health, University College London, London W1T 7DN, UK
| | - Francesmary Modugno
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15213, USA
- Ovarian Cancer Center of Excellence, Womens Cancer Research Program, Magee-Womens Research Institute and University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
| | - Alvaro N Monteiro
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Kirsten B Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Roberta B Ness
- The University of Texas School of Public Health, Houston, TX 77030, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki 00100, Finland
| | - James Paul
- The Beatson West of Scotland Cancer Centre, Glasgow G12 0YN, UK
| | - Celeste L Pearce
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Tanja Pejovic
- Department of Obstetrics & Gynecology, Oregon Health & Science University, Portland, OR 97239, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jennifer B Permuth
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Catherine Phelan
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Malcolm C Pike
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Elizabeth M Poole
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Susan J Ramus
- Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mary Anne Rossing
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98109, USA
| | - Helga B Salvesen
- Department of Gynecology and Obstetrics, Haukeland University Horpital, Bergen 5058, Norway
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen 5058, Norway
| | - Joellen M Schildkraut
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC 27710, USA
- Cancer Control and Population Sciences, Duke Cancer Institute, Durham, NC 27710, USA
| | - Thomas A Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Mark Sherman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Nadeem Siddiqui
- Department of Gynaecological Oncology, Glasgow Royal Infirmary, Glasgow G4 0SF, UK
| | - Weiva Sieh
- Department of Health Research and Policy—Epidemiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Honglin Song
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Melissa Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, VIC 3002, Australia
| | - Kathryn L Terry
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital, Boston, MA 02215, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - Shelley S Tworoger
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - Christine Walsh
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Alice S Whittemore
- Department of Health Research and Policy—Epidemiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Hannah Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center Medicine, Nashville, TN 37232, USA
| | - Argyrios Ziogas
- Department of Epidemiology, University of California Irvine, Irvine, CA 92697, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
| | - Simon A Gayther
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Kate Lawrenson
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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Chen L, Jin P, Qin ZS. DIVAN: accurate identification of non-coding disease-specific risk variants using multi-omics profiles. Genome Biol 2016; 17:252. [PMID: 27923386 PMCID: PMC5139035 DOI: 10.1186/s13059-016-1112-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/18/2016] [Indexed: 12/22/2022] Open
Abstract
Understanding the link between non-coding sequence variants, identified in genome-wide association studies, and the pathophysiology of complex diseases remains challenging due to a lack of annotations in non-coding regions. To overcome this, we developed DIVAN, a novel feature selection and ensemble learning framework, which identifies disease-specific risk variants by leveraging a comprehensive collection of genome-wide epigenomic profiles across cell types and factors, along with other static genomic features. DIVAN accurately and robustly recognizes non-coding disease-specific risk variants under multiple testing scenarios; among all the features, histone marks, especially those marks associated with repressed chromatin, are often more informative than others.
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Affiliation(s)
- Li Chen
- Department of Mathematics and Computer Science, Emory University, Atlanta, GA, 30322, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Zhaohui S Qin
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA. .,Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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Teerlink CC, Leongamornlert D, Dadaev T, Thomas A, Farnham J, Stephenson RA, Riska S, McDonnell SK, Schaid DJ, Catalona WJ, Zheng SL, Cooney KA, Ray AM, Zuhlke KA, Lange EM, Giles GG, Southey MC, Fitzgerald LM, Rinckleb A, Luedeke M, Maier C, Stanford JL, Ostrander EA, Kaikkonen EM, Sipeky C, Tammela T, Schleutker J, Wiley KE, Isaacs SD, Walsh PC, Isaacs WB, Xu J, Cancel-Tassin G, Cussenot O, Mandal D, Laurie C, Laurie C, Thibodeau SN, Eeles RA, Kote-Jarai Z, Cannon-Albright L. Genome-wide association of familial prostate cancer cases identifies evidence for a rare segregating haplotype at 8q24.21. Hum Genet 2016; 135:923-38. [PMID: 27262462 PMCID: PMC5020907 DOI: 10.1007/s00439-016-1690-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/26/2016] [Indexed: 10/21/2022]
Abstract
Previous genome-wide association studies (GWAS) of prostate cancer risk focused on cases unselected for family history and have reported over 100 significant associations. The International Consortium for Prostate Cancer Genetics (ICPCG) has now performed a GWAS of 2511 (unrelated) familial prostate cancer cases and 1382 unaffected controls from 12 member sites. All samples were genotyped on the Illumina 5M+exome single nucleotide polymorphism (SNP) platform. The GWAS identified a significant evidence for association for SNPs in six regions previously associated with prostate cancer in population-based cohorts, including 3q26.2, 6q25.3, 8q24.21, 10q11.23, 11q13.3, and 17q12. Of note, SNP rs138042437 (p = 1.7e(-8)) at 8q24.21 achieved a large estimated effect size in this cohort (odds ratio = 13.3). 116 previously sampled affected relatives of 62 risk-allele carriers from the GWAS cohort were genotyped for this SNP, identifying 78 additional affected carriers in 62 pedigrees. A test for an excess number of affected carriers among relatives exhibited strong evidence for co-segregation of the variant with disease (p = 8.5e(-11)). The majority (92 %) of risk-allele carriers at rs138042437 had a consistent estimated haplotype spanning approximately 100 kb of 8q24.21 that contained the minor alleles of three rare SNPs (dosage minor allele frequencies <1.7 %), rs183373024 (PRNCR1), previously associated SNP rs188140481, and rs138042437 (CASC19). Strong evidence for co-segregation of a SNP on the haplotype further characterizes the haplotype as a prostate cancer predisposition locus.
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Affiliation(s)
- Craig C Teerlink
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA.
| | - Daniel Leongamornlert
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, SW7 3RP, UK
| | - Tokhir Dadaev
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, SW7 3RP, UK
| | - Alun Thomas
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA
| | - James Farnham
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA
| | - Robert A Stephenson
- Department of Urology, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112, USA
| | - Shaun Riska
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Shannon K McDonnell
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Daniel J Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - William J Catalona
- Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - S Lilly Zheng
- Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Kathleen A Cooney
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Anna M Ray
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Kimberly A Zuhlke
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Ethan M Lange
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, 3010, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - Melissa C Southey
- Department of Pathology, University of Melbourne, Melbourne, 3010, Australia
| | - Liesel M Fitzgerald
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, 3004, Australia
| | - Antje Rinckleb
- Department of Urology, University Hospital Ulm, 53179, Ulm, Germany
| | - Manuel Luedeke
- Department of Urology, University Hospital Ulm, 53179, Ulm, Germany
| | - Christiane Maier
- Institute for Human Genetics, University of Ulm, 89081, Ulm, Germany
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, WA, 98109, USA
| | - Elaine A Ostrander
- Cancer Genetics Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Elina M Kaikkonen
- Department of Medical Biochemistry and Genetics, University of Turku, 20520, Turku, Finland
| | - Csilla Sipeky
- Department of Medical Biochemistry and Genetics, University of Turku, 20520, Turku, Finland
| | - Teuvo Tammela
- Department of Urology, University of Tampere and Tampere University Hospital, 33520, Tampere, Finland
| | - Johanna Schleutker
- Tyks Microbiology and Genetics, Department of Medical Genetics, Turku University Hospital, 20520, Turku, Finland
| | - Kathleen E Wiley
- Brady Urological Institute, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Sarah D Isaacs
- Brady Urological Institute, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Patrick C Walsh
- Brady Urological Institute, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - William B Isaacs
- Brady Urological Institute, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, IL, 60201, USA
| | | | - Olivier Cussenot
- CeRePP, Hopital Tenon, Assistance Publique-Hopitaux de Paris, 75020, Paris, France
| | - Diptasri Mandal
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA
| | - Cecelia Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Cathy Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Stephen N Thibodeau
- Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, SW7 3RP, UK
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, SW7 3RP, UK
| | - Lisa Cannon-Albright
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, 84148, USA
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Several Critical Cell Types, Tissues, and Pathways Are Implicated in Genome-Wide Association Studies for Systemic Lupus Erythematosus. G3-GENES GENOMES GENETICS 2016; 6:1503-11. [PMID: 27172182 PMCID: PMC4889647 DOI: 10.1534/g3.116.027326] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We aimed to elucidate the cell types, tissues, and pathways influenced by common variants in systemic lupus erythematosus (SLE). We applied a nonparameter enrichment statistical approach, termed SNPsea, in 181 single nucleotide polymorphisms (SNPs) that have been identified to be associated with the risk of SLE through genome-wide association studies (GWAS) in Eastern Asian and Caucasian populations, to manipulate the critical cell types, tissues, and pathways. In the two most significant cells’ findings (B lymphocytes and CD14+ monocytes), we subjected the GWAS association evidence in the Han Chinese population to an enrichment test of expression quantitative trait locus (QTL) sites and DNase I hypersensitivity, respectively. In both Eastern Asian and Caucasian populations, we observed that the expression level of SLE GWAS implicated genes was significantly elevated in xeroderma pigentosum B cells (P ≤ 1.00 × 10−6), CD14+ monocytes (P ≤ 2.74 × 10−4) and CD19+ B cells (P ≤ 2.00 × 10−6), and plasmacytoid dendritic cells (pDCs) (P ≤ 9.00 × 10−6). We revealed that the SLE GWAS-associated variants were more likely to reside in expression QTL in B lymphocytes (q1/q0 = 2.15, P = 1.23 × 10−44) and DNase I hypersensitivity sites (DHSs) in CD14+ monocytes (q1/q0 = 1.41, P = 0.08). We observed the common variants affected the risk of SLE mostly through by regulating multiple immune system processes and immune response signaling. This study sheds light on several immune cells and responses, as well as the regulatory effect of common variants in the pathogenesis of SLE.
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31
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Hashemi M, Moradi N, Ziaee SAM, Narouie B, Soltani MH, Rezaei M, Shahkar G, Taheri M. Association between single nucleotide polymorphism in miR-499, miR-196a2, miR-146a and miR-149 and prostate cancer risk in a sample of Iranian population. J Adv Res 2016; 7:491-8. [PMID: 27222754 DOI: 10.1016/j.jare.2016.03.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 03/23/2016] [Accepted: 03/24/2016] [Indexed: 01/29/2023] Open
Abstract
MicroRNAs (miRNAs) play an important role in regulating gene expression at the post-transcriptional level and are involved in numerous physiological processes. Accumulating evidence suggests that single-nucleotide polymorphisms (SNPs) in human miRNA genes may affect miRNA biogenesis pathway and influence the susceptibility to several diseases such as cancer. The present study aimed to evaluate the impact of miR-499 rs3746444, miR-196a2 rs11614913, miR-149 rs2292832, and miR-146a rs2910164 polymorphisms on prostate cancer (PCa) risk in a sample of Iranian population. This case-control study was done on 169 patients with pathologically confirmed PCa and 182 benign prostatic hyperplasia (BPH). The genotyping assays were done using T-ARMS-PCR or PCR-RFLP methods. The findings indicated that CC genotype of miR-499 rs3746444 polymorphism increased the risk of PCa (OR = 1.76, 95% CI = 1.12-2.79, P = 0.019) compared to TT genotype. No statistically significant association was found between miR-196a2 rs11614913, miR-149 rs2292832, and miR-146a rs2910164 polymorphisms and PCa risk. In summary, the findings indicated that miR-499 rs3746444 polymorphism increased the risk of PCa in an Iranian population. Further studies with larger sample sizes and different ethnicities are necessary to verify the findings of the present study.
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Affiliation(s)
- Mohammad Hashemi
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran; Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Nazanin Moradi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Seyed Amir Mohsen Ziaee
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Behzad Narouie
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Hosein Soltani
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Rezaei
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Ghazaleh Shahkar
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mohsen Taheri
- Genetics of Non Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
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