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Moya L, Lai J, Hoffman A, Srinivasan S, Panchadsaram J, Chambers S, Clements JA, Batra J. Association Analysis of a Microsatellite Repeat in the TRIB1 Gene With Prostate Cancer Risk, Aggressiveness and Survival. Front Genet 2018; 9:428. [PMID: 30337939 PMCID: PMC6180282 DOI: 10.3389/fgene.2018.00428] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 09/10/2018] [Indexed: 01/24/2023] Open
Abstract
With an estimated 1.1 million men worldwide diagnosed with prostate cancer yearly, effective and more specific biomarkers for early diagnosis could lead to better patient outcome. As such, novel genetic markers are sought for this purpose. The tribbles homologue 1 gene (TRIB1) has recently shown to have a role in prostate tumorigenesis and data-mining of prostate cancer expression data confirmed clinical significance of TRIB1 in prostate cancer. For the first time, a polymorphic microsatellite in this gene was studied for its potential association with prostate cancer risk and aggressiveness. Genomic DNA was extracted from a cohort of 1,152 prostate cancer patients and 1,196 cancer-free controls and the TTTTG-TRIB1 microsatellite was genotyped. The socio-demographic and clinical characteristics were analyzed using the non-parametric t-test and two-way ANOVA. Association of the TTTTG-TRIB1 microsatellite and prostate cancer risk and aggressiveness were analyzed by binary logistic regression and confirmed by bootstrapping. Total and prostate cancer mortality was analyzed using the Kaplan Meier test. Genotype and allele correlation with TRIB1 mRNA levels was analyzed using the non-parametric Kolmogorov-Smirnov test. To predict the effect that the TTTTG-TRIB1 polymorphisms had on the mRNA structure, the in silico RNA folding predictor tool, mfold, was used. By analyzing the publicly available data, we confirmed a significant over-expression of TRIB1 in prostate cancer compared to other cancer types, and an over-expression in prostate cancerous tissue compared to adjacent benign. Three alleles (three-five repeats) were observed for TTTTG-TRIB1. The three-repeat allele was associated with prostate cancer risk at the allele (OR = 1.16; P = 0.044) and genotypic levels (OR = 1.70; P = 0.006) and this association was age-independent. The four-repeat allele was inversely associated with prosatet cancer risk (OR = 0.57; P < 0.0001). TRIB1 expression was upregulated in tumors when compared to adjacent cancer-free tissue but was not allele specific. In silico analysis suggested that the TTTTG-TRIB1 alleles may alter TRIB1 mRNA structure. In summary, the three-repeat allele was significantly associated with prostate cancer risk, suggesting a biomarker potential for this microsatellite to predict prostate cancer. Further studies are needed to elucidate the functional role of this microsatellite in regulating TRIB1 expression, perhaps by affecting the TRIB1 mRNA structure and stability.
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Affiliation(s)
- Leire Moya
- Australian Prostate Cancer Research Centre – Queensland, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - John Lai
- Australian Prostate Cancer Research Centre – Queensland, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Andrea Hoffman
- Australian Prostate Cancer Research Centre – Queensland, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Srilakshmi Srinivasan
- Australian Prostate Cancer Research Centre – Queensland, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Janaththani Panchadsaram
- Australian Prostate Cancer Research Centre – Queensland, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Suzanne Chambers
- Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia
- Cancer Research Centre, Cancer Council Queensland, Brisbane, QLD, Australia
| | - Judith A. Clements
- Australian Prostate Cancer Research Centre – Queensland, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jyotsna Batra
- Australian Prostate Cancer Research Centre – Queensland, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
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A microsatellite repeat in PCA3 long non-coding RNA is associated with prostate cancer risk and aggressiveness. Sci Rep 2017; 7:16862. [PMID: 29203868 PMCID: PMC5715103 DOI: 10.1038/s41598-017-16700-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 11/10/2017] [Indexed: 01/08/2023] Open
Abstract
Short tandem repeats (STRs) are repetitive sequences of a polymorphic stretch of two to six nucleotides. We hypothesized that STRs are associated with prostate cancer development and/or progression. We undertook RNA sequencing analysis of prostate tumors and adjacent non-malignant cells to identify polymorphic STRs that are readily expressed in these cells. Most of the expressed STRs in the clinical samples mapped to intronic and intergenic DNA. Our analysis indicated that three of these STRs (TAAA-ACTG2, TTTTG-TRIB1, and TG-PCA3) are polymorphic and differentially expressed in prostate tumors compared to adjacent non-malignant cells. TG-PCA3 STR expression was repressed by the anti-androgen drug enzalutamide in prostate cancer cells. Genetic analysis of prostate cancer patients and healthy controls (N > 2,000) showed a significant association of the most common 11 repeat allele of TG-PCA3 STR with prostate cancer risk (OR = 1.49; 95% CI 1.11–1.99; P = 0.008). A significant association was also observed with aggressive disease (OR = 2.00; 95% CI 1.06–3.76; P = 0.031) and high mortality rates (HR = 3.0; 95% CI 1.03–8.77; P = 0.045). We propose that TG-PCA3 STR has both diagnostic and prognostic potential for prostate cancer. We provided a proof of concept to be applied to other RNA sequencing datasets to identify disease-associated STRs for future clinical exploratory studies.
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Dorn J, Bayani J, Yousef GM, Yang F, Magdolen V, Kiechle M, Diamandis EP, Schmitt M. Clinical utility of kallikrein-related peptidases (KLK) in urogenital malignancies. Thromb Haemost 2017; 110:408-22. [DOI: 10.1160/th13-03-0206] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Accepted: 05/25/2013] [Indexed: 12/19/2022]
Abstract
SummaryKallikrein-related peptidases (KLK), which represent a major tissue-associated proteolytic system, stand for a rich source of biomarkers that may allow molecular classification, early diagnosis and prognosis of human malignancies as well as prediction of response or failure to cancer-directed drugs. International research points to an important role of certain KLKs in female and male urogenital tract malignancies, in addition to cancers of the lung, brain, skin, head and neck, and the gastrointestinal tract. Regarding the female/male urogenital tract, remarkably, all of the KLKs are expressed in the normal prostate, testis, and kidney whereas the uterus, the ovary, and the urinary bladder are expressing a limited number of KLKs only. Most of the information regarding KLK expression in tumour-affected organs is available for ovarian cancer; all of the 12 KLKs tested so far were found to be elevated in the malignant state, depicting them as valuable biomarkers to distinguish between the normal and the cancerous phenotype. In contrast, for kidney cancer, a series of KLKs was found to be downregulated, while other KLKs were not expressed. Evidently, depending on the type of cancer or cancer stage, individual KLKs may show characteristics of a Janus-faced behaviour, by either expanding or inhibiting cancer progression and metastasis.
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Assis J, Pereira C, Nogueira A, Pereira D, Carreira R, Medeiros R. Genetic variants as ovarian cancer first-line treatment hallmarks: A systematic review and meta-analysis. Cancer Treat Rev 2017; 61:35-52. [PMID: 29100168 DOI: 10.1016/j.ctrv.2017.10.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 10/02/2017] [Accepted: 10/07/2017] [Indexed: 01/13/2023]
Abstract
BACKGROUND The potential predictive value of genetic polymorphisms in ovarian cancer first-line treatment is inconsistently reported. We aimed to review ovarian cancer pharmacogenetic studies to update and summarize the available data and to provide directions for further research. METHODS A systematic review followed by a meta-analysis was conducted on cohort studies assessing the involvement of genetic polymorphisms in ovarian cancer first-line treatment response retrieved through a MEDLINE database search by November 2016. Studies were pooled and summary estimates and 95% confidence intervals (CI) were calculated using random or fixed-effects models as appropriate. RESULTS One hundred and forty-two studies gathering 106871 patients were included. Combined data suggested that GSTM1-null genotype patients have a lower risk of death compared to GSTM1-wt carriers, specifically in advanced stages (hazard ratio (HR), 0.68; 95% CI, 0.48-0.97) and when submitted to platinum-based chemotherapy (aHR, 0.61; 95% CI, 0.39-0.94). ERCC1 rs11615 and rs3212886 might have also a significant impact in treatment outcome (aHR, 0.67; 95% CI, 0.51-0.89; aHR, 1.28; 95% CI, 1.01-1.63, respectively). Moreover, ERCC2 rs13181 and rs1799793 showed a distinct ethnic behavior (Asians: aHR, 1.41; 95% CI, 0.80-2.49; aHR, 1.07; 95% CI, 0.62-1.86; Caucasians: aHR, 0.10; 95% CI, 0.01-0.96; aHR, 0.18; 95% CI, 0.05-0.68, respectively). CONCLUSION(S) The definition of integrative predictive models should encompass genetic information, especially regarding GSTM1 homozygous deletion. Justifying additional pharmacogenetic investigation are variants in ERCC1 and ERCC2, which highlight the DNA Repair ability to ovarian cancer prognosis. Further knowledge could aid to understand platinum-treatment failure and to tailor chemotherapy strategies.
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Affiliation(s)
- Joana Assis
- Molecular Oncology and Viral Pathology Group - Research Center, Portuguese Institute of Oncology, Porto, Portugal; FMUP, Faculty of Medicine of Porto University, Porto, Portugal
| | - Carina Pereira
- Molecular Oncology and Viral Pathology Group - Research Center, Portuguese Institute of Oncology, Porto, Portugal; CINTESIS, Center for Health Technology and Services Research, FMUP, Porto, Portugal
| | - Augusto Nogueira
- Molecular Oncology and Viral Pathology Group - Research Center, Portuguese Institute of Oncology, Porto, Portugal; FMUP, Faculty of Medicine of Porto University, Porto, Portugal
| | - Deolinda Pereira
- Oncology Department, Portuguese Institute of Oncology, Porto, Portugal
| | - Rafael Carreira
- Centre of Biological Engineering, University of Minho, Braga, Portugal; SilicoLife, Lda, Braga, Portugal
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group - Research Center, Portuguese Institute of Oncology, Porto, Portugal; Research Department, Portuguese League Against Cancer (NRNorte), Porto, Portugal; CEBIMED, Faculty of Health Sciences of Fernando Pessoa University, Porto, Portugal.
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Involvement of Kallikrein-Related Peptidases in Normal and Pathologic Processes. DISEASE MARKERS 2015; 2015:946572. [PMID: 26783378 PMCID: PMC4689925 DOI: 10.1155/2015/946572] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/16/2015] [Accepted: 10/29/2015] [Indexed: 12/31/2022]
Abstract
Human kallikrein-related peptidases (KLKs) are a subgroup of serine proteases that participate in proteolytic pathways and control protein levels in normal physiology as well as in several pathological conditions. Their complex network of stimulatory and inhibitory interactions may induce inflammatory and immune responses and contribute to the neoplastic phenotype through the regulation of several cellular processes, such as proliferation, survival, migration, and invasion. This family of proteases, which includes one of the most useful cancer biomarkers, kallikrein-related peptidase 3 or PSA, also has a protective effect against cancer promoting apoptosis or counteracting angiogenesis and cell proliferation. Therefore, they represent attractive therapeutic targets and may have important applications in clinical oncology. Despite being intensively studied, many gaps in our knowledge on several molecular aspects of KLK functions still exist. This review aims to summarize recent data on their involvement in different processes related to health and disease, in particular those directly or indirectly linked to the neoplastic process.
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Sukumar N, Scott E, Dimitromanolakis A, Misiak A, Prassas I, Diamandis EP, Konvalinka A. Mining for single nucleotide variants (SNVs) at the kallikrein locus with predicted functional consequences. Biol Chem 2015; 395:1037-50. [PMID: 25153386 DOI: 10.1515/hsz-2014-0136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 07/03/2014] [Indexed: 12/17/2022]
Abstract
Kallikreins (KLKs) are a group of 15 serine proteases encoded by the KLK locus on chromosome 19. Certain single nucleotide variants (SNVs) within the KLK locus have been linked to human disease. Next-generation sequencing of large human cohorts enables reexamination of genomic variation at the KLK locus. We aimed to identify all KLK-related SNVs and examine their impact on gene regulation and function. To this end, we mined KLK SNVs across Ensembl and Exome Variant Server, with exome-sequencing data from 6503 individuals. PolyPhen-2-based prediction of damaging SNVs and population frequencies of these SNVs were examined. Damaging SNVs were plotted on protein sequence and structure. We identified 4866 SNVs, the largest number of KLK-related SNVs reported. Fourteen percent of noncoding SNVs overlapped with transcription factor binding sites. We identified 602 missense coding SNVs, among which 148 were predicted to be damaging. Nine missense SNVs were common (>1% frequency) and displayed significantly different frequencies between European-American and African-American populations. SNVs predicted to be damaging appeared to alter tertiary structure of KLK1 and KLK6. Similarly, these missense SNVs may affect KLK function, resulting in disease phenotypes. Our study represents a mine of information for those studying KLK-related SNVs and their associations with diseases.
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Engineered microenvironments provide new insights into ovarian and prostate cancer progression and drug responses. Adv Drug Deliv Rev 2014; 79-80:193-213. [PMID: 24969478 DOI: 10.1016/j.addr.2014.06.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 05/30/2014] [Accepted: 06/16/2014] [Indexed: 02/06/2023]
Abstract
Tissue engineering technologies, which have originally been designed to reconstitute damaged tissue structure and function, can mimic not only tissue regeneration processes but also cancer development and progression. Bioengineered approaches allow cell biologists to develop sophisticated experimentally and physiologically relevant cancer models to recapitulate the complexity of the disease seen in patients. Tissue engineering tools enable three-dimensionality based on the design of biomaterials and scaffolds that re-create the geometry, chemistry, function and signalling milieu of the native tumour microenvironment. Three-dimensional (3D) microenvironments, including cell-derived matrices, biomaterial-based cell culture models and integrated co-cultures with engineered stromal components, are powerful tools to study dynamic processes like proteolytic functions associated with cancer progression, metastasis and resistance to therapeutics. In this review, we discuss how biomimetic strategies can reproduce a humanised niche for human cancer cells, such as peritoneal or bone-like microenvironments, addressing specific aspects of ovarian and prostate cancer progression and therapy response.
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Chen X, Paranjape T, Stahlhut C, McVeigh T, Keane F, Nallur S, Miller N, Kerin M, Deng Y, Yao X, Zhao H, Weidhaas JB, Slack FJ. Targeted resequencing of the microRNAome and 3'UTRome reveals functional germline DNA variants with altered prevalence in epithelial ovarian cancer. Oncogene 2014; 34:2125-37. [PMID: 24909162 DOI: 10.1038/onc.2014.117] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 03/26/2014] [Indexed: 12/24/2022]
Abstract
Ovarian cancer is a major cause of cancer deaths, yet there have been few known genetic risk factors identified, the best known of which are disruptions in protein coding sequences (BRCA1 and 2). Recent findings indicate that there are powerful genetic markers of cancer risk outside of these regions, in the noncoding mRNA control regions. To identify additional cancer-associated, functional non-protein-coding sequence germline variants associated with ovarian cancer risk, we captured DNA regions corresponding to all validated human microRNAs and the 3' untranslated regions (UTRs) of ~6000 cancer-associated genes from 31 ovarian cancer patients. Multiple single-nucleotide polymorphisms in the 3'UTR of the vascular endothelial growth factor receptor/FLT1, E2F2 and PCM1 oncogenes were highly enriched in ovarian cancer patients compared with the 1000 Genome Project. Sequenom validation in a case-control study (267 cases and 89 controls) confirmed a novel variant in the PCM1 3'UTR is significantly associated with ovarian cancer (P=0.0086). This work identifies a potential new ovarian cancer locus and further confirms that cancer resequencing efforts should not ignore the study of noncoding regions of cancer patients.
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Affiliation(s)
- X Chen
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA [2] Program in Computational Biology and Bioinformatics, Yale University School of Medicine, New Haven, CT, USA
| | - T Paranjape
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
| | - C Stahlhut
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - T McVeigh
- Discipline of Surgery, National University of Ireland Galway and Galway University, Hospitals, Galway, Ireland
| | - F Keane
- Yale University School of Medicine, New Haven, CT, USA
| | - S Nallur
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
| | - N Miller
- Discipline of Surgery, National University of Ireland Galway and Galway University, Hospitals, Galway, Ireland
| | - M Kerin
- Discipline of Surgery, National University of Ireland Galway and Galway University, Hospitals, Galway, Ireland
| | - Y Deng
- Yale Center for Analytical Sciences, Yale University School of Medicine, New Haven, CT, USA
| | - X Yao
- Yale Center for Analytical Sciences, Yale University School of Medicine, New Haven, CT, USA
| | - H Zhao
- 1] Program in Computational Biology and Bioinformatics, Yale University School of Medicine, New Haven, CT, USA [2] Department of Genetics, Yale University School of Medicine, New Haven, CT, USA [3] Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - J B Weidhaas
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
| | - F J Slack
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
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Mavridis K, Stravodimos K, Scorilas A. Quantified KLK15 gene expression levels discriminate prostate cancer from benign tumors and constitute a novel independent predictor of disease progression. Prostate 2013; 73:1191-201. [PMID: 23620432 DOI: 10.1002/pros.22667] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 02/26/2013] [Indexed: 11/07/2022]
Abstract
BACKGROUND Several transcript variants of the kallikrein-related peptidase 15 gene (KLK15) have been identified up to now. The classical KLK15 mRNA isoform encodes for a non-truncated, functional protein. Aberrant KLK15 expression is found in breast, ovarian, and prostate cancers. Our aim in this present study was the specific quantitative expression analysis of the classical KLK15 mRNA transcript in prostate tumors and the examination of its clinical significance in prostate cancer. METHODS We isolated total RNA from 150 prostate tissue specimens and, following cDNA synthesis, the expression of KLK15 classical mRNA transcript was measured via quantitative Real-Time PCR using the TaqMan® chemistry. HPRT1 was used as a reference gene, and the absolute quantification approach, through the incorporation of standard curves, was applied for the calculation of normalized KLK15 expression. RESULTS KLK15 expression levels were significantly upregulated in malignant compared to benign samples (P < 0.001). The discriminatory value of KLK15 was confirmed by ROC curve and logistic regression analysis (both P < 0.001). KLK15 was also associated with advanced pathological stage (P = 0.023). KLK15-positive prostate cancer patients presented significantly shorter progression-free survival intervals, determined by biochemical relapse (P = 0.006), compared to KLK15-negative ones. Multivariate Cox regression analysis revealed that KLK15 expression is an independent predictor of biochemical recurrence (HR = 3.36, P = 0.038). CONCLUSIONS The present study unravels the important role of quantified KLK15 classical mRNA expression levels as a novel biomarker helpful for the differential diagnosis and prognosis of prostate cancer patients.
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Affiliation(s)
- Konstantinos Mavridis
- Department of Biochemistry and Molecular Biology, University of Athens, Athens, Greece
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Patnala R, Clements J, Batra J. Candidate gene association studies: a comprehensive guide to useful in silico tools. BMC Genet 2013; 14:39. [PMID: 23656885 PMCID: PMC3655892 DOI: 10.1186/1471-2156-14-39] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 04/15/2013] [Indexed: 01/01/2023] Open
Abstract
The candidate gene approach has been a pioneer in the field of genetic epidemiology, identifying risk alleles and their association with clinical traits. With the advent of rapidly changing technology, there has been an explosion of in silico tools available to researchers, giving them fast, efficient resources and reliable strategies important to find casual gene variants for candidate or genome wide association studies (GWAS). In this review, following a description of candidate gene prioritisation, we summarise the approaches to single nucleotide polymorphism (SNP) prioritisation and discuss the tools available to assess functional relevance of the risk variant with consideration to its genomic location. The strategy and the tools discussed are applicable to any study investigating genetic risk factors associated with a particular disease. Some of the tools are also applicable for the functional validation of variants relevant to the era of GWAS and next generation sequencing (NGS).
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Affiliation(s)
- Radhika Patnala
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia
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Association between Prostinogen (KLK15) genetic variants and prostate cancer risk and aggressiveness in Australia and a meta-analysis of GWAS data. PLoS One 2011; 6:e26527. [PMID: 22132073 PMCID: PMC3223160 DOI: 10.1371/journal.pone.0026527] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 09/28/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Kallikrein 15 (KLK15)/Prostinogen is a plausible candidate for prostate cancer susceptibility. Elevated KLK15 expression has been reported in prostate cancer and it has been described as an unfavorable prognostic marker for the disease. OBJECTIVES We performed a comprehensive analysis of association of variants in the KLK15 gene with prostate cancer risk and aggressiveness by genotyping tagSNPs, as well as putative functional SNPs identified by extensive bioinformatics analysis. METHODS AND DATA SOURCES: Twelve out of 22 SNPs, selected on the basis of linkage disequilibrium pattern, were analyzed in an Australian sample of 1,011 histologically verified prostate cancer cases and 1,405 ethnically matched controls. Replication was sought from two existing genome wide association studies (GWAS): the Cancer Genetic Markers of Susceptibility (CGEMS) project and a UK GWAS study. RESULTS Two KLK15 SNPs, rs2659053 and rs3745522, showed evidence of association (p<0.05) but were not present on the GWAS platforms. KLK15 SNP rs2659056 was found to be associated with prostate cancer aggressiveness and showed evidence of association in a replication cohort of 5,051 patients from the UK, Australia, and the CGEMS dataset of US samples. A highly significant association with Gleason score was observed when the data was combined from these three studies with an Odds Ratio (OR) of 0.85 (95% CI = 0.77-0.93; p = 2.7×10(-4)). The rs2659056 SNP is predicted to alter binding of the RORalpha transcription factor, which has a role in the control of cell growth and differentiation and has been suggested to control the metastatic behavior of prostate cancer cells. CONCLUSIONS Our findings suggest a role for KLK15 genetic variation in the etiology of prostate cancer among men of European ancestry, although further studies in very large sample sets are necessary to confirm effect sizes.
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Diaz-Padilla I, Amir E, Marsh S, Liu G, Mackay H. Genetic polymorphisms as predictive and prognostic biomarkers in gynecological cancers: a systematic review. Gynecol Oncol 2011; 124:354-65. [PMID: 22063461 DOI: 10.1016/j.ygyno.2011.10.034] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 10/28/2011] [Accepted: 10/29/2011] [Indexed: 11/15/2022]
Abstract
PURPOSE Numerous studies have explored the potential role of genetic polymorphisms as predictive or prognostic biomarkers in gynecologic malignancies. A systematic review for all eligible polymorphisms has not yet been reported. The aim of this study was to summarize the current status of the field and provide direction for future research. DESIGN We searched literature databases (MEDLINE, EMBASE, Cochrane) from 2006 to April 2011 to identify studies evaluating the association between gene polymorphisms and clinical outcome in ovarian, endometrial, cervical, or vulvar cancer. The main outcome measures were overall survival (OS) and progression-free survival (PFS). Studies reporting relationships between polymorphisms and toxicity were also included. RESULTS Sixty two studies met the inclusion criteria. The median sample size was 140. Most of the included studies (n=50, 81%) were conducted in ovarian cancer patients. Almost a third assessed potential predictive associations between gene polymorphism and outcome in ovarian cancer. The most commonly evaluated genes were ERCC1, VEGF, ABCB1 (MDR), and GSTP1. Most studies (n=44, 71%) were observational case-series. Only four studies (6%) included a validation arm and patient population ethnicity was explicitly stated only in 27% of included studies. CONCLUSION No consistent association between any gene polymorphism and clinical outcome in gynecological cancers has been found across studies. There is incomplete adherence to the REMARK guidelines and inadequate methodology reporting in most studies. Moving forward, analysis of large trial-based clinical samples; adherence to the highest methodological standards, and focus on validation analyses are necessary to identify clinically useful pharmacogenomic biomarkers of outcome.
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Affiliation(s)
- Ivan Diaz-Padilla
- Division of Medical Oncology, Princess Margaret Hospital, University of Toronto, Ontario, Canada.
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Bayani J, Diamandis EP. The physiology and pathobiology of human kallikrein-related peptidase 6 (KLK6). Clin Chem Lab Med 2011; 50:211-33. [PMID: 22047144 DOI: 10.1515/cclm.2011.750] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 09/21/2011] [Indexed: 12/11/2022]
Abstract
The human kallikrein-related peptidase 6 (KLK6) gene belongs to the 15-member kallikrein (KLK) gene family mapping to chromosome 19q13.3-13.4. Encoding for an enzyme with trypsin-like properties, KLK6 can degrade components of the extracellular matrix. The successful utilisation of another KLK member (KLK3/PSA) for prostate cancer diagnosis has led many to evaluate KLK6 as a potential biomarker for other cancer and diseased states. The observed dysregulated expression in cancers, neurodegenerative diseases and skin conditions has led to the discovery that KLK6 participates in other cellular pathways including inflammation, receptor activation and regulation of apoptosis. Moreover, the improvements in high-throughput genomics have not only enabled the identification of sequence polymorphisms, but of transcript variants, whose functional significances have yet to be realised. This comprehensive review will summarise the current findings of KLK6 pathophysiology and discuss its potential as a viable biomarker.
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Affiliation(s)
- Jane Bayani
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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