Cognitive outcome and gamma noise power unrelated to neuregulin 1 and 3 variation in schizophrenia

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License.[Background]: Neuregulins are a family of signalling proteins that orchestrate a broad range of cellular responses. Four genes encoding Neuregulins 1-4 have been identified so far in vertebrates. Among them, Neuregulin 1 and Neuregulin 3 have been reported to contribute to an increased risk for developing schizophrenia. We hypothesized that three specific variants of these genes (rs6994992 and rs3924999 for Neuregulin 1 and rs10748842 for Neuregulin 3) that have been related to this illness may modify information processing capacity in the cortex, which would be reflected in electrophysiological parameters (P3b amplitude or gamma noise power) and/or cognitive performance. [Methods]: We obtained DNA from 31 patients with schizophrenia and 23 healthy controls and analyzed NRG1 rs6994992, NRG1 rs3924999 and NRG3 rs10748842 promoter polymorphisms by allelic discrimination with real-time polymerase chain reaction (PCR). We compared cognitive outcome, P300 amplitude parameters and an electroencephalographic measure of noise power in the gamma band between the groups dichotomized according to genotype. [Results]: Contrary to our hypothesis, we could not detect any significant influence of variation in Neuregulin 1/Neuregulin 3 polymorphisms on cognitive performance or electrophysiological parameters of patients with schizophrenia. [Conclusions]: Despite our findings, we cannot discard that other genetic variants and, more likely, interactions between those variants and with genetic variation related to different pathways may still influence cerebral processing in schizophrenia.Funding for this study was provided by the Instituto de Salud Carlos III Grants 080017 and 1102203 to VM, Gerencia Regional de Salud de Castilla y León GRS 249/A/08 and 613/A/11, a postdoctoral Marie Curie Intra European Fellowship within the 7th European Commission Framework Programme for Research and Innovation (330156-CODIP) to ÁD, a predoctoral research grant from the Consejería de Educación - Junta de Castilla y León and the European Social Fund to ÁD (EDU/1486/2008) and CC (EDU/1064/2009), a predoctoral scholarship from the University of Salamanca and Santander Bank to VS, and the FIS Grant PI 1000219 to RG.Peer Reviewe

Urinary extracellular vesicles miRNA—A new era of prostate cancer biomarkers

Prostate cancer is the second most common male cancer worldwide showing the highest rates of incidence in Western Europe. Although the measurement of serum prostate-specific antigen levels is the current gold standard in PCa diagnosis, PSA-based screening is not considered a reliable diagnosis and prognosis tool due to its lower sensitivity and poor predictive score which lead to a 22%–43% overdiagnosis, unnecessary biopsies, and over-treatment. These major limitations along with the heterogeneous nature of the disease have made PCa a very unappreciative subject for diagnostics, resulting in poor patient management; thus, it urges to identify and validate new reliable PCa biomarkers that can provide accurate information in regard to disease diagnosis and prognosis. Researchers have explored the analysis of microRNAs (miRNAs), messenger RNAs (mRNAs), small proteins, genomic rearrangements, and gene expression in body fluids and non-solid tissues in search of lesser invasive yet efficient PCa biomarkers. Although the presence of miRNAs in body fluids like blood, urine, and saliva initially sparked great interest among the scientific community; their potential use as liquid biopsy biomarkers in PCa is still at a very nascent stage with respect to other well-established diagnostics and prognosis tools. Up to date, numerous studies have been conducted in search of PCa miRNA-based biomarkers in whole blood or blood serum; however, only a few studies have investigated their presence in urine samples of which less than two tens involve the detection of miRNAs in extracellular vesicles isolated from urine. In addition, there exists some discrepancy around the identification of miRNAs in PCa urine samples due to the diversity of the urine fractions that can be targeted for analysis such as urine circulating cells, cell-free fractions, and exosomes. In this review, we aim to discuss research output from the most recent studies involving the analysis of urinary EVs for the identification of miRNA-based PCa-specific biomarkers

MiR-21 is Required for the Epithelial–Mesenchymal Transition in MDA-MB-231 Breast Cancer Cells

Breast cancer (BCa) is one of the leading health problems among women. Although significant achievements have led to advanced therapeutic success with targeted therapy options, more efforts are required for different subtypes of tumors and according to genomic, transcriptomic, and proteomic alterations. This study underlines the role of microRNA-21 (miR-21) in metastatic MDA-MB-231 breast cancer cells. Following the knockout of miR-21 from MDA-MB-231 cells, which have the highest miR-21 expression levels compared to MCF-7 and SK-BR-3 BCa cells, a decrease in epithelial-mesenchymal transition (EMT) via downregulation of mesenchymal markers was observed. Wnt-11 was a critical target for miR-21, and the Wnt-11 related signaling axis was altered in the stable miR-21 knockout cells. miR-21 expression was associated with a significant increase in mesenchymal markers in MDA-MB-231 BCa cells. Furthermore, the release of extracellular vesicles (EVs) was significantly reduced in the miR-21 KO cells, alongside a significant reduction in relative miR-21 export in EV cargo, compared with control cells. We conclude that miR-21 is a leading factor involved in mesenchymal transition in MDA-MB-231 BCa. Future therapeutic strategies could focus on its role in the treatment of metastatic breast cancer

Telomere Length Shows No Association with BRCA1 and BRCA2 Mutation Status

This study aimed to determine whether telomere length (TL) is a marker of cancer risk or genetic status amongst two cohorts of BRCA1 and BRCA2 mutation carriers and controls. The first group was a prospective set of 665 male BRCA1/2 mutation carriers and controls (mean age 53 years), all healthy at time of enrolment and blood donation, 21 of whom have developed prostate cancer whilst on study. The second group consisted of 283 female BRCA1/2 mutation carriers and controls (mean age 48 years), half of whom had been diagnosed with breast cancer prior to enrolment. TL was quantified by qPCR from DNA extracted from peripheral blood lymphocytes. Weighted and unweighted Cox regressions and linear regression analyses were used to assess whether TL was associated with BRCA1/2 mutation status or cancer risk. We found no evidence for association between developing cancer or being a BRCA1 or BRCA2 mutation carrier and telomere length. It is the first study investigating TL in a cohort of genetically predisposed males and although TL and BRCA status was previously studied in females our results don't support the previous finding of association between hereditary breast cancer and shorter TL

A Single Nucleotide Polymorphism in the RASGRF2 Gene Is Associated with Alcoholic Liver Cirrhosis in Men

Background Genetic polymorphisms in the RAS gene family are associated with different diseases, which may include alcohol-related disorders. Previous studies showed an association of the allelic variant rs26907 in RASGRF2 gene with higher alcohol intake. Additionally, the rs61764370 polymorphism in the KRAS gene is located in a binding site for the let-7 micro-RNA family, which is potentially involved in alcohol-induced inflammation. Therefore, this study was designed to explore the association between these two polymorphisms and susceptibility to alcoholism or alcoholic liver disease (ALD). Methods We enrolled 301 male alcoholic patients and 156 healthy male volunteers in this study. Polymorphisms were genotyped by using TaqMan® PCR assays for allelic discrimination. Allelic and genotypic frequencies were compared between the two groups. Logistic regression analysis was performed to analyze the inheritance model. Results The A allele of the RASGRF2 polymorphism (rs26907) was significantly more prevalent among alcoholic patients with cirrhosis (23.2%) compared to alcoholic patients without ALD (14.2%). This difference remained significant in the group of patients with alcohol dependence (28.8% vs. 14.3%) but not in those with alcohol abuse (15.1% vs. 14.4%). Multivariable logistic regression analysis showed that the A allele of this polymorphism (AA or GA genotype) was associated with alcoholic cirrhosis both in the total group of alcoholics (odds ratio [OR]: 2.33, 95% confidence interval [CI]: 1.32–4.11; P = 0.002) and in the group of patients with alcohol dependence (OR: 3.1, 95% CI: 1.50–6.20; P = 0.001). Allelic distributions of the KRAS polymorphism (rs61764370) did not differ between the groups. Conclusions To our knowledge, this genetic association study represents the first to show an association of the RASGRF2 G>A (rs26907) polymorphism with ALD in men, particularly in the subgroup of patients with AD. The findings suggest the potential relevance of the RAS gene family in alcoholism and ALD

Rare germline variants in DNA repair genes and the angiogenesis pathway predispose prostate cancer patients to develop metastatic disease

Background Prostate cancer (PrCa) demonstrates a heterogeneous clinical presentation ranging from largely indolent to lethal. We sought to identify a signature of rare inherited variants that distinguishes between these two extreme phenotypes. Methods We sequenced germline whole exomes from 139 aggressive (metastatic, age of diagnosis < 60) and 141 non-aggressive (low clinical grade, age of diagnosis ≥60) PrCa cases. We conducted rare variant association analyses at gene and gene set levels using SKAT and Bayesian risk index techniques. GO term enrichment analysis was performed for genes with the highest differential burden of rare disruptive variants. Results Protein truncating variants (PTVs) in specific DNA repair genes were significantly overrepresented among patients with the aggressive phenotype, with BRCA2, ATM and NBN the most frequently mutated genes. Differential burden of rare variants was identified between metastatic and non-aggressive cases for several genes implicated in angiogenesis, conferring both deleterious and protective effects. Conclusions Inherited PTVs in several DNA repair genes distinguish aggressive from non-aggressive PrCa cases. Furthermore, inherited variants in genes with roles in angiogenesis may be potential predictors for risk of metastases. If validated in a larger dataset, these findings have potential for future clinical application

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Fine-mapping of prostate cancer susceptibility loci in a large meta-analysis identifies candidate causal variants

Prostate cancer is a polygenic disease with a large heritable component. A number of common, low-penetrance prostate cancer risk loci have been identified through GWAS. Here we apply the Bayesian multivariate variable selection algorithm JAM to fine-map 84 prostate cancer susceptibility loci, using summary data from a large European ancestry meta-analysis. We observe evidence for multiple independent signals at 12 regions and 99 risk signals overall. Only 15 original GWAS tag SNPs remain among the catalogue of candidate variants identified; the remainder are replaced by more likely candidates. Biological annotation of our credible set of variants indicates significant enrichment within promoter and enhancer elements, and transcription factor-binding sites, including AR, ERG and FOXA1. In 40 regions at least one variant is colocalised with an eQTL in prostate cancer tissue. The refined set of candidate variants substantially increase the proportion of familial relative risk explained by these known susceptibility regions, which highlights the importance of fine-mapping studies and has implications for clinical risk profiling. © 2018 The Author(s).Prostate cancer is a polygenic disease with a large heritable component. A number of common, low-penetrance prostate cancer risk loci have been identified through GWAS. Here we apply the Bayesian multivariate variable selection algorithm JAM to fine-map 84 prostate cancer susceptibility loci, using summary data from a large European ancestry meta-analysis. We observe evidence for multiple independent signals at 12 regions and 99 risk signals overall. Only 15 original GWAS tag SNPs remain among the catalogue of candidate variants identified; the remainder are replaced by more likely candidates. Biological annotation of our credible set of variants indicates significant enrichment within promoter and enhancer elements, and transcription factor-binding sites, including AR, ERG and FOXA1. In 40 regions at least one variant is colocalised with an eQTL in prostate cancer tissue. The refined set of candidate variants substantially increase the proportion of familial relative risk explained by these known susceptibility regions, which highlights the importance of fine-mapping studies and has implications for clinical risk profiling. © 2018 The Author(s).Peer reviewe

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Characterization of the new molecular profiles in sporadic endometrial carcinoma

[ES] Endometrial carcinoma is the most frequent gynaecological tumour in developed countries. The origin is sporadic in 95% of them and its main risk factor is hormone exposure. It has been proposed several classifications depending on the followed criteria to characterize sporadic endometrial carcinomas. Bearing in mind clinical-pathological characteristics, Bokhman et al., in 1983, proposed a dualistic model in which endometrial carcinomas were classified in two groups: type 1 or endometrioid carcinomas (with a good prognosis and estrogens-dependent) and type 2 or non-endometrioid carcinomas (with a poor prognosis and non-estrogens-dependent). Later, Vogelstein in 1988, developed a theory for colorectal cancer, embraced and adapted for endometrial carcinoma, which said that tumours are a consequence of an accumulation of genetic and epigenetic alterations. According to this fact, it has been observed that type 1 and type 2 endometrial carcinomas have specific molecular profiles. Type 1 carcinomas are mainly associated with MSI and mutations in PTEN, PIK3CA, KRAS, CTNNB1, FGFR2 and MMR genes and type 2 carcinomas are associated with mutations in TP53, CDKN2A, and CDH1 genes, loss of expression of HER2/ERBB2 and EGFR/ERBB1 proteins and loss of heterozigosity (LOH) in different chromosomes. Currently, whole exome sequencing studies are being carried out in order to look for new target genes in different types of tumours. Two of them are ARID1A and PPP2R1A genes that are highly mutated in endometrioid and non-endometrioid carcinomas respectively. On the other hand, telomere length variations have been associated with a susceptibility of developing different kind of tumours. However, it has not been yet clarified if the telomere shortening is a cause or a consequence of tumour development and the exact role of telomerase. Moreover, new criteria are being established with the aim of elaborate a more accurate classification that would help to better identify, characterize and treat the different types of endometrial carcinomas. The aim of the present work has been the analysis of 14 genes implicated in tumorigenesis (including PPP2R1A and ARID1A genes); MSI; LOH; as well as the methylation of the MMR genes promoter and HDACs expression; the telomere length and TERT-1327C>T and TERC-63G>A polymorphisms analysis in a cohort of 86 sporadic endometrial carcinomas and 23 blood samples. We have used a wide variety of techniques for the realization of our study. We have extracted DNA from tumour and blood samples, and RNA and total proteins from tumour samples. The analysis of different genes has been carried out by PCR, CSGE-Heteroduplex and Sanger sequencing using several databases in order to check if the mutations found had been previously described. For the characterization of the new mutations, we have performed RT-PCR and Western blot assays (as well as for HDAC protein expression analysis). Several prediction programs have helped us to determine the mutations pathogenicity. We also have studied LOH by qPCR and RFLP; gross alterations in MMR genes by MLPA; MMR promotermethylation by MS-MLPA; and telomere length and telomerase polymorphisms by real time PCR. Statistical analysis has been carried out with SPSS v18.0, GenEx 5.3.6 Enterprise, and MULTBiplot programs. We have found 213 mutations: 99 described mutations and other 114 non-previously described mutations that have been characterized in our work. The most mutated genes have been PTEN and ARID1A. MSI has been carried out when we have obtained DNA from both tumour and blood samples of the same patient observing that it is a frequent event in our patients. In contrast with Lynch syndrome, D17S250 was the most altered marked in our population. On the other hand, we have observed that the gross alterations and the point mutations do not explain the MSI and loss of expression of MMR genes. The most methylated gene has been hMLH1, but methylation of MMR genes has not been consistent with either the lack of MMR proteins expression and MSI. The HDAC2 protein has been the histone deacetylase which expression has been absent in a highest number of studied tumours. Both methylation and HDAC2 protein expression patterns have differed depending on the type of tumour. The telomere length has not shown any relation with neither type nor grade of tumour and C and G alleles of TERT-1327C>T and TERC-63G>A polymorphisms were only slightly related to mixed and grade 3 endometrioid carcinomas respectively (the groups with shortest telomeres). In our work, PPP2R1A gene has shown mutations mainly associated with serous carcinomas. We have described a new probably pathogenic mutation in the exon 2 of the gene, presented in a grade 1 endometrioid carcinoma, and a pole of polymorphisms situated in the promoter region implicated in the binding of several transcription factors. When we have analyzed PPP2R1A protein expression, we have observed a new pattern of protein expression at 110 kDa, maybe related to posttranslational modifications. On the other hand, we have observed that ARID1A gene appears commonly mutated in endometrioid and non-endometrioid carcinomas with a high number of nosense and frameshift mutations. We have described 32 new mutations including an inframe alteration that causes a change in the mRNA splicing. According to our results, the most adequate classification among those that have been proposed until now, is the classification that bears in mind the characteristics of the different histological subtypes. The clinical-pathological criteria are not accurate and they share a high identity with the classification by histological grades. We have observed that grade 1 and grade 2 endometrioid carcinomas could be grouped in a low-grade endometrioid cluster showing very similar molecular characteristics. At the same time the molecular profile of low-grade endometrioid carcinomas differs from grade 3 endometrioid carcinomas genetic profile. Grade 3 endometrioid carcinomas share characteristics with low-grade endometrioid and serous carcinomas and because of that, it is not possible to group them with any other histological subtype. Moreover, mixed carcinomas and carcinosarcomas show a molecular profile that depends on the type of their components suggesting the importance of making histological studies of this kind of tumours before their molecular analysis