Prognostic Classifier Based on Genome-Wide DNA Methylation Profiling in Well-Differentiated Thyroid Tumors

Made available in DSpace on 2018-12-11T17:23:43Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-11-01Context: Even though the majority of well-differentiated thyroid carcinoma (WDTC) is indolent, a number of cases display an aggressive behavior. Cumulative evidence suggests that the deregulation of DNA methylation has the potential to point out molecular markers associated with worse prognosis. Objective: To identify a prognostic epigenetic signature in thyroid cancer. Design: Genome-wide DNA methylation assays (450k platform, Illumina) were performed in a cohort of 50 nonneoplastic thyroid tissues (NTs), 17 benign thyroid lesions (BTLs), and 74 thyroid carcinomas (60 papillary, 8 follicular, 2 Hürthle cell, 1 poorly differentiated, and 3 anaplastic). A prognostic classifier for WDTC was developed via diagonal linear discriminant analysis. The results were compared with The Cancer Genome Atlas (TCGA) database. Results: A specific epigenetic profile was detected according to each histological subtype. BTLs and follicular carcinomas showed a greater number of methylated CpG in comparison with NTs, whereas hypomethylation was predominant in papillary and undifferentiated carcinomas. A prognostic classifier based on 21 DNA methylation probes was able to predict poor outcome in patients with WDTC (sensitivity 63%, specificity 92% for internal data; sensitivity 64%, specificity 88% for TCGA data). High-risk score based on the classifier was considered an independent factor of poor outcome (Cox regression, P < 0.001). Conclusions: The methylation profile of thyroid lesions exhibited a specific signature according to the histological subtype. A meaningful algorithm composed of 21 probes was capable of predicting the recurrence in WDTC.International Research Center, CIPE, A.C. Camargo Cancer Center and National Institute of Science and Technology in Oncogenomics, São Paulo 01509-010, SP, BrazilDepartment of Urology, Faculty of Medicine, UNESP, São Paulo State University, Botucatu 18618-970, SP, BrazilDepartment of Pathology, A.C. Camargo Cancer Center, São Paulo 01509-010, SP, BrazilEpigenetics Group; International Agency for Research on Cancer (IARC), Lyon 69372, FranceMRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 1TH, United KingdomDepartment of Head and Neck Surgery and Otorhinolaryngology, A.C. Camargo Cancer Center, São Paulo 01509-010, SP, BrazilDepartment of Clinical Genetics, Vejle Hospital and Institute of Regional Health Research, University of Southern Denmark, Vejle, 7100, Denmar

Perfil de metilação do DNA em lesões tireoidianas

Thyroid cancer (TC) is the most prevalent type of endocrine cancer. Papillary thyroid carcinoma (PTC) comprises 80-85% of the diagnosed thyroid cancers, followed by follicular (FTC), poorly differentiated (PDTC) and anaplastic carcinomas (ATC). Diagnosis of thyroid carcinomas, especially of well-differentiated carcinomas is a challenge due to morphological similarities between these tumors and benign lesions. The aim of this study was to evaluate the methylation profile to identify diagnostic markers involved in benign lesions and in different histological subtypes of carcinomas. Moreover, a search for reliable molecular prognostic markers was also performed in TC. The study included 17 benign lesions (8 adenomas, 6 goiters and 3 thyroiditis), 60 PTCs, 8 FTCs, 2 Hürthle cell carcinomas (HCC), 1 PDTC and 3 ATC, as well as 50 non-neoplastic tissues (NT) obtained from patients who had PTC. Differential methylation analyzes were performed using the Infinium® Human Methylation450 BeadChip microarray (Illumina). In the first stage of the study, the results of differentially methylated probes were used in the development of diagnostic classifier algorithm. In second step, the methylation profile of benign lesions and tumor subtypes was compared to data from non-neoplastic tissues. Only probes significantly altered in the current study and those confirmed by GEO data (Gene Expression Omnibus) were selected for the development of the algorithms. Three diagnostic algorithms were developed based on differential methylation of nine probes selected from area under the curve of 0.75 for BTL classifier and 0.90 for FTC and PTC classifiers and multivariate analysis. It was also applied linear classification methods. Application of the algorithm diagnosis allowed the correct classification of non-neoplastic tissues, benign and malignant lesions (sensitivity: 91.9% and specificity: 76.5%). The same strategy was performed using the GEO database...O câncer de tireoide (CT) é a neoplasia mais comum do sistema endócrino. O carcinoma papilífero da tireoide (CPT) compreende 80-85% dos casos, seguido dos carcinomas foliculares (CFT), pouco diferenciados (CPDT) e anáplasicos (CAT). O diagnóstico dos CT, principalmente nos casos bem diferenciados, ainda é um desafio devido a semelhanças morfológicas compartilhadas por esses tumores e lesões benignas (LBT). O objetivo desse estudo foi avaliar o perfil de metilação do DNA para identificar marcadores epigenéticos envolvidos no desenvolvimento das lesões benignas e dos diferentes subtipos histológicos de carcinomas. Além disso, buscou-se identificar marcadores prognósticos nos CT. Foram incluídos nesse estudo 17 lesões benignas da tireoide (8 adenomas, 6 bócios tireoideanos e 3 tireoidites), 60 CPT, 8 CFT, 2 carcinomas de células de Hurthle (CCH), 1 CPDT e 3 CAT, além de 50 tecidos não neoplásicos (TN) obtidos dos pacientes que tiveram CPT. As análises de metilação diferencial foram realizadas utilizando a plataforma microarray Infinium® Human Methylation450 BeadChip (Illumina). Na primeira etapa do estudo, os resultados obtidos de sondas diferencialmente metiladas foram utilizados na construção de um algoritmo útil como classificador diagnóstico. Na segunda etapa, o perfil de metilação do DNA das lesões benignas e dos diferentes subtipos tumorais foi comparado aos dados de tecidos não neoplásicos. Somente sondas significativamente alteradas no presente estudo e aquelas confirmadas no GEO (Gene Expression Omnibus) foram selecionadas para a construção de algoritmos. Foram delineados três algoritmos diagnósticos baseados na metilação diferencial de nove sondas selecionadas a partir de área abaixo da curva de 0,75 para o classificador de LBT e 0,90 para os classificadores CFT e CPT além de análise multivariada. Foram também aplicados métodos lineares de classificação. A aplicação do algoritmo...Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

Accuracy and Clinical Relevance of Intra-Tumoral Fusobacterium nucleatum Detection in Formalin-Fixed Paraffin-Embedded (FFPE) Tissue by Droplet Digital PCR (ddPCR) in Colorectal Cancer

The use of droplet digital PCR (ddPCR) to identify and quantify low-abundance targets is a significant advantage for accurately detecting potentially oncogenic bacteria. Fusobacterium nucleatum (Fn) is implicated in colorectal cancer (CRC) tumorigenesis and is becoming an important prognostic biomarker. We evaluated the detection accuracy and clinical relevance of Fn DNA by ddPCR in a molecularly characterized, formalin-fixed, paraffin-embedded (FFPE) CRC cohort previously analyzed by qPCR for Fn levels. Following a ddPCR assay optimization and an analytical evaluation, Fn DNA were measured in 139 CRC FFPE cases. The measures of accuracy for Fn status compared to the prior results generated by qPCR and the association with clinicopathological and molecular patients&rsquo; features were also evaluated. The ddPCR-based Fn assay was sensitive and specific to positive controls. Fn DNA were detected in 20.1% of cases and further classified as Fn-high and Fn-low/negative, according to the median amount of Fn DNA that were detected in all cases and associated with the patient&rsquo;s worst prognosis. There was a low agreement between the Fn status determined by ddPCR and qPCR (Cohen&rsquo;s Kappa = 0.210). Our findings show that ddPCR can detect and quantify Fn in FFPE tumor tissues and highlights its clinical relevance in Fn detection in a routine CRC setting

Defining suitable reference genes for RT-qPCR analysis on human sertoli cells after 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exposure

Quantitative real-time RT-PCR (qPCR) has proven to be a valuable molecular technique to quantify gene expression. There are few studies in the literature that describe suitable reference genes to normalize gene expression data. Studies of transcriptionally disruptive toxins, like tetrachlorodibenzo-p-dioxin (TCDD), require careful consideration of reference genes. The present study was designed to validate potential reference genes in human Sertoli cells after exposure to TCDD. 32 candidate reference genes were analyzed to determine their applicability. geNorm and NormFinder softwares were used to obtain an estimation of the expression stability of the 32 genes and to identify the most suitable genes for qPCR data normalization.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

In vivo assessment of DNA damage and protective effects of extracts from Miconia species using the comet assay and micronucleus test

The genus Miconia comprises similar to 1000 species belonging to the Melastomataceae family. Several crude plant extracts from Miconia and their isolated compounds have shown biological activities, such as analgesic and anti-neoplastic action; however, no studies concerning their effects on DNA are available. The present study aimed to evaluate, in vivo, the genotoxic and mutagenic effects of four species of plants from Miconia genus using the comet assay and micronucleus test. Their possible protective effects were also evaluated in experiments associating the plant extracts with cyclophosphamide (CPA). The methanolic extracts of Miconia albicans, Miconia cabucu, Miconia rubiginosa, Miconia stenostachya and the chloroformic extract of M. albicans were investigated. For genotoxic and mutagenic evaluations, three concentrations were tested, 200, 400 and 540 mg/kg body weight (bw), based on the solubility limit of the extract in distilled water. For the protective effects, only the highest dose was evaluated against 40 mg/kg bw of CPA. Blood was removed from mice tails pre- (T0) and post-treatment (T1-30 h) for the micronucleus test and 24 h post-treatment for the comet assay. The Student's t-test was used to compare data obtained at T0 and T1, the analysis of variance-Tukey test was used to compare between groups in the micronucleus test and the Kruskal-Wallis and Dunn's test were used to compare different groups in the comet assay. All the extracts induced alterations in DNA migration (comet assay); however, no mutagenic effect was observed in the micronucleus assay. All extracts showed a protective effect against CPA in both assays. Our study showed that the use of crude extracts could be more advantageous than the use of isolated compounds. The interaction between phytochemicals in the extracts showed efficacy in reducing mutagenicity and improving the protective effects.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

Mutagenicity and genotoxicity of isatin in mammalian cells in vivo

Isatin (1H-indole-2,3-dione) is a synthetically versatile substrate used for the synthesis of heterocyclic compounds and as a raw material for drug synthesis. Isatin and its derivatives demonstrate anticonvulsant, antibacterial, antifungal, antiviral, and anticancer properties. We evaluated the genotoxic and mutagenic effects of acute (24h) and repeated (14d) exposure to isatin in vivo. using the cornet assay and the micronucleus test. Three doses (50, 100, and 150 mg/kg b.w.) were administered to mice via gayage. Doses were selected according to the LD(50) of isatin, estimated in a preliminary test to be 1 g/kg b.w. To evaluate the results, parametric (ANOVA/Tukey) and non-parametric (Kruskal-Wallis/Dunn's post hoc test) tests were used, according to the nature of the data distribution. At all doses (50, 100 and 150 mg/kg b.w.), after acute treatment with isatin, alterations in DNA migration (comet assay) were not observed and mutagenic effects were not seen (micronucleus test on peripheral blood cells). After repeated doses, only the highest dose of isatin (150 mg/kg b.w.) induced alterations in the DNA that gave rise to micronuclei in the bone marrow and peripheral blood cells of the mice. Our results show that the mutagenic and genotoxic effects of isatin depend on dose and on period of exposure. (C) 2010 Elsevier B.V. All rights reserved.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

PFKFB2 Promoter Hypomethylation as Recurrence Predictive Marker in Well-Differentiated Thyroid Carcinomas

Despite the low mortality rates, well-differentiated thyroid carcinomas (WDTC) frequently relapse. BRAF and TERT mutations have been extensively related to prognosis in thyroid cancer. In this study, the methylation levels of selected CpGs (5-cytosine-phosphate-guanine-3) comprising a classifier, previously reported by our group, were assessed in combination with BRAF and TERT mutations. We evaluated 121 WDTC, three poorly-differentiated/anaplastic thyroid carcinomas (PDTC/ATC), 22 benign thyroid lesions (BTL), and 13 non-neoplastic thyroid (NT) tissues. BRAF (V600E) and TERT promoter (C228T and C250T) mutations were tested by pyrosequencing and Sanger sequencing, respectively. Three CpGs mapped in PFKFB2, ATP6V0C, and CXXC5 were evaluated by bisulfite pyrosequencing. ATP6V0C hypermethylation and PFKFB2 hypomethylation were detected in poor-prognosis (PDTC/ATC and relapsed WDTC) compared with good-prognosis (no relapsed WDTC) and non-malignant cases (NT/BTL). CXXC5 was hypomethylated in both poor and good-prognosis cases. Shorter disease-free survival was observed in WDTC patients presenting lower PFKFB2 methylation levels (p = 0.004). No association was observed on comparing BRAF (60.7%) and TERT (3.4%) mutations and prognosis. Lower PFKFB2 methylation levels was an independent factor of high relapse risk (Hazard Ratio = 3.2; CI95% = 1.1&ndash;9.5). PFKFB2 promoter methylation analysis has potential applicability to better stratify WDTC patients according to the recurrence risk, independently of BRAF and TERT mutations