HOXA1 3'UTR Methylation Is a Potential Prognostic Biomarker in Oral Squamous cell Carcinoma.

BACKGROUND: HOXA1 is a prognostic marker and a potential predictive biomarker for radioresistance in head and neck tumors. Its overexpression has been associated with promoter methylation and a worse prognosis in oral squamous cell carcinoma (OSCC) patients. However, opposite outcomes are also described. The effect of the methylation of this gene on different gene regions, other than the promoter, remains uncertain. We investigated the methylation profile at different genomic regions of HOXA1 in OSCC and correlated differentially methylated CpG sites with clinicopathological data. METHODS: The HOXA1 DNA methylation status was evaluated by analyzing data from The Cancer Genome Atlas and three Gene Expression Omnibus datasets. Significant differentially methylated CpG sites were considered with a |∆ß| ≥ 0.10 and a Bonferroni-corrected p-value < 0.01. Differentially methylated CpGs were validated by pyrosequencing using two independent cohorts of 15 and 47 OSCC patients, respectively. RESULTS: Compared to normal tissues, we found significantly higher DNA methylation levels in the 3'UTR region of HOXA1 in OSCC. Higher methylation levels in tumor samples were positively correlated with smoking habits and patients' overall survival. CONCLUSIONS: Our findings suggest that HOXA1 gene body methylation is a promising prognostic biomarker for OSCC with potential clinical applications in patient monitoring.

DNA Methylation-Based Method to Differentiate Malignant from Benign Thyroid Lesions.

Background: The differential diagnosis of thyroid nodules using fine-needle aspiration biopsy (FNAB) is challenging due to the inherent limitation of the cytology tests. The use of molecular markers has potential to complement the FNAB-based diagnosis and avoid unnecessary surgeries. In this study, we aimed to identify DNA methylation biomarkers and to develop a diagnostic tool useful for thyroid lesions. Methods: Genome-wide DNA methylation profiles (Illumina 450K) of papillary thyroid carcinoma (PTC = 60) and follicular thyroid carcinoma (FTC = 10) were compared with non-neoplastic thyroid tissue samples (NT = 50) and benign thyroid lesions (BTL = 17). The results were confirmed in publicly available databases from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) using the same DNA methylation platform. Two classifiers were trained to discriminate FTC and PTC from BTL. To increase the applicability of the method, six differentially methylated CpGs were selected and evaluated in 161 thyroid tumors and 69 BTL postsurgical specimens and 55 prospectively collected FNAB using bisulfite-pyrosequencing. Results: DNA methylation analysis revealed 2130 and 19 differentially methylated CpGs in PTC and FTC, respectively. The CpGs confirmed by GEO and TCGA databases showing high areas under the receiver operating characteristic curve in all sample sets were used to train our diagnostic classifier. The model based on six CpGs was able to differentiate benign from malignant thyroid lesions with 94.3% sensitivity and 82.4% specificity. A similar performance was found applying the algorithm to TCGA and GEO external data sets (91.3-97.4% sensitivity and 87.5% specificity). We successfully evaluated the classifiers using a bisulfite-pyrosequencing technique, achieving 90.7% sensitivity and 75.4% specificity in surgical specimens (five of six CpGs). The study comprising FNAB cytology materials corroborated the applicability and performance of the methodology, demonstrating 86.7% sensitivity and 89.5% specificity in confirmed malignant tumors, and 100% sensitivity and 89% specificity in cases with indeterminate cytology. Conclusions: A novel diagnostic tool with potential application in preoperative screening of thyroid nodules is reported here. The proposed protocol has the potential to avoid unnecessary thyroidectomies.

Alterações germinativas em pacientes com câncer de reto em idade jovem / Germline alterations in patients with rectal cancer at a young age

O câncer colorretal (CCR) é o terceiro tipo de câncer mais comum no mundo e a segunda causa de morte por câncer. Dados atuais apontam que o câncer de reto (CaRe) contribui para a maior incidência de CCR observada em pacientes jovens e é responsável por um aumento destes tumores em cerca de 75% nos últimos 40 anos. As variantes germinativas são reportadas em 14 a 16% dos indivíduos jovens com CCR, independente de história familiar de câncer. Ainda assim, a causa do desenvolvimento de CCR na maioria dos casos de indivíduos jovens ou famílias com múltiplos indivíduos afetados permanece desconhecida. Neste estudo, foram investigadas variantes germinativas em 76 pacientes com CaRe incluindo 29 classificados pelos critérios de Amsterdam I/II para a Síndrome de Lynch (Grupo 1) e 47 pacientes com idade igual ou inferior 40 anos (Grupo 2). O objetivo principal foi identificar variantes em 93 genes relacionados ao câncer que possam contribuir para o risco de desenvolvimento da doença usando sequenciamento de alto desempenho. Quinze variantes foram selecionadas e avaliadas em membros de oito famílias. Foram identificadas 153 variantes envolvendo 65 genes. Pacientes com câncer de reto apresentaram alta frequência de variantes germinativas em ATM (19%), APC (10%) e BRCA2 (9%). Variantes patogênicas ou likely-patogênicas foram identificadas em genes de alta (MSH2, MSH6, MLH1, MUTYH e BRCA2), moderada (ATM) e baixa (MTHFR e NOTCH1) penetrância, em 18% (14/76) dos pacientes, concordante com dados da literatura. Variantes características da Síndrome de Lynch foram identificadas em seis pacientes (6/76) e variantes associadas à polipose no gene MUTYH, em dois pacientes (2/76). Variantes patogênicas ou likely-patogênicas foram identificadas em 17% (8/47) dos pacientes jovens, especialmente em MUTYH (3/47), MTHFR (2/47), ATM, MSH6 e MLH1 (1/47 cada). Dentre estes, dois de 14 pacientes não reportaram câncer na família e seis tiveram pelo menos um caso de câncer na família, mas não preencheram os critérios clínicos para síndrome de predisposição hereditária ao câncer. Este estudo revelou 25 variantes novas (não identificadas em bancos de dados públicos ou reportadas em literatura). Em adição, foram observadas variantes germinativas em diferentes genes das vias MMR e de recombinação homóloga, incluindo ATM, BRCA2 e POLD1. Foram identificadas 15 variantes candidatas e ou associadas ao fenótipo nos genes ATM, APC, MSH2, MTHFR, CDKN2A, MUTYH e POLD1. Essas variantes foram avaliadas em 20 indivíduos de 8 famílias, sendo confirmadas nos probandos e identificadas em mais de um membro das famílias investigadas. A identificação de genes associados à predisposição ao CaRe tem potencial importância para o delineamento de estratégias mais eficientes de diagnóstico e aconselhamento genético em famílias com um alto risco de desenvolver este tumor (AU)

Colorectal cancer (CRC) is the third most common cancer worldwide and the second leading cause of cancer-related death. Recent studies suggest that rectal cancer (ReCa) contributes to the higher CRC incidence observed in young patients, and it is responsible for 75% of the increased incidence in colorectal tumors over the last 40 years. Germline variants have been reported in 14-16% of patients with early-onset CRC, regardless of family history of cancer. Nonetheless, the causes of CRC onset in most young patients or families with multiple affected cases remain unknown. We investigated germline variants in 76 ReCa patients, including 29 cases classified by the Amsterdam I/II criteria for Lynch Syndrome (Group 1) and 47 early-onset ReCa patients (≤40 years old, Group 2). The main objective was to identify variants in 93 cancer-related genes that can contribute to increased risk of the disease development using next-generation sequencing. Fifteen candidate variants were evaluated in eight selected families. Next-generation sequencing revealed 153 variants involving 65 genes. ReCa patients showed high frequency of germline variants in ATM (19%), APC (10%) and BRCA2 (9%). Pathogenic or likely-pathogenic variants were observed in high (MSH2, MSH6, MLH1, MUTYH, and BRCA2), moderate (ATM) and low (MTHFR and NOTCH1) penetrance genes, in 18% (14/76) of the patients, consistent with the literature data. Variants associated with Lynch Syndrome were identified in six patients (6/76), and variants involved in MUTYH-associated polyposis in two patients (2/76). Pathogenic or likely-pathogenic variants were identified in 17% (8/47) of early-onset patients, especially in the MUTYH (3/47), MTHFR (2/47), ATM, MSH6, and MLH1 (1/47 each) genes. Among these, two of fourteen patients had no family history of cancer and six reported at least one case of cancer in the family, but none of them met clinical criteria for the hereditary cancer syndrome. This study revealed 25 new variants (not reported in public databases or previous studies). In addition, germline variants were observed in several genes involved in MMR and homologous recombination (HR) pathways, including ATM, BRCA2 and POLD1. Fifteen candidates and associated to the phenotype variants were identified in the ATM, APC, MSH2, MTHFR, CDKN2A, MUTYH, and POLD1 genes. These variants were evaluated in 20 individuals (8 families), being confirmed in the index cases and identified in more than one relative of the evaluated families. The identification of genes associated with ReCa predisposition is crucial for outlining more efficient diagnostic strategies and for improving genetic counseling for families with high risk to develop this tumor type (AU)

Loss of DNA methylation is related to increased expression of miR-21 and miR-146b in papillary thyroid carcinoma.

BACKGROUND: DNA methylation in miRNA genes has been reported as a mechanism that may cause dysregulation of mature miRNAs and consequently impact the gene expression. This mechanism is largely unstudied in papillary thyroid carcinomas (PTC). METHODS: To identify differentially methylated miRNA-encoding genes, we performed global methylation analysis (Illumina 450 K), integrative analysis (TCGA database), data confirmation (pyrosequencing and RT-qPCR), and functional assays. RESULTS: Methylation analysis revealed 27 differentially methylated miRNA genes. The integrative analyses pointed out miR-21 and miR-146b as potentially regulated by methylation (hypomethylation and increased expression). DNA methylation and expression patterns of miR-21 and miR-146b were confirmed as altered, as well as seven of 452 mRNAs targets were down-expressed. The combined methylation and expression levels of miR-21 and miR-146b showed potential to discriminate malignant from benign lesions (91-96% sensitivity and 96-97% specificity). An increased expression of miR-146b due to methylation loss was detected in the TPC1 cell line. The miRNA mimic transfection highlighted putative target mRNAs. CONCLUSIONS: The increased expression of miR-21 and miR-146b due to loss of DNA methylation in PTC resulted in the disruption of the transcription machinery and biological pathways. These miRNAs are potential diagnostic biomarkers, and these findings provide support for future development of targeted therapies.

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

Context: 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.

Integrated data analysis reveals potential drivers and pathways disrupted by DNA methylation in papillary thyroid carcinomas.

BACKGROUND: Papillary thyroid carcinoma (PTC) is a common endocrine neoplasm with a recent increase in incidence in many countries. Although PTC has been explored by gene expression and DNA methylation studies, the regulatory mechanisms of the methylation on the gene expression was poorly clarified. In this study, DNA methylation profile (Illumina HumanMethylation 450K) of 41 PTC paired with non-neoplastic adjacent tissues (NT) was carried out to identify and contribute to the elucidation of the role of novel genic and intergenic regions beyond those described in the promoter and CpG islands (CGI). An integrative and cross-validation analysis were performed aiming to identify molecular drivers and pathways that are PTC-related. RESULTS: The comparisons between PTC and NT revealed 4995 methylated probes (88% hypomethylated in PTC) and 1446 differentially expressed transcripts cross-validated by the The Cancer Genome Atlas data. The majority of these probes was found in non-promoters regions, distant from CGI and enriched by enhancers. The integrative analysis between gene expression and DNA methylation revealed 185 and 38 genes (mainly in the promoter and body regions, respectively) with negative and positive correlation, respectively. Genes showing negative correlation underlined FGF and retinoic acid signaling as critical canonical pathways disrupted by DNA methylation in PTC. BRAF mutation was detected in 68% (28 of 41) of the tumors, which presented a higher level of demethylation (95% hypomethylated probes) compared with BRAF wild-type tumors. A similar integrative analysis uncovered 40 of 254 differentially expressed genes, which are potentially regulated by DNA methylation in BRAFV600E-positive tumors. The methylation and expression pattern of six selected genes (ERBB3, FGF1, FGFR2, GABRB2, HMGA2, and RDH5) were confirmed as altered by pyrosequencing and RT-qPCR. CONCLUSIONS: DNA methylation loss in non-promoter, poor CGI and enhancer-enriched regions was a significant event in PTC, especially in tumors harboring BRAFV600E. In addition to the promoter region, gene body and 3'UTR methylation have also the potential to influence the gene expression levels (both, repressing and inducing). The integrative analysis revealed genes potentially regulated by DNA methylation pointing out potential drivers and biomarkers related to PTC development.