Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors

Background: One of the most provocative recent observations in cancer epigenetics is the discovery of large hypomethylated blocks, including single copy genes, in colorectal cancer, that correspond in location to heterochromatic LOCKs (large organized chromatin lysine-modifications) and LADs (lamin-associated domains). Methods: Here we performed a comprehensive genome-scale analysis of 10 breast, 28 colon, nine lung, 38 thyroid, 18 pancreas cancers, and five pancreas neuroendocrine tumors as well as matched normal tissue from most of these cases, as well as 51 premalignant lesions. We used a new statistical approach that allows the identification of large hypomethylated blocks on the Illumina HumanMethylation450 BeadChip platform. Results: We find that hypomethylated blocks are a universal feature of common solid human cancer, and that they occur at the earliest stage of premalignant tumors and progress through clinical stages of thyroid and colon cancer development. We also find that the disrupted CpG islands widely reported previously, including hypermethylated island bodies and hypomethylated shores, are enriched in hypomethylated blocks, with flattening of the methylation signal within and flanking the islands. Finally, we found that genes showing higher between individual gene expression variability are enriched within these hypomethylated blocks. Conclusion: Thus hypomethylated blocks appear to be a universal defining epigenetic alteration in human cancer, at least for common solid tumors. Electronic supplementary material The online version of this article (doi:10.1186/s13073-014-0061-y) contains supplementary material, which is available to authorized users

Association of BRAFV600E Mutation and MicroRNA Expression with Central Lymph Node Metastases in Papillary Thyroid Cancer: A Prospective Study from Four Endocrine Surgery Centers

Background: Studies have demonstrated an association of the BRAFV600E mutation and microRNA (miR) expression with aggressive clinicopathologic features in papillary thyroid cancer (PTC). Analysis of BRAFV600E mutations with miR expression data may improve perioperative decision making for patients with PTC, specifically in identifying patients harboring central lymph node metastases (CLNM). Methods: Between January 2012 and June 2013, 237 consecutive patients underwent total thyroidectomy and prophylactic central lymph node dissection (CLND) at four endocrine surgery centers. All tumors were tested for the presence of the BRAFV600E mutation and miR-21, miR-146b-3p, miR-146b-5p, miR-204, miR-221, miR-222, and miR-375 expression. Bivariate and multivariable analyses were performed to examine associations between molecular markers and aggressive clinicopathologic features of PTC. Results: Multivariable logistic regression analysis of all clinicopathologic features found miR-146b-3p and miR-146b-5p to be independent predictors of CLNM, while the presence of BRAFV600E almost reached significance. Multivariable logistic regression analysis limited to only predictors available preoperatively (molecular markers, age, sex, and tumor size) found miR-146b-3p, miR-146b-5p, miR-222, and BRAFV600E mutation to predict CLNM independently. While BRAFV600E was found to be associated with CLNM (48% mutated in node-positive cases vs. 28% mutated in node-negative cases), its positive and negative predictive values (48% and 72%, respectively) limit its clinical utility as a stand-alone marker. In the subgroup analysis focusing on only classical variant of PTC cases (CVPTC), undergoing prophylactic lymph node dissection, multivariable logistic regression analysis found only miR-146b-5p and miR-222 to be independent predictors of CLNM, while BRAFV600E was not significantly associated with CLNM. Conclusion: In the patients undergoing prophylactic CLNDs, miR-146b-3p, miR-146b-5p, and miR-222 were found to be predictive of CLNM preoperatively. However, there was significant overlap in expression of these miRs in the two outcome groups. The BRAFV600E mutation, while being a marker of CLNM when considering only preoperative variables among all histological subtypes, is likely not a useful stand-alone marker clinically because the difference between node-positive and node-negative cases was small. Furthermore, it lost significance when examining only CVPTC. Overall, our results speak to the concept and interpretation of statistical significance versus actual applicability of molecular markers, raising questions about their clinical usefulness as individual prognostic markers.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/140269/1/thy.2015.0378.pd

Exploring the epigenetic regulation of telomerase reverse transcriptase (TERT) in human cancer cell lines

Telomerase regulation, including TERT promoter methylation, has been of long‐standing interest to cancer biologists. Rowland et al. have now vastly expanded their ongoing characterization of TERT promoter methylation in cancer cells, analyzing the methylation patterns of 833 cell lines from 23 human cancers. They document a highly conserved pattern of hypomethylation around the proximal promoter, as well as a more heterogeneous region of hypermethylation further upstream, both associated with active TERT expression in cancer cells. They further describe the interplay between activating TERT promoter mutations and allelic methylation and transcription patterns. This valuable dataset represents the most extensive characterization of TERT promoter methylation in cancer cells to date and will help guide the future study of transcriptional regulation of telomerase. Comment on: https://doi.org/10.1002/1878‐0261.1278

The Supreme Triumph of the Surgeon's Art': Narrative History of Endocrine Surgery

Endocrine surgery – the subspecialty of general surgery involving diseases of the thyroid, parathyroid, and adrenal glands as well as the endocrine pancreas – is a rapidly growing field of medicine that has a rich and fascinating history. As recently as the mid-19th Century, surgery for thyroid goiter was described as “horrid butchery” and believed by many to be too dangerous for any surgeon to attempt. Through the ingenuity and tireless efforts of surgeons in Europe and the U.S., thyroidectomy became a safe and even elegant operation, one that renowned Johns Hopkins surgeon William Halsted would describe in 1926 as representing “the supreme triumph of the surgeon’s art.” In this unique and captivating book, these and other seminal stories from the history of endocrine surgery are vividly retold by the current leaders in the field

Preoperative Molecular Markers in Thyroid Nodules

The need for distinguishing benign from malignant thyroid nodules has led to the pursuit of differentiating molecular markers. The most common molecular tests in clinical use are Afirma® Gene Expression Classifier (GEC) and Thyroseq® V2. Despite the rapidly developing field of molecular markers, several limitations exist. These challenges include the recent introduction of the histopathological diagnosis “Non-Invasive Follicular Thyroid neoplasm with Papillary-like nuclear features”, the correlation of genetic mutations within both benign and malignant pathologic diagnoses, the lack of follow-up of molecular marker negative nodules, and the cost-effectiveness of molecular markers. In this manuscript, we review the current published literature surrounding the diagnostic value of Afirma® GEC and Thyroseq® V2. Among Afirma® GEC studies, sensitivity (Se), specificity (Sp), positive predictive value (PPV), and negative predictive value (NPV) ranged from 75 to 100%, 5 to 53%, 13 to 100%, and 20 to 100%, respectively. Among Thyroseq® V2 studies, Se, Sp, PPV, and NPV ranged from 40 to 100%, 56 to 93%, 13 to 90%, and 48 to 97%, respectively. We also discuss current challenges to Afirma® GEC and Thyroseq® V2 utility and clinical application, and preview the future directions of these rapidly developing technologies

miR-126-3p Inhibits Thyroid Cancer Cell Growth and Metastasis, and Is Associated with Aggressive Thyroid Cancer

<div><p>Background</p><p>Previous studies have shown that microRNAs are dysregulated in thyroid cancer and play important roles in the post-transcriptional regulation of target oncogenes and/or tumor suppressor genes.</p><p>Methodology/Principal Findings</p><p>We studied the function of miR-126-3p in thyroid cancer cells, and as a marker of disease aggressiveness. We found that miR-126-3p expression was significantly lower in larger tumors, in tumor samples with extrathyroidal invasion, and in higher risk group thyroid cancer in 496 papillary thyroid cancer samples from The Cancer Genome Atlas study cohort. In an independent sample set, lower miR-126-3p expression was observed in follicular thyroid cancers (which have capsular and angioinvasion) as compared to follicular adenomas. Mechanistically, ectopic overexpression of miR-126-3p significantly inhibited thyroid cancer cell proliferation, <i>in vitro</i> (p<0.01) and <i>in vivo</i> (p<0.01), colony formation (p<0.01), tumor spheroid formation (p<0.05), cellular migration (p<0.05), VEGF secretion and endothelial tube formation, and lung metastasis <i>in vivo</i>. We found 14 predicted target genes, which were significantly altered upon miR-126-3p transfection in thyroid cancer cells, and which are involved in cancer biology. Of these 14 genes, <i>SLC7A5</i> and <i>ADAM9</i> were confirmed to be inhibited by miR-126-3p overexpression and to be direct targets of miR-136-3p.</p><p>Conclusions/Significance</p><p>To our knowledge, this is the first study to demonstrate that miR-126-3p has a tumor-suppressive function in thyroid cancer cells, and is associated with aggressive disease phenotype.</p></div

miR-126-3p overexpression inhibits cellular proliferation, and colony and spheroid formation.

<p><b>(A–C)</b> Thyroid cancer cell line proliferation with miR-126-3p overexpression. The Y axis represents the cell number. Error bars represent the standard error of the mean (SEM). (* indicates p<0.05; ** indicates p<0.01; *** indicates p<0.001). <b>(D)</b> miR-126-3p overexpression inhibits colony formation in thyroid cancer cells. Colony numbers in FTC-133 cell lines. The Y axis represents the number of colonies per field. Error bars represent SEM (*** indicates p<0.001). <b>(E)</b> miR-126-3p overexpression decreases the size and number of spheroids. Top panel: representative image of spheroids in culture with miR-126-3p overexpression (FTC-133 cells). Lower panel: Quantification of spheroid differences between XTC-1 and FTC-133 cells with miR-126-3p overexpression. The total area occupied by the spheroids within an image was measured by circumscribing the perimeter of each spheroid, marking the entire area, and calculating the pixel numbers with ImageJ software (National Institutes of Health, Bethesda, MD, USA). The Y axis represents the size and number of the spheroids. Error bars represent SEM (* indicates p<0.05).</p