Gene expression analysis reveals evidence for inactivation of the TGF-β signaling cascade in autonomously functioning thyroid nodules

Molecular Tests for Risk-Stratifying Cytologically Indeterminate Thyroid Nodules: An Overview of Commercially Available Testing Platforms in the United States

The past decade has witnessed significant advances in the application of molecular diagnostics for the pre-operative risk-stratification of cytologically indeterminate thyroid nodules. The tests that are currently marketed in the United States for this purpose combine aspects of tumor genotyping with gene and/or microRNA expression profiling. This review compares the general methodology and clinical validation studies for the three tests currently offered in the United States: ThyroSeq v3, Afirma GSC and Xpression Atlas, and ThyGeNEXT/ThyraMIR.

Updates in Thyroid Cytology

Genomic, clinical, and pathologic studies have prompted a more risk-stratified approach to the management of patients with thyroid nodules. The recent nomenclature change concerning noninvasive follicular thyroid neoplasm with papillary-like nuclear features reflects the clinical trend toward conservative treatment choices for carefully selected low-risk thyroid neoplasms. These developments have occurred in parallel with a growing array of molecular tests intended to improve clinical triage for patients with indeterminate fine needle aspiration diagnoses. This review discusses the implications of the nomenclature revision on the interpretation of thyroid fine needle aspiration and updates available ancillary molecular tests for thyroid fine needle aspirations.

Glycosylation in the Thyroid Gland: Vital Aspects of Glycoprotein Function in Thyrocyte Physiology and Thyroid Disorders

The key proteins responsible for hormone synthesis in the thyroid are glycosylated. Oligosaccharides strongly affect the function of glycosylated proteins. Both thyroid-stimulating hormone (TSH) secreted by the pituitary gland and TSH receptors on the surface of thyrocytes contain N-glycans, which are crucial to their proper activity. Thyroglobulin (Tg), the protein backbone for synthesis of thyroid hormones, is a heavily N-glycosylated protein, containing 20 putative N-glycosylated sites. N-oligosaccharides play a role in Tg transport into the follicular lumen, where thyroid hormones are produced, and into thyrocytes, where hyposialylated Tg is degraded. N-glycans of the cell membrane transporters sodium/iodide symporter and pendrin are necessary for iodide transport. Some changes in glycosylation result in abnormal activity of the thyroid and alteration of the metabolic clearance rate of hormones. Alteration of glycan structures is a pathological process related to the progression of chronic diseases such as thyroid cancers and autoimmunity. Thyroid carcinogenesis is accompanied by changes in sialylation and fucosylation, β1,6-branching of glycans, the content and structure of poly-LacNAc chains, as well as O-GlcNAcylation, while in thyroid autoimmunity the main processes affected are sialylation and fucosylation. The glycobiology of the thyroid gland is an intensively studied field of research, providing new data helpful in understanding the role of the sugar component in thyroid protein biology and disorders.

Molecular pathogenesis of nodular goiter

INTRODUCTION

Familial clustering of goiters mostly with an autosomal dominant pattern of inheritance has repeatedly been reported. Moreover, other environmental and etiologic factors are likely to be involved in the development of euthyroid goiter. Therefore, a multifactorial etiology based on complex interactions of both genetic predisposition and the individuals' environment is likely.

METHODS

The line of events from early thyroid hyperplasia to multinodular goiter argues for the predominant neoplastic (i.e., originating from a single mutated cell) character of nodular structures. Etiologically, relevant somatic mutations are known in two thirds of papillary and follicular thyroid carcinomas and hot thyroid nodules. In contrast, the somatic mutations relevant for benign cold or benign isocaptant thyroid nodules which constitute the majority of thyroid nodules are unknown.

RESULTS

The nodular process is triggered by the oxidative nature of thyroid hormone synthesis or additional oxidative stress caused by iodine deficiency or smoking. If the antioxidant defense is not effective, this oxidative stress will cause DNA damage followed by an increase of the spontaneous mutation rate which is a substrate for tumorogenesis.

CONCLUSIONS

Therefore, the hallmark of thyroid physiology--H(2)O(2) production during hormone synthesis--is very likely the ultimate cause for the frequent mutagenesis in the thyroid gland. Because iodine deficiency increases the oxidative burden, DNA damage and mutagenesis could provide the basis for the frequent nodular transformation of endemic goiters.

Role of transforming growth factor beta in the regulation of thyroid function and growth

Transforming growth factor beta (TGF-beta) exists in nature as three isoforms. They exert their effects by binding to a type II receptor located at the cell membrane. The TGF-beta-type II receptor complex then recruits type I receptor, and this new complex stimulates the phosphorylation of Smads 2 and 3, which are subsequently transferred to the nucleus, where they regulate gene transcription. The thyroid gland expresses the TGF-beta1 gene mRNA and synthesizes the protein, which under physiologic conditions regulates thyroid growth and function. Different studies have demonstrated that TGF-beta1 inhibits cell proliferation and a number of functional parameters. These include cyclic adenosine monophosphate (AMP) formation, iodine uptake and organification, hormone secretion, and the expression of thyroglobulin, thyroid peroxidase, and Na(+)/I(-) symporter. The expression of the TGF-beta1 gene and protein may be stimulated by iodine under normal conditions. Since TGF-beta1 mimics some of the inhibitory actions of iodine, its participation in thyroid autoregulation has been proposed; however, this concept is still debated. In thyroid tumors, the inhibitory action of TGF-beta1 on cell proliferation is progressively lost as the tumor becomes more undifferentiated. The alterations in the signaling pathway of TGF-beta1 are not the same in tumors from different species. Even within the same species, such as the pig thyroid, the results may be different depending on whether monolayers or follicular suspensions are employed. The data suggest that it is not entirely possible to apply the results obtained in animal studies to normal or pathological human thyroid tissue. More studies are required to provide the information needed to develop treatments, based on targeting the signaling pathway of TGF-beta1, for undifferentiated thyroid cancer and other thyroid diseases.

Proteomics in thyroid tumor research

BACKGROUND

In recent years, "OMICS" technologies have paved novel ways for the broad-scale identification of molecular signatures and signaling pathways specific to tumorigenesis. Related to this are high hopes for the discovery of biomarkers facilitating diagnosis and prognosis of cancer as well as the option for pathway-targeted tumor treatment. Among the different OMICS methods, the potential of proteomics is just beginning to emerge, and according to the current literature, the proteome is to date the most feasible tool to reflect tumor biology.

OBJECTIVE

In this review we discuss the application of proteomics to the field of thyroid tumor research.

CONTEXT

First, we provide an overview of different methods for protein expression profiling and then discuss specific requirements and challenges of thyroid proteomics. Furthermore, we summarize results of published proteomics studies on human thyroid tumors and finally explore perspectives of thyroid proteomics, which, combined with mRNA expression profiling and traditional biochemical methods, is increasingly contributing to an improved understanding of thyroid tumorigenesis and may in the future open novel avenues in thyroid cancer therapy.

Perspectives for improved and more accurate classification of thyroid epithelial tumors

CONTEXT

Histologic examination of thyroid nodules is the current standard to distinguish benign from malignant thyroid epithelial tumors and to classify histologic subtypes. This review analyzes the problems in histological differential diagnosis as well as contradictions between histology and molecular data and describes possibilities to combine histology with molecular data in an effort to more accurately classify thyroid epithelial tumors.

EVIDENCE ACQUISITION

Published literature, addressing the current recommendations for thyroid tumor classification, as well as literature on the application of histology and molecular studies on the etiology of thyroid tumors is analyzed.

EVIDENCE SYNTHESIS

The current histologic criteria to classify thyroid tumors, especially follicular-patterned tumors, are hampered by considerable interobserver variability. The detection of somatic mutations via genotyping and the definition of potentially informative gene expression signatures by microarray analyses, which can distinguish cancer subtypes as well as low- and high-risk cohorts, have recently demonstrated significant diagnostic potential. Moreover, in a routine diagnostic setting, micro-RNA profiling appears most promising due to their relative stability and the high accuracy of their expression profiles.

CONCLUSIONS

It is very likely that molecular definitions of thyroid tumors mentioned in the current World Health Organization classification will be further developed, leading to future progress in defining thyroid tumor types by an integrated histologic and molecular approach. These integrated classifications need to be evaluated for their specific impact on thyroid tumor diagnosis and prognosis.

Insights from molecular pathways: potential pharmacologic targets of benign thyroid nodules

PURPOSE OF REVIEW

To describe molecular pathways that might be of relevance for a potential pharmacologic therapy of benign thyroid nodules.

RECENT FINDINGS

Constitutively activating thyrotropin receptor mutations have been found in about 60% of hot nodules. Its predominant role for signaling in hot nodules has been confirmed by in-vitro mutagenesis studies, thyrotropin receptor modeling and microarray studies. In contrast, the basic molecular cause of cold thyroid nodules is so far largely unknown. Defective sodium/iodide symporter trafficking, accumulation of T4-deficient, insufficiently iodinated thyroglobulin, increased oxidative stress and differential expression of several Gqalpha-protein kinase C pathway-associated genes have, however, recently been identified in cold thyroid nodules.

SUMMARY

As disturbed thyrotropin receptor signaling plays a central role in hot thyroid nodules, the identification of effective low-molecular-weight thyrotropin receptor ligands, such as thyrotropin receptor agonists, inverse agonists and antagonists has a pharmacologic potential in the diagnosis and treatment of thyroid cancer, Graves' disease and hot thyroid nodules, respectively. Further studies have to clarify the pharmacologic potential of the enhancement of antioxidative mechanisms and the inhibition of Gqalpha-protein kinase C signaling in cold thyroid nodules.

A multi-gene approach to differentiate papillary thyroid carcinoma from benign lesions: gene selection using support vector machines with bootstrapping

Selection of novel molecular markers is an important goal of cancer genomics studies. The aim of our analysis was to apply the multivariate bioinformatical tools to rank the genes - potential markers of papillary thyroid cancer (PTC) according to their diagnostic usefulness. We also assessed the accuracy of benign/malignant classification, based on gene expression profiling, for PTC. We analyzed a 180-array dataset (90 HG-U95A and 90 HG-U133A oligonucleotide arrays), which included a collection of 57 PTCs, 61 benign thyroid tumors, and 62 apparently normal tissues. Gene selection was carried out by the support vector machines method with bootstrapping, which allowed us 1) ranking the genes that were most important for classification quality and appeared most frequently in the classifiers (bootstrap-based feature ranking, BBFR); 2) ranking the samples, and thus detecting cases that were most difficult to classify (bootstrap-based outlier detection). The accuracy of PTC diagnosis was 98.5% for a 20-gene classifier, its 95% confidence interval (CI) was 95.9-100%, with the lower limit of CI exceeding 95% already for five genes. Only 5 of 180 samples (2.8%) were misclassified in more than 10% of bootstrap iterations. We specified 43 genes which are most suitable as molecular markers of PTC, among them some well-known PTC markers (MET, fibronectin 1, dipeptidylpeptidase 4, or adenosine A1 receptor) and potential new ones (UDP-galactose-4-epimerase, cadherin 16, gap junction protein 3, sushi, nidogen, and EGF-like domains 1, inhibitor of DNA binding 3, RUNX1, leiomodin 1, F-box protein 9, and tripartite motif-containing 58). The highest ranking gene, metallophosphoesterase domain-containing protein 2, achieved 96.7% of the maximum BBFR score.

Modulation of TSHR signaling by posttranslational modifications

Posttranslational modifications of seven transmembrane receptors (7TMRs) affect their function to a large extent. Many studies of glycosylation or phosphorylation of 7TMRs have shown that these modifications influence the cell-surface expression or signaling of the receptor. Recently, other types of posttranslational modifications of the thyrotropin-stimulating hormone receptor (TSHR) have been characterized, including sialylation and dimerization. Increased TSHR sialylation results in increased TSHR cell-surface expression. Furthermore, TSHR oligomerization and the probable modification of TSHR signaling in lipid rafts require further clarification with regard to their functional consequences. In addition to its known coupling to Galphas and Galphaq, and possibly other G proteins, the TSHR also couples to further signaling pathways, such as the mitogen-activated protein kinase (MAPK) pathway, which involves G-protein-coupled receptor kinases (GRKs) and arrestins. We discuss these emerging new findings and their implications for signaling of the TSHR.

Perspectives and limitations of microarray-based gene expression profiling of thyroid tumors

Microarray technology has become a powerful tool to analyze the gene expression of tens of thousands of genes simultaneously. Microarray-based gene expression profiles are available for malignant thyroid tumors (i.e., follicular thyroid carcinoma, and papillary thyroid carcinoma), and for benign thyroid tumors (such as autonomously functioning thyroid nodules and cold thyroid nodules). In general, the two main foci of microarray investigations are improved understanding of the pathophysiology/molecular etiology of thyroid neoplasia and the detection of genetic markers that could improve the differential diagnosis of thyroid tumors. Their results revealed new features, not known from one-gene studies. Simultaneously, the increasing number of microarray analyses of different thyroid pathologies raises the demand to efficiently compare the data. However, the use of different microarray platforms complicates cross-analysis. In addition, there are other important differences between these studies: 1) some studies use intraindividual comparisons, whereas other studies perform interindividual comparisons; 2) the reference tissue is defined as strictly nonnodular healthy tissue or also contains benign lesions such as goiter, follicular adenoma, and hyperplastic nodules in some studies; and 3) the widely used Affymetrix GeneChip platform comprises several GeneChip generations that are only partially compatible. Moreover, the different studies are characterized by strong differences in data analysis methods, which vary from simple empiric filters to sophisticated statistic algorithms. Therefore, this review summarizes and compares the different published reports in the context of their study design. It also illustrates perspectives and solutions for data set integration and meta-analysis, as well as the possibilities to combine array analysis with other genetic approaches.

Comparison of Independent Samples of High-Dimensional Data by Pairwise Distance Measures

Pairwise distance or association measures of sample elements are often used as a basis for hierarchical cluster analyses. They can also be used in tests for the comparison of pre-defined subgroups of the total sample. Usually this is done with permutation tests In this paper, we compare such a procedure with alternative tests for high-dimensional data based on spherically distributed scores in simulation experiments and with real data. The tests based on the pairwise distance or similarity measures perform quite well in this comparison. As the number of possible permutations is small in very small samples, this might restrict the use of the test. Therefore, we propose an exact parametric small sample version of the test using randomly rotated samples.

Contemporary diagnostic approach to the thyroid nodule

Thyroid nodules are common, with an estimated incidence of 5%-10% in the United States. The current gold standard for diagnosis is fine needle aspiration biopsy (FNAB). The incidence of indeterminate diagnoses varies from 10% to 25%. Surgical resection is usually indicated to exclude the diagnosis of cancer in these patients. However, only a minority (about 20%) of indeterminate thyroid nodules actually harbor a malignancy, resulting in surgery for diagnostic purposes alone in many patients. The increased detection of benign nodules and microcarcinomas reinforces the need for improved non-operative methods to differentiate benign from malignant disease and discriminate low-risk from high-risk cancers. In this article we present a current, rational diagnostic approach to the patient with a thyroid nodule, evaluate new advances including thyroid genomic and predictor models, and propose the development of prospective trials to incorporate these new additions into clinical decision making. Given how many questions still exist for patients with thyroid nodules, partnership and collaboration, or the "bench to bedside" concept should find its way into most every thyroid surgeon and endocrinologist's lexicon.

Molecular determination of benign and malignant thyroid tumors

Recent molecular studies have revolutionized our understanding of the pathogenesis of thyroid tumors and particular advances have been made in three areas. First, toxic thyroid nodules, which originate from constitutive activation of thyroid-stimulating hormone receptor/Gs α signaling and represent the dominant cause of thyrotoxicosis in regions with iodine deficiency. Second, papillary thyroid cancer, the most frequent thyroid malignancy, which is characterized by a common fingerprint of constitutive mitogen-activated protein kinase activation. Importantly, this is caused by distinct genetic alterations in radiation-induced (RET/PTC, NTRK and AKAP9/BRAF rearrangements) and sporadic tumors (BRAF and RAS point mutation) and, recently, there exciting in vitro have emerged explaining the structural basis for this. These findings suggest a scenario in which the fate of a thyroid tumor is determined by the specific genetic defect at the beginning. Third, application of microarray analysis in nodular pathologies in which the oncogenic pathway is less clear, notably follicular neoplasia, has led to the identification of a number of promising genetic markers (TFF-3, Gal-3, PLAB, CCND2 and PCKD2) for the diagnostic distinction of follicular adenoma and carcinoma. In addition to the diagnostic perspective, the identification of molecular fingerprints of thyroid tumors opens novel avenues for an improved therapeutic approach; for example, selective antagonism of cell signaling in treatment-refractory thyroid cancer.

Meta- and reanalysis of gene expression profiles of hot and cold thyroid nodules and papillary thyroid carcinoma for gene groups

CONTEXT

There are an increasing number of studies analyzing gene expression profiles in various benign and malignant thyroid tumors. This creates the opportunity to validate results obtained from one microarray study with those from other data sets. This process requires rigorous methods for accurate comparison.

OBJECTIVE

The ability to compare data sets derived from different Affymetrix GeneChip generations and the influence of intra- and interindividual comparisons of gene expression data were evaluated to build multigene classifiers of benign thyroid nodules to verify a previously proposed papillary thyroid carcinoma (PTC) classifier and to look for molecular pathways essential for PTC oncogenesis.

METHODS

Gene expression profile data sets from autonomously functioning and cold thyroid nodules and from PTC were analyzed by support vector machines. GenMAPP analysis was used for PTC data analysis to examine the expression patterns of biologically relevant gene sets.

RESULTS

Only intraindividual reference samples allowed the identification of subtle changes in the expression patterns of relevant signaling cascades, such as the MAPK pathway in PTC. Using an artificial intelligence approach, the autonomously functioning and cold thyroid nodule multigene classifiers were derived and evaluated by cross-comparisons.

CONCLUSION

We recommend defining classifiers within one generation of gene chips and subsequently checking them across different array generations. Using this approach, we have demonstrated the specificity of a previously reported PTC classifier on an independent collection of benign tumors. Moreover, we propose multigene classifiers for different types of benign thyroid nodules.

Comparison of differential gene expression of hot and cold thyroid nodules with primary epithelial cell culture models by investigation of co-regulated gene sets

Both autonomously functioning thyroid nodules (AFTNs) and cold thyroid nodules (CTNs) are characterized by an increased proliferation, however, they have opposite functional activities. Therefore, with the aim to further understand the distinct molecular pathology of each entity and to discover common mechanisms like those leading to increased proliferation in both, AFTNs and CTNs, we now compared gene expression of AFTNs and CTNs with in vitro model systems (TSH-stimulated and ras-transfected primary cultures (PC)) whose gene expression patterns can be attributed to specific molecular alterations. Since combinations of co-regulated genes are more likely to reveal molecular mechanisms, we used a procedure which groups co-regulated genes within "gene sets". We found a co-regulated gene set in the AFTNs that overlaps with differential expression in TSH-stimulated PCs but not in CTNs or ras-transfected PCs. In addition to thyroid peroxidase and sialyltransferase 1, this set of co-regulated genes comprises metallothioneins and the G-protein-coupled receptor 56. Although their role in the thyroid is unknown so far, their appearance in one group indicates a functional relevance in TSH-TSH receptor-stimulated mechanisms. Furthermore, we identified down-regulated gene sets with concordant expression patterns in AFTNs, CTNs and ras-transfected PCs. However, these expression patterns are not of relevance in the TSH-stimulated PCs. These findings suggest that TSH-stimulated PCs can be used as a model of increased thyroid function (AFTNs), whereas the ras-transfected PCs better reflect the increased proliferation of both AFTNs and CTNs.

Gene expression in thyroid autonomous adenomas provides insight into their physiopathology

The purpose of this study was to use the microarray technology to define expression profiles characteristic of thyroid autonomous adenomas and relate these findings to physiological mechanisms. Experiments were performed on a series of separated adenomas and their normal counterparts on Micromax cDNA microarrays covering 2400 genes (analysis I), and on a pool of adenomatous tissues and their corresponding normal counterparts using microarrays of 18,000 spots (analysis II). Results for genes present on the two arrays corroborated and several gene regulations previously determined by Northern blotting or microarrays in similar lesions were confirmed. Five overexpressed and 24 underexpressed genes were also confirmed by real-time RT-PCR in some of the samples used for microarray analysis, and in additional tumor specimens. Our results show: (1) a change in the cell populations of the tumor, with a marked decrease in lymphocytes and blood cells and an increase in endothelial cells. The latter increase would correspond to the establishment of a close relation between thyrocytes and endothelial cells and is related to increased N-cadherin expression. It explains the increased blood flow in the tumor; (2) a homogeneity of tumor samples correlating with their common physiopathological mechanism: the constitutive activation of the thyrotropin (TSH)/cAMP cascade; (3) a low proportion of regulated genes consistent with the concept of a minimal deviation tumor; (4) a higher expression of genes coding for specific functional proteins, consistent with the functional hyperactivity of the tumors; (5) an increase of phosphodiesterase gene expression which explains the relatively low cyclic AMP levels measured in these tumors; (6) an overexpression of antiapoptotic genes and underexpression of proapoptotic genes compatible with their low apoptosis rate; (7) an overexpression of N-cadherin and downregulation of caveolins, which casts doubt about the use of these expressions as markers for malignancy.

Gene expression in human thyrocytes and autonomous adenomas reveals suppression of negative feedbacks in tumorigenesis

The cAMP signaling pathway regulates growth of many cell types, including somatotrophs, thyrocytes, melanocytes, ovarian follicular granulosa cells, adrenocortical cells, and keratinocytes. Mutations of partners from the cAMP signaling cascade are involved in tumor formation. Thyroid-stimulating hormone (TSH) receptor and Gsalpha activating mutations have been detected in thyroid autonomous adenomas, Gsalpha mutations in growth hormone-secreting pituitary adenomas, and PKAR1A mutations in Carney complex, a multiple neoplasia syndrome. To gain more insight into the role of cAMP signaling in tumor formation, human primary cultures of thyrocytes were treated for different times (1.5, 3, 16, 24, and 48 h) with TSH to characterize modulations in gene expression using cDNA microarrays. This kinetic study showed a clear difference in expression, early (1.5 and 3 h) and late (16-48 h) after the onset of TSH stimulation. This result suggests a progressive sequential process leading to a change of cell program. The gene expression profile of the long-term stimulated cultures resembled the autonomous adenomas, but not papillary carcinomas. The molecular phenotype of the adenomas thus confirms the role of long-term stimulation of the TSH-cAMP cascade in the pathology. TSH induced a striking up-regulation of different negative feedback modulators of the cAMP cascade, presumably insuring the one-shot effect of the stimulus. Some were down- or nonregulated in adenomas, suggesting a loss of negative feedback control in the tumors. These results suggest that in tumorigenesis, activation of proliferation pathways may be complemented by suppression of multiple corresponding negative feedbacks, i.e., specific tumor suppressors.

Modulation of thyroid-specific gene expression in normal and nodular human thyroid tissues from adults: an in vivo effect of thyrotropin

CONTEXT

Evidence from in vitro studies or animal models has shown that TSH affects thyrocytes by thyroid-specific expression modulation.

OBJECTIVE

The objective of our study was to analyze the role of TSH in human thyroid gene expression in vivo.

DESIGN/SETTING

Thirty-nine normal thyroid tissues were collected at the same center.

STUDY SUBJECTS

Patients were divided into two groups based on serum TSH levels: 17 with normal TSH levels (1-4 mU/liter; group 1) and 22 with TSH levels below 0.5 mU/liter (group 2).

INTERVENTION

Group 2 underwent thyroidectomy after suppressive L-T4 therapy.

MAIN OUTCOME MEASURES

mRNA levels of thyroid genes such as sodium/iodide symporter (NIS), apical iodide transporter, pendrin, thyroglobulin, thyroperoxidase, TSH receptor, paired box transcription factor 8, and thyroid transcription factor-1 were evaluated by quantitative PCR.

RESULTS

The reduction of TSH stimulation causes decreases in NIS and apical iodide transporter gene expression in normal tissues and more limited reductions in thyroglobulin, thyroperoxidase, and paired box transcription factor 8, but it has no significant effect on TSH receptor, pendrin, or thyroid transcription factor-1. Comparison of NIS levels in normal and nodular tissues from the same patient confirmed that it is differentially expressed in nodules only in the presence of normal TSH (P < 0.01). In patients with suppressed TSH, nodular NIS levels were similar to those in normal tissues.

CONCLUSIONS

Our data represent the first demonstration in human thyroid tissues that TSH contributes to the regulation of thyrocyte differentiation by modulating thyroid gene levels. It exerts a particularly important effect on the transcription of NIS, which becomes very low after prolonged TSH suppression.

Sialylation of human thyrotropin receptor improves and prolongs its cell-surface expression

Glycosylation of the thyrotropin receptor (TSHR) has been shown to be essential for correct protein folding and for cell-surface targeting. In a recent study, we detected increased expression of beta-galactoside alpha(2,6)-sialyltransferase (SIAT1) in toxic thyroid adenomas where gain-of-function mutations of the TSHR have been invoked as one of the major causes. To investigate the physiological meaning of these findings, we designed experiments to evaluate the consequences of sialylation for the expression of the TSHR. Hence, we investigated the effect of coexpressing the TSHR and different sialyltransferases (SIAT1, SIAT4a, and SIAT8a) for cell-surface expression of the receptor. Coexpression of each of the three SIAT isoforms and the TSHR in COS-7 cells increased TSHR expression on the cell surface in the range of 50 to 100%. Moreover, Western blot analysis with lectins specific for alpha(2,3) and alpha(2,6)-linked sialic acids and lectin-binding enzyme-linked immunosorbent assay support a direct effect on TSHR cell-surface expression mediated by sialic acid transfer to the TSHR. Finally, we treated living COS-7 cells after cotransfection of TSHR and SIAT8a with neuraminidase for 30 min to remove covalently linked sialic acid. Subsequent loss of TSHR cell-surface expression suggests that sialylation prolongs the resting time of the TSHR on the cell surface. Our data demonstrate for the first time that the transfer of sialic acid can improve and prolong cell-surface expression of a transmembrane receptor.

Increased power of microarray analysis by use of an algorithm based on a multivariate procedure

MOTIVATION

The power of microarray analyses to detect differential gene expression strongly depends on the statistical and bioinformatical approaches used for data analysis. Moreover, the simultaneous testing of tens of thousands of genes for differential expression raises the 'multiple testing problem', increasing the probability of obtaining false positive test results. To achieve more reliable results, it is, therefore, necessary to apply adjustment procedures to restrict the family-wise type I error rate (FWE) or the false discovery rate. However, for the biologist the statistical power of such procedures often remains abstract, unless validated by an alternative experimental approach.

RESULTS

In the present study, we discuss a multiplicity adjustment procedure applied to classical univariate as well as to recently proposed multivariate gene-expression scores. All procedures strictly control the FWE. We demonstrate that the use of multivariate scores leads to a more efficient identification of differentially expressed genes than the widely used MAS5 approach provided by the Affymetrix software tools (Affymetrix Microarray Suite 5 or GeneChip Operating Software). The practical importance of this finding is successfully validated using real time quantitative PCR and data from spike-in experiments.

AVAILABILITY

The R-code of the statistical routines can be obtained from the corresponding author.

CONTACT

Schuster@imise.uni-leipzig.de

Absence of a specific radiation signature in post-Chernobyl thyroid cancers

Thyroid cancers have been the main medical consequence of the Chernobyl accident. On the basis of their pathological features and of the fact that a large proportion of them demonstrate RET-PTC translocations, these cancers are considered as similar to classical sporadic papillary carcinomas, although molecular alterations differ between both tumours. We analysed gene expression in post-Chernobyl cancers, sporadic papillary carcinomas and compared to autonomous adenomas used as controls. Unsupervised clustering of these data did not distinguish between the cancers, but separates both cancers from adenomas. No gene signature separating sporadic from post-Chernobyl PTC (chPTC) could be found using supervised and unsupervised classification methods although such a signature is demonstrated for cancers and adenomas. Furthermore, we demonstrate that pooled RNA from sporadic and chPTC are as strongly correlated as two independent sporadic PTC pools, one from Europe, one from the US involving patients not exposed to Chernobyl radiations. This result relies on cDNA and Affymetrix microarrays. Thus, platform-specific artifacts are controlled for. Our findings suggest the absence of a radiation fingerprint in the chPTC and support the concept that post-Chernobyl cancer data, for which the cancer-causing event and its date are known, are a unique source of information to study naturally occurring papillary carcinomas.

Molecular pathogenesis of euthyroid and toxic multinodular goiter

The purpose of this review is to summarize current knowledge of the etiology of euthyroid and toxic multinodular goiter (MNG) with respect to the epidemiology, clinical characteristics, and molecular pathology. In reconstructing the line of events from early thyroid hyperplasia to MNG we will argue the predominant neoplastic character of nodular structures, the nature of known somatic mutations, and the importance of mutagenesis. Furthermore, we outline direct and indirect consequences of these somatic mutations for thyroid pathophysiology and summarize information concerning a possible genetic background of euthyroid goiter. Finally, we discuss uncertainties and open questions in differential diagnosis and therapy of euthyroid and toxic MNG.

Advancing the molecular diagnosis of thyroid nodules: defining benign lesions by molecular profiling

BACKGROUND

Thyroid nodules are common and most are benign. Previous data from our laboratory and others has suggested that gene profiling can accurately distinguish between benign and malignant thyroid nodules and provide new leads in the study of thyroid tumorigenesis. Current preoperative techniques do not permit distinction between neoplastic and hyperplastic follicular neoplasms. These studies were undertaken to determine whether benign follicular tumors could be subcategorized by molecular profiling.

METHODS

Molecular profiles of 8 follicular adenomas and 8 hyperplastic nodules were analyzed by oligonucleotide microarray analysis. A list of 402 differentially expressed genes was produced based on a comparison of these two groups. Seven additional benign follicular lesions were then added to the analysis. A hierarchical clustering analysis was performed on all 23 samples, utilizing the gene list generated from the test set, to examine the groups for potential differences and the ability of the gene list to distinguish tumor types.

RESULTS

Cluster analysis of all 23 samples produced two distinct groups, one containing the adenomas and one containing the hyperplastic lesions. The analysis was able to identify follicular adenomas with a sensitivity of 84.6% and a specificity of 100%.

CONCLUSIONS

These data indicate that benign thyroid lesions can be separated into distinct groups through molecular profiling. Analysis of the gene list may help further the understanding of thyroid tumorigenesis. Expression profiling may ultimately allow us to distinguish potentially malignant from benign follicular nodules.

Gene expression analysis reveals evidence for increased expression of cell cycle-associated genes and Gq-protein-protein kinase C signaling in cold thyroid nodules

In contrast to the molecular etiology of autonomously functioning thyroid nodules, the molecular cause of cold thyroid nodules (CTNs), their benign, functional inactive counterparts, are so far largely unknown. Because of the partially dedifferentiated phenotype of CTNs, alterations in signaling cascades that favor proliferation, but not differentiation, are likely candidates for tumor induction and progression. The importance of RAS mutations for the development of benign nodules with follicular histology is still in question. However, differentially expressed genes in the context of their signaling cascades could define aberrant signaling in CTNs. Therefore, we investigated gene expression in 22 CTNs and their normal surrounding tissue using Affymetrix GeneChips. Most prominently, data analysis revealed an increased expression of cell cycle-associated genes and a special relevance of protein kinase C signaling, whereas no evidence of RAS-MAPK signaling in CTNs was found. Moreover, we determined 31 differentially regulated genes in CTNs, including several histone mRNAs. Taken together, these results explain recent findings showing an increased proliferation in CTNs and draw attention to protein kinase C signaling, but away from RAS-MAPK signaling, as being involved in the etiology of CTNs.

Quantitative proteome analysis in benign thyroid nodular disease using the fluorescent ruthenium II tris(bathophenanthroline disulfonate) stain

Thyroid tumorigenesis involves qualitative and quantitative changes in protein expression, which can be comprehensively studied by proteome analysis. However, one of the technical bottlenecks of proteomics remains a reliable, sensitive and inexpensive method for quantification of differentially expressed proteins. This is due to the limited linear range of most available protein stains, i.e. silver and Coomassie blue, and high costs of commercially available fluorescent stains. In this paper we describe our experience with a lab-made ruthenium based fluorescent stain (ruthenium II tris(bathophenanthroline disulfonate) (RuBPs)) to perform proteome analysis of nodular thyroid disease. We first compared the properties of RuBPs with two highly sensitive protein stains: (1) silver staining and (2) the commercially available fluorescent dye Sypro Ruby. We show that in addition to its highly sensitive staining capabilities similar to Sypro Ruby and silver (2 ng), RuBPs offers several advantages such as a broad dynamic range (similar to Sypro Ruby and 500 times broader than the dynamic range of silver stain), low costs ( 0.03 per gel) and excellent compatibility with mass spectrometry. We then applied the inexpensive RuBPs stain to 2D gels (pH 4-7) of four benign thyroid nodules and normal thyroid tissue. We were able to detect approximately 1800 protein spots/gel in our thyroid samples. Quantitative changes in protein expression levels of at least 20-42 proteins were noted in the benign nodules compared with the normal thyroid tissue of the same patient. Differentially expressed spots were further characterised by nano-LC-FTICR and MALDI-TOF mass spectrometry. In summary we demonstrate, that the novel fluorescent ruthenium II tris(bathophenanthroline disulfonate) stain is a highly sensitive, reliable and inexpensive tool for quantitative proteome analysis in thyroid nodular disease.

Expression of regulators of g protein signaling mRNA is differentially regulated in hot and cold thyroid nodules

Because of their regulatory properties on cellular proliferation and differentiation, regulators of G protein signaling (RGS) have been suggested as potential tumor suppressors. The aim of this study was to describe the normal pattern of RGS transcripts in the thyroid gland systematically and to elucidate their potential role in common thyroid pathologies. Real-time polymerase chain reaction (PCR) was applied to quantify mRNA expression of RGS transcripts in 10 hot thyroid nodules (HTN), 10 cold thyroid nodules (CTN), and corresponding surrounding tissues (ST). We have found that 9 of 13 tested RGS transcripts were expressed in the human thyroid gland. Expression of several RGS transcripts was altered in thyroid nodules compared to corresponding normal tissue. In HTN and CTN, mRNA transcripts of RGS 2, 9, and 12 were significantly downregulated. In contrast, mRNA expression of RGS 3, 6, 10 was differentially regulated in HTN and CTN compared to corresponding normal tissue. RGS 3 transcripts were significantly upregulated in CTN. RGS 6 transcripts were significantly downregulated in CTN. RGS 10 mRNA was significantly reduced in HTN. We therefore propose that downregulation of several RGS transcripts in thyroid nodules might contribute to tumor growth within the thyroid gland.

Discrimination of benign and malignant thyroid nodules by molecular profiling

BACKGROUND

The evaluation of thyroid nodules by fine-needle aspiration has been the standard for almost 30 years, despite significant shortcomings in sensitivity and specificity. Recent data from our laboratory have suggested that molecular profiling permits the discrimination of specific types of thyroid nodules. These studies were undertaken to determine whether molecular profiling can discriminate between benign and malignant thyroid nodules with the necessary sensitivity and specificity required of a screening test.

METHODS

Molecular profiles of 11 papillary thyroid carcinomas, 13 follicular variant of papillary thyroid carcinomas, 9 follicular thyroid carcinomas, and 26 benign tumors (follicular adenomas and hyperplastic nodules) were analyzed by oligonucleotide microarray analysis. A gene list was created based on 45 samples. Seventeen samples were then added to the analysis as unknowns. A hierarchical clustering analysis was performed on all 62 samples to examine the groups for potential differences and the ability of the gene list to distinguish tumor types.

RESULTS

Cluster analysis of all 62 samples produced 2 distinct groups, 1 containing the carcinomas and 1 containing the benign lesions. The sensitivity for a diagnosis of cancer was 91.7% with a specificity of 96.2% (3 follicular variant of papillary thyroid carcinomas clustered with the benign lesions). The cancer gene profiles contained both known cancer-associated genes (MET, galectin-3) and previously unidentified genes.

CONCLUSIONS

Molecular profiling readily distinguishes between benign and malignant thyroid tumors with excellent sensitivity and specificity. Elucidated genes may provide insight into the molecular pathogenesis of thyroid cancer. Gene profiling may significantly enhance the evaluation of thyroid nodules in the future.