Molecular approaches to thyroid cancer diagnosis

Drug repositioning in thyroid cancer: from point mutations to gene fusions

The diagnosis of thyroid cancer (TC) has increased dramatically in recent years. Papillary TC is the most frequent type and has shown a good prognosis. Conventional treatments for TC are surgery, hormonal therapy, radioactive iodine, chemotherapy, and targeted therapy. However, resistance to treatments is well documented in almost 20% of all cases. Genomic sequencing has provided valuable information to help identify variants that hinder the success of chemotherapy as well as to determine which of those represent potentially druggable targets. There is a plethora of targeted therapies for cancer, most of them directed toward point mutations; however, chromosomal rearrangements that generate fusion genes are becoming relevant in cancer but have been less explored in TC. Therefore, it is relevant to identify new potential inhibitors for genes that are recurrent in the formation of gene fusions. In this review, we focus on describing potentially druggable variants and propose both point variants and fusion genes as targets for drug repositioning in TC.

Discriminating Interpatient Variabilities of RAS Gene Variants for Precision Detection of Thyroid Cancer

Importance

Interpatient variabilities in genomic variants may reflect differences in tumor statuses among individuals.

Objectives

To delineate interpatient variabilities in RAS variants in thyroid tumors based on the fifth World Health Organization classification of thyroid neoplasms and assess their diagnostic significance in cancer detection among patients with thyroid nodules.

Design, Setting, and Participants

This prospective diagnostic study analyzed surgically resected thyroid tumors obtained from February 2016 to April 2022 and residual thyroid fine-needle aspiration (FNA) biopsies obtained from January 2020 to March 2021, at Mount Sinai Hospital, Toronto, Ontario, Canada. Data were analyzed from June 20, 2022, to October 15, 2023.

Exposures

Quantitative detection of interpatient disparities of RAS variants (ie, NRAS, HRAS, and KRAS) was performed along with assessment of BRAF V600E and TERT promoter variants (C228T and C250T) by detecting their variant allele fractions (VAFs) using digital polymerase chain reaction assays.

Main Outcomes and Measures

Interpatient differences in RAS, BRAF V600E, and TERT promoter variants were analyzed and compared with surgical histopathologic diagnoses. Malignancy rates, sensitivity, specificity, positive predictive values, and negative predictive values were calculated.

Results

A total of 438 surgically resected thyroid tumor tissues and 249 thyroid nodule FNA biopsies were obtained from 620 patients (470 [75.8%] female; mean [SD] age, 50.7 [15.9] years). Median (IQR) follow-up for patients who underwent FNA biopsy analysis and subsequent resection was 88 (50-156) days. Of 438 tumors, 89 (20.3%) were identified with the presence of RAS variants, including 51 (11.6%) with NRAS, 29 (6.6%) with HRAS, and 9 (2.1%) with KRAS. The interpatient differences in these variants were discriminated at VAF levels ranging from 0.15% to 51.53%. The mean (SD) VAF of RAS variants exhibited no significant differences among benign nodules (39.2% [11.2%]), noninvasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTPs) (25.4% [14.3%]), and malignant neoplasms (33.4% [13.8%]) (P = .28), although their distribution was found in 41.7% of NIFTPs and 50.7% of invasive encapsulated follicular variant papillary thyroid carcinomas (P < .001). RAS variants alone, regardless of a low or high VAF, were significantly associated with neoplasms at low risk of tumor recurrence (60.7% of RAS variants vs 26.9% of samples negative for RAS variants; P < .001). Compared with the sensitivity of 54.2% (95% CI, 48.8%-59.4%) and specificity of 100% (95% CI, 94.8%-100%) for BRAF V600E and TERT promoter variant assays, the inclusion of RAS variants into BRAF and TERT promoter variant assays improved sensitivity to 70.5% (95% CI, 65.4%-75.2%), albeit with a reduction in specificity to 88.8% (95% CI, 79.8%-94.1%) in distinguishing malignant neoplasms from benign and NIFTP tumors. Furthermore, interpatient differences in 5 gene variants (NRAS, HRAS, KRAS, BRAF, and TERT) were discriminated in 54 of 126 indeterminate FNAs (42.9%) and 18 of 76 nondiagnostic FNAs (23.7%), and all tumors with follow-up surgical pathology confirmed malignancy.

Conclusions and Relevance

This diagnostic study delineated interpatient differences in RAS variants present in thyroid tumors with a variety of histopathological diagnoses. Discrimination of interpatient variabilities in RAS in combination with BRAF V600E and TERT promoter variants could facilitate cytology examinations in preoperative precision malignancy diagnosis among patients with thyroid nodules.

Elevated PDE4C level serves as a candidate diagnostic biomarker and correlates with poor survival in thyroid carcinoma

Thyroid carcinoma (THCA) is the most common endocrine cancer. Phosphodiesterase (PDE) 4 enzyme family, as specific regulator of cyclic adenosine monophosphate, may play a important role in THCA. However, few studies on PDE4 enzyme family in THCA have been reported yet. Therefore, this study aimed to systematically analyze the changes of PDE4 enzyme family in THCA, and look for potential target for THCA therapy. We systematically analyzed the expression differences, prognostic value, genetic alteration, methylation modification, and the correlation with tumor immune microenvironment of PDE4 family in THCA using several public databases, including TCGA, GEO, GSCA, TNMplot, cBioPortal, DiseaseMeth and TIMER. Besides, functional enrichment analysis and protein-protein interaction (PPI) network of PDE4 family was investigated using Metascape and STRING databases. The expression levels of PDE4A, PDE4B and PDE4D were down-regulated in THCA patients at different cancer stages, while the expression level of PDE4C was significantly up-regulated. Moreover, THCA patients with higher PDE4C expression had shorter progress free survival compared with those with lower PDE4C expression. The low genomic alteration frequencies and mildly increased methylation levels of PDE4 family were found in THCA patients. Except for PDE4A, the expression levels of PDE4B, PDE4C and PDE4D could affect many immune cells infiltration during THCA progression. Four PDE4 subtypes were all enriched in cAMP catabolic process. Nevertheless, PDE4C was not enriched in the cAMP binding signal pathway, and PDE4B was not enriched in the G alphas signaling events. Notably, PDE4C participated in cAMP metabolic process by regulating adenylate cyclases (ADCYs), which involved ADCY1, ADCY5, ADCY6, ADCY8 and ADCY9. The findings of this study provide a partial basis for the role of PDE4 family in the occurrence and development of THCA. In addition, this study also suggested that PDE4C might be a potential prognostic marker of THCA, which could serve as a reference for future basic and clinical research.

New Insights into Immune Cells and Immunotherapy for Thyroid Cancer

Thyroid cancer (TC) is the most common endocrine malignancy worldwide, and the incidence of TC has gradually increased in recent decades. Differentiated thyroid cancer (DTC) is the most common subtype and has a good prognosis. However, advanced DTC patients with recurrence, metastasis and iodine refractoriness, as well as more aggressive subtypes such as poorly differentiated thyroid cancer (PDTC) and anaplastic thyroid cancer (ATC), still pose a great challenge for clinical management. Therefore, it is necessary to continue to explore the inherent molecular heterogeneity of different TC subtypes and the global landscape of the tumor immune microenvironment (TIME) to find new potential therapeutic targets. Immunotherapy is a promising therapeutic strategy that can be used alone or in combination with drugs targeting tumor-driven genes. This article focuses on the genomic characteristics, tumor-associated immune cell infiltration and immune checkpoint expression of different subtypes of TC patients to provide guidance for immunotherapy.

Identification of crucial genes involved in thyroid cancer development

BACKGROUND

A malignancy of the endocrine system, one of the most common types, is thyroid cancer. It is proven that children who receive radiation treatment for leukemia or lymphoma are at a heightened risk of thyroid cancer due to low-dose radiation exposure throughout childhood. Several factors can increase the risk of thyroid cancer (ThyCa), such as chromosomal and genetic mutations, iodine intake, TSH levels, autoimmune thyroid disorders, estrogen, obesity, lifestyle changes, and environmental contaminants.

OBJECTIVES

The study aimed to identify a specific gene as an essential candidate for thyroid cancer progression. We might be able to focus on developing a better understanding of how thyroid cancer is inherited.

METHODS

The review article uses electronic databases such as PubMed, Google Scholar, Ovid MEDLINE, Embase, and Cochrane Central. The most frequently associated genes with thyroid cancer found on PubMed were BAX, XRCC1, XRCC3, XPO5, IL-10, BRAF, RET, and K-RAS. To perform an electronic literature search, genes derived from DisGeNET: a database of gene-disease associations, including PRKAR1A, BRAF, RET, NRAS, and KRAS, are used.

CONCLUSION

Examining the genetics of thyroid cancer explicitly emphasizes the primary genes associated with the pathophysiology of young and older people with thyroid cancer. Developing such gene investigations at the beginning of the thyroid cancer development process can identify better outcomes and the most aggressive thyroid cancers.

Novel thrombospondin-1 transcript exhibits distinctive expression and activity in thyroid tumorigenesis

Thrombospondin 1 (TSP1) is known for its cell-specific functions in cancer progression, such as proliferation and migration. It contains 22 exons that may potentially produce several different transcripts. Here, we identified TSP1V as a novel TSP1-splicing variant produced by intron retention (IR) in human thyroid cancer cells and tissues. We observed that TSP1V functionally inhibited tumorigenesis contrary to TSP1 wild-type, as identified in vivo and in vitro. These activities of TSP1V are caused by inhibiting phospho-Smad and phospho-focal adhesion kinase. Reverse transcription polymerase chain reaction and minigene experiments revealed that some phytochemicals/non-steroidal anti-inflammatory drugs enhanced IR. We further found that RNA-binding motif protein 5 (RBM5) suppressed IR induced by sulindac sulfide treatment. Additionally, sulindac sulfide reduced phospho-RBM5 levels in a time-dependent manner. Furthermore, trans-chalcone demethylated TSP1V, thereby preventing methyl-CpG-binding protein 2 binding to TSP1V gene. In addition, TSP1V levels were significantly lower in patients with differentiated thyroid carcinoma than in those with benign thyroid nodule, indicating its potential application as a diagnostic biomarker in tumor progression.

Identification of long non-coding RNA using single nucleotide epimutation analysis: a novel gene discovery approach

BACKGROUND

Long non-coding RNAs (lncRNAs) are involved in a variety of mechanisms related to tumorigenesis by functioning as oncogenes or tumor-suppressors or even harboring oncogenic and tumor-suppressing effects; representing a new class of cancer biomarkers and therapeutic targets. It is predicted that more than 35,000 ncRNA especially lncRNA are positioned at the intergenic regions of the human genome. Emerging research indicates that one of the key pathways controlling lncRNA expression and tissue specificity is epigenetic regulation.

METHODS

In the current article, a novel approach for lncRNA discovery based on the intergenic position of most lncRNAs and a single CpG site methylation level representing epigenetic characteristics has been suggested.

RESULTS

Using this method, a novel antisense lncRNA named LINC02892 presenting three transcripts without the capacity of coding a protein was found exhibiting nuclear, cytoplasmic, and exosome distributions.

CONCLUSION

The current discovery strategy could be applied to identify novel non-coding RNAs influenced by methylation aberrations.

Development of a Low-cost NGS Test for the Evaluation of Thyroid Nodules

Ultrasound-guided fine needle aspiration cytology (FNAC) is the preferred method of identifying malignancy in palpable thyroid nodules using the Bethesda reporting system. However, in around 30-40% of FNACs (Bethesda categories III, IV, and V), the results are indeterminate and surgery is required to confirm malignancy. Out of those who undergo surgery, only 10-40% of patients in these categories are found to have malignancies, thus proving surgery to be unnecessary for some patients or to be incomplete in others. While molecular testing on thyroid FNAC material is part of the American Thyroid Association (ATA) guidelines in evaluating thyroid nodules, it is currently unavailable in India due to cost constraints. In this study, we prospectively collected FNAC samples from sixty-nine patients who presented with palpable thyroid nodules. We designed a cost-effective next-generation sequencing (NGS) test to query multiple variants in the DNA and RNA isolated from the fine needle aspirate. The identification of oncogenic variants was considered to be indicative of malignancy, and confirmed by surgical histopathology. The panel showed an overall sensitivity of 81.25% and a specificity of 100%, while in the case of Bethesda categories III, IV, and V, the sensitivity was higher (87.5%) and the specificity was established at 100%. The panel could thereby serve as a rule-in test for the diagnosis of thyroid cancer and therefore help identify patients who require surgery, especially in the indeterminate Bethesda categories III, IV, and V.

Positive Correlation of Thyroid Nodule Cytology with Molecular Profiling-a Single-Center Experience

Despite several reports on the association between molecular profiling, aggressive histology, and clinical outcomes, the association between mutation expression and pre-operative cytology is yet to be demonstrated. Therefore, we performed a retrospective, single-center study, including all patients who underwent molecular profiling of thyroid nodules in Bethesda System for Reporting Thyroid Cytopathology (BSRTC) categories III to VI, between 2018 and 2019. Medical records were reviewed to collect demographics, cytology results according to BSRTC, final pathology (presence of malignancy and its type, as well as presence of aggressive features, including extrathyroidal extension, positive neck lymph nodes, and multifocality), and the identified genetic variants stratified by risk levels, according to the 2015 ATA guidelines. We supplemented this analysis with a systematic review to identify the variant distributions across the literature. We included data on 55 nodules from 48 patients for the final analysis. A significant positive correlation was found between BSRTC categories and the mutation risk level, shown by an increase in the intermediate to high-risk mutation rate in the higher BSRTC categories (Rs = 0.660, p ≤ 0.001). A significant positive correlation was also found between mutation risk levels and the presence of malignancy and aggressive tumor features (Rs = 0.637, p < 0.001 and Rs = 0.459, p = 0.006, respectively). This novel positive and significant correlation between BSRTC categories and the mutation risk level provides additional insight to aid clinicians in the interpretation of BSRTC results and may contribute to the discussion of appropriate management of thyroid nodule with patients.

Total thyroidectomy versus lobectomy: surgical approach to T1-T2 papillary thyroid cancer

The incidence of papillary thyroid carcinoma, which accounts for 80-90% of all thyroid cancers, has recently been increasing. The current study aimed to compare the oncological and functional outcomes of total thyroidectomy (TT) and thyroid lobectomy (TL). To this end, a retrospective single-centre cohort study involving a tertiary care institution was conducted. Data regarding demographics, clinicopathology and postoperative complications from 586 patients with papillary thyroid cancer treated in a single institution were collected. Cox proportional-hazards models were utilised to determine differences in outcomes stratified according to propensity score. Our data suggested no significant difference in the risk for locoregional recurrence or distant metastasis between TL and TT among patients with pT1-2 pN0 papillary carcinoma. TT plays an important role in improving prognosis among patients with metastatic lymph nodes in the central neck compartment (pN1a) (p = 0.001). Moreover, TT had significantly higher rates of postoperative hypocalcaemia and recurrent laryngeal nerve paralysis compared to TL (p < 0.001 and p = 0.02, respectively).

The Genomic Landscape of Thyroid Cancer Tumourigenesis and Implications for Immunotherapy

Thyroid cancer is the most prevalent endocrine malignancy that comprises mostly indolent differentiated cancers (DTCs) and less frequently aggressive poorly differentiated (PDTC) or anaplastic cancers (ATCs) with high mortality. Utilisation of next-generation sequencing (NGS) and advanced sequencing data analysis can aid in understanding the multi-step progression model in the development of thyroid cancers and their metastatic potential at a molecular level, promoting a targeted approach to further research and development of targeted treatment options including immunotherapy, especially for the aggressive variants. Tumour initiation and progression in thyroid cancer occurs through constitutional activation of the mitogen-activated protein kinase (MAPK) pathway through mutations in BRAF, RAS, mutations in the phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K) pathway and/or receptor tyrosine kinase fusions/translocations, and other genetic aberrations acquired in a stepwise manner. This review provides a summary of the recent genetic aberrations implicated in the development and progression of thyroid cancer and implications for immunotherapy.

The Combination of Sonographic Features and the Seven-Gene Panel May be Useful in the Management of Thyroid Nodules With Indeterminate Cytology

Introduction

The management of patients with indeterminate thyroid nodules, which account for 10-25% of thyroid fine needle aspiration biopsies (FNABs), is still very challenging.

Aim

To verify the utility of the seven-gene panel in combination with ultrasound features in the clinical management of indeterminate thyroid nodules.

Results

The study group included 188 indeterminate thyroid nodules, divided into TIR3A (56.4%) and TIR3B (43.6%). A significant correlation between US categories and both cytological and molecular results was observed. In detail, TIR3B cytology was more frequent in EU-TIRADS 4 and 5 nodules (54.7 and 50%, respectively) than in EU-TIRADS 2 and 3 nodules (31%, p = 0.04). Similarly, the rate of a nodule with a mutation increased with the increase of US risk class (6.0% in EU-TIRADS 2 and 3, 9.3% in EUTIRADS-4 and 27.8% in EUTIRAD-5, p = 0.01). Among thyroid nodules submitted to surgery, final histology was benign in 61.4% nodules, while malignancy was diagnosed in 38.6% nodules. Using US score as tool for decision-making in TIR3A subgroup, we correctly classified 64.5% of thyroid nodules. The second tool (seven-gene panel test) was used in the subgroup of US high-risk nodules. By multiple tests with a series approach (US in all cases and US plus seven-gene panel in US high risk nodules) 84% of cases were correctly classified. In TIR3B nodules, using only seven-gene panel as tool for decision making, we correctly classified 61.9% of indeterminate nodules. By multiple tests with series approach (seven-gene panel in all cases and seven-gene panel plus US score in non-mutated nodules) only a slight improvement of thyroid nodule classification (66.6%) was observed.

Conclusions

US score seems able to correctly discriminate between TIR3A nodules in which a conservative approach may be used, and those in which additional test, such as molecular test, may be indicated. On the contrary, in TIR3B nodules both US risk stratification and seven-gene panel seem to be of little use, because the risk of thyroid cancer remains high regardless of US score and mutational status.

From biomarkers to therapeutic targets: the promise of PD-L1 in thyroid autoimmunity and cancer

The programmed cell death-1/programmed cell death ligand-1 (PD-1/PD-L1) immune checkpoint proteins hold promise as diagnostic, prognostic, and therapeutic targets for precision oncology. By restoring antitumor T cell surveillance, the high degree of effectiveness of the immune checkpoint inhibitors (ICIs) has revolutionized cancer treatment. However, the majority of patients (65-80 %) treated with ICIs experience significant side effects, called immune-related adverse events (irAEs), resulting in autoimmune damage to various organs. Therefore, broadening the clinical applicability of these treatments to all cancer types requires an improved understanding of the mechanisms linking cancer immune evasion and autoimmunity. The thyroid is the endocrine gland the most frequently involved in autoimmunity and cancer, the growing incidence of which is raising serious public health issues worldwide. In addition, the risk of developing thyroid cancer is increased in patients with autoimmune thyroid disease and thyroid dysfunction is one of the most common irAEs, especially with PD‑1/PD-L1 blockade. Therefore, we chose the thyroid as a model for the study of the link between autoimmunity, irAEs, and cancer. We provide an update into the current knowledge of the PD‑1/PD-L1 axis and discuss the growing interest of this axis in the diagnosis, prognosis, and management of thyroid diseases within the context of autoimmunity and cancer, while embracing personalized medicine.

[The role of molecular testing in thyroid tumors]

&sup1;I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia; &sup2;Endocrinology Research Centre, Moscow, Russia Thyroid cancer is the most common endocrine gland cancer. In the last few decades, the molecular diagnostics for thyroid tumors have been widely researched. It is one of the few cancers whose incidence has increased in recent years from microcarcinomas to common, large forms, in all age groups, from children to the elder people. Most researches focus on the genetic basis, since our current knowledge of the genetic background of various forms of thyroid cancer is far from being complete. Molecular and genetic research has several main directions: firstly, differential diagnosis of thyroid tumors, secondly, the prognostic value of detected mutations in thyroid cancer, and thirdly, targeted therapy for aggressive or radioactive iodine-resistant forms of thyroid cancer. In this review, we wanted to update our understanding and describe the prevailing advances in molecular genetics of thyroid cancer, focusing on the main genes associated with the pathology and their potential application in clinical practice.

European perspective on the use of molecular tests in the diagnosis and therapy of thyroid neoplasms

Thyroid nodules are frequently observed, particularly in individuals of over 60 years of age. On the other hand, most of the detected changes are benign and they do not require surgery. Therefore, differentiation between benign and malignant lesions in preoperative diagnosis is of crucial importance. Currently, the use of fine-needle aspiration biopsy (FNAB) and cytological assessment are the gold standard in the diagnosis of thyroid nodules. This procedure significantly reduces the need for diagnostic surgical intervention. However, approximately 15-30% of cytological results are classified as indeterminate. This is mainly due to the lack of specific cytomorphologic features that would facilitate the diagnosis based on cell evaluation under microscopic assessment. For the diagnoses of atypia of undetermined significance/follicular lesion of undetermined significance (AUS/FLUS), the assessment of invasion is crucial. Such an evaluation is not possible in cytology. Recently, molecular tests have been developed. They improve cytological diagnosis, particularly in the case of indeterminate results. Commercially available tests are developed based on the North American population. It is important to assess whether such tests can be used in the evaluation of e.g., European population.

[Individualization of the surgical procedure in response to overdiagnosis and overtreatment in differentiated thyroid carcinomas]

BACKGROUND

Advances in diagnostic methods have led to an early detection of thyroid nodules with debatable malignant potential in numerous cases. This can result in a potential overtreatment of thyroid lesions with very good prognosis.

OBJECTIVES

To avoid surgical overtreatment, an individualized, risk-adapted management is required that respects the different tumor biology of the underlying histological entities.

METHODS

The current guidelines of the leading professional societies, the American Thyroid Association (ATA) and the German Association of Endocrine Surgeons (CAEK), were compared and critically studied, to describe risk-adapted, more conservative treatment options for certain types of thyroid neoplasms according to the 2017 WHO definition.

RESULTS

The German CAEK recommends thyroidectomy as a routine operation in the case of thyroid carcinoma. Exceptions are papillary thyroid microcarcinoma and minimally invasive follicular thyroid carcinoma, which can be treated by lobectomy. The ATA proposes an "active surveillance" for papillary thyroid microcarcinoma and lobectomy in cases of differentiated thyroid carcinoma <4 cm in diameter in the absence of clearly predefined risk factors.

CONCLUSIONS

The pre- or intraoperative pathological diagnosis of the underlying tumor entity is the key point, which allows for an adaption of the resection strategy for thyroid malignancy. Depending on the type of carcinoma, the current guidelines of international expert societies allow for parenchyma-sparing operations and, according to the ATA, even an "active surveillance."

Characterization of Activating Mutations of the MEK1 Gene in Papillary Thyroid Carcinomas

Background: Genetic alterations activating the mitogen-activated protein kinase (MAPK) signaling pathway, most commonly BRAF and RAS mutations, are common in papillary thyroid carcinoma (PTC). Somatic mutations of the MEK gene, also known as mitogen-activated protein kinase kinase 1 (MAP2K1), coding for a signaling protein downstream of BRAF, have been found in several cancer types. The goal of this study was to investigate if functional MEK1 mutations occur in thyroid cancer (TC). Methods: We analyzed MEK1 mutation status in a series of 101 PTCs lacking other known driver mutations using Sanger sequencing and targeted next-generation sequencing. In addition, 64 follicular and Hürthle cell carcinomas and 32 follicular adenomas were studied. The occurrence of MEK1 mutations was evaluated using another series of thyroid tumors studied by targeted next-generation sequencing. Western blot and RNA-seq analyses were performed on selected tumors. Results: We detected MEK1 mutations in 2/101 (2%) PTCs that otherwise had no known genetic alterations, in 0/64 follicular and Hürthle cell carcinomas, and in 0/32 follicular adenomas. Two positive tumors carried the same in-frame deletion p.L98_I103del; K104I (c.292_309del18; c.311A>T) located in exon 3 of the gene. One additional MEK1 mutation was identified following routine molecular tumor profiling. The tumor had an in-frame deletion p.I99_K104del (c.294_311del18) also located in exon 3. Western blot analysis of one of the tumors showed activation of the MAPK pathway. Using RNA-seq analysis to evaluate changes in gene expression, these tumors were RAS-like and showed a high thyroid differentiation score. Phenotypically, the MEK1-positive PTCs were all encapsulated and had a predominantly or exclusively follicular architecture, being diagnosed as a classic papillary type with a significant follicular pattern ( × 2) or follicular variant PTC ( × 1). Follow-up was available for 2 patients, with no evidence of disease found 2 and 10 years postsurgery. Conclusions: In this study, we report the occurrence of functional MEK1 mutations in PTC. All mutations are in-frame deletions in exon 3 of MEK1, representing another mechanism of activation of the MAPK pathway in papillary carcinomas with a predominantly follicular growth pattern.

American College of Radiology thyroid imaging report and data system combined with K-RAS mutation improves the management of cytologically indeterminate thyroid nodules

We investigated whether use of American College of Radiology thyroid imaging report and data system (ACR TIRADS) in combination with K-RAS mutation status may facilitate risk stratification of patients with cytological Bethesda Category III and IV thyroid nodules. Ultrasonographic, cytological, and histopathological diagnoses were retrospectively correlated with K-RAS mutation status in a series of 43 cytologically indeterminate thyroid nodules (CITNs) that were referred for surgical excision. K-RAS mutations were detected in 8/43 (18.6%) fine-needle aspiration (FNA) samples as against 11/43 (25.6%) surgical specimens. ACR TIRADS level (TR) TR3 lesions had a malignancy risk of 40%; the K-RAS mutation rate in FNA samples and surgical specimens of category TR3 lesions was 40% and 60%, respectively. K-RAS mutation-positive malignancy was significantly more frequently detected in follicular neoplasm/suspicious for follicular neoplasm (FN/SFN) lesions than that in atypia or follicular lesion of undetermined significance (AUS/FLUS) (P<0.01). Combined use of ACR TIRADS (TR5 as the diagnostic threshold) and K-RAS mutation status helped identify 83.3% (10/12) malignant nodules (58.6% specificity, 45.5% positive predictive value, 89.5% negative predictive value, and 65.9% accuracy). CITNs with ACR TIRADS category TR3 showed an unexpectedly high risk of malignancy. K-RAS mutation-positive FN/SFN nodules have a 50% risk of malignancy and surgery should be recommended. Combined use of ACR TIRADS and K-RAS mutation may facilitate risk-stratification of patients with CITNs. The high negative predictive value (NPV) for malignancy seems sufficient to allow conservative management of patients with active surveillance.

The roles and role-players in thyroid cancer angiogenesis

Thyroid cancer is the most prevalent endocrine cancer worldwide. Angiogenesis, the formation of new blood vessels, plays a pivotal role in the development and progression of tumors. Over the past years, cancer research has focused on the ability of tumors to induce newly formed blood vessel, because tumor growth and the process of cancer metastasis mainly depends on angiogenesis. Tumor neovascularization occurs following the imbalance between pro-angiogenic and anti-angiogenic factors until the tumor switches to an angiogenic phenotype. A number of signaling factors and receptors that are implicated in the regulation of angiogenesis have been identified and characterized; most notably, the vascular endothelial growth factors (VEGFs) family and their receptors, which are the main pro-angiogenic molecules during early development and in pathological conditions such as cancer. Although thyroid is a highly vascularized organ, angiogenic switch in tumors of this organ leads to the formation of a vast network of blood vessels that favors the dissemination of tumor cells to distant organs and results in deterioration of patient conditions. Accordingly, the identification of key angiogenic biomarkers for thyroid cancer can facilitate diagnosis, prognosis and clinical decision-making and also may help to discover targeting factors for effective cancer therapy as well as monitoring response to therapy. Hence, the main purposes of this review are to summarize the types and mechanisms of angiogenesis emphasizing the prominent factors implicated in thyroid cancer angiogenesis.

Creating Prognostic Systems for Well-Differentiated Thyroid Cancer Using Machine Learning

Updates to staging models are needed to reflect a greater understanding of tumor behavior and clinical outcomes for well-differentiated thyroid carcinomas. We used a machine learning algorithm and disease-specific survival data of differentiated thyroid carcinoma from the Surveillance, Epidemiology, and End Results Program of the National Cancer Institute to integrate clinical factors to improve prognostic accuracy. The concordance statistic (C-index) was used to cut dendrograms resulting from the learning process to generate prognostic groups. We created one computational prognostic model (7 prognostic groups with C-index = 0.8583) based on tumor size (T), regional lymph nodes (N), status of distant metastasis (M), and age to mirror the contemporary American Joint Committee on Cancer (AJCC) staging system (C-index = 0.8387). We showed that adding histologic type (papillary and follicular) improved the survival prediction of the model. We also showed that 55 is the best cutoff of age in the model, consistent with the changes from the most recent 8th edition staging manual from AJCC. The demonstrated approach has the potential to create prognostic systems permitting data driven and real time analysis that can aid decision-making in patient management and prognostication.

Lobular Breast Carcinoma Metastasis to the Thyroid Gland: Case Report and Literature Review

Metastasis from primary cancer to the thyroid is uncommon in breast cancer. Here we present a case of lobular breast carcinoma that metastasized to the thyroid. A 54-year-old woman without symptoms was admitted to our institution for staging of the lymph node above the left clavicle. An ¹⁸F-fluoro-deoxy-D-glucose positron emission tomography scan was performed for staging, and low uptakes were observed in the left supraclavicular and cervical lymph nodes. High uptake was seen in the posterior and lower left lobe of the thyroid. Histologic findings indicated lobular breast carcinoma (positive GATA3, loss of E-cadherin expression) metastatic to the thyroid with a luminal profile. Immunohistochemical analysis was negative for primary thyroid or parathyroid carcinoma. To our knowledge, this is the first report of a patient presenting a metastatic invasive lobular carcinoma in the thyroid and lymph nodes without a prior diagnosis of breast cancer.

Identification of potential functional genes in papillary thyroid cancer by co-expression network analysis

Interactions between multiple genes are involved in the development of complex diseases. However, there are few analyses of gene interactions associated with papillary thyroid cancer (PTC). Weighted gene co-expression network analysis (WGCNA) is a novel and powerful method that detects gene interactions according to their co-expression similarities. In the present study, WGCNA was performed in order to identify functional genes associated with PTC using R package. First, differential gene expression analysis was conducted in order to identify the differentially expressed genes (DEGs) between PTC and normal samples. Subsequently, co-expression networks of the DEGs were constructed for the two sample groups, respectively. The two networks were compared in order to identify a poorly preserved module. Concentrating on the significant module, validation analysis was performed to confirm the identified genes and combined functional enrichment analysis was conducted in order to identify more functional associations of these genes with PTC. As a result, 1062 DEGs were identified for network construction. A brown module containing 118 highly related genes was selected as it exhibited the lowest module preservation. After validation analysis, 61 genes in the module were confirmed to be associated with PTC. Following the enrichment analysis, two PTC-related pathways were identified: Wnt signal pathway and transcriptional misregulation in cancer. LRP4, KLK7, PRICKLE1, ETV4 and ETV5 were predicted to be candidate genes regulating the pathogenesis of PTC. These results provide novel insights into the etiology of PTC and the identification of potential functional genes.

Current methodologies for molecular screening of thyroid nodules

Several molecular tests have been developed for thyroid cytology with the main purpose to define the nature of indeterminate nodules in presurgical phase thus overcoming the limitations of cytological analysis. Molecular tests currently available for thyroid nodules are based on a variety of methodologies and display peculiar strengths and limitations: in this review of the literature they are summarized and critically discussed. The use of molecular diagnostics for thyroid cytology is increasingly widespread and accepted, however large, prospective validation studies are still needed to ultimately demonstrate the clinical efficacy of a wide incorporation of molecular tests into clinical practice.

Diagnostic value and lymph node metastasis prediction of a custom‑made panel (thyroline) in thyroid cancer

Differentiation of benign and malignant thyroid nodules is crucial for clinical management. Here, we explored the efficacy of next-generation sequencing (NGS) in predicting the classification of benign and malignant thyroid nodules and lymph node metastasis status, and simultaneously compared the results with ultrasound (US). Thyroline was designed to detect 15 target gene mutations and 2 fusions in 98 formalin-fixed, paraffin-embedded (FFPE) tissues, including those from 82 thyroid cancer (TC) patients and 16 patients with benign nodules. BRAF mutations were found in 57.69% of the papillary thyroid cancer (PTC) cases, while RET mutations were detected among all the medullary thyroid cancer (MTC) cases. Multiple mutations were positive but none showed dominance in anaplastic thyroid cancer (ATC) and follicular thyroid cancer (FTC). The sensitivity and specificity of NGS prediction in differentiation of benign and malignant thyroid nodules were 79.27 and 93.75%, respectively, and the positive predictive value (PPV) and negative predictive value (NPV) were 98.48 and 46.88%, respectively. The sensitivity and specificity of US were 76.83 and 6.25%, respectively, and the PPV and NPV were 80.77 and 5.00%, respectively. The area under curve (AUC) of NGS and US were 0.865 and 0.415, respectively. A total of 27 patients had ≥1 metastases to lymph nodes, 19 of which carried mutations, including BRAF, RET, NRAS, PIK3CA, TP53, CTNNB1 and PTEN. However, there was no correlation between the variant allele frequency of specific gene mutations and the number of metastatic lymph nodes. In conclusion, the prediction value of NGS was higher than the US-based Thyroid Imaging Reporting and Data System (TI-RADS). NGS is valuable for the accurate differentiation of benign and malignant thyroid nodules, and pathological subtypes in FFPE samples. The findings of the present study may pave the way for the application of NGS in analyzing fine-needle aspiration (FNA) biopsy samples.

Synchronous and Metastatic Papillary and Follicular Thyroid Carcinomas with Unique Molecular Signatures

Despite the relatively high prevalence of thyroid cancer, the occurrence of multiple synchronous, distinct subtypes of primary thyroid carcinoma is uncommon. The incidental finding of papillary thyroid microcarcinoma in a gland with a biologically relevant follicular or medullary carcinoma is more frequent than the synchronous occurrence of multiple clinically significant carcinomas. We report a case of synchronous papillary and follicular thyroid carcinomas metastatic to lymph node and bone, respectively. Next generation sequencing showed BRAF V600E mutation in the primary papillary carcinoma and NRAS Q61R mutation in the primary follicular carcinoma and bony metastasis. To our knowledge, this is the first reported case of synchronous and metastatic primary papillary and follicular carcinomas, and the first report of synchronous BRAF V600E mutated papillary and NRAS mutated follicular carcinoma.

Thyroid follicular adenomas and carcinomas: molecular profiling provides evidence for a continuous evolution

Non-autonomous thyroid nodules are common in the general population with a proportion found to be cancerous. A current challenge in the field is to be able to distinguish benign adenoma (FA) from preoperatively malignant thyroid follicular carcinoma (FTC), which are very similar both histologically and genetically. One controversial issue, which is currently not understood, is whether both tumor types represent different molecular entities or rather a biological continuum. To gain a better insight into FA and FTC tumorigenesis, we defined their molecular profiles by mRNA and miRNA microarray. Expression data were analyzed, validated by qRT-PCR and compared with previously published data sets. The majority of deregulated mRNAs were common between FA and FTC and were downregulated, however FTC showed additional deregulated mRNA. Both types of tumors share deregulated pathways, molecular functions and biological processes. The additional deregulations in FTC include the lipid transport process that may be involved in tumor progression. The strongest candidate genes which may be able to discriminate follicular adenomas and carcinomas, CRABP1, FABP4 and HMGA2, were validated in independent samples by qRT-PCR and immunohistochemistry. However, they were not able to adequately classify FA or FTC, supporting the notion of continuous evolving tumors, whereby FA and FTC appear to show quantitative rather than qualitative changes. Conversely, miRNA expression profiles showed few dysregulations in FTC, and even fewer in FA, suggesting that miRNA play a minor, if any, role in tumor progression.

Coupling of LETM1 up-regulation with oxidative phosphorylation and platelet-derived growth factor receptor signaling via YAP1 transactivation

Persistent cellular proliferation and metabolic reprogramming are essential processes in carcinogenesis. Here, we performed Gene Set Enrichment Analysis (GSEA) and found that that LETM1, a mitochondrial calcium transporter, is associated with cellular growth signals such as platelet-derived growth factor (PDGF) receptor signaling and insulin signaling pathways. These results were then verified by qRT-PCR and immnunoblotting. Mechanistically, up-regulation of LETM1 induced YAP1 nuclear accumulation, increasing the expression of PDGFB, PDGFRB and THBS4. Consistent with this, LETM1 silencing caused loss of YAP1 nuclear signal, decreasing the expression of PDGFB, PDGFRB and THBS4. Immunohistochemical staining consistently indicated a positive association between LETM1 up-regulation, YAP1 nuclear localization and high PDGFB expression. In clinical data analysis, LETM1 up-regulation in thyroid cancer was found to be related to aggressive tumor features such as lymphovascular invasion (LVI, P < 0.001) and lymph node metastasis (LNM, P = 0.011). Multivariate analysis demonstrated that LETM1 up-regulation increases the risk of LVI and LNM (OR = 3.455, 95% CI = 1.537–7.766 and OR = 3.043, 95% CI = 1.282–7.225, respectively). Collectively, these data suggest that up-regulation of LETM1 induces sustained activation of proliferative signaling pathways, such as PDGF signal pathway by AKT induced YAP1 transactivation, resulting in aggressive thyroid cancer phenotypes.

Oncogenesis of Thyroid Cancer

Thyroid neoplasms encompass a variety of lesions that range from benign adenomas to malignancies. These latter can be well-differentiated, poorly differentiated or undifferentiated (anaplastic) carcinomas. More than 95% of thyroid cancers are derived from thyroid follicular cells, while 2-3% (medullary thyroid cancers, MTC) originate from calcitonin producing C-cells. Over the last decade, investigators have developed a clearer understanding of genetic alterations underlying thyroid carcinogenesis. A number of point mutations and translocations are involved, not only in its tumorigenesis, but also as have potential use as diagnostic and prognostic indicators and therapeutic targets. Many occur in genes for several important signaling pathways, in particular the mitogen-activated protein kinase (MAPK) pathway. Sporadic (isolated) lesions account for 75% of MTC cases, while inherited MTC, often in association with multiple endocrine neoplasia (MEN) type 2A and 2B syndromes, constitute the remainder. However, non-MEN familial MTC may also occur. Advances in genetic testing have revolutionized the management of MTC, with prospects of genetic screening, testing and early prophylactic thyroidectomy. Ethical concerns of these advances are addressed.

Nodular Thyroid Disease and Thyroid Cancer in the Era of Precision Medicine

The management of thyroid nodules, one of the main clinical challenges in endocrine clinical practice, is usually straightforward. Although the most important concern is ruling out malignancy, there are grey areas where uncertainty is frequently present: the nodules labelled as indeterminate by cytology and the extent of therapy when thyroid cancer is diagnosed pathologically. There is evidence that the current available precision medicine tools (from all the "-omics" to molecular analysis, fine-tuning imaging or artificial intelligence) may help to fill present gaps in the future. We present here a commentary on some of the current challenges faced by endocrinologists in the field of thyroid nodules and cancer, and illustrate how precision medicine may improve their diagnostic and therapeutic capabilities in the future.

Thyroid sclerosing mucoepidermoid carcinoma with eosinophilia: a clinicopathologic and molecular analysis of a distinct entity

Sclerosing mucoepidermoid carcinoma with eosinophilia is a rare thyroid neoplasm of uncertain pathogenesis that resembles salivary gland mucoepidermoid carcinoma. This multi-institutional study characterizes the clinicopathologic and molecular features of this tumor by utilizing next-generation sequencing to assess common mutations and gene fusions involved in thyroid carcinogenesis as well as fluorescence in-situ hybridization for MAML2 translocations typical of salivary gland mucoepidermoid carcinoma. Nine cases (6 females and 3 males, mean age: 59 years, range 30-77 years) were identified. All cases were comprised of nests and strands of tumor cells with both squamous and mucinous differentiation embedded in a fibrohyaline stroma with an inflammatory infiltrate replete with eosinophils. All cases were p63 positive, thyroglobulin negative and showed variable expression of TTF-1. All nine cases were negative for MAML2 rearrangements. Five cases successfully tested by next-generation sequencing (ThyroSeq v.2 assay) were negative for mutations and translocations commonly involved in thyroid carcinogenesis. NTRK1 showed overexpression but no evidence of translocation. On follow-up, one patient died of persistent disease, whereas one of four remaining patients with available follow-up (mean: 7.3 years, range 4-11 years) demonstrated recurrence at 4 years. Thus, we show that sclerosing mucoepidermoid carcinoma with eosinophilia appears molecularly and morphologically distinct from follicular and C-cell-derived thyroid tumors as well as from salivary gland mucoepidermoid carcinoma. The overall and recurrence-free survival for these patients may be lower than for other well-differentiated thyroid cancers.

A Concise Atlas of Thyroid Cancer Next-Generation Sequencing Panel ThyroSeq v.2

The next-generation sequencing technology allows high out-put genomic analysis. An innovative assay in thyroid cancer, ThyroSeq® was developed for targeted mutation detection by next generation sequencing technology in fine needle aspiration and tissue samples. ThyroSeq v.2 next generation sequencing panel offers simultaneous sequencing and detection in >1000 hotspots of 14 thyroid cancer-related genes and for 42 types of gene fusions known to occur in thyroid cancer. ThyroSeq is being increasingly used to further narrow the indeterminate category defined by cytology for thyroid nodules. From a surgical perspective, genomic profiling also provides prognostic and predictive information and closely relates to determination of surgical strategy. Both the genomic analysis technology and the informatics for the cancer genome data base are rapidly developing. In this paper, we have gathered existing information on the thyroid cancer-related genes involved in the initiation and progression of thyroid cancer. Our goal is to assemble a glossary for the current ThyroSeq genomic panel that can help elucidate the role genomics play in thyroid cancer oncogenesis.

Molecular Diagnosis Using Residual Liquid-Based Cytology Materials for Patients with Nondiagnostic or Indeterminate Thyroid Nodules

BACKGROUND

Molecular analysis for common somatic mutations in thyroid cancer can improve diagnostic accuracy of fine-needle aspiration cytology (FNAC) in the nondiagnostic or indeterminate category of thyroid nodules. In this study, we evaluated the feasibility of molecular diagnosis from residual liquid-based cytology (LBC) material after cytological diagnosis.

METHODS

This prospective study enrolled 53 patients with thyroid nodules diagnosed as nondiagnostic, atypia of undetermined significance (AUS), or follicular lesion of undetermined significance (FLUS) after FNAC. DNAs and RNAs were isolated from residual LBC materials. BRAF(V600E) and RAS point mutations, PAX8/peroxisome proliferator-activated receptor γ (PPARγ), RET/PTC1, and RET/PTC3 rearrangements were evaluated by real-time polymerase chain reaction and pyrosequencing.

RESULTS

All DNAs from 53 residual LBC samples could be analysed and point mutations were detected in 10 samples (19%). In 17 AUS nodules, seven samples (41%) had point mutations including BRAF (n=4), NRAS (n=2), and KRAS (n=1). In 20 FLUS nodules, three samples (15%) had NRAS point mutations. RNA from only one FLUS nodule could be analysed for rearrangements and there was no abnormality.

CONCLUSION

Molecular analysis for BRAF and RAS mutations was feasible in residual LBC materials and might be useful for diagnosis of indeterminate thyroid nodules.

Papillary Thyroid Carcinoma: Association Between Germline DNA Variant Markers and Clinical Parameters

BACKGROUND

Papillary thyroid cancer (PTC) is reported to be highly heritable in epidemiological studies. Genome-wide association studies (GWAS) have uncovered several variants associated with PTC predisposition. It remains unknown whether these variants might contribute to better clinical stratification of PTC patients.

METHODS

In order to assess the usefulness of germline genetic analyses in the management of PTC patients, the genotypes of five variants (rs965513, rs944289, rs116909374, rs2439302, and rs966423) were determined in 1216 PTC patients and 1416 controls. Additionally, the expression of seven genes located close to GWAS variants (PTCSC3, MBIP, NKX2-1, FOXE1, DIRC3, PTCSC2, and NRG1) were measured in 73 PTC paired tumor/normal tissues, respectively. Next, the association was analyzed between the genotypes of the germline variants and the levels of gene expression with clinical/pathological features such as age, sex, TNM staging, multifocality status, extrathyroidal expansion, and MACIS score.

RESULTS

The risk allele of rs965513 was associated with larger tumor size (p = 0.025) and extrathyroidal expansion (odd ratio [OR] = 1.29, p = 0.045). The variant rs2439302 showed association with lymph node metastasis (OR = 1.24, p = 0.016), and multifocality status of the tumor (OR = 1.24, p = 0.012). The expression of MBIP was associated with T stage (p = 0.010). MBIP and PTCSC3 displayed lower expression in PTC tissue in males than in females (p = 0.025 and p = 0.036, respectively). NKX2-1 displayed lower expression in patients with N1 stage (p = 0.040).

CONCLUSIONS

The studied germline risk alleles predisposing to PTC were associated with a more aggressive course of the disease reflected by larger tumor diameter, higher multifocality rate, and more advanced N stage at the time of diagnosis. These results show that germline variants not only predispose to PTC but also might impact its clinical course. However, these associations were only moderate, and further large multi-ethnic studies are required to evaluate the usefulness of these germline variants in the clinical stratification of PTC patients.

Thyroid Hormone Receptor-β (TRβ) Mediates Runt-Related Transcription Factor 2 (Runx2) Expression in Thyroid Cancer Cells: A Novel Signaling Pathway in Thyroid Cancer

Dysregulation of the thyroid hormone receptor (TR)β is common in human cancers. Restoration of functional TRβ delays tumor progression in models of thyroid and breast cancers implicating TRβ as a tumor suppressor. Conversely, aberrant expression of the runt-related transcription factor 2 (Runx2) is established in the progression and metastasis of thyroid, breast, and other cancers. Silencing of Runx2 diminishes tumor invasive characteristics. With TRβ as a tumor suppressor and Runx2 as a tumor promoter, a compelling question is whether there is a functional relationship between these regulatory factors in thyroid tumorigenesis. Here, we demonstrated that these proteins are reciprocally expressed in normal and malignant thyroid cells; TRβ is high in normal cells, and Runx2 is high in malignant cells. T3 induced a time- and concentration-dependent decrease in Runx2 expression. Silencing of TRβ by small interfering RNA knockdown resulted in a corresponding increase in Runx2 and Runx2-regulated genes, indicating that TRβ levels directly impact Runx2 expression and associated epithelial to mesenchymal transition molecules. TRβ specifically bound to 3 putative thyroid hormone-response element motifs within the Runx2-P1 promoter ((-)105/(+)133) as detected by EMSA and chromatin immunoprecipitation. TRβ suppressed Runx2 transcriptional activities, thus confirming TRβ regulation of Runx2 at functional thyroid hormone-response elements. Significantly, these findings indicate that a ratio of the tumor-suppressor TRβ and tumor-promoting Runx2 may reflect tumor aggression and serve as biomarkers in biopsy tissues. The discovery of this TRβ-Runx2 signaling supports the emerging role of TRβ as a tumor suppressor and reveals a novel pathway for intervention.

Evolutionary features of thyroid cancer in patients with thyroidectomies from 2008 to 2013 in China

To evaluate the characteristics of thyroid carcinoma over time, we carried out a retrospective study to illustrate the evolutionary features of thyroid carcinoma. All records of thyroidectomies from the First Affiliated Hospital of Nanjing Medical University from 2008 to 2013 were obtained focusing on pathological diagnosis, size, local lymph node metastasis (LNM) of the tumors. The thyroid cancer detection rate increased from 24.6% to 41.5% significantly (P < 0.05). Papillary thyroid carcinoma (PTC) remained to be the most common type counting 86.4% of all thyroid carcinomas. In all 1,704 PTCs, microPTC (mPTC) with maximum diameter less than or equal to 10 mm has become the dominant form taking up 56.5% of all PTCs in 2013 while only 43.1% in 2008. The mean maximum tumor size has decreased from 17.8 mm to 12.2 mm significantly (P < 0.05). However, the average age, female dominance, and local LNM remained similarly in the past six years. Logistic regression test showed that the determinants for local LNM were age, gender and tumor size. mPTC has become the most common form of thyroid carcinoma detected during thyroidectomies in China while other features of thyroid carcinoma remained similarly in the recent years.

Genomic Profiling of Thyroid Cancer Reveals a Role for Thyroglobulin in Metastasis

Papillary thyroid carcinoma (PTC) has a wide geographic variation in incidence; it is most common in Saudi Arabia, where it is only second to breast cancer as the most common cancer among females. Genomic profiling of PTC from Saudi Arabia has not been attempted previously. We performed whole-exome sequencing of 101 PTC samples and the corresponding genomic DNA to identify genes with recurrent somatic mutations, then sequenced these genes by using a next-generation gene-panel approach in an additional 785 samples. In addition to BRAF, N-RAS, and H-RAS, which have previously been shown to be recurrently mutated in PTC, our analysis highlights additional genes, including thyroglobulin (TG), which harbored somatic mutations in 3% of the entire cohort. Surprisingly, although TG mutations were not exclusive to mutations in the RAS-MAP kinase pathway, their presence was associated with a significantly worse clinical outcome, which suggests a pathogenic role beyond driving initial oncogenesis. Analysis of metastatic PTC tissue revealed significant enrichment for TG mutations (p < 0.001), including events of apparent clonal expansion. Our results suggest a previously unknown role of TG somatic mutations in the pathogenesis of PTC and its malignant evolution.

The immune network in thyroid cancer

The immune system plays critical roles in tumor prevention, but also in its initiation and progression. Tumors are subjected to immunosurveillance, but cancer cells generate an immunosuppressive microenvironment that favors their escape from immune-mediated elimination. During chronic inflammation, immune cells can contribute to the formation and progression of tumors by producing mitogenic, prosurvival, proangiogenic and lymphangiogenic factors. Thyroid cancer is the most frequent type of endocrine neoplasia and is the most rapidly increasing cancer in the US. In this review, we discuss recent findings on how different immune cells and mediators can contribute to thyroid cancer development and progression.

Molecular classification of thyroid lesions by combined testing for miRNA gene expression and somatic gene alterations

Multiple molecular markers contribute to the pathogenesis of thyroid cancer and can provide valuable information to improve disease diagnosis and patient management. We performed a comprehensive evaluation of miRNA gene expression in diverse thyroid lesions (n = 534) and developed predictive models for the classification of thyroid nodules, alone or in combination with genotyping. Expression profiling by reverse transcription-quantitative polymerase chain reaction in surgical specimens (n = 257) identified specific miRNAs differentially expressed in 17 histopathological categories. Eight supervised machine learning algorithms were trained to discriminate benign from malignant lesions and evaluated for accuracy and robustness. The selected models showed invariant area under the receiver operating characteristic curve (AUC) in cross-validation (0.89), optimal AUC (0.94) in an independent set of preoperative thyroid nodule aspirates (n = 235), and classified 92% of benign lesions as low risk/negative and 92% of malignant lesions as high risk/positive. Surgical and preoperative specimens were further tested for the presence of 17 validated oncogenic gene alterations in the BRAF, RAS, RET or PAX8 genes. The miRNA-based classifiers complemented and significantly improved the diagnostic performance of the 17-mutation panel (p < 0.001 for McNemar's tests). In a subset of resected tissues (n = 54) and in an independent set of thyroid nodules with indeterminate cytology (n = 42), the optimized ThyraMIR Thyroid miRNA Classifier increased diagnostic sensitivity by 30-39% and correctly classified 100% of benign nodules negative by the 17-mutation panel. In contrast, testing with broad targeted next-generation sequencing panels decreased diagnostic specificity by detecting additional mutations of unknown clinical significance in 19-39% of benign lesions. Our results demonstrate that, independent of mutational status, miRNA expression profiles are strongly associated with altered molecular pathways underlying thyroid tumorigenesis. Combined testing for miRNA gene expression and well-established somatic gene alterations is a novel diagnostic strategy that can improve the preoperative diagnosis and surgical management of patients with indeterminate thyroid nodules.

The Management of Thyroid Nodules

Thyroid nodules are extremely common and are detected in 3%-7% of the general population by palpation and in 70% of the population by ultrasonography (USG). Approximately 5%-15% of these nodules are malignant. Therefore, in nodule examination, our primary aim is to detect malignant nodules. Besides the medical history and the findings of the physical examination, USG and fine-needle aspiration biopsy (FNAB) are the most commonly used methods to examine these nodules. Ultrasound-guided FNAB and on-site assessment of FNA specimens are suggested to decrease false negative and non-diagnostic test results. FNAB results in the "atypia of undetermined significance" group is challenging in the follow-up or treatment of the nodule. In this group, to differentiate the malignant nodules, other developing methods, such as analyzing molecular genetic markers, protein markers, and elastography, are generally studied. However, these methods are not used in a routine nodule examination because of cost-benefit analysis.

A 3-bp Deletion VK600-1E in the BRAF Gene Detected in a Young Woman with Papillary Thyroid Carcinoma

Papillary thyroid cancer (PTC) derived from follicular cells is a frequent thyroid tumor. The incidence of this type of malignancy is still growing worldwide. Several major genetic causes are recognized to cause PTC-mutations in the BRAF and RAS genes or rearrangements with the RET proto-oncogene. The most common genetic change found in PTC is a V600E mutation in the BRAF gene presented in 36-69 % of all PTC cases. For routine purposes, several methods were developed to selectively detect only this mutation. However, these methods miss other mutations in the BRAF gene located elsewhere. We focused on the analysis of the exon 15 of the BRAF gene by next-generation sequencing. Here we report a three nucleotide deletion VK600-1E in one patient and present this finding in the context of 13 previously described PTC cases with this deletion. Our patient is the second youngest one among the reported cases. Clinical features of PTC patients with VK600-1E are summarized. For the future, it is important to evaluate genotype-phenotype characteristics of patients with rare BRAF mutations and to follow up them for years.

The combination of four molecular markers improves thyroid cancer cytologic diagnosis and patient management

Background

Papillary thyroid cancer is the most common endocrine malignancy. The most sensitive and specific diagnostic tool for thyroid nodule diagnosis is fine-needle aspiration (FNA) biopsy with cytological evaluation. Nevertheless, FNA biopsy is not always decisive leading to “indeterminate” or “suspicious” diagnoses in 10 %–30 % of cases. BRAF V600E detection is currently used as molecular test to improve the diagnosis of thyroid nodules, yet it lacks sensitivity. The aim of the present study was to identify novel molecular markers/computational models to improve the discrimination between benign and malignant thyroid lesions.

Methods

We collected 118 pre-operative thyroid FNA samples. All 118 FNA samples were characterized for the presence of the BRAF V600E mutation (exon15) by pyrosequencing and further assessed for mRNA expression of four genes (KIT, TC1, miR-222, miR-146b) by quantitative polymerase chain reaction. Computational models (Bayesian Neural Network Classifier, discriminant analysis) were built, and their ability to discriminate benign and malignant tumors were tested. Receiver operating characteristic (ROC) analysis was performed and principal component analysis was used for visualization purposes.

Results

In total, 36/70 malignant samples carried the V600E mutation, while all 48 benign samples were wild type for BRAF exon15. The Bayesian neural network (BNN) and discriminant analysis, including the mRNA expression of the four genes (KIT, TC1, miR-222, miR-146b) showed a very strong predictive value (94.12 % and 92.16 %, respectively) in discriminating malignant from benign patients. The discriminant analysis showed a correct classification of 100 % of the samples in the malignant group, and 95 % by BNN. KIT and miR-146b showed the highest diagnostic accuracy of the ROC curve, with area under the curve values of 0.973 for KIT and 0.931 for miR-146b.

Conclusions

The four genes model proposed in this study proved to be highly discriminative of the malignant status compared with BRAF assessment alone. Its implementation in clinical practice can help in identifying malignant/benign nodules that would otherwise remain suspicious.

Electronic supplementary material

The online version of this article (doi:10.1186/s12885-015-1917-2) contains supplementary material, which is available to authorized users.

Genome-wide CpG island methylation and intergenic demethylation propensities vary among different tumor sites

The epigenetic landscape of cancer includes both focal hypermethylation and broader hypomethylation in a genome-wide manner. By means of a comprehensive genomic analysis on 6637 tissues of 21 tumor types, we here show that the degrees of overall methylation in CpG island (CGI) and demethylation in intergenic regions, defined as ‘backbone’, largely vary among different tumors. Depending on tumor type, both CGI methylation and backbone demethylation are often associated with clinical, epidemiological and biological features such as age, sex, smoking history, anatomic location, histological type and grade, stage, molecular subtype and biological pathways. We found connections between CGI methylation and hypermutability, microsatellite instability, IDH1 mutation, 19p gain and polycomb features, and backbone demethylation with chromosomal instability, NSD1 and TP53 mutations, 5q and 19p loss and long repressive domains. These broad epigenetic patterns add a new dimension to our understanding of tumor biology and its clinical implications.

A metabolic phenotype based on mitochondrial ribosomal protein expression as a predictor of lymph node metastasis in papillary thyroid carcinoma

Metabolic reprogramming has been regarded as an essential component of malignant transformation. However, the clinical significance of metabolic heterogeneity remains poorly characterized. The aim of this study was to characterize metabolic heterogeneity in thyroid cancers via the analysis of the expression of mitochondrial ribosomal proteins (MRPs) and genes involved in oxidative phosphorylation (OxPhos), and investigate potential prognostic correlations. Gene set enrichment analysis (GSEA) verified by reverse transcription polymerase chain reaction and gene network analysis was performed using public repository data. Cross-sectional observational study was conducted to classify papillary thyroid cancer (PTC) by the expression of MRP L44 (MRPL44) messenger RNA (mRNA), and to investigate the clinicopathological features. GSEA clearly showed that the expression of OxPhos and MRP gene sets was significantly lower in primary thyroid cancer than in matched normal thyroid tissue. However, 8 of 49 primary thyroid tumors (16.3%) in the public repository did not show a reduction in OxPhos mRNA expression. Remarkably, strong positive correlations between MRPL44 expression and those of OxPhos and MRPs such as reduced nicotinamide adenine dinucleotide dehydrogenase (ubiquinone) 1 α subcomplex, 5; succinate dehydrogenase complex, subunit D; cytochrome c, somatic; adenosine triphosphate synthase, H+ transporting, mitochondrial Fo complex, subunit C1 (subunit 9); and MRP S5 (MRPS5) (P < 0.0001) were clearly denoted, suggesting that MRPL44 is a representative marker of OxPhos and MRP expressions. In laboratory experiments, metabolic heterogeneity in oxygen consumption, extracellular acidification rates (ECARs), and amounts of OxPhos complexes were consistently observed in BCPAP, TPC1, HTH-7, and XTC.UC1 cell lines. In PTCs, metabolic phenotype according to OxPhos amount defined by expression of MRPL44 mRNA was significantly related to lymph node metastasis (LNM) (P < 0.001). Furthermore, multivariate analysis clearly indicated that expression of MRPL44 is associated with an increased risk of lateral neck LNM (odds ratio 9.267, 95% confidence interval 1.852-46.371, P = 0.007). MRPL44 expression may be a representative marker of metabolic phenotype according to OxPhos amount and a useful predictor of LNM.