A novel complex BRAF mutation detected in a solid variant of papillary thyroid carcinoma

Unveiling a rare BRAF mutation in minimally invasive follicular thyroid carcinoma: A case report

RATIONALE

Molecular testing is becoming more widely used; however, the accuracy of diagnostic testing remains a primary consideration, especially for molecular testing that detects specific mutations associated with cancers.

PATIENT CONCERNS

A 45-year-old female without documented comorbidities presented a thyroid nodule during a routine health examination. Initial evaluation revealed a 3.8-cm nodule in the left lobe of thyroid, classified as Bethesda System category III on fine needle aspiration cytology. Genetic molecular testing detected the BRAF V600E mutation via quantitative polymerase chain reaction assay, raising concern for papillary thyroid cancer (PTC).

DIAGNOSES

The preoperative impression was PTC based on the detection of BRAF V600E mutation.

INTERVENTIONS

The patient underwent thyroidectomy as well as lymph node dissection with the expectation to treat PTC.

OUTCOMES

The final pathology unexpectedly revealed minimally invasive follicular carcinoma. Confirmatory Sanger sequencing unveiled a novel sequence variation involving nucleotide duplication within the range of 1794 to 1802, a non-V600E BRAF mutation not previously reported in follicular thyroid carcinoma.

LESSONS

This case study demonstrates the clinical relevance of exercising caution in molecular testing and its interpretation of results. For genetic testing used for diagnostic purposes, rigorous validation or cross-checking using different methods should always be considered to ensure appropriate interpretation of molecular results.

Thyroid Carcinoma: Phenotypic Features, Underlying Biology and Potential Relevance for Targeting Therapy

Thyroid carcinoma consists a group of phenotypically heterogeneous cancers. Recent advances in biological technologies have been advancing the delineation of genetic, epigenetic, and non-genetic factors that contribute to the heterogeneities of these cancers. In this review article, we discuss new findings that are greatly improving the understanding of thyroid cancer biology and facilitating the identification of novel targets for therapeutic intervention. We review the phenotypic features of different subtypes of thyroid cancers and their underlying biology. We discuss recent discoveries in thyroid cancer heterogeneities and the critical mechanisms contributing to the heterogeneity with emphases on genetic and epigenetic factors, cancer stemness traits, and tumor microenvironments. We also discuss the potential relevance of the intratumor heterogeneity in understanding therapeutic resistance and how new findings in tumor biology can facilitate designing novel targeting therapies for thyroid cancer.

Solid variant of papillary thyroid carcinoma: an under-recognized entity

Solid variant of papillary thyroid carcinoma (SVPTC) is a rare morphological variant of papillary thyroid carcinoma (PTC). SVPTC is histologically characterized by predominant solid, trabecular and insular nests of tumor cells while cytological features of PTC such as nuclear grooves and nuclear inclusions are preserved. In fine needle aspiration cytology smears, tumor cells of SVPTC may be presented in cohesive, syncytial or trabecular clusters accompanied by some discohesiveness in the absence of necrosis. Although SVPTC and poorly differentiated thyroid carcinoma (PDTC) share similar histological findings of solid nests, SVPTC can be differentiated from PDTC in the lack of tumor necrosis, severe nuclear atypia, and a higher mitotic index. Immunohistochemical expression of CK19 and HBME-1, common markers of PTC, is decreased in solid nests of SVPTC. In pediatric patients exposed to radiation after the Chernobyl nuclear accident, there was a higher prevalence of SVPTC with RET/PTC3 type rearrangement. BRAF mutations are also reported in a small number of adult patients with SVPTC without any prior radiation exposure. Patients with SVPTC may have a slightly higher incidence of metastasis and recurrence of the tumor compared to conventional PTC, although overall survival rate is comparable. In this article, the current knowledge of SVPTC will be reviewed and discussed with an emphasis on the histopathological feature.

New insights into intranuclear inclusions in thyroid carcinoma: Association with autophagy and with BRAFV600E mutation

Background

Intranuclear inclusions (NI) in normal and neoplastic tissues have been known for years, representing one of the diagnostic criteria for papillary thyroid carcinoma (PTC). BRAF activation is involved among others in autophagy. NI in hepatocellular carcinoma contain autophagy-associated proteins. Our aim was to clarify if NI in thyroid carcinoma (TC) have a biological function.

Methods

NI in 107 paraffin-embedded specimens of TC including all major subtypes were analyzed. We considered an inclusion as positive if it was delimited by a lamin AC (nuclear membrane marker) stained intact membrane and completely closed. Transmission electron microscopy (TEM), immunohistochemistry (IHC), immunofluorescence (IF) and 3D reconstruction were performed to investigate content and shape of NI; BRAF^V600E mutation was analyzed by next generation sequencing.

Results

In 29% of the TCs at least one lamin AC positive intranuclear inclusion was detected; most frequently (76%) in PTCs. TEM analyses revealed degenerated organelles and heterolysosomes within such NI; 3D reconstruction of IF stained nuclei confirmed complete closure by the nuclear membrane without any contact to the cytoplasm. NI were positively stained for the autophagy-associated proteins LC3B, ubiquitin, cathepsin D, p62/sequestosome1 and cathepsin B in 14–29% of the cases. Double-IF revealed co-localization of LC3B & ubiquitin, p62 & ubiquitin and LC3B & p62 in the same NI. BRAF^V600E mutation, exclusively detected in PTCs, was significantly associated with the number of NI/PTC (p = 0.042) and with immunoreactivity for autophagy-associated proteins in the NI (p≤0.035). BRAF-IHC revealed that some of these BRAF-positive thyrocytes contained mutant BRAF in their NI co-localized with autophagy-associated proteins.

Conclusions

NI are completely delimited by nuclear membrane in TC. The presence of autophagy-associated proteins within the NI together with degenerated organelles and lysosomal proteases suggests their involvement in autophagy and proteolysis. Whether and how BRAF^V600E protein is degraded in NI needs further investigation.

Solid papillary thyroid carcinoma with Hashimoto's thyroiditis: description of a further case with challenging cytological features

Solid papillary thyroid carcinoma (SV-PTC) is a rare variant which is mainly observed in young patients with a history of exposure to ionising radiations. Neoplasms belonging to such category generally carry RET-PTC (REarranged during Transfection- Papillary Thyroid Carcinoma) fusions and seem to have a slightly worse prognosis with respect to classical and follicular variants of papillary thyroid carcinoma (PTC), though consistent prognostic and survival data are scarce. SV-PTC should be differentiated from trabecular-insular poorly differentiated thyroid carcinomas, which occur in a different age group and carry a dismal prognosis. These latter tumours do not show the typical nuclear features of PTC and show tumour necrosis with an high mitotic activity. In this report a further case of SV-PTC is described which was associated to Hashimoto's thyroiditis, a finding never described in the cytological literature up to now for SV-PTC; this association created further differential diagnostic problems. The neoplasm displayed RET-PTC1 fusion.

Cytopathology of Solid Variant of Papillary Thyroid Carcinoma: Differential Diagnoses with other Thyroid Tumors

OBJECTIVES

Solid variant of papillary thyroid carcinoma (SVPTC) is rare, differing from classical PTC (cPTC) in architecture and outcome. We evaluated the cytomorphology of SVPTC cases to assess the feasibility of a preoperative diagnosis.

STUDY DESIGN

SVPTC cases were evaluated for architecture, nuclear features, and Bethesda category and were compared with noninvasive follicular thyroid neoplasm with papillary-like nuclear features/follicular variant of PTC (NIFTP/FVPTC), cPTC, and poorly differentiated thyroid carcinoma (PDTC).

RESULTS

Nine SVPTCs, 29 NIFTP/FVPTCs, 12 cPTCs, and 4 PDTCs were included. The predominant architecture in most SVPTCs was solid fragment, which is helpful in differentiating them from NIFTP/FVPTC (p < 0.001) and cPTC (p = 0.006) but not from PDTC. The presence of microfollicles led to misinterpretation as NIFTP/FVPTC/follicular neoplasm in 4 patients. All but 1 SVPTC showed diffuse nuclear features. Intranuclear pseudoinclusions (INIs) were seen in 67% of SVPTCs as compared to 83% of cPTCs, 14% of NIFTP/FVPTCs (p = 0.005), and none of PDTCs. SVPTC cases were commonly (78%) categorized as intermediate/suspicious.

CONCLUSIONS

The presence of solid fragments and lack of true papillae are helpful in differentiating SVPTC from cPTC. Solid fragments, trabeculae, the extent of nuclear features, and INIs should be looked for in cases with prominent microfollicles for distinguishing SVPTC from NIFTP/FVPTC. None of the features were helpful in differentiating SVPTC from PDTC.

Special types of thyroid carcinoma

This article reviews the small percentage of thyroid tumours that are not classified as classic papillary thyroid carcinoma, follicular thyroid carcinoma, and medullary thyroid carcinoma. It includes subtypes of papillary thyroid carcinoma, including, tall-cell, hobnail/micropapillary, columnar cell, diffuse sclerosing and solid variants. Poorly differentiated carcinoma, high-grade carcinoma and anaplastic thyroid carcinoma are reviewed. Also discussed are entities that are unusual but need to be recognized as primary thyroid neoplasms, i.e. mucoepidermoid carcinoma, sclerosing mucoepidermoid carcinoma with eosinophilia, and mammary analogue secretory carcinoma/secretory carcinoma. The pathological features and prognostic factors are described; a brief review of molecular correlates of these neoplasms is included.

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.

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.

Fine needle aspiration cytology of the papillary thyroid carcinoma with a solid component: A cytological and clinical correlation

BACKGROUND

Solid variant of papillary thyroid carcinoma is a rare subtype of papillary thyroid carcinoma (PTC) containing a solid component (SC), and thus its cytological and clinicopathological features remain elusive. We examined fine needle aspiration (FNA) cytological features of PTC with variable degrees of SC (20-80% of the tumor)(PTCSC) in comparison to well-differentiated PTC (WPTC).

METHODS

Twenty-six cases of PTCSC were histologically stratified into major-SC (SC >50% of the tumor) and minor-SC (<49%) groups. Pre-operative FNA smears were compared between major-SC (n = 11) and minor-SC (n = 15) groups, and between PTCSC and WPTC (n = 39) groups.

RESULTS

In FNA smears of PTCSC, the presence of cohesive solid nests, trabecular patterns, overlapping, enlarged nuclei, pleomorphism, and distinct nucleolus, and the absence of colloid and psammoma bodies were noted more often than in WPTC, while classical cytological features of PTC, such as nuclear grooves and/or pseudo-nuclear inclusions, were preserved. There was no significant difference in FNA findings between the major-SC and minor-SC groups. The presence of either solid nests or trabecular patterns, and overlapping in FNA smears of PTCSC was associated with a higher recurrence rate of the tumor (P = 0.007 and P < 0.001, respectively).

CONCLUSION

PTCSC may pre-operatively be identified by detecting its characteristic cytological features in FNA smears, regardless of the proportion of SC within the tumor. Because clinical outcomes of PTCSC remain undetermined, it is imperative to postulate PTCSC as a differential diagnosis, even when classical nuclear features of PTC are present. Diagn. Cytopathol. 2017;45:391-398. © 2017 Wiley Periodicals, Inc.

Novel BRAFI599Ins Mutation Identified in a Follicular Variant of a Papillary Thyroid Carcinoma: A Molecular Modeling Approach

OBJECTIVE

BRAF mutations are the most common genetic alteration found in papillary thyroid carcinoma (PTC). Approximately, 90% correspond to BRAFV600E, although other less common BRAF mutations have been described. The aim of this study was to describe a new mutation on BRAF gene discovered on the previous thyroid cytology of a patient diagnosed with a follicular variant of PTC (FV-PTC).

METHODS

The mutation was identified by independent cloning of the 2 alleles and direct sequencing in the previous cytology and tumor tissue samples from a patient diagnosed with FV-PTC. To elucidate the effect of the mutation on the structure and hence on the activating mechanism of the protein, the structures of BRAFI599Ins, BRAFT599Ins, BRAFV599Ins and BRAFV600E were modeled by using the reconstructed wild-type BRAF (BRAFWT) crystal structure.

RESULTS

The novel mutation in BRAF consisted in the in-frame insertion of 3 nucleotides (TAA) after nucleotide 1795, resulting in the incorporation of an extra isoleucine residue at position 599 (BRAFI599Ins) of the protein. The structural comparison of BRAFI599Ins, BRAFT599Ins, BRAFV599Ins with BRAFWT, and BRAFV600E models revealed that the overall shape of the kinase was conserved in the protein produced by this novel mutation, except for the displacement of the activation loop (A-loop), as a direct consequence of the increase in loop size, and the exposition of 1 of the 2 residues involved in BRAF activation (T599), probably facilitating its phosphorylation.

CONCLUSION

BRAFI599Ins mutation constitutes a new BRAF mutation affecting the length of the A-loop, which most likely facilitates BRAF activation by altering the A-loop conformation.

Classical V600E and other non-hotspot BRAF mutations in adult differentiated thyroid cancer

BACKGROUND

BRAF is the most frequently mutated gene in differentiated thyroid cancer (DTC). Previous studies on DTC have well documented high rates of the BRAF (V600E) mutation in patients of mixed ages. Previous studies either included a mix of pediatric and adult patients or pediatric patients only. However, the prevalence of hotspot and non-hotspot BRAF mutations and its significance in pure adult DTCs is not yet well determined. In this study we determine the frequency of this classical BRAF mutation and other rare BRAF mutations in pure adult DTCs.

METHODS

A total of 204 adult DTC samples (Age >18 years) were analyzed for mutations in exon 15 of the BRAF gene by performing polymerase chain reaction (PCR) amplification of tumor genomic DNAs and direct sequencing of amplicons using Sanger sequencing. Obtained results were correlated to clinical and pathological characteristics of DTCs. Statistical analyses were performed using SPSS (The Statistical Package for Social Sciences) version 20 software.

RESULTS

Overall, BRAF mutations were identified in 48.5 % (99/204) of adult DTCs. Three rare non-hotspot mutations (T599I, T599dup and K601E) were detected in four tumor samples (2 %). One (K601E) of these non-hotspot mutations occurred in conventional papillary thyroid cancer (CPTC) and other three (T599I, T599dup and K601E) were found in follicular variant PTC. We found significant association between BRAF (V600E) mutation and age (P < 0.0001), extrathyroidal invasion (P = 0.017), lymph node metastasis (P = 0.038) and TNM stage III/IV (P = 0.001).

CONCLUSIONS

Our study is the first to report BRAF mutations in a pure adult sample of DTCs of Saudi Arabian ethnicity. Our results show a high rate and a strong prognostic role of the classical BRAF (V600E) mutation and also suggest a common occurrence of non-hot spot mutations in adult DTC from this highly inbred population.

B-Raf mutation and papillary thyroid carcinoma patients

Thyroid carcinoma is the most prevalent endocrine neoplasm globally. In the majority of thyroid carcinoma cases, a positive prognosis is predicted following administration of the appropriate treatment. A wide range of genetic alterations present in thyroid carcinoma exert their oncogenic actions partially through the activation of the mitogen-activated protein kinase pathway, with the B-Raf mutation in particular being focused on by experts for decades. The B-Raf gene has numerous mutations, however, V600E presents with the highest frequency. It is believed that the existence of the V600E mutation may demonstrate an association with the clinicopathological characteristics of patients, however, inconsistencies remain in the literature. A number of explanatory theories have been presented in order to resolve these discrepancies. Recently, it has been suggested that the V600E mutation may function as a target in a novel approach that may aid the diagnosis and prognosis of thyroid carcinoma, with a number of vying methods put forward to that effect. The current review aims to assist researchers in further understanding the possible association between B-Raf mutations and thyroid carcinoma.

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 management of thyroid nodules and cancer in the molecular era

The incidence of thyroid cancer is increasing worldwide. Current standards in the diagnosis and management of thyroid cancer are limited by the uncertainty of fine-needle aspiration samples that are indeterminate in nature. Molecular markers have the potential to improve the accuracy of thyroid fine-needle aspiration and to aid the physician in giving a more accurate diagnosis and prognosis. This paper summarizes the various molecular markers currently available.

Fine-needle aspiration cytology of the solid variant of papillary thyroid carcinoma: a study of 13 cases with clinical, histologic, and ultrasound correlations

BACKGROUND

The solid variant of papillary thyroid carcinoma (SVPTC) comprises approximately 3% of thyroid cancers, and there are conflicting reports about its behavior in the literature. The cytology of SVPTC is limited to 3 single case reports, a review article, and a monograph. We present the first cytologic study of SVPTC.

METHODS

Fine-needle aspiration smears obtained with ultrasound guidance from 13 patients with histologically pure SVPTC were reviewed, and the cytologic features recorded. Ultrasound images were retrieved from radiology and were correlated with low-power histology images. Intratumor vascularity on Doppler imaging was correlated with cellularity in cytology samples.

RESULTS

Three cytomorphologic patterns of SVPTC were identified: cohesive, syncytial-type tissue fragments; microfollicles/trabeculae; and dyshesive single cells. All 3 SVPTCs in the first group were encapsulated without invasion. Two of 6 SVPTCs in the second group had a single lymph node metastasis; 4 were encapsulated, and 2 had pushing borders. Ultrasound images in the first and second SVPTC groups were similar, with the majority revealing a well defined, solid nodule with minimal intranodular vascularity. All 4 SVPTCs in the third group had infiltrative borders; and, with the exception of one 0.8-cm tumor, all had multiple lymph node metastases. Ultrasound in the third group revealed irregular borders. RET/PTC1 and RET/PTC3 mutations were found in 2 cases of the third group.

CONCLUSIONS

SVPTCs are heterogeneous tumors. The cohesive, syncytial tissue-fragment pattern can be recognized as SVPTC in smears and is associated with encapsulation and indolent behavior. The microfollicular/trabecular pattern is indistinguishable from that of the follicular variant of papillary thyroid carcinoma and has intermediate behavior. The dyshesive single-cell pattern correlates with infiltrative tumor growth and may not be unique to SVPTC.

Universal BRAF State Detection by the Pyrosequencing®-Based U-BRAF(V⁶⁰⁰) Assay

Malignant melanoma is a highly aggressive type of malignancy with considerable metastatic potential and frequent resistance to cytotoxic agents. BRAF mutant protein was recently recognized as therapeutic target in metastatic melanoma.We present the newly developed U-BRAF(V600) approach (Patent No. 12153477.0-1404)-a universal Pyrosequencing(®)-based assay for mutation detection within the activation segment in exon 15 of human BRAF. We identified five different BRAF mutations in a single assay analyzing 75 different formalin-fixed paraffin-embedded samples of cutaneous melanoma metastases from 29 patients. All mutant variants were quantitatively detectable by the newly developed U-BRAF(V600) assay. These results were confirmed by ultra-deep sequencing. In contrast to all other BRAF state detection methods, the U-BRAF(V600) assay is capable of automated quantitative identification of at least 36 previously published BRAF mutations. Under the precaution of a minimum of 5 % mutated cells in a background of wild-type cells, the U-BRAF(V600) assay design completely excludes false-negative wild-type results. The corresponding algorithm for classification of BRAF-mutated variants is provided in this chapter together with a detailed step-by-step protocol for the Pyrosequencing reaction.The single-reaction format and automation of data analysis make our approach suitable for the assessment of large clinical cohorts. Therefore, we suggest U-BRAF(V600) assay as a powerful sequencing-based diagnostic tool to automatically identify BRAF status.

Best practice of BRAF V600E mutation testing for the diagnosis and management of thyroid cancers

BRAF V600E mutation is the single most common genetic alteration identified in papillary thyroid carcinoma. There is significant association between BRAF V600E mutation and aggressive tumor behavior. BRAF V600E mutation has also been found to be an independent predictor of treatment failure and tumor recurrence even in patients with low-stage disease. Pre-operative BRAF mutation testing of thyroid fine needle aspiration specimens has become a routine clinical practice that enhances the predictability of malignancy in indeterminate fine needle aspiration cytology specimens especially those in the follicular lesion of undetermined significance/atypia of undetermined significance category. In addition to histological evaluation of subsequent core needle biopsy and BRAF immunohistochemistry, an expanded panel of mutation testing including BRAF V600E, NRAS, HRAS, RET/papillary thyroid carcinoma and PAX8/PPARγ rearrangements are currently advocated to further improve the diagnostic predictability in the detection of thyroid carcinomas using cytological specimens.

Molecular approaches to thyroid cancer diagnosis

Thyroid nodules are common, and the accurate diagnosis of cancer or benign disease is important for the effective clinical management of patients. Molecular markers are a helpful diagnostic tool, particularly for cytologically indeterminate thyroid nodules. In the past few years, significant progress has been made in developing molecular markers for clinical use in fine-needle aspiration specimens, including gene mutation panels and gene expression classifiers. With the availability of next generation sequencing technology, gene mutation panels can be expanded to interrogate multiple genes simultaneously and to provide yet more accurate diagnostic information. In addition, recently several new molecular markers of thyroid cancer have been identified that offer diagnostic, prognostic, and therapeutic information that might be of value in guiding individualized management of patients with thyroid nodules.

Clinicopathological features of rare BRAF mutations in Korean thyroid cancer patients

The most common BRAF mutation in thyroid cancer is c.1799T>A (p.Val600Glu), and other BRAF mutations are rarely reported. We investigated the clinicopathological features of thyroid cancer with rare BRAF mutations. A total of 2,763 patients with thyroid cancer underwent molecular testing by direct DNA sequencing for mutations in BRAF exon 15. Among them, 2,110 (76.4%) had BRAF mutations. The c.1799T>A mutation was found in 2,093 (76.9%) of 2,722 papillary carcinomas and in one of 7 medullary carcinomas. Sixteen cases (0.76%) harbored rare mutation types. Five cases had single-nucleotide substitutions, 5 cases had small in-frame deletion or insertion, and one harbored a two-nucleotide substitution. Of these mutations, 2 were novel (c.1797_1798insGAGACTACA, c.[1799T>A; 1801_1812del]). The c.1801A>G mutation was identified in 4 follicular variant papillary carcinomas and one follicular carcinoma. None of the patients with the c.1801A>G mutation showed extrathyroidal extension or lymph node metastasis. The prevalence of rare BRAF mutations was 0.76% of all BRAF-positive thyroid cancers, and the rare mutations were associated with less aggressive pathologic features. Although BRAF mutations are detected exclusively in papillary carcinoma, they are also found in medullary carcinoma and follicular carcinoma. [Corrected]

Molecular diagnostics for thyroid nodules: the current state of affairs

Molecular diagnostics offers great promise for the evaluation of cytologically indeterminate thyroid nodules. Numerous molecular genetic and immunohistochemical tests have been developed that may be performed on thyroid specimens obtained during standard fine-needle aspiration, some of which may greatly improve diagnostic yield. A sound understanding of the diagnostic performance of these tests, and how they can enhance clinical practice, is important. This article reviews the diagnostic utility of immunohistochemical and molecular testing for the clinical assessment of thyroid nodules, and makes recommendations about how these tests can be integrated into clinical practice for patients with cytologically indeterminate thyroid nodules.

Aggressive variants of follicular cell-derived thyroid carcinomas: a cytopathologist's perspective

Follicular cell-derived carcinomas of the thyroid gland comprise a heterogeneous group of malignant neoplasms of the thyroid gland with varied histologic appearance and molecular profiles. In most patients, these tumors represent relatively indolent neoplasms; however, certain subtypes/variants behave in an aggressive manner, and the recognition of this subset of tumors is essential because of their variable response to therapy and significant morbidity and mortality. Fine-needle aspiration is considered an essential tool for the diagnosis of suspicious thyroid nodules. In this review, the authors discuss the clinical, histologic, and molecular findings and the prognostic implications of aggressive thyroid neoplasms with emphasis on the characteristic cytomorphologic features on fine-needle aspiration smears.

Eruptive squamous cell carcinomas after vemurafenib therapy

BACKGROUND

Vemurafenib is an oral BRAF inhibitor recently approved for the treatment of metastatic melanoma. Patients treated with this medication have been reported to have the occurrence of squamous cell carcinoma (SCC) and/or actinic keratosis (AK).

OBJECTIVE

We report the case of a patient treated with vemurafenib for papillary thyroid carcinoma who subsequently developed multiple SCCs and AK of the skin. The lesions were deemed related to the medication and treated with excision. In addition, subsequent development of SCCs and AK was successfully prevented with a combination of isotretinoin and 5-fluorouracil in this patient. We discuss postulated mechanisms for these findings, as well as potential preventive therapy with the aforementioned combination regimen in patients undergoing treatment with vemurafenib.

Peptide nucleic acid clamp polymerase chain reaction reveals a deletion mutation of the BRAF gene in papillary thyroid carcinoma: A case report

The BRAF point mutation is the most common genetic event in papillary thyroid carcinoma (PTC), occurring in 29–69% of such tumors. The V600E mutation accounts for up to 95% of all BRAF mutations. Therefore, the majority of diagnostic assays have been developed to detect only the V600E mutation of the BRAF gene. A peptide nucleic-acid (PNA)-clamp quantitative polymerase chain reaction (qPCR) was developed to detect the V600E mutation and other mutations in the BRAF gene. In this study, a 3-bp deletion mutation (c.1799_ 1801delTGA) was detected in a subject with a PTC by PNA clamp qPCR, in contrast with the results of allele-specific (AS)-PCR. The mutant allele was not detected by AS-PCR, but was detected using PNA-clamp PCR. The atypical 3-bp deletion mutation (c.1799_1801delTGA) was identified by confirmatory PCR combined with sequencing. The conversion of codons 600 (GTG) and 601 (AAA) into a single codon (GAA) resulted in the insertion of a glutamic acid residue into the activation segment of the B-raf protein (p.V600_K601delinsE). In cases where PTC is highly suspected but no mutation is detected by AS-PCR specific for V600E, PNA clamp qPCR, which is complementary to other sequencing methods, should be performed in order to detect other mutations in the BRAF gene.

Aggressive variants of follicular cell derived thyroid carcinoma; the so called 'real thyroid carcinomas'

The pathological diagnoses and classification schemes for thyroid carcinoma have changed over the past 20 years and continue to do so. New entities have been described and molecular analyses have suggested better characterisation and grouping of certain tumours. Because some of the lesions have been named differently by different authors, clinicians and patients may be confused as to what a specific patient's lesion represents. In this review, we discuss the thyroid tumours of follicular origin which are clinically unusual but important to recognise as their behaviour may be aggressive, they may not respond to radioiodine treatment and they may cause significant mortality. This paper describes these important but rare lesions, their pathological features, important clinicopathological correlations, molecular correlates and prognostic implications.

Genetic mutations, molecular markers and future directions in research

Recent molecular studies have described a number of abnormalities associated with the pathogenesis of thyroid carcinoma. These distinct molecular events are often associated with specific stages of tumor development and may serve as prognostic factors and therapeutic targets. A better understanding of the mechanisms involved in thyroid cancer pathogenesis, will hopefully help translate these discoveries to improved patient care.

Automated universal BRAF state detection within the activation segment in skin metastases by pyrosequencing-based assay U-BRAF(V600)

Malignant melanoma is a highly-aggressive type of malignancy with considerable metastatic potential and frequent resistance to cytotoxic agents. BRAF mutant protein was recently recognized as therapeutic target in metastatic melanoma. We present a newly-developed U-BRAF^V600 approach – a universal pyrosequencing-based assay for mutation detection within activation segment in exon 15 of human braf. We identified 5 different BRAF mutations in a single assay analyzing 75 different formalin-fixed paraffin-embedded (FFPE) samples of cutaneous melanoma metastases from 29 patients. We found BRAF mutations in 21 of 29 metastases. All mutant variants were quantitatively detectable by the newly-developed U-BRAF^V600 assay. These results were confirmed by ultra-deep-sequencing validation (^∼60,000-fold coverage). In contrast to all other BRAF state detection methods, the U-BRAF^V600 assay is capable of automated quantitative identification of at least 36 previously-published BRAF mutations. Under the precaution of a minimum of 3% mutated cells in front of a background of wild type cells, U-BRAFV600 assay design completely excludes false wild-type results. The corresponding algorithm for classification of BRAF-mutated variants is provided. The single-reaction assay and data analysis automation makes our approach suitable for the assessment of large clinical sample sizes. Therefore, we suggest U-BRAF^V600 assay as a most powerful sequencing-based diagnostic tool to automatically identify BRAF state as a prerequisite to targeted therapy.

BRAF mutations in thyroid tumors from an ethnically diverse group

BACKGROUND

The molecular etiology of thyroid carcinoma (TC) and other thyroid diseases which may present malignant precursor lesions is not fully explored yet. The purpose of this study was to estimate frequency, type and clinicopathological value of BRAF exon 15 mutations in different types of cancerous and non-cancerous thyroid lesions originating in an ethnically diverse population.

METHODS

BRAF exon 15 was sequenced in 381 cases of thyroid lesions including Hashimoto´s thyroiditis, nodular goiters, hyperplastic nodules, follicular adenomas (FA), papillary TC (PTC), follicular variant PTC (FVPTC), microcarcinomas of PTC (micro PTC; tumor size ≤ 1 cm), follicular TC (FTC), and non-well differentiated TC (non-WDTC).

RESULTS

We identified BRAF mutations in one of 69 FA, 72 of 115 (63%) PTC, seven of 42 (17%) FVPTC, 10 of 56 (18%) micro PTC, one of 17 (6%) FTC, and one of eight (13%) non-WDTC. Most of the cases showed the common V600E mutation. One case each of PTC, FVPTC, and FTC harbored a K601E mutation. A novel BRAF mutation was identified in a FA leading to deletion of threonine at codon 599 (p.T599del). A rare 3-base pair insertion was detected in a stage III PTC resulting in duplication of threonine at codon 599 (p.T599dup). Patients with PTC harboring no BRAF mutation (BRAFwt) were on average younger than those with a BRAF mutation (BRAFmut) in the PTC (36.6 years vs. 43.8 years). Older age (≥ 45 years) in patients with PTC was significantly associated with tumor size ≥ 4 cm (P = 0.018), vessel invasion (P = 0.004), and distant metastasis (P = 0.001). Lymph node (LN) involvement in PTC significantly correlated with tumor size (P = 0.044), and vessel invasion (P = 0.013). Of notice, taken the whole TC group, family history of thyroid disease positively correlated with capsular invasion (P = 0.025).

CONCLUSIONS

Older age is manifold associated with unfavorable tumor markers in our series. The K601E identified in a PTC, FVPTC, and FTC seems to be more distributed among different histological types of TC than previously thought. The T599del is a yet undescribed mutation and the rare T599dup has not been reported as a mutation in PTC so far.

Diagnostic and prognostic markers in differentiated thyroid cancer

The MAPK/ERK (mitogen-activated protein kinase/extracellular signal- regulated kinase signaling pathway) and PI3K/Akt (lipid kinase phoshoinositide-3-kinase signaling pathway) play an important role in transmission of cell signals through transduction systems as ligands, transmembrane receptors and cytoplasmic secondary messengers to cell nucleus, where they influence the expression of genes that regulate important cellular processes: cell growth, proliferation and apoptosis. The genes, coding the signaling cascade proteins (RET, RAS, BRAF, PI3K, PTEN, AKT), are mutated or aberrantly expressed in thyroid cancer derived from follicular thyroid cell. Genetic and epigenetic alternations, concerning MAPK/ERK and PI3K/Akt signaling pathways, contribute to their activation and interaction in consequence of malignant follicular cell transformation. Moreover, it is additionally pointed out that genetic, as well as epigenetic DNA changing via aberrant methylation of several tumor suppressor and thyroid-specific genes is associated with tumor aggressiveness, being a jointly responsible mechanism for thyroid tumorigenesis. In the present manuscript the currently developed diagnostic and prognostic genetic/epigenetic markers are presented; the understanding of this molecular mechanism provides access to novel molecular therapeutic strategies.

BRAF mutation detection in indeterminate thyroid cytology specimens: underlying cytologic, molecular, and pathologic characteristics of papillary thyroid carcinoma

BACKGROUND

BRAF mutations are highly specific for papillary thyroid carcinoma (PTC) and many cytology specimens with BRAF mutations are expected to demonstrate cytologic features typical of PTC. However, indeterminate thyroid cytology cases are inevitable and understanding the significance of the BRAF mutation within the context of the Bethesda System for Reporting Thyroid Cytopathology would be valuable.

METHODS

Thyroid cytology cases submitted for conventional cytomorphologic evaluation and BRAF mutational analyses were selected from the authors' cytopathology files from April 2007 to October 2011. From this group, the diagnostic usefulness of BRAF mutations in indeterminate and malignant cases was assessed and analyses of cytologic and histopathologic features associated with the mutations in this gene were performed.

RESULTS

A total of 131 cases with a BRAF mutation were identified. Of these, 119 underwent surgical pathology resection follow-up and demonstrated PTC. Approximately 75% of the cases were cytologically diagnosed as being positive for malignancy and these cases were associated with both the classic and tall cell variants of PTC at the time of resection, a greater likelihood of extrathyroidal extension, and the V600E type of BRAF mutation. In contrast, BRAF-mutated cases with diagnoses of atypia of undetermined significance/follicular lesion of undetermined significance (AUS/FLUS) and follicular neoplasm/suspicious for follicular neoplasm were found to be more strongly associated with the follicular variant of PTC, a K601E BRAF mutation, and a lower likelihood of extrathyroidal extension. However, a subset of AUS/FLUS cases with the V600E BRAF mutation appeared to represent sampling variability of the classic or tall cell variants of PTC.

CONCLUSIONS

Bethesda thyroid diagnoses in the setting of a BRAF mutation reflect differences in PTC subtypes, the nature of cytology specimens, and molecular characteristics.

Mutational patterns and novel mutations of the BRAF gene in a large cohort of Korean patients with papillary thyroid carcinoma

BACKGROUND

BRAF mutation is the most common genetic event in papillary thyroid carcinoma (PTC); however, the prevalence and patterns of the mutation vary worldwide. We investigated the frequency and type of BRAF mutations based on the histologic subtypes in a large cohort of Korean patients with PTC.

METHODS

A total of 1041 consecutive PTCs were classified according to histologic subtypes. BRAF mutations were examined by denaturing high-performance liquid chromatography and direct sequencing. Rare complex mutations were confirmed by molecular cloning of polymerase chain reaction amplicons and sequencing of the products.

RESULTS

BRAF mutations were found in 839 (80.6%) of 1041 patients with PTC. The histologic subtype-specific prevalence of BRAF mutation was as follows: 85.3% (249/292) were classic, 45.8% (11/24) were follicular, 79.9% (576/721) were microcarcinoma, and 75.0% (3/4) were other variants. In addition to the usual c.1799T>A mutation, we identified other four mutation types: c.[1795_1796insA;1770_1795dup26], c.[1742-10T>C;1799T>A] and c.[1796C>G;1799T>A], and c.1799_1800TG>AA, respectively. The former three were novel mutations in thyroid tumors. Within the series of microcarcinoma variants, the BRAF mutation rate was lower in tumors with follicular morphology than those with nonfollicular types (66.7% vs. 80.9%, p=0.0145).

CONCLUSION

Out of 1041 Korean patients with PTC, 0.4% had rare types of BRAF mutation and three new somatic mutations were identified. The BRAF mutation rate was quite low in PTC with follicular morphology regardless of tumor size. However, the prevalence of BRAF mutation in microcarcinoma and follicular variants of PTC is relatively high in Korea and its analysis may be clinically useful for managing the patients.

Functional characterization of the novel BRAF complex mutation, BRAF(V600delinsYM) , identified in papillary thyroid carcinoma

An activating mutation in the BRAF gene is the most common genetic alteration in papillary thyroid carcinomas (PTCs). The mutation in PTCs is almost a c.1799T>A transversion, resulting in a p.V600E amino acid substitution (BRAF(V600E) ). Here, we report a novel complex BRAF mutation identified in 4/492 Japanese PTC cases (0.81%). The mutation was comprised of one nucleotide substitution at position 1798, followed by an in-frame insertion of three nucleotides, c.1798delinsTACA in Exon 15, resulting in p.V600delinsYM. In silico three-dimensional protein structure prediction implied altered kinase activity of this mutant. In vitro kinase assay and western blotting revealed that this mutation conferred high kinase activity on the BRAF protein, leading to constitutive activation of the MAPK signaling pathway. The mutation also showed high transforming ability in focus formation assay using NIH3T3 cells. The degree of all the functional characteristics was comparable to that of BRAF(V600E) , and treatment with a BRAF inhibitor Sorafenib was also equally effective in this mutant. These findings suggest that the novel BRAF mutation, BRAF(V600delinsYM) , is a gain-of-function mutation and plays an important role in PTC development.

Pediatric thyroid cancer

Thyroid cancer is an uncommon childhood malignancy that presents primarily in young children or adolescent females and may be related to radiation exposure or genetic predisposition. Gene alterations, such as RET mutation or RET/PTC rearrangement, are not uncommon. Recent studies have lead to an increased understanding of the role of these particular gene alterations in the diagnosis, prognosis, and treatment of thyroid cancer. Surgery remains the mainstay of treatment for thyroid cancer followed by radioactive iodine when appropriate. In patients with MEN2, prophylactic thyroidectomy is recommended, although a delay in the initial diagnosis is common. With early aggressive treatment and long-term follow-up, these patients generally have excellent outcomes. Recent research suggests potential usefulness of novel therapies directed at oncogenic signaling pathways, modulators of growth, angiogenesis inhibitors, immunomodulators, and gene therapy.

Molecular analysis of thyroid tumors

Thyroid cancer is the most common endocrine malignancy, and its incidence is rising in the USA and other countries. Papillary and follicular thyroid carcinomas are the two most common types of thyroid cancer. Non-overlapping genetic alterations, including BRAF and RAS point mutations, and RET/PTC and PAX8/PPARγ rearrangements, are found in more than 70% of papillary and follicular thyroid carcinomas. These represent the most common genetic alterations in thyroid cancer, as well as molecular markers of diagnostic and prognostic significance. The use of these and other emerging molecular markers will likely improve the diagnosis of malignancy in thyroid nodules as well as facilitate more individualized operative and postoperative management. Herein, we provide a brief overview of the common genetic alterations in papillary and follicular thyroid carcinoma and discuss the diagnostic and prognostic significance thereof.

Molecular genetics and diagnosis of thyroid cancer

Thyroid cancer is a common type of endocrine malignancy, and its incidence has been steadily increasing in many regions of the world. Initiation and progression of thyroid cancer involves multiple genetic and epigenetic alterations, of which mutations leading to the activation of the MAPK and PI3K-AKT signaling pathways are crucial. Common mutations found in thyroid cancer are point mutation of the BRAF and RAS genes as well as RET/PTC and PAX8/PPARγ chromosomal rearrangements. The mutational mechanisms seem to be linked to specific etiologic factors. Chromosomal rearrangements have a strong association with exposure to ionizing radiation and possibly with DNA fragility, whereas point mutations probably arise as a result of chemical mutagenesis. A potential role of dietary iodine excess in the generation of BRAF point mutations has also been proposed. Somatic mutations and other molecular alterations have been recognized as helpful diagnostic and prognostic markers for thyroid cancer and are beginning to be introduced into clinical practice, to offer a valuable tool for the management of patients with thyroid nodules.

Molecular diagnostics of thyroid tumors

CONTEXT

Thyroid cancer is the most common type of endocrine malignancy and its incidence is steadily increasing. Papillary carcinoma and follicular carcinoma are the most common types of thyroid cancer and represent those tumor types for which use of molecular markers for diagnosis and prognostication is of high clinical significance.

OBJECTIVE

To review the most common molecular alterations in thyroid cancer and their diagnostic and prognostic utility.

DATA SOURCES

PubMed (US National Library of Medicine)-available review articles, peer-reviewed original articles, and experience of the author.

CONCLUSIONS

The most common molecular alterations in thyroid cancer include BRAF and RAS point mutations and RET/PTC and PAX8/PPAR γ rearrangements. These nonoverlapping genetic alterations are found in more than 70% of papillary and follicular thyroid carcinomas. These molecular alterations can be detected in surgically resected samples and fine-needle aspiration samples from thyroid nodules and can be of significant diagnostic use. The diagnostic role of BRAF mutations has been studied most extensively, and recent studies also demonstrated a significant diagnostic utility of RAS, RET/PTC, and PAX8/PPAR γ mutations, particularly in thyroid fine-needle aspiration samples with indeterminate cytology. In addition to the diagnostic use, BRAF V600E mutation can also be used for tumor prognostication, as this mutation is associated with higher rate of tumor recurrence and tumor-related mortality. The use of these and other emerging molecular markers is expected to improve significantly the accuracy of cancer diagnosis in thyroid nodules and allow more individualized surgical and postsurgical management of patients with thyroid cancer.

Molecular analysis of thyroid tumors

In the recent years, a large number of molecular alterations in thyroid cancer has been discovered and characterized. Some of these markers may have significant diagnostic utility, can be used for tumor prognostication, and serve as potential therapeutic targets. The diagnostic utility of these markers is of particular importance in thyroid fine-needle aspiration samples. Some molecular markers, such as BRAF, offer help in risk stratification and can be potentially used to optimize surgical and postsurgical management of patients with thyroid cancer. This review discusses major molecular alterations known to occur in thyroid cancer, focusing on those markers that have been extensively characterized, carry clinical significance, and are being introduced into pathology practice.

The utility of BRAF testing in the management of papillary thyroid cancer

This review summarizes the current literature surrounding BRAF and its significance in thyroid cancer.

Over the last decade, investigators have developed a clearer understanding of the genetic alterations underlying thyroid carcinogenesis. A number of biomarkers involved in the pathogenesis of differentiated thyroid cancer have undergone intensive study, not only for their role in tumorigenesis, but also for their potential utility as diagnostic and prognostic indicators and therapeutic targets. This review summarizes the current literature surrounding BRAF and its significance in thyroid cancer. Further, we discuss how molecular analysis can be integrated into management algorithms for thyroid nodules and papillary thyroid cancer. We also review what is known, to date, about the association of BRAF and papillary microcarcinoma as well as using targeted therapies for BRAF as adjuvant treatment for metastatic papillary thyroid cancer.

High Prevalence of B-RAF Mutation in Papillary Carcinoma of the Thyroid in North-East Italy

B-RAF V600E mutation is frequently observed in several tumors, including papillary thyroid carcinomas (PTCs), where it is considered of potential diagnostic and prognostic value. The reported prevalence of B-RAF mutation in PTCs in different Italian populations varies from 14% to 69%. The authors investigate the prevalence and utility of the B-RAF V600E mutation in a series of 91 fine needle aspiration biopsies (FNABs) of the thyroid and in 60 histologically proven PTCs in a well-defined north Italian population. In their series, the B-RAF mutation was detected in 43 (72%) PTCs and was more frequent in classic (34 out of 44, 77%) versus variant follicular PTCs (PTCVF; 9 out of 16, 56%). In all, 41 (46%) FNABs showed B-RAF mutation and corresponded to histologically proven PTCs (33 classic type and 8 PTCVF), which had been cytologically classified as malignant (28 cases), atypical/suspicious (10), inadequate (1), and benign (2). B-RAF mutations were never seen in non-PTC/ PTCVF FNAB cases, implying a 100% positive predictive value.These data demonstrate a high prevalence of B-RAF mutations in the present study population, underscoring the possibility of strong regional differences in B-RAF mutation prevalence in PTCs and further confirming its high diagnostic value on FNAB.

Molecular diagnostics and predictors in thyroid cancer

BACKGROUND

The accuracy of cancer detection in thyroid nodules by fine-needle aspiration (FNA) cytology and prognostication of thyroid cancer needs further improvement and can benefit from testing for molecular alterations known to occur in thyroid tumors.

SUMMARY

Recent studies have demonstrated the feasibility of mutation detection in clinical FNA samples from thyroid nodules and their contribution to improving the diagnostic accuracy of FNA cytology. It appears that molecular testing is most beneficial for thyroid FNA samples with indeterminate cytology, where it can resolve the diagnosis in a significant number of cases. In addition to BRAF mutation, which has been studied most extensively, detection of RAS, RET/PTC, and PAX8/PPARgamma mutations also contribute substantially to cancer diagnosis. Some of these molecular markers, particularly BRAF, can also be used for tumor prognostication. In clinical setting, molecular testing of thyroid FNA samples and surgically removed tumors should utilize a restricted number of techniques that provide high accuracy and specificity of mutation detection.

CONCLUSION

Testing for cancer-specific mutations in thyroid FNA samples and surgically removed tumor tissues increases diagnostic accuracy of FNA cytology and offers better prognostication of thyroid cancer.