Characterization of a novel complex BRAF mutation in a follicular variant 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.

The changing characteristics and molecular profiles of papillary thyroid carcinoma over time: a systematic review

BACKGROUND

The genetic alterations of papillary thyroid carcinoma (PTC) have been reported to change over the past few decades. We performed this systematic review to further examine the trends and modifications of patient demographic, clinicopathological features and molecular profiles of PTC over time.

METHODS

A literature search was performed within six electronic databases to identify relevant articles. The inclusion criteria were published studies investigating BRAF mutations, RET/PTC rearrangements or RAS mutations in PTCs or classical PTCs. Two teams of reviewers independently screened titles and abstracts of all articles. Full texts of potential articles were read and extracted data were listed and stratified into an excel file according to country, city, institution, and surgical time period. Student t test and Pearson Chi-square were used to analyze the trends of demographic and clinicopathological features of PTC patients and the prevalence of each genetic alteration in individual institutions.

RESULTS

From 3139 articles, we included 16 articles for final analysis. Our results showed an increasing trend of BRAF and a decreasing trend of RET/PTC prevalence over time in PTCs and classical PTCs, accompanied by an older age of PTC patients, an increase in proportion of PTMC and less aggressive behaviours of tumours.

CONCLUSIONS

The demographic and clinicopathological characteristics and molecular profile of PTCs have been changing over the past few decades. These modifications suggest changes in etiologies and risk factors of thyroid cancer that influence the tumorigenesis of PTCs.

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.

Follicular variant of papillary thyroid carcinoma with B-type Raf(V600E) showing higher frequency of suspicious sonographic features and multifocality

BACKGROUND

The purpose of this study was to investigate the correlation between B-type Raf (BRAF) kinase mutation and clinicopathological features of follicular variant of papillary thyroid carcinoma (PTC).

METHODS

Eighty-four patients with pathologically confirmed follicular variant of PTC, who underwent a preoperative BRAF(V600E) study, were analyzed. Clinicopathological parameters and ultrasonographic features were compared between the BRAF(V600E) -positive and negative groups.

RESULTS

A total of 41.7% of the patients showed BRAF(V600E) . The BRAF(V600E) -positive group showed the smaller tumor size (7.3 ± 3.6 mm vs 10.7 ± 8.9 mm; p = .018) and the more frequent multifocality (25.7% vs 8.2%; p = .028). Follicular variant of PTC with BRAF(V600E) showed suspicious ultrasonographic features (88.6% vs 57.1%; p = .002) more frequently. BRAF(V600E) positivity is associated with multifocality after adjusting for age, sex, the presence of suspicious ultrasonographic features, pathological tumor size, and thyrotropin level.

CONCLUSION

BRAF(V600E) was correlated with smaller tumor size and suspicious ultrasonographic features in follicular variant of PTC. BRAF(V600E) was a significant parameter for predicting multifocality of follicular variant of PTC.

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]

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.

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.

Follicular variant of papillary carcinoma: reproducibility of histologic diagnosis and utility of HBME-1 immunohistochemistry and BRAF mutational analysis as diagnostic adjuncts

CONTEXT

Despite the recognition of the follicular variant of papillary carcinoma of the thyroid (FVPTC) for over 50 years, reproducibility of this diagnostic category has remained poor. Architectural features have been of variable utility as some FVPTC seem encapsulated, whereas others are multifocal and may be confused with nodular hyperplasia. Nuclear features are important for diagnosis of FVPTC, but some authors have discounted the utility of nuclear grooves and inclusions. More recently, BRAF and HBME-1 (Human Bone Marrow Endothelial Cell-1) have been suggested as markers for FVPTC.

OBJECTIVE

To investigate the frequency of BRAF mutations and HBME-1 immunopositivity, in a series of FVPTCs in which the diagnosis was established by 100% consensus among a panel of 6 surgical pathologists.

DESIGN

Twenty-eight specimens with an original diagnosis of FVPTC and 10 cases with other diagnoses were obtained from the surgical pathology files of the University of Utah School of Medicine. All specimens were independently reviewed by 6 surgical pathologists. Tissue blocks were analyzed for BRAF exon 15 mutations and HMBE-1 expression.

RESULTS

Complete agreement among pathologists for the diagnosis of FVPTC was obtained in 28.6% (8/28) of cases originally diagnosed as FVPTC. Mutations in BRAF exon 15 were found in 25% (2/8) of cases with a 100% consensus diagnosis of FVPTC and 32% (6/19) of cases unanimously diagnosed as a type of papillary carcinoma (classic or follicular variant). HBME-1 was expressed in 87.5% (7/8) of lesions with a 100% consensus diagnosis of FVPTC and 84.2% (16/19) of lesions with a unanimous diagnosis of a type of papillary carcinoma of the thyroid (classic or follicular variant).

CONCLUSIONS

Interobserver agreement for the diagnosis of FVPTC is poor and testing for the BRAF mutation is only marginally helpful because a minority of FVPTCs possess the mutation. HBME-1 expression when coupled with a BRAF mutation, results in 100% specificity but low sensitivity for the presence of papillary carcinoma of the thyroid including the follicular variant.

Genetic alterations in the RAS/RAF/mitogen-activated protein kinase and phosphatidylinositol 3-kinase/Akt signaling pathways in the follicular variant of papillary thyroid carcinoma

BACKGROUND

The follicular variant of papillary thyroid carcinoma (FVPTC) is the second most common histotype among papillary thyroid cancers (PTCs). Although the prognosis of FVPTC is similar to the conventional phenotype, differential diagnostic difficulties may not be uncommon with other follicular thyroid neoplasms, and little is known about their genetic alterations. Defining these alterations may lead to the identification of diagnostic and biologic markers.

METHODS

In this study, the authors evaluated genetic alterations and downstream-activated signals of the Ras/Raf-mitogen-activated protein kinase (MAPK) and phosphatidylinositol 3-kinase (PI3K)/v-akt murine thymoma viral oncogene (Akt) (PI3K/Akt) signaling pathways in 30 FVPTC tissue specimens. Tumors and matched normal thyroid samples were tested for RAS, for the v-raf murine sarcoma viral oncogene (BRAF) substitution of valine (V) for glutamate (E) at codon 600 (the V600E mutation), for phosphatase and tensin homolog (PTEN), for catalytic PI3k p110 subunit alpha (PIK3CA), for AKT, and for the presence of rearranged during transfection (ret) proto-oncogene/PTC (RET-PTC) and paired box-8 (PAX8)/peroxisome proliferator-activated receptor gamma (PPARgamma) fusion protein (PAX8-PPARgamma) rearrangements by direct sequencing and reverse transcriptase-polymerases chain reaction analyses, respectively. Western blot analysis was used to assess the effects of these gene abnormalities on the activation of the 2 pathways.

RESULTS

Genetic alterations were identified in 70% of FVPTCs. Activation of the MAPK and PI3K pathways was observed in 74% and 22% of tumors, respectively. The alterations that were identified in the genes of the 2 pathways were mutually exclusive. Chromosomal RET-PTC and PAX8-PPARgamma rearrangements were observed in 20% and 17% of tumors, respectively. It was noteworthy that some FVPTCs with RET-PTC had the coactivation of both pathways.

CONCLUSIONS

RET-PTC and PAX8-PPARgamma rearrangements and mutations of the neuroblastoma RAS viral oncogene homolog N-RAS at codon 61 were the most common genetic alterations in FVPTCs. Activation of the MAPK pathway was a frequent event in FVPTCs, and the PI3K signaling pathway could be coactivated in RET-PTC tumors. These findings may have important therapeutic implication in patients with FVPTC.

Investigation of BRAF and CTNNB1 activating mutations in adrenocortical tumors

BACKGROUND

Activating mutations of the BRAF oncogene play a central role in the development of various cancer types, but their role in human adrenocortical tumors is unknown. At variance, activating mutations of another oncogene, CTNNB1, which encodes beta-catenin, have been shown to be common events in both benign and malignant adrenocortical tumors.

AIM

To investigate the prevalence of BRAF and CTNNB1 activating mutations in sporadic adrenocortical tumors.

MATERIALS AND METHODS

Tissue samples from 15 adrenocortical carcinomas and 41 adrenocortical adenomas were investigated for the presence of BRAF and CTNNB1 activating mutations by PCR amplification and direct sequencing.

RESULTS

An advanced invasive non-functioning adrenocortical carcinoma carried a somatic heterozygous BRAF V600E mutation, while 4 functioning and 4 non-functioning adenomas and 3 functioning carcinomas carried different CTNNB1 activating mutations.

CONCLUSIONS

Activating BRAF somatic mutations may be occasionally found in advanced adrenocortical carcinomas, while CTNNB1 activating mutations are early and common events in adrenal tumorigenesis.

Detection and molecular characterization of a novel BRAF activated domain mutation in follicular variant of papillary thyroid carcinoma

To assess the mutational status of BRAF in FVPTC, we directly sequenced the genomic DNA of 30 primary FVPTC samples. BRAF mutations were found in only 4 (13%) tumors. We also identified a previously unknown (novel) mutation in the activation kinase domain of the BRAF (A598V), replacing alanine with valine. Functional analysis showed that this mutation led to the up-regulation of the BRAF kinase activity and its downstream signaling factors. The effect of this mutation on the structural formation of the protein is highlighted. Our results confirm the infrequency of BRAF (V600E) mutation in FVPTC and identify a novel (A598V) mutation of this gene.