Is immunohistochemistry of BRAF V600E useful as a screening tool and during progression disease of melanoma patients?

Effective detection of BRAFV595E mutation in canine urothelial and prostate carcinomas using immunohistochemistry

Canine urothelial carcinoma (UC) and prostate carcinoma (PC) frequently exhibit the BRAFV595E mutation, akin to the BRAFV600E mutation common in various human cancers. Since the initial discovery of the BRAF mutation in canine cancers in 2015, PCR has been the standard method for its detection in both liquid and tissue biopsies. Considering the similarity between the canine BRAFV595E and human BRAFV600E mutations, we hypothesized that immunohistochemistry (IHC) using a BRAFV600E-specific antibody could effectively identify the canine mutant BRAFV595E protein. We tested 122 canine UC (bladder n = 108, urethra n = 14), 21 PC, and benign tissue using IHC and performed digital droplet PCR (ddPCR) on all 122 UC and on 14 IHC positive PC cases. The results from ddPCR and IHC were concordant in 99% (135/136) of the tumours. Using IHC, BRAFV595E was detected in 72/122 (59%) UC and 14/21 (65%) PC. Staining of all benign bladder and prostate tissues was negative. If present, mutant BRAF staining was homogenous, with rare intratumour heterogeneity in three (4%) cases of UC. Additionally, the BRAFV595E mutation was more prevalent in tumours with urothelial morphology, and less common in glandular PC or UC with divergent differentiation. This study establishes that BRAFV600-specific IHC is a reliable and accurate method for detecting the mutant BRAFV595E protein in canine UC and PC. Moreover, the use of IHC, especially with tissue microarrays, provides a cost-efficient test for large-scale screening of canine cancers for the presence of BRAF mutations. This advancement paves the way for further research to define the prognostic and predictive role of this tumour marker in dogs and use IHC to stratify dogs for the treatment with BRAF inhibitors.

Academic dermatology in Australia and New Zealand between 2017 and 2022: A cross‐sectional bibliometric analysis

INTRODUCTION

Academic dermatologists in Australia and New Zealand provide high-quality and meaningful contributions to the understanding of disease and therapeutic translational research. Concerns have been raised by the Australian Medical Association regarding the decline of clinical academics in Australia as a whole, however, such trends in scholarly output have not previously been analysed for Australasian dermatologists.

METHODS

A bibliometric analysis of dermatologists in Australia and New Zealand was conducted in January and February 2023. Available Scopus profiles for all dermatologists were used to measure lifetime H index, scholarly output, citation counts and field-weighted citation impact (FWCI) in the last 5 years (2017-2022). Trends in output over time were measured using non-parametric tests. Differences in output between subgroups stratified by gender and academic leadership positions (associate professor or professor) were measured using Wilcoxon rank-sum and one-way ANOVA tests. The scholarly output of recent College graduates was also analysed as a subgroup, comparing the same bibliographic variables in the 5 years preceding and 5 years following awarding of their fellowships.

RESULTS

From the 463 practising dermatologists in Australia and New Zealand, 372 (80%) were successfully matched to Scopus researcher profiles. Of these dermatologists, 167 were male (45%) and 205 (55%) were female, and 31 (8%) held academic leadership positions. Most dermatologists (67%) published at least one paper in the last 5 years. The median lifetime H index was 4, and between 2017 and 2022 median scholarly output was 3, the median citations were 14 and the median FWCI was 0.64. There was a non-significant trend towards fewer publications per year, however, citation count and FWCI decreased significantly. By subgroups, female dermatologists published significantly more papers between 2017 and 2022, and other bibliographic variables were comparable to male dermatologists. However, women were underrepresented in positions of academic leadership-comprising only 32% of this cohort despite representing 55% of dermatologists. Professors were also significantly more likely to have higher bibliographic outcomes than associate professors. Finally, analysis of recent College graduates highlighted a significant decline in bibliometric outcomes pre- and post-fellowship.

CONCLUSION

Overall, our analysis identifies a trend towards decreased research output by dermatologists in Australia and New Zealand in the last 5 years. Strategies to support dermatologists in research endeavours, particularly women and recent graduates, will be essential in maintaining strong scholarly output among Australasian dermatologists and thereby sustaining optimal evidence-based patient care.

Robustness Evaluation of a Deep Learning Model on Sagittal and Axial Breast DCE-MRIs to Predict Pathological Complete Response to Neoadjuvant Chemotherapy

To date, some artificial intelligence (AI) methods have exploited Dynamic Contrast-Enhanced Magnetic Resonance Imaging (DCE-MRI) to identify finer tumor properties as potential earlier indicators of pathological Complete Response (pCR) in breast cancer patients undergoing neoadjuvant chemotherapy (NAC). However, they work either for sagittal or axial MRI protocols. More flexible AI tools, to be used easily in clinical practice across various institutions in accordance with its own imaging acquisition protocol, are required. Here, we addressed this topic by developing an AI method based on deep learning in giving an early prediction of pCR at various DCE-MRI protocols (axial and sagittal). Sagittal DCE-MRIs refer to 151 patients (42 pCR; 109 non-pCR) from the public I-SPY1 TRIAL database (DB); axial DCE-MRIs are related to 74 patients (22 pCR; 52 non-pCR) from a private DB provided by Istituto Tumori “Giovanni Paolo II” in Bari (Italy). By merging the features extracted from baseline MRIs with some pre-treatment clinical variables, accuracies of 84.4% and 77.3% and AUC values of 80.3% and 78.0% were achieved on the independent tests related to the public DB and the private DB, respectively. Overall, the presented method has shown to be robust regardless of the specific MRI protocol.

A ultrasound-based radiomic approach to predict the nodal status in clinically negative breast cancer patients

In breast cancer patients, an accurate detection of the axillary lymph node metastasis status is essential for reducing distant metastasis occurrence probabilities. In case of patients resulted negative at both clinical and instrumental examination, the nodal status is commonly evaluated performing the sentinel lymph-node biopsy, that is a time-consuming and expensive intraoperative procedure for the sentinel lymph-node (SLN) status assessment. The aim of this study was to predict the nodal status of 142 clinically negative breast cancer patients by means of both clinical and radiomic features extracted from primary breast tumor ultrasound images acquired at diagnosis. First, different regions of interest (ROIs) were segmented and a radiomic analysis was performed on each ROI. Then, clinical and radiomic features were evaluated separately developing two different machine learning models based on an SVM classifier. Finally, their predictive power was estimated jointly implementing a soft voting technique. The experimental results showed that the model obtained by combining clinical and radiomic features provided the best performances, achieving an AUC value of 88.6%, an accuracy of 82.1%, a sensitivity of 100% and a specificity of 78.2%. The proposed model represents a promising non-invasive procedure for the SLN status prediction in clinically negative patients.

Immunohistochemistry as an accurate tool for the assessment of BRAF V600E and TP53 mutations in primary and metastatic melanoma

Metastatic melanoma is a fatal disease with poor prognosis. Ever since targeted therapy against oncogenic BRAF was approved, molecular profiling has become an integral part of the management of such patients. While molecular testing is not available in all pathology laboratories, immunohistochemistry (IHC) is a reliable screening option. The major objective of the present study was to evaluate whether IHC detection of BRAF and the tumor (suppressor) protein 53 gene (TP53) are reliable surrogates for mutation detection. Formalin-fixed paraffin-embedded samples of melanomas for which molecular data were previously obtained by targeted next-generation sequencing (NGS) between January 2014 and February 2019 were immunostained with BRAF V600E and p53 antibodies. A blinded evaluation of the IHC slides was performed by two pathologists in order to evaluate inter-observer concordance (discordant cases were reviewed by a third observer). The associations between the results of IHC and molecular profiling were evaluated. The study included a series of 37 cases of which 15 harbored a BRAF mutation and five a TP53 mutation. IHC had an overall diagnostic accuracy of 93.9% for BRAF V600E and 68.8% for TP53 compared to NGS. A statistically significant association between the two diagnostic methods was obtained for BRAF V600E (P=0.0004) but not for p53 (P=0.3098) IHC. The κ coefficient for IHC assessment of p53 was 0.55 and that for BRAF V600E was 0.72. In conclusion, the present results evidenced that IHC staining is a reliable surrogate for NGS in identifying the BRAF V600E mutation, which may become an efficient screening tool. Aberrant expression of p53 on IHC is at times associated with TP53 mutations but it was not possible to establish a direct link.

Predictive Evaluation on Cytological Sample of Metastatic Melanoma: The Role of BRAF Immunocytochemistry in the Molecular Era

BACKGROUND

Cutaneous malignant melanoma is an aggressive neoplasm. In advanced cases, the therapeutic choice depends on the mutational status of BRAF. Fine needle aspiration cytology (FNA) is often applied to the management of patients affected by melanoma, mainly for the diagnosis of metastases. The evaluation of BRAF mutational status by sequencing technique on cytological samples may be inconvenient, as it is a time and biomaterial-consuming technique. Recently, BRAF immunocytochemistry (ICC) was applied for the evaluation of BRAF V600E mutational status. Although it may be useful mainly in cytological samples, data about BRAF ICC on cytological samples are missing.

METHODS

We performed BRAF ICC on a series of 50 FNA samples of metastatic melanoma. BRAF molecular analysis was performed on the same cytological samples or on the corresponding histological samples. Molecular analysis was considered the gold standard.

RESULTS

BRAF ICC results were adequate in 49 out of 50 (98%) cases, positive in 15 out of 50 (30%) cases and negative in 34 out of 50 (68%) of cases. Overall, BRAF ICC sensitivity, specificity, positive predictive value and negative predictive value results were 88.2%, 100%, 100% and 94.1%, respectively. The diagnostic performance of BRAF ICC results was perfect when molecular evaluation was performed on the same cytological samples. Hyperpigmentation represents the main limitation of the technique.

CONCLUSIONS

BRAF ICC is a rapid, cost-effective method for detecting BRAF V600E mutation in melanoma metastases, applicable with high diagnostic performance to cytological samples. It could represent the first step to evaluate BRAF mutational status in cytological samples, mainly in poorly cellular cases.

BRAF Gene and Melanoma: Back to the Future

As widely acknowledged, 40-50% of all melanoma patients harbour an activating BRAF mutation (mostly BRAF V600E). The identification of the RAS-RAF-MEK-ERK (MAP kinase) signalling pathway and its targeting has represented a valuable milestone for the advanced and, more recently, for the completely resected stage III and IV melanoma therapy management. However, despite progress in BRAF-mutant melanoma treatment, the two different approaches approved so far for metastatic disease, immunotherapy and BRAF+MEK inhibitors, allow a 5-year survival of no more than 60%, and most patients relapse during treatment due to acquired mechanisms of resistance. Deep insight into BRAF gene biology is fundamental to describe the acquired resistance mechanisms (primary and secondary) and to understand the molecular pathways that are now being investigated in preclinical and clinical studies with the aim of improving outcomes in BRAF-mutant patients.

A highly sensitive and specific real-time quantitative PCR for BRAF V600E/K mutation screening

Mutations that lead to constitutive activation of key regulators in cellular processes are one of the most important drivers behind vigorous growth of cancer cells, and are thus prime targets in cancer treatment. BRAF V600E mutation transduces strong growth and survival signals for cancer cells, and is widely present in various types of cancers including lung cancer. A combination of BRAF inhibitor (dabrafenib) and MEK inhibitor (trametinib) has recently been approved and significantly improved the survival of patients with advanced NSCLC harboring BRAF V600E/K mutation. To improve the detection of BRAF V600E/K mutation and investigate the incidence and clinicopathological features of the mutation in lung cancer patients of southern Taiwan, a highly sensitive and specific real-time quantitative PCR (RT-qPCR) method, able to detect single-digit copies of mutant DNA, was established and compared with BRAF V600E-specific immunohistochemistry. Results showed that the BRAF V600E mutation was present at low frequency (0.65%, 2/306) in the studied patient group, and the detection sensitivity and specificity of the new RT-qPCR and V600E-specific immunohistochemistry both reached 100% and 97.6%, respectively. Screening the BRAF V600E/K mutation with the RT-qPCR and V600E-specific immunohistochemistry simultaneously could help improve detection accuracy.

BRAF as a positive predictive biomarker: Focus on lung cancer and melanoma patients

In the era of personalized medicine, BRAF mutational assessment is mandatory in advanced-stage melanoma and non-small cell lung cancer (NSCLC) patients. The identification of actionable mutations is crucial for the adequate management of these patients. To date various drugs have been implemented in clinical practice. Similarly, various methods may be adopted for the identification of BRAF mutations. Here, we briefly review the current literature on BRAF in melanoma and NSCLC, focusing attention in particular on the different methods and drugs adopted in these patients. In addition, an overview of the real-world practice in different Italian laboratories with high expertise in molecular predictive pathology testing is provided.

Detection of BRAF V600E Mutation in Ganglioglioma and Pilocytic Astrocytoma by Immunohistochemistry and Real-Time PCR-Based Idylla Test

The BRAF V600E mutation is an important oncological target in certain central nervous system (CNS) tumors, for which a possible application of BRAF-targeted therapy grows continuously. In the present study, we aim to determine the prevalence of BRAF V600E mutations in a series of ganglioglioma (GG) and pilocytic astrocytoma (PA) cases. Simultaneously, we decided to verify whether the combination of fully automated tests—BRAF-VE1 immunohistochemistry (IHC) and Idylla BRAF mutation assay—may be useful to accurately predict it in the case of specified CNS tumors. The study included 49 formalin-fixed, paraffin-embedded tissues, of which 15 were GG and 34 PA. Immunohistochemistry with anti-BRAF V600E (VE1) antibody was performed on tissue sections using the VentanaBenchMark ULTRA platform. All positive or equivocal cases on IHC and selected negative ones were further assessed using the Idylla BRAF mutation assay coupled with the Idylla platform. The BRAF-VE1 IHC was positive in 6 (6/49; 12.3%) and negative in 39 samples (39/49; 79.6%). The interpretation of immunostaining results was complicated in 4 cases, of which 1 tested positive for the Idylla BRAF mutation assay. Therefore, the overall positivity rate was 14.3%. This included 2 cases of GG and 5 cases of PA. Our study found that BRAF V600E mutations are moderately frequent in PA and GG and that for these tumor entities, IHC VE1 is suitable for screening purposes, but all negative, equivocal, and weak positive cases should be further tested with molecular biology techniques, of which the Idylla system seems to be a promising tool.

Protein Expression in Metastatic Melanoma and the Link to Disease Presentation in a Range of Tumor Phenotypes

Malignant melanoma is among the most aggressive skin cancers and it has among the highest metastatic potentials. Although surgery to remove the primary tumor is the gold standard treatment, once melanoma progresses and metastasizes to the lymph nodes and distal organs, i.e., metastatic melanoma (MM), the usual outcome is decreased survival. To improve survival rates and life span, advanced treatments have focused on the success of targeted therapies in the MAPK pathway that are based on BRAF (BRAF V600E) and MEK. The majority of patients with tumors that have higher expression of BRAF V600E show poorer prognosis than patients with a lower level of the mutated protein. Based on the molecular basis of melanoma, these findings are supported by distinct tumor phenotypes determined from differences in tumor heterogeneity and protein expression profiles. With these aspects in mind, continued challenges are to: (1) deconvolute the complexity and heterogeneity of MM; (2) identify the signaling pathways involved; and (3) determine protein expression to develop targeted therapies. Here, we provide an overview of the results from protein expression in MM and the link to disease presentation in a variety of tumor phenotypes and how these will overcome the challenges of clinical problems and suggest new promising approaches in metastatic melanoma and cancer therapy.

The Hidden Story of Heterogeneous B-raf V600E Mutation Quantitative Protein Expression in Metastatic Melanoma-Association with Clinical Outcome and Tumor Phenotypes

In comparison to other human cancer types, malignant melanoma exhibits the greatest amount of heterogeneity. After DNA-based detection of the BRAF V600E mutation in melanoma patients, targeted inhibitor treatment is the current recommendation. This approach, however, does not take the abundance of the therapeutic target, i.e., the B-raf V600E protein, into consideration. As shown by immunohistochemistry, the protein expression profiles of metastatic melanomas clearly reveal the existence of inter- and intra-tumor variability. Nevertheless, the technique is only semi-quantitative. To quantitate the mutant protein there is a fundamental need for more precise techniques that are aimed at defining the currently non-existent link between the levels of the target protein and subsequent drug efficacy. Using cutting-edge mass spectrometry combined with DNA and mRNA sequencing, the mutated B-raf protein within metastatic tumors was quantitated for the first time. B-raf V600E protein analysis revealed a subjacent layer of heterogeneity for mutation-positive metastatic melanomas. These were characterized into two distinct groups with different tumor morphologies, protein profiles and patient clinical outcomes. This study provides evidence that a higher level of expression in the mutated protein is associated with a more aggressive tumor progression. Our study design, comprised of surgical isolation of tumors, histopathological characterization, tissue biobanking, and protein analysis, may enable the eventual delineation of patient responders/non-responders and subsequent therapy for malignant melanoma.

Immunohistochemical Study Using Monoclonal VE1 Antibody Can Substitute the Molecular Tests for Apprehension of BRAF V600E Mutation in Patients with Non-small-Cell Lung Carcinoma

In patients with non-small-cell lung carcinoma (NSCLC), the analysis of BRAF V600E mutation has become more and more applied since the introduction of many mutation-targeted medications. In this regard, the advantage of immunohistochemistry (IHC) as a reliable diagnostic test substitute to other molecular studies has not been approved yet. Objective. To examine the dependability of using immunohistochemical method utilizing monoclonal VE1 antibody in the detection of BRAF V600 E mutation in patients with non-small-cell lung carcinoma and compare the results there with that of polymerase chain reaction (SSCP-PCR). Materials and Methods. We retrospectively identified 53 patients of whom their histopathological diagnosis was non-small-cell carcinoma of different types. Evaluation of BRAF V600E mutation was assessed using polymerase chain reaction (SSCP-PCR) and IHC using VE1 antibody. This approach was applied to all cases under the study. Results. Among the 53 NSCLC samples, only 5 (9.3%) cases harbored BRAF V600E mutation, 80% were of adenocarcinoma type, and the rest (20%) was of squamous cell carcinoma. IHC analysis for VE1 was positive in 4 out of 5 (80%) BRAF-mutated tumors and negative in all nonmutated BRAF V600 E NSCLC. Conclusion. Our results revealed that VE1 antibody IHC analysis is a promising technique that can be used to detect BRAF V600-mutated NSCLC with relatively high specificity and sensitivity and might become a potential alternative to the current molecular biological methods that are in use for this purpose.

Immunohistochemistry as a Genetic Surrogate in Dermatopathology: Pearls and Pitfalls

Immunohistochemistry (IHC) is routinely performed in most laboratories, and other than purchase of commercially available antibodies, requires no additional equipment or reagents. As such, IHC is an accessible and relatively inexpensive test and one that can be performed quite quickly. This is in sharp contrast to genomic or mutational testing methodologies that are routinely "send out" tests as they require specialized equipment and reagents as well as individuals with expertise in the performance of the tests and analysis of the results, resulting in a prolonged turn-round-time and enhanced associated costs. However, many open questions remain in a rapidly changing therapeutic and scientific landscape with most obvious one being what exactly is the utility of "good old fashioned" IHC in the age of targeted therapy? For molecular applications, is a negative immunohistochemical result enough as a stand-alone diagnostic or predictive product? Is a positive immunohistochemical result perhaps more suitable for a role in screening for molecular alterations rather than a definitive testing modality? This review is an attempt to answer those very questions. We elucidate the broad range of entities in which IHC is currently used as a molecular surrogate and underscore pearls and pitfalls associated with each. Special attention is given to entities for which targeted therapies are currently available and to entities in which molecular data is of clinical utility as a prognosticator.

Concordance in BRAF V600E status over time in malignant melanoma and corresponding metastases

AIMS

The aims of the present study were to analyse the usability of an immunohistochemical (IHC) analysis as compared with a frequently used mutation detection analysis, and to examine the extent of intratumour and intertumour heterogeneity of BRAF V600E in primary tumours and their corresponding metastases. In the development of intertumour heterogeneity between the primary tumour and the corresponding metastases, time as a factor was also investigated.

METHODS AND RESULTS

In total, 227 samples from 224 melanoma patients were analysed with both the Cobas 4800 BRAF V600 Mutation Test and IHC anti-BRAF V600E staining. In 82 primary tumours and 224 corresponding metastases, the extents of intertumour and intratumour heterogeneity were investigated with IHC staining. In 15 cases, disagreement between IHC analysis and the Cobas test was seen. In all but one of the examined patients, homogeneity between the primary tumour and the corresponding metastasis was found. Except for this one case, no heterogeneity developed over longer periods.

CONCLUSION

IHC analysis can be safely used as a BRAF pretreatment screening tool, and no additional test is needed when staining is positive. However, if stains are negative, additional tests are essential for detection of other BRAF mutations. We suggest that using primary melanoma tissues is just as safe as using metastatic tissue for detection of BRAF V600E, as BRAF intertumour heterogeneity is extremely rare. In addition, the time between diagnosis of the primary tumour and diagnosis of the corresponding metastasis seems not to increase the risk of intertumour heterogeneity.

Prognostic Role of BRAFV600E Cellular Localization in Melanoma

BACKGROUND

Approximately half of cutaneous melanoma tissues harbor BRAF^V600E mutations, resulting in a constitutive activation of the mitogen-activated protein kinase (MAPK) pathway. Nuclear-cytoplasmic transport machinery is dysregulated in neoplastic cells and alters the key regulatory proteins that can lead to tumor progression and drug resistance. The significance of nuclear localization of BRAF^V600E has not been fully understood. We examined the clinical significance of intracellular localization of BRAF^V600E in cutaneous melanoma.

STUDY DESIGN

Immunohistochemical analysis of BRAF^V600E was performed on formalin-fixed, paraffin-embedded specimens of cutaneous melanoma (n = 91). Staining intensity was graded in a blinded manner. Correlations to clinical factors were analyzed by Fisher's exact test and 2-tailed t-test. Localization of BRAF^V600E was determined in melanoma cells, and we investigated their resistance to BRAF^V600E-specific inhibitor according to nuclear localization in both in vitro and in vivo models.

RESULTS

We included 91 patients, of whom 32% (29 of 91) had cytoplasmic BRAF^V600E. Nuclear BRAF^V600E was observed in 30% (27 of 91). Overall, BRAF^V600E expression correlated with TNM stage (p = 0.011), mitotic activity (p = 0.010), and ulceration (p = 0.045). Nuclear BRAF^V600E expression correlated with overall clinical stage (p < 0.001), tumor size (p < 0.001), regional lymph node (p < 0.017), depth of invasion (p = 0.005), Clark level (p < 0.001), mitotic activity (p < 0.001), ulceration (p < 0.001), and margin status (p = 0.017). On a cellular level, BRAF^V600E was identified in the nucleus, and its translocation was serum dependent. Our in vitro and in vivo data revealed sequestration of BRAF^V600E in the cytosol-sensitized resistant cells to vemurafenib; nuclear retention of BRAF^V600E was associated with aggressiveness and drug resistance.

CONCLUSIONS

Nuclear localization of BRAF^V600E is associated with melanoma aggressiveness. Further multi-institutional studies are warranted to confirm the clinical relevance of nuclear localization of BRAF^V600E.

Molecular testing for BRAF mutations to inform melanoma treatment decisions: a move toward precision medicine

Approximately one-half of advanced (unresectable or metastatic) melanomas harbor a mutation in the BRAF gene, with V600E being the most common mutation. Targeted therapy with BRAF and MEK inhibitors is associated with significant long-term treatment benefit in patients with BRAF V600-mutated melanoma. Therefore, molecular testing for BRAF mutations is a priority in determining the course of therapy. A literature search was performed using MEDLINE/PubMed and scientific congress databases using the terms 'BRAF,' 'mutation,' and 'cancer/tumor.' These results were filtered to include manuscripts that focused on diagnostic tests for determining BRAF mutation status. Numerous BRAF testing methods were identified, including DNA-based companion diagnostic tests and DNA- and protein-based laboratory-developed tests. Herein we review the characteristics of each method and highlight the strengths and weaknesses that should be considered before use and when interpreting results for each patient. Molecular profiling has shown that mutation load increases with melanoma tumor progression and that unique patterns of genetic changes and evolutionary trajectories for different melanoma subtypes can occur. Discordance in the BRAF mutational status between primary and metastatic lesions, as well as intratumoral heterogeneity, is known to occur. Additionally, the development of acquired resistance to combination BRAF and MEK inhibitor therapy is still a formidable obstacle. Therefore, tumor heterogeneity and the development of acquired resistance have important implications for molecular testing and ultimately the treatment of patients with advanced-stage melanoma. Overall, this information may help community oncologists more accurately and effectively interpret results of diagnostic tests within the context of recent data characterizing melanoma tumor progression.

Intratumor and Intertumor Heterogeneity in Melanoma

Melanoma is a cancer that exhibits one of the most aggressive and heterogeneous features. The incidence rate escalates. A high number of clones harboring various mutations contribute to an exceptional level of intratumor heterogeneity of melanoma. It also refers to metastases which may originate from different subclones of primary lesion. Such component of the neoplasm biology is termed intertumor and intratumor heterogeneity. These levels of tumor heterogeneity hinder accurate diagnosis and effective treatment. The increasing number of research on the topic reflects the need for understanding limitation or failure of contemporary therapies. Majority of analyses concentrate on mutations in cancer-related genes. Novel high-throughput techniques reveal even higher degree of variations within a lesion. Consolidation of theories and researches indicates new routes for treatment options such as targets for immunotherapy. The demand for personalized approach in melanoma treatment requires extensive knowledge on intratumor and intertumor heterogeneity on the level of genome, transcriptome/proteome, and epigenome. Thus, achievements in exploration of melanoma variety are described in details. Particularly, the issue of tumor heterogeneity or homogeneity given BRAF mutations is discussed.

BRAF V600 mutation detection in melanoma: a comparison of two laboratory testing methods

Aims

The assessment of B-raf proto-oncogene, serine/threonine kinase (BRAF) gene status is now standard practice in patients diagnosed with metastatic melanoma with its presence predicting a clinical response to treatment with BRAF inhibitors. The gold standard in determining BRAF status is currently by DNA-based methods. More recently, a BRAF V600E antibody has been developed. We aim to investigate whether immunohistochemical detection of BRAF mutation is a suitable alternative to molecular testing by polymerase chain reaction (PCR).

Methods

We assessed the incidence of BRAF mutation in our cohort of 132 patients, as determined by PCR, as well as examining clinical and histopathological features. We investigated the sensitivity and specificity of the anti-BRAF V600E VE1 clone antibody in detecting the presence of the BRAF V600E mutation in 122 cases deemed suitable for testing.

Results

The incidence of BRAF mutation in our cohort was 28.8% (38/132). Patients with the BRAF mutation were found to be significantly younger at age of diagnosis. BRAF-mutated melanomas tended to be thinner and more mitotically active. The antibody showed a sensitivity of 86.1% with a specificity of 96.9%. The positive predictive value was 96.9%; the negative predictive value was 94.4%. The concordance rate between PCR and immunohistochemical BRAF status was 95.1% (116/122).

Conclusions

The rate of BRAF mutation in our cohort (28.8%) was lower than international published rates of 40%–60%. This may reflect ethnic or geographic differences within population cohorts. The high concordance rate of PCR and immunohistochemical methods in determining BRAF status suggests that immunohistochemistry is potentially a viable, cost-effective alternative to PCR testing and suitable as a screening test for the BRAF mutation.

Investigation of BRAF mutation analysis with different technical platforms in metastatic melanoma

In metastatic melanoma, the detection of somatic mutations in the BRAF gene is crucial regarding patient selection for targeted therapy. Several screening methods have been developed to identify BRAF gene mutations. In this study, our objective was to evaluate the detection of the BRAF V600 mutations using two molecular methods, real-time polymerase chain (real-time PCR) assay and pyrosequencing, and immunohistochemistry (IHC), and to compare the results of these different technical platforms. This study included 98 patients diagnosed with metastatic melanoma at the Hacettepe University, Department of Pathology between 2002 and 2014. BRAF mutation analysis was tested with real-time PCR, pyrosequencing and IHC methods. The results of all three tests were compared with a reference test, and the sensitivity, specificity rates and kappa coefficient values were analysed for each test. We successfully analysed BRAF mutations using all three methods in 92 patients. According to our findings, the pyrosequencing method had the highest kappa value regarding the determination of BRAF V600 mutations. The kappa values were at almost perfect agreement levels in pyrosequencing and real-time PCR assay (kappa coefficient for pyrosequencing=0.895 (95% CI: 0.795-0.995); kappa coefficient for real-time PCR=0.871 (95% CI: 0.761-0.981). The kappa value was at a substantial agreement level in the IHC analysis (kappa coefficient=0.776 (95% CI: 0.629-0.923). According to our results, we found that real-time PCR and pyrosequencing methods were equally excellent in determination of BRAF V600 mutations. The IHC method, which is commonly used in routine pathology practice, can also be safely used as a screening test for determination of BRAF V600 mutations.