Molecular testing in melanoma

BRAFV600E Metastatic Melanoma Journey: A Perspective from a Patient and his Oncologist

BACKGROUND

This article is co-authored by a patient with BRAFV600E metastatic melanoma and his treating oncologist.

CASE DESCRIPTION

The patient describes how he coped with his diagnosis and treatment. He details the pathway of his melanoma treatment, which has spanned over 10 years, including surgical interventions, medical treatment, and participation in clinical trials. He relates his experience of living with the disease-and the adverse effects of treatment-in the long term. The clinical perspective of his treating oncologist reviews the diagnostic process and explains how the therapeutic options were selected for and with the patient. The oncologist also addresses the integration of the patient into clinical trials involving programmed death-1 (PD-1) inhibitors and BRAF/MEK inhibitors. Challenges related to the adverse effects that occurred and the personalised treatment of the patient are also discussed. Finally, the article evaluates current advances in treatment and future therapeutic approaches.

CONCLUSIONS

This case highlights the challenges of identifying which therapeutic options are most appropriate for individual patients with BRAFV600E metastatic melanoma.

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.

Sensitivity and Usefulness of VE1 Immunohistochemical Staining in Acral Melanomas with BRAF Mutation

Background

Acral melanomas are known to have a low frequency of BRAF mutation, in contrary to higher KIT mutation. Recently, VE1 immunostaining was reported to have a good correlation with BRAF mutation status.

Objective

We aimed to evaluate the clinicopathological features of BRAF-mutated acral melanomas and validate the correlation of the VE1 immunohistochemical stains in those cases.

Methods

The clinical features (age, sex, anatomical site), and histopathological characteristics of 41 patients with acral melanoma were evaluated. We performed a next-generation sequencing to detect BRAF mutation status. We also determined the correlation of VE1 immunohistochemical staining with BRAF mutation status.

Results

Among 19 acral melanomas with BRAF mutation, common histopathological subtype was acral lentiginous melanoma (8/19, 42%) and nodular melanoma (8/19, 42%) and superficial spreading melanoma (3/19, 16%) followed. VE1 immunostaining results were positive in all 15 cases with BRAF V600E mutation (sensitivity 100%), and negative in 4 cases of BRAF non-V600E mutation. However, VE1 immunostaining was negative in all 22 patients with BRAF wild-type.

Conclusion

VE1 immunostaining had a good correlation with BRAF V600E mutation status.

Immunohistochemistry as a reliable method for detection of BRAF-V600E mutation in melanoma: a systematic review and meta-analysis of current published literature

BACKGROUND

The BRAF-V600E mutation is associated with tumor aggressiveness and poor prognosis in melanoma patients. Identification of this mutation is clinically important as we now have Food and Drug Administration-approved targeted therapies, such as BRAF and MEK inhibitors, which have been shown to retard disease progression in these patients. Detection of BRAF-V600E by genetic analysis using polymerase chain reaction is the gold standard method for melanoma cases. However, immunohistochemistry (IHC) using a VE1 antibody is rapidly emerging as a trustworthy method for the determination of mutation status in patients' specimens. Our objective in this study was to assess the reliability of IHC compared with genetic methods for successful identification of BRAF-V600E mutation in melanoma tissue specimens.

METHODS

A literature search of PubMed, Web of Science, and Embase was performed for studies comparing IHC with genetic analysis for the detection of BRAF in melanoma patients published through May 28, 2015. Pooled sensitivity, specificity, diagnostic odds ratio, positive, and negative likelihood ratios were calculated using a bivariate model. Logit estimates of sensitivity and specificity with their respective variances were used to plot a hierarchical receiver operating characteristic curve and area under the curve. Heterogeneity was assessed using the Q- and I-squared statistics.

RESULTS

An initial literature search resulted in 287 articles. After two independent reviews and consensus-based discussion to resolve disparities, 21 studies involving a total of 1687 cases met the eligibility criteria and were included in the analysis. The pooled sensitivity of IHC for BRAF-V600E detection was 0.96; 95% confidence interval (CI, 0.94-0.98), specificity 1.00; 95% CI (0.97-1.00), positive likelihood ratio 194.2; 95% CI (37.6-1003.3), negative likelihood ratio 0.04; 95% CI (0.02-0.07), and diagnostic odds ratio 5503 (1199-25,263), as compared with genetic analysis. A high heterogeneity was observed between these studies (Q value of 40.17 & I(2) = 95%; 95% CI (91-99, P < 0.001) which may be explained by studies using different cutoff values for labeling IHC as positive. High accuracy of IHC was depicted by area under the curve in the receiver operating characteristic curve which was 0.99; 95 % CI (0.98-1.00).

CONCLUSIONS

Meta-analysis demonstrates that IHC is highly sensitive and specific for the detection of BRAF-V600E in melanoma cases. IHC is likely to be useful in BRAF mutation detection because it is highly comparable with the genetic methods. Any negative or low staining cases may be selected to undergo genetic analysis based on other clinical and histopathologic features.

Melanoma: Advances in Targeted Therapy and Molecular Markers

PURPOSE AND DESIGN

In recent years, there have been dramatic improvements in the diagnosis and treatment of patients with melanoma. The development of molecular markers and associated targeted therapies have given new hope to subsets of patients with advanced disease. Here we discuss the most important advances in molecular targeted therapy and how these developments are likely to affect the practice of the clinical surgeon.

RESULTS AND CONCLUSIONS

Germ-line and somatic mutations are common in melanoma and provide prognostic information that can now be harnessed to provide a more personalized approach to cancer treatment. BRAF mutation at the V600 position is the most commonly identified mutation in patients with melanoma. Treatment with targeted inhibitors in patients with BRAF-mutant melanoma has afforded dramatic responses in about half of selected patients. Unfortunately, disease control is not durable and recurrences are common. We predict an increasing role for the surgeon in the multidisciplinary treatment of patients with metastatic disease, as well as a role for molecular profiling in patients with high-risk early stage disease. Further, we are only beginning to understand the prognostic significance of various gene mutations in patients with melanoma.

Comparison between two widely used laboratory methods in BRAF V600 mutation detection in a large cohort of clinical samples of cutaneous melanoma metastases to the lymph nodes

AIMS

The study compares detection rates of oncogenic BRAF mutations in a homogenous group of 236 FFPE cutaneous melanoma lymph node metastases, collected in one cancer center. BRAF mutational status was verified by two independent in-house PCR/Sanger sequencing tests, and the Cobas® 4800 BRAF V600 Mutation Test.

RESULTS

The best of two sequencing approaches returned results for 230/236 samples. In 140 (60.9%), the mutation in codon 600 of BRAF was found. 91.4% of all mutated cases (128 samples) represented p.V600E. Both Sanger-based tests gave reproducible results although they differed significantly in the percentage of amplifiable samples: 230/236 to 109/143. Cobas generated results in all 236 cases, mutations changing codon V600 were detected in 144 of them (61.0%), including 5 not amplifiable and 5 negative in the standard sequencing. However, 6 cases positive in sequencing turned out to be negative in Cobas. Both tests provided us with the same BRAF V600 mutational status in 219 out of 230 cases with valid results (95.2%).

CONCLUSIONS

The total BRAF V600 mutation detection rate didn't differ significantly between the two methodological approaches (60.9% vs. 61.0%). Sequencing was a reproducible method of V600 mutation detection and more powerful to detect mutations other than p.V600E, while Cobas test proved to be less susceptible to the poor DNA quality or investigator's bias. The study underlined an important role of pathologists in quality assurance of molecular diagnostics.

Validation of the VE1 immunostain for the BRAF V600E mutation in melanoma

BACKGROUND

BRAF mutation status, and therefore eligibility for BRAF inhibitors, is currently determined by sequencing methods. We assessed the validity of VE1, a monoclonal antibody against the BRAF V600E mutant protein, in the detection of mutant BRAF V600E melanomas as classified by DNA pyrosequencing.

METHODS

The cases were 76 metastatic melanoma patients with only one known primary melanoma who had had BRAF codon 600 pyrosequencing of either their primary (n = 19), metastatic (n = 57) melanoma, or both (n = 17). All melanomas (n = 93) were immunostained with the BRAF VE1 antibody using a red detection system. The staining intensity of these specimens was scored from 0 to 3+ by a dermatopathologist. Scores of 0 and 1+ were considered as negative staining while scores of 2+ and 3+ were considered positive.

RESULTS

The VE1 antibody showed a sensitivity of 85% and a specificity of 100% as compared to DNA pyrosequencing results. There was 100% concordance between VE1 immunostaining of primary and metastatic melanomas from the same patient. V600K, V600Q, and V600R BRAF melanomas did not positively stain with VE1.

CONCLUSIONS

This hospital-based study finds high sensitivity and specificity for the BRAF VE1 immunostain in comparison to pyrosequencing in detection of BRAF V600E in melanomas.

A meta-analysis of somatic mutations from next generation sequencing of 241 melanomas: a road map for the study of genes with potential clinical relevance

Next generation sequencing (NGS) has been used to characterize the overall genomic landscape of melanomas. Here, we systematically examined mutations from recently published melanoma NGS data involving 241 paired tumor-normal samples to identify potentially clinically relevant mutations. Melanomas were characterized according to an in-house clinical assay that identifies well-known specific recurrent mutations in five driver genes: BRAF (affecting V600), NRAS (G12, G13, and Q61), KIT (W557, V559, L576, K642, and D816), GNAQ (Q209), and GNA11 (Q209). Tumors with none of these mutations are termed "pan negative." We then mined the driver mutation-positive and pan-negative melanoma NGS data for mutations in 632 cancer genes that could influence existing or emerging targeted therapies. First, we uncovered several genes whose mutations were more likely associated with BRAF- or NRAS-driven melanomas, including TP53 and COL1A1 with BRAF, and PPP6C, KALRN, PIK3R4, TRPM6, GUCY2C, and PRKAA2 with NRAS. Second, we found that the 69 "pan-negative" melanoma genomes harbored alternate infrequent mutations in the five known driver genes along with many mutations in genes encoding guanine nucleotide binding protein α-subunits. Third, we identified 12 significantly mutated genes in "pan-negative" samples (ALK, STK31, DGKI, RAC1, EPHA4, ADAMTS18, EPHA7, ERBB4, TAF1L, NF1, SYK, and KDR), including five genes (RAC1, ADAMTS18, EPHA7, TAF1L, and NF1) with a recurrent mutation in at least two "pan-negative" tumor samples. This meta-analysis provides a road map for the study of additional potentially actionable genes in both driver mutation-positive and pan-negative melanomas.

Molecular pathology of melanocytic tumors

Genetic and genomic analyses of melanocytic tumors have yielded new opportunities for improvements in diagnostic accuracy for the distinction of nevus from melanoma and better selection of patients affected by melanoma for targeted treatment. Since chromosomal copy number changes are commonly found in malignant melanoma, but rare in melanocytic nevi, cytogenetic assays have emerged as a promising ancillary study for the workup of melanocytic tumors with ambiguous light microscopic features. Comparative genomic hybridization (CGH) permits assessment of the full set of chromosomes, but requires a significant amount of lesional tissue, and may fail to detect aberrations in a minor subpopulation of tumor cells. Fluorescence in situ hybridization (FISH) is the cytogenetic assay of choice for limited amounts of tissue. FISH targets only specific chromosomes, with inherent limitations in test sensitivity and specificity. FISH analysis is also heavily dependent on individual experience. Molecular studies have identified distinct sets of mutations in melanoma and/or nevi. These mutations have become clinically relevant for targeted therapy of patients with advanced disease, especially for the treatment of patients with metastatic melanoma carrying the BRAF(V600) or KIT mutations. However, mutation analysis can on occasion also be used for diagnostic purposes.

Combined BRAF(V600E)-positive melanocytic lesions with large epithelioid cells lacking BAP1 expression and conventional nevomelanocytes

Recently a group of spitzoid melanocytic proliferations with loss of BAP1 expression has been reported. The lesions may occur sporadically or as part of a familial cancer syndrome. They have distinct histopathologic features characterized by a nevus-like silhouette and cytologic composition of large epithelioid melanocytes with oval vesicular nuclei, distinct nucleoli, and abundant cytoplasm with well-defined cytoplasmic borders. A characteristic immunohistochemical finding is loss of nuclear labeling for BAP1. In contrast to classic Spitz nevi, the lesions carry the BRAF mutation. They may present as a pure large epithelioid cell proliferation or as a combined lesion in association with a conventional nevus. Here we report a series of 8 combined melanocytic lesions, in which a dominant large epithelioid cell proliferation with loss of BAP1 expression was associated and intimately admixed with a BAP1-positive conventional nevus. These biphenotypic lesions were from 6 patients, 3 female and 3 male, ranging in age from 16 to 59 years. Immunohistochemical analysis for BAP1 showed loss of nuclear labeling confined to the large epithelioid melanocyte subpopulation. The conventional melanocytes retained BAP1 expression. Both large epithelioid and conventional melanocytes were immunoreactive with the monoclonal antibody VE1, which recognizes the protein encoded by mutant BRAF. In 6 cases the conventional nevus component was a compound nevus of small "type B" melanocytes. In 2 cases, the nevus remnant was entirely intradermal. The lesions described herein may represent a peculiar combined melanocytic nevus variant. However, longer follow-up and more studies are needed to determine the biological potential of the BAP1-negative melanocyte proliferations.

Cytogenetic and mutational analyses of melanocytic tumors

Analyses of genetic and genomic alterations of melanocytic tumors have not only led to a better understanding of the pathogenesis of melanocytic tumors but also created new opportunities for improvements in diagnostic accuracy in distinguishing nevus from melanoma, and more effective treatments for patients affected by melanoma. Cytogenetic tests have emerged as a promising ancillary method for the workup of diagnostically problematic melanocytic tumors with ambiguous light microscopic features. Mutation analysis not only is important in treatment decision making but also can be used for improved diagnostic accuracy, staging, and prognosis.