Beyond BRAF(V600): clinical mutation panel testing by next-generation sequencing in advanced melanoma

The management of melanoma has evolved due to improved understanding of its molecular drivers. To augment the current understanding of the prevalence, patterns, and associations of mutations in this disease, the results of clinical testing of 699 advanced melanoma patients using a pan-cancer next generation sequencing (NGS) panel of hotspot regions in 46 genes were reviewed. Mutations were identified in 43 of the 46 genes on the panel. The most common mutations were BRAF^V600 (36%), NRAS (21%), TP53 (16%), BRAF^Non-V600 (6%), and KIT (4%). Approximately one-third of melanomas had >1 mutation detected, and the number of mutations per tumor was associated with melanoma subtype. Concurrent TP53 mutations were the most frequent event in tumors with BRAF^V600 and NRAS mutations. Melanomas with BRAF^Non-V600 mutations frequently harbored concurrent NRAS mutations (18%), which were rare in tumors with BRAF^V600 mutations (1.6%). The prevalence of BRAF^V600 and KIT mutations were significantly associated with melanoma subtypes, and BRAF^V600 and TP53 mutations were significantly associated with cutaneous primary tumor location. Multiple potential therapeutic targets were identified in metastatic unknown primary and cutaneous melanomas that lacked BRAF^V600 and NRAS mutations. These results enrich our understanding of the patterns and clinical associations of oncogenic mutations in melanoma.

Novel algorithmic approach predicts tumor mutation load and correlates with immunotherapy clinical outcomes using a defined gene mutation set

BACKGROUND

While clinical outcomes following immunotherapy have shown an association with tumor mutation load using whole exome sequencing (WES), its clinical applicability is currently limited by cost and bioinformatics requirements.

METHODS

We developed a method to accurately derive the predicted total mutation load (PTML) within individual tumors from a small set of genes that can be used in clinical next generation sequencing (NGS) panels. PTML was derived from the actual total mutation load (ATML) of 575 distinct melanoma and lung cancer samples and validated using independent melanoma (n = 312) and lung cancer (n = 217) cohorts. The correlation of PTML status with clinical outcome, following distinct immunotherapies, was assessed using the Kaplan-Meier method.

RESULTS

PTML (derived from 170 genes) was highly correlated with ATML in cutaneous melanoma and lung adenocarcinoma validation cohorts (R2 = 0.73 and R2 = 0.82, respectively). PTML was strongly associated with clinical outcome to ipilimumab (anti-CTLA-4, three cohorts) and adoptive T-cell therapy (1 cohort) clinical outcome in melanoma. Clinical benefit from pembrolizumab (anti-PD-1) in lung cancer was also shown to significantly correlate with PTML status (log rank P value < 0.05 in all cohorts).

CONCLUSIONS

The approach of using small NGS gene panels, already applied to guide employment of targeted therapies, may have utility in the personalized use of immunotherapy in cancer.

Acneiform eruptions associated with epidermal growth factor receptor–targeted chemotherapy

A relatively newer class of chemotherapy agents, known as the epidermal growth factor receptor inhibitors (EGF-RIs), is being used to treat advanced stages of solid tumors. Acneiform eruptions are a frequent adverse effect and one which has been associated with increased survival in some studies. We describe 3 patients who presented shortly after initiation of EGF-RI therapy. Characteristics included an absence of comedones, facial and truncal involvement, and a perifollicular lymphoneutrophilic infiltrate detected on biopsy. Lesion counts were reduced with topical adapalene and oral tetracyclines in two patients. Patient 3 had dramatic clearance with low-dose isotretinoin (20 mg daily) until completion of EGF-RI therapy. Acneiform eruptions are a common adverse reaction to EGF-RI therapy and can be treated with traditional acne therapy. This should not be considered a drug hypersensitivity eruption or allergy, and patients should continue therapy. For patients with severe eruptions, oral isotretinoin is a consideration.

Clinicopathological features and clinical outcomes associated with TP53 and BRAFNon-V600 mutations in cutaneous melanoma patients

BACKGROUND

BRAFV600 , NRAS, TP53, and BRAFNon-V600 are among the most common mutations detected in non-acral cutaneous melanoma patients. Although several studies have identified clinical and pathological features associated with BRAFV600 and NRAS mutations, limited data are available regarding the correlates and significance of TP53 and BRAFNon-V600 mutations.

METHODS

This study analyzed the patient demographics, primary tumor features, and clinical outcomes of a large cohort of non-acral cutaneous melanoma patients who had undergone clinically indicated molecular testing (n = 926).

RESULTS

The prevalence of BRAFV600 , NRAS, TP53, and BRAFNon-V600 mutations was 43%, 21%, 19%, and 7%, respectively. The presence of a TP53 mutation was associated with older age (P = .019), a head and neck primary tumor site (P = .0001), and longer overall survival (OS) from the diagnosis of stage IV disease in univariate (P = .039) and multivariate analyses (P = .015). BRAFNon-V600 mutations were associated with older age (P = .005) but not with primary tumor features or OS from stage IV. Neither TP53 nor BRAFNon-V600 mutations correlated significantly with OS with frontline ipilimumab treatment, and the TP53 status was not significantly associated with outcomes with frontline BRAF inhibitor therapy. Eleven patients with BRAFNon-V600 mutations were treated with a BRAF inhibitor. Three patients were not evaluable for a response because of treatment cessation for toxicities; the remaining patients had disease progression as the best response to therapy.

CONCLUSIONS

These results add to the understanding of the clinical features associated with TP53 and BRAFNon-V600 mutations in advanced cutaneous melanoma patients, and they support the rationale for evaluating the prognostic significance of TP53 in other cohorts of melanoma patients. Cancer 2017;123:1372-1381. © 2016 American Cancer Society.

Somatic Copy Number Alterations at Oncogenic Loci Show Diverse Correlations with Gene Expression

Somatic copy number alterations (SCNAs) affecting oncogenic drivers have a firmly established role in promoting cancer. However, no agreed-upon standard exists for calling locus-specific amplifications and deletions in each patient sample. Here, we report the correlative analysis of copy number amplitude and length with gene expression across 6,109 samples from The Cancer Genome Atlas (TCGA) dataset across 16 cancer types. Using specificity, sensitivity, and precision-based scores, we assigned optimized amplitude and length cutoffs for nine recurrent SCNAs affecting known oncogenic drivers, using mRNA expression as a functional readout. These cutoffs captured the majority of SCNA-driven, highly-expression-altered samples. The majority of oncogenes required only amplitude cutoffs, as high amplitude samples were almost invariably focal; however, CDKN2A and PTEN uniquely required both amplitude and length cutoffs as primary predictors. For PTEN, these extended to downstream AKT activation. In contrast, SCNA genes located peri-telomerically or in fragile sites showed poor expression-copy number correlations. Overall, our analyses identify optimized amplitude and length cutoffs as efficient predictors of gene expression changes for specific oncogenic SCNAs, yet warn against one-size-fits-all interpretations across all loci. Our results have implications for cancer data analyses and the clinic, where copy number and mutation data are increasingly used to personalize cancer therapy.

Anti-MDA-5 Dermatomyositis With Development of Drug-Mediated Necrolytic Skin Lesions

A 59-year-old male presented with 1 month of progressive dyspnea, 30-lb weight loss, and skin changes on the digits of the hands. In the 4 weeks prior to admission, he was admitted and treated twice for pneumonia at another hospital and received intravenous (IV) vancomycin, ceftriaxone, and azithromycin for a total of 10 days. After admission, he underwent computed tomography imaging of chest, which revealed findings suggestive of interstitial lung disease but given the fact that infection was not ruled out, empiric antibiotics were initiated. The skin lesions on the fingers were felt to be consistent with Gottron’s papules, and his overall constellation of findings were felt to be consistent with dermatomyositis (DM). Over the following 3 days, he developed diffuse, violaceous skin lesions, elevation of liver transaminases, and severe thrombocytopenia. The skin lesions progressed to epidermal necrosis. He developed erosions of the oral mucosa and scrotum. Before skin biopsy results were finalized, IV immunoglobulin and IV dexamethasone were started empirically for suspected DM and immune-mediated thrombocytopenia. His laboratory abnormalities normalized within a week. Biopsy results of the skin were consistent with Stevens-Johnson syndrome (SJS). Autoantibody test for anti-MDA5 were positive, confirming a diagnosis of anti-MDA5 associated DM. Subsequent development of SJS was likely due to antibiotic exposure in the preceding month. Simultaneous development of anti-MDA5 DM and SJS raises the question of a link between the 2 conditions. To our knowledge, this is the first reported association of these 2 conditions reported in the literature.

A novel approach: chest wall cyst excised by MIS

We present a 62-year-old male with a recurrent cyst in the left posterior chest. MRI demonstrated a fluid-filled cavity measuring 23 cm in length and 11 cm in width. The cyst was aspirated demonstrating clear serous fluid. However, the cyst returned and he was referred to us for further treatment. The cyst was excised through a minimally invasive approach using a combination of blunt and electrocautery dissection. The cystic lesion was circumferentially freed from the trapezius muscle and cervical structures. Pathologic examination revealed a benign, fibrous-walled cyst without a true epithelial lining. There are no published reports of a deep thoracic wall cyst resembling this case in terms of histology or location. This patient is free of recurrence 1 year later.

Granuloma Annulare Secondary to Vemurafenib Therapy for Lung Adenocarcinoma

Numerous cutaneous manifestations have been associated with use of BRAF inhibitors, including two previously reported cases of granuloma annulare (GA) eruptions associated with vemurafenib therapy. Both of these patients were being treated for metastatic melanoma. In this report, we describe the case of a 71-year-old man who developed classic GA lesions while being treated with vemurafenib monotherapy for nonmelanoma cancer, specifically metastatic lung adenocarcinoma positive for BRAF V600 mutation. <p><em>J Drugs Dermatol. 2017;16(10):1050-1052.</em></p>.