Development of a prognostic genetic signature to predict the metastatic risk associated with cutaneous melanoma

Clinical validation of a prognostic 11-gene expression profiling score in prospectively collected FFPE tissue of patients with AJCC v8 stage II cutaneous melanoma

BACKGROUND

Adjuvant therapies have been approved for patients with AJCC (American Joint Committee on Cancer) stage III and stage IV cutaneous melanoma (CM) after complete resection. These therapies might also be indicated for patients with high-risk stage II CM.

MATERIAL AND METHODS

We included patients diagnosed with stage II melanoma between 2000 and 2016 and for which primary tumour tissue was available. The prognostic value of the 11-gene expression profiling score (GEPS) was evaluated as a dichotomized parameter (GEPS ≤0 vs. >0). Endpoints of the analysis were melanoma specific survival (MSS), distant metastasis-free survival (DMFS) and relapse-free survival (RFS).

RESULTS

GEPS was determined in 245 patients ranging between -0.7 and 3.53. A total of 111 females and 134 males were included; the median follow-up was 41 months. Kaplan Meier analyses showed statistically significant survival differences between patients with high GEPS (n = 154) and low GEPS (n = 91) for MSS (p = 0.018), DMFS (p = 0.005) and RFS (p = 0.009). The 5-year and 10-year MSS was 92% in the low-GEPS and 82% and 67% in the high-GEPS group, respectively. Multivariate Cox regression analysis showed independent significance for MSS of GEPS (HR = 1.55; p = 0.006), tumor thickness (HR = 1.21; p < 0.001) and age (HR1.05; p = 0.002).

CONCLUSION

GEPS was validated as independent prognostic factor for MSS in stage II CM and could be used for therapeutic decisions when systemic therapies become available in stage II CM.

Potential Prognostic Predictors and Molecular Targets for Skin Melanoma Screened by Weighted Gene Co-expression Network Analysis

AIMS AND OBJECTIVES

Among skin cancers, malignant skin melanoma is the leading cause of death. Identification of gene markers of malignant skin melanoma associated with survival may provide new clues for prognosis prediction and treatment. This research aimed to screen out potential prognostic predictors and molecular targets for malignant skin melanoma.

INTRODUCTION

Information regarding gene expression in skin melanoma and patients' clinical traits was obtained from the Gene Expression Omnibus database. Weighted gene co-expression network analysis (WGCNA) was applied to build co-expression modules and investigate the association between the modules and clinical traits. Moreover, functional enrichment analysis was performed for clinically significant co-expression modules. Hub genes of these modules were validated via Gene Expression Profiling Interactive Analysis (GEPIA) and the Human Protein Atlas (http:// www.proteinatlas.org).

METHODS

First, using WGCNA, 9 co-expression modules were constructed by the top 25% differentially expressed genes (4406 genes) from 77 human melanoma samples. Two co-expression modules (magenta and blue modules) were significantly correlated with survival months (r = -0.27, p = 0.02; r = 0.27, p = 0.02, respectively). The results of functional enrichment analysis demonstrated that the magenta module was mainly enriched in the cell cycle process and the blue module was mainly enriched in the immune response process. Additionally, the GEPIA and Human Protein Atlas results suggested that the hub genes CCNB2, ARHGAP30, and SEMA4D were associated with relapse-free survival and overall survival (all p-values < 0.05) and were differentially expressed in melanoma tumors and normal skin.

RESULTS AND CONCLUSION

The results provided the framework of co-expression gene modules of skin melanoma and screened out CCNB2, ARHGAP30, and SEMA4D associated with survival as potential prognostic predictors and molecular targets of treatment.

Towards Improving Skin Cancer Diagnosis by Integrating Microarray and RNA-Seq Datasets

Many clinical studies have revealed the high biological similarities existing among different skin pathological states. These similarities create difficulties in the efficient diagnosis of skin cancer, and encourage to study and design new intelligent clinical decision support systems. In this sense, gene expression analysis can help find differentially expressed genes (DEGs) simultaneously discerning multiple skin pathological states in a single test. The integration of multiple heterogeneous transcriptomic datasets requires different pipeline stages to be properly designed: from suitable batch merging and efficient biomarker selection to automated classification assessment. This article presents a novel approach addressing all these technical issues, with the intention of providing new sights about skin cancer diagnosis. Although new future efforts will have to be made in the search for better biomarkers recognizing specific skin pathological states, our study found a panel of 8 highly relevant multiclass DEGs for discerning up to 10 skin pathological states: 2 healthy skin conditions a priori, 2 cataloged precancerous skin diseases and 6 cancerous skin states. Their power of diagnosis over new samples was widely tested by previously well-trained classification models. Robust performance metrics such as overall and mean multiclass F1-score outperformed recognition rates of 94% and 80%, respectively. Clinicians should give special attention to highlighted multiclass DEGs that have high gene expression changes present among them, and understand their biological relationship to different skin pathological states.

Prognostic gene expression profiling in melanoma: necessary steps to incorporate into clinical practice

Prognostic gene expression profiling (GEP) tests for cutaneous melanoma (CM) are not recommended in current guidelines outside of a clinical trial. However, their use is becoming more prevalent and some practitioners are using GEP tests to guide patient management. Thus, there is an urgent need to bridge this gap between test usage and clinical guideline recommendations by obtaining high-quality evidence to guide us toward best practice use of GEP testing in CM patients. We focus here on the opportunities and uncertainties associated with prognostic GEP testing in CM, review how GEP testing was incorporated into clinical care guidelines for uveal melanoma and breast cancer and discuss the role of clinical trials to determine best use in patients with CM.

Transcriptomic Analysis Reveals Prognostic Molecular Signatures of Stage I Melanoma

PURPOSE

Previously identified transcriptomic signatures have been based on primary and metastatic melanomas with relatively few American Joint Committee on Cancer (AJCC) stage I tumors, given difficulties in sampling small tumors. The advent of adjuvant therapies has highlighted the need for better prognostic and predictive biomarkers, especially for AJCC stage I and stage II disease.

EXPERIMENTAL DESIGN

A total of 687 primary melanoma transcriptomes were generated from the Leeds Melanoma Cohort (LMC). The prognostic value of existing signatures across all the AJCC stages was tested. Unsupervised clustering was performed, and the prognostic value of the resultant signature was compared with that of sentinel node biopsy (SNB) and tested as a biomarker in three published immunotherapy datasets.

RESULTS

Previous Lund and The Cancer Genome Atlas signatures predicted outcome in the LMC dataset (P = 10-8 to 10-4) but showed a significant interaction with AJCC stage (P = 0.04) and did not predict outcome in stage I tumors (P = 0.3-0.7). Consensus-based classification of the LMC dataset identified six classes that predicted outcome, notably in stage I disease. LMC class was a similar indicator of prognosis when compared with SNB, and it added prognostic value to the genes reported by Gerami and colleagues. One particular LMC class consistently predicted poor outcome in patients receiving immunotherapy in two of three tested datasets. Biological characterization of this class revealed high JUN and AXL expression and evidence of epithelial-to-mesenchymal transition.

CONCLUSIONS

A transcriptomic signature of primary melanoma was identified with prognostic value, including in stage I melanoma and in patients undergoing immunotherapy.

Adjuvant Treatment of Melanoma: Recent Developments and Future Perspectives

Surgical excision is the treatment of choice for early stage melanoma, and this strategy is initially curative for the vast majority of patients. However, only approximately 40-60% of high-risk patients who undergo surgery alone will be disease-free at 5 years. These patients will ultimately experience loco-regional relapse or relapse at distant sites. The main aim of adjuvant therapies is to reduce the recurrence rate of radically operated patients at high risk and to potentially improve survival. Recent practice changing results with immune checkpoint inhibitors and targeted therapies have been published in stage III/IV melanoma patients, after surgical complete resection, and have dramatically improved the landscape of adjuvant therapy. Interferon-α, ipilimumab, and more recently anti-programmed cell death protein-1 antibodies and BRAF inhibitors plus MEK inhibitors have been approved in the adjuvant setting by the US Food and Drug Administration; similarly, the same drugs are approved by the European Medicines Agency with the exception of ipilimumab. A completely new scenario is emerging in the neoadjuvant setting as well: in locally advanced or metastatic disease, patients may partially respond to neoadjuvant therapy and become virtually resectable with systemic control of disease. This review summarizes the current state of the field and describes new strategies tracing the history of adjuvant therapy in melanoma, with a view on future projects.

Level of Evidence Review for a Gene Expression Profile Test for Cutaneous Melanoma

BACKGROUND

The advent of molecular medicine may allow for individualized cancer prognostication, which should enable better clinical management and, hopefully, improve patient outcomes. A 31-gene expression profile (31-GEP) test is currently available for patients diagnosed with cutaneous melanoma; this test helps inform patients' individual treatment plans, especially when combined with traditional biomarkers.

OBJECTIVE

The objective of this study was to review the current literature and establish the level of evidence for a cutaneous melanoma 31-GEP test.

METHODS

A review of seven development and validation studies for the 31-GEP test was conducted. The respective strengths and weaknesses of each study were applied to the level of evidence criteria from major organizations that publish guidelines for melanoma management: American Joint Committee on Cancer, National Comprehensive Cancer Network, and American Academy of Dermatology.

RESULTS

Evaluating each study led to classifying the 31-GEP test as level I/II, I-IIIB, and IIA according to American Joint Committee on Cancer, National Comprehensive Cancer Network, and American Academy of Dermatology criteria, respectively. This stands in contrast to the official unrated status conferred by the American Joint Committee on Cancer and National Comprehensive Cancer Network and the II/IIIC rating designated by the American Academy of Dermatology.

CONCLUSIONS

Differences between the authors' findings and official published ratings may be attributed to chronological issues, as many of the studies were not yet published when the aforementioned organizations conducted their reviews. There was also difficulty in applying the National Comprehensive Cancer Network criteria to this prognostic test, as their guidelines were intended for evaluation of predictive markers. Nevertheless, based upon the most current data available, integration of the 31-GEP test into clinical practice may be warranted in certain clinical situations.

Evolving management of positive regional lymph nodes in melanoma: Past, present and future directions

Sentinel lymph node (SLN) biopsy has become the standard of care for lymph node staging in melanoma and the most important predictor of survival in clinically node-negative disease. Previous guidelines recommend completion lymph node dissection (CLND) in cases of positive SLN; however, the lymph nodes recovered during CLND are only positive in a minority of these cases. Recent evidence suggests that conservative management (i.e. observation) has similar outcomes compared to CLND. We sought to review the most current literature regarding the management of SLN in metastatic melanoma and to discuss potential future directions.

Nonsurgical Management of Lymph Node Basins in Melanoma

In this article we provide a critical review of the evidence available for surgical management of the nodal basin in melanoma, with an aim to ensure an understanding of risks and benefits for all lymph node surgery offered to patients, and alternatives to surgical management where appropriate.

Comparative gene expression analysis in melanocytes driven by tumor cell-derived exosomes

Abundant with organelle-like membranous structures, the tumor microenvironment is composed of cancer cells that secrete exosomes. Studies have shown that these secreted exosomes transport RNA and active molecules to other cells to reshape the tumor microenvironment and promote tumor growth. In fact, we found that exosomes derived from melanoma cells drive pre-malignant transition in primary melanocytes. However, there is little available in the scientific literature on how exosomes modulate melanocytes in the microenvironment to optimize conditions for tumor progression and metastasis. We therefore focused this current study on identifying these conditions genetically. Through RNA sequencing, we analyzed gene expression levels of melanocytes driven by exosomes derived from melanoma and lung cancer cells compared with those without exosome controls. Significant differences were found in gene expression patterns of melanocytes driven by exosomes derived from melanoma and lung cancer cells. In the melanocytes responding to exosomes derived from melanoma cells, genes of lipopolysaccharide and regulation of leukocyte chemotaxis were predominant. In the melanocytes responding to exosomes derived from lung cancer cells, genes of DNA replication and mitotic nuclear division played an important role. These results provide further mechanistic understanding of tumor progression promoted by tumor-derived exosomes. This will also help identify potential therapeutic targets for melanoma progression.

Development and Initial Validation of Calculated Tumor Area as a Prognostic Tool in Cutaneous Malignant Melanoma

IMPORTANCE

Breslow thickness is a 1-dimensional surrogate prognostic feature for tumor size, yet tissue sections have 2 dimensions. Therefore, a 2-dimensional feature, calculated tumor area (CTA), was devised.

OBJECTIVE

To determine CTA precision and prognostic value.

DESIGN, SETTING, AND PARTICIPANTS

This retrospective cohort of patients with cutaneous melanoma presented to the Leicester and Nottingham National Health Service hospital trusts in the United Kingdom. Eligible patients in the Leicester development sample had available primary tumor tissue; a diagnosis from January 1, 2004, through December 31, 2011; invasive disease; and Leicestershire residency. Patients in the Nottingham validation sample had an anonymized spreadsheet with primary melanoma diagnosed from January 1, 2003, through December 31, 2005, or from January 1, 2008, through December 31, 2010. From a starting population of 1463 patients in both data sets, a total of 224 (15.3%) were excluded to yield a study population of 1239. Data were analyzed from April 30, 2018, through January 10, 2019.

INTERVENTION

An observational analysis of the prognostic value of CTA in patients with cutaneous melanoma.

MAIN OUTCOMES AND MEASURES

Independent association of CTA with melanoma-specific survival and confounding effect of CTA on Breslow thickness in survival analysis.

RESULTS

A total of 1239 patients with melanoma were assessed, including 649 (52.4%) women, with a median age of 60 years (interquartile range, 47-71 years). An intraclass correlation coefficient for CTA on 13 cases was 0.99. In 918 patients in the Leicester cohort, CTA was an independent prognostic factor in Cox proportional hazards regression models after adjusting for Breslow thickness, age, sex, ulcer, mitotic rate, and microsatellites (hazard ratio [HR], 1.87; 95% CI, 1.49-2.34; P < .001). Validation in 321 patients in the Nottingham cohort showed an HR of 1.55 (95% CI, 1.15-2.09; P = .005) and in the combined 1239 cases, an HR of 1.70 (95% CI, 1.43-2.03; P < .001). Breslow thickness was significant in multivariable analysis only when CTA was not in the model. The relative importance of CTA was shown by its retention in all 100 bootstrap multivariable models with backward selection, whereas Breslow thickness was retained in only 53. Melanomas stratified by CTA showed wider separation of survival curves than those stratified by Breslow thickness using the American Joint Committee on Cancer Staging Manual, 8th Edition (HRs, 1.00 to 41.46 vs 1.00 to 36.95, respectively), and the model with CTA categories had a Bayesian information criterion difference of 13.9 compared with T category, indicating substantially better fit. This model had a Harrell C index of 83.7%, and bootstrap analysis showed little evidence of model optimism, with a corrected calibration slope of 0.99.

CONCLUSIONS AND RELEVANCE

This study provides a novel microscopic feature, CTA, with evidence of its independent prognostic value. This evidence suggests that CTA should be a priority for further study.

Lung-Seeking Metastases

Metastases from different cancer types most often affect the lung parenchyma. Moreover, the lungs are among the most frequent sites of growth of metastatic masses of uncertain/unknown lineage of origin. Thus, with regards to pulmonary neoplastic parenchymal nodules, the critical issue is to determine if they are IN the lung or OF the lung. In this review, we highlight the clinical, instrumental and molecular features which characterize lung metastases, mainly focusing on recently advancing and emerging concepts regarding the metastatic niche, inflammation, angiogenesis, immune modulation and gene expression. A novel issue is related to the analysis of biomechanical forces which cooperate in the expansion of tumor masses in the lungs. We here aim to analyze the biological, genetic and pathological features of metastatic lesions to the lungs, here referred to as site of metastatic growth. This point should be a crucial part of the algorithm for a proper diagnostic and therapeutic approach in the era of personalized medicine.

Molecular Testing for Cutaneous Melanoma: An Update and Review

CONTEXT.—

The steady rise in the incidence of cutaneous malignant melanoma and its inherently difficult-to-interpret histopathology continues to fuel an increasing demand for diagnostically and prognostically insightful adjunctive molecular tests among both clinicians and dermatopathologists. A number of DNA, RNA, and epigenetically based assays have now been developed and are at various stages of experimental and/or clinical use.

OBJECTIVE.—

To examine the evidence for the utility and limitations of these leading candidates for the diagnosis and risk stratification of melanoma and related melanocytic neoplasms.

DATA SOURCES.—

The available English medical literature was reviewed in the preparation of this manuscript.

CONCLUSIONS.—

Comparative genomic hybridization, fluorescence in situ hybridization, RNA-based gene expression profiling, and immunohistochemical assays for novel genetic and epigenetic markers will help bring diagnostic and prognostic accuracy to the assessment of melanocytic neoplasms.

Integration of protein interaction and gene co-expression information for identification of melanoma candidate genes

Cutaneous melanoma is an aggressive form of skin cancer that causes death worldwide. Although much has been learned about the molecular basis of melanoma genesis and progression, there is also increasing appreciation for the continuing discovery of melanoma genes to improve the genetic understanding of this malignancy. In the present study, melanoma candidate genes were identified by analysis of the common network from cancer type-specific RNA-Seq co-expression data and protein-protein interaction profiles. Then, an integrated network containing the known melanoma-related genes represented as seed genes and the putative genes represented as linker genes was generated using the subnetwork extraction algorithm. According to the network topology property of the putative genes, we selected seven key genes (CREB1, XPO1, SP3, TNFRSF1B, CD40LG, UBR1, and ZNF484) as candidate genes of melanoma. Subsequent analysis showed that six of these genes are melanoma-associated genes and one (ZNF484) is a cancer-associated gene on the basis of the existing literature. A signature comprising these seven key genes was developed and an overall survival analysis of 461 cutaneous melanoma cases was carried out. This seven-gene signature can accurately determine the risk profile for cutaneous melanoma tumors (log-rank P=3.27E-05) and be validated on an independent clinical cohort (log-rank P=0.028). The presented seven genes might serve as candidates for studying the molecular mechanisms and help improve the prognostic risk assessment, which have clinical implications for melanoma patients.

Prospective validation of the prognostic 31-gene expression profiling test in primary cutaneous melanoma

BACKGROUND

Gene expression profiling (GEP) has been integrated into cancer treatment decision-making in multiple neoplasms. We prospectively evaluated the prognostic utility of the 31-GEP test (DecisionDx-Melanoma, Castle Biosciences, Inc) in cutaneous melanoma (CM) patients undergoing sentinel node biopsy (SNB).

METHODS

One hundred fifty-nine patients (age 26-88) diagnosed with melanoma between 01/2013 and 8/2015 underwent SNB and concurrent GEP testing. GEP results were reported as low-risk Class 1 (subclasses 1A and 1B) or high-risk Class 2 (subclasses 2A and 2B). Statistical analyses were performed with chi-square analysis, t tests, log-rank tests, and Cox proportional hazard models. Recurrence-free survival (RFS) and distant metastasis-free survival (DMFS) were estimated using Kaplan-Meier method.

RESULTS

Median follow-up was 44.9 months for event-free cases. Median Breslow thickness was 1.4 mm (0.2-15.0 mm). There were 117 Class 1 and 42 Class 2 patients. Gender, age, Breslow thickness, ulceration, SNB positivity, and AJCC stage were significantly associated with GEP classification (P < 0.05 for all). Recurrence and distant metastasis rates were 5% and 1% for Class 1 patients compared with 55% and 36% for Class 2 patients. Sensitivities of Class 2 and SNB for recurrence were 79% and 34%, respectively. Of 10 SNB-positive/Class 2 patients, 9 recurred. By multivariate analysis, only SNB result and GEP class were statistically associated with both RFS (P = 0.008 and 0.0001) and DMFS (P = 0.019 and 0.001).

CONCLUSIONS

Gene expression profiling Class 2 result and SNB positivity were independently associated with recurrence and distant metastasis in primary CM patients. GEP testing may have additive prognostic utility in initial staging work-up of these patients.

Identification of gene expression levels in primary melanoma associated with clinically meaningful characteristics

Factors influencing melanoma survival include sex, age, clinical stage, lymph node involvement, as well as Breslow thickness, presence of tumor-infiltrating lymphocytes based on histological analysis of primary melanoma, mitotic rate, and ulceration. Identification of genes whose expression in primary tumors is associated with these key tumor/patient characteristics can shed light on molecular mechanisms of melanoma survival. Here, we show results from a gene expression analysis of formalin-fixed paraffin-embedded primary melanomas with extensive clinical annotation. The Cancer Genome Atlas data on primary melanomas were used for validation of nominally significant associations. We identified five genes that were significantly associated with the presence of tumor-infiltrating lymphocytes in the joint analysis after adjustment for multiple testing: IL1R2, PPL, PLA2G3, RASAL1, and SGK2. We also identified two genes significantly associated with melanoma metastasis to the regional lymph nodes (PIK3CG and IL2RA), and two genes significantly associated with sex (KDM5C and KDM6A). We found that LEF1 was significantly associated with Breslow thickness and CCNA2 and UBE2T with mitosis. RAD50 was the gene most significantly associated with survival, with a higher level of expression associated with worse survival.

Guidance of sentinel lymph node biopsy decisions in patients with T1–T2 melanoma using gene expression profiling

Aim: Can gene expression profiling be used to identify patients with T1–T2 melanoma at low risk for sentinel lymph node (SLN) positivity? Patients & methods: Bioinformatics modeling determined a population in which a 31-gene expression profile test predicted <5% SLN positivity. Multicenter, prospectively-tested (n = 1421) and retrospective (n = 690) cohorts were used for validation and outcomes, respectively. Results: Patients 55–64 years and ≥65 years with a class 1A (low-risk) profile had SLN positivity rates of 4.9% and 1.6%. Class 2B (high-risk) patients had SLN positivity rates of 30.8% and 11.9%. Melanoma-specific survival was 99.3% for patients ≥55 years with class 1A, T1–T2 tumors and 55.0% for class 2B, SLN-positive, T1–T2 tumors. Conclusion: The 31-gene expression profile test identifies patients who could potentially avoid SLN biopsy.

Updates in Melanoma

Skin cancer is reaching epidemic levels in the United States. Recent advances in the understanding of the pathophysiology of melanoma have allowed improved risk stratification in the revised American Joint Committee on Cancer (AJCC) criteria, new tests to capture patients at higher risk than their stage may indicate, and new treatments to offer hope and cures to patients with advanced disease.

Estimation of Prognosis in Invasive Cutaneous Melanoma: An Independent Study of the Accuracy of a Gene Expression Profile Test

BACKGROUND

Cutaneous melanomas (CMs) with similar clinical and histopathologic features can harbor differing capacities for metastasis. A validated gene expression profile (GEP) test offers prognostic information by classifying CMs as low risk (Class 1A/1B) or high risk (Class 2A/2B) for metastasis.

OBJECTIVE

The authors sought to perform an independent study of the predictive accuracy of the GEP test, to determine what clinical and histopathologic features predict high-risk classification, and to evaluate how intermediate classes (1B & 2A) performed clinically.

MATERIALS AND METHODS

Using our institution's prospectively collected melanoma registry, the authors identified patients who had been treated for CM within the last 5 years and undergone GEP testing. Clinical, histopathologic, and outcomes data were analyzed. A subcohort of patients with known metastatic disease were identified and tested.

RESULTS

The GEP test accurately identified 77% of metastatic CMs as high risk (Class 2). The GEP had a negative predictive value of 99% for Class 1 CMs. Class 2 CMs were 22 times more likely to metastasize.

CONCLUSION

The GEP test's performance in our independent cohort corresponded with previous industry-sponsored studies and proved to be a helpful clinical prognostic tool with the potential to direct patient care protocols.

Surveillance imaging for metastasis in high-risk melanoma: importance in individualized patient care and survivorship

Most patients newly diagnosed with melanoma have early-stage disease considered of good prognosis. However, with a risk of recurrence, appropriate follow-up may include surveillance imaging for early relapse detection. Previously, surveillance imaging to detect recurrences was considered unjustified, given the lack of effective treatments. Now, systemic therapies have improved, and patients with low tumor burden may derive benefit from surveillance imaging. Despite this, controversy exists regarding the role of surveillance imaging in early-stage melanoma survivorship, in part reflected by the lack of consensus on specific imaging protocols and broad guidelines. This review discusses published evidence on surveillance imaging to detect metastasis in high-risk melanoma, the need for early recurrence detection and implications for value-based clinical decision-making, survivorship care and multidisciplinary patient management.

Early outcome of a 31-gene expression profile test in 86 AJCC stage IB-II melanoma patients. A prospective multicentre cohort study

Background

The clinical and pathological features of primary melanoma are not sufficiently sensitive to accurately predict which patients are at a greater risk of relapse. Recently, a 31‐gene expression profile (DecisionDx‐Melanoma) test has shown promising results.

Objectives

To evaluate the early prognostic performance of a genetic signature in a multicentre prospectively evaluated cohort.

Methods

Inclusion of patients with AJCC stages IB and II conducted between April 2015 and December 2016. All patients were followed up prospectively to assess their risk of relapse. Prognostic performance of this test was evaluated individually and later combined with the AJCC staging system. Prognostic accuracy of disease‐free survival was determined using Kaplan–Meier curves and Cox regression analysis. Results of the gene expression profile test were designated as Class 1 (low risk) and Class 2 (high risk).

Results

Median follow‐up time was 26 months (IQR 22–30). The gene expression profile test was performed with 86 patients; seven had developed metastasis (8.1%) and all of them were in the Class 2 group, representing 21.2% of this group. Gene expression profile was an independent prognostic factor for relapse as indicated by multivariate Cox regression analysis, adjusted for AJCC stages and age.

Conclusions

This prospective multicentre cohort study, performed in a Spanish Caucasian cohort, shows that this 31‐gene expression profile test could correctly identify patients at early AJCC stages who are at greater risk of relapse. We believe that gene expression profile in combination with the AJCC staging system could well improve the detection of patients who need intensive surveillance and optimize follow‐up strategies.

Current controversies in early-stage melanoma: Questions on management and surveillance

There are a number of controversies and uncertainties relating to the management and surveillance of patients with early-stage, localized (ie, stage 0, I, and II) cutaneous melanoma. While tumor stage is a critical predictor of clinical outcome and guides treatment, accurate determination of stage may be affected by the biopsy technique used and the method of sectioning before histologic review. A new molecular prognostic test is available but has not been formally incorporated into staging or treatment guidelines. There are no randomized controlled clinical trials to support guidelines for surveillance following the treatment of early-stage melanoma. In the second article in this continuing medical education series, we review the controversies and uncertainties relating to these issues. The questions we address are controversial because they speak to clinical scenarios for which there are no evidence-based guidelines or randomized clinical trials with the consequence of considerable variability in clinical practice. Our goal is to provide the clinician with up-to-date contextual knowledge to appreciate the multiple sides of each controversy and to suggest pathways to resolution.

Cyst Fluid Biosignature to Predict Intraductal Papillary Mucinous Neoplasms of the Pancreas with High Malignant Potential

BACKGROUND

Current standard-of-care technologies, such as imaging and cyst fluid analysis, are unable to consistently distinguish intraductal papillary mucinous neoplasms (IPMNs) of the pancreas at high risk of pancreatic cancer from low-risk IPMNs. The objective was to create a single-platform assay to identify IPMNs that are at high risk for malignant progression.

STUDY DESIGN

Building on the Verona International Consensus Conference branch duct IPMN biomarker review, additional protein, cytokine, mucin, DNA, and microRNA cyst fluid targets were identified for creation of a quantitative polymerase chain reaction-based assay. This included messenger RNA markers: ERBB2, GNAS, interleukin 1β, KRAS, MUCs1, 2, 4, 5AC, 7, prostaglandin E2R, PTGER2, prostaglandin E synthase 2, prostaglandin E synthase 1, TP63; microRNA targets: miRs 101, 106b, 10a, 142, 155, 17, 18a, 21, 217, 24, 30a, 342, 532, 92a, and 99b; and GNAS and KRAS mutational analysis. A multi-institutional international collaborative contributed IPMN cyst fluid samples to validate this platform. Cyst fluid gene expression levels were normalized, z-transformed, and used in classification and regression analysis by a support vector machine training algorithm.

RESULTS

From cyst fluids of 59 IPMN patients, principal component analysis confirmed no institutional bias/clustering. Lasso (least absolute shrinkage and selection operator)-penalized logistic regression with binary classification and 5-fold cross-validation used area under the curve as the evaluation criterion to create the optimal signature to discriminate IPMNs as low risk (low/moderate dysplasia) or high risk (high-grade dysplasia/invasive cancer). The most predictive signature was achieved with interleukin 1β, MUC4, and prostaglandin E synthase 2 to accurately discriminate high-risk cysts from low-risk cysts with an area under the curve of up to 0.86 (p = 0.002).

CONCLUSIONS

We have identified a single-platform polymerase chain reaction-based assay of cyst fluid to accurately predict IPMNs with high malignant potential for additional studies.

Genomic Copy Number Variations in the Autism Clinic-Work in Progress

The development of advanced technology for microarray-based chromosomal studies helped discover increased prevalence of genomic copy number variants (CNVs) in individuals with autism spectrum disorder (ASD). Chromosomal microarray analysis (CMA) is now an important tool for clinical investigations in patients with ASD. While this technology helps identify high proportion of CNV positive individuals among patients with autism, the clinical interpretation of such genomic rearrangements is often challenged by inconsistent genotype-phenotype correlations. Possible explanations of such inconsistencies may involve complex interactions of potentially pathogenic CNV with additional (secondary) CNVs or single nucleotide variants (SNVs). Other involved factors may include gender-specific effects or environmental contributions. Development of risk models for interpreting such complex interactions may be necessary in order to provide better informed genetic counseling to the affected families.

An Update Regarding the Molecular Genetics of Melanocytic Neoplasms and the Current Applications of Molecular Genetic Technologies in Their Diagnosis and Treatment

Molecular genetic technologies are used to aid in diagnosis and treatment of borderline melanocytic tumors as an adjuvant to the gold standard histopathologic evaluation. A specific set of fluorescence in situ hybridization probes is widely used to aid in diagnosing challenging melanocytic lesions. New melanoma probe cocktails have revealed increased sensitivity and specificity in ambiguous melanocytic cases. Array comparative genomic hybridization is a more complex technology used for the work-up of diagnostically problematic Spitzoid melanocytic proliferations. Cutting-edge technologies, including next-generation sequencing and cell-free nucleic acid analysis, are promising biomarker applications for mutation detection towards personalized patient management.

Performance of a 31-gene expression profile test in cutaneous melanomas of the head and neck

Background

We report the performance of a gene expression profile test to classify the recurrence risk of cutaneous melanoma tumors of the head and neck as low‐risk Class 1 or high‐risk Class 2.

Methods

Of note, 157 primary head and neck cutaneous melanoma tumors were identified. Survival analyses were performed using Kaplan‐Meier and Cox methods.

Results

Gene expression profile class and node status stratified tumors into significantly different 5‐year survival groups by Kaplan‐Meier method (P < .0001 for all end points), and both were independent predictors of recurrence in multivariate analysis. Overall, 74% of distant metastases and 88% of melanoma‐specific deaths had Class 2 risk.

Conclusion

The gene expression profile test identifies cases at increased risk for metastasis and death independent of a clinically or pathologically negative nodal status, suggesting that incorporation of this molecular tool could improve clinical management of patients with head and neck cutaneous melanoma, especially in those with a negative sentinel lymph node biopsy.

Malignant Melanoma: Diagnostic and Management Update

LEARNING OBJECTIVES

After studying this article, the participant should be able to: 1. Summarize the changes to the American Joint Committee on Cancer Eighth Edition Melanoma Staging System. 2. List advances in genetic, molecular, and histopathologic melanoma diagnosis and prognostication. 3. Recommend sentinel lymph node biopsy and appropriate surgical margins based on individualized patient needs. 4. Recognize the currently available treatments for in-transit metastasis and advanced melanoma. 5. Describe current and future therapies for melanoma with distant visceral or brain metastases.

SUMMARY

Strides in melanoma surveillance, detection, and treatment continue to be made. The American Joint Committee on Cancer Eighth Edition Cancer Staging System has improved risk stratification of patients, introduced new staging categories, and resulted in stage migration of patients with improved outcomes. This review summarizes melanoma advances of the recent years with an emphasis on the surgical advances, including techniques and utility of sentinel node biopsy, controversies in melanoma margin selection, and the survival impact of time-to-treatment metrics. Once a disease manageable only with surgery, a therapeutic paradigm shift has given a more promising outlook to melanoma patients at any stage. Indeed, a myriad of novel, survival-improving immunotherapies have been introduced for metastatic melanoma and more recently in the high-risk adjuvant setting.

Identification of risk in cutaneous melanoma patients: Prognostic and predictive markers

New therapeutic modalities for melanoma promise benefit in selected individuals. Efficacy appears greater in patients with lower tumor burden, suggesting an important role for risk-stratified surveillance. Robust predictive markers might permit optimization of agent to patient, while low-risk prognostic markers might guide more conservative management. This review evaluates protein, gene, and multiplexed marker panels that may contribute to better risk assessment and improved management of patients with cutaneous melanoma.

Predictive genetic profiles for regional lymph node metastasis in primary cutaneous melanoma: a case-matched pilot study

Melanoma confers an estimated lifetime risk of one in 50 for 2016. Clinicopathologic staging and sentinel lymph node biopsy (SLNB) have been the standard of care for T2 and T3 lesions. Molecular biomarkers identified in the primary lesion suggestive of metastatic potential may offer a more conclusive prognosis of these lesions. Our purpose was to investigate molecular mutations in primary melanoma that were predictive for micrometastasis as defined by a positive sentinel lymph node (SLN) in a case-controlled manner: nine patients with negative SLN and nine with positive SLN. The two cohorts were statistically identical as shown by a t-test for age (P=0.17), race (P=0.18), Breslow depth (P=0.14), Clark level (P=0.33), host response (P=0.17), ulceration (P=0.50), satellite nodules (P=0.17), lymphovascular invasion (P=0.50), and mitotic activity (P=0.09). While no single gene was significantly associated with SLN status, multivariate analysis using classification and regression tree assessment revealed two unique gene profiles that completely represented regional metastases in our cohort as defined by a positive SLN: PIK3CA (+) NRAS (-) and PIK3CA (-) ERBB4 (-) TP53 (+) SMAD4 (-). These profiles were identified in 89% of the patients with positive SLN; none of these profiles were identified in the SLN-negative cohort. We identified two unique gene profiles associated with positive SLN that do not overlap other studies and highlight the genetic complexity that portends the metastatic phenotype in cutaneous melanoma.

Use of gene expression profile testing as a prognostic tool in early-stage cutaneous melanoma - compelling but not ready for primetime

Advances in the field of molecular genetics have led to the development of multiple tests capable of identifying genetic changes within cutaneous melanoma. Although the majority of these tests are currently used for diagnostic purposes, their potential use as prognostic tools is rapidly emerging. A new 31-gene expression profile test has been developed that promises to accurately predict metastatic risk in patients with early-stage cutaneous melanoma. Although current data are promising, many questions remain in terms of its potential effects in patient care. Thus, before this test is used routinely in clinical practice, we recommend that it first be performed as part of current adjuvant treatment trials as a potential predictive marker or other high-quality studies investigating relevant outcomes resulting from changes in the clinical management of patients on the basis of the gene expression profile test results.

Gene expression profiling in melanoma: past results and future potential

The field of melanoma oncology is rapidly evolving with advances in detection, staging and treatment. There is heterogeneity in all stages of melanoma where some patients fare better than others for reasons currently unknown and it is sometimes unclear which patients warrant closer surveillance, multidisciplinary care, increased imaging, more aggressive surgery or adjuvant therapy. Early studies have shown the predictive ability of gene expression profiling (GEP) and institutions that have adopted GEP for melanoma treatment have demonstrated changes in practice patterns and patient management. The goal of this paper is to review the clinical evidence for a new diagnostic test, DecisionDx-Melanoma, the only GEP test for cutaneous melanoma with prospective studies analyzing its utility.

Guidelines of care for the management of primary cutaneous melanoma

The incidence of primary cutaneous melanoma continues to increase each year. Melanoma accounts for the majority of skin cancer-related deaths, but treatment is usually curative following early detection of disease. In this American Academy of Dermatology clinical practice guideline, updated treatment recommendations are provided for patients with primary cutaneous melanoma (American Joint Committee on Cancer stages 0-IIC and pathologic stage III by virtue of a positive sentinel lymph node biopsy). Biopsy techniques for a lesion that is clinically suggestive of melanoma are reviewed, as are recommendations for the histopathologic interpretation of cutaneous melanoma. The use of laboratory, molecular, and imaging tests is examined in the initial work-up of patients with newly diagnosed melanoma and for follow-up of asymptomatic patients. With regard to treatment of primary cutaneous melanoma, recommendations for surgical margins and the concepts of staged excision (including Mohs micrographic surgery) and nonsurgical treatments for melanoma in situ, lentigo maligna type (including topical imiquimod and radiation therapy), are updated. The role of sentinel lymph node biopsy as a staging technique for cutaneous melanoma is described, with recommendations for its use in clinical practice. Finally, current data regarding pregnancy and melanoma, genetic testing for familial melanoma, and management of dermatologic toxicities related to novel targeted agents and immunotherapies for patients with advanced disease are summarized.

Identification of patients at risk of metastasis using a prognostic 31-gene expression profile in subpopulations of melanoma patients with favorable outcomes by standard criteria

BACKGROUND

A substantial number of patients who relapse and die from cutaneous melanoma (CM) are categorized as being at low risk by traditional staging factors. The 31-gene expression profile (31-GEP) test independently stratifies metastatic risk of patients with CM as low (Class 1, with 1A indicating lowest risk) or high (Class 2,with 2B indicating highest risk).

OBJECTIVE

To assess risk prediction by the 31-GEP test within 3 low-risk (according to the American Joint Committee on Cancer) populations of patients with CM: those who are sentinel lymph node (SLN) negative, those with stage I to IIA tumors, and those with thin (≤1 mm [T1]) tumors.

METHODS

A total of 3 previous validation studies provided a nonoverlapping cohort of 690 patients with 31-GEP results, staging information, and survival outcomes. Kaplan-Meier and Cox regression analysis were performed.

RESULTS

The results included the identification of 70% of SLN-negative patients who experienced metastasis as Class 2, the discovery of reduced recurrence-free survival for patients with thin tumors and Class 2B biology compared with that of those with Class 1A biology (P < .0001); and determination of the 31-GEP test as an independent predictor of risk compared with traditional staging factors in patients with stage I to IIA tumors.

LIMITATIONS

Diagnoses spanned multiple versions of pathologic staging criteria.

CONCLUSIONS

The 31-GEP test identifies high-risk patients who are likely to experience recurrence or die of melanoma within low-risk groups of subpopulations of patients with CM who have SLN-negative disease, stage I to IIA tumors, and thin tumors.

Update on systemic therapy for advanced cutaneous melanoma and recent development of novel drugs

Malignant melanoma is generally chemo- and radio-resistant, and patients with advanced melanoma have a poor prognosis. However, with our increased understanding of the checkpoint immune molecules and genetic alterations of melanoma cells, more effective immunotherapy, such as anti CTLA4 antibody and anti PD-1 antibodies, and targeted drug therapy, such as BRAF inhibitors and MEK inhibitors, have been developed, resulting in improved overall survival and quality of life of patients with advanced melanoma. In addition, emerging technologies to develop prognostic and predictive biomarkers for response to systemic therapy could help clinicians make more accurate assessments of the disease and formulate more effective treatment plans. In this review, current standard systemic therapy options and recently developed novel drugs for advanced melanoma are discussed.

A Prognostic Gene Signature Expressed in Primary Cutaneous Melanoma: Synergism With Conventional Staging

Background

Current clinico-pathological American Joint Committee on Cancer (AJCC) staging of primary cutaneous melanoma is limited in its ability to determine clinical outcome, and complementary biomarkers are not available for routine prognostic assessment. We therefore adapted a gene signature, previously identified in fresh-frozen (FF) melanomas and adjacent stroma, to formalin-fixed paraffin-embedded (FFPE) melanomas. The aim was to develop a gene expression profiling (GEP) score to define patient survival probability at the time of first diagnosis.

Methods

Expression of 11 FF melanoma signature genes was quantified by reverse transcription polymerase chain reaction in an FFPE melanoma training cohort (n = 125), corresponding to the combined FF melanoma training and validation cohorts. The resulting GEP score was validated technically and clinically in an independent FFPE melanoma cohort (n = 211). All statistical tests were two-sided.

Results

We identified a prognostic eight-gene signature in the tumor area (tumor and adjacent tissue) of AJCC stage I–III melanomas. A signature-based GEP score correlated with melanoma-specific survival (MSS; Kaplan-Meier analysis: P < .0001) was independent of tumor stage (multivariable regression analysis: P = .0032) and stroma content (<5%–90%) and complemented conventional AJCC staging (receiver operating characteristic curve analysis: area under the curve = 0.91). In the clinical validation cohort, the GEP score remained statistically significant (P = .0131) in a multivariable analysis accounting for conventional staging. The GEP score was technically robust (reproducibility: 93%; n = 84) and clinically useful, as a binary as well as a continuous score, in predicting stage-specific patient MSS.

Conclusions

The GEP score is a clinically significant prognostic tool, contributes additional information regarding the MSS of melanoma patients, and complements conventional staging.

An update on the Society for Immunotherapy of Cancer consensus statement on tumor immunotherapy for the treatment of cutaneous melanoma: version 2.0

BACKGROUND

Cancer immunotherapy has been firmly established as a standard of care for patients with advanced and metastatic melanoma. Therapeutic outcomes in clinical trials have resulted in the approval of 11 new drugs and/or combination regimens for patients with melanoma. However, prospective data to support evidence-based clinical decisions with respect to the optimal schedule and sequencing of immunotherapy and targeted agents, how best to manage emerging toxicities and when to stop treatment are not yet available.

METHODS

To address this knowledge gap, the Society for Immunotherapy of Cancer (SITC) Melanoma Task Force developed a process for consensus recommendations for physicians treating patients with melanoma integrating evidence-based data, where available, with best expert consensus opinion. The initial consensus statement was published in 2013, and version 2.0 of this report is an update based on a recent meeting of the Task Force and extensive subsequent discussions on new agents, contemporary peer-reviewed literature and emerging clinical data. The Academy of Medicine (formerly Institute of Medicine) clinical practice guidelines were used as a basis for consensus development with an updated literature search for important studies published between 1992 and 2017 and supplemented, as appropriate, by recommendations from Task Force participants.

RESULTS

The Task Force considered patients with stage II-IV melanoma and here provide consensus recommendations for how they would incorporate the many immunotherapy options into clinical pathways for patients with cutaneous melanoma.

CONCLUSION

These clinical guidleines provide physicians and healthcare providers with consensus recommendations for managing melanoma patients electing treatment with tumor immunotherapy.

A unique gene expression signature is significantly differentially expressed in tumor-positive or tumor-negative sentinel lymph nodes in patients with melanoma

The purpose of this study was to learn whether molecular characterization through gene expression profiling of node-positive and node-negative sentinel lymph nodes (SLNs) in patients with clinical stage I and II melanoma may improve the understanding of mechanisms of metastasis and identify gene signatures for SLNs/SLNs that correlate with diagnosis or clinical outcome. Gene expression profiling was performed on SLN biopsies of 48 (24 SLN and 24 SLN) patients (T3a/b-T4a/b) who underwent staging of SLNs using transcriptome profiling analysis on 5 μm sections of fresh SLNs. U133A 2.0 Affymetrix gene chips were used. Significance analysis of microarrays was used to test the association between gene expression level and SLN status. Genes with fold change more than 1.5 and q value less than 0.05 were considered differentially expressed. Pathway analysis was performed using Ingenuity Pathway Analysis. The Benjamini and Hochberg method was used to adjust for multiple testing in pathway analysis. We identified 89 probe sets that were significantly differentially expressed (1.5-27-fold; q<0.05). Upon performing the pathway analysis, it was found that 25 genes were common among the most significant and biologically relevant canonical pathways. The molecules and pathways that achieved differential expression of highest statistical significance were notably related to melanoma and its microenvironment and to signaling pathways implicated in immunosuppression and development of cancer. A 25-gene signature is significantly differentially expressed between SLN and SLN and is related to melanoma oncogenesis and immunosuppression. The identified expression profile provides a signature of melanoma nodal involvement. These findings warrant further investigation into the mechanisms of metastasis, melanoma metastasis diagnosis, and prediction of outcome.

Review of diagnostic, prognostic, and predictive biomarkers in melanoma

Melanoma is an aggressive cutaneous malignancy with rapidly rising incidence. Diagnosis of controversial melanocytic lesions, correct prognostication of patients, selection of appropriate adjuvant and systemic therapies, and prediction of response to a given therapy remain very real challenges. Despite these challenges, multiple high throughput, nucleic-acid based biomarkers have been developed that can be assayed from histologic tissue specimens. FISH, CGH, Decision-Dx, and other multi-marker assays have been combined to improve overall predictability. This review discusses some of the most promising nucleic acid based assays that can be obtained from tissue specimens to assist with diagnosis, prognostication, and prediction of treatment response.

Emerging Biomarkers in Cutaneous Melanoma

Earlier identification of aggressive melanoma remains a goal in the field of melanoma research. With new targeted and immune therapies that have revolutionized the care of patients with melanoma, the ability to predict progression and monitor or predict response to therapy has become the new focus of research into biomarkers in melanoma. In this review, promising biomarkers are highlighted. These biomarkers have been used to diagnose melanoma as well as predict progression to advanced disease and response to therapy. The biomarkers take various forms, including protein expression at the level of tissue, genetic mutations of cancer cells, and detection of circulating DNA. First, a brief description is provided about the conventional tissue markers used to stage melanoma, including tumor depth. Next, protein biomarkers, which provide both diagnostic and prognostic information, are described. This is followed by a discussion of important genetic mutations, microRNA, and epigenetic modifications that can provide therapeutic and prognostic material. Finally, emerging serologic biomarkers are reviewed, including circulating melanoma cells and exosomes. Overall the goal is to identify biomarkers that aid in the earlier identification and improved treatment of aggressive melanoma.

Mapping heterogeneity in patient-derived melanoma cultures by single-cell RNA-seq

Recent technological advances in single-cell genomics make it possible to analyze cellular heterogeneity of tumor samples. Here, we applied single-cell RNA-seq to measure the transcriptomes of 307 single cells cultured from three biopsies of three different patients with a BRAF/NRAS wild type, BRAF mutant/NRAS wild type and BRAF wild type/NRAS mutant melanoma metastasis, respectively. Analysis based on self-organizing maps identified sub-populations defined by multiple gene expression modules involved in proliferation, oxidative phosphorylation, pigmentation and cellular stroma. Gene expression modules had prognostic relevance when compared with gene expression data from published melanoma samples and patient survival data. We surveyed kinome expression patterns across sub-populations of the BRAF/NRAS wild type sample and found that CDK4 and CDK2 were consistently highly expressed in the majority of cells, suggesting that these kinases might be involved in melanoma progression. Treatment of cells with the CDK4 inhibitor palbociclib restricted cell proliferation to a similar, and in some cases greater, extent than MAPK inhibitors. Finally, we identified a low abundant sub-population in this sample that highly expressed a module containing ABC transporter ABCB5, surface markers CD271 and CD133, and multiple aldehyde dehydrogenases (ALDHs). Patient-derived cultures of the BRAF mutant/NRAS wild type and BRAF wild type/NRAS mutant metastases showed more homogeneous single-cell gene expression patterns with gene expression modules for proliferation and ABC transporters. Taken together, our results describe an intertumor and intratumor heterogeneity in melanoma short-term cultures which might be relevant for patient survival, and suggest promising targets for new treatment approaches in melanoma therapy.

Prospective evaluation of prognostic indicators for early recurrence of cutaneous melanoma

The majority of melanomas are thin lesions with an excellent prognosis; however, significant tumor heterogeneity exists, and a small percentage of patients with early-stage disease may progress to metastatic recurrence. This study aimed to assess whether prognostic factors previously shown to be significant in predicting stage I and stage II melanoma recurrence were consistent in a large prospectively collected patient cohort, and to identify novel prognostic factors associated with early recurrence to inform follow-up protocols. There were 1029 patients with stage I and stage II melanoma included in the analysis, of whom 123 developed a recurrence during follow-up (median 2.13 years). Multivariable analysis identified ulceration, presence of mitoses, Clark level, presence of lymphovascular invasion, and a history of autoimmune disease as factors independently associated with recurrence. These data identified patients with stage I-II melanoma with very low-risk for recurrence: no ulceration, zero mitoses, a low Clark level, no lymphovascular invasion, and possibly no history of autoimmune disease. These patients do not require intensive follow-up: 12 monthly reviews and full skin checks may be appropriate. Ongoing research into prognostic factors for recurrence in early-stage melanoma is important.

Analytic validity of DecisionDx-Melanoma, a gene expression profile test for determining metastatic risk in melanoma patients

BACKGROUND

The DecisionDx-Melanoma test provides prognostic information for patients with cutaneous melanoma (CM). Using formalin-fixed paraffin-embedded primary tumor tissue, the RT-PCR-based test classifies patients into a low- (Class 1) or high-risk (Class 2) category for recurrence based on expression of 31 genes. The current study was designed to assess the analytical validity of this test.

METHODS

Inter-assay, inter-instrument, and inter-operator studies were performed to evaluate reliability of the 31-gene expression test results, sample stability and reagent stability. From March 2013 through June 2016, the gene expression test was performed on 8244 CM tumors. De-identified data from Pathology Reports were used to assess technical success.

RESULTS

Robust sample and reagent stability was observed. Inter-assay concordance on 168 specimens run on 2 consecutive days was 99% and matched probability scores were significantly correlated (R² = 0.96). Inter-instrument concordance was 95%, and probability scores had a correlation R² of 0.99 (p < 0.001). From 8244 CM specimens submitted since 2013, 85% (7023) fulfilled pre-specified tumor content parameters. In these samples with sufficient tumor requirements, the technical success of the test was 98%.

CONCLUSION

DecisionDx-Melanoma is a robust gene expression profile test that demonstrates strong reproducibility between experiments and has high technical reliability on clinical samples.

Performance of a prognostic 31-gene expression profile in an independent cohort of 523 cutaneous melanoma patients

BACKGROUND

The heterogeneous behavior of patients with melanoma makes prognostication challenging. To address this, a gene expression profile (GEP) test to predict metastatic risk was previously developed. This study evaluates the GEP's prognostic accuracy in an independent cohort of cutaneous melanoma patients.

METHODS

This multi-center study analyzed primary melanoma tumors from 523 patients, using the GEP to classify patients as Class 1 (low risk) and Class 2 (high risk). Molecular classification was correlated to clinical outcome and assessed along with AJCC v7 staging criteria. Primary endpoints were recurrence-free (RFS) and distant metastasis-free (DMFS) survival.

RESULTS

The 5-year RFS rates for Class 1 and Class 2 were 88% and 52%, respectively, and DMFS rates were 93% versus 60%, respectively (P < 0.001). The GEP was a significant predictor of RFS and DMFS in univariate analysis (hazard ratio [HR] = 5.4 and 6.6, respectively, P < 0.001 for each), along with Breslow thickness, ulceration, mitotic rate, and sentinel lymph node (SLN) status (P < 0.001 for each). GEP, tumor thickness and SLN status were significant predictors of RFS and DMFS in a multivariate model that also included ulceration and mitotic rate (RFS HR = 2.1, 1.2, and 2.5, respectively, P < 0.001 for each; and DMFS HR = 2.7, 1.3 and 3.0, respectively, P < 0.01 for each).

CONCLUSIONS

The GEP test is an objective predictor of metastatic risk and provides additional independent prognostic information to traditional staging to help estimate an individual's risk for recurrence. The assay identified 70% of stage I and II patients who ultimately developed distant metastasis. Its role in consideration of patients for adjuvant therapy should be examined prospectively.

Impact of genomics on the surgical management of melanoma

BACKGROUND

Although surgery for early-stage melanoma offers the best chance of cure, recent advances in molecular medicine have revolutionized the management of late-stage melanoma, leading to significant improvements in clinical outcomes. Research into the genomic drivers of disease and cancer immunology has not only ushered in a new era of targeted and immune-based therapies for patients with metastatic melanoma, but has also provided new tools for monitoring disease recurrence and selecting therapeutic strategies. These advances present new opportunities and challenges to the surgeon treating patients with melanoma.

METHODS

The literature was reviewed to evaluate diagnostic and therapeutic advances in the management of cutaneous melanoma, and to highlight the impact of these advances on surgical decision-making.

RESULTS

Genomic testing is not required in the surgical management of primary melanoma, although it can provide useful information in some situations. Circulating nucleic acids from melanoma cells can be detected in peripheral blood to predict disease recurrence before it manifests clinically, but validation is required before routine clinical application. BRAF mutation testing is the standard of care for all patients with advanced disease to guide therapy, including the planning of surgery in adjuvant and neoadjuvant settings.

CONCLUSION

Surgery remains central for managing primary melanoma, and is an important element of integrated multidisciplinary care in advanced disease, particularly for patients with resectable metastases. The field will undergo further change as clinical trials address the relationships between surgery, radiotherapy and systemic therapy for patients with high-risk, early-stage and advanced melanoma.