Chromosomal copy number analysis in melanoma diagnostics

Treatment resistance to melanoma therapeutics on a single cell level

Therapy targeting the BRAF-MEK cascade created a treatment revolution for patients with BRAF mutant advanced melanoma. Unfortunately, 80% patients treated will progress by 5 years follow-up. Thus, it is imperative we study mechanisms of melanoma progression and therapeutic resistance. We created a scRNA (single cell RNA) atlas of 128,230 cells from 18 tumors across the treatment spectrum, discovering melanoma cells clustered strongly by transcriptome profiles of patients of origins. Our cell-level investigation revealed gains of 1q and 7q as likely early clonal events in metastatic melanomas. By comparing patient tumors and their derivative cell lines, we observed that PD1 responsive tumor fraction disappears when cells are propagated in vitro. We further established three anti-BRAF-MEK treatment resistant cell lines using three BRAF mutant tumors. ALDOA and PGK1 were found to be highly expressed in treatment resistant cell populations and metformin was effective in targeting the resistant cells. Our study suggests that the investigation of patient tumors and their derivative lines is essential for understanding disease progression, treatment response and resistance.

Expanding Our Understanding of Nevogenesis: Copy Number Gain of Chromosome 15q in Melanocytic Nevi Is Associated With Distinct Histomorphologic Findings

As the landscape of melanomagenesis becomes better refined through increasingly detailed schema grounded in distinct clinicopathologic-molecular pathways, the stepwise process and variations of molecular nevogenesis have largely remained elusive. Herein, we present a series of 8 melanocytic nevi in patients ranging from 40 to 74 years of age (median: 59.5 y), which demonstrated a reproducible constellation of histomorphologic features as well as a copy number gain of the long arm of chromosome 15 (15q). The most characteristic histologic feature was sclerosis with maturation at the base of the lesion. All cases demonstrated a dome-shaped configuration and epidermal acanthosis with hyperpigmentation. However, the cytologic features ranged in their appearances from that of a banal nevus with ovoid nuclei, inconspicuous nucleoli, and minimal cytoplasm to enlarged, epithelioid forms with central nucleoli and abundant cytoplasm. No lesions showed staining with BRAF V600E or NRAS Q61R immunohistochemistry. Single-nucleotide polymorphism-based chromosome microarray analysis revealed a monoaberrant 15q gain in all cases. The histology was sufficiently distinctive in the initial 6 cases encountered to allow for prospective identification of 2 additional cases harboring a 15q gain. The clinical follow-up did not reveal recurrence in any case. Although adverse outcomes were not observed in our cohort, future studies are needed to more adequately characterize the clinical and biological behavior of these lesions.

Ciliation Index Is a Useful Diagnostic Tool in Challenging Spitzoid Melanocytic Neoplasms

The loss of primary cilia on melanocytes is a useful biomarker for the distinction of melanoma from conventional melanocytic nevi. It is unknown whether ciliation status is beneficial for diagnosing spitzoid tumors-a subclass of melanomas that present inherently ambiguous histology and are challenging to classify. We evaluated the Ciliation Index (CI) in 68 cases of spitzoid tumors ranging from Spitz nevi and atypical Spitz tumors to spitzoid melanoma. We found a significant decrease in CI within the spitzoid melanoma group when compared with either the Spitz nevi or atypical Spitz tumors groups. In addition, we used a machine-learning-based algorithm to determine the value of CI when considered in combination with other histopathologic and molecular features commonly used for diagnosis. We found that a low CI was consistently ranked as a top predictive feature in the diagnosis of malignancy. Predictive models trained on only the top four predictive features (CI, asymmetry, hyperchromatism, and cytologic atypia) outperformed standard histologic assessment in an independent validation cohort of 56 additional cases. The results provide an alternative approach to evaluate diagnostically challenging melanocytic lesions, and further support the use of CI as an ancillary diagnostic test.

Through the looking glass and what you find there: making sense of comparative genomic hybridization and fluorescence in situ hybridization for melanoma diagnosis

Melanoma is the leading cause of death among cutaneous neoplasms. Best outcome relies on early detection and accurate pathologic diagnosis. For the great majority of melanocytic tumors, histopathologic examination can reliably distinguish nevi from melanomas. However, there is a subset of melanocytic tumors that cannot be definitively classified as benign or malignant using histopathological criteria alone. These tumors are usually diagnosed using terms that imply various degrees of uncertainty in regards to their malignant potential and create the possibility for over or undertreatment. For such tumors, additional ancillary tests would be beneficial in adjudicating a more definitive diagnosis. In recent years, DNA-based molecular ancillary tests, specifically comparative genomic hybridization and fluorescence in situ hybridization, have been developed to help guide the diagnosis of ambiguous melanocytic proliferations. This study will present an updated overview of these two major ancillary tests, which are currently being used in clinical practice to assist in the diagnosis of challenging melanocytic neoplasms.

Targeted next generation sequencing (NGS) to classify melanocytic neoplasms

This study piloted a pan-solid-tumor next generation sequence (NGS)-based laboratory developed test as a diagnostic aid in melanocytic tumors. 31 cases (4 "epithelioid" nevi, 5 blue nevi variants, 7 Spitz tumors [3 benign and 4 malignant] and 15 melanomas) were evaluated. All tumors [median diameter 7 mm (range 4-15 mm); median thickness 2.25 mm (range 0.25-12 mm)] yielded satisfactory results. The number of small nucleotide variants/tumor was significantly different between melanoma (median 18/tumor, range 4-71) and all other lesions (median 8/tumor, range 3-17) (P < 0.004) and malignant (median 16/tumor, range 4-71) vs benign lesions (median 7/tumor, range 3-14) (P = 0.01). BRAF, MET, NTRK1, and ROS fusions only occurred in benign Spitz tumors; EML4 fusion, BRAF, MAP2K1 and TERT mutations occurred in malignant Spitz tumors and/or melanoma. Amplifications and NRAS and NF1 mutations only occurred in melanoma. Most melanomas contained >1 pathogenic alteration. Developed NGS-based criteria correctly classified all malignant lesions in this series. 10/12 cases showed concordance with FISH; consensus diagnosis agreed with NGS classification in FISH-non-concordant cases. This pilot study suggests that NGS may be an effective diagnostic adjunct comparable to FISH, but further studies with larger numbers of cases are needed.

An independent validation of a gene expression signature to differentiate malignant melanoma from benign melanocytic nevi

BACKGROUND

Recently, a 23-gene signature was developed to produce a melanoma diagnostic score capable of differentiating malignant and benign melanocytic lesions. The primary objective of this study was to independently assess the ability of the gene signature to differentiate melanoma from benign nevi in clinically relevant lesions.

METHODS

A set of 1400 melanocytic lesions was selected from samples prospectively submitted for gene expression testing at a clinical laboratory. Each sample was tested and subjected to an independent histopathologic evaluation by 3 experienced dermatopathologists. A primary diagnosis (benign or malignant) was assigned to each sample, and diagnostic concordance among the 3 dermatopathologists was required for inclusion in analyses. The sensitivity and specificity of the score in differentiating benign and malignant melanocytic lesions were calculated to assess the association between the score and the pathologic diagnosis.

RESULTS

The gene expression signature differentiated benign nevi from malignant melanoma with a sensitivity of 91.5% and a specificity of 92.5%.

CONCLUSIONS

These results reflect the performance of the gene signature in a diverse array of samples encountered in routine clinical practice. Cancer 2017;123:617-628. © 2016 American Cancer Society.

Copy number variation in archival melanoma biopsies versus benign melanocytic lesions

BACKGROUND

Skin melanocytes can give rise to benign and malignant neoplasms. Discrimination of an early melanoma from an unusual/atypical benign nevus can represent a significant challenge. However, previous studies have shown that in contrast to benign nevi, melanoma demonstrates pervasive chromosomal aberrations.

OBJECTIVE

This substantial difference between melanoma and benign nevi can be exploited to discriminate between melanoma and benign nevi.

METHODS

Array-comparative genomic hybridization (aCGH) is an approach that can be used on DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissues to assess the entire genome for the presence of changes in DNA copy number. In this study, high resolution, genome-wide single-nucleotide polymorphism (SNP) arrays were utilized to perform comprehensive and detailed analyses of recurrent copy number aberrations in 41 melanoma samples in comparison with 21 benign nevi.

RESULTS

We found statistically significant copy number gains and losses within melanoma samples. Some of the identified aberrations are previously implicated in melanoma. Moreover, novel regions of copy number alterations were identified, revealing new candidate genes potentially involved in melanoma pathogenesis.

CONCLUSIONS

Taken together, these findings can help improve melanoma diagnosis and introduce novel melanoma therapeutic targets.

A p16-Ki-67-HMB45 immunohistochemistry scoring system as an ancillary diagnostic tool in the diagnosis of melanoma

BACKGROUND

Melanoma is a skin cancer which treatment requires early diagnosis and large surgical removal. The histopathological diagnosis of a melanocytic tumour is sometimes difficult between a benign nevus and a malignant melanoma. We built an immunomarker-based score to differentiate nevi from melanomas.

METHODS

Two independent sets of 308 (first set) and 62 (validation set) formalin-fixed and paraffin embedded tumour samples were studied using p16-Ki-67 and HMB45-MelanA dual-staining immunohistochemistry.

RESULTS

In the first set of tumours, high Ki-67 index, low to null p16 immunohistochemistry and absence of HMB45 immunohistochemistry gradient were more frequent in melanomas (156 primary tumours and 78 metastases) than in nevi (74 tumours). Nevertheless, none of these single parameters was able to differentiate all primary melanomas from all nevi. We built a scoring system based on the addition of semi-quantitative scorings of Ki-67 (0: <2%; 1:2-5%; 2:6-10%, 3:11-20%; 4:>20%) and p16 (0:>50% stained cells; 1:11-50%; 2:1-10%; 3:0%) and HMB45 staining (0: gradient present; 1: doubtful/inconclusive gradient; 2: gradient absent). A p16-Ki-67-HMB45 total score from 0 to 9 permitted to classify nevi (score <4) and primary melanomas (score ≥4) with a sensitivity of 97.4% and a specificity of 97.3% in the first set of tumours. Sensibility and specificity of 100 % were obtained in a second set (validation set) of 62 tumours (46 melanomas and 16 nevi). The total scoring also allowed analyzing 11 difficult or initially misdiagnosed tumours in our files.

CONCLUSIONS

We propose a valuable triple p16-Ki-67-HMB45 immunohistochemistry scoring system to help pathologists in the differential diagnosis of melanomas and nevi.

Spitzoid melanoma of childhood: a case series and review

Spitzoid melanomas (SM) and atypical Spitz tumors (AST) are rare pediatric neoplasms. We performed a retrospective, single-institution review and report our institutional experience. We identified 10 patients (median age: 12.5 years). A sentinel node biopsy (SNB) was performed in 8/10 (80%) patients, and interestingly 7/8 (87.5%) were found to be positive for malignant cells. A complete regional lymphadenectomy was performed in all SNB-positive patients, but only 2/8 (25%) were found to have additional lymph node spread. Adjuvant therapy was administered in 5/8 SLNB-positive and 2/2 (100%) regional LN-positive cases. All patients had excellent long-term outcomes (100% survival). This report highlights the excellent outcomes associated with SNB + pediatric SM and AST.

Budget impact analysis of a novel gene expression assay for the diagnosis of malignant melanoma

BACKGROUND

Traditional pathology techniques alone can be insufficient to reliably distinguish between malignant melanoma, dysplastic nevi, and benign nevi in biopsies of suspicious pigmented lesions. Numerous studies have shown high rates of ambiguity when assessing such samples. A novel gene expression assay has been developed to objectively differentiate malignant melanoma from benign nevi.

OBJECTIVE

The purpose of this study was to quantify the economic impact of the gene expression assay on a US commercial health plan.

METHODS

The clinical paradigm of care was modeled for a hypothetical cohort of patients with suspicious pigmented lesions that are difficult-to-diagnose. Costs were assigned to each unit of care provided based on 2013 Medicare fee-for-service rates. Patients were followed for 10 years and were modeled to progress according to the natural history of their disease. The total cost of care was calculated for two scenarios: a Reference Scenario, representing current clinical practice, and a Test Scenario, in which each lesion was tested with the gene expression assay and diagnosed. Total cost of care was compared between the two scenarios to determine overall budget impact. Sensitivity analyses were performed to test the robustness of the model.

RESULTS

The gene expression assay reduces costs by $1268 per patient tested over 10 years, a decrease of 8.3%, after accounting for the cost of the assay. For a health plan with 10 million members, this would translate to over $8 million in savings. The largest portion of this saving comes from reducing the number of missed melanomas, which would otherwise progress to advanced disease. In sensitivity analyses, no single model input changed within a reasonable range of values caused the model to show that the assay was not cost-saving.

CONCLUSION

In addition to improving the diagnosis of melanoma, this gene expression assay would likely reduce costs for health plans that choose to cover it.