Faculty Bibliography

Background: Efforts to identify targeted therapies that can improve treatment outcome in metastatic ALM have been unsuccessful. In a previous genomic screening, we identified copy number amplification of the histone methyltransferase EZH2 in 47% of ALM cases, a higher frequency than previously reported in cutaneous melanomas (CM) (5%). Here, we tested the hypothesis that increased EZH2 expression contributes to ALM progression and may confer selective sensitivity to EZH2 inhibition. Methods: EZH2 expression was examined by immunohistochemistry (IHC) in 51 primary (21 stage I, 13 Stage II and 17 Stage III) and 23 metastatic (11 in transit, 8 nodal and 4 visceral) ALM cases with extensive clinicopathological data and protocol-driven follow up. Colony formation and cell proliferation was assessed following treatment of ALM and CM cell lines with three EZH2 inhibitors, including GSK126, currently in clinical trials. The effect of GSK126 on H3K27me3 and downstream EZH2 targets was analyzed by western blotting. Results: EZH2 is commonly overexpressed in both primary (30/51; 65%) and metastatic (20/23; 87%) ALM cases, with a significant increase in mean IHC score between primary and metastatic tumors (1.9 vs. 2.7, respectively, p = 0.047). EZH2 expression increased in 6/10 metastatic ALM tumors compared to their matched primary tumors. ALM tumors with EZH2 gene amplification showed increased EZH2 protein expression; however more cases showed overexpression with no amplification suggesting a potential epigenetic component of EZH2 regulation. GSK126 significantly suppressed ALM colony formation at lower doses compared to CM (1 muM vs. 5 muM, respectively). EZH2 inhibition also increased expression of the downstream tumor suppressor E-cadherin in ALM but not in CM cell lines. Finally, ALM cell lines had significantly lower basal H3K27me3 levels than CM cell lines, suggesting an additional, histone methyltransferase-independent function of EZH2 in ALM. Conclusions: Our data demonstrate thatEZH2 upregulation is common in ALM, and suggest that it may play a role in ALM's metastatic progression that requires further investigation. Selective sensitivity of ALM cell lines to EZH2 inhibitors supports the therapeutic potential of EZH2-targeted therapy in ALM

Background: Recently, tumor mutation burden (TMB) has been shown to increase the presentation of neoantigens that stimulate immune tumor recognition, resulting in improved immunotherapy (IT) outcomes in melanoma and other cancers. As melanoma is highly immunogenic, here we tested whether TMB associates with immune recognition during tumor progression, hence impacting melanoma overall survival (OS), independently of IT treatment. Methods: We have generated somatic mutation data from 314 IT-naive metastatic melanomas from The Cancer Genome Atlas (TCGA). In the TCGA cohort, TMB has been calculated for 210 genes (200GS) previously established from TMB studies of anti-CTLA4 and anti-PD1/PD-L1 IT. For validation, we have sequenced exonic regions of 20 genes (20GS) with the highest TMB among 200GS in 89 IT-naive metastatic melanomas ascertained at New York University Langone Medical Center. The TMB was defined using total number of somatic, non-synonymous mutations in either 200GS (TCGA discovery) or 20GS (validation), respectively. For discovery and validation cohorts, OS from primary diagnosis of samples with high TMB was compared against low TMB, using thresholds established in previous studies. Results: We found that total TMB predicts better OS (p = 0.03, HR = 2.64) in TCGA melanomas. Restricting the analysis only to the established 200GS, this association became more significant in all patients (p = 0.01, HR = 2.67) as well as in patients without IT (p = 0.01, HR = 2.67). In the validation stage of 89 melanomas without prior IT treatment, a high TMB in a subset of 20GS accurately determined favorable OS (p = 0.02, HR = 2.69) and confirmed TCGA observations from the 200GS. Conclusions: Here we show, for the first time, that in addition to IT, high TMB predicts more favorable OS in patients that never received IT, potentially serving as a novel marker of prognosis of melanoma and likely other immunogenic tumors at early stages. In addition, our study suggests that TMB test can be robust when applied to only a small subset of genes that trigger significantly higher immunogenicity. This may also eventually assist with accurate sub-selection of early stage patients likely to respond to IT regimens

Background: Unlike other solid tumors, the impact of primary HS on melanoma survival and response to systemic therapy is not well studied. Nodular melanoma (NM) has a worse prognosis than superficial spreading melanoma (SSM), which is usually attributed to thicker primary tumors. Herein, we examine the hypothesis that HS might have an impact on MSS independent of thickness and that NM and SSM exhibit different mutational landscapes that associate with response to checkpoint inhibitor immunotherapy (IT) and BRAF targeted therapy (TT) in the metastatic setting. Methods: Primary NM and SSM patients prospectively enrolled at NYU (2002 - 2016) were compared to the most recent SEER cohort (1973 - 2012) and analyzed with respect to MSS. Next-Generation Sequencing (NGS) was performed on a subset of matched tumor-germline pairs, allowing a comparison of the mutational landscape between NM and SSM. In the metastatic setting, survival analyses were used to compare outcomes and responses to treatment across HS. Results: The NYU cohort of 1,621 patients with either NM (n = 510) or SSM (n = 1,111) was representative of the analogous SEER cohort (21,339 NM, 97,169 SSM), with NM presenting as thicker, more ulcerated, and later stage (all p < 0.001). Among the NYU cohort, NM was found to have lower rates of TIL (p = 0.047), higher mitotic index (p < 0.001), and higher rates of NRAS mutation (p < 0.001). In multivariate Cox models, NM was a significant predictor of worse MSS, independent of thickness and stage (p = 0.01). NM had a significantly lower mutational burden across the exome (p < 0.001). Some of the most under-mutated genes noted in NM were NOTCH4, BCL2L12 and RPS6KA6 (all p < 0.01). Among patients treated with TT (n = 56), NM remained a significant predictor of worse MSS (p = 0.004). However, there was no difference in response to IT. Conclusions: NM and SSM show divergent mutational patterns which may contribute to their different clinical behaviors and responses to BRAF targeted therapy. More studies are needed to better understand the key molecular and cellular processes driving such differences. Integration of HS data into prospective clinical trial reporting is needed to better assess its impact on response to treatment

Association of aberrant glycosylation with melanoma progression is based mainly on analyses of cell lines. Here we present a systems-based study of glycomic changes and corresponding enzymes associated with melanoma metastasis in patient samples. Upregulation of core fucosylation (FUT8) and downregulation of alpha-1,2 fucosylation (FUT1, FUT2) were identified as features of metastatic melanoma. Using both in vitro and in vivo studies, we demonstrate FUT8 is a driver of melanoma metastasis which, when silenced, suppresses invasion and tumor dissemination. Glycoprotein targets of FUT8 were enriched in cell migration proteins including the adhesion molecule L1CAM. Core fucosylation impacted L1CAM cleavage and the ability of L1CAM to support melanoma invasion. FUT8 and its targets represent therapeutic targets in melanoma metastasis.

Despite increasing amounts of experimental evidence depicting the involvement of non-coding RNAs in cancer, the study of BRAFV600E-regulated genes has thus far focused mainly on protein-coding ones. Here, we identify and study the microRNAs that BRAFV600E regulates through the ERK pathway.By performing small RNA sequencing on A375 melanoma cells and a vemurafenib-resistant clone that was taken as negative control, we discover miR-204 and miR-211 as the miRNAs most induced by vemurafenib. We also demonstrate that, although belonging to the same family, these two miRNAs have distinctive features. miR-204 is under the control of STAT3 and its expression is induced in amelanotic melanoma cells, where it acts as an effector of vemurafenib's anti-motility activity by targeting AP1S2. Conversely, miR-211, a known transcriptional target of MITF, is induced in melanotic melanoma cells, where it targets EDEM1 and consequently impairs the degradation of TYROSINASE (TYR) through the ER-associated degradation (ERAD) pathway. In doing so, miR-211 serves as an effector of vemurafenib's pro-pigmentation activity. We also show that such an increase in pigmentation in turn represents an adaptive response that needs to be overcome using appropriate inhibitors in order to increase the efficacy of vemurafenib.In summary, we unveil the distinct and context-dependent activities exerted by miR-204 family members in melanoma cells. Our work challenges the widely accepted "same miRNA family = same function" rule and provides a rationale for a novel treatment strategy for melanotic melanomas that is based on the combination of ERK pathway inhibitors with pigmentation inhibitors.

Patients with stage IB melanoma have a 10% risk of melanoma-specific mortality within five years. The current prognostic paradigm, however, is insufficient to predict which of these patients are most likely to recur. Additional prognostic characteristics of stage IB melanoma are needed to identify this patient subset who are at highest risk of recurrence, and may benefit from closer follow-up. We evaluated a prospective cohort of stage IB patients (n = 655) treated at NYU Langone Medical Center. In a research subset (n = 149) composed of patients with recurrent (n = 63) and nonrecurrent (n = 86) disease matched for age, sex, thickness, ulceration and mitoses, primary tumors were independently reviewed for digitally calculated area, manually calculated area (depth x width), width, and conformation (contiguous versus noncontiguous) using computer-assisted histopathological analysis (Aperio, Vista, CA USA). We tested the association between histologic variables and recurrence-free survival (RFS) using Cox univariate analysis. Increasing digital area (HR 1.08, P < 0.01), tumor width (HR 1.17, P = 0.01), and non-contiguous conformation (HR 0.57, P = 0.05) were independently prognostic of RFS. Linear regression analysis showed a significant correlation between the manual and digital area (estimate 0.64, P < 0.01), which became even stronger when restricted to patients with contiguous tumors (estimate 0.75, P < 0.01), suggesting manually calculated tumor area may also provide useful prognostic information for providers without access to similar software. Computer-assisted measurement of cross-sectional tumor area, width, and contiguity may help risk-stratification in stage IB patients. Independent validation of these primary tumor characteristic is needed to fully comprehend their prognostic role in stage IB melanoma

Patients with thick (>4 mm) primary melanomas have highly variable outcomes. Current staging criteria for these patients are based primarily on the presence of nodal disease, which often serves as the basis for adjuvant trial eligibility. Identification of novel biomarkers could help identify patients who may benefit from promising, new adjuvant therapies or, alternatively, spare patients with good prognoses the cost and potential toxicity of these drugs. We examined patients with thick primary melanoma to determine whether proliferation markers (mitotic index and Ki- 67) and other clinicopatholgical features were associated with survival. We studied 171 patients with thick primary melanomas; median thickness was 6.0 mm (median follow-up, 3.0 years). In clinically node-negative patients, Ki-67 expression was an independent predictor of worse RFS (HR 2.19, P = 0.024) and OS (HR 2.49, P = 0.028). In a separate model, moderate (>1 to <5 per mm²) and many (>5 per mm²) mitoses were each significantly associated with RFS (HR = 9.97, P = 0.035 and HR = 11.93, P = 0.025, respectively); and OS (HR = 12.79, P = 0.033 and HR = 18.68, P = 0.017, respectively). In the same model, natural log-transformed tumor thickness was also significantly associated with worse OS (HR 2.37, P = 0.009). In sum, we identified cell proliferation markers Ki-67 and mitotic index as independent predictors of survival in clinically nodenegative patients with thick primary melanoma. Greater tumor thickness was also an independent predictor of survival in this cohort. With further investigation, these measures may improve risk-stratification for patients with thick primary melanoma

Purpose To identify MR imaging features of melanoma brain metastases (MBM) that correlate with genetic profile of melanoma and patient survival. Materials and methods Patients with newly diagnosed melanoma metastases were identified from institutional database A retrospective review of brain MRI was performed focusing on lesion number, size, T1-, T2- and diffusion-weighted signal characteristics, hemorrhage, necrosis, enhancement pattern and edema. Genomic (BRAF status), treatment and survival data was collected. Results 98 patients were included in final analysis. A strong correlation was found between size of the largest lesion and the percent of lesions with T1-weighted hyperintense signal (R = 0.49), percent of lesions with size >1 cm (0.55), and the lesions that are clearly hemorrhagic (0.43). The analyzed imaging parameters were found to be independent of BRAF mutation status. The median survival of subjects with single lesion (9.1 months) was significantly higher than the median survival of subjects with more than 1 lesion (4.9 months) (p = 0.002). Patients with 2-18 lesions had significantly longer survival (5.6 months) than with >18 lesions (2 months) (p < 0.001). Other imaging parameters such as lesion size, T1-weighted hyperintensity, number of lesions with edema and hemorrhage were not found to be significantly related to survival. BRAF inhibitor treatment was found to be the most significant prognostic factor (p = 0.002) among patients with multiple lesions. Conclusion There is a statistically significant correlation between number of brain metastases and survival. In patients with multiple lesions, BRAF inhibitor treatment was the most significant prognostic factor.