Faculty Bibliography

Background: There are no predictive biomarkers of ipilimumab (IPI) toxicity. Of metastatic melanoma (MM) patients (pts) receiving IPI (3mg/kg), 35% require systemic therapies to treat immune-related adverse events (irAEs) and 20% must terminate treatment (Horvat et al., JCO 2015). Here we tested the hypothesis that a pre-existing autoantibody (autoAb) profile is predictive of IPI irAEs. Methods: We measured autoAb levels in pre- and post-treatment sera from mm pts who received IPI (3mg/kg) monotherapy on a proteome microarray containing ~20,000 unique full-length human proteins (HuProt array, CDI Laboratories). Clinical data were prospectively collected with protocol-driven follow-up. IrAEs were categorized by CTCAE guidelines as none (grade 0), mild (grade 1-2), or severe (grade 3-4). AutoAb levels were standardized using median quantile normalization and considered positive hits if > 2-SD above the peak array signal and differed by >=2 fold with p < 0.05 between toxicity groups (Non-parametric Analysis/Wilcox test). Results: Seventy-eight sera from 37 mm pts were analyzed. Antibodies against CTLA-4 were significantly elevated post IPI treatment (p < 0.0001), validating the assay. The pre-treatment levels of 190 IgG autoAbs were significantly diferent in pts who experienced irAEs (n = 28) compared to those with no irAEs (n = 9). Comparison of severe irAE (n = 9) and no irAE (n = 9) groups revealed 129 IgG autoAbs that significantly differed in pre-treatment sera. Localization and pathway analysis (UniProt, KEGG, Reactome) showed 81/190 (43%) of the autoAbs targeted nuclear and mitochondrial antigens and were enriched in metabolic pathways (p = 0.015). AutoAbs associated with irAEs did not correlate with treatment response. Conclusions: AutoAbs to antigens enriched in metabolic pathways prior to treatment may predict IPI-induced toxicity in MM. The subcellular localization of targeted antigens could explain the autoimmune toxicities associated with IPI. Studies in larger cohorts and in pts receiving other checkpoint inhibitors and/or combination therapies are essential to determine the validity of the data. If validated, our results would support the discovery of the first toxicity predictor in cancer immunotherapy

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 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

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

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.

OBJECTIVES: Since 2011, metastatic melanoma treatment has evolved with commercial approval of BRAF- and MEK-targeted therapy and CTLA-4- and PD-1-blocking antibodies (immune checkpoint inhibitors, ICI). While novel therapies have demonstrated improved prognosis in clinical trials, few studies have examined the evolution of prognosis and toxicity of these drugs among an unselected population. We assess whether survival and toxicity reported in trials, which typically exclude most patients with brain metastases and poor performance status, are recapitulated within a commercial access population. METHODS: 182 patients diagnosed with stage IV melanoma from July 2006 to December 2013 and treated with BRAF- and/or MEK-targeted therapy or ICI were prospectively studied. Outcomes and clinicopathologic differences between trial and commercial cohorts were assessed. RESULTS: Patients receiving commercial therapy (vs. on trial) had poorer prognostic features (i.e., brain metastases) and lower median overall survival (mOS) when assessed across all treatments (9.2 vs. 17.5 months, p = 0.0027). While toxicity within trial and commercial cohorts did not differ, patients who experienced toxicity had increased mOS (p < 0.001), irrespective of stratification by trial status or therapy. CONCLUSION: Metastatic melanoma patients receiving commercial treatment may represent a different clinical population with poor prognostic features compared to trial patients. Toxicity may prognosticate treatment benefit.