PDF - 313KB, Supplementary Table S2. List of genes downregulated in HN5-ER cells relative to HN5 cells.

PDF - 706KB, Supplementary Table S3. Functional pathways associated with acquired erlotinib resistance in HN5-ER cells.

PDF - 22KB, Supplementary Figure S1. Cross-resistance of HN5-ER cells to gefitinib and stability of erlotinib resistance in HN5-ER cells grown in the absence of erlotinib.

Our Ion Torrent targeted sequencing assay consists of a single ultraplex PCR reaction with primer sets for 207 amplicons. Data were filtered to exclude all synonymous and intronic variants. A quality score cutoff of 100 and an allele frequency of >5 were applied to eliminate low frequency artifacts.

Kaplan-Meier analysis shows no significant difference in overall survival of melanoma patients from the validation cohort based on KDR status (TA,AA: Q472H variant, TT: WT variant).

PDF - 47KB, Supplementary Figure S5. Sensitivity of HN5-ER cells to erlotinib following Axl knockdown by RNAi.

Sequencing data of paired primary/metastatic tumor samples from two patients.

PDF - 59KB, Supplementary Figure S3. Inhibition of Axl activity in HN5-ER cells and EGFR activity in HN5 cells with the Axl inhibitor R428.

PDF - 27KB, Supplementary Figure S2. Immunoblotting analysis of EGFR, Akt and E-cadherin in HN5-ER2 cells.

Somatic mutations (top column) identified by Ion Torrent sequencing of the pilot melanoma cohort are listed for each patient (left hand column).

PDF - 771KB, Supplementary Table S4. Functional pathways associated with acquired erlotinib resistance in HNC and NSCLC.

PDF - 13KB, Supplementary Figure S4. Sensitivity of HN5-ER cells to co-treatment with gefitinib and R428.

PDF - 75KB, Supplementary Figure S6. Analysis of NF-kB activity between HN5 and HN5-ER cells and following transfection of HN5-ER cells with miR-34a or Axl siRNAs.

PDF - 197KB, Supplementary Table S1. List of genes upregulated in HN5-ER cells relative to HN5 cells.

PDF - 101KB, Legends for Supplemental Figures 1 through 6 and Supplemental Tables 1 through 4.

Clinically relevant somatic mutations identified in WT melanoma patients in the pilot cohort

Frataxin deficiency in Friedreich’s ataxia results from transcriptional downregulation of the FXN gene caused by expansion of the intronic trinucleotide guanine-adenine-adenine (GAA) repeats. We used multiple transcriptomic approaches to determine the molecular mechanism of transcription inhibition caused by long GAAs. We uncovered that transcription of FXN in patient cells is prematurely terminated upstream of the expanded repeats leading to the formation of a novel, truncated and stable RNA. This FXN early terminated transcript (FXN-ett) undergoes alternative, non-productive splicing and does not contribute to the synthesis of functional frataxin. The level the FXN-ett RNA directly correlates with the length of the longer of the two expanded GAA tracts. Targeting GAAs with antisense oligonucleotides or excision of the repeats eliminates the transcription impediment, diminishes expression of the aberrant FXN-ett, while increasing levels of FXN mRNA and frataxin. Non-productive transcription may represent a common phenomenon and attractive therapeutic target in diseases caused by repeat-mediated transcription aberrations.

3069 Background: Immune checkpoint inhibitors (ICIs), e.g., ipilimumab (IPI) and/or nivolumab (NIVO), produce durable survival benefit in a substantial proportion of melanoma patients but can also induce severe immune-related adverse events (irAEs) requiring treatment discontinuation. There is no biomarker to predict irAEs in ICI-treated melanoma patients. Given the similar clinical manifestation between irAEs and autoimmune disorders, we hypothesized that a subset of patients possess a subclinical baseline predisposition to developing irAEs that is characterized by specific autoantibodies (autoAbs). Methods: Pre-treatment melanoma patient sera from the CheckMate-238 Phase III trial of adjuvant IPI vs. NIVO were used for autoAb profiling with HuProt proteomic arrays (CDI Labs). The outcome of interest is to predict toxicity events that caused treatment discontinuation. For each treatment arm, we allocated patients to training and testing datasets in a 3:1 ratio. We calculated the area under the curve (AUC) of the receiver operating characteristic curve to select a probability threshold, which was applied to the testing dataset to assess accuracy, sensitivity, and specificity. Functional enrichment among autoAb protein targets was assessed using Metascape. Results: There were 707 irAEs among 597 patients (IPI = 423, NIVO = 174), of which 355 required treatment discontinuation (IPI = 287, NIVO = 68). In the training sets, we identified a 170 autoAbs signature consisting of 102 autoAbs for IPI treatment and 68 autoAbs for NIVO treatment. In the independent testing set, the signatures showed AUC of 0.85 (0.78, 0.92), 82% sensitivity, 78% specificity, and overall accuracy of 81% to predict IPI discontinuation, and AUC of 0.87 (0.74, 0.99), 75% sensitivity, 97% specificity, and overall accuracy of 88% to predict NIVO discontinuation. Enrichment of nuclear lumen-associated protein targets was identified among autoAb signatures that predict IPI or NIVO discontinuation. Conclusions: The identified signature within a large Phase III trial cohort highlights the potential utility of pre-treatment autoAbs for prediction of patients at high risk of developing irAEs in the adjuvant setting necessitating treatment termination. We are currently validating and refining toxicity-associated autoAb signatures with the goal of developing a Clinical Laboratory Improvement Amendments (CLIA)-certified assay to enable clinicians to optimize immunotherapy delivery and patient selection.

Dermal invasion is a hallmark of malignant melanoma. Although the molecular alterations that drive the progression of primary melanoma to metastatic disease have been studied extensively, the early progression of noninvasive primary melanoma to an invasive state is poorly understood. To elucidate the mechanisms underlying the transition from radial to vertical growth, the first step in melanoma invasion, we developed a zebrafish melanoma model in which constitutive activation of ribosomal protein S6 kinase A1 drives tumor invasion. Transcriptomic analysis of ribosomal protein S6 kinase A1-activated tumors identified metabolic changes, including up-regulation of genes associated with oxidative phosphorylation. Vertical growth phase human melanoma cells show higher oxygen consumption and preferential utilization of glutamine compared to radial growth phase melanoma cells. Peroxisome proliferator activated receptor γ coactivator (PGC)-1α, has been proposed as a master regulator of tumor oxidative phosphorylation. In human primary melanoma specimens, PGC1α protein expression was found to be positively associated with increased tumor thickness and expression of the proliferative marker Ki-67 and the reactive oxygen species scavenger receptor class A member 3. PGC1α depletion modulated cellular processes associated with primary melanoma growth and invasion, including oxidative stress. These results support a role for PGC1α in mediating glutamine-driven oxidative phosphorylation to facilitate the invasive growth of primary melanoma.

e22075 Background: NF1-mutant melanoma (NF1-MT) is a distinct molecular subtype with worse overall prognosis than NF1-wild melanoma (NF1-WT). Despite its prevalence in 20% of patients and associated clinical disadvantage, there is no specific targeted therapy available to treat NF1-MT as its biological impact remains understudied. We tested the hypothesis that NF1-MT possess distinct genomic and transcriptomic characteristics from NF1-WT, which can potentially inform therapeutic innovation. Methods: Tumor DNA from metastatic melanoma (MM) patients treated with checkpoint inhibition at NYU was genotyped using exome sequencing. Microenvironment-related transcripts (n = 770) were then compared in NF1-MT versus NF1-WT using unsupervised clustering, differential gene expression, and gene set enrichment analyses. Verification of genomic and transcriptional findings was performed using qPCR and immunohistochemistry (IHC). TCGA melanoma (SKCM) data were analyzed as an independent cohort. Results: Pathogenic NF1 mutations were detected in 31/121 (27%) cases and were significantly associated with higher tumor mutational burden (P = 0.02). NF1-MT showed recurrent homozygous deletion in the membrane regulatory gene SYT1 and amplifications in oncogenes including CCND1 and MDM2, verified by qPCR. NF1-MT showed upregulation of proliferation with significantly increased expression of Ki-67 and cell division cycle protein 20 CDC20 (P = 0.03) validated by IHC (P = 0.03). Cell cycle was the top enriched pathway in NF1-MT (P = 0.003, FDR = 0.04). Analysis of TCGA melanoma data (n = 440) corroborated upregulation of MKI67 and CDC20 in NF1-MT melanoma (P = 0.01, P = 0.03). Conclusions: NF1-MT is associated with a hyper-proliferative tumor phenotype that cannot be only attributed to MAP kinase activation. Our data suggest that NF1-MT may be vulnerable to pharmacological inhibitors of cell cycle progression and proliferation, such as those targeting CDC20 or CDK4/6.