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Supplemental Figure 1. Three melanoma cell lines (CHL1, Mel888, and WM793) were treated with DMSO (0), 10uM, or 50uM of dabrafenib (BRAFi) for 3 hours. Whole cell lysates were prepared, and levels of phospho-ERK and total ERK were analyzed by immunoblotting. Supplemental Figure 2. Mel888 cells were treated with vehicle (DMSO) or 50 uM of BRAFi for 3 hours. Following treatment, cells were stained with fluorescently-labeled antibodies specific for MHC-I (HLA-A,B,C), MHC-II (HLA-DR), PD-L1, or melanoma-associated chondroitin sulfate proteoglycan (MCSP), and analyzed by flow cytometry. Data shown are representative of at least three replicate experiments with similar results. * indicates p < 0.05; ns, not significant. Supplemental Figure 3. HLA-A2-transduced Mel888 melanoma cell lines were treated with vehicle DMSO (0), 10uM, or 50uM of BRAFi for 3 hours. Whole cell lysates were prepared and levels of phospho-ERK and total ERK were analyzed by immunoblotting. Supplemental Figure 4. HLA-A2-transduced Mel888 or WM793 cells were treated with DMSO or MEKi for 3 hours. Following treatment, cells were stained with a fluorescently-labeled HLA-A2-specific antibody and analyzed by flow cytometry. These experiments were repeated at least four times with similar results. *** indicates p < 0.005; ns, not significant. Supplemental Figure 5. T2 cells were pulsed with titrated amounts of MART-1(27-35) peptide, washed, and then used as stimulator cells for MART1-specific CD8+ TILs. Supernatants were collected after 8 hours of co-culture and analyzed by ELISA to measure interferon-gamma (IFNgamma) release. Supplemental Figure 6. Percentage of intracellular IFNgamma-positive TILs following 3 hours of co-culture with DMSO- or BRAFi-treated HLA-A*0201-transduced Mel888 cells or MART-1(27-35) peptide-pulsed WM793 cells, as measured by flow cytometry. All data are representative of experiments performed at least 3 times with similar results. *, p

Testing of T cell–based cancer therapeutics often involves measuring cancer antigen–specific T-cell populations with the assumption that they arise from in vivo clonal expansion. This analysis, using peptide/MHC tetramers, is often ambiguous. From a leukemia cell line, we identified a CDK4-derived peptide epitope, UNC-CDK4-1 (ALTPVVVTL), that bound HLA-A*02:01 with high affinity and could induce CD8+ T-cell responses in vitro. We identified UNC-CDK4-1/HLA-A*02:01 tetramer+ populations in 3 of 6 patients with acute myeloid leukemia who had undergone allogeneic stem cell transplantation. Using tetramer-based, single-cell sorting and T-cell receptor β (TCRβ) sequencing, we identified recurrent UNC-CDK4-1 tetramer–associated TCRβ clonotypes in a patient with a UNC-CDK4-1 tetramer+ population, suggesting in vivo T-cell expansion to UNC-CDK4-1. In parallel, we measured the patient's TCRβ repertoire and found it to be highly restricted/oligoclonal. The UNC-CDK4-1 tetramer–associated TCRβ clonotypes represented >17% of the entire TCRβ repertoire—far in excess of the UNC-CDK4-1 tetramer+ frequency—indicating that the recurrent TCRβ clonotypes identified from UNC-CDK-4-1 tetramer+ cells were likely a consequence of the extremely constrained T-cell repertoire in the patient and not in vivo UNC-CDK4-1–driven clonal T-cell expansion. Mapping recurrent TCRβ clonotype sequences onto TCRβ repertoires can help confirm or refute antigen-specific T-cell expansion in vivo. Cancer Immunol Res; 3(3); 228–35. ©2015 AACR.

PTEN loss in melanoma promotes resistance to T cell-mediated anti-tumor activity in the context of concurrent a selective inhibitor for mutant BRAF.

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Supplemental Methods and Figure Legends

S1. Ectopic expression of HLA allotypes in melanoma cell line Mel888. S2. SLC45A2 expression is restricted to melanoma tumor cells. S3. SLC45A2 gene expression in Cancer Cell Line Encyclopedia (CCLE) cell lines. S4. Quantitative comparison of SLC45A2 gene expression in various normal tissues and cancers. S5. Generation of HLA-A*0201-restricted SLC45A2 antigen-specific CTLs from multiple normal donor PBMC. S6. SLC45A2-specific CTLs demonstrate lytic activity against uveal and mucosal melanoma cell lines. S7. IFN-gamma release by MDA-specific CTLs in response to titrated HLA-A*0201 restricted peptides. S8. Primary melanocytes express HLA-A*0201 but are only killed by SLC45A2 T cells after peptide pulsing. S9. SLC45A2-specific CTLs from different donors preferentially kill melanoma tumor cells over primary melanocytes. Supplemental Table S1.Human MDA gene primer pair sequences used for RT-PCR. Supplemental Table S2. SLC45A2-derived peptides detected by mass spectrometric analysis of melanoma cell lines. Supplemental Table S3. Confirmation of natural SLC45A2 peptide processing and presentation by HLA transduction. Supplemental Table S4.Sequences and predicted binding affinities of HLA-A2-restricted MDA peptides.

The document contains 4 supplemental tables: 1. RT-PCR Primers for TCRbeta sequencing 2. HPLC-MS identified peptide sequences 3. The amino acid sequences of recurrent TCRbeta clonotypes 4. The distribution of the CDR3 amino acid length in the analyzed patient. There are 2 supplementary figures: 1. Tetramer flow cytometry showing the generation of an oligoclonal T-cell population with a UNC-CDK4-1 high affinity T-cell population. 2. More detailed information regarding the tetramer gating strategy employed.

Oncogene activation in tumor cells induces broad and complex cellular changes that contribute significantly to disease initiation and progression. In melanoma, oncogenic BRAFV600E has been shown to drive the transcription of a specific gene signature that can promote multiple mechanisms of immune suppression within the tumor microenvironment. We show here that BRAFV600E also induces rapid internalization of MHC class I (MHC-I) from the melanoma cell surface and its intracellular sequestration within endolysosomal compartments. Importantly, MAPK inhibitor treatment quickly restored MHC-I surface expression in tumor cells, thereby enhancing melanoma antigen-specific T-cell recognition and effector function. MAPK pathway–driven relocalization of HLA-A*0201 required a highly conserved cytoplasmic serine phosphorylation site previously implicated in rapid MHC-I internalization and recycling by activated immune cells. Collectively, these data suggest that oncogenic activation of BRAF allows tumor cells to co-opt an evolutionarily conserved MHC-I trafficking pathway as a strategy to facilitate immune evasion. This link between MAPK pathway activation and the MHC-I cytoplasmic tail has direct implications for immunologic recognition of tumor cells and provides further evidence to support testing therapeutic strategies combining MAPK pathway inhibition with immunotherapies in the clinical setting. Cancer Immunol Res; 3(6); 602–9. ©2015 AACR.

Cytotoxic T lymphocyte (CTL)–based immunotherapies have had remarkable success at generating objective clinical responses in patients with advanced metastatic melanoma. Although the melanocyte differentiation antigens (MDA) MART-1, PMEL, and tyrosinase were among the first melanoma tumor-associated antigens identified and targeted with immunotherapy, expression within normal melanocytes of the eye and inner ear can elicit serious autoimmune side effects, thus limiting their clinical potential as CTL targets. Using a tandem mass spectrometry (MS) approach to analyze the immunopeptidomes of 55 melanoma patient–derived cell lines, we identified a number of shared HLA class I–bound peptides derived from the melanocyte-specific transporter protein SLC45A2. Antigen-specific CTLs generated against HLA-A*0201- and HLA-A*2402–restricted SLC45A2 peptides effectively killed a majority of HLA-matched cutaneous, uveal, and mucosal melanoma cell lines tested (18/25). CTLs specific for SLC45A2 showed significantly reduced recognition of HLA-matched primary melanocytes that were, conversely, robustly killed by MART1- and PMEL-specific T cells. Transcriptome analysis revealed that SLC45A2 mRNA expression in normal melanocytes was less than 2% that of other MDAs, therefore providing a more favorable melanoma-to-melanocyte expression ratio. Expression of SLC45A2 and CTL sensitivity could be further upregulated in BRAF(V600E)-mutant melanoma cells upon treatment with BRAF or MEK inhibitors, similarly to other MDAs. Taken together, our study demonstrates the feasibility of using tandem MS as a means of discovering shared immunogenic tumor-associated epitopes and identifies SLC45A2 as a promising immunotherapeutic target for melanoma with high tumor selectivity and reduced potential for autoimmune toxicity. Cancer Immunol Res; 5(8); 618–29. ©2017 AACR.

Interleukin (IL)-1–mediated inflammation is proposed to contribute to the development and progression of some cancers. IL-1 family member proteins are known to be expressed constitutively in many melanoma tumor cells, and we hypothesize that these support molecular pathways of inflammation and facilitate tumor growth. To investigate the expression of IL-1α and IL-1β in melanoma patients, and their association with disease progression, immunohistochemical staining was carried out on tissues from 170 patients including benign nevi, primary melanomas, and metastatic melanomas. IL-1β levels were low (or zero) in benign nevi and higher in primary and metastatic melanomas (P < 0.0001). IL-1α was expressed in about 73% of nevi and 55% of metastatic melanomas, with levels significantly higher in primary tumors (P < 0.0001); most (98%) primary melanoma samples were positive for IL-1α. In vitro studies with seven human melanoma cell lines showed that five cell lines expressed IL-1α and IL-1β proteins and mRNA. We identified for the first time several important downstream signaling pathways affected by endogenous IL-1, including reactive oxygen and nitrogen species, COX-2, and phosphorylated NF-κB inhibitor (IκB) and stress-activated protein kinase/c-jun-NH2-kinase; all of which were decreased by siRNA to IL-1s. Downregulation of IL-1α, IL-1β, or MyD88 substantially increased p21 and p53 levels. Treatment with IL-1 receptor type I neutralizing antibody or IL-1 pathway–specific siRNAs led to growth arrest in IL-1–positive melanoma cells. Furthermore, blocking the IL-1 pathway increased autophagy in IL-1–positive melanoma cells. These results indicate that the endogenous IL-1 system is functional in most human melanoma and interrupting its signaling inhibits the growth of IL-1–positive melanoma cells. Mol Cancer Res; 9(11); 1537–50. ©2011 AACR.

Supplementary Table S1. Patient characteristics of the single-agent anti-PD-1 cohort. Supplementary Table S2. List of primers used for gene expression analysis by real-time PCR. Supplementary Table S3. List of autophagy-related genes for overexpressing experiment.

PDF file, 212K, (A) H&E staining of representative, A375 human xenograft tumor sections excised from NOD/SCID mice. Prior to excision, mice with established tumors were treated for 3 days with either PLX4720 or DMSO vehicle control. Magnification: 4x. (B) RT-PCR analysis of human IL1α, IL1β, IL-8, GRO-α, PD-L1, and PD-L2 transcripts derived from A375 xenografts shown in (A). Data show the average of 3 mice per group, and are representative of 3 separate experiments.

PDF file - 19K, Melanoma antigen expression is decreased at time of progression.

PDF file, 78K, (A) Dose titration curve showing surface expression of PD-L1 on TAFs as measured by flow cytometry 18 hours following exposure to titrated doses of IL-1α or IL-1β. (B) Time course experiment assessing surface expression of PD-L1 by flow cytometry following exposure of TAFs to 1 ng/ml IL-1β.

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PDF file - 349K, Inhibition of BRAFV600E is not associated with a significant increase in HLA expression in patients with metastatic melanoma.

PDF file - 30K, VEGF production by A375/H-2Db/gp100 melanoma cells

PDF file - 56K, Methods for determination of tumor antigen-specific CD8+ population in TIL.

PDF file - 127K, CD8+CD27+CD57+ subset in TIL can persist, proliferate, and expand ex vivo in high-dose IL-2 culture.

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PDF file, 188K, Tumor-associated fibroblasts (TAF) cultures were derived from three separate metastatic melanoma biopsies from three distinct anatomical sites: lymph node, lung and soft tissue. Cultured TAFs were exposed overnight to IL-1α, and treated and untreated cells were subjected to Affymetrix gene expression analysis. (A) Heatmap displaying the 197 most differentially expressed genes selected at FDR 0.01. Relative expression values are indicated by the color bar. (B) Gene set enrichment analysis of IL-1α-treated TAFs demonstrates a strong correlation with gene sets previously identified to be associated with NF-kappaB upregulation and the interferon response. (C) Heatmap showing IL-1α induced expression of nine genes previously reported to be associated with T-cell suppression.

PDF file - 117K, CD8+CD57+ T cells in TIL can further differentiate into CD27-CD57+, Perfhigh effector cells ex vivo.

PDF file - 72K, PLX4720 treatment does not increase infiltration of adoptively transferred T cells into tumors containing WT BRAF

PDF file - 38K, mRNA levels of VEGF in patients with metastatic melanoma undergoing treatment with a selective inhibitor of BRAF(V600E)

PDF file - 82K, Administration of PLX4720 in vivo increases tumor infiltration of adoptively transferred T cells and enhances antitumor responses

Purpose: In this study, we assessed the specific role of BRAF(V600E) signaling in modulating the expression of immune regulatory genes in melanoma, in addition to analyzing downstream induction of immune suppression by primary human melanoma tumor-associated fibroblasts (TAF).Experimental Design: Primary human melanocytes and melanoma cell lines were transduced to express WT or V600E forms of BRAF, followed by gene expression analysis. The BRAF(V600E) inhibitor vemurafenib was used to confirm targets in BRAF(V600E)-positive melanoma cell lines and in tumors from melanoma patients undergoing inhibitor treatment. TAF lines generated from melanoma patient biopsies were tested for their ability to inhibit the function of tumor antigen-specific T cells, before and following treatment with BRAF(V600E)-upregulated immune modulators. Transcriptional analysis of treated TAFs was conducted to identify potential mediators of T-cell suppression.Results: Expression of BRAF(V600E) induced transcription of interleukin 1 alpha (IL-1α) and IL-1β in melanocytes and melanoma cell lines. Further, vemurafenib reduced the expression of IL-1 protein in melanoma cell lines and most notably in human tumor biopsies from 11 of 12 melanoma patients undergoing inhibitor treatment. Treatment of melanoma-patient–derived TAFs with IL-1α/β significantly enhanced their ability to suppress the proliferation and function of melanoma-specific cytotoxic T cells, and this inhibition was partially attributable to upregulation by IL-1 of COX-2 and the PD-1 ligands PD-L1 and PD-L2 in TAFs.Conclusions: This study reveals a novel mechanism of immune suppression sensitive to BRAF(V600E) inhibition, and indicates that clinical blockade of IL-1 may benefit patients with BRAF wild-type tumors and potentially synergize with immunotherapeutic interventions. Clin Cancer Res; 18(19); 5329–40. ©2012 AACR.

PDF file - 24K, Pmel-1 T cells in the peripheral blood of tumor-bearing mice

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PDF file, 303K, IL-1α production is reduced by BRAF knockdown shRNA expression in melanoma cells. IL-1α staining in WM793 melanoma cells transduced with scrambled shRNA vector, BRAF targeting shRNA vectors, or untranduced as indicated. Expression of shRNA is indicated by coexpression of RFP (x-axis) and is induced by treatment with 2 ug/mL Doxycycline (DOX) (Lower). Cells were treated with DOX for one week prior to flow analysis by intracellular staining for IL-1α.

PDF file - 68K, CD8+CD27+CD57- and CD8+CD27+CD57+ subsets in bulk TIL could further differentiate into CD27-CD57- and CD27-CD57+ subsets, respectively, and up-regulate perforin expression upon TCR stimulation, which were both inhibited by the addition of TGF-b1.

Purpose: To evaluate the effects of BRAF inhibition on the tumor microenvironment in patients with metastatic melanoma.Experimental Design: Thirty-five biopsies were collected from 16 patients with metastatic melanoma pretreatment (day 0) and at 10 to 14 days after initiation of treatment with either BRAF inhibitor alone (vemurafenib) or BRAF + MEK inhibition (dabrafenib + trametinib) and were also taken at time of progression. Biopsies were analyzed for melanoma antigens, T-cell markers, and immunomodulatory cytokines.Results: Treatment with either BRAF inhibitor alone or BRAF + MEK inhibitor was associated with an increased expression of melanoma antigens and an increase in CD8+ T-cell infiltrate. This was also associated with a decrease in immunosuppressive cytokines [interleukin (IL)-6 and IL-8] and an increase in markers of T-cell cytotoxicity. Interestingly, expression of exhaustion markers TIM-3 and PD1 and the immunosuppressive ligand PDL1 was increased on treatment. A decrease in melanoma antigen expression and CD8 T-cell infiltrate was noted at time of progression on BRAF inhibitor alone and was reversed with combined BRAF and MEK inhibition.Conclusions: Together, these data suggest that treatment with BRAF inhibition enhances melanoma antigen expression and facilitates T-cell cytotoxicity and a more favorable tumor microenvironment, providing support for potential synergy of BRAF-targeted therapy and immunotherapy. Interestingly, markers of T-cell exhaustion and the immunosuppressive ligand PDL1 are also increased with BRAF inhibition, further implying that immune checkpoint blockade may be critical in augmenting responses to BRAF-targeted therapy in patients with melanoma. Clin Cancer Res; 19(5); 1225–31. ©2013 AACR.

PDF file - 26K, Chromium release assay

PDF file - 491K, Administration of PLX4720 in vivo increases tumor infiltration of adoptively transferred T cells

Purpose: Treatment of melanoma patients with selective BRAF inhibitors results in objective clinical responses in the majority of patients with BRAF-mutant tumors. However, resistance to these inhibitors develops within a few months. In this study, we test the hypothesis that BRAF inhibition in combination with adoptive T-cell transfer (ACT) will be more effective at inducing long-term clinical regressions of BRAF-mutant tumors.Experimental Design:BRAF-mutated human melanoma tumor cell lines transduced to express gp100 and H-2Db to allow recognition by gp100-specific pmel-1 T cells were used as xenograft models to assess melanocyte differentiation antigen–independent enhancement of immune responses by BRAF inhibitor PLX4720. Luciferase-expressing pmel-1 T cells were generated to monitor T-cell migration in vivo. The expression of VEGF was determined by ELISA, protein array, and immunohistochemistry. Importantly, VEGF expression after BRAF inhibition was tested in a set of patient samples.Results: We found that administration of PLX4720 significantly increased tumor infiltration of adoptively transferred T cells in vivo and enhanced the antitumor activity of ACT. This increased T-cell infiltration was primarily mediated by the ability of PLX4720 to inhibit melanoma tumor cell production of VEGF by reducing the binding of c-myc to the VEGF promoter. Furthermore, analysis of human melanoma patient tumor biopsies before and during BRAF inhibitor treatment showed downregulation of VEGF consistent with the preclinical murine model.Conclusion: These findings provide a strong rationale to evaluate the potential clinical application of combining BRAF inhibition with T-cell–based immunotherapy for the treatment of patients with melanoma. Clin Cancer Res; 19(2); 393–403. ©2012 AACR.

PDF file - 52K, PLX4720 exposure reduces binding of c-myc to the VEGF promoter in BRAF mutant melanoma cells

PDF file - 74K, PD-1 expression is enriched in the CD8+CD27+CD57+ TIL subset freshly isolated from melanoma metastases (n=10).

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A list of all 384 ORFs in the library

PDF file - 30K, Inhibition of BRAFV600E increases expression of MDAs in tumors of patients with metastatic melanoma.

PDF file - 112K, Inhibition of BRAFV600E increases expression of MART-1 in tumors of patients with metastatic melanoma.

Purpose: Tumor‐specific T cells are frequently induced naturally in melanoma patients and infiltrate tumors. It is enigmatic why these patients fail to experience tumor regression. Given that CD8+ T cells mediate antigen‐specific killing of tumor cells, the focus of this study was to identify alterations in the differentiation of CD8+ residing at the tumor site, with emphasis on a population expressing CD57, a marker for terminal differentiation.Experimental Design: We conducted flow cytometric analysis of CD8+ tumor‐infiltrating lymphocytes (TIL) isolated from 44 resected melanoma metastases with known T‐cell differentiation markers. For comparison, peripheral blood mononuclear cells were isolated from matched melanoma patients. We sorted different CD8+ subsets found in TIL and determined their effector functions. In addition, we carried out Vβ clonotype expression analysis of T‐cell receptors to determine lineage relationship between the CD8+ TIL subsets.Results: The majority of CD8+ TIL was in the early-effector memory stage of differentiation. A significant population consisted of an oligoclonal subset of cells coexpressing CD27, CD28, CD57, and Granzyme B, with little or no perforin. These cells could be induced to proliferate, produce a high level of IFN-γ, and differentiate into CD27−CD57+, perforinhigh mature CTL in vitro. Addition of TGF‐β1 prevented further differentiation.Conclusions: Our studies identified a novel subset of incompletely differentiated CD8+ CTL coexpressing early effector memory and late CTL markers. This population resembles that found in patients with uncontrolled chronic viral infections. TGF-β1, frequently produced by melanoma tumors, may be a key cytokine inhibiting further maturation of this subset. Clin Cancer Res; 18(9); 2465–77. ©2012 AACR.