Genetic and Genomic Characterization of 462 Melanoma Patient-Derived Xenografts, Tumor Biopsies, and Cell Lines

Tumor-sequencing studies have revealed the widespread genetic diversity of melanoma. Sequencing of 108 genes previously implicated in melanomagenesis was performed on 462 patient-derived xenografts (PDXs), cell lines, and tumors to identify mutational and copy number aberrations. Samples came from 371 unique individuals: 263 were naive to treatment, and 108 were previously treated with targeted therapy (34), immunotherapy (54), or both (20). Models of all previously reported major melanoma subtypes (BRAF, NRAS, NF1, KIT, and WT/WT/WT) were identified. Multiple minor melanoma subtypes were also recapitulated, including melanomas with multiple activating mutations in the MAPK-signaling pathway and chromatin-remodeling gene mutations. These well-characterized melanoma PDXs and cell lines can be used not only as reagents for a large array of biological studies but also as pre-clinical models to facilitate drug development.

Abstract A01: A comprehensive collection of patient derived xenografts of human melanoma with clinical, genomic, and biological characterization

Advanced melanoma has seen dramatic changes in standard of care in the last years and many novel targeted small molecules and immune checkpoint inhibitors are in development. More than 200 clinical trials are currently ongoing for metastatic melanoma. Thus, accurate pre-clinical models to predict clinical responses are urgently needed. We have established a large bank of live tumor tissue (n=500) with more than 300 models expanded as PDX. Melanoma tumor tissue is uniquely suited to establish patient-derived xenograft (PDX) models, since only one tumor cell can initiate tumor growth. Thus, our success rate is at 90% using NSG mice and matrigel for s.c. implantation of minced tissue chunks. We have opted for such a large number of models due to the genomic and clinical heterogeneity of melanoma based on available TCGA data. Although almost half of all melanomas harbor BRAF V600 hotspot mutations, followed in frequency by NRAS and NF1 mutations, many driver mutations are only found in a small subset and many mutations are occurring concurrently in various confirmations. We used a custom targeted capture of 108 genes previously implicated in melanoma, and performed massively parallel sequencing on currently 200 PDX. Samples were then clustered into groups based on deleterious mutations which were detected in all but a very small subset of samples. The biological relevance of these multiple genomic subsets was then tested against latency, growth rate, and spontaneous metastasis in PDX. Further, clinical information such as age, gender, history, and response to therapies provided additional parameters to classify this collection into meaningful subgroups. In conclusion, this collection of melanoma PDX recapitulates the breadth of advanced melanoma in the clinic and therefore a comprehensive resource for precision medicine testing in an increasingly scattered therapy landscape.

Citation Format: Clemens Krepler, Katrin Sproesser, Marilda Beqiri, Min Xiao, Patricia Brafford, Wei Xu, Bradley Garman, Jennifer Wargo, Michael A. Davies, Dennie T. Frederick, Keith T. Flaherty, David Hoon, Joseph J. Bennett, Michael Guarino, Nicholas J. Petrelli, David Elder, Xiaowei Xu, Giorgos Karakousis, KATHERINE L. NATHANSON, Lynn Schuchter, Meenhard Herlyn. A comprehensive collection of patient derived xenografts of human melanoma with clinical, genomic, and biological characterization. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr A01.

Abstract 4668: Targeted, massively parallel sequencing identifies novel genetic subsets of cutaneous melanoma

Despite the prevalence of recurrent, high activating BRAF V600 mutations in 45% of tumors, cutaneous melanoma (CM) is a heterogeneous malignancy resulting from aberrant signaling in multiple pathways. It has been traditionally characterized by activation of the MAPK and PI3K signaling pathways, as well as cell cycle disruption. In recent years, whole-genome and exome sequencing studies have identified several new genes associated with melanomagenesis. However, a comprehensive understanding of concurrent, and mutually exclusive, mutations in tumors is currently lacking. Using a custom targeted capture of 108 genes previously implicated in melanoma pathogenesis, massively parallel sequencing was performed on 94 human melanoma cell lines, 67 patient-derived xenografts (PDX), and 5 cell lines made from PDX, all untreated. Samples were then clustered into groups based on deleterious mutations. 83% of samples had deleterious mutations in the MAPK signaling pathway, including 92 high activity BRAF (55%), 35 RAS codon 61 (21%), 7 with multiple mutations (e.g. low activity BRAF/RAS codons 12/13) (4%) and 10 NF1 (6%) mutated samples. Likely deleterious NF1 mutations were found in several BRAF or NRAS-mutated samples. PI3K pathway mutations were found in 10% of samples, predominantly associated with BRAF mutations. TP53 mutations were found in 24% of samples and were associated with all MAPK signaling mutations. Mutations in chromatin remodeling genes (ARID1A/1B, ARID2, TRRAP, and BAP1) were mutually exclusive with each other and primarily found in tumors with high activity BRAF or NRAS mutations. The majority of BRAF or RAS-mutated samples with a mutation in a chromatin remodeling gene lacked mutations in cell cycle, TP53, and PI3K signaling genes; however, 100% of deleterious, or likely deleterious, NF1-mutated samples with a chromatin remodeling gene mutation harbored additional mutations in cell cycle, TP53, and/or PI3K signaling genes. Of particular interest, five of the 10 NF1-mutated samples (50%) lacked BRAF, RAS, and MEK1/2 mutations but harbored likely deleterious mutations in MAP3K5 or MAP3K9, suggesting the potential involvement of the JNK signal transduction pathway in this particular cohort. Only 4% of samples did not have a deleterious mutation in any of the genes on the panel. These data reveal novel insights into the genetics of melanomas lacking a canonical BRAF V600 mutation. Functional assays are needed to confirm the biological relevance of likely deleterious mutations, which will further facilitate a more thorough classification of CM subsets.

Citation Format: Bradley Garman, Clemens Krepler, Katrin Sproesser, Patrica Brafford, Melissa Wilson, Bradley Wubbenhorst, Ravi Amaravadi, Joseph Bennett, Marilda Beqiri, Michael Davies, David Elder, Keith Flaherty, Dennie Frederick, Tara C. Gangadhar, Michael Guarino, David Hoon, Giorgos Karakousis, Nandita Mitra, Nicholas J. Petrelli, Lynn Schuchter, Batool Shannan, Jennifer Wargo, Min Xiao, Wei Xu, Xaiowei Xu, Meenhard Herlyn, Katherine Nathanson. Targeted, massively parallel sequencing identifies novel genetic subsets of cutaneous melanoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4668. doi:10.1158/1538-7445.AM2015-4668

Transcriptional repression of IFNβ1 by ATF2 confers melanoma resistance to therapy

The resistance of melanoma to current treatment modalities represents a major obstacle for durable therapeutic response, and thus, the elucidation of mechanisms of resistance is urgently needed. The crucial functions of Activating Transcription Factor-2 (ATF2) in the development and therapeutic resistance of melanoma have been previously reported, although the precise underlying mechanisms remain unclear. Here, we report a protein kinase C epsilon (PKCε)- and Activating Transcription Factor-2 (ATF2)-mediated mechanism that facilitates resistance by transcriptionally repressing the expression of IFNβ1 and downstream type-I IFN signaling, which is otherwise induced upon exposure to chemotherapy. Treatment of early stage melanomas expressing low levels of PKCε with chemotherapies relieves its transcriptional repression of IFNB1, resulting in impaired S-phase progression, a senescence-like phenotype, and increased cell death. This response is lost in late stage metastatic melanomas expressing high levels of PKCε. Notably, nuclear ATF2 and low expression of IFNβ1 in melanoma tumor samples correlates with poor patient responsiveness to biochemotherapy or neoadjuvant IFN-α2a. Conversely, cytosolic ATF2 and induction of IFNβ1 coincides with therapeutic responsiveness. Collectively, we identify an IFNβ1-dependent, cell autonomous mechanism that contributes to the therapeutic resistance of melanoma via the PKCε-ATF2 regulatory axis.

Protective immunization against melanoma by gp100 DNA-HVJ-liposome vaccine

DNA-based vaccine immunization effectively induces both humoral and cell-mediated immunity to antigens and can confer protection against numerous infectious diseases as well as some cancers. Human and mouse melanomas consistently express the tumor-associated antigen interacted with the melanogenesis pathway. Gp100 is immunogenic and has been shown to induce both antibody and cytotoxic T cell (CTL) responses in humans. To explore the potential use of DNA immunization to induce melanoma-specific immune responses, we assessed HVJ-AVE liposome incorporated with plasmid DNA encoding human gp100. The gp100 DNA vaccine was used in a mouse melanoma model to assess immunity against the B16 melanoma of C57BL/6 mice. Intramuscular injection of the DNA-HVJ-AVE liposomes induced both anti-gp100 antibody and CTL responses. Gp100 DNA-HVJ-AVE liposome immunization significantly delayed tumor development in mice challenged with B16 melanoma cells. Mice immunized with gp100 DNA-HVJ-AVE liposomes survived longer compared with control mice immunized with HVJ-AVE liposome alone. These results indicate that immunization with human gp100 DNA by HVJ-AVE liposomes can induce protective immunity against melanoma in this pre-clinical mouse model. This strategy may provide an effective approach for vaccine therapy with tumor-associated antigens against human melanoma.

Modulation of histamine type II receptors on CD8+ T cells by interleukin-2 and cimetidine

CD8+ T cells are known to play a major role in regulating immune functions under normal and disease conditions. In this study a radioligand binding assay was used to quantitate histamine type II (H2) receptors on activated T cells. The objective was to examine the expression of H2 receptors on T cells during activation with interleukin-2 (IL-2) and treatment with cimetidine. Activated suppressor T cells induced by concanavalin A+IL-2 showed a significant (p less than 0.01) increase in H2 receptors compared to the control nonactivated T cells. The T cells expressing the H2 receptors were identified as CD8+ cells; those among them that had an enhanced level of H2 receptors were identified as CD25+. Treatment of activated suppressor cells with the H2 receptor antagonist cimetidine at a concentration of 10(-5) M significantly reduced the number of H2 receptors. Suppressor cells induced by Con A+IL-2 were able to suppress both IgG and IgM production that was reversible with cimetidine. Incubation of lymphocytes with 50 U/ml IL-2 alone in 3-day culture significantly (p less than 0.005) enhanced H2 receptor expression. These studies demonstrate that activated suppressor T cells that are CD8+CD25+ have enhanced levels of H2 receptors and can be modulated by cimetidine.

A 6-thioguanine-resistant variant of the 13762 cell line which is no longer tumorigenic or metastatic

A 6-thioguanine resistant (TGR) variant of the highly tumorigenic and metastatic mammary adenocarcinoma cell line 13762 was obtained. This variant was no longer tumorigenic or metastatic in normal syngeneic rats but did grow as a primary tumor in irradiated animals. Our results suggest that the TGR cell line was rejected by an irradiation-sensitive immunological mechanism. Although the TGR cells produced primary tumors in irradiated animals, there was no evidence of the extensive metastasis seen with the 13762 cells. This apparent inability to metastasize was confirmed by injecting the TGR cells intravenously. Whereas the 13762 cells produced large numbers of metastatic lung foci, there was no evidence of lung metastasis with the TGR cells, even in irradiated animals. Revertant cells for the 6-thioguanine-resistant phenotype were still non-tumorigenic and non-metastatic in normal rats, suggesting that 6-thioguanine resistance is not associated with the altered tumorigenic phenotype. From the TGR variant, cell lines were selected with an increased ability to produce tumors in normal rats. Although some of these revertants were capable of producing limited lung metastases in normal animals, extensive metastases were always seen when the cells were injected into irradiated animals. Differences between the 13762 and the TGR variants were also found in their ability to produce plasminogen activator. The TGR cells released far less plasminogen activator in culture than the 13762 cells. This could be a contributing factor in their different metastatic potentials.