NUMB as a Therapeutic Target for Melanoma

The upregulation of the adaptor protein NUMB triggers melanocytic differentiation from multipotent skin stem cells, which share many properties with aggressive melanoma cells. Although NUMB acts as a tumor suppressor in various human cancer types, little is known about its role in melanoma. In this study, we investigated the role of NUMB in melanoma progression and its regulatory mechanism. Analysis of The Cancer Genome Atlas melanoma datasets revealed that high NUMB expression in melanoma tissues correlates with improved patient survival. Moreover, NUMB expression is downregulated in metastatic melanoma cells. NUMB knockdown significantly increased the invasion potential of melanoma cells in a three-dimensional collagen matrix in vitro and in the lungs of a mouse model in vivo; it also significantly upregulated the expression of the NOTCH target gene CCNE. Previous studies suggested that Wnt signaling increases NUMB expression. By mimicking Wnt stimulation through glycogen synthase kinase-3 inhibition, we increased NUMB expression in melanoma cells. Furthermore, a glycogen synthase kinase-3 inhibitor reduced the invasion of melanoma cells in a NUMB-dependent manner. Together, our results suggest that NUMB suppresses invasion and metastasis in melanoma, potentially through its regulation of the NOTCH‒CCNE axis and that the inhibitors that upregulate NUMB can exert therapeutic effects in melanoma.

Neural Crest-Like Stem Cell Transcriptome Analysis Identifies LPAR1 in Melanoma Progression and Therapy Resistance

Metastatic melanoma is challenging to clinically address. Although standard-of-care targeted therapy has high response rates in patients with BRAF-mutant melanoma, therapy relapse occurs in most cases. Intrinsically resistant melanoma cells drive therapy resistance and display molecular and biologic properties akin to neural crest-like stem cells (NCLSC) including high invasiveness, plasticity, and self-renewal capacity. The shared transcriptional programs and vulnerabilities between NCLSCs and cancer cells remains poorly understood. Here, we identify a developmental LPAR1-axis critical for NCLSC viability and melanoma cell survival. LPAR1 activity increased during progression and following acquisition of therapeutic resistance. Notably, genetic inhibition of LPAR1 potentiated BRAFi ± MEKi efficacy and ablated melanoma migration and invasion. Our data define LPAR1 as a new therapeutic target in melanoma and highlights the promise of dissecting stem cell-like pathways hijacked by tumor cells. SIGNIFICANCE: This study identifies an LPAR1-axis critical for melanoma invasion and intrinsic/acquired therapy resistance.

Tumor-infiltrating mast cells are associated with resistance to anti-PD-1 therapy

Anti-PD-1 therapy is used as a front-line treatment for many cancers, but mechanistic insight into this therapy resistance is still lacking. Here we generate a humanized (Hu)-mouse melanoma model by injecting fetal liver-derived CD34⁺ cells and implanting autologous thymus in immune-deficient NOD-scid IL2Rγ^null (NSG) mice. Reconstituted Hu-mice are challenged with HLA-matched melanomas and treated with anti-PD-1, which results in restricted tumor growth but not complete regression. Tumor RNA-seq, multiplexed imaging and immunohistology staining show high expression of chemokines, as well as recruitment of FOXP3⁺ Treg and mast cells, in selective tumor regions. Reduced HLA-class I expression and CD8⁺/Granz B⁺ T cells homeostasis are observed in tumor regions where FOXP3⁺ Treg and mast cells co-localize, with such features associated with resistance to anti-PD-1 treatment. Combining anti-PD-1 with sunitinib or imatinib results in the depletion of mast cells and complete regression of tumors. Our results thus implicate mast cell depletion for improving the efficacy of anti-PD-1 therapy.

Immune checkpoint therapies (ICT) are promising for treating various cancers, but response rates vary. Here the authors show, in mouse models, that tumor-infiltrating mast cells colocalize with regulatory T cells, coincide with local reduction of MHC-I and CD8 T cells, and is associated with resistance to ICT, which can be reversed by c-kit inhibitor treatment.

Abstract 5651: JNJ-61186372, an Fc enhanced EGFR/cMet bispecific antibody, mediates EGFR and cMet downmodulation and therapeutic efficacy preclinically through monocyte / macrophage mediated trogocytosis

Small molecule inhibitors targeting EGFR are now standard of care in NSCLC patients harboring EGFR mutations, but acquired resistance invariably develops through secondary mutations within EGFR and/or through activation of compensatory pathways such as cMet. JNJ-61186372 (JNJ-372) is an anti-EGFR and cMet bispecific antibody with enhanced binding to immune cell Fcγ receptors, designed to target tumors with activated EGFR and cMet signaling through a distinct mechanism of action. Ongoing first-in-human study in patients with advanced, treatment refractory EGFR mutant NSCLC revealed JNJ-372 to have clinical activity in patients with diverse EGFR-mutated NSCLC, including Exon 20 mutations, TKI resistance mutations (T790M, C797S), and resistance due to MET amplification.

However preclinically, despite potent anti-tumor activity in NSCLC xenograft models, only modest anti-proliferative effects were observed with JNJ-372 in cell lines in vitro. Interestingly, the addition of isolated human immune cells (PBMCs) to the in vitro assays enhanced JNJ-372-mediated EGFR and cMet downregulation, and dose-dependent tumor cell killing. Through depletion or enrichment of individual immune cell types, we demonstrated that monocytes and/or macrophages are necessary for JNJ-372 Fc interaction-mediated EGFR/cMet downmodulation. Depletion of macrophages in mice showed that they are required for JNJ-372 anti-tumor efficacy. Finally, we showed that the down-modulation of EGFR and cMet receptors occurs through monocyte or macrophage-mediated trogocytosis. Collectively, these results demonstrate a novel Fc-dependent mechanism of action for JNJ-372 and support its continued clinical development in patients with aberrant EGFR and cMet signaling.

Citation Format: Smruthi Vijayaraghavan, Lorraine Lipfert, Barbara Bushey, Kristen Chevalier, Benjamin Henley, Ryan Lenhart, Marilda Beqiri, Hillary J. Millar, Kathryn Packman, Matthew V. Lorenzi, Sylvie Laquerre, Sheri Moores. JNJ-61186372, an Fc enhanced EGFR/cMet bispecific antibody, mediates EGFR and cMet downmodulation and therapeutic efficacy preclinically through monocyte / macrophage mediated trogocytosis [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5651.

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.

Tumor-associated B-cells induce tumor heterogeneity and therapy resistance

In melanoma, therapies with inhibitors to oncogenic BRAFV600E are highly effective but responses are often short-lived due to the emergence of drug-resistant tumor subpopulations. We describe here a mechanism of acquired drug resistance through the tumor microenvironment, which is mediated by human tumor-associated B cells. Human melanoma cells constitutively produce the growth factor FGF-2, which activates tumor-infiltrating B cells to produce the growth factor IGF-1. B-cell-derived IGF-1 is critical for resistance of melanomas to BRAF and MEK inhibitors due to emergence of heterogeneous subpopulations and activation of FGFR-3. Consistently, resistance of melanomas to BRAF and/or MEK inhibitors is associated with increased CD20 and IGF-1 transcript levels in tumors and IGF-1 expression in tumor-associated B cells. Furthermore, first clinical data from a pilot trial in therapy-resistant metastatic melanoma patients show anti-tumor activity through B-cell depletion by anti-CD20 antibody. Our findings establish a mechanism of acquired therapy resistance through tumor-associated B cells with important clinical implications.Resistance to BRAFV600E inhibitors often occurs in melanoma patients. Here, the authors describe a potential mechanism of acquired drug resistance mediated by tumor-associated B cells-derived IGF-1.

Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance

Therapies targeting signaling molecules mutated in cancers can often have striking short-term effects, but the emergence of resistant cancer cells is a major barrier to full cures^1,2. Resistance can result from a secondary mutations^3,4, but other times there is no clear genetic cause, raising the possibility of non-genetic rare cell variability^5–11. Here, we show that melanoma cells can display profound transcriptional variability at the single cell level that predicts which cells will ultimately resist drug treatment. This variability involves infrequent, semi-coordinated transcription of a number of resistance markers at high levels in a very small percentage of cells. The addition of drug then induces epigenetic reprogramming in these cells, converting the transient transcriptional state to a stably resistant state. This reprogramming begins with a loss of SOX10-mediated differentiation followed by activation of new signaling pathways, partially mediated by activity of Jun-AP-1 and TEAD. Our work reveals the multistage nature of the acquisition of drug resistance and provides a framework for understanding resistance dynamics in single cells. We find that other cell types also exhibit sporadic expression of many of these same marker genes, suggesting the existence of a general rare-cell expression program.

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 A02: A novel orthotopic ovarian patient derived xenograft model platform to investigate novel therapies for BRCA deficient ovarian cancers

Introduction: To create a personalized, targeted approach to high grade serous ovarian cancers (HGSOC), reliable preclinical models are essential. About ~50% of HGSOC have defects in genes involved in homologous recombination (HR) such as BRCA. PARP inhibitors (PARPi) capitalize on synthetic lethality in HR-deficient tumors, however, clinical efficacy is limited (response rate only ~40%). Patient derived xenografts (PDXs) are emerging as a reliable preclinical model that recapitulates principal characteristics of the patients' tumor while remaining biologically stable while passaged in mice. We developed a BRCA1/2 orthotopic PDX experimental platform to study alternative strategies for synthetic lethality. We hypothesized that targeting the ATR/CHK1 axis is synthetically lethal in BRCA mutant HGSOC models.

Experimental Procedures: Fresh HGSOC tumor was transplanted orthotopically to the fallopian tube/ovary of NSG 5-8 wk mice. Tumor growth was followed. Tumors were evaluated by IHC, genomic and proteomic analysis. Alu II probe staining was used to evaluate human stroma content. DNA sequencing was performed using a 153 OVCA gene panel. Reverse Phase Protein Array Analysis (RPPA) was evaluated for signaling pathway activation. Primary ovarian tumor cultures were developed from patients' tumor for mechanistic studies. To study the ATR/CHK1 axis in HR-deficient HGSOC, PARPi (Olaparib), CHK1 inhibitor (CHK1i, MK8776), and ATR inhibitor (ATRi, AZD6738) were evaluated. PEO1 (BRCA2 mutant), PEO4 (BRCA wildtype) and JHOS4 (BRCA1 mutant) HGSOC cells were evaluated for cell proliferation, survival, and genome stability before and after treatment. BRCA2 mutant (8945delAA) PDX (WO-2-1) was expanded in 70 mice. Mice were randomized into 5 gps: untreated, carboplatin, PARPi, CHK1i, and ATRi. Treatment was initiated when tumors were 70-100mm3 and volume was assessed weekly with ultrasound. PARP tumor activity and response to PARPi was assessed with a PET PARP1 radiotracer [18F]FTT (fluorthanatrace).

Results: We developed a pipeline to study HR deficient HGSOC. We created an orthotopic PDX platform from 15 BRCA mutant patients in order to accurately study OVCA tumorigenicity and metastasis in the native environment with a 90% take rate in generating tumors in mouse passage 1 (MP1), and 100% take rate for MP2 and MP3. The PDX model (WO-2-1) was similarly platinum sensitive as the patient after platinum treatment. Tumors were evaluated by genomic and proteomic analysis to identify a target population and streamline therapeutic approaches. Pathogenic mutation profiles from the original patient tumor were preserved in PDXs serially passaged (MP1-3). High pCHK1 (s345) was used as a marker for investigation of ATR/CHK1 inhibition in BRCA mutant PDX models. We showed that ATRi and CHK1i are similarly effective to PARPi in a BRCA2 mutant PDX. A novel PET PARP1 radiotracer [18F]FTT was used and demonstrated co-localization of signal in a BRCA2 mutant PDX, which was diminished with olaparib treatment.

Conclusions: Although technically more challenging, the orthotopic transplantation technique is feasible in generating HGSOC PDX models with a high success rate that more closely resembles the natural environment for HGSOC progression. Evaluation of genomic and proteomic profiles of a tumor allows one to streamline targeted therapies for testing in PDX preclinical trials that may in the future be translated back to the patient.

Citation Format: Erin George, Hyoung Kim, Janos Tanyi, Ryan Ragland, Eric Brown, Rugang Zhang, Patricia Brafford, Katrin Sproesser, Marilda Beqiri, Adina Vultur, Clemens Krepler, Brandon Weis, Kate Nathanson, Yuling Lu, Gordon Mills, Mehran Makvandi, Robert Mach, Mark Morgan, Fiona Simpkins. A novel orthotopic ovarian patient derived xenograft model platform to investigate novel therapies for BRCA deficient ovarian cancers. [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 A02.

Abstract PR02: Humanized mouse melanoma model using patient-derived xenografts

Melanoma patients develop resistance to both chemo- and targeted-therapy drugs. Promising pre-clinical and clinical results with immune checkpoint inhibitors using antibodies directed against CTLA4 and PD1 have re-energized the field of immune-based therapies in melanoma. However, similar to chemo- or targeted-therapies only subsets of melanoma patients respond to immune checkpoint blockade. Currently available immunodeficient mouse xenograft and transgenic mouse melanoma models have a number of short comings and are unable to address the basis of drug resistance and immune non-responsiveness frequently observed in melanoma patients treated either with chemo- and targeted-therapy drugs or immune checkpoint inhibitors. Thus there is an urgent need to establish a mouse model with an immune microenvironment that can address the above issues encountered in melanoma patients. For this, our laboratory has developed a humanized mouse melanoma model using patient-derived xenograft (PDX). Immunodeficient (NOD/Shi-SCID/IL-2Rgnull [NOG; Taconic]/ NOD.Cg-Prkdcscid IL2rgtm1Wjl/SzJ [NSG; Jackson Laboratory]) mice were reconstituted with human CD34+ cells and after 12 weeks, mature human CD45+ cells are observed in mouse peripheral blood and in the lymphoid organs. Humanized mice with optimum number of mature human CD45+ cells in peripheral blood were challenged with HLA-matched melanoma PDX and the immune response to melanoma associated antigens were monitored. Lymphoid cells derived from humanized mice that are challenged with human leukocyte antigen (HLA) matched melanoma cells in vivo showed enhanced cytokine expression to in vitro stimulation with peptides derived from melanoma antigens. In addition, cytotoxic T-cells were able to functionally lyse tumor cells in vitro, infiltrate and restrict in vivo tumor growth. We are currently refining our model to establish an autologous mouse melanoma model. Our innovative humanized mouse melanoma model will enable one to understand the causes of therapy resistance and immune non-responsiveness in patients.

This abstract is also being presented as Poster B33.

Citation Format: Clemens Krepler, Michela Perego, Mizuho Kalabis, Marilda Beqiri, Denitsa Hristova, Min Xiao, Nicholas J. Petrelli, Rajasekharan Somasundaram, Meenhard Herlyn. Humanized mouse melanoma model using patient-derived xenografts. [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 PR02.

Abstract B46: Use of a novel orthotopic ovarian cancer transplant patient derived xenograft model as a preclinical platform for bench to bedside research

Introduction: Treatment for cancer is moving from a “one size fits all” to a personalized and targeted approach addressing the unique biology of each patients' tumor. Preclinical research in ovarian cancer (OVCA) has relied on established cell lines that have recently been shown to have marked differences in molecular profiles when compared to ovarian tumors from the TCGA. Patient derived xenografts (PDXs) are emerging as a reliable preclinical model that can recapitulate the principal characteristics of the patients' original tumor while remaining biologically stable while passaged in mice. We developed an orthotopic model that involves transplanting tumor directly to the fallopian tube/ovary in order to accurately study ovarian cancer tumorigenicity and metastasis in the native environment.

Experimental Procedures: Fresh OVCA tumor was transplanted orthotopically to the fallopian tube/ovary of NSG 5-8 week female mice. Tumor growth was followed over time with ultrasound. Tumors were evaluated by IHC, genomic and proteomic analysis. Alu II probe staining was performed to evaluate human stroma content. DNA sequencing analysis was performed using a 153 ovarian cancer gene panel, which includes all genes relevant to OVCA, including homologous recombination and all actionable genes. Reverse Phase Protein Array Analysis (RPPA) was used to evaluate signaling pathway activation. Several primary ovarian tumor cultures were also developed from the patients' tumor for mechanistic studies.

Results: To date, we have transplanted tumor from 18 primary, 4 interval, and 6 recurrent ovarian debulking surgeries using an orthotopic ovarian tumor transplant approach with an 90% success rate in generating tumors in mouse passage 1 (MP1) and 100% in generating MP2 and MP3. The mean time for tumors to reach ~1 cm (first passage in mice) was 8 weeks and ~6 weeks when tumors were then passaged again (MP2/MP3). We have generated 12 BRCA1/2 deleterious mutation positive carrier PDXs. Alu staining of PDXs demonstrated human cells in the stroma. We have generated several primary tumor cell lines from the original tumors/PDXs. These primary cells express ovarian epithelial markers CK7, and PAX8. Targeted DNA sequencing analysis showed that P53 and BRCA1/2 pathogenic mutations were highly conserved from the patient tumor, to the PDXs (MP1-3) and primary tumor cell lines. We evaluated 280 phospho/total proteins in our tumor samples by RPPA. Unsupervised cluster analysis of 24 patient tumors and correlating PDX (MP1-3) and 6 cell lines showed that several parent tumors clustered together with their MP1-3 PDXs. WO-2-1 BRCA 2 mutant PDXs were sensitive to platinum treatment demonstrating a response similar to that noted in the original patient after platinum chemotherapy.

Conclusions: Although technically more challenging the orthotopic transplantation technique is feasible in generating ovarian cancer PDX models that more closely resemble the natural environment for ovarian cancer tumor growth and metastasis. PDXs maintain consistent gene alterations and signaling pathway activation to the original patient tumor. Given PDXs maintain the characteristics of the patients' original tumor, they are excellent models to study therapeutic response.

Citation Format: Erin George, Hyoung Kim, Clemens Krepler, Janos Tanyi, Zhi Wei, Katrin Sproesser, Patricia Brafford, Marilda Beqiri, Adina-Monica Vultur, Rachel Lee, Mark Morgan, Ronny Drapkin, Tan Ince, Meenhard Herlyn, Fiona Simpkins. Use of a novel orthotopic ovarian cancer transplant patient derived xenograft model as a preclinical platform for bench to bedside research. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr B46.

Personalized Preclinical Trials in BRAF Inhibitor-Resistant Patient-Derived Xenograft Models Identify Second-Line Combination Therapies

PURPOSE

To test second-line personalized medicine combination therapies, based on genomic and proteomic data, in patient-derived xenograft (PDX) models.

EXPERIMENTAL DESIGN

We established 12 PDXs from BRAF inhibitor-progressed melanoma patients. Following expansion, PDXs were analyzed using targeted sequencing and reverse-phase protein arrays. By using multi-arm preclinical trial designs, we identified efficacious precision medicine approaches.

RESULTS

We identified alterations previously described as drivers of resistance: NRAS mutations in 3 PDXs, MAP2K1 (MEK1) mutations in 2, BRAF amplification in 4, and aberrant PTEN in 7. At the protein level, re-activation of phospho-MAPK predominated, with parallel activation of PI3K in a subset. Second-line efficacy of the pan-PI3K inhibitor BKM120 with either BRAF (encorafenib)/MEK (binimetinib) inhibitor combination or the ERK inhibitor VX-11e was confirmed in vivo Amplification of MET was observed in 3 PDX models, a higher frequency than expected and a possible novel mechanism of resistance. Importantly, MET amplification alone did not predict sensitivity to the MET inhibitor capmatinib. In contrast, capmatinib as single agent resulted in significant but transient tumor regression in a PDX with resistance to BRAF/MEK combination therapy and high pMET. The triple combination capmatinib/encorafenib/binimetinib resulted in complete and sustained tumor regression in all animals.

CONCLUSIONS

Genomic and proteomic data integration identifies dual-core pathway inhibition as well as MET as combinatorial targets. These studies provide evidence for biomarker development to appropriately select personalized therapies of patients and avoid treatment failures. See related commentary by Hartsough and Aplin, p. 1550.

Abstract 2842: Personalized pre-clinical trials in BRAF inhibitor resistant patient derived xenograft models of melanoma identify c-Met as an effective second line combination therapy target

Melanoma has seen a remarkable improvement in the treatment of advanced disease. However, the majority of patients still relapse with the emergence of resistant disease. This is especially true for BRAF inhibitors, were multiple mechanisms of resistance have been uncovered. However, the lack of dependable models to develop approaches to overcome resistance, poses a real challenge for clinical decisions on second line therapies. In addition, combination therapies necessary to achieve long term responses increase the number of possibilities to be assessed. In this study, we developed patient derived xenograft (PDX) models from BRAF inhibitor resistant patients and, after characterization, tested rational second line combination therapies in co-clinical trials.Fresh tumor tissue from 12 patients after progression on vemurafenib or dabrafenib was implanted into immune deficient NSG mice. Once the tumor grafts were established, mice were continually dosed with PLX4720 to approximate clinical plasma levels to preserve the resistant phenotype. Xenografts were then characterized for genomic alterations and pathway activation status using a targeted sequencing array and a reverse phase protein array, respectively. We found at least 2 and up to 9 known deleterious alterations in all samples, many of which have been described as conferring resistance. The protein array clustered into two major groups: MAPK pathway activated and PI3K pathway activated, again consistent with previous reports. Integrating these data allowed us to design rational combination therapies for in vivo testing. We treated a PDX model with MET amplification and high phospho c-Met with the BRAF inhibitor LGX818 20mg/kg QD, the MEK inhibitor MEK162 3mg/kg QD, and the c-Met inhibitor INC280 25mg/kg QD (all p.o.). Although INC280 alone led to significant decrease in tumor growth, only the LGX818/ MEK162/ INC280 triple combination led to complete and sustained tumor regression in all mice. Further, we tested a second PDX model with a MET amplification (albeit broader and lower) but baseline pMET on the protein level. In this model, INC280 did not show any antitumor effect confirming the specificity for c-Met and the importance of validating genomic data.In summary, using our BRAF inhibitor resistant PDX model pipeline we were not only able to identify actionable alterations in all models, but also to test rational second line combination therapies in pre-clinical in vivo trials. Genomic data alone might not be sufficient to accurately predict therapy responses and protein arrays were a valuable tool to validate deleterious alteration calls. This study represents an important step towards improving personalized medicine in melanoma, and highlights the potential use of c-Met inhibitors in melanoma combination therapy in a defined subset of patients.

Citation Format: Clemens Krepler, Min Xiao, Katrin Sproesser, Patricia Brafford, Batool Shannan, Marilda Beqiri, Wei Xu, Bradley Garman, Katherine L. Nathanson, Xiaowei Xu, Giorgos Karakousis, Gordon B. Mills, Yiling Lu, Giordano Caponigro, Markus Boehm, Malte Peters, Lynn Schuchter, Meenhard Herlyn. Personalized pre-clinical trials in BRAF inhibitor resistant patient derived xenograft models of melanoma identify c-Met as an effective second line combination therapy target. [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 2842. doi:10.1158/1538-7445.AM2015-2842

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

miR-200c/Bmi1 axis and epithelial-mesenchymal transition contribute to acquired resistance to BRAF inhibitor treatment

Resistance to BRAF inhibitors (BRAFi) is one of the major challenges for targeted therapies for BRAF-mutant melanomas. However, little is known about the role of microRNAs in conferring BRAFi resistance. Herein, we demonstrate that miR-200c expression is significantly reduced whereas miR-200c target genes including Bmi1, Zeb2, Tubb3, ABCG5, and MDR1 are significantly increased in melanomas that acquired BRAFi resistance compared to pretreatment tumor biopsies. Similar changes were observed in BRAFi-resistant melanoma cell lines. Overexpression of miR-200c or knock-down of Bmi1 in resistant melanoma cells restores their sensitivities to BRAFi, leading to deactivation of the PI3K/AKT and MAPK signaling cascades, and acquisition of epithelial-mesenchymal transition-like phenotypes, including upregulation of E-cadherin, downregulation of N-cadherin, and ABCG5 and MDR1 expression. Conversely, knock-down of miR-200c or overexpression of Bmi1 in BRAFi-sensitive melanoma cells activates the PI3K/AKT and MAPK pathways, upregulates N-cadherin, ABCG5, and MDR1 expression, and downregulates E-cadherin expression, leading to BRAFi resistance. Together, our data identify miR-200c as a critical signaling node in BRAFi-resistant melanomas impacting the MAPK and PI3K/AKT pathways, suggesting miR-200c as a potential therapeutic target for overcoming acquired BRAFi resistance.

Abstract 1182: Patient derived xenograft (PDX) of human melanoma to predict clinical responses

The approval of three drugs targeting the MAPK pathway has led to new standard therapies for melanoma with BRAFV600E mutations. The excitement about these therapeutic successes is somewhat dampened by the relapse of most if not all treated patients due to the development of acquired (secondary) resistance. Early clinical trial results indicate that combining BRAF and MEK inhibitors can improve survival and delay the onset of resistance. Currently, there is a lack of good translational models to study resistance pathways found in patients. We have developed a patient-derived xenograft (PDX) bank for assessing patients' responses to therapies.

Human melanoma tissues were obtained following surgery, and small pieces were implanted subcutaneously with Matrigel® into NSG mice. This technique was advantageous over injecting single tumor cells. It also allows prior dissociation and freezing for extended time periods prior to injection. The xenografts maintained a histological architecture similar to the respective patients' lesions. NSG mice injected with tumor fragments and single cells allow a high rate of tumor growth of approximately 90%, even if few malignant cells from fine needle aspirates are injected. When injecting decreasing numbers of tumor cells after removal of endothelial cells, hematopoietic cells and red blood cells (but not fibroblasts), in 5 out of 7 cases single malignant cells induced tumors. Our current tumor bank contains 125 samples linked to patients' clinical data and characterized for mutational status and spontaneous metastasis rates (25%). DNA fingerprinting was matched to normal blood DNA if available to assure identity of the samples. The samples had a similar distribution pattern of genetic abnormalities to those in patients, thus allowing their use for mutation-specific therapy strategies. As an example, a PDX from a patient with intrinsic resistance to vemurafenib was grown to compare tumor growth on a 200 ppm BRAF inhibitor (PLX4720) diet, 200 ppm PLX4720 + 7 ppm MEK inhibitor (PD0325901) combination diet, or control diet for 21 days. As in the original patient, the BRAF inhibitor alone did not inhibit tumor growth, while the combination of BRAF and MEK inhibition showed significant tumor growth inhibition demonstrating that a PDX can predict clinical outcome.

Citation Format: Clemens Krepler, Katrin Sproesser, Patricia Brafford, Min Xiao, Marilda Beqiri, Wei Xu, Katherine Nathanson, Jennifer Wargo, Keith Flaherty, Donald L. Morton, Dave S. Hoon, Randall Ryan, Michael Guarino, Nicholas J. Petrelli, David Elder, Xiawei Xu, Giorgos Karakousis, Lynn Schuchter, Meenhard Herlyn. Patient derived xenograft (PDX) of human melanoma to predict clinical responses. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1182. doi:10.1158/1538-7445.AM2014-1182