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Small bowel adenocarcinomas (SBAs) are rare and frequently treated like large intestinal adenocarcinomas. However, SBAs have a very different microenvironment and could respond differently to the same therapies. Our previous data suggested that SBAs might benefit from targeting the PD-1/PD-L1 axis based on PD-L1 staining in almost 50% of SBA tissue samples tested. Thus, we designed a phase 2 study to explore safety and efficacy of avelumab in SBA.Patients with advanced or metastatic disease were enrolled; ampullary tumors were considered part of the duodenum and allowed. Prior PD-1/PD-L1 inhibition was not allowed. Avelumab (10 mg/kg) was given every 2 weeks, and imaging was performed every 8 weeks. Primary endpoint was response rate.Eight patients (n = 5, small intestine; n = 3, ampullary) were enrolled, with a majority (88%) being male and a median age of 61 years. Of 7 efficacy-evaluable patients, 2 (29%) experienced partial responses; stable disease occurred in 3 additional patients (71%). Median progression-free survival was 3.35 months. Most frequent, related toxicities were anemia, fatigue, and infusion-related reaction (25% each), mostly grade ≤2; grade 3 hypokalemia and hyponatremia occurred in one patient, and another reported grade 4 diabetic ketoacidosis.Despite the observed benefit, accrual was slower than expected and the study was closed early due to feasibility. A general clinic observation was that patients were receiving immunotherapy off-label as the availability of these agents increased. Off-label availability and disease rarity were likely drivers of insufficient accrual.

XLS file 56K, List of called variants re-sequenced by Sanger, their gene identities, protein sequences, and the primers used for Sanger sequencing

PDF - 160K, Supplementary Table S1. Summary of the six next-generation sequencing (NGS) studies containing 241 paired melanoma tumor/normal samples. Supplementary Table S2. Summary of known driver mutations detected in the 241 melanoma samples. Table S3. Mutated genes significantly associated with BRAF-mutated samples (frequencygreater than or equal to 10% and p-value < 0.05) in the Hodis et al. study. Table S4. Mutated genes significantly associated with NRAS-mutated samples (frequencygreater than or equal to 10% and p-value < 0.05) in the Hodis et al. study. Table S5. Mutated genes significantly associated with BRAF-mutated samples (frequencygreater than or equal to 10% and p-value < 0.05) in the Krauthammer et al. study. Table S6. Mutated genes significantly associated with NRAS-mutated samples (frequencygreater than or equal to 10% and p-value < 0.05) in the Krauthammer et al. study. Table S7. Mutated genes significantly associated with BRAF-mutated samples identified by the meta-analysis but not significantly BRAF-associated in the Hodis et al. study (corresponds with Table 1). Table S8. Mutated genes significantly associated with NRAS-mutated samples identified by the meta-analysis but some of them not significantly NRAS-associated in the Hodis et al. study (corresponds with Table 2). Table S9. Mutated genes significantly associated with BRAF-mutated samples as identified by the meta-analysis but not significantly BRAF-associated in the Krauthammer et al. study (corresponds with Table 1). Table S10. Mutated genes significantly associated with NRAS-mutated samples as identified by the meta-analysis but most of them not significantly NRAS-associated in the Krauthammer et al. study. Supplementary Table S11. Meta-analysis defined mutated genes associated with BRAF-mutated samples (frequencygreater than or equal to 10%, p-value < 0.05 is shown in red) by histological subtype. Supplementary Table S12. Meta-analysis defined mutated genes associated with NRAS-mutated samples (frequencygreater than or equal to 10%, p-value < 0.05 is shown in red) by histological subtype. Supplementary Table S13. Meta-analysis identified guanine nucleotide-binding protein alpha-subunit (GNA) mutations in the 69 pan-negative melanoma samples. Table S15. Summary of Meta-analysis identified genes with mutations enriched in pan-negative sun-exposed melanoma samples (mutation frequency greater than or equal to 10% and p-value < 0.05).

PDF file - 76K, Relative expression levels of WT vs. P124SMEK1 in the YUKSI B-RAF/MEK1 double-mutant melanoma short-term culture. Genomic DNA (gDNA) and cDNA derived from YUKSI were subjected to exon 3 sequencing by the Sanger method. Relative peaks of WT vs. P124SMEK1 is shown to be 1:1 for both gDNA and cDNA based on nucleotide chromatograms, showing no allelic bias in RNA expression.

PDF file 6308K, This includes all supplementary figures except S2 and contains additional clinical data, sequence and copy number analysis as well as immunohistochemical and functional studies

PDF file - 46K, Rapid symptomatic relief in patient 12 treated with GSK2118436/dabrafenib. This patient's right axillary nodal tumor was punch-biopsied at baseline (prior to B-RAFi therapy), showing concurrent B-RAF/MEK1 mutations, and became non-palpable after eleven days of continuous GSK2118436 dosing. This tumor shrinkage was associated with increased right shoulder mobility, decreased pain and right axillary and breast swelling, despite the best overall response in this patient (Table 1) not achieving partial response by RECIST criteria.

XLSX - 17K, Supplementary File S1. 632 melanoma candidate genes.

PDF file - 188K, Effects of MEK1 P124S co-expression with B-RAF V600K on cellular p-ERK levels and growth inhibitory sensitivities to B-RAFi and MEKi. (A) The YULAC V600KB-RAF melanoma cell line was stably introduced with the doxycycline-repressible tetracycline transactivator (tTA) and subsequently with vector, FLAG-MEK1, or FLAG-MEK1 P124S expression constructs. Stable cell lines incubated with doxycycline (100 ng/ml) or washed from doxycycline for 2 days were lysed, and the lysates probed for levels of indicated proteins by Western blotting. Tubulin, loading controls. (B) Survival curves for indicated YULAC stable cell lines treated with the indicated PLX4032 or AZD6244 for 72 h in the presence of doxycycline (top) or its absence (bottom). Data represent percent surviving cells relative to DMSO-treated controls (mean +/- SEM, n = 5). The dashed line corresponds to 50% cell killing.

PDF file - 181K, Patient tissues harboring concurrent and somatic B-RAF and MEK1 mutations. Chromatograms showing B-RAF exon 15 at V600 codon and MEK1 exon 3 at I111 or P124 codons in patient-matched normal tissue, baseline melanomas (prior to B-RAFi therapy), and melanomas on disease progression (i.e. at acquisition of B-RAFi resistance). Specific codons in red; N/A, not available.

PDF file - 76K, B-RAFi and MEKi combinatorial treatments lead to strong synergistic growth inhibition of V600EB-RAF cell lines regardless of concurrent P124SMEK1 expression. M229 and M238 vector vs. MEK1 stable cell lines were cultured with different levels of doxycycline (ng/ml), treated with constant ratios of B-RAFi (vemurafenib) and MEK1/2i (selumetinib), as indicated (muM), and measured for survival after 72h. Relative synergy of indicated drug combinations (expressed as log10 of CI values) is shown. Calculations were made by CalcuSyn software using the method of Chou and Taladay. Interpretation of CI values is summarized as follows: CI < 0.1 (very strong synergy); = 0.1-0.3 (strong synergy); = 0.3-0.7 (synergy); 0.7-0.85 (moderate synergy); = 0.85-0.9 (slight synergy); = 0.90-1.10 (nearly additive); and = 1.10-1.20 (slight antagonism). The relevant correlated Log10 (CI) values are shown as follow: Log10 (CI 0.1) = -1; Log10 (CI 0.3) = -0.5228787452803376; Log10 (CI 0.7) = -0.1549019599857432, and Log10 (CI 0.85) = -0.07058107428570727.

PDF file 8842K, Supplementary Figure S2 contains Sanger re-sequencing to estimate the specificity of WES

PDF file - 144K, Long-term effects of P124SMEK1 expression on population doubling and p-ERK levels. (A) Impact of regulated expression of P124SMEK1 on long-term growth of M238. Stable lines expressing empty vector, FLAG-MEK1 WT or FLAG-MEK1 P124S were cultured with different levels of doxycycline, enabling low (0.1 ng/ml) or high (0 ng/ml) expression levels of exogenous MEK1. Equal number of cells were serially plated every 4 days and fold growth calculated by dividing the number of viable cells (trypan-blue negative) at the end of each four day period over the starting seeding number. (B) Long-term, regulated expression of WTMEK or P124SMEK and corresponding levels of ERK activation in a clonogenic assay (Fig. 2G). Doxycycline-controlled expression of vector (control), FLAG-MEK1 WT, vs. FLAG-MEK1 P124S in the V600EB-RAF melanoma cell line, M238. Protein lysates (192 h post seeding at 0, 0.1, and 100 ng/ml doxycycline) were probed by Western blotting for the indicated phospho- and total protein levels. Tubulin, loading control.

Next generation sequencing (NGS) has been used to characterize the overall genomic landscape of melanomas. Here, we systematically examined mutations from recently published melanoma NGS data involving 241 paired tumor-normal samples to identify potentially clinically relevant mutations. Melanomas were characterized according to an in-house clinical assay that identifies well-known specific recurrent mutations in five driver genes: BRAF (affecting V600), NRAS (G12, G13, and Q61), KIT (W557, V559, L576, K642, and D816), GNAQ (Q209), and GNA11 (Q209). Tumors with none of these mutations are termed “pan negative.” We then mined the driver mutation-positive and pan-negative melanoma NGS data for mutations in 632 cancer genes that could influence existing or emerging targeted therapies. First, we uncovered several genes whose mutations were more likely associated with BRAF- or NRAS-driven melanomas, including TP53 and COL1A1 with BRAF, and PPP6C, KALRN, PIK3R4, TRPM6, GUCY2C, and PRKAA2 with NRAS. Second, we found that the 69 “pan-negative” melanoma genomes harbored alternate infrequent mutations in the five known driver genes along with many mutations in genes encoding guanine nucleotide binding protein α-subunits. Third, we identified 12 significantly mutated genes in “pan-negative” samples (ALK, STK31, DGKI, RAC1, EPHA4, ADAMTS18, EPHA7, ERBB4, TAF1L, NF1, SYK, and KDR), including five genes (RAC1, ADAMTS18, EPHA7, TAF1L, and NF1) with a recurrent mutation in at least two “pan-negative” tumor samples. This meta-analysis provides a road map for the study of additional potentially actionable genes in both driver mutation-positive and pan-negative melanomas. Mol Cancer Ther; 13(7); 1918–28. ©2014 AACR.

PDF - 912K, Supplementary Figure S1. NRAS mutations in the 69 pan-negative melanoma samples. Supplementary Figure S2. KIT mutations in the 69 pan-negative melanoma samples. Supplementary Figure S3. GNAQ mutations in the 69 pan-negative melanoma samples.Supplementary Figure S4. GNA11 mutations in the 69 pan-negative melanoma samples. Supplementary Figure S5. RAC1 mutations in the 69 pan-negative melanoma samples. Supplementary Figure S6. ADAMTS18 mutations in the 69 pan-negative melanoma samples. Supplementary Figure S7. EPHA7 mutations in the 69 pan-negative melanoma samples. Supplementary Figure S8. TAF1L mutations in the 69 pan-negative melanoma samples. Supplementary Figure S9. NF1 mutations in the 69 pan-negative melanoma samples. Supplementary Figure S10. ALK mutations in the 69 pan-negative melanoma samples. Supplementary Figure S11. STK31 mutations in the 69 pan-negative melanoma samples. Supplementary Figure S12. DGKI mutations in the 69 pan-negative melanoma samples. Supplementary Figure S13. EPHA4 mutations in the 69 pan-negative melanoma samples. Supplementary Figure S14. ERBB4 mutations in the 69 pan-negative melanoma samples. Supplementary Figure S15. SYK mutations in the 69 pan-negative melanoma samples. Supplementary Figure S16. KDR mutations in the 69 pan-negative melanoma samples.

PDF file - 181K, WTMEK and P124SMEK activated by V600EB-RAF display similar in vitro kinase activities toward recombinant ERK1. HEK293T cells were transfected with vector, FLAG-MEK1 WT, or FLAG-MEK1 P124S in the absence or presence of co-transfected V600EB-RAF. Cells were lysed and exogenous MEK1 immunoprecipitated (IP) using isotype (I) control or anti-FLAG (F) antibody (ab), washed, and subjected to in vitro kinase assay. Pre-IP lysates were immunoblotted for FLAG levels. After the kinase reaction, the supernatant (sup) or ab-bead fractions were mixed with denaturing loading buffers, fractionated and immunoblotted against indicated phospho- or total protein levels (rERK, recombinant ERK).

Supplementary Figure S3: Alterations in Protein Expression Associated with D+T Response in Group I PDX lines.

Supplementary Table S1. A. NGS Summary.

Purpose:Over 60% of patients with melanoma respond to immune checkpoint inhibitor (ICI) therapy, but many subsequently progress on these therapies. Second-line targeted therapy is based on BRAF mutation status, but no available agents are available for NRAS, NF1, CDKN2A, PTEN, and TP53 mutations. Over 70% of melanoma tumors have activation of the MAPK pathway due to BRAF or NRAS mutations, while loss or mutation of CDKN2A occurs in approximately 40% of melanomas, resulting in unregulated MDM2-mediated ubiquitination and degradation of p53. Here, we investigated the therapeutic efficacy of over-riding MDM2-mediated degradation of p53 in melanoma with an MDM2 inhibitor that interrupts MDM2 ubiquitination of p53, treating tumor-bearing mice with the MDM2 inhibitor alone or combined with MAPK-targeted therapy.Experimental Design:To characterize the ability of the MDM2 antagonist, KRT-232, to inhibit tumor growth, we established patient-derived xenografts (PDX) from 15 patients with melanoma. Mice were treated with KRT-232 or a combination with BRAF and/or MEK inhibitors. Tumor growth, gene mutation status, as well as protein and protein–phosphoprotein changes, were analyzed.Results:One-hundred percent of the 15 PDX tumors exhibited significant growth inhibition either in response to KRT-232 alone or in combination with BRAF and/or MEK inhibitors. Only BRAFV600WT tumors responded to KRT-232 treatment alone while BRAFV600E/M PDXs exhibited a synergistic response to the combination of KRT-232 and BRAF/MEK inhibitors.Conclusions:KRT-232 is an effective therapy for the treatment of either BRAFWT or PANWT (BRAFWT, NRASWT) TP53WT melanomas. In combination with BRAF and/or MEK inhibitors, KRT-232 may be an effective treatment strategy for BRAFV600-mutant tumors.

Purpose: Over 60% of patients with melanoma respond to immune checkpoint inhibitor (ICI) therapy, but many subsequently progress on these therapies. Second-line targeted therapy is based on BRAF mutation status, but no available agents are available for NRAS, NF1, CDKN2A, PTEN, and TP53 mutations. Over 70% of melanoma tumors have activation of the MAPK pathway due to BRAF or NRAS mutations, while loss or mutation of CDKN2A occurs in approximately 40% of melanomas, resulting in unregulated MDM2-mediated ubiquitination and degradation of p53. Here, we investigated the therapeutic efficacy of over-riding MDM2-mediated degradation of p53 in melanoma with an MDM2 inhibitor that interrupts MDM2 ubiquitination of p53, treating tumor-bearing mice with the MDM2 inhibitor alone or combined with MAPK-targeted therapy. Experimental Design: To characterize the ability of the MDM2 antagonist, KRT-232, to inhibit tumor growth, we established patient-derived xenografts (PDX) from 15 patients with melanoma. Mice were treated with KRT-232 or a combination with BRAF and/or MEK inhibitors. Tumor growth, gene mutation status, as well as protein and protein–phosphoprotein changes, were analyzed. Results: One-hundred percent of the 15 PDX tumors exhibited significant growth inhibition either in response to KRT-232 alone or in combination with BRAF and/or MEK inhibitors. Only BRAFV600WT tumors responded to KRT-232 treatment alone while BRAFV600E/M PDXs exhibited a synergistic response to the combination of KRT-232 and BRAF/MEK inhibitors. Conclusions: KRT-232 is an effective therapy for the treatment of either BRAFWT or PANWT (BRAFWT, NRASWT) TP53WT melanomas. In combination with BRAF and/or MEK inhibitors, KRT-232 may be an effective treatment strategy for BRAFV600-mutant tumors.

Proliferating tricholemmal tumors (PTTs) are rare benign neoplasms that arise from the outer sheath of a hair follicle. Occasionally, these PTTs undergo malignant transformation to become malignant proliferating tricholemmal tumors (MPTTs). Little is known about the molecular alterations, malignant progression, and management of MPTTs. Here, we describe the case of a 58-year-old female that had a widely metastatic MPTT that harbored an activating PIK3CA mutation and was sensitive to the PI3K inhibitor, alpelisib (BYL719). We review the available literature on metastatic MPTT, detail the patient’s course, and present a whole genome analysis of this rare tumor.

International audience; Retrospective studies suggest that chimeric antigen receptor T-cell (CAR T) therapy may lead to cardiac injury, but this has not been assessed systematically or prospectively. In this prospective study of 40 patients who received CAR T, we systematically measured high-sensitivity troponin T (hsTropT) and N-terminal pro-B natriuretic peptide (NTproBNP) at baseline and on day 1, days 7, and 21 after CAR T. Biomarker elevations with respect to timepoint and cytokine release syndrome (CRS) status were examined using repeated measure analysis of variance. hsTropT did not differ with time or with the presence of grade 2 CRS. Median hsTropT was 12.1 ng/L [interquartile range (IQR): 9.2, 20.1] at baseline, 13.1 ng/L (IQR: 9.6, 24.2) at day 1, 11.9 ng/L (IQR: 9.6, 18.0) at day 7, and 15.3 ng/L (10.8, 20.2) at day 21. In contrast, NTproBNP rose on day 1 (PWilcox = 0.0002) and day 7 (PWilcox = 2.7 × 10−5), and the degree of elevation differed by the presence of grade 2 CRS (Pinteraction = 0.002). Median NTproBNP was 179 pg/mL (IQR: 116, 325) at baseline, 357 pg/mL (IQR: 98, 813) at day 1, 420 pg/mL (IQR: 239, 1242) at day 7, and 177 pg/mL (IQR: 80, 278) at day 21. In conclusion, hsTropT l did not differ across timepoints after CAR T therapy, but NTproBNP rose at day 7, the prognostic implications of which should be the target of future research, as the indications for this therapy expand.

PURPOSE: Precision medicine is revolutionizing healthcare practices, most notably in oncology. With cancer being the second leading cause of death in the USA, it is important to integrate precision oncology content in undergraduate medical education. METHODS: In 2015, we launched a Clinical Cancer Medicine Integrated Science Course (ISC) for post-clerkship medical students at Vanderbilt University School of Medicine (VUSM). In this ISC, students learned cancer biology and clinical oncology concepts through a combination of classroom and patient care activities. Student feedback from mid- and end-of-course surveys and student match data were analyzed and used to develop ongoing course improvements. RESULTS: To date, 72 medical students have taken the Clinical Cancer Medicine ISC. Over 90% of students who completed end-of-course surveys agreed or strongly agreed that this course advanced their foundational science knowledge in clinical cancer medicine, that clinical relevance was provided during non-clinical foundational science learning activities, and that foundational science learning was embedded in course clinical experiences. Students who took this course most commonly matched in Internal Medicine, Pathology, Pediatrics, and Radiation Oncology. VUSM students who matched into Pathology and Radiation Oncology were more likely to take this ISC than students who matched in other specialties. CONCLUSION: The Clinical Cancer Medicine ISC serves as a model for incorporating precision oncology, cancer biology foundational science, and oncology patient care activities in undergraduate medical education. The course prepares students to care for oncology patients in their fields of interests during their future career in medicine.

This study aims to design, implement, and launch courses that integrate foundational science learning and clinical application in a post-clerkship undergraduate medical school curriculum. In academic year 2015–2016 (AY15–16), as part of a comprehensive curricular revision, Vanderbilt University School of Medicine (VUSM) formally implemented “Integrated Science Courses” (ISCs) that combined rigorous training in the foundational sciences with meaningful clinical experiences. These courses integrated foundational sciences that could be leveraged in the clinical environment, utilized a variety of instructional modalities, and included quantitative and qualitative (competency-based milestones) student assessments. Each ISC underwent a rigorous quality-improvement process that required input on foundational science content, student experience, and student performance assessment. Eleven ISCs were delivered to 173 students in AY15–16, with some students taking more than one ISC. Immediately after completing each course, 93% (n = 222) of ISC enrollees completed a course evaluation. Students (91%; n = 201) “agreed” or “strongly agreed” that foundational science learning informed and enriched the clinical experiences. Furthermore, 94% (n = 209) of students thought that the clinical experiences informed and enriched the foundational science learning. Ninety-four percent of the students anticipated using the foundational science knowledge acquired in future clinical training and practice. The teaching of foundational sciences in the clinical workplace in the post-clerkship medical curriculum is challenging and resource intensive, yet feasible. Additional experience with the model will inform the mix of courses as well as the breadth and depth of foundational science instruction that is necessary to foster scientifically based clinical reasoning skills in each student.

Dual MAPK pathway inhibition (dMAPKi) with BRAF and MEK inhibitors improves survival in BRAF V600E/K mutant melanoma, but the efficacy of dMAPKi in non-V600 BRAF mutant tumors is poorly understood. We sought to characterize the responsiveness of class II (enhanced kinase activity, dimerization dependent) BRAF mutant melanoma to dMAPKi.Tumors from patients with BRAF wild-type (WT), V600E (class I), and L597S (class II) metastatic melanoma were used to generate patient-derived xenografts (PDX). We assembled a panel of melanoma cell lines with class IIa (activation segment) or IIb (p-loop) mutations and compared these with WT or V600E/K BRAF mutant cells. Cell lines and PDXs were treated with BRAFi (vemurafenib, dabrafenib, encorafenib, and LY3009120), MEKi (cobimetinib, trametinib, and binimetinib), or the combination. We identified 2 patients with BRAF L597S metastatic melanoma who were treated with dMAPKi.BRAFi impaired MAPK signaling and cell growth in class I and II BRAF mutant cells. dMAPKi was more effective than either single MAPKi at inhibiting cell growth in all class II BRAF mutant cells tested. dMAPKi caused tumor regression in two melanoma PDXs with class II BRAF mutations and prolonged survival of mice with class II BRAF mutant melanoma brain metastases. Two patients with BRAF L597S mutant melanoma clinically responded to dMAPKi.Class II BRAF mutant melanoma is growth inhibited by dMAPKi. Responses to dMAPKi have been observed in 2 patients with class II BRAF mutant melanoma. These data provide rationale for clinical investigation of dMAPKi in patients with class II BRAF mutant metastatic melanoma.

Background and Objectives: The World Health Organization (WHO) 2010 has classified GI neuroendocrine neoplasms into neuroendocrine tumor (NET) and high-grade neuroendocrine carcinoma (NEC). The genetic underpinnings of NEC are poorly understood. The aim of the study was to perform genomic profiling of NEC to better characterize this aggressive disease. Methods: We identified nine patients with colonic NEC between January 1, 2005 and June 30, 2013. Whole exome sequencing (WES) was performed on tumor DNA from two patients with ≥80% tumor cellularity and matched normal tissue available. Focused BRAF mutational analysis was performed on an additional seven patients via sanger sequencing of BRAF exons 11 and 15. Results: We identified BRAF exon 15 mutations (c.A1781G: p.D594G and c.T1799A: p.V600E) by WES in two patients. Upon additional screening of seven colonic NECs for BRAF exon 11 and 15 mutations, we identified BRAF V600E mutations in two of seven specimens (29%). Overall, BRAF exon 15 mutations were present in four of nine colonic NECs. Conclusion: Colonic NEC is a rare but aggressive tumor with high frequency (44%) of BRAF mutations. Further investigation is warranted to ascertain the incidence of BRAF mutations in a larger population as BRAF inhibition may be a potential avenue of targeted treatment for these patients.

Wilms tumor (WT) is the most common renal neoplasm of childhood and affects 1 in 10 000 children aged less than 15 years. These embryonal tumors are thought to arise from primitive nephrogenic rests that derive from the metanephric mesenchyme during kidney development and are characterized partly by increased Wnt/β-catenin signaling. We previously showed that coordinate activation of Ras and β-catenin accelerates the growth and metastatic progression of a murine WT model. Here, we show that activating KRAS mutations can be found in human WT. In addition, high levels of phosphorylated AKT are present in the majority of WT. We further show in a mouse model and in renal epithelial cells that Ras cooperates with β-catenin to drive metastatic disease progression and promotes in vitro tumor cell growth, migration, and colony formation in soft agar. Cellular transformation and metastatic disease progression of WT cells are in part dependent on PI3K/AKT activation and are inhibited via pharmacological inhibition of this pathway. Our studies suggest both KRAS mutations and AKT activation are present in WT and may represent novel therapeutic targets for this disease.

Background: Cytomegalovirus (CMV) serostatus is associated with transplant related mortality, relapse and survival following allogeneic stem cell transplant (SCT). Prior studies have demonstrated that CMV seronegative recipients (R-) receiving a CMV seropositive graft (D+) experience inferior outcomes compared to the R-/D- combination, an observation that is independent of viral reactivation and due to increased bacterial and fungal sepsis (Nichols WG et al, J. Infect. Dis. 2002; 185:273-82). We therefore investigated the hypothesis that CMV exposure, including that by the donor only prior to transplant, promotes endogenous and long-term immunodeficiency after SCT. Methods: A total of 108 patient peripheral blood samples were obtained from the Chronic Graft-vs.-Disease (GVHD) Consortium, which includes both patients with and without chronic GVHD. Seventy-three baseline samples were taken at an average of 458 days (range 63 to 1,965) after SCT, and 35 paired blood samples were taken at an average of 94 days follow-up. Transplant parameters, CMV serostatus, and CMV viral titers after SCT were collected. We performed multiparameter flow cytometry to assess innate and adaptive immunity after SCT in the context of CMV, including transcription factor and cytokine expression, together with TCR/BCR sequencing to assess immune diversity. Results: We demonstrate that CMV exposure (including solely in the donor prior to transplant or in the recipient after transplant) is strongly associated with long-lasting expansion of a terminally differentiated MHC class II-restricted donor memory T cell subset identifiable by the surface markers CD4+/CD57+/CD27-(Figure 1). These cells are CCR7neg/CD45RO+/CD45RA+/-, express T-bet, eomesodermin (EOMES), granzyme B, and secret high amounts of Th1 cytokines IFNγ and TNF (Figure 1). This T cell subset represents an average of 2.8% for D-/R- transplants and >10% (and up to 70%) of total CD4+ T cells in all other serostatus combinations irrespective of the presence or absence of measurable CMV reactivation after SCT (p Conclusion: These data describe a temporally stable, expanded MHC class II-restricted memory T cell population with high cytotoxic potential and putative mechanisms by which CMV exposure modifies immune function in the peri-transplant period, namely the limitation of TCR diversity and antigen presentation. This cell population is expanded even in the absence of detectable CMV reactivation post SCT and can be observed for several years following transplant. We thus provide a potential mechanism for the immunodeficiency and broad increase in infection mortality invoked by CMV exposure. In particular, these findings may provide a rationale for supporting the selection of CMV- donors for R- SCT recipients. Disclosures Jagasia: Ocugen: Other; Mallinckrodt: Research Funding; Janssen: Research Funding. Dahlman:Kadmon Holdings, Inc: Other. Lee:Syndax: Research Funding; Pfizer: Consultancy, Research Funding; AstraZeneca: Research Funding; Amgen: Research Funding; Kadmon: Research Funding; Takeda: Research Funding; Novartis: Research Funding; Incyte: Consultancy, Research Funding. Hill:Generon: Consultancy; Roche: Research Funding; Compass Pharmaceuticals: Research Funding; CSL: Research Funding; Implicit Bioscience: Research Funding; Pharmacyclics: Research Funding.

797 Background: SBA is rare and often grouped with, and treated like, large intestinal adenocarcinomas. However, SBA has a very different microenvironment and could respond differently to the same therapies, potentially lowering efficacy. Also no standard treatments exist due to the lack of prospective randomized trials. We presented data at GI ASCO 2016 that suggested SBAs might benefit from targeting the PD-1/PD-L1 axis based on strong PD-L1 staining in ~50% of SBAs tested. Thus, we designed a pilot phase 2 trial to study safety and efficacy of avelumab in SBA. Methods: Patients (pts) with advanced (not amenable to surgery) or metastatic disease were eligible; ampullary tumors were considered part of the duodenum and allowed. Pts with prior PD-1/PD-L1 were excluded. Avelumab (10 mg/kg) was given every 2 weeks in 14-day cycles, and imaging was performed every 8 weeks. Primary endpoint was response rate (RR). Enrollment of 25 pts were planned, and avelumab would be considered active if ≥4 responses (RR≥16%) were observed (80% power, a = 5%). Secondary endpoints included disease-control rate (DCR) and progression-free survival (PFS). Results: Eight SBA pts (5 small intestine; 3 ampullary) were enrolled, with a majority (88%) being male and a median age of 61 years. Median time on treatment was 3.4 months; 1 patient is still on study with an ongoing partial response (PR). Of 7 efficacy-evaluable patients, 2 had a PR for a RR of 29%; DCR was 71% (5/7). Median PFS was 8.0 months. Most frequent, related adverse events were fatigue (38%), elevated alkaline phosphatase (25%), and infusion related reaction (25%), all ≤G2; a G3 (not serious) hypokalemia and a G4 (serious) diabetic ketoacidosis occurred in 1 pt each. Conclusions: Avelumab was considered safe, and antitumor activity was observed as evidenced by a 29% RR and 71% DCR. Despite this benefit, accrual was slower than expected and the study was closed early due to feasibility. A general clinical observation is that more pts are receiving immunotherapy off-label as the availability of these agents increases. This was a likely contributor to slow accrual, in addition to disease rarity. Analysis of PD-L1 expression, MSI status, and other immune cell markers is planned and will be compared to response. Clinical trial information: NCT03000179 .

Resistance to current therapies still impacts a significant number of melanoma patients and can be regulated by epigenetic alterations. Analysis of global cytosine methylation in a cohort of primary melanomas revealed a pattern of early demethylation associated with overexpression of oncogenic transcripts. Loss of methylation and associated overexpression of the CSF 1 receptor (CSF1R) was seen in a majority of tumors and was driven by an alternative, endogenous viral promoter in a subset of samples. CSF1R was particularly elevated in melanomas with BRAF and other MAPK activating mutations. Furthermore, rebound ERK activation after BRAF inhibition was associated with RUNX1-mediated further upregulation of CSF-1R and its ligand IL-34. Importantly, increased CSF-1R and IL-34 overexpression were detected in an independent cohort of resistant melanomas. Inhibition of CSF-1R kinase or decreased CSF-1R expression by RNAi reduced 3-D growth and invasiveness of melanoma cells. Coinhibition of CSF-1R and BRAF resulted in synergistic efficacy in vivo. To our knowledge, our data unveil a previously unknown role for the autocrine-regulated CSF-1R in BRAF V600E resistance and provide a preclinical rationale for targeting this pathway in melanoma.

Little is known about the in vivo impacts of targeted therapy on melanoma cell abundance and protein expression. Here, 21 antibodies were added to an established melanoma mass cytometry panel to measure 32 cellular features, distinguish malignant cells, and characterize dabrafenib and trametinib responses in BRAF(V600mut) melanoma. Tumor cells were biopsied before neoadjuvant therapy and compared to cells surgically resected from the same site after 4 weeks of therapy. Approximately 50,000 cells per tumor were characterized by mass cytometry and computational tools t-SNE/viSNE, FlowSOM, and MEM. The resulting single cell view of melanoma treatment response revealed initially heterogeneous melanoma tumors were consistently cleared of Nestin expressing melanoma cells. Melanoma cells subsets that persisted to week 4 were heterogeneous but expressed SOX2 or SOX10 proteins and specifically lacked surface expression of MHC I proteins by MEM analysis. Traditional histology imaging of tissue microarrays from the same tumors confirmed mass cytometry results, including persistence of NES-SOX10+ S100β+ melanoma cells. This quantitative single cell view of melanoma treatment response revealed protein features of malignant cells that are not eliminated by targeted therapy.

The pathogenesis of mycosis fungoides (MF), the most common cutaneous T-cell lymphoma (CTCL), is unknown. Although genetic alterations have been identified, none are considered consistently causative in MF. To identify potential drivers of MF, we performed whole-genome sequencing of MF tumors and matched normal skin. Targeted ultra-deep sequencing of MF samples and exome sequencing of CTCL cell lines were also performed. Multiple mutations were identified that affected the same pathways, including epigenetic, cell-fate regulation, and cytokine signaling, in MF tumors and CTCL cell lines. Specifically, interleukin-2 signaling pathway mutations, including activating Janus kinase 3 (JAK3) mutations, were detected. Treatment with a JAK3 inhibitor significantly reduced CTCL cell survival. Additionally, the mutation data identified 2 other potential contributing factors to MF, ultraviolet light, and a polymorphism in the tumor suppressor p53 (TP53). Therefore, genetic alterations in specific pathways in MF were identified that may be viable, effective new targets for treatment.

The mechanisms by which some melanoma cells adapt to Serine/threonine-protein kinase B-Raf (BRAF) inhibitor therapy are incompletely understood. In the present study, we used mass spectrometry-based phosphoproteomics to determine how BRAF inhibition remodeled the signaling network of melanoma cell lines that were BRAF mutant and PTEN null. Short-term BRAF inhibition was associated with marked changes in fibronectin-based adhesion signaling that were PTEN dependent. These effects were recapitulated through BRAF siRNA knockdown and following treatment with chemotherapeutic drugs. Increased fibronectin expression was also observed in mouse xenograft models as well as specimens from melanoma patients undergoing BRAF inhibitor treatment. Analysis of a melanoma tissue microarray showed loss of PTEN expression to predict for a lower overall survival, with a trend for even lower survival being seen when loss of fibronectin was included in the analysis. Mechanistically, the induction of fibronectin limited the responses of these PTEN-null melanoma cell lines to vemurafenib, with enhanced cytotoxicity observed following the knockdown of either fibronectin or its receptor α5β1 integrin. This in turn abrogated the cytotoxic response to BRAF inhibition via increased AKT signaling, which prevented the induction of cell death by maintaining the expression of the pro-survival protein Mcl-1. The protection conveyed by the induction of FN expression could be overcome through combined treatment with a BRAF and PI3K inhibitor.

Increased understanding of intertumoral heterogeneity at the genomic level has led to significant advancements in the treatment of solid tumors. Functional genomic alterations conferring sensitivity to targeted therapies can take many forms, and appropriate methods and tools are needed to detect these alterations. This review provides an update on genetic variability among solid tumors of similar histologic classification, using non–small cell lung cancer and melanoma as examples. We also discuss relevant technological platforms for discovery and diagnosis of clinically actionable variants and highlight the implications of specific genomic alterations for response to targeted therapy. Clin Cancer Res; 20(9); 2264–75. ©2014 AACR.

Somatic mutations in kinase genes are associated with sensitivity of solid tumors to kinase inhibitors, but patients with metastatic cancer eventually develop disease progression. In EGFR mutant lung cancer, modeling of acquired resistance (AR) with drug-sensitive cell lines has identified clinically relevant EGFR tyrosine kinase inhibitor (TKI) resistance mechanisms such as the second-site mutation, EGFR T790M, amplification of the gene encoding an alternative kinase, MET, and epithelial–mesenchymal transition (EMT). The full spectrum of DNA changes associated with AR remains unknown. We used next-generation sequencing to characterize mutational changes associated with four populations of EGFR mutant drug-sensitive and five matched drug-resistant cell lines. Comparing resistant cells with parental counterparts, 18–91 coding SNVs/indels were predicted to be acquired and 1–27 were lost; few SNVs/indels were shared across resistant lines. Comparison of two related parental lines revealed no unique coding SNVs/indels, suggesting that changes in the resistant lines were due to drug selection. Surprisingly, we observed more CNV changes across all resistant lines, and the line with EMT displayed significantly higher levels of CNV changes than the other lines with AR. These results demonstrate a framework for studying the evolution of AR and provide the first genome-wide spectrum of mutations associated with the development of cellular drug resistance in an oncogene-addicted cancer. Collectively, the data suggest that CNV changes may play a larger role than previously appreciated in the acquisition of drug resistance and highlight that resistance may be heterogeneous in the context of different tumor cell backgrounds.

Kinase inhibitors are accepted treatment for metastatic melanomas that harbor specific driver mutations in BRAF or KIT, but only 40% to 50% of cases are positive. To uncover other potential targetable mutations, we conducted whole-genome sequencing of a highly aggressive BRAF (V600) and KIT (W557, V559, L576, K642, and D816) wild-type melanoma. Surprisingly, we found a somatic BRAFL597R mutation in exon 15. Analysis of BRAF exon 15 in 49 tumors negative for BRAFV600 mutations as well as driver mutations in KIT, NRAS, GNAQ, and GNA11, showed that two (4%) harbored L597 mutations and another two involved BRAF D594 and K601 mutations. In vitro signaling induced by L597R/S/Q mutants was suppressed by mitogen-activated protein (MAP)/extracellular signal–regulated kinase (ERK) kinase (MEK) inhibition. A patient with BRAFL597S mutant metastatic melanoma responded significantly to treatment with the MEK inhibitor, TAK-733. Collectively, these data show clinical significance to BRAFL597 mutations in melanoma. Significance: This study shows that cells harboring BRAFL597 mutants are sensitive to MEK inhibitor treatment, providing a rationale for routine screening and therapy of BRAFL597-mutant melanoma. Cancer Discov; 2(9); 791–7. ©2012 AACR. Read the Commentary on this article by Garraway and Baselga, p. 766. This article is highlighted in the In This Issue feature, p. 753.

BRAF inhibitors (BRAFi) induce antitumor responses in nearly 60% of patients with advanced V600E/KBRAF melanomas. Somatic activating MEK1 mutations are thought to be rare in melanomas, but their potential concurrence with V600E/KBRAF may be selected for by BRAFi. We sequenced MEK1/2 exon 3 in melanomas at baseline and upon disease progression. Of 31 baseline V600E/KBRAF melanomas, 5 (16%) carried concurrent somatic BRAF/MEK1 activating mutations. Three of 5 patients with BRAF/MEK1 double-mutant baseline melanomas showed objective tumor responses, consistent with the overall 60% frequency. No MEK1 mutation was found in disease progression melanomas, except when it was already identified at baseline. MEK1-mutant expression in V600E/KBRAF melanoma cell lines resulted in no significant alterations in p-ERK1/2 levels or growth-inhibitory sensitivities to BRAFi, MEK1/2 inhibitor (MEKi), or their combination. Thus, activating MEK1 exon 3 mutations identified herein and concurrent with V600E/KBRAF do not cause BRAFi resistance in melanoma. Cancer Discov; 2(5); 414–24. ©2012 AACR. Significance: As BRAF inhibitors gain widespread use for treatment of advanced melanoma, biomarkers for drug sensitivity or resistance are urgently needed. We identify here concurrent activating mutations in BRAF and MEK1 in melanomas and show that the presence of a downstream mutation in MEK1 does not necessarily make BRAF–mutant melanomas resistant to BRAF inhibitors. Read the Commentary on this article by Paraiso and Smalley, p. 390. This article is highlighted in the In This Issue feature, p. 377.

Human lung adenocarcinomas with activating mutations in EGFR (epidermal growth factor receptor) often respond to treatment with EGFR tyrosine kinase inhibitors (TKIs), but the magnitude of tumour regression is variable and transient. This heterogeneity in treatment response could result from genetic modifiers that regulate the degree to which tumour cells are dependent on mutant EGFR. Through a pooled RNA interference screen, we show that knockdown of FAS and several components of the NF-κB pathway specifically enhanced cell death induced by the EGFR TKI erlotinib in EGFR-mutant lung cancer cells. Activation of NF-κB through overexpression of c-FLIP or IKK (also known as CFLAR and IKBKB, respectively), or silencing of IκB (also known as NFKBIA), rescued EGFR-mutant lung cancer cells from EGFR TKI treatment. Genetic or pharmacologic inhibition of NF-κB enhanced erlotinib-induced apoptosis in erlotinib-sensitive and erlotinib-resistant EGFR-mutant lung cancer models. Increased expression of the NF-κB inhibitor IκB predicted for improved response and survival in EGFR-mutant lung cancer patients treated with EGFR TKI. These data identify NF-κB as a potential companion drug target, together with EGFR, in EGFR-mutant lung cancers and provide insight into the mechanisms by which tumour cells escape from oncogene dependence.

Epigenetic changes in cancer are thought to contribute to the regulation of invasion and metastasis. To study this at a genome-wide level in melanoma, we analyzed the methylome of 44 cases of malignant melanoma. We saw widespread demethylation occurring preferentially outside of CpG islands. Comparison of primary and metastatic lesions showed demethylation occurs early during carcinogenesis with few additional alterations in advanced tumors. The colony stimulating factor-1 receptor was aberrantly expressed and hypomethylated in nearly all cases. Its expression was validated by IHC and RNA-FISH on primary tumors and by qPCR, Western blotting and FACS in BRAF mutant and WT cell lines. CSF1R can be aberrantly expressed via an upstream LTR element in Hodgkin's lymphoma. After analyzing our patient samples and cell lines, we have found this aberrant transcript may be the dominant form in melanoma as well. Expression of one of its ligands IL34 was also shown in the cell lines by both ELISA and qPCR pointing to a potential autocrine regulatory loop. The effects of a small molecule inhibitor, PLX3397 as well as shRNA-mediated knockdown of the receptor were investigated in 2D and 3D cell culture. We saw inhibition of cell growth, smaller colony size, increased apoptosis and decreased invasiveness suggesting a functional role for CSF-1R in melanoma. Treatment of melanoma with BRAF-V600E inhibitors is effective for a time, but resistance invariably develops. The feedback activation of EGFR, BRAF amplification, BRAF splice variants and others are known to aid in the acquisition of resistance and the rebound activation of the MAPK-pathway. We are suggesting a role for CSF1R in this process. In Western experiments, the rebound of phospho-ERK after BRAF inhibitor treatment was accelerated with the addition of CSF1R ligands, or delayed with PLX3397, also attenuating AKT phosphorylation. Melanoma cells stably expressing shRNA against CSF1R recapitulated the effects of the inhibitor. Assaying the cells at different time points during a long-term V600E inhibitory experiment, we saw increasing levels of the transcription factor RUNX1, followed by increasing levels of IL34 and of the receptor, as well as its maturation, and presentation on the cell surface. shRNA-mediated knockdown of RUNX1 resulted in lower levels of the CSF1R and IL34 transcripts and delayed the rebound. Analysis of primary RNA-Seq data showed an increase in RUNX1, CSF1R and IL34 expression in resistant tumors. Co-inhibition of CSF1R and BRAF was also tested and resulted in synergistic blockade of cell growth in vitro and xenograft growth in vivo.The CSF1R inhibitor, PLX3397 is currently in clinical trials for glioblastoma, prostate, breast cancers and other cancers. These data present a preclinical rationale for its study in malignant melanoma. Citation Format: Orsolya Giricz, Yongkai Mo, Kimberly B. Dahlman, Xiomaris M. Cotto-Rios, Chiara Vardabasso, Hoa Nguyen, Bernice Matusow, Matthias Bartenstein, Veronika Polishchuck-Lee, Douglas B. Johnson, Tushar B. Bhagat, Rafe Shellooe, Elizabeth Burton, Gaston Habets, John M. Greally, Yiting Yu, Gideon Bollag, Paraic A. Kenny, Kith Pradhan, E. Richard Stanley, Emily Bernstein, Evripidis Gavathiotis, Brian L. West, Jeffrey A. Sosman, Amit Verma. Aberrant expression of CSF1R in melanoma is driven through an endogenous viral promoter and it contributes to malignant growth and BRAF-inhibitor resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2515.

SummaryClinically acquired resistance to MAPK inhibitor (MAPKi) therapies for melanoma cannot be fully explained by genomic mechanisms and may be accompanied by co-evolution of intra-tumoral immunity. We sought to discover non-genomic mechanisms of acquired resistance and dynamic immune compositions by a comparative, transcriptomic-methylomic analysis of patient-matched melanoma tumors biopsied before therapy and during disease progression. Transcriptomic alterations across resistant tumors were highly recurrent, in contrast to mutations, and were frequently correlated with differential methylation of tumor cell-intrinsic CpG sites. We identified in the tumor cell compartment supra-physiologic c-MET up-expression, infra-physiologic LEF1 down-expression and YAP1 signature enrichment as drivers of acquired resistance. Importantly, high intra-tumoral cytolytic T cell inflammation prior to MAPKi therapy preceded CD8 T cell deficiency/exhaustion and loss of antigen presentation in half of disease-progressive melanomas, suggesting cross-resistance to salvage anti-PD-1/PD-L1 immunotherapy. Thus, melanoma acquires MAPKi resistance with highly dynamic and recurrent non-genomic alterations and co-evolving intra-tumoral immunity.

Combined BRAF- and MEK-targeted therapy improves upon BRAF inhibitor (BRAFi) therapy but is still beset by acquired resistance. We show that melanomas acquire resistance to combined BRAF and MEK inhibition by augmenting or combining mechanisms of single-agent BRAFi resistance. These double-drug resistance-associated genetic configurations significantly altered molecular interactions underlying MAPK pathway reactivation. (V600E)BRAF, expressed at supraphysiological levels because of (V600E)BRAF ultra-amplification, dimerized with and activated CRAF. In addition, MEK mutants enhanced interaction with overexpressed (V600E)BRAF via a regulatory interface at R662 of (V600E)BRAF. Importantly, melanoma cell lines selected for resistance to BRAFi+MEKi, but not those to BRAFi alone, displayed robust drug addiction, providing a potentially exploitable therapeutic opportunity.

As the use of lenalidomide expands, the poorly understood phenomenon of lenalidomide-induced thyroid abnormalities will increase. In this study, we compared rates of therapy-induced hypothyroidism in 329 patients with diffuse large B-cell lymphoma (DLBCL) treated with conventional chemotherapy (DLBCL-c) or conventional chemotherapy plus lenalidomide (DLBCL-len). We measured serum levels of tumor necrosis factor α, interferon gamma, interleukin 6, interleukin 12, and interleukin 15 before and after treatment. We found a significantly higher rate of therapy-induced hypothyroidism in the DLBCL-len group (25.8% vs. 1.3%), and we found a statistically significant increase in serum tumor necrosis factor α in patients with lenalidomide-induced hypothyroidism.

Epigenetic changes in cancer are thought to contribute to regulation of invasion and metastasis. To study this at a genome-wide level in melanoma we analyzed the methylome of 44 cases of malignant melanoma. We saw widespread demethylation in melanoma occurring preferentially outside of CpG islands. Comparison of primary and metastatic lesions showed demethylation occurs early during carcinogenesis with few additional alterations in advanced tumors. The colony stimulating factor-1 receptor was aberrantly expressed and hypomethylated in nearly all cases. The expression of CSF1R was validated by IHC on primary tumors and by qPCR and Western blotting in BRAF mutant and WT cell lines. CSF1R can be aberrantly expressed via an upstream LTR element in Hodgkin’s lymphoma. After analyzing our patient samples and the cell lines, we have found this aberrant transcript may be the dominant form in melanoma as well. Expression of one of its ligands IL34 was also shown in the cell lines by both ELISA and qPCR pointing to a potential autocrine regulatory loop. The effects of a small molecule inhibitor, PLX3397 as well as shRNA-mediated knockdown of the receptor were investigated in 2D and 3D cell culture. We saw inhibition of cell growth, smaller colony size, increased apoptosis and decreased invasiveness - suggesting a functional role for CSF1R in melanoma. Treatment of melanoma with small molecule inhibitors of BRAF V600E is effective for a time, but resistance invariably develops. The feedback activation of EGFR, BRAF amplification, BRAF splice variants and others are known to aid in the acquisition of resistance and the rebound activation of the MAPK-pathway. We are suggesting a role for CSF1R in this process. In Western experiments, the rebound of phospho-ERK after BRAF inhibitor treatment was accelerated with the addition of CSF1R ligands, or delayed with PLX3397, also attenuating AKT phosphorylation. Melanoma cells stably expressing shRNA against CSF1R recapitulated the effects of the inhibitor. Assaying the cells at different time points during a long-term V600E inhibitory experiment, we saw increasing levels of the transcription factor RUNX1, followed by increasing levels of IL34 and of the receptor, as well as its maturation, evidenced by the appearance of the high MW form. Utilizing shRNA-mediated knockdown of RUNX1 resulted in lower levels of the CSF1R and IL34 transcripts and delayed the rebound. Analysis of primary RNA-Seq data showed an increase in RUNX1, CSF1R and IL34 expression in resistant tumors. Co-inhibition of CSF1R and BRAF was also tested and resulted in synergistic blockade of cell growth in vitro and xenograft growth in vivo. The CSF1R inhibitor, PLX3397 is currently in clinical trials for glioblastoma, prostate, breast cancers and other cancers. These data present a preclinical rationale for its study in malignant melanoma. Citation Format: Orsolya Giricz, Yongkai Mo, Caroline Y. Hu, Yiting Yu, Kith Pradhan, Matthias Bartenstein, Nandini Ramachandra, Veronika Polishchuck, Kimberly B. Dahlman, Tushar Bhagat, Hoa Nguyen, Bernice Matusow, Rafe Shellooe, Elizabeth Burton, Paraic Kenny, John Greally, Jeffrey Sosman, Gideon Bollag, Brian West, Amit Verma. Aberrant expression of CSF1R in melanoma is driven through an endogenous viral promoter and it contributes to malignant growth and the acquisition of resistance against BRAF inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3332. doi:10.1158/1538-7445.AM2017-3332

Next generation sequencing (NGS) has been used to characterize the overall genomic landscape of melanomas. Here, we systematically examined mutations from recently published melanoma NGS data involving 241 paired tumor-normal samples to identify potentially clinically relevant mutations. Melanomas were characterized according to an in-house clinical assay that identifies well-known specific recurrent mutations in five driver genes: BRAF (affecting V600), NRAS (G12, G13, and Q61), KIT (W557, V559, L576, K642, and D816), GNAQ (Q209), and GNA11 (Q209). Tumors with none of these mutations are termed “pan negative.” We then mined the driver mutation-positive and pan-negative melanoma NGS data for mutations in 632 cancer genes that could influence existing or emerging targeted therapies. First, we uncovered several genes whose mutations were more likely associated with BRAF- or NRAS-driven melanomas, including TP53 and COL1A1 with BRAF, and PPP6C, KALRN, PIK3R4, TRPM6, GUCY2C, and PRKAA2 with NRAS. Second, we found that the 69 “pan-negative” melanoma genomes harbored alternate infrequent mutations in the five known driver genes along with many mutations in genes encoding guanine nucleotide binding protein α-subunits. Third, we identified 12 significantly mutated genes in “pan-negative” samples (ALK, STK31, DGKI, RAC1, EPHA4, ADAMTS18, EPHA7, ERBB4, TAF1L, NF1, SYK, and KDR), including five genes (RAC1, ADAMTS18, EPHA7, TAF1L, and NF1) with a recurrent mutation in at least two “pan-negative” tumor samples. This meta-analysis provides a road map for the study of additional potentially actionable genes in both driver mutation-positive and pan-negative melanomas. Mol Cancer Ther; 13(7); 1918–28. ©2014 AACR.