Driver Mutations In Melanoma Research Articles

Efficacy and toxicity of BRAF targeted therapy in elderly patients with melanoma.

e23270 Background: Melanoma is the most lethal form of skin cancer which have seen drastic improvement in patient survival over the last decade. BRAF is the most common driver mutation in melanoma, seen in ≈50% of all patients (≈30% of patients > 65). The use of BRAF & MEK inhibitors yields high response rates, though it is limited by toxicity and development of acquired resistance. Acknowledging these limitations, we aimed at assessing the efficacy and toxicity of these agents in melanoma patients > 65. Methods: We identified electronic medical records of all melanoma patients > 65 that were treated with BRAF & MEK inhibitors at our institution over the years 2017-2023. Data was retrospectively collected including demographics, disease characteristics, treatment given, response patterns and toxicity. Results: 106 patients were identified. The median age was 71 (65-89), 55% were males. The median follow up was 28.9 months. 32 (30%) patients were treated at first line, 58 (55%) at second line and 16 (15%) at third line. 88 (83%) evaluable patients received treatment for unresectable/metastatic disease of which 84% had an objective response (60% partial response, 24% complete response). Response rate (RR) was 82%, 85% and 87% for first, second and third line respectively. RR was 86% for patients with an increased serum lactate dehydrogenase. 33% of patients had active central nervous system (CNS) metastases at treatment initiation, for whom the systemic RR was 80% and the CNS RR was 39%. The median progression free survival (PFS) was 7.9 months, with a PFS of 6, 8.3 and 13.4 months for first, second and third line respectively. The median PFS was 5.7 months for patients with active CNS disease. The median overall survival (OS) from treatment initiation was 15.7 months (12.5, 14.5, 31.9 for first, second & third line respectively). The median OS for patients with CNS disease was 9.8 months. 16 patients were treated in the adjuvant setting, of which 6 (37%) finished treatment as planned, 3 stopped due to disease progression (19%) and 6 stopped due to toxicity (37%). 88% of patients experienced adverse events (AEs) of any grade, with 27% having grade 3-4 toxicity. There were no grade 5 toxicities reported. 36% of patients experienced one AE, while 52% experienced two or more. 21% of patients stopped treatment due to toxicity, 28% needed a dose reduction and 20% changed to different BRAF/MEK inhibitors. 10% of patients needed systemic corticosteroids to treat AEs. The most common toxicities seen were fever (30%), fatigue (30%), skin rash (22%), elevated liver function tests (20%), arthralgia/myalgia (15%), nausea (14%) and diarrhea (11%). 7% had decrease in cardiac ejection fraction with one grade 3 leading to treatment discontinuation. Conclusions: Treatment with BRAF & MEK inhibitors is challenging in older patients, with a high prevalence of toxicity leading to treatment modifications and discontinuation. Efficacy seems to be the same as in the general population.

Abstract 4384: Differential epitope tagging of oncogenic GNAQ mutants produces distinct effects on downstream signaling of GNAQ

Abstract GNAQ Q209P and Q209L are common driver mutations in uveal melanoma, leading to constitutive activation of downstream signaling of GNAQ. It is not fully understood whether the two GNAQ mutants have similar effects on downstream signaling pathways. Due to lack of available specific GNAQ antibody, epitope tagging is a well-established tool for protein interaction studies using mass spectrometry. Several studies used an epitope tag inserted into an internal region or the c-terminus of GNAQ to study its function. However, the functional consequences of these modalities on effector engagement are not fully elucidated. Here, we engineered both GNAQ wild-type and GNAQ mutants (Q209L and Q209P) without epitope tag as well as three different commonly used tagging modalities. A 3xflag tag of 22 amino acids was inserted after residue 122 of GNAQ. A MYC/DDK tag consisting of 18 amino acids was incorporated before the stop codon of GNAQ. An internal Glu-Glu epitope tag (EE tag) of 6 amino acids was introduced internally by mutating residues AYLPTQ(171-176) of GNAQ to EYMPTE. To assess the impact of the different modalities on the function of GNAQ mutants, we introduced them into 293FT cells and examined the known oncogenic signaling outputs downstream of GNAQ: MAPK, PKC and FAK signaling. We found that all three tags of both GNAQQ209L and GNAQQ209P activated MAPK signaling at similar levels as the corresponding untagged GNAQ mutants as evidenced by increases of pERK and pp90RSK level compared to GNAQ wild-type controls. By contrast, both GNAQQ209L and GNAQQ209P tagged with MYC/DDK induced lower p-PKD (a readout of PKC) and p-FAK (a readout of FAK activation) compared to EE-tagged or untagged, suggesting that MYC/DDK tag fused to the c-terminus of GNAQ affects specific effectors downstream of GNAQ. Furthermore, GNAQQ209P with the 3xflag tag induced lower levels of p-PKD and p-FAK than 3xflag tagged GNAQQ209L did, indicating that GNAQQ209P may have a different three-dimensional conformation compared to GNAQQ209L with different downstream effectors engagement. Moreover, the GNAQ/11 inhibitor YM-254890 inhibited phosphorylation of ERK, PKD, FAK in a concentration dependent manner in 293FT cells transfected with GNAQ mutants tagged with MYC/DDK but had no effect on MAPK, PKC and FAK signaling in cells expressing EE-tagged GNAQ mutants. These data suggest that EE tag has no effect on the function of GNAQ , but interferes with YM-254890 binding. Our findings highlight unappreciated consequences of epitope-tagging of the oncogene GNAQ that are relevant for studies on the interactome of mutant GNAQ and drug response. Citation Format: Chinchu Jagadan Ushakumari, Aashish Manglik, Boris C Bastian, Xu Chen. Differential epitope tagging of oncogenic GNAQ mutants produces distinct effects on downstream signaling of GNAQ [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4384.

The Surprising Diversity of UV‐Induced Mutations

AbstractUltraviolet (UV) light is the most pervasive environmental mutagen and the primary cause of skin cancer. Genome sequencing of melanomas and other skin cancers has revealed that the vast majority of somatic mutations in these tumors are cytosine‐to‐thymine (C>T) substitutions in dipyrimidine sequences, which, together with tandem CC>TT substitutions, comprise the canonical UV mutation “signature”. These mutation classes are caused by DNA damage directly induced by UV absorption, namely cyclobutane pyrimidine dimers (CPDs) or 6‐4 pyrimidine‐pyrimidone photoproducts (6‐4PP), which form between neighboring pyrimidine bases. However, many of the key driver mutations in melanoma do not fit this mutation signature, but instead are caused by T>A, T>C, C>A, or AC>TT substitutions, frequently occurring in non‐dipyrimidine sequence contexts. This article describes recent studies indicating that UV light causes a more diverse spectrum of mutations than previously appreciated, including many of the mutation classes observed in melanoma driver mutations. Potential mechanisms for these diverse mutation signatures are discussed, including UV‐induced pyrimidine‐purine photoproducts and indirect DNA damage induced by UVA light. Finally, the article reviews recent findings indicating that human DNA polymerase eta normally suppresses these non‐canonical UV mutation classes, which can potentially explain why canonical C>T substitutions predominate in human skin cancers.

Abstract PR002: Somatic mutation rates and strength of selection on driver genes change by age in melanoma

Abstract The frequencies of driver mutations in melanoma vary in patients of different ages. However, it is unclear whether these differences in frequency are driven by variation in underlying mutation rates or by a changing selective regime in the aging body. Employing a bulk tumor sequence dataset from 5472 melanomas (459 whole-exome sequences and 5013 cancer gene-panel sequences) analyzed with the cancereffectsizeR package, we quantified somatic mutation rates and the strength of selection on somatic mutations, measuring the survival advantage conferred by a somatic mutation across the tumorigenic trajectory. Likelihood ratio tests were used to compare cancer effect sizes between age groups: <40 y/o, 40-59 y/o and ≥ 60 y/o. The proportion of cancer effect attributable to each mutational source was calculated by averaging over bootstrapped resample of mutational signature weights. Mann-Whitney U statistics were used to test the difference in signature weights and cancer effect sources across the groups.The underlying mutation rate increased with age, with a mean of 4.49e-6, 4.88e-6, 6.45e-6 in patients <40 y/o, 40-59 y/o and ≥ 60 y/o respectively. From the whole-exome and panel data, 23 variants differed significantly across age groups, among which BRAF V600E had the largest effect sizes, followed by NRAS Q61R, NRAS Q61K, NRAS Q61L. BRAF V600E were significantly larger in patients <40 y/o, while NRAS Q61R, NRAS Q61K, NRAS Q61L were significantly larger in patients 40-59 y/o and ≥ 60 y/o. Although underlying mutation rates and strengths of selection varied across age groups, the origin of melanomas from patients in all three age groups was predominantly attributed to UV light. These observations illuminate numerous theoretical questions regarding the origins of cancer at different ages. They are helpful to widespread implementation of prevention strategies. Moreover, understanding the relative strength of selection on driver mutations within patients at distinct ages is crucial for improving precision therapeutic interventions. Citation Format: Yihan Liu, Moein Rajaei, Jeff Mandell, Jeffrey Townsend. Somatic mutation rates and strength of selection on driver genes change by age in melanoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr PR002.

Utility of sequencing for ATP6AP1 and ATP6AP2 to distinguish between atypical granular cell tumor with junctional component and melanoma.

Granular cell tumor (GCT) is a S100+ neoplasm with atypical and malignant variants. Similar to melanocytic neoplasms, the tumors make nests and can have junctional components raising a differential diagnosis of melanoma. Nevi and melanomas may also have granular cell cytoplasm. MelanA is useful in distinguishing melanocytic from granular cell lineage, but increasingly MelanA/SOX10 negative melanomas have been recognized by correlation with molecular methods. We encountered several cases with morphologic overlap between melanoma and atypical GCT necessitating additional molecular workup. We sequenced two cases and searched our archive for similar cases of GCT with overlapping features of melanocytic lineage. In our two index cases, we excluded melanoma driver mutations and identified frameshift or premature stop codons in ATP6AP1/2 pathognomonic of granular cell lineage. Data retrieved from Cosmic identified 24 melanomas with missense single nucleotide variants (SNVs) in ATP6AP1 but no frameshift or premature stop codons. Twenty-one melanomas had missense SNVs in ATP6AP2. One melanoma had a premature stop codon in ATP6AP2, but this lesion also had a melanoma-associated driver mutation NRASQ61K. We found 1 of 23 additional cases of GCT in our archives with a junctional component and no additional cases with maturation. Atypical and malignant GCT can have histopathologic overlap with melanoma. Frameshift and premature stop codons in ATP6AP1/2 are specific for granular cell lineage, and capable of excluding melanoma, in the absence of known melanoma-associated driver mutations.

Outcomes of patients with advanced NF1-mutant melanoma treated with MEK inhibitors.

e21513 Background: Mutations in neurofibromin 1 ( NF1) constitute the third most frequent driver mutation in melanoma, occurring in approximately 15% of patients. NF1 is a tumor suppressor gene that negatively regulates the MAPK pathway by inactivating RAS through the hydrolysis of RAS-GTP to the inactive form, RAS-GDP. Preclinical studies have demonstrated that NF1 mutations induce the activation of the MAPK pathway through constitutively maintaining the active form of RAS protein, and that MEK inhibitors cause growth arrest of NF1-mutant melanoma in vitro and tumor regressions in vivo. Methods: We conducted a retrospective analysis to evaluate the outcomes of patients with NF1-mutant melanoma who were treated with MEK inhibitors using our institutional melanoma database. We searched for all melanoma patients whose melanoma was analyzed with next generation sequencing (NGS), and their clinical, pathological and molecular characteristics were examined along with the details of MEK inhibitor treatment and clinical outcomes. Results: Among 229 patients whose melanoma was analyzed with the NGS, we identified 32 patients whose melanoma harbored a pathogenic or likely pathogenic NF1 mutation, of which four were treated with trametinib. The clinical, molecular characteristics and the outcomes of the 4 patients are summarized in the table. All had previously experienced disease progression following anti-PD1 antibody therapy. One patient with metastatic mucosal melanoma had a confirmed partial response to trametinib treatment with time to progression of 18 months. Two patients had regression of the metastatic lesions at the initial tumor response evaluation, but due to significant toxicity, treatment was discontinued. Their disease progressed within 3 months after treatment discontinuation. Two patients with initial tumor regression had a mucosal primary melanoma. Interestingly, the patient with a prolonged response had the highest variant allele frequency (VAF) of NF1 whereas the early progressor had the lowest VAF (Table). All responders (including the unconfirmed responders) had a VAF of >35%. Conclusions: Despite the small sample size, our findings suggest a potential promising efficacy of trametinib in the setting of NF1-mutant melanoma, particularly those with high allelic frequency, thereby providing a strong rationale for a prospective study to evaluate the clinical efficacy of MEK inhibitors in this molecular subtype of melanoma. [Table: see text]

Genome-wide maps of UVA and UVB mutagenesis in yeast reveal distinct causative lesions and mutational strand asymmetries.

Ultraviolet (UV) light primarily causes C > T substitutions in lesion-forming dipyrimidine sequences. However, many of the key driver mutations in melanoma do not fit this canonical UV signature, but are instead caused by T > A, T > C, or C > A substitutions. To what extent exposure to the UVB or UVA spectrum of sunlight can induce these noncanonical mutation classes, and the molecular mechanism involved is unclear. Here, we repeatedly exposed wild-type or repair-deficient yeast (Saccharomyces cerevisiae) to UVB or UVA light and characterized the resulting mutations by whole genome sequencing. Our data indicate that UVB induces C > T and T > C substitutions in dipyrimidines, and T > A substitutions that are often associated with thymine-adenine (TA) sequences. All of these mutation classes are induced in nucleotide excision repair-deficient cells and show transcriptional strand asymmetry, suggesting they are caused by helix-distorting UV photoproducts. In contrast, UVA exposure induces orders of magnitude fewer mutations with a distinct mutation spectrum. UVA-induced mutations are elevated in Ogg1-deficient cells, and the resulting spectrum consists almost entirely of C > A/G > T mutations, indicating they are likely derived from oxidative guanine lesions. These mutations show replication asymmetry, with elevated G > T mutations on the leading strand, suggesting there is a strand bias in the removal or bypass of guanine lesions during replication. Finally, we develop a mutation reporter to show that UVA induces a G > T reversion mutation in yeast that mimics the oncogenic NRAS Q61K mutation in melanoma. Taken together, these findings indicate that UVA and UVB exposure can induce many of the noncanonical mutation classes that cause driver mutations in melanoma.

Contributions of replicative and translesion DNA polymerases to mutagenic bypass of canonical and atypical UV photoproducts

UV exposure induces a mutation signature of C > T substitutions at dipyrimidines in skin cancers. We recently identified additional UV-induced AC > TT and A > T substitutions that could respectively cause BRAF V600K and V600E oncogenic mutations. The mutagenic bypass mechanism past these atypical lesions, however, is unknown. Here, we whole genome sequenced UV-irradiated yeast and used reversion reporters to delineate the roles of replicative and translesion DNA polymerases in mutagenic bypass of UV-lesions. Our data indicates that yeast DNA polymerase eta (pol η) has varied impact on UV-induced mutations: protecting against C > T substitutions, promoting T > C and AC > TT substitutions, and not impacting A > T substitutions. Surprisingly, deletion rad30Δ increased novel UV-induced C > A substitutions at CA dinucleotides. In contrast, DNA polymerases zeta (pol ζ) and epsilon (pol ε) participated in AC > TT and A > T mutations. These results uncover lesion-specific accurate and mutagenic bypass of UV lesions, which likely contribute to key driver mutations in melanoma.

Undifferentiated and Dedifferentiated Metastatic Melanomas Masquerading as Soft Tissue Sarcomas: Mutational Signature Analysis and Immunotherapy Response

The distinction between undifferentiated melanoma (UM) or dedifferentiated melanoma (DM) from undifferentiated or unclassifiable sarcoma can be difficult and requires the careful correlation of clinical, pathologic, and genomic findings. In this study, we examined the utility of mutational signatures to identify patients with UM/DM with particular attention as to whether this distinction matters for treatment because the survival of patients with metastatic melanoma has dramatically improved with immunologic therapy, whereas durable responses are less frequent in sarcomas. We identified 19 cases of UM/DM that were initially reported as unclassified or undifferentiated malignant neoplasm or sarcoma and submitted for targeted next-generation sequencing analysis. These cases were confirmed as UM/DM by harboring melanoma driver mutations, UV signature, and high tumor mutation burden. One case of DM showed melanoma in situ. Meanwhile, 18 cases represented metastatic UM/DM. Eleven patients had a prior history of melanoma. Thirteen of 19 (68%) of the tumors were immunohistochemically completely negative for 4 melanocytic markers (S100, SOX10, HMB45, and MELAN-A). All cases harbored a dominant UV signature. Frequent driver mutations involved BRAF (26%), NRAS (32%), and NF1 (42%). In contrast, the control cohort of undifferentiated pleomorphic sarcomas (UPS) of deep soft tissue exhibited a dominant aging signature in 46.6% (7/15) without evidence of UV signature. The median tumor mutation burden for DM/UM vs UPS was 31.5 vs 7.0 mutations/Mb (P < .001). A favorable response to immune checkpoint inhibitor therapy was observed in 66.6% (12/18) of patients with UM/DM. Eight patients exhibited a complete response and were alive with no evidence of disease at the last follow-up (median 45.5 months). Our findings support the usefulness of the UV signature in discriminating DM/UM vs UPS. Furthermore, we present evidence suggesting that patients with DM/UM and UV signatures can benefit from immune checkpoint inhibitor therapy.

Damage mapping techniques and the light they have shed on canonical and atypical UV photoproducts.

Ultraviolet (UV) light is a pervasive threat to the DNA of terrestrial organisms. UV light induces helix-distorting DNA lesions, primarily cyclobutane pyrimidine dimers (CPDs) that form between neighboring pyrimidine bases. Unrepaired CPD lesions cause cytosine-to-thymine (C>T) substitutions in dipyrimidine sequences, which is the predominant mutation class in skin cancer genomes. However, many driver mutations in melanoma (e.g., in the BRAF and NRAS oncogenes) do not fit this UV mutation signature. Recent studies have brought to light the intriguing hypothesis that these driver mutations may be induced by infrequent or atypical UV photoproducts, including pyrimidine 6-4 pyrimidone photoproducts (6-4PP) and thymine-adenine (TA) photoproducts. Here, we review innovative methods for mapping both canonical and atypical UV-induced photoproducts across the genome.

Genomic comparison between an in vitro three-dimensional culture model of melanoma and the original primary tumor.

Three-dimensional (3D) melanoma culture is a personalized in vitro model that can be used for high-fidelity pre-clinical testing and validation of novel therapies. However, whether the genomic landscape of 3D cultures faithfully reflects the original primary tumor which remains unknown. The purpose of our study was to compare the genomic landscapes of 3D culture models with those of the original tumors. Patient-derived xenograft (PDX) tumors were established by engrafting fresh melanoma tissue from each patient. Then, a 3D culture model was generated using cryopreserved PDX tumors embedded in pre-gelled porcine skin decellularized extracellular matrix with normal human dermal fibroblasts. Using whole-exome sequencing, the genomic landscapes of 3D cultures, PDX tumors, and the original tumor were compared. We found that 91.4% of single-nucleotide variants in the original tumor were detected in the 3D culture and PDX samples. Putative melanoma driver mutations (BRAF p.V600E, CDKN2A p.R7*, ADAMTS1 p.Q572*) were consistently identified in both the original tumor and 3D culture samples. Genome-wide copy number alteration profiles were almost identical between the original tumor and 3D culture samples, including the driver events of ARID1B loss, BRAF gain, and CCND1 gain. In conclusion, our study revealed that the genomic profiles of the original tumor and our 3D culture model showed high concordance, indicating the reliability of our 3D culture model in reflecting the original characteristics of the tumor.

Pervasive conditional selection of driver mutations and modular epistasis networks in cancer.

Cancer driver mutations often display mutual exclusion or co-occurrence, underscoring the key role of epistasis in carcinogenesis. However, estimating the magnitude of epistasis and quantifying its effect on tumor evolution remains a challenge. We develop a method (Coselens) to quantify conditional selection on the excess of nonsynonymous substitutions in cancer genes. Coselens infers the number of drivers per gene in different partitions of a cancer genomics dataset using covariance-based mutation models and determines whether coding mutations in a gene affect selection for drivers in any other gene. Using Coselens, we identify 296 conditionally selected gene pairs across 16 cancer types in the TCGA dataset. Conditional selection affects 25%-50% of driver substitutions in tumors with >2 drivers. Conditionally co-selected genes form modular networks, whose structures challenge the traditional interpretation of within-pathway mutual exclusivity and across-pathway synergy, suggesting a more complex scenario where gene-specific across-pathway epistasis shapes differentiated cancer subtypes.

Undifferentiated pleomorphic sarcoma of the breast with neoplastic fever: case report and genomic characterization

PurposePrimary breast sarcomas are extraordinary rare, in particular undifferentiated pleomorphic sarcoma (UPS). UPS with neoplastic fever (UPS-NF) of the breast has not been reported yet. Here, we present an extended UPS-NF of the breast including its comprehensive molecular workup.MethodsA 58-year-old female presented with general malaise, fever spikes, weight loss, and a massively swollen left breast. C-reactive protein and blood leucocytes were significantly increased. However, repeated blood cultures and smears were all sterile. Histopathology of the abscess-forming tumor revealed an undifferentiated malignancy with numerous of tumor giant cells as well as spindle-shaped cells with nuclear pleomorphism and hyperchromasia. Immunohistochemistry demonstrated partial, patchy desmin staining and weak heterogonous neuron-specific enolase immunoreactivity of tumor cells, but a focal staining for Melan-A.ResultsNeither common melanoma driver mutations nor an ultraviolet mutational signature was detected by whole genome sequencing. Using FISH and RT-PCR we also excluded translocations characteristic for clear cell sarcoma. Thus, the diagnosis of inflammatory UPS-NF of the breast was considered highly probable. Despite a complete mastectomy, the tumor recurred after only three months. This recurrence was treated with a combination of ipilimumab and nivolumab based on the primary tumor’s TPS score for PD-L1 of 30%. After an initial response, however, the tumor was progressive again.ConclusionWe describe here the first case of UPS-NF of the breast, which shows great clinical and histopathologic resemblances to previously reported UPS-NF of other anatomic localizations.

STAT3 promotes melanoma metastasis by CEBP-induced repression of the MITF pathway.

Metastatic melanoma is hallmarked by its ability of phenotype switching to more slowly proliferating, but highly invasive cells. Here, we tested the impact of signal transducer and activator of transcription 3 (STAT3) on melanoma progression in association with melanocyte inducing transcription factor (MITF) expression levels. We established a mouse melanoma model for deleting Stat3 in melanocytes with specific expression of human hyperactive NRASQ61K in an Ink4a deficient background, two frequent driver mutations in human melanoma. Mice devoid of Stat3 showed early disease onset with higher proliferation in primary tumors, but displayed significantly diminished lung, brain and liver metastases. Whole genome expression profiling of tumor-derived cells also showed a reduced invasion phenotype, which was further corroborated by 3D melanoma model analysis. Notably, loss or knockdown of STAT3 in mouse or human cells resulted in up-regulation of MITF and induction of cell proliferation. Mechanistically we show that STAT3-induced CEBPa/b expression was sufficient to suppress MITF transcription. Epigenetic analysis by ATAC-seq confirmed that CEBPa/b binding to the MITF enhancer region silenced the MITF locus. Finally, by classification of patient-derived melanoma samples, we show that STAT3 and MITF act antagonistically and hence contribute differentially to melanoma progression. We conclude that STAT3 is a driver of the metastatic process in melanoma and able to antagonize MITF via direct induction of CEBP family member transcription.

Atypical UV Photoproducts Induce Non-canonical Mutation Classes Associated with Driver Mutations in Melanoma

SUMMARYSomatic mutations in skin cancers and other ultraviolet (UV)-exposed cells are typified by C>T and CC>TT substitutions at dipyrimidine sequences; however, many oncogenic “driver” mutations in melanoma do not fit this UV signature. Here, we use genome sequencing to characterize mutations in yeast repeatedly irradiated with UV light. Analysis of ~50,000 UV-induced mutations reveals abundant non-canonical mutations, including T>C, T>A, and AC>TT substitutions. These mutations display transcriptional asymmetry that is modulated by nucleotide excision repair (NER), indicating that they are caused by UV photoproducts. Using a sequencing method called UV DNA endonuclease sequencing (UVDE-seq), we confirm the existence of an atypical thymine-adenine photoproduct likely responsible for UV-induced T>A substitutions. Similar non-canonical mutations are present in skin cancers, which also display transcriptional asymmetry and dependence on NER. These include multiple driver mutations, most prominently the recurrent BRAF V600E and V600K substitutions, suggesting that mutations arising from rare, atypical UV photoproducts may play a role in melanomagenesis.

Dynamics of nevus development implicate cell cooperation in the growth arrest of transformed melanocytes.

Mutational activation of the BRAF proto-oncogene in melanocytes reliably produces benign nevi (pigmented 'moles'), yet the same change is the most common driver mutation in melanoma. The reason nevi stop growing, and do not progress to melanoma, is widely attributed to a cell-autonomous process of 'oncogene-induced senescence'. Using a mouse model of Braf-driven nevus formation, analyzing both proliferative dynamics and single-cell gene expression, we found no evidence that nevus cells are senescent, either compared with other skin cells, or other melanocytes. We also found that nevus size distributions could not be fit by any simple cell-autonomous model of growth arrest, yet were easily fit by models based on collective cell behavior, for example in which arresting cells release an arrest-promoting factor. We suggest that nevus growth arrest is more likely related to the cell interactions that mediate size control in normal tissues, than to any cell-autonomous, 'oncogene-induced' program of senescence.

Abstract A21: Identification of putative melanoma driver mutations in the ErbB4 receptor tyrosine kinase gene

Abstract Introduction: Despite the advances in targeted therapies and immunotherapeutics, the 5-year survival rate of metastatic melanoma patients remains about 20%. In part, the high mortality rate is due to the fact that there are currently no other clinically actionable targets other than those that have been identified in the RAS/RAF/MEK/MAPK pathway. Our analyses of The Cancer Genome Atlas (TCGA) Skin Cutaneous Melanoma (SKCM) data set revealed that 15% of the cases harbor at least one nonsynonymous missense mutation in the gene that encodes the ErbB4 receptor tyrosine kinase. This mutation incidence is significantly higher than that of the other ERBB genes in the same data set. However, unlike the validated V600E/K/D/R mutations in the BRAF oncogene, ERBB4 mutations in melanoma are extremely heterogenous with 76 unique ERBB4 nonsynonymous missense mutations, none of which have incidence rates of greater than 1%. Furthermore, some of these ERBB4 mutations have already been shown to be necessary for the proliferation of some human melanoma cell lines, demonstrating a need to determine which ERBB4 mutations contribute to melanoma tumorigenesis. Experimental Procedures/Summary of Data: Consequently, we have used various in silico approaches to predict the functional role of ERBB4 nonsynonymous missense mutations in melanoma. We found that many TCGA-SKCM ERBB4 mutations affect highly conserved regions. Indeed, 57 ERBB4 mutations affect a residue that is conserved in at least one other ErbB receptor. Moreover, 7 ERBB4 mutations affect a residue that is conserved in another ErbB receptor and is the location of a gain-of-function mutation in the other ERBB gene. Fifteen (15) of the putative ERBB4 melanoma driver mutations are found in other tumor types, and 3 transform the growth of fibroblasts and exhibit ligand-independent signaling. Finally, we found that the combination of the ERBB4 E542K and E872K mutations and the E452K mutation alone are necessary for the proliferation of some human melanoma cell lines. Conclusions: Unlike genes such as BRAF or NRAS, which contain a single or a small number of “hot spot(s)” for driver mutations, the ERBB4 gene appears to harbor numerous mutations that are likely to function as drivers of melanoma tumorigenesis. Whereas some of the ERBB4 mutations found in melanoma have been identified as bona fide melanoma drivers, most remain uncharacterized. The results of these analyses indicate that many of these uncharacterized mutations are likely to contribute to the malignant phenotype of melanoma. Therefore, there remains a need to distinguish which ERBB4 mutations function as drivers and can serve as biomarkers for response to therapies that disrupt ErbB4 signaling. Citation Format: Richard L. Cullum, Taraswi M. Ghosh, Lauren M. Lucas, Damien Waits, Kenneth M. Halanych, David J. Riese. Identification of putative melanoma driver mutations in the ErbB4 receptor tyrosine kinase gene [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr A21.

The RAC1 Target NCKAP1 Plays a Crucial Role in the Progression of Braf;Pten-Driven Melanoma in Mice

BRAFV600E is the most common driver mutation in human cutaneous melanoma and is frequently accompanied by loss of the tumor-suppressing phosphatase PTEN. Recent evidence suggests a co-operative role for RAC1 activity in BRAFV600E-driven melanoma progression and drug resistance. However, the underlying molecular mechanisms and the role of RAC1 downstream targets are not well-explored. In this study, we examine the role of the NCKAP1 subunit of the pentameric cytoskeletal SCAR/WAVE complex, a major downstream target of RAC1, in a mouse model of melanoma driven by BRAFV600E;PTEN loss. The SCAR/WAVE complex is the major driver of lamellipodia formation and cell migration downstream of RAC1 and depends on NCKAP1 for its integrity. Targeted deletion of Nckap1 in the melanocyte lineage delayed tumor onset and progression of a mutant Braf;Pten loss‒driven melanoma mouse model. Nckap1-depleted tumors displayed fibrotic stroma withincreased collagen deposition concomitant with enhanced immune infiltration. Nckap1 loss slowed proliferation and tumor growth, highlighting a role in cell-cycle progression. Altogether, we propose that NCKAP1-orchestrated actin polymerization is essential for tumor progression and maintenance of tumor tissue integrity in a mutant Braf/Pten loss‒driven mouse model for melanoma.

Abstract IA03: The Hippo pathway in melanoma

Abstract Melanoma is usually driven by mutations in BRAF or NRAS that trigger hyperactivation of mitogen-activated protein kinase (MAPK) signaling. However, MAPK targeted therapies are not sustainably effective in most patients. Accordingly, characterizing mechanisms that cooperatively drive melanoma progression is key to improving patient outcomes. One possible mechanism is the Hippo signaling pathway, which regulates cancer progression via its central oncoproteins YAP and TAZ, although it is relatively rarely affected by direct mutation. As YAP hyperactivation occurs in uveal melanoma, we investigated this oncogene in cutaneous melanoma. YAP protein expression was elevated in most benign nevi and primary cutaneous melanomas but present at only very low levels in normal melanocytes. In patient-derived xenografts and melanoma cell lines, we observed variable reliance of cell viability on Hippo pathway signaling that was independent of classical melanoma driver mutations such as BRAF and NRAS. YAP activity was enriched in invasive melanoma cell lines and was necessary for their invasive properties in culture. In in vivo studies, we found that expression of hyperactive YAP induced spontaneous melanoma metastasis in mice. Finally, in genotyping studies of melanoma, we observed the first ever hyperactivating YAP mutations in a human cancer, manifest as seven distinct missense point mutations that caused serine to alanine transpositions. Strikingly, these mutate four of five known serine residues targeted by the Hippo pathway, and we show that they lead to hyperactivation of YAP function. Our studies highlight the YAP oncoprotein as a potential therapeutic target in select subgroups of melanoma patients, although successful treatment with anti-YAP therapies will depend on identification of biomarkers other than YAP protein expression. Citation Format: Xiaomeng Zhang, Lie Yang, Ismael Vergara, Pacman Szeto, Youfang Zhang, Anthony Papenfuss, Mark Shackleton, Kieran Harvey. The Hippo pathway in melanoma [abstract]. In: Proceedings of the AACR Special Conference on the Hippo Pathway: Signaling, Cancer, and Beyond; 2019 May 8-11; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(8_Suppl):Abstract nr IA03.

Update on GNA Alterations in Cancer: Implications for Uveal Melanoma Treatment.

Tumorigenesis is correlated with abnormal expression and activity of G protein-coupled receptors (GPCRs) and associated G proteins. Oncogenic mutations in both GPCRs and G proteins (GNAS, GNAQ or GNA11) encoding genes have been identified in a significant number of tumors. Interestingly, uveal melanoma driver mutations in GNAQ/GNA11 were identified for a decade, but their discovery did not lead to mutation-specific drug development, unlike it the case for BRAF mutations in cutaneous melanoma which saw enormous success. Moreover, new immunotherapies strategies such as immune checkpoint inhibitors have given underwhelming results. In this review, we summarize the current knowledge on cancer-associated alterations of GPCRs and G proteins and we focus on the case of uveal melanoma. Finally, we discuss the possibilities that this signaling might represent in regard to novel drug development for cancer prevention and treatment.