James B. Massengill

Germline BAP1 mutation predisposes to uveal melanoma, lung adenocarcinoma, meningioma, and other cancers.

Objective To investigate the potential contribution of germline sequence alterations in the BAP1 gene in uveal melanoma (UM) patients with possible predisposition to hereditary cancer. Design A total of 53 unrelated UM patients with high risk for hereditary cancer and five additional family members of one proband were studied. Mutational screening was carried out by direct sequencing. Results Of the 53 UM patients studied, a single patient was identified with a germline BAP1 truncating mutation, c. 799 C→T (p.Q267X), which segregated in several family members and was associated with UM and other cancers. Biallelic inactivation of BAP1 and decreased BAP1 expression were identified in the UM, lung adenocarcinoma and meningioma tumours from three family members with this germline BAP1 mutation. Germline BAP1 variants of uncertain significance, likely non-pathogenic, were also identified in two additional UM patients. Conclusion This study reports a novel hereditary cancer syndrome caused by a germline BAP1 mutation that predisposes patients to UM, lung carcinoma, meningioma, and possibly other cancers. The results indicate that BAP1 is the candidate gene in only a small subset of hereditary UM, suggesting the contribution of other candidate genes.

Expanding the clinical phenotype of hereditary BAP1 cancer predisposition syndrome, reporting three new cases

The clinical phenotype of BAP1 hereditary cancer predisposition syndrome (MIM 614327) includes uveal melanoma (UM), cutaneous melanoma (CM), renal cell carcinoma (RCC), and mesothelioma. However, the frequency of the syndrome in patients with UM and the association with other cancers are still not clear. In this study, we screened 46 previously untested, unrelated UM patients with high risk for hereditary cancer for germline mutation in BAP1. We also studied four additional patients with a personal or family history suggestive of BAP1 hereditary cancer syndrome. We identified three patients with germline pathogenic mutations (c.2050 C>T, pGln684*; c.1182C>G, p.Tyr394*, and c.1882_1885delTCAC, p. Ser628Profs*8) in BAP1. Two of these three patients presented with UM and the third with a metastatic adenocarcinoma likely from a hepatic cholangiocarcinoma. Reported family histories included UM, mesothelioma, RCC, CM, and several other internal malignancies. The results of this study confirm the association between germline BAP1 mutation and predisposition to UM, mesothelioma, CM and RCC. However, other cancers, such as cholangiocarcinoma and breast carcinoma may be part of the phenotype of this hereditary cancer predisposition syndrome. In addition, the results support the existence of other candidate genes in addition to BAP1 contributing to hereditary predisposition to UM.

MET oncogene inhibition as a potential target of therapy for uveal melanomas.

PURPOSE. The purposes of this study were to investigate the frequency of MET activation in uveal melanomas (UMs), to study the potential molecular mechanism for its activation, and to assess the utility of MET inhibition as a potential therapy for UM. METHODS. The frequency of MET activation in UMs was studied by using immunohistochemistry and Western blot analysis in 46 primary UMs and six UM cell lines. Sequencing was used for detection of activating mutations in the MET gene, and the effect of selective MET inhibition was assessed by cell proliferation and migration assays. RESULTS. The results showed that the majority (82.5%) of the 46 UMs expressed activated MET protein. Three of the UM cell lines, C918, 92.1, and MEL202, showed strong MET and pMET expression, whereas the other three showed weaker expression. Sequence analysis identified no activating mutations in MET in any of the 22 tumors or in the six UM cell lines. Selective MET blocking showed inhibition of tumor cell proliferation at an IC(50) ranging from 2.5 to 5.2 microM. A significant inhibition of UM cell migration was also observed starting at 1.25 microM. CONCLUSIONS. The results indicate that MET is activated in a significant number of UMs and also that MET activation in UMs is most likely through indirect gene activation rather than copy number alteration or mutation involving the MET gene. MET inhibition could be a target of therapy for UM.

Analysis of BAP1 Germline Gene Mutation in Young Uveal Melanoma Patients

Abstract Background: To evaluate the prevalence of BAP1 germline mutations in a series of young patients with uveal melanoma (UM), diagnosed before age 30. Materials and Methods: The study was carried out on 14 young uveal melanoma patients (average age 21.4 years, range 3 months to 29 years). Germline DNA was extracted from peripheral blood. BAP1 sequencing was carried out using direct sequencing of all exons and adjacent intronic sequences. We also tested for germline mutations in additional melanoma-associated candidate genes CDKN2A and CDK4 (exon 4). Results: We identified one patient with a pathogenic mutation (c. 1717delC, p.L573fs*3) in BAP1. This patient was diagnosed with UM at age 18 years and had a family history of a father with UM and a paternal grandfather with cancer of unknown origin. One additional patient had an intronic variant of uncertain significance (c.123-48T > G) in BAP1 while the remaining 12 patients had no alteration. None of the patients had CDKN2A or CDK4 (Exon 4) mutations. Family history was positive for a number of additional malignancies in this series, in particular for cutaneous melanoma, prostate, breast and colon cancers. There were no families with a history of mesothelioma or renal cell carcinoma. Conclusions: This study suggests that a small subset of patients with early onset UM has germline mutation in BAP1. While young patients with UM should be screened for germline BAP1 mutations, our results suggest that there is a need to identify other candidate genes which are responsible for UM in young patients.

Germline BAP1 alterations in familial uveal melanoma

Uveal melanoma (UM) is the most commonly diagnosed primary intraocular tumor in adults. Familial UM (FUM), defined as two or more family members diagnosed with UM, is rare and estimated at less than 1% of all UM. Currently, BAP1 is the only gene known to contribute significant risk for UM. In this study we aimed to estimate the frequency of BAP1 mutation in FUM and to characterize the family and personal histories of other cancers in these families. We identified 32 families with FUM, including seven families previously reported by our group. BAP1 mutation testing was carried out by direct sequencing of the coding exons and the adjacent untranslated regions of the gene. Germline deletion and duplication analysis of BAP1 was assessed by multiplex ligation‐dependent probe amplification (MLPA). Germline BAP1 mutations were found in 6/32 (19%) families. No deletions or duplications were identified in any of the 24 samples tested by MLPA. Combined with published studies, the frequency of BAP1 mutations was 14/64 (22%) in FUM. FUM families without BAP1 mutations have distinct family histories with high rates of prostate cancer in first‐ and second‐degree relatives. It is likely that additional genes conferring risk for FUM exist. It is important to understand key shared features of FUM to focus future research on identifying these additional tumor predisposition syndromes. Though BAP1 should be tested first in these families, FUM families without BAP1 mutation should be explored for additional predisposition genes.

Melanoma candidate genes CDKN2A/p16/INK4A, p14ARF, and CDK4 sequencing in patients with uveal melanoma with relative high-risk for hereditary cancer predisposition.

The reported frequencies of germline mutations in the melanoma candidate genes are low in patients with uveal melanoma (UM). However, the number of families studied is limited and the majority of the published reports used low-sensitivity techniques for mutational screening. Identifying the frequency of alterations in any of the melanoma genes in patients with UM with increased hereditary cancer risk is important for proper counseling of these patients. We studied a total of 47 patients with UM including three with a family history of UM, 18 with a family and/or personal history of cutaneous melanoma (CM), three with early age at diagnosis (<30), 11 with increased risk for a known familial cancer syndrome, and 12 with a second primary tumor. Germline screening for mutations in CDKN2A, p14ARF, and exon 2 of CDK4 was carried out by direct sequencing. We identified a variant (IVS1-69 C>T) of uncertain significance in exon 1b of p14ARF in one of the patients with UM and his mother who also had UM. The variant was neither detected in any of the other patients with UM nor in 146 controls. We did not identify pathogenic mutations in CDKN2A nor exon 2 of CDK4 gene. Our study supports the low frequency of germline mutation of the CM candidate genes in patients with UM with family histories suggestive of a high risk for hereditary cancer. Germline testing for CDKN2A might be reserved for patients with UM with a family history of two or more CM.

Investigation of the potential utility of a linomide analogue for treatment of choroidal neovascularization

The aim of this study was to test the selectivity, in-vivo effectiveness, and potential mechanism of action of a linomide analogue (N-phenyl-1,2-dihydro-4-hydroxyl-2-oxo-quinoline-3-carboxamide, Lin05) for inhibition of choroidal neovascularization. The selectivity of Lin05 was tested in cell proliferation assays with human umbilical vein endothelial cells (HUVEC) and a retinal pigmented epithelial cell line(ARPE-19). In-vivo anti-angiogenic effect of Lin05 was investigated utilizing an experimental laser-induced choroidal neovascularization (ECNV) model in adult Brown Norway rats. Western blot and/or reverse transcriptase-PCR was used to test the effect of Lin05 on potential targets. Our results indicate that Lin05 is at least an 8-fold more selective inhibitor of endothelial cell proliferation compared to RPE cells. Systemic administration of Lin05 in an ECNV model was associated with a significant decrease in both vascular leakage on fluorescein angiography and lesion size by histopathology (p = 0.02). No systemic toxicity was detected for Lin05 in major organs such as the liver, lung and kidneys. Lin05 did not inhibit VEGF-induced VEGFR2 (KDR) phosphorylation in HUVEC nor was associated with decreased VEGF gene expression. Also it did not inhibit insulin-like growth factor (IGF-1) and Epidermal Growth Factor (EGF) induced activation of p42/p44 MAPK activation. It inhibited both PDGF- and bFGF-induced p42/p44 MAPK phosphorylation. However, the effect on PDGF was variable in different HUVEC cells. In conclusion, Lin05 is a potential anti-angiogenic agent for the treatment of eye diseases associated with pathological neovascularization. The anti-angiogenic effect of Lin05 is likely through inhibition of bFGF but not through inhibition of the VEGF/KDR pathway.

Analysis of the exome aggregation consortium (ExAC) database suggests that the BAP1-tumor predisposition syndrome is underreported in cancer patients

The BAP1‐tumor predisposition syndrome (BAP1‐TPDS) has been recently identified to predispose patients to a variety of cancers and preneoplastic lesions. About 130 unrelated probands have been identified worldwide; however, the impact of the syndrome is suspected to be much larger given the diversity of the cancer phenotype. To evaluate the frequency of germline BAP1 mutations in the general and cancer populations, we analyzed the Exome Aggregation Consortium (ExAC), a database that contains 53105 exomes of unrelated individuals unaffected by cancer (general population) and exomes of 7601 unrelated individuals affected by cancer provided by the Cancer Genome Atlas (TCGA, cancer subjects). BAP1 null variants were seen at much higher frequency in the cancer subjects (0.0526%) compared to the general population (0.00188%) with a relative risk of 27.93 and (P = 0.0011, [95% CI: 3.122‐249.883], Fishers exact test). We also studied a reported BAP1 null variant, c.1203T > G, p.T401* (rs200156887), observed commonly in the general population. Sequencing and restriction fragment polymorphism of the RT‐4 cell line that contains this variant revealed that it is in fact a 3bp deletion/insertion, c.1201_1203delinsGAG, a likely benign missense alteration p.Y401E explaining the relative high frequency of this variant in the general population. In conclusion, germline null mutations in BAP1 have a significantly higher frequency in cancer patients than the general population. Given the low frequency of reported families with BAP1‐TPDS, our results suggest that the syndrome is underreported especially in patients with cancer.

Abstract 1127: Lack of MAPK activation in significant number of uveal melanomas with somatic mutation in GNAQ and GNA11

Purpose: The aims of this study were to investigate the correlation between MAPK activation and somatic mutation in GNAQ and GNA11 genes in uveal melanoma (UM) and to investigate the potential utility of MEK inhibition as a target for therapy of UM in tumors with GNAQ and GNA11 mutations. Methods: Sequencing and restriction fragment length polymorphism (RFLP) were utilized for detection of activating mutations in codon 209 of the GNAQ and GNA11 genes in 44 primary UMs. The expression of phospho p44/42 MAPK (pERK1/2) was assessed by immunohistochemistry in 44 UMs. In addition, the expression of pERK1/2 and pMEK 1/2 were studied using Western blot analysis in 17 primary UMs (14 with GNAQ or GNA11 mutations) and five UM cell lines (C918, 92.1, OCM3, MEL202, MEL270). Three of the UM cell lines (92.1, MEL202 and MEL270) have GNAQ codon 209 mutations. The effect of three different selective MEK inhibitors (U126, PD98059 and PD184352) on UM cell proliferation and apoptosis were studied. Results: The majority (30/44, 68.2%) of the primary UM tumors showed somatic mutation in codon 209 of either the GNAQ or the GNA11 genes. With the exception of one tumor, the mutations in either gene were mutually exclusive. Of the 30 UM primary tumors with GNAQ and/or GNA11 mutation, pERK1/2 expression was absent in 26.7%, weak in 33.3%, moderate in 23.3%, and high in only 16.7%. Western blot showed no pMEK1/2 expression in 6/14 (42.9%) of UM with either GNAQ or GNA11 mutations. Two of the UM cell lines with GNAQ mutation showed weak pERK1/2 expression. In addition one showed no pMEK1/2 expression while the other one showed very weak pMEK1/2 expression. Selective MEK inhibitors slowed UM cell proliferation but didn9t induce significant apoptosis in UM cell lines regardless of GNAQ status. Conclusions: Our results indicate that a significant number of UM with somatic mutations in GNAQ or GNA11 showed no MAPK pathway activation. In UM, MEK inhibition is mostly cytostatic suggesting that selective MEK inhibitors alone may not be sufficient to control UM. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1127. doi:10.1158/1538-7445.AM2011-1127

Abstract C162: MET oncogen inhibition as a potentitial target for therapy of uveal melanoma

Purpose: Uveal melanomas (UM), including choroidal, iris and ciliary body melanomas, are the most common intraocular malignancy in adult. The tumor spreads through a hematogenous route mostly to the liver in about 50% of the patients. Once metastatic, UMs are highly fatal and currently there is no available therapy for these tumors. Identifying novel therapy is crucial to improve the survival of these patients. The aim of this study is to investigate the utility of MET inhibition as a potential therapy for UM. Methods: The frequency of MET activation (phospho‐MET expression) in UM was studied using immunohistochemistry in 46 tumors. The half maximum inhibitory concentration (IC50) of selective MET inhibitor SU11274 was assessed on the five UM cell lines using cell proliferation assay. Inhibition of MET activation in UM cells treated with the SU11274 was confirmed using Western blot analysis. Effect of MET inhibition on cell migration was also studied. Results: Our results showed that the majority (82.5%) of the 46 UM studied showed strong to moderate expression of phospho‐MET. Selective MET blocking showed inhibition of tumor cell proliferation at an IC50 ranging from 2∼ 10 µM. In addition significant inhibition UM cell line migration was observed. Conclusions: Our results indicate that MET is activated in a significant number of uveal melanomas. Our results also indicate the potential utility of MET inhibition as a target for therapy of UM. Citation Information: Mol Cancer Ther 2009;8(12 Suppl):C162.