Association of specific chromosome alterations with tumour phenotype in posterior uveal melanoma

Deferral of Treatment for Small Choroidal Melanoma and the Risk of Metastasis: An Investigation Using the Liverpool Uveal Melanoma Prognosticator Online (LUMPO)

BACKGROUND

We estimated metastatic-death risk when the treatment of small choroidal melanomas is deferred until growth is observed.

METHODS

In 24 patients with choroidal melanoma (median diameter 5.85 mm), the exponential growth rate estimated by a mixed-effects model was 4.3% per year. Using the Liverpool Uveal Melanoma Prognosticator Online v.3 (LUMPO3), we measured changes in 15-year metastatic and non-metastatic death risks according to whether the tumor is treated immediately or after observing growth 4 or 12 months later, considering age, sex, and metastasis predictors.

RESULTS

In 40-year-old females with 10 mm, disomy 3 and monosomy 3 choroidal melanomas (prevalence 16%), the 15-year absolute risks of metastatic death are 4.2% and 76.6%, respectively, increasing after a 4-month delay by 0.0% and 0.2% and by 3.0% and 2.3% with tumor growth rates of 5.0% and 20.0%, respectively. With 12-month delays, these risks increase by 0.0% and 0.5% and by 1.0% and 7.1%, respectively. Increases in metastatic-death risk are less with smaller tumors and with a higher risk of non-metastatic death.

CONCLUSIONS

Deferring treatment of choroidal melanomas until documentation of growth may delay iatrogenic visual loss by months or years and is associated with minimal increase in metastatic mortality, at least with small tumors with usual growth rates of up to 40% per year.

New Treatment Horizons in Uveal and Cutaneous Melanoma

Melanoma is a complex and heterogeneous malignant tumor with distinct genetic characteristics and therapeutic challenges in both cutaneous melanoma (CM) and uveal melanoma (UM). This review explores the underlying molecular features and genetic alterations in these melanoma subtypes, highlighting the importance of employing specific model systems tailored to their unique profiles for the development of targeted therapies. Over the past decade, significant progress has been made in unraveling the molecular and genetic characteristics of CM and UM, leading to notable advancements in treatment options. Genetic mutations in the mitogen-activated protein kinase (MAPK) pathway drive CM, while UM is characterized by mutations in genes like GNAQ, GNA11, BAP1, EIF1AX, and SF3B1. Chromosomal aberrations, including monosomy 3 in UM and monosomy 10 in CM, play significant roles in tumorigenesis. Immune cell infiltration differs between CM and UM, impacting prognosis. Therapeutic advancements targeting these genetic alterations, including oncolytic viruses and immunotherapies, have shown promise in preclinical and clinical studies. Oncolytic viruses selectively infect malignant cells, inducing oncolysis and activating antitumor immune responses. Talimogene laherparepvec (T-VEC) is an FDA-approved oncolytic virus for CM treatment, and other oncolytic viruses, such as coxsackieviruses and HF-10, are being investigated. Furthermore, combining oncolytic viruses with immunotherapies, such as CAR-T cell therapy, holds great potential. Understanding the intrinsic molecular features of melanoma and their role in shaping novel therapeutic approaches provides insights into targeted interventions and paves the way for more effective treatments for CM and UM.

Genetics and RNA Regulation of Uveal Melanoma

Uveal melanoma (UM) is the most common intraocular malignant tumor and the most frequent melanoma not affecting the skin. While the rate of UM occurrence is relatively low, about 50% of patients develop metastasis, primarily to the liver, with lethal outcome despite medical treatment. Notwithstanding that UM etiopathogenesis is still under investigation, a set of known mutations and chromosomal aberrations are associated with its pathogenesis and have a relevant prognostic value. The most frequently mutated genes are BAP1, EIF1AX, GNA11, GNAQ, and SF3B1, with mutually exclusive mutations occurring in GNAQ and GNA11, and almost mutually exclusive ones in BAP1 and SF3B1, and BAP1 and EIF1AX. Among chromosomal aberrations, monosomy of chromosome 3 is the most frequent, followed by gain of chromosome 8q, and full or partial loss of chromosomes 1 and 6. In addition, epigenetic mechanisms regulated by non-coding RNAs (ncRNA), namely microRNAs and long non-coding RNAs, have also been investigated. Several papers investigating the role of ncRNAs in UM have reported that their dysregulated expression affects cancer-related processes in both in vitro and in vivo models. This review will summarize current findings about genetic mutations, chromosomal aberrations, and ncRNA dysregulation establishing UM biology.

Scientific and clinical implications of genetic and cellular heterogeneity in uveal melanoma

Here, we discuss the presence and roles of heterogeneity in the development of uveal melanoma. Both genetic and cellular heterogeneity are considered, as their presence became undeniable due to single cell approaches that have recently been used in uveal melanoma analysis. However, the presence of precursor clones and immune infiltrate in uveal melanoma have been described as being part of the tumour already decades ago. Since uveal melanoma grow in the corpus vitreous, they present a unique tumour model because every cell present in the tumour tissue is actually part of the tumour and possibly plays a role. For an effective treatment of uveal melanoma metastasis, it should be clear whether precursor clones and normal cells play an active role in progression and metastasis. We propagate analysis of bulk tissue that allows analysis of tumour heterogeneity in a clinical setting.

Increased Non-Homologous End Joining Makes DNA-PK a Promising Target for Therapeutic Intervention in Uveal Melanoma

Uveal melanoma (UM) is the most common primary intraocular tumour in adults, with a mean survival of six months following metastasis. The survival rates have not improved in over 30 years. This study has shown that sister chromatid exchange (SCE) is low in UM which is likely due to a reduced expression of FANCD2. As FANCD2 can function to suppress non-homologous end joining (NHEJ), this study therefore investigated NHEJ in UM. The activation of the catalytic subunit of the NHEJ pathway protein DNA-dependent protein kinase (DNA-PK) was measured by analysing the foci formation and the ligation efficiency by NHEJ determined using a plasmid-based end-joining assay. Using small-interfering RNA (siRNA) knock-down, and chemical inhibitors of DNA-PK, the survival of primary UM cultures and two cell lines were determined. To assess the homologous recombination capacity in response to the inhibition of DNA-PK, a SCE analysis was performed. In addition, to support the findings, the messenger RNA (mRNA) expression of genes associated with NHEJ was analysed using the Cancer Genome Atlas (TCGA)-UM RNAseq data (n = 79). The NHEJ activity and DNA-PKcs activation was upregulated in UM and the inhibition of DNA-PK selectively induced apoptosis and sensitized to ionising radiation and inter-strand cross-linking agents. The inhibition of the NHEJ protein DNA-PK is lethal to UM, indicating a potentially effective therapeutic option, either alone or as a sensitizer for other treatments.

ICG-001 Exerts Potent Anticancer Activity Against Uveal Melanoma Cells

Purpose

Uveal melanoma (UM) is uniformly refractory to all available systemic chemotherapies, thus creating an urgent need for novel therapeutics. In this study, we investigated the sensitivity of UM cells to ICG-001, a small molecule reported to suppress the Wnt/β-catenin–mediated transcriptional program.

Methods

We used a panel of UM cell lines to examine the effects of ICG-001 on cellular proliferation, migration, and gene expression. In vivo efficacy of ICG-001 was evaluated in a UM xenograft model.

Results

ICG-001 exerted strong antiproliferative activity against UM cells, leading to cell cycle arrest, apoptosis, and inhibition of migration. Global gene expression profiling revealed strong suppression of genes associated with cell cycle proliferation, DNA replication, and G1/S transition. Gene set enrichment analysis revealed that ICG-001 suppressed Wnt, mTOR, and MAPK signaling. Strikingly, ICG-001 suppressed the expression of genes associated with UM aggressiveness, including CDH1, CITED1, EMP1, EMP3, SDCBP, and SPARC. Notably, the transcriptomic footprint of ICG-001, when applied to a UM patient dataset, was associated with better clinical outcome. Lastly, ICG-001 exerted anticancer activity against a UM tumor xenograft in mice.

Conclusions

Using in vitro and in vivo experiments, we demonstrate that ICG-001 has strong anticancer activity against UM cells and suppresses transcriptional programs critical for the cancer cell. Our results suggest that ICG-001 holds promise and should be examined further as a novel therapeutic agent for UM.

Characterization of luteinizing hormone-releasing hormone receptor type I (LH-RH-I) as a potential molecular target in OCM-1 and OCM-3 human uveal melanoma cell lines

Introduction

Uveal melanoma (UM) is the most common primary intraocular malignancy with very poor prognosis. Conventional chemotherapy only rarely prolongs the survival, therefore patients require novel treatment modalities. The discovery of specific receptors for hypothalamic hormones on cancer cells has led to the development of radiolabeled and cytotoxic hormone analogs.

Materials and methods

In the present study, our aim was to investigate the expression of mRNA for receptors of luteinizing hormone-releasing hormone type I (LH-RH-I) and LH-RH ligand in OCM-1 and OCM-3 human uveal melanoma cell lines. The presence and binding characteristics of LH-RH-I receptor protein was further studied by Western blot, immunocytochemistry and ligand competition assay. The expression of mRNA and protein for LH-RH-I receptors has been also studied using tumor samples originating from nude mice xenografted with OCM-1 or OCM-3 cells.

Results

The mRNA for LH-RH-I receptor has been detected in OCM-1 and OCM-3 cell lines and was found markedly higher in OCM-3 cells. The mRNA for LH-RH-I receptors was also observed in both UM xenograft models in vivo with higher levels in OCM-3. The presence of LH-RH-I receptor protein was found in both cell lines in vitro by immunocytochemistry and Western blot, and also in tumor tissue samples grown in nude mice by Western blot. Both human uveal melanoma models investigated showed specific high affinity receptors for LH-RH-I using ligand competition assay. The mRNA for LH-RH ligand has also been detected in OCM-1 and OCM-3 cell lines and cancer tissues.

Conclusion

The demonstration of the expression of LH-RH-I receptors in OCM-1 and OCM-3 human UM cell lines suggests that they could serve as potential molecular target for therapy. Our findings support the development of new therapeutic approaches based on cytotoxic LH-RH analogs or modern powerful antagonistic analogs of LH-RH targeting LH-RH-I receptors in UM.

Personalized Prognosis of Uveal Melanoma Based on Cytogenetic Profile in 1059 Patients over an 8-Year Period: The 2017 Harry S. Gradle Lecture

PURPOSE

To determine the personalized rate of uveal melanoma-related metastasis on the basis of individual tumor cytogenetic profile.

DESIGN

Retrospective case series.

PARTICIPANTS

A total of 1059 patients with uveal melanoma.

METHODS

Fine-needle aspiration biopsy (FNAB) for DNA amplification and whole genome array-based assay were performed for analysis of chromosomes 3, 6, and 8.

MAIN OUTCOME MEASURES

Melanoma-related metastasis.

RESULTS

The mean patient age was 57 years, and most were white (1026/1059, 97%). The melanoma involved the choroid (938/1059, 89%), ciliary body (85/1059, 8%), or iris (36/1059, 3%), with 19% being macular in location. The mean largest basal diameter was 11 mm (median, 12 mm; range, 3-24 mm), and mean thickness was 5 mm (median, 4 mm; range, 1-20 mm). On the basis of individual chromosomal mutations, risk for metastasis was increased for chromosome 3 partial monosomy (hazard ratio [HR], 2.84; P = 0.001), 3 complete monosomy (HR, 6.7, P < 0.001), 6q loss (HR, 3.1, P = 0.003), 8p loss (HR, 21.5, P < 0.001), and 8q gain (HR, 9.8, P < 0.001). Kaplan-Meier estimate for melanoma-related metastasis in 1, 3, 5, and 7 years for 3 partial monosomy was 1%, 5%, 14%, and 17%; for 3 complete monosomy was 3%, 19%, 28%, and 37%; for 6q loss was 8%, 23%, 49%, and 49%; for 8p loss was 8%, 29%, not estimable (NE), and NE; and for 8q gain was 6%, 21%, 35%, 48%, respectively. On the basis of personalized cytogenetic profiles, Kaplan-Meier estimates (1, 3, and 5 years) for melanoma-related metastasis for 3, 6, and 8 disomy (1%, 1%, 4% [HR, 1]) were low compared with the higher-risk combinations of 3 complete monosomy, 6p gain, and 8q gain (0%, 29%, 29% [HR, 10.6, P = 0.02]); 3 complete monosomy, 6 disomy, 8q gain, and 8p gain (14%, 14%, NE [HR, 18.3, P = 0.02]); 3 complete monosomy, 6 disomy, and 8q gain (8%, 27%, 39% [HR, 19.5, P < 0.001]); and 3 complete monosomy, 6 disomy, 8q gain, and 8p loss (3%, 28%, NE [HR, 31.6, P < 0.001]), respectively.

CONCLUSIONS

Risk for melanoma-related metastasis strongly correlates with personalized cytogenetic profiles, with 5-year Kaplan-Meier estimates ranging from 4% with chromosomes 3, 6, and 8 disomy up to 39% for 3 complete monosomy, 6 disomy, and 8q gain.

Heterogeneity revealed by integrated genomic analysis uncovers a molecular switch in malignant uveal melanoma

Gene expression profiles as well as genomic imbalances are correlated with disease progression in uveal melanoma (UM). We integrated expression and genomic profiles to obtain insight into the oncogenic mechanisms in development and progression of UM. We used tumor tissue from 64 enucleated eyes of UM patients for profiling. Mutations and genomic imbalances were quantified with digital PCR to study tumor heterogeneity and molecular pathogenesis. Gene expression analysis divided the UM panel into three classes. Class I presented tumors with a good prognosis and a distinct genomic make up that is characterized by 6p gain. The UM with a bad prognosis were subdivided into class IIa and class IIb. These classes presented similar survival risks but could be distinguished by tumor heterogeneity. Class IIa presented homogeneous tumors while class IIb tumors, on average, contained 30% of non-mutant cells. Tumor heterogeneity coincided with expression of a set of immune genes revealing an extensive immune infiltrate in class IIb tumors. Molecularly, class IIa and IIb presented the same genomic configuration and could only be distinguished by 8q copy number. Moreover, UM establish in the void of the immune privileged eye indicating that in IIb tumors the infiltrate is attracted by the UM. Combined our data show that chromosome 8q contains the locus that causes the immune phentotype of UM. UM thereby provides an unique opportunity to study immune attraction by tumors.

Association of tumor and plasma microRNA expression with tumor monosomy-3 in patients with uveal melanoma

BACKGROUND

Epigenetic events mediated by methylation and histone modifications have been associated with the development of metastasis in patients with uveal melanoma. The role of epigenetic events mediated by microRNA (miR) is less clear. Tumor and plasma miR expression was examined in patients with primary uveal melanoma with tumor monosomy-3, a predictor of metastasis.

RESULTS

miR profiling of tumors by microarray found six miRs over-expressed and 19 under-expressed in 33 tumors with monosomy-3 compared to 22 without. None of the miRs differentially expressed in tumors with and without monosomy-3 was differentially expressed in tumors with and without tumor infiltrating lymphocytes. Tumors manifesting monosomy-3 were also characterized by higher levels of TARBP2 and DDX17 and by lower levels of XPO5 and HIWI, miR biogenesis factors. miR profiling of plasma by a quantitative nuclease protection assay found elevated levels of 11 miRs and reduction in four in patients with tumor monosomy-3. Only three miRs differentially expressed in the tumor arrays were detectable in plasma. miRs implicated in uveal melanoma development were not differentially expressed. Elevated plasma levels in patients with tumor monosomy-3 of miR-92b, identified in the tumor array, and of miR-199-5p and miR-223, identified in the plasma array, were confirmed by quantitative real-time polymerase chain reaction. Levels were also higher in patients compared to normal controls.

CONCLUSIONS

These results support a role for epigenetic mechanisms in the development of metastasis in patients with uveal melanoma and the analysis of miRs as biomarkers of metastatic risk. They also suggest that potentially useful blood miRs may be derived from the host response as well as the tumor.

Uveal Melanoma UK National Guidelines

The United Kingdom (UK) uveal melanoma guideline development group used an evidence based systematic approach (Scottish Intercollegiate Guidelines Network (SIGN)) to make recommendations in key areas of uncertainty in the field including: the use and effectiveness of new technologies for prognostication, the appropriate pathway for the surveillance of patients following treatment for primary uveal melanoma, the use and effectiveness of new technologies in the treatment of hepatic recurrence and the use of systemic treatments. The guidelines were sent for international peer review and have been accredited by NICE. A summary of key recommendations is presented. The full documents are available on the Melanoma Focus website.

[Prognostic factors for uveal melanoma]

Uveal melanoma is a malignant intraocular tumor associated with poor vital prognosis, process generalization, and death from metastatic disease. A number of factors are considered undesirable in the presence of a tumor. This paper provides a review of the literature on major prognostic factors for uveal melanoma development and their contribution to vital prognosis.

Clinical significance of immunohistochemistry for detection of BAP1 mutations in uveal melanoma

Uveal melanoma is a lethal cancer with a strong propensity to metastasize. Limited therapeutic options are available once the disease has disseminated. A strong predictor for metastasis is the loss of chromosome 3. Inactivating mutations in BAP1 encoding the BRCA1-associated protein 1 and located on chromosome 3p21.1, have been described in uveal melanoma and other types of cancer. In this study, we determined the prevalence of somatic BAP1 mutations and examined whether these mutations correlate with the functional expression of BAP1 in uveal melanoma tissue and with other clinical, histopathological and chromosomal parameters. We screened a cohort of 74 uveal melanomas for BAP1 mutations, using different deep sequencing methods. The frequency of BAP1 mutations in our study group was 47%. The expression of BAP1 protein was studied using immunohistochemistry. BAP1 staining was absent in 43% of the cases. BAP1 mutation status was strongly associated with BAP1 protein expression (P<0.001), loss of chromosome 3 (P<0.001), and other aggressive prognostic factors. Patients with a BAP1 mutation and absent BAP1 expression had an almost eightfold higher chance of developing metastases compared with those without these changes (P=0.002). We found a strong correlation between the immunohistochemical and sequencing data and therefore propose that, immunohistochemical screening for BAP1 should become routine in the histopathological work-up of uveal melanoma. Furthermore, our analysis indicates that loss of BAP1 may be particularly involved in the progression of uveal melanoma to an aggressive, metastatic phenotype.

Uveal melanoma dormancy: an acceptable clinical endpoint?

Uveal melanoma is a rare but life-threatening malignancy. Over the past decades, the morbidity of uveal melanoma has been markedly reduced as a result of advances in the diagnostic ability to detect smaller tumors at an earlier stage. This has allowed for the use of more conservative treatments, avoiding enucleation. Mortality, however, has remained unchanged. This indicates that life expectancy is independent of local tumor control. Metastatic disease, the leading cause of death, is usually diagnosed many years later, despite successful treatment of the primary tumor, and at a late stage, when no effective therapy is available. These observations suggest that the disease was already disseminated at the time of tumor diagnosis. The detection of circulating malignant cells in the bloodstream of patients at different time points in the course of the disease supports this observation. Tumor dormancy has been considered as the leading theory for this intriguing delayed appearance of metastasis. Recent knowledge gained about the biological behavior of uveal melanoma as well as novel potential therapeutic targets are presented in this review.

Chromosome 3 status in uveal melanoma: a comparison of fluorescence in situ hybridization and single-nucleotide polymorphism array

PURPOSE

To compare fluorescence in situ hybridization (FISH) using a centromeric probe for chromosome 3 (CEP3) and 3p26 locus-specific probe with single-nucleotide polymorphism array (SNP-A) analysis in the detection of high-risk uveal melanoma.

METHODS

Fifty cases of uveal melanoma (28 males, 22 females) treated by enucleation between 2004 and 2010 were analyzed. Fresh tissue was used for FISH and SNP-A analysis. FISH was performed using a CEP3 and a 3p26 locus-specific probe. Tumor size, location, and clinical outcome were recorded during the 7-year study period (median follow-up: 35.5 months; mean: 38.5 months). The sensitivity, specificity, positive predictive value, and negative predictive value were calculated.

RESULTS

Monosomy 3 was detected by FISH-CEP3 in 27 tumors (54%), FISH-3p26 deletion was found in 30 (60%), and SNP-A analysis identified 31 (62%) of the tumors with monosomy 3. Due to technical failures, FISH and SNP-A were noninterpretable in one case (2%) and two cases (4%), respectively. In both cases of SNP-A failure, tumors were positive for FISH 3p26 deletion and in a single case of FISH failure, monosomy 3 was found using SNP-A. No statistically significant differences were observed in any of the sensitivity or specificity measures.

CONCLUSIONS

For prediction of survival at 36 months, FISH CEP3, FISH 3p26, and SNP-A were comparable. A combination of prognostication techniques should be used in an unlikely event of technical failure (2%-4%).

Monosomy 3 by FISH in uveal melanoma: variability in techniques and results

Tumor monosomy 3 confers a poor prognosis in patients with uveal melanoma. We critically review the techniques used for fluorescence in situ hybridization (FISH) detection of monosomy 3 in order to assess variability in practice patterns and to explain differences in results. Significant variability that has likely affected reported results was found in tissue sampling methods, selection of FISH probes, number of cells counted, and the cut-off point used to determine monosomy 3 status. Clinical parameters and specific techniques employed to report FISH results should be specified so as to allow meta-analysis of published studies. FISH-based detection of monosomy 3 in uveal melanoma has not been performed in a standardized manner, which limits conclusions regarding its clinical utility. FISH is a widely available, versatile technology, and when performed optimally has the potential to be a valuable tool for determining the prognosis of uveal melanoma.

Locoregional management of hepatic metastasis from primary uveal melanoma

Uveal melanoma is the most common primary ocular malignancy in adults and has a significant predilection for metastasis to the liver. Despite successful treatment of the primary uveal melanoma, up to 50% of patients will subsequently develop a systemic metastasis, with the liver involved in up to 90% of these individuals. Metastatic uveal melanoma has proven to be resistant to currently available systemic chemotherapies. Recognition of the poor prognosis associated with liver metastasis has led to the evaluation of various locoregional treatment modalities primarily designed to control tumor progression in the liver, including surgical resection, hepatic arterial chemotherapy, transarterial chemoembolization (TACE), immunoembolization, radiosphere, drug-eluting beads, isolated hepatic perfusion (IHP), and percutaneous hepatic perfusion. This article reviews the efficacies, and morbidities of currently available locoregional therapies.

Genetics of uveal melanoma and cutaneous melanoma: two of a kind?

Cutaneous melanoma and uveal melanoma both derive from melanocytes but show remarkable differences in tumorigenesis, mode of metastatic spread, genetic alterations, and therapeutic response. In this review we discuss the differences and similarities along with the genetic research techniques available and the contribution to our current understanding of melanoma. The several chromosomal aberrations already identified prove to be very strong predictors of decreased survival in CM and UM patients. Especially in UM, where the overall risk of metastasis is high (45%), genetic research might aid clinicians in selecting high-risk patients for future systemic adjuvant therapies.

Chromosomal 3 and 8 status within hepatic metastasis of uveal melanoma

CONTEXT

Several studies have evaluated clinical, histopathologic, cytogenetic, and molecular prognostic variables in uveal melanoma. However, it is not known whether the primary tumor cells maintain these aggressive attributes at the metastatic sites.

OBJECTIVE

To determine the status of chromosomes 3 and 8q and c-myc amplification using fluorescence in situ hybridization on hepatic metastatic lesions of primary uveal melanoma.

DESIGN

Ten patients with uveal melanoma with needle core biopsy-confirmed hepatic metastasis. Representative paraffin blocks were selected based on review of hematoxylin-eosin-stained sections. Fluorescence in situ hybridization was performed for detection of monosomy 3 and amplification at the 8q24 MYC locus using standard methods. The tricolor chromosome enumeration probe 8 (CEP8)/IGH/MYC and the Urovysion probe consisting of CEP3, CEP7, CEP17, and 9P21 probes were used. A total of 200 interphase cells were scored.

RESULTS

Hepatic metastasis was confirmed in each case by needle core biopsy. Fluorescence in situ hybridization analysis revealed chromosome 3 monosomy in 5 of the 8 cases that could be satisfactorily evaluated. Aneusomy of chromosome 8 was observed in 2 cases. MYC amplification was observed in 5 samples. In a single case where the primary tumor was treated by enucleation, the chromosomal monosomy 3 and aneusomy of chromosome 8 were present both in the primary tumor and its hepatic metastatic lesion.

CONCLUSIONS

The presence of cytogenetic changes within the metastatic lesions confirms that chromosome 3 monosomy and aneusomy of chromosome 8 are not just markers of metastatic potential of the primary tumor but are also present within the hepatic metastatic lesions.

The biology and management of uveal melanoma

Uveal melanoma is the most common primary intraocular malignancy in adults. Overall mortality rate remains high because of the frequent development of metastatic disease, especially hepatic metastasis. While traditional systemic chemotherapies provide only marginal benefit to patients, local treatments for hepatic metastases, such as immunoembolization, have improved patient prognoses. Progress has also been made in identifying potential targets in the pathways involved in apoptosis, proliferation, invasion, metastasis, and angiogenesis of uveal melanoma. Among these pathways, the c-Kit, c-Met, and IGF-1R signal pathways and the PTEN-related PI3K-Akt pathway are the most important targets. Clinical trials using blockades of these pathways in conjunction with strategies to facilitate apoptosis is a direction for future clinical trials. Application of these approaches in the adjuvant setting after primary therapy for high-risk uveal melanoma patients is also a future consideration to improve the clinical outcome of this disease.

Integrative genomic analysis of aneuploidy in uveal melanoma

PURPOSE

Aneuploidy is a hallmark of cancer and is closely linked to metastasis and poor clinical outcome. Yet, the mechanisms leading to aneuploidy and its role in tumor progression remain poorly understood. The extensive and complex karyotypic abnormalities seen in many solid tumors could hinder the identification of pathogenetically relevant chromosomal alterations. Uveal melanoma is an attractive solid tumor for studying aneuploidy because it is a relatively homogeneous cancer that is highly metastatic and has low nonspecific chromosomal instability.

EXPERIMENTAL DESIGN

Comparative genomic hybridization and gene expression profiling were used to analyze patterns of aneuploidy in 49 primary uveal melanomas. This analysis was supplemented by a review of cytogenetic findings in 336 published cases.

RESULTS

Three prognostically significant tumor subgroups were identified based on the status of chromosomes 3 and 6p. Discrete patterns of chromosomal alterations accumulated in these three subgroups in a nonrandom temporal sequence. Poor clinical outcome was associated with early chromosomal alterations rather than overall aneuploidy. A gene expression signature associated with aneuploidy was enriched for genes involved in cell cycle regulation, centrosome function, and DNA damage repair. One of these genes was PTEN, a tumor suppressor and genomic integrity guardian, which was down-regulated in association with increasing aneuploidy (P = 0.003).

CONCLUSIONS

The relationship between aneuploidy and poor prognosis may be determined by specific, pathogenetically relevant chromosomal alterations, rather than overall aneuploidy. Such alterations can be identified using integrative genomic methods and may provide insights for novel therapeutic approaches.

Small Choroidal Melanoma with Chromosome 3 Monosomy on Fine-Needle Aspiration Biopsy

PURPOSE

To evaluate the presence of chromosome 3 monosomy in small choroidal melanoma using fine-needle aspiration biopsy (FNAB).

DESIGN

Noncomparative case series.

PARTICIPANTS

Fifty-six patients with small choroidal melanoma measuring 3 mm or less in thickness who were undergoing plaque radiotherapy.

METHODS

Fine-needle aspiration biopsy was used at the time of plaque radiotherapy to sample tumor cells using a 27-gauge long needle via an indirect transvitreal approach into the tumor apex for postequatorial tumors or a 30-gauge short needle via a direct transscleral approach into the tumor base for preequatorial tumors.

MAIN OUTCOME MEASURES

Chromosome 3 monosomy in small choroidal melanoma.

RESULTS

The median tumor thickness was 2.6 mm. Monosomy 3 was found in 15 (27%) cases and disomy 3 was found in 32 (57%) cases. In 9 (16%) cases, genomic DNA yield was insufficient for genetic analysis. Fine-needle aspiration biopsy with a 27-gauge needle transvitreal approach provided quantity sufficient for genetic testing in 31 (97%) of 32 cases versus 16 (67%) of 24 cases sampled with a 30-gauge transscleral technique. Compared with disomy 3 tumors, monosomy 3 tumors were statistically more likely to occur in older patients (P = 0.040). Monosomy 3 (versus disomy 3) tumors showed thickness of more than 2 mm in 100% (vs. 84%), subretinal fluid in 87% (vs. 94%), symptoms in 40% (vs. 56%), orange pigment in 93% (vs. 81%), and margin of 3 mm or less to the optic disc in 20% (vs. 50%). There was no statistical difference between monosomy 3 and disomy 3 tumors in the presence or number of these clinical factors. However, small choroidal melanomas with monosomy 3 mutation were more likely to have had documented growth (63%) compared with those with disomy 3 (25%; P = 0.025; odds ratio, 5.00).

CONCLUSIONS

Using FNAB at the time of plaque radiotherapy, monosomy 3 was found in approximately 27% of small choroidal melanomas, more often in older patients and tumors with documented growth. Transvitreal biopsy into the tumor apex provided better yield compared with transscleral biopsy into the tumor base.

Monosomy 7 mosaicism in metastatic choroidal melanoma

Uveal melanoma is the most common primary intraocular malignancy in adults. Several cytogenetic studies on uveal melanoma cells have revealed that the majority of these cells harbor alterations in chromosomes 3, 6, and 8. This report describes the results of cytogenetic analysis performed on a fresh choroidal melanoma tissue sample from a patient with cerebellar metastasis. Monosomy 7 mosaicism was observed. To our knowledge, monosomy 7 has not been reported in patients with uveal melanoma. We suggest that observation of monosomy 7 may be related to an aggressive clinical behavior and unusual cerebellar metastasis in uveal melanoma. Further data are necessary to define the exact role of monosomy 7 in the pathogenesis and evolution of uveal melanoma.

An alternative hypothesis for observed mortality rates due to metastasis after treatment of choroidal melanomas of different sizes

PURPOSE

To propose an alternative hypothesis for the observed differential survival of patients with small, medium, and large choroidal melanomas based on recently uncovered cytogenetic evidence about melanocytic choroidal tumors.

METHODS

Review and analysis of published data.

RESULTS

Recent evidence has shown that recurring nonrandom cytogenetic abnormalities are present within virtually all cytomorphologically malignant cells that compose choroidal melanomas and that certain individual cytogenetic abnormalities and combinations of these abnormalities are important prognostic factors for metastasis and metastatic death. Although these cytogenetic abnormalities are strongly correlated with recognized clinical prognostic factors (tumor size, intraocular tumor location) and histomorphologic prognostic factors (melanoma cell type, vascular mimicry pattern) for metastasis, most laboratories have found these cytogenetic abnormalities to be much more robust indicators that metastasis will or will not develop than these clinical and histopathologic factors. In most series of uveal melanomas evaluated by current cytogenetic methods, approximately 30% to 60% of the tumors have cytogenetic abnormalities indicative of high likelihood of metastasis posttreatment. Evidence suggests that these abnormalities are more frequent in larger tumors than in smaller ones. Survival analyses of uveal melanoma patients whose tumors have been evaluated cytogenetically have shown rates of metastasis that approach 100% for patients with a tumor exhibiting monosomy 3 or a class 2 gene expression profile but are very low for those with a tumor that did not exhibit these cytogenetic abnormalities.

CONCLUSION

The better prognosis of patients with smaller choroidal melanomas is likely to be attributable to a lower probability of cytogenetic abnormalities indicative of metastatic capability among smaller tumors and not to effectiveness of treatment at preventing metastasis.

Chromosome 3 analysis of uveal melanoma using fine-needle aspiration biopsy at the time of plaque radiotherapy in 140 consecutive cases

PURPOSE

To evaluate the feasibility of genetic testing of uveal melanoma using fine-needle aspiration biopsy (FNAB).

METHODS

Noncomparative case series of 140 patients in which FNAB was performed immediately prior to plaque radiotherapy. The specimen was sent for genetic analysis using DNA amplification and microsatellite assay for evaluation for monosomy 3.

RESULTS

Monosomy 3 was found in 44 cases (32%) and disomy 3 in 76 cases (54%); genomic DNA yield was insufficient for genetic analysis in 20 cases (14%). Monosomy 3 was found in 26% of small melanomas (16/61), 36% of medium melanomas (24/67), and 33% of large melanomas (4/12). Adequate DNA was achieved in 97% of cases using a 27-gauge needle via transvitreal tumor apex approach and in 75% of cases using a 30-gauge needle via transscleral tumor base approach. Factors predictive of monosomy 3 included greater tumor basal dimension (P = .016) and greater distance from the optic disc (P = .019). Transient localized vitreous hemorrhage was found in 46% of eyes. There was no case of diffuse vitreous hemorrhage, retinal detachment, or tumor recurrence along the biopsy tract.

CONCLUSIONS

FNAB provides adequate DNA in most cases for genetic analysis of uveal melanoma using microsatellite assay.

Correlation of comparative genomic hybridization results of 100 archival uveal melanomas with patient survival

Comparative genomic hybridization (CGH) was used to elucidate DNA sequence copy number imbalances in 100 archival formalin-fixed, paraffin-embedded (FFPE) uveal melanoma cases. Of these 100 cases, 51 were from patients who survived >or=9 years post diagnosis without evidence of metastasis; the remaining 49 patients died from metastatic disease. Viable probe was generated from 82 of the 100 cases, allowing correlation of CGH findings with survival for all but 18 cases. Copy number imbalances revealed by CGH were tested for univariate prognostic significance. The most powerful predictor of a poor prognosis was gain of 18q11.2, which was subsequently compared with other significant chromosomal regions, as well as histologic and clinical factors, in a multivariate analysis. There was also evidence of differential X chromosome involvement in the survival correlations between male and female cases, which may be of significance to prognosis. This large-scale CGH analysis of archival material is intended to direct further gene-specific study of malignancy in uveal melanoma.

Multiple locations on chromosome 3 are the targets of specific deletions in uveal melanoma

PURPOSE

Loss of chromosome 3 is a frequent event in uveal melanomas, which is associated with hepatic metastases and a poor prognosis. The entire copy of chromosome 3 is usually lost (monosomy 3); however, a small subset of tumours demonstrate partial deletions of chromosome 3. Analysis of these tumours may allow the identification of tumour suppressor genes (TSGs) that are the molecular target of monosomy 3. Therefore, the purpose of this investigation was to determine the location of these partial deletions of chromosome 3 in uveal melanomas.

METHODS

Microsatellite analysis and restriction fragment-length polymorphism analysis were performed on 52 primary uveal melanomas using 19 markers located on both arms of chromosome 3. Cytogenetic analysis and fluorescence in situ hybridisation were performed, where possible, to confirm molecular findings.

RESULTS

Of 52 tumours studied, five tumours (10%) demonstrated LOH at one or more informative markers, but retention of heterozygosity was observed at other loci on chromosome 3, consistent with the presence of structural abnormalities to chromosome 3. Consistent with previous findings, the pattern of LOH in these tumours indicates the presence of deletions around 3p25-26 and on 3q, and that a new target region at 3p11-14 is preferentially deleted.

CONCLUSIONS

These results indicate the presence of several tumour suppressor loci on chromosome 3 and support the notion that the high rate of monosomy 3 in uveal melanoma is driven by disruption of several TSGs located on both arms of chromosome 3.

Multiplex fluorescence in situ hybridization identifies novel rearrangements of chromosomes 6, 15, and 18 in primary uveal melanoma

Uveal melanomas are the commonest ocular tumour of adults and are characterized by reproducible alterations of chromosomes 1, 3, 6 and 8. These alterations are of prognostic relevance and have also be shown to correlate to high risk and low risk metastatic categories of uveal melanoma as defined by micro-array analysis. It is, however, possible that a catalogue of relevant genetic alterations, involving gene rearrangement rather than amplification, have as yet eluded identification. To address this point we examined 14 primary uveal melanomas, using 24 colour multiplex fluorescence in situ hybridization (M-FISH). All tumours were karyotyped following G-Banding, and M-FISH was performed to confirm and clarify the identity of abnormal chromosomes. M-FISH data were obtained from all tumours and was able to establish the nature of most abnormalities not fully characterized by cytogenetics. Abnormalities of chromosome 6 were far more frequent than previously indicated, in approximately 70% of cases, indicating they have been substantially underrepresented in past studies of uveal melanoma. Spindle melanomas were found to have novel rearrangements affecting in particular chromosomes 6, 15 and 18, suggesting that juxtaposition of genes through translocational events may play a role in the development of some uveal melanomas. In conclusion, this study is the largest of primary uveal melanoma analysed by M-FISH and indicates that alterations of chromosome 6 have previously been underestimated. Furthermore spindle melanomas are prone to rearrangements affecting chromosomes 6, 15 and 18, which may relate to early changes in uveal melanoma development or associate with those melanomas of a more differentiated status.

Loss of heterozygosity of 1p in uveal melanomas with monosomy 3

Gains and losses of chromosomes 1, 3, 6 and 8 are nonrandom chromosomal aberrations in uveal melanoma. Monosomy 3 is the most frequent abnormality and is associated with poor prognosis. To identify regions of allelic loss on the short arm of chromosome 1 and to investigate if these alterations contribute to uveal melanoma progression, we performed microsatellite analysis of 10 loci in 70 uveal melanomas. A total of 51 tumors were obtained from patients with clinical follow-up data, 19 tumors were from recent patients without follow-up. Loss of heterozygosity (LOH) of at least 1 marker was more frequent in tumors with monosomy 3 (40%) than in tumors with disomy 3 (10%). In particular, loss of the entire short arm of chromosome 1 was only observed in tumors with monosomy 3 (p = 0.0001). By comparing the extent of 1p LOH in all tumors with monosomy 3, we were able to define a smallest region of overlap (SRO) of approximately 55 Mb, which is flanked by markers D1S507 and D1S198. On the basis of our data and published cytogenetic data, we propose that 1p31 harbors genes involved in the progression of uveal melanoma with monosomy 3.

The identification of chromosome abnormalities associated with the invasive phenotype of uveal melanoma in vitro

Tumour cell cultures are often highly heterogeneous, containing sub-populations of cells with differing characteristics. To identify chromosome abnormalities that are associated with the invasive phenotype, we isolated highly invasive uveal melanoma cell populations using the Transwell assay. Using this invasion assay, invasive sub-populations of primary uveal melanoma short-term cultures, and an established cell line, were specifically isolated. A series of sequential assays were undertaken to enrich the invasive population, and the enhanced invasive ability was confirmed by Transwell invasion assay. Chromosome abnormalities in invasive and parental cells were identified by karyotyping and confirmed by comparative genome hybridisation. Invasive sub-populations of uveal melanoma cells were isolated from 3 uveal melanoma short term cultures and a uveal melanoma cell line. In all cases, invasive sub-populations had either acquired additional chromosome abnormalities to those present in the parental cell line, or other abnormalities present in the parental lines were lost. In the established cell line (SOM 157), invasive cells were characterised by widespread chromosomal instability, frequent telomere associations and additional copies of chromosome 20. The invasive phenotype of SOM 196 associated with the presence of a derivative chromosome 5, der(5)t(5;11)(q35;q12) whilst a translocation t(17;20)(q12;q13) was predominant amongst non-invasive cells. In two additional cultures, deletions on chromosome 6q were associated with reduced invasive ability. In conclusion, highly invasive populations of uveal melanoma cells demonstrate chromosomal abnormalities that differ from non-invasive cells. These include chromosome instability and abnormalities of chromosome 20, observations echoing those seen in metastatic uveal melanoma.

Identification of monosomy 3 in choroidal melanoma by chromosome in situ hybridisation

BACKGROUND/AIMS

In uveal melanoma monosomy 3 is emerging as a significant indicator of a poor prognosis. To date most cytogenetic studies of uveal melanoma have utilised fresh tissue or DNA extracted from tissue sections. In this study chromosome in situ hybridisation (CISH) was used to study monosomy 3 in tissue sections. The copy number of chromosome 3 was determined and related to patient survival.

METHODS

Archival glutaraldehyde or formalin fixed, paraffin embedded material was obtained from 30 metastasising and 26 non-metastasising choroidal melanomas. Hybridisations were performed using centromere specific probes to chromosomes 3 and 18. Chromosome 18 was included as a control as previous abnormalities in uveal melanoma have not been described. Chromosomal imbalance was defined on the basis of changes in both chromosome index and signal distribution.

RESULTS

CISH was successfully performed on both glutaraldehyde and formalin fixed tissue. Four cases were unsuccessful because of extensive tumour necrosis. All cases were balanced for chromosome 18. Monosomy 3 was detected in 15 of the 26 cases of metastasising melanoma; the 26 non-metastasising tumours were all balanced for chromosome 3. Monosomy 3 was significantly associated with metastases related death.

CONCLUSION

CISH can successfully identify monosomy 3 in archival glutaraldehyde or formalin fixed, paraffin embedded tissue sections. Similar to previous studies monosomy 3 is a significant predictor of metastases related death.

Absence of BRAF gene mutations in uveal melanomas in contrast to cutaneous melanomas

The recent discovery of activating mutations in the BRAF gene in many cutaneous melanomas led us to screen the genomic sequence of BRAF exons 11 and 15 in a series of 48 intraocular (uveal) melanomas, together with control samples from three cutaneous melanomas and the SK-Mel-28 cell line, which has a BRAF mutation. The same mutation was detected in two-thirds of our cutaneous melanoma samples, but was not present in any uveal melanomas. This finding further underlines the distinction between uveal and cutaneous melanomas, and suggests that BRAF inhibitors are unlikely to benefit patients with uveal melanoma.

Deregulation of the Rb and p53 pathways in uveal melanoma

Uveal melanoma is the most common primary eye cancer, yet its molecular pathogenesis is poorly understood. In this study, we investigated the immunohistochemical expression of proteins in the Rb and p53 tumor suppressor pathways in 33 uveal melanomas from enucleated eyes. Strong nuclear staining for Rb was present in most tumors. However, a few cases displayed weak nuclear staining and strong cytoplasmic staining (possibly indicating Rb mutation), and this aberrant staining correlated strongly with failed radiotherapy or thermotherapy before enucleation. Staining for cyclin D1 was positive in most tumors and was associated with advanced age and larger tumor size, which are both poor prognostic factors. Generally, immunostaining for p53 was weak (suggesting a lack of p53 mutations), although p53 positivity correlated strongly with staining for phosphorylated Rb, supporting the notion that inappropriate phosphorylation of Rb can induce p53. Strong immunostaining for MDM2, which can functionally block p53 activity, was observed in most tumors and correlated significantly with female sex. Strong cytoplasmic staining was observed for Bcl2, which can inhibit both p53-dependent and -independent apoptosis. We conclude that Rb and p53 are mutated infrequently in uveal melanoma, but their respective pathways may be functionally inactivated.