Uveal Melanoma with Histopathologic Intratumoral Heterogeneity Associated with Gene Expression Profile Discordance

Microdissection of Distinct Morphological Regions Within Uveal Melanomas Identifies Novel Drug Targets

Background/Objectives: Uveal melanomas (UMs) are rare but often deadly malignancies that urgently require viable treatment options. UMs often exhibit tumour heterogeneity, with macroscopic and microscopic differences in morphology between different regions of the same tumour. However, to date, the clinical significance of this and how it may help guide personalised therapy have not been realised. Methods: Using targeted DNA and RNA sequencing of a small case series of large, high-risk primary UMs, we explored whether morphologically distinct regions of the same tumour were associated with distinct molecular profiles. Results: In four of the seven tumours analysed, we detected different sets of genetic variants following the separate analysis of microdissected melanotic and amelanotic regions of the same tumour. These included a MET exon 14 skipping RNA transcript that predicts sensitivity to crizotinib and variants in other genes that are important in active clinical trials for patients with UM and advanced solid tumours. The integration of TCGA data also identified recurrent mutational events in genes that were not previously implicated in UM development (FANCA, SLX4, BRCA2, and ATRX). Conclusions: Our findings show that the molecular analysis of spatially separated and morphologically distinct regions of the same tumour may yield additional, therapeutically relevant genetic variants in uveal melanomas and have implications for the future molecular testing of UMs to identify targeted therapies.

Eye-specific quantitative dynamic contrast-enhanced MRI analysis for patients with intraocular masses

OBJECTIVE

Dynamic contrast enhanced (DCE)-MRI is currently not generally used for intraocular masses as lesions are small, have an inhomogeneous T₁ and the eye is prone to motion. The aim of this paper is to address these eye-specific challenges, enabling accurate ocular DCE-MRI.

MATERIALS & METHODS

DCE-MRI of 19 uveal melanoma (UM) patients was acquired using a fat-suppressed 3D spoiled gradient echo sequence with TWIST (time-resolved angiography with stochastic trajectories sequence). The analysis consisted of a two-step registration method to correct for both head and eye motion. A T₁ map was calculated to convert signal intensities to concentrations. Subsequently, the Tofts model was fitted voxel wise to obtain K^trans and v_e.

RESULTS

Registration significantly improved the concentration curve quality (p < 0.001). The T₁ of melanotic lesions was significantly lower than amelanotic lesions (888 ms vs 1350 ms, p = 0.03). The average achieved B₁⁺ in the lesions was 91%. The average K^trans was 0.46 min^-1 (range 0.13-1.0) and the average v_e was 0.22 (range 0.10-0.51).

CONCLUSION

Using this eye-specific analysis, DCE of intraocular masses is possible which might aid in the diagnosis, prognosis and follow-up of UM.

Small High-Risk Uveal Melanomas Have a Lower Mortality Rate

Simple Summary

The current paradigm concerning metastatic spread in uveal melanoma is that the critical point for dissemination occurs prior to presentation and that treatment of the primary tumor does not change outcome. However, we show that patients with small uveal melanomas with genetic characteristics typical for high risk for metastatic disease have a lower mortality rate from metastatic disease, if treated earlier. Our data demonstrate that such small melanomas are potentially lethal (like larger tumors), but that there is a window of opportunity to prevent life-threatening metastatic spread if actively treated, rather than being monitored, as is often done currently.

Abstract

Our aim was to determine whether size impacts on the difference in metastatic mortality of genetically high-risk (monosomy 3) uveal melanomas (UM). We undertook a retrospective analysis of data from a patient cohort with genetically characterized UM. All patients treated for UM in the Liverpool Ocular Oncology Centre between 2007 and 2014, who had a prognostic genetic tumor analysis. Patients were subdivided into those with small (≤2.5 mm thickness) and large (>2.5 mm thickness) tumors. Survival analyses were performed using Gray rank statistics to calculate absolute probabilities of dying as a result of metastatic UM. The 5-year absolute risk of metastatic mortality of those with small monosomy 3 UM was significantly lower (23%) compared to the larger tumor group (50%) (p = 0.003). Small disomy 3 UM also had a lower absolute risk of metastatic mortality (0.8%) than large disomy 3 UM (6.4%) (p = 0.007). Hazard rates showed similar differences even with lead time bias correction estimates. We therefore conclude that earlier treatment of all small UM, particularly monosomy 3 UM, reduces the risk of metastatic disease and death. Our results would support molecular studies of even small UM, rather than ‘watch-and-wait strategies’.

Incomplete multi-view gene clustering with data regeneration using Shape Boltzmann Machine

Deciphering patterns in the structural and functional anatomy of genes can prove to be very helpful in understanding genetic biology and genomics. Also, the availability of the multiple omics data, along with the advent of machine learning techniques, aids medical professionals in gaining insights about various biological regulations. Gene clustering is one of the many such computation techniques that can help in understanding gene behavior. However, more comprehensive and reliable insights can be gained if different modalities/views of biomedical data are considered. However, in most multi-view cases, each view contains some missing data, leading to incomplete multi-view clustering. In this study, we have presented a deep Boltzmann machine-based incomplete multi-view clustering framework for gene clustering. Here, we seek to regenerate the data of the three NCBI datasets in the incomplete modalities using Shape Boltzmann Machines. The overall performance of the proposed multi-view clustering technique has been evaluated using the Silhouette index and Davies-Bouldin index, and the comparative analysis shows an improvement over state-of-the-art methods. Finally, to prove that the improvement attained by the proposed incomplete multi-view clustering is statistically significant, we perform Welch's t-test. AVAILABILITY OF DATA AND MATERIALS: https://github.com/piyushmishra12/IMC.

Comparative Cytogenetic Abnormalities in Paired Choroidal Melanoma Samples Obtained Before and After Proton Beam Irradiation by Transscleral Fine-Needle Aspiration Biopsy and Endoresection

This study compared the cytogenetic profiles of choroidal melanoma samples retrieved before and after proton beam irradiation. Twenty-four consecutive patients who underwent both fine-needle aspiration biopsy (FNAB) during tantalum clip positioning, and endoresection within three months of irradiation, were retrospectively included. Chromosome alterations were explored by array comparative genomic hybridization. Age at diagnosis was 50 ± 14 years, tumor thickness was 8.6 ± 1.7 mm and tumor diameter was 12.4 ± 2.3 mm. Six FNAB samples were non-contributive (25%), versus one endoresection sample (4%) (p = 0.049). Among 17 cases with paired contributive samples, the profiles of chromosomes 3 and 8 were identical in all cases, except one with partial chromosome 3 loss on the FNAB sample only. Three cases presented additional discordant aberrations on chromosomes other than 3 or 8q. Overall, we identified monosomy 3 in two cases, 8q gain in six cases, and both alterations in three cases. All cases presented GNAQ or GNA11 mutations assessed by a custom next-generation sequencing panel. Among the six cases with non-contributive initial FNAB, three cases presented abnormal 3 or 8q chromosomes detected on the endoresection material. These results demonstrate the higher rentability of endoresection material for cytogenetic analysis compared to FNAB, and provide clinical evidence of tumor heterogeneity in choroidal melanoma.

Uptake of Ranibizumab but Not Bevacizumab into Uveal Melanoma Cells Correlates with a Sustained Decline in VEGF-A Levels and Metastatic Activities

Despite the implication of vascular endothelial growth factor-A (VEGF-A) in the pathophysiology of uveal melanoma (UM), the anti-VEGF-A antibody bevacizumab yielded conflicting results on UM growth. Here, we evaluated whether bevacizumab and ranibizumab, a humanized Fab-fragment against VEGF-A, can enter UM cells and induce a sustained physiological response. The primary and metastatic UM cell lines Mel-270 and OMM-2.5 were exposed to bevacizumab or ranibizumab for one day and were maintained further in untreated medium for a total of three days. Both antibodies significantly reduced the levels of extracellular VEGF-A and the angiogenic potential of the conditioned medium after one day. These inhibitory effects of bevacizumab diminished by day three. Ranibizumab suppressed the metabolic activity, proliferation, and intracellular VEGF-A levels in a cell-type and concentration-dependent manner, whereas bevacizumab exerted no effect. Both drugs were detected inside early endosomes within the UM cells, with the stronger and sustained colocalization of ranibizumab. Our results therefore demonstrated the more potent and persistent suppressive activity of ranibizumab on the UM cells, possibly due to its higher level of uptake and prolonged intracellular retention. Further research on the endosome dynamics in UM cells might provide valuable insight into the response of these heterogenous tumors to therapeutic antibodies.

Spatial intratumor heterogeneity in uveal melanoma: Tumor cell subtypes with a presumed invasive potential exhibit a particular epigenetic staining reaction

Cancer evolves from a combination of genetic and epigenetic abnormalities resulting in aberrant gene expression profiles as well as altered epigenomic patterns. Epigenetic alterations such as DNA methylation and histone modification play an important role in tumorigenesis. While in the pathobiology of uveal melanoma (UM) genetic changes have been well characterized, there is growing evidence suggesting that epigenetic changes are also involved. We investigated whether epigenetic modifications (global levels of histone acetylation, DNA methylation, ubiquitination) are detectable in UM tissues compared to healthy controls with respect to inter- and intratumoral heterogeneity. Formalin-fixed paraffin-embedded tissues of primary UM (n = 15), UM metastasis (n = 13), and control choroid (n = 12) were immunohistochemically investigated by two ophthalmic pathologists for global levels of histone acetylation (Histone 3 acetylation, H3Ac; Histone 4 acetylation, H4Ac), DNA methylation (5-methylcytosine, 5-MeC; 5'-hydroxymethylcytosine, 5-hMeC), global ubiquitination (UBC) as well as Ubiquityl-Histone H2A (H2Aub). The nuclear staining intensity of primary tumors, metastases and control choroids was evaluated using a score from 0 to 3, which was multiplied with the percentage of stained cells (score from 0 to 4). The control choroid and the choroid next to the tumor showed a more intense nuclear staining than the primary tumor tissue. The choroid next to the tumor was stained less than the control choroid. The nuclear staining intensity in the tumor was comparable to that in the metastases. The tumor tissue itself often exhibited a heterogeneous staining pattern, as nuclei in the tumor center were less intensely stained than in the periphery. Cells with a presumed invasive potential (extraocular extension, growth along emissary canals) showed also an intense staining reaction. Although no prognostically relevant pattern of global epigentic markers could be identified, our results suggest that epigenetic changes play a role in UM pathogenesis and metastasis. In particular the staining reaction of tumor cell subtypes with a presumed invasive potential warrants further attention. The role of epigenetically relevant interactions with the tumor micromilieu should be further investigated as immune cells are predominantly located in the tumor periphery which showed a different staining intensity than the tumor center. However, as considerable epigenetic diversity exists in primary tumors, studies on biopsy tissue are not recommended for the immunohistochemical investigation of epigenetic markers.

Do Largest Basal Tumor Diameter and the American Joint Committee on Cancer's Cancer Staging Influence Prognostication by Gene Expression Profiling in Choroidal Melanoma

PURPOSE

To evaluate the prognostication of choroidal melanoma (CM) by the gene expression profiling (GEP) test.

DESIGN

Cohort study.

METHODS

Retrospective review of 293 CM patients from 2 centers.

RESULTS

Of 293 patients, 132 (45%) were class 1A by GEP, 63 (22%) were class 1B, and 98 (33%) were class 2. Class 2 tumors had more ciliary body involvement and greater largest basal dimension (LBD), and were thicker. GEP results and increasing LBD were independently predictive of time to metastasis. Kaplan-Meier survival analysis estimated the probability of 3-year metastasis-free survival (MFS) of 0.99 in class 1A, 0.90 in class 1B, and 0.60 in class 2. The probability of 3-year MFS was 0.49 in class 2 patients with LBD ≥ 12 mm vs 1.00 in those with LBD < 12 mm, 0.89 in class 1B with LBD ≥ 12 mm vs 0.93 in those with LBD < 12 mm, and 0.99 in class 1A with LBD ≥ 12 mm vs 1.00 in those with LBD < 12 mm. In American Joint Committee on Cancer (AJCC) stage I CMs, the probability of 3-year MFS was 1.0 for class 1A and 1B, and 0.79 for class 2. In stage II CMs, the probability of 3-year MFS was 0.99 for class 1A, 0.89 for class 1B, and 0.61 for class 2. In stage III CM, the probability of 3-year MFS was 1.0 for class 1A, 0.60 for class 1B, and 0.41 for class 2.

CONCLUSIONS

GEP testing provided significant prognostic information for CM. Class 2 tumors with LBD ≥ 12 mm and class 2 and 1B tumors with AJCC stage III showed significantly worse prognosis.

Genetic prognostication in uveal melanoma

Uveal melanoma (UM) is a rare tumour with a high propensity to metastasize. Although no effective treatment for metastases yet exists, prognostication in UM is relevant for patient counselling, planning of follow-up and stratification in clinical trials. Besides conventional clinicopathologic characteristics, genetic tumour features with prognostic significance have been identified. Non-random chromosome aberrations such as monosomy 3 and gain of chromosome 8q are strongly correlated with metastatic risk, while gain of chromosome 6p indicates a low risk. Recently, mutations in genes such as BAP1, SF3B1 and EIF1AX have been shown to be related to patient outcome. Genetics of UM is a rapidly advancing field, which not only contributes to the understanding of the pathogenesis of this cancer, but also results in further refinement of prognostication. Concomitantly, advances have been made in the use of genetic tests. New methods for genetic typing of UM have been developed. Despite the considerable progress made recently, many questions remain, such as those relating to the reliability of prognostic genetic tests, and the use of biopsied or previously irradiated tumour tissue for prognostication by genetic testing. In this article, we review genetic prognostic indicators in UM, also comparing available genetic tests, addressing the clinical application of genetic prognostication and discussing future perspectives for improving genetic prognostication in UM.

Correlation of Immunocytochemistry of BRCA1-associated Protein-1 (BAP1) With Other Prognostic Markers in Uveal Melanoma

PURPOSE

Prior studies have shown that nuclear reactivity for BRCA1-associated protein-1 (BAP1) yields prognostic information for paraffin-embedded uveal melanomas. Lacking are immunocytochemical studies of BAP1 on fine needle aspiration biopsies of uveal melanoma that correlate with prognosis or other markers of prognosis. Our purpose was to fill this gap.

DESIGN

Experimental laboratory study.

METHODS

Fine needle aspiration biopsies were performed prospectively on 113 patients with uveal melanomas, garnering limited subsets of cases for comparison. Agreement between immunocytochemistry for BAP1 nuclear staining vs chromosome 3 ploidy analysis and gene expression profiling was assessed by 2 × 2 contingency table analysis.

RESULTS

The presence or absence of suppression of nuclear expression of BAP1 was strongly associated (73%, P = .000002) with monosomy and disomy chromosome 3, respectively. BAP1 nuclear expression was also correlated with gene expression profiling. Chromosome 3 ploidy analysis correlated with gene expression profiles.

CONCLUSION

When adequate material is obtained, immunocytology using BAP1 is a potentially informative tool for prognostication of uveal melanoma.

An Ensemble Method to Predict Target Genes and Pathways in Uveal Melanoma

Objective: This work proposes to predict target genes and pathways for uveal melanoma (UM) based on an ensemble method and pathway analyses.

METHODS

The ensemble method integrated a correlation method (Pearson correlation coefficient, PCC), a causal inference method (IDA) and a regression method (Lasso) utilizing the Borda count election method. Subsequently, to validate the performance of PIL method, comparisons between confirmed database and predicted miRNA targets were performed. Ultimately, pathway enrichment analysis was conducted on target genes in top 1000 miRNA-mRNA interactions to identify target pathways for UM patients.

RESULTS

Thirty eight of the predicted interactions were matched with the confirmed interactions, indicating that the ensemble method was a suitable and feasible approach to predict miRNA targets. We obtained 50 seed miRNA-mRNA interactions of UM patients and extracted target genes from these interactions, such as ASPG, BSDC1 and C4BP. The 601 target genes in top 1,000 miRNA-mRNA interactions were enriched in 12 target pathways, of which Phototransduction was the most significant one.

CONCLUSION

The target genes and pathways might provide a new way to reveal the molecular mechanism of UM and give hand for target treatments and preventions of this malignant tumor.