The Cancer Genome Atlas Project: An Integrated Molecular View of Uveal Melanoma

Aqueous Humor Liquid Biopsy as a Companion Diagnostic for Retinoblastoma: Implications for Diagnosis, Prognosis, and Therapeutic Options: Five Years of Progress

PURPOSE

To define the prospective use of the aqueous humor (AH) as a molecular diagnostic and prognostic liquid biopsy for retinoblastoma (RB).

METHODS

This is a prospective, observational study wherein an AH liquid biopsy is performed at diagnosis and longitudinally through therapy for patients with RB. Tumor-derived cell-free DNA is isolated and sequenced for single nucleotide variant analysis of the RB1 gene and detection of somatic copy number alterations (SCNAs). The SCNAs are used to determine tumor fraction (TFx). Specific SCNAs, including 6p gain and focal MycN gain, along with TFx, are prospectively correlated with intraocular tumor relapse, response to therapy, and globe salvage.

RESULTS

A total of 26 eyes of 21 patients were included with AH taken at diagnosis. Successful ocular salvage was achieved in 19 of 26 (73.1%) eyes. Mutational analysis of 26 AH samples identified 23 pathogenic RB1 variants and 2 focal RB1 deletions; variant allele fraction ranged from 30.5% to 100% (median 93.2%). At diagnosis, SCNAs were detectable in 17 of 26 (65.4%) AH samples. Eyes with 6p gain and/or focal MycN gain had significantly greater odds of poor therapeutic outcomes (odds ratio = 6.75, 95% CI = 1.06-42.84, P = .04). Higher AH TFx was observed in eyes with vitreal progression (TFx = 46.0% ± 40.4) than regression (22.0 ± 29.1; difference: -24.0; P = .049).

CONCLUSIONS

Establishing an AH liquid biopsy for RB is aimed at addressing (1) our inability to biopsy tumor tissue and (2) the lack of molecular biomarkers for intraocular prognosis. Current management decisions for RB are made based solely on clinical features without objective molecular testing. This prognostic study shows great promise for using AH as a companion diagnostic. NOTE: Publication of this article is sponsored by the American Ophthalmological Society.

Recent Advances in Molecular and Genetic Research on Uveal Melanoma

Uveal melanoma (UM), a distinct subtype of melanoma, presents unique challenges in its clinical management due to its complex molecular landscape and tendency for liver metastasis. This review highlights recent advancements in understanding the molecular pathogenesis, genetic alterations, and immune microenvironment of UM, with a focus on pivotal genes, such as GNAQ/11, BAP1, and CYSLTR2, and delves into the distinctive genetic and chromosomal classifications of UM, emphasizing the role of mutations and chromosomal rearrangements in disease progression and metastatic risk. Novel diagnostic biomarkers, including circulating tumor cells, DNA and extracellular vesicles, are discussed, offering potential non-invasive approaches for early detection and monitoring. It also explores emerging prognostic markers and their implications for patient stratification and personalized treatment strategies. Therapeutic approaches, including histone deacetylase inhibitors, MAPK pathway inhibitors, and emerging trends and concepts like CAR T-cell therapy, are evaluated for their efficacy in UM treatment. This review identifies challenges in UM research, such as the limited treatment options for metastatic UM and the need for improved prognostic tools, and suggests future directions, including the discovery of novel therapeutic targets, immunotherapeutic strategies, and advanced drug delivery systems. The review concludes by emphasizing the importance of continued research and innovation in addressing the unique challenges of UM to improve patient outcomes and develop more effective treatment strategies.

Enhancing the utility of chromosome 6 and 8 testing in uveal melanoma biopsies

BACKGROUND

The aim of this study was to evaluate the significance of testing the gain of chromosome 8 and the gain of chromosome 6 as prognostic markers in histopathological samples of enucleated eyes in with uveal melanoma.

METHODS

This is a retrospective study of 54 enucleated eyes. The status of chromosomes 3, 8 and 6 was tested by CISH, and FISH was used in a few samples. A follow-up for the detection of metastases was conducted in all patients. The statistical significance of chromosomal abnormalities as a prognostic factor for the development of metastases was determined.

RESULTS

The study group consists of 54 patients (average age 63 years), 28 men (51.9%) Monosomy 3 together with gain of chromosome 8 was found in 10 samples (18.5%). Both chromosomal abnormalities were detected in 6 (11%) patients. No chromosomal abnormality in 3 or 8 was detected in 21 (38.9%) patients. Abnormalities of chromosome 6 were present in 6 (11%) patients. Progression free survival after 5 years was 33.3% (95% CI 0.0; 83.3) in these patients.

CONCLUSIONS

Our findings indicate a correlation between progression-free survival and the presence of changes in chromosome 3 and e 8 in uveal melanomas. The results underline the necessity of testing for both chromosomal aberrations.

Pathological and Molecular Diagnosis of Uveal Melanoma

(1) Background: Uveal melanoma (UM) is a common malignant intraocular tumor that presents with significant genetic differences to cutaneous melanoma and has a high genetic burden in terms of prognosis. (2) Methods: A systematic literature search of several repositories on uveal melanoma diagnosis, prognosis, molecular analysis, and treatment was conducted. (3) Results: Recent genetic understanding of oncogene-initiation mutations in GNAQ, GNA11, PLCB4, and CYSLTR2 and secondary progression drivers of BAP1 inactivation and SF3B1 and EIF1AX mutations offers an appealing explanation to the high prognostic impact of adding genetic profiling to clinical UM classification. Genetic information could help better explain peculiarities in uveal melanoma, such as the low long-term survival despite effective primary tumor treatment, the overwhelming propensity to metastasize to the liver, and possibly therapeutic behaviors. (4) Conclusions: Understanding of uveal melanoma has improved step-by-step from histopathology to clinical classification to more recent genetic understanding of oncogenic initiation and progression.

Updates in the Management of Uveal Melanoma

ABSTRACT

Uveal melanoma (UM), arising from intraocular melanocytes, poses a complex clinical challenge with a substantial risk of distant metastasis, often to the liver. Molecular profiling, encompassing genetic, cytogenetic, gene expression, and immunological subsets, plays a pivotal role in determining prognoses. The evolving landscape includes promising systemic treatments, such as tebentafusp, a novel immune-modulating bispecific fusion protein, and targeted therapies. Combined regional and systemic approaches, including immune checkpoint inhibitors and innovative liver-directed therapy, are also under investigation. Although recent progress has improved outcomes, ongoing research aims to address the unique challenges of UM and develop effective therapies, particularly for HLA-A*02:01-negative patients who represent a significant unmet medical need. This review comprehensively discusses the molecular characteristics of UM, risk stratification methods, and the current and future spectrum of regional and systemic therapeutic modalities.

Uveal melanoma: Current evidence on prognosis, treatment and potential developments

Uveal Melanoma (UM) is a rare disease, yet it is the most common primary intraocular malignancy in adult patients. Despite continuous advancements and research, the risk of metastasis remains high. It is possible to stratify patients according to their risk of metastases using a variety of known risk factors. Even though there is no gold standard for the prognostication of patients with uveal melanoma, it is becoming increasingly clear that combining histo-pathological, patient-related and molecular prognostic markers allows a more accurate prediction of the metastatic risk than by using one parameter. Primary UM in the eye are treated very effectively with eye-sparing radiation-based techniques or enucleation. However, it is not yet possible to prevent or treat metastases with the current therapeutic options. Nonetheless, the efforts to find new therapeutic targets continue and progress is being made, especially in the field of targeted therapy, as exemplified by the anti-gp100 bispecific molecule Tebentafusp. This review delves into the history of uveal melanoma, its incidence, presentation and diagnosis, the known prognostic factors and the treatment options, both for the primary tumour and for metastases. We show that different populations may have different risks for developing UM, and that each country should evaluate their own patients.

The Cancer Genome Atlas for uveal melanoma is predictive of patient outcomes

Uveal melanoma (UM) is the most common primary eye malignancy. Despite excellent local tumor rates, UM is a life-threatening disease with moderate systemic metastatic rates. In the past, certain clinical features were shown to be predictive of patient prognosis, including tumor thickness, tumor diameter, ciliary body involvement, and histopathologic factors. Genetic markers have lately been used to predict patient outcomes. The Cancer Genome Atlas (TCGA) is a worldwide effort developed by the National Cancer Institute and the National Human Genome Research Institute to study numerous mutations in various cancer types. TCGA has explored chromosome copy number alterations in UM, messenger RNA, micro-RNA, and long noncoding RNA expression levels and established four prognostic classes: group A (chromosome 3 and 8 disomy), group B (chromosome 3 disomy and 8q gain), group C (chromosome 3 monosomy and/or 8q gain), and group D (chromosome 3 monosomy and multiple 8q gains). Multiple studies have validated TCGA classification and have reported that it has been highly predictive of UM metastasis and patient survival.

PRAME Expression: A Target for Cancer Immunotherapy and a Prognostic Factor in Uveal Melanoma

Purpose

Uveal melanoma (UM) is a rare disease with a high mortality, and new therapeutic options are being investigated. Preferentially Expressed Antigen in Melanoma (PRAME) is a cancer testis antigen, expressed in the testis, but also in cancers, including uveal melanoma. PRAME is considered a target for immune therapy in several cancers, and PRAME-specific T cell clones have been shown to kill UM cells.

Methods

We studied the literature on PRAME expression in hematological and solid malignancies, including UM, and its role as a target for immunotherapy. The distribution of tumor features was compared between PRAME-high and PRAME-low UM in a 64-patient cohort from the Leiden University Medical Center (LUMC) and in the Cancer Genome Atlas (TCGA) cohort of 80 cases and differential gene expression analysis was performed in the LUMC cohort.

Results

PRAME is expressed in many malignancies, it is frequently associated with a negative prognosis, and can be the target of T cell receptor (TCR)-transduced T cells, a promising treatment option with high avidity and safety. In UM, PRAME is expressed in 26% to 45% of cases and is correlated with a worse prognosis. In the LUMC and the TCGA cohorts, high PRAME expression was associated with larger diameter, higher Tumor-Node-Metastasis (TNM) stage, more frequent gain of chromosome 8q, and an inflammatory phenotype.

Conclusions

We confirm that PRAME is associated with poor prognosis in UM and has a strong connection with extra copies of 8q. We show that PRAME-specific immunotherapy in an adjuvant setting is promising in treatment of malignancies, including UM.

Multicentre analysis of nucleic acid quantification using aqueous humour liquid biopsy in uveal melanoma: implications for clinical testing

OBJECTIVE

Uveal melanoma (UM) tumour biopsy is limited by size and intratumour heterogeneity. We explored the potential of aqueous humour (AH) liquid biopsy for UM by quantifying analytes in samples collected at diagnosis and after brachytherapy to look for clinical correlations with tumour features.

DESIGN

Case-series study.

PARTICIPANTS

Sixty-six UM patients and 16 control subjects from a tertiary care hospital.

METHODS

The study included 119 UM AH samples and 16 control samples analyzed for unprocessed analytes (i.e., dsDNA, miRNA, and protein) using Qubit fluorescence assays.

RESULTS

Analytes were widely quantifiable among available UM AH samples (dsDNA: 94.1%; miRNA: 88.0%; protein: 95.2%) at significantly higher concentrations than among control samples (dsDNA, p = 0.008; miRNA, p < 0.0001; protein, p = 0.007). In samples taken at diagnosis, concentrations were higher at more advanced American Joint Cancer Commission stages; when comparing most advanced stage III with least advanced stage I, median dsDNA was 4 times greater (p < 0.0001), miRNA was 2 times greater (p = 0.001), and protein was 3 times greater (p < 0.0001). Analytes were quantifiable in >70% of diagnostic samples from eyes with tumours <2 mm tall. Height had a positive association with diagnostic analyte concentrations (dsDNA: R = 0.43, p = 0.0007; miRNA: R = 0.35, p = 0.01; protein: R = 0.39, p = 0.005). Samples taken after brachytherapy showed significantly higher concentrations than diagnostic samples (p < 0.01 for all).

CONCLUSIONS

UM AH is a rich repository of analytes. Samples from eyes with more advanced stage and larger tumours had higher concentrations, though analytes also were quantifiable in eyes with smaller, less advanced tumours. Future analysis of AH analytes may be informative in the pursuit of personalized UM treatments.

Immuno-oncology approaches in uveal melanoma: tebentafusp and beyond

Uveal melanoma (UM) is the most common ocular malignancy in adults, associated with the poorest prognosis, with metastatic disease occurring in up to 50% of patients. In contrast to metastatic cutaneous melanoma, the use of immune checkpoint inhibitors is associated with poor outcomes in metastatic uveal melanoma (mUM). Tebentafusp, a bispecific molecule, has recently become the first treatment in decades to improve overall survival for mUM. This review summarises the existing and emerging immuno-oncology approaches for the treatment of mUM, and biomarkers of response and resistance to the same. Finally, we propose future research directions that could maximise treatment benefit to a wider pool of patients with UM.

Integration of bulk RNA sequencing data and single-cell RNA sequencing analysis on the heterogeneity in patients with colorectal cancer

The cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway has emerged as a critical innate immune pathway that could virtually impact nearly all aspects of tumorigenesis including colorectal cancer. This work aimed to develop and validate molecular subtypes related to cGAS-STING pathways for colorectal cancer using Bulk RNA-seq and single-cell RNA-seq (scRNA-seq) data. Bulk RNA-seq data were acquired from The Cancer Genome Atlas dataset (training dataset) and Gene Expression Omnibus dataset (validation dataset). Univariate COX survival analysis was utilized to identify prognostic differentially expressed genes (DEGs) from 6 immune pathways related to cGAS-STING. ConsensusClusterPlus package was used to classify different subtypes based on DEGs. scRNA-seq data were used to validate differences in immune status between different subtypes. Two clusters with distinct prognosis were identified based on 27 DEGs. The six cGAS-STING-related pathways had different levels of significance between the two clusters. Clust1 had most number of amplified CNVs and clust2 had the most number of loss CNVs. TP53 was the top mutated gene of which missense mutations contributed the most of single-nucleotide variants. Immune score of clust1 was higher than that in clust2, as reflected in macrophages, T cells, and natural killer cells. Three unfavorable genes and 31 protection factors were screened between the two clusters in three datasets. ScRNA-seq data analysis demonstrated that macrophages were more enriched in clust1, and tumor cells and immune cells had close interaction. We classified two distinct subtypes with different prognosis, mutation landscape, and immune characteristics.

Tumor subtypes and signature model construction based on chromatin regulators for better prediction of prognosis in uveal melanoma

Background: Uveal Melanoma (UM) is the most prevalent primary intraocular malignancy in adults. This study assessed the importance of chromatin regulators (CRs) in UM and developed a model to predict UM prognosis. Methods: Gene expression data and clinical information for UM were obtained from public databases. Samples were typed according to the gene expression of CRs associated with UM prognosis. The prognostic key genes were further screened by the protein interaction network, and the risk model was to predict UM prognosis using the least absolute shrinkage and selection operator (LASSO) regression analysis and performed a test of the risk mode. In addition, we performed gene set variation analysis, tumor microenvironment, and tumor immune analysis between subtypes and risk groups to explore the mechanisms influencing the development of UM. Results: We constructed a signature model consisting of three CRs (RUVBL1, SIRT3, and SMARCD3), which was shown to be accurate, and valid for predicting prognostic outcomes in UM. Higher immune cell infiltration in poor prognostic subtypes and risk groups. The Tumor immune analysis and Tumor Immune Dysfunction and Exclusion (TIDE) score provided a basis for clinical immunotherapy in UM. Conclusion: The risk model has prognostic value for UM survival and provides new insights into the treatment of UM.

Glutamine metabolism-related genes predict prognosis and reshape tumor microenvironment immune characteristics in diffuse gliomas

Background

Diffuse gliomas possess a kind of malignant brain tumor with high mortality. Glutamine represents the most abundant and versatile amino acid in the body. Glutamine not only plays an important role in cell metabolism but also involves in cell survival and malignancies progression. Recent studies indicate that glutamine could also affect the metabolism of immune cells in the tumor microenvironment (TME).

Materials and methods

The transcriptome data and clinicopathological information of patients with glioma were acquired from TCGA, CGGA, and West China Hospital (WCH). The glutamine metabolism-related genes (GMRGs) were retrieved from the Molecular Signature Database. Consensus clustering analysis was used to discover expression patterns of GMRGs, and glutamine metabolism risk scores (GMRSs) were established to model tumor aggressiveness-related GMRG expression signature. ESTIMATE and CIBERSORTx were applied to depict the TME immune landscape. The tumor immunological phenotype analysis and TIDE were utilized for predicting the therapeutic response of immunotherapy.

Results

A total of 106 GMRGs were retrieved. Two distinct clusters were established by consensus clustering analysis, which showed a close association with the IDH mutational status of gliomas. In both IDH-mutant and IDH-wildtype gliomas, cluster 2 had significantly shorter overall survival compared with cluster 1, and the differentially expressed genes between the two clusters enriched in pathways related to malignant transformation as well as immunity. In silico TME analysis of the two IDH subtypes revealed not only significantly different immune cell infiltrations and immune phenotypes between the GMRG expression clusters but also different predicted responses to immunotherapy. After the screening, a total of 10 GMRGs were selected to build the GMRS. Survival analysis demonstrated the independent prognostic role of GMRS. Prognostic nomograms were established to predict 1-, 2-, and 3-year survival rates in the four cohorts.

Conclusion

Different subtypes of glutamine metabolism could affect the aggressiveness and TME immune features of diffuse glioma, despite their IDH mutational status. The expression signature of GMRGs could not only predict the outcome of patients with glioma but also be combined into an accurate prognostic nomogram.

A Novel Glycolysis-Related Signature for Predicting the Prognosis and Immune Infiltration of Uveal Melanoma

INTRODUCTION

As the most common aggressive intraocular cancer in adults, uveal melanoma (UVM) threatens the survival and vision of many people. Glycolysis is a novel hallmark of cancer, but the role of glycolysis-related genes in UVM prognosis remains unknown. The purpose of the study was to establish a glycolysis-related gene signature (GRGS) to predict UVM prognosis.

METHODS

Raw data were obtained from TCGA-UVM and GSE22138 datasets. The GRGS was established by univariate, LASSO, and multivariate Cox regression analyses. Kaplan-Meier survival and time-dependent receiver operating characteristic curves were used to evaluate the predictive ability of the GRGS. The relationships of the GRGS with infiltrating immune cell levels and mutations were analyzed with CIBERSORT and maftools.

RESULTS

A novel GRGS (risk score = 0.690861*ISG20 + 0.070991*MET - 0.227520*SDC2 + 0.690223*FBP1 + 0.048008*CLN6 - 0.128520*SDC3) was developed for predicting UVM prognosis. The GRGS had robust predictive stability in UVM. Enrichment annotation suggested that the high-risk group had stronger adaptive immune responses and that the low-risk group had more innate immune cell infiltration. Moreover, BAP1 mutation was related to high risk, and SF3B1 mutation was related to low risk.

CONCLUSIONS

This study developed and validated a novel GRGS to predict UVM prognosis and immune infiltration. The signature revealed an association between glycolysis-related genes and the tumor microenvironment, providing new insights into the role of glycolysis in UVM.

A prognostic classification system for uveal melanoma based on a combination of patient age and sex, the American Joint Committee on Cancer and the Cancer Genome Atlas models

PURPOSE

To revisit the independent importance of ciliary body involvement (CBI), monosomy 3 (M3), tumour size, histological and clinical factors in uveal melanoma (UM) and to devise a new prognostic classification based on a combination of the American Joint Committee on Cancer (AJCC) and the Cancer Genome Atlas (TCGA) models.

METHODS

Two cohorts with a total of 1796 patients were included. Clinicopathological factors were compared between patients with and without CBI and M3. Development of the prognostic classification was performed in a training cohort and was then tested in two independent validation cohorts.

RESULTS

Tumours with CBI were more common in women, had greater apical thickness, greater basal tumour diameter, greater rates of vasculogenic mimicry and greater rates of M3, were more often asymptomatic at diagnosis and had poorer 5- and 10-year globe conservation rates (p < 0.023). In multivariate logistic regression, patient age at diagnosis, tumour diameter and CBI were independent predictors of M3 (p < 0.001). In multivariate Cox regression, male sex, age at diagnosis, tumour diameter, M3 and CBI were independent predictors of metastasis. The proposed prognostic classification combined patient age, sex, CBI, extraocular extension, M3, 8q (optional) and tumour size, and demonstrated greater prognostic acumen than both AJCC 4 T categories and TCGA groups A to D in validation cohorts.

CONCLUSIONS

Tumour size does not confound the prognostic implication of CBI, M3, male sex and age at diagnosis in UM. These factors were included in a new prognostic classification that outperforms AJCC T category and TCGA groups.

Lipid metabolism-related gene signature predicts prognosis and depicts tumor microenvironment immune landscape in gliomas

Background

Glioma is the most common primary brain tumor in adults and accounts for more than 70% of brain malignancies. Lipids are crucial components of biological membranes and other structures in cells. Accumulating evidence has supported the role of lipid metabolism in reshaping the tumor immune microenvironment (TME). However, the relationship between the immune TME of glioma and lipid metabolism remain poorly described.

Materials and methods

The RNA-seq data and clinicopathological information of primary glioma patients were downloaded from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA). An independent RNA-seq dataset from the West China Hospital (WCH) also included in the study. Univariate Cox regression and LASSO Cox regression model was first to determine the prognostic gene signature from lipid metabolism-related genes (LMRGs). Then a risk score named LMRGs-related risk score (LRS) was established and patients were stratified into high and low risk groups according to LRS. The prognostic value of the LRS was further demonstrated by construction of a glioma risk nomogram. ESTIMATE and CIBERSORTx were used to depicted the TME immune landscape. Tumor Immune Dysfunction and Exclusion (TIDE) was utilized to predict the therapeutic response of immune checkpoint blockades (ICB) among glioma patients.

Results

A total of 144 LMRGs were differentially expressed between gliomas and brain tissue. Finally, 11 prognostic LMRGs were included in the construction of LRS. The LRS was demonstrated to be an independent prognostic predictor for glioma patients, and a nomogram consisting of the LRS, IDH mutational status, WHO grade, and radiotherapy showed a C-index of 0.852. LRS values were significantly associated with stromal score, immune score, and ESTIMATE score. CIBERSORTx indicated remarkable differences in the abundance of TME immune cells between patients with high and low LRS risk levels. Based on the results of TIDE algorithm, we speculated that the high-risk group had a greater chance of benefiting from immunotherapy.

Conclusion

The risk model based upon LMRGs could effectively predict prognosis in patients with glioma. Risk score also divided glioma patients into different groups with distinct TME immune characteristics. Immunotherapy is potentially beneficial to glioma patients with certain lipid metabolism profiles.

Iris melanoma outcomes based on the Cancer Genome Atlas (TCGA) classification in 78 consecutive patients

BACKGROUND

The Cancer Genome Atlas (TCGA) classification of genetic alterations in uveal melanoma is widely used for prognostication. We present novel observations on the impact of TCGA Group specifically for iris melanoma.

METHODS

This was a retrospective cohort study at a tertiary referral ocular oncology center. All patients with a diagnosis of iris melanoma who underwent genetic evaluation and assessment for TCGA classification between 20 November 1995 and 5 April 2021 were included. The main outcome measures were visual acuity, secondary glaucoma, tumor recurrence, melanoma-related metastasis and death per TCGA group.

RESULTS

There were a total of 78 patients included. The mean patient age was 49.6 years (median 53.0, range 3.0-85.0), mean tumor basal diameter was 6.7 mm (median 6.0, range 1.5-22.0), and mean tumor thickness was 2.6 mm (median 2.5, range 0.5-8.5). Cytology results confirmed iris melanoma (93%) or were inconclusive (7%). The TCGA groups included Group A (n = 36, 46%), Group B (n = 7, 9%), Group C (n = 34, 44%), and Group D (n = 1, 1%). There was no statistically significant difference in outcomes of visual acuity, tumor thickness reduction, secondary glaucoma, tumor recurrence, melanoma-related metastasis or death per individual TCGA group (A vs. B vs. C vs. D) and per bimodal comparison (A/B vs. C/D).

CONCLUSIONS

In this analysis, iris melanoma was classified as TCGA group A or B in 55% and as C or D in 45%. The TCGA classification was not predictive of melanoma-related metastasis or death.

Relationship between Fitzpatrick Skin Type and The Cancer Genome Atlas Classification with Melanoma-Related Metastasis and Death in 854 Patients at a Single Ocular Oncology Center

BACKGROUND

The Fitzpatrick Skin Type (FST) is an objective method of classifying patients based on skin color and sunburn sensitivity. The Cancer Genome Atlas (TCGA) is a method of determining the prognosis of patients with uveal melanoma based on genetic composition of the tumor. There is no literature studying the relationship of FST and TCGA groups.

MATERIALS AND METHODS

Retrospective cohort study on 854 patients with uveal melanoma treated at a single tertiary ocular oncology center between April 2006 and June 2020, classified based on FST on a scale of I-VI and based on genetic analysis with TCGA classification on a scale of A, B, C, and D. Outcome measures included uveal melanoma-related metastasis and death per FST and TCGA group.

RESULTS

Patients classified as FST I (compared to FST II and III-V) had higher odds of being TCGA group D (OR 2.34, p = 0.002). Patients classified as FST III-V (compared to FST I and II) had higher odds of being TCGA group B (OR 2.26, p = 0.002). Kaplan-Meier survival analysis showed no difference in melanoma-related metastasis or death comparing FST I vs. II vs. III-V within each TCGA group at 5, 10, and 15 years.

CONCLUSIONS

Patients classified as FST I are more likely to have a higher grade melanoma on genetic testing whereas those classified as FST III-V show lower grade melanoma. Despite differences in tumor features and genetic profile with various FST, survival analysis at 5, 10, and 15 years revealed no difference in melanoma-related metastasis or death within each TCGA group per skin tone.

Tebentafusp for the treatment of HLA-A*02:01-positive adult patients with unresectable or metastatic uveal melanoma

INTRODUCTION

: Metastatic uveal melanoma is associated with poor prognosis and few treatment options. Tebentafusp recently became the first FDA-approved agent for metastatic uveal melanoma.

AREAS COVERED

In this review, we describe the mechanism of action of tebentafusp as well as preclinical data showing high tumor specificity of the drug. We also review promising early phase trials in which tebentafusp demonstrated activity in metastatic uveal melanoma patients with an acceptable toxicity profile that included cytokine-mediated, dermatologic-related, and liver-related adverse events. Finally, we summarize findings from a pivotal phase III randomized trial in which tebentafusp demonstrated significant improvement in overall survival in comparison with investigator choice therapy.

EXPERT OPINION

Tebentafusp has transformed the treatment paradigm for metastatic uveal melanoma and should be the preferred frontline agent for most HLA-A*0201 positive patients. However, patients with rapidly progressing disease or high tumor benefit may not derive the same benefit. Areas of future study should focus on its role in the adjuvant setting as well as strategies to improve efficacy of tebentafusp in the metastatic setting.

Characterizing metastatic uveal melanoma patients who develop symptomatic brain metastases

Metastatic uveal melanoma (mUM) is an advanced ocular malignancy characterized by a hepatotropic pattern of spread. As the incidence of brain metastases (BM) in mUM patients has been thought to be low, routine CNS surveillance has not been recommended. Notably, no formal assessment of BM incidence in mUM has to date been published to support this clinical practice. We aimed to determine the true rate of BM in mUM and to clarify the clinical and genomic risk factors associated with BM patients through a collaborative multicenter, retrospective research effort. Data collected from 1,845 mUM patients in databases across four NCI-designated comprehensive cancer centers from 2006-2021 were retrospectively analyzed to identify patients with BM. Brain imaging in most cases were performed due to onset of neurological symptoms and not for routine surveillance. An analysis of demographics, therapies, gene expression profile, tumor next generation sequencing (NGS) data, time to metastasis (brain or other), and survival in the BM cohort was completed. 116/1,845 (6.3%) mUM patients were identified with BM. The median age at time of UM diagnosis was 54 years old (range: 18-77). The median time to any metastasis was 4.2 years (range: 0-30.8). The most common initial metastatic site was the liver (75.9%). 15/116 (12.9%) BM patients presented with BM at the time of initial metastatic diagnosis. Median survival after a diagnosis of BM was 7.6 months (range: 0.4-73.9). The median number of organs involved at time of BM diagnosis was 3 (range: 1-9). DecisionDX-UM profiling was completed on 13 patients: 10-Class 2, 2-Class 1B, and 1-Class 1A. NGS and cytogenetic data were available for 34 and 21 patients, respectively. BM was identified in 6.3% of mUM cases and was associated with high disease burden and a median survival of under 8 months once diagnosed. Since most patients in this cohort were symptomatic, the incidence of asymptomatic BM remains unknown. These data suggest the use of routine brain imaging in all mUM patients at risk for developing BM for early detection.

Inflammatory landscape in Xeroderma pigmentosum patients with cutaneous melanoma

Xeroderma pigmentosum (XP) is a DNA repair disease that predisposes to early skin cancers as cutaneous melanoma. Melanoma microenvironment contains inflammatory mediators, which would be interesting biomarkers for the prognosis or for the identification of novel therapeutic targets. We used a PCR array to evaluate the transcriptional pattern of 84 inflammatory genes in melanoma tumors obtained from XP patients (XP-Mel) and in sporadic melanoma (SP-Mel) compared to healthy skin. Commonly expressed inflammatory genes were further explored via GTEx and GEPIA databases. The differentially expressed inflammatory genes in XP were compared to their expression in skin exposed to UVs, and evaluated on the basis of the overall survival outcomes of patients with melanoma. Monocyte subsets of patients with SP-Mel, XP and healthy donors were also assessed. PCR array data revealed that 34 inflammatory genes were under-expressed in XP-Mel compared to SP-Mel. Differentially expressed genes that were common in XP-Mel and SP-Mel were correlated with the transcriptomic datasets from GEPIA and GTEx and highlighted the implication of KLK1 and IL8 in the tumorigenesis. We showed also that in XP-Mel tumors, there was an overexpression of KLK6 and KLK10 genes, which seems to be associated with a bad survival rate. As for the innate immunity, we observed a decrease of intermediate monocytes in patients with SP-Mel and in XP. We highlight an alteration in the immune response in XP patients. We identified candidate biomarkers involved in the tumorigenesis, and in the survival of patients with melanoma. Intermediate monocyte's in patients at risk could be a prognostic biomarker for melanoma outcome.

Recent Advances and Challenges in Uveal Melanoma Immunotherapy

Simple Summary

Uveal melanoma is the most common primary intraocular malignancy in adults. Although it can be controlled locally, half of the patients still develop metastases. To date, there have been no standard therapeutic strategies for the prevention or treatment of metastases. Existing therapies, such as chemotherapy and targeted therapies, induce only minimal responses. This review focuses on newly published research on immunotherapy. We highlight expanding treatments and their clinical outcomes, as well as propose promising new treatments and feasible checkpoints. Based on these findings, we provide innovative insights into feasible strategies for the treatment of patients with uveal melanoma.

Abstract

Uveal melanoma (UM) is the most common primary intraocular malignancy in adults. Compared to cutaneous melanoma (CM), which mainly harbors BRAF or NRAS mutations, UM predominantly harbors GNAQ or GNA11 mutations. Although primary UM can be controlled locally, approximately 50% of patients still develop metastases. To date, there have been no standard therapeutic strategies for the prevention or treatment of metastases. Unfortunately, chemotherapy and targeted therapies only induce minimal responses in patients with metastatic UM, with a median survival time of only 4–5 months after metastasis detection. Immunotherapy agents, such as immune checkpoint inhibitors, have achieved pioneering outcomes in CM but have shown limited effects in UM. Researchers have explored several feasible checkpoints to identify options for future therapies. Cancer vaccines have shown little in the way of therapeutic benefit in patients with UM, and there are few ongoing trials providing favorable evidence, but adoptive cell transfer-related therapies seem promising and deserve further investigation. More recently, the immune-mobilizing monoclonal T-cell receptor against the cancer molecule tebentafusp showed impressive antitumor effects. Meanwhile, oncolytic viruses and small molecule inhibitors have also gained ground. This review highlights recent progress in burgeoning treatments and provides innovative insights on feasible strategies for the treatment of UM.

A Novel and Easy-to-Promote Prognostic Model for Patients With Uveal Melanoma

Purpose

To establish an easy and widely applicable prognostic prediction model for uveal melanoma (UM) based on a Chinese population.

Patients and Methods

A total of 295 consecutive cases treated at the Eye & ENT Hospital of Fudan University were included as the primary cohort, and 256 cases were included in the validation cohorts from two external Caucasian databases. Clinicopathological data were collected retrospectively, and nomogram models were formulated based on multivariable analysis. The concordance index (C-index), AUC (area under the Receiver Operating Characteristic, ROC curve), and Brier score were calculated and compared.

Results

Based on the training cohort, a nomogram model was established with five relevant variables: age, tumor size, ciliary body involvement, non-spindle cell type and extra-scleral extension. The C-index was 0.737, the 3- and 5-year AUCs were 0.767 and 0.742, and the Brier scores for 3- and 5-year survival were 0.082 and 0.129, respectively, which showed superior prediction compared to that of the Tumor, Node and Metastasis staging system. The model also displayed good discrimination and calibration in the external validation cohorts. By risk stratification, patients could be divided into low- and high-risk groups, and the overall survival curves displayed significant differences in the training and validation cohorts.

Conclusion

Our nomogram model was simple and accurate at predicting the overall survival of patients with UM. It was established based on Asian patients and proved suitable for Caucasian patients; thus, it has a wide range of potential applications, especially for patients living in less medically developed countries and regions.

Potential of Aqueous Humor as a Liquid Biopsy for Uveal Melanoma

Tumor biopsy can identify prognostic biomarkers for metastatic uveal melanoma (UM), however aqueous humor (AH) liquid biopsy may serve as an adjunct. This study investigated whether the AH of UM eyes has sufficient circulating tumor DNA (ctDNA) to perform genetic analysis. This is a case series of 37 AH samples, taken before or after radiation, and one tumor wash sample, from 12 choroidal and 8 ciliary body (CB) melanoma eyes. AH was analyzed for nucleic acid concentrations. AH DNA and one tumor wash sample underwent shallow whole-genome sequencing followed by Illumina sequencing to detect somatic copy number alterations (SCNAs). Four post-radiation AH underwent targeted sequencing of BAP1 and GNAQ genes. Post-radiation AH had significantly higher DNA and miRNA concentrations than paired pre-radiation samples. Highly recurrent UM SCNAs were identified in 0/11 post-radiation choroidal and 6/8 post-radiation CB AH. SCNAs were highly concordant in a CB post-radiation AH with its matched tumor (r = 0.978). BAP1 or GNAQ variants were detected in 3/4 post-radiation AH samples. AH is a source of ctDNA in UM eyes, particularly in post-radiation CB eyes. For the first time, UM SCNAs and mutations were identified in AH-derived ctDNA. Suggesting that AH can serve as a liquid biopsy for UM.

Identification of prognostic genes in oral squamous cell carcinoma microenvironment

BACKGROUND

Numerous studies reveal the clinical significance of tumor microenvironment (TME) in multiple cancers. The association between TME in oral squamous cell carcinoma (OSCC) and clinical outcomes remains unsolved.

OBJECTIVE

This study aims to exhibit the TME of OSCC and identified the prognostic marker.

METHODS

Gene expression profile and clinical data OSCC patients were from the TCGA database. The validated stage data was from the Gene Expression Omnibus (GSE65858). Immune/stromal scores of each patient were calculated by ESTIMATE algorithm. Biological functional prediction was conducted. Prognostic genes identified by survival analysis. Nomogram and Receiver operating characteristic curves were employed to test the predicting power. TIMER database was applied to evaluated the immune infiltrates.

RESULTS

Lower immune scores were observed in male patients (P= 0.0107) and different primary tumor sites of oral cavity with different stromal scores (P= 0.0328). The Differentially expressed genes (DEGs) were involved in immune related pathways. HGF gene (hepatocyte growth factor) was prognostic related and with a better prognostic performance when combined with clinical features (AUC=TCGA 0.638, AUC=GEO 0.714). HGF was significantly related with B cell, CD4ï⁢¼⁢T cell, CD8+T cell, macrophage, neutrophils, and dendritic cell infiltration.

CONCLUSION

The current study analyzed the TME and presented immune related prognostic biomarkers for OSCC.

The Interplay between Tumour Microenvironment Components in Malignant Melanoma

Malignant melanoma has shown an increasing incidence during the last two decades, exhibiting a large spectrum of locations and clinicopathological characteristics. Although current histopathological, biochemical, immunohistochemical, and molecular methods provide a deep insight into its biological behaviour and outcome, melanoma is still an unpredictable disease, with poor outcome. This review of the literature is aimed at updating the knowledge regarding melanoma’s clinicopathological and molecular hallmarks, including its heterogeneity and plasticity, involving cancer stem cells population. A special focus is given on the interplay between different cellular components and their secretion products in melanoma, considering its contribution to tumour progression, invasion, metastasis, recurrences, and resistance to classical therapy. Furthermore, the influences of the specific tumour microenvironment or “inflammasome”, its association with adipose tissue products, including the release of “extracellular vesicles”, and distinct microbiota are currently studied, considering their influences on diagnosis and prognosis. An insight into melanoma’s particular features may reveal new molecular pathways which may be exploited in order to develop innovative therapeutic approaches or tailored therapy.

PRRX1 Is a Novel Prognostic Biomarker and Facilitates Tumor Progression Through Epithelial–Mesenchymal Transition in Uveal Melanoma

Uveal melanoma (UM) is the most common primary intraocular malignancy in adults. UM develops and is sustained by inflammation and immunosuppression from the tumor microenvironment (TME). This study sought to identify a reliable TME-related biomarker that could provide survival prediction and new insight into therapy for UM patients. Based on clinical characteristics and the RNA-seq transcriptome data of 80 samples from The Cancer Genome Atlas (TCGA) database, PRRX1 as a TME- and prognosis-related gene was identified using the ESTIMATE algorithm and the LASSO–Cox regression model. A prognostic model based on PRRX1 was constructed and validated with a Gene Expression Omnibus (GEO) dataset of 63 samples. High PRRX1 expression was associated with poorer overall survival (OS) and metastasis-free survival (MFS) in UM patients. Comprehensive results of the prognostic analysis showed that PRRX1 was an independent and reliable predictor of UM. Then the results of immunological characteristics demonstrated that higher expression of PRRX1 was accompanied by higher expression of immune checkpoint genes, lower tumor mutation burden (TMB), and greater tumor cell infiltration into the TME. Gene set enrichment analysis (GSEA) showed that high PRRX1 expression correlated with angiogenesis, epithelial–mesenchymal transition (EMT), and inflammation. Furthermore, downregulation of PRRX1 weakened the process of EMT, reduced cell invasion and migration of human UM cell line MuM-2B in vitro. Taken together, these findings indicated that increased PRRX1 expression is independently a prognostic factor of poorer OS and MFS in patients with UM, and that PRRX1 promotes malignant progression of UM by facilitating EMT, suggesting that PRRX1 may be a potential target for UM therapy.

Biopsy for molecular risk stratification in uveal melanoma: Yields and molecular characteristics in 119 patients

BACKGROUND

Prognostic cytological and molecular features of uveal melanoma have been well researched and are essential in management. Samples can be obtained in vivo through fine needle aspirate biopsy, vitrector cutter, forceps or post-enucleation for off-site testing. This study aims to examine cytological and chromosome microarray yields of these samples.

METHODS

A retrospective cohort analysis of 119 uveal melanoma biopsies submitted to our laboratory. Samples included those taken in vivo (n = 57) and post-enucleation (n = 62). Patient and tumour features were collected including age, sex, primary tumour location, basal diameter and tumour height. Prognostic outcomes measured include cell morphology, chromosomal status and immunohistochemistry.

RESULTS

Post-enucleation biopsies accounted for just over half of our samples (52%). Post-enucleation samples had a more successful genetic yield than in vivo biopsies (77% vs. 50%, p = 0.04) though there was no difference for cytological yields. There was no difference in cytological or microarray yields between instruments. The vitrector biopsy group had the smallest tumour thickness (5 mm vs. 10 mm [fine-needle aspirate biopsy], p = 0.003). There was a strong correlation between monosomy 3, BAP1 aberrancy and epithelioid cell type in post-enucleation samples (Tb  = 0.742, p = 0.005). However, epithelioid morphology was not associated with either monosomy 3 (p = 0.07) or BAP1 aberrancy (p = 0.24) for in vivo biopsies.

CONCLUSIONS

All three biopsy instruments provide similar cytological yields as post-enucleation sampling, although post-enucleation samples had a more successful chromosome microarray yield. Epithelioid cytomorphology alone is insufficient for prognostication in in vivo biopsies, immunohistochemistry would be a useful surrogate test.

Prognostic Biomarkers in Uveal Melanoma: The Status Quo, Recent Advances and Future Directions

Simple Summary

Although rare, uveal melanoma (UM) is the most common cancer that develops inside adult eyes. The prognosis is poor, since 50% of patients will develop lethal metastases in the first decade, especially to the liver. Once metastases are detected, life expectancy is limited, given that the available treatments are mostly unsuccessful. Thus, there is a need to find methods that can accurately predict UM prognosis and also effective therapeutic strategies to treat this cancer. In this manuscript, we initially compile the current knowledge on epidemiological, clinical, pathological and molecular features of UM. Then, we cover the most relevant prognostic factors currently used for the evaluation and follow-up of UM patients. Afterwards, we highlight emerging molecular markers in UM published over the last three years. Finally, we discuss the problems preventing meaningful advances in the treatment and prognostication of UM patients, as well as forecast new roadblocks and paths of UM-related research.

Abstract

Uveal melanoma (UM) is the most common malignant intraocular tumour in the adult population. It is a rare cancer with an incidence of nearly five cases per million inhabitants per year, which develops from the uncontrolled proliferation of melanocytes in the choroid (≈90%), ciliary body (≈6%) or iris (≈4%). Patients initially present either with symptoms like blurred vision or photopsia, or without symptoms, with the tumour being detected in routine eye exams. Over the course of the disease, metastases, which are initially dormant, develop in nearly 50% of patients, preferentially in the liver. Despite decades of intensive research, the only approach proven to mildly control disease spread are early treatments directed to ablate liver metastases, such as surgical excision or chemoembolization. However, most patients have a limited life expectancy once metastases are detected, since there are limited therapeutic approaches for the metastatic disease, including immunotherapy, which unlike in cutaneous melanoma, has been mostly ineffective for UM patients. Therefore, in order to offer the best care possible to these patients, there is an urgent need to find robust models that can accurately predict the prognosis of UM, as well as therapeutic strategies that effectively block and/or limit the spread of the metastatic disease. Here, we initially summarized the current knowledge about UM by compiling the most relevant epidemiological, clinical, pathological and molecular data. Then, we revisited the most important prognostic factors currently used for the evaluation and follow-up of primary UM cases. Afterwards, we addressed emerging prognostic biomarkers in UM, by comprehensively reviewing gene signatures, immunohistochemistry-based markers and proteomic markers resulting from research studies conducted over the past three years. Finally, we discussed the current hurdles in the field and anticipated the future challenges and novel avenues of research in UM.

Regulation of epigenetic homeostasis in uveal melanoma and retinoblastoma

Uveal melanoma (UM) and retinoblastoma (RB), which cause blindness and even death, are the most frequently observed primary intraocular malignancies in adults and children, respectively. Epigenetic studies have shown that changes in the epigenome contribute to the rapid progression of both UM and RB following classic genetic changes. The loss of epigenetic homeostasis plays an important role in oncogenesis by disrupting the normal patterns of gene expression. The targetable nature of epigenetic modifications provides a unique opportunity to optimize treatment paradigms and establish new therapeutic options for both UM and RB with these aberrant epigenetic modifications. We aimed to review the research findings regarding relevant epigenetic changes in UM and RB. Herein, we 1) summarize the literature, with an emphasis on epigenetic alterations, including DNA methylation, histone modifications, RNA modifications, noncoding RNAs and an abnormal chromosomal architecture; 2) elaborate on the regulatory role of epigenetic modifications in biological processes during tumorigenesis; and 3) propose promising therapeutic candidates for epigenetic targets and update the list of epigenetic drugs for the treatment of UM and RB. In summary, we endeavour to depict the epigenetic landscape of primary intraocular malignancy tumorigenesis and provide potential epigenetic targets in the treatment of these tumours.

Adding TCGA chromosome classes to AJCC system allows for more precise prognostication in uveal melanoma patients

PURPOSE

Uveal melanoma (UM) is a rare disease and the most common primary intraocular malignancy in adults, with a high risk of metastases. Reliable prognostication systems are based on anatomical features, as in the Tumor Node Metastasis / American Joint Committee on Cancer (TNM/AJCC) staging, or on genetic information, as in The Cancer Genome Atlas (TCGA) system. Prior evidence suggests that combining both systems may be beneficial. We evaluated the benefit of combining the TCGA and AJCC systems in a large cohort of patients.

DESIGN

Retrospective case series of UM patients.

PARTICIPANTS

979 patients with a choroidal/ciliary body melanoma treated at the Wills Eye Hospital between 1998 and 2020, 94% of whom received eye-sparing treatment.

METHODS

Tumors were classified into four TCGA groups based on chromosome copy number: A (disomy 3, normal 8q), B (disomy 3, any 8q gain), C (monosomy 3, one extra copy of 8q), D (monosomy 3, multiple 8q gain). The AJCC staging manual, 8th edition was used for AJCC staging. Cox regression and log-rank test were used for survival analysis.

MAIN OUTCOME MEASURE

Metastasis-free survival.

RESULTS

Combining information of the two systems improved prognostication in intermediate groups: in TCGA group C, we saw an increased rate of metastasis in AJCC stage III (28%) compared to stage II (8.9%); the same was seen in AJCC stage II, going from TCGA group C (8.9%) to group D (46%) and in AJCC stage III going from group C (28%) to group D (49%). In AJCC stage II or III patients, loss of chromosome 3 and gain of 8q (TCGA group C and D) significantly worsened the prognosis, with multiple 8q gain (TCGA group D) having a greater impact.

CONCLUSIONS

Combining information from AJCC stage and TCGA groups yields a better predictive power even in this set of relatively small tumors and we propose that physicians take both systems into account whenever possible, especially in moderate-risk groups.

Intra- and intertumoral heterogeneity of liver metastases in a patient with uveal melanoma revealed by single-cell RNA sequencing

Tumor heterogeneity is a major obstacle to the success of cancer treatment. An accurate understanding and recognition of tumor heterogeneity is critical in the clinical management of cancer patients. Here, we utilized single-cell RNA sequencing (scRNA-seq) to uncover the intra- and intertumoral heterogeneity of liver metastases from a patient with metastatic uveal melanoma. The two metastases analyzed were largely infiltrated by noncancerous cells with significant variability in the proportion of different cell types. Analysis of copy-number variations (CNVs) showed gain of 8q and loss of 6q in both tumors, but loss of Chromosome 3 was only detected in one of the tumors. Single-nucleotide polymorphism (SNP) array revealed a uniparental isodisomy 3 in the tumor with two copies of Chromosome 3, indicating a regain of Chromosome 3 during the development of the metastatic disease. In addition, both tumors harbored subclones with additional CNVs. Pathway enrichment analysis of differentially expressed genes revealed that cancer cells in the metastasis with isodisomy 3 showed up-regulation in epithelial-mesenchymal transition and myogenesis related genes. In contrast, up-regulation in interferon signaling was observed in the metastasis with monosomy 3 and increased T-cell infiltrate. This study highlights the complexity and heterogeneity of different metastases within an individual case of uveal melanoma.

Ten-year outcomes of uveal melanoma based on The Cancer Genome Atlas (TCGA) classification in 1001 cases

Purpose

To understand the prognostic value of The Cancer Genome Atlas (TCGA) for uveal melanoma metastasis, using a simplified 4-category classification, based on tumor DNA.

Methods

A retrospective cohort study of 1001 eyes with uveal melanoma at a single center, categorized according to TCGA as Group A, B, C, or D (by fine-needle aspiration biopsy for DNA analysis), and treated with standard methods, was studied for melanoma-related metastasis at 5 and 10 years.

Results

Of 1001 eyes with uveal melanoma, the TCGA categories included Group A (n = 486, 49%), B (n = 141, 14%), C (n = 260, 26%), and D (n = 114, 11%). By comparison, increasing category (A vs. B vs. C vs. D) was associated with features of older age at presentation (56.8 vs. 52.8 vs. 61.1 vs. 63.5 years, P < 0.001), less often visual acuity of 20/20-20/50 (80% vs. 67% vs. 70% vs. 65%, P = 0.001), tumor location further from the optic disc (P < 0.001) and foveola (P < 0.001), and greater median tumor basal diameter (10.0 vs. 13.0 vs. 14.0 vs. 16.0 mm, P < 0.001) and tumor thickness (3.5 vs. 5.2 vs. 6.0 vs. 7.1 mm, P < 0.001). The Kaplan-Meier (5-year/10-year) rate of metastasis was 4%/6% for Group A, 12%/20% for Group B, 33%/49% for Group C, and 60%/not available for Group D.

Conclusion

A simplified 4-category classification of uveal melanoma using TCGA, based on tumor DNA, is highly predictive of risk for metastatic disease.

Identification of survival-related genes and a novel gene-based prognostic signature involving the tumor microenvironment of uveal melanoma

Uveal melanoma (UM) is the most common primary intraocular malignant tumor in adults and almost fifty percent of patients subsequently develop systemic metastases usually involving the liver. The tumor microenvironment (TME) is crucial to the initiation and progression of tumors. In the present study, we comprehensively evaluated the TME of primary UM samples from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database by using several bioinformatic algorithms. The prognostic value of immune score and infiltrating immune cells in the TME were evaluated. Differentially expressed genes between the low- and high-immune score groups were also identified. The majority of tumor-infiltrating lymphocytes in UM have been determined to be activated CD8 + T cells. Therefore, weighted gene co-expression network analysis (WGCNA) was performed to identify the co-expression modules and genes significantly associated with the level of infiltrating CD8 + T cells in UM. Survival-related genes involved in the TME were identified by univariate Cox regression analysis. Furthermore, an eight-gene-based prognostic signature was established in the training dataset TCGA-UM via Lasso-penalized and multivariate Cox regression analyses. The predictive value of this signature was validated in two testing datasets. Besides, a nomogram was established to serve clinical practice. Moreover, hub genes involved in the infiltrating CD8 + T cells were identified and a potential targeted therapy for preventing metastasis of UM was proposed based on the results. In summary, our results provided a robust gene-based prognostic signature for predicting prognosis of UM patients and proposed a potential targeted therapy for preventing UM metastasis.

Uveal melanoma: laboratory advances and new frontiers in patient care

PURPOSE OF REVIEW

To review recent advancements in the genetic understanding, diagnosis, prognosis, and treatment of uveal melanoma (UM).

RECENT FINDINGS

UM is a molecularly distinct melanocytic malignancy driven by mutations in GNAQ or GNA11, with mitogen-activated protein kinase pathway upregulation. Earlier diagnosis and treatment are important factors for improving life prognosis. These goals can be aided by more objective multimodal imaging risk factors for the prediction of malignant nevus transformation and novel treatment strategies such as customized radiation fields and nanoparticle therapy to reduce vision-threatening treatment side effects. The risk for metastatic disease can be reliably predicted through gene expression profiling or the Cancer Genome Atlas project classification, and combined use of clinical tumor features with molecular data allows for highly individualized patient prognosis. Patients with high-risk UM should be considered for clinical trials of adjuvant therapy to prevent metastatic disease. For patients with clinically evident metastasis, combination immunotherapy regimens, T cell-based therapies, and focal adhesion kinase inhibitors offer hope for improved clinical response rates.

SUMMARY

Improved understanding of UM molecular pathogenesis and clinical trials of targeted therapy for prevention and treatment of metastatic disease may improve patient survival for this challenging disease.

Development of new therapeutic options for the treatment of uveal melanoma

Uveal melanoma (UM) is the most common primary intraocular malignancy in adults. Important cytogenetic and genetic risk factors for the development of UM include chromosome 3 monosomy, mutations in the guanine nucleotide-binding proteins GNAQ/GNA11, and loss of the BRACA1-associated protein 1 (BAP 1). Most primary UMs are treated conservatively with radiotherapy, but enucleation is necessary for large tumours. Despite the effectiveness of local control, up to 50% of UM patients develop metastasis for which there are no effective therapies. Attempts to utilise the targeted therapies that have been developed for the treatment of other cancers, including a range of signal transduction pathway inhibitors, have rarely produced significant outcomes in UM. Similarly, the application of immunotherapies that are effective in cutaneous melanoma to treat UM have also been disappointing. Other approaches that have been initiated involve proteasomal inhibitors and histone deacetylase inhibitors which are approved for the treatment of other cancers. Nevertheless, there have been occasional positive outcomes from these treatments in UM. Moreover, combination approaches in UM have also yielded some positive developments. It would be valuable to identify how to apply such therapies efficiently in UM, potentially via individualised tumour profiling. It would also be important to characterise UM tumours to differentiate the potential drivers of progression from those in other types of cancers. The recent identification of novel kinases and metastatic genes in UM tumours makes the development of new UM-specific treatments feasible.

Optimising prediction of early metastasis-free survival in uveal melanoma using a four-category model incorporating gene expression profile and tumour size

BACKGROUND

Largest basal diameter (LBD) appears to have independent prognostic value in uveal melanoma (UM).

METHODS

All patients undergoing plaque brachytherapy or enucleation for UM involving the choroid and/or ciliary body between 2012 and 2019.

RESULTS

A total of 348 patients with a mean age of 60±14 years were included and followed for a mean of 40±26 months (3.3±2.2 years). On multivariate analysis, LBD >12 mm remained a significant independent predictor of metastasis for both class 1 (HR 21.90; 95% CI 2.69 to 178.02; p=0.004) and class 2 (HR 2.45; 95% CI, 1.03 to 5.83; p=0.04) tumours. Four prognostic groups were created: group 1 (class 1, LBD <12 mm), group 2 (class 1, LBD ≥12 mm), group 3 (class 2, LBD <12 mm) and group 4 (class 2, LBD ≥12 mm). Life tables were used to calculate the 3-year and 5-year metastasis-free survival: group 1 (98 and 98%), group 2 (86 and 86%), group 3 (81 and 62%) and group 4 (54 and 47%). Compared with the reference category (group 1), the Cox proportional hazard model demonstrated a significant worsening of survival for each progressive category (group 2 (HR 21.59; p=0.004), group 3 (HR 47.12, p<0.001), and group 4 (HR 114.24; p<0.001)). In our dataset, the four-category Cox model performed poorer compared with the American Joint Committee on Cancer (AJCC) and gene expression profile (AJCC+GEP) in the Akaike's information criteria (AIC) (297 vs 291), fit better with the Bayesian information criteria (BIC) (309 vs 313) and performed similarly with the Harrel's C (0.86 (95% CI 0.80 to 0.91) vs 0.89 (0.84 to 0.94), respectively).

CONCLUSIONS

Combination of GEP and LBD allows separation of patients into four easy-to-use prognostic groups and was similar to a model combining AJCC stage with GEP.

Accuracy of The Cancer Genome Atlas Classification vs American Joint Committee on Cancer Classification for Prediction of Metastasis in Patients With Uveal Melanoma

Importance

The Cancer Genome Atlas (TCGA) classification is a newly emerging method for prediction of uveal melanoma (UM)-related metastasis and death. Limited information is available regarding the accuracy of the TCGA classification for prediction of metastasis in patients with UM.

Objective

To investigate the accuracy of the TCGA classification for predicting UM-related metastasis compared with the American Joint Committee on Cancer (AJCC) classification.

Design, Setting, and Participants

In this retrospective cohort study, patients with UM treated with plaque radiotherapy at a tertiary referral center from October 1, 2008, to December 31, 2018, were evaluated. All patients with tumors classified according to the American Joint Committee on Cancer Staging Manual, 8th Edition, and who completed pretreatment fine-needle aspiration biopsy sampling for genetic analysis of chromosomes 3 and 8 for TCGA classification were included. Tumors were classified into 4 categories, 17 subcategories, and 4 stages using AJCC classification and further grouped into 4 classes using TCGA classification.

Main Outcomes and Measures

Value of TCGA classification vs AJCC classification for predicting UM-related metastasis.

Results

Of 642 included patients, 331 (51.6%) were women, and the mean (SD) age was 58.0 (13.8) years. There were 642 tumors from 642 patients classified according to both AJCC and TCGA classifications. The mean (range) follow-up time for the entire cohort was 43.7 (1.4-159.2) months. At 5 years, TCGA classification showed higher value for prediction of metastasis (4 TCGA classes: Wald statistic, 94.8; hazard ratio [HR], 2.8; 95% CI, 2.3-3.5; P < .001; 4 AJCC categories: Wald statistic, 67.5; HR, 2.6; 95% CI, 2.1-3.2; P < .001; 17 AJCC subcategories: Wald statistic, 74.3; HR, 1.3; 95% CI, 1.2-1.3; P < .001; 4 AJCC stages: Wald statistic, 67.0; HR, not applicable; P < .001). After entering TCGA and AJCC classifications into a multivariate model, TCGA classification still showed higher value for prediction of metastasis (TCGA classification: Wald statistic, 61.5; HR, 2.4; 95% CI, 1.9-2.9; P < .001; AJCC classification: Wald statistic, 35.5; HR, 1.9; 95% CI, 1.5-2.4; P < .001).

Conclusions and Relevance

These results suggest that TCGA classification provides accuracy that is superior to AJCC categories, subcategories, and stages for predicting metastasis from UM. When genetic testing is available, TCGA classification can provide a more accurate way to identify patients at high risk of metastasis who might benefit from adjuvant therapy.

Development and validation of an immune and stromal prognostic signature in uveal melanoma to guide clinical therapy

The tumor microenvironment is known to play an important role in uveal melanoma. Reliable prognostic signatures are needed to aid high risk patients and improve prognosis. Uveal melanoma tissues from three public datasets were analyzed. RNA sequence data of uveal melanoma and corresponding clinical features were obtained from The Cancer Genome Atlas database. Immune and stromal scores were calculated by applying the "ESTIMATE" algorithm. The samples were divided into high and low immune or stromal score groups. We constructed prognostic models by using the 'lasso' package and tested them for 500 iterations. The cell signature was validated in another GSE44295 and GSE84976 datasets. We found that the median survival time of the low immune/stromal score group is longer than that of the high-score group. Thirteen immune cells and one stromal cell were concerned significant in predicting poor overall survival rate. Finally, a four-cell model was identified. Further validation revealed that the low-risk group has a significantly better survival than the high-risk group in another two datasets (P < 0.05). Moreover, the high-risk group is more sensitive to immunotherapy and chemotherapy. Summarizing, the proposed immune cells signature is a promising biomarker for estimating overall survival in uveal melanoma.

Uveal Melanoma-Derived Extracellular Vesicles Display Transforming Potential and Carry Protein Cargo Involved in Metastatic Niche Preparation

Extracellular vesicles (EVs) carry molecules derived from donor cells and are able to alter the properties of recipient cells. They are important players during the genesis and progression of tumors. Uveal melanoma (UM) is the most common primary intraocular tumor in adults and is associated with a high rate of metastasis, primarily to the liver. However, the mechanisms underlying this process are poorly understood. In the present study, we analyzed the oncogenic potential of UM-derived EVs and their protein signature. We isolated and characterized EVs from five UM cell lines and from normal choroidal melanocytes (NCMs). BRCA1-deficient fibroblasts (Fibro-BKO) were exposed to the EVs and analyzed for their growth in vitro and their reprograming potential in vivo following inoculation into NOD-SCID mice. Mass spectrometry of proteins from UM-EVs and NCM-EVs was performed to determine a protein signature that could elucidate potential key players in UM progression. In-depth analyses showed the presence of exosomal markers, and proteins involved in cell-cell and focal adhesion, endocytosis, and PI3K-Akt signaling pathway. Notably, we observed high expression levels of HSP90, HSP70 and integrin V in UM-EVs. Our data bring new evidence on the involvement of UM-EVs in cancer progression and metastasis.

Molecular Insights and Emerging Strategies for Treatment of Metastatic Uveal Melanoma

Uveal melanoma (UM) is the most common intraocular cancer. In recent decades, major advances have been achieved in the diagnosis and prognosis of UM allowing for tailored treatments. However, nearly 50% of patients still develop metastatic disease with survival rates of less than 1 year. There is currently no standard of adjuvant and metastatic treatment in UM, and available therapies are ineffective resulting from cutaneous melanoma protocols. Advances and novel treatment options including liver-directed therapies, immunotherapy, and targeted-therapy have been investigated in UM-dedicated clinical trials on single compounds or combinational therapies, with promising results. Therapies aimed at prolonging or targeting metastatic tumor dormancy provided encouraging results in other cancers, and need to be explored in UM. In this review, the latest progress in the diagnosis, prognosis, and treatment of UM in adjuvant and metastatic settings are discussed. In addition, novel insights into tumor genetics, biology and immunology, and the mechanisms underlying metastatic dormancy are discussed. As evident from the numerous studies discussed in this review, the increasing knowledge of this disease and the promising results from testing of novel individualized therapies could offer future perspectives for translating in clinical use.

Lower Levels of Adiponectin and Its Receptor Adipor1 in the Uveal Melanomas With Monosomy-3

Purpose

Adiponectin is an insulin-sensitizing and anticarcinogenic hormone that is encoded by a gene on chromosome 3. Here, we analyzed the expression of adiponectin and its receptor Adipor1 in primary uveal melanoma (UM) with regard to the monosomy-3 status and clinical factors, as well as the physiological response of UM cells to adiponectin.

Methods

Immunohistochemistry was performed on the primary UM of 34 patients. Circulating melanoma cells (CMC) were isolated by immunomagnetic enrichment. Monosomy-3 was evaluated by Immuno-FISH. Gene expression was analyzed using the RNAseq data of The Cancer Genome Atlas study. Cultures of choroidal melanocytes and UM were established from the samples of two patients. The proliferative potential of the UM cell lines Mel-270 and OMM-2.5 was determined by immunocytochemistry, immunoblotting, cell cycle analysis, nucleolar staining, and adenosine triphosphate (ATP) levels.

Results

UM with monosomy-3 exhibited a lower immunoreactivity for adiponectin and Adipor1, which was associated with monosomy-3-positive CMC and the development of extraocular growth or metastases. Both proteins were more abundant in the irradiated tumors and present in the cultured cells. Gene expression profile indicated the impairment of adiponectin-mediated signaling in the monosomy-3 tumors. Adiponectin induced a significant decline in the ATP levels, Ki-67 expression, cells in the G2/M phase, and nucleolar integrity in UM cultures.

Conclusions

Adiponectin deficiency appears to enhance the metastatic potential of the UM cells with monosomy-3 and the termination of tumor dormancy. Counteracting insulin resistance and improving the serum adiponectin levels might therefore be a valuable approach to prevent or delay the UM metastases.

Uncommon Subtypes of Malignant Melanomas: A Review Based on Clinical and Molecular Perspectives

Malignant melanoma represents the most aggressive type of skin cancer. Modern therapies, including targeted agents and immune checkpoint inhibitors, have changed the dismal prognosis that characterized this disease. However, most evidence was obtained by studying patients with frequent subtypes of cutaneous melanoma (CM). Consequently, there is an emerging need to understand the molecular basis and treatment approaches for unusual melanoma subtypes. Even a standardized definition of infrequent or rare melanoma is not clearly established. For that reason, we reviewed this challenging topic considering clinical and molecular perspectives, including uncommon CMs-not associated with classical V600E/K BRAF mutations-malignant mucosal and uveal melanomas, and some unusual independent entities, such as amelanotic, desmoplastic, or spitzoid melanomas. Finally, we collected information regarding melanomas from non-traditional primary sites, which emerge from locations as unique as meninges, dermis, lymph nodes, the esophagus, and breasts. The aim of this review is to summarize and highlight the main scientific evidence regarding rare melanomas, with a particular focus on treatment perspectives.

Genetic Biomarkers in Melanoma of the Ocular Region: What the Medical Oncologist Should Know

Melanoma of the ocular region (ocular melanoma) comprises about 5% of all patients with melanoma and covers posterior uveal melanoma, iris melanoma, and conjunctival melanoma. The risk of metastasis is much higher in patients with ocular melanoma compared to a primary melanoma of the skin. The subtypes of ocular melanoma have distinct genetic features, which should be taken into consideration when making clinical decisions. Most relevant for current practice is the absence of BRAF mutations in posterior uveal melanoma, although present in some iris melanomas and conjunctival melanomas. In this review, we discuss the genetic biomarkers of the subtypes of ocular melanoma and their impacts on the clinical care of these patients.

Uveal melanoma pathobiology: Metastasis to the liver

Uveal melanoma (UM) is a type of intraocular tumor with a propensity to disseminate to the liver. Despite the identification of the early driver mutations during the development of the pathology, the process of UM metastasis is still not fully comprehended. A better understanding of the genetic, molecular, and environmental factors participating to its spread and metastatic outgrowth could provide additional approaches for UM treatment. In this review, we will discuss the advances made towards the understanding of the pathogenesis of metastatic UM, summarize the current and prospective treatments, and introduce some of the ongoing research in this field.

The prognostic landscape of adaptive immune resistance signatures and infiltrating immune cells in the tumor microenvironment of uveal melanoma

Uveal melanoma (UM) is the most common primary intraocular malignancy in adults and has a high mortality rate. Tumor microenvironment (TME) is crucial in controlling and influencing the behavior of malignant tumors. Thus, illustrating the prognostic values of adaptive immune resistance signatures and infiltrating immune cells in the TME of UM may provide scientific rationales for immunotherapy. In this study, the gene expression data of 80 primary UM and 103 primary skin cutaneous melanoma (SKCM) samples with relevant clinical information were obtained from The Cancer Genome Atlas (TCGA) database. The TME was analyzed by the xCell, EPIC, ESTIMATE and TIMER algorithms. The relationships and prognostic values of immune infiltrates and mutated genes were further investigated. We found that primary UM and primary SKCM exhibited distinct TMEs. Higher levels of infiltrating stromal and immune cells in UM were related to more aggressive biology and poor prognosis. Increased CD8⁺ T cell level, as well as several adaptive immune resistance markers, was a predictive factor of poor prognosis in UM. Furthermore, some common mutations of UM were associated with its TME. This study analyzed the immune landscape of adaptive immune resistance signatures and infiltrating immune cells in the TME of UM. Identification of these immune-related biomarkers may thus enable the prediction of prognosis and the selection of optimal immunotherapy strategies in UM.