Frequent mutation of BAP1 in metastasizing uveal melanomas

A novel FTO-targeting nanodrug induces disulfidptosis and ameliorates the suppressive tumor immune environment to treat uveal melanoma

Uveal melanoma (UM) is the most prevalent primary ocular malignancy in adults, with high lethality and limited effective treatment options. Despite identified driver mutations in GNAQ, GNA11, and BAP1, therapeutic advancements have been minimal. This study highlights the pivotal role of N6-methyladenosine (m6A) modifications in UM pathogenesis and progression, focusing on the demethylase FTO as a therapeutic target. Elevated FTO expression in UM tissues correlates with decreased m6A levels, increased aggressiveness, and poor prognosis. The FTO inhibitor meclofenamic acid (MA) restored m6A levels, upregulated SLC7A11, and induced disulfidptosis, a unique form of cell death triggered by GSH depletion and NADPH consumption. To address MA's limitations in bioavailability and tumor targeting, we developed an MA-loaded nucleic acid nanodrug (SNAMA). SNAMA demonstrated effective tumor growth inhibition in orthotopic and metastatic UM models through GSH-responsive release and m6A-mediated disulfidptosis activation. Incorporating a PD-L1 aptamer into SNAMA further improved tumor targeting and immune modulation, enhancing therapeutic efficacy. This study identifies FTO as a critical target for UM therapy and introduces SNAMA-apt as a promising nanodrug. The findings offer a foundation for m6A-targeted approaches in UM and other malignancies, addressing bioavailability, targeting, and immune evasion challenges.

Co-occurrence of EIF1AX, SF3B1, or BAP1 variants in uveal melanomas: A case series and review

Purpose

The purpose of this study is to present a case series of patients with co-occurrence of either BRCA1 associated protein-1 (BAP1), eukaryotic translation initiation factor 1A, X-chromosomal (EIF1AX), or splicing factor 3B subunit 1 (SF3B1) in the detection and treatment of a uveal melanoma (UM) prior to the development of metastatic disease.

Observations

This is a retrospective case series of ten patients with UM demonstrating co-occurrence of either BAP1, EIF1AX, or SF3B1 variants treated at a single ocular oncology clinic by a senior ocular oncologist between 2020 and 2024. Charts were reviewed and data on medical history, demographics, tumor characteristics, genetic testing, follow up, as well as fundus photo and B-scan ocular ultrasound were collected. The average age of the patients was 58.5 years old. The mean length of follow up was 18.2 months. Four patients had guanosine nucleotide-binding protein alpha-11 (GNA11) variants and six had guanosine nucleotide-binding protein Q (GNAQ) variants. Four patients had germline BAP1 variants. Four patients had a combination of EIF1AX and BAP1 variants. Three patients had a combination of EIF1AX and SF3B1 variants. Three patients had a combination of SF3B1 and BAP1 variants. Eight UM were gene expression profile (GEP) Class 1A and two UM were GEP Class 1B. Seven UM were preferentially expressed antigen in melanoma (PRAME) negative and three UM were PRAME positive. All patients had cytologic confirmation of the diagnosis of UM: seven had cytology results of spindle cells and three had results of mixed spindle and epithelioid cells. All patients were treated with Iodine-125 (I-125) plaque brachytherapy.

Conclusions and importance

We present a case series of patients with the co-occurrence of EIF1AX, SF3B1, or BAP1. With distinct genomic aberrations, transcriptional features, and clinical outcomes, EIF1AX, SF3B1, and BAP1 are thought to be mutually exclusive. The present case series demonstrates rare exceptions to this general pattern and speculates on the early molecular steps of UM which may lead to these rare mutation combinations.

Genetic analysis of metastatic versus nonmetastatic conjunctival melanoma using a cutaneous melanoma gene expression panel

OBJECTIVE

Conjunctival melanoma (CJM) is a rare subtype of mucosal melanomas. Despite an increasing understanding of CJM genetics, predicting patient prognosis remains challenging. Here we sought to see if a 31-gene expression profile (31-GEP) test (i.e., DecisionDx-Melanoma) originally developed and validated for cutaneous melanoma (CM) could be useful in the prognostication of patients with CJM.

DESIGN/PARTICIPANTS

We performed a single-center retrospective review and gene expression profiling of 10 patients with CJM.

METHODS

Deidentified archived samples of each primary tumor were sent to Castle Biosciences, where 31-GEP testing was performed. Patients were followed until death or a minimum of 5 years postexcision and monitored for tumor recurrence or metastatic spread. Mean fold change in individual gene expression was compared between nonmetastatic and metastatic groups via independent t-tests.

RESULTS

Fifty percent of patients developed metastatic disease and had reduced overall survival (3.6 vs 9.3 months; p = 0.018). In 4 of 10 patients, two nonmetastatic and two metastatic, tumor samples passed Castle Biosciences quality control allowing for class designation. All metastatic patients and one nonmetastatic patient were designated as class 2B. The final nonmetastatic patient was designated as class 1B. In individual gene analysis, BAP1 expression was significantly reduced in the metastatic group (p = 0.03).

CONCLUSIONS

In assessing if a CM gene expression panel could aid in the risk stratification of patients with CJM, we found that the uveal melanoma-relevant gene, BAP1, may be important. Additional studies with larger sample sizes are needed to determine the relevance of this and other differentially expressed genes in CJM prognostication.

Role of miRNA in adult ocular tumorigenesis

In recent years, cancer research has made huge advances also thanks to the discovery of the role of non-coding RNAs in the control of tumorigenesis, tumor proliferation, migration and metastasis and therefore also in the diagnosis and therapy of tumors. This work aims to review the most recent literature involving the study of miRNAs in ocular tumors affecting adult patients. We will introduce the role of miRNAs in tumorigenesis, and we will focus on summarizing the studies on uveal intraocular melanomas in which a role of microRNAs has been demonstrated. Similarly, we will also cover observations on miRNAs and eyelid cancers, especially sebaceous gland carcinoma, and cancers of the conjunctiva and the retina, excluding retinoblastoma which is typically a pediatric-onset tumor. We will summarize specific miRNAs that could be considered as diagnostic molecules or as therapeutic targets against some ocular cancer diseases, indicating their potentialities and limitations, considering also their administration as nanomedicine for the eye.

A model workflow for microfluidic enrichment and genetic analysis of circulating melanoma cells

Circulating melanoma cells (CMCs) are responsible for the hematogenous spread of melanoma and, ultimately, metastasis. However, their study has been limited by the low abundance in patient blood and the heterogeneous expression of surface markers. The FDA-approved CellSearch platform enriches CD146-positive CMCs, whose number correlates with progression-free survival and overall survival. However, a single marker may not be sufficient to identify them all. The Parsortix system allows enrichment of CMCs based on their size and deformability, keeping them viable and suitable for downstream molecular analyses. In this study, we tested the strengths, weaknesses and potential convergences of both platforms to integrate the counting of CMCs with a protocol for their genetic analysis. Samples run on Parsortix were labeled with a customized melanoma antibody cocktail, which efficiently labeled and distinguished CMCs from endothelial cells/leukocytes. The capture rate of CellSearch and Parsortix was comparable for cell lines, but Parsortix had a higher capture rate in real-life samples. Moreover, double enrichment with both CellSearch and Parsortix succeeded in removing most of the leukocyte contamination, resulting in an almost pure CMC sample suitable for genetic analysis. In this regard, a proof-of-concept analysis of CMCs from a paradigmatic case of a metastatic uveal melanoma patient led to the identification of multiple genetic alterations. In particular, the GNAQ p.Q209L was identified as homozygous, while a deletion in BAP1 exon 9 was found hemizygous. Moreover, an isochromosome 8 and a homozygous deletion of the CDKN2A gene were detected. In conclusion, we have optimized an approach to successfully enrich and retrieve viable CMCs from metastatic melanoma patients. Moreover, this study provides proof-of-principle for the feasibility of a marker-agnostic CMC enrichment followed by CMC phenotypic identification and genetic analysis.Kindly check and confirm the processed contributed equally is correctly identify We confirm.

AlphaMissense Predictions and ClinVar Annotations: A Deep Learning Approach to Uveal Melanoma

Objective

Uveal melanoma (UM) poses significant diagnostic and prognostic challenges due to its variable genetic landscape. We explore the use of a novel deep learning tool to assess the functional impact of genetic mutations in UM.

Design

A cross-sectional bioinformatics exploratory data analysis of genetic mutations from UM cases.

Subjects

Genetic data from patients diagnosed with UM were analyzed, explicitly focusing on missense mutations sourced from the Catalogue of Somatic Mutations in Cancer (COSMIC) database.

Methods

We identified missense mutations frequently observed in UM using the COSMIC database, assessed their potential pathogenicity using AlphaMissense, and visualized mutations using AlphaFold. Clinical significance was cross-validated with entries in the ClinVar database.

Main Outcome Measures

The primary outcomes measured were the agreement rates between AlphaMissense predictions and ClinVar annotations regarding the pathogenicity of mutations in critical genes associated with UM, such as GNAQ, GNA11, SF3B1, EIF1AX, and BAP1.

Results

Missense substitutions comprised 91.35% (n = 1310) of mutations in UM found on COSMIC. Of the 151 unique missense mutations analyzed in the most frequently mutated genes, only 40.4% (n = 61) had corresponding data in ClinVar. Notably, AlphaMissense provided definitive classifications for 27.2% (n = 41) of the mutations, which were labeled as "unknown significance" in ClinVar, underscoring its potential to offer more clarity in ambiguous cases. When excluding these mutations of uncertain significance, AlphaMissense showed perfect agreement (100%) with ClinVar across all analyzed genes, demonstrating no discrepancies where a mutation predicted as "pathogenic" was classified as "benign" or vice versa.

Conclusions

Integrating deep learning through AlphaMissense offers a promising approach to understanding the mutational landscape of UM. Our methodology holds the potential to improve genomic diagnostics and inform the development of personalized treatment strategies for UM.

Financial Disclosures

Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

BAP1 Loss Affords Lipotoxicity Resistance in Uveal Melanoma

Uveal melanoma (UM) is an aggressive intraocular malignancy. Despite effective control of primary tumors, ~50% of UM patients develop metastases, with the liver being the predominant secondary site. BAP1 deficiency, present in ~80% of metastatic UM cases, is strongly associated with increased metastatic risk and poor prognosis. In silico analysis of UM patient samples suggests that reduced BAP1 is linked to enhanced expression of genes involved in fatty acid processing; therefore, we hypothesize that BAP1 deficiency primes UM cells for survival in the hepatic microenvironment by enhancing lipid tolerance and oxidative stress responses. Our findings demonstrate BAP1-mutant UM resist lipotoxicity, whereas BAP1-competent UM exhibit sensitivity due to lipid peroxide accumulation-a hallmark of ferroptotic-like stress, and a response that can be mitigated by ferroptosis inhibition. Using an ex vivo liver slice model, we found that disrupting lipid metabolism with atorvastatin, an HMG-CoA reductase inhibitor, reduced tumor burden of BAP1-mutant UM. Moreover, we demonstrate a positive correlation between BAP1 and an epigenetic regulator of lipid homeostasis, ASXL2. Notably, ASXL2 depletion in BAP1-competent UM phenocopies the lipotoxicity resistance observed in BAP1-mutant UM-an effect that may be mediated by altered PPAR expression. This study reveals a novel mechanism linking BAP1 expression to lipid sensitivity via ASXL2, providing insights into liver tropism and potential therapeutic avenues for metastatic uveal melanoma.

Genetics and current research models of Mendelian tumor predisposition syndromes with ocular involvement

In this review, we aim to provide a survey of hereditable tumor predisposition syndromes with a Mendelian inheritance pattern and ocular involvement. We focus our discussion on von Hippel-Lindau disease, neurofibromatosis type 1, NF2-related schwannomatosis, tuberous sclerosis complex, retinoblastoma, and the BAP1 tumor predisposition syndrome. For each of the six diseases, we discuss the clinical presentation and the molecular pathophysiology. We emphasize the genetics, current research models, and therapeutic developments. After reading each disease section, readers should possess an understanding of the clinical presentation, genetic causes and inheritance patterns, and current state of research in disease modeling and treatment.

Prognostic value of PRAME expression in uveal melanoma: a meta-analysis

INTRODUCTION

Overexpression of Preferentially Expressed Melanoma Antigen (PRAME) is associated with melanoma progression. In the case of uveal melanoma (UM), PRAME expression was identified as conferring a metastatic risk.

AIM

This study aimed to review the available evidence regarding the prognostic value of PRAME expression in UM.

METHODS

This study adhered to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We included cohort studies and randomised clinical trials. The methodological quality of the studies was assessed by the Methodological Index for Non-Randomised Studies (MINORS). The meta-analysis was performed using Review Manager V.5.4. Heterogeneity was checked with the I2 test. If there was no heterogeneity, a fixed-effects model was adopted.

RESULTS

Nine studies were included. The PRAME+ group showed significant differences in the development of metastases OR (M-H, Fixed, 95% CI): 3.46 (2.84, 4.22). The PRAME+ group had a significantly shorter time to metastasis MD (IV, Random, 95% CI): -28.31 (-55.41, -1.22) and a significantly lower percentage metastasis-free survival at 5-year follow-up MD (IV, Fixed, 95% CI): -21.67 (-25.74,-17.61). PRAME expression was an independent marker for the development of metastatic disease at any follow-up HR (IV, Fixed, 95% CI): 2.00 (1.60, 2.49). In addition, PRAME+tumours were significantly larger than PRAME-tumours MD (IV, Random, 95% CI): 0.22 (0.01, 0.42).

CONCLUSIONS

PRAME is a good prognostic marker in UM. We believe that further studies are needed to determine the most cost-effective method for reporting PRAME overexpression.

Prognostic significance of pigmentation and stem cell markers in Indian population of uveal melanoma

BACKGROUND

Increased pigmentation has been associated with cancer stem-cell-like behaviour and chemoresistance in uveal melanoma (UM) and cutaneous melanoma. Therefore, our present study determines the correlation between pigmentation and cancer stem cell markers in UM patients.

METHODS

Expression of PAX3, CD133, ABCG2, TRYP1, TRYP2 and microphthalmia-associated transcription factor (MITF) was assessed by immunohistochemistry along with mRNA expression level of PAX3 using quantitative real-time PCR in 70 prospective UM cases. Kaplan-Meier analysis and Cox-proportional hazards model were used to analyse the correlation of protein expression with clinicopathological parameters and patient outcome.

RESULTS

We found significant expression of PAX3, CD133 and ABCG2 proteins in 28/70 (40%), 34/70 (49%) and 31/70 (44%) cases, respectively. There was a positive correlation between nuclear expression of PAX3 and high-risk clinicopathological parameters such as necrosis and scleral invasion (p<0.01). CD133 and ABCG2 expression were positively correlated with distant metastasis (p=0.03 and 0.01). Immunoexpression of PAX3, CD133 and ABCG2 proteins was positively correlated with MITF. TYRP2 expression correlated with PAX3 and ABCG2 immunoexpression. Tumour pigmentation was not correlated with any of the markers. PAX3 mRNA expression was positively correlated with immunoexpression of CD133 (p<0.01), ABCG2 (p=0.01) and distant metastasis (p<0.01). On Kaplan-Meier survival analysis, reduced metastasis-free survival was observed in patients with tumours showing high CD133 and ABCG2 expression. No significant correlation was observed between tumour pigmentation and overall survival.

CONCLUSION

Our study highlights the association between PAX3 expression, pigmentation markers such as MITF and TRYP2 and cancer stem-cell markers in UM progression.

Digital PCR-based genetic profiling from vitreous fluid as liquid biopsy for primary uveal melanoma: a proof-of-concept study

BACKGROUND

Uveal melanoma is an aggressive ocular malignancy. Early molecular characterisation of primary tumours is crucial to identify those at risk of metastatic dissemination. Although tumour biopsies are being taken, liquid biopsies of ocular fluids may form a less invasive but relatively unexplored alternative. In this study, we aim to evaluate the DNA content of vitreous fluid from eyes with a uveal melanoma to obtain molecular tumour information.

METHODS

DNA was isolated from 65 vitreous fluid samples from enucleated eyes with a uveal melanoma and studied using digital PCR. Primary and additional driver mutations (in GNAQ, GNA11, PLCB4, CYSLTR2, BAP1, SF3B1 and EIF1AX) were investigated using accustomed targeted and drop-off assays. The copy numbers of chromosome 3p and 8q were measured using multiplex and single-nucleotide polymorphism-based assays. Our findings were compared to the molecular profile of matched primary tumours and to the clinicopathological tumour characteristics.

RESULTS

Almost all (63/65) vitreous fluids had measurable levels of DNA, but melanoma-cell derived DNA (containing the primary driver mutation) was detected in 45/65 samples (median proportion 15.5%, range 0.03-94.4%) and was associated with a larger tumour prominence, but not with any of the molecular tumour subtypes. Among the vitreous fluids with melanoma-cell derived DNA, not all samples harboured (analysable) other mutations or had sufficient statistical power to measure copy numbers. Still, additional mutations in BAP1, SF3B1 and EIF1AX were detected in 15/17 samples and chromosome 3p and 8q copy numbers matched the primary tumour in 19/21 and 18/20 samples, respectively. Collectively, a clinically-relevant molecular classification of the primary tumour could be inferred from 29/65 vitreous fluids.

CONCLUSIONS

This proof-of-concept study shows that substantial amounts of DNA could be detected in vitreous fluids from uveal melanoma patients, including melanoma-cell derived DNA in 69% of the samples. Prognostically-relevant genetic alterations of the primary tumour could be identified in 45% of the patients. A follow-up study is needed to evaluate our approach in a prospective clinical context. Additionally, our work highlights improved possibilities to sensitively analyse scarce and heterogeneous tumour biopsies, with potential application in other malignancies.

Evolution of the tumor immune landscape during treatment with tebentafusp, a T cell receptor-CD3 bispecific

Metastatic uveal melanoma is an aggressive disease with poor outcome, which is refractory to immune checkpoint inhibitors. A T cell receptor (TCR)-based CD3 bispecific, tebentafusp, delivers clinical benefit in patients with metastatic uveal melanoma. Understanding the molecular basis for the anti-tumor activity of tebentafusp in an indication where checkpoint inhibitors are ineffective could aid in identification of other solid tumor indications where CD3 bispecifics may serve an unmet need. By analyzing tumor biopsies taken prior to treatment, early on-treatment, and at progression (NCT02570308), using RNA sequencing (RNA-seq) and immunohistochemistry (IHC), we show that expression of interferon-related genes in the tumor prior to treatment is associated with improved overall survival and tumor reduction on tebentafusp, that T cell recruitment occurs even in tumors with a low baseline level of T cell infiltration, and that durability of changes induced in the tumor microenvironment is key for survival duration.

Exploring recent advances in signaling pathways and hallmarks of uveal melanoma: a comprehensive review

The purpose of this review was to provide a comprehensive review of the latest insights on the pathogenesis of uveal melanoma (UM) and its intracellular pathways. This article covers the epidemiology of UM, racial predispositions, cytogenetic and chromosomal alterations, gene mutations, key defective pathways, and their underlying mechanisms, as well as the application of hallmarks of cancer to UM. A key knowledge gap remains in identifying the most effective targeted therapy and determining the central pathway linking multiple signaling networks. UM is a malignant tumor arising from uveal melanocytes, predominantly affecting the choroid, with both genetic and epigenetic contributors. Key cytogenetic alterations include monosomy 3, chromosome 6p gain, chromosome 1p loss, and chromosome 8q gain. The most important UM-related signaling pathways are RAS/MAPK, PI3K/Akt/mTOR, Hippo-YAP, retinoblastoma (Rb), and p53 pathways. In the RAS/MAPK pathway, GNAQ/GNA11 mutations occur which account for more than 80% of UM cases. The PI3K/Akt/mTOR pathway promotes cyclin D1 overexpression and MDM2 upregulation, leading to p53 pathway inhibition. GNAQ/GNA11 mutations activate YAP via the Trio-RhoGTPase/RhoA/Rac1 signaling circuit in the Hippo-YAP pathway. Rb pathway dysregulation results from cyclin D1 overexpression or cyclin-dependent kinase inhibitor (CDKI) inactivation. In the p53 pathway, UM is characterized by p53 mutations, MDM2 overexpression, and Bcl-2 deregulation. Eventually, the ARF-MDM2 axis serves as a critical link between the RAS and p53 pathways. Hallmarks of cancer, such as evasion of growth suppression and self-sufficiency in growth signals, are also evident in UM. Genetic and epigenetic alterations, including NSB1, MDM2 and CCND1 amplification, and BAP1 mutations, play pivotal roles in UM pathobiology. Thus, UM exhibits a multifactorial pathology. By consolidating key mechanisms underlying UM pathogenesis, this review provides a comprehensive perspective on the involved pathways, offering insights that may facilitate the development of effective therapeutic strategies.

An overview of BAP1 biological functions and current therapeutics

BRCA1-associated protein 1 (BAP1) is a tumor suppressor gene that was first identified in 1998. Germline loss-of-function variants in BAP1 are associated with a tumor predisposition syndrome with at least four cancers: uveal melanoma (UM), malignant mesothelioma (MMe), renal cell carcinoma (RCC), and cutaneous melanoma (CM). Furthermore, somatic BAP1 mutations are important drivers for several cancers most notably UM, MMe, RCC, intrahepatic cholangiocarcinoma (ICC) and hepatocellular carcinoma (HCC). Emerging evidence substantiates the fundamental role of BAP1 in suppressing cancer initiation and progression by tuning DNA damage repair, apoptosis, ferroptosis, immune response, Warburg phenomenon, and metastasis. Multiple treatment strategies such as poly (ADP-ribose) polymerase (PARP) inhibitors, EZH2 inhibitors, alkylating agents, and immunotherapy have been used as potential therapies for BAP1-mutated tumors. Although these agents showed promising results in BAP1-mutated tumors in preclinical studies, the results of most clinical trials are still dismal. The objectives of this review are to summarize the current state of knowledge regarding the biological functions of BAP1, the implications of these functions in tumorigenesis, and the current progress in BAP1-targeted therapy.

Metabolic Inhibition Induces Pyroptosis in Uveal Melanoma

Few treatment options are available for patients with metastatic uveal melanoma. Although the bispecific tebentafusp is FDA approved, immunotherapy has largely failed, likely given the poorly immunogenic nature of uveal melanoma. Treatment options that improve the recognition of uveal melanoma by the immune system may be key to reducing disease burden. We investigated whether uveal melanoma has the ability to undergo pyroptosis, a form of immunogenic cell death. Publicly available patient data and cell line analysis showed that uveal melanoma expressed the machinery needed for pyroptosis, including gasdermins D and E (GSDMD and E), caspases 1, 3, 4, and 8, and ninjurin-1. We induced cleavage of GSDMs in uveal melanoma cell lines treated with metabolic inhibitors. In particular, the carnitine palmitoyltransferase 1 (CPT1) inhibitor, etomoxir, induced propidium iodide uptake, caspase 3 cleavage, and the release of HMGB1 and IL-1β, indicating that the observed cleavage of GSDMs led to pyroptosis. Importantly, a gene signature reflecting CPT1A activity correlated with poor prognosis in patients with uveal melanoma and knockdown of CPT1A also induced pyroptosis. Etomoxir-induced pyroptosis was dependent on GSDME but not on GSDMD, and a pyroptosis gene signature correlated with immune infiltration and improved response to immune checkpoint blockade in a set of patients with uveal melanoma. Together, these data show that metabolic inhibitors can induce pyroptosis in uveal melanoma cell lines, potentially offering an approach to enhance inflammation-mediated immune targeting in patients with metastatic uveal melanoma. Implications: Induction of pyroptosis by metabolic inhibition may alter the tumor immune microenvironment and improve the efficacy of immunotherapy in uveal melanoma.

Molecular genomic insights into melanoma associated proteins PRAME and BAP1

Melanoma, a globally prevalent skin cancer with over 325,000 new cases annually, necessitates a comprehensive under- standing of its molecular components. This study looks at the PRAME (cutaneous melanoma-associated antigen) and BAP1 (gene controlling gene-environment interactions) proteins. Both PRAME and BAP1 are associated with critical genomic alterations that significantly influence melanoma progression and patient outcomes. PRAME is overexpressed in various cancers, especially uveal melanoma (UM), where high levels correlate with poor prognosis and genomic instability linked to chromosome 8q12 alterations. Meanwhile, mutations in BAP1 contribute to increased genomic instability and a higher risk of metastasis in UM, highlighting its importance as a key prognostic marker in tumorigenesis. Established approaches along with features proposed in this work are used to investigate sequence conservation, polyglutamic acid presence, intrinsic disorder of proteins, polar-nonpolar residues arrangement PRAME and BAP1 conserved residues highlight their critical roles in protein function and interaction. Sequence invariance indicates the possibility of functional relevance and evolutionary conservation. PRAME has enhanced intrinsic disorder and flexibility, whereas BAP1 has changed disorder-promoting residue sequences. Polyglutamic acid strings are found in both proteins, emphasizing their modulatory involvement in protein interactions. The ratios and spatial arrangement of amino acids have a profound influence on interactions and gene dysregulation. This work contributes to a better knowledge of the two melanoma-associated proteins viz. PRAME and BAP1 by unraveling their structural and functional complexities.

Characterizing uveal melanoma patients with peritoneal metastases: A retrospective single-center analysis

BACKGROUND

Metastatic uveal melanoma (mUM) is an aggressive cancer predominately affecting the liver. Peritoneal metastases (PM) occur rarely, and there is limited knowledge about this subgroup´s clinical course and biology.

METHODS

We analyzed 41 mUM patients with confirmed PM from the Charité-Universitätsmedizin Berlin database, focusing on clinical characteristics, immune cell infiltrates, genetic alterations and tumor mutational burden (TMB).

RESULTS

The incidence of PM in mUM was 4.27 %. Metastatic disease was diagnosed 3.6 years after primary UM, with PM developing later (median: 4.7 years). Median overall survival (OS) from mUM diagnosis was 22.4 months. Prognosis correlated with metastatic pattern. Patients presenting with synchronous liver and peritoneal metastases or primary hepatic metastases followed by secondary peritoneal dissemination showed a median OS of 19.7 and 17.7 months, respectively. However, PM patients with exclusive extrahepatic disease at diagnosis of mUM had a significantly longer OS of 48.6 months and this metastatic pattern showed highly significant correlation with low and intermediate genetic risk. Metastasis-free survival and OS upon mUM diagnosis were significantly shorter in patients with high-risk UM tumors. TMB also correlated with metastatic pattern, being lowest in patients presenting with only extrahepatic disease. Higher TMB was generally associated with shorter OS.

CONCLUSION

PM in mUM patients is rare and in contrast to other extra-abdominal tumors does not worsen prognosis. Prognosis is greatly influenced by the metastatic pattern, which is determined by tumor biology, as evidenced by its correlation with genetic risk groups and TMB.

Identification of diagnostic and prognostic genetic alterations in uveal melanoma using RNA sequencing

Uveal melanoma is a lethal intraocular tumour, in which the presence of various genetic alterations correlates with the risk of metastatic dissemination and survival. Here, we tested the detectability of all key mutations and chromosomal changes from RNA sequencing data in 80 primary uveal melanomas studied by The Cancer Genome Atlas (TCGA) initiative, and in five prospective cases. Whereas unsupervised gene expression profiling strongly indicated the presence of chromosome 3 alterations, it was not reliable in identifying other alterations. Though, the presence of both chromosome 3 and 8q copy number alterations could be successfully inferred from expressed allelic imbalances of heterozygous common single nucleotide polymorphisms. Most mutations were adequately recognised in the RNA by their nucleotide changes (all genes), alternative splicing around the mutation (BAP1) and transcriptome-wide aberrant splicing (SF3B1). Notably, in the TCGA cohort we detected previously unreported mutations in BAP1 (n = 3) and EIF1AX (n = 5), that were missed by the original DNA sequencing. In our prospective cohort, all genetic alterations were successfully identified by combining the described approaches. In conclusion, a transcriptional analysis presents insights into the expressed tumour genotype and its phenotypic consequences and may augment or even substitute DNA-based approaches, with potential applicability in research and clinical practice.

RNA methylation homeostasis in ocular diseases: All eyes on Me

RNA methylation is a pivotal epigenetic modification that adjusts various aspects of RNA biology, including nuclear transport, stability, and the efficiency of translation for specific RNA candidates. The methylation of RNA involves the addition of methyl groups to specific bases and can occur at different sites, resulting in distinct forms, such as N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), and 7-methylguanosine (m7G). Maintaining an optimal equilibrium of RNA methylation is crucial for fundamental cellular activities such as cell survival, proliferation, and migration. The balance of RNA methylation is linked to various pathophysiological conditions, including senescence, cancer development, stress responses, and blood vessel formation, all of which are pivotal for comprehending a spectrum of eye diseases. Recent findings have highlighted the significant role of diverse RNA methylation patterns in ophthalmological conditions such as age-related macular degeneration, diabetic retinopathy, cataracts, glaucoma, uveitis, retinoblastoma, uveal melanoma, thyroid eye disease, and myopia, which are critical for vision health. This thorough review endeavors to dissect the influence of RNA methylation on common and vision-impairing ocular disorders. It explores the nuanced roles that RNA methylation plays in key pathophysiological mechanisms, such as oxidative stress and angiogenesis, which are integral to the onset and progression of these diseases. By synthesizing the latest research, this review offers valuable insights into how RNA methylation could be harnessed for therapeutic interventions in the field of ophthalmology.

Identification of targetable epigenetic vulnerabilities for uveal melanoma

Uveal melanoma (UM) is the most common primary intraocular malignancy in adults, with a strong predilection for hepatic metastasis, occurring in approximately 50% of cases. Metastatic UM remains highly resistant to therapy and is almost invariably fatal. The strongest genetic drivers of UM metastasis are loss-of-function mutations in tumor suppressor BAP1, an epigenetic regulator that serves as the ubiquitin hydrolase subunit of the polycomb repressive deubiquitinase (PR-DUB) complex, and a key player in global epigenetic regulation. Inactivation of BRCA Associated Protein 1 (BAP1) has been shown to induce widespread epigenetic alterations across multiple model systems. To identify novel therapeutic strategies, we investigated whether targeting the epigenome could reveal new vulnerabilities in UM. We performed high-throughput compound screening using a curated epigenetic inhibitor library and identified BET (bromodomain and extra-terminal domain) inhibition as a particularly promising approach. Interestingly, we observed significant heterogeneity in the efficacy of different BET inhibitors in UM. While previous clinical trials with two BET inhibitors have failed to show efficacy in UM, our findings highlight substantial differences in the potency of specific BET inhibitors for this malignancy. Notably, the BET inhibitor mivebresib (ABBV-075) significantly improved survival rates by 50% in a metastatic UM xenograft mouse model and completely prevented detectable metastases in the bones, spinal cord, and brain. Unexpectedly, RNA sequencing revealed a strong transcriptional overlap between BET inhibition and histone deacetylase (HDAC) inhibition-- an approach currently under clinical evaluation for UM treatment. Both BET and HDAC inhibitors reversed gene expression signatures associated with high metastatic risk and induced a neuronal differentiation-like phenotype in UM cells. Together, our findings demonstrate that UM cells exhibit a distinct vulnerability to BET inhibition and establish BET inhibitors as promising candidates for further clinical evaluation for metastatic UM.

Prognostic significance of melanogenesis pathway and its association with the ultrastructural characterisation of melanosomes in uveal melanoma

BACKGROUND

Pigmentation could be a relevant prognostic factor in uveal melanoma (UM) development. Microphthalmia-associated transcription factor (MITF) regulates melanin synthesis by activating tyrosinase-related protein 2 (TYRP2) and silver protein (SILV) that induce the melanogenesis pathway. Although their oncogenic potential has been observed in various malignancies but has not been investigated in UM Asian population. Our aim is to study the ultrastructure of melanosomes and the prognostic significance of pigmentation markers such as TYRP2, MITF and SILV in UM.

METHODS

Transmission electron microscopy was performed to compare the ultrastructure of melanosomes in the normal choroid and UM cases. Immunoexpression of TYRP2, SILV and MITF was analysed in 82 UM samples. The mRNA expression level of all genes was measured in 70 UM cases. A statistical correlation was performed to determine the prognostic significance of all markers.

RESULTS

Premelanosomes and mature melanosomes undergoing dedifferentiation were observed in high-pigmented UM cases as compared with low-pigmented UM cases. Seventy per cent of UM cases showed high SILV expression while TYRP2 and MITF expression was present in 58% and 56% of cases, respectively. At the mRNA level, upregulation of TYRP2, SILV and MITF markers was seen in around 50% of UM cases, which was statistically significant with high pigmentation. Reduced metastatic-free survival was statistically significant with the MITF protein expression.

CONCLUSION

Our results demonstrated that ultrastructural changes in melanosomes and high expression of TYRP2, MITF and SILV could dysregulate the melanogenesis pathway and might be responsible for the aggressive behaviour of UM.

BAP1 Represses Sequential Activation of IRAKs and NF-κB Signaling in Pancreatic Cancer

The deubiquitinating enzyme BRCA1 Associated Protein-1 (BAP1) has been reported to be shallowly deleted in a subset of pancreatic ductal adenocarcinomas (PDAC) and is believed to play a significant role in the development of chronic pancreatitis-driven PDAC. However, evidence suggests that BAP1 may also be involved in the progression and metastasis of PDAC, though the underlying mechanism remains unclear. Here, we demonstrate that BAP1 deletion leads to the overactivation of the nuclear factor-κB (NF-κB) signaling in PDAC, thereby promoting the proliferation, migration, and invasion of PDAC models both in vivo and in vitro. Mechanistically, BAP1 inhibits the sequential activation of interleukin-1 receptor-associated kinases (IRAKs) in an enzyme-independent manner. BAP1 binds to IRAK1 and inhibits the interaction between IRAK4 and IRAK1, as well as the IRAK4-mediated initiation of IRAK1 phosphorylation and autophosphorylation. This, in turn, prevents the dissociation of IRAK1 from the Myddosome complex and sequential activation of NF-κB. Based on this, we further identified that dual-target inhibitors of IRAK1/4 exhibited significant inhibitory effects on BAP1-deficient tumors in both in vivo and in vitro PDAC models. Our findings elucidate the mechanism by which BAP1 inhibits the NF-κB signaling and present a promising strategy for the targeted treatment of BAP1-deficient pancreatic cancer.

Targeting ocular malignancies using a novel light-activated virus-like drug conjugate

Background

Targeted therapy is a promising approach to improve the treatment of tumors, including ocular malignancies. Current therapies, such as radiotherapy and surgery, often lead to serious damage to vision or to loss of the eye. New approaches have examined nanoparticles for use as targeted delivery vehicles for drugs. A newly-developed virus-like drug conjugate is a promising nanoparticle with a defined target: the novel virus-like particle-photosensitizer conjugate Belzupacap sarotalocan (Bel-sar, previous name AU-011).

Main text

In this review, we summarize the application of this novel light-activated virus-like particle conjugate in pre-clinical and clinical studies and discuss its potential to treat ocular malignancies, such as uveal melanoma and conjunctival melanoma. We furthermore discuss the combination with immunotherapy and its application on pigmented and non-pigmented tumors as well as its effect on macrophage polarization, which is important to achieve effective results in immunotherapy.

Conclusions

Belzupacap sarotalocan (Bel-sar) is a promising targeted drug carrier that enhances tumor-specific delivery and minimizes off-target effects. Its photodynamic therapy effectively treats pigmented and non-pigmented tumors while inducing immunogenic cell death through DAMP exposure, triggering local and systemic immune responses. Combining Bel-sar PDT with immunotherapy improves efficacy in preclinical models, warranting further clinical investigation.

Loss of histone deubiquitinase Bap1 triggers anti-tumor immunity

PURPOSE

Immunotherapy using PD-L1 blockade is effective in only a small group of cancer patients, and resistance is common. This emphasizes the importance of understanding the mechanisms of cancer immune evasion and resistance.

METHODS

A genome-scale CRISPR-Cas9 screen identified Bap1 as a regulator of PD-L1 expression. To measure tumor size and survival, tumor cells were subcutaneously injected into both syngeneic WT mice and immunocompromised mice. The phenotypic and transcriptional characteristics of Bap1-deleted tumors were examined using flow cytometry, RNA-seq, and CUT&Tag-seq analysis.

RESULTS

We found that loss of histone deubiquitinase Bap1 in cancer cells activates a cDC1-CD8+ T cell-dependent anti-tumor immunity. The absence of Bap1 leads to an increase in genes associated with anti-tumor immune response and a decrease in genes related to immune evasion. As a result, the tumor microenvironment becomes inflamed, with more cDC1 cells and effector CD8+ T cells, but fewer neutrophils and regulatory T cells. We also found that the elimination of Bap1-deleted tumors depends on the tumor MHCI molecule and Fas-mediated CD8+ T cell cytotoxicity. Our analysis of TCGA data further supports these findings, showing a reverse correlation between BAP1 expression and mRNA signatures of activated DCs and T-cell cytotoxicity in various human cancers.

CONCLUSION

The histone deubiquitinase Bap1 could be used as a biomarker for tumor stratification and as a potential therapeutic target for cancer immunotherapies.

Lineage commitment pathways epigenetically oppose oncogenic Gαq/11-YAP1 signaling in dormant disseminated uveal melanoma

Uveal melanoma (UM) can remain in clinical dormancy for decades only to later produce lethal metastases. Using Gαq/11 mut /BAP1 wt UM xenograft models and human metastatic samples, we identified NR2F1 as a key inducer of UM disseminated cancer cell (DCC) dormancy. Dormant UM DCCs upregulate NR2F1, neural crest genes and, along with suppression of proliferation programs, NR2F1 silences YAP1/TEAD1 transcription by altering histone H3 activation marks. YAP1 can reciprocally repress NR2F1, but inhibiting Gαq/11 signaling or activating NR2F1 can arrest UM growth. NR2F1 knockout led to dormant DCC awakening and liver metastatic growth. NR2F1 and YAP1 inverse expression was confirmed in human livers carrying UM solitary, small DCC clusters as well as large metastases. Intriguingly, RNA-seq and Cut&Run analysis revealed that NR2F1 short-circuits oncogene signaling by repressing multiple G-protein signaling components. Our work provides previously unrecognized mechanistic insight into UM DCC dormancy and potential pathways for interception.

Statement of significance

NR2F1 epigenetically suppresses genes associated with G-protein signaling, cell cycle, and YAP1/TEAD1 pathways, inducing dormancy in uveal melanoma (UM) disseminated cancer cells. This study unveils novel markers for UM dormancy and reactivation, positioning NR2F1 as a promising target for intercepting residual and UM metastatic disease.

An epigenetic pathway regulates MHC-II expression and function in B cell lymphoma models

Mutations or homozygous deletions of MHC class II (MHC-II) genes are commonly found in B cell lymphomas that develop in immune-privileged sites and have been associated with patient survival. However, the mechanisms regulating MHC-II expression, particularly through genetic and epigenetic factors, are not yet fully understood. In this study, we identified a key signaling pathway involving the histone H2AK119 deubiquitinase BRCA1 associated protein 1 (BAP1), the interferon regulatory factor interferon regulatory factor 1 (IRF1), and the MHC-II transactivator class II transactivator (CIITA), which directly activates MHC-II gene expression. Disruption of the BAP1/IRF1/CIITA axis leads to a functional attenuation of MHC-II expression and MHC-II-dependent immune cell infiltration, leading to accelerated tumor growth in immunocompetent mice. Additionally, we demonstrated that pharmacological inhibition of polycomb repressive complex 1 (PRC1) - which deposits histone H2K119Ub and opposes BAP1 activity - can restore MHC-II gene expression in BAP1-deficient B cell lymphoma cells. These findings suggest that BAP1 may function as a tumor suppressor by regulating the tumor microenvironment and immune response. Our study also establishes the rationale for therapeutic strategies to restore tumor-specific MHC-II expression and enhance immunotherapy outcomes at epigenetic levels in B cell lymphoma treatment.

Direct Prediction of 48 Month Survival Status in Patients with Uveal Melanoma Using Deep Learning and Digital Cytopathology Images

BACKGROUND

Uveal melanoma (UM) is the most common primary intraocular malignancy in adults. The median overall survival time for patients who develop metastasis is approximately one year. In this study, we aim to leverage deep learning (DL) techniques to analyze digital cytopathology images and directly predict the 48 month survival status on a patient level.

METHODS

Fine-needle aspiration biopsy (FNAB) of the tumor was performed in each patient diagnosed with UM. The cell aspirate was smeared on a glass slide and stained with H&E. Each slide then underwent whole-slide scanning. Within each whole-slide image, regions of interest (ROIs) with UM cells were automatically extracted. Each ROI was converted into super pixels, and the super pixels were automatically detected, segmented and annotated as "tumor cell" or "background" using DL. Cell-level features were extracted from the segmented tumor cells. The cell-level features were aggregated into slide-level features which were learned by a fully connected layer in an artificial neural network, and the patient survival status was predicted directly from the slide-level features. The data were partitioned at the patient level (78% training and 22% testing). Our DL model was trained to perform the binary prediction of yes-versus-no survival by Month 48. The ground truth for patient survival was established via a retrospective chart review.

RESULTS

A total of 74 patients were included in this study (43% female; mean age at the time of diagnosis: 61.8 ± 11.6 years), and 207,260 unique ROIs were generated for model training and testing. By Month 48 after diagnosis, 18 patients (24%) died from UM metastasis. Our hold-out test set contained 16 patients, where 6 patients had passed away and 10 patients were alive at Month 48. When using a sensitivity threshold of 80% in predicting UM-specific death by Month 48, our model achieved an overall accuracy of 75%. Within the subgroup of patients who died by Month 48, our model achieved a prediction accuracy of 83%. Of note, one patient in our test set was a clinical surprise, namely death by Month 48 despite having a GEP class 1A tumor, which typically portends a good prognosis. Our model correctly predicted this clinical surprise as well.

CONCLUSIONS

Our DL model was able to predict the Month 48 survival status directly from digital cytopathology images obtained from FNABs of UM tumors with reasonably robust performance. This approach, if validated prospectively, could serve as an alternative survival prediction tool for patients with UM to whom GEP is not available.

Knockdown of PR-DUB subunit calypso in the developing Drosophila eye and wing results in mis-patterned tissues with altered size and shape

The deubiquitinating enzyme BAP1, the catalytic subunit of the PR-DUB complex, is implicated in several cancers, in the familial cancer syndrome BAP1 Tumor Predisposition Syndrome, and in the neurodevelopmental disorder Küry -Isidor syndrome. In Drosophila, there are numerous reports in the literature describing developmental patterning phenotypes for several chromatin regulators including the discovery of Polycomb itself, but corresponding adult morphological phenotypes caused by developmental dysregulation of Drosophila BAP1 ortholog calypso ( caly ) are less well-described. We report here that knockdown of caly in the eye and wing produce concomitant chromatin dysregulation phenotypes. RNAi to caly in the early eye reduces survival and leads to changes in eye size and shape including eye outgrowths, some of which resemble homeotic transformations whereas others resemble tumor-like outgrowths seen in other fly cancer models. Mosaic eyes containing caly loss-of-function tissue phenocopy caly RNAi. Knocking down caly across the wing disrupts wing shape and patterning including effects on wing vein pattern. This phenotypic characterization reinforces the growing body of literature detailing developmental mis-patterning driven by chromatin dysregulation and serves as a baseline for future mechanistic studies to understand the role of BAP1 in development and disease.

ARTICLE SUMMARY

PR-DUB catalytic subunit deubiquitinating enzyme BAP1 plays an important role in tumor suppression and chromatin regulation. Whereas many chromatin regulators are well-characterized for their roles in patterning, the mis-patterning phenotypes in adult structure for dysregulating BAP1 ortholog calypso ( caly ) in development are less well described. We report mis-patterned adult eye and wing phenotypes caused by caly RNAi in the developing eye and wing respectively.

Liver cancer multiomics reveals diverse protein kinase A disruptions convergently produce fibrolamellar hepatocellular carcinoma

Fibrolamellar Hepatocellular Carcinoma (FLC) is a rare liver cancer characterized by a fusion oncokinase of the genes DNAJB1 and PRKACA, the catalytic subunit of protein kinase A (PKA). A few FLC-like tumors have been reported showing other alterations involving PKA. To better understand FLC pathogenesis and the relationships among FLC, FLC-like, and other liver tumors, we performed a massive multi-omics analysis. RNA-seq data of 1412 liver tumors from FLC, hepatocellular carcinoma, hepatoblastoma and intrahepatic cholangiocarcinoma are analyzed, obtaining transcriptomic signatures unrestricted by experimental processing methods. These signatures reveal which dysregulations are unique to specific tumors and which are common to all liver cancers. Moreover, the transcriptomic FLC signature identifies a unifying phenotype for all FLC tumors regardless of how PKA was activated. We study this signature at multi-omics and single-cell levels in the first spatial transcriptomic characterization of FLC, identifying the contribution of tumor, normal, stromal, and infiltrating immune cells. Additionally, we study FLC metastases, finding small differences from the primary tumors.

TGFβ signaling sensitizes MEKi-resistant human melanoma to targeted therapy-induced apoptosis

The TGFβ signaling pathway is known for its pleiotropic functions in a plethora of biological processes. In melanoma, TGFβ signaling promotes invasiveness and metastasis formation. However, its involvement in the response to therapy is controversial. While several studies have linked TGFβ signaling to elevated resistance to targeted therapy in melanoma, separate findings have indicated a favorable treatment response through TGFβ-mediated increase of cell death. We now found that the outcome of TGFβ signaling in the context of targeted therapy is dose dependent. Unlike low doses, high levels of TGFβ signal activation induce apoptosis upon simultaneous MAPK pathway inhibition, even in targeted therapy resistant melanoma cell lines. Using transcriptomic analyses, combined with genomic target identification of the critical TGFβ signaling effector SMAD4, we demonstrate that parallel activation of TGFβ signaling and MAPK pathway inhibition causes a complete switch of TGFβ target genes from promoting pro-invasive processes to fueling pro-apoptotic pathways. Investigations of underlying mechanisms identified a novel apoptosis-inducing gene signature. Functional validation of signature members highlighted a central role of the pro-apoptotic BCL2 family member BCL2L11 (BIM) in mediating apoptosis in this condition. Using a modified, synthetic version of the TGFB1 mRNA for intra-tumoral injections, we additionally showcase a potential therapeutic application of this treatment combination.

Optimized and Robust Workflow for Quantifying the Canonical Histone Ubiquitination Marks H2AK119ub and H2BK120ub by LC-MS/MS

The eukaryotic genome is packaged around histone proteins, which are subject to a myriad of post-translational modifications. By controlling DNA accessibility and the recruitment of protein complexes that mediate chromatin-related processes, these modifications constitute a key mechanism of epigenetic regulation. Since mass spectrometry can easily distinguish between these different modifications, it has become an essential technique in deciphering the histone code. Although robust LC-MS/MS methods are available to analyze modifications on the histone N-terminal tails, routine methods for characterizing ubiquitin marks on histone C-terminal regions, especially H2AK119ub, are less robust. Here, we report the development of a simple workflow for the detection and improved quantification of the canonical histone ubiquitination marks H2AK119ub and H2BK120ub. The method entails a fully tryptic digestion of acid-extracted histones, followed by derivatization with heavy or light propionic anhydride. A pooled sample is then spiked into oppositely labeled single samples as a reference channel for relative quantification, and data is acquired using PRM-based nano-LC-MS/MS. We validated our approach with synthetic peptides as well as treatments known to modulate the levels of H2AK119ub and H2BK120ub. This new method complements existing histone workflows, largely focused on the lysine-rich N-terminal regions, by extending modification analysis to other sequence contexts.

A comprehensive review of PRAME and BAP1 in melanoma: Genomic instability and immunotherapy targets

In a thorough review of the literature, the complex roles of PRAME (preferentially expressed Antigen of Melanoma) and BAP1 (BRCA1-associated protein 1) have been investigated in uveal melanoma (UM) and cutaneous melanoma. High PRAME expression in UM is associated with poor outcomes and correlated with extraocular extension and chromosome 8q alterations. BAP1 mutations in the UM indicate genomic instability and a poor prognosis. Combining PRAME and BAP1 immunohistochemical staining facilitates effective risk stratification. Mechanistically, both genes are associated with genomic instability, making them promising targets for cancer immunotherapy. Hypomethylation of PRAME, specifically in its promoter regions, is critical for UM progression and contributes to epigenetic reprogramming. Additionally, miR-211 regulation is crucial in melanoma and has therapeutic potential. The way PRAME changes signaling pathways provides clues about the cause of cancer due to genomic instability related to modifications in DNA repair. Inhibition of poly(ADP-ribose) polymerase-1 (PARP-1) and PARP-2 in cells expressing PRAME could lead to potential therapeutic applications. Pathway enrichment analysis underscores the significance of PRAME and BAP1 in melanoma pathogenesis.

Deciphering the Intricate Relationship Between Macrophages, Pigmentation, and Prognosis in Uveal Melanoma

High pigmentation and the abundance of M2 macrophages have been identified as negative predictors in uveal melanoma (UM). Risk factors associated with UM that are prevalent in high-risk White populations are still present, although less common, in relatively low-risk Asian populations. Research indicates that proangiogenic M2 macrophages and monosomy 3 play significant roles in UM progression. Our aim was to investigate the impact of tumor-associated macrophages in UM and examine their correlation with monosomy 3 and pigmentation. Transmission electron microscopy was used to analyze the morphology of macrophages in UM. Forty UM samples underwent fluorescent in situ hybridization for monosomy 3 identification. Immunohistochemistry was done to assess M2/M1 macrophages on 82 UM tissue samples. IL-10 and IL-12 expressions were quantified in UM serum samples by enzyme-linked immunosorbent assay. The expression of all markers was correlated with pigmentation markers (tyrosinase-related protein 1, tyrosinase-related protein 2, silver protein, and microphthalmia-associated transcription factor). Prognostic outcomes were determined using the Cox proportional hazard model and log-rank tests. Increased expression of M2/M1 macrophages was observed in 31 UM cases, which correlated with the high expression of pigmentation markers. IL-10 concentration was high in UM cases. Monosomy 3 was evident in 50% of UM cases and significantly associated with increased immunoexpression of M2/M1 macrophages and pigmentation markers. Reduced metastasis-free survival was observed in patients with UM with high M2/M1 macrophage expression (P = .001). High pigmentation and increased M2 macrophage density could impact the tumor microenvironment in UM. This could contribute to ineffective antitumor immune responses in patients with UM. Our findings suggest avenues for developing novel therapeutic approaches to counteract these immunosuppressive effects in UM.

Imipridones inhibit tumor growth and improve survival in an orthotopic liver metastasis mouse model of human uveal melanoma

BACKGROUND

Uveal melanoma (UM) is a highly aggressive disease with very few treatment options. We previously demonstrated that mUM is characterized by high oxidative phosphorylation (OXPHOS). Here we tested the anti-tumor, signaling and metabolic effects of imipridones, which are CLPP activators, which inhibit OXPHOS indirectly and have demonstrated safety in patients.

METHODS

We assessed CLPP expression in UM patient samples. We tested the effects of imipridones (ONC201 and ONC212) on the growth, survival, signaling and metabolism of UM cell lines in vitro, and for therapeutic efficacy in vivo in UM liver metastasis models.

RESULTS

CLPP expression was detected in primary and mUM patient samples. ONC201 and 212 decreased OXPHOS effectors, inhibited cell growth and migration, and induced apoptosis in human UM cell lines in vitro. ONC212 inhibited OXPHOS, increased metabolic stress and apoptotic pathways, inhibited amino acid metabolism, and induced cell death-related lipids. ONC212 also decreased tumor burden and increased survival in vivo in two UM liver metastasis models.

CONCLUSIONS

Imipridones are a promising strategy for further testing and development in mUM.

Base-excision repair pathway shapes 5-methylcytosine deamination signatures in pan-cancer genomes

Transition of cytosine to thymine in CpG dinucleotides is the most frequent type of mutation in cancer. This increased mutability is commonly attributed to the spontaneous deamination of 5-methylcytosine (5mC), which is normally repaired by the base-excision repair (BER) pathway. However, the contribution of 5mC deamination in the increasing diversity of cancer mutational signatures remains poorly explored. We integrate mutational signatures analysis in a large series of tumor whole genomes with lineage-specific epigenomic data to draw a detailed view of 5mC deamination in cancer. We uncover tumor type-specific patterns of 5mC deamination signatures in CpG and non-CpG contexts. We demonstrate that the BER glycosylase MBD4 preferentially binds to active chromatin and early replicating DNA, which correlates with lower mutational burden in these domains. We validate our findings by modeling BER deficiencies in isogenic cell models. Here, we establish MBD4 as the main actor responsible for 5mC deamination repair in humans.

Malignant melanoma complicated with cataract and secondary glaucoma: A case report

Uveal melanoma is the most common intraocular malignant tumor in adults. For patients presenting with cataracts and glaucoma, it is recommended to assess whether an intraocular lesion is present as the primary cause. The present study describes the case of a 52-year-old man with primary intraocular malignant melanoma. The patient experienced painless vision loss in the right eye for 1 year, with recent onset of eye swelling and pain in the week prior to seeking medical attention. A slit-lamp examination revealed a shallow anterior chamber in the right eye, a visibly opaque lens and a faint reflection of the tumor surface in the vitreous humor. In addition, the intraocular pressure of this eye was >60 mmHg. Magnetic resonance imaging revealed a large tumor behind the lens measuring 16×18×14 mm. Pathological examination confirmed the diagnosis of malignant melanoma. No BRCA-associated protein-1 somatic mutation was detected, whereas germline mutations of MutL protein homolog 1, RAD54 like, and SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 were identified. Extensive systemic examination excluded the possibility that the tumors originated from another part of the body. The present case report highlights the crucial role of slit-lamp examination in the detection of ocular tumors. It is advocated that for patients presenting with cataracts, attention should be paid to the possibility of intraocular tumors. Meticulous slit-lamp microscopy may reveal a reflection of the surface of a malignant melanoma, preventing misdiagnosis.

Radiogenomics of Intrahepatic Cholangiocarcinoma: Correlation of Imaging Features With BAP1 and FGFR Molecular Subtypes

PURPOSE

Clinical research has shown unique tumor behavioral characteristics of BRCA -associated protein-1- ( BAP1 -) and fibroblast growth factor receptor ( FGFR )-mutated intrahepatic cholangiocarcinomas (CCAs), with BAP1 -mutated tumors demonstrating more aggressive forms of disease and FGFR -altered CCAs showing more indolent behavior. We performed a retrospective case-control study to evaluate for unique imaging features associated with BAP1 and FGFR genomic markers in intrahepatic CCA (iCCA).

METHODS

Multiple imaging features of iCCA at first staging were analyzed by 2 abdominal radiologists blinded to genomic data. Growth and development of metastases at available follow-up imaging were also recorded, as were basic clinical cohort data. Types of iCCA analyzed included those with BAP1 , FGFR , or both alterations, as well as cases with low mutational burden or mutations with low clinical impact, which served as a control or "wild-type" group. There were 18 cases in the FGFR group, 10 with BAP1 mutations, and 31 wild types (controls).

RESULTS

Cases with BAP1 mutations showed significantly larger growth at first year of follow-up ( P = 0.03) and more frequent tumor-associated biliary ductal dilatation ( P = 0.04) compared with controls. FGFR -altered cases showed more infiltrative margins compared with controls ( P = 0.047) and demonstrated less enhancement between arterial to portal venous phases ( P = 0.02). BAP1 and FGFR groups had more cases with stage IV disease at presentation than controls ( P = 0.025, P = 0.006).

CONCLUSION

Compared with wild-type iCCAs, FGFR -mutated tumors often demonstrate infiltrative margins, and BAP1 tumors show increased biliary ductal dilatation at presentation. BAP1 -mutated cases had significantly larger growth at first-year restaging.

Genetic Features of Uveal Melanoma

BACKGROUND/OBJECTIVES

Although it comprises only 5% of all melanomas, uveal melanoma (UM) is the most commonly observed primary intraocular cancer.

METHODS

Poor patient survival persists in spite of innovative systemic therapies. In fact, approximately fifty percent of UM patients develop metastases from micro-metastases that remain undetected at the exact time of diagnosis.

RESULTS

The molecular understanding of UM is significantly enhanced by the recent identification of several mutations that are responsible for the metastasis, growth, and survival of UM. The crucial point is a more accurate genetic analysis for patient follow-up and metastatic risk prediction.

CONCLUSIONS

This review provides a brief summary of the molecular features of UM that are recently discovered, as well as cytogenetic markers and biochemical pathways that are associated with the development of UM metastases.

Azacytidine treatment affects the methylation pattern of genomic and cell-free DNA in uveal melanoma cell lines

BACKGROUND

Uveal melanoma (UM) is the most common primary intraocular tumour in adults, and approximately 50% of patients will develop metastasis. Epigenetic changes are a major factor in cancer progression. We aimed to determine whether methylation profiles could be altered using a DNA methyltransferase (DNMT) inhibitor in UM cell lines.

METHODS

Four primary and metastatic UM cell lines were treated with azacytidine and analysed for cell proliferation, colony formation, and BAP1 protein expression. Genomic and cell-free (cf)DNA methylation were compared.

RESULTS

In all cell lines, azacytidine treatment resulted in dose-dependent effects on proliferation, colony formation, and radiosensitivity. Methylation profiling revealed differences in methylation between cell lines according to BAP1 expression. Matched primary and metastatic cell lines showed very similar patterns. Alterations were seen in pathways known to be important in UM progression, such as PI3K/Akt and MAPK signaling, and in pathways involved in cancer progression, such as regulation of stemlike potential, cell motility, and invasion. These changes were maintained in genomic and cell-free DNA.

CONCLUSIONS

This data suggests that DNMT inhibitors cause changes in UM cells that are maintained in cfDNA. The results suggest that targeting methylation in UM treatment and monitoring response to treatment using cfDNA methylation could be a valuable tool.

Plaque Radiotherapy for Ocular Melanoma

Plaque radiotherapy is an effective treatment modality for medium-sized ocular tumors such as uveal melanoma. The authors review the available literature and concisely summarize the current state of the art of ophthalmic plaque brachytherapy. The choice of radioisotope, which includes Ruthenium-106 and Iodine-125, depends on the intended treatment duration, tumor characteristics, and side effect profiles. Ophthalmic plaques may be customized to allow for the delivery of a precise radiation dose by adjusting seed placement and plaque shape to minimize collateral tissue radiation. High dose rate (HDR) brachytherapy, using beta (e.g., Yttrium-90) and photon-emitting sources (e.g., Ytterbium-169, Selenium-75), allows for rapid radiation dose delivery, which typically lasts minutes, compared to multiple days with low-dose plaque brachytherapy. The efficacy of Ruthenium-106 brachytherapy for uveal melanoma varies widely, with reported local control rates between 59.0% and 98.0%. Factors influencing outcomes include tumor size, thickness, anatomical location, and radiation dose at the tumor apex, with larger and thicker tumors potentially exhibiting poorer response and a higher rate of complications. Plaque brachytherapy is effective for selected tumors, particularly uveal melanoma, providing comparable survival rates to enucleation for medium-sized tumors. The complications of plaque brachytherapy are well described, and many of these are treatable.

Assessment of ferroptosis as a promising candidate for metastatic uveal melanoma treatment and prognostication

Uveal melanoma (UM) is the most common primary intraocular tumour in adults. Local resection, radiation therapy, and enucleation are the current first-line, primary UM treatments. However, regardless of the treatment received, around 50% of UM patients will develop metastatic disease within five to 7 years. In the largest published series of unselected patients with metastatic UM (mUM), the median survival time after diagnosis of metastasis was 3.6 months, with less than 1% of patients surviving beyond 5 years. Approved drugs for treatment of mUM include systemic treatment with tebentafusp-tebn or isolated hepatic perfusion (IHP) with melphalan. However, these drugs are only available to a subset of patients and improve survival by only a few months, highlighting the urgent need for new mUM treatments. Accurately predicting which patients are at high risk for metastases is also crucial. Researchers are developing gene expression signatures in primary UM to create reliable prognostic models aimed at improving patient follow-up and treatment strategies. In this review we discuss the evidence supporting ferroptosis, a non-apoptotic form of cell death, as a potential novel treatment target and prognosticator for UM.

L3MBTL2 maintains MYCN-amplified neuroblastoma cell proliferation through silencing NRIP3 and BRME1 genes

Epigenetic alterations critically affect tumor development. Polycomb-group complexes constitute an evolutionarily conserved epigenetic machinery that regulates stem cell fate and development. They are implicated in tumorigenesis, primarily via histone modification. Polycomb repressive complex 1 (PRC1) complexes 1-6 (PRC1.1-6) mediate the ubiquitination of histone H2A on lysine 119 (H2AK119ub). Here, we studied the functional roles of a PRC1.6 molecule, L3MBTL2, in neuroblastoma (NB) cells. L3MBTL2-knockout and knockdown revealed that L3MBTL2 depletion suppressed NB cell proliferation via cell-cycle arrest and gamma-H2A.X upregulation. L3MBTL2-knockout profoundly suppressed xenograft tumor formation. Transcriptome analysis revealed suppressed cell-cycle-related and activated differentiation-related pathways. Break repair meiotic recombinase recruitment factor 1 (BRME1) and nuclear receptor interacting protein 3 (NRIP3) were notably de-repressed by L3MBTL2-knockout. The deletion of L3MBTL2 reduced enrichment of H2AK119ub and PCGF6 at transcriptional start site proximal regions of the targets. Add-back studies unveiled the importance of L3MBTL2-BRME1 and -NRIP3 axes for NB cell proliferation. We further manifested the association of MYCN with de-repression of NRIP3 in an L3MBTL2-deficient context. Therefore, this study first revealed the significance of L3MBTL2-mediated gene silencing in MYCN-amplified NB cells.

Immunotherapy response and resistance in patients with advanced uveal melanoma: a retrospective cohort study

Metastatic uveal melanoma (mUM) is associated with poor prognosis. Ipilimumab/nivolumab has shown antitumor efficacy in phase II studies. Tebentafusp resulted in longer overall survival (OS) compared to investigator`s choice in a phase III study. We sought to describe the radiological response patterns of mUM patients treated with immunotherapy. Patients with mUM treated with ipilimumab/nivolumab and tebentafusp between July 2018 and December 2022, with available radiological assessment per RECISTv1.1 and/or imPERCIST5, were retrospectively identified and included. Progression-free survival (PFS) and OS rates, liver-specific response and pathological assessment in available liver biopsies were evaluated. In the ipilimumab/nivolumab group, median PFS (mPFS) was 2.9 months (95% CI 2.2-28.6) and mOS 28.9 months (95% CI 12.7-NR). Complete (CMR) and partial (PMR) metabolic response per imPERCIST5, and partial response (PR) per RECISTv1.1 were associated with longer PFS and OS by trend, compared to morphologically and metabolically stable or progressive disease. In the tebentafusp group, mPFS was 2.7 months (95% CI 2.2-3) and mOS 18.6 months (95% CI 11.5-NR). PMR and PR were associated with longer PFS by trend. In both treatments, the overall treatment response was associated with the radiological response at the liver site. In available liver tumor biopsies, differences in pathological and radiological responses were noted. ImPERCIST5 and RECIST v1.1 are valuable tools in the radiological response assessment, but both methods display limitations. Accurate biomarkers to stratify patients at risk for disease progression and future translational studies to investigate mechanisms of response and resistance are required.

Cell Senescence and the Genetics of Melanoma Development

Cutaneous malignant melanoma is an aggressive skin cancer with an approximate lifetime risk of 1 in 38 in the UK. While exposure to ultraviolet radiation is a key environmental risk factor for melanoma, up to ~10% of patients report a family history of melanoma, and ~1% have a strong family history. The understanding of causal mutations in melanoma has been critical to the development of novel targeted therapies that have contributed to improved outcomes for late-stage patients. Here, we review current knowledge of the genes affected by familial melanoma mutations and their partial overlap with driver genes commonly mutated in sporadic melanoma development. One theme linking a set of susceptibility loci/genes is the regulation of skin pigmentation and suntanning. The largest functional set of susceptibility variants, typically with high penetrance, includes CDKN2A, RB1, and telomerase reverse transcriptase (TERT) mutations, associated with attenuation of cell senescence. We discuss the mechanisms of action of these gene sets in the biology and progression of nevi and melanoma.

15-Gene Expression Profile and PRAME as Integrated Prognostic Test for Uveal Melanoma: First Report of Collaborative Ocular Oncology Group Study No. 2 (COOG2.1)

PURPOSEValidated and accurate prognostic testing is critical for precision medicine in uveal melanoma (UM). Our aims were to (1) prospectively validate an integrated prognostic classifier combining a 15-gene expression profile (15-GEP) and PRAME RNA expression and (2) identify clinical variables that enhance the prognostic accuracy of the 15-GEP/PRAME classifier.MATERIALS AND METHODSThis study included 1,577 patients with UM of the choroid and/or ciliary body who were enrolled in the Collaborative Ocular Oncology Group Study Number 2 (COOG2) and prospectively monitored across 26 North American centers. Test results for 15-GEP (class 1 or class 2) and PRAME expression status (negative or positive) were available for all patients. The primary end point was metastasis-free survival (MFS).RESULTS15-GEP was class 1 in 1,082 (68.6%) and class 2 in 495 (31.4%) patients. PRAME status was negative in 1,106 (70.1%) and positive in 471 (29.9%) patients. Five-year MFS was 95.6% (95% CI, 93.9 to 97.4) for class 1/PRAME(-), 80.6% (95% CI, 73.9 to 87.9) for class 1/PRAME(+), 58.3% (95% CI, 51.1 to 66.4) for class 2/PRAME(-), and 44.8% (95% CI, 37.9 to 52.8) for class 2/PRAME(+). By multivariable Cox proportional hazards analysis, 15-GEP was the most important independent predictor of MFS (hazard ratio [HR], 5.95 [95% CI, 4.43 to 7.99]; P < .001), followed by PRAME status (HR, 1.82 [95% CI, 1.42 to 2.33]; P < .001). The only clinical variable demonstrating additional prognostic value was tumor diameter.CONCLUSIONIn the largest prospective multicenter prognostic biomarker study performed to date in UM to our knowledge, the COOG2 study validated the superior prognostic accuracy of the integrated 15-GEP/PRAME classifier over 15-GEP alone and clinical prognostic variables. Tumor diameter was found to be the only clinical variable to provide additional prognostic information. This prognostic classifier provides an advanced resource for risk-adjusted metastatic surveillance and adjuvant trial stratification in patients with UM.

Impact of Metastatic Pattern on Survival in Patients with Posterior Uveal Melanoma: A Retrospective Cohort Study

Background/Objectives: Metastatic posterior uveal melanoma (PUM) is one of the deadliest types of melanomas. Though the median survival is short, some patients with metastatic disease live for a long time. In this study, we investigated whether the anatomical location of the metastatic lesions is associated with differences in survival. Methods: One hundred and seventy-eight patients with metastatic PUM with baseline whole-body imaging were retrospectively included. The patients were divided into three groups based on the anatomical location of metastases: (1) exclusive liver metastases (hepatic pattern), (2) both hepatic and extrahepatic metastatic lesions (hepatic-extrahepatic pattern), and (3) exclusive extrahepatic lesions (extrahepatic pattern). Survival was investigated using Kaplan-Meier plots, log-rank test, and the Cox proportional hazard model. Results: In total, 95 patients (53%) presented with hepatic pattern, 66 patients (37%) presented with hepatic-extrahepatic pattern, and 17 patients (10%) presented with extrahepatic pattern. Overall survival was significantly longer in patients with extrahepatic pattern (median 17.0 months) compared to those with hepatic pattern (median 11.0 months) and hepatic-extrahepatic pattern (median 7.0 months) (p < 0.001, log-rank test). Multivariate Cox regression analysis showed increased hazard ratios (HR) for hepatic pattern (HR 2.37, 95% CI 1.08-5.17, p = 0.031) and hepatic-extrahepatic pattern (3.25, 95% CI 1.42-7.41, p = 0.005) compared to extrahepatic pattern. Most patients with hepatic (95%) and hepatic-extrahepatic patterns (82%) were diagnosed with metastases by liver ultrasonography screening, whereas 81% of patients with extrahepatic pattern developed symptoms that led to the diagnosis. Conclusions: Extrahepatic pattern was associated with prolonged survival in patients with metastatic PUM, despite there being a larger proportion of symptomatic patients. It is therefore important to consider the anatomical location of the metastatic lesions when stratifying patients into clinical trials.

A Multi-Omics Prognostic Model Capturing Tumor Stemness and the Immune Microenvironment in Clear Cell Renal Cell Carcinoma

Background: Cancer stem-like cells (CSCs), a distinct subset recognized for their stem cell-like abilities, are intimately linked to the resistance to radiotherapy, metastatic behaviors, and self-renewal capacities in tumors. Despite their relevance, the definitive traits and importance of CSCs in the realm of oncology are still not fully comprehended, particularly in the context of clear cell renal cell carcinoma (ccRCC). A comprehensive understanding of these CSCs' properties in relation to stemness, and their impact on the efficacy of treatment and resistance to medication, is of paramount importance. Methods: In a meticulous research effort, we have identified new molecular categories designated as CRCS1 and CRCS2 through the application of an unsupervised clustering algorithm. The analysis of these subtypes included a comprehensive examination of the tumor immune environment, patterns of metabolic activity, progression of the disease, and its response to immunotherapy. In addition, we have delved into understanding these subtypes' distinctive clinical presentations, the landscape of their genomic alterations, and the likelihood of their response to various pharmacological interventions. Proceeding from these insights, prognostic models were developed that could potentially forecast the outcomes for patients with ccRCC, as well as inform strategies for the surveillance of recurrence after treatment and the handling of drug-resistant scenarios. Results: Compared with CRCS1, CRCS2 patients had a lower clinical stage/grading and a better prognosis. The CRCS2 subtype was in a hypoxic state and was characterized by suppression and exclusion of immune function, which was sensitive to gefitinib, erlotinib, and saracatinib. The constructed prognostic risk model performed well in both training and validation cohorts, helping to identify patients who may benefit from specific treatments or who are at risk of recurrence and drug resistance. A novel therapeutic target, SAA2, regulating neutrophil and fibroblast infiltration, and, thus promoting ccRCC progression, was identified. Conclusions: Our findings highlight the key role of CSCs in shaping the ccRCC tumor microenvironment, crucial for therapy research and clinical guidance. Recognizing tumor stemness helps to predict treatment efficacy, recurrence, and drug resistance, informing treatment strategies and enhancing ccRCC patient outcomes.

The role of signaling pathways mediated by the GPCRs CysLTR1/2 in melanocyte proliferation and senescence

In contrast with sun exposure-induced melanoma, rarer melanocytic tumors and neoplasms with low mutational burden present opportunities to study isolated signaling mechanisms. These include uveal melanoma and blue nevi, which are often driven by mutations within the G protein-coupled signaling cascade downstream of cysteinyl leukotriene receptor 2. Here, we review how the same mutations within this pathway drive the growth of melanocytes in one tissue but can inhibit the growth of those in another, exemplifying the role of the tissue environment in the delicate balance between uncontrolled cell growth and senescence.

Tumor suppressor BAP1 suppresses disulfidptosis through the regulation of SLC7A11 and NADPH levels

BAP1, BRCA1-Associated Protein 1, serves as a novel tumor suppressor through the deubiquitination of monoubiquitination of H2A and subsequent gene transcriptional regulation. Regulated cell death like apoptosis or ferroptosis is considered an essential mechanism mediating tumor suppression. Previous reports, including ours, have demonstrated that BAP1 could promote apoptosis and ferroptosis to inhibit tumor development. Whether BAP1 regulated additional types of cell death remains unclear. Disulfidptosis is a recently identified novel cell death mode characterized by aberrant accumulation of intracellular disulfide (e.g., cystine) and depletion of NADPH. In this study, we first demonstrated that BAP1 could significantly protect disulfidptosis induced by glucose starvation, which is validated by various cell death inhibitors and the accumulation of disulfide bonds in the cytoskeleton proteins. BAP1 is known to inhibit SLC7A11 expression. We found that the protective effect of BAP1 against disulfidptosis was counteracted when overexpressing SLC7A11 or adding additional cystine. Conversely, BAP1-mediated suppression of disulfidptosis was largely abrogated when SLC7A11-mediated cystine uptake was inhibited by the knockout of SLC7A11 or erastin treatment. Besides, high BAP1 expression showed lower NADP+/NADPH levels, which might confer resistance to disulfidptosis. Consistent with these observations, the expression level of BAP1 was also positively correlated with NADPH-related genes in KIRC patients, though the underlying mechanism mediating NADPH regulation remains further investigation. In summary, our results revealed the role of BAP1 in the regulation disulfidptosis and provided new insights into the understanding of disulfidptosis in tumor development.