Uveal Melanoma Tumors Research Articles

The Impact of Spliceosome Inhibition in SF3B1-Mutated Uveal Melanoma.

Unfortunately, treatment of patients with uveal melanoma (UM) with metastatic disease is limited. Twenty percent of patients with UM harbor a mutation in the splicing factor gene SF3B1, suggesting that aberrant spliceosome function plays a vital role in tumorigenesis. Splicing inhibitors exploit the preferential sensitivity of spliceosome-compromised leukemic cells to these compounds. We studied the effect of the splicing inhibitor E7107 using two UM cell lines and ex vivo cultured SF3B1- and BAP1-mutated primary UM tumor slices. These UM cell lines and ex vivo tumor slices were exposed for 24 hours to different concentrations of E7107. Tumor slices were stained with hematoxylin and eosin (H&E) and incubated with BAP1, MelanA, MIB-1, and caspase-3 antisera. The E7107-exposed UM cell lines exhibited decreased cell viability and increased apoptosis, with the greatest effect on SF3B1-mutated UM cells. A similar effect on UM tumor slices was observed upon exposure to E7107. Additionally, RNA was isolated for differential isoform expression analysis. No significant difference in isoform usage was found genome-wide. However, specific genes were differentially expressed after E7107 treatment in the SF3B1-mutated samples. Moreover, E7107 had the greatest effect on intron retention. This study indicates/suggests that mutated SF3B1 UM cells are more sensitive to the splicing inhibitor E7107 than wild-type SF3B1 UM cells.

The Phenotypical Characterization of Dual-Nature Hybrid Cells in Uveal Melanoma.

Metastasis, occurring years after primary diagnosis, represents a poor prognosis in uveal melanoma (UM)-affected individuals. The nature of cells involved in this process is under debate. Circulating hybrid cells that have combined tumor and immune cell features found in blood were predictive of metastasis and may correspond to dual-nature cells (DNC) in the primary tumor. Herein, we sought to determine the presence of DNCs in primary UM tumors, the cell types involved in their genesis, and their ability to be formed in vitro. UM lesions (n = 38) were immunolabeled with HMB45 in combination with immune-cell-specific antibodies. In parallel, we co-cultured UM cells and peripheral blood mononuclear cells (PBMCs) to analyze DNC formation. HMB45+/CD45+ DNCs were present in 90% (26/29) of the tumors, HMB45+/CD8+ DNCs were present in 93% (26/28), and HMB45+/CD68+ DNCs were present in 71% (17/24). DNCs formed with CD8+ and CD68+ cells were positively correlated to the infiltration of their respective immune cells. Notably, UM cells were prone to hybridize with PBMCs in vitro. This phenotypical characterization of DNCs in UM demonstrates that CD8+ T-cells and macrophages are capable of DNC formation, and they are important for better understanding metastatic dissemination, thus paving the path towards novel therapeutic avenues.

The roles of genetic mutation and cytokines/chemokines in immune response and their association with uveal melanoma patient outcome

The impact of tumor mutations and the interplay of cytokines and chemokines on the immune response and clinical outcomes in uveal melanoma (UM) warrants further exploration. In our study, we delved into the correlation between genetic alterations and survival rates in a cohort of 188 UM patients, utilizing data from cBioPortal. We assessed the composition of immune cell populations within 80 UM tumors by examining RNA sequence-based gene expression data from The Cancer Genome Atlas (TCGA). Furthermore, we scrutinized the relationship between genetic mutations and the expression of cytokines and chemokines, as well as their influence on various immune cell subsets. Our investigation revealed a significant association between the presence of mutated GNAQ or SF3B1 genes and improved progression-free survival (PFS), disease-specific survival (DSS), and overall survival (OS) when compared to patients with non-mutated counterparts. In contrast, the presence of immune response gene mutations was associated with a detrimental effect on PFS, DSS, and OS. We also observed that the expression levels of cytokines and chemokines were positively linked to the infiltration of immune killer cells and inversely related to the populations of B cells and dendritic cells. Elevated expression levels of PDCD1, TNF, IL6, CXCL9, and CXCL10 were found to be correlated with reduced OS. Intriguingly, an increase in CD8+ T cell populations was associated with a poorer OS, a finding that warrants further investigation. These findings underscore the potential utility of cytokines/chemokines expression levels, immune cell subsets, and mutation status as critical biomarkers for the selection of patients who are most likely to benefit from immunotherapeutic interventions. Our research provides valuable insights that could guide the development of more targeted and effective treatment strategies for UM patients.

Inhibition of Heme Oxygenase 1 Suppresses Growth, Migration, and Invasion, and Regulates Tumor-Infiltrating CD8+ T Cells and in Uveal Melanoma.

Metastatic uveal melanoma (UM) treatment is difficult, and effective treatments are urgently needed. We aimed to explore the role of heme oxygenase 1 (HO-1) in UM and provide new therapeutic strategies for UM. Bioinformatics was used to analyze the relationship between HMOX1 and immunity in UM and other tumors. Cell Counting Kit-8, Western blot, immunofluorescence staining, wound healing, and Transwell assays were used. A subcutaneous transplanted UM tumor model was used in mice to verify the therapeutic effect. In UM, the expression level of HMOX1 was strongly correlated with the immune score and the infiltration level of various immune cells. ZnPP can inhibit the growth of UM cells, promote cell apoptosis, and block the cell cycle at G0/G1 phase in vitro. HO-1 knockout can effectively inhibit the proliferation of UM cells. ZnPP effectively inhibited the growth of UM and promoted the infiltration of CD8+ T cells in a subcutaneous tumor transplantation model. These results indicate that targeting HO-1 in UM has the potential for independent targeted immunotherapy or adjuvant immunotherapy.

Detection of neoplastic-immune hybrid cells with metastatic properties in uveal melanoma

BackgroundUveal melanoma is the most common non-cutaneous melanoma and is an intraocular malignancy affecting nearly 7,000 individuals per year worldwide. Of these, approximately 50% will progress to metastatic disease for which there are currently no effective curative therapies. Despite advances in molecular profiling and metastatic stratification of uveal melanoma tumors, little is known regarding their underlying biology of metastasis. Our group has identified a disseminated neoplastic cell population characterized by co-expression of immune and melanoma proteins, circulating hybrid cells (hybrids), in patients with uveal melanoma. Compared to circulating tumor cells, which lack expression of immune proteins, hybrids are detected at an increased prevalence in peripheral blood and can be used as a non-invasive biomarker to predict metastatic progression.MethodsTo ascertain mechanisms underlying enhanced hybrid cell dissemination we identified hybrid cells within primary uveal melanoma tumors using single cell RNA sequencing (n = 8) and evaluated their gene expression and predicted ligand-receptor interactions in relation to other melanoma and immune cells within the primary tumor. We then verified expression of upregulated hybrid pathways within patient-matched tumor and peripheral blood hybrids (n = 4) using cyclic immunofluorescence and quantified their protein expression relative to other non-hybrid tumor and disseminated tumor cells.ResultsAmong the top upregulated genes and pathways in hybrid cells were those involved in enhanced cell motility and cytoskeletal rearrangement, immune evasion, and altered cellular metabolism. In patient-matched tumor and peripheral blood, we verified gene expression by examining concordant protein expression for each pathway category: TMSB10 (cell motility), CD74 (immune evasion) and GPX1 (metabolism). Both TMSB10 and GPX1 were expressed on significantly higher numbers of disseminated hybrid cells compared to circulating tumor cells, and CD74 and GPX1 were expressed on more disseminated hybrids than tumor-resident hybrids. Lastly, we identified that hybrid cells express ligand-receptor signaling pathways implicated in promoting metastasis including GAS6-AXL, CXCL12-CXCR4, LGALS9-P4HB and IGF1-IGFR1.ConclusionThese findings highlight the importance of TMSB10, GPX1 and CD74 for successful hybrid cell dissemination and survival in circulation. Our results contribute to the understanding of uveal melanoma tumor progression and interactions between tumor cells and immune cells in the tumor microenvironment that may promote metastasis.

Erdafitinib promotes ferroptosis in human uveal melanoma by inducing ferritinophagy and lysosome biogenesis via modulating the FGFR1/mTORC1/TFEB signaling axis

Uveal melanoma (UM) is a rare yet lethal primary intraocular malignancy affecting adults. Analysis of data from The Cancer Genome Atlas (TCGA) database revealed that FGFR1 expression was increased in UM tumor tissues and was linked to aggressive behavior and a poor prognosis. This study assessed the anti-tumor effects of Erdafitinib, a selective pan-FGFR inhibitor, in both in vitro and in vivo UM models. Erdafitinib exhibited a robust anti-cancer activity in UM through inducing ferroptosis in the FGFR1-dependent manner. Transcriptomic data revealed that Erdafitinib mediated its anti-cancer effects via modulating the ferritinophagy/lysosome biogenesis. Subsequent research revealed that Erdafitinib exerted its effects by reducing the expression of FGFR1 and inhibiting the activity of mTORC1 in UM cells. Concurrently, it enhanced the dephosphorylation, nuclear translocation, and transcriptional activity of TFEB. The aggregation of TFEB in nucleus triggered FTH1-dependent ferritinophagy, leading to lysosomal activation and iron overload. Conversely, the overexpression of FGFR1 served to mitigate the effects of Erdafitinib on ferritinophagy, lysosome biogenesis, and the activation of the mTORC1/TFEB signaling pathway. In vivo experiments have convincingly shown that Erdafitinib markedly curtails tumor growth in an UM xenograft mouse model, an effect that is closely correlated with a decrease in FGFR1 expression levels. The present study is the first to demonstrate that Erdafitinib powerfully induces ferroptosis in UM by orchestrating the ferritinophagy and lysosome biogenesis via modulating the FGFR1/mTORC1/TFEB signaling. Consequently, Erdafitinib emerges as a strong candidate for clinical trial investigation, and FGFR1 emerges as a novel and promising therapeutic target in the treatment of UM.

Slow proliferation of BAP1-deficient uveal melanoma cells is associated with reduced S6 signaling and resistance to nutrient stress.

Uveal melanoma (UM) is the deadliest form of eye cancer in adults. Inactivating mutations and/or loss of expression of the gene encoding BRCA1-associated protein 1 (BAP1) in UM tumors are associated with an increased risk of metastasis. To investigate the mechanisms underlying this risk, we explored the functional consequences of BAP1 deficiency. UM cell lines expressing mutant BAP1 grew more slowly than those expressing wild-type BAP1 in culture and in vivo. The ability of BAP1 reconstitution to restore cell proliferation in BAP1-deficient cells required its deubiquitylase activity. Proteomic analysis showed that BAP1-deficient cells had decreased phosphorylation of ribosomal S6 and its upstream regulator, p70S6K1, compared with both wild-type and BAP1 reconstituted cells. In turn, expression of p70S6K1 increased S6 phosphorylation and proliferation of BAP1-deficient UM cells. Consistent with these findings, BAP1 mutant primary UM tumors expressed lower amounts of p70S6K1 target genes, and S6 phosphorylation was decreased in BAP1 mutant patient-derived xenografts (PDXs), which grew more slowly than wild-type PDXs in the liver (the main metastatic site of UM) in mice. BAP1-deficient UM cells were also more resistant to amino acid starvation, which was associated with diminished phosphorylation of S6. These studies demonstrate that BAP1 deficiency slows the proliferation of UM cells through regulation of S6 phosphorylation. These characteristics may be associated with metastasis by ensuring survival during amino acid starvation.

Chimeric Antigen Receptor T Cell with an Inducible Caspase-9 Suicide Gene Eradicates Uveal Melanoma Liver Metastases via B7-H3 Targeting.

Uveal melanoma (UM) is the most common intraocular malignant tumor. Despite successful treatment of the primary tumor, about 50% of patients will recur with systemic diseases for which there are no effective treatment strategies. Here we investigated the preclinical efficacy of a chimeric antigen receptor (CAR) T-cell-based immunotherapy targeting B7-H3. B7-H3 expression on primary and metastatic human UM samples and cell lines was assessed by RNA sequencing, flow cytometry, and immunohistochemistry. Antitumor activity of CAR T cells targeting B7-H3 was tested in vitro with UM cell lines, patient-derived organotypic tumor spheroids from patients with metastatic UM, and in immunodeficient and humanized murine models. B7-H3 is expressed at high levels in >95% UM tumor cells in vitro and in vivo. We generated a B7-H3 CAR with an inducible caspase-9 (iCas9) suicide gene controlled by the chemical inducer of dimerization AP1903, which effectively kills UM cells in vitro and eradicates UM liver metastases in murine models. Delivery of iCas9.B7-H3 CAR T cells in experimental models of UM liver metastases demonstrates a durable antitumor response, even upon tumor rechallenge or in the presence of a significant metastatic disease burden. We demonstrate effective iCas9.B7-H3 CAR T-cell elimination in vitro and in vivo in response to AP1903. Our studies demonstrate more effective tumor suppression with iCas9.B7-H3 CAR T cells as compared to a B7-H3-targeted humanized monoclonal antibody. These studies support a phase I clinical trial with iCas9.B7-H3 CAR T cells to treat patients with metastatic UM.

Combination of Molecule-Targeted Therapy and Photodynamic Therapy Using Nanoformulated Verteporfin for Effective Uveal Melanoma Treatment.

Uveal melanoma (UM) is the most common primary ocular malignancy in adults and has high mortality. Recurrence, metastasis, and therapeutic resistance are frequently observed in UM, but no beneficial systemic therapy is available, presenting an urgent need for developing effective therapeutic drugs. Verteporfin (VP) is a photosensitizer and a Yes-Associated Protein (YAP) inhibitor that has been used in clinical practice. However, VP's lack of tumor targetability, poor biocompatibility, and relatively low treatment efficacy hamper its application in UM management. Herein, we developed a biocompatible CD44-targeting hyaluronic acid nanoparticle (HANP) carrying VP (HANP/VP) to improve UM treatment efficacy. We found that HANP/VP showed a stronger inhibitory effect on cell proliferation than that of free VP in UM cells. Systemic delivery of HANP/VP led to targeted accumulation in the UM-tumor-bearing mouse model. Notably, HANP/VP mediated photodynamic therapy (PDT) significantly inhibited UM tumor growth after laser irradiation compared with no treatment or free VP treatment. Consistently, in HANP/VP treated tumors after laser irradiation, the tumor proliferation and YAP expression level were decreased, while the apoptotic tumor cell and CD8+ immune cell levels were elevated, contributing to effective tumor growth inhibition. Overall, the results of this preclinical study showed that HANP/VP is an effective nanomedicine for tumor treatment through PDT and inhibition of YAP in the UM tumor mouse model. Combining phototherapy and molecular-targeted therapy offers a promising approach for aggressive UM management.

Abstract 1529: Development of lymphoid aggregates in metastatic uveal melanoma tumors treated with tebentafusp

Abstract Tebentafusp (tebe), targeting gp100, is the first TCR-CD3 bispecific to demonstrate overall survival (OS) benefit and is approved for the treatment of metastatic uveal melanoma (mUM). We have previously shown B cell recruitment into the tumor associates with OS on tebe [1]. We explored further the formation of lymphoid aggregates (LA) within the tumor microenvironment in response to tebe. HLA-A*02:01+ 2L+ adult patients (pts) with mUM were treated with tebe (NCT02570308). Paired tumor biopsies were collected at baseline (n=70), after 3 doses of tebe (n=48), and at radiographical progression (n=17). Presence of B cells, T cells and macrophages was assessed by immunohistochemistry, using antibodies against CD20, CD3 and CD163 respectively, and digitally quantified. Using digital density analysis, aggregates of ≥10 CD20+ B cells within CD3+ T cell area in a 100µm radius were defined as LA. At progression pts were categorized by OS ≥12 or <12 months. Mean fold change (FC) was used. At baseline, B cells were detected in 90% of pts (median 5 B cells/mm2) with those pts having no more than 2 LA/mm2 (17% pts with 1 LA/mm2 and 3% pts with 2 LA/mm2). The median number of B cells in the biggest LA per sample was 24.B cells were recruited into the tumor after 3 doses of tebe (median 32 B cells/mm2, FC 3, p=6.5e-05). The LA density increased up to 6 LA/mm2 (23% pts with 1 LA/mm2, 8% pts with 2 LA/mm2, 6% pts with 3 LA/mm2 and 2% pts with 6 LA/mm2) with a trend for an increase in LA size (median B cell number in biggest LA = 30, p = 0.67). Tumors with a low baseline CD163+ macrophage to CD3+ T cell ratio, which was previously associated with longer OS on tebe, tended to have more LA/mm2 at baseline and on-treatment than those with a high ratio. At progression, pts with long OS had more B cells in the tumor compared to short OS (median 20 vs 2 B cells/mm2; FC 5, p=0.05). Additionally, more pts with long OS had LA than pts with short OS (6/12 pts vs 1/5 pts respectively) with a density not exceeding 1 LA/mm2. LA size was larger in pts with long OS compared to short OS (median B cell number in biggest LA 30 vs 10 respectively). LA in the short OS patient was found in the normal adjacent tissue compared to the LA in long OS patients which were located in the tumor and invasive margin. Tebe enhanced the formation of LA in the tumor microenvironment, notably in the low immunosuppressed tumors, which is consistent with the hypothesis that it results in epitope spread. These observations provide deeper insight into the mechanism of action of tebe and helps to explain prolonged survival of mUM pts beyond radiographical progression. [1] Greenshields-Watson A. et al., 619, SITC 2022 Citation Format: Takami Sato, Camille Britton-Rivet, Sophie Khakoo, Alistair Easton, Anastasiya Kazachenka, Laura Collins, Emma Leach, Adel Benlarech, Sarah Stanhope, Marcus O. Butler. Development of lymphoid aggregates in metastatic uveal melanoma tumors treated with tebentafusp [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1529.

Calcium Electroporation versus Electrochemotherapy with Bleomycin in an In Vivo CAM-Based Uveal Melanoma Xenograft Model.

Despite recent advancements in the diagnosis and treatment of uveal melanoma (UM), its metastatic rate remains high and is accompanied by a highly dismal prognosis, constituting an unmet need for the development of novel adjuvant therapeutic strategies. We established an in vivo chick chorioallantoic membrane (CAM)-based UM xenograft model from UPMD2 and UPMM3 cell lines to examine its feasibility for the improvement of selection of drug candidates. The efficacy of calcium electroporation (CaEP) with 5 or 10 mM calcium chloride (Ca) and electrochemotherapy (ECT) with 1 or 2.5 µg/mL bleomycin in comparison to monotherapy with the tested drug or electroporation (EP) alone was investigated on the generated UM tumors. CaEP and ECT showed a similar reduction of proliferation and melanocytic expansion with a dose-dependent effect for bleomycin, whereas CaEP induced a significant increase of the apoptosis and a reduction of vascularization with varying sensitivity for the two xenograft types. Our in vivo results suggest that CaEP and ECT may facilitate the adequate local tumor control and contribute to the preservation of the bulbus, potentially opening new horizons in the adjuvant treatment of advanced UM.

Ruthenium brachytherapie and sandwich therapy for medium sized uveal melanomas

Aims/Purpose: Brachytherapy using ruthenium is an established procedure for the treatment of uveal melanomas, the most common malignant primary intraocular tumour in adults. The supplementary use of transpupillary thermotherapy (TTT) with brachytherapy is known as sandwich therapy. Due to the rarity of uveal melanomas, long‐term outcome of large cohorts treated by ruthenium brachytherapy with and without TTT is of special clinical and scientific interest.Methods: Based on a retrospective longitudinal study, patients with uveal melanoma who received treatment using ruthenium brachytherapy at the Department of Ophthalmology from 1994 to 2021, were analysed. The evaluation includes tumour height, visual acuity, radiation data, side effects, local recurrence, bulbus preservation and occurrence of metastasis.Results: Overall, 150 patients with medium sized uveal melanoma (tumour height >3.0 and ≤7.0 mm) who received ruthenium brachytherapy were included. The mean age of patients at diagnosis was 63.5 ± 12.9 years (median 65), the proportion of women was 60.0%. Tumours were located centrally in 48.7% of cases; ciliary body involvement was seen in 4%. Additive transpupillary thermotherapy (TTT) was performed in 70.7% of cases as part of a sandwich therapy. After therapy and a mean follow‐up of 68.0 ± 58.3 years tumours height was significantly reduced from 4.5 ± 1.1 to 1.4 ± 1.6 mm (p < 0.001). Visual acuity showed deterioration from 0.25 ± 0.43 to 1.0 ± 0.85 logMAR (p < 0.001) due to the large proportion of centrally located tumours. In 29.9% of cases no side effects requiring therapy occurred. Within the remaining cases cataracta complicata (41.3%) and radiation retinopathy (30.0%) were observed. Local tumour control was achieved in 86.0% of patients, in 91.3% of cases the ocular globe was preserved. Metastatic free survival was seen in 86.4% of patients.Conclusions: Brachytherapy using ruthenium plaque with and without TTT represents a safe procedure in the treatment of uveal melanomas over the last three decades.

Familial uveal melanoma and other tumors in 25 families with monoallelic germline MBD4 variants.

Monoallelic germline MBD4 pathogenic variants were recently reported to cause a predisposition to uveal melanoma, associated with a specific tumor mutational signature and good response to immunotherapy. Monoallelic tumor pathogenic variants have also been described in brain tumors, breast cancers, and myxofibrosarcomas, whereas biallelic germline MBD4 pathogenic variants have been involved in a recessive hereditary adenomatous polyposis and a specific type of acute myeloid leukemia. We analyzed MBD4 for all patients with a diagnosis of uveal melanoma at Institut Curie since July 2021 and in the 3240 consecutive female probands explored at the Institut Curie for suspicion of predisposition to breast cancer between July 2021 and February 2023. We describe 25 families whose probands carry a monoallelic germline pathogenic variant in MBD4. Eighteen of these families presented with uveal melanoma (including a case patient with multiple uveal melanoma), and 7 families presented with breast cancer. Family histories showed the first familial case of uveal melanoma in monoallelic MBD4 pathogenic variant carriers and other various types of cancers in relatives, especially breast, renal, and colorectal tumors. Monoallelic MBD4 pathogenic variant may explain some cases of familial and multiple uveal melanoma as well as various cancer types, expanding the tumor spectrum of this predisposition. Further genetic testing in relatives combined with molecular tumor analyses will help define the tumor spectrum and estimate each tumor's risk.

Abstract A041: FHD-286, a potent and selective inhibitor of BRG1 and BRM, shifts metastatic uveal melanoma tumor towards a less immunosuppressive state in patient samples

Abstract BRG1/BRM are key components of the SWI/SNF complex that are critical in regulation of transcriptional programs that control cell fate and identity. Tumor cells aberrantly hijack and upregulated BRG1 levels, hijacking “stemness features”. Furthermore, BRG1 has been shown to impact immune cell polarization, driving programs associated with T cell exhaustion and an immunosuppressive cell state. Our group previously demonstrate that the combination of FHD-286 and anti-PD-1 antibody is synergistic in syngeneic mouse models from various lineages, and substantially shifted with tumor microenvironment (TME) towards a more tumor killing state (Ichikawa, K. 2022, SITC). FHD-286 was evaluated in a phase 1 dose escalation (FHD-286-001, NCT04879017), in metastatic uveal melanoma (mUM) a tumor with low response rate to standard immune checkpoint therapy as well as high levels of immunosuppressive cell infiltration. Thus, we endeavored to determine if there was evidence of biological changes in peripheral blood and TME shifts in samples taken from our phase 1 dose escalation in patients with metastatic uveal melanoma. Subjects were on a daily dosing regimen ranging from 2.5 to 10 mg or an intermittent regimen of 1-week on/1-week-off ranging from 10 to 22.5 mg in 73 patients. RNA sequencing was performed in 46 patient blood samples collected in Paxgene tubes during dose escalation (2.5 mg- 15mg, C1D1, C1D15, C3D1 and other intermediate timepoints) and analyzed for transcriptional changes associated with shifts in immune polarization and activation. Tumor biopsies were collected at screening and either Cycle 3 or end of treatment. Biomarker changes in the tumor were quantified using multiplex IF (mIF) panel (Neogenomics) to assess co-localization and spatial orientation of 20 different immune related markers in 16 patients, 13 of which had samples from screening and on-treatment. Further changes were assessed using RNA sequencing of paired biopsies in 9 patients. Analysis of peripheral blood identified changes in expression of genes associated with a reduction in immunosuppressive signatures, particularly a dose dependent reduction of FOXP3 from baseline, as well as an increase in transcripts associated with activation of neutrophils. The mIF panel highlighted a reduction in immunosuppressive cells of multiple lineages including in on treatment samples, with 12/13 patients showing a reduction of one or more of the following: FOXP3+ Tregs (8/13), PD-L1+ Macrophages (8/13), an increase in the M2 Mf to tumor cells distance (8/13), markers of T cell exhaustion (PD1) on both CD4 (7/13) and CD8 T cells (8/13), or an increase in CD8/Treg ratio (5/13). Taken together these results suggest FHD-286 may reduce the immunosuppressive “blockade”, priming mUM patients to response in combination with an immune checkpoint inhibitor. Citation Format: Liv H Johannessen, Jessica Wan, Kim Horrigan, Mike Collins, GiNell Elliott, Kana Ichikawa, Ammar Adam, Sam Agresta, Jessica Piel, Martin Hentemann. FHD-286, a potent and selective inhibitor of BRG1 and BRM, shifts metastatic uveal melanoma tumor towards a less immunosuppressive state in patient samples [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A041.

Abstract LB_C16: Long-read sequencing reveals alternative splicing driven, shared immunogenic neoepitopes regardless SF3B1 status in uveal melanoma

Abstract Tumor-specific neoepitopes are promising targets in cancer immunotherapy. However, identification of functional tumor-specific neoepitopes remains challenging. In addition to the most common source single-nucleotide variants (SNVs), alternative splicing (AS) represents another rich source of neoepitopes and can be particularly useful to certain cancers with low SNVs such as Uveal melanoma (UM). UM, the most prevalent adult ocular malignancy, has poor clinical outcomes due to a lack of effective therapies. Recent studies have manifested the promise of harnessing tumor neoepitopes to treat UM. Notably, previous studies have focused on neoepitope targets associated with mutations in splicing factor 3b subunit 1 (SF3B1), a key splicing factor, however little is known about the neoepitopes that are commonly shared by patients but independent of SF3B1 status. To identify the AS-derived neoepitopes regardless SF3B1, we herein used a comprehensive Nanopore long-read-sequencing approach to elucidate the landscape of AS and novel isoforms in UM. We also performed high-resolution mass-spectrometry to further validate the presence of neoepitope candidates, and analyzed their structures using AlphaFold2 algorithm. We experimentally evaluated the anti-tumor effects of these neoepitopes, and found they induced profound immune responses by stimulating interferon (IFN)-g production and activating T-cell-based UM tumor killing. These results provide novel insights into UM-specific neoepitopes independent of SF3B1, and lay the foundation for developing therapies by targeting these actionable neoepitopes. Citation Format: Jianfeng Shen, Zhe Zhang. Long-read sequencing reveals alternative splicing driven, shared immunogenic neoepitopes regardless SF3B1 status in uveal melanoma [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr LB_C16.

Tryptophan metabolism-related gene expression patterns: unveiling prognostic insights and immune landscapes in uveal melanoma.

Uveal melanoma (UVM) remains the leading intraocular malignancy in adults, with a poor prognosis for those with metastatic disease. Tryptophan metabolism plays a pivotal role in influencing cancerous properties and modifying the tumor's immune microenvironment. In this study, we explore the relationship between tryptophan metabolism-related gene (TRMG) expression and the various features of UVM, including prognosis and tumor microenvironment. Our analysis included 143 patient samples sourced from public databases. Using K-means clustering, we categorized UVM patients into two distinct clusters. Further, we developed a prognostic model based on five essential genes, effectively distinguishing between low-risk and high-risk patients. This distinction underscores the importance of TRMGs in UVM prognostication. Combining TRMG data with gender to create nomograms demonstrated exceptional accuracy in predicting UVM patient outcomes. Moreover, our analysis reveals correlations between risk assessments and immune cell infiltrations. Notably, the low-risk group displayed a heightened potential response to immune checkpoint inhibitors. In conclusion, our findings underscore the dynamic relationship between TRMG expression and various UVM characteristics, presenting a novel prognostic framework centered on TRMGs. The deep connection between TRMGs and UVM's tumor immune microenvironment emphasizes the crucial role of tryptophan metabolism in shaping the immune landscape. Such understanding paves the way for designing targeted immunotherapy strategies for UVM patients.

Long-Read Sequencing Reveals Alternative Splicing-Driven, Shared Immunogenic Neoepitopes Regardless of SF3B1 Status in Uveal Melanoma.

Tumor-specific neoepitopes are promising targets in cancer immunotherapy. However, the identification of functional tumor-specific neoepitopes remains challenging. In addition to the most common source, single-nucleotide variants (SNV), alternative splicing (AS) represents another rich source of neoepitopes and can be utilized in cancers with low SNVs such as uveal melanoma (UM). UM, the most prevalent adult ocular malignancy, has poor clinical outcomes due to a lack of effective therapies. Recent studies have revealed the promise of harnessing tumor neoepitopes to treat UM. Previous studies have focused on neoepitope targets associated with mutations in splicing factor 3b subunit 1 (SF3B1), a key splicing factor; however, little is known about the neoepitopes that are commonly shared by patients independent of SF3B1 status. To identify the AS-derived neoepitopes regardless of SF3B1 status, we herein used a comprehensive nanopore long-read-sequencing approach to elucidate the landscape of AS and novel isoforms in UM. We also performed high-resolution mass spectrometry to further validate the presence of neoepitope candidates and analyzed their structures using the AlphaFold2 algorithm. We experimentally evaluated the antitumor effects of these neoepitopes and found they induced robust immune responses by stimulating interferon (IFN)γ production and activating T cell-based UM tumor killing. These results provide novel insights into UM-specific neoepitopes independent of SF3B1 and lay the foundation for developing therapies by targeting these actionable neoepitopes.

Protein Kinase Signaling Networks Driven by Oncogenic Gq/11 in Uveal Melanoma Identified by Phosphoproteomic and Bioinformatic Analyses

Metastatic uveal melanoma (UM) patients typically survive only 2 to 3years because effective therapy does not yet exist. Here, to facilitate the discovery of therapeutic targets in UM, we have identified protein kinase signaling mechanisms elicited by the drivers in 90% of UM tumors: mutant constitutively active G protein α-subunits encoded by GNAQ (Gq) or GNA11 (G11). We used the highly specific Gq/11 inhibitor FR900359 (FR) to elucidate signaling networks that drive proliferation, metabolic reprogramming, and dedifferentiation of UM cells. We determined the effects of FR on the proteome and phosphoproteome of UM cells as indicated by bioinformatic analyses with CausalPath and site-specific gene set enrichment analysis. We found that inhibition of oncogenic Gq/11 caused deactivation of PKC, Erk, and the cyclin-dependent kinases CDK1 and CDK2 that drive proliferation. Inhibition of oncogenic Gq/11 in UM cells with low metastatic risk relieved inhibitory phosphorylation of polycomb-repressive complex subunits that regulate melanocytic redifferentiation. Site-specific gene set enrichment analysis, unsupervised analysis, and functional studies indicated that mTORC1 and 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 drive metabolic reprogramming in UM cells. Together, these results identified protein kinase signaling networks driven by oncogenic Gq/11 that regulate critical aspects of UM cell biology and provide targets for therapeutic investigation.

Validation of an Ultraviolet Light Response Gene Signature for Predicting Prognosis in Patients with Uveal Melanoma.

Uveal melanoma (UVM) is a highly aggressive ocular cancer with limited therapeutic options and poor prognosis particularly for patients with liver metastasis. As such, the identification of new prognostic biomarkers is critical for developing effective treatment strategies. In this study, we aimed to investigate the potential of an ultraviolet light response gene signature to predict the prognosis of UVM patients. Our approach involved the development of a prognostic model based on genes associated with the cellular response to UV light. By employing this model, we generated risk scores to stratify patients into high- and low-risk groups. Furthermore, we conducted differential expression analysis between these two groups and explored the estimation of immune infiltration. To validate our findings, we applied our methodology to an independent UVM cohort. Through our study, we introduced a novel survival prediction tool and shed light on the underlying cellular processes within UVM tumors, emphasizing the involvement of immune subsets in tumor progression.

Combined Mcl-1 and YAP1/TAZ inhibition for treatment of metastatic uveal melanoma.

Uveal melanoma is the most common intraocular tumor in adults, representing approximately 5% of all melanoma cases. Up to 50% of uveal melanoma patients develop metastases that are resistant to most of the commonly used antineoplastic treatments. Virtually all uveal melanoma tumors harbor activating mutations in GNAQ or GNA11 , encoding Gαq and Gα11, respectively. Constant activity of these proteins causes deregulation of multiple downstream signaling pathways including PKC, MAPK and YAP1/TAZ. While the importance of YAP1 signaling for the proliferation of uveal melanoma has recently been demonstrated, much less is known about the paralog of YAP1 transcriptional coactivator, named TAZ; however, similar to YAP1, TAZ is expected to be a therapeutic target in uveal melanoma. We performed a small-scale drug screen to discover a compound synergistically inhibiting uveal melanoma proliferation/survival in combination with YAP1/TAZ inhibition. We found that the combination of genetic depletion of YAP1/TAZ together with Mcl-1 inhibition demonstrates a synergistic inhibitory effect on the viability of uveal melanoma cell lines. Similarly, indirect attenuation of the YAP1/TAZ signaling pathway with an inhibitor of the mevalonate pathway, that is, the geranyl-geranyl transferase inhibitor GGTI-298, synergizes with Mcl-1 inhibition. This combination could be potentially used as a treatment for metastatic uveal melanoma.