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Lalonde E, Li D, Ewens K, Shields CL, Ganguly A. Genome-Wide Methylation Patterns in Primary Uveal Melanoma: Development of MethylSig-UM, an Epigenomic Prognostic Signature to Improve Patient Stratification. Cancers (Basel) 2024; 16:2650. [PMID: 39123378 PMCID: PMC11312132 DOI: 10.3390/cancers16152650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Despite studies highlighting the prognostic utility of DNA methylation in primary uveal melanoma (pUM), it has not been translated into a clinically useful tool. We sought to define a methylation signature to identify newly diagnosed individuals at high risk for developing metastasis. Methylation profiling was performed on 41 patients with pUM with stage T2-T4 and at least three years of follow-up using the Illumina Infinium HumanMethylation450K BeadChip (N = 24) and the EPIC BeadChip (N = 17). Findings were validated in the TCGA cohort with known metastatic outcome (N = 69). Differentially methylated probes were identified in patients who developed metastasis. Unsupervised consensus clustering revealed three epigenomic subtypes associated with metastasis. To identify a prognostic signature, recursive feature elimination and random forest models were utilized within repeated cross-validation iterations. The 250 most commonly selected probes comprised the final signature, named MethylSig-UM. MethylSig-UM could distinguish individuals with pUM at diagnosis who develop future metastasis with an area under the curve of ~81% in the independent validation cohort, and remained significant in Cox proportional hazard models when combined with clinical features and established genomic biomarkers. Altered expression of immune-modulating genes were detected in MethylSig-UM positive tumors, providing clues for pUM resistance to immunotherapy. The MethylSig-UM model is available to enable additional validation in larger cohort sizes including T1 tumors.
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Affiliation(s)
- Emilie Lalonde
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Schulich School Medicine & Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Dong Li
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathryn Ewens
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Carol L. Shields
- Oncology Services, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Arupa Ganguly
- Department of Pathology and Laboratory Medicine, Schulich School Medicine & Dentistry, Western University, London, ON N6A 5C1, Canada
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2
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Reveneau MF, Masliah-Planchon J, Fernandez M, Ouikene A, Dron B, Dadamessi I, Dayen C, Golmard L, Chauffert B. Major response of a peritoneal mesothelioma to nivolumab and ipilimumab: a case report, molecular analysis and review of literature. Front Oncol 2024; 14:1410322. [PMID: 39091916 PMCID: PMC11291227 DOI: 10.3389/fonc.2024.1410322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 07/05/2024] [Indexed: 08/04/2024] Open
Abstract
Malignant peritoneal mesothelioma (MPM) is a rare tumor associated with a poor prognosis and a lack of consensus regarding treatment strategies. While the Checkmate 743 trial demonstrated the superiority of first-line nivolumab and ipilimumab over chemotherapy in malignant pleural mesothelioma (MPlM), few studies have assessed the effectiveness of immunotherapy against MPM, due to its rarity. Here, we report a major and sustained 12-month response in a 74-year-old female patient who received the anti-PD-1 nivolumab and the anti-CTLA4 ipilimumab as first-line therapy for diffuse MPM. PD-L1 was expressed and BAP1 expression was lost, as shown by immunohistochemistry, however the BAP1 gene was not mutated. Our findings suggest a role for ICI in non-resectable diffuse MPM exhibiting PD-L1 overexpression and loss of BAP1 expression, and instill new hope in their treatment. To our knowledge, this is the second reported case of dual immunotherapy used as first-line in MPM with a major clinical response. To investigate the clinical outcome, we conducted additional molecular analyses of the MPM tumor and we reviewed the literature on immunotherapy in MPM to discuss the role of PD-L1 and BAP1.
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Affiliation(s)
- Marie-Florence Reveneau
- Department of Genetics, Institut Curie, Paris, France
- Department of Medical Oncology, Saint Quentin Hospital, Saint Quentin, France
| | | | - Manuel Fernandez
- Department of Radiology, Saint Quentin Hospital, Saint Quentin, France
| | - Abdenour Ouikene
- Department of Medical Oncology, Saint Quentin Hospital, Saint Quentin, France
| | - Bernard Dron
- Department of Digestive Surgery, Saint Quentin Hospital, Saint Quentin, France
| | - Innocenti Dadamessi
- Department of Digestive Surgery, Saint Quentin Hospital, Saint Quentin, France
| | - Charles Dayen
- Department of Pneumology, Saint Quentin Hospital, Saint Quentin, France
| | - Lisa Golmard
- Department of Genetics, Institut Curie, Paris, France
| | - Bruno Chauffert
- Department of Medical Oncology, Saint Quentin Hospital, Saint Quentin, France
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3
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Doddi S, Hamoud AR, Eby HM, Zhang X, Imami AS, Shedroff E, Schiefer I, Moreno-Lopez J, Gamm D, Meller J, McCullumsmith RE. Transcriptomic Analysis of Metastatic Uveal Melanoma and Differences in Male and Female Patients. Cancer Genomics Proteomics 2024; 21:350-360. [PMID: 38944422 PMCID: PMC11215432 DOI: 10.21873/cgp.20452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 03/20/2024] [Accepted: 04/02/2024] [Indexed: 07/01/2024] Open
Abstract
BACKGROUND/AIM Uveal melanoma is an ocular malignancy whose prognosis severely worsens following metastasis. In order to improve the understanding of molecular physiology of metastatic uveal melanoma, we identified genes and pathways implicated in metastatic vs non-metastatic uveal melanoma. PATIENTS AND METHODS A previously published dataset from Gene Expression Omnibus (GEO) was used to identify differentially expressed genes between metastatic and non-metastatic samples as well as to conduct pathway and perturbagen analyses using Gene Set Enrichment Analysis (GSEA), EnrichR, and iLINCS. RESULTS In male metastatic uveal melanoma samples, the gene LOC401052 is significantly down-regulated and FHDC1 is significantly up-regulated compared to non-metastatic male samples. In female samples, no significant differently expressed genes were found. Additionally, we identified many significant up-regulated immune response pathways in male metastatic uveal melanoma, including "T cell activation in immune response". In contrast, many top up-regulated female pathways involve iron metabolism, including "heme biosynthetic process". iLINCS perturbagen analysis identified that both male and female samples have similar discordant activity with growth factor receptors, but only female samples have discordant activity with progesterone receptor agonists. CONCLUSION Our results from analyzing genes, pathways, and perturbagens demonstrate differences in metastatic processes between sexes.
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Affiliation(s)
- Sishir Doddi
- Department of Neurosciences, University of Toledo College of Medicine, Toledo, OH, U.S.A
| | - Abdul-Rizaq Hamoud
- Department of Neurosciences, University of Toledo College of Medicine, Toledo, OH, U.S.A
| | - Hunter M Eby
- Department of Neurosciences, University of Toledo College of Medicine, Toledo, OH, U.S.A
| | - Xiaolu Zhang
- Department of Neurosciences, University of Toledo College of Medicine, Toledo, OH, U.S.A
| | - Ali Sajid Imami
- Department of Neurosciences, University of Toledo College of Medicine, Toledo, OH, U.S.A
| | - Elizabeth Shedroff
- Department of Neurosciences, University of Toledo College of Medicine, Toledo, OH, U.S.A
| | - Isaac Schiefer
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH, U.S.A
| | - Jose Moreno-Lopez
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH, U.S.A
| | - David Gamm
- McPherson Eye Research Institute and Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, U.S.A
| | - Jaroslaw Meller
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, U.S.A
| | - Robert E McCullumsmith
- Department of Neurosciences, University of Toledo College of Medicine, Toledo, OH, U.S.A.;
- Neurosciences Institute, ProMedica, Toledo, OH, U.S.A
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4
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Booth L, Roberts JL, Spasojevic I, Baker KC, Poklepovic A, West C, Kirkwood JM, Dent P. GZ17-6.02 kills PDX isolates of uveal melanoma. Oncotarget 2024; 15:328-344. [PMID: 38758815 PMCID: PMC11101052 DOI: 10.18632/oncotarget.28586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 05/06/2024] [Indexed: 05/19/2024] Open
Abstract
GZ17-6.02 has undergone phase I evaluation in patients with solid tumors (NCT03775525). The RP2D is 375 mg PO BID, with an uveal melanoma patient exhibiting a 15% reduction in tumor mass for 5 months at this dose. Studies in this manuscript have defined the biology of GZ17-6.02 in PDX isolates of uveal melanoma cells. GZ17-6.02 killed uveal melanoma cells through multiple convergent signals including enhanced ATM-AMPK-mTORC1 activity, inactivation of YAP/TAZ and inactivation of eIF2α. GZ17-6.02 significantly enhanced the expression of BAP1, predictive to reduce metastasis, and reduced the levels of ERBB family RTKs, predicted to reduce growth. GZ17-6.02 interacted with doxorubicin or ERBB family inhibitors to significantly enhance tumor cell killing which was associated with greater levels of autophagosome formation and autophagic flux. Knock down of Beclin1, ATG5 or eIF2α were more protective than knock down of ATM, AMPKα, CD95 or FADD, however, over-expression of FLIP-s provided greater protection compared to knock down of CD95 or FADD. Expression of activated forms of mTOR and STAT3 significantly reduced tumor cell killing. GZ17-6.02 reduced the expression of PD-L1 in uveal melanoma cells to a similar extent as observed in cutaneous melanoma cells whereas it was less effective at enhancing the levels of MHCA. The components of GZ17-6.02 were detected in tumors using a syngeneic tumor model. Our data support future testing GZ17-6.02 in uveal melanoma as a single agent, in combination with ERBB family inhibitors, in combination with cytotoxic drugs, or with an anti-PD1 immunotherapy.
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Affiliation(s)
- Laurence Booth
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Jane L Roberts
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Ivan Spasojevic
- Department of Medicine, and PK/PD Core Laboratory, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kaitlyn C Baker
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Andrew Poklepovic
- Department of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Cameron West
- Genzada Pharmaceuticals, Hutchinson, KS 67502, USA
- Department of Dermatology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - John M Kirkwood
- Melanoma and Skin Cancer Program, Hillman Cancer Research Pavilion Laboratory, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
| | - Paul Dent
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23298, USA
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5
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Loda A, Semeraro F, Parolini S, Ronca R, Rezzola S. Cancer stem-like cells in uveal melanoma: novel insights and therapeutic implications. Biochim Biophys Acta Rev Cancer 2024; 1879:189104. [PMID: 38701937 DOI: 10.1016/j.bbcan.2024.189104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/24/2024] [Accepted: 04/27/2024] [Indexed: 05/06/2024]
Abstract
Uveal melanoma (UM) is the most common primary ocular tumor in the adult population. Even though these primary tumors are successfully treated in 90% of cases, almost 50% of patients ultimately develop metastasis, mainly in the liver, via hematological dissemination, with a median survival spanning from 6 to 12 months after diagnosis. In this context, chemotherapy regimens and molecular targeted therapies have demonstrated poor response rates and failed to improve survival. Among the multiple reasons for therapy failure, the presence of cancer stem-like cells (CSCs) represents the main cause of resistance to anticancer therapies. In the last few years, the existence of CSCs in UM has been demonstrated both in preclinical and clinical studies, and new molecular pathways and mechanisms have been described for this subpopulation of UM cells. Here, we will discuss the state of the art of CSC biology and their potential exploitation as therapeutic target in UM.
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Affiliation(s)
- Alessandra Loda
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Francesco Semeraro
- Eye Clinic, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy
| | - Silvia Parolini
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy; National Center for Gene Therapy and Drugs based on RNA Technology - CN3, Padova, Italy; Consorzio Interuniversitario per le Biotecnologie (CIB), Italy
| | - Roberto Ronca
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy; Consorzio Interuniversitario per le Biotecnologie (CIB), Italy
| | - Sara Rezzola
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.
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6
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Pašalić D, Nikuševa-Martić T, Sekovanić A, Kaštelan S. Genetic and Epigenetic Features of Uveal Melanoma-An Overview and Clinical Implications. Int J Mol Sci 2023; 24:12807. [PMID: 37628989 PMCID: PMC10454135 DOI: 10.3390/ijms241612807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/09/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
Uveal melanoma (UM) is rare, but it is the most common primary intraocular malignancy among adults. This review represents the molecular, genetic, and immunobiological mechanisms involved in UM carcinogenesis and progression, as well as data about the association of chromosomal changes, genetic mutations, selective proteins, and biochemical biomarkers with the clinical implications of UM. Genetic analysis has the potential to identify patients with a high risk of UM metastasis, enabling management that is more effective and allowing for the follow-up of patients. Advancements in molecular characterization of UM offer opportunities to develop targeted therapeutic strategies by focusing on relevant signaling pathways. Changes in miRNA expression could be useful in the diagnosis and prognosis of UM, due to unique miRNA profiles in melanoma cells or tissue and its association with metastasis. Although liver function tests do not provide enough data on the prognosis of UM, due to the high frequency of liver metastasis, liver function tests (LFTs) might be useful indicators; however, the absence of rising LFT values cannot lead to the exclusion of liver metastases. Molecular analysis of tumor tissue will allow us to identify patients with the added benefit of new therapeutic agents and provide a better insight into melanoma pathogenesis and its biological behavior.
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Affiliation(s)
- Daria Pašalić
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Tamara Nikuševa-Martić
- Department of Biology and Genetics, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Ankica Sekovanić
- Institute for Medical Research and Occupational Health, 10000 Zagreb, Croatia;
| | - Snježana Kaštelan
- Department of Ophthalmology and Optometry, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
- Department of Ophthalmology, Clinical Hospital Dubrava, 10000 Zagreb, Croatia
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7
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Miguez S, Lee RY, Chan AX, Demkowicz PC, Jones BSCL, Long CP, Abramson DH, Bosenberg M, Sznol M, Kluger H, Goldbaum MH, Francis JH, Pointdujour-Lim R, Bakhoum MF. Validation of the Prognostic Usefulness of the Gene Expression Profiling Test in Patients with Uveal Melanoma. Ophthalmology 2023; 130:598-607. [PMID: 36739981 PMCID: PMC10619207 DOI: 10.1016/j.ophtha.2023.01.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/11/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
PURPOSE To validate the prognostic usefulness of gene expression profile (GEP) testing in patients with uveal melanoma. To determine whether combining tumor size with the GEP classification provides additional prognostic value. DESIGN Retrospective analysis. PARTICIPANTS Patients with a diagnosis of choroidal melanoma examined at Yale New Haven Hospital; University of California, San Diego; and Memorial Sloan Kettering Cancer Center. METHODS Patients' demographic and clinical data and tumor characteristics were collected. Univariate and multivariate Cox hazard regression analysis were used to assess the association between tumor characteristics and GEP classification with metastasis as an outcome. MAIN OUTCOME MEASURES Metastasis-free survival (MFS). RESULTS Of the 337 individuals included in the study, 87 demonstrated metastases. The mean follow-up time was 37.2 (standard deviation [SD], 40.2) months for patients with metastases and 55.0 (SD, 49.3) months for those without metastases. Tumors of larger thickness and GEP class 2 (vs. class 1) were associated significantly with increased risk of metastasis. Tumor thickness showed better prognostic usefulness than GEP classification (Wald statistic, 40.7 and 24.2, respectively). Class 2 tumors with a thickness of 7.0 mm or more were associated with increased risk of metastasis than tumors with a thickness of < 7.0 mm (hazard ratio [HR], 3.23; 95% confidence interval [CI], 1.61-6.51), whereas class 1 tumors with a thickness of 9.0 mm or more were associated with increased risk of metastasis than tumors with a thickness of < 9.0 mm (HR, 2.07; 95% CI, 0.86-4.99). No difference in MFS was found between patients with class 1A tumors compared with those with class 1B tumors (P = 0.8). Patients with class 2 tumors showed an observed 5-year MFS of 47.5% (95% CI, 36.0%-62.8%). CONCLUSIONS Tumor size was the most significant predictor of metastasis and provided additional prognostic value independent of GEP classification. In addition, rates of metastasis for class 2 tumors were lower than estimates reported by Castle Bioscience, and no difference in rates of metastasis were found between class 1A and 1B tumors. This indicates that tumor size should be accounted for when relying on GEP for prognostication and that patients with GEP class 1A or 1B tumors may benefit from the same metastatic surveillance protocols. FINANCIAL DISCLOSURE(S) The author(s) have no proprietary or commercial interest in any materials discussed in this article.
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Affiliation(s)
- Sofia Miguez
- Yale University School of Medicine, New Haven, Connecticut
| | - Ryan Y Lee
- Yale University School of Medicine, New Haven, Connecticut
| | - Alison X Chan
- The Viterbi Family Department of Ophthalmology, University of California, San Diego, La Jolla, California
| | | | - Bailey S C L Jones
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, Connecticut
| | - Christopher P Long
- Department of Ophthalmology, University of Southern California, Los Angeles, California
| | - David H Abramson
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marcus Bosenberg
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut; Yale Cancer Center, Yale University, New Haven, Connecticut
| | - Mario Sznol
- Yale Cancer Center, Yale University, New Haven, Connecticut; Department of Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Harriet Kluger
- Yale Cancer Center, Yale University, New Haven, Connecticut; Department of Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Michael H Goldbaum
- The Viterbi Family Department of Ophthalmology, University of California, San Diego, La Jolla, California
| | - Jasmine H Francis
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Renelle Pointdujour-Lim
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, Connecticut; Yale Cancer Center, Yale University, New Haven, Connecticut
| | - Mathieu F Bakhoum
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, Connecticut; Department of Pathology, Yale University School of Medicine, New Haven, Connecticut; Yale Cancer Center, Yale University, New Haven, Connecticut.
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8
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Yin J, Zhao G, Kalirai H, Coupland SE, Jochemsen AG, Forn-Cuní G, Wierenga APA, Jager MJ, Snaar-Jagalska BE, Groenewoud A. Zebrafish Patient-Derived Xenograft Model as a Preclinical Platform for Uveal Melanoma Drug Discovery. Pharmaceuticals (Basel) 2023; 16:ph16040598. [PMID: 37111355 PMCID: PMC10141637 DOI: 10.3390/ph16040598] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/06/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Uveal melanoma (UM) is a rare malignant cancer of the eye, with up to 50% of patients dying from metastasis, for which no effective treatment is available. Due to the rarity of the disease, there is a great need to harness the limited material available from primary tumors and metastases for advanced research and preclinical drug screening. We established a platform to isolate, preserve, and transiently recover viable tissues, followed by the generation of spheroid cultures derived from primary UM. All assessed tumor-derived samples formed spheroids in culture within 24 h and stained positive for melanocyte-specific markers, indicating the retention of their melanocytic origin. These short-lived spheroids were only maintained for the duration of the experiment (7 days) or re-established from frozen tumor tissue acquired from the same patient. Intravenous injection of fluorescently labeled UM cells derived from these spheroids into zebrafish yielded a reproducible metastatic phenotype and recapitulated molecular features of the disseminating UM. This approach allowed for the experimental replications required for reliable drug screening (at least 2 individual biological experiments, with n > 20). Drug treatments with navitoclax and everolimus validated the zebrafish patient-derived model as a versatile preclinical tool for screening anti-UM drugs and as a preclinical platform to predict personalized drug responses.
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Affiliation(s)
- Jie Yin
- Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
| | - Gangyin Zhao
- Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
| | - Helen Kalirai
- Liverpool Ocular Oncology Research Centre, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool L69 3BX, UK
| | - Sarah E Coupland
- Liverpool Ocular Oncology Research Centre, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool L69 3BX, UK
| | - Aart G Jochemsen
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Gabriel Forn-Cuní
- Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
| | - Annemijn P A Wierenga
- Department of Ophthalmology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Martine J Jager
- Department of Ophthalmology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | | | - Arwin Groenewoud
- Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
- Experimental Renal and Cardiovascular Research, Department of Nephropathology, Institute of Pathology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
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9
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Nan X, Liu Y, Gao Y, Nan X. Multiple epigenetic modification profiles reveal the tumor immune microenvironment and clinical outcomes of uveal melanoma. Front Genet 2023; 14:1155199. [PMID: 37124608 PMCID: PMC10132731 DOI: 10.3389/fgene.2023.1155199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/16/2023] [Indexed: 05/02/2023] Open
Abstract
Uveal melanoma (UM) is an aggressive intraocular cancer that, in 50% of cases, spreads to the patient's other systems. The exact cause of the increased metastatic rate is still unknown. Methylation and immune response, metastasis, and the expansion of cancer cells are closely related. Additionally, proteins linked to RNA methylation have come to light as possible cancer treatment targets. However, the relationship between methylation-related genes (MRGs) and the tumor microenvironment (TME) is still not understood. The goal of this work was to discover important MRGs and create a signature for UM patients' prognosis prediction. Using two different data sets, we examined the MRG expression patterns in the transcriptional and genomic regions of 106 UM samples. We discovered a connection between the clinicopathological traits of the patients, their prognosis, the capability of TME cells to infiltrate, and various MRG changes. Following that, we developed an MRGs signature to forecast prognosis, and we evaluated the model's precision in patients with UM. We grouped the patients into multiple categories based on their clinical traits, looked at the survival rates for various groups within various groupings, and tested their accuracy. Additionally, to increase the practical usability of the MRGs model, we created a very accurate nomogram. TIDE scores were higher in the low-risk group. We go over how MGRs could impact UM's TME, immunotherapy responsiveness, prognosis, and clinically significant features. We looked for different chemotherapeutic drugs and cutting-edge targeted agents for patients in diverse subgroups in order to better understand MRGs in UM. This helped in the creation of customized therapy to open new doors. We could also further research the prognosis and develop more efficient immunotherapy regimens.
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Affiliation(s)
- Xinshuai Nan
- Department of Ophthalmology, Subei Peoples’ Hospital Affiliated to Yangzhou University, Yangzhou, China
| | - Yuchen Liu
- Department of Ophthalmology, Yangzhou Aier New Vision Eye Hospital, Yangzhou, China
| | - Yuzhen Gao
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinshan Nan
- Department of ICU, Hua Xin Hospital, Ningbo, China
- *Correspondence: Xinshan Nan,
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10
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Pergaris A, Danas E, Gajdzis P, Levidou G, Gajdzis M, Cassoux N, Gardrat S, Donizy P, Korkolopoulou P, Kavantzas N, Klijanienko J, Theocharis S. EPHA2, EPHA4, and EPHA6 Expression in Uveal Melanomas: Searching for the Culprits of Neoplasia. Diagnostics (Basel) 2022; 12:diagnostics12051025. [PMID: 35626181 PMCID: PMC9139903 DOI: 10.3390/diagnostics12051025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/07/2022] [Accepted: 04/14/2022] [Indexed: 12/02/2022] Open
Abstract
Uveal melanomas (UMs) comprise the most common primary intraocular malignancies in adults, with the eye representing the second most common site for melanoma, following the skin. Prognosis remains poor, with approximately half of the cases presenting with metastatic disease at the time of diagnosis. Erythropoietin-producing human hepatocellular receptors (EPHs) comprise the largest known family of tyrosine receptors, in which, along with their ligands, ephrins, play an important role in a plethora of processes in human physiology, and are implicated in key steps of carcinogenesis. In the present study, EPHA2, EPHA4, and EPHA6 immunohistochemical expressions were investigated in UM tissues and further correlated to a multitude of clinicopathological parameters, including disease stage and patients’ overall survival (OS). High levels of EPHA2 expression were significantly associated with increased tumor vertical thickness (p = 0.03) and the presence of intrascleral involvement (p = 0.05), whereas high EPHA6 nuclear expression was associated with older age at diagnosis (p = 0.03) and absence of retinal detachment (p = 0.05). In a multivariate survival analysis, increased EPHA4 expression was associated with shortened OS along with the presence of metastasis (p < 0.001) and monosomy 3 (p = 0.02). In a separate model, the concurrent overexpression of at least two of the investigated EPHs (HR = 14.7, p = 0.03) also proved to be an independent poor prognostic factor. In conclusion, our results implicate these specific members of the EPHA group as potential biomarkers for disease prognosis as well as possible targets for the development of novel therapeutic interventions.
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Affiliation(s)
- Alexandros Pergaris
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, Bld. 10, Goudi, 11527 Athens, Greece; (A.P.); (E.D.); (G.L.); (P.K.); (N.K.)
| | - Eugene Danas
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, Bld. 10, Goudi, 11527 Athens, Greece; (A.P.); (E.D.); (G.L.); (P.K.); (N.K.)
| | - Pawel Gajdzis
- Department of Clinical and Experimental Pathology, Division of Clinical Pathology, Wroclaw Medical
University, 50-556 Wroclaw, Poland; (P.G.); (P.D.)
| | - Georgia Levidou
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, Bld. 10, Goudi, 11527 Athens, Greece; (A.P.); (E.D.); (G.L.); (P.K.); (N.K.)
- Department of Pathology, Paracelsus Medical University, 90419 Nuremberg, Germany
| | - Malgorzata Gajdzis
- Department of Ophthalmology, Wroclaw Medical University, 50-556 Wroclaw, Poland;
| | - Nathalie Cassoux
- Department of Ophthalmology, Institut Curie, 75005 Paris, France;
| | - Sophie Gardrat
- Department of Biopathology, Institut Curie, PSL Research University, 75005 Paris, France;
| | - Piotr Donizy
- Department of Clinical and Experimental Pathology, Division of Clinical Pathology, Wroclaw Medical
University, 50-556 Wroclaw, Poland; (P.G.); (P.D.)
| | - Penelope Korkolopoulou
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, Bld. 10, Goudi, 11527 Athens, Greece; (A.P.); (E.D.); (G.L.); (P.K.); (N.K.)
| | - Nikolaos Kavantzas
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, Bld. 10, Goudi, 11527 Athens, Greece; (A.P.); (E.D.); (G.L.); (P.K.); (N.K.)
| | | | - Stamatios Theocharis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, Bld. 10, Goudi, 11527 Athens, Greece; (A.P.); (E.D.); (G.L.); (P.K.); (N.K.)
- Correspondence: ; Tel.: +30-210-746-2116; Fax: +30-210-746-2157
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Prognostic Biomarkers in Uveal Melanoma: The Status Quo, Recent Advances and Future Directions. Cancers (Basel) 2021; 14:cancers14010096. [PMID: 35008260 PMCID: PMC8749988 DOI: 10.3390/cancers14010096] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/15/2021] [Accepted: 12/23/2021] [Indexed: 01/18/2023] Open
Abstract
Simple Summary Although rare, uveal melanoma (UM) is the most common cancer that develops inside adult eyes. The prognosis is poor, since 50% of patients will develop lethal metastases in the first decade, especially to the liver. Once metastases are detected, life expectancy is limited, given that the available treatments are mostly unsuccessful. Thus, there is a need to find methods that can accurately predict UM prognosis and also effective therapeutic strategies to treat this cancer. In this manuscript, we initially compile the current knowledge on epidemiological, clinical, pathological and molecular features of UM. Then, we cover the most relevant prognostic factors currently used for the evaluation and follow-up of UM patients. Afterwards, we highlight emerging molecular markers in UM published over the last three years. Finally, we discuss the problems preventing meaningful advances in the treatment and prognostication of UM patients, as well as forecast new roadblocks and paths of UM-related research. Abstract Uveal melanoma (UM) is the most common malignant intraocular tumour in the adult population. It is a rare cancer with an incidence of nearly five cases per million inhabitants per year, which develops from the uncontrolled proliferation of melanocytes in the choroid (≈90%), ciliary body (≈6%) or iris (≈4%). Patients initially present either with symptoms like blurred vision or photopsia, or without symptoms, with the tumour being detected in routine eye exams. Over the course of the disease, metastases, which are initially dormant, develop in nearly 50% of patients, preferentially in the liver. Despite decades of intensive research, the only approach proven to mildly control disease spread are early treatments directed to ablate liver metastases, such as surgical excision or chemoembolization. However, most patients have a limited life expectancy once metastases are detected, since there are limited therapeutic approaches for the metastatic disease, including immunotherapy, which unlike in cutaneous melanoma, has been mostly ineffective for UM patients. Therefore, in order to offer the best care possible to these patients, there is an urgent need to find robust models that can accurately predict the prognosis of UM, as well as therapeutic strategies that effectively block and/or limit the spread of the metastatic disease. Here, we initially summarized the current knowledge about UM by compiling the most relevant epidemiological, clinical, pathological and molecular data. Then, we revisited the most important prognostic factors currently used for the evaluation and follow-up of primary UM cases. Afterwards, we addressed emerging prognostic biomarkers in UM, by comprehensively reviewing gene signatures, immunohistochemistry-based markers and proteomic markers resulting from research studies conducted over the past three years. Finally, we discussed the current hurdles in the field and anticipated the future challenges and novel avenues of research in UM.
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