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Beigi YZ, Lanjanian H, Fayazi R, Salimi M, Hoseyni BHM, Noroozizadeh MH, Masoudi-Nejad A. Heterogeneity and molecular landscape of melanoma: implications for targeted therapy. MOLECULAR BIOMEDICINE 2024; 5:17. [PMID: 38724687 PMCID: PMC11082128 DOI: 10.1186/s43556-024-00182-2] [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: 11/19/2023] [Accepted: 04/08/2024] [Indexed: 05/12/2024] Open
Abstract
Uveal cancer (UM) offers a complex molecular landscape characterized by substantial heterogeneity, both on the genetic and epigenetic levels. This heterogeneity plays a critical position in shaping the behavior and response to therapy for this uncommon ocular malignancy. Targeted treatments with gene-specific therapeutic molecules may prove useful in overcoming radiation resistance, however, the diverse molecular makeups of UM call for a patient-specific approach in therapy procedures. We need to understand the intricate molecular landscape of UM to develop targeted treatments customized to each patient's specific genetic mutations. One of the promising approaches is using liquid biopsies, such as circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA), for detecting and monitoring the disease at the early stages. These non-invasive methods can help us identify the most effective treatment strategies for each patient. Single-cellular is a brand-new analysis platform that gives treasured insights into diagnosis, prognosis, and remedy. The incorporation of this data with known clinical and genomics information will give a better understanding of the complicated molecular mechanisms that UM diseases exploit. In this review, we focused on the heterogeneity and molecular panorama of UM, and to achieve this goal, the authors conducted an exhaustive literature evaluation spanning 1998 to 2023, using keywords like "uveal melanoma, "heterogeneity". "Targeted therapies"," "CTCs," and "single-cellular analysis".
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Affiliation(s)
- Yasaman Zohrab Beigi
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Hossein Lanjanian
- Software Engineering Department, Engineering Faculty, Istanbul Topkapi University, Istanbul, Turkey
| | - Reyhane Fayazi
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Mahdieh Salimi
- Department of Medical Genetics, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Behnaz Haji Molla Hoseyni
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Ali Masoudi-Nejad
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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Kadamb R, Anton ML, Purwin TJ, Chua V, Seeneevassen L, Teh J, Angela Nieto M, Sato T, Terai M, Roman SR, De Koning L, Zheng D, Aplin AE, Aguirre-Ghiso J. Lineage commitment pathways epigenetically oppose oncogenic Gαq/11-YAP signaling in dormant disseminated uveal melanoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.05.583565. [PMID: 38496663 PMCID: PMC10942354 DOI: 10.1101/2024.03.05.583565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The mechanisms driving late relapse in uveal melanoma (UM) patients remains a medical mystery and major challenge. Clinically it is inferred that UM disseminated cancer cells (DCCs) persist asymptomatic for years-to-decades mainly in the liver before they manifest as symptomatic metastasis. Here we reveal using Gαq/11 mut /BAP wt human uveal melanoma models and human UM metastatic samples, that the neural crest lineage commitment nuclear receptor NR2F1 is a key regulator of spontaneous UM DCC dormancy in the liver. Using a quiescence reporter, RNA-seq and multiplex imaging we revealed that rare dormant UM DCCs upregulate NR2F1 expression and genes related to neural crest programs while repressing gene related to cell cycle progression. Gain and loss of function assays showed that NR2F1 silences YAP1/TEAD1 transcription downstream of Gαq/11 signaling and that NR2F1 expression can also be repressed by YAP1. YAP1 expression is repressed by NR2F1 binding to its promoter and changing the histone H3 tail activation marks to repress YAP1 transcription. In vivo CRISPR KO of NR2F1 led dormant UM DCCs to awaken and initiate relentless liver metastatic growth. Cut&Run and bulk RNA sequencing further confirmed that NR2F1 epigenetically stimulates neuron axon guidance and neural lineage programs, and it globally represses gene expression linked to G-protein signaling to drive dormancy. Pharmacological inhibition of Gαq/11 mut signaling resulted in NR2F1 upregulation and robust UM growth arrest, which was also achieved using a novel NR2F1 agonist. Our work sheds light on the molecular underpinnings of UM dormancy revealing that transcriptional programs driven by NR2F1 epigenetically short-circuit Gαq/11 signaling to its downstream target YAP1. Highlights Quiescent solitary uveal melanoma (UM) DCCs in the liver up- and down-regulate neural crest and cell cycle progression programs, respectively.NR2F1 drives solitary UM DCC dormancy by antagonizing the Gαq/11-YAP1 pathway; small molecule Gαq/11 inhibition restores NR2F1 expression and quiescence. NR2F1 short-circuits oncogenic YAP1 and G-protein signaling via a chromatin remodeling program. Loss of function of NR2F1 in dormant UM DCCs leads to aggressive liver metastasis. Graphical abstract
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Barbi M, Carvajal RD, Devoe CE. Updates in the Management of Uveal Melanoma. Cancer J 2024; 30:92-101. [PMID: 38527262 DOI: 10.1097/ppo.0000000000000708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
ABSTRACT Uveal melanoma (UM), arising from intraocular melanocytes, poses a complex clinical challenge with a substantial risk of distant metastasis, often to the liver. Molecular profiling, encompassing genetic, cytogenetic, gene expression, and immunological subsets, plays a pivotal role in determining prognoses. The evolving landscape includes promising systemic treatments, such as tebentafusp, a novel immune-modulating bispecific fusion protein, and targeted therapies. Combined regional and systemic approaches, including immune checkpoint inhibitors and innovative liver-directed therapy, are also under investigation. Although recent progress has improved outcomes, ongoing research aims to address the unique challenges of UM and develop effective therapies, particularly for HLA-A*02:01-negative patients who represent a significant unmet medical need. This review comprehensively discusses the molecular characteristics of UM, risk stratification methods, and the current and future spectrum of regional and systemic therapeutic modalities.
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Affiliation(s)
| | | | - Craig E Devoe
- From the Northwell Health Cancer Institute, New Hyde Park
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Ma S, Huis in't Veld RV, Hao Y, Gu Z, Rich C, Gelmi MC, Mulder AA, van Veelen PA, Vu TKH, van Hall T, Ossendorp FA, Jager MJ. Tumor Pigmentation Does Not Affect Light-Activated Belzupacap Sarotalocan Treatment but Influences Macrophage Polarization in a Murine Melanoma Model. Invest Ophthalmol Vis Sci 2024; 65:42. [PMID: 38271187 PMCID: PMC10829805 DOI: 10.1167/iovs.65.1.42] [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: 09/15/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024] Open
Abstract
Purpose Pigmentation in uveal melanoma is associated with increased malignancy and is known as a barrier for photodynamic therapy. We investigated the role of pigmentation in tumor behavior and the response to light-activated Belzupacap sarotalocan (Bel-sar) treatment in a pigmented (wild type) and nonpigmented (tyrosinase knock-out [TYR knock-out]) cell line in vitro and in a murine model. Methods The B16F10 (TYR knock-out) was developed using CRISPR/Cas9. After the treatment with light-activated Bel-sar, cytotoxicity and exposure of damage-associated molecular patterns (DAMPs) were measured by flow cytometry. Treated tumor cells were co-cultured with bone marrow-derived macrophages (BMDMs) and dendritic cells (DCs) to assess phagocytosis and activation. Both cell lines were injected subcutaneously in syngeneic C57BL/6 mice. Results Knock-out of the tyrosinase gene in B16F10 led to loss of pigmentation and immature melanosomes. Pigmented tumors contained more M1 and fewer M2 macrophages compared with amelanotic tumors. Bel-sar treatment induced near complete cell death, accompanied with enhanced exposure of DAMPs in both cell lines, resulting in enhanced phagocytosis of BMDMs and maturation of DCs. Bel-sar treatment induced a shift to M1 macrophages and delayed tumor growth in both in vivo tumor models. Following treatment, especially the pigmented tumors and their draining lymph nodes contained IFN-gamma positive CD8+T cells. Conclusions Pigmentation influenced the type of infiltrating macrophages in the tumor, with more M1 macrophages in pigmented tumors. Belzupacap sarotalocan treatment induced immunogenic cell death and tumor growth delay in pigmented as well as in nonpigmented models and stimulated M1 macrophage influx in both models.
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Affiliation(s)
- Sen Ma
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Ruben V. Huis in't Veld
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
- Department of Radiology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Yang Hao
- Department of Radiology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, China
| | - Zili Gu
- Department of Radiology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Cadmus Rich
- Aura Biosciences, Inc., Boston, Massachusetts, United States
| | - Maria Chiara Gelmi
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Aat A. Mulder
- Department of Electron Microscopy, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Peter A. van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - T. Khanh H. Vu
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Thorbald van Hall
- Department of Medical Oncology, Oncology Institute, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Ferry A. Ossendorp
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Martine J. Jager
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
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Pérez-Pérez M, Agostino A, de Sola-Llamas CG, Ruvolo M, Vilches-Arenas A, Relimpio-López MI, Espejo-Arjona F, Macías-García L, De Miguel-Rodríguez M, García-Escudero A, Idoate MA, Ríos-Martín JJ. Next-generation sequencing of uveal melanoma with clinical and histological correlations: Prognostic value of new mutations in the PI3K/AKT/mTOR pathway. Clin Exp Ophthalmol 2023; 51:822-834. [PMID: 37803816 DOI: 10.1111/ceo.14302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 09/10/2023] [Accepted: 09/19/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND Uveal melanoma (UM) is the eye's most common primary malignancy and there are no effective therapies for disseminated disease. It is important to try to know the patient's prognosis. The aim of this study was to reflect genetic variants, studied using NGS, of a series of 69 cases of UM and its correlation with histopathology and clinical progression. METHODS We performed targeted NGS using a 519-gene panel. RESULTS There were selected 28 different mutated genes, showing a total of 231 genetic variants that affected the function of the protein. The most common secondary mutations occurred in SF3B1 (in 26%), followed by BAP1 (in 23%), LRP1B (22%) and FGFR4 (20%). BAP1 mutation was associated with a greater likelihood of metastases and with greater presence of epithelioid cells. LRP1B was also associated with presence of epithelioid cells SF3B1 mutation was significantly associated with a spindle morphology. We found variants in the RAD51B, TOP2A, PTPRD, TSC2, DHX9, PDK1 and MTOR that have not been previously reported in consulted databases. The presence of a mutation in: CHEK2, DHX9 and PDK1 was associated with metastases. CONCLUSIONS BAP1 is the most solid biomarker of a poor prognosis in UM and mutations can be detected using NGS. SF3B1 is associated with the spindle cell subtype of UM, which gives it probably a favourable prognostic value. Our study suggests that mutations in DHX9 and PDK1 can have prognostic value. These potential biomarkers are related to the PI3K/AKT/mTOR pathway and makes them candidates for developing new directed therapies.
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Affiliation(s)
- Manuel Pérez-Pérez
- Department of Anatomic Pathology, Virgen Macarena University Hospital, Seville, Spain
| | - Alessandro Agostino
- Diagnostics and Genomics Division, Agilent Technologies Italia S.p.A. Cernusco sul Naviglio, Milan, Italy
| | | | - Michael Ruvolo
- Diagnostics and Genomics Division, Agilent Technologies, Inc., Santa Clara, California, USA
| | - Angel Vilches-Arenas
- Department of Preventive Medicine and Public Health, Faculty of Medicine, University of Seville, Seville, Spain
| | | | | | - Laura Macías-García
- Department of Normal and Pathological Histology and Cytology, Faculty of Medicine, University of Seville, Seville, Spain
| | - Manuel De Miguel-Rodríguez
- Department of Normal and Pathological Histology and Cytology, Faculty of Medicine, University of Seville, Seville, Spain
| | | | - Miguel A Idoate
- Department of Anatomic Pathology, Virgen Macarena University Hospital, Seville, Spain
- Department of Normal and Pathological Histology and Cytology, Faculty of Medicine, University of Seville, Seville, Spain
| | - Juan J Ríos-Martín
- Department of Anatomic Pathology, Virgen Macarena University Hospital, Seville, Spain
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Liu X, Yue H, Jiang S, Kong L, Xu Y, Chen Y, Wang C, Wang Y, Zhu X, Kong Y, Zhang X, Qian J, Luo Z. Clinical features and prognosis of patients with metastatic ocular and orbital melanoma: A bi-institutional study. Cancer Med 2023; 12:16163-16172. [PMID: 37409486 PMCID: PMC10469730 DOI: 10.1002/cam4.6273] [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: 11/09/2022] [Revised: 03/14/2023] [Accepted: 05/06/2023] [Indexed: 07/07/2023] Open
Abstract
PURPOSE Metastatic ocular and orbital melanomas are extremely rare. The clinical characteristics and standard treatments for these patients are not fully established. MATERIALS AND METHODS We retrospectively analyzed patients with metastatic ocular and orbital melanoma from Fudan University Shanghai Cancer Center and Eye & ENT Hospital of Fudan University between January 2012 and May 2022. RESULTS Overall, 51 patients with metastatic ocular and orbital melanoma were included. The most common primary sites were uvea (73%), followed by conjunctiva (22%), lacrimal sac (4%), and orbit (2%). Patients with uveal melanoma (UM) had a significantly younger age (48 vs. 68 years, p < 0.001), higher incidence of liver metastases (89% vs. 9%, p<0.001), a lower incidence of lymph nodes metastases (16% vs. 46%, p = 0.043) and a lower incidence of BRAF mutation (0% vs. 55%, p<0.001) compared with patients with conjunctival melanoma (CM). The overall response rate of the first-line treatment was 18%. Three of the four patients with BRAF-mutated CM responded to dabrafenib and trametinib treatment. The median progression-free survival (PFS) and overall survival (OS) of first-line treatment were 5.1 and 11.9 months, respectively. Among patients with liver metastases, liver-directed treatment was correlated with better patient PFS (p < 0.001) and OS (p < 0.001) after adjusting for number of metastatic sites and primary sites. CONCLUSION CM and UM have different characteristics. Patient with CM had a high incidence of BRAF mutation, and the treatment of BRAF and MEK inhibitors conferred clinical benefit. Liver directed therapies had a potential benefit in disease control in patients with liver metastases.
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Affiliation(s)
- Xin Liu
- Department of Head & Neck tumors and Neuroendocrine tumorsFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
| | - Han Yue
- Department of OphthalmologyEye & ENT Hospital of Fudan UniversityShanghaiChina
| | - Shiyu Jiang
- Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
- Department of LymphomaFudan University Shanghai Cancer CenterShanghaiChina
| | - Lin Kong
- Department of Radiation Oncology, Shanghai Proton and Heavy Ion CenterFudan University Cancer HospitalShanghaiChina
- Shanghai Key Laboratory of radiation oncologyShanghaiChina
- Shanghai Engineering Research Center of Proton and Heavy Ion Radiation TherapyShanghaiChina
| | - Yu Xu
- Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
- Department of Musculoskeletal OncologyFudan University Shanghai Cancer CenterShanghaiChina
| | - Yong Chen
- Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
- Department of Musculoskeletal OncologyFudan University Shanghai Cancer CenterShanghaiChina
| | - Chunmeng Wang
- Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
- Department of Musculoskeletal OncologyFudan University Shanghai Cancer CenterShanghaiChina
| | - Yan Wang
- Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
- Department of Radiation OncologyFudan University Shanghai Cancer CenterShanghaiChina
| | - Xiaoli Zhu
- Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
- Department of PathologyFudan University Shanghai Cancer CenterShanghaiChina
| | - Yunyi Kong
- Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
- Department of PathologyFudan University Shanghai Cancer CenterShanghaiChina
| | - Xiaowei Zhang
- Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
- Department of gastrointestinal medical oncologyFudan University Shanghai Cancer CenterShanghaiChina
| | - Jiang Qian
- Department of OphthalmologyEye & ENT Hospital of Fudan UniversityShanghaiChina
| | - Zhiguo Luo
- Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
- Department of gastrointestinal medical oncologyFudan University Shanghai Cancer CenterShanghaiChina
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7
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O'Day RF, McKelvie P, Cherepanoff S, McKay D. Trans-scleral uveal melanoma biopsy: can it be safely and accurately incorporated into a medium volume ocular oncology service? Int Ophthalmol 2023; 43:2139-2141. [PMID: 36864122 DOI: 10.1007/s10792-023-02647-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 02/19/2023] [Indexed: 03/04/2023]
Affiliation(s)
- Roderick F O'Day
- Centre for Eye Research Australia, 32 Gisborne Street, East Melbourne, Victoria, 3022, Australia.
- Ocular Oncology Clinic, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia.
| | - Penny McKelvie
- St Vincent's Hospital Melbourne, Fitzroy, Victoria, Australia
| | - Svetlana Cherepanoff
- Sydpath St Vincent's Hospital, Darlinghurst, NSW, Australia
- University of Notre Dame Australia, Darlinghurst, NSW, Australia
- St Vincent's Clinical School, University of NSW Sydney, Darlinghurst, NSW, Australia
| | - Daniel McKay
- Centre for Eye Research Australia, 32 Gisborne Street, East Melbourne, Victoria, 3022, Australia
- Ocular Oncology Clinic, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
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Rantala ES, Parrozzani R, Hernberg MM, Chiarion-Sileni V, Kivelä TT, Midena E. Determinants of Long-Term Survival in Metastatic Choroidal and Ciliary Body Melanoma. Am J Ophthalmol 2023; 246:258-272. [PMID: 36328199 DOI: 10.1016/j.ajo.2022.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/26/2022] [Accepted: 10/18/2022] [Indexed: 12/15/2022]
Abstract
PURPOSE To build and validate a prognostic model that predicts long-term overall survival (OS) in metastatic choroidal and ciliary body melanoma (CCBM) to facilitate patient counseling and planning, reporting, and interpreting clinical trials. DESIGN Retrospective cohort study with validation. METHODS We analyzed predictors of intermediate (IMT; 25-<42 months) and long-term (LT; ≥42 months) OS in a Finnish nationwide cohort of 330 patients with metastatic CCBM. Short-term (<25 months), IMT, and LT survival were compared with pairwise and ordinal logistic regression. A single-center cohort of 259 patients from Italy was used for validation. Models were compared with a deviance test. RESULTS Median OS was 12 and 17 months in the building and validation datasets, respectively; 40 (12%) and 31 (9%) compared with 44 (17%) and 32 (12%) patients were IMT and LT survivors, respectively. Alkaline phosphatase or lactate dehydrogenase level never exceeded 2 times the upper normal limit (UNL) in either LT cohort. Conditional to both being ≤2 times the UNL, distant metastasis-free interval (DMFI) >42 months (odds ratio [OR] 4.09-4.64; P < .001) paired with age <60 years (OR 3.23; P = .002), having no symptoms (OR 4.19; P = .005), and the largest diameter of the largest metastasis <30 mm (Tumor, Node, Metastasis stage M1a; OR 3.05; P = .001) independently predicted higher odds of surviving longer (IMT or LT) without model preference. These results were confirmed in the validation dataset. CONCLUSIONS Alkaline phosphatase or lactate dehydrogenase >2 times the UNL essentially precluded LT survival. The most robust predictor otherwise was DMFI >42 months, followed by age <60 years, absence of symptoms, and Tumor, Node, Metastasis stage M1a.
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Affiliation(s)
- Elina S Rantala
- From the Ocular Oncology Service (E.S.R., T.T.K.), Department of Ophthalmology.
| | | | - Micaela M Hernberg
- The Comprehensive Cancer Centre (M.M.H.), Department of Oncology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | | | - Tero T Kivelä
- From the Ocular Oncology Service (E.S.R., T.T.K.), Department of Ophthalmology
| | - Edoardo Midena
- Department of Ophthalmology (R.P., E.M.), University of Padova; IRCCS-Fondazione Bietti (E.M.), Rome, Italy
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Barbagallo C, Stella M, Broggi G, Russo A, Caltabiano R, Ragusa M. Genetics and RNA Regulation of Uveal Melanoma. Cancers (Basel) 2023; 15:775. [PMID: 36765733 PMCID: PMC9913768 DOI: 10.3390/cancers15030775] [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: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
Uveal melanoma (UM) is the most common intraocular malignant tumor and the most frequent melanoma not affecting the skin. While the rate of UM occurrence is relatively low, about 50% of patients develop metastasis, primarily to the liver, with lethal outcome despite medical treatment. Notwithstanding that UM etiopathogenesis is still under investigation, a set of known mutations and chromosomal aberrations are associated with its pathogenesis and have a relevant prognostic value. The most frequently mutated genes are BAP1, EIF1AX, GNA11, GNAQ, and SF3B1, with mutually exclusive mutations occurring in GNAQ and GNA11, and almost mutually exclusive ones in BAP1 and SF3B1, and BAP1 and EIF1AX. Among chromosomal aberrations, monosomy of chromosome 3 is the most frequent, followed by gain of chromosome 8q, and full or partial loss of chromosomes 1 and 6. In addition, epigenetic mechanisms regulated by non-coding RNAs (ncRNA), namely microRNAs and long non-coding RNAs, have also been investigated. Several papers investigating the role of ncRNAs in UM have reported that their dysregulated expression affects cancer-related processes in both in vitro and in vivo models. This review will summarize current findings about genetic mutations, chromosomal aberrations, and ncRNA dysregulation establishing UM biology.
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Affiliation(s)
- Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy
| | - Michele Stella
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy
| | - Giuseppe Broggi
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia—Section of Anatomic Pathology, University of Catania, 95123 Catania, Italy
| | - Andrea Russo
- Department of Ophthalmology, University of Catania, 95123 Catania, Italy
| | - Rosario Caltabiano
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia—Section of Anatomic Pathology, University of Catania, 95123 Catania, Italy
| | - Marco Ragusa
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy
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10
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Neoantigens: promising targets for cancer therapy. Signal Transduct Target Ther 2023; 8:9. [PMID: 36604431 PMCID: PMC9816309 DOI: 10.1038/s41392-022-01270-x] [Citation(s) in RCA: 145] [Impact Index Per Article: 145.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/14/2022] [Accepted: 11/27/2022] [Indexed: 01/07/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development and regulatory approval of tumor immunotherapies, including cancer vaccines, adoptive cell therapy and antibody-based therapies, especially for solid tumors. Neoantigens are newly formed antigens generated by tumor cells as a result of various tumor-specific alterations, such as genomic mutation, dysregulated RNA splicing, disordered post-translational modification, and integrated viral open reading frames. Neoantigens are recognized as non-self and trigger an immune response that is not subject to central and peripheral tolerance. The quick identification and prediction of tumor-specific neoantigens have been made possible by the advanced development of next-generation sequencing and bioinformatic technologies. Compared to tumor-associated antigens, the highly immunogenic and tumor-specific neoantigens provide emerging targets for personalized cancer immunotherapies, and serve as prospective predictors for tumor survival prognosis and immune checkpoint blockade responses. The development of cancer therapies will be aided by understanding the mechanism underlying neoantigen-induced anti-tumor immune response and by streamlining the process of neoantigen-based immunotherapies. This review provides an overview on the identification and characterization of neoantigens and outlines the clinical applications of prospective immunotherapeutic strategies based on neoantigens. We also explore their current status, inherent challenges, and clinical translation potential.
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Chalise P, Kwon D, Fridley BL, Mo Q. Statistical Methods for Integrative Clustering of Multi-omics Data. Methods Mol Biol 2023; 2629:73-93. [PMID: 36929074 PMCID: PMC10950392 DOI: 10.1007/978-1-0716-2986-4_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Cancers are heterogeneous diseases caused by accumulated mutations or abnormal alterations at multi-levels of biological processes including genomics, epigenomics, transcriptomics, and proteomics. There is a great clinical interest in identifying cancer molecular subtypes for disease prognosis and personalized medicine. Integrative clustering is a powerful unsupervised learning method that has been increasingly used to identify cancer molecular subtypes using multi-omics data including somatic mutations, DNA copy numbers, DNA methylation, and gene expression. Integrative clustering methods are generally classified into model-based or nonparametric approaches. In this chapter, we will give an overview of the frequently used model-based methods, including iCluster, iClusterPlus, and iClusterBayes, and the nonparametric method, integrative nonnegative matrix factorization (intNMF). We will use the integrative analyses of uveal melanoma and lower-grade glioma to illustrate these representative methods. Finally, we will discuss the strengths and limitations of these representative methods and give suggestions for performing integrative analyses of cancer multi-omics data in practice.
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Affiliation(s)
- Prabhakar Chalise
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, USA
| | - Deukwoo Kwon
- Department of Population Health Science & Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brooke L Fridley
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Qianxing Mo
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
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Switzer B, Piperno-Neumann S, Lyon J, Buchbinder E, Puzanov I. Evolving Management of Stage IV Melanoma. Am Soc Clin Oncol Educ Book 2023; 43:e397478. [PMID: 37141553 DOI: 10.1200/edbk_397478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Significant advancements have been made in the treatment of advanced melanoma with the use of immune checkpoint inhibitors, novel immunotherapies, and BRAF/MEK-targeted therapies with numerous frontline treatment options. However, there remains suboptimal evidence to guide treatment decisions in many patients. These include patients with newly diagnosed disease, immune checkpoint inhibitor (ICI)-resistant/ICI-refractory disease, CNS metastases, history of autoimmune disease, and/or immune-related adverse events (irAEs). Uveal melanoma (UM) is a rare melanoma associated with a poor prognosis in the metastatic setting. Systemic treatments, including checkpoint inhibitors, failed to demonstrate any survival benefit. Tebentafusp, a bispecific molecule, is the first treatment to improve overall survival (OS) in patients with HLA A*02:01-positive metastatic UM.
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Affiliation(s)
- Benjamin Switzer
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | | | - James Lyon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Igor Puzanov
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY
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13
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Lactate Rewrites the Metabolic Reprogramming of Uveal Melanoma Cells and Induces Quiescence Phenotype. Int J Mol Sci 2022; 24:ijms24010024. [PMID: 36613471 PMCID: PMC9820521 DOI: 10.3390/ijms24010024] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Uveal melanoma (UM), the most common primary intraocular cancer in adults, is among the tumors with poorer prognosis. Recently, the role of the oncometabolite lactate has become attractive due to its role as hydroxycarboxylic acid receptor 1 (HCAR1) activator, as an epigenetic modulator inducing lysine residues lactylation and, of course, as a glycolysis end-product, bridging the gap between glycolysis and oxidative phosphorylation. The aim of the present study was to dissect in UM cell line (92.1) the role of lactate as either a metabolite or a signaling molecule, using the known modulators of HCAR1 and of lactate transporters. Our results show that lactate (20 mM) resulted in a significant decrease in cell proliferation and migration, acting and switching cell metabolism toward oxidative phosphorylation. These results were coupled with increased euchromatin content and quiescence in UM cells. We further showed, in a clinical setting, that an increase in lactate transporters MCT4 and HCAR1 is associated with a spindle-shape histological type in UM. In conclusion, our results suggest that lactate metabolism may serve as a prognostic marker of UM progression and may be exploited as a potential therapeutic target.
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14
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Sen M, Card KR, Caudill GB, Spitofsky NR, Dockery PW, Zaloga AR, Zeiger JS, DeYoung CF, Hamou SJ, Shields CL. Relationship between Fitzpatrick Skin Type and The Cancer Genome Atlas Classification with Melanoma-Related Metastasis and Death in 854 Patients at a Single Ocular Oncology Center. Ophthalmic Genet 2022; 43:742-755. [PMID: 36369870 DOI: 10.1080/13816810.2022.2141799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
BACKGROUND The Fitzpatrick Skin Type (FST) is an objective method of classifying patients based on skin color and sunburn sensitivity. The Cancer Genome Atlas (TCGA) is a method of determining the prognosis of patients with uveal melanoma based on genetic composition of the tumor. There is no literature studying the relationship of FST and TCGA groups. MATERIALS AND METHODS Retrospective cohort study on 854 patients with uveal melanoma treated at a single tertiary ocular oncology center between April 2006 and June 2020, classified based on FST on a scale of I-VI and based on genetic analysis with TCGA classification on a scale of A, B, C, and D. Outcome measures included uveal melanoma-related metastasis and death per FST and TCGA group. RESULTS Patients classified as FST I (compared to FST II and III-V) had higher odds of being TCGA group D (OR 2.34, p = 0.002). Patients classified as FST III-V (compared to FST I and II) had higher odds of being TCGA group B (OR 2.26, p = 0.002). Kaplan-Meier survival analysis showed no difference in melanoma-related metastasis or death comparing FST I vs. II vs. III-V within each TCGA group at 5, 10, and 15 years. CONCLUSIONS Patients classified as FST I are more likely to have a higher grade melanoma on genetic testing whereas those classified as FST III-V show lower grade melanoma. Despite differences in tumor features and genetic profile with various FST, survival analysis at 5, 10, and 15 years revealed no difference in melanoma-related metastasis or death within each TCGA group per skin tone.
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Affiliation(s)
- Mrittika Sen
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, PA, USA
| | - Kevin R Card
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, PA, USA
| | - G Brandon Caudill
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, PA, USA
| | - Nina R Spitofsky
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, PA, USA
| | - Philip W Dockery
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, PA, USA
| | - Alexandra R Zaloga
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jennifer S Zeiger
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, PA, USA
| | - Charles F DeYoung
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, PA, USA
| | - Samara J Hamou
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, PA, USA
| | - Carol L Shields
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, PA, USA
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15
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Jiang Y, Wang J, Sun M, Zuo D, Wang H, Shen J, Jiang W, Mu H, Ma X, Yin F, Lin J, Wang C, Yu S, Jiang L, Lv G, Liu F, Xue L, Tian K, Wang G, Zhou Z, Lv Y, Wang Z, Zhang T, Xu J, Yang L, Zhao K, Sun W, Tang Y, Cai Z, Wang S, Hua Y. Multi-omics analysis identifies osteosarcoma subtypes with distinct prognosis indicating stratified treatment. Nat Commun 2022; 13:7207. [PMID: 36418292 PMCID: PMC9684515 DOI: 10.1038/s41467-022-34689-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 11/03/2022] [Indexed: 11/27/2022] Open
Abstract
Osteosarcoma (OS) is a primary malignant bone tumor that most commonly affects children, adolescents, and young adults. Here, we comprehensively analyze genomic, epigenomic and transcriptomic data from 121 OS patients. Somatic mutations are diverse within the cohort, and only TP53 is significantly mutated. Through unsupervised integrative clustering of the multi-omics data, we classify OS into four subtypes with distinct molecular features and clinical prognosis: (1) Immune activated (S-IA), (2) Immune suppressed (S-IS), (3) Homologous recombination deficiency dominant (S-HRD), and (4) MYC driven (S-MD). MYC amplification with HR proficiency tumors is identified with a high oxidative phosphorylation signature resulting in resistance to neoadjuvant chemotherapy. Potential therapeutic targets are identified for each subtype, including platinum-based chemotherapy, immune checkpoint inhibitors, anti-VEGFR, anti-MYC and PARPi-based synthetic lethal strategies. Our comprehensive integrated characterization provides a valuable resource that deepens our understanding of the disease, and may guide future clinical strategies for the precision treatment of OS.
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Affiliation(s)
- Yafei Jiang
- grid.16821.3c0000 0004 0368 8293Department of Orthopedic Oncology, Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080 PR China
| | - Jinzeng Wang
- grid.16821.3c0000 0004 0368 8293National Research Center for Translational Medicine (Shanghai), State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 PR China
| | - Mengxiong Sun
- grid.16821.3c0000 0004 0368 8293Department of Orthopedic Oncology, Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080 PR China
| | - Dongqing Zuo
- grid.16821.3c0000 0004 0368 8293Department of Orthopedic Oncology, Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080 PR China
| | - Hongsheng Wang
- grid.16821.3c0000 0004 0368 8293Department of Orthopedic Oncology, Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080 PR China
| | - Jiakang Shen
- grid.16821.3c0000 0004 0368 8293Department of Orthopedic Oncology, Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080 PR China
| | - Wenyan Jiang
- grid.16821.3c0000 0004 0368 8293Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, 200001 Shanghai, PR China
| | - Haoran Mu
- grid.16821.3c0000 0004 0368 8293Department of Orthopedic Oncology, Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080 PR China
| | - Xiaojun Ma
- grid.16821.3c0000 0004 0368 8293Department of Orthopedic Oncology, Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080 PR China
| | - Fei Yin
- grid.16821.3c0000 0004 0368 8293Department of Orthopedic Oncology, Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080 PR China
| | - Jun Lin
- grid.16821.3c0000 0004 0368 8293Department of Pathology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080 PR China
| | - Chongren Wang
- grid.16821.3c0000 0004 0368 8293Department of Orthopedic Oncology, Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080 PR China
| | - Shuting Yu
- grid.16821.3c0000 0004 0368 8293National Research Center for Translational Medicine (Shanghai), State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 PR China
| | - Lu Jiang
- grid.16821.3c0000 0004 0368 8293National Research Center for Translational Medicine (Shanghai), State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 PR China
| | - Gang Lv
- grid.16821.3c0000 0004 0368 8293National Research Center for Translational Medicine (Shanghai), State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 PR China
| | - Feng Liu
- grid.16821.3c0000 0004 0368 8293National Research Center for Translational Medicine (Shanghai), State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 PR China
| | - Linghang Xue
- grid.16821.3c0000 0004 0368 8293Department of Orthopedic Oncology, Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080 PR China
| | - Kai Tian
- grid.16821.3c0000 0004 0368 8293Department of Orthopedic Oncology, Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080 PR China
| | - Gangyang Wang
- grid.16821.3c0000 0004 0368 8293Department of Orthopedic Oncology, Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080 PR China
| | - Zifei Zhou
- grid.16821.3c0000 0004 0368 8293Department of Orthopedic Oncology, Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080 PR China
| | - Yu Lv
- grid.16821.3c0000 0004 0368 8293Department of Orthopedic Oncology, Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080 PR China
| | - Zhuoying Wang
- grid.16821.3c0000 0004 0368 8293Department of Orthopedic Oncology, Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080 PR China
| | - Tao Zhang
- grid.16821.3c0000 0004 0368 8293Department of Orthopedic Oncology, Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080 PR China
| | - Jing Xu
- grid.16821.3c0000 0004 0368 8293Department of Orthopedic Oncology, Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080 PR China
| | - Liu Yang
- grid.16821.3c0000 0004 0368 8293National Research Center for Translational Medicine (Shanghai), State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 PR China
| | - Kewen Zhao
- grid.16821.3c0000 0004 0368 8293Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, 200001 Shanghai, PR China
| | - Wei Sun
- grid.16821.3c0000 0004 0368 8293Department of Orthopedic Oncology, Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080 PR China
| | - Yujie Tang
- grid.16821.3c0000 0004 0368 8293Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, 200001 Shanghai, PR China
| | - Zhengdong Cai
- grid.16821.3c0000 0004 0368 8293Department of Orthopedic Oncology, Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080 PR China
| | - Shengyue Wang
- grid.16821.3c0000 0004 0368 8293National Research Center for Translational Medicine (Shanghai), State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 PR China
| | - Yingqi Hua
- grid.16821.3c0000 0004 0368 8293Department of Orthopedic Oncology, Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080 PR China
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16
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Cole YC, Zhang YZ, Gallo B, Januszewski AP, Nastase A, Essex DJ, Thaung CMH, Cohen VML, Sagoo MS, Bowcock AM. Correlation between BAP1 Localization, Driver Mutations, and Patient Survival in Uveal Melanoma. Cancers (Basel) 2022; 14:cancers14174105. [PMID: 36077643 PMCID: PMC9454448 DOI: 10.3390/cancers14174105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 12/02/2022] Open
Abstract
Uveal melanoma (UM) is an uncommon but highly aggressive ocular malignancy. Poor overall survival is associated with deleterious BAP1 alterations, which frequently occur with monosomy 3 (LOH3) and a characteristic gene expression profile. Tumor DNA from a cohort of 100 UM patients from Moorfields Biobank (UK) that had undergone enucleation were sequenced for known UM driver genes (BAP1, SF3B1, EIF1AX, GNAQ, and GNA11). Immunohistochemical staining of BAP1 and interphase FISH for chromosomes 3 and 8 was performed, and cellular localization of BAP1 was correlated with BAP1 mutations. Wildtype (WT) BAP1 staining was characterized by nBAP1 expression with <10% cytoplasmic BAP1 (cBAP1). Tumors exhibited heterogeneity with respect to BAP1 staining with different percentages of nBAP1 loss: ≥25% loss of nuclear BAP1 (nBAP1) was superior to chr8q and LOH3 as a prognostic indicator. Of the successfully sequenced UMs, 38% harbored oncogenic mutations in GNA11 and 48% harbored mutations in GNAQ at residues 209 or 183. Of the secondary drivers, 39% of mutations were in BAP1, 11% were in EIF1AX, and 20% were in the SF3B1 R625 hotspot. Most tumors with SF3B1 or EIF1AX mutations retained nuclear BAP1 (nBAP1). The majority of tumor samples with likely pathogenic BAP1 mutations, regardless of mutation class, displayed ≥25% loss of nBAP1. This included all tumors with truncating mutations and 80% of tumors with missense mutations. In addition, 60% of tumors with truncating mutations and 82% of tumors with missense mutations expressed >10% cBAP1.
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Affiliation(s)
- Yasemin C. Cole
- National Heart and Lung Institute, Imperial College London, London SW3 6LR, UK
| | - Yu-Zhi Zhang
- National Heart and Lung Institute, Imperial College London, London SW3 6LR, UK
- Department of Histopathology, Royal Brompton and Harefield NHS Foundation Trust, London SW3 6NP, UK
| | - Beatrice Gallo
- Ocular Oncology Service, Moorfields Eye Hospital & St. Bartholomew’s Hospital, London EC1V 2PD, UK
| | - Adam P. Januszewski
- National Heart and Lung Institute, Imperial College London, London SW3 6LR, UK
| | - Anca Nastase
- National Heart and Lung Institute, Imperial College London, London SW3 6LR, UK
| | - David J. Essex
- Ocular Oncology Service, Moorfields Eye Hospital & St. Bartholomew’s Hospital, London EC1V 2PD, UK
| | - Caroline M. H. Thaung
- Moorfields Eye Hospital, London EC1V 2PD, UK
- Department of Eye Pathology, UCL Institute of Ophthalmology, London EC1V 9EL, UK
| | - Victoria M. L. Cohen
- Ocular Oncology Service, Moorfields Eye Hospital & St. Bartholomew’s Hospital, London EC1V 2PD, UK
- Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Mandeep S. Sagoo
- Ocular Oncology Service, Moorfields Eye Hospital & St. Bartholomew’s Hospital, London EC1V 2PD, UK
- Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Anne M. Bowcock
- National Heart and Lung Institute, Imperial College London, London SW3 6LR, UK
- Departments of Oncological Sciences, Dermatology and Genetics & Genome Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Correspondence: ; Tel.: +1-212-659-8256
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17
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In uveal melanoma Gα-protein GNA11 mutations convey a shorter disease-specific survival and are more strongly associated with loss of BAP1 and chromosomal alterations than Gα-protein GNAQ mutations. Eur J Cancer 2022; 170:27-41. [DOI: 10.1016/j.ejca.2022.04.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/08/2022] [Accepted: 04/04/2022] [Indexed: 12/21/2022]
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18
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Leyvraz S, Konietschke F, Peuker C, Schütte M, Kessler T, Ochsenreither S, Ditzhaus M, Sprünken ED, Dörpholz G, Lamping M, Rieke DT, Klinghammer K, Burock S, Ulrich C, Poch G, Schäfer R, Klauschen F, Joussen A, Yaspo ML, Keilholz U. Biomarker-driven therapies for metastatic uveal melanoma: A prospective precision oncology feasibility study. Eur J Cancer 2022; 169:146-155. [DOI: 10.1016/j.ejca.2022.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 02/07/2023]
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19
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Sabat‐Pośpiech D, Fabian‐Kolpanowicz K, Kalirai H, Kipling N, Coupland SE, Coulson JM, Fielding AB. Aggressive uveal melanoma displays a high degree of centrosome amplification, opening the door to therapeutic intervention. J Pathol Clin Res 2022; 8:383-394. [PMID: 35474453 PMCID: PMC9161346 DOI: 10.1002/cjp2.272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/18/2022] [Accepted: 03/28/2022] [Indexed: 11/22/2022]
Abstract
Uveal melanoma (UM) is the most common intraocular cancer in adults. Whilst treatment of primary UM (PUM) is often successful, around 50% of patients develop metastatic disease with poor outcomes, linked to chromosome 3 loss (monosomy 3, M3). Advances in understanding UM cell biology may indicate new therapeutic options. We report that UM exhibits centrosome abnormalities, which in other cancers are associated with increased invasiveness and worse prognosis, but also represent a potential Achilles' heel for cancer-specific therapeutics. Analysis of 75 PUM patient samples revealed both higher centrosome numbers and an increase in centrosomes with enlarged pericentriolar matrix (PCM) compared to surrounding normal tissue, both indicative of centrosome amplification. The PCM phenotype was significantly associated with M3 (t-test, p < 0.01). Centrosomes naturally enlarge as cells approach mitosis; however, whilst UM with higher mitotic scores had enlarged PCM regardless of genetic status, the PCM phenotype remained significantly associated with M3 in UM with low mitotic scores (ANOVA, p = 0.021) suggesting that this is independent of proliferation. Phenotypic analysis of patient-derived cultures and established UM lines revealed comparable levels of centrosome amplification in PUM cells to archetypal triple-negative breast cancer cell lines, whilst metastatic UM (MUM) cell lines had even higher levels. Importantly, many UM cells also exhibit centrosome clustering, a common strategy employed by other cancer cells with centrosome amplification to survive cell division. As UM samples with M3 display centrosome abnormalities indicative of amplification, this phenotype may contribute to the development of MUM, suggesting that centrosome de-clustering drugs may provide a novel therapeutic approach.
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Affiliation(s)
- Dorota Sabat‐Pośpiech
- Molecular Physiology and Cell Signalling, Institute of Systems Molecular & Integrative BiologyUniversity of LiverpoolLiverpoolUK
- Molecular and Clinical Cancer Medicine, Institute of Systems Molecular & Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Kim Fabian‐Kolpanowicz
- Biomedical and Life Sciences, Faculty of Health and MedicineLancaster UniversityLancasterUK
| | - Helen Kalirai
- Molecular and Clinical Cancer Medicine, Institute of Systems Molecular & Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Natalie Kipling
- Molecular and Clinical Cancer Medicine, Institute of Systems Molecular & Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Sarah E Coupland
- Molecular and Clinical Cancer Medicine, Institute of Systems Molecular & Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Judy M Coulson
- Molecular Physiology and Cell Signalling, Institute of Systems Molecular & Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Andrew B Fielding
- Molecular Physiology and Cell Signalling, Institute of Systems Molecular & Integrative BiologyUniversity of LiverpoolLiverpoolUK
- Biomedical and Life Sciences, Faculty of Health and MedicineLancaster UniversityLancasterUK
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20
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Novel Treatments of Uveal Melanoma Identified with a Synthetic Lethal CRISPR/Cas9 Screen. Cancers (Basel) 2022; 14:cancers14133186. [PMID: 35804957 PMCID: PMC9264875 DOI: 10.3390/cancers14133186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 01/30/2023] Open
Abstract
Simple Summary We performed a CRISPR-Cas9 synthetic lethality screen in order to identify molecular targets whose inhibition would synergistically enhance the effect of everolimus in uveal melanoma cells. IGF1R and PRKDC, among others, were identified as hits. We verified these hits effects genetically: we treated the uveal melanoma cell lines depleted of PRKDC or IGF1R with everolimus and, in case of IGF1R, observed a synergistic effect. Additionally, we found synergistic growth inhibition with the inhibitors targeting DNA-PKcs or IGF1R in combination with everolimus. Moreover, we investigated the combination of targeted inhibitors of DNA-PKcs and IGF1R with everolimus on uveal melanoma in an in vivo model. The dual DNA-PKcs/mTOR inhibitor CC-115 demonstrated activity in vivo. Abstract Currently, no systemic treatment is approved as the standard of care for metastatic uveal melanoma (UM). mTOR has been evaluated as a drug target in UM. However, one of the main limitations is dose reduction due to adverse effects. The combination of everolimus with another targeted agent would allow the reduction of the dose of a single drug, thus widening the therapeutic window. In our study, we aimed to identify a synergistic combination with everolimus in order to develop a novel treatment option for metastatic UM. We exploited CRISPR-Cas9 synthetic lethality screening technology to search for an efficient combination. IGF1R and PRKDC and several other genes were identified as hits in the screen. We investigated the effect of the combination of everolimus with the inhibitors targeting IGF1R and DNA-PKcs on the survival of UM cell lines. These combinations synergistically slowed down cell growth but did not induce apoptosis in UM cell lines. These combinations were tested on PDX UM in an in vivo model, but we could not detect tumor regression. However, we could find significant activity of the dual DNA-PKcs/mTOR inhibitor CC-115 on PDX UM in the in vivo model.
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21
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GNAQ and GNA11 Genes: A Comprehensive Review on Oncogenesis, Prognosis and Therapeutic Opportunities in Uveal Melanoma. Cancers (Basel) 2022; 14:cancers14133066. [PMID: 35804836 PMCID: PMC9264989 DOI: 10.3390/cancers14133066] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 11/17/2022] Open
Abstract
The GNAQ and GNA11 genes are mutated in almost 80–90% of uveal melanomas in a mutually exclusive pattern. These genes encode the alpha subunits of the heterotrimeric G proteins, Gq and G11; thus, mutations of these genes result in the activation of several important signaling pathways, including phospholipase C, and activation of the transcription factor YAP. It is well known that both of them act as driver genes in the oncogenic process and it has been assumed that they do not play a role in the prognosis of these tumours. However, it has been hypothesised that mutations in these genes could give rise to molecularly and clinically distinct types of uveal melanomas. It has also been questioned whether the type and location of mutation in the GNAQ and GNA11 genes may affect the progression of these tumours. All of these questions, except for their implications in carcinogenesis, remain controversial. Uveal melanoma has a distinctive genetic profile, and specific recurrent mutations, which make it a potential candidate for treatment with targeted therapy. Given that the most frequent mutations are those observed in the GNAQ and GNA11 genes, and that both genes are involved in oncogenesis, these molecules, as well as the downstream signalling pathways in which they are involved, have been proposed as promising potential therapeutic targets. Therefore, in this review, special attention is paid to the current data related to the possible prognostic implications of both genes from different perspectives, as well as the therapeutic options targeting them.
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22
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Bendall ML, Francis JH, Shoushtari AN, Nixon DF. Specific human endogenous retroviruses predict metastatic potential in uveal melanoma. JCI Insight 2022; 7:e147172. [PMID: 35349481 PMCID: PMC9090245 DOI: 10.1172/jci.insight.147172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/23/2022] [Indexed: 11/17/2022] Open
Abstract
Uveal melanoma (UM) is a unique disease in that patients with primary UM are well stratified based on their risk of developing metastasis, yet there are limited effective treatments once metastases occur. There is an urgent need to better understand the distinct molecular pathogenesis of UM and the characteristics of patients at high risk for metastasis to identify neoantigenic targets that can be used in immunotherapy and to develop novel therapeutic strategies that may effectively target this lethal transition. An important and overlooked area of molecular pathogenesis and neoantigenic targets in UM comes from human endogenous retroviruses (HERVs). We investigated the HERV expression landscape in primary UM and found that tumors were stratified into 4 HERV-based subsets that provide clear delineation of risk outcome and support subtypes identified by other molecular indicators. Specific HERV loci are associated with the risk of uveal melanoma metastasis and may offer mechanistic insights into this process, including dysregulation of HERVs on chromosomes 3 and 8. A HERV signature composed of 17 loci was sufficient to classify tumors according to subtype with greater than 95% accuracy, including at least 1 intergenic HERV with coding potential (HERVE_Xp11.23) that could represent a potential HERV E target for immunotherapy.
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Affiliation(s)
- Matthew L. Bendall
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | | | - Alexander N. Shoushtari
- Melanoma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Douglas F. Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
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Steckler AM, Francis JH, Shoushtari AN, Abramson DH, Barker CA. Uveal melanoma metastatic at initial diagnosis: a case series. Melanoma Res 2022; 32:120-123. [PMID: 35152255 PMCID: PMC8901542 DOI: 10.1097/cmr.0000000000000807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Detectable metastasis at the time of initial diagnosis of uveal melanoma (UM) is rare. The purpose of this investigation was to evaluate the characteristics and outcomes in patients with metastatic UM (MUM) at initial diagnosis. An institutional review board-approved retrospective case series analysis was performed in 21 patients that presented for management of MUM at initial diagnosis. Patient, tumor and treatment parameters were recorded, and ophthalmic symptoms, metastasis response and overall survival were assessed. Among 21 patients, median tumor diameter was 18 mm (range, 9.1-35 mm), with 76% classified as a Collaborative Ocular Melanoma Study (COMS) large size. Sites of metastasis included liver (95%), bone (29%) and lung (29%), among others, and were confirmed by biopsy in 95% of patients studied. Symptomatic primary tumors were present in 81%, causing pain (24%) or vision loss (57%). Primary tumor therapy (PTT) was provided upfront for 52% of patients with enucleation (24%) and brachytherapy (29%). Eye pain developed 3-6 months after diagnosis in four of 10 patients who did not receive upfront PTT, whereas it did not occur in any of the 11 patients who received upfront PTT (P = 0.04). PTT palliated pain in all cases. The median overall survival was 11.9 months (range, 2.5-21.1 months). Patients presenting with MUM at initial diagnosis have high-risk tumors and experience survival like patients who develop metastases metachronously. PTT is not associated with survival but may mitigate ophthalmic symptoms, especially in patients with large tumors at risk for causing symptoms.
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Affiliation(s)
- Alexa M. Steckler
- Department of Radiation Oncology (Brachytherapy Service), Memorial Sloan Kettering Cancer Center
| | - Jasmine H. Francis
- Department of Surgery (Ophthalmic Oncology Service), Memorial Sloan Kettering Cancer Center
| | | | - David H. Abramson
- Department of Surgery (Ophthalmic Oncology Service), Memorial Sloan Kettering Cancer Center
| | - Christopher A. Barker
- Department of Radiation Oncology (Brachytherapy Service), Memorial Sloan Kettering Cancer Center
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24
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Genome-wide aberrant methylation in primary metastatic UM and their matched metastases. Sci Rep 2022; 12:42. [PMID: 34997020 PMCID: PMC8742000 DOI: 10.1038/s41598-021-03964-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/01/2021] [Indexed: 12/20/2022] Open
Abstract
Uveal melanoma (UM) is an aggressive intra-ocular cancer with a strong tendency to metastasize. Metastatic UM is associated with mutations in BAP1 and SF3B1, however only little is known about the epigenetic modifications that arise in metastatic UM. In this study we aim to unravel epigenetic changes contributing to UM metastasis using a new genome-wide methylation analysis technique that covers over 50% of all CpG’s. We identified aberrant methylation contributing to BAP1 and SF3B1-mediated UM metastasis. The methylation data was integrated with expression data and surveyed in matched UM metastases from the liver, skin and bone. UM metastases showed no commonly shared novel epigenetic modifications, implying that epigenetic changes contributing to metastatic spreading and colonization in distant tissues occur early in the development of UM and epigenetic changes that occur after metastasis are mainly patient-specific. Our findings reveal a plethora of epigenetic modifications in metastatic UM and its metastases, which could subsequently result in aberrant repression or activation of many tumor-related genes. This observation points towards additional layers of complexity at the level of gene expression regulation, which may explain the low mutational burden of UM.
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25
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Rantala ES, Hernberg MM, Piperno-Neumann S, Grossniklaus HE, Kivelä TT. Metastatic uveal melanoma: The final frontier. Prog Retin Eye Res 2022; 90:101041. [PMID: 34999237 DOI: 10.1016/j.preteyeres.2022.101041] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 12/31/2021] [Accepted: 01/03/2022] [Indexed: 12/11/2022]
Abstract
Treatment of primary intraocular uveal melanoma has developed considerably, its driver genes are largely unraveled, and the ways to assess its risk for metastases are very precise, being based on an international staging system and genetic data. Unfortunately, the risk of distant metastases, which emerge in approximately one half of all patients, is unaltered. Metastases are the leading single cause of death after uveal melanoma is diagnosed, yet no consensus exists regarding surveillance, staging, and treatment of disseminated disease, and survival has not improved until recently. The final frontier in conquering uveal melanoma lies in solving these issues to cure metastatic disease. Most studies on metastatic uveal melanoma are small, uncontrolled, retrospective, and do not report staging. Meta-analyses confirm a median overall survival of 10-13 months, and a cure rate that approaches nil, although survival exceeding 5 years is possible, estimated 2% either with first-line treatment or with best supportive care. Hepatic ultrasonography and magnetic resonance imaging as surveillance methods have a sensitivity of 95-100% and 83-100%, respectively, to detect metastases without radiation hazard according to prevailing evidence, but computed tomography is necessary for staging. No blood-based tests additional to liver function tests are generally accepted. Three validated staging systems predict, each in defined situations, overall survival after metastasis. Their essential components include measures of tumor burden, liver function, and performance status or metastasis free interval. Age and gender may additionally influence survival. Exceptional mutational events in metastases may make them susceptible to checkpoint inhibitors. In a large meta-analysis, surgical treatment was associated with 6 months longer median overall survival as compared to conventional chemotherapy and, recently, tebentafusp as first-line treatment at the first interim analysis of a randomized phase III trial likewise provided a 6 months longer median overall survival compared to investigator's choice, mostly pembrolizumab; these treatments currently apply to selected patients. Promoting dormancy of micrometastases, harmonizing surveillance protocols, promoting staging, identifying predictive factors, initiating controlled clinical trials, and standardizing reporting will be critical steppingstones in reaching the final frontier of curing metastatic uveal melanoma.
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Affiliation(s)
- Elina S Rantala
- Ocular Oncology Service, Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 4 C, PL 220, FI-00029, HUS, Helsinki, Finland.
| | - Micaela M Hernberg
- Comprehensive Cancer Center, Department of Oncology, Helsinki University Hospital and University of Helsinki, Paciuksenkatu 3, PL 180, FI-00029, HUS, Helsinki, Finland.
| | | | - Hans E Grossniklaus
- Section of Ocular Oncology, Emory Eye Center, 1365 Clifton Road B, Atlanta, GA, 30322, USA.
| | - Tero T Kivelä
- Ocular Oncology Service, Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 4 C, PL 220, FI-00029, HUS, Helsinki, Finland.
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26
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Optimisation of the Chicken Chorioallantoic Membrane Assay in Uveal Melanoma Research. Pharmaceutics 2021; 14:pharmaceutics14010013. [PMID: 35056909 PMCID: PMC8778438 DOI: 10.3390/pharmaceutics14010013] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/04/2021] [Accepted: 12/19/2021] [Indexed: 01/07/2023] Open
Abstract
The treatment of uveal melanoma and its metastases has not evolved sufficiently over the last decades in comparison to other tumour entities, posing a great challenge in the field of ocular oncology. Despite improvements in the conventional treatment regime and new discoveries about the genetic and molecular background of the primary tumour, effective treatment strategies to either prevent tumours or treat patients with advanced or metastatic disease are still lacking. New therapeutic options are necessary in order to achieve satisfactory local tumour control, reduce the risk of metastasis development, and preserve the eyeball and possibly the visual function of the eye. The development of in vivo model systems remains crucial for the identification and investigation of potential novel treatment modalities. The aim of this study was the optimisation of the chorioallantoic membrane (CAM) model for uveal melanoma research. We analysed the established CAM assay and its modification after the implantation of three-dimensional spheroids. The chorioallantoic membrane of a chick embryo was used to implant uveal melanoma-cell-line-derived spheroids in order to study their growth rate, angiogenic potential, and metastatic capability. Using the UM 92.1, UPMD2, UPMM3, and Mel270 cell lines, we were able to improve the viability of the embryos from 20% to >80% and to achieve up to a fourfold volume increase of the transplanted spheroid masses. The results point to the value of an optimised chicken embryo assay as an in vivo model for testing novel therapies for uveal melanoma by simplifying the research conditions and by contributing to a considerable reduction in animal experiments.
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Luo X, Ren C, Liu X, Zhang G, Huang S, Yu L, Li Y. [Screening of drugs that selectively inhibit uveal melanoma cells with SF3B1 mutations]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021; 41:1835-1842. [PMID: 35012916 DOI: 10.12122/j.issn.1673-4254.2021.12.12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVE To screen compounds that can selectively inhibit uveal melanoma cells with splicing factor 3B subunit 1 (SF3B1) mutations in comparison with isogenic SF3B1 wild-type counterparts in a cell model of SF3B1 mutant allele knockout. METHODS Principal component analysis was used to analyze transcriptome alternative splicing in TCGA cohorts of uveal melanoma with wild-type SF3B1 and SF3B1 mutations, and abnormal alternative splicing events derived from SF3B1 mutations were identified. The SF3B1 mutant allele in Mel202 cells was knocked out using CRISPR-Cas9 technology, and Sanger sequencing was used to verify the edited sequence. MTT and colony formation assays were used to assess the proliferation of Mel202 and Mut-KO cells. RT-PCR agarose electrophoresis combined with Sanger sequencing was used to determine alternative splicing events in Mel202 and Mut-KO cells. MTT assay was performed to screen the compounds that showed selective inhibitory effect against Mel202 cells with SF3B1 mutation. RESULTS Specific knockout of SF3B1 mutant allele in Mel202 cells obviously promoted the cell proliferation and caused changes in alternative splicing of ZDHHC16 and DYNLL1 transcripts. The screening data showed that 13 compounds had selective inhibitory activity against Mel202 cells with SF3B1 mutation (Fold change≥2), and among them, tetrandrine and lapatinib showed good dose-effect curves. CONCLUSION This study provides a cell screening model for identification of potential individualized treatment drugs for patients with uveal melanoma with SF3B1 mutation.
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Affiliation(s)
- X Luo
- Department of Pharmacy, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - C Ren
- College of Medical Information Engineering, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - X Liu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - G Zhang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - S Huang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - L Yu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Y Li
- Department of Pharmacy, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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Mo Q, Wan L, Schell MJ, Jim H, Tworoger SS, Peng G. Integrative Analysis Identifies Multi-Omics Signatures That Drive Molecular Classification of Uveal Melanoma. Cancers (Basel) 2021; 13:6168. [PMID: 34944787 PMCID: PMC8699355 DOI: 10.3390/cancers13246168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/21/2021] [Accepted: 12/01/2021] [Indexed: 01/21/2023] Open
Abstract
By iCluster analysis, we found that the integrative molecular classification of the UM was primarily driven by DNA copy number variation on chromosomes 3, 6 and 8, differential methylation and expression of genes involved in the immune system, cell morphogenesis, movement and migration, and differential mutation of genes including GNA11, BAP1, EIF1AX, SF3B1 and GNAQ. Integrative analysis revealed that pathways including IL6/JAK/STAT3 signaling, angiogenesis, allograft rejection, inflammatory response and interferon gamma response were hypomethylated and up-regulated in the M3 iSubtype, which was associated with a worse overall survival, compared to the D3 iSubtype. Using two independent gene expression datasets, we demonstrated that the subtype-driving genes had an excellent prognostic power in classifying UM into high- or low-risk groups for metastasis. Integrative analysis of UM multi-omics data provided a comprehensive view of UM biology for understanding the underlying mechanism leading to UM metastasis. The concordant molecular alterations at multi-omics levels revealed by our integrative analysis could be used for patient stratification towards personalized management and surveillance.
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Affiliation(s)
- Qianxing Mo
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA;
| | - Lixin Wan
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA;
| | - Michael J. Schell
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA;
| | - Heather Jim
- Department of Health Outcomes & Behavior, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA;
| | - Shelley S. Tworoger
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA;
| | - Guang Peng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
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Chai P, Jia R, Li Y, Zhou C, Gu X, Yang L, Shi H, Tian H, Lin H, Yu J, Zhuang A, Ge S, Jia R, Fan X. Regulation of epigenetic homeostasis in uveal melanoma and retinoblastoma. Prog Retin Eye Res 2021; 89:101030. [PMID: 34861419 DOI: 10.1016/j.preteyeres.2021.101030] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 12/13/2022]
Abstract
Uveal melanoma (UM) and retinoblastoma (RB), which cause blindness and even death, are the most frequently observed primary intraocular malignancies in adults and children, respectively. Epigenetic studies have shown that changes in the epigenome contribute to the rapid progression of both UM and RB following classic genetic changes. The loss of epigenetic homeostasis plays an important role in oncogenesis by disrupting the normal patterns of gene expression. The targetable nature of epigenetic modifications provides a unique opportunity to optimize treatment paradigms and establish new therapeutic options for both UM and RB with these aberrant epigenetic modifications. We aimed to review the research findings regarding relevant epigenetic changes in UM and RB. Herein, we 1) summarize the literature, with an emphasis on epigenetic alterations, including DNA methylation, histone modifications, RNA modifications, noncoding RNAs and an abnormal chromosomal architecture; 2) elaborate on the regulatory role of epigenetic modifications in biological processes during tumorigenesis; and 3) propose promising therapeutic candidates for epigenetic targets and update the list of epigenetic drugs for the treatment of UM and RB. In summary, we endeavour to depict the epigenetic landscape of primary intraocular malignancy tumorigenesis and provide potential epigenetic targets in the treatment of these tumours.
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Affiliation(s)
- Peiwei Chai
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Ruobing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Yongyun Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Chuandi Zhou
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Xiang Gu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Ludi Yang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Hanhan Shi
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Hao Tian
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Huimin Lin
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Jie Yu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Ai Zhuang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China.
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30
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Postpartum breast cancer has a distinct molecular profile that predicts poor outcomes. Nat Commun 2021; 12:6341. [PMID: 34732713 PMCID: PMC8566602 DOI: 10.1038/s41467-021-26505-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 10/06/2021] [Indexed: 12/21/2022] Open
Abstract
Young women's breast cancer (YWBC) has poor prognosis and known interactions with parity. Women diagnosed within 5-10 years of childbirth, defined as postpartum breast cancer (PPBC), have poorer prognosis compared to age, stage, and biologic subtype-matched nulliparous patients. Genomic differences that explain this poor prognosis remain unknown. In this study, using RNA expression data from clinically matched estrogen receptor positive (ER+) cases (n = 16), we observe that ER+ YWBC can be differentiated based on a postpartum or nulliparous diagnosis. The gene expression signatures of PPBC are consistent with increased cell cycle, T-cell activation and reduced estrogen receptor and TP53 signaling. When applied to a large YWBC cohort, these signatures for ER+ PPBC associate with significantly reduced 15-year survival rates in high compared to low expressing cases. Cumulatively these results provide evidence that PPBC is a unique entity within YWBC with poor prognostic phenotypes.
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Yavuzyigitoglu S, Tang MCY, Jansen M, Geul KW, Dwarkasing RS, Vaarwater J, Drabarek W, Verdijk RM, Paridaens D, Naus NC, Brosens E, de Klein A, Kilic E. Radiological Patterns of Uveal Melanoma Liver Metastases in Correlation to Genetic Status. Cancers (Basel) 2021; 13:cancers13215316. [PMID: 34771480 PMCID: PMC8582397 DOI: 10.3390/cancers13215316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 10/15/2021] [Indexed: 11/16/2022] Open
Abstract
This study reports the role played by the mutation status of Uveal Melanoma (UM) in relation to hepatic metastatic patterns as seen on imaging modalities. Radiological images were obtained from 123 patients treated at the Erasmus Medical Center Rotterdam or the Rotterdam Eye Hospital. Radiological images were derived from either computed tomography or magnetic resonance imaging. Hepatic metastatic patterns were classified by counting the number of metastases found in the liver. Miliary metastatic pattern (innumerable small metastases in the entire liver) was analyzed separately. Mutation status was determined in 85 patients. Median disease-free survival (DFS) and survival with metastases differed significantly between each of the metastatic patterns (respectively, p = 0.009, p < 0.001), both in favor of patients with less hepatic metastases. The mutation status of the primary tumor was not correlated with any hepatic tumor profiles (p = 0.296). Of the patients who had a solitary metastasis (n = 18), 11 originated from a primary BAP1-mutated tumors and one from a primary SF3B1-mutated tumor. Of the patients who had a miliary metastasis pattern (n = 24), 17 had a primary BAP1-mutated tumor and two had a primary SF3B1-mutated tumor. Chromosome 8p loss was significantly more in patients with more metastases (p = 0.045). Moreover, the primary UMs of patients with miliary metastases harbored more chromosome 8p and 1p loss, compared to patients with single solitary metastasis (p = 0.035 and p = 0.026, respectively). In conclusion, our study shows that there is an inverse correlation of the number of metastasis with the DFS and metastasized survival, indicating separate growth patterns. We also revealed that the number and type of metastases is irrelevant to the prognostic mutation status of the tumor, showing that both BAP1- and SF3B1-mutated UM can result in solitary and miliary metastases, indicating that other processes lay ground to the different metastatic patterns.
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Affiliation(s)
- Serdar Yavuzyigitoglu
- Department of Ophthalmology, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (S.Y.); (M.C.Y.T.); (M.J.); (J.V.); (W.D.); (D.P.); (N.C.N.)
- Department of Clinical Genetics, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (E.B.); (A.d.K.)
| | - Michael C. Y. Tang
- Department of Ophthalmology, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (S.Y.); (M.C.Y.T.); (M.J.); (J.V.); (W.D.); (D.P.); (N.C.N.)
| | - Miguel Jansen
- Department of Ophthalmology, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (S.Y.); (M.C.Y.T.); (M.J.); (J.V.); (W.D.); (D.P.); (N.C.N.)
| | - Kaspar W. Geul
- Department of Internal Medicine, Sint Franciscus Gasthuis Rotterdam, 3045 PM Rotterdam, The Netherlands;
| | - Roy S. Dwarkasing
- Department of Radiology, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands;
| | - Jolanda Vaarwater
- Department of Ophthalmology, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (S.Y.); (M.C.Y.T.); (M.J.); (J.V.); (W.D.); (D.P.); (N.C.N.)
- Department of Clinical Genetics, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (E.B.); (A.d.K.)
| | - Wojtek Drabarek
- Department of Ophthalmology, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (S.Y.); (M.C.Y.T.); (M.J.); (J.V.); (W.D.); (D.P.); (N.C.N.)
- Department of Clinical Genetics, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (E.B.); (A.d.K.)
| | - Robert M. Verdijk
- Department of Pathology, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands;
| | - Dion Paridaens
- Department of Ophthalmology, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (S.Y.); (M.C.Y.T.); (M.J.); (J.V.); (W.D.); (D.P.); (N.C.N.)
- The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands
| | - Nicole C. Naus
- Department of Ophthalmology, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (S.Y.); (M.C.Y.T.); (M.J.); (J.V.); (W.D.); (D.P.); (N.C.N.)
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (E.B.); (A.d.K.)
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (E.B.); (A.d.K.)
| | - Emine Kilic
- Department of Ophthalmology, Erasmus Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (S.Y.); (M.C.Y.T.); (M.J.); (J.V.); (W.D.); (D.P.); (N.C.N.)
- Correspondence:
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32
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Wang H, Yang X, Sun G, Yang Q, Cui C, Wang X, Ye H, Dai L, Shi J, Zhang J, Wang P. Identification and Evaluation of Autoantibody to a Novel Tumor-Associated Antigen GNA11 as a Biomarker in Esophageal Squamous Cell Carcinoma. Front Oncol 2021; 11:661043. [PMID: 34568004 PMCID: PMC8462091 DOI: 10.3389/fonc.2021.661043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022] Open
Abstract
The study aims to explore the diagnostic value of anti-GNA11 autoantibody in esophageal squamous cell carcinoma (ESCC) from multiple levels. Autoantibody against GNA11 with the highest diagnostic performance was screened out from the customized protein microarray. A total of 486 subjects including ESCC patients and matched normal controls were recruited in the verification and validation phases by using enzyme-linked immunosorbent assay (ELISA). Western blotting analysis was used to verify the ELISA results. Immunohistochemistry (IHC) was used to evaluate GNA11 expression in ESCC tissues and para-tumor tissues. In addition, a bioinformatics approach was adopted to investigate the mRNA expression of GNA11 in ESCC. Results indicated that the level of anti-GNA11 autoantibody in ESCC patients was significantly higher than that in the normal controls, and it can be used to distinguish ESCC patients from normal individuals in clinical subgroups (p < 0.05), as revealed by both ELISA and Western blotting. The receiver operating characteristic (ROC) curve analysis showed that anti-GNA11 autoantibody could distinguish ESCC patients from normal controls with an area under the ROC curve (AUC) of 0.653, sensitivity of 10.96%, and specificity of 98.63% in the verification cohort and with an AUC of 0.751, sensitivity of 38.24%, and specificity of 88.82% in the validation cohort. IHC manifested that the expression of GNA11 can differentiate ESCC tissues with para-tumor tissues (p < 0.05), but it cannot be used to differentiate different pathological grades and clinical stages (p > 0.05). The mRNA expression of GNA11 in ESCC patients and normal controls was different with a bioinformatics mining with The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) data in Gene Expression Profiling Interactive Analysis (GEPIA). In summary, anti-GNA11 autoantibody has the potential to be a new serological marker in the diagnosis of ESCC.
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Affiliation(s)
- Huimin Wang
- Henan Institute of Medical and Pharmaceutical Sciences in Academy of Medical Science, Zhengzhou University, Zhengzhou, China.,School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China.,College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xiaoang Yang
- Henan Institute of Medical and Pharmaceutical Sciences in Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Guiying Sun
- Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China.,College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Qian Yang
- Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China.,College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Chi Cui
- Henan Institute of Medical and Pharmaceutical Sciences in Academy of Medical Science, Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China
| | - Xiao Wang
- Henan Institute of Medical and Pharmaceutical Sciences in Academy of Medical Science, Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China
| | - Hua Ye
- Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China.,College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences in Academy of Medical Science, Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China
| | - Jianxiang Shi
- Henan Institute of Medical and Pharmaceutical Sciences in Academy of Medical Science, Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China
| | - Jianying Zhang
- Henan Institute of Medical and Pharmaceutical Sciences in Academy of Medical Science, Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China
| | - Peng Wang
- Henan Institute of Medical and Pharmaceutical Sciences in Academy of Medical Science, Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China.,College of Public Health, Zhengzhou University, Zhengzhou, China
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Busso-Lopes AF, Carnielli CM, Winck FV, Patroni FMDS, Oliveira AK, Granato DC, E Costa RAP, Domingues RR, Pauletti BA, Riaño-Pachón DM, Aricetti J, Caldana C, Graner E, Coletta RD, Dryden K, Fox JW, Paes Leme AF. A Reductionist Approach Using Primary and Metastatic Cell-Derived Extracellular Vesicles Reveals Hub Proteins Associated with Oral Cancer Prognosis. Mol Cell Proteomics 2021; 20:100118. [PMID: 34186243 PMCID: PMC8350068 DOI: 10.1016/j.mcpro.2021.100118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/28/2021] [Accepted: 06/20/2021] [Indexed: 12/12/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) has high mortality rates that are largely associated with lymph node metastasis. However, the molecular mechanisms that drive OSCC metastasis are unknown. Extracellular vesicles (EVs) are membrane-bound particles that play a role in intercellular communication and impact cancer development and progression. Thus, profiling EVs would be of great significance to decipher their role in OSCC metastasis. For that purpose, we used a reductionist approach to map the proteomic, miRNA, metabolomic, and lipidomic profiles of EVs derived from human primary tumor (SCC-9) cells and matched lymph node metastatic (LN1) cells. Distinct omics profiles were associated with the metastatic phenotype, including 670 proteins, 217 miRNAs, 26 metabolites, and 63 lipids differentially abundant between LN1 cell– and SCC-9 cell–derived EVs. A multi-omics integration identified 11 ‘hub proteins’ significantly decreased at the metastatic site compared with primary tumor–derived EVs. We confirmed the validity of these findings with analysis of data from multiple public databases and found that low abundance of seven ‘hub proteins’ in EVs from metastatic lymph nodes (ALDH7A1, CAD, CANT1, GOT1, MTHFD1, PYGB, and SARS) is correlated with reduced survival and tumor aggressiveness in patients with cancer. In summary, this multi-omics approach identified proteins transported by EVs that are associated with metastasis and which may potentially serve as prognostic markers in OSCC. Proteomic, miRNA, metabolomic, and lipidomic profiles were mapped in oral cancer EVs. The molecular profile of EVs was associated with the lymph node metastatic phenotype. A multi-omics integrative analysis revealed 11 highly connected ‘hub proteins.’ ‘Hub proteins’ from EVs are candidates as prognostic markers in oral cancer.
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Affiliation(s)
- Ariane Fidelis Busso-Lopes
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Carolina Moretto Carnielli
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Flavia Vischi Winck
- Laboratório de Biologia de Sistemas Regulatórios, Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Fábio Malta de Sá Patroni
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Ana Karina Oliveira
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Daniela Campos Granato
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Rute Alves Pereira E Costa
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Romênia Ramos Domingues
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Bianca Alves Pauletti
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Diego Mauricio Riaño-Pachón
- Laboratório de Biologia de Sistemas Regulatórios, Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Juliana Aricetti
- Laboratório Nacional de Biorrenováveis - LNBR, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Camila Caldana
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | - Edgard Graner
- Departamento de Diagnóstico Oral, Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, Piracicaba, SP, Brazil
| | - Ricardo Della Coletta
- Departamento de Diagnóstico Oral, Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, Piracicaba, SP, Brazil
| | - Kelly Dryden
- Molecular Electron Microscopy Core, University of Virginia, Charlottesville, Virginia, USA
| | - Jay William Fox
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Adriana Franco Paes Leme
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil.
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Luo X, Xu Y, Li Y, Zhang G, Huang S, Liu X, Ren Z, Liu S, Yu L. BAP1 deletion abrogates growth and metastasis of murine cutaneous melanoma. Melanoma Res 2021; 31:119-129. [PMID: 33347048 DOI: 10.1097/cmr.0000000000000714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Although germline mutations in BRCA-associated protein-1 (BAP1) predispose to cutaneous melanoma (CM), BAP1 is rarely mutated in primary CM outside the familial context. The role of BAP1 in the pathogenesis of CM remains obscure. Here, we discovered an unexpected role of BAP1 in suppressing CM growth and metastasis. BAP1 deletion by CRISPR-Cas9 system severely compromises colony-forming capability of murine CM cell line B16-F10 and human CM cell lines, SK-MEL-28 and A375. Furthermore, BAP1 loss abrogates tumor growth and lung metastasis in murine syngeneic tumor models. Deletion of BAP1 in B16-F10 cells leads to preferential downregulation of genes accompanied with increased H2A ubiquitination at lysine 119. Transcriptomic characterization of BAP1 deletion reveals multiple deregulated cellular functions including extracellular matrix-receptor interaction and MAPK signaling pathway which may contribute to BAP1's effect on metastasis and proliferation. Our findings indicate that BAP1 could be a potential therapeutic target for CM.
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Affiliation(s)
- Xin Luo
- School of Pharmaceutical Sciences, Southern Medical University
- Department of Pharmacy, Nanfang Hospital, Southern Medical University
| | - Yuyan Xu
- School of Pharmaceutical Sciences, Southern Medical University
- Department of Pharmacy, Nanfang Hospital, Southern Medical University
| | - Yilei Li
- Department of Pharmacy, Nanfang Hospital, Southern Medical University
| | - Guiming Zhang
- School of Pharmaceutical Sciences, Southern Medical University
| | - Sisi Huang
- School of Pharmaceutical Sciences, Southern Medical University
| | - Xiaolian Liu
- School of Pharmaceutical Sciences, Southern Medical University
| | - Zhonglu Ren
- College of Medical Information Engineering, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Shuwen Liu
- School of Pharmaceutical Sciences, Southern Medical University
| | - Le Yu
- School of Pharmaceutical Sciences, Southern Medical University
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Yang H, Chen R, Li D, Wang Z. Subtype-GAN: a deep learning approach for integrative cancer subtyping of multi-omics data. Bioinformatics 2021; 37:2231-2237. [PMID: 33599254 DOI: 10.1093/bioinformatics/btab109] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 02/04/2021] [Accepted: 02/16/2021] [Indexed: 12/14/2022] Open
Abstract
MOTIVATION The discovery of cancer subtyping can help explore cancer pathogenesis, determine clinical actionability in treatment, and improve patients' survival rates. However, due to the diversity and complexity of multi-omics data, it is still challenging to develop integrated clustering algorithms for tumor molecular subtyping. RESULTS We propose Subtype-GAN, a deep adversarial learning approach based on the multiple-input multiple-output neural network to model the complex omics data accurately. With the latent variables extracted from the neural network, Subtype-GAN uses consensus clustering and the Gaussian Mixture model to identify tumor samples' molecular subtypes. Compared with other state-of-the-art subtyping approaches, Subtype-GAN achieved outstanding performance on the benchmark data sets consisting of ∼4,000 TCGA tumors from 10 types of cancer. We found that on the comparison data set, the clustering scheme of Subtype-GAN is not always similar to that of the deep learning method AE but is identical to that of NEMO, MCCA, VAE, and other excellent approaches. Finally, we applied Subtype-GAN to the BRCA data set and automatically obtained the number of subtypes and the subtype labels of 1031 BRCA tumors. Through the detailed analysis, we found that the identified subtypes are clinically meaningful and show distinct patterns in the feature space, demonstrating the practicality of Subtype-GAN. AVAILABILITY The source codes, the clustering results of Subtype-GAN across the benchmark data sets are available at https://github.com/haiyang1986/Subtype-GAN. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hai Yang
- Department of Computer Science and Engineering, East China University of Science and Technology, Shanghai 200237, PR China
| | - Rui Chen
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America.,Vanderbilt Genetics Institute, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Dongdong Li
- Department of Computer Science and Engineering, East China University of Science and Technology, Shanghai 200237, PR China
| | - Zhe Wang
- Department of Computer Science and Engineering, East China University of Science and Technology, Shanghai 200237, PR China
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Zhang Q, Lin ZN, Chen J, Zheng WX. A multi-omics study on cutaneous and uveal melanoma. Int J Ophthalmol 2021; 14:32-41. [PMID: 33469481 DOI: 10.18240/ijo.2021.01.05] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 09/15/2020] [Indexed: 12/20/2022] Open
Abstract
AIM To present the multi-omics landscape of cutaneous melanoma (CM) and uveal melanoma (UM) from The Cancer Genome Atlas (TCGA). METHODS The differentially expressed genes (DEGs) between CM and UM were found and integrated into a gene ontology enrichment analysis. Besides, the differentially expressed miRNAs were also identified. We also compared the methylation level of CM with UM and identified the differentially methylated regions to integrate with the DEGs to display the relationship between the gene expression and DNA methylation. The differentially expressed transcription factors (TFs) were identified. RESULTS Though CM had more mutational burden than UM, they shared several similarities such as the same rankings in diverse variant types. Except GNAQ and GNA11, the other top 18 mutated genes of the combined group were mostly detected in CM instead of UM. On the transcriptomic level, 4610 DEGs were found and integrated into a gene ontology enrichment analysis. We also identified 485 differentially expressed miRNAs. The methylation analysis showed that UM had a significantly higher methylation level than CM. The integration of differentially methylated regions and DEGs demonstrated that most DEGs were downregulated in UM and the hypo- and hypermethylation presented no obvious difference within these DEGs. Finally, 116 hypermethylated TFs and 114 hypomethylated TFs were identified as differentially expressed TFs in CM when compared with UM. CONCLUSION This multi-omics study on comparing CM with UM confirms that they differ in all analyzed levels. Of notice, the results also offer new insights with implications for elucidating certain unclear problems such as the distinct role of epithelial mesenchymal transition in two melanomas, the different metastatic routes of CM and UM and the liver tropism of metastatic UM.
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Affiliation(s)
- Qi Zhang
- Institute of Pathology and Neuropathology, University of Tuebingen, Tuebingen 72076, Germany
| | - Ze-Nan Lin
- University Eye Hospital, Center for Ophthalmology, University of Tuebingen, Tuebingen 72076, Germany
| | - Jie Chen
- Department of Ophthalmology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Wen-Xu Zheng
- Department of Ophthalmology, the Second Hospital Affiliated to Jilin University, Jilin University, Changchun 130041, Jilin Province, China
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Genomic and transcriptomic landscape of conjunctival melanoma. PLoS Genet 2020; 16:e1009201. [PMID: 33383577 PMCID: PMC7775126 DOI: 10.1371/journal.pgen.1009201] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 10/14/2020] [Indexed: 02/07/2023] Open
Abstract
Conjunctival melanoma (CJM) is a rare but potentially lethal and highly-recurrent cancer of the eye. Similar to cutaneous melanoma (CM), it originates from melanocytes. Unlike CM, however, CJM is relatively poorly characterized from a genomic point of view. To fill this knowledge gap and gain insight into the genomic nature of CJM, we performed whole-exome (WES) or whole-genome sequencing (WGS) of tumor-normal tissue pairs in 14 affected individuals, as well as RNA sequencing in a subset of 11 tumor tissues. Our results show that, similarly to CM, CJM is also characterized by a very high mutation load, composed of approximately 500 somatic mutations in exonic regions. This, as well as the presence of a UV light-induced mutational signature, are clear signs of the role of sunlight in CJM tumorigenesis. In addition, the genomic classification of CM proposed by TCGA seems to be well-applicable to CJM, with the presence of four typical subclasses defined on the basis of the most frequently mutated genes: BRAF, NF1, RAS, and triple wild-type. In line with these results, transcriptomic analyses revealed similarities with CM as well, namely the presence of a transcriptomic subtype enriched for immune genes and a subtype enriched for genes associated with keratins and epithelial functions. Finally, in seven tumors we detected somatic mutations in ACSS3, a possible new candidate oncogene. Transfected conjunctival melanoma cells overexpressing mutant ACSS3 showed higher proliferative activity, supporting the direct involvement of this gene in the tumorigenesis of CJM. Altogether, our results provide the first unbiased and complete genomic and transcriptomic classification of CJM. Conjunctival melanoma is an extremely rare form of cancer of the eye that arises from melanocytes–the cells producing the protective pigment melanin–in the outmost layer of the eye: the conjunctiva. This tissue, similarly to the skin, can also be exposed to UV light radiation from the sun. We investigated the genetic background of this rare form of cancer in samples from fourteen patients, by global DNA and RNA sequencing. Our results showed that conjunctival melanoma is genetically very similar to cutaneous melanoma. More precisely, in tumor DNA we detected signs of damage caused by UV light, as well as mutations in the genes BRAF, NF1 and NRAS/HRAS, previously described to be involved in cutaneous melanoma. Analysis of tumor gene expression also revealed similarities between these two types of cancer, some of which could be used as prognostic factors or as indicators of a patients’ response to therapy. In addition, we identified frequent somatic mutations in ACSS3, a gene not yet associated with either conjunctival or cutaneous melanoma, which represents a potential key player in oncogenesis of conjunctival melanoma.
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Ness C, Katta K, Garred Ø, Kumar T, Olstad OK, Petrovski G, Moe MC, Noer A. Integrated differential DNA methylation and gene expression of formalin-fixed paraffin-embedded uveal melanoma specimens identifies genes associated with early metastasis and poor prognosis. Exp Eye Res 2020; 203:108426. [PMID: 33387485 DOI: 10.1016/j.exer.2020.108426] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 12/09/2020] [Accepted: 12/22/2020] [Indexed: 12/23/2022]
Abstract
PURPOSE Uveal melanoma (UM) is an aggressive malignancy, in which nearly 50% of the patients die from metastatic disease. Aberrant DNA methylation is recognized as an important epigenomic event in carcinogenesis. Formalin-fixed paraffin-embedded (FFPE) samples represent a valuable source of tumor tissue, and recent technology has enabled the use of these samples in genome-wide DNA methylation analyses. Our aim was to investigate differential DNA methylation in relation to histopathological classification and survival data. In addition we sought to identify aberrant DNA methylation of genes that could be associated with metastatic disease and poor survival. METHODS FFPE samples from UM patients (n = 23) who underwent enucleation of the eye in the period 1976-1989 were included. DNA methylation was assessed using the Illumina Infinium HumanMethylation450 array and coupled to histopathological data, Cancer Registry of Norway- (registered UM metastasis) and Norwegian Cause of Death Registry- (time and cause of death) data. Differential DNA methylation patterns contrasting histological classification, survival data and clustering properties were investigated. Survival groups were defined as "Early metastasis" (metastases and death within 2-5 years after enucleation, n = 8), "Late metastasis" (metastases and death within 9-21 years after enucleation, n = 7) and "No metastasis" (no detected metastases ≥18 years after enucleation, n = 8). A subset of samples were selected based on preliminary multi-dimensional scaling (MDS) plots, histopathological classification, chromosome 3 status, survival status and clustering properties; "Subset Early metastasis" (n = 4) vs "Subset No metastasis" (n = 4). Bioinformatics analyses were conducted in the R statistical software. Differentially methylated positions (DMPs) and differentially methylated regions (DMRs) in various comparisons were assessed. Gene expression of relevant subgroups was determined by microarray analysis and quantitative reverse-transcription polymerase chain reaction (qRT-PCR). RESULTS DNA methylation analyses identified 2 clusters that separated the samples according to chromosome 3 status. Cluster 1 consisted of samples (n = 5) with chromosome 3 disomy (D3), while Cluster 2 was comprised of samples (n = 15) with chromosome 3 monosomy (M3). 1212 DMRs and 9386 DMPs were identified in M3 vs D3. No clear clusters were formed based on our predefined survival groups ("Early", "Late", "No") nor histopathological classification (Epithelioid, Mixed, Spindle). We identified significant changes in DNA methylation (beta FC ≥ 0.2, adjusted p < 0.05) between two sample subsets (n = 8). "Subset Early metastasis" (n = 4) vs "Subset No metastasis" (n = 4) identified 348 DMPs and 36 DMRs, and their differential gene expression by microarray showed that 14 DMPs and 2 DMRs corresponded to changes in gene expression (FC ≥ 1.5, p < 0.05). RNF13, ZNF217 and HYAL1 were hypermethylated and downregulated in "Subset Early metastasis" vs "Subset No metastasis" and could be potential tumor suppressors. TMEM200C, RGS10, ADAM12 and PAM were hypomethylated and upregulated in "Subset Early metastasis vs "Subset No metastasis" and could be potential oncogenes and thus markers of early metastasis and poor prognosis in UM. CONCLUSIONS DNA methylation profiling showed differential clustering of samples according to chromosome 3 status: Cluster 1 (D3) and Cluster 2 (M3). Integrated differential DNA methylation and gene expression of two subsets of samples identified genes associated with early metastasis and poor prognosis. RNF13, ZNF217 and HYAL1 are hypermethylated and candidate tumor suppressors, while TMEM200C, RGS10, ADAM12 and PAM are hypomethylated and candidate oncogenes linked to early metastasis. UM FFPE samples represent a valuable source for methylome studies and enable long-time follow-up.
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Affiliation(s)
- Charlotte Ness
- Center for Eye Research, Department of Ophthalmology, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Kirankumar Katta
- Center for Eye Research, Department of Ophthalmology, Oslo University Hospital, Oslo, Norway
| | - Øystein Garred
- Department of Pathology, Oslo University Hospital, Norway
| | - Theresa Kumar
- Department of Pathology, Oslo University Hospital, Norway
| | | | - Goran Petrovski
- Center for Eye Research, Department of Ophthalmology, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Morten C Moe
- Center for Eye Research, Department of Ophthalmology, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Agate Noer
- Center for Eye Research, Department of Ophthalmology, Oslo University Hospital, Oslo, Norway.
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LncRNA LINC00518 Acts as an Oncogene in Uveal Melanoma by Regulating an RNA-Based Network. Cancers (Basel) 2020; 12:cancers12123867. [PMID: 33371395 PMCID: PMC7767460 DOI: 10.3390/cancers12123867] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Uveal melanoma (UM) is the most frequent primary tumor of the eye in adults. Although molecular alterations on protein-coding genes have been associated with the development of UM, the role of non-coding RNAs and their competitive endogenous networks remain poorly investigated. Starting from a computational analysis on UM expression dataset deposited in The Cancer Genome Atlas, we identified the long non-coding RNA LINC00518 as a potential oncogene. We then experimentally evaluated LINC00518 and its supposed RNA signaling in human biopsies and in vitro functional assays. The results obtained suggest that LINC00518, under potential transcriptional control by MITF, regulates an RNA–RNA network promoting cancer-related processes (i.e., cell proliferation and migration). These findings open the way to the characterization of the unknown RNA signaling associated with UM and pave the way to the exploitation of a potential target for RNA-based therapeutics. Abstract Uveal melanoma (UM) is the most common primary intraocular malignant tumor in adults; little is known about the contribution of non-coding RNAs (ncRNAs) to UM pathogenesis. Competitive endogenous RNA (ceRNA) networks based on RNA–RNA interactions regulate physiological and pathological processes. Through a combined approach of in silico and experimental biology, we investigated the expression of a set of long non-coding RNAs (lncRNAs) in patient biopsies, identifying LINC00518 as a potential oncogene in UM. The detection of LINC00518 dysregulation associated with several in vitro functional assays allowed us to investigate its ceRNA regulatory network and shed light on its potential involvement in cancer-related processes, such as epithelial to mesenchymal transition (EMT) and CoCl2-induced hypoxia-like response. In vitro transient silencing of LINC00518 impaired cell proliferation and migration, and affected mRNA expression of LINGO2, NFIA, OTUD7B, SEC22C, and VAMP3. A “miRNA sponge” and “miRNA protector” model have been hypothesized for LINC00518-induced regulation of mRNAs. In vitro inhibition of MITF suggested its role as a potential activator of LINC00518 expression. Comprehensively, LINC00518 may be considered a new oncogene in UM and a potential target for RNA-based therapeutic approaches.
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Spliceosome Mutations in Uveal Melanoma. Int J Mol Sci 2020; 21:ijms21249546. [PMID: 33333932 PMCID: PMC7765440 DOI: 10.3390/ijms21249546] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 12/13/2022] Open
Abstract
Uveal melanoma (UM) is the most common primary intraocular malignancy of the eye. It has a high metastatic potential and mainly spreads to the liver. Genetics play a vital role in tumor classification and prognostication of UM metastatic disease. One of the driver genes mutated in metastasized UM is subunit 1 of splicing factor 3b (SF3B1), a component of the spliceosome complex. Recurrent mutations in components of the spliceosome complex are observed in UM and other malignancies, suggesting an important role in tumorigenesis. SF3B1 is the most common mutated spliceosome gene and in UM it is associated with late-onset metastasis. This review summarizes the genetic and epigenetic insights of spliceosome mutations in UM. They form a distinct subgroup of UM and have similarities with other spliceosome mutated malignancies.
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Rodrigues M, Ait Rais K, Salviat F, Algret N, Simaga F, Barnhill R, Gardrat S, Servois V, Mariani P, Piperno-Neumann S, Roman-Roman S, Delattre O, Cassoux N, Savignoni A, Stern MH, Pierron G. Association of Partial Chromosome 3 Deletion in Uveal Melanomas With Metastasis-Free Survival. JAMA Ophthalmol 2020; 138:182-188. [PMID: 31895446 DOI: 10.1001/jamaophthalmol.2019.5403] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Importance Studies on uveal melanomas (UMs) have demonstrated the prognostic value of 8q gain and monosomy 3, but the prognosis of UMs with partial deletion of chromosome 3 remains to be defined. Objective To examine the association of partial chromosome 3 deletion in UMs with metastasis-free survival. Design, Setting, and Participants This retrospective cohort study of 1088 consecutive comparative genomic hybridization arrays performed from May 1, 2006, to July 31, 2015, assessed patients presenting with UMs with and without partial loss of chromosome 3 at a referral center. Data analysis was performed from September 1, 2017, to November 30, 2017. Exposure Uveal melanoma with or without partial loss of chromosome 3. Main Outcomes and Measures Metastasis-free survival and overall survival at 60 months. Results Of the 1088 consecutive comparative genomic hybridization arrays that were performed, 43 UMs (4.0%) in 43 patients (median age, 58 years [range, 12-79 years]; 22 [51%] female) carried partial deletions of chromosome 3. Median follow-up was 66 months (range, 1.2-126.2 months). Metastasis-free survival at 60 months was 33.6% (95% CI, 15.8%-71.4%) for UMs that carried a deletion of the BAP1 (BRCA1 associated protein 1) locus (BAP1del; 24 tumors) and 80.5% (95% CI, 64.8%-100%) for UMs without the loss of the BAP1 locus (BAP1 normal [BAP1nl]; 19 tumors) (log-rank P = .001). Overall survival at 60 months was 64.5% (95% CI, 43.5%-95.8%) in the BAP1del group vs 84.1% (95% CI, 69.0%-100%) in the BAP1nl group (log-rank P < .001). In these 43 cases, metastasis-free survival at 60 months was 100% for UMs without loss of the BAP1 locus or 8q gain, 70.0% (95% CI, 50.5%-96.9%) for UMs that carried 1 of these alterations, and 12.5% (95% CI, 2.1%-73.7%) for those that carried both (log-rank P < .001). Similarly, overall survival at 60 months was 100% for UMs without loss of the BAP1 locus or 8q gain, 80.8% (95% CI, 63.3%-100%) for UMs that carried 1 of these alterations, and 46.7% (95% CI, 23.3%-93.6%) for those that carried both (log-rank P < .001). Conclusions and Relevance These findings suggest that partial deletion of chromosome 3 encompassing the BAP1 locus is associated with poor prognosis. A cytogenetic classification of UMs could be proposed based on the status of the BAP1 locus instead of the chromosome 3 locus, while also taking chromosome 8q into account.
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Affiliation(s)
- Manuel Rodrigues
- Unit 830 (Cancer, Heterogeneity, Instability and Plasticity) INSERM, Institut Curie, PSL Research University, Paris, France.,Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France
| | - Khadija Ait Rais
- Department of Genetics, Institut Curie, PSL Research University, Paris, France
| | - Flore Salviat
- Department of Biometry, Institut Curie, PSL Research University, Paris, France
| | - Nathalie Algret
- Department of Biometry, Institut Curie, PSL Research University, Paris, France
| | - Fatoumata Simaga
- Department of Genetics, Institut Curie, PSL Research University, Paris, France
| | - Raymond Barnhill
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France.,Faculty of Medicine, University of Paris Descartes, Paris, France
| | - Sophie Gardrat
- Unit 830 (Cancer, Heterogeneity, Instability and Plasticity) INSERM, Institut Curie, PSL Research University, Paris, France.,Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Vincent Servois
- Department of Medical Imaging, Institut Curie, PSL Research University, Paris, France
| | - Pascale Mariani
- Department of Surgical Oncology, Institut Curie, PSL Research University, Paris, France
| | | | - Sergio Roman-Roman
- Department of Translational Research, Institut Curie, PSL Research University, Paris, France
| | - Olivier Delattre
- Unit 830 (Cancer, Heterogeneity, Instability and Plasticity) INSERM, Institut Curie, PSL Research University, Paris, France.,Department of Genetics, Institut Curie, PSL Research University, Paris, France
| | - Nathalie Cassoux
- Faculty of Medicine, University of Paris Descartes, Paris, France.,Department of Ocular Oncology, Institut Curie, PSL Research University, Paris, France
| | - Alexia Savignoni
- Department of Biometry, Institut Curie, PSL Research University, Paris, France
| | - Marc-Henri Stern
- Unit 830 (Cancer, Heterogeneity, Instability and Plasticity) INSERM, Institut Curie, PSL Research University, Paris, France.,Department of Genetics, Institut Curie, PSL Research University, Paris, France
| | - Gaëlle Pierron
- Department of Genetics, Institut Curie, PSL Research University, Paris, France
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Mazloumi M, Vichitvejpaisal P, Dalvin LA, Yaghy A, Ewens KG, Ganguly A, Shields CL. Accuracy of The Cancer Genome Atlas Classification vs American Joint Committee on Cancer Classification for Prediction of Metastasis in Patients With Uveal Melanoma. JAMA Ophthalmol 2020; 138:260-267. [PMID: 31944225 DOI: 10.1001/jamaophthalmol.2019.5710] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Importance The Cancer Genome Atlas (TCGA) classification is a newly emerging method for prediction of uveal melanoma (UM)-related metastasis and death. Limited information is available regarding the accuracy of the TCGA classification for prediction of metastasis in patients with UM. Objective To investigate the accuracy of the TCGA classification for predicting UM-related metastasis compared with the American Joint Committee on Cancer (AJCC) classification. Design, Setting, and Participants In this retrospective cohort study, patients with UM treated with plaque radiotherapy at a tertiary referral center from October 1, 2008, to December 31, 2018, were evaluated. All patients with tumors classified according to the American Joint Committee on Cancer Staging Manual, 8th Edition, and who completed pretreatment fine-needle aspiration biopsy sampling for genetic analysis of chromosomes 3 and 8 for TCGA classification were included. Tumors were classified into 4 categories, 17 subcategories, and 4 stages using AJCC classification and further grouped into 4 classes using TCGA classification. Main Outcomes and Measures Value of TCGA classification vs AJCC classification for predicting UM-related metastasis. Results Of 642 included patients, 331 (51.6%) were women, and the mean (SD) age was 58.0 (13.8) years. There were 642 tumors from 642 patients classified according to both AJCC and TCGA classifications. The mean (range) follow-up time for the entire cohort was 43.7 (1.4-159.2) months. At 5 years, TCGA classification showed higher value for prediction of metastasis (4 TCGA classes: Wald statistic, 94.8; hazard ratio [HR], 2.8; 95% CI, 2.3-3.5; P < .001; 4 AJCC categories: Wald statistic, 67.5; HR, 2.6; 95% CI, 2.1-3.2; P < .001; 17 AJCC subcategories: Wald statistic, 74.3; HR, 1.3; 95% CI, 1.2-1.3; P < .001; 4 AJCC stages: Wald statistic, 67.0; HR, not applicable; P < .001). After entering TCGA and AJCC classifications into a multivariate model, TCGA classification still showed higher value for prediction of metastasis (TCGA classification: Wald statistic, 61.5; HR, 2.4; 95% CI, 1.9-2.9; P < .001; AJCC classification: Wald statistic, 35.5; HR, 1.9; 95% CI, 1.5-2.4; P < .001). Conclusions and Relevance These results suggest that TCGA classification provides accuracy that is superior to AJCC categories, subcategories, and stages for predicting metastasis from UM. When genetic testing is available, TCGA classification can provide a more accurate way to identify patients at high risk of metastasis who might benefit from adjuvant therapy.
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Affiliation(s)
- Mehdi Mazloumi
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Pornpattana Vichitvejpaisal
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania.,Chulabhorn Hospital, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Lauren A Dalvin
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania.,Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota
| | - Antonio Yaghy
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Kathryn G Ewens
- Perelman School of Medicine, Department of Genetics, University of Pennsylvania, Philadelphia
| | - Arupa Ganguly
- Perelman School of Medicine, Department of Genetics, University of Pennsylvania, Philadelphia
| | - Carol L Shields
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania
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Li Y, Shi J, Yang J, Ge S, Zhang J, Jia R, Fan X. Uveal melanoma: progress in molecular biology and therapeutics. Ther Adv Med Oncol 2020; 12:1758835920965852. [PMID: 33149769 PMCID: PMC7586035 DOI: 10.1177/1758835920965852] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 09/16/2020] [Indexed: 12/15/2022] Open
Abstract
Uveal melanoma (UM) is the most common intraocular malignancy in adults. So far, no systemic therapy or standard treatment exists to reduce the risk of metastasis and improve overall survival of patients. With the increased knowledge regarding the molecular pathways that underlie the oncogenesis of UM, it is expected that novel therapeutic approaches will be available to conquer this disease. This review provides a summary of the current knowledge of, and progress made in understanding, the pathogenesis, genetic mutations, epigenetics, and immunology of UM. With the advent of the omics era, multi-dimensional big data are publicly available, providing an innovation platform to develop effective targeted and personalized therapeutics for UM patients. Indeed, recently, a great number of therapies have been reported specifically for UM caused by oncogenic mutations, as well as other etiologies. In this review, special attention is directed to advancements in targeted therapies. In particular, we discuss the possibilities of targeting: GNAQ/GNA11, PLCβ, and CYSLTR2 mutants; regulators of G-protein signaling; the secondary messenger adenosine diphosphate (ADP)-ribosylation factor 6 (ARF6); downstream pathways, such as those involving mitogen-activated protein kinase/MEK/extracellular signal-related kinase, protein kinase C (PKC), phosphoinositide 3-kinase/Akt/mammalian target of rapamycin (mTOR), Trio/Rho/Rac/Yes-associated protein, and inactivated BAP1; and immune-checkpoint proteins cytotoxic T-lymphocyte antigen 4 and programmed cell-death protein 1/programmed cell-death ligand 1. Furthermore, we conducted a survey of completed and ongoing clinical trials applying targeted and immune therapies for UM. Although drug combination therapy based on the signaling pathways involved in UM has made great progress, targeted therapy is still an unmet medical need.
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Affiliation(s)
- Yongyun Li
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Jiahao Shi
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Jie Yang
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Jianming Zhang
- National Research Center for Translational Medicine, Shanghai State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Renbing Jia
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Huangpu District, Shanghai 200001, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200001, China
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Huangpu District, Shanghai 200001, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, 833 Zhizaoju Road, Huangpu District, Shanghai 200001, China
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The Role of Non-Coding RNAs in Uveal Melanoma. Cancers (Basel) 2020; 12:cancers12102944. [PMID: 33053887 PMCID: PMC7600503 DOI: 10.3390/cancers12102944] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/01/2020] [Accepted: 10/09/2020] [Indexed: 12/21/2022] Open
Abstract
Simple Summary The development of uveal melanoma is a multifactorial and multi-step process, in which abnormal gene expression plays a key role. Recently, several studies have highlighted the role of non-coding RNAs in the progression of uveal melanoma by affecting different signaling pathways. As important agents in the regulation of genes, non-coding RNAs have enormous potential to open up therapeutic pathways, predict response to treatment, and anticipate patient outcome for uveal melanoma. This review aims to provide a comprehensive view of what we know about ncRNAs in uveal melanoma currently. Abstract Uveal melanoma (UM) is the most common primary intraocular tumor in adulthood. Approximately 50% of patients develop metastatic disease, which typically affects the liver and is usually fatal within one year. This type of cancer is heterogeneous in nature and is divided into two broad groups of tumors according to their susceptibility to develop metastasis. In the last decade, chromosomal abnormalities and the aberrant expression of several signaling pathways and oncogenes in uveal melanomas have been described. Recently, importance has been given to the association of the mentioned deregulation with the expression of non-coding RNAs (ncRNAs). Here, we review the different classes of ncRNAs—such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs)—and their contribution to the development of UM. Special attention is given to miRNAs and their regulatory role in physiopathology and their potential as biomarkers. As important agents in gene regulation, ncRNAs have a huge potential for opening up therapeutic pathways, predicting response to treatment, and anticipating patient outcome for UM.
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Tura A, Thieme C, Brosig A, Merz H, Ranjbar M, Vardanyan S, Zuo H, Maassen T, Kakkassery V, Grisanti S. Lower Levels of Adiponectin and Its Receptor Adipor1 in the Uveal Melanomas With Monosomy-3. Invest Ophthalmol Vis Sci 2020; 61:12. [PMID: 32396633 PMCID: PMC7405622 DOI: 10.1167/iovs.61.5.12] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Purpose Adiponectin is an insulin-sensitizing and anticarcinogenic hormone that is encoded by a gene on chromosome 3. Here, we analyzed the expression of adiponectin and its receptor Adipor1 in primary uveal melanoma (UM) with regard to the monosomy-3 status and clinical factors, as well as the physiological response of UM cells to adiponectin. Methods Immunohistochemistry was performed on the primary UM of 34 patients. Circulating melanoma cells (CMC) were isolated by immunomagnetic enrichment. Monosomy-3 was evaluated by Immuno-FISH. Gene expression was analyzed using the RNAseq data of The Cancer Genome Atlas study. Cultures of choroidal melanocytes and UM were established from the samples of two patients. The proliferative potential of the UM cell lines Mel-270 and OMM-2.5 was determined by immunocytochemistry, immunoblotting, cell cycle analysis, nucleolar staining, and adenosine triphosphate (ATP) levels. Results UM with monosomy-3 exhibited a lower immunoreactivity for adiponectin and Adipor1, which was associated with monosomy-3-positive CMC and the development of extraocular growth or metastases. Both proteins were more abundant in the irradiated tumors and present in the cultured cells. Gene expression profile indicated the impairment of adiponectin-mediated signaling in the monosomy-3 tumors. Adiponectin induced a significant decline in the ATP levels, Ki-67 expression, cells in the G2/M phase, and nucleolar integrity in UM cultures. Conclusions Adiponectin deficiency appears to enhance the metastatic potential of the UM cells with monosomy-3 and the termination of tumor dormancy. Counteracting insulin resistance and improving the serum adiponectin levels might therefore be a valuable approach to prevent or delay the UM metastases.
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MicroRNAs and Uveal Melanoma: Understanding the Diverse Role of These Small Molecular Regulators. Int J Mol Sci 2020; 21:ijms21165648. [PMID: 32781746 PMCID: PMC7460624 DOI: 10.3390/ijms21165648] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 07/31/2020] [Accepted: 08/04/2020] [Indexed: 12/12/2022] Open
Abstract
Uveal melanoma (UM) is a rare tumour of the eye, characterised by a high propensity to metastasise in half of all patients, most frequently to the liver. Although there are effective treatment options for the primary tumour, once metastasis has occurred prognosis is poor, with overall survival limited to months. Currently, there are no effective treatments for metastatic UM, despite the tumour having a well-defined signalling pathway to which many therapies have been directed. In an effort to develop novel treatment approaches, understanding the role of other signalling molecules, such as microRNAs, is fundamental. MicroRNAs (miRNAs) are small non-coding RNA molecules involved in posttranscriptional gene regulation, resulting in reduced target gene expression and subsequent protein translation. In UM, several dysregulated miRNAs have been proposed to play a functional role in disease progression, whereas others have been put forward as clinical biomarkers of high-risk disease following isolation from blood, plasma and exosomes. Most recently, analyses of large datasets have identified promising prognostic miRNA signatures and panels. This review navigates the plethora of aberrant miRNAs disclosed so far in UM, and maps these to signalling pathways, which could be targeted in future therapies for the disseminated disease.
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47
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Tang J, Wan Q, Lu J. The prognostic values of m6A RNA methylation regulators in uveal melanoma. BMC Cancer 2020; 20:674. [PMID: 32682400 PMCID: PMC7368742 DOI: 10.1186/s12885-020-07159-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 07/09/2020] [Indexed: 12/18/2022] Open
Abstract
Background The aim of this study was to identify gene signatures and prognostic values of m6A methylation regulators in uveal melanoma (UM). Methods The RNA sequencing dataset and corresponding clinical information were downloaded from TCGA and GEO database. Based on the expression of m6A RNA methylation regulators, the patients were further clustered into different groups by applying the “ClassDiscovery” algorithm. Best survival analysis was performed to select prognostic m6A regulators and multivariate cox regression analysis was applied to constructed m6A regulators signature. The association between mutations and m6A regulators was assessed by Kruskal−Wallis tests and clinical characteristics were examined by using chi-square test. Results Totally, we identified two molecular subtypes of UM (C1/2) by applying consensus clustering to m6A RNA methylation regulators. In contrast to the C1 subtype, the C2 subtype associates with a better prognosis, has higher percentage of subtype 1 and lower percentage of Monosomy 3 which have been regarded as the well established prognostic markers for UM. The malignant hallmarks of mTORC1 signaling, oxidative phosphorylation, interferon-a response and apoptosis signaling are also significantly enriched in the C1 subtype. Moreover, a 3-m6A regulators signature was constructed by multivariate cox regression analysis method, which closely correlated with chromosome 3 status, subtype 1 of UM and can robustly predict patients’ overall survival time. Conclusions m6A RNA methylation regulators take a crucial role in the potential malignant progression and prognostic value of UM and might be regarded as a new promising biomarker for UM prognosis and treatment strategy development.
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Affiliation(s)
- Jing Tang
- Department of Ophthalmology, The People's Hospital of Leshan, city, Leshan, China
| | - Qi Wan
- Department of Ophthalmology, The People's Hospital of Leshan, city, Leshan, China. .,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, 510064, China.
| | - Jianqun Lu
- Department of Ophthalmology, The People's Hospital of Leshan, city, Leshan, China
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Figueiredo CR, Kalirai H, Sacco JJ, Azevedo RA, Duckworth A, Slupsky JR, Coulson JM, Coupland SE. Loss of BAP1 expression is associated with an immunosuppressive microenvironment in uveal melanoma, with implications for immunotherapy development. J Pathol 2020; 250:420-439. [PMID: 31960425 PMCID: PMC7216965 DOI: 10.1002/path.5384] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/28/2019] [Accepted: 01/14/2020] [Indexed: 12/22/2022]
Abstract
Immunotherapy using immune checkpoint inhibitors (ICIs) induces durable responses in many metastatic cancers. Metastatic uveal melanoma (mUM), typically occurring in the liver, is one of the most refractory tumours to ICIs and has dismal outcomes. Monosomy 3 (M3), polysomy 8q, and BAP1 loss in primary uveal melanoma (pUM) are associated with poor prognoses. The presence of tumour‐infiltrating lymphocytes (TILs) within pUM and surrounding mUM – and some evidence of clinical responses to adoptive TIL transfer – strongly suggests that UMs are indeed immunogenic despite their low mutational burden. The mechanisms that suppress TILs in pUM and mUM are unknown. We show that BAP1 loss is correlated with upregulation of several genes associated with suppressive immune responses, some of which build an immune suppressive axis, including HLA‐DR, CD38, and CD74. Further, single‐cell analysis of pUM by mass cytometry confirmed the expression of these and other markers revealing important functions of infiltrating immune cells in UM, most being regulatory CD8+ T lymphocytes and tumour‐associated macrophages (TAMs). Transcriptomic analysis of hepatic mUM revealed similar immune profiles to pUM with BAP1 loss, including the expression of IDO1. At the protein level, we observed TAMs and TILs entrapped within peritumoural fibrotic areas surrounding mUM, with increased expression of IDO1, PD‐L1, and β‐catenin (CTNNB1), suggesting tumour‐driven immune exclusion and hence the immunotherapy resistance. These findings aid the understanding of how the immune response is organised in BAP1− mUM, which will further enable functional validation of detected biomarkers and the development of focused immunotherapeutic approaches. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Carlos R Figueiredo
- Department of Molecular and Clinical Cancer Medicine, ITM, University of Liverpool, Liverpool, UK.,Department of the Faculty of Medicine, MediCity Research Laboratory and Institute of Biomedicine, University of Turku, Turku, Finland
| | - Helen Kalirai
- Department of Molecular and Clinical Cancer Medicine, ITM, University of Liverpool, Liverpool, UK
| | - Joseph J Sacco
- Department of Molecular and Clinical Cancer Medicine, ITM, University of Liverpool, Liverpool, UK.,Department of Medical Oncology, The Clatterbridge Cancer Centre, Wirral, UK
| | - Ricardo A Azevedo
- Department of Cancer Biology, The University of Texas-MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew Duckworth
- Department of Molecular and Clinical Cancer Medicine, ITM, University of Liverpool, Liverpool, UK
| | - Joseph R Slupsky
- Department of Molecular and Clinical Cancer Medicine, ITM, University of Liverpool, Liverpool, UK
| | - Judy M Coulson
- Department of Cellular and Molecular Physiology, University of Liverpool, Liverpool, UK
| | - Sarah E Coupland
- Department of Molecular and Clinical Cancer Medicine, ITM, University of Liverpool, Liverpool, UK.,Liverpool Clinical Laboratories, Royal Liverpool University Hospital, Liverpool, UK
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Dogrusöz M, Brouwer NJ, de Geus SJR, Ly LV, Böhringer S, van Duinen SG, Kroes WGM, van der Velden PA, Haasnoot GW, Marinkovic M, Luyten GPM, Kivelä TT, Jager MJ. Prognostic Factors Five Years After Enucleation for Uveal Melanoma. Invest Ophthalmol Vis Sci 2020; 61:31. [PMID: 32186672 PMCID: PMC7401572 DOI: 10.1167/iovs.61.3.31] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Purpose A subgroup of uveal melanoma (UM) gives rise to metastases at a late stage. Our objective was to identify patient and tumor characteristics that are associated with UM-related death in patients who survived 5 years following enucleation. Methods A retrospective analysis was performed in 583 primary UM cases, enucleated at the Leiden University Medical Center between 1983 and 2013. Univariable and multivariable Cox regression analyses were performed in the total cohort and separately in those surviving more than 5 years (n = 297). Results In the total cohort, the median age was 62.6 years, and the median tumor diameter was 12.0 mm. Monosomy 3 was detected in 53% of cases and gain of 8q in 47%. In the cohort surviving 5 years, the median age was 59.5 years, and the median tumor diameter was 11.0 mm. Monosomy 3 and gain of 8q were detected in 33% and 31% of cases, respectively. In the total cohort, male gender (P = 0.03), tumor diameter (P < 0.001), mitotic count (P < 0.001), extravascular matrix loops (P = 0.03), extraocular growth (P < 0.001), and gain of 8q (P < 0.001) were independently associated with UM-related death. In patients surviving 5 years after enucleation, univariable analysis revealed that age (P = 0.03), tumor diameter (P < 0.001), monosomy 3 (P = 0.04), and 8q gain (P = 0.003) were associated with subsequent UM-related death. Using a multivariable analysis, only male gender (P = 0.03) and gain of 8q (P = 0.01) remained significant. Conclusions Predictors of UM-related death change over time. Among UM patients who survived the initial 5 years following enucleation, male gender and chromosome 8q status were the remaining factors related to UM-related death later on.
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Hussain RN, Coupland SE, Khzouz J, Kalirai H, Parsons JL. Inhibition of ATM Increases the Radiosensitivity of Uveal Melanoma Cells to Photons and Protons. Cancers (Basel) 2020; 12:cancers12061388. [PMID: 32481544 PMCID: PMC7352388 DOI: 10.3390/cancers12061388] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/20/2020] [Accepted: 05/25/2020] [Indexed: 02/06/2023] Open
Abstract
Treatment of uveal melanoma (UM) is generally successful, with local primary tumour control being at 90%-95%. Localized radiotherapy in the form of plaque brachytherapy or proton beam radiotherapy is the most common treatment modality in the UK. However, the basic mechanisms of radiation response, DNA repair and tissue reactions in UM have not been well documented previously. We have investigated the comparative radiosensitivity of four UM cell lines in response to exogenous radiation sources (both X-rays and protons), and correlated this with DNA repair protein expression and repair efficiency. We observed a broad range of radiosensitivity of different UM cell lines to X-rays and protons, with increased radioresistance correlating with elevated protein expression of ataxia telangiectasia mutated (ATM), a protein kinase involved in the signaling and repair of DNA double strand breaks. The use of an ATM inhibitor in UM cell lines enhanced radiosensitivity following both X-ray and proton irradiation, particularly in cells that contained high levels of ATM protein which are otherwise comparatively radioresistant. In proton-irradiated compared with non-irradiated primary enucleated UM patient samples, there was no significant difference in ATM protein expression. Our study therefore suggests that ATM is a potential target for increasing the radiosensitivity of more resistant UM subgroups.
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Affiliation(s)
- Rumana N. Hussain
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, William Henry Duncan Building, University of Liverpool, Liverpool L7 8TX, UK; (R.N.H.); (S.E.C.); (J.K.); (H.K.)
- St Paul’s Eye Clinic, Liverpool University Hospitals Foundation Trust, Prescot Street, Liverpool L7 8XP, UK
| | - Sarah E. Coupland
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, William Henry Duncan Building, University of Liverpool, Liverpool L7 8TX, UK; (R.N.H.); (S.E.C.); (J.K.); (H.K.)
- Liverpool Clinical Laboratories, Duncan Building, Liverpool University Hospitals NHS Foundation Trust, Liverpool L69 3GA, UK
| | - Jakub Khzouz
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, William Henry Duncan Building, University of Liverpool, Liverpool L7 8TX, UK; (R.N.H.); (S.E.C.); (J.K.); (H.K.)
| | - Helen Kalirai
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, William Henry Duncan Building, University of Liverpool, Liverpool L7 8TX, UK; (R.N.H.); (S.E.C.); (J.K.); (H.K.)
| | - Jason L. Parsons
- Cancer Research Centre, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 200 London Road, Liverpool L3 9TA, UK
- Clatterbridge Cancer Centre NHS Foundation Trust, Clatterbridge Road, Bebington CH63 4JY, UK
- Correspondence: ; Tel.: +44-151-794-8848
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