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Fuentes-Rodriguez A, Mitchell A, Guérin SL, Landreville S. Recent Advances in Molecular and Genetic Research on Uveal Melanoma. Cells 2024; 13:1023. [PMID: 38920653 PMCID: PMC11201764 DOI: 10.3390/cells13121023] [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: 04/10/2024] [Revised: 06/08/2024] [Accepted: 06/09/2024] [Indexed: 06/27/2024] Open
Abstract
Uveal melanoma (UM), a distinct subtype of melanoma, presents unique challenges in its clinical management due to its complex molecular landscape and tendency for liver metastasis. This review highlights recent advancements in understanding the molecular pathogenesis, genetic alterations, and immune microenvironment of UM, with a focus on pivotal genes, such as GNAQ/11, BAP1, and CYSLTR2, and delves into the distinctive genetic and chromosomal classifications of UM, emphasizing the role of mutations and chromosomal rearrangements in disease progression and metastatic risk. Novel diagnostic biomarkers, including circulating tumor cells, DNA and extracellular vesicles, are discussed, offering potential non-invasive approaches for early detection and monitoring. It also explores emerging prognostic markers and their implications for patient stratification and personalized treatment strategies. Therapeutic approaches, including histone deacetylase inhibitors, MAPK pathway inhibitors, and emerging trends and concepts like CAR T-cell therapy, are evaluated for their efficacy in UM treatment. This review identifies challenges in UM research, such as the limited treatment options for metastatic UM and the need for improved prognostic tools, and suggests future directions, including the discovery of novel therapeutic targets, immunotherapeutic strategies, and advanced drug delivery systems. The review concludes by emphasizing the importance of continued research and innovation in addressing the unique challenges of UM to improve patient outcomes and develop more effective treatment strategies.
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Affiliation(s)
- Aurélie Fuentes-Rodriguez
- Department of Ophthalmology and Otorhinolaryngology-Cervico-Facial Surgery, Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada; (A.F.-R.); (A.M.); (S.L.G.)
- Hôpital du Saint-Sacrement, Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC G1S 4L8, Canada
- Centre de Recherche en Organogénèse Expérimentale de l‘Université Laval/LOEX, Quebec City, QC G1J 1Z4, Canada
- Université Laval Cancer Research Center, Quebec City, QC G1R 3S3, Canada
| | - Andrew Mitchell
- Department of Ophthalmology and Otorhinolaryngology-Cervico-Facial Surgery, Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada; (A.F.-R.); (A.M.); (S.L.G.)
- Hôpital du Saint-Sacrement, Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC G1S 4L8, Canada
- Centre de Recherche en Organogénèse Expérimentale de l‘Université Laval/LOEX, Quebec City, QC G1J 1Z4, Canada
- Université Laval Cancer Research Center, Quebec City, QC G1R 3S3, Canada
| | - Sylvain L. Guérin
- Department of Ophthalmology and Otorhinolaryngology-Cervico-Facial Surgery, Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada; (A.F.-R.); (A.M.); (S.L.G.)
- Hôpital du Saint-Sacrement, Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC G1S 4L8, Canada
- Centre de Recherche en Organogénèse Expérimentale de l‘Université Laval/LOEX, Quebec City, QC G1J 1Z4, Canada
| | - Solange Landreville
- Department of Ophthalmology and Otorhinolaryngology-Cervico-Facial Surgery, Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada; (A.F.-R.); (A.M.); (S.L.G.)
- Hôpital du Saint-Sacrement, Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC G1S 4L8, Canada
- Centre de Recherche en Organogénèse Expérimentale de l‘Université Laval/LOEX, Quebec City, QC G1J 1Z4, Canada
- Université Laval Cancer Research Center, Quebec City, QC G1R 3S3, Canada
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Wang L, Lu Y, Li D, Zhou Y, Yu L, Mesa Eguiagaray I, Campbell H, Li X, Theodoratou E. The landscape of the methodology in drug repurposing using human genomic data: a systematic review. Brief Bioinform 2024; 25:bbad527. [PMID: 38279645 PMCID: PMC10818097 DOI: 10.1093/bib/bbad527] [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: 07/17/2023] [Revised: 11/24/2023] [Accepted: 12/19/2023] [Indexed: 01/28/2024] Open
Abstract
The process of drug development is expensive and time-consuming. In contrast, drug repurposing can be introduced to clinical practice more quickly and at a reduced cost. Over the last decade, there has been a significant expansion of large biobanks that link genomic data to electronic health record data, public availability of various databases containing biological and clinical information and rapid development of novel methodologies and algorithms in integrating different sources of data. This review aims to provide a thorough summary of different strategies that utilize genomic data to seek drug-repositioning opportunities. We searched MEDLINE and EMBASE databases to identify eligible studies up until 1 May 2023, with a total of 102 studies finally included after two-step parallel screening. We summarized commonly used strategies for drug repurposing, including Mendelian randomization, multi-omic-based and network-based studies and illustrated each strategy with examples, as well as the data sources implemented. By leveraging existing knowledge and infrastructure to expedite the drug discovery process and reduce costs, drug repurposing potentially identifies new therapeutic uses for approved drugs in a more efficient and targeted manner. However, technical challenges when integrating different types of data and biased or incomplete understanding of drug interactions are important hindrances that cannot be disregarded in the pursuit of identifying novel therapeutic applications. This review offers an overview of drug repurposing methodologies, providing valuable insights and guiding future directions for advancing drug repurposing studies.
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Affiliation(s)
- Lijuan Wang
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Lu
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Doudou Li
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yajing Zhou
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lili Yu
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ines Mesa Eguiagaray
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Harry Campbell
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Xue Li
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, The University of Edinburgh MRC Institute of Genetics and Cancer, Edinburgh, UK
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Li K, Sun L, Wang Y, Cen Y, Zhao J, Liao Q, Wu W, Sun J, Zhou M. Single-cell characterization of macrophages in uveal melanoma uncovers transcriptionally heterogeneous subsets conferring poor prognosis and aggressive behavior. Exp Mol Med 2023; 55:2433-2444. [PMID: 37907747 PMCID: PMC10689813 DOI: 10.1038/s12276-023-01115-9] [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: 09/09/2022] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 11/02/2023] Open
Abstract
Uveal melanoma (UM) is the most frequent primary intraocular malignancy with high metastatic potential and poor prognosis. Macrophages represent one of the most abundant infiltrating immune cells with diverse functions in cancers. However, the cellular heterogeneity and functional diversity of macrophages in UM remain largely unexplored. In this study, we analyzed 63,264 single-cell transcriptomes from 11 UM patients and identified four transcriptionally distinct macrophage subsets (termed MΦ-C1 to MΦ-C4). Among them, we found that MΦ-C4 exhibited relatively low expression of both M1 and M2 signature genes, loss of inflammatory pathways and antigen presentation, instead demonstrating enhanced signaling for proliferation, mitochondrial functions and metabolism. We quantified the infiltration abundance of MΦ-C4 from single-cell and bulk transcriptomes across five cohorts and found that increased MΦ-C4 infiltration was relevant to aggressive behaviors and may serve as an independent prognostic indicator for poor outcomes. We propose a novel subtyping scheme based on macrophages by integrating the transcriptional signatures of MΦ-C4 and machine learning to stratify patients into MΦ-C4-enriched or MΦ-C4-depleted subtypes. These two subtypes showed significantly different clinical outcomes and were validated through bulk RNA sequencing and immunofluorescence assays in both public multicenter cohorts and our in-house cohort. Following further translational investigation, our findings highlight a potential therapeutic strategy of targeting macrophage subsets to control metastatic disease and consistently improve the outcome of patients with UM.
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Affiliation(s)
- Ke Li
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, China
| | - Lanfang Sun
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, China
| | - Yanan Wang
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, China
| | - Yixin Cen
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, China
| | - Jingting Zhao
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, China
| | - Qianling Liao
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, China
| | - Wencan Wu
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, China.
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, China.
| | - Jie Sun
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, China.
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, China.
| | - Meng Zhou
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, China.
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, China.
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Tan Y, Pan J, Deng Z, Chen T, Xia J, Liu Z, Zou C, Qin B. Monoacylglycerol lipase regulates macrophage polarization and cancer progression in uveal melanoma and pan-cancer. Front Immunol 2023; 14:1161960. [PMID: 37033945 PMCID: PMC10076602 DOI: 10.3389/fimmu.2023.1161960] [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: 02/09/2023] [Accepted: 03/13/2023] [Indexed: 04/11/2023] Open
Abstract
Background Although lipid metabolism has been proven to play a key role in the development of cancer, its significance in uveal melanoma (UM) has not yet been elucidated in the available literature. Methods To identify the expression patterns of lipid metabolism in 80 UM patients from the TCGA database, 47 genes involved in lipid metabolism were analyzed. Consensus clustering revealed two distinct molecular groups. ESTIMATE, TIMER, and ssGSEA analyses were done to identify the differences between the two subgroups in tumor microenvironment (TME) and immune state. Using Cox regression and Lasso regression analysis, a risk model based on differentially expressed genes (DEGs) was developed. To validate the expression of monoacylglycerol lipase (MGLL) and immune infiltration in diverse malignancies, a pan-cancer cohort from the UCSC database was utilized. Next, a single-cell sequencing analysis on UM patients from the GEO data was used to characterize the lipid metabolism in TME and the role of MGLL in UM. Finally, in vitro investigations were utilized to study the involvement of MGLL in UM. Results Two molecular subgroups of UM patients have considerably varied survival rates. The majority of DEGs between the two subgroups were associated with immune-related pathways. Low immune scores, high tumor purity, a low number of immune infiltrating cells, and a comparatively low immunological state were associated with a more favorable prognosis. An examination of GO and KEGG data demonstrated that the risk model based on genes involved with lipid metabolism can accurately predict survival in patients with UM. It has been demonstrated that MGLL, a crucial gene in this paradigm, promotes the proliferation, invasion, and migration of UM cells. In addition, we discovered that MGLL is strongly expressed in macrophages, specifically M2 macrophages, which may play a function in the M2 polarization of macrophages and M2 macrophage activation in cancer cells. Conclusion This study demonstrates that the risk model based on lipid metabolism may be useful for predicting the prognosis of patients with UM. By promoting macrophage M2 polarization, MGLL contributes to the evolution of malignancy in UM, suggesting that it may be a therapeutic target for UM.
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Affiliation(s)
- Yao Tan
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, China
| | - Juan Pan
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, Guangxi, China
- Department of Clinical Medical Research Center, The Second Clinical Medical College, The First Affiliated Hospital of Southern University of Science and Technology, Jinan University (Shenzhen People’s Hospital), Shenzhen, Guangdong, China
| | - Zhenjun Deng
- Department of Dermatology, The Second Clinical Medical College, Jinan University (Shenzhen People’s Hospital), Shenzhen, China
- The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Tao Chen
- School of Medicine, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Jinquan Xia
- Department of Clinical Medical Research Center, The Second Clinical Medical College, The First Affiliated Hospital of Southern University of Science and Technology, Jinan University (Shenzhen People’s Hospital), Shenzhen, Guangdong, China
| | - Ziling Liu
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, China
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Chang Zou
- School of Life and Health Sciences, The Chinese University of Kong Hong, Shenzhen, China
- *Correspondence: Bo Qin, ; Chang Zou,
| | - Bo Qin
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, China
- Shenzhen Aier Ophthalmic Technology Institute, Shenzhen, China
- *Correspondence: Bo Qin, ; Chang Zou,
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