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Seedor RS, Orloff M, Sato T. Genetic Landscape and Emerging Therapies in Uveal Melanoma. Cancers (Basel) 2021; 13:5503. [PMID: 34771666 PMCID: PMC8582814 DOI: 10.3390/cancers13215503] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/26/2021] [Accepted: 10/30/2021] [Indexed: 12/12/2022] Open
Abstract
Despite successful treatment of primary uveal melanoma, up to 50% of patients will develop systemic metastasis. Metastatic disease portends a poor outcome, and no adjuvant or metastatic therapy has been FDA approved. The genetic landscape of uveal melanoma is unique, providing prognostic and potentially therapeutic insight. In this review, we discuss our current understanding of the molecular and cytogenetic mutations in uveal melanoma, and the importance of obtaining such information. Most of our knowledge is based on primary uveal melanoma and a better understanding of the mutational landscape in metastatic uveal melanoma is needed. Clinical trials targeting certain mutations such as GNAQ/GNA11, BAP1, and SF3B1 are ongoing and promising. We also discuss the role of liquid biopsies in uveal melanoma in this review.
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Affiliation(s)
- Rino S. Seedor
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; (M.O.); (T.S.)
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2
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Fallico M, Raciti G, Longo A, Reibaldi M, Bonfiglio V, Russo A, Caltabiano R, Gattuso G, Falzone L, Avitabile T. Current molecular and clinical insights into uveal melanoma (Review). Int J Oncol 2021; 58:10. [PMID: 33649778 PMCID: PMC7910016 DOI: 10.3892/ijo.2021.5190] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022] Open
Abstract
Uveal melanoma (UM) represents the most prominent primary eye cancer in adults. With an incidence of approximately 5 cases per million individuals annually in the United States, UM could be considered a relatively rare cancer. The 90-95% of UM cases arise from the choroid. Diagnosis is based mainly on a clinical examination and ancillary tests, with ocular ultrasonography being of greatest value. Differential diagnosis can prove challenging in the case of indeterminate choroidal lesions and, sometimes, monitoring for documented growth may be the proper approach. Fine needle aspiration biopsy tends to be performed with a prognostic purpose, often in combination with radiotherapy. Gene expression profiling has allowed for the grading of UMs into two classes, which feature different metastatic risks. Patients with UM require a specialized multidisciplinary management. Primary tumor treatment can be either enucleation or globe preserving. Usually, enucleation is reserved for larger tumors, while radiotherapy is preferred for small/medium melanomas. The prognosis is unfavorable due to the high mortality rate and high tendency to metastasize. Following the development of metastatic disease, the mortality rate increases to 80% within one year, due to both the absence of an effective treatment and the aggressiveness of the condition. Novel molecular studies have allowed for a better understanding of the genetic and epigenetic mechanisms involved in UM biological activity, which differs compared to skin melanomas. The most commonly mutated genes are GNAQ, GNA11 and BAP1. Research in this field could help to identify effective diagnostic and prognostic biomarkers, as well as novel therapeutic targets.
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Affiliation(s)
- Matteo Fallico
- Department of Ophthalmology, University of Catania, I‑95123 Catania, Italy
| | - Giuseppina Raciti
- Department of Drug Sciences, Section of Biochemistry, University of Catania, I‑95125 Catania, Italy
| | - Antonio Longo
- Department of Ophthalmology, University of Catania, I‑95123 Catania, Italy
| | - Michele Reibaldi
- Department of Surgical Sciences, Eye Clinic Section, University of Turin, I‑10122 Turin, Italy
| | - Vincenza Bonfiglio
- Department of Experimental Biomedicine and Clinical Neuroscience, Ophthalmology Section, University of Palermo, I‑90127 Palermo, Italy
| | - Andrea Russo
- Department of Ophthalmology, University of Catania, I‑95123 Catania, Italy
| | - Rosario Caltabiano
- Department 'G.F. Ingrassia', Section of Anatomic Pathology, University of Catania, I‑95123 Catania, Italy
| | - Giuseppe Gattuso
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Luca Falzone
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori 'Fondazione G. Pascale', I‑80131 Naples, Italy
| | - Teresio Avitabile
- Department of Ophthalmology, University of Catania, I‑95123 Catania, Italy
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Yang C, Wang Y, Hardy P. Emerging roles of microRNAs and their implications in uveal melanoma. Cell Mol Life Sci 2021; 78:545-559. [PMID: 32783068 PMCID: PMC11072399 DOI: 10.1007/s00018-020-03612-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/14/2020] [Accepted: 07/30/2020] [Indexed: 12/19/2022]
Abstract
Uveal melanoma (UM) is the most common intraocular malignant tumor in adults with an extremely high mortality rate. Genetic and epigenetic dysregulation contribute to the development of UM. Recent discoveries have revealed dysregulation of the expression levels of microRNAs (miRNAs) as one of the epigenetic mechanisms underlying UM tumorigenesis. Based on their roles, miRNAs are characterized as either oncogenic or tumor suppressive. This review focuses on the roles of miRNAs in UM tumorigenesis, diagnosis, and prognosis, as well as their therapeutic potentials. Particularly, the actions of collective miRNAs are summarized with respect to their involvement in major, aberrant signaling pathways that are implicated in the development and progression of UM. Elucidation of the underlying functional mechanisms and biological aspects of miRNA dysregulation in UM is invaluable in the development of miRNA-based therapeutics, which may be used in combination with conventional treatments to improve therapeutic outcomes. In addition, the expression levels of some miRNAs are correlated with UM initiation and progression and, therefore, may be used as biomarkers for diagnosis and prognosis.
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Affiliation(s)
- Chun Yang
- Departments of Pediatrics, Pharmacology, and Physiology, University of Montréal, Montréal, Québec, H3T 1C5, Canada
| | - Yuejiao Wang
- Department of Gynecological Endocrinology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Pierre Hardy
- Departments of Pediatrics, Pharmacology, and Physiology, University of Montréal, Montréal, Québec, H3T 1C5, Canada.
- Research Center of CHU Sainte-Justine, 3175 Côte-Sainte-Catherine, Room 2.17.004, Montréal, Québec, H3T 1C5, Canada.
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Targeting Epigenetic Modifications in Uveal Melanoma. Int J Mol Sci 2020; 21:ijms21155314. [PMID: 32726977 PMCID: PMC7432398 DOI: 10.3390/ijms21155314] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/21/2020] [Accepted: 07/25/2020] [Indexed: 12/17/2022] Open
Abstract
Uveal melanoma (UM), the most common intraocular malignancy in adults, is a rare subset of melanoma. Despite effective primary therapy, around 50% of patients will develop the metastatic disease. Several clinical trials have been evaluated for patients with advanced UM, though outcomes remain dismal due to the lack of efficient therapies. Epigenetic dysregulation consisting of aberrant DNA methylation, histone modifications, and small non-coding RNA expression, silencing tumor suppressor genes, or activating oncogenes, have been shown to play a significant role in UM initiation and progression. Given that there is no evidence any approach improves results so far, adopting combination therapies, incorporating a new generation of epigenetic drugs targeting these alterations, may pave the way for novel promising therapeutic options. Furthermore, the fusion of effector enzymes with nuclease-deficient Cas9 (dCas9) in clustered regularly interspaced short palindromic repeats (CRISPR) associated protein 9 (Cas9) system equips a potent tool for locus-specific erasure or establishment of DNA methylation as well as histone modifications and, therefore, transcriptional regulation of specific genes. Both, CRISPR-dCas9 potential for driver epigenetic alterations discovery, and possibilities for their targeting in UM are highlighted in this review.
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Li YF, Dong L, Li Y, Wei WB. A Review of MicroRNA in Uveal Melanoma. Onco Targets Ther 2020; 13:6351-6359. [PMID: 32669855 PMCID: PMC7335863 DOI: 10.2147/ott.s253946] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 06/12/2020] [Indexed: 12/24/2022] Open
Abstract
Uveal melanoma (UM) is the most common and aggressive primary intraocular tumor in adults. UM is classified as a malignant tumor with a strong tendency of metastasis, which always leads to poor outcomes. At present, the pathogenesis of UM remains unclear and lacks effective therapies. Recent studies have shown that microRNAs (miRNAs), defined as a group of 21-23 nucleotides single-stranded noncoding RNAs, play a significant role in UM. By binding to the complementary sites within the 3' untranslated region (3'UTR) of message RNAs (mRNAs), miRNAs regulate genes by decaying mRNAs or inhibiting their translation. Thus, miRNAs can modulate various biological behaviors of tumors, including cell proliferation, invasion and metastasis. Furthermore, miRNAs have shown clinical applications by serving as biomarkers for diagnosis and prognosis, regulating immune response, and functioning as epigenetic regulators. It is reasonable to believe that miRNAs have wide application prospects in the early diagnosis and therapy of UM.
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Affiliation(s)
- Yi Fan Li
- Department of Ophthalmology, Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Li Dong
- Department of Ophthalmology, Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Yang Li
- Department of Ophthalmology, Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Wen Bin Wei
- Department of Ophthalmology, Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China
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Zhang Y, Xue Z, Guo F, Yu F, Xu L, Chen H. Nc2Eye: A Curated ncRNAomics Knowledgebase for Bridging Basic and Clinical Research in Eye Diseases. Front Cell Dev Biol 2020; 8:75. [PMID: 32117995 PMCID: PMC7033623 DOI: 10.3389/fcell.2020.00075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 01/29/2020] [Indexed: 01/24/2023] Open
Abstract
Eye diseases (EDs) represent a group of disorders affecting the visual system, most of which can lead to visual impairment and blindness. Accumulating evidence reveals that non-coding RNAs (ncRNAs) are closely associated with a wide variety of EDs. However, abundant associations between ncRNAs and EDs are scattered across the published literature, obstructing a global view of ncRNA-ED associations. A public resource of high-quality manually curated ncRNAomics knowledge associated with EDs remains unavailable. To address this gap, we thus developed Nc2Eye (http://nc2eye.bio-data.cn/), which is the first knowledgebase dedicated to providing a comprehensive ncRNAomics resource for bridging basic and clinical research in EDs. Through a comprehensive review of more than 2400 published papers, Nc2Eye catalogs 7088 manually curated ncRNA-ED associations involving 4363 ncRNAs across eight species. We also provide detailed descriptions and annotation information for each ncRNA-disease association such as ncRNA categories, experimental methods, expression pattern and related clinical drugs. To further expand the pathogenic ncRNAs, we also collected more than 90 high-throughput EDs-related transcriptome datasets. Furthermore, a user-friendly interface was constructed for convenient and flexible data browsing, querying, and retrieving. We believe that Nc2Eye is a timely and valuable knowledgebase for significantly improving and useful for discovery of new diagnostic and therapeutic biomarkers.
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Affiliation(s)
- Yan Zhang
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Zhengbo Xue
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Fangjie Guo
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Fulong Yu
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Liangde Xu
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Hao Chen
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
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Xia Z, Yang C, Yang X, Wu S, Feng Z, Qu L, Chen X, Liu L, Ma Y. miR-652 Promotes Proliferation and Migration of Uveal Melanoma Cells by Targeting HOXA9. Med Sci Monit 2019; 25:8722-8732. [PMID: 31740654 PMCID: PMC6880646 DOI: 10.12659/msm.917099] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Background Dysregulation of the microRNA (miRNA) network is a typical feature of many cancers. However, the key specific miRNAs involved in uveal melanoma carcinogenesis are largely unknown. Material/Methods RT-qPCR was used to detected miR-652 expression in uveal melanoma tissues and cell lines. miR-652 inhibitor was transfected into uveal melanoma cells to decrease miR-652 expression and determine the biological role of miR-652 by CCK-8 and wound healing assays. Bioinformatic analysis and dual luciferase reporter assay were used to predict and validate the target gene of miR-652. HOXA9 siRNA was transfected into cells to confirm that miR-652 relies on regulation of HOXA9 to regulate cell proliferation and migration. Results RT-qPCR showed that miR-652 was overexpressed in uveal melanoma cell lines (MUM-2B, MEL270) compared with melanocyte cells (ARPE-19). Overexpression of miR-652 was also observed in uveal melanoma compared to paired non-tumor tissues. Downregulation of miR-652 inhibited the cell proliferation ability and migration ability of uveal melanoma cells. Using bioinformatic analysis, HOXA9 was found to be a potential target gene of miR-652. The direct regulation of HOXA9 by miR-652 was experimentally validated in uveal melanoma cells by dual luciferase assay and Western blotting. We also observed that miR-652 promoted HIF-1α signaling via repression of HOXA9 in uveal melanoma cells. Silencing of HOXA9 attenuated the miR-652 inhibitor decreased cell growth rate and decreased migration ability in uveal melanoma cells. Conclusions Our data demonstrate an oncogenic role of miR-652 in uveal melanoma, showing that miR-652 may be a useful biomarker for prediction of prognosis for patients with uveal melanoma.
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Affiliation(s)
- Zhaoxia Xia
- Department of Ophthalmology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China (mainland)
| | - Chaoying Yang
- Department of Dermatology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China (mainland)
| | - Xiaoxi Yang
- Department of Ophthalmology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China (mainland)
| | - Shuduan Wu
- Department of Ophthalmology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China (mainland)
| | - Zhizhen Feng
- Department of Ophthalmology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China (mainland)
| | - Lei Qu
- Department of Ophthalmology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China (mainland)
| | - Xianghua Chen
- Department of Ophthalmology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China (mainland)
| | - Lingyu Liu
- Department of Ophthalmology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China (mainland)
| | - Yanling Ma
- Department of Ophthalmology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China (mainland)
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Abstract
Objective: The objective of the study was to summarize the role of DNA methylation in the development and metastasis of uveal melanoma (UM). Data Sources: The relevant studies in MEDLINE were searched. Study Selection: In this review, we performed a comprehensive literature search in MEDLINE using “uveal melanoma” AND (“DNA methylation” OR “epigenetics”) for original research/review articles published before February 2018 on the relationship between DNA methylation and UM. References of the retrieved studies were also examined to search for potentially relevant papers. Results: Previous studies on the relationship between DNA methylation and UM covered many genes including tumor suppressor genes (TSGs), cyclin-dependent kinase genes, and other genes. Among them, the TSG genes such as RASSF1A and p16INK4a, which encodes a cyclin-dependent kinase inhibitor, are relatively well-studied genes. Specifically, a high percentage of promoter methylation of RASSF1A was observed in UM cell lines and/or patients with UM. Promoter methylation of RASSF1A was also associated with the development of metastasis. Similarly, a high percentage of promoter hypermethylation of p16INK4a was found in UM cell lines. DNA promoter methylation can control the expression of p16INK4a, which affect cell growth, migration, and invasion in UM. Many other genes might also be involved in the pathogenesis of UM such as the Ras and EF-hand domain containing (RASEF) gene, RAB31, hTERT, embryonal fyn-associated substrate, and deleted in split-hand/split-foot 1. Conclusions: Our review reveals the complex mechanisms underlying the tumorigenesis of UM and highlights the great needs of future studies to discover more genes/5’-C-phosphate-G-3’ sites contributing to the development/metastasis of UM and explore the mechanisms through which epigenetic changes exert their function in UM.
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Affiliation(s)
- Zhi-Kun Yang
- Department of Ophthalmology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jing-Yun Yang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL 60612, USA
| | - Zhuo-Zai Xu
- Department of Ophthalmology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Wei-Hong Yu
- Department of Ophthalmology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
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Li Y, Jia R, Ge S. Role of Epigenetics in Uveal Melanoma. Int J Biol Sci 2017; 13:426-433. [PMID: 28529451 PMCID: PMC5436563 DOI: 10.7150/ijbs.18331] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 01/04/2017] [Indexed: 01/02/2023] Open
Abstract
Uveal melanoma (UM) is a severe human malignancy with a high mortality rate that demands continued research into new and alternative forms of prevention and treatment. The emerging field of epigenetics is beginning to unfold an era of contemporary approaches to reducing the risk and improving the clinical treatment of UM. Epigenetic changes have a high prevalence rate in cancer, are reversible in nature, and can lead to cancer characteristics even in mutation-free cells. The information contained in this review highlights and expands on the main mechanisms of epigenetic dysregulation in UM tumorigenesis, progression and metastasis, including microRNA expression, hypermethylation of genes and histone modification. Epigenetic drugs have been shown to enhance tumor suppressor gene expression and drug sensitivity in many other cancer cell lines and animal models. An increased understanding of epigenetic mechanisms in UM will be invaluable in the design of more potent epigenetic drugs, which when used in combination with traditional therapies, may permit improved therapeutic outcomes.
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Affiliation(s)
| | - Renbing Jia
- ✉ Corresponding authors: Shengfang Ge or Renbing Jia. or
| | - Shengfang Ge
- ✉ Corresponding authors: Shengfang Ge or Renbing Jia. or
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Venkatesan N, Kanwar J, Deepa PR, Khetan V, Crowley TM, Raguraman R, Sugneswari G, Rishi P, Natarajan V, Biswas J, Krishnakumar S. Clinico-Pathological Association of Delineated miRNAs in Uveal Melanoma with Monosomy 3/Disomy 3 Chromosomal Aberrations. PLoS One 2016; 11:e0146128. [PMID: 26812476 PMCID: PMC4728065 DOI: 10.1371/journal.pone.0146128] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 12/14/2015] [Indexed: 12/15/2022] Open
Abstract
Purpose To correlate the differentially expressed miRNAs with clinico-pathological features in uveal melanoma (UM) tumors harbouring chromosomal 3 aberrations among South Asian Indian cohort. Methods Based on chromosomal 3 aberration, UM (n = 86) were grouped into monosomy 3 (M3; n = 51) and disomy 3 (D3; n = 35) by chromogenic in-situ hybridisation (CISH). The clinico-pathological features were recorded. miRNA profiling was performed in formalin fixed paraffin embedded (FFPE) UM samples (n = 6) using Agilent, Human miRNA microarray, 8x15KV3 arrays. The association between miRNAs and clinico-pathological features were studied using univariate and multivariate analysis. miRNA-gene targets were predicted using Target-scan and MiRanda database. Significantly dys-regulated miRNAs were validated in FFPE UM (n = 86) and mRNAs were validated in frozen UM (n = 10) by qRT-PCR. Metastasis free-survival and miRNA expressions were analysed by Kaplen-Meier analysis in UM tissues (n = 52). Results Unsupervised analysis revealed 585 differentially expressed miRNAs while supervised analysis demonstrated 82 miRNAs (FDR; Q = 0.0). Differential expression of 8 miRNAs: miR-214, miR-149*, miR-143, miR-146b, miR-199a, let7b, miR-1238 and miR-134 were studied. Gene target prediction revealed SMAD4, WISP1, HIPK1, HDAC8 and C-KIT as the post-transcriptional regulators of miR-146b, miR-199a, miR-1238 and miR-134. Five miRNAs (miR-214, miR146b, miR-143, miR-199a and miR-134) were found to be differentially expressed in M3/ D3 UM tumors. In UM patients with liver metastasis, miR-149* and miR-134 expressions were strongly correlated. Conclusion UM can be stratified using miRNAs from FFPE sections. miRNAs predicting liver metastasis and survival have been identified. Mechanistic linkage of de-regulated miRNA/mRNA expressions provide new insights on their role in UM progression and aggressiveness.
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Affiliation(s)
- Nalini Venkatesan
- Larsen & Toubro Department of Ocular Pathology, Vision Research Foundation, Sankara Nethralaya, 18/41, College road, Chennai—600006, India
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani-333031, Rajasthan, India
| | - Jagat Kanwar
- Nanomedicine-Laboratory of Immunology and Molecular Biomedical Research (NLIMBR), School of Medicine (SoM), Molecular and Medical Research (MMR) Strategic Research Centre, Faculty of Health, Deakin University, Pigdons Road, Waurn Ponds, Geelong, Victoria 3217, Australia
| | - Perinkulam Ravi Deepa
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani-333031, Rajasthan, India
| | - Vikas Khetan
- Department of Vitreoretinal and Ocular Oncology, Medical Research Foundation, Sankara Nethralaya, 18/41, College road, Chennai—600006, India
| | - Tamsyn M. Crowley
- School of Medicine, Deakin University, and Australian Animal Health Laboratories, CSIRO, Australia
| | - Rajeswari Raguraman
- Larsen & Toubro Department of Ocular Pathology, Vision Research Foundation, Sankara Nethralaya, 18/41, College road, Chennai—600006, India
| | - Ganesan Sugneswari
- Department of Vitreoretinal and Ocular Oncology, Medical Research Foundation, Sankara Nethralaya, 18/41, College road, Chennai—600006, India
| | - Pukhraj Rishi
- Department of Vitreoretinal and Ocular Oncology, Medical Research Foundation, Sankara Nethralaya, 18/41, College road, Chennai—600006, India
| | - Viswanathan Natarajan
- Department of Bio-statistics, Medical Research Foundation, Sankara Nethralaya, 41, College road, Chennai—600006, India
| | - Jyotirmay Biswas
- Larsen & Toubro Department of Ocular Pathology, Vision Research Foundation, Sankara Nethralaya, 18/41, College road, Chennai—600006, India
| | - Subramanian Krishnakumar
- Larsen & Toubro Department of Ocular Pathology, Vision Research Foundation, Sankara Nethralaya, 18/41, College road, Chennai—600006, India
- * E-mail:
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CancerNet: a database for decoding multilevel molecular interactions across diverse cancer types. Oncogenesis 2015; 4:e177. [PMID: 26690544 PMCID: PMC4688397 DOI: 10.1038/oncsis.2015.40] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/21/2015] [Accepted: 10/15/2015] [Indexed: 02/08/2023] Open
Abstract
Protein–protein interactions (PPIs) and microRNA (miRNA)–target interactions are important for deciphering the mechanisms of tumorigenesis. However, current PPI databases do not support cancer-specific analysis. Also, no available databases can be used to retrieve cancer-associated miRNA–target interactions. As the pathogenesis of human cancers is affected by several miRNAs rather than a single miRNA, it is needed to uncover miRNA synergism in a systems level. Here for each cancer type, we constructed a miRNA–miRNA functionally synergistic network based on the functions of miRNA targets and their topological features in that cancer PPI network. And for the first time, we report the cancer-specific database CancerNet (http://bis.zju.edu.cn/CancerNet), which contains information about PPIs, miRNA–target interactions and functionally synergistic miRNA–miRNA pairs across 33 human cancer types. In addition, PPI information across 33 main normal tissues and cell types are included. Flexible query methods are allowed to retrieve cancer molecular interactions. Network viewer can be used to visualize interactions that users are interested in. Enrichment analysis tool was designed to detect significantly overrepresented Gene Ontology categories of miRNA targets. Thus, CancerNet serves as a comprehensive platform for assessing the roles of proteins and miRNAs, as well as their interactions across human cancers.
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Venza I, Visalli M, Beninati C, Benfatto S, Teti D, Venza M. IL-10Rα expression is post-transcriptionally regulated by miR-15a, miR-185, and miR-211 in melanoma. BMC Med Genomics 2015; 8:81. [PMID: 26631117 PMCID: PMC4668633 DOI: 10.1186/s12920-015-0156-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/18/2015] [Indexed: 12/14/2022] Open
Abstract
Background IL-10 is an immunoregulatory cytokine that increases during malignant diseases. The purpose of this study was to: i) determine the mRNA amounts of IL-10, IL-10Rα, and IL-10Rβ in cutaneous and uveal melanoma cells and specimens; ii) evaluate their post-transcriptional regulation by miRNAs; iii) ascertain whether miRNA dysregulation may affect IL-10-induced proliferation. Methods Genome-wide miRNA expression profiling was performed using a human microarray platform. The reference gene mRNA was measured through qPCR. miRNAs/mRNAs interactions were predicted by TargetScan, microRNA, and PITA. Transfections of specific miRNA mimics/inhibitors were carried out. Cell proliferation was assessed by MTT assay in the presence of IL-10 after transfection with miRNA mimics/inhibitors. Results There were no differences in IL-10 mRNA levels between any of the 3 melanoma cell lines tested and normal melanocytes. However, lower IL-10Rα expression was found in G361 and OCM-1 cells, and higher levels of IL-10Rβ were observed in G361 cells compared with normal melanocytes. GR-M cells did not exhibit any modifications in IL-10Rα and IL-10Rβ expression. miR-15a, miR-185, miR-211, and miR-30d were upregulated in G361 and OCM-1 cells, remaining at similar levels in GR-M cells. miR-409-3p and miR-605were down-regulated exclusively in G361 cells. Prediction tools revealed that miR-15a, miR-185, and miR-211 targeted IL-10Rα whereas none of the miRNAs exclusively downregulated in G361 cells targeted IL-10Rβ. Luciferase reporter and western blot assays showed that IL-10Rα expression is directly regulated by miR-15a, miR-185, and miR-211, either alone or in combination. An inverse expression pattern between IL-10Rα, on one side, and miR-15a, miR-185, and miR-211 on the other one was also shown in melanoma samples. Ectopic expression of individual miR-15a, miR-185, and miR-211, and even more their co-expression, caused a marked decrease in the proliferation rate of all the cell lines. Likewise, inhibition of any specific miRNA promoted cell growth, an effect that further increased when inhibition concerned all three miRNA. Moreover, specific knockdown of IL-10Rα prevented the proliferative effect of miRNA inhibitors. Conclusions Our results support a key role of IL-10Rα in the development and progression of melanoma and suggest that the IL-10/IL-10 receptor system may become a new therapeutic target for melanoma treatment.
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Affiliation(s)
- Isabella Venza
- Department of Clinical and Experimental Medicine, Azienda Policlinico Universitario G. Martino, viaConsolare Valeria, 1, Messina, 98125, Italy.
| | - Maria Visalli
- Department of Clinical and Experimental Medicine, Azienda Policlinico Universitario G. Martino, viaConsolare Valeria, 1, Messina, 98125, Italy.
| | - Concetta Beninati
- Department of Human Pathology of Adult and Developmental Age "Gaetano Barresi", Azienda PoliclinicoUniversitario G. Martino, via Consolare Valeria, 1, Messina, 98125, Italy. .,Scylla Biotech Srl, University of Messina, Messina, Italy.
| | - Salvatore Benfatto
- Department of Human Pathology of Adult and Developmental Age "Gaetano Barresi", Azienda PoliclinicoUniversitario G. Martino, via Consolare Valeria, 1, Messina, 98125, Italy.
| | - Diana Teti
- Department of Clinical and Experimental Medicine, Azienda Policlinico Universitario G. Martino, viaConsolare Valeria, 1, Messina, 98125, Italy.
| | - Mario Venza
- Department of Clinical and Experimental Medicine, Azienda Policlinico Universitario G. Martino, viaConsolare Valeria, 1, Messina, 98125, Italy.
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Cellular Mechanisms of Oxidative Stress and Action in Melanoma. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2015; 2015:481782. [PMID: 26064422 PMCID: PMC4438193 DOI: 10.1155/2015/481782] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 04/21/2015] [Indexed: 12/14/2022]
Abstract
Most melanomas occur on the skin, but a small percentage of these life-threatening cancers affect other parts of the body, such as the eye and mucous membranes, including the mouth. Given that most melanomas are caused by ultraviolet radiation (UV) exposure, close attention has been paid to the impact of oxidative stress on these tumors. The possibility that key epigenetic enzymes cannot act on a DNA altered by oxidative stress has opened new perspectives. Therefore, much attention has been paid to the alteration of DNA methylation by oxidative stress. We review the current evidence about (i) the role of oxidative stress in melanoma initiation and progression; (ii) the mechanisms by which ROS influence the DNA methylation pattern of transformed melanocytes; (iii) the transformative potential of oxidative stress-induced changes in global and/or local gene methylation and expression; (iv) the employment of this epimutation as a biomarker for melanoma diagnosis, prognosis, and drug resistance evaluation; (v) the impact of this new knowledge in clinical practice for melanoma treatment.
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14
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Li Z, Yu X, Shen J, Jiang Y. MicroRNA dysregulation in uveal melanoma: a new player enters the game. Oncotarget 2015; 6:4562-8. [PMID: 25682876 PMCID: PMC4467099 DOI: 10.18632/oncotarget.2923] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 12/15/2014] [Indexed: 12/15/2022] Open
Abstract
Uveal melanoma is the second most common form of melanoma and a predominant intraocular malignant tumor in adults. The development of uveal melanoma is a multistep process involving genetic and epigenetic alteration of proto-oncogenes and tumor-suppressor genes. Recent discoveries have shed a new light on the involvement of a class of noncoding RNA known as microRNAs (miRNAs) in uveal melanoma. A lot of miRNAs show differential expressions in uveal melanoma tissues and cell lines. Genes coding for these miRNAs have been characterized as novel oncogene and tumor-suppressor genes based on findings that these miRNAs control malignant phenotypes of uveal melanoma cells. Several studies have confirmed that dysregulation of miRNAs promotes cell-cycle progression, confers resistance to apoptosis, and enhances invasiveness and metastasis. Moreover, several miRNAs have also been shown to correlate with uveal melanoma initiation and progression, and thus may be used as biomarkers for early diagnosis and prognosis. Elucidating the biological aspects of miRNA dysregulation may help us better understand the pathogenesis of uveal melanoma and promote the development of miRNA directed-therapeutics against this disease.
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Affiliation(s)
- Zheng Li
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xin Yu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jianxiong Shen
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yang Jiang
- Department of Ophthalmology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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15
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Venza M, Visalli M, Biondo C, Oteri R, Agliano F, Morabito S, Caruso G, Caffo M, Teti D, Venza I. Epigenetic effects of cadmium in cancer: focus on melanoma. Curr Genomics 2015; 15:420-35. [PMID: 25646071 PMCID: PMC4311387 DOI: 10.2174/138920291506150106145932] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 11/07/2014] [Accepted: 11/17/2014] [Indexed: 01/01/2023] Open
Abstract
Cadmium is a highly toxic heavy metal, which has a destroying impact on organs. Exposure to cadmium causes severe health problems to human beings due to its ubiquitous environmental presence and features of the pathologies associated with pro-longed exposure. Cadmium is a well-established carcinogen, although the underlying mechanisms have not been fully under-stood yet. Recently, there has been considerable interest in the impact of this environmental pollutant on the epigenome. Be-cause of the role of epigenetic alterations in regulating gene expression, there is a potential for the integration of cadmium-induced epigenetic alterations as critical elements in the cancer risk assessment process. Here, after a brief review of the ma-jor diseases related to cadmium exposure, we focus our interest on the carcinogenic potential of this heavy metal. Among the several proposed pathogenetic mechanisms, particular attention is given to epigenetic alterations, including changes in DNA methylation, histone modifications and non-coding RNA expression. We review evidence for a link between cadmium-induced epigenetic changes and cell transformation, with special emphasis on melanoma. DNA methylation, with reduced expression of key genes that regulate cell proliferation and apoptosis, has emerged as a possible cadmium-induced epigenetic mechanism in melanoma. A wider comprehension of mechanisms related to this common environmental contaminant would allow a better cancer risk evaluation.
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Affiliation(s)
- Mario Venza
- Department of Experimental Specialistic Medical, Surgical and Odontostomatology Sciences, University of Messina, Messina, Italy
| | - Maria Visalli
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Carmelo Biondo
- Department of Pediatric, Gynecological, Microbiological and Biomedical Sciences, University of Messina, Messina, Italy
| | - Rosaria Oteri
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Federica Agliano
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Silvia Morabito
- Department of Experimental Specialistic Medical, Surgical and Odontostomatology Sciences, University of Messina, Messina, Italy
| | - Gerardo Caruso
- Department of Neurosciences, University of Messina, Messina, Italy
| | - Maria Caffo
- Department of Neurosciences, University of Messina, Messina, Italy
| | - Diana Teti
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Isabella Venza
- Department of Experimental Specialistic Medical, Surgical and Odontostomatology Sciences, University of Messina, Messina, Italy
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16
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Audano M, Ferrari A, Fiorino E, Kuenzl M, Caruso D, Mitro N, Crestani M, De Fabiani E. Energizing Genetics and Epi-genetics: Role in the Regulation of Mitochondrial Function. Curr Genomics 2015; 15:436-56. [PMID: 25646072 PMCID: PMC4311388 DOI: 10.2174/138920291506150106151119] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 11/11/2014] [Accepted: 11/18/2014] [Indexed: 12/15/2022] Open
Abstract
Energy metabolism and mitochondrial function hold a core position in cellular homeostasis. Oxidative metabolism is regulated at multiple levels, ranging from gene transcription to allosteric modulation. To accomplish the fine tuning of these multiple regulatory circuits, the nuclear and mitochondrial compartments are tightly and reciprocally controlled. The fact that nuclear encoded factors, PPARγ coactivator 1α and mitochondrial transcription factor A, play pivotal roles in the regulation of oxidative metabolism and mitochondrial biogenesis is paradigmatic of this crosstalk. Here we provide an updated survey of the genetic and epigenetic mechanisms involved in the control of energy metabolism and mitochondrial function. Chromatin dynamics highly depends on post-translational modifications occurring at specific amino acids in histone proteins and other factors associated to nuclear DNA. In addition to the well characterized enzymes responsible for histone methylation/demethylation and acetylation/deacetylation, other factors have gone on the "metabolic stage". This is the case of the new class of α-ketoglutarate-regulated demethylases (Jumonji C domain containing demethylases) and of the NAD+-dependent deacetylases, also known as sirtuins. Moreover, unexpected features of the machineries involved in mitochondrial DNA (mtDNA) replication and transcription, mitochondrial RNA processing and maturation have recently emerged. Mutations or defects of any component of these machineries profoundly affect mitochondrial activity and oxidative metabolism. Finally, recent evidences support the importance of mtDNA packaging in replication and transcription. These observations, along with the discovery that non-classical CpG islands present in mtDNA undergo methylation, indicate that epigenetics also plays a role in the regulation of the mitochondrial genome function.
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Affiliation(s)
- Matteo Audano
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
| | - Alessandra Ferrari
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
| | - Erika Fiorino
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
| | - Martin Kuenzl
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
| | - Donatella Caruso
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
| | - Nico Mitro
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
| | - Maurizio Crestani
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
| | - Emma De Fabiani
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
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