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da Costa Nunes GG, de Freitas LM, Monte N, Gellen LPA, Santos AP, de Moraes FCA, da Costa ACA, de Lima MC, Fernandes MR, dos Santos SEB, dos Santos NPC. Genomic Variants and Worldwide Epidemiology of Breast Cancer: A Genome-Wide Association Studies Correlation Analysis. Genes (Basel) 2024; 15:145. [PMID: 38397135 PMCID: PMC10888129 DOI: 10.3390/genes15020145] [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: 11/30/2023] [Revised: 12/29/2023] [Accepted: 01/01/2024] [Indexed: 02/25/2024] Open
Abstract
Breast cancer (BCa) is the most common cancer and leading cause of cancer death among women globally. This can be explained by the genetic factor of this disease. This article aims to correlate the epidemiological data, worldwide incidence, and mortality of BCa with the Single-Nucleotide Polymorphisms (SNPs) associated with the susceptibility and severity in different populations. Two hundred and forty genetic variants associated with BCa susceptibility/severity were selected from the literature through Genome-Wide Association Studies (GWAS). The allele frequencies were obtained from the 1000 Genomes Project, and the epidemiological data were obtained from the World Health Organization (WHO). The BCa incidence, mortality rates, and allele frequencies of the variants were evaluated using Pearson's correlation. Our study demonstrated that 11 SNPs (rs3817578, rs4843437, rs3754934, rs61764370, rs780092, rs2290203, rs10411161, rs6001930, rs16886165, rs8051542 and rs4973768) were significantly correlated with the epidemiological data in different ethnic groups. Seven polymorphisms (rs3817578, rs3754934, rs780092, rs2290203, rs10411161, rs6001930 and rs16886165) were inversely correlated with the incidence rate and four polymorphisms (rs4843437, rs61764370, rs8051542 and rs4973768) were directly correlated with the incidence rate. African and South-East Asian populations have a lower risk of developing BCa when evaluated in terms of genetic factors since they possess variants characterized as protective, as their higher incidence is associated with a lower frequency of BCa cases. The genetic variants investigated here are likely to predispose individuals to BCa. The genetic study described here is promising for implementing personalized strategies to screen for breast cancer in diverse populations.
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Affiliation(s)
| | | | - Natasha Monte
- Research Center of Oncology, Federal University of Pará Belém, Belém 66073-000, Brazil
| | | | - Aline Pasquini Santos
- Research Center of Oncology, Federal University of Pará Belém, Belém 66073-000, Brazil
| | | | | | | | | | - Sidney Emanuel Batista dos Santos
- Research Center of Oncology, Federal University of Pará Belém, Belém 66073-000, Brazil
- Laboratory of Human and Medical Genetics, Institute of Biological Science, Federal University of Pará, Belém 66075-110, Brazil
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Kolenda T, Poter P, Guglas K, Kozłowska-Masłoń J, Braska A, Kazimierczak U, Teresiak A. Biological role and diagnostic utility of ribosomal protein L23a pseudogene 53 in cutaneous melanoma. Rep Pract Oncol Radiother 2023; 28:255-270. [PMID: 37456695 PMCID: PMC10348336 DOI: 10.5603/rpor.a2023.0030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/02/2023] [Indexed: 07/18/2023] Open
Abstract
Background Skin melanoma is one of the deadliest types of skin cancer and develops from melanocytes. The genetic aberrations in protein-coding genes are well characterized, but little is known about changes in non-coding RNAs (ncRNAs) such as pseudogenes. Ribosomal protein pseudogenes (RPPs) have been described as the largest group of pseudogenes which are dispersed in the human genome. Materials and methids We looked deeply at the role of one of them, ribosomal protein L23a pseudogene 53 (RPL23AP53), and its potential diagnostic use. The expression level of RPL23AP53 was profiled in melanoma cell lines using real time quantitative reverse transcription polymerase chain reaction (qRT-PCR) and analyzed based on the Cancer Genome Atlas (TCGA) data depending on BRAF status and clinicopathological parameters. Cellular phenotype, which was associated with RPL23AP53 levels, was described based on the REACTOME pathway browser, Gene Set Enrichment Analysis (GSEA) analysis as well as Immune and ESTIMATE Scores. Results We indicted in vitro changes in RPL23AP53 level depending on a cell line, and based on in silico analysis of TCGA samples demonstrated significant differences in RPL23AP53 expression between primary and metastatic melanoma, as well as correlation between RPL23AP53 and overall survival. No differences depending on BRAF status were observed. RPL23AP53 is associated with several signaling pathways and cellular processes. Conclusions This study showed that patients with higher expression of RPL23AP53 displayed changed infiltration of lymphocytes, macrophages, and neutrophils compared to groups with lower expression of RPL23AP53. RPL23AP53 pseudogene is differently expressed in melanoma compared with normal tissue and its expression is associated with cellular proliferation. Thus, it may be considered as an indicator of patients' survival and a marker for the immune profile assessment.
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Affiliation(s)
- Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Centre, Poznan, Poland
| | - Paulina Poter
- Department of Oncologic Pathology and Prophylaxis, Poznan University of Medical Sciences, Greater Poland Cancer Center, Poznan, Poland
- Department of Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Centre, Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warszawa, Poland
| | - Joanna Kozłowska-Masłoń
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Centre, Poznan, Poland
- Faculty of Biology, Institute of Human Biology and Evolution, Adam Mickiewicz University, Poznań, Poland
| | - Alicja Braska
- Research and Implementation Unit, Greater Poland Cancer Centre, Poznan, Poland
| | - Urszula Kazimierczak
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Poznan, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Centre, Poznan, Poland
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Caetano AR, Oliveira RD, Celeiro SP, Freitas AS, Cardoso SM, Gonçalves MST, Baltazar F, Almeida-Aguiar C. Phenolic Compounds Contribution to Portuguese Propolis Anti-Melanoma Activity. Molecules 2023; 28:molecules28073107. [PMID: 37049869 PMCID: PMC10096369 DOI: 10.3390/molecules28073107] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/25/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Melanoma is the deadliest type of skin cancer, with about 61,000 deaths annually worldwide. Late diagnosis increases mortality rates due to melanoma’s capacity to metastasise rapidly and patients’ resistance to the available conventional therapies. Consequently, the interest in natural products as a strategy for drug discovery has been emerging. Propolis, a natural product produced by bees, has several biological properties, including anticancer effects. Propolis from Gerês is one of the most studied Portuguese propolis. Our group has previously demonstrated that an ethanol extract of Gerês propolis collected in 2018 (G18.EE) and its fractions (n-hexane, ethyl acetate, and n-butanol) decrease melanoma cell viability. Out of all the fractions, G18.EE-n-BuOH showed the highest potential as a melanoma pharmacological therapy. Thus, in this work, G18.EE-n-BuOH was fractioned into 17 subfractions whose effect was evaluated in A375 BRAF-mutated melanoma cells. The subfractions with the highest cytotoxic activity were analysed by UPLC-DAD-ESI/MSn in an attempt to understand which phenolic compounds could account for the anti-melanoma activity. The compounds identified are typical of the Gerês propolis, and some of them have already been linked with antitumor effectiveness. These results reaffirm that propolis compounds can be a source of new drugs and the isolation of compounds could allow its use in traditional medicine.
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Affiliation(s)
- Ana Rita Caetano
- Department of Biology, School of Sciences, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
| | - Rafaela Dias Oliveira
- Department of Biology, School of Sciences, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
- ICVS/3B’s-PT Government Associate Laboratory, 4710-057 Braga, Portugal
| | - Sónia Pires Celeiro
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
- ICVS/3B’s-PT Government Associate Laboratory, 4710-057 Braga, Portugal
| | - Ana Sofia Freitas
- Department of Biology, School of Sciences, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
| | - Susana M. Cardoso
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - M. Sameiro T. Gonçalves
- Centre of Chemistry (CQ/UM), Department of Chemistry, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
| | - Fátima Baltazar
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
- ICVS/3B’s-PT Government Associate Laboratory, 4710-057 Braga, Portugal
| | - Cristina Almeida-Aguiar
- Department of Biology, School of Sciences, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
- Correspondence: ; Tel.: +351-253-601-513
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Portuguese Propolis Antitumoral Activity in Melanoma Involves ROS Production and Induction of Apoptosis. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27113533. [PMID: 35684471 PMCID: PMC9182411 DOI: 10.3390/molecules27113533] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/27/2022] [Accepted: 05/29/2022] [Indexed: 12/15/2022]
Abstract
Melanoma is the most aggressive and life-threatening skin cancer type. The melanoma genome is the most frequently mutated, with the BRAF mutation present in 40–60% of melanoma cases. BRAF-mutated melanomas are characterized by a higher aggressiveness and progression. Adjuvant targeted treatments, such as BRAF and MEK inhibitors, are added to surgical excision in BRAF-mutated metastatic melanomas to maximize treatment effectiveness. However, resistance remains the major therapeutic problem. Interest in natural products, like propolis, for therapeutic applications, has increased in the last years. Propolis healing proprieties offer great potential for the development of novel cancer drugs. As the activity of Portuguese propolis has never been studied in melanoma, we evaluated the antitumoral activity of propolis from Gerês (G18.EE) and its fractions (n-hexane, ethyl acetate (EtOAc), and n-butanol) in A375 and WM9 melanoma cell lines. Results from DPPH•/ABTS• radical scavenging assays indicated that the samples had relevant antioxidant activity, however, this was not confirmed in the cell models. G18.EE and its fractions decreased cell viability (SRB assay) and promoted ROS production (DHE/Mitotracker probes by flow cytometry), leading to activation of apoptotic signaling (expression of apoptosis markers). Our results suggest that the n-BuOH fraction has the potential to be explored in the pharmacological therapy of melanoma.
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Wozniak M, Czyz M. The Functional Role of Long Non-Coding RNAs in Melanoma. Cancers (Basel) 2021; 13:cancers13194848. [PMID: 34638331 PMCID: PMC8508152 DOI: 10.3390/cancers13194848] [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: 08/23/2021] [Revised: 09/23/2021] [Accepted: 09/25/2021] [Indexed: 12/15/2022] Open
Abstract
Melanoma is the most lethal skin cancer, with increasing incidence worldwide. The molecular events that drive melanoma development and progression have been extensively studied, resulting in significant improvements in diagnostics and therapeutic approaches. However, a high drug resistance to targeted therapies and adverse effects of immunotherapies are still a major challenge in melanoma treatment. Therefore, the elucidation of molecular mechanisms of melanomagenesis and cancer response to treatment is of great importance. Recently, many studies have revealed the close association of long noncoding RNAs (lncRNAs) with the development of many cancers, including melanoma. These RNA molecules are able to regulate a plethora of crucial cellular processes including proliferation, differentiation, migration, invasion and apoptosis through diverse mechanisms, and even slight dysregulation of their expression may lead to tumorigenesis. lncRNAs are able to bind to protein complexes, DNA and RNAs, affecting their stability, activity, and localization. They can also regulate gene expression in the nucleus. Several functions of lncRNAs are context-dependent. This review summarizes current knowledge regarding the involvement of lncRNAs in melanoma. Their possible role as prognostic markers of melanoma response to treatment and in resistance to therapy is also discussed.
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Peng Q, Wang J. Non-coding RNAs in melanoma: Biological functions and potential clinical applications. MOLECULAR THERAPY-ONCOLYTICS 2021; 22:219-231. [PMID: 34514101 PMCID: PMC8424110 DOI: 10.1016/j.omto.2021.05.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Malignant melanoma (MM) is a malignant tumor that originates from melanocytes and has a high mortality rate. Therefore, early diagnosis and treatment are very important for survival. So far, the exact molecular mechanism leading to the occurrence of melanoma, especially the molecular metastatic mechanism, remains largely unknown. Non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNA (circRNAs), have been investigated and found to play vital roles in regulating tumor occurrence and development, including melanoma. In this review, we summarize the progress of recent research on the effects of ncRNAs on melanoma and attempt to elucidate the role of ncRNAs as molecular markers or potential targets that will provide promising application perspectives on melanoma.
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Affiliation(s)
- Qiu Peng
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410008, China
| | - Jia Wang
- Department of Immunology, Changzhi Medical College, Changzhi, Shanxi 046000 China
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Huang T, Wang M, Huang B, Chang A, Liu F, Zhang Y, Jiang B. Long noncoding RNAs in the mTOR signaling network: biomarkers and therapeutic targets. Apoptosis 2019; 23:255-264. [PMID: 29556906 DOI: 10.1007/s10495-018-1453-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
As an evolutionarily conserved serine/threonine kinase of the phosphoinositide 3-kinase (PI3K) related kinase family, the mechanistic/mammalian target of rapamycin (mTOR) plays vital roles in the PI3K/AKT/mTOR pathway, participating in different cellular processes including cell survival, metabolism and proliferation. Aberrant activity of this signaling pathway may lead to oncogenesis. Over the last two decades, great progress has been made in the understanding of mTOR activation and how its response is counteracted for maintaining tissue homeostasis. Besides regulatory proteins and microRNAs, long noncoding RNA (lncRNA) is another emerging critical layer of the intricate modulatory architecture for the control of the mTOR signaling circuit. Also, the production of numerous lncRNAs is induced by mTOR treatment. These findings offer new perspectives for designing novel diagnostic and therapeutic strategies. In this review, we summarize the interactions between the mTOR signaling pathway and lncRNAs in the development and progression of various types of tumors, focusing on the mechanisms of these interactions, and also discuss the potential use of lncRNAs as biomarkers and therapeutic targets for malignancies.
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Affiliation(s)
- Tinglei Huang
- Oncology Department, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 201900, China
| | - Meiling Wang
- Oncology Department, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 201900, China
| | - Bo Huang
- Oncology Department, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 201900, China
| | - Augustus Chang
- Rutgers University, 604 Allison Road, Piscataway, NJ, 08854, USA
| | - Feng Liu
- Oncology Department, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 201900, China
| | - Yanjie Zhang
- Oncology Department, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 201900, China.
| | - Bin Jiang
- Oncology Department, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 201900, China.
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Siena ÁDD, Plaça JR, Araújo LF, de Barros II, Peronni K, Molfetta G, de Biagi CAO, Espreafico EM, Sousa JF, Silva WA. Whole transcriptome analysis reveals correlation of long noncoding RNA ZEB1-AS1 with invasive profile in melanoma. Sci Rep 2019; 9:11350. [PMID: 31383874 PMCID: PMC6683136 DOI: 10.1038/s41598-019-47363-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 07/09/2019] [Indexed: 02/07/2023] Open
Abstract
Melanoma is the deadliest form of skin cancer, and little is known about the impact of deregulated expression of long noncoding RNAs (lncRNAs) in the progression of this cancer. In this study, we explored RNA-Seq data to search for lncRNAs associated with melanoma progression. We found distinct lncRNA gene expression patterns across melanocytes, primary and metastatic melanoma cells. Also, we observed upregulation of the lncRNA ZEB1-AS1 (ZEB1 antisense RNA 1) in melanoma cell lines. Data analysis from The Cancer Genome Atlas (TCGA) confirmed higher ZEB1-AS1 expression in metastatic melanoma and its association with hotspot mutations in BRAF (B-Raf proto-oncogene, serine/threonine kinase) gene and RAS family genes. In addition, a positive correlation between ZEB1-AS1 and ZEB1 (zinc finger E-box binding homeobox 1) gene expression was verified in primary and metastatic melanomas. Using gene expression signatures indicative of invasive or proliferative phenotypes, we found an association between ZEB1-AS1 upregulation and a transcriptional profile for invasiveness. Enrichment analysis of correlated genes demonstrated cancer genes and pathways associated with ZEB1-AS1. We suggest that the lncRNA ZEB1-AS1 could function by activating ZEB1 gene expression, thereby influencing invasiveness and phenotype switching in melanoma, an epithelial-to-mesenchymal transition (EMT)-like process, which the ZEB1 gene has an essential role.
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Affiliation(s)
- Ádamo Davi Diógenes Siena
- Department of Genetics at Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Center for Cell-Based Therapy (CEPID/FAPESP); National institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil
| | - Jéssica Rodrigues Plaça
- Center for Cell-Based Therapy (CEPID/FAPESP); National institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil.,Center for Integrative Systems Biology (CISBi) - NAP/USP, Ribeirão Preto, Brazil
| | - Luiza Ferreira Araújo
- Department of Genetics at Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Center for Cell-Based Therapy (CEPID/FAPESP); National institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil.,Center for Integrative Systems Biology (CISBi) - NAP/USP, Ribeirão Preto, Brazil
| | - Isabela Ichihara de Barros
- Department of Genetics at Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Center for Cell-Based Therapy (CEPID/FAPESP); National institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil
| | - Kamila Peronni
- Center for Cell-Based Therapy (CEPID/FAPESP); National institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil
| | - Greice Molfetta
- Department of Genetics at Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Center for Cell-Based Therapy (CEPID/FAPESP); National institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil.,Center for Medical Genomics, HCFMRP/USP, Ribeirão Preto, Brazil
| | - Carlos Alberto Oliveira de Biagi
- Department of Genetics at Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Center for Cell-Based Therapy (CEPID/FAPESP); National institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil
| | - Enilza Maria Espreafico
- Department of Cellular and Molecular Biology at Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Josane Freitas Sousa
- Center for Cell-Based Therapy (CEPID/FAPESP); National institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil.,Center for Integrative Systems Biology (CISBi) - NAP/USP, Ribeirão Preto, Brazil.,Institute of Biological Sciences, Federal University of Para, Belem, Brazil
| | - Wilson Araújo Silva
- Department of Genetics at Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil. .,Center for Cell-Based Therapy (CEPID/FAPESP); National institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil. .,Center for Integrative Systems Biology (CISBi) - NAP/USP, Ribeirão Preto, Brazil. .,Center for Medical Genomics, HCFMRP/USP, Ribeirão Preto, Brazil.
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Cardoso C, Serafim RB, Kawakami A, Gonçalves Pereira C, Roszik J, Valente V, Vazquez VL, Fisher DE, Espreafico EM. The lncRNA RMEL3 protects immortalized cells from serum withdrawal-induced growth arrest and promotes melanoma cell proliferation and tumor growth. Pigment Cell Melanoma Res 2018; 32:303-314. [PMID: 30457212 DOI: 10.1111/pcmr.12751] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 12/12/2022]
Abstract
RMEL3 is a recently identified lncRNA associated with BRAFV600E mutation and melanoma cell survival. Here, we demonstrate strong and moderate RMEL3 upregulation in BRAF and NRAS mutant melanoma cells, respectively, compared to melanocytes. High expression is also more frequent in cutaneous than in acral/mucosal melanomas, and analysis of an ICGC melanoma dataset showed that mutations in RMEL3 locus are preponderantly C > T substitutions at dipyrimidine sites including CC > TT, typical of UV signature. RMEL3 mutation does not correlate with RMEL3 levels, but does with poor patient survival, in TCGA melanoma dataset. Accordingly, RMEL3 lncRNA levels were significantly reduced in BRAFV600E melanoma cells upon treatment with BRAF or MEK inhibitors, supporting the notion that BRAF-MEK-ERK pathway plays a role to activate RMEL3 gene transcription. RMEL3 overexpression, in immortalized fibroblasts and melanoma cells, increased proliferation and survival under serum starvation, clonogenic ability, and xenografted melanoma tumor growth. Although future studies will be needed to elucidate the mechanistic activities of RMEL3, our data demonstrate that its overexpression bypasses the need of mitogen activation to sustain proliferation/survival of non-transformed cells and suggest an oncogenic role for RMEL3.
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Affiliation(s)
- Cibele Cardoso
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil.,Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Rodolfo B Serafim
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Akinori Kawakami
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Cristiano Gonçalves Pereira
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Valeria Valente
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil.,School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil.,Center for Cell-Based Therapy CEPID/FAPESP, Ribeirão Preto, Brazil
| | - Vinicius L Vazquez
- Molecular Oncology Research Center (CPOM) and Melanoma/Sarcoma Surgery Department, Barretos Cancer Hospital, Barretos, Brazil
| | - David E Fisher
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Enilza M Espreafico
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
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Fattore L, Mancini R, Ascierto PA, Ciliberto G. The potential of BRAF-associated non-coding RNA as a therapeutic target in melanoma. Expert Opin Ther Targets 2018; 23:53-68. [PMID: 30507327 DOI: 10.1080/14728222.2019.1554057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION The advent of targeted therapies and immune checkpoints inhibitors has enhanced the treatment of metastatic melanomas. Despite striking improvements of patients' survival, drug resistance continues to limit the efficacy of such treatments. Genetic and nongenetic/adaptive mechanisms of resistance could be involved; in the latter mechanism, noncoding RNAs (ncRNAs) are emerging as key players. Areas covered: This article outlines the current knowledge of ncRNA involvement in BRAF-mutant melanomas and the development of resistance to targeted/immunotherapies. We also discuss how ncRNAs can be exploited for the development of therapeutic and diagnostic approaches. Expert opinion: ncRNAs can be envisaged as powerful diagnostics and therapeutics. Despite progress in our knowledge about their deregulation in cancer, it is still difficult to derive universal and robust ncRNAs unique signatures of malignancy for diagnostic purposes, which need validation in large cohort of patients. Also, ncRNA specific targeting to melanoma cells in vivo requires the development of improved systemic delivery tools. In this regard, the development of stable nanodelivery particles seems to offer renewed hope for success in the clinic.
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Affiliation(s)
- Luigi Fattore
- a IRCCS , Regina Elena National Cancer Institute , Rome , Italy
| | - Rita Mancini
- b Department of Molecular and Clinical Medicine , University of Roma "Sapienza" , Rome , Italy
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Araujo LF, Siena ADD, Plaça JR, Brotto DB, Barros II, Muys BR, Biagi CAO, Peronni KC, Sousa JF, Molfetta GA, West LC, West AP, Leopoldino AM, Espreafico EM, Silva WA. Mitochondrial transcription factor A (TFAM) shapes metabolic and invasion gene signatures in melanoma. Sci Rep 2018; 8:14190. [PMID: 30242167 PMCID: PMC6155108 DOI: 10.1038/s41598-018-31170-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 07/27/2018] [Indexed: 12/27/2022] Open
Abstract
Mitochondria are central key players in cell metabolism, and mitochondrial DNA (mtDNA) instability has been linked to metabolic changes that contribute to tumorigenesis and to increased expression of pro-tumorigenic genes. Here, we use melanoma cell lines and metastatic melanoma tumors to evaluate the effect of mtDNA alterations and the expression of the mtDNA packaging factor, TFAM, on energetic metabolism and pro-tumorigenic nuclear gene expression changes. We report a positive correlation between mtDNA copy number, glucose consumption, and ATP production in melanoma cell lines. Gene expression analysis reveals a down-regulation of glycolytic enzymes in cell lines and an up-regulation of amino acid metabolism enzymes in melanoma tumors, suggesting that TFAM may shift melanoma fuel utilization from glycolysis towards amino acid metabolism, especially glutamine. Indeed, proliferation assays reveal that TFAM-down melanoma cell lines display a growth arrest in glutamine-free media, emphasizing that these cells rely more on glutamine metabolism than glycolysis. Finally, our data indicate that TFAM correlates to VEGF expression and may contribute to tumorigenesis by triggering a more invasive gene expression signature. Our findings contribute to the understanding of how TFAM affects melanoma cell metabolism, and they provide new insight into the mechanisms by which TFAM and mtDNA copy number influence melanoma tumorigenesis.
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Affiliation(s)
- L F Araujo
- Department of Genetics-Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- National institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell-based Therapy-CEPID/FAPESP, Ribeirão Preto, Brazil
- Medical Genomics Laboratory, CIPE, AC Camargo Cancer Center, São Paulo, Brazil
| | - A D D Siena
- Department of Genetics-Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- National institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell-based Therapy-CEPID/FAPESP, Ribeirão Preto, Brazil
| | - J R Plaça
- National institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell-based Therapy-CEPID/FAPESP, Ribeirão Preto, Brazil
| | - D B Brotto
- Department of Genetics-Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- National institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell-based Therapy-CEPID/FAPESP, Ribeirão Preto, Brazil
| | - I I Barros
- Department of Genetics-Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- National institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell-based Therapy-CEPID/FAPESP, Ribeirão Preto, Brazil
| | - B R Muys
- Department of Genetics-Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- National institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell-based Therapy-CEPID/FAPESP, Ribeirão Preto, Brazil
| | - C A O Biagi
- Department of Genetics-Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- National institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell-based Therapy-CEPID/FAPESP, Ribeirão Preto, Brazil
| | - K C Peronni
- National institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell-based Therapy-CEPID/FAPESP, Ribeirão Preto, Brazil
| | - J F Sousa
- Department of Genetics-Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- National institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell-based Therapy-CEPID/FAPESP, Ribeirão Preto, Brazil
| | - G A Molfetta
- Department of Genetics-Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- National institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell-based Therapy-CEPID/FAPESP, Ribeirão Preto, Brazil
| | - L C West
- Microbial Pathogenesis & Immunology, Health Science Center, Texas A&M University, College Station, USA
| | - A P West
- Microbial Pathogenesis & Immunology, Health Science Center, Texas A&M University, College Station, USA
| | - A M Leopoldino
- Department of Clinical Analysis-Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - E M Espreafico
- Department of Cellular and Molecular Biology-Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - W A Silva
- Department of Genetics-Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
- National institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell-based Therapy-CEPID/FAPESP, Ribeirão Preto, Brazil.
- Center for Integrative System Biology-CISBi-NAP/USP, University of São Paulo, Ribeirão Preto, Brazil.
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12
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Goedert L, Pereira CG, Roszik J, Plaça JR, Cardoso C, Chen G, Deng W, Yennu-Nanda VG, Silva WA, Davies MA, Espreafico EM. RMEL3, a novel BRAFV600E-associated long noncoding RNA, is required for MAPK and PI3K signaling in melanoma. Oncotarget 2017; 7:36711-36718. [PMID: 27167340 PMCID: PMC5095033 DOI: 10.18632/oncotarget.9164] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 04/16/2016] [Indexed: 11/25/2022] Open
Abstract
Previous work identified RMEL3 as a lncRNA with enriched expression in melanoma. Analysis of The Cancer Genome Atlas (TCGA) data confirmed RMEL3 enriched expression in melanoma and demonstrated its association with the presence of BRAFV600E. RMEL3 siRNA-mediated silencing markedly reduced (95%) colony formation in different BRAFV600E melanoma cell lines. Multiple genes of the MAPK and PI3K pathways found to be correlated with RMEL3 in TCGA samples were experimentally confirmed. RMEL3 knockdown led to downregulation of activators or effectors of these pathways, including FGF2, FGF3, DUSP6, ITGB3 and GNG2. RMEL3 knockdown induces gain of protein levels of tumor suppressor PTEN and the G1/S cyclin-Cdk inhibitors p21 and p27, as well as a decrease of pAKT (T308), BRAF, pRB (S807, S811) and cyclin B1. Consistently, knockdown resulted in an accumulation of cells in G1 phase and subG0/G1 in an asynchronously growing population. Thus, TCGA data and functional experiments demonstrate that RMEL3 is required for MAPK and PI3K signaling, and its knockdown decrease BRAFV600E melanoma cell survival and proliferation.
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Affiliation(s)
- Lucas Goedert
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.,National Institute of Science and Technology in Stem Cell and Cell Therapy and Center for Cell-Based Therapy, Ribeirão Preto, São Paulo, Brazil
| | - Cristiano G Pereira
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Jessica R Plaça
- National Institute of Science and Technology in Stem Cell and Cell Therapy and Center for Cell-Based Therapy, Ribeirão Preto, São Paulo, Brazil.,Clinical Oncology, Stem Cell and Cell Therapy Program, Ribeirão Preto Medical School, Ribeirão Preto, São Paulo, Brazil
| | - Cibele Cardoso
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Guo Chen
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Wanleng Deng
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Vashisht Gopal Yennu-Nanda
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Wilson A Silva
- National Institute of Science and Technology in Stem Cell and Cell Therapy and Center for Cell-Based Therapy, Ribeirão Preto, São Paulo, Brazil.,Department of Genetics, Ribeirão Preto Medical School, and Center for Integrative System Biology (CISBi-NAP/USP), University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Michael A Davies
- Clinical Oncology, Stem Cell and Cell Therapy Program, Ribeirão Preto Medical School, Ribeirão Preto, São Paulo, Brazil
| | - Enilza M Espreafico
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
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13
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Bird AD, Greatorex S, Reser D, Lavery GG, Cole TJ. Hydroxysteroid dehydrogenase HSD1L is localised to the pituitary-gonadal axis of primates. Endocr Connect 2017; 6:489-499. [PMID: 28871060 PMCID: PMC5592779 DOI: 10.1530/ec-17-0119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 08/07/2017] [Indexed: 01/03/2023]
Abstract
Steroid hormones play clinically important and specific regulatory roles in the development, growth, metabolism, reproduction and brain function in human. The type 1 and 2 11-beta hydroxysteroid dehydrogenase enzymes (11β-HSD1 and 2) have key roles in the pre-receptor modification of glucocorticoids allowing aldosterone regulation of blood pressure, control of systemic fluid and electrolyte homeostasis and modulation of integrated metabolism and brain function. Although the activity and function of 11β-HSDs is thought to be understood, there exists an open reading frame for a distinct 11βHSD-like gene; HSD11B1L, which is present in human, non-human primate, sheep, pig and many other higher organisms, whereas an orthologue is absent in the genomes of mouse, rat and rabbit. We have now characterised this novel HSD11B1L gene as encoded by 9 exons and analysis of EST library transcripts indicated the use of two alternate ATG start sites in exons 2 and 3, and alternate splicing in exon 9. Relatively strong HSD11B1L gene expression was detected in human, non-human primate and sheep tissue samples from the brain, ovary and testis. Analysis in non-human primates and sheep by immunohistochemistry localised HSD11B1L protein to the cytoplasm of ovarian granulosa cells, testis Leydig cells, and gonadatroph cells in the anterior pituitary. Intracellular localisation analysis in transfected human HEK293 cells showed HSD1L protein within the endoplasmic reticulum and sequence analysis suggests that similar to 11βHSD1 it is membrane bound. The endogenous substrate of this third HSD enzyme remains elusive with localisation and expression data suggesting a reproductive hormone as a likely substrate.
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Affiliation(s)
- A Daniel Bird
- Department of Biochemistry and Molecular BiologyMonash University, Melbourne, Victoria, Australia
| | - Spencer Greatorex
- Department of Biochemistry and Molecular BiologyMonash University, Melbourne, Victoria, Australia
| | - David Reser
- Department of PhysiologyMonash University, Melbourne, Victoria, Australia
| | - Gareth G Lavery
- Institute of Metabolism and Systems Research2nd Floor IBR Tower, University of Birmingham, Birmingham, UK
- Centre for EndocrinologyDiabetes and Metabolism, Birmingham Health Partners, Birmingham, UK
| | - Timothy J Cole
- Department of Biochemistry and Molecular BiologyMonash University, Melbourne, Victoria, Australia
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14
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Hulstaert E, Brochez L, Volders PJ, Vandesompele J, Mestdagh P. Long non-coding RNAs in cutaneous melanoma: clinical perspectives. Oncotarget 2017; 8:43470-43480. [PMID: 28415644 PMCID: PMC5522162 DOI: 10.18632/oncotarget.16478] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/13/2017] [Indexed: 02/06/2023] Open
Abstract
Metastatic melanoma of the skin has a high mortality despite the recent introduction of targeted therapy and immunotherapy. Long non-coding RNAs (lncRNAs) are defined as transcripts of more than 200 nucleotides in length that lack protein-coding potential. There is growing evidence that lncRNAs play an important role in gene regulation, including oncogenesis. We present 13 lncRNA genes involved in the pathogenesis of cutaneous melanoma through a variety of pathways and molecular interactions. Some of these lncRNAs are possible biomarkers or therapeutic targets for malignant melanoma.
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Affiliation(s)
- Eva Hulstaert
- Department of Dermatology, Ghent University Hospital, Ghent, Belgium
| | - Lieve Brochez
- Department of Dermatology, Ghent University Hospital, Ghent, Belgium
| | - Pieter-Jan Volders
- Center for Medical Genetics, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Pieter Mestdagh
- Center for Medical Genetics, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
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15
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Richtig G, Ehall B, Richtig E, Aigelsreiter A, Gutschner T, Pichler M. Function and Clinical Implications of Long Non-Coding RNAs in Melanoma. Int J Mol Sci 2017; 18:E715. [PMID: 28350340 PMCID: PMC5412301 DOI: 10.3390/ijms18040715] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 03/16/2017] [Accepted: 03/17/2017] [Indexed: 02/06/2023] Open
Abstract
Metastatic melanoma is the most deadly type of skin cancer. Despite the success of immunotherapy and targeted agents, the majority of patients experience disease recurrence upon treatment and die due to their disease. Long non-coding RNAs (lncRNAs) are a new subclass of non-protein coding RNAs involved in (epigenetic) regulation of cell growth, invasion, and other important cellular functions. Consequently, recent research activities focused on the discovery of these lncRNAs in a broad spectrum of human diseases, especially cancer. Additional efforts have been undertaken to dissect the underlying molecular mechanisms employed by lncRNAs. In this review, we will summarize the growing evidence of deregulated lncRNA expression in melanoma, which is linked to tumor growth and progression. Moreover, we will highlight specific molecular pathways and modes of action for some well-studied lncRNAs and discuss their potential clinical implications.
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Affiliation(s)
- Georg Richtig
- Institute of Experimental and Clinical Pharmacology, Medical University of Graz, Graz 8010, Austria.
- Department of Dermatology, Medical University of Graz, Graz 8036, Austria.
| | - Barbara Ehall
- Institute for Pathology, Medical University of Graz, Graz 8036, Austria.
- Division of Hematology, Department of Internal Medicine, Medical University of Graz, Graz 8036, Austria.
| | - Erika Richtig
- Department of Dermatology, Medical University of Graz, Graz 8036, Austria.
| | | | - Tony Gutschner
- Faculty of Medicine, Martin-Luther-University Halle-Wittenberg, Halle (Saale) 06120, Germany.
| | - Martin Pichler
- Division of Clinical Oncology, Department of Medicine, Medical University of Graz, Graz 8036, Austria.
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16
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Silva-Oliveira RJ, Silva VAO, Martinho O, Cruvinel-Carloni A, Melendez ME, Rosa MN, de Paula FE, de Souza Viana L, Carvalho AL, Reis RM. Cytotoxicity of allitinib, an irreversible anti-EGFR agent, in a large panel of human cancer-derived cell lines: KRAS mutation status as a predictive biomarker. Cell Oncol (Dordr) 2016; 39:253-63. [DOI: 10.1007/s13402-016-0270-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2016] [Indexed: 12/27/2022] Open
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17
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TANG MINGRUI, WANG YUXIN, GUO SHU, HAN SIYUAN, LI HEHUAN, JIN SHIFENG. Prognostic significance of in situ and plasma levels of transforming growth factor β1, -2 and -3 in cutaneous melanoma. Mol Med Rep 2015; 11:4508-12. [DOI: 10.3892/mmr.2015.3250] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 01/02/2015] [Indexed: 11/05/2022] Open
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18
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Akrami R, Jacobsen A, Hoell J, Schultz N, Sander C, Larsson E. Comprehensive analysis of long non-coding RNAs in ovarian cancer reveals global patterns and targeted DNA amplification. PLoS One 2013; 8:e80306. [PMID: 24265805 PMCID: PMC3827191 DOI: 10.1371/journal.pone.0080306] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 10/01/2013] [Indexed: 12/19/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging as potent regulators of cell physiology, and recent studies highlight their role in tumor development. However, while established protein-coding oncogenes and tumor suppressors often display striking patterns of focal DNA copy-number alteration in tumors, similar evidence is largely lacking for lncRNAs. Here, we report on a genomic analysis of GENCODE lncRNAs in high-grade serous ovarian adenocarcinoma, based on The Cancer Genome Atlas (TCGA) molecular profiles. Using genomic copy-number data and deep coverage transcriptome sequencing, we derived dual copy-number and expression data for 10,419 lncRNAs across 407 primary tumors. We describe global correlations between lncRNA copy-number and expression, and associate established expression subtypes with distinct lncRNA signatures. By examining regions of focal copy-number change that lack protein-coding targets, we identified an intergenic lncRNA on chromosome 1, OVAL, that shows narrow focal genomic amplification in a subset of tumors. While weakly expressed in most tumors, focal amplification coincided with strong OVAL transcriptional activation. Screening of 16 other cancer types revealed similar patterns in serous endometrial carcinomas. This shows that intergenic lncRNAs can be specifically targeted by somatic copy-number amplification, suggestive of functional involvement in tumor initiation or progression. Our analysis provides testable hypotheses and paves the way for further study of lncRNAs based on TCGA and other large-scale cancer genomics datasets.
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Affiliation(s)
- Rozita Akrami
- Department of Medical Biochemistry & Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anders Jacobsen
- Computational Biology Center, Memorial Sloan- Kettering Cancer Center, New York, New York, United States of America
| | - Jessica Hoell
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Nikolaus Schultz
- Computational Biology Center, Memorial Sloan- Kettering Cancer Center, New York, New York, United States of America
| | - Chris Sander
- Computational Biology Center, Memorial Sloan- Kettering Cancer Center, New York, New York, United States of America
| | - Erik Larsson
- Department of Medical Biochemistry & Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- * E-mail:
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