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Hossain A, Ahsan A, Hasan I, Sohel, Khan A, Somadder PD, Monjur S, Miah S, Kibria KMK, Ahmed K, Rahman H. Screening out molecular pathways and prognostic biomarkers of ultraviolet-mediated melanoma through computational techniques. Int J Biol Markers 2024; 39:118-129. [PMID: 38410032 DOI: 10.1177/03936155241230968] [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] [Indexed: 02/28/2024]
Abstract
PURPOSE Ultraviolet radiation causes skin cancer, but the exact mechanism by which it occurs and the most effective methods of intervention to prevent it are yet unknown. For this purpose, our study will use bioinformatics and systems biology approaches to discover potential biomarkers of skin cancer for early diagnosis and prevention of disease with applicable clinical treatments. METHODS This study compared gene expression and protein levels in ultraviolet-mediated cultured keratinocytes and adjacent normal skin tissue using RNA sequencing data from the National Center for Biotechnology Information-Gene Expression Omnibus (NCBI-GEO) database. Then, pathway analysis was employed with a selection of hub genes from the protein-protein interaction (PPI) network and the survival and expression profiles. Finally, potential clinical biomarkers were validated by receiver operating characteristic (ROC) curve analysis. RESULTS We identified 32 shared differentially expressed genes (DEGs) by analyzing three different subsets of the GSE85443 dataset. Skin cancer development is related to the control of several DEGs through cyclin-dependent protein serine/threonine kinase activity, cell cycle regulation, and activation of the NIMA kinase pathways. The cytoHubba plugin in Cytoscape identified 12 hub genes from PPI; among these 3 DEGs, namely, AURKA, CDK4, and PLK1 were significantly associated with survival (P < 0.05) and highly expressed in skin cancer tissues. For validation purposes, ROC curve analysis indicated two biomarkers: AURKA (area under the curve (AUC) value = 0.8) and PLK1 (AUC value = 0.7), which were in an acceptable range. CONCLUSIONS Further translational research, including clinical experiments, teratogenicity tests, and in-vitro or in-vivo studies, will be performed to evaluate the expression of these identified biomarkers regarding the prognosis of skin cancer patients.
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Affiliation(s)
- Arju Hossain
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Asif Ahsan
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Imran Hasan
- Department of Computer Science and Engineering, Islamic University, Kushtia, Bangladesh
| | - Sohel
- Department of Biochemistry and Molecular Biology, Primeasia University, Dhaka, Bangladesh
| | - Arif Khan
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Dhaka, Bangladesh
| | - Pratul Dipta Somadder
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Sumaiya Monjur
- Department of Otolaryngology and Head-Neck Surgery, Dhaka Medical College and Hospital, Dhaka, Bangladesh
| | - Sipon Miah
- Department of Information and communication Technology, Islamic University, Kushtia, Bangladesh
| | - K M Kaderi Kibria
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Kawsar Ahmed
- Department of Electrical and Computer Engineering, University of Saskatchewan, Saskatoon, Canada
- Group of Biophotomatiχ, Department of Information and Communication Technology, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia, Bangladesh
- Center for Advanced Bioinformatics and Artificial Intelligence Research, Islamic University, Kushtia, Bangladesh
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DeSouza NR, Quaranto D, Carnazza M, Jarboe T, Tiwari RK, Geliebter J. Interactome of Long Non-Coding RNAs: Transcriptomic Expression Patterns and Shaping Cancer Cell Phenotypes. Int J Mol Sci 2023; 24:9914. [PMID: 37373059 DOI: 10.3390/ijms24129914] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
RNA biology has gained extensive recognition in the last two decades due to the identification of novel transcriptomic elements and molecular functions. Cancer arises, in part, due to the accumulation of mutations that greatly contribute to genomic instability. However, the identification of differential gene expression patterns of wild-type loci has exceeded the boundaries of mutational study and has significantly contributed to the identification of molecular mechanisms that drive carcinogenic transformation. Non-coding RNA molecules have provided a novel avenue of exploration, providing additional routes for evaluating genomic and epigenomic regulation. Of particular focus, long non-coding RNA molecule expression has been demonstrated to govern and direct cellular activity, thus evidencing a correlation between aberrant long non-coding RNA expression and the pathological transformation of cells. lncRNA classification, structure, function, and therapeutic utilization have expanded cancer studies and molecular targeting, and understanding the lncRNA interactome aids in defining the unique transcriptomic signatures of cancer cell phenotypes.
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Affiliation(s)
- Nicole R DeSouza
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Danielle Quaranto
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Michelle Carnazza
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Tara Jarboe
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Raj K Tiwari
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
- Department of Otolaryngology, New York Medical College, Valhalla, NY 10591, USA
| | - Jan Geliebter
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
- Department of Otolaryngology, New York Medical College, Valhalla, NY 10591, USA
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3
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de Souza IR, Iulini M, Galbiati V, Silva EZM, Sivek TW, Rodrigues AC, Gradia DF, Pestana CB, Leme DM, Corsini E. An integrated in silico-in vitro investigation to assess the skin sensitization potential of 4-Octylphenol. Toxicology 2023; 493:153548. [PMID: 37207816 DOI: 10.1016/j.tox.2023.153548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/04/2023] [Accepted: 05/16/2023] [Indexed: 05/21/2023]
Abstract
One of the major challenges in chemical toxicity testing is the possibility to protect human health against adverse effects with non-animal methods. In this paper, 4-Octylphenol (OP) was tested for skin sensitization and immunomodulatory effects using an integrated in silico-in vitro test approach. In silico tools (QSAR TOOLBOX 4.5, ToxTree and VEGA) were used together with several in vitro tests including HaCaT cells (quantification of IL-6; IL-8; IL-1α and IL-18 by ELISA and expression of genes TNF, IL1A, IL6 and IL8 by RT- qPCR), RHE model (quantification of IL-6; IL-8; IL-1α and IL-18 by ELISA) and THP-1 activation assay (CD86/CD54 expression and IL-8 release). Additionally, the immunomodulatory effect of OP was investigated using lncRNAs MALAT1 and NEAT1 expression and LPS-induced THP-1 activation (CD86/CD54 expression and IL-8 release). The in silico tools predicted OP as a sensitizer. In vitro tests are also concordant with the in silico prediction. OP increased IL-6 expression (HaCaT cells); IL-18 and IL-8 expressions (RHE model). An irritant potential was also shown by a great expression of IL-1α (RHE model); and increased expression of CD54 marker and IL-8 in THP-1 cells. Immunomodulatory effects of OP were demonstrated by the downregulation of NEAT1, MALAT1 (epigenetic markers), IL6 and IL8; and an increase in LPS-induced CD54 and IL-8 expressions. Overall, results indicate that OP is a skin sensitizer, being positive in three key events of the AOP for skin sensitization, also showing immunomodulatory effects.
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Affiliation(s)
- Isisdoris Rodrigues de Souza
- Graduate Program in Genetics, Department of Genetics - Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Martina Iulini
- Laboratory of Toxicology, Department of Pharmacological and Biomolecular Sciences 'Rodolfo Paoletti', Università Degli Studi di Milano, Milan, Italy
| | - Valentina Galbiati
- Laboratory of Toxicology, Department of Pharmacological and Biomolecular Sciences 'Rodolfo Paoletti', Università Degli Studi di Milano, Milan, Italy.
| | - Enzo Zini Moreira Silva
- Graduate Program in Genetics, Department of Genetics - Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Tainá Wilke Sivek
- Graduate Program in Genetics, Department of Genetics - Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Ana Carolina Rodrigues
- Graduate Program in Genetics, Department of Genetics - Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Daniela Fiori Gradia
- Graduate Program in Genetics, Department of Genetics - Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Cynthia Bomfim Pestana
- Graduate Program in Genetics, Department of Genetics - Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Daniela Morais Leme
- Graduate Program in Genetics, Department of Genetics - Federal University of Paraná (UFPR), Curitiba, PR, Brazil; National Institute for Alternative Technologies of Detection, Toxicological Evaluation and Removal of Micropollutants and Radioactives (INCT-DATREM), Institute of Chemistry, Araraquara, SP, Brazil
| | - Emanuela Corsini
- Laboratory of Toxicology, Department of Pharmacological and Biomolecular Sciences 'Rodolfo Paoletti', Università Degli Studi di Milano, Milan, Italy
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Pan W, Chai B, Li L, Lu Z, Ma Z. p53/MicroRNA-34 axis in cancer and beyond. Heliyon 2023; 9:e15155. [PMID: 37095919 PMCID: PMC10121403 DOI: 10.1016/j.heliyon.2023.e15155] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/25/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
Cancer is serious endangers human life. After a long period of research and accumulation, people's understanding of cancer and the corresponding treatment methods are constantly developing. p53 is an important tumor suppressor gene. With the more in-depth understanding of the structure and function of p53, the more importance of this tumor suppressor gene is realized in the process of inhibiting tumor formation. MicroRNAs (miRNAs) are important regulatory molecules with a length of about 22nucleotides (nt), which belong to non-coding RNA and play an important role in the occurrence and development of tumors. miR-34 is currently considered to be a master regulator of tumor suppression. The positive feedback regulatory network formed by p53 and miR-34 can inhibit the growth and metastasis of tumor cells and inhibit tumor stem cells. This review focuses on the latest progress of p53/miR-34 regulatory network, and discusses its application in tumor diagnosis and treatment.
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Leitner N, Ertl R, Gabner S, Fuchs-Baumgartinger A, Walter I, Hlavaty J. Isolation and Characterization of Novel Canine Osteosarcoma Cell Lines from Chemotherapy-Naïve Patients. Cells 2023; 12:cells12071026. [PMID: 37048099 PMCID: PMC10093184 DOI: 10.3390/cells12071026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
The present study aimed to establish novel canine osteosarcoma cell lines (COS3600, COS3600B, COS4074) and characterize the recently described COS4288 cells. The established D-17 cell line served as a reference. Analyzed cell lines differed notably in their biological characteristics. Calculated doubling times were between 22 h for COS3600B and 426 h for COS4074 cells. COS3600B and COS4288 cells produced visible colonies after anchorage-independent growth in soft agar. COS4288 cells were identified as cells with the highest migratory capacity. All cells displayed the ability to invade through an artificial basement membrane matrix. Immunohistochemical analyses revealed the mesenchymal origin of all COS cell lines as well as positive staining for the osteosarcoma-relevant proteins alkaline phosphatase and karyopherin α2. Expression of p53 was confirmed in all tested cell lines. Gene expression analyses of selected genes linked to cellular immune checkpoints (CD270, CD274, CD276), kinase activity (MET, ERBB2), and metastatic potential (MMP-2, MMP-9) as well as selected long non-coding RNA (MALAT1) and microRNAs (miR-9, miR-34a, miR-93) are provided. All tested cell lines were able to grow as multicellular spheroids. In all spheroids except COS4288, calcium deposition was detected by von Kossa staining. We believe that these new cell lines serve as useful biological models for future studies.
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Affiliation(s)
- Natascha Leitner
- Institute of Morphology, Working Group Histology, University of Veterinary Medicine, Veterinaerplatz 1, A-1210 Vienna, Austria
| | - Reinhard Ertl
- VetCore Facility for Research, University of Veterinary Medicine, Veterinaerplatz 1, A-1210 Vienna, Austria
| | - Simone Gabner
- Institute of Morphology, Working Group Histology, University of Veterinary Medicine, Veterinaerplatz 1, A-1210 Vienna, Austria
| | | | - Ingrid Walter
- Institute of Morphology, Working Group Histology, University of Veterinary Medicine, Veterinaerplatz 1, A-1210 Vienna, Austria
- VetCore Facility for Research, University of Veterinary Medicine, Veterinaerplatz 1, A-1210 Vienna, Austria
| | - Juraj Hlavaty
- Institute of Morphology, Working Group Histology, University of Veterinary Medicine, Veterinaerplatz 1, A-1210 Vienna, Austria
- Correspondence: ; Tel.: +431-250-77-3402; Fax: +431-250-77-3490
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Mekky RY, Ragab MF, Manie T, Attia AA, Youness RA. MALAT-1: Immunomodulatory lncRNA hampering the innate and the adaptive immune arms in triple negative breast cancer. Transl Oncol 2023; 31:101653. [PMID: 36907052 PMCID: PMC10025146 DOI: 10.1016/j.tranon.2023.101653] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/05/2023] [Accepted: 03/05/2023] [Indexed: 03/13/2023] Open
Abstract
BACKGROUND Triple negative breast cancer (TNBC) is known as hot immunogenic tumor. Yet, it is one of the most aggressive BC subtypes. TNBC evolve several tactics to evade the immune surveillance phenomena, one of which is shedding of natural killer (NK) cells activating immune ligands such as MICA/B and/or by inducing the expression of the immune checkpoints such as PD-L1 and B7-H4. MALAT-1 is an oncogenic lncRNA. MALAT-1 immunogenic profile is not well investigated. AIM The study aims at exploring the immunogenic role of MALAT-1 in TNBC patients and cell lines and to identify its molecular mechanism in altering both innate and adaptive immune cells present at the tumor microenvironment of TNBC METHODS: BC patients (n = 35) were recruited. Primary NK cells and cytotoxic T lymphocytes were isolated from normal individuals using the negative selection method. MDA-MB-231 cells were cultured and transfected by several oligonucleotides by lipofection technique. Screening of ncRNAs was performed using q-RT-PCR. Immunological functional analysis experiments were performed upon co-culturing primary natural killer cells and cytotoxic T lymphocytes using LDH assay. Bioinformatics analysis was performed to identify potential microRNAs targeted by MALAT-1. RESULTS MALAT-1 expression was significantly upregulated in BC patinets with a profound expression in TNBC patients compared to their normal counterparts. Correlation analysis revealed a positive correlation between MALAT-1, tumor size and lymph node metastasis. Knocking down of MALAT-1 in MDA-MB-231 cells resulted in a significant induction of MICA/B, repression of PD-L1 and B7-H4 expression levels. Enhancement of cytotoxic activity of co-cultured NK and CD8+ cells with MALAT-1 siRNAs transfected MDA-MB-231 cells. In silico analysis revealed that miR-34a and miR-17-5p are potential targets to MALAT-1; accordingly, they were found to be downregulated in BC patients. Forcing the expression of miR-34a in MDA-MB-231 cells resulted in a significant induction in MICA/B levels. Ectopic expression of miR-17-5p in MDA-MB-231 cells significantly repressed the expression of PD-L1 and B7-H4 checkpoints. Validations of MALAT-1/miR-34a" and "MALAT-1/miR-17-5p axes were performed by a series of co-transfections and functional assessment of cytotoxic profile of primary immune cells. CONCLUSION This study proposes a novel epigenetic alteration exerted by TNBC cells mainly by inducing the expression of MALAT-1 lncRNA. MALAT-1 mediates innate and adaptive immune suppression events partially via targeting miR-34a/MICA/B and miR-175p/PD-L1/B7-H4 axes in TNBC patients and cell lines.
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Affiliation(s)
- Radwa Y Mekky
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA University), Cairo 12622, Egypt
| | - Mai F Ragab
- Pharmacology Department, School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, Cairo 11835, Egypt
| | - Tamer Manie
- Department of Breast Surgery, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Abdelrahman A Attia
- General Surgery Department, Ain Shams University, Demerdash Hospital, Cairo, Egypt
| | - Rana A Youness
- Biology and Biochemistry Department, Molecular Genetics Research Team (MGRT), School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, Cairo 11835, Egypt.
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Saklani N, Chauhan V, Akhtar J, Upadhyay SK, Sirdeshmukh R, Gautam P. In silico analysis to identify novel ceRNA regulatory axes associated with gallbladder cancer. Front Genet 2023; 14:1107614. [PMID: 36873948 PMCID: PMC9978489 DOI: 10.3389/fgene.2023.1107614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/03/2023] [Indexed: 02/18/2023] Open
Abstract
Competitive endogenous RNA (ceRNA) networks are reported to play a crucial role in regulating cancer-associated genes. Identification of novel ceRNA networks in gallbladder cancer (GBC) may improve the understanding of its pathogenesis and might yield useful leads on potential therapeutic targets for GBC. For this, a literature survey was done to identify differentially expressed lncRNAs (DELs), miRNAs (DEMs), mRNAs (DEGs) and proteins (DEPs) in GBC. Ingenuity pathway analysis (IPA) using DEMs, DEGs and DEPs in GBC identified 242 experimentally observed miRNA-mRNA interactions with 183 miRNA targets, of these 9 (CDX2, MTDH, TAGLN, TOP2A, TSPAN8, EZH2, TAGLN2, LMNB1, and PTMA) were reported at both mRNA and protein levels. Pathway analysis of 183 targets revealed p53 signaling among the top pathway. Protein-protein interaction (PPI) analysis of 183 targets using the STRING database and cytoHubba plug-in of Cytoscape software revealed 5 hub molecules, of which 3 of them (TP53, CCND1 and CTNNB1) were associated with the p53 signaling pathway. Further, using Diana tools and Cytoscape software, novel lncRNA-miRNA-mRNA networks regulating the expression of TP53, CCND1, CTNNB1, CDX2, MTDH, TOP2A, TSPAN8, EZH2, TAGLN2, LMNB1, and PTMA were constructed. These regulatory networks may be experimentally validated in GBC and explored for therapeutic applications.
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Affiliation(s)
- Neeraj Saklani
- Laboratory of Molecular Oncology, ICMR- National Institute of Pathology, New Delhi, India
| | - Varnit Chauhan
- Department of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, India
| | - Javed Akhtar
- Laboratory of Molecular Oncology, ICMR- National Institute of Pathology, New Delhi, India
| | - Santosh Kumar Upadhyay
- Department of Biotechnology, Sir J. C. Bose Technical Campus, Bhimtal, Kumaun University, Nainital, Uttarakhand, India
| | - Ravi Sirdeshmukh
- Manipal Academy of Higher Education (MAHE), Manipal, India.,Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - Poonam Gautam
- Laboratory of Molecular Oncology, ICMR- National Institute of Pathology, New Delhi, India
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Zhou W, Xu X, Cen Y, Chen J. The role of lncRNAs in the tumor microenvironment and immunotherapy of melanoma. Front Immunol 2022; 13:1085766. [PMID: 36601121 PMCID: PMC9806239 DOI: 10.3389/fimmu.2022.1085766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Melanoma is one of the most lethal tumors with highly aggressive and metastatic properties. Although immunotherapy and targeted therapy have certain therapeutic effects in melanoma, a significant proportion of patients still have drug resistance after treatment. Recent studies have shown that long noncoding RNAs (lncRNAs) are widely recognized as regulatory factors in cancer. They can regulate numerous cellular processes, including cell proliferation, metastasis, epithelial-mesenchymal transition (EMT) progression and the immune microenvironment. The role of lncRNAs in malignant tumors has received much attention, whereas the relationship between lncRNAs and melanoma requires further investigation. Our review summarizes tumor suppressive and oncogenic lncRNAs closely related to the occurrence and development of melanoma. We summarize the role of lncRNAs in the immune microenvironment, immunotherapy and targeted therapy to provide new targets and therapeutic methods for clinical treatment.
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Long Noncoding RNA LINC02249 Is a Prognostic Biomarker and Correlates with Immunosuppressive Microenvironment in Skin Cutaneous Melanoma. JOURNAL OF ONCOLOGY 2022; 2022:2054901. [PMID: 36117849 PMCID: PMC9473915 DOI: 10.1155/2022/2054901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/08/2022] [Accepted: 08/11/2022] [Indexed: 11/25/2022]
Abstract
Skin cutaneous melanoma (SKCM) is one of the most aggressive and life-threatening tumors. It has a high incidence rate, as well as significant metastasis and fatality rates. To successfully treat SKCM and to increase the overall survival rate, early identification and risk stratification are both absolutely necessary. Long noncoding RNAs (lncRNAs) play a significant regulatory role in a variety of cancers. However, the expression and function of many lncRNAs have not been investigated. We evaluated the expression profile of the long noncoding RNA LINC02249 (LINC02249) in pan-cancers by using data on gene expression obtained from TCGA and GTEx. The biological function of LINC02249 was determined by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The prognostic value of LINC02249 expression in SKCM patients was statistically analyzed. Besides, the ssGSEA approach was utilized in order to investigate the degree to which LINC02249 expression is correlated with tumor immune infiltration. In this study, the expression of LINC02249 was found to be abnormally high in a variety of tumors, according to our findings. When compared with nontumor specimens, the level of expression of LINC02249 was shown to be significantly elevated in SKCM samples. GO and KEGG assays revealed LINC02249 may be involved in tumor progression. High expression of LINC02249 was associated with shorter overall survival and disease-specific survival of SKCM patients. More importantly, multivariate methods revealed that LINC02249 expression was an independent prognostic factor for SKCM cases. Using ssGSEA, we found that the expression of LINC02249 was negatively associated with different tumor-infiltrating immune cells, especially aDC, Treg, and macrophages. Overall, our findings suggested that LINC02249 can serve as a novel biomarker to predict the prognosis and immune infiltration in SKCM.
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Zhou X, Rong R, Xiong S, Song W, Ji D, Xia X. Integrated analysis to reveal potential therapeutic targets and prognostic biomarkers of skin cutaneous melanoma. Front Immunol 2022; 13:914108. [PMID: 36032150 PMCID: PMC9402985 DOI: 10.3389/fimmu.2022.914108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/21/2022] [Indexed: 11/24/2022] Open
Abstract
Skin cutaneous melanoma (SKCM) is a malignant tumor with high mortality rate in human, and its occurrence and development are jointly regulated by genes and the environment. However, the specific pathogenesis of SKCM is not completely understood. In recent years, an increasing number of studies have reported the important role of competing endogenous RNA (ceRNA) regulatory networks in various tumors; however, the complexity and specific biological effects of the ceRNA regulatory network of SKCM remain unclear. In the present study, we obtained a ceRNA regulatory network of long non-coding RNAs, microRNAs, and mRNAs related to the phosphatase and tensin homolog (PTEN) in SKCM and identified the potential diagnostic and prognostic markers related to SKCM. We extracted the above three types of RNA involved in SKCM from The Cancer Genome Atlas database. Through bioinformatics analysis, the OIP5-AS1-hsa-miR-186-5p/hsa-miR-616-3p/hsa-miR-135a-5p/hsa-miR-23b-3p/hsa-miR-374b-5p-PTPRC/IL7R/CD69 and MALAT1-hsa-miR-135a-5p/hsa-miR-23b-3p/hsa-miR-374b-5p-IL7R/CD69 ceRNA networks were found to be related to the prognosis of SKCM. Finally, we determined the OIP5-AS1-PTPRC/IL7R/CD69 and MALAT1-IL7R/CD69 axes in ceRNA as a clinical prognostic model using correlation and Cox regression analyses. Additionally, we explored the possible role of these two axes in affecting gene expression and immune microenvironment changes and the occurrence and development of SKCM through methylation and immune infiltration analyses. In summary, the ceRNA-based OIP5-AS1-PTPRC/IL7R/CD69 and MALAT1-IL7R/CD69 axes may be a novel and important approach for the diagnosis and prognosis of SKCM.
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Affiliation(s)
- Xuezhi Zhou
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Changsha, China
- National Clinical Research Center for Geriatric Diseases (Xiangya Hospital), Changsha, China
| | - Rong Rong
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Changsha, China
- National Clinical Research Center for Geriatric Diseases (Xiangya Hospital), Changsha, China
| | - Siqi Xiong
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Changsha, China
- National Clinical Research Center for Geriatric Diseases (Xiangya Hospital), Changsha, China
| | - Weitao Song
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Changsha, China
- National Clinical Research Center for Geriatric Diseases (Xiangya Hospital), Changsha, China
| | - Dan Ji
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Changsha, China
- National Clinical Research Center for Geriatric Diseases (Xiangya Hospital), Changsha, China
| | - Xiaobo Xia
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Changsha, China
- National Clinical Research Center for Geriatric Diseases (Xiangya Hospital), Changsha, China
- *Correspondence: Xiaobo Xia,
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Hair Follicle-Related MicroRNA-34a Serum Expression and rs2666433A/G Variant in Patients with Alopecia: A Cross-Sectional Analysis. Biomolecules 2022; 12:biom12050602. [PMID: 35625530 PMCID: PMC9138785 DOI: 10.3390/biom12050602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/10/2022] [Accepted: 04/14/2022] [Indexed: 01/10/2023] Open
Abstract
Alopecia areata (AA) is a type of immune-mediated alopecia. Recent studies have suggested microRNAs’ (miRNAs) implication in several cellular processes, including epidermal and hair follicle biology. Single nucleotide polymorphisms (SNPs) can modify gene expression levels, which may induce an autoimmune response. This case−control study included 480 participants (240 for each case/control group). MicroRNA-34a gene (MIR-34A) rs2666433A/G variant was genotyped using real-time allelic discrimination polymerase chain reaction (PCR). Additionally, circulatory miR-34a levels were quantified by quantitative reverse transcription PCR (qRT-PCR). On comparing between alopecia and non-alopecia cohorts, a higher frequency of A variant was noted among patients when compared to controls—A allele: 28 versus 18% (p < 0.001); A/A genotype: 9 versus 2%; A/G genotype: 39 versus 32% (p < 0.001). A/A and A/G carriers were more likely to develop alopecia under heterozygote comparison (OR = 1.83, 95% CI = 1.14−2.93), homozygote comparison (OR = 4.19, 95% CI = 1.33−13.1), dominant (OR = 2.0, 95% CI = 1.27−3.15), recessive (OR = 3.36, 95% CI = 1.08−10.48), over-dominant (OR = 1.65, 95% CI = 1.04−32.63), and log additive (OR = 1.91, 95% CI = 1.3−2.82) models. Serum miR-34a expression levels were upregulated in alopecia patients with a median and quartile fold change of 27.3 (1.42−2430). Significantly higher levels were more pronounced in A/A genotype patients (p < 0.01). Patients carrying the heterozygote genotype (rs2666433 * A/G) were two times more likely to develop more severe disease grades. Stratified analysis by sex revealed the same results. A high expression level was associated with concomitant autoimmune comorbidities (p = 0.001), in particular SLE (p = 0.007) and vitiligo (p = 0.049). In conclusion, the MIR34A rs2666433 (A/G) variant is associated with AA risk and severity in the studied population. Furthermore, high miR-34a circulatory levels could play a role in disease pathogenesis.
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Jiang X, Liu Y, Wang Y, Zhou Y, Miao H, Zhang P, Ma J. Long non‑coding RNA MALAT1 is involved in retinal pigment epithelial cell damage caused by high glucose treatment. Mol Med Rep 2022; 25:177. [PMID: 35315497 DOI: 10.3892/mmr.2022.12693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 03/02/2022] [Indexed: 11/06/2022] Open
Abstract
The present study aimed to explore the role of long non‑coding RNA metastasis associated lung adenocarcinoma transcript 1 (lncRNA MALAT1) in high glucose (HG)‑induced ARPE‑19 cell damage. ARPE‑19 cells were cultured and treated with HG (25 mmol/l glucose). MALAT1 expression was silenced following transfection of small interfering RNA. Cell apoptosis was measured using flow cytometry. The cellular levels of reactive oxygen species (ROS), malondialdehyde and superoxide dismutase activity were all measured to examine oxidative stress. Gene expression levels of MALAT1 were determined by reverse transcription‑quantitative (RT‑q)PCR, while expression of tumor necrosis factor (TNF)‑α, monocyte chemotactic protein 1 (MCP‑1), intercellular cell adhesion molecule 1 (ICAM‑1) and vascular endothelial growth factor (VEGF) was detected using RT‑qPCR and western blotting. MALAT1 expression was markedly increased in ARPE‑19 cells treated with HG. HG treatment caused increased apoptosis and elevated ROS‑induced stress in ARPE‑19 cells and these effects could be partly attenuated by MALAT1 knockdown. Increased gene expression levels of TNF‑α, MCP‑1, ICAM‑1 and VEGF induced by HG were also alleviated by MALAT1 inhibition. Therefore, lncRNA MALAT1 is the key factor in ARPE‑19 cell damage caused by HG and may be a promising therapeutic target for clinical DR therapy. However, further studies are still required to reveal the detailed mechanisms underlying lncRNA MALAT1 function.
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Affiliation(s)
- Xinli Jiang
- Department of Ophthalmology, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Yan Liu
- Department of Endocrinology, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Yuling Wang
- Department of Neurology, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Yaru Zhou
- Department of Endocrinology, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Huipeng Miao
- Department of Ophthalmology, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Peng Zhang
- Department of Ophthalmology, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Jingxue Ma
- Department of Ophthalmology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, P.R. China
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Ma J, Shi Q, Guo S, Xu P, Yi X, Yang Y, Zhang W, Liu Y, Liu L, Yue Q, Zhao T, Gao T, Guo W, Li C. Long Non-Coding RNA CD27-AS1-208 Facilitates Melanoma Progression by Activating STAT3 Pathway. Front Oncol 2022; 11:818178. [PMID: 35096622 PMCID: PMC8791859 DOI: 10.3389/fonc.2021.818178] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/17/2021] [Indexed: 11/21/2022] Open
Abstract
Melanoma is the most lethal skin cancer that originates from epidermal melanocytes. Recently, long non-coding RNAs (lncRNAs) are emerging as critical regulators of cancer pathogenesis and potential therapeutic targets. However, the expression profile of lncRNAs and their role in melanoma progression have not been thoroughly investigated. Herein, we firstly obtained the expression profile of lncRNAs in primary melanomas using microarray analysis and unveiled the differentially-expressed lncRNAs compared with nevus. Subsequently, a series of bioinformatics analysis showed the great involvement of dysregulated lncRNAs in melanoma biology and immune response. Further, we identified lncRNA CD27-AS1-208 as a novel nuclear-localized factor with prominent facilitative role in melanoma cell proliferation, invasion and migration. Mechanistically, CD27-AS1-208 could directly interact with STAT3 and contribute to melanoma progression in a STAT3-dependent manner. Ultimately, the role of CD27-AS1-208 in melanoma progression in vivo was also investigated. Collectively, the present study offers us a new horizon to better understand the role of lncRNAs in melanoma pathogenesis and demonstrates that CD27-AS1-208 up-regulation contributes to melanoma progression by activating STAT3 pathway. Targeting CD27-AS1-208 in melanoma cells can be exploited as a potential therapeutic approach that needs forward validation in clinical trials in the future.
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Affiliation(s)
- Jingjing Ma
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Qiong Shi
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Sen Guo
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Peng Xu
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiuli Yi
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yuqi Yang
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Weigang Zhang
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yu Liu
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Lin Liu
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Qiao Yue
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Tao Zhao
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Tianwen Gao
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Weinan Guo
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Chunying Li
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
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Ruan L, Mendhe B, Parker E, Kent A, Isales CM, Hill WD, McGee-Lawrence M, Fulzele S, Hamrick MW. Long Non-coding RNA MALAT1 Is Depleted With Age in Skeletal Muscle in vivo and MALAT1 Silencing Increases Expression of TGF-β1 in vitro. Front Physiol 2022; 12:742004. [PMID: 35126169 PMCID: PMC8814451 DOI: 10.3389/fphys.2021.742004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/16/2021] [Indexed: 01/10/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are thought to function as “sponges” for microRNAs, but a role for such competing endogenous RNAs (ceRNAs) in muscle aging is not well understood. We therefore examined in skeletal muscles of young (4–6 months) and aged (22–24) male and female mice the expression of lncRNA MALAT1, which is predicted in silico to bind the senescence-associated microRNA miR-34a-5p. Results indicate a significant decrease in lncRNA MALAT1 expression in mouse skeletal muscle with age that coincides with an age-related increase in miR-34a-5p expression. In vitro studies using mouse C2C12 myoblasts demonstrate that MALAT1 silencing using siRNA increases miR-34a expression, consistent with a role for MALAT1 as an inhibitor of miR-34a-5p activity. Levels of reactive oxygen species (ROS) are known to increase in muscle with age, and so we treated C2C12 cells with hydrogen peroxide (10 and 100 μM) to examine changes in MALAT1 expression. MALAT1 expression decreased significantly with H2O2 treatment, but this effect was attenuated with p53 siRNA. Finally, miR-34a-5p is implicated in tissue fibrosis, and so we assessed the expression of TGF-β1 after MALAT1 silencing. MALAT1 siRNA significantly increased the expression of TGF-β1 in C2C12 cells. These findings suggest that age-related fibrosis and muscle atrophy mediated by ROS may result at least in part from an increase in miR-34a bioavailability resulting from a decline in miR-34a “sponging” due to ceRNA MALAT1 depletion. Crosstalk between MALAT1 and miR-34a may therefore represent a therapeutic target for improving muscle function with aging.
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Affiliation(s)
- Ling Ruan
- Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Bharati Mendhe
- Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Emily Parker
- Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Andrew Kent
- Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Carlos M. Isales
- Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - William D. Hill
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, United States
| | | | - Sadanand Fulzele
- Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Mark W. Hamrick
- Medical College of Georgia, Augusta University, Augusta, GA, United States
- *Correspondence: Mark W. Hamrick,
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Chai P, Jia R, Li Y, Zhou C, Gu X, Yang L, Shi H, Tian H, Lin H, Yu J, Zhuang A, Ge S, Jia R, Fan X. Regulation of epigenetic homeostasis in uveal melanoma and retinoblastoma. Prog Retin Eye Res 2021; 89:101030. [PMID: 34861419 DOI: 10.1016/j.preteyeres.2021.101030] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 12/13/2022]
Abstract
Uveal melanoma (UM) and retinoblastoma (RB), which cause blindness and even death, are the most frequently observed primary intraocular malignancies in adults and children, respectively. Epigenetic studies have shown that changes in the epigenome contribute to the rapid progression of both UM and RB following classic genetic changes. The loss of epigenetic homeostasis plays an important role in oncogenesis by disrupting the normal patterns of gene expression. The targetable nature of epigenetic modifications provides a unique opportunity to optimize treatment paradigms and establish new therapeutic options for both UM and RB with these aberrant epigenetic modifications. We aimed to review the research findings regarding relevant epigenetic changes in UM and RB. Herein, we 1) summarize the literature, with an emphasis on epigenetic alterations, including DNA methylation, histone modifications, RNA modifications, noncoding RNAs and an abnormal chromosomal architecture; 2) elaborate on the regulatory role of epigenetic modifications in biological processes during tumorigenesis; and 3) propose promising therapeutic candidates for epigenetic targets and update the list of epigenetic drugs for the treatment of UM and RB. In summary, we endeavour to depict the epigenetic landscape of primary intraocular malignancy tumorigenesis and provide potential epigenetic targets in the treatment of these tumours.
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Affiliation(s)
- Peiwei Chai
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Ruobing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Yongyun Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Chuandi Zhou
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Xiang Gu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Ludi Yang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Hanhan Shi
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Hao Tian
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Huimin Lin
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Jie Yu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Ai Zhuang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China.
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Cui Y, Zheng Y, Lu Y, Zhang M, Yang L, Li W. LINC01224 facilitates the proliferation and inhibits the radiosensitivity of melanoma cells through the miR-193a-5p/NR1D2 axis. Kaohsiung J Med Sci 2021; 38:196-206. [PMID: 34783160 DOI: 10.1002/kjm2.12467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 07/08/2021] [Accepted: 10/04/2021] [Indexed: 12/22/2022] Open
Abstract
Melanoma is a skin cancer characterized by early metastasis and high mortality. Radiotherapy is a common treatment for melanoma in patients. Long noncoding RNAs play pivotal roles in regulating the radiosensitivity of many tumors, including melanomas. In this study, the role of LINC01224 in the radiosensitivity of melanoma cells was explored. The expression of LINC01224 in melanoma was examined by reverse transcription-quantitative polymerase chain reaction, and the results showed that LINC01224 was upregulated in melanoma tissues and cells. The effects of LINC01224 on cell proliferation and apoptosis in melanoma were assessed by 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide (MTT), colony formation, and flow cytometry assays. The effects of LINC01224 on the radiosensitivity of melanoma were analyzed by colony formation assay. The results implied that LINC01224 knockdown inhibited cell viability and proliferation but enhanced cell apoptosis and radiosensitivity. Luciferase reporter and RNA pull-down assays were performed to evaluate the relationships between LINC01224 and miR-193a-5p or miR-193a-5p and nuclear receptor subfamily 1 group D member 2 (NR1D2). We found that LINC01224 binds to miR-193a-5p, which directly targets NR1D2. In addition, we discovered that LINC01224 upregulated NR1D2 expression by sponging miR-193a-5p in melanoma cells. Overall, the data collected in this study suggest that LINC01224 exerts oncogenic effects in melanoma via the miR-193a-5p/NR1D2 axis.
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Affiliation(s)
- Yu Cui
- Department of CT, Chengde Central Hospital, Chengde, China
| | - Yi Zheng
- Department of CT, Chengde Central Hospital, Chengde, China
| | - Yue Lu
- Department of Ultrasound Diagnosis, Chengde Central Hospital, Chengde, China
| | - Muyuan Zhang
- Department of CT, Chengde Central Hospital, Chengde, China
| | - Lei Yang
- Department of CT, Chengde Central Hospital, Chengde, China
| | - Wei Li
- Department of CT, Chengde Central Hospital, Chengde, China
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Non-coding RNA dysregulation in skin cancers. Essays Biochem 2021; 65:641-655. [PMID: 34414406 DOI: 10.1042/ebc20200048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 07/16/2021] [Accepted: 08/04/2021] [Indexed: 02/07/2023]
Abstract
Skin cancers are the most common cancers worldwide. They can be classified in melanoma and non-melanoma skin cancer (NMSC), the latter includes squamous cell carcinoma (SCC), basal cell carcinoma (BCC) and merkel cell carcinoma (MCC). In recent years, the crucial role of non-coding RNAs (ncRNAs) in skin cancer pathogenesis has become increasingly evident. NcRNAs are functional RNA molecules that lack any protein-coding activity. These ncRNAs are classified based on their length: small, medium-size, and long ncRNAs. Among the most studied ncRNAs there are microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNA (circRNAs). ncRNAs have the ability to regulate gene expression at transcriptional and post-transcriptional levels and are involved in skin cancer cell proliferation, angiogenesis, invasion, and metastasis. Many ncRNAs exhibit tissue- or cell-specific expression while others have been correlated to tumor staging, drug resistance, and prognosis. For these reasons, ncRNAs have both a diagnostic and prognostic significance in skin cancers. Our review summarizes the functional role of ncRNAs in skin cancers and their potential clinical application as biomarkers.
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Down-regulated expression of miR-582 predicts poor prognosis and facilitates melanoma progression by targeting FOXC1. Arch Dermatol Res 2021; 314:759-766. [PMID: 34628519 DOI: 10.1007/s00403-021-02285-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 08/31/2021] [Accepted: 09/24/2021] [Indexed: 10/20/2022]
Abstract
Melanoma is one of the most common malignant tumors that originate from nerve sheath melanocytes and are produced in the skin and other organs. This paper mainly studied the role of miR-582 in melanoma. The expression of miR-582 in melanoma cell lines and tissues was evaluated by real-time quantitative PCR. Kaplan-Meier curve and Cox proportional hazards model analysis were used to investigate the prognostic value of miR-582 in melanoma. Cell proliferation, invasion, and migration were analyzed using CCK-8 and transwell assays. The results showed that miR-582 was significantly decreased in melanoma cells and tissues. Downregulation of miR-582 was associated with ulceration, lymph node metastasis, TNM stage, and poor overall survival. The functional results showed that low expression of miR-582 can promote cell proliferation, migration, and invasion. FOXC1 was a direct target of miR-582. Overall, the expression of miR-582 is downregulated in melanoma tissues and cell lines. Low expression of miR-582 is associated with prognosis and progression of melanoma by targeting FOXC1. miR-582 may be a prognostic biomarker and a new therapeutic strategy for 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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LncRNA MALAT1 Facilitates Ovarian Cancer Progression through Promoting Chemoresistance and Invasiveness in the Tumor Microenvironment. Int J Mol Sci 2021; 22:ijms221910201. [PMID: 34638541 PMCID: PMC8508663 DOI: 10.3390/ijms221910201] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/18/2021] [Accepted: 09/18/2021] [Indexed: 01/06/2023] Open
Abstract
Upregulation of metastasis-associated lung adenocarcinoma transcript 1 (MALAT1, also known as nuclear-enriched abundant transcript 2 (NEAT2) or LINC00047) was found in various solid tumors, including epithelial ovarian cancer (EOC). MALAT1 is a long noncoding (lnc)RNA that regulates many functional signaling pathways, including tumorigenesis. Herein, we observed the consistent upregulation of MALAT1 in MYST4-overexpressing cell lines, while MALAT1 was frequently found to be upregulated in various types of clinical carcinoma tissues, especially EOC. To further investigate the lncRNA MALAT1 in EOC progression, the transduced overexpression of MALAT1 in EOC cell lines and cancer-associated fibroblasts (CAFs) was employed. We found that MALAT1 overexpression in EOC cell lines significantly increased drug resistance, cell migration, and invasion. Furthermore, the concomitant overexpression of MALAT1 in EOC cells and CAFs dramatically increased EOC cell invasion. Accordingly, a mechanistic investigation of MALAT1 overexpression in EOC cells showed that expressions of the cytokines interleukin (IL)-1β and p-P38/p-NFκB/Cox2/prostaglandin E2 (PGE2) signaling were significantly increased, which stimulated inflammatory responses, whereas cell apoptosis was inhibited due to increased Bcl-2 levels and reduced Caspase3 levels. After MALAT1 was overexpressed in EOC cells, and the cyclin D1, p-PI3K, and p-Akt expressions increased, suggesting the promotion of tumor cell proliferation, while increased zinc finger E-box-binding homeobox-2 (ZEB2), yes-associated protein (YAP), and vimentin expression with E-cadherin downregulation indicated the enhancement of the epithelial-to-mesenchymal transition (EMT) in terms of metastasis, thereby triggering EOC progression. Together, our findings demonstrate how MALAT1 overexpression facilitates an oncogenic function through inhibiting tumor cell apoptosis, combined with increasing tumor cell inflammation, proliferation, and invasion in the EOC tumor microenvironment. MALAT1 is thus a potential diagnostic marker and therapeutic for this malignancy.
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Lange M, Begolli R, Giakountis A. Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine. Noncoding RNA 2021; 7:47. [PMID: 34449663 PMCID: PMC8395730 DOI: 10.3390/ncrna7030047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/26/2021] [Accepted: 08/01/2021] [Indexed: 12/11/2022] Open
Abstract
The cancer genome is characterized by extensive variability, in the form of Single Nucleotide Polymorphisms (SNPs) or structural variations such as Copy Number Alterations (CNAs) across wider genomic areas. At the molecular level, most SNPs and/or CNAs reside in non-coding sequences, ultimately affecting the regulation of oncogenes and/or tumor-suppressors in a cancer-specific manner. Notably, inherited non-coding variants can predispose for cancer decades prior to disease onset. Furthermore, accumulation of additional non-coding driver mutations during progression of the disease, gives rise to genomic instability, acting as the driving force of neoplastic development and malignant evolution. Therefore, detection and characterization of such mutations can improve risk assessment for healthy carriers and expand the diagnostic and therapeutic toolbox for the patient. This review focuses on functional variants that reside in transcribed or not transcribed non-coding regions of the cancer genome and presents a collection of appropriate state-of-the-art methodologies to study them.
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Affiliation(s)
- Marios Lange
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece; (M.L.); (R.B.)
| | - Rodiola Begolli
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece; (M.L.); (R.B.)
| | - Antonis Giakountis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece; (M.L.); (R.B.)
- Institute for Fundamental Biomedical Research, B.S.R.C “Alexander Fleming”, 34 Fleming Str., 16672 Vari, Greece
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Song Z, Lin J, Li Z, Huang C. The nuclear functions of long noncoding RNAs come into focus. Noncoding RNA Res 2021; 6:70-79. [PMID: 33898883 PMCID: PMC8053782 DOI: 10.1016/j.ncrna.2021.03.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/16/2022] Open
Abstract
Long noncoding RNAs (lncRNAs), defined as untranslated and tightly-regulated transcripts with a length exceeding 200 nt, are common outputs of the eukaryotic genome. It is becoming increasingly apparent that many lncRNAs likely serve as important regulators in a variety of biological processes. In particular, some of them accumulate in the nucleus and function in diverse nuclear events, including chromatin remodeling, transcriptional regulation, RNA processing, DNA damage repair, etc. Here, we unite recent progresses on the functions of nuclear lncRNAs and provide insights into the future research directions of this field.
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Affiliation(s)
- Zhenxing Song
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Jiamei Lin
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Zhengguo Li
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
- Corresponding author. School of Life Sciences, Chongqing University, Chongqing, 401331, China.
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Wu X, Cheng YSL, Matthen M, Yoon A, Schwartz GK, Bala S, Taylor AM, Momen-Heravi F. Down-regulation of the tumor suppressor miR-34a contributes to head and neck cancer by up-regulating the MET oncogene and modulating tumor immune evasion. J Exp Clin Cancer Res 2021; 40:70. [PMID: 33596979 PMCID: PMC7890893 DOI: 10.1186/s13046-021-01865-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/02/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND MicroRNAs (miRs) have been shown to play an important role in tumorigenesis, including in head and neck squamous cell carcinoma (HNSCC). The miR-34 family is thought to play a role in tumor suppression, but the exact mechanism of their action in HNSCC is not well understood. Moreover, the impact of chromosomal changes and mutation status on miR-34a expression remains unknown. METHODS Differential expression of miR-34a, MET, and genomic alterations were assessed in the Cancer Genome Atlas (TCGA) datasets as well as in primary HNSCC and adjacent normal tissue. The biological functions of miR-34a in HNSCC were investigated in samples derived from primary human tumors and HNSCC cell lines. The expression of MET was evaluated using immunohistochemistry, and the molecular interaction of miR-34a and MET were demonstrated by RNA pulldown, RNA immunoprecipitation, luciferase reporter assay, and rescue experiments. Lastly, locked nucleic acid (LNA) miRs in mouse xenograft models were used to evaluate the clinical relevance of miR-34a in HNSCC tumor growth and modulation of the tumor microenvironment in vivo. RESULTS Chromosome arm 1p loss and P53 mutations are both associated with lower levels of miR-34a. In HNSCC, miR-34a acts as a tumor suppressor and physically interacts with and functionally targets the proto-oncogene MET. Our studies found that miR-34a suppresses HNSCC carcinogenesis, at least in part, by downregulating MET, consequently inhibiting HNSCC proliferation. Consistent with these findings, administration of LNA-miR-34a in an in vivo model of HNSCC leads to diminished HNSCC cell proliferation and tumor burden in vitro and in vivo, represses expression of genes involved in epithelial-mesenchymal transition, and negates the oncogenic effect of MET in mouse tumors. Consistently, LNA-miR-34a induced a decreased number of immunosuppressive PDL1-expressing tumor-associated macrophages in the tumor microenvironment. In HNSCC patient samples, higher levels of miR-34a are significantly associated with a higher frequency of Th1 cells and CD8 naïve T cells. CONCLUSIONS Our results demonstrate that miR-34a directly targets MET and maintains anti-tumor immune activity. We propose miR-34a as a potential new therapeutic approach for HNSCC.
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Affiliation(s)
- Xun Wu
- Cancer Biology and Immunology Laboratory, College of Dental Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Division of Periodontics, Section of Oral, Diagnostic and Rehabilitation Sciences, Columbia University College of Dental Medicine, New York, NY, USA
- Department of Maxillofacial Surgery, Guangxi Medical University College of Stomatology, Nanning, Guangxi, China
| | - Yi-Shing Lisa Cheng
- Department of Diagnostic Sciences, Texas A&M University College of Dentistry, Dallas, TX, USA
| | - Mathew Matthen
- Department of Medicine Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
| | - Angela Yoon
- Division of Pathology, Columbia University College of Dental Medicine, New York, NY, USA
| | - Gary K Schwartz
- Department of Medicine Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
| | - Shashi Bala
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Alison M Taylor
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.
| | - Fatemeh Momen-Heravi
- Cancer Biology and Immunology Laboratory, College of Dental Medicine, Columbia University Irving Medical Center, New York, NY, USA.
- Division of Periodontics, Section of Oral, Diagnostic and Rehabilitation Sciences, Columbia University College of Dental Medicine, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
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24
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De Falco V, Napolitano S, Esposito D, Guerrera LP, Ciardiello D, Formisano L, Troiani T. Comprehensive Review on the Clinical Relevance of Long Non-Coding RNAs in Cutaneous Melanoma. Int J Mol Sci 2021; 22:1166. [PMID: 33503876 PMCID: PMC7865742 DOI: 10.3390/ijms22031166] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 02/06/2023] Open
Abstract
Cutaneous melanoma is considered a rare tumor, although it is one of the most common cancers in young adults and its incidence has risen in the last decades. Targeted therapy, with BRAF and MEK inhibitors, and immunotherapy revolutionized the treatment of metastatic melanoma but there is still a considerable percentage of patients with primary or acquired resistance to these therapies. Recently, oncology researchers directed their attention at the role of long non-coding RNAs (lncRNAs) in different types of cancers, including melanoma. lncRNAs are RNA transcripts, initially considered "junk sequences", that have been proven to have a crucial role in the fine regulation of physiological and pathological processes of different tissues. Furthermore, they are more expressed in tumors than protein-coding genes, constituting perfect candidates either as biomarkers (diagnostic, prognostic, predictive) or as therapeutic targets. In this work, we reviewed all the literature available for lncRNA in melanoma, elucidating all the potential roles in this tumor.
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Affiliation(s)
- Vincenzo De Falco
- Department of Precision Medicine, Università della Campania “Luigi Vanvitelli”, 80131 Napoli, Italy; (V.D.F.); (S.N.); (L.P.G.); (D.C.)
| | - Stefania Napolitano
- Department of Precision Medicine, Università della Campania “Luigi Vanvitelli”, 80131 Napoli, Italy; (V.D.F.); (S.N.); (L.P.G.); (D.C.)
| | - Daniela Esposito
- Department of Clinical Medicine and Surgery, University of Naples “Federico II”, 80131 Napoli, Italy; (D.E.); (L.F.)
| | - Luigi Pio Guerrera
- Department of Precision Medicine, Università della Campania “Luigi Vanvitelli”, 80131 Napoli, Italy; (V.D.F.); (S.N.); (L.P.G.); (D.C.)
| | - Davide Ciardiello
- Department of Precision Medicine, Università della Campania “Luigi Vanvitelli”, 80131 Napoli, Italy; (V.D.F.); (S.N.); (L.P.G.); (D.C.)
| | - Luigi Formisano
- Department of Clinical Medicine and Surgery, University of Naples “Federico II”, 80131 Napoli, Italy; (D.E.); (L.F.)
| | - Teresa Troiani
- Department of Precision Medicine, Università della Campania “Luigi Vanvitelli”, 80131 Napoli, Italy; (V.D.F.); (S.N.); (L.P.G.); (D.C.)
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25
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De Novo Profiling of Long Non-Coding RNAs Involved in MC-LR-Induced Liver Injury in Whitefish: Discovery and Perspectives. Int J Mol Sci 2021; 22:ijms22020941. [PMID: 33477898 PMCID: PMC7833382 DOI: 10.3390/ijms22020941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/08/2021] [Accepted: 01/15/2021] [Indexed: 12/18/2022] Open
Abstract
Microcystin-LR (MC-LR) is a potent hepatotoxin for which a substantial gap in knowledge persists regarding the underlying molecular mechanisms of liver toxicity and injury. Although long non-coding RNAs (lncRNAs) have been extensively studied in model organisms, our knowledge concerning the role of lncRNAs in liver injury is limited. Given that lncRNAs show low levels of sequence conservation, their role becomes even more unclear in non-model organisms without an annotated genome, like whitefish (Coregonus lavaretus). The objective of this study was to discover and profile aberrantly expressed polyadenylated lncRNAs that are involved in MC-LR-induced liver injury in whitefish. Using RNA sequencing (RNA-Seq) data, we de novo assembled a high-quality whitefish liver transcriptome. This enabled us to find 94 differentially expressed (DE) putative evolutionary conserved lncRNAs, such as MALAT1, HOTTIP, HOTAIR or HULC, and 4429 DE putative novel whitefish lncRNAs, which differed from annotated protein-coding transcripts (PCTs) in terms of minimum free energy, guanine-cytosine (GC) base-pair content and length. Additionally, we identified DE non-coding transcripts that might be 3′ autonomous untranslated regions (3′UTRs) of mRNAs. We found both evolutionary conserved lncRNAs as well as novel whitefish lncRNAs that could serve as biomarkers of liver injury.
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26
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Karagkouni D, Karavangeli A, Paraskevopoulou MD, Hatzigeorgiou AG. Characterizing miRNA-lncRNA Interplay. Methods Mol Biol 2021; 2372:243-262. [PMID: 34417757 DOI: 10.1007/978-1-0716-1697-0_21] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Long noncoding RNAs (lncRNAs) are noncoding transcripts, usually longer than 200 nt, that constitute one of the largest and significantly heterogeneous RNA families. The annotation of lncRNAs and the characterization of their function is a constantly evolving field. LncRNA interplay with microRNAs (miRNAs) is thoroughly studied in several physiological and disease states. miRNAs are small noncoding RNAs (~22 nt) that posttranscriptionally regulate the expression of protein coding genes, through mRNA target cleavage, degradation or direct translational suppression. miRNAs can affect lncRNA half-life by promoting their degradation, or lncRNAs can act as miRNA "sponges," reducing miRNA regulatory effect on target mRNAs. This chapter outlines the miRNA-lncRNA interplay and provides hands-on methodologies for experimentally supported and in silico-guided analyses. The proposed techniques are a valuable asset to further understand lncRNA functions and can be appropriately adapted to become the backbone for further downstream analyses.
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Affiliation(s)
- Dimitra Karagkouni
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece. .,Hellenic Pasteur Institute, Athens, Greece.
| | - Anna Karavangeli
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece.,Hellenic Pasteur Institute, Athens, Greece
| | - Maria D Paraskevopoulou
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Artemis G Hatzigeorgiou
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece. .,Hellenic Pasteur Institute, Athens, Greece.
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Zhang J, Liu H, Zhang W, Li Y, Fan Z, Jiang H, Luo J. Identification of lncRNA-mRNA Regulatory Module to Explore the Pathogenesis and Prognosis of Melanoma. Front Cell Dev Biol 2020; 8:615671. [PMID: 33392203 PMCID: PMC7773644 DOI: 10.3389/fcell.2020.615671] [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: 10/09/2020] [Accepted: 11/24/2020] [Indexed: 12/21/2022] Open
Abstract
Skin cutaneous melanoma (SKCM) is an aggressive form of skin cancer that results in high mortality rate worldwide. It is vital to discover effective prognostic biomarkers and therapeutic targets for the treatment of melanoma. Long non-coding RNA (lncRNA) has been verified to play an essential role in the regulation of gene expression in diseases and tumors. Therefore, it is significant to explore the function of lncRNAs in the development and progression of SKCM. In this paper, a set of differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) were first screened out using 471 cutaneous melanoma samples and 813 normal skin samples. Gene Ontology and KEGG pathway enrichment analysis were performed to obtain the significant function annotations and pathways of DEmRNAs. We also ran survival analysis on both DElncRNAs and DEmRNAs to identify prognostic-related lncRNAs and mRNAs. Next, a set of hub genes derived from protein-protein interaction (PPI) network analysis and lncRNA target genes screened from starbase-ENCORI database were integrated to construct a lncRNA-mRNA regulatory module, which includes 6 lncRNAs 4 target mRNAs. We further checked the capacity of these lncRNA and mRNA in the diagnosis of melanoma, and found that single lncRNA can effectively distinguish tumor and normal tissue. Moreover, we ran CMap analysis to select a list of small molecule drugs for SKCM, such as EGFR inhibitor AG-490, growth factor receptor inhibitor GW-441756 and apoptosis stimulant betulinic-acid, which have shown therapeutic effect in the treatment of melanoma.
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Affiliation(s)
- Jiaqi Zhang
- Department of Radiotherapy, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China.,Department of Dermatology, Graduate School of Dalian Medical University, Dalian, China
| | - Hui Liu
- Aliyun School of Big Data, Changzhou University, Changzhou, China
| | - Wenhao Zhang
- Aliyun School of Big Data, Changzhou University, Changzhou, China
| | - Yinfang Li
- Aliyun School of Big Data, Changzhou University, Changzhou, China
| | - Zhigang Fan
- Department of Oncology, Affiliated 3201 Hospital of Xi'an Jiaotong University, Hanzhong, China
| | - Hua Jiang
- Department of Oncology, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Judong Luo
- Department of Radiotherapy, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
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LncRNA MALAT1 Regulates miR-144-3p to Facilitate Epithelial-Mesenchymal Transition of Lens Epithelial Cells via the ROS/NRF2/Notch1/Snail Pathway. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:8184314. [PMID: 33274006 PMCID: PMC7683160 DOI: 10.1155/2020/8184314] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/10/2020] [Accepted: 10/20/2020] [Indexed: 12/18/2022]
Abstract
Diabetic cataract is a common complication of diabetes. The epithelial-mesenchymal transition (EMT) of lens epithelial cells (LECs) is a key event in the development of diabetic cataracts. Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) has been reported to be highly expressed in different tissues of diabetic patients. This study is aimed at investigating the function and mechanism of MALAT1 in the regulation of EMT in human LECs under high glucose conditions. MALAT1, α-smooth muscle actin (α-SMA), fibronectin (FN), and nuclear factor erythroid-derived 2-like 2 (NRF2) were highly expressed in the LECs of diabetic cataract patients and in the human LECs under high glucose conditions; meanwhile, the decreased expressions of E-cadherin and zonula occludens 1 (ZO-1) were detected. Knockdown of MALAT1 could significantly reduce ROS, prevent EMT, arrest S phase cell cycle, and suppress the expression of total NRF2 and its nucleus translocation in LECs. Furthermore, after NRF2 was knocked down, total NRF2, α-SMA, and FN in cells, and NRF2, Notch intracellular domain (NICD), and Snail were decreased in the nucleus. Using bioinformatics methods, we predicted that MALAT1 and NRF2 shared the same microRNA-144-3p (miR-144-3p) combining site. Luciferase reporter coupled with qRT-PCR assays revealed that miR-144-3p was a target of MALAT1, which was confirmed to downregulate miR-144-3p in the LECs. In addition, after transfection of miR-144-3p mimics or inhibitor, western blot assay demonstrated that miR-144-3p negatively regulated the expression of total NRF2, α-SMA, and FN in cells, and NRF2, NICD, and Snail in the nucleus without affecting Kelch-like ECH-associated protein 1 (KEAP1). Finally, we confirmed that transfection of shMALAT1 inhibited NRF2 expression, and its mediated EMT could be rescued by miR-144-3p inhibitor; transfection of pcDNA3.1-MALAT1 promoted NRF2 expression, and its mediated EMT could be reversed by miR-144-3p inhibitor. In summary, we demonstrate that MALAT1 regulates miR-144-3p to facilitate EMT of LECs via the ROS/NRF2/Notch1/Snail pathway.
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The Role of Non-Coding RNAs in Uveal Melanoma. Cancers (Basel) 2020; 12:cancers12102944. [PMID: 33053887 PMCID: PMC7600503 DOI: 10.3390/cancers12102944] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/01/2020] [Accepted: 10/09/2020] [Indexed: 12/21/2022] Open
Abstract
Simple Summary The development of uveal melanoma is a multifactorial and multi-step process, in which abnormal gene expression plays a key role. Recently, several studies have highlighted the role of non-coding RNAs in the progression of uveal melanoma by affecting different signaling pathways. As important agents in the regulation of genes, non-coding RNAs have enormous potential to open up therapeutic pathways, predict response to treatment, and anticipate patient outcome for uveal melanoma. This review aims to provide a comprehensive view of what we know about ncRNAs in uveal melanoma currently. Abstract Uveal melanoma (UM) is the most common primary intraocular tumor in adulthood. Approximately 50% of patients develop metastatic disease, which typically affects the liver and is usually fatal within one year. This type of cancer is heterogeneous in nature and is divided into two broad groups of tumors according to their susceptibility to develop metastasis. In the last decade, chromosomal abnormalities and the aberrant expression of several signaling pathways and oncogenes in uveal melanomas have been described. Recently, importance has been given to the association of the mentioned deregulation with the expression of non-coding RNAs (ncRNAs). Here, we review the different classes of ncRNAs—such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs)—and their contribution to the development of UM. Special attention is given to miRNAs and their regulatory role in physiopathology and their potential as biomarkers. As important agents in gene regulation, ncRNAs have a huge potential for opening up therapeutic pathways, predicting response to treatment, and anticipating patient outcome for UM.
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Wang P, Hu L, Fu G, Lu J, Zheng Y, Li Y, Jia L. LncRNA MALAT1 Promotes the Proliferation, Migration, and Invasion of Melanoma Cells by Downregulating miR-23a. Cancer Manag Res 2020; 12:6553-6562. [PMID: 32801893 PMCID: PMC7397564 DOI: 10.2147/cmar.s249348] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 06/17/2020] [Indexed: 12/20/2022] Open
Abstract
Purpose This study was designed to investigate the relationship between long-chain non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (lncRNA MALAT1)/miR-23a-23a and melanoma. Patients and Methods Fifty-two cases of corresponding non-tumor normal tissues and 109 cases (including 62 cases of primary melanoma and 47 cases of metastatic melanoma) were collected. Real-time fluorescent PCR quantified lncRNA MALAT1 and miR-23a, and counted the 3-year survival of high/low miR-23 and high/low lncRNA MALAT1 populations. We predicted the binding site according to the sequence information of lncRNA MALAT1 and miR-23a. lncRNA MALAT1 siRNA and miR-23a mimics vectors were constructed and transfected into melanoma cell lines respectively to observe their effects on cells. Results Compared with corresponding non-tumor normal tissues, lncRNA MALAT1 in melanoma tissue increased while miR-23a decreased. Compared with primary melanoma, metastatic melanoma was higher and miR-23a was lower. Downregulation of lncRNA MALAT1 caused upregulation of miR-23a, and lncRNA MALAT1 could bind to miR-23a. Downregulating lncRNA MALAT1 or upregulating miR-23a inhibited cell proliferation, migration and invasion and promoted apoptosis. Rescue experiments revealed that downregulation of miR-23a could offset cell changes caused by downregulation of lncRNA MALAT1. Conclusion lncRNA MALAT1 promotes malignant proliferation of melanoma cells through miR-23a.
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Affiliation(s)
- Pan Wang
- Department of Dermatology, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430015, Hubei Province, People's Republic of China
| | - Liu Hu
- Department of Radiotherapy, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, 430071, People's Republic of China
| | - Guili Fu
- Department of Dermatology, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430015, Hubei Province, People's Republic of China
| | - Jingjing Lu
- Department of Dermatology, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430015, Hubei Province, People's Republic of China
| | - Yuanquan Zheng
- Department of Dermatology, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430015, Hubei Province, People's Republic of China
| | - Ying Li
- Department of Radiotherapy, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, 430071, People's Republic of China
| | - Lin Jia
- Department of Nephrology, The Central Hosptial of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430015, Hubei Province, People's Republic of China
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He B, Zhao Z, Cai Q, Zhang Y, Zhang P, Shi S, Xie H, Peng X, Yin W, Tao Y, Wang X. miRNA-based biomarkers, therapies, and resistance in Cancer. Int J Biol Sci 2020; 16:2628-2647. [PMID: 32792861 PMCID: PMC7415433 DOI: 10.7150/ijbs.47203] [Citation(s) in RCA: 249] [Impact Index Per Article: 62.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 07/04/2020] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs), small non-coding RNAs (ncRNAs) of about 22 nucleotides in size, play important roles in gene regulation, and their dysregulation is implicated in human diseases including cancer. A variety of miRNAs could take roles in the cancer progression, participate in the process of tumor immune, and function with miRNA sponges. During the last two decades, the connection between miRNAs and various cancers has been widely researched. Based on evidence about miRNA, numerous potential cancer biomarkers for the diagnosis and prognosis have been put forward, providing a new perspective on cancer screening. Besides, there are several miRNA-based therapies among different cancers being conducted, advanced treatments such as the combination of synergistic strategies and the use of complementary miRNAs provide significant clinical benefits to cancer patients potentially. Furthermore, it is demonstrated that many miRNAs are engaged in the resistance of cancer therapies with their complex underlying regulatory mechanisms, whose comprehensive cognition can help clinicians and improve patient prognosis. With the belief that studies about miRNAs in human cancer would have great clinical implications, we attempt to summarize the current situation and potential development prospects in this review.
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Affiliation(s)
- Boxue He
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Zhenyu Zhao
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Qidong Cai
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Yuqian Zhang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Pengfei Zhang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Shuai Shi
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Hui Xie
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Xiong Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Wei Yin
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Yongguang Tao
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, Hunan, 410078 China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, Hunan, 410078 China
| | - Xiang Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
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García-Guede Á, Vera O, Ibáñez-de-Caceres I. When Oxidative Stress Meets Epigenetics: Implications in Cancer Development. Antioxidants (Basel) 2020; 9:antiox9060468. [PMID: 32492865 PMCID: PMC7346131 DOI: 10.3390/antiox9060468] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 02/06/2023] Open
Abstract
Cancer is one of the leading causes of death worldwide and it can affect any part of the organism. It arises as a consequence of the genetic and epigenetic changes that lead to the uncontrolled growth of the cells. The epigenetic machinery can regulate gene expression without altering the DNA sequence, and it comprises methylation of the DNA, histones modifications, and non-coding RNAs. Alterations of these gene-expression regulatory elements can be produced by an imbalance of the intracellular environment, such as the one derived by oxidative stress, to promote cancer development, progression, and resistance to chemotherapeutic treatments. Here we review the current literature on the effect of oxidative stress in the epigenetic machinery, especially over the largely unknown ncRNAs and its consequences toward cancer development and progression.
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Affiliation(s)
- Álvaro García-Guede
- Epigenetics Laboratory, INGEMM, Hospital La PAZ. 28046 Madrid, Spain; (Á.G.-G.); (I.I.-d.-C.)
- Experimental Therapies and Novel Biomarkers in Cancer, Instituto de Investigación Sanitaria del Hospital La Paz. IdiPAZ, 28046 Madrid, Spain
| | - Olga Vera
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
- Correspondence:
| | - Inmaculada Ibáñez-de-Caceres
- Epigenetics Laboratory, INGEMM, Hospital La PAZ. 28046 Madrid, Spain; (Á.G.-G.); (I.I.-d.-C.)
- Experimental Therapies and Novel Biomarkers in Cancer, Instituto de Investigación Sanitaria del Hospital La Paz. IdiPAZ, 28046 Madrid, Spain
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Zhang Y, Mou C, Shang M, Jiang M, Xu C. Long noncoding RNA RP11-626G11.3 promotes the progression of glioma through miR-375-SP1 axis. Mol Carcinog 2020; 59:492-502. [PMID: 32128886 DOI: 10.1002/mc.23173] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/10/2020] [Accepted: 02/21/2020] [Indexed: 12/16/2022]
Abstract
Gliomas are the most common malignant tumor in the central nervous system and are also one of the leading causes of death in cancer patients. Recently, mounting evidence suggested that both long noncoding RNAs (lncRNAs) and microRNAs play important roles in the proliferation and invasion of cancers, including gliomas. However, the role of lncRNA RP11-626G11.3 in glioma-genesis is still uncovered. Results indicated that lncRNA RP11-626G11.3 was up-regulated in glioma tissues and cell lines, moreover, its overexpression positively correlated with the poor prognosis and advanced pathological stages. Gain and loss of functional experiments demonstrated that lncRNA RP11-626G11.3 promoted the proliferation and invasion of glioma cells in vitro. The knockdown of lncRNA RP11-626G11.3 repressed the tumor growth in vivo. Mechanistically, lncRNA RP11-626G11.3 positively regulated the SP1 expression via competitively sponging with miR-375. Overall, our study shows that lncRNA RP11-626G11.3 promotes glioma progression by sponging miR-375 to regulate SP1 expression, which may provide a novel therapeutic strategy for glioma.
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Affiliation(s)
- Yahui Zhang
- Department of Pharmacy, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Chengzhi Mou
- Department of Neurosurgery, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Miaomiao Shang
- Department of Neurosurgery, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Meng Jiang
- Department of Neurosurgery, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Chunyang Xu
- Department of Surgical Intensive Care Unit, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, Shandong, China
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Agostini M, Ganini C, Candi E, Melino G. The role of noncoding RNAs in epithelial cancer. Cell Death Discov 2020; 6:13. [PMID: 32194993 PMCID: PMC7067833 DOI: 10.1038/s41420-020-0247-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/11/2020] [Accepted: 02/17/2020] [Indexed: 02/06/2023] Open
Abstract
Regulatory noncoding RNAs (ncRNAs) are a class of RNAs transcribed by regions of the human genome that do not encode for proteins. The three main members of this class, named microRNA, long noncoding RNA, and circular RNA play a key role in the regulation of gene expression, eventually shaping critical cellular processes. Compelling experimental evidence shows that ncRNAs function either as tumor suppressors or oncogenes by participating in the regulation of one or several cancer hallmarks, including evading cell death, and their expression is frequently deregulated during cancer onset, progression, and dissemination. More recently, preclinical and clinical studies indicate that ncRNAs are potential biomarkers for monitoring cancer progression, relapse, and response to cancer therapy. Here, we will discuss the role of noncoding RNAs in regulating cancer cell death, focusing on those ncRNAs with a potential clinical relevance.
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Affiliation(s)
- Massimiliano Agostini
- Department of Experimental Medicine, TOR, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Carlo Ganini
- Department of Experimental Medicine, TOR, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Eleonora Candi
- Department of Experimental Medicine, TOR, University of Rome “Tor Vergata”, 00133 Rome, Italy
- IDI-IRCCS, Via Monti di Creta 106, 00166 Rome, Italy
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome “Tor Vergata”, 00133 Rome, Italy
- MRC Toxicology Unit, University of Cambridge, Department of Pathology, Tennis Court Road, Cambridge, CB2 1QP UK
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Chen Q, Zhu C, Jin Y. The Oncogenic and Tumor Suppressive Functions of the Long Noncoding RNA MALAT1: An Emerging Controversy. Front Genet 2020; 11:93. [PMID: 32174966 PMCID: PMC7056701 DOI: 10.3389/fgene.2020.00093] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/28/2020] [Indexed: 12/22/2022] Open
Abstract
Long noncoding RNAs are recently emerging as critical factors of tumorigenesis. Originally regarded as a pre-messenger RNA (mRNA) splicing regulator, the long noncoding RNA MALAT1 has been demonstrated to regulate gene transcription by binding histone modification enzymes and transcription factors, and to regulate mRNA and protein expression post-transcriptionally by binding microRNAs (miRNAs) and acting as a sponge. Early studies consistently report that MALAT1 is up-regulated in human cancer tissues of various organ origins, particularly metastatic cancer tissues, that high levels of MALAT1 expression in cancer tissues are associated with poor patient prognosis, and that MALAT1 induces cancer cell proliferation, migration, and invasion in vitro and tumor metastasis in mice. By contrast, by analyzing multiple independent large datasets, MALAT1 have very recently been found to be down-regulated in human colorectal and breast cancer tissues, and low MALAT1 expression is associated with decreased patient survival. By binding to the transcription factor TEAD, MALAT1 suppresses metastasis gene expression, colorectal and breast cancer cell migration, invasion, and metastasis in vitro and in mice. MALAT1 has therefore been proposed to function as a tumor suppressor in colorectal and breast cancers. More comprehensive studies with multiple independent cohorts of human cancer tissues of various organ origins, in vitro and in vivo function, and mechanism studies with rescue experiments are required to confirm the oncogenic or tumor suppressive role of MALAT1 in other cancers.
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Affiliation(s)
- Qingjuan Chen
- Department of Oncology, Yongchuan Hospital, Chongqing Medical University, Chongqing, China
| | - Chenjing Zhu
- Department of Radiation Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Yingying Jin
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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Wu S, Chen H, Zuo L, Jiang H, Yan H. Suppression of long noncoding RNA MALAT1 inhibits the development of uveal melanoma via microRNA-608-mediated inhibition of HOXC4. Am J Physiol Cell Physiol 2020; 318:C903-C912. [PMID: 31913701 DOI: 10.1152/ajpcell.00262.2019] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This study explored the effects of the metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) on the development of uveal melanoma. Moreover, the role of the MALAT1/microRNA-608 (miR-608)/homeobox C4 (HOXC4) axis was assessed by evaluating the proliferation, invasion, and migration, as well as the cell cycle distribution of uveal melanoma in vitro after knocking down MALAT1 or HOXC4 and/or overexpression of miR-608 in uveal melanoma cells (MUM-2B and C918). Moreover, the effects of the MALAT1/miR-608/HOXC4 axis in uveal melanoma in vivo were further evaluated by injecting the C918 cells into the NOD/SCID mice. HOXC4 was found to be a gene upregulated in uveal melanoma, while knockdown of its expression resulted in suppression of uveal melanoma cell migration, proliferation, and invasion, as well as cell cycle progression. In addition, the upregulation of miR-608 reduced the expression of HOXC4 in the uveal melanoma cells, which was rescued by overexpression of MALAT1. Hence, MALAT1 could upregulate the HOXC4 by binding to miR-608. The suppressed progression of uveal melanoma in vitro by miR-608 was rescued by overexpression of MALAT1. Additionally, in vivo assays demonstrated that downregulation of MALAT1 could suppress tumor growth through downregulation of HOXC4 expression via increasing miR-608 in uveal melanoma. In summary, MALAT1 downregulation functions to restrain the development of uveal melanoma via miR-608-mediated inhibition of HOXC4.
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Affiliation(s)
- Shuai Wu
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, People's Republic of China
| | - Han Chen
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, People's Republic of China
| | - Ling Zuo
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, People's Republic of China
| | - Hai Jiang
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, People's Republic of China
| | - Hongtao Yan
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, People's Republic of China
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