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Gene-Specific Intron Retention Serves as Molecular Signature that Distinguishes Melanoma from Non-Melanoma Cancer Cells in Greek Patients
Background: Skin cancer represents the most common human malignancy, and it includes BCC, SCC, and melanoma. Since melanoma is one of the most aggressive types of cancer, we have herein attempted to develop a gene-specific intron retention signature that can distinguish BCC and SCC from melanoma bio...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6412294/ https://www.ncbi.nlm.nih.gov/pubmed/30795533 http://dx.doi.org/10.3390/ijms20040937 |
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author | Giannopoulou, Aikaterini F. Konstantakou, Eumorphia G. Velentzas, Athanassios D. Avgeris, Socratis N. Avgeris, Margaritis Papandreou, Nikos C. Zoi, Ilianna Filippa, Vicky Katarachia, Stamatia Lampidonis, Antonis D. Prombona, Anastasia Syntichaki, Popi Piperi, Christina Basdra, Efthimia K. Iconomidou, Vassiliki Papadavid, Evangelia Anastasiadou, Ema Papassideri, Issidora S. Papavassiliou, Athanasios G. Voutsinas, Gerassimos E. Scorilas, Andreas Stravopodis, Dimitrios J. |
author_facet | Giannopoulou, Aikaterini F. Konstantakou, Eumorphia G. Velentzas, Athanassios D. Avgeris, Socratis N. Avgeris, Margaritis Papandreou, Nikos C. Zoi, Ilianna Filippa, Vicky Katarachia, Stamatia Lampidonis, Antonis D. Prombona, Anastasia Syntichaki, Popi Piperi, Christina Basdra, Efthimia K. Iconomidou, Vassiliki Papadavid, Evangelia Anastasiadou, Ema Papassideri, Issidora S. Papavassiliou, Athanasios G. Voutsinas, Gerassimos E. Scorilas, Andreas Stravopodis, Dimitrios J. |
author_sort | Giannopoulou, Aikaterini F. |
collection | PubMed |
description | Background: Skin cancer represents the most common human malignancy, and it includes BCC, SCC, and melanoma. Since melanoma is one of the most aggressive types of cancer, we have herein attempted to develop a gene-specific intron retention signature that can distinguish BCC and SCC from melanoma biopsy tumors. Methods: Intron retention events were examined through RT-sqPCR protocols, using total RNA preparations derived from BCC, SCC, and melanoma Greek biopsy specimens. Intron-hosted miRNA species and their target transcripts were predicted via the miRbase and miRDB bioinformatics platforms, respectively. Ιntronic ORFs were recognized through the ORF Finder application. Generation and visualization of protein interactomes were achieved by the IntAct and Cytoscape softwares, while tertiary protein structures were produced by using the I-TASSER online server. Results: c-MYC and Sestrin-1 genes proved to undergo intron retention specifically in melanoma. Interaction maps of proteins encoded by genes being potentially targeted by retained intron-accommodated miRNAs were generated and SRPX2 was additionally delivered to our melanoma-specific signature. Novel ORFs were identified in MCT4 and Sestrin-1 introns, with potentially critical roles in melanoma development. Conclusions: The property of c-MYC, Sestrin-1, and SRPX2 genes to retain specific introns could be clinically used to molecularly differentiate non-melanoma from melanoma tumors. |
format | Online Article Text |
id | pubmed-6412294 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-64122942019-04-05 Gene-Specific Intron Retention Serves as Molecular Signature that Distinguishes Melanoma from Non-Melanoma Cancer Cells in Greek Patients Giannopoulou, Aikaterini F. Konstantakou, Eumorphia G. Velentzas, Athanassios D. Avgeris, Socratis N. Avgeris, Margaritis Papandreou, Nikos C. Zoi, Ilianna Filippa, Vicky Katarachia, Stamatia Lampidonis, Antonis D. Prombona, Anastasia Syntichaki, Popi Piperi, Christina Basdra, Efthimia K. Iconomidou, Vassiliki Papadavid, Evangelia Anastasiadou, Ema Papassideri, Issidora S. Papavassiliou, Athanasios G. Voutsinas, Gerassimos E. Scorilas, Andreas Stravopodis, Dimitrios J. Int J Mol Sci Article Background: Skin cancer represents the most common human malignancy, and it includes BCC, SCC, and melanoma. Since melanoma is one of the most aggressive types of cancer, we have herein attempted to develop a gene-specific intron retention signature that can distinguish BCC and SCC from melanoma biopsy tumors. Methods: Intron retention events were examined through RT-sqPCR protocols, using total RNA preparations derived from BCC, SCC, and melanoma Greek biopsy specimens. Intron-hosted miRNA species and their target transcripts were predicted via the miRbase and miRDB bioinformatics platforms, respectively. Ιntronic ORFs were recognized through the ORF Finder application. Generation and visualization of protein interactomes were achieved by the IntAct and Cytoscape softwares, while tertiary protein structures were produced by using the I-TASSER online server. Results: c-MYC and Sestrin-1 genes proved to undergo intron retention specifically in melanoma. Interaction maps of proteins encoded by genes being potentially targeted by retained intron-accommodated miRNAs were generated and SRPX2 was additionally delivered to our melanoma-specific signature. Novel ORFs were identified in MCT4 and Sestrin-1 introns, with potentially critical roles in melanoma development. Conclusions: The property of c-MYC, Sestrin-1, and SRPX2 genes to retain specific introns could be clinically used to molecularly differentiate non-melanoma from melanoma tumors. MDPI 2019-02-21 /pmc/articles/PMC6412294/ /pubmed/30795533 http://dx.doi.org/10.3390/ijms20040937 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Giannopoulou, Aikaterini F. Konstantakou, Eumorphia G. Velentzas, Athanassios D. Avgeris, Socratis N. Avgeris, Margaritis Papandreou, Nikos C. Zoi, Ilianna Filippa, Vicky Katarachia, Stamatia Lampidonis, Antonis D. Prombona, Anastasia Syntichaki, Popi Piperi, Christina Basdra, Efthimia K. Iconomidou, Vassiliki Papadavid, Evangelia Anastasiadou, Ema Papassideri, Issidora S. Papavassiliou, Athanasios G. Voutsinas, Gerassimos E. Scorilas, Andreas Stravopodis, Dimitrios J. Gene-Specific Intron Retention Serves as Molecular Signature that Distinguishes Melanoma from Non-Melanoma Cancer Cells in Greek Patients |
title | Gene-Specific Intron Retention Serves as Molecular Signature that Distinguishes Melanoma from Non-Melanoma Cancer Cells in Greek Patients |
title_full | Gene-Specific Intron Retention Serves as Molecular Signature that Distinguishes Melanoma from Non-Melanoma Cancer Cells in Greek Patients |
title_fullStr | Gene-Specific Intron Retention Serves as Molecular Signature that Distinguishes Melanoma from Non-Melanoma Cancer Cells in Greek Patients |
title_full_unstemmed | Gene-Specific Intron Retention Serves as Molecular Signature that Distinguishes Melanoma from Non-Melanoma Cancer Cells in Greek Patients |
title_short | Gene-Specific Intron Retention Serves as Molecular Signature that Distinguishes Melanoma from Non-Melanoma Cancer Cells in Greek Patients |
title_sort | gene-specific intron retention serves as molecular signature that distinguishes melanoma from non-melanoma cancer cells in greek patients |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6412294/ https://www.ncbi.nlm.nih.gov/pubmed/30795533 http://dx.doi.org/10.3390/ijms20040937 |
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