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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...

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Autores principales: 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.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
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.
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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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