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...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2019-02-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/20/4/937 |
| id |
doaj-ed11c2f6e4f14023b0dc2b60b609ceef |
|---|---|
| record_format |
Article |
| collection |
DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Aikaterini F. Giannopoulou Eumorphia G. Konstantakou Athanassios D. Velentzas Socratis N. Avgeris Margaritis Avgeris Nikos C. Papandreou Ilianna Zoi Vicky Filippa Stamatia Katarachia Antonis D. Lampidonis Anastasia Prombona Popi Syntichaki Christina Piperi Efthimia K. Basdra Vassiliki Iconomidou Evangelia Papadavid Ema Anastasiadou Issidora S. Papassideri Athanasios G. Papavassiliou Gerassimos E. Voutsinas Andreas Scorilas Dimitrios J. Stravopodis |
| spellingShingle |
Aikaterini F. Giannopoulou Eumorphia G. Konstantakou Athanassios D. Velentzas Socratis N. Avgeris Margaritis Avgeris Nikos C. Papandreou Ilianna Zoi Vicky Filippa Stamatia Katarachia Antonis D. Lampidonis Anastasia Prombona Popi Syntichaki Christina Piperi Efthimia K. Basdra Vassiliki Iconomidou Evangelia Papadavid Ema Anastasiadou Issidora S. Papassideri Athanasios G. Papavassiliou Gerassimos E. Voutsinas Andreas Scorilas Dimitrios J. Stravopodis Gene-Specific Intron Retention Serves as Molecular Signature that Distinguishes Melanoma from Non-Melanoma Cancer Cells in Greek Patients International Journal of Molecular Sciences BCC cancer intron melanoma SCC splicing transcription |
| author_facet |
Aikaterini F. Giannopoulou Eumorphia G. Konstantakou Athanassios D. Velentzas Socratis N. Avgeris Margaritis Avgeris Nikos C. Papandreou Ilianna Zoi Vicky Filippa Stamatia Katarachia Antonis D. Lampidonis Anastasia Prombona Popi Syntichaki Christina Piperi Efthimia K. Basdra Vassiliki Iconomidou Evangelia Papadavid Ema Anastasiadou Issidora S. Papassideri Athanasios G. Papavassiliou Gerassimos E. Voutsinas Andreas Scorilas Dimitrios J. Stravopodis |
| author_sort |
Aikaterini F. Giannopoulou |
| title |
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_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_sort |
gene-specific intron retention serves as molecular signature that distinguishes melanoma from non-melanoma cancer cells in greek patients |
| publisher |
MDPI AG |
| series |
International Journal of Molecular Sciences |
| issn |
1422-0067 |
| publishDate |
2019-02-01 |
| 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: <i>c-MYC</i> and <i>Sestrin-1</i> 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 <i>SRPX2</i> was additionally delivered to our melanoma-specific signature. Novel ORFs were identified in <i>MCT4</i> and <i>Sestrin-1</i> introns, with potentially critical roles in melanoma development. Conclusions: The property of <i>c-MYC</i>, <i>Sestrin-1</i>, and <i>SRPX2</i> genes to retain specific introns could be clinically used to molecularly differentiate non-melanoma from melanoma tumors. |
| topic |
BCC cancer intron melanoma SCC splicing transcription |
| url |
https://www.mdpi.com/1422-0067/20/4/937 |
| work_keys_str_mv |
AT aikaterinifgiannopoulou genespecificintronretentionservesasmolecularsignaturethatdistinguishesmelanomafromnonmelanomacancercellsingreekpatients AT eumorphiagkonstantakou genespecificintronretentionservesasmolecularsignaturethatdistinguishesmelanomafromnonmelanomacancercellsingreekpatients AT athanassiosdvelentzas genespecificintronretentionservesasmolecularsignaturethatdistinguishesmelanomafromnonmelanomacancercellsingreekpatients AT socratisnavgeris genespecificintronretentionservesasmolecularsignaturethatdistinguishesmelanomafromnonmelanomacancercellsingreekpatients AT margaritisavgeris genespecificintronretentionservesasmolecularsignaturethatdistinguishesmelanomafromnonmelanomacancercellsingreekpatients AT nikoscpapandreou genespecificintronretentionservesasmolecularsignaturethatdistinguishesmelanomafromnonmelanomacancercellsingreekpatients AT iliannazoi genespecificintronretentionservesasmolecularsignaturethatdistinguishesmelanomafromnonmelanomacancercellsingreekpatients AT vickyfilippa genespecificintronretentionservesasmolecularsignaturethatdistinguishesmelanomafromnonmelanomacancercellsingreekpatients AT stamatiakatarachia genespecificintronretentionservesasmolecularsignaturethatdistinguishesmelanomafromnonmelanomacancercellsingreekpatients AT antonisdlampidonis genespecificintronretentionservesasmolecularsignaturethatdistinguishesmelanomafromnonmelanomacancercellsingreekpatients AT anastasiaprombona genespecificintronretentionservesasmolecularsignaturethatdistinguishesmelanomafromnonmelanomacancercellsingreekpatients AT popisyntichaki genespecificintronretentionservesasmolecularsignaturethatdistinguishesmelanomafromnonmelanomacancercellsingreekpatients AT christinapiperi genespecificintronretentionservesasmolecularsignaturethatdistinguishesmelanomafromnonmelanomacancercellsingreekpatients AT efthimiakbasdra genespecificintronretentionservesasmolecularsignaturethatdistinguishesmelanomafromnonmelanomacancercellsingreekpatients AT vassilikiiconomidou genespecificintronretentionservesasmolecularsignaturethatdistinguishesmelanomafromnonmelanomacancercellsingreekpatients AT evangeliapapadavid genespecificintronretentionservesasmolecularsignaturethatdistinguishesmelanomafromnonmelanomacancercellsingreekpatients AT emaanastasiadou genespecificintronretentionservesasmolecularsignaturethatdistinguishesmelanomafromnonmelanomacancercellsingreekpatients AT issidoraspapassideri genespecificintronretentionservesasmolecularsignaturethatdistinguishesmelanomafromnonmelanomacancercellsingreekpatients AT athanasiosgpapavassiliou genespecificintronretentionservesasmolecularsignaturethatdistinguishesmelanomafromnonmelanomacancercellsingreekpatients AT gerassimosevoutsinas genespecificintronretentionservesasmolecularsignaturethatdistinguishesmelanomafromnonmelanomacancercellsingreekpatients AT andreasscorilas genespecificintronretentionservesasmolecularsignaturethatdistinguishesmelanomafromnonmelanomacancercellsingreekpatients AT dimitriosjstravopodis genespecificintronretentionservesasmolecularsignaturethatdistinguishesmelanomafromnonmelanomacancercellsingreekpatients |
| _version_ |
1725078307627597824 |
| spelling |
doaj-ed11c2f6e4f14023b0dc2b60b609ceef2020-11-25T01:33:16ZengMDPI AGInternational Journal of Molecular Sciences1422-00672019-02-0120493710.3390/ijms20040937ijms20040937Gene-Specific Intron Retention Serves as Molecular Signature that Distinguishes Melanoma from Non-Melanoma Cancer Cells in Greek PatientsAikaterini F. Giannopoulou0Eumorphia G. Konstantakou1Athanassios D. Velentzas2Socratis N. Avgeris3Margaritis Avgeris4Nikos C. Papandreou5Ilianna Zoi6Vicky Filippa7Stamatia Katarachia8Antonis D. Lampidonis9Anastasia Prombona10Popi Syntichaki11Christina Piperi12Efthimia K. Basdra13Vassiliki Iconomidou14Evangelia Papadavid15Ema Anastasiadou16Issidora S. Papassideri17Athanasios G. Papavassiliou18Gerassimos E. Voutsinas19Andreas Scorilas20Dimitrios J. Stravopodis21Section of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, 15701 Athens, GreeceSection of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, 15701 Athens, GreeceSection of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, 15701 Athens, GreeceLaboratory of Molecular Carcinogenesis and Rare Disease Genetics, Institute of Biosciences and Applications, National Center for Scientific Research “Demokritos”, 15310 Athens, GreeceSection of Biochemistry and Molecular Biology, Department of Biology, School of Science, National and Kapodistrian University of Athens, 15701 Athens, GreeceSection of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, 15701 Athens, GreeceDepartment of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, GreeceCenter of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, GreeceSection of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, 15701 Athens, GreeceSection of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, 15701 Athens, GreeceLaboratory of Chronobiology, Institute of Biosciences and Applications, National Center for Scientific Research “Demokritos”, 15310 Athens, GreeceCenter of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, GreeceDepartment of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, GreeceDepartment of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, GreeceSection of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, 15701 Athens, Greece2nd Department of Dermatology and Venereology, Medical School, National and Kapodistrian University of Athens, “Attikon” University Hospital, 12462 Athens, GreeceCenter of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, GreeceSection of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, 15701 Athens, GreeceDepartment of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, GreeceLaboratory of Molecular Carcinogenesis and Rare Disease Genetics, Institute of Biosciences and Applications, National Center for Scientific Research “Demokritos”, 15310 Athens, GreeceSection of Biochemistry and Molecular Biology, Department of Biology, School of Science, National and Kapodistrian University of Athens, 15701 Athens, GreeceSection of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, 15701 Athens, GreeceBackground: 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: <i>c-MYC</i> and <i>Sestrin-1</i> 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 <i>SRPX2</i> was additionally delivered to our melanoma-specific signature. Novel ORFs were identified in <i>MCT4</i> and <i>Sestrin-1</i> introns, with potentially critical roles in melanoma development. Conclusions: The property of <i>c-MYC</i>, <i>Sestrin-1</i>, and <i>SRPX2</i> genes to retain specific introns could be clinically used to molecularly differentiate non-melanoma from melanoma tumors.https://www.mdpi.com/1422-0067/20/4/937BCCcancerintronmelanomaSCCsplicingtranscription |