Gene-Specific Intron Retention Serves as Molecular Signature that Distinguishes Melanoma from Non-Melanoma Cancer Cells in Greek Patients

International Journal of Molecular Sciences
Aikaterini F GiannopoulouDimitrios J Stravopodis

Abstract

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. 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. 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 developm...Continue Reading

References

Jul 4, 2001·Nature Reviews. Molecular Cell Biology·M Holcik, R G Korneluk
Mar 26, 2002·FEBS Letters·Lei Zeng, Ming Ming Zhou
Jan 10, 2003·The Journal of Investigative Dermatology. Symposium Proceedings·Andrzej DlugoszStuart H Yuspa
Feb 13, 2003·Journal of the American Chemical Society·Cyril DominguezAlexandre M J J Bonvin
Jul 21, 2004·Journal of Computational Chemistry·Eric F PettersenThomas E Ferrin
Sep 15, 2004·Genome Research·Antony RodriguezAllan Bradley
Sep 24, 2004·Physiological Reviews·Andrzej SlominskiJacobo Wortsman
Feb 25, 2006·Human Molecular Genetics·Patrice RollPierre Szepetowski
Jul 28, 2007·Nature Clinical Practice. Oncology·Julie A NevilleDavid J Leffell
Dec 14, 2007·Nature Reviews. Cancer·Dario C Altieri
Sep 25, 2008·Nature Reviews. Cancer·Ervin H Epstein
Dec 10, 2008·International Journal of Cancer. Journal International Du Cancer·Kaoru TanakaKazuto Nishio
Apr 23, 2009·Molecular Oncology·Anna BergamaschiJonathan R Pollack
Aug 12, 2009·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Marijana Miljkovic-LicinaBeat A Imhof
Nov 3, 2010·Nucleic Acids Research·Ana Kozomara, Sam Griffiths-Jones
Nov 26, 2010·Transplantation·Oliver P GüntherUNKNOWN Biomarkers in Transplantation Team
Oct 21, 2011·Nature·Corine BertolottoBrigitte Bressac-de Paillerets
Dec 17, 2011·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Keryn M LucasJohn D Allen
Jan 25, 2012·Nature Reviews. Cancer·Ermanno GherardiGeorge Vande Woude
Apr 6, 2012·Nature Reviews. Cancer·Keith T FlahertyDavid E Fisher
Apr 17, 2012·Cell·Mathieu Laplante, David M Sabatini
Aug 23, 2012·Clinical & Translational Oncology : Official Publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico·Chunmei GuoMing-Zhong Sun
Oct 10, 2012·Molecular Cancer·Jonhan HoStergios J Moschos
Dec 19, 2012·The International Journal of Biochemistry & Cell Biology·Ying JiYouquan Bu
Jan 26, 2013·Science·Susanne HornRajiv Kumar
Jan 26, 2013·Science·Franklin W HuangLevi A Garraway
Mar 13, 2013·Pathology·Andrew C ChenDiona L Damian
Apr 23, 2013·Scientific Reports·Jeyanthy EswaranRakesh Kumar

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Citations

Mar 19, 2020·Frontiers in Cell and Developmental Biology·Monica NeaguSabina Zurac
Mar 25, 2020·Computational and Structural Biotechnology Journal·Lucile Broseus, William Ritchie
Oct 14, 2020·Cancer Research·Geoffray MonteuuisJohn E J Rasko

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Datasets Mentioned

BETA
AAL55828.1
AF318321.1

Methods Mentioned

BETA
biopsy
PCR
biopsies
chips
electrophoresis

Software Mentioned

miRbase
Clustal X2
Ensembl Browser
Clustal Omega
TASSER
HADDOCK2
ORF Finder
HADDOCK
PyMol Visualization System
Ensembl Genome Browser

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