Radiation-induced alternative transcription and splicing events and their applicability to practical biodosimetry

Scientific Reports
Ellina MacaevaRoel Quintens

Abstract

Accurate assessment of the individual exposure dose based on easily accessible samples (e.g. blood) immediately following a radiological accident is crucial. We aimed at developing a robust transcription-based signature for biodosimetry from human peripheral blood mononuclear cells irradiated with different doses of X-rays (0.1 and 1.0 Gy) at a dose rate of 0.26 Gy/min. Genome-wide radiation-induced changes in mRNA expression were evaluated at both gene and exon level. Using exon-specific qRT-PCR, we confirmed that several biomarker genes are alternatively spliced or transcribed after irradiation and that different exons of these genes exhibit significantly different levels of induction. Moreover, a significant number of radiation-responsive genes were found to be genomic neighbors. Using three different classification models we found that gene and exon signatures performed equally well on dose prediction, as long as more than 10 features are included. Together, our results highlight the necessity of evaluating gene expression at the level of single exons for radiation biodosimetry in particular and transcriptional biomarker research in general. This approach is especially advisable for practical gene expression-based biodosime...Continue Reading

Associated Datasets

References

May 16, 2002·Proceedings of the National Academy of Sciences of the United States of America·Robert TibshiraniGilbert Chu
Jun 4, 2004·Nature Biotechnology·Zhijin Wu, Rafael A Irizarry
Jun 16, 2004·Annals of Internal Medicine·Jamie K WaselenkoUNKNOWN Strategic National Stockpile Radiation Working Group
Sep 18, 2004·Cancer Research·Sally A AmundsonAlbert J Fornace
Oct 19, 2006·Radiation and Environmental Biophysics·H D Dörr, V Meineke
Apr 5, 2007·PLoS Medicine·Holly K DressmanJohn P Chute
Apr 26, 2007·Genome Biology·Tyson A ClarkJohn E Blume
Jun 24, 2008·International Journal of Radiation Oncology, Biology, Physics·Sunirmal Paul, Sally A Amundson
Jan 13, 2010·Health Physics·Muriel BrenguesFrederic Zenhausern
Jun 2, 2010·Nucleic Acids Research·Dorothea EmigMario Albrecht
Nov 12, 2010·International Journal of Radiation Biology·Sylwia KabacikChristophe Badie
Dec 25, 2010·American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics : the Official Publication of the International Society of Psychiatric Genetics·Yingfang TianFrank R Sharp
Aug 2, 2011·International Journal of Radiation Biology·Sunirmal Paul, Sally A Amundson
Nov 1, 2011·PloS One·Carl N SprungHelen B Forrester
Nov 30, 2011·Nucleic Acids Research·Pascal GellertShizuka Uchida
Dec 1, 2011·Cell Cycle·Krassimira BotchevaCarl W Anderson
Jan 12, 2012·International Journal of Radiation Biology·Sonja BoldtOlaf Wolkenhauer
Jan 18, 2013·Nature·Geoff Brumfiel
Feb 1, 2013·International Journal of Radiation Biology·Grainne ManningChristophe Badie
Jun 26, 2013·International Journal of Bioinformatics Research and Applications·Daniel R HydukeAlbert J Fornace
Jan 18, 2014·International Journal of Oncology·Houssein El-SaghireHubert Thierens
Sep 6, 2014·Scientific Reports·Tzu-Pin LuEric Y Chuang
Sep 26, 2014·PloS One·Joseph LucasJohn P Chute

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Citations

May 16, 2017·Radiation Research·Jerome LacombeFrederic Zenhausern
Sep 25, 2018·International Journal of Radiation Biology·Ellina MacaevaRoel Quintens
Sep 12, 2019·International Journal of Radiation Biology·Danijela StanisavljevicMilena Stevanovic
Jun 4, 2020·International Journal of Molecular Sciences·Jessica VanderstraetenHanane Derradji
Sep 11, 2020·International Journal of Radiation Biology·Ben C ShirleyPeter K Rogan
May 20, 2020·Dose-response : a Publication of International Hormesis Society·Ruixue HuangPing-Kun Zhou
Dec 6, 2019·Scientific Reports·Shanaz A GhandhiDavid J Brenner
Oct 30, 2020·International Journal of Molecular Sciences·Lourdes Cruz-GarciaChristophe Badie
Feb 15, 2021·Translational Research : the Journal of Laboratory and Clinical Medicine·Jared M MayMolykutty J Aryankalayil
Sep 16, 2020·Mutation Research. Genetic Toxicology and Environmental Mutagenesis·Shangamithra VisweswaranVenkatachalam Perumal
Apr 8, 2021·International Journal of Radiation Biology·Farah NasserChristophe Badie
May 11, 2021·International Journal of Radiation Biology·Sally A Amundson
Sep 30, 2021·International Journal of Radiation Biology·Sally A Amundson

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Datasets Mentioned

BETA
E-MTAB-3463
GSE23515

Methods Mentioned

BETA
X-ray
immunoprecipitation
PCA

Software Mentioned

PGE
Partek Genomics Suite
AltAnalyze
PAM ( Prediction Analysis for Microarrays )
Excel
Venny
Gene Array Analyzer
7500
Partek

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