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

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 biodosimetry, for which primer- or probe-based techniques would be the method of choice.

Comparable dose estimates of blinded whole blood samples are obtained independently of culture conditions and analytical approaches. Second RENEB gene expression study

“…Dose assessment in irradiated blood samples can be obtained by either using dose predictive gene or exon signatures (Paul & Amundson 2008;Kabacik et al 2011;Boldt et al 2012;Knops et al 2012;Lucas et al 2014;Macaeva et al 2016) or by monitoring the modification of transcription of single radiation-responsive genes like ferredoxin reductase (FDXR) (Manning et al 2013;Abend et al 2016).…”

“…In ex vivo studies, several protocols have been used such as cultured peripheral blood mononuclear cells (PBMC) (Dressman et al 2007;Meadows et al 2008Meadows et al , 2010Sprung et al 2011;Boldt et al 2012;Knops et al 2012;Riecke et al 2012;Macaeva et al 2016), cultured whole blood diluted with media Brzoska andKruszewski 2015, Abend et al 2016) or undiluted whole blood (Manning et al 2013). However, none of these studies have addressed the role of blood culture methods during the incubation time at 37 C following radiation exposure.…”

“…A wide range of methodologies, reagents and analysis techniques are available for studying gene expression and it is important to identify external factors, apart from radiation exposure, which may cause 'artificial' transcriptional modifications in ex vivo studies, like culture conditions or the type of analytical approaches; this is particularly relevant for the calibration curves generated as they are the reference used for in vivo dose assessments. This concern was briefly addressed in Macaeva et al (2016), where they compared gene expression levels in their study to others in the literature and found that despite varying cell types, radiation quality, dose rate, a core signature of genes was found in common among the studies. However, the role of ex vivo blood preservation has yet to be addressed.…”

“…As a consequence, this could introduce differences between participating labs and most importantly affect the shape of the calibration curves, hence providing inaccurate dose estimates. The use of different platforms may also introduce variability in the dose estimates provided, however, in a recent paper by Macaeva et al (2016), gene expression profiles from different platforms were used and very comparable gene signatures were obtained. Also, in the first RENEB exercise (Abend et al 2016) different platforms were also used and again comparable results were obtained.…”

Analysis of Saliva Gene Expression during Head and Neck Cancer Radiotherapy: A Pilot Study

“…However, this approach is time consuming and highly technique dependent, and detection of very low or high dose is limited. Because of these limitations, studies published over the past several years have suggested the development of gene expression profiles in biological fluid, especially in blood, as an alternative approach for identifying exposed individuals and assessing absorbed dose (2–8). These studies have shown promising results indicating that distinctive gene expression patterns could be highly correlated with different radiation doses.…”