Deconvolution of expression microarray data reveals 131I-induced responses otherwise undetected in thyroid tissue

PloS One
Britta LangenEva Forssell-Aronsson

Abstract

High-throughput gene expression analysis is increasingly used in radiation research for discovery of damage-related or absorbed dose-dependent biomarkers. In tissue samples, cell type-specific responses can be masked in expression data due to mixed cell populations which can preclude biomarker discovery. In this study, we deconvolved microarray data from thyroid tissue in order to assess possible bias from mixed cell type data. Transcript expression data [GSE66303] from mouse thyroid that received 5.9 Gy from 131I over 24 h (or 0 Gy from mock treatment) were deconvolved by cell frequency of follicular cells and C-cells using csSAM and R and processed with Nexus Expression. Literature-based signature genes were used to assess the relative impact from ionizing radiation (IR) or thyroid hormones (TH). Regulation of cellular functions was inferred by enriched biological processes according to Gene Ontology terms. We found that deconvolution increased the detection rate of significantly regulated transcripts including the biomarker candidate family of kallikrein transcripts. Detection of IR-associated and TH-responding signature genes was also increased in deconvolved data, while the dominating trend of TH-responding genes was repro...Continue Reading

References

Jan 1, 1986·International Journal of Radiation Applications and Instrumentation. Part A, Applied Radiation and Isotopes·I Brown
Jan 1, 1982·Acta Endocrinologica·V Thurston, E D Williams
Sep 1, 1996·The Journal of Histochemistry and Cytochemistry : Official Journal of the Histochemistry Society·R E FeinsteinL Grimelius
Jun 1, 1954·Proceedings of the Society for Experimental Biology and Medicine·J G HAMILTONM W PARROTT
Oct 1, 1954·The Journal of Clinical Endocrinology and Metabolism·J G HAMILTONM PARROTT
Jun 16, 2004·Cancer Metastasis Reviews·Andrew R Snyder, William F Morgan
Jan 30, 2007·Cancer Biotherapy & Radiopharmaceuticals·Charlotta LundhEva Forssell-Aronsson
May 6, 2008·Journal of Biomedical Science·M Ahmad Chaudhry
Jun 16, 2009·Journal of Nuclear Medicine : Official Publication, Society of Nuclear Medicine·Charlotta LundhEva Forssell-Aronsson
Mar 9, 2010·Nature Methods·Shai S Shen-OrrAtul J Butte
Dec 30, 2011·Nature Methods·Yi Zhong, Zhandong Liu
May 10, 2013·Journal of Nuclear Medicine : Official Publication, Society of Nuclear Medicine·Britta LangenEva Forssell-Aronsson
Jun 25, 2013·Cancer Biotherapy & Radiopharmaceuticals·Johan SpetzEva Forssell-Aronsson
Oct 24, 2013·Current Opinion in Immunology·Shai S Shen-Orr, Renaud Gaujoux
Jan 18, 2014·Nuclear Medicine and Biology·Emil SchülerEva Forssell-Aronsson
Jul 10, 2014·EJNMMI Research·Anders Josefsson, Eva Forssell-Aronsson
Aug 27, 2014·Nuclear Medicine and Biology·Emil SchülerEva Forssell-Aronsson
Dec 17, 2014·Nuclear Medicine and Biology·Nils RudqvistEva Forssell-Aronsson
Oct 24, 2015·EJNMMI Research·Nils RudqvistEva Forssell-Aronsson
Oct 27, 2015·Recent Results in Cancer Research. Fortschritte Der Krebsforschung. Progrès Dans Les Recherches Sur Le Cancer·Gilbert J CoteMarie-Claude Hofmann
Oct 22, 2016·Journal of Nuclear Medicine : Official Publication, Society of Nuclear Medicine·Britta LangenEva Forssell-Aronsson
Feb 22, 2017·PloS One·Nils RudqvistEva Forssell-Aronsson

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Datasets Mentioned

BETA
GSE66303

Methods Mentioned

BETA
PCR

Software Mentioned

csSAM
Elements F
gplots
Nexus Expression
R
NIS
csSAM ( analysis of microarrays )

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