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  • Langen, BrittaGothenburg University,Göteborgs universitet,Sahlgrenska Cancer Center,Institutionen för kliniska vetenskaper, Avdelningen för radiofysik,Institute of Clinical Sciences, Department of Radiation Physics,Sahlgrenska universitetssjukhuset,Sahlgrenska University Hospital,Chalmers tekniska högskola,Chalmers University of Technology (author)

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

  • Article/chapterEnglish2018

Publisher, publication year, extent ...

  • 2018-07-12
  • Public Library of Science (PLoS),2018

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  • LIBRIS-ID:oai:gup.ub.gu.se/277272
  • https://gup.ub.gu.se/publication/277272URI
  • https://doi.org/10.1371/journal.pone.0197911DOI
  • https://research.chalmers.se/publication/504145URI

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  • Language:English

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  • Subject category:ref swepub-contenttype
  • Subject category:art swepub-publicationtype

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  • 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 I-131 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 reproduced. Importantly, responses in biological processes for DNA integrity, gene expression integrity, and cellular stress were not detected in convoluted data-which was in disagreement with expected dose-response relationships-but upon deconvolution in follicular cells and C-cells. In conclusion, previously reported trends of I-131-induced transcriptional responses in thyroid were reproduced with deconvolved data and usually with a higher detection rate. Deconvolution also resolved an issue with detecting damage and stress responses in enriched data, and may reduce false negatives in other contexts as well. These findings indicate that deconvolution can optimize microarray data analysis of heterogeneous sample material for biomarker screening or other clinical applications.

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  • Rudqvist, NilsGothenburg University,Göteborgs universitet,Sahlgrenska Cancer Center,Institutionen för kliniska vetenskaper, Avdelningen för radiofysik,Institute of Clinical Sciences, Department of Radiation Physics,Sahlgrenska universitetssjukhuset,Sahlgrenska University Hospital(Swepub:gu)xrudni (author)
  • Spetz, JohanGothenburg University,Göteborgs universitet,Sahlgrenska Cancer Center,Institutionen för kliniska vetenskaper, Avdelningen för radiofysik,Institute of Clinical Sciences, Department of Radiation Physics,Sahlgrenska universitetssjukhuset,Sahlgrenska University Hospital(Swepub:gu)xspetj (author)
  • Helou, Khalil,1966Gothenburg University,Göteborgs universitet,Institutionen för kliniska vetenskaper, Avdelningen för onkologi,Sahlgrenska Cancer Center,Institute of Clinical Sciences, Department of Oncology,Sahlgrenska universitetssjukhuset,Sahlgrenska University Hospital(Swepub:gu)xhelkh (author)
  • Forssell-Aronsson, Eva,1961Gothenburg University,Göteborgs universitet,Institutionen för kliniska vetenskaper, Avdelningen för radiofysik,Sahlgrenska Cancer Center,Institute of Clinical Sciences, Department of Radiation Physics,Sahlgrenska universitetssjukhuset,Sahlgrenska University Hospital(Swepub:gu)xforev (author)
  • Göteborgs universitetSahlgrenska Cancer Center (creator_code:org_t)

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  • In:Plos One: Public Library of Science (PLoS)13:71932-6203

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Langen, Britta
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MEDICAL AND HEALTH SCIENCES
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Plos One
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University of Gothenburg
Chalmers University of Technology

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