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Comparative toxicoproteogenomics of mouse and rat liver identifies TCDD-resistance genes

  • Stephenie D. Prokopec
  • Aileen Lu
  • Sandy Che-Eun S. Lee
  • Cindy Q. Yao
  • Ren X. Sun
  • John D. Watson
  • Rabah Soliymani
  • Richard de Borja
  • Ada Wong
  • Michelle Sam
  • Philip Zuzarte
  • John D. McPherson
  • Allan B. OkeyEmail author
  • Raimo PohjanvirtaEmail author
  • Paul C. BoutrosEmail author
Organ Toxicity and Mechanisms

Abstract

The aryl hydrocarbon receptor (AHR) mediates many toxic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). However, the AHR alone does not explain the widely different outcomes among organisms. To identify the other factors involved, we evaluated three transgenic mouse lines, each expressing a different rat AHR isoform (rWT, DEL, and INS) providing widely different resistance to TCDD toxicity, as well as C57BL/6 and DBA/2 mice which exhibit a ~ tenfold divergence in TCDD sensitivity (exposures of 5-1000 μg/kg TCDD). We supplement these with whole-genome sequencing, together with transcriptomic and proteomic analyses of the corresponding rat models, Long–Evans (L–E) and Han/Wistar (H/W) rats (having a ~ 1000-fold difference in their TCDD sensitivities; 100 μg/kg TCDD), to identify genes associated with TCDD-response phenotypes. Overall, we identified up to 50% of genes with altered mRNA abundance following TCDD exposure are associated with a single AHR isoform (33.8%, 11.7%, 5.2% and 0.3% of 3076 genes altered unique to rWT, DEL, C57BL/6 and INS respectively following 1000 μg/kg TCDD). Hepatic Pxdc1 was significantly repressed in all three TCDD-sensitive animal models (C57BL/6 and rWT mice, and L–E rat) after TCDD exposure. Three genes, including Cxxc5, Sugp1 and Hgfac, demonstrated different AHRE-1 (full) motif occurrences within their promoter regions between rat strains, as well as different patterns of mRNA abundance. Several hepatic proteins showed parallel up- or downward alterations with their RNAs, with three genes (SNRK, IGTP and IMPA2) showing consistent, strain-dependent changes. These data show the value of integrating genomic, transcriptomic and proteomic evidence across multi-species models in toxicologic studies.

Keywords

Model organisms Whole-genome sequencing Transcriptomics Proteomics TCDD AhR 

Notes

Acknowledgements

The authors thank Hanbert Chen, Alexander Wu, Ashley Smith, Janne Korkalainen, Arja Moilanen, and Virpi Tiihonen for excellent technical assistance and support. Additional thanks to Marc Baumann and staff at the Meilahti Clinical & Basic Proteomics Core Facility. This work was supported by the Canadian Institutes of Health Research [grant number MOP-57903 to ABO and PCB], the Academy of Finland [grant number 123345 to RP], and with the support of the Ontario Institute for Cancer Research to PCB through funding provided by the Government of Ontario. PCB was supported by a Terry Fox Research Institute New Investigator Award and a Canadian Institutes of Health Research New Investigator Award.

Author contributions

JDW and SDP carried out the sample preparation for transcriptomic analyses. AW, MS and PZ were involved in library preparation and genome sequencing. RS performed proteomics work. AL, SDP, SL and RDB performed statistical and bioinformatics analyses. AL and SDP wrote the first draft of the manuscript. AL, CQY, SDP, RXS and RP generated tools and reagents. ABO, RP and PCB initiated the project. JDM, ABO, RP and PCB supervised the research. All authors approved the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

All study plans were approved by the Finnish National Animal Experiment Board (Eläinkoelautakunta, ELLA; permit code: ESLH-2008-07223/Ym-23). All animal handling and reporting comply with ARRIVE guidelines (Kilkenny et al. 2010).

Supplementary material

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Supplementary material 1 (XLSX 19 kb)
204_2019_2560_MOESM2_ESM.pdf (1.9 mb)
Supplementary material 2 (PDF 1937 kb)
204_2019_2560_MOESM3_ESM.xlsx (15.3 mb)
Supplementary material 3 (XLSX 15684 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Stephenie D. Prokopec
    • 1
  • Aileen Lu
    • 1
    • 2
  • Sandy Che-Eun S. Lee
    • 1
  • Cindy Q. Yao
    • 1
  • Ren X. Sun
    • 1
  • John D. Watson
    • 1
  • Rabah Soliymani
    • 3
  • Richard de Borja
    • 1
  • Ada Wong
    • 4
  • Michelle Sam
    • 4
  • Philip Zuzarte
    • 4
  • John D. McPherson
    • 4
  • Allan B. Okey
    • 2
    Email author
  • Raimo Pohjanvirta
    • 5
    • 6
    Email author
  • Paul C. Boutros
    • 1
    • 2
    • 7
    • 8
    • 9
    • 10
    • 11
    Email author
  1. 1.Computational BiologyOntario Institute for Cancer ResearchTorontoCanada
  2. 2.Department of Pharmacology and ToxicologyUniversity of TorontoTorontoCanada
  3. 3.Department of Biochemistry and Developmental Biology, Meilahti Clinical and Basic Proteomics Core FacilityUniversity of HelsinkiHelsinkiFinland
  4. 4.Genome Technologies ProgramOntario Institute for Cancer ResearchTorontoCanada
  5. 5.Laboratory of ToxicologyNational Institute for Health and WelfareKuopioFinland
  6. 6.Department of Food Hygiene and Environmental HealthUniversity of HelsinkiHelsinkiFinland
  7. 7.Department of Medical BiophysicsUniversity of TorontoTorontoCanada
  8. 8.Department of Human GeneticsUniversity of CaliforniaLos AngelesUSA
  9. 9.Department of UrologyUniversity of CaliforniaLos AngelesUSA
  10. 10.Institute for Precision HealthUniversity of CaliforniaLos AngelesUSA
  11. 11.Jonsson Comprehensive Cancer CenterUniversity of CaliforniaLos AngelesUSA

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