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Global gene expression profiling using heterologous DNA microarrays to analyze alterations in the transcriptome of Mus spretus mice living in a heavily polluted environment

Abstract

Microarray platforms are a good approach for assessing biological responses to pollution as they enable the simultaneous analyses of changes in the expression of thousands of genes. As an omic and non-targeted methodology, this technique is open to unforeseen responses under particular environmental conditions. In this study, we successfully apply a commercial oligonucleotide microarray containing Mus musculus whole-genome probes to compare and assess the biological effects of living in a heavily polluted settlement, the Domingo Rubio stream (DRS), at the Huelva Estuary (SW Spain), on inhabitant free-living Mus spretus mice. Our microarray results show that mice living in DRS suffer dramatic changes in gene and protein expression compared with reference specimens. DRS mice showed alteration in the oxidative status of hepatocytes, with activation of both the innate and the acquired immune responses and the induction of chronic inflammation, accompanied by metabolic alterations that imply the accumulation of lipids in the liver (hepatic steatosis). The identified deregulated genes may be useful as biomarkers of environmental pollution.

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Acknowledgments

The authors thank the European Regional Development Fund, the Spanish Ministry of Economy and Competitiveness (MINECO, CTM2012-38720.C03-02), the Agency of Economy, Competitiveness, Science, and Employment, Andalusian Government (CVI-3829 and BIO1657), and the Andalusian Plan of Research, Development, and Innovation (PAIDI) to group BIO187, for funding this work.

Authors’ contributions

N.A. and J. R-L. contributed equally to this work and merit equal consideration as first authors.

Author information

Correspondence to Nieves Abril.

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Conflict of interest

The authors declare that there are no conflicts of interest.

Funding resources

This study was co-funded by European Regional Development Fund and MINECO (CTM2012-38720-C03-02) and the Agency of Economy, Competitiveness, Science, and Employment from the Andalusian Government (CVI-3829 and BIO1657), and by the Andalusian Plan of Research, Development, and Innovation (PAIDI) to group BIO187.

Additional information

Animal rights

This work was performed in accordance with EU Directive 2010/63/EU for animal experiments and was approved by the Ethical Committees of the University of Cordoba. Animal collection at the Doñana Natl. Park had the corresponding authorizations from the General Direction of Natural Environments of the Andalusian Ministry of Agriculture, Fisheries, and Environment.

Highlights

• Commercial oligonucleotide microarrays containing the lab mouse Mus musculus whole-genome probes are useful tools to assess the biological effects of polluted environment on free-living Mus spretus mice.

• qRT-PCR and Western blot data confirm the upregulation or downregulation of a selected group of transcripts.

• Mice living in polluted areas show a set of deregulated hepatic genes involved in a variety of biological functions, affecting mainly the immune and stress responses.

• Pollution modifies the genetic expression of hepatic cells, leading to metabolic changes that might cause a higher incidence of a variety of hepatic pathologies.

• The identified deregulated genes may be useful as biomarkers of environmental pollution.

TOC

Responsible editor: Philippe Garrigues

Electronic supplementary material

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ESM 1

Supplementary Information Figure 1. Location of SOL and DRS mice sampling areas. (A) Location of the studied area in SW Spain. (B) Location of the Santa Olalla Lagoon (SOL), the reference site located in the heart of Doñana National Park. (C) Close-up view of Huelva Estuary with the location of the Domingo Rubio Stream (DRS) sampling area. (PPTX 480 kb)

ESM 2

Supplementary Information Figure 2. Experimental design. (PPTX 211 kb)

ESM 3

Supplementary Information Figure 3. Functional classification of deregulated hepatic genes in DRS mice. (PPTX 456 kb)

ESM 4

Supplementary Information Table 1. Primers used in this work. (XLSX 23 kb)

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Ruiz-Laguna, J., Vélez, J.M., Pueyo, C. et al. Global gene expression profiling using heterologous DNA microarrays to analyze alterations in the transcriptome of Mus spretus mice living in a heavily polluted environment. Environ Sci Pollut Res 23, 5853–5867 (2016). https://doi.org/10.1007/s11356-015-5824-5

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Keywords

  • Environmental pollution
  • Transcriptomics
  • Mus spretus
  • Heterologous microarray
  • Biomonitoring