RESEARCH ARTICLE Global gene expression profiling using heterologous DNA microarrays to analyze alterations in the transcriptome of Mus spretus mice living in a heavily polluted environment Julia Ruiz-Laguna 1 & José M. Vélez 1 & Carmen Pueyo 1 & Nieves Abril 1 Received: 23 July 2015 /Accepted: 16 November 2015 /Published online: 21 November 2015 # Springer-Verlag Berlin Heidelberg 2015 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 thou- sands 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 dra- matic changes in gene and protein expression compared with reference specimens. DRS mice showed alteration in the oxi- dative 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. Keywords Environmental pollution . Transcriptomics . Mus spretus . Heterologous microarray . Biomonitoring Introduction The environment is continuously loaded with natural and ex- ogenous chemicals released by anthropogenic activities. As a result, many wildlife and human populations are exposed to a variety of chemical agents that may lead to several adverse biological effects. The Domingo Rubio Stream (DRS) flows through a highly industrialized area close to Huelva City (SW Spain) (Suppl. Inf. Fig. 1). DRS is located at the confluence of the Tinto and Odiel Rivers (SW Spain), an estuarine area of salt marshes (the Huelva Estuary) with great ecological value but highly polluted. One main pollution source is the mining activity from the Iberian Pyrite Belt, which continuously lib- erates large amounts of acid, sulfate, and heavy metals into the Environ Sci Pollut Res (2016) 23:5853–5867 DOI 10.1007/s11356-015-5824-5 Responsible editor: Philippe Garrigues 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 downreg- ulation 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 envi- ronmental pollution. TOC Electronic supplementary material The online version of this article (doi:10.1007/s11356-015-5824-5) contains supplementary material, which is available to authorized users. * Nieves Abril bb1abdim@uco.es 1 Department of Biochemistry and Molecular Biology and Agrifood Campus of International Excellence (ceiA3-UCO), University of Córdoba, Severo Ochoa Building, Rabanales Campus, 14071 Córdoba, Spain