Transcriptomic markers meet the real world: finding diagnostic signatures of corticosteroid treatment in commercial beef samples

Quantitative determination of Dexamethasone (DEX) residues in the urine collected at the slaughterhouse was performed by Liquid Chromatography-Mass Spectrometry (LC-MS). DNA-microarray technology was used to obtain transcriptomic profiles of skeletal muscle in commercial samples and negative controls. LC-MS confirmed the presence of low level of DEX residues in the urine of the commercial samples suspect for histological classification. Principal Component Analysis (PCA) on microarray data identified two clusters of samples. One cluster included negative controls and a subset of commercial samples, while a second cluster included part of the specimens collected at the slaughterhouse together with positives for corticosteroid treatment based on thymus histology and LC-MS. Functional analysis of the differentially expressed genes (3961) between the two groups provided further evidence that animals clustering with positive samples might have been treated with corticosteroids. These suspect samples could be reliably classified with a specific classification tool (Prediction Analysis of Microarray) using just two genes.Despite broad variation observed in gene expression profiles, the present study showed that DNA-microarrays can be used to find transcriptomic signatures of putative anabolic treatments and that gene expression markers could represent a useful screening tool.The use of growth promoters in meat production has been banned in the European Union since 1988 due to the potentially adverse effects of hormone residues for the consumer. Council Directive 23/96/EC requires the EU member States to adopt National Monitoring Plans to control the illegal use of these compounds. Despite the ban, these substances are still administered and a black-market for the production, distribution, and use of multiple steroids has flourished [1]. To elude official controls, new anabolic compounds are developed and growth promoters are administered at low doses or combining different