title: The potential of circulating extracellular small RNAs (smexRNA) in veterinary diagnostics-Identifying biomarker signatures by multivariate data analysis.
abstract: Worldwide growth and performance-enhancing substances are used in cattle husbandry to increase productivity. In certain countries however e.g., in the EU, these practices are forbidden to prevent the consumers from potential health risks of substance residues in food. To maximize economic profit, 'black sheep' among farmers might circumvent the detection methods used in routine controls, which highlights the need for an innovative and reliable detection method. Transcriptomics is a promising new approach in the discovery of veterinary medicine biomarkers and also a missing puzzle piece, as up to date, metabolomics and proteomics are paramount. Due to increased stability and easy sampling, circulating extracellular small RNAs (smexRNAs) in bovine plasma were small RNA-sequenced and their potential to serve as biomarker candidates was evaluated using multivariate data analysis tools. After running the data evaluation pipeline, the proportion of miRNAs (microRNAs) and piRNAs (PIWI-interacting small non-coding RNAs) on the total sequenced reads was calculated. Additionally, top 10 signatures were compared which revealed that the readcount data sets were highly affected by the most abundant miRNA and piRNA profiles. To evaluate the discriminative power of multivariate data analyses to identify animals after veterinary drug application on the basis of smexRNAs, OPLS-DA was performed. In summary, the quality of miRNA models using all mapped reads for both treatment groups (animals treated with steroid hormones or the β-agonist clenbuterol) is predominant to those generated with combined data sets or piRNAs alone. Using multivariate projection methodologies like OPLS-DA have proven the best potential to generate discriminative miRNA models, supported by small RNA-Seq data. Based on the presented comparative OPLS-DA, miRNAs are the favorable smexRNA biomarker candidates in the research field of veterinary drug abuse.
authors.affiliation: Chair of Physiology, Technical University Munich, TUM School of Life Sciences Weihenstephan, Weihenstephaner Berg 3, 85354 Freising-Weihenstephan, Germany.
authors.forename: Spornraft
authors.initials: S
authors.lastname: Melanie
authors.affiliation: Chair of Physiology, Technical University Munich, TUM School of Life Sciences Weihenstephan, Weihenstephaner Berg 3, 85354 Freising-Weihenstephan, Germany.
authors.forename: Kirchner
authors.initials: K
authors.lastname: Benedikt
authors.affiliation: Chair of Physiology, Technical University Munich, TUM School of Life Sciences Weihenstephan, Weihenstephaner Berg 3, 85354 Freising-Weihenstephan, Germany.
authors.forename: Michael W
authors.initials: MW
authors.lastname: Pfaffl
authors.affiliation: Chair of Physiology, Technical University Munich, TUM School of Life Sciences Weihenstephan, Weihenstephaner Berg 3, 85354 Freising-Weihenstephan, Germany.
authors.forename: Riedmaier
authors.initials: R
authors.lastname: Irmgard
keywords: Biomarker signatures; CLEN, treated group with clenbuterol-hydrochloride; CON, control group; Circulating small RNAs; DA, discriminant analysis; EU, European Union; Multivariate data analysis; OPLS, orthogonal partial least-squares; PCA, principal component analysis; PLS, partial least-squares projection; P + EB, treated group with steroid hormone implant: progesterone plus estradiol benzoate; Small RNA-Sequencing; Transcriptomics; Veterinary diagnostics; exRNA, extracellular RNA; miRNA, microRNA; piRNA, PIWI-interacting small non-coding RNA; rpm, reads per million; small RNA-Seq, small RNA-Sequencing; smexRNA, circulating extracellular small RNA