Harmonization of pipeline for preclinical multicenter plasma protein and miRNA biomarker discovery in a rat model of post-traumatic epileptogenesis

• Published in: Epilepsy research 2019-01, Vol.149, p.92-101
• Main Authors: Kamnaksh, Alaa, Puhakka, Noora, Ali, Idrish, Smith, Gregory, Aniceto, Roxanne, McCullough, Jesse, Das Gupta, Shalini, Ndode-Ekane, Xavier Ekolle, Brady, Rhys, Casillas-Espinosa, Pablo, Hudson, Matt, Santana-Gomez, Cesar, Immonen, Riikka, Abreu, Pedro Andrade de, Jones, Nigel, Shultz, Sandy, Staba, Richard J., O’Brien, Terence J., Agoston, Denes, Pitkänen, Asla
• Format: Article
• Language: English
• Subjects: Animals; Biomarkers - metabolism; Blood Proteins - metabolism; Case report form; Common data elements; Computational Biology; Disease Models, Animal; Epilepsy, Post-Traumatic - metabolism; Hemoglobins - metabolism; Homeostasis - physiology; International Cooperation; MicroRNAs - genetics; MicroRNAs - metabolism; Nerve Tissue Proteins - metabolism; Post-traumatic epilepsy; Protein Array Analysis; Proteomics; Quality control; Rats; Rats, Sprague-Dawley; RNA, Messenger - metabolism; Standardization; Statistics, Nonparametric; Time Factors; Traumatic brain injury
• ISSN: 0920-1211; 1872-6844
• DOI: 10.1016/j.eplepsyres.2018.11.009

•Our analysis of harmonization parameters and plasma sample quality indicates.•Personnel training can significantly improve plasma quality for biomarker discovery.•High-hemolysis samples show more variable hemoglobin protein concentrations.•Hemoglobin content may interfere with protein biomarkers measured in plasma.•RBC miRNAs correlate with platelet contamination even in low-hemolysis samples. The Epilepsy Bioinformatics Study for Antiepileptogenic Therapy (EpiBioS4Rx) is an international, multicenter, multidisciplinary study aimed at preventing epileptogenesis (EpiBioS4Rx: https://epibios.loni.usc.edu/). One of the study’s major objectives is the discovery of diagnostic, prognostic, and predictive plasma protein and microRNA (miRNA) biomarkers that are sensitive, specific, and translatable to the human condition. Epilepsy due to structural brain abnormalities, secondary to neurological insults such as traumatic brain injury (TBI), currently represents ∼50% of all epilepsy cases. In the preclinical EpiBioS4Rx study, TBI was induced in adult male Sprague Dawley rats using a standardized protocol for lateral fluid-percussion injury. Whole blood was collected from the tail vein at baseline and 2, 9 and 30 days post-injury and processed for plasma separation. Biomaterial properties, sample preparation and integrity, and choice of analysis platform can significantly impact measured marker levels and, in turn, interpretation with respect to injury and/or other variables. We present here the results of procedural harmonization for the first 320 rats included in the EpiBioS4Rx study study, from three international research centers, and preliminary proteomic and miRNA analyses. We also discuss experimental considerations for establishing rigorous quality controls with the goal of harmonizing operating procedures across study sites, and delivering high-quality specimens for preclinical biomarker discovery in a rat model of post-traumatic epilepsy (PTE).