Longitudinal assessment and stability of long non-coding RNA gene expression profiles measured in human peripheral whole
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(2020) 13:531 Wylezinski et al. BMC Res Notes https://doi.org/10.1186/s13104-020-05360-3
Open Access
RESEARCH NOTE
Longitudinal assessment and stability of long non‑coding RNA gene expression profiles measured in human peripheral whole blood collected into PAXgene blood RNA tubes Lukasz S. Wylezinski1,2,3†, Guzel I. Shaginurova1† and Charles F. Spurlock III1,2,3*
Abstract Objective: Long non-coding RNAs (lncRNAs) are emerging as novel biomarkers for a variety of chronic conditions including autoimmune disease. PAXgene Blood RNA tubes are routinely used in clinical research and molecular diagnostic development to capture RNA profiles in peripheral whole blood. While the stability of mRNA expression profiles captured using PAXgene tubes has been documented previously, no previous work has determined the stability of lncRNA expression profiles observed in PAXgene tubes stored at − 80 °C. Here we sought to determine the effects on lncRNA expression profiles following − 80 °C storage of total RNA templates, cDNA synthesized using fresh or frozen total RNA template, and the impact of freeze–thaw cycles on both total RNA and cDNA obtained from PAXgene tubes. Results: We find that storage of whole blood in PAXgene tubes, total RNA and cDNA for up to 1 year at − 80 °C or up to ten total RNA or cDNA freeze–thaw cycles do not significantly alter lncRNA expression profiles compared to baseline. As monthly expression profiles were determined, some month to month lncRNA expression variability was observed. However, all monthly observations fell within the 95% confidence interval calculated at baseline. Keywords: Long non-coding RNA, Multiple sclerosis, Messenger RNA, PAXgene blood RNA tube, Quantitative real time PCR, Storage Introduction Long non-coding RNAs (lncRNAs) play pivotal roles in gene regulation, protein synthesis, sex chromosome compensation and telomere maintenance [1–5]. Work over the past decade has also implicated specific lncRNAs in a variety of pathological processes and human diseases including cancer, autoimmune disease and neurodegenerative disorders like Parkinson’s and Alzheimer’s [6–13]. Apart from mechanistic studies ascribing *Correspondence: [email protected] † Lukasz S. Wylezinski and Guzel I. Shaginurova contributed equally to this work. 1 IQuity, Inc, 111, 10th Avenue South, Suite 100, Nashville, TN 37203, USA Full list of author information is available at the end of the article
biological outcomes to over- or under-expression of specific lncRNAs, lncRNAs that exhibit expression differences are often proposed as candidate biomarkers that could be measured in novel RNA-based assays to aid in the diagnosis of disease or to monitor disease progression [14–17]. Our own cross-sectional studies in human disease have included extensive RNA sequencing and quantitative real time PCR (qRT-PCR) studies to measure a variety of RNA species including protein-coding and non-coding genes, with a particular focus on lncRNAs. We identified a series of mRNAs, annotated and novel lncRNA genes that are differen
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