Next Article in Journal
Screening of Anaesthetics in Adult Zebrafish (Danio rerio) for the Induction of Euthanasia by Overdose
Next Article in Special Issue
Procollagen C-Endopeptidase Enhancer 2 Secreted by Tonsil-Derived Mesenchymal Stem Cells Increases the Oxidative Burst of Promyelocytic HL-60 Cells
Previous Article in Journal
The Identification of RNA Modification Gene PUS7 as a Potential Biomarker of Ovarian Cancer
Previous Article in Special Issue
ARGEOS: A New Bioinformatic Tool for Detailed Systematics Search in GEO and ArrayExpress
Article

Oxford Nanopore MinION Direct RNA-Seq for Systems Biology

1
Institute of Biomedical Chemistry, 119121 Moscow, Russia
2
Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
*
Author to whom correspondence should be addressed.
Academic Editors: Ioannis Michalopoulos and Apostolos Malatras
Biology 2021, 10(11), 1131; https://doi.org/10.3390/biology10111131
Received: 8 October 2021 / Revised: 28 October 2021 / Accepted: 2 November 2021 / Published: 4 November 2021
(This article belongs to the Special Issue Differential Gene Expression and Coexpression)
A new technology has been recently developed by Oxford Nanopore Technologies, enabling researchers to investigate the structure and relative abundance of specific molecules, ribonucleic acids. The ribonucleic acids carry information from the genes to proteins, which are responsible for virtually every process in the human organism, including disease progression and response to therapies. Special computational methods allow identification of various activated biological processes by analyzing the changes in concentrations of ribonucleic acids. This is of particular interest for precision medicine which aims at single-patient analysis. Here we evaluated whether ribonucleic acid abundances measured by new technology are suited for robust predictions of activated biological processes in single samples. We performed simulations varying the number of experimental replicates and analysed activated biological processes’ predictions using two algorithms. In brief, we found that at least two replicates are required to obtain reproducible results. We hope that our findings may be of interest to researchers planning their nanopore experiments and may stimulate further development of clinical applications of this technology.
Long-read direct RNA sequencing developed by Oxford Nanopore Technologies (ONT) is quickly gaining popularity for transcriptome studies, while fast turnaround time and low cost make it an attractive instrument for clinical applications. There is a growing interest to utilize transcriptome data to unravel activated biological processes responsible for disease progression and response to therapies. This trend is of particular interest for precision medicine which aims at single-patient analysis. Here we evaluated whether gene abundances measured by MinION direct RNA sequencing are suited to produce robust estimates of pathway activation for single sample scoring methods. We performed multiple RNA-seq analyses for a single sample that originated from the HepG2 cell line, namely five ONT replicates, and three replicates using Illumina NovaSeq. Two pathway scoring methods were employed—ssGSEA and singscore. We estimated the ONT performance in terms of detected protein-coding genes and average pairwise correlation between pathway activation scores using an exhaustive computational scheme for all combinations of replicates. In brief, we found that at least two ONT replicates are required to obtain reproducible pathway scores for both algorithms. We hope that our findings may be of interest to researchers planning their ONT direct RNA-seq experiments. View Full-Text
Keywords: transcriptomics; nanopore technology; RNA-seq; MinION; pathway activation; systems biology; HepG2 transcriptomics; nanopore technology; RNA-seq; MinION; pathway activation; systems biology; HepG2
Show Figures

Graphical abstract

MDPI and ACS Style

Pyatnitskiy, M.A.; Arzumanian, V.A.; Radko, S.P.; Ptitsyn, K.G.; Vakhrushev, I.V.; Poverennaya, E.V.; Ponomarenko, E.A. Oxford Nanopore MinION Direct RNA-Seq for Systems Biology. Biology 2021, 10, 1131. https://doi.org/10.3390/biology10111131

AMA Style

Pyatnitskiy MA, Arzumanian VA, Radko SP, Ptitsyn KG, Vakhrushev IV, Poverennaya EV, Ponomarenko EA. Oxford Nanopore MinION Direct RNA-Seq for Systems Biology. Biology. 2021; 10(11):1131. https://doi.org/10.3390/biology10111131

Chicago/Turabian Style

Pyatnitskiy, Mikhail A., Viktoriia A. Arzumanian, Sergey P. Radko, Konstantin G. Ptitsyn, Igor V. Vakhrushev, Ekaterina V. Poverennaya, and Elena A. Ponomarenko. 2021. "Oxford Nanopore MinION Direct RNA-Seq for Systems Biology" Biology 10, no. 11: 1131. https://doi.org/10.3390/biology10111131

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop