» Articles » PMID: 33914880

Application of a Bioinformatic Pipeline to RNA-seq Data Identifies Novel Virus-like Sequence in Human Blood

Overview
Journal G3 (Bethesda)
Date 2021 Apr 29
PMID 33914880
Citations 4
Authors
Affiliations
Soon will be listed here.
Abstract

Numerous reports have suggested that infectious agents could play a role in neurodegenerative diseases, but specific etiological agents have not been convincingly demonstrated. To search for candidate agents in an unbiased fashion, we have developed a bioinformatic pipeline that identifies microbial sequences in mammalian RNA-seq data, including sequences with no significant nucleotide similarity hits in GenBank. Effectiveness of the pipeline was tested using publicly available RNA-seq data and in a reconstruction experiment using synthetic data. We then applied this pipeline to a novel RNA-seq dataset generated from a cohort of 120 samples from amyotrophic lateral sclerosis patients and controls, and identified sequences corresponding to known bacteria and viruses, as well as novel virus-like sequences. The presence of these novel virus-like sequences, which were identified in subsets of both patients and controls, were confirmed by quantitative RT-PCR. We believe this pipeline will be a useful tool for the identification of potential etiological agents in the many RNA-seq datasets currently being generated.

Citing Articles

Aspergillus flavipes L-methionine γ-lyase-β-cyclodextrin conjugates with improved stability, catalytic efficiency and anticancer activity.

El-Sayed A, Shindia A, Emam E, Labib M, El-Deen E, Seadawy M Sci Rep. 2024; 14(1):27715.

PMID: 39532921 PMC: 11557573. DOI: 10.1038/s41598-024-78368-5.


Profiling of Microbial Landscape in Lung of Chronic Obstructive Pulmonary Disease Patients Using RNA Sequencing.

Shin D, Kim J, Lee J, Kim J, Oh Y Int J Chron Obstruct Pulmon Dis. 2023; 18:2531-2542.

PMID: 38022823 PMC: 10644840. DOI: 10.2147/COPD.S426260.


RNA sequencing of peripheral blood in amyotrophic lateral sclerosis reveals distinct molecular subtypes: Considerations for biomarker discovery.

Grima N, Liu S, Southwood D, Henden L, Smith A, Lee A Neuropathol Appl Neurobiol. 2023; 49(6):e12943.

PMID: 37818590 PMC: 10946588. DOI: 10.1111/nan.12943.


Is There a Brain Microbiome?.

Link C Neurosci Insights. 2021; 16:26331055211018709.

PMID: 34104888 PMC: 8165828. DOI: 10.1177/26331055211018709.

References
1.
Kohne D, GIBBS C, White L, Tracy S, Meinke W, Smith R . Virus detection by nucleic acid hybridization: examination of normal and ALS tissues for the presence of poliovirus. J Gen Virol. 1981; 56(Pt 2):223-33. DOI: 10.1099/0022-1317-56-2-223. View

2.
Trageser K, Smith C, Herman F, Ono K, Pasinetti G . Mechanisms of Immune Activation by Expansions in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Front Neurosci. 2020; 13:1298. PMC: 6914852. DOI: 10.3389/fnins.2019.01298. View

3.
Parker J, Chen J . Application of next generation sequencing for the detection of human viral pathogens in clinical specimens. J Clin Virol. 2016; 86:20-26. PMC: 5182090. DOI: 10.1016/j.jcv.2016.11.010. View

4.
Westermann A, Barquist L, Vogel J . Resolving host-pathogen interactions by dual RNA-seq. PLoS Pathog. 2017; 13(2):e1006033. PMC: 5313147. DOI: 10.1371/journal.ppat.1006033. View

5.
Reddy K, Zamiri B, Stanley S, Macgregor Jr R, Pearson C . The disease-associated r(GGGGCC)n repeat from the C9orf72 gene forms tract length-dependent uni- and multimolecular RNA G-quadruplex structures. J Biol Chem. 2013; 288(14):9860-9866. PMC: 3617286. DOI: 10.1074/jbc.C113.452532. View