Transcriptomic Profiling of Extracellular RNAs Present in Cerebrospinal Fluid Identifies Differentially Expressed Transcripts in Parkinson's Disease

Journal of Parkinson's Disease
Arash Hossein-NezhadMohammad Ali Faghihi

Abstract

Parkinson's disease (PD) is a debilitating neurological disorder for which prognostic and diagnostic biomarkers are lacking. Cerebrospinal fluid (CSF) is an accessible body fluid that comes into direct contact with the central nervous system (CNS) and acts as a nuclease-free repository where RNA transcripts shed by brain tissues can reside for extended periods of time. We studied the RNA species present in the CSF of PD patients to identify novel diagnostic biomarkers. Small volumes of CSF from 27 PD patients and 30 healthy age- and sex-matched controls were used for RNA extraction followed by next-generation sequencing (RNA-seq) using the Illumina platform. CSF contains a number of fragmented RNA species that were individually sequenced and analyzed. Comparing PD to control subjects, we observed a pool of dysregulated sequencing tags that were further analyzed and validated by quantitative real-time PCR (qRT-PCR). A total of 201 differentially expressed sequencing tags (DETs), including 92 up-regulated and 109 down-regulated DETs were identified. We validated the following DETs by real time PCR in the patient samples: Dnmt1, Ezh2, CCR3, SSTR5,PTPRC, UBC, NDUFV2, BMP7, SCN9, SCN9 antisense (AC010127.3), and long noncoding RNAs ...Continue Reading

References

Jun 1, 1988·Journal of Neurology, Neurosurgery, and Psychiatry·W R Gibb, A J Lees
Mar 7, 2003·Journal of Neuroimmunology·Geraldine FlynnDavid Male
May 23, 2006·Lancet Neurology·Lonneke M L de Lau, Monique M B Breteler
Sep 1, 2007·Science·Jongpil KimAsa Abeliovich
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Oct 13, 2009·Mini Reviews in Medicinal Chemistry·M RealeM A Kamal
Feb 17, 2010·Brain : a Journal of Neurology·Zhen HongJing Zhang
Jul 10, 2010·Proceedings of the National Academy of Sciences of the United States of America·Sharon HaramatiEran Hornstein
Nov 10, 2010·Archives of Neurology·Ignacio F MataCyrus P Zabetian
Feb 8, 2011·The Journal of Biological Chemistry·Paula DesplatsEliezer Masliah
Mar 15, 2011·Annals of Neurology·Min ShiJing Zhang
May 12, 2011·FEBS Letters·John S Mattick
Sep 29, 2011·Neurobiology of Disease·Teresa Botta-OrfilaMario Ezquerra
Mar 1, 2012·Frontiers in Neurology·Véronique Dorval, Sébastien S Hébert
Apr 5, 2012·European Journal of Pain : EJP·L GreenbaumR Djaldetti
Jun 6, 2012·Annual Review of Biochemistry·John L Rinn, Howard Y Chang
Sep 11, 2012·Bioinformatics·Enrico GlaabAlfonso Valencia
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Dec 4, 2012·Nucleic Acids Research·Andrea FranceschiniLars J Jensen
Feb 20, 2013·Nature Reviews. Neurology·Lucilla ParnettiPaolo Calabresi
Mar 26, 2013·RNA·Kasandra Lovette BurgosKendall Van Keuren-Jensen
Aug 14, 2013·Journal of Parkinson's Disease·Brenna A CholertonJames B Leverenz
Dec 17, 2014·Metabolism: Clinical and Experimental·Diane B Miller, James P O'Callaghan
Jan 18, 2015·Neurology·Manja MarzChristine Klein

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Citations

Jan 13, 2017·Epigenetics : Official Journal of the DNA Methylation Society·Suzanne AcklooSusanne Müller
Nov 22, 2017·International Journal of Molecular Sciences·Maria Michela PallottaTeresa Capriglione
Jan 23, 2018·Omics : a Journal of Integrative Biology·Sara RedenšekTanja Kunej
Feb 28, 2019·Molecular Biology Reports·Annamaria VallelungaMaria Teresa Pellecchia
May 13, 2018·Non-coding RNA·Gabriel A CipollaDaniela F Gradia
Dec 6, 2016·Frontiers in Molecular Neuroscience·Ariadna RecasensCarolyn M Sue
Sep 25, 2018·Journal of Parkinson's Disease·Virginie BotteroJudith A Potashkin
Jan 6, 2019·Molecular Neurobiology·Silvia ZucchelliStefano Gustincich
May 22, 2020·Frontiers in Cell and Developmental Biology·Beatrice SalvatoriMariangela Morlando
Oct 27, 2017·The European Journal of Neuroscience·Genevie BorrageiroSoraya Bardien
Dec 16, 2019·Neurochemistry International·Mario J BertogliatRaghu Vemuganti
Apr 18, 2020·Neurobiology of Disease·Simon M BenoitMatthew O Hebb
Apr 30, 2021·Ageing Research Reviews·Harald HampelUNKNOWN Alzheimer Precision Medicine Initiative (APMI)
May 14, 2021·Frontiers in Genetics·Adrienne R HendersonTravis Dunckley
Jul 29, 2021·Journal of Cellular and Molecular Medicine·Xiaoyu Dong, Shuyan Cong

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Methods Mentioned

BETA
RNA-seq
PCR

Software Mentioned

SPSS
DAVID
EdgeR
Database for Annotation Visualization and Integrated Discovery...
Trim Galore
Spliced Transcripts Alignment to Reference ( STAR )
EnrichNet
Bowtie
STAR
Bioconductor

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