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Series GSE221185 Query DataSets for GSE221185
Status Public on Jun 08, 2023
Title Small RNA sequencing analysis of peptide-affinity isolated plasma extracellular vesicles distinguishes pancreatic cancer patients from non-affected individuals
Organism Homo sapiens
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Pancreatic ductal adenocarcinoma (PDAC) has a high fatality rate, mainly due to its asymptomatic nature until late-stage disease and therefore delayed diagnosis that leads to a lack of timely treatment intervention. Consequently, there is a significant need for better methods to screen populations that are at high risk of developing PDAC. Such advances would result in earlier diagnosis, more treatment options, and ultimately better outcomes for patients. Several recent studies have applied the concept of liquid biopsy, which is the sampling of a biofluid (such as blood plasma) for the presence of disease biomarkers, to develop screening approaches for PDAC; several of these studies have focused on analysis of extracellular vesicles (EVs) and their cargoes. While these studies have identified many potential biomarkers for PDAC that are present within EVs, their application to clinical practice is hindered by the lack of a robust, reproducible method for EV isolation and analysis that is amenable to a clinical setting. Our previous research has shown that the Vn96 synthetic peptide is indeed a robust and reproducible method for EV isolation that has the potential to be used in a clinical setting. We have therefore chosen to investigate the utility of the Vn96 synthetic peptide for this isolation of EVs from human plasma and the subsequent detection of small RNA biomarkers of PDAC by Next-generation sequencing (NGS) analysis. We find that analysis of small RNA from Vn96-isolated EVs permits the robust discrimination of PDAC patients from non-affected individuals. Moreover, analyses of all small RNA species, miRNAs, and lncRNAs are most effective at segregating PDAC patients from non-affected individuals. We further identified 34 chromosomal regions that encode small RNAs whose differential expression in Vn96-isolated EVs strongly distinguishes PDAC patients from non-affected individuals. Several of the identified small RNA biomarkers have been previously associated with and/or characterized in PDAC, indicating the validity of our findings, whereas other identified small RNA biomarkers may have novel roles in PDAC or cancer in general. Overall, our results provide a basis for a clinically-amendable detection and/or screening strategy for PDAC using a liquid biopsy approach that relies on Vn96-mediated isolation of EVs from plasma. 
Overall design Small RNA sequencing was performed on extracellular vesicle RNA derived from plasma of PDAC patients (n = 16) and non-affected individuals (n = 13).
Contributor(s) Roy JW, Wajnberg G, Ouellette A, Boucher JE, Lacroix J, Chacko S, Ghosh A, Ouellette RJ, Lewis SM
Citation(s) 37286718
Submission date Dec 16, 2022
Last update date Sep 07, 2023
Contact name Eric P Allain
Phone 5068697347
Organization name Vitalité Health Network
Department Medical Genetics
Lab Bioinformatics
Street address 330 University ave
City Moncton
State/province New Brunswick
ZIP/Postal code E1C 2Z3
Country Canada
Platforms (1)
GPL17303 Ion Torrent Proton (Homo sapiens)
Samples (29)
GSM6850216 ACRI169
GSM6850217 ACRI176
GSM6850218 ACRI247
BioProject PRJNA913165

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Supplementary file Size Download File type/resource
GSE221185_panc_counts_GEO.txt.gz 6.1 Mb (ftp)(http) TXT
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