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| 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
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| 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.
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| 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).
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| Contributor(s) |
Roy JW, Wajnberg G, Ouellette A, Boucher JE, Lacroix J, Chacko S, Ghosh A, Ouellette RJ, Lewis SM |
| Citation(s) |
37286718 |
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| Submission date |
Dec 16, 2022 |
| Last update date |
Sep 07, 2023 |
| Contact name |
Eric P Allain |
| E-mail(s) |
eric.allain@vitalitenb.ca
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| Phone |
5068697347
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| Organization name |
Vitalité Health Network
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| Department |
Medical Genetics
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| Lab |
Bioinformatics
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| Street address |
330 University ave
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| City |
Moncton |
| State/province |
New Brunswick |
| ZIP/Postal code |
E1C 2Z3 |
| Country |
Canada |
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| Platforms (1) |
| GPL17303 |
Ion Torrent Proton (Homo sapiens) |
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| Samples (29)
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| Relations |
| BioProject |
PRJNA913165 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE221185_panc_counts_GEO.txt.gz |
6.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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