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Transcriptomic analysis of pancreatic cyst fluid in patients with pancreatic cysts reveals novel biomarkers of pancreatic cancer risk

ABSTRACT: Transcriptomic analysis of pancreatic cyst fluid in patients with pancreatic cysts reveals novel biomarkers of pancreatic cancer risk

PROVIDER: PRJNA1180512 | ENA |

REPOSITORIES: ENA

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Transcriptomic analysis of pancreatic cyst fluid in patients with pancreatic cysts reveals novel biomarkers of pancreatic cancer risk

Project description:Integration of multi-omic data for the purposes of biomarker discovery can provide novel and robust panels across multiple biological compartments. Appropriate analytical methods are key to ensuring accurate and meaningful outputs in the multi-omic setting. Here, we extensively profile the proteome and transcriptome of patient pancreatic cyst fluid (PCF) (n=32) and serum (n=68), before integrating matched omic and biofluid data, to identify biomarkers of pancreatic cancer risk. Differential expression analysis, feature reduction, multi-omic data integration, unsupervised hierarchical clustering, principal component analysis, spearman correlations and leave-one-out cross-validation were performed using RStudio and CombiROC software. An 11-feature multi-omic panel in PCF [PIGR, S100A8, REG1A, LGALS3, TCN1, LCN2, PRSS8, MUC6, SNORA66, miR-216a-5p, miR-216b-5p] generated an AUC=0.80. A 13-feature multi-omic panel in serum [SHROOM3, IGHV3-72, IGJ, IGHA1, PPBP, APOD, SFN, IGHG1, miR-197-5p, miR-6741-5p, miR-3180, miR-3180-3p, miR-6782-5p] produced an AUC=0.824. Integration of the strongest performing biomarkers generated a 10-feature cross-biofluid multi-omic panel [S100A8, LGALS3, SNORA66, miR-216b-5p, IGHV3-72, IGJ, IGHA1, PPBP, miR-3180, miR-3180-3p] with an AUC=0.970. Multi-omic profiling provides an abundance of potential biomarkers. Integration of data from different omic compartments, and across biofluids, produced a biomarker panel that performs with high accuracy, showing promise for the risk stratification of these patients.

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Metabolic profiling of cyst fluid from patients with Intraductal Pancreatic Mucinous Neoplasm

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Quantitative Proteomic Analysis of Pancreatic Cyst Fluid Proteins Associated with Malignancy in Intraductal Papillary Mucinous Neoplasms

Project description:Intraductal papillary mucinous neoplasm (IPMN) is a benign tumor that grows within the pancreatic ducts characterized by the production of thick mucinous fluid by surrounding tumor cells. IPMN is the most important precursor lesion for pancreatic cancer that is the fourth most common cause of cancer deaths. Differentiating between low-grade dysplasia (LGD), high-grade dysplasia (HGD), and invasive intraductal papillary mucinous neoplasms (IPMNs) remains a diagnostic challenge with current biomarkers, necessitating the development of novel biomarkers that can distinguish IPMN malignancy. We investigated differentially expressed proteins among pancreatic cyst fluids consisted of LGD, HGD, and invasive IPMN patients by using our novel proteomic strategy, and finally we discovered pancreatic cyst fluid protein marker candidates that can predict the malignant potential of IPMNs.

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Metabolic profiling of cyst fluid from patients with Intraductal Pancreatic Mucinous Neoplasm (part II)

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Proteomic profiling of pancreatic cyst fluid in patients with pancreatic cystic lesions identifies novel biomarkers of pancreatic cancer risk

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Transcriptomic analysis of serum in patients with pancreatic cysts reveals novel biomarkers of pancreatic cancer risk

Project description:Transcriptomic analysis of serum in patients with pancreatic cysts reveals novel biomarkers of pancreatic cancer risk

| PRJNA1180499 | ENA