Proteomics

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Biomarkers of Cholangiocarcinoma and Pancreatic adenocarcinoma

ABSTRACT: Cholangiocarcinoma (CCA) and pancreatic adenocarcinoma (PDAC) may lead to the development of extrahepatic obstructive cholestasis. However, biliary stenoses can also be caused by benign conditions, and the identification of their etiology still remains a clinical challenge. We performed metabolomic and proteomic analyses of bile from patients with benign (n=36) and malignant conditions, CCA (n=36) or PDAC (n=57), undergoing endoscopic retrograde cholangiopancreatography with the aim of characterizing bile composition in biliopancreatic disease and identifying biomarkers for the differential diagnosis of biliary strictures. Comprehensive analyses of lipids, bile acids and small molecules were carried out using mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (1H-NMR) in all patients. MS analysis of bile proteome was performed in five patients per group. We implemented artificial intelligence tools for the selection of biomarkers and algorithms with predictive capacity. Our machine-learning pipeline included the generation of synthetic data with properties of real data, the selection of potential biomarkers (metabolites or proteins) and their analysis with neural networks (NN). Selected biomarkers were then validated with real data. We identified panels of lipids (n=10) and proteins (n=5) that when analyzed with NN algorithms discriminated between patients with and without cancer with an unprecedented accuracy.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Bile

DISEASE(S): Pancreas Adenocarcinoma,Cholangiocarcinoma

SUBMITTER: Antonio Ramos Fernández  

LAB HEAD: Fernando J. Corrales

PROVIDER: PXD019924 | Pride | 2021-09-09

REPOSITORIES: Pride

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Dataset's files

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Action DRS
20190623_03_MAvila_18123-C.wiff Wiff
20190623_03_MAvila_18123-C.wiff.scan Wiff
20190623_05_MAvila_188-CCA.wiff Wiff
20190623_05_MAvila_188-CCA.wiff.scan Wiff
20190623_07_MAvila_18135-C.wiff Wiff
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Publications

Pilot Multi-Omic Analysis of Human Bile from Benign and Malignant Biliary Strictures: A Machine-Learning Approach.

Urman Jesús M JM   Herranz José M JM   Uriarte Iker I   Rullán María M   Oyón Daniel D   González Belén B   Fernandez-Urién Ignacio I   Carrascosa Juan J   Bolado Federico F   Zabalza Lucía L   Arechederra María M   Alvarez-Sola Gloria G   Colyn Leticia L   Latasa María U MU   Puchades-Carrasco Leonor L   Pineda-Lucena Antonio A   Iraburu María J MJ   Iruarrizaga-Lejarreta Marta M   Alonso Cristina C   Sangro Bruno B   Purroy Ana A   Gil Isabel I   Carmona Lorena L   Cubero Francisco Javier FJ   Martínez-Chantar María L ML   Banales Jesús M JM   Romero Marta R MR   Macias Rocio I R RIR   Monte Maria J MJ   Marín Jose J G JJG   Vila Juan J JJ   Corrales Fernando J FJ   Berasain Carmen C   Fernández-Barrena Maite G MG   Avila Matías A MA  

Cancers 20200621 6

Cholangiocarcinoma (CCA) and pancreatic adenocarcinoma (PDAC) may lead to the development of extrahepatic obstructive cholestasis. However, biliary stenoses can also be caused by benign conditions, and the identification of their etiology still remains a clinical challenge. We performed metabolomic and proteomic analyses of bile from patients with benign (<i>n</i> = 36) and malignant conditions, CCA (<i>n</i> = 36) or PDAC (<i>n</i> = 57), undergoing endoscopic retrograde cholangiopancreatograph  ...[more]

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