Dataset Information

Label-free shotgun proteomics analysis in zebrafish liver following dietary exposure to the pesticide dieldrin

ABSTRACT: The objective of this study was to determine the effect of dieldrin on the hepatic proteome in the zebrafish liver following dietary exposure. Female zebrafish were fed a control dose or one of three doses of DLD-contaminated food pellets over 21 days.

INSTRUMENT(S): 6520 Quadrupole Time-of-Flight LC/MS

ORGANISM(S): Danio Rerio (zebrafish) (brachydanio Rerio)

TISSUE(S): Liver

SUBMITTER: Denina Simmons

LAB HEAD: Denina Bobbie Dawn Simmons

PROVIDER: PXD014480 | Pride | 2019-08-29

REPOSITORIES: Pride

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Publications

Hepatic proteome network data in zebrafish (<i>Danio rerio</i>) liver following dieldrin exposure.

Simmons Denina B D DBD Cowie Andrew M AM Koh Jin J Sherry James P JP Martyniuk Christopher J CJ

Data in brief 20190805

Dieldrin is an environmental contaminant that adversely affects aquatic organisms. The data presented in this study are proteomic data collected in liver of zebrafish that were exposed to the pesticide in a dietary exposure. For label free proteomics, data were collected with a quadrupole Time-of-Flight mass spectrometer and for iTRAQ proteomics, data were acquired using a hybrid quadrupole Orbitrap (Q Exactive) MS system. Using formic acid digestion and label free proteomics, 2,061 proteins wer ...[more]

PMID: 31453304

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Project description:Colorectal cancer is the third most common cancer worldwide, with 1.4 million people diagnosed in 2012 according to GLOBOCAN 2012. 95% of the colon cancer cases are that of adenocarcinomas. Removal of high-risk adenomas and tumors at early stage of colorectal cancer (CRC) can prevent its onset/progression into higher grades of cancer. The prognosis of colorectal cancer and the stage of diagnosis are closely correlated. 5-year survival rate is observed among 90% patients when diagnosed early and in less than 10% when the metastases develop. This makes the implementation of screening methods aimed at early detection paramount for reduced incidence and mortality rate. Adenocarcinomas are the cancers originating from the gland forming cells of the colon and rectal lining and are known to be the most common type of colorectal cancer. The current diagnosis options for colorectal cancers are limited to biopsy, stool tests and other laboratory tests, barium enema based imaging and other imaging techniques, colonoscopy and other endoscopic procedures which are time consuming. In this study, we used proteomics approach with an aim to identify protein biomarkers which can aid in early detection of colon adenocarcinomas to be precise. Proteins from tumor tissue of colon adenocarcinoma subjects (n=11) and their matched controls were subjected to 4-plex iTRAQ labelling followed by off-gel fractionation prior to LC-MS/MS run. The mass spectrometry data was analysed independently using two different analysis software - Spectrum Mill (SM) and Trans Proteome Pipeline (TPP). The proteins identified using either SM and/or TPP were subjected to pathway analysis using the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.8 and the proteins common between the two analyses were compared with the data from CPTAC portal and Human Protein Atlas. The expression level of the shortlisted panel of proteins was studied in brain cancers as a non-colon adenocarcinoma control group and validated using MRM approach. A list of 285 unique proteins was identified to be significantly dysregulated in colon adenocarcinoma as compared to its matched controls. These proteins were found to be involved in glycolysis, pentose phosphate pathway, biosynthesis of amino acids, protein processing, spliceosome, proteosome, focal adhesion and proteoglycans in cancer. 94 of the 285 proteins were identified by both- SM and TPP. 34 of these 94 proteins were found to be dysregulated with same trend as that in data reported on CPTAC portal and 9 of these 34 proteins were validated using MRM approach. The proteins identified from this study could be validated further to investigate the role of these proteins as potential biomarkers for early detection of colon adenocarcinoma.

Dataset Information

Label-free shotgun proteomics analysis in zebrafish liver following dietary exposure to the pesticide dieldrin

Publications

Hepatic proteome network data in zebrafish (<i>Danio rerio</i>) liver following dieldrin exposure.

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