Dataset Information

Serum glycoprotein biomarker discovery and qualification pipeline reveals novel diagnostic biomarkers for esophageal adenocarcinoma

ABSTRACT: The aim of this project is to identify circulatory diagnostic glycoprotein biomarkers for Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC). Serum samples from healthy, BE and EAC patients were screened using LeMBA-LC-MS/MS-GlycoSelector pipeline as described in the manuscript.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Serum

DISEASE(S): Barrett's Esophagus,Barrett's Adenocarcinoma

SUBMITTER: Alok Shah

LAB HEAD: Dr. Michelle M. Hill

PROVIDER: PXD002442 | Pride | 2015-09-25

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20120727_AShah_AAL-2.d.tar.bz2	Other
	20120727_AShah_BPL-2.d.tar.bz2	Other
	20120727_AShah_ConA-2.d.tar.bz2	Other
	20120727_AShah_Ctrl-2.d.tar.bz2	Other
	20120727_AShah_DSA-2.d.tar.bz2	Other

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Publications

Serum Glycoprotein Biomarker Discovery and Qualification Pipeline Reveals Novel Diagnostic Biomarker Candidates for Esophageal Adenocarcinoma.

Shah Alok K AK Cao Kim-Anh Lê KA Choi Eunju E Chen David D Gautier Benoît B Nancarrow Derek D Whiteman David C DC Saunders Nicholas A NA Barbour Andrew P AP Joshi Virendra V Hill Michelle M MM

Molecular & cellular proteomics : MCP 20150924 11

We report an integrated pipeline for efficient serum glycoprotein biomarker candidate discovery and qualification that may be used to facilitate cancer diagnosis and management. The discovery phase used semi-automated lectin magnetic bead array (LeMBA)-coupled tandem mass spectrometry with a dedicated data-housing and analysis pipeline; GlycoSelector (http://glycoselector.di.uq.edu.au). The qualification phase used lectin magnetic bead array-multiple reaction monitoring-mass spectrometry incorpo ...[more]

PMID: 26404905

Similar Datasets

Project description:Esophageal adenocarcinoma (EAC) has become a major concern in Western countries due to rapid rises in incidence coupled with very poor survival rates. One of the key risk factors for the development of this cancer is the presence of Barrett’s esophagus (BE), which is believed to form in response to repeated gastro-esophageal reflux. In this study we performed comparative, genome-wide expression profiling (using Illumina whole-genome Beadarray) on total RNA extracted from esophageal biopsy tissues from individuals with EAC, BE (in the absence of EAC) and those with normal squamous epithelium. We combined these data with publically accessible raw data from three similar studies to investigate key gene and ontology differences between these three tissue states. The results support the deduction that BE is a tissue with enhanced glycoprotein synthesis machinery (DPP4, ATP2A3, AGR2) designed to provide strong mucosal defenses aimed at resisting gastro-esophageal reflux. EAC exhibits the enhanced extracellular matrix remodeling (collagens, IGFBP7, PLAU) effects expected in an aggressive form of cancer, as well as evidence of reduced expression of genes associated with mucosal (MUC6, CA2, TFF1) and xenobiotic (AKR1C2, AKR1B10) defenses. When our results are compared to previous whole-genome expression profiling studies keratin, mucin, annexin and trefoil factor gene families are the most frequently represented gene families. Eleven genes identified here are also represented in at least 3 other profiling studies. We used these genes to discriminate squamous, BE and EAC within the two largest cohorts using a support vector machine leave one out cross validation analysis. While this method was satisfactory for discriminating squamous and BE, it demonstrates the need for more detailed investigations into profiling changes within BE leading to the progression towards EAC. A comparison of three esophageal biopsy groups from separate individuals: normal squamous (n=9), Barrett's esophagus without dysplasia (n=22) & adenocarcinoma (n=23). Adenocarcinoma samples overlap with members of DNA copy number analysis GEO series GSE10506 such that, in each case genomic DNA and total RNA were extracted from the same biopsy. The matching copy number data GEO samples IDs are noted in characteristics: Matching CN Sample ID