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

Abstract

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 incorporating an interactive web-interface, Shiny mixOmics (http://mixomics-projects.di.uq.edu.au/Shiny), for univariate and multivariate statistical analysis. Relative quantitation was performed by referencing to a spiked-in glycoprotein, chicken ovalbumin. We applied this workflow to identify diagnostic biomarkers for esophageal adenocarcinoma (EAC), a life threatening malignancy with poor prognosis in the advanced setting. EAC develops from metaplastic condition Barrett's esophagus (BE). Currently diagnosis and monitoring of at-risk patients is through endoscopy and biopsy, which is expensive and requires hospital admission. Hence there is a clinical need for a noninvasive diagnostic biomarker of EAC. In total 89 patient samples from healthy controls, and patients with BE or EAC were screened in discovery and qualification stages. Of the 246 glycoforms measured in the qualification stage, 40 glycoforms (as measured by lectin affinity) qualified as candidate serum markers. The top candidate for distinguishing healthy from BE patients' group was Narcissus pseudonarcissus lectin (

Transglutaminase 3 protein modulates human esophageal cancer cell growth by targeting the NF-κB signaling pathway

“…Recently, several research groups have reported certain genes and signaling molecules that are potentially involved in EC initiation and progression (24,25). These molecular targets may provide significant clues for early diagnosis, prognosis and new targeted therapies (26)(27)(28). Previous studies have found that TGM3 expression is downregulation in head and neck cancer, laryngeal carcinoma and oral squamous cell carcinoma (29)(30)(31)(32), other reports found that TGM3 expression is decreased in EC tissues compared with normal tissues (29).…”

The omics revolution: beyond genomics. A meeting report

“…Michelle's studies have focussed on the potential of disease-related glycoproteins as potential markers of early stage disease. To assist in this goal a lectin magnetic bead array (LeMBA) coupled with a mass spectrometry biomarker pipeline was developed which revealed novel potential diagnostic biomarkers for EAC [3]. The data were further validated in independent cohorts [4] and a candidate biomarker panel for BE surveillance developed.…”

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