Journal of Pathology Informatics

RESEARCH ARTICLE
Year
: 2019  |  Volume : 10  |  Issue : 1  |  Page : 40-

A digital pathology-based shotgun-proteomics approach to biomarker discovery in colorectal cancer


Stefan Zahnd1, Sophie Braga-Lagache2, Natasha Buchs2, Alessandro Lugli1, Heather Dawson1, Manfred Heller2, Inti Zlobec1 
1 Institute of Pathology, University of Bern, Bern, Switzerland
2 Department for BioMedical Research, Proteomics and Mass Spectrometry Core Facility, University of Bern, Bern, Switzerland

Correspondence Address:
Prof. Inti Zlobec
Institute of Pathology, University of Bern, Murtenstrasse 31, 3008 Bern
Switzerland

Background: Biomarkers in colorectal cancer are scarce, especially for patients with Stage 2 disease. The aim of our study was to identify potential prognostic biomarkers from colorectal cancers using a novel combination of approaches, whereby digital pathology is coupled to shotgun proteomics followed by validation of candidates by immunohistochemistry (IHC) using digital image analysis (DIA). Methods and Results: Tissue cores were punched from formalin-fixed paraffin-embedded colorectal cancers from patients with Stage 2 and 3 disease (n = 26, each). Protein extraction and liquid chromatography-mass spectrometry (MS) followed by analysis using three different methods were performed. Fold changes were evaluated. The candidate biomarker was validated by IHC on a series of 413 colorectal cancers from surgically treated patients using a next-generation tissue microarray. DIA was performed by using a pan-cytokeratin serial alignment and quantifying staining within the tumor and normal tissue epithelium. Analysis was done in QuPath and Brightness_Max scores were used for statistical analysis and clinicopathological associations. MS identified 1947 proteins with at least two unique peptides. To reinforce the validity of the biomarker candidates, only proteins showing a significant (P < 0.05) fold-change using all three analysis methods were considered. Eight were identified, and of these, cathepsin B was selected for further validation. DIA revealed strong associations between higher cathepsin B expression and less aggressive tumor features, including tumor node metastasis stage and lymphatic vessel and venous vessel invasion (P < 0.001, all). Cathepsin B was associated with more favorable survival in univariate analysis only. Conclusions: Our results present a novel approach to biomarker discovery that includes MS and digital pathology. Cathepsin B expression analyzed by DIA within the tumor epithelial compartment was identified as a strong feature of less aggressive tumor behavior and favorable outcome, a finding that should be further investigated on a more functional level.


How to cite this article:
Zahnd S, Braga-Lagache S, Buchs N, Lugli A, Dawson H, Heller M, Zlobec I. A digital pathology-based shotgun-proteomics approach to biomarker discovery in colorectal cancer.J Pathol Inform 2019;10:40-40


How to cite this URL:
Zahnd S, Braga-Lagache S, Buchs N, Lugli A, Dawson H, Heller M, Zlobec I. A digital pathology-based shotgun-proteomics approach to biomarker discovery in colorectal cancer. J Pathol Inform [serial online] 2019 [cited 2020 Jan 21 ];10:40-40
Available from: http://www.jpathinformatics.org/article.asp?issn=2153-3539;year=2019;volume=10;issue=1;spage=40;epage=40;aulast=Zahnd;type=0