Comparison of Proteomic Technologies for Blood-Based Detection of Colorectal Cancer.

Megha Bhardwaj,Tobias Terzer,Petra Schrotz-King,Hermann Brenner

doi:10.3390/ijms22031189

Abstract

Blood-based protein biomarkers are increasingly being explored as supplementary or efficient alternatives for population-based screening of colorectal cancer (CRC). The objective of the current study was to compare the diagnostic potential of proteins measured with different proteomic technologies. The concentrations of protein biomarkers were measured using proximity extension assays (PEAs), liquid chromatography/multiple reaction monitoring–mass spectrometry (LC/MRM-MS) and quantibody microarrays (QMAs) in plasma samples of 56 CRC patients and 99 participants free of neoplasms. In another approach, proteins were measured in serum samples of 30 CRC cases and 30 participants free of neoplasm using immunome full-length functional protein arrays (IpAs). From all the measurements, 9, 6, 35 and 14 protein biomarkers overlapped for comparative evaluation of (a) PEA and LC/MRM-MS, (b) PEA and QMA, (c) PEA and IpA, and (d) LC/MRM-MS and IpA measurements, respectively. Correlation analysis was performed, along with calculation of the area under the curve (AUC) for assessing the diagnostic potential of each biomarker. DeLong’s test was performed to assess the differences in AUC. Evaluation of the nine biomarkers measured with PEA and LC/MRM-MS displayed correlation coefficients >+0.6, similar AUCs and DeLong’s p-values indicating no differences in AUCs for biomarkers like insulin-like growth factor binding protein 2 (IGFBP2), matrix metalloproteinase 9 (MMP9) and serum paraoxonase lactonase 3 (PON3). Comparing six proteins measured with PEA and QMA showed good correlation and similar diagnostic performance for only one protein, growth differentiation factor 15 (GDF15). The comparison of 35 proteins measured with IpA and PEA and 14 proteins analyzed with IpA and LC/MRM-MS revealed poor concordance and comparatively better AUCs when measured with PEA and LC/MRM-MS. The comparison of different proteomic technologies suggests the superior performance of novel technologies like PEA and LC/MRM-MS over the assessed array-based technologies in blood-protein-based early detection of CRC.

Highlights

Licensee MDPI, Basel, Switzerland.Colorectal cancer (CRC) is the third most common cancer globally, accounting for approximately 1.85 million incident cases and 880,000 deaths per year [1]
The comparisons were established for protein biomarkers that overlapped between measurements from different technologies
The study population for immunome protein array (IpA) assays consisted of 30 participants in screening colonoscopy with colorectal cancer (CRC) and 30 controls free of neoplasms, with a median age of 64.5 years and males representing 60% of the study populations in both the groups

Summary

Introduction

Licensee MDPI, Basel, Switzerland.Colorectal cancer (CRC) is the third most common cancer globally, accounting for approximately 1.85 million incident cases and 880,000 deaths per year [1]. Utilizing novel high-throughput approaches that enable simultaneous screening of hundred-plex targets, research studies have explored the blood proteome and identified signatures for early detection of CRC [7,8,9,10,11]. Previous studies from our group utilizing proximity extension assays (PEA) and liquid chromatography/multiple reaction monitoring–mass spectrometry (LC/MRM-MS) have identified several individual markers and multimarker protein signatures for the detection of CRC [13,14,15,16,17,18]. The objective of the current study was to evaluate and compare the diagnostic potential of overlapping protein biomarkers measured with PEA, LC/MRM-MS, quantibody microarrays (QMAs) and immunome full-length functional protein arrays (IpAs)

Objectives

Methods

Results

Conclusion