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

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.

Methylation Status of Corticotropin-Releasing Factor (CRF) Receptor Genes in Colorectal Cancer

“…In this context, guaiac-based fecal occult blood test (gFOBT), a method that detects blood in feces, has demonstrated low sensitivity (51%) in detecting cancer cells [ 10 ], whereas DNA stool tests (i.e., Cologuard ® ) have high sensitivity for early CRC detection (92%) but lower performance in perceiving advanced pre-cancerous lesions (42.4%) [ 11 ]. Blood-based protein biomarkers have been suggested for the early detection of CRC [ 12 ]. Circulating cfDNA has been considered as a liquid biopsy material able to provide insights in cancer initiation and progression, meeting the need for a convenient, minimally invasive tool for precision medicine [ 13 , 14 , 15 ].…”

Development and validation of circulating protein signatures as diagnostic biomarkers for biliary tract cancer

“… 30 The proximity extension assay platform has been widely used for biomarker studies, the method has high accuracy and results obtained using this method correlate well with results obtained using other platforms such as multiple reaction monitoring–mass spectrometry and enzyme-linked immunosorbent assays. [30] , [31] , [32] This panel was chosen because BTC is characterized by a high degree of inflammation and an immunosuppressive environment, 6 , 17 , 18 , 22 and the Olink I-O panel has previously been used to generate potential diagnostic protein signatures in pancreatic ductal adenocarcinoma. 26 The analyses were performed blinded at BioXpedia, Aarhus, Denmark according to the manufacturer’s instructions.…”

Quantification of 782 Plasma Peptides by Multiplexed Targeted Proteomics

“…1−5 As many described biomarkers are derived from the direct analysis of the affected tissue or tumor material, they usually do not directly translate into valid biomarkers in blood samples, making further studies and method development necessary. 1,6,7 As a multiplexed technique, mass spectrometry plays an integrated role in discovering and verifying biomarker candidates and is an alternative to antibody-based analysis techniques. 8−10 While shotgun proteomics measurements are excellent tools for the initial discovery of regulated proteins, the inherent risk of not detecting proteins in samples of a cohort due to the random selection of ions for fragmentation is mitigated by switching to targeted acquisition.…”

“…Recently, several studies showed that protein panels provide a better diagnostic or predictive power than single protein markers. − As many described biomarkers are derived from the direct analysis of the affected tissue or tumor material, they usually do not directly translate into valid biomarkers in blood samples, making further studies and method development necessary. ,, …”