Abstract Background There is currently no screening test to detect oesophageal adenocarcinoma (OAC) at an earlier stage, leading to poor survival outcomes; hence, a non-endoscopic approach to diagnosis is required. This project aims for a diagnostic via plasma proteomics, which experienced remarkable progress in recent years in both mass spectrometry and affinity binders technology. We conducted three pilot studies in OAC, Barrett’s and normal patients using the Olink Explore HT platform and data independent acquisition (DIA) on the Astral mass spectrometer and generated proteomic signatures that distinguish normal and Barrett’s (BO/LGD) patients from Barrett’s with high grade dysplasia (HGD) and OAC. Methods These pilot studies used 119 samples from the PROBENET study and an additional biobank. DIA protein quantitation was generated for 80 samples in two separate batches (n = 10 normal, n = 10 Barrett’s, n = 10 HGD Barrett’s and n = 10 OAC each), with quantitation extraction via Spectronaut. Olink Explore quantitation (NPX values) was obtained for 88 samples (n = 10 normal, n = 10 Barrett’s, n = 9 LGD, n = 7 IMC, n = 8 HGD Barrett’s and n = 45 OAC). The effect of clinical variables was assessed for all datasets, and the correlation of the two proteomic techniques was calculated on common samples. Differential expression was determined using the limma package. Results In total, 1681 protein groups were quantitated in two Astral batches, whilst Olink HT evaluated 5416 targeted immunoassays. Assays correlating with storage age were removed from biomarker discovery workflows; patient age differed between comparison groups (range: median age 57–68 years). Correlations between Astral and Olink data were as previously reported between Olink and Somascan and stratified by protein abundance: more abundant blood proteins exhibited more consistent quantitation. A proteomic signature comprising 5 proteins trained on the Astral study (AUC = 0.86 in batch 1, AUC = 0.82 in batch 2) was validated in the Olink data (AUC = 0.85). Conclusion The depth of coverage now achieved in plasma proteomics enables diagnostics discovery from both mass spectrometry and affinity platforms, although care is required with varying sample storage ages, reconciling different quantitative techniques and accounting for patient age differences where disease categories cannot be fully age matched. Protein signatures with useful clinical performance in detecting OAC via plasma samples can be determined using these approaches, and signatures obtained by mass spectrometry can be validated using Olink.
Pascovici et al. (Fri,) studied this question.