Emerging Affinity-Based Proteomic Technologies for Large-Scale Plasma Profiling in Cardiovascular Disease

Abstract

Plasma biomarkers that reflect molecular states of the cardiovascular system are central for clinical decision-making. Routinely used plasma biomarkers include troponins, natriuretic peptides and lipoprotein particles, yet interrogate only a modest subset of pathways relevant to cardiovascular disease. Systematic profiling of a larger portion of circulating plasma proteins (the plasma proteome) will provide opportunities for unbiased discovery of novel markers to improve diagnostic or predictive accuracy. In addition, proteomic profiling may inform pathophysiological understanding and point to novel therapeutic targets. Obstacles for comprehensive proteomic profiling include the immense size and structural heterogeneity of the proteome, as well as the broad range of abundance levels. Proteome-wide, untargeted profiling can be performed in tissues and cells with tandem mass spectrometry. However, applications to plasma are limited by the need for complex preanalytical sample preparation stages limiting sample throughput. Multiplexing of targeted methods based on capture and detection of specific proteins are therefore receiving increasing attention in plasma proteomics. Immunoaffinity assays are the workhorse for measuring individual proteins but have been limited for proteomic applications by long development times, cross-reactivity preventing multiplexing, specificity issues, and incomplete sensitivity to detect proteins in the lower range of the abundance spectrum (below picograms per milliliter). Emerging technologies to address these issues include nucleotide-labeled immunoassays and aptamer reagents which can be automated for efficient multiplexing of thousands of proteins at high sample throughput, coupling of affinity capture methods to mass spectrometry for improved specificity, and ultrasensitive detection systems to measure low-abundance proteins. In addition, proteomics can now be integrated with modern genomics tools to comprehensively relate proteomic profiles to genetic variants, which may both influence binding of affinity reagents and serve to validate the target specificity of affinity assays. The application of deep quantitative proteomic profiling to large cohorts has thus become increasingly feasible with emerging affinity methods. The aims of this article are to provide the broad readership of Circulation with a timely overview of emerging methods for affinity proteomics and recent progress in cardiovascular medicine based on such methods.

The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays

“…In the long run, technologies that are capable of measuring proteins in multiplex and in a large number of samples will be beneficial for rapid analysis of plasma (69). One attractive solution is described for coupling multiplexed protein detection with read-out by DNA and to profile more than 90 proteins in a single assay (70, 71); they have been used and applied in extensive sample sets (72, 73).…”

Facets of individual-specific health signatures determined from longitudinal plasma proteome profiling

“…The blood proteome, consisting of both cellular and soluble proteins, has received a revived interest due to advances in protein technologies. This includes mass cytometry [5] to study immune systems, as well as mass spectrometry [6] and affinity assays [7] for profiling serum or plasma. For the circulating plasma proteome, nearly 5,000 proteins have this far been detected when combing discoveries from all assays and technologies [8].…”

Coding and regulatory variants affect serum protein levels and common disease

“…It remains a possibility that the influence of some structural variants on protein levels reflect effects mediated by regulatory variants that are in linkage disequilibrium with the pQTL of interest. In addition, protein coding variants may cause technical artifacts in both affinity proteomics and mass spectrometry 43,44 . However, systematic conditional and colocalization analyses in causality testing using the aptamer-based technology have shown that pQTLs driven by common missense variants being artefactual is an unlikely event 11,45 .…”