Crossing the Halfway Point: Aptamer-Based, Highly Multiplexed Assay for the Assessment of the Proteome

Measuring
responses in the proteome to various perturbations
improves
our understanding of biological systems. The value of information
gained from such studies is directly proportional to the number of
proteins measured. To overcome technical challenges associated with
highly multiplexed measurements, we developed an affinity reagent-based
method that uses aptamers with protein-like side chains along with
an assay that takes advantage of their unique properties. As hybrid
affinity reagents, modified aptamers are fully comparable to antibodies
in terms of binding characteristics toward proteins, including epitope
size, shape complementarity, affinity and specificity. Our assay combines
these intrinsic binding properties with serial kinetic proofreading
steps to allow highly effective partitioning of stable specific complexes
from unstable nonspecific complexes. The use of these orthogonal methods
to enhance specificity effectively overcomes the severe limitation
to multiplexing inherent to the use of sandwich-based methods. Our
assay currently measures half of the unique proteins encoded in the
human genome with femtomolar sensitivity, broad dynamic range and
exceptionally high reproducibility. Using machine learning to identify
patterns of change, we have developed tests based on measurement of
multiple proteins predictive of current health states and future disease
risk to guide a holistic approach to precision medicine.