Large-Scale Plasma Proteome Epitome Profiling is an Efficient Tool for the Discovery of Cancer Biomarkers.

Current proteomic technologies focus on the quantification of protein levels, while little effort is dedicated to the development of system approaches to simultaneously monitor proteome variability and abundance. Protein variants may display different immunogenic epitopes detectable by monoclonal antibodies. Epitope variability results from alternative splicing, posttranslational modifications, processing, degradation, and complex formation and possesses dynamically changing availability of interacting surface structures that frequently serve as reachable epitopes and often carry different functions. Thus, it is highly likely that the presence of some of the accessible epitopes correlates with function under physiological and pathological conditions. To enable the exploration of the impact of protein variation on the immunogenic epitome first, here, we present a robust and analytically validated PEP technology for characterizing immunogenic epitopes of the plasma. To this end, we prepared mAb libraries directed against the normalized human plasma proteome as a complex natural immunogen. Antibody producing hybridomas were selected and cloned. Monoclonal antibodies react with single epitopes, thus profiling with the libraries is expected to profile many epitopes which we define by the mimotopes, as we present here. Screening blood plasma samples from control subjects (n = 558) and cancer patients (n = 598) for merely 69 native epitopes displayed by 20 abundant plasma proteins resulted in distinct cancer-specific epitope panels that showed high accuracy (AUC 0.826-0.966) and specificity for lung, breast, and colon cancer. Deeper profiling (≈290 epitopes of approximately 100 proteins) showed unexpected granularity of the epitope-level expression data and detected neutral and lung cancer-associated epitopes of individual proteins. Biomarker epitope panels selected from a pool of 21 epitopes of 12 proteins were validated in independent clinical cohorts. The results demonstrate the value of PEP as a rich and thus far unexplored source of protein biomarkers with diagnostic potential.

Specific detection and quantitation of bovine IgG in bioreactor derived mouse mAb preparations.

Monoclonal antibody and recombinant protein production benefits greatly from bovine serum as an additive. The caveat is that bovine serum IgG, co-purifies with mAbs and IgG Fc-containing fusion proteins and it presents a contaminant in the end products. In order to analytically validate the products, species specific reagents are needed that react with bovine IgG exclusively. Our attempts to find such commercially available reagents failed. Here, we report the production of species specific mAbs which recognize bovine IgG even in the presence of excess amount of mouse IgG. We present five mAbs: Bsi4028, Bsi4032, Bsi4033, Bsi4034 and Bsi4035 suitable to determine the presence of bovine IgG contamination via ELISA or immunoblotting in bioreactor derived mouse mAb preparations. To quantitate bovine IgG content we developed sensitive sandwich ELISAs capable to detect bovine IgG contaminant in the ng/ml (~10-11M/l) range. Finally, we show that bovine IgG is efficiently removed from bioreactor produced mouse mAb preparation via affinity depletion columns prepared with Bsi4028, Bsi4032, Bsi4033, Bsi4034, Bsi4035 mAbs.