Sample-Treatment with the Virucidal β‑Propiolactone Does Not Preclude Analysis by Large Panel Affinity Proteomics, Including the Discovery of Biomarker Candidates

Virus inactivation is a prerequisite for safe handling
of high-risk
infectious samples. β-Propiolactone (BPL) is an established
reagent with proven virucidal efficacy. BPL primarily reacts with
DNA, RNA, and amino acids. The latter may modify antigenic protein
epitopes interfering with binding properties of affinity reagents
such as antibodies and aptamers used in affinity proteomic screens.
We investigated (i) the impact of BPL treatment on the analysis of
protein levels in plasma samples using the aptamer-based affinity
proteomic platform SomaScan and (ii) effects on protein detection
in conditioned medium samples using the proximity extension assay-based
Olink Target platform. In the former setup, BPL-treated and native
plasma samples from patients with ovarian cancer (n = 12) and benign diseases (n = 12) were analyzed
using the SomaScan platform. In the latter, conditioned media samples
collected from cultured T cells with (n = 3) or without
(n = 3) anti-CD3 antibody stimulation were analyzed
using the Olink Target platform. BPL-related changes in protein detection
were evaluated comparing native and BPL-treated states, simulating
virus inactivation, and impact on measurable group differences was
assessed. While approximately one-third of SomaScan measurements were
significantly changed by the BPL treatment, a majority of antigen/aptamer
interactions remained unaffected. Interaction effects of BPL treatment
and disease state, potentially altering detectability of group differences,
were observable for less than one percent of targets (0.6%). BPL effects
on protein detection with Olink Target were also limited, affecting
3.6% of detected proteins with no observable interaction effects.
Thus, effects of BPL treatment only moderately interfere with affinity
proteomic detectability of differential protein expression between
different experimental groups. Overall, the results prove high-throughput
affinity proteomics well suited for the analysis of high-risk samples
inactivated using BPL.