Plasma-treatment with the virucidal beta-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. Beta-propiolactone (BPL) is an established and commonly used reagent with proven virucidal efficacy. BPL primarily reacts with DNA and RNA, but also amino acids. The latter may yield modified antigenic protein epitopes and thus interfere with the binding properties of affinity reagents such as antibodies and aptamers, including panels of such reagents used in affinity proteomic screens. We investigated the impact of BPL-treatment on the analysis of protein levels in plasma samples using the commercial aptamer-based affinity proteomic platform SomaScan. Heparin-plasma samples from patients with ovarian cancer (n = 12) and benign tumors (n = 12) were analyzed using the SomaScan v4.1 platform, which led to the identification of COL10A1 as a novel ovarian cancer biomarker, a protein strongly associated with poor clinical outcome. BPL-related changes in protein detection were evaluated comparing native and BPL-treated state, simulating virus inactivation, and impact on measurable group differences was assessed. While approximately one third of protein 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%). Accordingly, noticeable global effects of BPL treatment did not interfere with detectability of differential protein expression between benign and ovarian cancer samples, as measurements are altered in both groups to the same extent. Global effect sizes (Cohen’s d) between benign and cancer in BPL-treated samples and the number of significantly altered protein abundance observed in limma-based linear modeling appeared minimally increased, slightly enhancing the probability of false positive hits. Taken together, the results indicate the SomaScan platform as well suited for the analysis of high biosafety risk samples inactivated using BPL and the identification of novel biomarkers. ### Competing Interest Statement Sample analysis on the SomaScan platform was provided by SomaLogic Operating Co., Inc. free of charge. The authors affirm the study to have been conducted independently and without undue influence from SomaLogic Co., Inc. The researchers involved maintained full control over the design, data analysis, and interpretation of the results, ensuring scientific rigor. The authors declare no further conflicts of interest. ### Funding Statement Sample analysis on the SomaScan platform was provided by SomaLogic Operating Co., Inc. free of charge. This study did not receive any further funding. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethics committee of the Philipps-University Marburg gave ethical approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors