Comprehensive characterization of multivalent mRNA vaccines functionality by flow cytometry and mass spectrometry

The number of clinical trials involving mRNA vaccines has increased considerably over the past few years, increasing the demand for analysis and quantification of their biological activity in vitro. This present challenges due to mRNA vaccines' complex mechanism of action. As the mRNA platform requires minimal adaptations between projects, analytical methods should be quickly adaptable to maximize the technology's benefits. In the literature, mRNA vaccines biological activity is assessed using antibody-based methods that compare percentages of positive cells. However, these methods do not allow quantification of different antigen expression levels between samples, and require using specific antibodies, limiting platform applicability. This study aimed to identify the most relevant read-out using an antibody-based method, and to compare it with an antibody-independent quantifiable method (liquid chromatography coupled with mass spectrometry; LCMS). Both approaches were used to analyze multivalent mRNA samples in stability studies. Results showed that reporting transfection efficiency by percentage of positive cells does not capture differences in protein expression between samples. Integrated median fluorescence intensity (iMFI) highlights these differences and shows trends consistent with antigens quantification by LCMS, confirming the relevance of the latter. However, the LCMS method does not allow relative potency analyses, as the parallelism between samples' dose-responses can be lost due to sample degradation. In summary, iMFI can provide a more comprehensive view of mRNA vaccine's in vitro functionality than the percentage of positive cells. Additionally, this work demonstrates that LCMS is indeed a viable antibody-free alternative to quantify mRNA vaccine functionality. However, neither method allows for calculating relative potencies as prescribed in the US pharmacopeias guidelines.