Longitudinal proteomic and autoantibody signatures after mRNA vaccination in healthy individuals

Longitudinal analysis of the circulating proteome after SARS-CoV-2 mRNA vaccination provides insights into immune adaptation, optimizing vaccination strategies, and understanding long-term molecular effects.

We analyzed 120 paired plasma samples from 114 healthy participants at six time points: pre-vaccination, 3 days and 7-21 days post-dose 1, 7-21 days post-dose 2, and at 8-, 16-, and 24-weeks post-dose 2. IgG antibody responses to SARS-CoV-2 structural proteins and autoantibody profiles were assessed using a multiplex platform, and plasma proteome changes were quantified by mass spectrometry.

IgG antibodies against spike protein regions (RBD, S1, S2) produced sustained responses for up to 24 weeks, with no detection of nucleocapsid or membrane antibodies, confirming that there was no prior infection. Younger participants (<45 years) presented stronger responses, with no significant sex differences. Proteomics identified 342 proteins, of which 214 proteins were significantly altered, predominantly at 16-24 weeks. Key changes included upregulation of C1 complex proteins (C1R, C1QC, C1S) and downregulations of the C1 inhibitor SERPING1, indicating complement activation. Platelet-associated proteins showed minimal changes, suggesting a limited thrombosis risk. Altered proteins were enriched in carbohydrate metabolism, cofactors/vitamin metabolism, and thyroid hormone pathways. Autoantibody profiling showed stable responses for most self-antigens, with modest increased in several interleukin specific autoantibodies, including IL-1B, at later time points.

Integrated plasma proteomics and autoantibody profiling demonstrated sustained immunogenicity and safety of SARS-CoV-2 mRNA vaccines, characterized by durable spike-specific antibody responses, late-onset complement activation, and limited autoantibody induction. These findings enhance our understanding of vaccine-induced immunity and inform long-term monitoring and optimization of mRNA vaccine strategies.