Isoform-level analysis reveals conserved early changes in transcript usage during human vaccine responses

Methods

We re-analyzed longitudinal whole-blood RNA-seq data from two independent cohorts of mRNA COVID-19 vaccine recipients using the IsoformSwitchAnalyzeR framework. Key findings were validated by full-length RNA long-read sequencing and extended to four additional vaccine cohorts covering distinct platforms and pathogens. Results: mRNA vaccination induced a rapid and transient wave of differential transcript usage, peaking at 24 hours post-vaccination with 131 isoforms significantly altered across 107 genes, before largely resolving by day 14.

Isoform switching events were reproducible across independent cohorts and confirmed by full-length RNA long-read sequencing. Structural annotation of switching transcripts, including RMI2, WARS1, and NT5C3A, revealed changes affecting predicted protein domains and signal peptides. Notably, highly concordant isoform switching patterns were observed across MVA-based SARS-CoV-2, influenza, and Ebola vaccine cohorts, and showed dose-dependent modulation.

Conclusions: Differential transcript isoform usage is a rapid, transient, and conserved feature of the early human immune response to vaccination, independent of platform or pathogen. These findings reveal an underappreciated layer of transcriptional regulation that complements conventional gene-level analyses and warrants integration into future vaccine immunogenicity studies.