Code from: A distinct antigen presentation pathway drive potent T-cell immunity in lipid nanoparticle-based mRNA vaccines
Abstract
In the paper by Muro et al (Science Advances 2026), to investigate whether mRNA-LNP affects the TCR repertoire of the induced CD8 T cells, we performed bulk TCR sequencing on the TCRα chains in retrogenic mice expressing a rearranged TCRβ chain. Retrogenic mice were immunized with OVA mRNA-LNP or OVA protein + poly I/C, and SIINFEKL/Kb tetramer-positive CD8 T cells were analyzed on day 14. TCR sequencing analysis showed that the number of TCR clonotypes was markedly reduced in SIINFEKL/Kb tetramer-positive CD8 T cells compared to total CD8 T cells before immunization. Principal component analysis revealed a marked similarity in the composition of OVA peptide-reactive TCRs between mice immunized with OVA mRNA-LNP and those receiving OVA protein + poly I/C. These results showed similar TCR repertoires induced by OVA mRNA-LNP and OVA + poly I/C, suggesting that the robust expansion of CD8 T cells by mRNA-LNP is primarily due to differences that are quantitative rather than qualitative compared to antigen protein and conventional adjuvants. The sequencing data have been deposited in the DDBJ Sequence Read Archive under BioProject accession number PRJDB40453.
Dataset DOI: 10.5061/dryad.h44j0zq25
Description of the data and file structure
The source code for the principal component analysis of TCR frequency, shown in Figure S5B (Muro et al, Science Advances 2026).
Files and variables
File: R_script
Description: The source code for the principal component analysis of TCR frequency, shown in Figure S5B
Code/software
This is an R script for performing principal component analysis on the frequencies of TCR-alpha clones obtained from bulk TCR sequence analysis.
Access information
Other publicly accessible locations of the data:
- GitHub (https://github.com/nittatakeshi)
Data was derived from the following sources:
- The raw TCR sequencing data have been deposited in the DDBJ Sequence Read Archive under BioProject accession number PRJDB40453.
