SARS-CoV-2 infection and mRNA vaccination promote a transcriptionally distinct CD4+ T cell memory landscape

In a recent study posted on Bio Rxiv*, researchers reported that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and mRNA vaccination induced clear memory T cells.

Background

T-cell memory is critical for long-term defense against viruses and correlates with immune defense. Many develop her T-cell memory for the SARS-CoV-2 spike as a result of natural infection or vaccination. In particular, differentiation 4-positive clusters (CD4⁺) T cell responses target epitopes that are conserved among variants.

During initial priming, sites and antigen Exposure, inflammatory signals, cytokine milieu, and cell-cell interactions imprint the resulting memory pool and influence T-cell responses upon re-exposure to antigen. Viral infection causes a highly inflammatory state not seen with vaccination.Effect of infection-associated inflammation on memory CD4⁺ T cells have not yet been studied.

Research and Findings

In the present study, researchers investigated the transcriptional landscape of CD4.⁺ T cells specific for SARS-CoV-2 spike protein Before and after the third vaccination (booster). Peripheral blood mononuclear cells (PBMC) were obtained in his 14 mice approximately 8 months after the second vaccination (pre-boost) and after the booster vaccination (post-boost) to longitudinally examine immunological memory. collected from adults.

Seven adults contracted coronavirus disease 2019 (COVID-19) in the spring of 2020 and were designated for infection priming. Thus, the initial exposure to the SARS-CoV-2 spike was due to infection. The remaining 7 of her were infection-naive and were considered vaccine-primed (the first spike exposure was her BNT162b2 mRNA vaccine). Additionally, five of her vaccine-primed subjects later experienced breakthrough infections during her Omicron wave.

We identified memory CD4 using an activation-induced marker (AIM) assay.⁺ T cells. PBMC were stimulated with spiked peptide pools and AIM-reactive CD4.⁺ T cells were detected by flow cytometry. After the AIM assay, the authors performed multimodal single-cell RNA-sequencing to examine differences in transcript levels of spike-specific memory CD4.⁺ T cells.

Seven major clusters were identified in stimulated PBMCs, two of which were largely absent in unstimulated controls. Activation-related genes such as interferon gamma (IFNGMore), interleukin 2 (IL2), and lymphotoxin-α (LTA), highly enriched in these two clusters. Dimensionality reduction applied with 27 parameters to identify AIM-reactive CD4⁺ T cell clusters revealed 11 different clusters.

The distribution of cells across these 11 clusters was similar between the two cohorts at pre- and post-boost time points. Most CD4⁺ T cells in both cohorts were identified with cluster 0 expression. CD27selectin L (sell), and transcription factor 7 (TCF7), suggesting a central memory state. Infection-primed CD4 after booster vaccination⁺ T cells were more represented in cluster 1 expressing cytotoxic genes than in other clusters. Multifunctionality of CD4⁺ T cells were similar between the two cohorts and were not significantly altered by booster vaccination.

69 and 220 genes were differentially expressed in CD4⁺ T cells before and after booster vaccination between the two cohorts. CD4⁺ Adult-derived T cells primed with infection differentially expressed IFN-stimulated genes. In contrast, CD4⁺ T cells from vaccinated individuals showed differential expression of genes involved in nuclear factor kappa B (NF-kB) signaling. Gene set enrichment analysis (GSEA) was performed to test differences at the pathway level.

We found a significant enrichment of the IFN α and γ responsive gene sets in CD4.⁺ Infected primed target T cells at the pre-boost time point. Booster vaccination did not substantially alter gene set enrichment and CD4⁺ T cells were imprinted differently upon priming, and transcriptional profiles changed minimally upon re-exposure to spikes during mRNA vaccination.

In contrast, GSEA revealed a significant enrichment of the NF-kB signaling gene set in vaccine-primed individuals at post-boost time points. In addition, the mitotic spindle and G2M checkpoint gene sets were enriched at pre- and post-boost time points, suggesting strong expression of proliferation-related genes in vaccine-primed CD4.⁺ T cells.

Therefore, CD4⁺ T-cell frequencies were 2-fold higher in vaccine-primed adults than in infection-primed individuals one month after the second mRNA vaccination.⁺ T cells can have a lasting effect on cell activation and can also affect their proliferative capacity.

Finally, SARS-CoV-2 vaccine breakthrough infection in five vaccinated participants caused subtle changes in the transcriptional profile of CD4⁺ T cells.However, it did not recapitulate the transcriptional landscape of infection-primed CD4⁺ T cells.

Conclusion

In summary, the findings suggest that inflammatory signatures during the formation of SARS-CoV-2 spike-specific memory CD4⁺ T cells, compared with CD4, conferred persistent transcriptional changes that persisted even after mRNA vaccination⁺ Primed T cells during mRNA vaccination. SARS-CoV-2 vaccine breakthrough infection did not cause dramatic changes in the vaccine-stimulated CD4 transcriptional landscape⁺ T cells. Taken together, this study provided valuable insight into the factors that influence memory CD4 function and quality.⁺ T-cell responses to aid future vaccine design.

*Important Notices

bioRxiv publishes non-peer-reviewed, preliminary scientific reports and should not be considered conclusive, to guide clinical practice/health-related actions, or to be treated as established information .