The Promotion of Humoral Immune Responses in Humans via SOCS1-Mediated Th2-Bias Following SARS-CoV-2 Vaccination

Abstract

The effectiveness of SARS-CoV-2 vaccines varies among individuals. During the COVID-19 global pandemic, SARS-CoV-2 infection showed significant Th1 characteristics, suggesting that the immune disorder and production of SARS-CoV-2 antibodies may be related to Th1/Th2 bias. However, the molecular mechanisms underlying Th1/Th2 bias effects on host immune responses to viruses remain unclear. In this study, the top three subjects with the highest and lowest changes in anti-SARS-CoV-2 antibodies after receiving three doses of SARS-CoV-2 vaccination were selected and defined as the elevated group (E) and the control group (C), respectively. Peripheral blood was collected, single-cell sequencing was performed before and after the third dose of the SARS-CoV-2 vaccine, and the changes in T cell clusters were analyzed. Compared with the C group, the Treg pre-vaccination proportion was lower in E, while the post-vaccination proportion was higher, suggesting that Tregs may be crucial in this process. Differential analysis results of Tregs between the two groups revealed that differentially expressed genes (DEGs) were significantly enriched in the IL4 pathway. Correlation analysis between DEGs and serum antibody showed that the expression of NR4A2, SOCS1, and SOCS3 in Tregs was significantly correlated with serum antibodies, suggesting that the immune response in E group changed to Th2 bias, thereby promoting host humoral immune responses. On the other hand, antibody-related genes SOCS1 and NR4A2, as well as lnc-RNA MALAT1 and NEAT1, were highly expressed in the CD4-MALAT1 subclusters. In summary, our study revealed that Th2 bias promotes humoral immune responses in humans by increasing SOCS1 in T cells after SARS-CoV-2 vaccination. Moreover, NR4A2, SOCS1, MALAT1, and NEAT1 were identified as the potential key biomarkers or treatment targets for enhanced SARS-CoV-2 antibody production by influencing the Th1/Th2 balance in T cells. Our findings have important implications for population stratification and tailored therapeutics for more effective SARS-CoV-2 vaccines.

Keywords: SARS-CoV-2 vaccine; Treg cells; humoral immune responses; single-cell sequencing; the Th1/Th2 balance.

Figure 1

Study design and expression profiling of 84,331 single cells in pre- and post-vaccinated PBMCs. (A) Schematic of the study design of the sample composition, processing, and bioinformatic analyses for 12 samples. (B) Serum neutralizing antibody and IgG antibody levels in control vs. elevated groups. Median ± IQR; Mann–Whitney U test. (C) UMAP plot showing the clusters of all high-quality cells. (D) UMAP plot showing clusters of all T cells. (E) Heatmap of the marker genes utilized to annotate T cell clusters.

Figure 2

Changes in the Treg cell expression atlas of pre- and post-vaccination were different between the C and E groups. (A) UMAP plots showing the clusters of four groups: B_C, Af_C, B_E, and Af_E (arrows indicate Treg cells). (B) The ratios of Treg cells in the C vs. E groups. Median ± IQR; Mann–Whitney U test. (C) Schematic of the differential analysis design for the four groups. (D) Venn plot showing the number of DEGs per group.

Figure 3

Enrichment pathway analysis of significantly changed genes. (A) Top 10 enriched pathways of the DEGs in the E group (n = 99) via Metascape (https://metascape.org) (accessed on 7 September 2023). (B) Heatmap of the significant antibody-related genes (n = 31). Hierarchical clustering identifies four groups. (C) Top 10 enriched pathways of the 31 antibody-related genes via Metascape. (D) Top enriched KEGG pathways of the 31 antibody-related genes via “clusterProfiler” R package.

Figure 4

Differential expression atlas of CD4 effector T cells was correlated with host humoral immune responses. (A) UMAP plots of four groups with no clustering: B_C, Af_C, B_E, and Af_E. (B) Volcano plots showing the increase in CD4 differentiation genes NR4A2, SOCS1, and SOCS3 in Af_E cells compared with in Af_C. (C) Heatmaps of the significantly expressed antibody-related genes (n = 41) in all T cell clusters. (D) Heatmaps of marker genes and key transcription factors.

Figure 5

Schematic diagram of the differential immune response mechanism. The up and down arrows indicate increases and decreases, respectively.