Altered expression of miRNA profile in peripheral blood mononuclear cells following the third dose of inactivated COVID-19 vaccine

Abstract

COVID-19 vaccination is the most effective strategy for preventing severe disease and death. Inactivated vaccines are the most accessible type of COVID-19 vaccines in developing countries. Several studies, including work from our group, have demonstrated that the third dose (booster vaccination) of inactivated COVID-19 vaccine induces robust humoral and cellular immune responses. The present study aimed to examine miRNA expression profile in participants who received a homologous third dose of the CoronaVac vaccine. Samples of peripheral blood mononuclear cells (PBMCs) were collected from healthcare volunteers both before and 1-2 weeks after the booster dose. miRNA microarray analysis in a discovery cohort of six volunteers identified 67 miRNAs with differential expression. Subsequently, the expression of six miRNAs related to immune responses was examined in a validation cohort of 31 participants via qRT-PCR. Our results validated the differential expression of miR-25-5p, miR-34c-3p, and miR-206 post-booster, with a significant correlation to the receptor binding domain (RBD)-specific antibody. Bioinformatic analysis suggested that miR-25-5p, miR-34c-3p, and miR-206 may target multiple pathways involved in immune regulation and inflammation. Therefore, our study highlights miR-25-5p, miR-34c-3p, and miR-206 in PBMCs as promising biomarkers for assessing the immune response induced by the booster dose of the CoronaVac vaccine.

Keywords: COVID-19; CoronaVac; Immune response; Inactivated vaccine; MicroRNA; Peripheral blood mononuclear cells.

Figure 1. miRNA profile of PBMCs in the discovery cohort before and after the booster dose of CoronaVac.

(A) A miRNA microarray was performed on PBMCs from six volunteers before and 1–2 weeks after the booster dose. There were 30 upregulated miRNAs and 37 downregulated miRNAs (greater than 1.5 fold, nominal p < 0.05). (B) The volcano plot illustrates the identification of differentially expressed miRNAs. Red dots represent miRNAs with a nominal p-value < 0.05 and a fold change > 1.5, while green dots indicate miRNAs with a nominal p-value < 0.05 and a fold change < −1.5. Black dots show 1,724 unaltered miRNAs.

Figure 2. Altered expression of miR-25-5p, miR-34c-3p, and miR-206 after the booster dose of CoronaVac in the validation cohort.

qRT-PCR was performed on PBMCs from 31 volunteers for the expression of six immune response-related miRNAs with differential expression. n = 31. The plot shows a median (lines within boxes), interquartile range (bounds of boxes), and error bars (upper and lower ranges). *p < 0.05.

Figure 3. Correlation between expression of miRNAs and levels of anti-RBD IgG.

(A) Levels of anti-RBD IgG were determined via ELISA and represented by OD₄₅₀ value. Each dot represents a subject. The plot shows a median (lines within boxes), interquartile range (bounds of boxes), and error bars (upper and lower ranges). ****p < 0.001. (B) The curve was plotted by the relative expression of miR-25-5p, miR-34c-3p, and miR-206 after booster dose to their respective OD₄₅₀ value of anti-RBD IgG. OD, Optical density.

Figure 4. KEGG pathways significantly enriched in target genes of miR-25-5p, miR-34c-3p, and miR-206.

KEGG pathway analysis was conducted for miR-25-5p, miR-34c-3p, and miR-206. There were 13 over-represented biological pathways for mRNA targets of the three miRNAs. Data shown are the negative log p-value (nominal) of the Fisher’s exact test.

Figure 5. Target gene network for miR-25-5p, miR-34c-3p, and miR-206 with relevance to immune response.

Solid and dashed arrows show experimentally validated and predicted targets, respectively.