Fig. 4

KR-incubated cells display enhanced expression of interferon-stimulated and immune processes related proteins. A PCA on proteomic data (obtained by data independent acquisition (DIA) mass spectrometry) of control HEK293T cell lines and incubated with four SARS-CoV-2 VLP variants (WT, KR, D614G, and D614G-KR). PCA plot is generated by Spectronaut software version 15) and is based on all differentially expressed (DE) proteins (n = 4 independent experiments). B–C Volcano plot displaying differentially expressed proteins. B Comparing KR VLP incubated cells with WT (KR versus WT). C Comparing D614G-KR VLP incubated cells with WT (D614G-KR versus WT). Proteins with statistically significant (adjusted p-value ≤ 0.05) differences between KR/D614G-KR mutant and WT conditions are shown in red (candidates) and all other non-significant proteins (non-candidates) are shown in gray. The names of top differentially expressed proteins common between KR and D614G-KR conditions are shown and highlighted in blue (selected). D Venn diagram shows the overlap of all significantly (adj p-value < 0.05 and Log2 ratio ≥ 1) down-regulated proteins between KR, D614G-KR, and D614G SARS-CoV-2 VLP incubated cells. E Venn diagram shows the overlap of all significantly (adj p-value < 0.05 and Log2 ratio ≥ 1) up-regulated proteins between KR, D614G-KR, and D614G SARS-CoV-2 VLP-infected cells. F Plot showing GO-enrichment analysis (top 30 GO-Biological Processes (BP) enriched pathways are shown) for significantly up-regulated proteins common between KR and D614G-KR conditions (adj p-value < 0.05 and log2 fold-change ≥ 1). GO term analysis was performed by ShinyGO (version 0.074)