Intracellular peptides in SARS-CoV-2-infected patients

Abstract

Intracellular peptides (InPeps) generated by the orchestrated action of the proteasome and intracellular peptidases have biological and pharmacological significance. Here, human plasma relative concentration of specific InPeps was compared between 175 patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and 45 SARS-CoV-2 non-infected patients; 2,466 unique peptides were identified, of which 67% were InPeps. The results revealed differences of a specific group of peptides in human plasma comparing non-infected individuals to patients infected by SARS-CoV-2, following the results of the semi-quantitative analyses by isotope-labeled electrospray mass spectrometry. The protein-protein interactions networks enriched pathways, drawn by genes encoding the proteins from which the peptides originated, revealed the presence of the coronavirus disease/COVID-19 network solely in the group of patients fatally infected by SARS-CoV-2. Thus, modulation of the relative plasma levels of specific InPeps could be employed as a predictive tool for disease outcome.

Keywords: Microbiology; Public health; Virology.

Graphical abstract

Figure 1

Plasma peptides frequency and their respective p value when comparing peptide ratios M/C, S/C, and D/C. Colored dots represent peptides whose relative ratio either remained unaltered (gray dots), significantly increased (red dots) or significantly decreased (green dots) [p value ≤ -log₁₀ (5·10⁻²)]. See also Table S4.

Figure 2

Comparative analyzes of human plasma peptidome studies (A) subcellular localization of proteins that originated the identified peptides. (B) Venn diagram of peptides identified across studies. sA, present report; sB, Magalhães et al. and sC, Parker et al. See also Table S6.

Figure 3

Biochemical comparisons between plasma and urine peptides Identified plasma peptides (P) were both herein and previously by Magalhães et al. and sC, Parker et al., and urine peptides (U) from previously reports by Magalhães et al. and Wendt et al. (A) Peptide mass. (B) Number of residues. (C) Net charge. (D) Isoelectric point. (E) Hydrophobicity. (F) Aliphatic index. (G) Instability index. ∗p ≤ 0.05 vs. P.

Figure 4

PathfindR bubble plot of Biogrid PIN represented by Kyoto Encyclopedia of Genes and Genomes (KEGG) terms Enriched PIN were identified using genes encoding the proteins that originated the differentially expressed peptides. The x axis corresponds to fold enrichment values, while the y axis indicates the enriched pathways with at least two genes. Bubble size indicates number of differentially expressed genes (DEGs) in the given pathway. Color indicates −log₁₀(p value) value; the more it shifts from purple to red, the more significant the PIN was enriched.

Figure 5

Bubble plot of overrepresented differentially regulated peptides docking or SLiMs KEGG terms On Y axis are terms with p value ≤ -log10(p value) and part of top three lowest p values of at least one group comparison (M/C, S/C or D/C). Bold terms were enriched on groups M/C and S/C, or exclusively on group D/C. Bubble size represents number of SLiMs related to a given term. Color scale indicates -log10(p value); redder the color, more significantly pathway is enriched.

Figure 6

Multiple sequence alignment of plasma peptides identified herein that contain the RGD or LDS SLiMs (A) Peptides containing either the motif RGD, (B) or LDS, (C) and their respective relative ratios in M/C, S/C, or D/C. For better visualization, extreme peptides ratios values used to produce the plot were capped at 10 and 0.5. ∗Peptide ratio significantly greater than one (p ≤ 0.05). The peptide-precursor protein was shown after each peptide sequence. Proteins which generated more than one peptide were identified with unique ID in parentheses.