Coxsackievirus B Persistence Modifies the Proteome and the Secretome of Pancreatic Ductal Cells

Figures

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  Figure 1. Establishment of Persistent CVB1 Infections in PANC-1 Cells (A) Both CVB1 strains (ATCC and 10796) were replicating in PANC-1 cells for nearly 1 year. The amount of viral RNA was measured by RT-qPCR, and the results were converted into genome copy numbers/sample (140 μL). Sample collection for proteomics was performed 300, 315, and 322 days post-infection, as indicated in the figure. (B) Viral capsid protein VP1 (brown) was detected by IHC at 362 days post-infection. Scale bar, 25 μm.

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  Figure 2. Persistent CVB1 Infection Results in Changes in Intracellular Protein Expression and Protein Secretion (A) Numbers of differentially expressed proteins in cells with persistent CVB1 ATCC and 10796 infection. (B) Heatmap of Z-score normalized data for the 605 proteins with similar responses to persistent CVB1 infection with both virus strains in the PANC-1 cells. (C) Numbers of proteins whose secretion is significantly changed during persistent CVB1 ATCC and 10796 infections. (D) Heatmap of Z-score normalized data showing the 363 proteins whose secretion is changed similarly from cells with persistent CVB1 ATCC and 10796 infections.

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  Figure 3. Both Persistent CVB1 Infections Modulate the Expression of Multiple Host Cell Proteins (A) eIF4G is cleaved in PANC-1 cells with persistent CVB1 ATCC and 10796 infection. Western blot analyses were performed for two biological replicates from each condition. (B) IPA canonical pathways that are significantly enriched among the upregulated proteins in both persistent CVB1 infection models. (C) Several nuclear complex proteins are downregulated during persistent CVB1 infection. Nuclear pore complex proteins were assigned based on Knockenhauer and Schwartz (2016). ∗FDR < 0.05 and |Fold change| ≥ 1.5. (D) Raw intensities of three CXADR peptides in the PANC-1 cells. For each sample, median intensity of three technical replicates is shown. (E) IPA canonical pathways that are significantly enriched among the downregulated proteins in both persistent CVB1 infection models. FDR, false discovery rate.

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  Figure 4. Mitochondrial Networks in Non-infected PANC-1 Cells and Cells with Persistent CVB1 Infections Cell imaging analysis was carried out on three biological replicates of CVB1 ATCC persistent infection model and four biological replicates of CVB1 10796 persistent infection model and non-infected control cells. (A) Mitochondrial network is visualized in living cells using MitoTracker staining. Representative examples of cells with persistent CVB1 ATCC and 10796 infection and non-infected control cells are shown. (B) Cells were grouped into four different categories based on the morphology of their mitochondrial network. The data are presented as mean ± SD. Total numbers of cells used for the grouping: control N = 784, CVB1 ATCC N = 546, CVB1 10796 N = 709.

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  Figure 5. Persistent CVB1 Infection Influences the Secretion of Several Proteins (A) Secretion of exosome marker proteins CD9, CD63, and CD81 from PANC-1 cells. For each sample, the median intensity of three technical replicates is shown. Statistically significant differences are marked with ∗. (B and C) Persistent CVB1 ATCC (B) and 10796 (C) infection induced changes in the levels of extended granin family proteins, CPE and peptidylglycine α-amidating monooxygenase (PAM) in the cell culture supernatants. (D–F) RT-qPCR analyses of CHGB (D), SCG3 (E), and CPE (F) in PANC-1 cells. The measurements were performed for the three biological replicates from each condition, and results are shown as Delta Ct ± SD. Primer sequences are presented in Table S7.

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  Figure 6. Persistent CVB1 Infections Influence the Expression of Several Proteins Associated with Beta-Cell Differentiation, Growth, and Survival Persistent CVB1 infection induced changes in the expression levels of (A) ALDH1A3 (cell lysates), (B) SPARC (cell culture supernatants), (C) SUSD2 (cell lysates), and (D) HSPG2 (cell lysates). For each sample, median intensity of the three technical replicates is shown. Statistically significant differences are marked with ∗. ND, not detected.

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  Figure 7. Antiviral Immune Responses during Persistent CVB1 Infections (A) Changes in IFNL1 secretion from PANC-1 cells. For each sample, median intensity of three technical replicates is shown. ND, not detected. (B) IFNL1 mRNA expression in PANC-1 cells. The measurements were performed for the three biological replicates from each condition. Primer sequences are presented in Table S7. (C-D) Differentially expressed IFNL1 downstream target proteins in cells with persistent (C) CVB1 ATCC and (D) CVB1 10796 infection based on IPA analysis. Red, significantly upregulated; blue, significantly downregulated; white node with red lines, detected only in the cells with persistent CVB1 ATCC infection; white node with blue lines, not detected in the cells with persistent CVB1 10796 infection. (E) IFIH1 expression in PANC-1 cells based on in situ hybridization. TP1, 102 days post-infection; TP2, 228 days post-infection. Scale bar, 50 μm. In each bright-field image, fluorescent channel from the bright-field image is condensed into corner.