Journal: iScience

Article Title: Persistent coxsackievirus B1 infection triggers extensive changes in the transcriptome of human pancreatic ductal cells

doi: 10.1016/j.isci.2021.103653

Figure Lengend Snippet: Persistent carrier-state-type CVB1 infection revealed changes in the transcriptome of pancreatic cell line (A and B) Detection of viral capsid protein VP1 in non-infected PANC-1 cells and cells with persistent CVB1-ATCC and 10796 infections by immunoblotting at 300, 315, and 322 days post infection with β-Actin as loading control (M, molecular weight marker) and (B) by immunofluorescence. Representative cell images show VP1 protein in red and nuclei in blue (DAPI); scale bar, 50 μm. (C) Heatmap of Z score standardized expression for the 3,936 differentially expressed genes in the persistent CVB1 infection models with false discovery rate (FDR) of <0.05 and fold-change (FC) ≥2. (D) Venn diagram demonstrating the number of overlapping up- and downregulated genes in cells with persistent CVB1-ATCC and 10796 infections. (E and F) The log2 transformed counts per million (CPM) expression of CXADR and CD55 are shown as mean ± SD for three biological replicates (∗ FDR <0.05).

Article Snippet: Two carrier-state-type persistent CVB1 infection models were established in human pancreatic ductal cell lines (PANC-1) with two virus strains, the ATCC strain Conn-5 and the wild-type strain 10796, as reported recently ( ).

Techniques: Infection, Western Blot, Control, Molecular Weight, Marker, Immunofluorescence, Expressing, Transformation Assay

Journal: iScience

Article Title: Persistent coxsackievirus B1 infection triggers extensive changes in the transcriptome of human pancreatic ductal cells

doi: 10.1016/j.isci.2021.103653

Figure Lengend Snippet: Persistent CVB1 infection modulates innate immune response (A) Significantly enriched GO biological processes, based on the DAVID database tool, are shown with FDR <0.05 for the upregulated differentially expressed genes in the persistent CVB1-ATCC infection model and the downregulated differentially expressed genes in persistent CVB1-10796 infection. (B) A signature of 25 genes with opposite expression pattern between the two CVB1 strains reveals an interconnected cluster with central role in antiviral immune response. Protein-protein interactions were downloaded from the STRING database (only high-confidence interactions with a combined interaction score of ≥0.7 are included). The color of the nodes in the network represents the expression of the genes as logFC: downregulation (blue) or upregulation (red) of persistent CVB1-10796 (outer circle) and CVB1-ATCC (inner circle) infections. (C and D) Differently expressed PARP9 and IFNL1 downstream target genes in cells with persistent CVB1-ATCC (C) and CVB1-10796 infection (D) are depicted based on IPA analysis (red, significantly upregulated; blue, significantly downregulated). (E) The log 2 transformed CPM expression of proinflammatory cytokines IL32, IL18, CCL5, IL34, CSF1, and CXCL5 in both persistent CVB1 infection models are shown as mean ± SD for three biological replicates (∗ FDR <0.05; ns, not significant).

Article Snippet: Two carrier-state-type persistent CVB1 infection models were established in human pancreatic ductal cell lines (PANC-1) with two virus strains, the ATCC strain Conn-5 and the wild-type strain 10796, as reported recently ( ).

Techniques: Infection, Expressing, Protein-Protein interactions, Transformation Assay

Journal: iScience

Article Title: Persistent coxsackievirus B1 infection triggers extensive changes in the transcriptome of human pancreatic ductal cells

doi: 10.1016/j.isci.2021.103653

Figure Lengend Snippet: Genes associated with beta cell communication and function are strongly affected in persistent CVB1 infection (A and B) Significantly enriched GO biological processes, based on the DAVID database tool, are shown with FDR <0.05 for the 2,460 and 2,606 differentially expressed genes in persistent CVB1-ATCC and 10796 infection models, respectively. (C) Persistent CVB1 infections induced changes in the gene expression of GJA1, CADM1, SPARC, CLDNs, EPHAs, and EPHBs (red color means upregulated, blue downregulated, and gray non-differentially expressed). (D) Common downregulated genes in both persistent CVB1 infection models form an interconnected cluster related to secretion. All genes in the network are included in the gene ontology term GO:0030141∼secretory granule and/or in the UniProt keyword KW-0964∼secretory. Network nodes included in the GO:0030141 term are indicated with a green inner color. (E and F) The log2 transformed CPM expression of TGFBI (E), IGFBP1-3 (F) in both persistent CVB1 infection models are shown as mean ± SD for three biological replicates (∗ FDR <0.05; ND, not detected).

Article Snippet: Two carrier-state-type persistent CVB1 infection models were established in human pancreatic ductal cell lines (PANC-1) with two virus strains, the ATCC strain Conn-5 and the wild-type strain 10796, as reported recently ( ).

Techniques: Infection, Gene Expression, Transformation Assay, Expressing

Journal: iScience

Article Title: Persistent coxsackievirus B1 infection triggers extensive changes in the transcriptome of human pancreatic ductal cells

doi: 10.1016/j.isci.2021.103653

Figure Lengend Snippet: Persistent CVB1 infection impairs the expression of lysosome genes and autophagy-related SNAREs (A) Heatmap of Z score standardized expression of differentially expressed genes in the cellular components GO: 0005764 (lysosome) of persistent CVB1-10796 infection. (B) The log2 transformed CPM expression of VAMP7 and VAMP8 in both persistent CVB1 infection models are shown as mean ± SD for three biological replicates (∗ FDR <0.05; ns, not significant). (C and D) SNAP29 gene expression was validated by real-time qPCR (C) and immunoblotting, with β-Actin as a loading control. Quantification of SNAP29 protein was normalized to loading control (D). (E and F) Autophagy-related SNARE proteins (STX7, STX17, and YKT6) (E) and LC3B expression (F) was analyzed in both CVB1 infection models by immunoblotting, with β-Actin as a loading control (M, molecular weight marker). Band intensities of target proteins were normalized to loading control. (G) For autophagic flux analysis, CVB1-infected PANC-1 cells were treated for 2 h with bafilomycin A1 (BafA1) and immunofluorescence stained with anti-LC3 (green) and DAPI (blue). The cells were analyzed with Nikon A1R + laser scanning confocal microscope; scale bar, 50 μm (representative images). (H) Immunofluorescence images were analyzed using ImageJ Fiji and the total area of LC3 puncta per cell was calculated using 3D object counter analysis tool; (n = 30 cells per group). Data are represented as mean ± SD from three biological replicates; statistical analysis: (C, D, E, F, and H) Student's t test (unpaired, two-tailed, unequal variance), ns, not significant; ∗p < 0.05; ∗∗p < 0.01; ∗∗∗∗p < 0.0001.

Article Snippet: Two carrier-state-type persistent CVB1 infection models were established in human pancreatic ductal cell lines (PANC-1) with two virus strains, the ATCC strain Conn-5 and the wild-type strain 10796, as reported recently ( ).

Techniques: Infection, Expressing, Transformation Assay, Gene Expression, Western Blot, Control, Molecular Weight, Marker, Immunofluorescence, Staining, Microscopy, Two Tailed Test

Journal: iScience

Article Title: Persistent coxsackievirus B1 infection triggers extensive changes in the transcriptome of human pancreatic ductal cells

doi: 10.1016/j.isci.2021.103653

Figure Lengend Snippet:

Article Snippet: Two carrier-state-type persistent CVB1 infection models were established in human pancreatic ductal cell lines (PANC-1) with two virus strains, the ATCC strain Conn-5 and the wild-type strain 10796, as reported recently ( ).

Techniques: Immunofluorescence, Virus, Control, Recombinant, Reverse Transcription, Gene Expression, Software, Transformation Assay