Fig 1.
Effect of NDV LaSota strain in KKU-055 and KKU-100 CCA cells.
(A) Overview of the experiments conducted to assess the impact of NDV in KKU-055 and KKU-100 CCA cell lines. (B-C) Representative bright-field microscopy images of CCA cells. Cells were cultured for 24 hours in complete media before being infected with a viral dilution of 16 HAU per 10,000 cells. Images depicting KKU-055 (B) and KKU-100 (C) CCA cells at 72 hours after NDV infection.(D-G) Evaluation of cell number after NDV infection. Cells were trypsinized, stained with trypan blue, and counted at 72 hours after infection. Bar graphs show the percentage of total KKU-055 cells (D), total KKU-100 cells (E), live KKU-055 cells (F) and live KKU-100 cells (G) in comparison to the mock controls (* p < 0.05). The data presented were acquired from three experiments, each comprising three replicates within each condition.
Fig 2.
Differential expression and pathway analysis of RNA-seq data in NDV LaSota strain-treated CCA cells.
(A-B) Volcano plots, generated by the Limma-voom tool in the Galaxy-based platform, illustrate the differential expression patterns in KKU-055 (A) and KKU-100 (B) CCA cells at 24 hours after NDV LaSota strain infection. Significantly upregulated and downregulated genes in comparison to mock controls (adjusted p-value < 0.05) are represented by red and blue dots, respectively. (C-D) Heat maps of the differentially expressed genes in KKU-055 (C) and KKU-100 (D) cells after NDV LaSota infection. The range of expression levels is represented by the colors. (E-F) Pathways significantly enriched by hallmark analysis in KKU-055 (E) and KKU-100 (F) cells following NDV LaSota strain exposure.
Fig 3.
Potential key genes associated with oncolytic impact of NDV LaSota strain in CCA cells.
(A) Venn diagram illustrates the number of genes altered in KKU-055 and KKU-100 cells following 24 hours of exposure to NDV LaSota strain. The analysis solely incorporates genes identified in the RNA sequencing results of both cells. (B-D) Hub genes identified based on protein-protein interaction network. The top 10 genes identified and ranked using five methods including node degree, maximal clique centrality (MCC), maximum neighborhood component (MNC), betweenness, and closeness, were selected. The hub genes identified by node degree, MCC, and MNC are shown in the topmost and middle rows. The topmost row displays hub genes identified by all five methods. Hub genes were identified from 3 groups of genes: genes with the same expression pattern in KKU-055 and KKU-100 cells (B), genes exclusively altered in KKU-055 cells (C), and genes exclusively altered in KKU-100 cells (D). (E) Association among 6 hub genes with the same expression pattern in KKU-055 and KKU-100 cells, 8 hub genes exclusively altered in KKU-055 cells, 4 hub genes exclusively altered in KKU-100 cells and 4 genes altered in opposite directions in two CCA cells. (F-I) Gene expression changes compared between NDV LaSota- and mock- treated cells. The bar graph illustrates differential expression of the genes exhibited significant changes in expression: 4 genes altered in opposite directions in two CCA cells (F), 6 hub genes with the same expression pattern in KKU-055 and KKU-100 cells (G), 8 hub genes exclusively altered in KKU-055 cells (H), and 4 hub genes exclusively altered in KKU-100 cells (I).