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Fig. 4 | Journal of Translational Medicine

Fig. 4

From: Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products

Fig. 4

Effect of viral vector integration into the gene promoter and untranslated region. A, B Volcano plots show the differentially expressed genes between control non-transduced cells vs. CAR T-cells transduced for lentiviral (A) and γ-retroviral vectors (B). The number of DEGs were indicated in the volcano plot. Significantly downregulated genes are highlighted in blue (A) or green (B) and upregulated genes are highlighted in red (A) or brown (B). Differential expression analysis was performed using the built-in function from limma package in Rstudio with custom scripts. Wald’s test was used to calculate the adjusted p-value or significance that a gene is differentially expressed. Genes with | FoldChange | >=2 and adj.P.value < 0.05 were considered significantly expressed. C The number of DEGs and integration events occurring at promoter and untranslated region of these DEGs is summarized. DEGs indicates differentially expressed genes; IS events indicates integration site events; and utr, untranslated region. NA means no value is available in the p-value column. Percentage = sequencing reads mapped on each feature/sequencing reads mapped on genome. The boxplots show the expression of 34 genes with integration events at untranslated region (D) and promoter (E) and whose expression differed in control non-transduced vs. transduced CAR T-cells

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