RNA sequencing of chronic and acute coxsackievirus B3 (CVB3) infection

The goal of this study was to examine gene expression changes associated with CVB3 infection in cell culture. Induced pluripotent stem cell (iPSC)-derived cardiomyocytes and AC16 cells were used to study acute infection. AC16 cells expressing low levels of CVB3 RNA were used to study chronic infection. Overall design: iPSC-derived cardiomyocytes (iCell Cardiomyocytes²) were differentiated for two or four days before infection with wildype CVB3 (MOI 10 for 8 hours) or encapsidation-deficient CVB3 (VP4 A67G - MOI of 3 for 16 hours). AC16 cells with ectopic CXADR overexpression (AC16-CAR) were infected with wildype CVB3 (MOI 10 for 8 hours) or encapsidation-deficient CVB3 (VP4 A67G - MOI of 3 for 16 hours). The uninfected AC16-CAR cell RNA-seq is in GSE155312. AC16 cells were stably transfected with encapsidation-deficient pSLIK CVB3 (VP4 A67G) under the control of a tetracycline-inducible promoter that permits only leaky expression in the absence of tetracycline. 12 clones were then isolated. 9 of the CVB3+ AC16 clones were genetically perturbed with constitutively active MKK6 (MKK6-EE), constitutively active IKK2 (IKK2-EE), or degradation resistant I?Ba (I?Ba-SR) or pharmacologically perturbed using BIRB796 (p38 inhibitor).