IFN-I and CD8 T cells increase intestinal barrier permeability after chronic viral infection

Intestinal barrier leakage constitutes a potential therapeutic target for many inflammatory diseases and represents a disease progression marker during chronic viral infections. The causes of altered gut barrier remain, however, mostly unknown. By using murine infection with lymphocytic choriomeningitis virus we demonstrated that, in contrast to an acute viral strain, a persistent viral isolate led to long-term viral replication in hematopoietic and mesenchymal, but not epithelial (IEC), cells in the intestine. Viral persistence drove sustained intestinal epithelial barrier leakage, which was characterized by increased paracellular flux of small molecules and was associated with enhanced colitis susceptibility. IFN-I signaling caused tight junction dysregulation in IEC, promoted gut microbiome shifts and enhanced intestinal CD8 T cell responses. Notably, both IFN-I receptor blockade and CD8 T cell depletion prevented infection-induced barrier leakage. Our study demonstrated that infection with a virus that persistently replicated in intestinal mucosa increased epithelial barrier permeability, and revealed IFN-I and CD8 T cells as causative factors of intestinal leakage during chronic infections. 6 to 10 week old C57BL/6 female mice were left uninfected or infected with 2x10^6 pfu of LCMV ARM or LCMV Cl13 intravenously. In a different set of experiments, mice were infected with 2x10^6 pfu of LCMV Cl13 and intraperitoneally injected with IFNAR neutralizing antibody (MAR1-5A3; BioXCell) or mouse IgG1 isotype control (MOPC-21; BioXcell) on days -1 and 0 p.i. (500 µg/mouse) as well as on days 2, 4 and 6 p.i. (250 µg/mouse) with Cl13. For both experimental set ups, intestinal epithelial cells (IEC) from the small intestine were obtained (from pools of 3 mice per group) after FACS sorting based on a CD45-EpCAM+ gate at day 9 post-infection. We performed 3 experimental repeats with uninfected, LCMV ARM-infected and LCMV Cl13-infected mice where the average IEC purity was 96.4%±4.4, and 2 experimental repeats with LCMV Cl13-infected mice treated with isotype or IFNAR neutralizing antibody where the average IEC purity was 96.5%±3.2. Total RNA was extracted from 50,000 IEC and downstream processing was performed by the UCSD Institute for Genomic Medicine. mRNA stranded libraries were constructed by using TruSeq RNA Library Prep Kit v2 (Illumina) followed by single-end sequencing of 75 base-pair fragments with a HiSeq 4000 (Illumina). Raw sequencing files were processed with CASAVA 1.8.2 (Illumina) to generate .fastq files.