Characterization of Transcriptional Changes in a Vimentin Knock‐out Mouse Model Following Influenza A Infection Using RNAseq

/Rationale Our group has previously demonstrated that vimentin, an intermediate filament, is required for the assembly and activation of the NLRP3 inflammasome in an infection model of Influenza A virus (IAV). To further investigate the role of vimentin in the response to IAV, our aim was to compare wild‐type and vimentin‐null mice and study changes in specific cell populations of the lung following IAV infection using RNAseq as an unbiased approach to study transcriptional changes. Methods Wild‐type and vimentin‐null 129S mice were infected with 200pfu of Influenza A/WSN/33 virus. Lungs were collected on days 0, 2, 3, 4, and 6 post‐infection (p.i.) and tissue was processed into single‐cell suspension. AM, MoDC, and ATII cells were flow‐sorted and total RNA was subsequently isolated using an RNeasy Plus Mini extraction kit (Qiagen). Following mRNA‐enrichment, libraries were prepared and sequenced using Illumina NextSeq 500. Results RNA sequencing data demonstrated significant differences in gene expression between the wild‐type and vimentin‐null ATII, AM, and MoDC cells post‐IAV infection in three cell sub‐populations of the lung. Differential gene expression analysis and pairwise comparison between wild‐type and vimentin‐null cells identified a significant number of differentially expressed genes between the two groups. The newly identified gene clusters were grouped into multiple GO processes involved in the innate immune response and cellular structure. Conclusions Our RNAseq data demonstrated that following IAV infection, vimentin‐null mice have a strikingly different response compared to the wild‐type animals, which was evident in the alveolar macrophages (AM), monocyte‐derived cells (MoDC), and to a lesser extent in the alveolar type II (ATII) cell subpopulations and their respective differential gene analyses. Support or Funding Information Funding: HL128194 and HL071643