Innate immune response to homologous rotavirus infection in the small intestinal villous epithelium at single-cell resolution

Adrish Sen, Michael E. Rothenberg, Gourab Mukherjee, Ningguo Feng, Tomer Kalisky, Nitya Nair, Iain M. Johnstone, Michael F. Clarke, Harry B. Greenberg

Research output: Contribution to journalArticlepeer-review

71 Scopus citations


“Bulk” measurements of antiviral innate immune responses from pooled cells yield averaged signals and do not reveal underlying signaling heterogeneity in infected and bystander single cells. We examined such heterogeneity in the small intestine during rotavirus (RV) infection. Murine RV EW robustly activated type I IFNs and several antiviral genes (IFN-stimulated genes) in the intestine by bulk analysis, the source of induced IFNs primarily being hematopoietic cells. Flow cytometry and microfluidics-based single-cell multiplex RT-PCR allowed dissection of IFN responses in single RV-infected and bystander intestinal epithelial cells (IECs). EW replicates in IEC subsets differing in their basal type I IFN transcription and induces IRF3-dependent and IRF3-augmented transcription, but not NF-κB–dependent or type I IFN transcripts. Bystander cells did not display enhanced type I IFN transcription but had elevated levels of certain IFN-stimulated genes, presumably in response to exogenous IFNs secreted from immune cells. Comparison of IRF3 and NF-κB induction in STAT1/ mice revealed that murine but not simian RRV mediated accumulation of IkB-α protein and decreased transcription of NF-κB–dependent genes. RRV replication was significantly rescued in IFN types I and II, as well as STAT1 (IFN types I, II, and III) deficient mice in contrast to EW, which was only modestly sensitive to IFNs I and II. Resolution of “averaged” innate immune responses in single IECs thus revealed unexpected heterogeneity in both the induction and subversion of early host antiviral immunity, which modulated host range.

Original languageEnglish
Pages (from-to)20667-20672
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number50
StatePublished - 11 Dec 2012
Externally publishedYes

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© 2017, National Academy of Sciences. All rights reserved.


  • IRF3 signaling
  • Innate immunity
  • Interferon and antiviral response
  • NF-κB signaling
  • Single-cell analysis


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