Poster Presentation CD1-MR1 2024

A single-cell analysis of the role of Mucosal Associated Invariant T cells in influenza A virus infection (#218)

Yuqing Long 1 2 , Xiawei Zhang 1 , Theodoros Kapellos 3 , Paul Klenerman 1 , Timothy SC Hinks 1
  1. University of Oxford, Oxford, OXFORDSHIRE, United Kingdom
  2. Chinese Academy of Medical Sciences Oxford Institute, Oxford, UK
  3. Helmholtz Munich, Comprehensive Pneumology Center (CPC), Institute of Lung Health and Immunity (LHI), Munich, Germany

Introduction: We previously demonstrated TCR-independent MAIT cell protection against severe influenza A virus (IAV) infection in vivo in mice, with upregulation of CD25, CD69 and Granzyme B, mediated at least partially via IFN-γ. To understand how MAIT cells regulate the immune response during virus infection, we performed single cell analysis and spectral flow cytometry on whole lungs from wild-type and MAIT cell deficient mice post IAV infection.

 

Methods: C57BL/6 and MR1-/- mice were infected intranasally with 100 PFU of IAV PR8 strain, and lung tissues analysed at days 0, 3, 5, 7 post-infection. Samples were processed using 3' Chromium 10x and 71,762 cells were Illumina sequenced to 25,000 reads/cell. QC, integration, and clustering were performed by CellRanger mapping to an integrated reference genome which includes both the virus and mouse genome enabling assessment of both infected and bystander cells. To date we analysed pseudobulk expression (Muscat) by cluster, differential gene expression between experimental groups, and gene set enrichment analysis (fgsea) of GO terms, KEGG pathways, Reactome pathways, and the MSigDB Hallmark gene sets, and explored cell communication networks (NicheNet).

 

Results: 1) Genome mapping, detected the virus and revealed it is predominantly present in myeloid cells. 2) A specific subtype of neutrophil emerges during viral infection. 3) Gene expression profile differs between infected and bystander cells within the same cell type. 4) In comparison to C57BL/6 mice, MAIT cell deficient mice exhibited an altered microenvironment and immune responses during viral infection. 5) In MAIT cells the main pathways upregulated were related to antiviral response, response to interferon γ/β, and cytokine-mediated signalling. 6) In the absence of riboflavin-producing bacterial infection viral infection induces a previously-described tissue repair signature peaking at day 3.

 

Conclusions: MAIT cells are activated by viral infection contributing to type-1 IFN-driven antiviral responses and a contemporaneous tissue repair programme.