Characterising the Transcriptomic Response to Interferon and Infection in European Domestic Ferret Respiratory Tissues Using Long‐Read RNA Sequencing

TL;DR

This study uses long-read RNA sequencing to explore how ferrets respond to interferon and influenza virus, identifying new genes and changes in RNA structure.

Contribution

The study identifies novel interferon-stimulated genes and transcripts in ferrets, along with poly(A) tail elongation in key pathways.

Findings

A panel of ferret genes orthologous to human ISGs was identified as upregulated by IFN-α and IAV infection.

Novel IFN-stimulated genes and transcripts were discovered in ferret respiratory tissues.

Poly(A) tail elongation was observed in ribosome and Coronavirus Disease-19 pathways following IFN-α treatment.

Abstract

The European domestic ferret (
Mustela putorius furo
) is considered the gold standard small animal model for studying human and avian influenza virus infections. However, experimental characterisation of the transcriptomic response to interferon (IFN) stimulation and/or influenza virus infection has been limited, particularly in defining the induction of interferon‐stimulated genes (ISGs), with most being computationally predicted. In this study, we present a comprehensive transcriptome‐wide assessment of the ferret transcriptome following IFN‐α treatment of a ferret lung (FRL) cell line, as well as in nasal turbinates from influenza A virus (IAV)‐infected ferrets using long‐read RNA sequencing. We have identified a panel of ferret genes orthologous to human ISGs that are upregulated both in response to IFN‐α stimulation in vitro and IAV infection in vivo. We have also identified novel IFN‐stimulated genes and transcripts. Furthermore, we observed elongation of the poly(A) tails of genes in the ribosome and Coronavirus Disease‐19 pathways in response to IFN‐α treatment in vitro, suggesting a relationship between poly(A) elongation and the antiviral responses of the host. These results illuminate the dynamics of the transcriptional innate immune response of the domestic ferret and provide an important resource for better utilising ferrets as a small animal model to study influenza virus infections.

We utilised long‐read Nanopore sequencing to characterise the transcriptome of ferret cell lines stimulated with IFN‐α as well as nasal turbinates from ferrets infected with influenza A virus. We identified novel genes and isoforms and observed elongation of poly(A) tails in the ribosome and Coronavirus Disease‐19 pathways in response to IFN‐α treatment.

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