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Series GSE188122 Query DataSets for GSE188122
Status Public on May 15, 2023
Title Influenza defective interfering virus promotes multiciliated cell differentiation and reduces the inflammatory response in mice
Organisms Mus musculus; Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Experiment type Expression profiling by high throughput sequencing
Other
Non-coding RNA profiling by high throughput sequencing
Summary Influenza defective interfering (DI) viruses have long been considered promising antiviral candidates because of their ability to interfere with replication-competent viruses and to induce antiviral immunity. However, the mechanisms underlying DI-mediated antiviral immunity have not been extensively explored. Here, we demonstrated interferon (IFN) independent protection conferred by influenza DI virus against homologous virus infection in mice deficient in type I and III IFN signaling. By integrating transcriptional and post-transcriptional regulatory data we identified unique host signatures in response to DI co-infection. DI-treated mice exhibited reduced viral transcription, less intense inflammatory and innate immune responses, and primed multiciliated cell differentiation in their lungs at an early stage of infection, even in the absence of type I or III IFNs. This increased multiciliogenesis could also be detected at the protein level by immunofluorescence staining of lung tissue from DI-treated mice. Overall, our study provides mechanistic insight into the protection mediated by DIs, implying a unifying theme involving inflammation and multiciliogenesis in maintaining respiratory homeostasis, and reveals their IFN-independent antiviral activity.
 
Overall design The firs Dataset consists of a bulk RNA-seq dataset containing 36 libraries generated with NEBNext Ultra II RNA library prep kit and poly(A) mRNA magnetic isolation module, a miRNA-seq dataset containing 36 libraries generated with QIAseq miRNA library kit, and a viral genome sequencing dataset containing 52 libraries generated from multi-segment reverse-transcription PCR (M-RT-PCR) products followed by library preparation with Nextera XT DNA library prep kit. This second dataset consists of 31 libraries generated with NEBNext Ultra II RNA library prep kit and poly(A) mRNA magnetic isolation module from the first in vivo study presented in the manuscript.
 
Contributor(s) Wang C, Honce R, Salvatore M, Chow D, Randazzo D, Yang J, Twells NM, Mahal LK, Schultz-Cherry S, Ghedin E
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Submission date Nov 04, 2021
Last update date May 15, 2023
Contact name Matthew Chung
E-mail(s) matt.chung@nih.gov
Organization name NIAID (National Institute of Allergy and Infectious Diseases)
Street address 50 South Dr
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platforms (3)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL30927 Illumina NextSeq 500 (Influenza A virus (A/Puerto Rico/8/1934(H1N1)))
GPL30928 Illumina NextSeq 500 (Influenza A virus (A/Puerto Rico/8/1934(H1N1)); Mus musculus)
Samples (155)
GSM5670771 RNA-seq dataset: mock-infected IFNAR-/- mouse #1
GSM5670772 RNA-seq dataset: mock-infected IFNAR-/- mouse #2
GSM5670773 RNA-seq dataset: mock-infected IFNAR-/- mouse #3
Relations
BioProject PRJNA777796
SRA SRP344536

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE188122_DIinfKOmice_mRNAseq_counts.txt.gz 1.7 Mb (ftp)(http) TXT
GSE188122_DIinfKOmice_miRNAseq_counts.txt.gz 82.4 Kb (ftp)(http) TXT
GSE188122_DIinfmice_mRNAseq_processed_data_matrix.txt.gz 1.3 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record
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