Exploring the host response in infected lung organoids using NanoString technology: A statistical analysis of gene...

Area of Science:

• Virology and Immunology
• Respiratory Tract Infections
• Gene Expression Analysis

Background:

• Human airway physiology is complex and challenging to model in vitro.
• Understanding differential gene expression in response to respiratory viruses is crucial for developing effective treatments.
• Existing models may not fully capture the dynamic interplay between host and virus at the cellular level.

Purpose of the Study:

• To investigate the host gene expression response to Influenza A virus (IAV), Human metapneumovirus (MPV), and Parainfluenza virus type 3 (PIV3) using a 3D airway organ tissue equivalent (OTE) model.
• To analyze gene expression profiles at 24 and 72 hours post-infection.
• To introduce and utilize a novel Magnitude-Altitude Score (MAS) algorithm for robust identification of biologically relevant differentially expressed genes.

Main Methods:

• Development and utilization of a three-dimensional airway organ tissue equivalent (OTE) model at an air-liquid interface (ALI).
• Infection of OTE models with IAV, MPV, and PIV3, with appropriate control conditions.
• Gene expression profiling of 773 specific genes using the NanoString platform at 24 and 72 hours post-infection.
• Application of the novel Magnitude-Altitude Score (MAS) algorithm to integrate fold change and adjusted p-values for gene identification.

Main Results:

• IAV infection induced a strong interferon-stimulated gene (ISG) response at 24 hours, which persisted at 72 hours.
• MPV infection elicited a dual innate and adaptive immune response at 24 hours, shifting towards IL17A and signaling genes by 72 hours.
• PIV3 infection triggered an ISG-dominant response with immune cell recruitment and inflammation modulation at 24 hours, maintaining an interferon-centric profile at 72 hours.
• The MAS algorithm successfully identified biologically significant differentially expressed genes, revealing distinct host responses to each virus.

Conclusions:

• Interferon-stimulated genes (ISGs) play a pivotal and universal role in the host's antiviral defense against IAV, MPV, and PIV3.
• Temporal gene expression patterns demonstrate host adaptation and fine-tuning of the immune response over time.
• Distinct host-specific responses were identified for each virus, with IAV showing sustained impact and PIV3 exhibiting a delayed genomic response.