Transcriptomic analysis of primary nasal epithelial cells reveals altered interferon signalling in preterm birth survivors at one year of age

Denby J Evans; Jessica K Hillas; Thomas Iosifidis; Shannon J Simpson; Anthony Kicic; Patricia Agudelo-Romero

doi:10.3389/fcell.2024.1399005

Transcriptomic analysis of primary nasal epithelial cells reveals altered interferon signalling in preterm birth survivors at one year of age

Front Cell Dev Biol. 2024 Jul 24:12:1399005. doi: 10.3389/fcell.2024.1399005. eCollection 2024.

Authors

Denby J Evans^{1

2

3}, Jessica K Hillas¹, Thomas Iosifidis^{1

3

4}, Shannon J Simpson^{1

5}, Anthony Kicic^{1

3

4

6}, Patricia Agudelo-Romero^{1

7

8}

Affiliations

¹ Wal-yan Respiratory Research Centre, Telethon Kids Institute, Nedlands, WA, Australia.
² Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute and The University of Western Australia, Crawley, WA, Australia.
³ School of Population Health, Curtin University, Bentley, WA, Australia.
⁴ Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia and Harry Perkins Institute of Medical Research, Nedlands, WA, Australia.
⁵ School of Allied Health, Curtin University, Bentley, WA, Australia.
⁶ Department of Respiratory and Sleep Medicine, Perth Children's Hospital, Nedlands, WA, Australia.
⁷ School of Molecular Science, University of Western Australia, Nedlands, WA, Australia.
⁸ European Virus Bioinformatics Centre, Jena, Thuringia, Germany.

Abstract

Introduction: Many survivors of preterm birth (<37 weeks gestation) have lifelong respiratory deficits, the drivers of which remain unknown. Influencers of pathophysiological outcomes are often detectable at the gene level and pinpointing these differences can help guide targeted research and interventions. This study provides the first transcriptomic analysis of primary nasal airway epithelial cells in survivors of preterm birth at approximately 1 year of age. Methods: Nasal airway epithelial brushings were collected, and primary cell cultures established from term (>37 weeks gestation) and very preterm participants (≤32 weeks gestation). Ex vivo RNA was collected from brushings with sufficient cell numbers and in vitro RNA was extracted from cultured cells, with bulk RNA sequencing performed on both the sample types. Differential gene expression was assessed using the limma-trend pipeline and pathway enrichment identified using Reactome and GO analysis. To corroborate gene expression data, cytokine concentrations were measured in cell culture supernatant. Results: Transcriptomic analysis to compare term and preterm cells revealed 2,321 genes differentially expressed in ex vivo samples and 865 genes differentially expressed in cultured basal cell samples. Over one third of differentially expressed genes were related to host immunity, with interferon signalling pathways dominating the pathway enrichment analysis and IRF1 identified as a hub gene. Corroboration of disrupted interferon release showed that concentrations of IFN-α2 were below measurable limits in term samples but elevated in preterm samples [19.4 (76.7) pg/ml/µg protein, p = 0.03]. IFN-γ production was significantly higher in preterm samples [3.3 (1.5) vs. 9.4 (17.7) pg/ml/µg protein; p = 0.01] as was IFN-β [7.8 (2.5) vs. 13.6 (19.5) pg/ml/µg protein, p = 0.01]. Conclusion: Host immunity may be compromised in the preterm nasal airway epithelium in early life. Altered immune responses may lead to cycles of repeated infections, causing persistent inflammation and tissue damage which can have significant impacts on long-term respiratory function.

Keywords: RNA seq analysis; airway epithelial; bronchopulmonary dysplasia; interferon; preterm.

Grants and funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This work was supported by Perpetual IMPACT Philanthropy Grant: IPAP2017/1355 and a Wal-yan Respiratory Research Centre Inspiration Award 2021–2022. DE received PhD scholarship funding from the Australian Government Research Training Program, the Wesfarmers Centre of Vaccines and Infectious Diseases and the Stan and Jean Perron Foundation. AK is a Rothwell Family Fellow. TI is a Future Health, Research and Innovation Fund (FHRIF) Innovation Fellow.