Introduction: Childhood acute wheeze and asthma remain poorly understood at a biological level, contributed to by the multifactorial and complex immune pathways involved. Long non-coding RNA (lncRNA) often act as regulators of biological processes and work closely with other types of RNA, including mRNA. We sought to identify key lncRNA in peripheral blood mononuclear cells (PBMCs) and nasal cells during acute wheeze/asthma, and to elucidate how they interacted in networks with other RNA during these acute respiratory illnesses.
Methods: Utilising our Perth-based paediatric acute wheeze/asthma cohort (Mechanisms of Acute Viral Infection in Children, MAVRIC), we measured gene expression in acute, convalescent and control samples using microarray. Analysis was focused around the paired acute and convalescent PBMC (n = 21 pairs) and nasal swab samples (n = 7 pairs), and the >2,500 lncRNA probes of each dataset, although control and unpaired samples, and mRNA, were incorporated where necessary for specific analyses. Differential gene expression between paired samples was determined using paired linear modelling for microarray (limma). Gene networks on all samples were generated using weighted gene co-expression network analysis (WGCNA), and functional enrichment analysis was undertaken on the lncRNA-mRNA networks using Reactome.
Results: Children with acute wheeze had differentially expressed lncRNA (DE-lncRNA) and mRNA (DE-mRNA) compared to their paired convalescent samples in both PBMCs and nasal cells. In the PBMCs 10 WGCNA modules were identified, with the strongest module correlating with acute wheeze/asthma - compared to convalescence and control - having a negative correlation of r = -0.575 (p <0.001). Co-expression networks were built around five ‘hub’ lncRNA obtained from acute illness-associated modules, including LINC02432 and HEIH. LINC02432 and HEIH were upregulated during acute wheeze/asthma (logFC = 1.60, p<0.001 and logFC = 0.71, p<0.001, respectively). Functional enrichment analysis of PBMC DE-lncRNA and DE-mRNA correlating with each of these two transcripts found similar processes such as interferon signalling, neutrophil degranulation and cytokine signalling to be positively associated and cholesterol metabolic processes to be negatively associated. In the nasal cells, there was one WGCNA module correlating with acute wheeze, and HEIH was identified as the key lncRNA associated with acute wheeze overlapping both the nasal and PBMC datasets.
Conclusions: LncRNA HEIH and LINC02432 were identified as potential hub genes in acute wheeze/asthma pathways of immune cells. Our findings warrant further investigation into lncRNA, especially HEIH and LINC0432, and how they may shape immune responses in acute respiratory exacerbations and chronic asthma.