BALF gene expression profiling reveals innate immune activation bias in persistent post-COVID-19 ILD

Survivors of COVID-19 can experience long-term lung complications (pulmonary sequelae), but the underlying mechanisms remain unclear. While most patients with major COVID-19 lung injury eventually recover essentially completely, some experience significant residual damage. To investigate the underlying differences, we analyzed, using bronchoalveolar lavage fluid (BALF), the alveolar immune cell compartments of a group of patients with post-COVID-19 interstitial lung disease (ILD) six months after acute COVID-19. Patients were categorized into two groups, based on High-Resolution Computed Tomography (HRCT) evaluation a year later: those with persistent HRCT abnormalities compatible with fibrosis (persistent post-COVID-19 ILD, n=6) and those with resolved lung lesions (resolved post-COVID-19 ILD, n=13). Additionally, 6 patients with pre-existing ILD were included in the study, after recovery from COVID-19. Bulk RNA transcriptomics analyses of BALF cells revealed pathways of neutrophil and monocyte chemotaxis to be enriched in patients with persistent HRCT abnormalities, consistent with increased monocyte-like cell recruitment in the lungs. Furthermore, increased gene expression of markers of pro-fibrotic macrophages/monocytes, such as SPP1 and pro-inflammatory cytokines, such as Il-1b, was also observed. Conversely, patients with resolved post-COVID-19 ILD displayed BALF cell gene expression signatures indicative of T-cell activation. Additionally, BALF gene expression patterns associated with pro-fibrotic macrophage activation, neutrophil chemotaxis and downregulation of T-cell activation were also observed in patients with pre-existing fibrotic ILD following COVID-19. These findings suggest that immune response imbalance leading to prolonged activation of innate immunity and subdued adaptive immune responses may be associated with persistent post-COVID-19 ILD.