The immune landscape in SSc-ILD and tow genes are potential risk factors for pulmonary fibrosis

Abstract Background Interstitial lung disease (ILD) is the most common cause of death in patients with systemic sclerosis (SSc-ILD) and immune cells are crucial in the onset and development of ILD. The aim of this study was to compare the molecular fingerprint of lung tissue from patients with SSc-ILD with that of lung tissue from normal donors, and to determine the immune landscape according to their gene expression profiles. Methods Two gene expression omnibus (GEO) datasets were merged as a test set, and another dataset was selected as the validation set. Lung biopsies and alveolar macrophages from 2 SSc-ILD patients and 2 healthy controls were obtained for further validation. Machine-learning algorithms were used to filter and identify potential diagnostic biomarkers of SSc-ILD in the test set. These biomarkers were examined in a validation dataset and further validated by quantitative real-time PCR and western blotting. CIBERSORT was used to quantify the proportions of immune cells in lung samples from SSc-ILD patients and healthy controls. The link between potential biomarkers and immune infiltration cells was established using a logistic regression approach. Results CDH3 upregulated and TNFAIP3 downregulated in SSc-ILD, and their encoded proteins (Cadherin 3 and TNFAIP3, respectively) also showed the same trend of changes. TNFAIP3 protein in alveolar macrophages derived from the alveolar lavage fluid of patients with SSc-ILD was decreased too. The proportion of M2 macrophages in SSc-ILD was significantly higher. TNFAIP3 was negatively correlated with M2 macrophages. CDH3 was positively correlated with plasma cells, M0 macrophages, and resting mast cells, and negatively correlated with M1 macrophages, resting NK cells, activated mast cells, eosinophils, and monocytes. Conclusions TNFAIP3 and CDH3 are two potential factors for pulmonary fibrosis. In particular, the lower expression of TNFAIP3 in alveolar macrophages of SSc-ILD patients may be linked to the maintenance of the profibrotic phenotype of macrophages. This research offers a fresh viewpoint on how SSc-ILD manifests itself at the transcriptomic and immune cell level, and may be useful in future therapeutic strategies.