PTK2-associated gene signature could predict the prognosis of IPF.

Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disease with a poor prognosis. Current/available clinical prediction tools have limited sensitivity and accuracy when evaluating clinical outcomes of IPF. Research has shown that focal adhesion kinase (FAK), produced by the protein tyrosine kinase 2 (PTK2) gene, is crucial in IPF development. FAK activation is a characteristic of lesional fibroblasts; Thus, FAK may be a valuable therapeutic target or prognostic biomarker for IPF. This study aimed to create a gene signature based on PTK2-associated genes and microarray data from blood cells to predict disease prognosis in patients with IPF. PTK2 levels were found to be higher in lung tissues of IPF patients compared to healthy controls, and PTK2 inhibitor Defactinib was found to reduce TGFß-induced FAK activation and increase α-smooth muscle actin. Although the blood PTK2 levels were higher in IPF patients, blood PTK level alone could not predict IPF prognosis. From 196 PTK2-associated genes, 11 genes were prioritized to create a gene signature (PTK2 molecular signature) and a risk score system using univariate and multivariate Cox regression analysis. Patients were divided into high-risk and low-risk groups using PTK2 molecular signature. Patients in the high-risk group experienced decreased survival rates compared to patients in the low-risk group across all discovery and validation cohorts. Further functional enrichment and immune cell proportion analyses revealed that the PTK2 molecular signature strongly reflected the activation levels of immune pathways and immune cells. These findings suggested that PTK2 is a molecular target of IPF and the PTK2 molecular signature is an effective IPF prognostic biomarker.

Carbon nanotube stimulation of human mononuclear cells to model granulomatous inflammation.

OBJECTIVES: Sarcoidosis is a multisystem inflammatory granulomatous disease of unknown etiology. The disease most often affects the lung and leads to death in 5% of patients. Patients who die often succumb due to progressive fibrotic lung disease. Translational research in sarcoidosis is significantly limited by a paucity of available experimental models. Carbon nanotubes are released into the environment during fuel combustion, manufacturing, and natural fires. Exposed individuals are at risk for cancer, lung inflammation and other chronic pulmonary disorders, including diseases resembling sarcoidosis and pulmonary fibrosis. In this study, we developed and characterized an in vitro experimental model relevant to sarcoidosis using human peripheral blood mononuclear cells (PBMCs) exposed to multiwalled carbon nanotubes (MWCNTs). METHODS: MWCNT-exposed PBMCs were cultured and analyzed by Giemsa staining, immunohistochemistry (IHC) and RNA-seq analysis on days 1 and 7. Normalization and differential expression were calculated using DESeq2, Limma and edgeR methods from Bioconductor (adjP, log2Fold change and rawP). RESULTS: MWCNT stimulation of PBMCs from healthy subjects leads to the formation of granuloma-like cell clusters and stereotypical inflammatory cytokine secretion. PBMC transcriptomic analysis demonstrated activation of defense- and inflammation-related pathways, including the Jak-Stat pathway and TNF signaling pathway. CONCLUSIONS: This model is unique, as cell clustering is seen in the absence of specific antigenic stimulation (e.g., mycobacterial) or the addition of exogenous cytokines. Modeling with PBMCs provides a platform for precision medicine and evaluation of future therapies for granulomatous and fibrotic lung diseases.