Idiopathic pulmonary fibrosis: current and future directions

Identification of genetic indicators linked to immunological infiltration in idiopathic pulmonary fibrosis

This study employed bioinformatics to investigate potential molecular markers associated with idiopathic pulmonary fibrosis (IPF) and examined their correlation with immune-infiltrating cells. Microarray data for IPF were retrieved from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and module genes were identified through Limma analysis and weighted gene co-expression network analysis. Enrichment analysis and protein-protein interaction network development were performed on the DEGs. Machine learning algorithms, including least absolute shrinkage and selection operator regression, random forest, and extreme gradient boosting, were applied to identify potential key genes. The predictive accuracy was assessed through a nomogram and a receiver operating characteristic (ROC) curve. Additionally, the correlation between core genes and immune-infiltrating cells was assessed utilizing the CIBERSORT algorithm. An IPF model was established in a human fetal lung fibroblast 1 (HFL-1) through induction with transforming growth factor β1 (TGF-β1), and validation was conducted via reverse transcription-quantitative polymerase chain reaction. A sum of 1246 genes exhibited upregulation, whereas 879 genes were downregulated. Pathway enrichment analysis and functional annotation revealed that DEGs were predominantly involved in extracellular processes. Four key genes - cd19, cxcl13, fcrl5, and slamf7 - were identified. Furthermore, ROC analysis demonstrated high predictive accuracy for these 4 genes. Compared to healthy individuals, lung tissues from IPF patients exhibited an increased presence of plasma cells, CD4 memory-activated T cells, M0 macrophages, activated dendritic cells, resting NK cells, and M2 macrophage infiltration. The upregulation of cd19, cxcl13, fcrl5, and slamf7 in TGF-β1-treated HFL-1 cells was confirmed, aligning with the findings from the microarray data analysis. cd19, cxcl13, fcrl5, and slamf7 serve as diagnostic markers for IPF, providing fresh perspectives regarding the fundamental pathogenesis and molecular mechanisms associated with this condition.

Identification of diagnostic gene biomarkers related to immune infiltration in patients with idiopathic pulmonary fibrosis based on bioinformatics strategies

Objective

The study aims to identify potential diagnostic markers of idiopathic pulmonary fibrosis (IPF) and analyze the significance of immune cell infiltration in this pathology.

Materials and methods

Download two publicly available gene expression profiles (GSE10667 and GSE24206 datasets) from the GEO database including 48 Idiopathic pulmonary fibrosis (IPF) samples and 21 human control samples and select for distinctly expressed genes (DEG) from them. Lasso regression model and support vector machine recursive feature elimination S,V,R,F analysis were used to check candidate biomarkers. The area under the subject's work characteristic curve (AUC) value is used to evaluate its recognition ability. The GSE53845 dataset (40 IPF patients and 8 controls) continue to validate the expression level and diagnostic value of biomarkers in IPF. Comprehensive analysis of immune infiltrated cells of IPF was performed using R software and immune cell infiltration estimation analysis tool- deconvolution algorithm (CIBERSORT).

Results

43 DEGs were identified in total. The identified DEGs mostly involve pneumonia, lung disease, collagen disease, obstructive pulmonary disease and other diseases. The activation of IL-17 signaling pathways, amoebic disease, interaction of viral proteins with cytokines and cytokine receptors, protein digestion and absorption, and flaccid hormone signaling pathways in IPF were different from the control group. The expression degree of CRTAC1, COL10A1, COMP, RPS4Y1, IGFL2, NECAB1, SCG5, SLC6A4, and SPP1 in IPF tissue were prominently higher than the normal group. Immune cell infiltration analysis showed that CRTAC1, COL10A1, COMP, IGFL2, NECAB1, SCG5, SLC6A4, and SPP1 were associated with monocytes, plasma cells, neutrophils, and regulatory (treg) T cells.

Conclusion

CRTAC1, COL10A1, COMP, IGFL2, NECAB1, SCG5, SLC6A4, and SPP1 can be used as diagnostic markers for IPF, providing new ideas for the future study of IPF occurrence and molecular mechanisms.

Reference values for high attenuation areas on chest CT in a healthy, never-smoker, multi-ethnic sample: The MESA study

BACKGROUND AND OBJECTIVE

Normative values for HAA-a quantitative, CT-based measure of subclinical ILD-in healthy adults are needed to improve interpretability in clinical and research settings.

METHODS

HAA was measured on full-lung CT in 3110 participants in the MESA study. Clinical prediction models were developed using a healthy never-smoker subset with normal spirometry (n = 696). RMSE on cross-validation was used as the primary criterion for model selection. Parametric and non-parametric methods were considered. z-Scores were calculated for the entire study sample. Associations between z-scores and several ILD features were estimated.

RESULTS

In the healthy never-smoker subset, the mean age was 69 years with a range of 54-93 years. The median HAA was 4.3% with a range of 2.7-17.8%. Linear regression had better predictive performance than other methods. The final model included race, height, weight, age and sex. The standard error of the estimate was 1.62 with a cross-validated RMSE of 1.64 and an adjusted R² of 0.139. z-Scores were associated with several ILD outcomes in adjusted models, including ILA (OR: 1.40 per z-unit; 95% CI: 1.30, 1.52), exertional dyspnoea (OR: 1.08 per z-unit; 95% CI: 1.02, 1.15) and FVC (expected increase per z-unit: -2.49; 95% CI: -2.95, - 2.03).

CONCLUSION

We present a reference equation and z-scores to define expected values of HAA on full-lung CT to aid HAA interpretation in middle-aged and older adults.

Impact of serum SP-A and SP-D levels on comparison and prognosis of idiopathic pulmonary fibrosis: A systematic review and meta-analysis

BACKGROUND AND OBJECTIVE

Idiopathic pulmonary fibrosis (IPF) has a poor prognosis in general; however, it is heterogeneous to detect relative biomarkers for predicting the disease progression. Serum biomarkers can be conveniently collected to detect and help to differentially diagnose IPF and predict IPF prognosis. This meta-analysis aimed to evaluate the use of serum surfactant proteins A and D (SP-A and SP-D) for differential diagnosis and prognosis of IPF.

METHODS

Relevant articles were searched in PubMed, Embase, and Chinese National Knowledge Infrastructure databases and reviewed by 2 independent readers. Standard mean difference (SMD) and 95% confidence interval (CI) were calculated to assess the difference in serum levels of SP-A/D among patients with IPF, when compared to patients with non-IPF interstitial lung disease (ILD), pulmonary infection, and healthy control. Hazard ratio (HR) and 95% CI were used to compare the relative risk of mortality.

RESULTS

Twenty-one articles (totalling 1289 IPF patients) were included in final meta-analysis. Serum SP-A levels were significantly higher in patients with IPF than in patients with non-IPF ILD (SMD: 1.108 [0.584, 1.632], P < .001), or pulmonary infection (SMD: 1.320 [0.999, 1.640], P < .001) and healthy controls (SMD: 2.802 [1.901, 3.702], P < .001). There was no significant difference in serum SP-D levels between patients with IPF and those with non-IPF ILD patients (SMD: 0.459 [-0.000, 0.919], P = .050). Serum SP-D levels were significantly higher in patients with IPF than in patients with pulmonary infection (SMD: 1.308 [0.813, 1.803], P < .001) and healthy controls (SMD: 2.235 [1.739, 2.731], P < .001). Risk of death in patients with IPF and elevated serum SP-A was increased 39% compared to patients with low SP-A groups. Elevated SP-D increased risk by 111% when compared to low SP-D. In acute exacerbation of IPF, serum SP-A/D were higher than those in stable stage. The comparisons and prognosis might be different in Asian and Caucasian patients.

CONCLUSIONS

Serum SP-A/D detection might be useful for differential diagnosis and prediction of survival in patients with IPF.

The earlier, the better: Impact of early diagnosis on clinical outcome in idiopathic pulmonary fibrosis

BACKGROUND

Idiopathic pulmonary fibrosis (IPF) is a complex disease with a highly variable clinical course and generally poor prognosis. Classified as a rare disease, significant increases in incidence have been recorded worldwide in recent years. Left untreated IPF is extremely debilitating with substantial personal, social and economic implications.

OBJECTIVES

To discuss how IPF is diagnosed and managed in real life clinical practice with particular reference to Italy and to determine how new and effective therapies can be incorporated into a patient-centred management approach in order to improve the lives of patients with IPF.

OUTCOMES

Barriers to early diagnosis are discussed. Cited reasons for delays in diagnosing IPF in Italy include: inherent difficulties in diagnosis; lack of knowledge/awareness of the condition among point-of-contact healthcare professionals; delays in referral to centres of excellence and underestimation of symptoms by both patients and healthcare workers. Valid therapeutic options with demonstrated efficacy in slowing the decline in lung function are now available for patients with IPF. The ASCEND trial confirmed the effects of pirfenidone, approved for the treatment of IPF on the basis of the four phase III trials. Nintedanib, a tyrosine kinase inhibitor that targets the PDGF receptors α/β, FGF receptors 1 to 3, and VEGF receptors 1-3, is approved in the USA and the EU for the treatment of IPF. The TOMORROW and the INPULSIS placebo controlled trials in patients with IPF confirm the efficacy and safety of nintedanib and recent interim analyses endorse its long-term effects in slowing disease progression.

CONCLUSIONS

The importance of early and accurate diagnosis of IPF cannot be underestimated and it is the duty of all healthcare professionals to be vigilant to the symptoms of IPF and to involve a multidisciplinary team in diagnosing and managing IPF early in the course of disease.