Fatty acid metabolism-related genes in bronchoalveolar lavage fluid unveil prognostic and immune infiltration in idiopathic pulmonary fibrosis

Identification of fatty acid metabolism hub genes in endometriosis using integrative bioinformatics analysis

Background

Fatty acid metabolism plays a major role in several inflammatory diseases such as endometriosis. However, its specific mechanism in endometriosis remains unclear. Therefore, this study aimed to investigate the hub genes involved in endometriosis and fatty acid metabolism using bioinformatics analyses.

Methods

The R package sva was used to remove batch effects from the GSE120103 and GSE25628 datasets, resulting in the creation of a combined GEO dataset. Differential analysis of the combined GEO dataset was interposed with fatty acid metabolism-related genes. Differentially expressed genes associated with fatty acid metabolism (FAMRDEGs) were subsequently identified. Functional enrichment analyses were performed using the clusterProfiler package, whereas gene set enrichment analysis (GSEA) was used to identify significant pathways. Protein-protein interaction (PPI) networks were constructed using STRING and visualized using Cytoscape to identify hub genes. Moreover, regulatory networks involving transcription factors and microRNAs were constructed using ChIPBase and ENCORI databases, respectively. Hub genes were validated via expression comparison and receiver operating characteristic curve analysis.

Results

We identified 405 DEGs in the combined dataset, including 168 and 237 with upregulated and downregulated expression, respectively. Of these, 17 were FAMRDEGs. These genes were significantly involved in arachidonic acid and fatty acid metabolic processes. GSEA highlighted pathways such as Hamai_apoptosis_via_trail_dn for genes whose expression was downregulated, along with nuclear receptors in lipid metabolism and toxicity for genes with upregulated expression. The PPI network identified six hub genes: PTGS2, CYP2C9, HSDL2, HSD17B3, ACSL4, and CYP2C18. ACSL4 showed the strongest positive correlation with immune cell effector memory CD8 T cells, whereas HSDL2 showed the strongest negative correlation with immune cell-activated CD8 T cells.

Conclusion

The identified hub genes may be potential biomarkers of fatty acid metabolism in endometriosis. This reveals the potential molecular mechanisms underlying this metabolic process and identifies therapeutic targets for future interventions.

Higher mitochondrial protein-Succinylation detected in lung tissues of idiopathic pulmonary fibrosis patients

A new pathogenic role for mitochondrial dysfunction has been associated with the development of idiopathic pulmonary fibrosis (IPF). Lysine succinylation (Ksucc) is involved in many energy metabolism pathways in mitochondria, making Ksucc highly valuable for studying IPF. We used liquid chromatography with tandem mass spectrometry (LC-MS/MS) to perform the first global profiling of Ksucc in fibrotic lung tissues from IPF patients, providing a proof of concept for the alteration of Ksucc in IPF and highlighting its potential as a therapeutic target. Selected candidate proteins were further verified by targeted proteomics using parallel reaction monitoring (PRM). In this study, we identified 1964 Ksucc sites on 628 modified proteins, with675 of these Ksucc sites on 124 modified proteins closely related to mitochondrial metabolism. 117 succinylated proteins were associated with energy metabolism in mitochondria by comparing these proteins with those previously reported in normal lung tissues. The Ksucc levels in KYAT3, HSD17B8, GRHPR, and IDH2 were different between control and IPF groups by Using PRM. This study provides insight into Ksucc profile alterations in IPF pathogenesis and Ksucc sites in proteins associated with mitochondrial energy metabolism can also serve as candidate molecules for future mechanism exploration and drug target selection in IPF.

Integrating cellular experiments, single-cell sequencing, and machine learning to identify endoplasmic reticulum stress biomarkers in idiopathic pulmonary fibrosis

BACKGROUND

Idiopathic Pulmonary Fibrosis (IPF) presents a severe respiratory challenge with a poor prognosis due to the lack of reliable biomarkers. Recent evidence suggests that Endoplasmic Reticulum Stress (ERS) may be associated with IPF pathogenesis. This study focuses on uncovering ERS-associated biomarkers for IPF.

METHODS

Sequencing data from diverse datasets were analyzed, utilizing differential gene expression analysis and Weighted Gene Co-expression Network Analysis (WGCNA). Endoplasmic Reticulum Stress (ERS)-related genes were extracted from the GeneCards database. Hub genes were identified through Protein-Protein Interaction (PPI) analysis. Diagnostic and prognostic models were developed using machine learning algorithms and validated across both training and validation sets. Additionally, techniques such as Cell-type Identification by Estimating Relative Subsets of RNA Transcripts and single-cell RNA sequencing were employed to identify potential IPF-related cells. These findings were further investigated to elucidate their underlying mechanisms through in vitro experiments.

RESULTS

Differentially expressed genes, WGCNA-identified blue module genes, and ERS-related genes extracted from the GeneCards database were intersected, and the resulting genes were used to construct diagnostic and prognostic models. Validation using multiple datasets indicated that both the diagnostic and prognostic models possess strong predictive capabilities. PPI analysis highlighted SPP1 as a potential hub gene in IPF. Moreover, M2 macrophages were found in higher quantities in the lung tissue of IPF patients, with a significant increase in SPP1-expressing M2 macrophages compared to the control group. In vitro experiments demonstrated that exogenous SPP1 inhibited the proliferation and migration of M2 macrophages and promoted apoptosis within a certain concentration range.

CONCLUSION

This study identifies ERS-related biomarkers in IPF, highlighting SPP1 and M2 macrophages. The resulting diagnostic and prognostic models offer strong predictive capabilities, unveiling new therapeutic avenues.

Circulating metabolic profile in idiopathic pulmonary fibrosis: data from the IPF-PRO Registry

BACKGROUND

The circulating metabolome, reflecting underlying cellular processes and disease biology, has not been fully characterized in patients with idiopathic pulmonary fibrosis (IPF). We evaluated whether circulating levels of metabolites correlate with the presence of IPF, with the severity of IPF, or with the risk of clinically relevant outcomes among patients with IPF.

METHODS

We analyzed enrollment plasma samples from 300 patients with IPF in the IPF-PRO Registry and 100 individuals without known lung disease using a set of targeted metabolomics and clinical analyte modules. Linear regression was used to compare metabolite and clinical analyte levels between patients with IPF and controls and to determine associations between metabolite levels and measures of disease severity in patients with IPF. Unadjusted and adjusted univariable Cox regression models were used to evaluate associations between circulating metabolites and the risk of mortality or disease progression among patients with IPF.

RESULTS

Levels of 64 metabolites and 5 clinical analytes were significantly different between patients with IPF and controls. Among analytes with greatest differences were non-esterified fatty acids, multiple long-chain acylcarnitines, and select ceramides, levels of which were higher among patients with IPF versus controls. Levels of the branched-chain amino acids valine and leucine/isoleucine were inversely correlated with measures of disease severity. After adjusting for clinical factors known to influence outcomes, higher levels of the acylcarnitine C:16-OH/C:14-DC were associated with all-cause mortality, lower levels of the acylcarnitine C16:1-OH/C14:1DC were associated with all-cause mortality, respiratory death, and respiratory death or lung transplant, and higher levels of the sphingomyelin d43:2 were associated with the risk of respiratory death or lung transplantation.

CONCLUSIONS

IPF has a distinct circulating metabolic profile characterized by increased levels of non-esterified fatty acids, long-chain acylcarnitines, and ceramides, which may suggest a more catabolic environment that enhances lipid mobilization and metabolism. We identified select metabolites that were highly correlated with measures of disease severity or the risk of disease progression and that may be developed further as biomarkers.

TRIAL REGISTRATION

ClinicalTrials.gov; No: NCT01915511; URL: www.

CLINICALTRIALS

gov .

Predictive biomarkers of disease progression in idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a chronic interstitial disease that cannot be cured, and treatment options for IPF are very limited. Early diagnosis, close monitoring of disease progression, and timely treatment are therefore the best options for patients due to the irreversibility of IPF. Effective markers help doctors judge the development and prognosis of disease. Recent research on traditional biomarkers (KL-6, SP-D, MMP-7, TIMPs, CCL18) has provided novel ideas for predicting disease progression and prognosis. Some emerging biomarkers (HE4, GDF15, PRDX4, inflammatory cells, G-CSF) also provide more possibilities for disease prediction. In addition to markers in serum and bronchoalveolar lavage fluid (BALF), some improvements related to the GAP model and chest HRCT also show good predictive ability for disease prognosis.

Codium fragile Suppressed Chronic PM2.5-Exposed Pulmonary Dysfunction via TLR/TGF-β Pathway in BALB/c Mice

This study investigated the ameliorating effect of the aqueous extract of Codium fragile on PM2.5-induced pulmonary dysfunction. The major compounds of Codium fragile were identified as palmitic acid, stearic acid, and oleamide using GC/MS2 and hexadecanamide, oleamide, and 13-docosenamide using UPLC-Q-TOF/MSE. Codium fragile improved pulmonary antioxidant system deficit by regulating SOD activities and reducing GSH levels and MDA contents. It suppressed pulmonary mitochondrial dysfunction by regulating ROS contents and mitochondrial membrane potential levels. It regulated the inflammatory protein levels of TLR4, MyD88, p-JNK, p-NF-κB, iNOS, Caspase-1, TNF-α, and IL-1β. In addition, it improved the apoptotic protein expression of BCl-2, BAX, and Caspase-3 and attenuated the fibrous protein expression of TGF-β1, p-Smad-2, p-Smad-3, MMP-1, and MMP-2. In conclusion, this study suggests that Codium fragile might be a potential material for functional food or pharmaceuticals to improve lung damage by regulating oxidative stress inflammation, cytotoxicity, and fibrosis via the TLR/TGF-β1 signaling pathway.