Identification and validation of INHBE and P4HA1 as hub genes in non-alcoholic fatty liver disease

ASS1 is a hub gene and possible therapeutic target for regulating metabolic dysfunction-associated steatotic liver disease modulated by a carbohydrate-restricted diet

Metabolic dysfunction-associated steatotic liver disease (MASLD) is the leading cause of chronic liver disease globally. A low-carbohydrate diet (LCD) offers benefits to MASLD patients, albeit its exact mechanism is not fully understood. Using public liver transcriptome data from MASLD patients before/after LCD intervention, we applied differential expression analysis and machine learning to identify key genes. We initially identified 162 differentially expressed genes in the GSE107650 dataset. Secondly, employing two machine learning algorithms, we found that PRAMENP, LEAP2, LOC105379013, and argininosuccinate synthetase 1 (ASS1) are potential hub genes. Additionally, protein-protein interaction and single-cell RNA location analyses suggested that ASS1 was the most crucial hub gene. Then, L1000CDS2 analysis of the gene-expression signatures was employed for drug repurposing studies. CGP71683, an appetite suppressant, was predicted to improve MASLD and may mimic the ASS1 expression pattern induced by an LCD. Molecular dynamics confirmed spontaneous, stable CGP71683-ASS1 complex formation. Overall, this work based on analysis of machine learning algorithms, essential gene identification, and drug repurposing studies suggested that ASS1 is an essential gene in MASLD and CGP71683 is a potential drug candidate for treating MASLD by targeting ASS1 and mimicking the beneficial effects of an LCD. However, due to the inherent limitations of a purely computational approach, further experimental investigation is necessary to validate the anticipated results.

Nonylphenol exposure increases the risk of Hirschsprung's disease by inducing macrophage M1 polarization

Nonylphenol (NP), a ubiquitous environmental contaminant used as a surfactant in industrial production and classified as an endocrine disruptor, could interfere hormone secretion and exhibit neurotoxicity in organisms. Hirschsprung's disease (HSCR), one of the most frequently observed congenital malformations of the digestive system, arises mainly due to the failure of enteric neural crest cells to migrate to the distal colon during embryonic development. However, the effects of NP exposure on HSCR are largely unknown. Herein, we identified the content of NP and expression of lncRNA LINC00294/Inhibin Subunit Beta E (INHBE) axis in clinical samples and evaluated the crucial role of lncRNA LINC00294/INHBE axis in the neurogenic potential of neurons and the neurotoxicity effects of NP in the SH-SY5Y cells and female specific pathogen-free (SPF) rat model. Our results showed that NP concentration and LINC00294 were significantly associated with HSCR occurrence and macrophage polarization in human HSCR specimens. Moreover, NP promoted macrophage M1 polarization. The proliferation and migration were weakened, and apoptosis was heightened by the conditioned medium of NP-treated macrophages in SH-SY5Y cells. Contrarily, LINC00294 overexpression and INHBE knockdown reversed the neurotoxicity effect of NP on SH-SY5Y cells. Furthermore, the neurotoxicity effect of NP was abolished by clodronate liposomes in the rat model. In conclusion, NP could induce macrophage M1 polarization via the LINC00294/INHBE axis and increase the risk of Hirschsprung's disease. Our findings would provide a foundation for the toxicity study and risk assessments of NP.

Unveiling functionality and conducting two-sample mendelian randomization on WGCNA-identified oxidative stress-related hub genes in metabolic dysfunction-associated fatty liver disease

Metabolic dysfunction-associated fatty liver disease (MAFLD) shows accelerated development under the impact of oxidative stress (OS). There is an imperative to identify OS-related biomarkers in MAFLD and explore their potential mechanistic insights. The objective of this study was to identify OS-related biomarkers in MAFLD and explore their potential mechanisms. DEG analysis was performed using GSE17470 and GSE24807 datasets. An investigative exploration utilizing WGCNA was executed to elucidate hub OS-related genes. The intersection of OS-related hub genes identified by WGCNA and DEGs was systematically employed for thorough analyses. A mendelian randomization (MR) study examined the causal effect of C-reactive protein (CRP) on MAFLD. 59 OS-related DEGs were identified in MAFLD. WGCNA revealed 100 OS-related hub genes in MAFLD. Sixteen OS-related genes have been delineated as critical components in MAFLD. Enrichment analyses, employing GO and KEGG pathways, revealed pathways enriched with these genes. Following PPI analyses, the highest-ranking ten hub genes demonstrating abnormal expression were determined. Ultimately, a two-sample MR analysis demonstrated a causal link between the hub gene CRP and the occurrence of MAFLD. In this study, we harnessed WGCNA to formulate a co-expression network and identified hub OS-related DEGs in MAFLD. Additionally, the hub gene CRP exhibited a significant correlation with the predisposition to MAFLD. These findings offer innovative perspectives on the applications of OS-associated genes in individuals afflicted with MAFLD.

Screening, identification and targeted intervention of necroptotic biomarkers of asthma

BACKGROUND

As a pivotal pathway of programmed cell death, necroptosis significantly contributes to the pathogenesis of respiratory disorders. However, its role in asthma is not yet fully elucidated. Therefore, this study aimed to identify markers associated with necroptosis, evaluate their functions in asthma, and explore potential therapeutic agents targeting necroptosis for the management of asthma.

METHODS

Firstly, machine learning algorithms, including Least Absolute Shrinkage and Selection Operator (LASSO), Random Forest, and Support Vector Machine-Recursive Feature Elimination (SVM-RFE), were utilized to identify necroptosis-related differentially expressed genes (NRDEGs) in asthma patients compared to healthy controls. Concurrently, the expression of NRDEGs was validated using external datasets, Western blot, and quantitative real-time polymerase chain reaction (qPCR). Secondly, the clinical relevance of NRDEGs was assessed through Receiver Operating Characteristic (ROC) curve analysis and correlation with clinical indicators. Thirdly, the relationship between NRDEGs and pulmonary immune cell infiltration, as well as the signaling interactions between different cells types, were analyzed through immune infiltration and single-cell analysis. Fourthly, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA), were conducted to elucidate the functional roles of NRDEGs. Finally, compounds targeting NRDEGs were screened, and their binding affinities were evaluated using molecular docking studies.

RESULTS

In asthma, necroptosis is activated, leading to the identification of four NRDEGs: NLRP3, PYCARD, ALOX15, and VDAC3. Among these, NLRP3, PYCARD, and ALOX15 are upregulated, whereas VDAC3 is downregulated in asthma. Comprehensive clinical evaluations indicated that NRDEGs hold diagnostic value for asthma. Specifically, NLRP3 was inversely correlated with forced expiratory volume in 1 s (FEV1) and forced vital capacity (FVC), while VDAC3 showed an inverse correlation with sputum neutrophils. Conversely, ALOX15 expression was positively correlated with fractional exhaled nitric oxide (FeNO) levels, as well as sputum eosinophils, blood eosinophils, and blood IgE levels. Subsequent immune infiltration analysis revealed associations between NRDEGs and activated dendritic cells, mast cells, and eosinophils. Single-cell RNA sequencing (scRNA-seq) further confirmed the communication signals between myeloid dendritic cells, fibroblasts, neutrophils, and helper T cells, predominantly related to fibrosis and immune-inflammatory responses. Pathway enrichment analysis demonstrated that NRDEGs are involved in ribosomal function, oxidative phosphorylation, and fatty acid metabolism. Finally, resveratrol and triptonide were identified as potential therapeutic agents targeting the proteins encoded by NRDEGs for asthma treatment.

CONCLUSIONS

The necroptosis pathway is activated in asthma, with NRDEGs-namely PYCARD, NLRP3, ALOX15, and VDAC3-correlated with declines in lung function and airway inflammation. These genes serve as reliable predictors of asthma risk and are involved in the regulation of the immune-inflammatory microenvironment. Resveratrol and triptolide have been identified as promising therapeutic candidates due to their potential to target the proteins encoded by these genes.

P4HA1: an important target for treating fibrosis related diseases and cancer

Fibrosis is significantly associated with a wide variety of diseases and is involved in their progression. Fibrosis activated under the influence of different combinations of factors is considered a double-edged sword. Although there has been much research on organ fibrosis in recent years, a variety of organ fibrosis diseases and cancers are not well controlled in terms of prevention, treatment, and prognosis. Clinical studies still lack exploration and discovery of effective targets for the pathogenesis of organ fibrosis. Prolyl 4-hydroxylase subunit alpha 1 (P4HA1) is a protein kinase and the synthesis and secretion of collagen are related to the sustained activation of P4HA1. As further studies are being conducted, the potential role of P4HA1 in the development of fibrosis-associated diseases and cancer is becoming clear. Consequently, we conducted a systematic review and discussion on the role of P4HA1 in the pathogenesis of various fibrosis-related diseases and cancers. We reviewed the possible strategies of P4HA1 in the diagnosis and treatment of fibrosis-related diseases and cancers, and analyzed its potential relevance as a biomarker in the diagnosis and treatment of fibrosis-related diseases and cancer.

Activin E upregulates uncoupling protein 1 and fibroblast growth factor 21 in brown adipocytes

Activin E activates brown and beige adipocytes and has been controversially implicated as a factor that induces obesity and fatty liver. Here, we sought to address this controversial issue by producing recombinant human activin E to evaluate its effects on HB2 brown adipocytes in vitro. Activin E increased uncoupling protein 1 (Ucp1) and fibroblast growth factor 21 (Fgf21) mRNA expression in the adipocytes. This upregulation was suppressed by SB431542, an inhibitor of activin receptor-like kinase (Alk) TGF-β type I receptors. SB431542 also inhibited the activin E-induced phosphorylation of Smad2/3. A promoter assay using a CAGA-Luc reporter and Alk expression vectors revealed that activin E activated the TGF-β/activin pathway via Alk7. The upregulation of Ucp1 and Fgf21 mRNA might be mediated through Alk7 and Smad2/3 phosphorylation. Activin E is a potential stimulator of energy expenditure by activating brown adipocytes and highlights its potential as a therapeutic target for treating obesity.

Unveiling the mitophagy puzzle in non-alcoholic fatty liver disease (NAFLD): Six hub genes for early diagnosis and immune modulatory roles

Background

Non-alcoholic fatty liver disease (NAFLD) stands as a predominant chronic liver ailment globally, yet its pathogenesis remains elusive. This study aims to identify Hub mitophagy-related genes (MRGs), and explore the underlying pathological mechanisms through which these hub genes regulate NAFLD.

Methods

A total of 3 datasets were acquired from the GEO database and integrated to identify differentially expressed genes (DEGs) in NAFLD and perform Gene Set Enrichment Analysis (GSEA). By intersecting DEGs with MRGs, mitophagy-related differentially expressed genes (MRDEGs) were obtained. Then, hub MRGs with diagnostic biomarker capability for NAFLD were screened and a diagnostic prediction model was constructed and assessed using Nomogram, Decision Curve Analysis (DCA), and ROC curves. Functional enrichment analysis was conducted on the identified hub genes to explore their biological significance. Additionally, regulatory networks were constructed using databases. NAFLD was stratified into high and low-risk groups based on the Riskscore from the diagnostic prediction model. Furthermore, single-sample gene set enrichment analysis (ssGSEA) and CIBERSORT algorithms were employed to analyze immune cell infiltration patterns and the relationship between Hub MRGs and immune cells.

Results

The integrated dataset comprised 122 NAFLD samples and 31 control samples. After screening, 18 MRDEGs were identified. Subsequently, six hub MRGs (NR4A1, PPP2R2A, P4HA1, TUBB6, DUSP1, NAMPT) with diagnostic potential were selected through WGCNA, logistic regression, SVM, RF, and LASSO models, all significantly downregulated in NAFLD samples compared to the control group. A diagnostic prediction model based on these six genes demonstrated robust predictive performance. Functional enrichment analysis of the six hub genes revealed involvement in processes such as protein phosphorylation or dephosphorylation. Correlation analysis demonstrated a significant association between hub MRGs and infiltrating immune cells.

Conclusion

We identified six hub MRGs in NAFLD and constructed a diagnostic prediction model based on these six genes, applicable for early NAFLD diagnosis. These genes may participate in regulating NAFLD progression through the modulation of mitophagy and immune activation. Our findings may contribute to subsequent clinical and basic research on NAFLD.

Drug development advances in human genetics-based targets

Drug development is a long and costly process, with a high degree of uncertainty from the identification of a drug target to its market launch. Targeted drugs supported by human genetic evidence are expected to enter phase II/III clinical trials or be approved for marketing more quickly, speeding up the drug development process. Currently, genetic data and technologies such as genome-wide association studies (GWAS), whole-exome sequencing (WES), and whole-genome sequencing (WGS) have identified and validated many potential molecular targets associated with diseases. This review describes the structure, molecular biology, and drug development of human genetics-based validated beneficial loss-of-function (LOF) mutation targets (target mutations that reduce disease incidence) over the past decade. The feasibility of eight beneficial LOF mutation targets (PCSK9, ANGPTL3, ASGR1, HSD17B13, KHK, CIDEB, GPR75, and INHBE) as targets for drug discovery is mainly emphasized, and their research prospects and challenges are discussed. In conclusion, we expect that this review will inspire more researchers to use human genetics and genomics to support the discovery of novel therapeutic drugs and the direction of clinical development, which will contribute to the development of new drug discovery and drug repurposing.