Roles of transducin-like enhancer of split (TLE) family proteins in tumorigenesis and immune regulation

Helicobacter pylori induced miR-362-5p upregulation drives gastric cancer progression and links hepatocellular carcinoma through an exosome-dependent pathway

Introduction

Helicobacter pylori (H. pylori) infection induced miRNA dysregulation plays an important role in gastric cancer (GC) and exosomes mediate the spread of pathogenic effects.

Methods

Expression of miR-362-5p and its clinical significance in GC were analyzed using data from TCGA. The effects of miR-362-5p on GC cells' proliferation and migration were examined by using CCK-8, EdU, transwell and scratch assays. MKN45 xenograft model in nude mice was employed to evaluate impacts of miR-362-5p on GC progression in vivo. Target gene of miR-362-5p was screened by bioinformatic analysis and verified by using dual-luciferase assay. Exosomes from H. pylori-infected GES-1 cell (Hp-GES-EVs) were isolated and miR-362-5p inside the exosome was detected. The uptake of exosome by GC cells was observed through fluorescence imaging and exosome-mediated pathogenesis was explored. Furthermore, the transport of exosome-mediated miR-362-5p via blood was examined. The effect of exosome-carried miR-362-5p on hepatocellular carcinoma (HCC) progression was investigated by hepatocyte's uptake, proliferation and migration assays.

Results

miR-362-5p was significantly upregulated in GC tissues associated with H. pylori infection. Downregulation of miR-362-5p in GC cells inhibited proliferation and migration in vitro and suppressed tumor growth in vivo, counteracting H. pylori-induced carcinogenesis. TLE4 was confirmed as a direct target of miR-362-5p, and miR-362-5p/TLE4 axis implicated in H. pylori-driven neoplastic transformations in GC cells. Hp-GES-EVs mediated the transport of miR-362-5p, was absorbed by GC cells and detected at elevated levels in the serum of infected mice. Moreover, Hp-GES-EVs were diffused to liver and taken up by liver cells, enhancing HCC cell proliferation and migration by targeting TLE4.

Conclusion

H. pylori infection upregulates miR-362-5p, facilitating GC progression via TLE4 targeting. Exosome-mediated transfer amplifies its effects, contributing to liver damage and potentially facilitating HCC.

Transducin-like enhancer of split 3 protects against lipopolysaccharide-induced inflammation through DEAD-box helicase 5-activating transcription factor 1-protein phosphatase 2 regulatory subunit 5A signaling

INTRODUCTION

Sepsis consists of life-threatening multi-organ dysfunction caused by an excessive systemic inflammatory response to infection. Therefore, identifying negative regulators of innate inflammation is crucial for treating this condition.

OBJECTIVES

In this study, we aimed to understand how transducin-like enhancer of split 3 (TLE3) regulates inflammatory responses.

METHODS

We detected Tle3 changes in sepsis patients by analyzing public databases, which were confirmed in septic survivors, septic mouse models, and inflammatory macrophages using Western blotting, qRT-PCR, and immunohistochemistry staining. We investigated the role and mechanism of TLE3 in sepsis by utilizing bone marrow-transplantation (BMT) and adenovirus-infected mice. Furthermore, Protein-Protein Docking, BiFC, LC-MS/MS analysis, CUT & Tag-seq, and CHIP experiments were utilized to disclose the mechanism underlying TLE3 involving macrophage inflammation.

RESULTS

In this study, we found that Tle3 transcript is upregulated in peripheral blood samples of sepsis survivors and is decreased in non-survivors, suggesting the critical role of TLE3 in sepsis outcomes. TLE3 is also upregulated in lipopolysaccharide (LPS)-stimulated human monocyte-derived macrophages (MDMs), murine bone marrow-derived macrophages (BMDMs), and septic mice. Gain-of- and loss-of-function of TLE3 in LPS-stimulated murine BMDMs, human MDMs, and mouse models of sepsis showed that TLE3 alleviates LPS-induced cytokine production, as well as nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) and mitogen-activated protein kinase (MAPK) activation in macrophages, which protects against LPS-induced acute systemic inflammation, multi-organ injury, and death caused by sepsis. Mechanistically, upregulated TLE3 interacts with the transcriptional coactivator, DEAD-box helicase 5 (DDX5), promoting its retention in the cytoplasm and ultimately decreasing transcription of the DDX5/ activating transcription factor 1 (ATF1)-targeted gene Ppp2r5a. Furthermore, the TLE3-DDX5-ATF1 axis downregulates PPP2R5A, a negative regulatory subunit of protein phosphatase 2A (PP2A), thereby increasing PP2A activity and promoting the dephosphorylation of NF-κB and MAPK.

CONCLUSION

Our study shows that TLE3 represents a novel suppressor of LPS-induced inflammatory signaling in macrophages.

Identification of HES4 as a novel prognostic marker and therapeutic target in hepatocellular carcinoma

Hairy and enhancer of Split 4 (HES4) is thought to have a substantial impact on the pathogenesis and progression of malignancies. However, the prognostic significance and mechanism of HES4 have not been reported in Hepatocellular carcinoma (HCC). A comprehensive bioinformatics analysis of HES4 expression, clinicopathological characteristics, tumor microenvironment status, and drug sensitivity were performed based on TCGA, GTEx, and GEO. Paired HCC samples and cell lines were used to validate the dysfunction of HES4 in vitro. The expression of HES4 at both mRNA and protein levels was significantly upregulated in HCC tissues. High level of HES4 was associated with unfavorable outcomes. Enrichment analysis demonstrated strong associations of HES4 with HCC progression pathways. In addition, elevated HES4 expression was positively correlated with increased sensitivity to various chemotherapy drugs and associated with resistance to immunotherapy. As a transcription factor, the target genes regulated by HES4 were mostly risky genes, and a novel prediction model based on HES4 target genes was generated for HCC risk stratification. The AUCs of 1-, 3-, and 5-year year overall survival (OS) were 0.829, 0.732, and 0.700, respectively. HES4 overexpression is associated with poor clinical outcomes and tumor progression. HES4 may serve as a novel prognostic marker and therapeutic target in HCC.

Profiling Genome-Wide Methylation Patterns in Cattle Infected with Ostertagia ostertagi

DNA methylation (DNAm) regulates gene expression and genomic imprinting. This study aimed to investigate the effect of gastrointestinal (GI) nematode infection on host DNAm. Helminth-free Holstein steers were either infected with Ostertagia ostertagi (the brown stomach worm) or given tap water only as a control. Animals were euthanized 30 days post-infection, and tissues were collected at necropsy. We conducted epigenome-wide profiling using a mammalian methylation array to explore the impact of infection on methylation patterns in the mucosa from abomasal fundus (FUN), pylorus (PYL), draining lymph nodes (dLNs), and the duodenum (DUO). The analysis covered 31,107 cattle CpGs of 5082 genes and revealed infection-driven, tissue-specific, differential methylation patterns. A total of 389 shared and 2770 tissue-specific, differentially methylated positions (DMPs) were identified in dLN and FUN, particularly in genes associated with immune responses. The shared DMPs were found in 263 genes, many of which are involved in immune responses. Furthermore, 282, 244, 52, and 24 differentially methylated regions (DMRs) were observed in dLN, FUN, PYL, and DUO, respectively. More hypomethylated DMRs were detected in dLN and FUN, while more hypermethylated DMRs were found in PYL and DUO. Genes carrying DMPs and DMRs and enriched pathways relating to immune functions/responses were detected in infected animals, indicating a link between DNA methylation and the infection. The data may implicate a crucial role of DNAm in regulating the nature/strength of host immunity to infection and contribute to a deeper understanding of the epigenetic regulatory landscape in cattle infected by GI nematodes.

Multi-ancestry GWAS meta-analyses of lung cancer reveal susceptibility loci and elucidate smoking-independent genetic risk

Lung cancer remains the leading cause of cancer mortality, despite declining smoking rates. Previous lung cancer GWAS have identified numerous loci, but separating the genetic risks of lung cancer and smoking behavioral susceptibility remains challenging. Here, we perform multi-ancestry GWAS meta-analyses of lung cancer using the Million Veteran Program cohort (approximately 95% male cases) and a previous study of European-ancestry individuals, jointly comprising 42,102 cases and 181,270 controls, followed by replication in an independent cohort of 19,404 cases and 17,378 controls. We then carry out conditional meta-analyses on cigarettes per day and identify two novel, replicated loci, including the 19p13.11 pleiotropic cancer locus in squamous cell lung carcinoma. Overall, we report twelve novel risk loci for overall lung cancer, lung adenocarcinoma, and squamous cell lung carcinoma, nine of which are externally replicated. Finally, we perform PheWAS on polygenic risk scores for lung cancer, with and without conditioning on smoking. The unconditioned lung cancer polygenic risk score is associated with smoking status in controls, illustrating a reduced predictive utility in non-smokers. Additionally, our polygenic risk score demonstrates smoking-independent pleiotropy of lung cancer risk across neoplasms and metabolic traits.

TLE4 downregulation identified by WGCNA and machine learning algorithm promotes papillary thyroid carcinoma progression via activating JAK/STAT pathway

Background: Papillary Thyroid Carcinoma (PTC), a common type of thyroid cancer, has a pathogenesis that is not fully understood. This study utilizes a range of public databases, sophisticated bioinformatics tools, and empirical approaches to explore the key genetic components and pathways implicated in PTC, particularly concentrating on the Transducin-Like Enhancer of Split 4 (TLE4) gene. Methods: Public databases such as TCGA and GEO were utilized to conduct differential gene expression analysis in PTC. Hub genes were identified using Weighted Gene Co-expression Network Analysis (WGCNA), and machine learning techniques, including Random Forest, LASSO regression, and SVM-RFE, were employed for biomarker identification. The clinical impact of the TLE4 gene was assessed in terms of diagnostic accuracy, prognostic value, and its functional enrichment analysis in PTC. Additionally, the study focused on understanding the role of TLE4 in the dynamics of immune cell infiltration, gene function enhancement, and behaviors of PTC cells like growth, migration, and invasion. To complement these analyses, in vivo studies were performed using a xenograft mouse model. Results: 244 genes with significant differential expression across various databases were identified. WGCNA indicated a strong link between specific gene modules and PTC. Machine learning analysis brought the TLE4 gene into focus as a key biomarker. Bioinformatics studies verified that TLE4 expression is lower in PTC, linking it to immune cell infiltration and the JAK-STAT signaling pathways. Experimental data revealed that decreased TLE4 expression in PTC cell lines leads to enhanced cell growth, migration, invasion, and activates the JAK/STAT pathway. In contrast, TLE4 overexpression in these cells inhibited tumor growth and metastasis. Conclusions: This study sheds light on TLE4's crucial role in PTC pathogenesis, positioning it as a potential biomarker and target for therapy. The integration of multi-omics data and advanced analytical methods provides a robust framework for understanding PTC at a molecular level, potentially guiding personalized treatment strategies.

Foxq1 Promotes Alveolar Epithelial Cell Death through Tle1-mediated Inhibition of the NF-κB Signaling Pathway

Acute lung injury (ALI) is a common respiratory disease characterized by diffuse alveolar injury and interstitial edema, as well as a hyperinflammatory response, lung cell damage, and oxidative stress. Foxq1, a member of the FOX family of transcription factors, is expressed in various tissues, such as the lungs, liver, and kidneys, and contributes to various biological processes, such as stress, metabolism, cell cycle arrest, and aging-related apoptosis. However, the role of Foxq1 in ALI is unknown. We constructed ex vivo and in vivo ALI models by LPS tracheal perfusion of ICR mice and conditioned medium stimulation of injured MLE-12 cells. Foxq1 expression was increased, and its localization was altered, in our ALI model. In normal or injured MLE-12 cells, knockdown of Foxq1 promoted cell survival, and overexpression had the opposite effect. This regulatory effect was likely mediated by Tle1 and the NF-κB/Bcl2/Bax signaling pathway. These data suggest a potential link between Foxq1 and ALI, indicating that Foxq1 can be used as a biomarker for the diagnosis of ALI. Targeted inhibition of Foxq1 expression could promote alveolar epithelial cell survival and may provide a strategy for mitigating ALI.

Sox10 Activity and the Timing of Schwann Cell Differentiation Are Controlled by a Tle4-Dependent Negative Feedback Loop

The HMG-domain containing transcription factor Sox10 plays a crucial role in regulating Schwann cell survival and differentiation and is expressed throughout the entire Schwann cell lineage. While its importance in peripheral myelination is well established, little is known about its role in the early stages of Schwann cell development. In a search for direct target genes of Sox10 in Schwann cell precursors, the transcriptional co-repressor Tle4 was identified. At least two regions upstream of the Tle4 gene appear involved in mediating the Sox10-dependent activation. Once induced, Tle4 works in tandem with the bHLH transcriptional repressor Hes1 and exerts a dual inhibitory effect on Sox10 by preventing the Sox10 protein from transcriptionally activating maturation genes and by suppressing Sox10 expression through known enhancers of the gene. This mechanism establishes a regulatory barrier that prevents premature activation of factors involved in differentiation and myelin formation by Sox10 in immature Schwann cells. The identification of Tle4 as a critical downstream target of Sox10 sheds light on the gene regulatory network in the early phases of Schwann cell development. It unravels an elaborate regulatory circuitry that fine-tunes the timing and extent of Schwann cell differentiation and myelin gene expression.

Bioinformatics and Experimental Validation for Identifying Biomarkers Associated with AMG510 (Sotorasib) Resistance in KRASG12C-Mutated Lung Adenocarcinoma

The Kirsten rat sarcoma viral oncogene homolog (KRAS)G12C mutation is prevalent in lung adenocarcinoma (LUAD), driving tumor progression and indicating a poor prognosis. While the FDA-approved AMG510 (Sotorasib) initially demonstrated efficacy in treating KRASG12C-mutated LUAD, resistance emerged within months. Data from AMG510 treatment-resistant LUAD (GSE204753) and single-cell datasets (GSE149655) were analyzed. Gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA) were used to explore enriched signaling pathways, nomogram models were constructed, and transcription factors predicting resistance biomarkers were predicted. CIBERSORT identified immune cell subpopulations, and their association with resistance biomarkers was assessed through single-cell analysis. AMG510-resistant LUAD cells (H358-AR) were constructed, and proliferative changes were evaluated using a CCK-8 assay. Key molecules for AMG510 resistance, including SLC2A1, TLE1, FAM83A, HMGA2, FBXO44, and MTRNR2L12, were recognized. These molecules impacted multiple signaling pathways and the tumor microenvironment and were co-regulated by various transcription factors. Single-cell analysis revealed a dampening effect on immune cell function, with associations with programmed cell death ligand 1 (PDL1) expression, cytokine factors, and failure factors. The findings indicate that these newly identified biomarkers are linked to the abnormal expression of PDL1 and have the potential to induce resistance through immunosuppression. These results highlight the need for further research and therapeutic intervention to address this issue effectively.

Regulation of phosphosignaling pathways involved in transcription of cell cycle target genes by TRH receptor activation in GH1 cells

Thyrotropin-releasing hormone (TRH) is known to activate several cellular signaling pathway, but the activation of the TRH receptor (TRH-R) has not been reported to regulate gene transcription. The aim of this study was to identify phosphosignaling pathways and phosphoprotein complexes associated with gene transcription in GH1 pituitary cells treated with TRH or its analog, taltirelin (TAL), using label-free bottom-up mass spectrometry-based proteomics. Our detailed analysis provided insight into the mechanism through which TRH-R activation may regulate the transcription of genes related to the cell cycle and proliferation. It involves control of the signaling pathways for β-catenin/Tcf, Notch/RBPJ, p53/p21/Rbl2/E2F, Myc, and YY1/Rb1/E2F through phosphorylation and dephosphorylation of their key components. In many instances, the phosphorylation patterns of differentially phosphorylated phosphoproteins in TRH- or TAL-treated cells were identical or displayed a similar trend in phosphorylation. However, some phosphoproteins, especially components of the Wnt/β-catenin/Tcf and YY1/Rb1/E2F pathways, exhibited different phosphorylation patterns in TRH- and TAL-treated cells. This supports the notion that TRH and TAL may act, at least in part, as biased agonists. Additionally, the deficiency of β-arrestin2 resulted in a reduced number of alterations in phosphorylation, highlighting the critical role of β-arrestin2 in the signal transduction from TRH-R in the plasma membrane to transcription factors in the nucleus.

From viral load to survival: Unveiling new genetic links for resistance against PMCV in Atlantic Salmon (Salmo salar)

The infectious agent piscine myocarditis virus (PMCV) causes cardiomyopathy syndrome (CMS) and is responsible for substantial mortality and economic losses in the Atlantic salmon (Salmo salar) farming industry. Previous research has demonstrated that breeding for resistance against PMCV is an effective approach to mitigate the disease's impact. In this study, a new quantitative trait locus (QTL) is described on chromosome 23, together with previously described QTLs on chromosomes 12 and 27. The findings are based on two genome-wide association studies conducted on two different year-classes of Atlantic salmon of the Rauma strain. In this study, we utilized data from an experimental challenge trial with the viral load as the phenotype and a field outbreak of CMS with survival data as the phenotype. The estimated SNP-based heritability was 0.55 and 0.44 in the two studies, respectively. In the infection trial, the top associated SNP on chromosome 23 accounted for approximately 46% of the genetic and 25.53% of the phenotypic variations in the viral load. In the field outbreak, we identified a QTL on the same genomic region of chromosome 23. The most significantly associated marker on this chromosome explained 13.57% and 5.97% of the genetic and phenotypic variations. The QTL on chromosome 23 is in proximity to delta-5 fatty acyl desaturase and fatty acid desaturase 2 genes, both of which play a role in the production of polyunsaturated fatty acids. This proximity is particularly interesting as it offers valuable insights into enhancing our understanding of resistance against PMCV.

Identification of anoikis-related genes classification patterns and immune infiltration characterization in ischemic stroke based on machine learning

Introduction

Ischemic stroke (IS) is a type of stroke that leads to high mortality and disability. Anoikis is a form of programmed cell death. When cells detach from the correct extracellular matrix, anoikis disrupts integrin junctions, thus preventing abnormal proliferating cells from growing or attaching to an inappropriate matrix. Although there is growing evidence that anoikis regulates the immune response, which makes a great contribution to the development of IS, the role of anoikis in the pathogenesis of IS is rarely explored.

Methods

First, we downloaded GSE58294 set and GSE16561 set from the NCBI GEO database. And 35 anoikis-related genes (ARGs) were obtained from GSEA website. The CIBERSORT algorithm was used to estimate the relative proportions of 22 infiltrating immune cell types. Next, consensus clustering method was used to classify ischemic stroke samples. In addition, we used least absolute shrinkage and selection operator (LASSO), support vector machine-recursive feature elimination (SVM-RFE) and random forest (RF) algorithms to screen the key ARGs in ischemic stroke. Next, we performed receiver operating characteristics (ROC) analysis to assess the accuracy of each diagnostic gene. At the same time, the nomogram was constructed to diagnose IS by integrating trait genes. Then, we analyzed the correlation between gene expression and immune cell infiltration of the diagnostic genes in the combined database. And gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analysis were performed on these genes to explore differential signaling pathways and potential functions, as well as the construction and visualization of regulatory networks using NetworkAnalyst and Cytoscape. Finally, we investigated the expression pattern of ARGs in IS patients across age or gender.

Results

Our study comprehensively analyzed the role of ARGs in IS for the first time. We revealed the expression profile of ARGs in IS and the correlation with infiltrating immune cells. And The results of consensus clustering analysis suggested that we can classify IS patients into two clusters. The machine learning analysis screened five signature genes, including AKT1, BRMS1, PTRH2, TFDP1 and TLE1. We also constructed nomogram models based on the five risk genes and evaluated the immune infiltration correlation, gene-miRNA, gene-TF and drug-gene interaction regulatory networks of these signature genes. The expression of ARGs did not differ by sex or age.

Discussion

This study may provide a beneficial reference for further elucidating the pathogenesis of IS, and render new ideas for drug screening, individualized therapy and immunotherapy of IS.