Isavuconazonium sulfate induces heart development defects in zebrafish larvae by upregulation of oxidative stress.

Environmental pollution remains a pressing global concern, with a substantial number of annual fatalities attributed to pollution-induced diseases. One emerging facet of environmental pollution is drug contamination, whereby pharmaceutical compounds can readily infiltrate water sources during manufacturing or utilization, subsequently being detected in various aquatic ecosystems. Some drugs have been detected in many watersheds at concentrations that can cause toxicity to aquatic organisms. Isavuconazonium sulfate (ISAV-SF), a prevalent antifungal medication, is no exception, warranting an exploration of its potential toxicity. However, limited research has been conducted in this domain. In this investigation, zebrafish were employed as a model organism to scrutinize the cardiotoxicity of ISAV-SF. Exposure of zebrafish embryos to concentrations of 0.5, 0.75, and 1 mg/L of ISAV-SF resulted in noteworthy cardiac developmental aberrations. These anomalies encompassed enlarged pericardial area, diminished heart rate, alterations in SV-BA distance, and the detachment of cardiomyocytes from the endocardium. Exposure to ISAV-SF caused disruption of the expression of genes related to cardiac development (gata4, klf2a, nkx2.5, vmhc, tbx2b), especially in the high concentration group. Moreover, the Notch signaling pathway was inhibited and oxidative stress levels were upregulated in all exposed groups. Remarkably, the administration of the antioxidant astaxanthin effectively mitigated oxidative stress levels, thus ameliorating heart developmental impairments. These results suggest that ISAV-SF may contribute to cardiac developmental defects by upregulating oxidative stress. This study serves as a pivotal reference for the utilization of ISAV-SF within the market, emphasizing the necessity to curtail its introduction into aquatic environments during production and consumption and to evaluate its repercussions on aquatic organisms.

ß-elemene alleviates esophageal fibrosis after endoscopic submucosal dissection via the FAP-mediated PTEN-PI3K/AKT signaling pathway.

Esophageal stricture caused by fibrosis is a serious complication after esophageal Endoscopic submucosal dissection (ESD). Myofibroblasts play a crucial role in esophageal fibrosis, so inhibiting activated myofibroblasts is a promising approach for treating esophageal fibrosis. ß-Elemene, a natural product with anti-tumor and anti-fibrotic properties, has not been thoroughly examined in esophageal fibrosis. Additionally, fibroblast activation protein (FAP) and PTEN-PI3K/AKT signaling pathway are both notably linked to fibrotic diseases. Therefore, we investigated the potential mechanisms of ß-elemene in esophageal fibrosis by treating primary human esophageal granulation fibroblasts (PHEGFs) with gradient concentrations of ß-elemene. Our findings demonstrated that ß-elemene inhibited the activity of PHEGFs in a dose-dependent manner, accompanied by downregulation of FAP, p-PI3K, and p-AKT protein expression, along with upregulation of p-PTEN protein expression. In addition, we substantiated the potential correlation between FAP and the PTEN-PI3K/AKT signaling pathway by establishing models of FAP overexpression and silencing. These results provide a new perspective on the potential mechanism of ß-elemene in relieving esophageal fibrosis and offer novel therapeutic strategies for managing post-esophageal ESD stricture in clinical practice.

Changes in the intestinal microbiota of individuals with non-alcoholic fatty liver disease based on sequencing: An updated systematic review and meta-analysis.

BACKGROUND: Alterations in the composition and abundance of the intestinal microbiota occur in non-alcoholic fatty liver disease (NAFLD). However, the results are inconsistent because of differences in the study design, subject area, and sequencing methodology. In this study, we compared the diversity and abundance of the intestinal microbiota of patients with NAFLD and healthy individuals through a systematic review and meta-analysis. METHODS: Three databases (PubMed, EMBASE, and Cochrane Library) were searched from their inception to March 20, 2023. A meta-analysis was performed using Stata software to analyze variations in the richness and abundance of the intestinal microbiota in patients with NAFLD. The Newcastle-Ottawa Quality Assessment Scale (NOS) was used for quality assessment. RESULTS: A total of 28 articles were included. Shannon diversity was reduced in patients with NAFLD (SMD = -0.24 (95% CI -0.43-0.05, I2 = 71.7%). The relative abundance of Ruminococcus, Faecalibacterium, and Coprococcus all decreased, with total SMDs of -0.96 (95% CI -1.29 to -0.63, I2 = 4.8%), -1.13 (95% CI -2.07 to -0.19, I2 = 80.5%), and -1.66 (95% CI -3.04 to -0.28, I2 = 91.5%). Escherichia was increased in individuals with NAFLD (SMD = 1.78, 95% CI 0.12 to 3.45, I2 = 94.4%). CONCLUSION: Increasing the species diversity and altering the abundance of specific gut microbiota, including Coprococcus, Faecalibacterium, Ruminococcus, and Escherichia, may be beneficial for improving NAFLD.

Iprodione induces hepatotoxicity in zebrafish by mediating ROS generation and upregulating p53 signalling pathway.

Iprodione is an effective and broad-spectrum fungicide commonly used for early disease control in fruit trees and vegetables. Due to rainfall, iprodione often finds its way into water bodies, posing toxicity risks to non-target organisms and potentially entering the human food chain. However, there is limited information available regarding the developmental toxicity of iprodione specifically on the liver in existing literature. In this study, we employed larval and adult zebrafish as models to investigate the toxicity of iprodione. Our findings revealed that iprodione exposure led to yolk sac edema and increased mortality in zebrafish. Notably, iprodione exhibited specific effects on zebrafish liver development. Additionally, zebrafish exposed to iprodione experienced an overload of reactive oxygen species, resulting in the upregulation of p53 gene expression. This, in turn, triggered hepatocyte apoptosis and disrupted carbohydrate/lipid metabolism as well as energy demand systems. These results demonstrated the substantial impact of iprodione on zebrafish liver development and function. Furthermore, the application of astaxanthin (an antioxidant) and p53 morpholino partially mitigated the liver toxicity caused by iprodione. To summarize, iprodione induces apoptosis through the upregulation of p53 mediated by oxidative stress signals, leading to liver toxicity in zebrafish. Our study highlights that exposure to iprodione can result in hepatotoxicity in zebrafish, and it may potentially pose toxicity risks to other aquatic organisms and even humans.

Endoscopic papillectomy combined with endoscopic retrograde cholangio-pancreatography for duodenal gangliocytic paraganglioma: A case report.

RATIONALE: Gangliocytic paraganglioma is a rare tumor that can occur in several organs throughout the body. Gangliocytic paraganglioma of the main duodenal papilla is even rarer. This study analyzes and discusses the endoscopic management of a case of gangliocytic paraganglioma of the main duodenal papilla and reviews the relevant literature. It is hoped that this study will increase clinicians' awareness of this disease. PATIENT CONCERNS: Electron endoscopy reveals a duodenal main papillary tumor, and the patient desires further clarification of the nature of the tumor and the next step in the treatment plan. DIAGNOSES: Duodenal gangliocytic paraganglioma. INTERVENTIONS: As the patient lesion was located in the main duodenal papilla, we successfully performed endoscopic minimally invasive treatment of the tumor by endoscopic papillectomy combined with endoscopic retrograde cholangiopancreatography. OUTCOMES: The patient was discharged after the postoperative removal of the nasobiliary drain and returned to the hospital 2 months later to have the biliary stent removed; the patient was in good general condition at follow-up. LESSONS: For duodenal main papillary tumor, we need to be alert to the possibility of gangliocytic paraganglioma. Since the tumor is located in the submucosa of the juxta-abdominal region, the preoperative biopsy positivity rate is low, and the tumor is often adjacent to or involves the biliopancreatic duct, endoscopic resection combined with endoscopic retrograde cholangiopancreatography can be considered for diagnosis and treatment.

Exploration of key ferroptosis-related genes and immune infiltration in Crohn's disease using bioinformatics.

Crohn's disease (CD) is a type of inflammatory bowel disease (IBD) that manifests mainly as chronic inflammation in different parts of the gastrointestinal tract, and its incidence has come to be increasing in recent years. Ferroptosis, a novel type of programmed cell death, it seems the role of ferroptosis-related biomarkers in CD has not been mentioned. Thus, the role of ferroptosis in CD and its relationship with immune infiltration were explored in this study. The CD dataset was downloaded from the Gene Expression Omnibus database. The validated ferroptosis genes (FRGs) were retrieved from the public FerrDb database. The gene expression matrix of the CD dataset was analyzed with the "limma" package in R language to obtain differentially expressed genes (DEGs) between diseased and healthy samples. Then, intersecting genes between DEGs and FRGs were identified as differentially expressed ferroptosis-associated genes (DE-FRGs). Protein-protein interaction (PPI) network analysis and visualization were carried out with STRING and Cytoscape, and key CD ferroptosis-related genes (CD-FRGs) were identified along with their Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways using the clusterProfiler package. Immune cell infiltration was analyzed with CIBERSORT. The correlation between key CD-FRGs and immune-infiltrated cells in CD was studied by Spearman's correlation method. A total of 37 DE-FRGs and 6 key CD-FRGs (CAV1, CD44, HIF1A, IFNG, TIMP1 and TLR4) were identified. GO and KEGG functional analysis indicated these genes enrichment in programmed cell death and apoptotic process, HIF-1 signaling pathway and IBD. Infiltration matrix analysis of immune cells showed abundant T cells CD4 memory activated, M1 macrophages, M2 macrophages, Mast cells activated and Neutrophils in CD intestinal tissues. The 6 key CD-FRGs were correlated with immune-infiltrated cells in CD based on correlation analysis. Taken together, immune cells with abnormal infiltration can be implicated in CD due to ferroptosis. This study identified 6 key CD-FRGs that may be key biomarkers of ferroptosis in CD; they include CAV1, CD44, HIF1A, IFNG, TIMP1 and TLR4. These findings suggest that the immune response is critical in CD caused by ferroptosis through the interaction between key CD-FRGs and immune infiltrating cells.

A case report of heterotopic gastric mucosa in the rectum treated by endoscopic submucosal dissection and a systematic review.

RATIONALE: Heterotopic gastric mucosa (HGM) can occur in all segments of the gastrointestinal tract, but rectal is very rare. In recent years, rectal HGM is more often treated by endoscopic resection (ER). PATIENT CONCERNS: A 28-year-old female was admitted to the hospital with the chief complaint of "a rectal lesion found on physical examination". DIAGNOSES: Heterotopic gastric mucosa (HGM). INTERVENTIONS: An endoscopic submucosal dissection (ESD) was performed to completely dissect the lesion. OUTCOMES: The patient recovered well at 1 month of follow-up and did not suffer from further blood in the stool. LESSONS: Rectal HGM has acid secretion function and HP can be colonized, causing a variety of symptoms such as abdominal pain, bloody stool, and anal pain and has the potential risk of malignant transformation; resection is the best treatment method, and ESD has its unique advantages and can be promoted in the clinic.

Boron-peptide conjugates with angiopep-2 for boron neutron capture therapy.

Boron neutron capture therapy (BNCT) induces intracellular nuclear reaction to destroy cancer cells during thermal neutron irradiation. To selectively eliminate cancer cells but avoid harmful effects on normal tissues, novel boron-peptide conjugates with angiopep-2, namely ANG-B, were constructed and evaluated in preclinical settings. Boron-peptide conjugates were synthesized using solid-phase peptide synthesis, and the molecular mass was validated by mass spectrometry afterwards. Boron concentrations in 6 cancer cell lines and an intracranial glioma mouse model after treatments were analyzed by inductively coupled plasma atomic emission spectroscopy (ICP-AES). Phenylalanine (BPA) was tested in parallel for comparison. In vitro treatment with boron delivery peptides significantly increased boron uptake in cancer cells. BNCT with 5 mM ANG-B caused 86.5% ± 5.3% of clonogenic cell death, while BPA at the same concentration caused 73.3% ± 6.0% clonogenic cell death. The in vivo effect of ANG-B in an intracranial glioma mouse model was evaluated by PET/CT imaging at 31 days after BNCT. The mouse glioma tumours in the ANG-B-treated group were shrunk by 62.9% on average, while the BPA-treated tumours shrank by only 23.0%. Therefore, ANG-B is an efficient boron delivery agent, which has low cytotoxicity and high tumour-to-blood ratio. Based on these experimental results, we expected that ANG-B may leverage BNCT performance in clinical applications in future.

Identification of hub genes and immune infiltration in ulcerative colitis using bioinformatics.

Ulcerative colitis (UC) is a chronic inflammatory disease of the intestine, whose pathogenesis is not fully understood. Given that immune infiltration plays a key role in UC progression, our study aimed to assess the level of immune cells in UC intestinal mucosal tissues and identify potential immune-related genes. The GSE65114 UC dataset was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) between healthy and UC tissues were identified using the "limma" package in R, while their Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were determined with the clusterProfiler package. Protein-protein interaction network analysis and visualization were performed with STRING and Cytoscape. Immune cell infiltration was calculated with CIBERSORT. The relationship between hub genes and immune-infiltrated cells in UC was determined by Pearson correlation. A total of 206 DEGs were identified, of which 174 were upregulated and 32 downregulated. GO and KEGG functional classification indicated DEG enrichment in immune response pathways, including Toll-like receptor signaling, IL-17 signaling, and immune system process and chemokine signaling. 13 hub genes were identified. Infiltration matrix analysis of immune cells showed abundant plasma cells, memory B cells, resting CD4 memory T cells, γδ T cells, M0 and M1 macrophages, and neutrophils in UC intestinal tissues. Correlation analysis revealed 13 hub genes associated with immune-infiltrated cells in UC. 13 hub genes associated with immune-infiltrated cells in UC were identified; they included CXCL13, CXCL10, CXCL9, CXCL8, CCL19, CTLA4, CCR1, CD69, CD163, IL7R, PECAM1, TLR8 and TLR2. These genes could potentially serve as markers for the diagnosis and treatment of UC.

Human papillomavirus associated XPF deficiency increases alternative end joining and cisplatin sensitivity in head and neck squamous cell carcinoma.

OBJECTIVES: Human papillomavirus (HPV) positive head and neck squamous cell carcinoma (HNSCC) showed a considerably better prognosis with greater cisplatin sensitivity compared to their HPV-negative counterparts. Deciphering the underlying molecular mechanisms for HPV-induced cisplatin sensitivity is imperative to improve the prognosis of HPV-negative HNSCC. MATERIALS AND METHODS: The Fanconi anemia (FA) pathway status in HNSCC cells was analysed by detecting the cell cycle and chromosomal aberrations. XPF expression was validated using PCR, western blot, and immunohistochemistry. Droplet digital PCR and GFP expressing reporter assay were used to analyse the changes in alternative end-joining (alt-EJ) levels. The cisplatin sensitization was verified by cell proliferation assay, clonogenic cell survival assay, and TUNEL. RESULTS: HPV-positive HNSCC cells showed significant prolonged G2-M cell cycle arrest and aberrant chromosome formation under interstrand crosslinker treatment. Both mRNA and protein expression of XPF were considerably decreased in HPV-positive HNSCC, according to the analysis of cellular and clinical data. XPF inhibition upregulated the activity of the alt-EJ pathway in HPV-negative HNSCC cells by 32.02% (P < 0.001) but had little effect on HPV-positive HNSCC. Consistent with this, simultaneous suppression of XPF and alt-EJ enhanced cisplatin sensitivity of HPV-negative HNSCC in vitro and in vivo. CONCLUSION: HPV-positive HNSCC cells exhibit a profound FA pathway deficiency associated with reduced XPF expression. HNSCC cells with compromised XPF function are more reliant on the alt-EJ pathway for genomic stability. Combining FA and alt-EJ inhibition may be used to cope with the hard-to-treat HPV-negative HNSCC.

Identifying differentially expressed genes and miRNAs in Kawasaki disease by bioinformatics analysis.

Kawasaki disease (KD) is an acute systemic immune vasculitis caused by infection, and its etiology and underlying mechanisms are not completely clear. This study aimed to identify differentially expressed genes (DEGs) with diagnostic and treatment potential for KD using bioinformatics analysis. In this study, three KD datasets (GSE68004, GSE73461, GSE18606) were downloaded from the Gene Expression Omnibus (GEO) database. Identification of DEGs between normal and KD whole blood was performed using the GEO2R online tool. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis of DEGs was undertaken with Metascape. Analysis and visualization of protein-protein interaction networks (PPI) were carried out with STRING and Cytoscape. Lastly, miRNA-genes regulatory networks were built by Cytoscape to predict the underlying microRNAs (miRNAs) associated with DEGs. Overall, 269 DEGs were identified, including 230 up-regulated and 39 down-regulated genes. The enrichment functions and pathways of DEGs involve regulation of defense response, inflammatory response, response to bacterium, and T cell differentiation. KEGG analysis indicates that the genes were significantly enriched in Neutrophil extracellular trap formation, TNF signaling pathway, Cytokine-cytokine receptor interaction, and Primary immunodeficiency. After combining the results of the protein-protein interaction (PPI) network and CytoHubba, 9 hub genes were selected, including TLR8, ITGAX, HCK, LILRB2, IL1B, FCGR2A, S100A12, SPI1, and CD8A. Based on the DEGs-miRNAs network construction, 3 miRNAs including mir-126-3p, mir-375 and mir-146a-5p were determined to be potential key miRNAs. To summarize, a total of 269 DEGs, 9 hub genes and 3 miRNAs were identified, which could be considered as KD biomarkers. However, further studies are needed to clarify the biological roles of these genes in KD.

The molecular basis of the associations between non-alcoholic fatty liver disease and colorectal cancer.

Background: Given the ongoing research on non-alcoholic fatty liver disease (NAFLD) and colorectal cancer (CRC), the number of studies suggesting a strong link between NAFLD and CRC is on the rise, while its underlying pathological mechanisms remain uncertain. This study aims to explore the shared genes and mechanisms and to reveal the molecular basis of the association between CRC and NAFLD through bioinformatics approaches. Methods: The Gene Expression Omnibus (GEO) dataset GSE89632 is downloaded for NAFLD cases and healthy controls. Additionally, the GSE4107 and GSE9348 datasets are obtained for CRC cases and healthy controls. Differentially expressed genes (DEGs) are obtained for NAFLD and CRC datasets, as well as shared genes between the two disorders. GO and KEGG enrichment analyses are further conducted. Subsequently, the STRING database and Cytoscape software are utilized to establish the PPI network and identify the hub genes. Then, co-expression analysis is performed using GeneMANIA. Subsequently, ROC curves and external datasets validation were applied to further screen the candidate markers. Finally, NetworkAnalyst is available as a means to construct a miRNA-gene regulatory network. Results: Under the threshold of FDR ≤ 0.01, 147 common genes are obtained in NAFLD and CRC. Categorization of GO functions shows that DEGs are predominantly enriched in "response to organic substance", "cellular response to chemical stimulus", and "response to external stimulus". The predominant KEGG pathways in DEGs are the "IL-17 signaling pathway", the "TNF signaling pathway", "Viral protein interaction with cytokine and cytokine receptor", "Cytokine-cytokine receptor interaction", and the "Toll-like receptor signaling pathway". Additionally, MYC, IL1B, FOS, CXCL8, PTGS2, MMP9, JUN, and IL6 are identified as hub genes by the evaluation of 7 algorithms. With the construction of miRNA-gene networks, 2 miRNAs, including miR-106a-5p, and miR-204-5p are predicted to be potential key miRNAs. Conclusion: This study identifies possible hub genes acting in the co-morbidity of NAFLD and CRC and discovers the interaction of miRNAs and hub genes, providing a novel understanding of the molecular basis for the relevance of CRC and NAFLD, thus contributing to the development of new therapeutic strategies to combat NAFLD and CRC.

Identification of hub ferroptosis-related genes and immune infiltration in lupus nephritis using bioinformatics.

Lupus nephritis (LN) is one of the most severe and more common organ manifestations of the autoimmune disease, systemic lupus erythematosus. Ferroptosis, a novel type of programmed cell death, so far its role in LN remains uncertain. In the present study, we explored the role of ferroptosis in LN and its relationship with the immune response. The GSE112943 LN dataset was downloaded from the Gene Expression Omnibus database. Ferroptosis-Related Genes (FRGs) that drive, suppress or mark ferroptosis were retrieved from the public FerrDb database. The gene expression matrix of the GSE112943 dataset was analyzed with the "limma" package in R to obtain differentially expressed genes (DEGs) between LN and healthy samples. Subsequently, the crossover genes between DEGs and FRGs were identified as differentially expressed ferroptosis-related genes (DE-FRGs). Protein-protein interaction (PPI) network analysis, visualization, and identification of hub lupus nephritis ferroptosis-related genes (LN-FRGs) were performed with STRING and Cytoscape, while their Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were determined with the clusterProfiler package. Immune cell infiltration was calculated with CIBERSORT. The relationship between hub LN-FRGs and immune-infiltrated cells in LN was determined by Pearson correlation. A total of 96 DE-FRGs and 8 hub LN-FRGs (KRAS, PIK3CA, EGFR, MAPK14, SRC, MAPK3, VEGFA, and ATM) were identified. GO and KEGG functional classification indicated these genes enrichment in apoptotic process, programmed cell death, autophagy-animal, FoxO signaling pathway, relaxin signaling pathway, and VEGF signaling pathway. Infiltration matrix analysis of immune cells showed abundant Monocytes and M0/M1/M2 macrophages in LN kidney tissues. Correlation analysis revealed 8 hub LN-FRGs associated with immune-infiltrated cells in LN. In summary, overproduction of ROS and abnormal infiltration of immune cells would be implicated in the LN caused by ferroptosis. 8 hub lupus nephritis ferroptosis-related genes (LN-FRGs) which might be good biomarkers of ferroptosis in LN were identified in this study. These findings point to the immune response playing an important role in LN caused by ferroptosis via mutual regulation between hub LN-FRGs and immune-infiltrated cells.

Tumor cell-derived exosomal lncRNA LOC441178 inhibits the tumorigenesis of esophageal carcinoma through suppressing macrophage M2 polarization.

Esophageal carcinoma (EC) is a highly malignant type of tumor. In a previous study, the authors found that long non-coding RNA (lncRNA) LOC441178 inhibited the tumorigenesis of EC. Moreover, exosomes derived from tumor cells containing lncRNAs were found to play a key role in the tumor environment; however, whether exosomes can affect the tumor microenvironment by carrying LOC441178 remains unclear. Thus, the present study aimed to clarify this. In order to assess the effects of exosomal LOC441178 in EC, cell invasion and migration were examined using the Transwell assay. Exosomes were identified using transmission electron microscopy, western blot analysis and nanoparticle tracking analysis. Furthermore, macrophage surface makers (CD206 and CD86) were analyzed using flow cytometry. Moreover, a subcutaneous xenograft mouse model was constructed to assess the role of TE-9 cells-derived exosomal LOC441178 in EC. The results revealed that LOC441178 overexpression notably suppressed the metastasis of EC cells. In addition, exosomes were successfully isolated from EC cells, and LOC441178 level was upregulated in exosomes derived from LOC441178-overexpressed EC cells. Exosomal LOC441178 also suppressed macrophage M2 polarization, and the polarized macrophages decreased EC cell invasion. Exosomes containing LOC441178 notably inhibited the growth of EC in mice. On the whole, the present study demonstrated that the delivery of LOC441178 by EC cell-secreted exosomes inhibited the tumorigenesis of EC by suppressing the polarization of M2 macrophages. These findings may provide a new theoretical basis for discovering new strategies against EC.

Detection of Alternative End-Joining in HNSC Cell Lines Using DNA Double-Strand Break Reporter Assays.

The main cellular pathways to repair DNA double-strand breaks (DSBs) and protect the integrity of the genome are homologous recombination (HR), non-homologous end-joining (NHEJ), and alternative end-joining (Alt-EJ). Polymerase theta-regulated Alt-EJ is an error-prone DSB repair pathway characterized by microhomology usage. Considering its importance in cancer treatment, technologies for detection of Alt-EJ in cancer cells may facilitate the study of the mechanisms of carcinogenesis and the development of new therapeutic targets. DSB reporter assay is the classical method for detecting Alt-EJ, which is primarily based on components of EJ2-puro cassette integration, I-SceI cleaving, and flow cytometry analysis. Here, we described an assay based on a modified I-Scel plasmid that can screen head and neck squamous cell carcinoma (HNSC) cells that were successfully transfected using selection medium with hygrovetine. We expect that this protocol will improve the fidelity and accuracy of reporter assays. Graphical abstract: Schematic overview of the workflow for establishment of Alt-EJ reporters.

Identifying hub genes and miRNAs in Crohn's disease by bioinformatics analysis.

Introduction: Crohn's disease (CD) is a disease that manifests mainly as chronic inflammation of the gastrointestinal tract, which is still not well understood in terms of its pathogenesis. The aim of this study was to use bioinformatics analysis to identify differentially expressed genes (DEGs) and miRNAs with diagnostic and therapeutic potential in CD. Materials and methods: Three CD datasets (GSE179285, GSE102133, GSE75214) were downloaded from the Gene Expression Omnibus (GEO) database. DEGs between normal and CD tissues were identified using the GEO2R online tool. The Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the DEGs were conducted using the clusterProfiler function in the R package. Protein-protein interaction network (PPI) analysis and visualization were performed with STRING and Cytoscape. Ten hub genes were identified using cytoHubba's MCC algorithm and validated with datasets GSE6731 and GSE52746. Finally, the miRNA gene regulatory network was constructed by Cytoscape and NetworkAnalyst to predict potential microRNAs (miRNAs) associated with DEGs. Results: A total of 97 DEGs were identified, consisting of 88 downregulated genes and 9 upregulated genes. The enriched functions and pathways of the DEGs include immune system process, response to stress, response to cytokine and extracellular region. KEGG pathway analysis indicates that the genes were significantly enriched in Cytokine-cytokine receptor interaction, IL-17 signaling pathway, Rheumatoid arthritis and TNF signaling pathway. In combination with the results of the protein-protein interaction (PPI) network and CytoHubba, 10 hub genes including IL1B, CXCL8, CXCL10, CXCL1, CXCL2, CXCL5, ICAM1, IL1RN, TIMP1 and MMP3 were selected. Based on the DEG-miRNAs network construction, 5 miRNAs including hsa-mir-21-5p, hsa-mir-93-5p, hsa-mir-98-5p, hsa-mir-1-3p and hsa-mir-335-5p were identified as potential critical miRNAs. Conclusion: In conclusion, a total of 97 DEGs, 10 hub genes and 5 miRNAs that may be involved in the progression or occurrence of CD were identified in this study, which could be regarded as biomarkers of CD.

Synthesis of Multisubstituted Allylic Alcohols via a Nickel-Catalyzed Cross-Electrophile Ring-Opening Reaction.

Herein we report a nickel-catalyzed cross-electrophile ring-opening reaction of vinyl epoxides wherein aryl iodides, alkyl iodides, and benzyl chlorides can all serve as the electrophilic coupling partners, providing a new approach to preparing multisubstituted allylic alcohols. This new method features broad substrate scope (76 examples), good step-economy, and high L/B- and E/Z selectivity as well as mild reaction conditions.

Identification of Differentially Expressed Genes and miRNAs for Ulcerative Colitis Using Bioinformatics Analysis.

Introduction: Ulcerative colitis (UC) is a chronic inflammatory disease of the intestine whose cause and underlying mechanisms are not fully understood. The aim of this study was to use bioinformatics analysis to identify differentially expressed genes (DEGs) with diagnostic and therapeutic potential in UC. Materials and methods: Three UC datasets (GSE179285, GSE75214, GSE48958) were downloaded from the Gene Expression Omnibus (GEO) database. DEGs between normal and UC tissues were identified using the GEO2R online tool. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the DEGs were performed using Metascape. Protein-protein interaction network (PPI) analysis and visualization using STRING and Cytoscape. Finally, the miRNA gene regulatory network was constructed by Cytoscape to predict potential microRNAs (miRNAs) associated with DEGs. Results: A total of 446 DEGs were identified, consisting of 309 upregulated genes and 137 downregulated genes. The enriched functions and pathways of the DEGs include extracellular matrix, regulation of cell adhesion, inflammatory response, response to cytokine, monocarboxylic acid metabolic process, response to toxic substance. The analysis of KEGG pathway indicates that the DEGs were significantly enriched in Complement and coagulation cascades, Amoebiasis, TNF signaling pathway, bile secretion, and Mineral absorption. Combining the results of the PPI network and CytoHubba, 9 hub genes including CXCL8, ICAM1, CXCR4, CD44, IL1B, MMP9, SPP1, TIMP1, and HIF1A were selected. Based on the DEG-miRNAs network construction, 7 miRNAs including miR-335-5p, mir-204-5p, miR-93-5p, miR106a-5p, miR-21-5p, miR-146a-5p, and miR-155-5p were identified as potential critical miRNAs. Conclusion: In summary, we identified DEGs that may be involved in the progression or occurrence of UC. A total of 446 DEGs,9 hub genes and 7 miRNAs were identified, which may be considered as biomarkers of UC. Further studies, however, are needed to elucidate the biological functions of these genes in UC.

Long noncoding RNA EIF1AX-AS1 promotes endometrial cancer cell apoptosis by affecting EIF1AX mRNA stabilization.

Long noncoding RNAs (lncRNAs) have been found to play an important role in the occurrence and development of endometrial carcinoma (EC). Here, using RNA sequencing analysis, we systemically screened and identified the lncRNA eukaryotic translation initiation factor 1A, X-linked (EIF1AX)-AS1, which is aberrantly downregulated in clinical EC tissues and closely correlated with tumor type. EIF1AX-AS1 markedly inhibited EC cell proliferation and promoted apoptosis in vitro and in vivo. Mechanistically, EIF1AX-AS1 interacts with EIF1AX mRNA and poly C binding protein 1 (PCBP1), which promote EIF1AX mRNA degradation. Intriguingly, by interacting with internal ribosome entry site-related protein Y-box binding protein 1 (YBX-1), EIF1AX promotes c-Myc translation through the internal ribosome entry site pathway. c-Myc promotes EIF1AX transcription and thus forms a feed-forward loop to regulate EC cell proliferation. Taken together, these data reveal new insights into the biology driving EC proliferation and highlights the potential of lncRNAs as biomarkers for prognosis and future therapeutic targets for cancer.

Trps1 targets Ccnd1 to regulate mouse Leydig cell proliferation.

BACKGROUND: The tricho-rhino-phalangeal syndrome-1 gene (Trps1) is an atypical GATA family member. Although current studies of Trps1 mainly focus on tumors, whether Trps1 plays a role in the male reproductive system remains unknown. OBJECTIVES: The purpose of this study was to elucidate the function of Trps1 in Leydig cells, indicating its regulatory mechanism on the cell cycle. METHODS: Gene-silencing technology, RNA-seq, RT-qPCR, and western blotting were used to evaluate the function of Trps1 in mouse primary Leydig cells and MLTC-1 cells. In addition, ChIP-base sets and ChIP-qPCR were employed to further assess the regulatory mechanism of Trps1 in MLTC-1 cells. RESULTS: Knockdown of Trps1 in Leydig cells significantly suppressed phosphorylation of Src and Akt and expression of Ccnd1, which was accompanied by impairment of cell proliferative ability. Trps1 may affect the cell cycle through the Src/Akt/Ccnd1 signaling pathway. In addition, Trps1 may bind to the promoter of Srcin1 to regulate its transcription, thus influencing Src phosphorylation levels and the proliferation of Leydig cells. DISCUSSION AND CONCLUSION: Src increases in Leydig cells during pubertal development, suggesting its functional involvement in differentiated adult Leydig cells. Inhibition of the Src/Akt pathway would reduce Ccnd1 expression. In the present study, we found that Trps1 may regulate the phosphorylation level of Src and Akt through Srcin1, targeting Ccnd1 to influence mouse Leydig cell proliferation. These findings shed light on the regulation of Trps1 on cell proliferation and differentiation of mouse Leydig cells.