Correlation between Complement C1q A Chain (C1QA) and Macrophages in the Progression of Carotid Atherosclerosis.

Background: There is increasing evidence that macrophages are involved in the development of carotid atherosclerosis (CAS), but the specific mechanism is still unclear. We aimed to explore the key genes that play a regulatory role on macrophages in the progression of CAS. Methods: From 2021 August to 2023 August, GEO datasets GSE100927 and GSE43292 were downloaded and the key gene modules related to CAS were identified by weighted Gene co-expression network analysis (WGCNA). Kyoto Encyclopedia of Genes and Genes (KEGG) pathway analysis was performed on the genes of the key modules to identify common gene enrichment pathways. Differential expression analysis of pathway-related genes was performed by the "limma" package of R software. Case groups were categorized into high and low expression groups based on the expression levels of key genes, and ssGSEA immune infiltration analysis was performed. Results: The turquoise module of GSE100924 (threshold=12) and the brown module of GSE43292 (threshold=7) were obtained through WGCNA analysis. The analysis of KEGG showed that the differentially expressed genes in the turquoise and brown modules were co-enriched in the staphylococcus aureus infection signaling pathway. Differential expression analysis identified 18 common differentially expressed genes, all of which were highly expressed in the case group. C1QA is the gene of interest. According to ssGSEA analysis, the high expression group of C1QA showed a significant increase in the number of macrophages (GSE43292, P=0.0011; GSE100927, P=0.025). Conclusion: This study identified the key gene C1QA involved in regulating macrophage functional activity during the CAS process, providing new ideas for effective control of CAS.

Identification of deregulated lncRNAs in Alzheimer's disease: an integrated gene co-expression network analysis of hippocampus and fusiform gyrus RNA-seq datasets.

Introduction: The deregulation of lncRNAs expression has been associated with neuronal damage in Alzheimer's disease (AD), but how or whether they can influence its onset is still unknown. We investigated 2 RNA-seq datasets consisting, respectively, of the hippocampal and fusiform gyrus transcriptomic profile of AD patients, matched with non-demented controls. Methods: We performed a differential expression analysis, a gene correlation network analysis (WGCNA) and a pathway enrichment analysis of two RNA-seq datasets. Results: We found deregulated lncRNAs in common between hippocampus and fusiform gyrus and deregulated gene groups associated to functional pathways related to neurotransmission and memory consolidation. lncRNAs, co-expressed with known AD-related coding genes, were identified from the prioritized modules of both brain regions. Discussion: We found common deregulated lncRNAs in the AD hippocampus and fusiform gyrus, that could be considered common signatures of AD pathogenesis, providing an important source of information for understanding the molecular changes of AD.

Combined salt and low nitrate stress conditions lead to morphophysiological changes and tissue-specific transcriptome reprogramming in tomato.

Despite intense research towards the understanding of abiotic stress adaptation in tomato, the physiological adjustments and transcriptome modulation induced by combined salt and low nitrate (low N) conditions remain largely unknown. Here, three traditional tomato genotypes were grown under long-term single and combined stresses throughout a complete growth cycle. Physiological, molecular, and growth measurements showed extensive morphophysiological modifications under combined stress compared to the control, and single stress conditions, resulting in the highest penalty in yield and fruit size. The mRNA sequencing performed on both roots and leaves of genotype TRPO0040 indicated that the transcriptomic signature in leaves under combined stress conditions largely overlapped that of the low N treatment, whereas root transcriptomes were highly sensitive to salt stress. Differentially expressed genes were functionally interpreted using GO and KEGG enrichment analysis, which confirmed the stress and the tissue-specific changes. We also disclosed a set of genes underlying the specific response to combined conditions, including ribosome components and nitrate transporters, in leaves, and several genes involved in transport and response to stress in roots. Altogether, our results provide a comprehensive understanding of above- and below-ground physiological and molecular responses of tomato to salt stress and low N treatment, alone or in combination.

Identification of differentially expressed genes, pathways, and immune infiltration in diabetes.

This study aimed to perform exhaustive bioinformatic analysis by using GSE29221 micro-array maps obtained from healthy controls and Type 2 Diabetes (T2DM) patients. Raw data are downloaded from the Gene Expression Omnibus database and processed by the limma package in R software to identify Differentially Expressed Genes (DEGs). Gene ontology functional analysis and Kyoto Gene Encyclopedia and Genome Pathway analysis are performed to determine the biological functions and pathways of DEGs. A protein interaction network is constructed using the STRING database and Cytoscape software to identify key genes. Finally, immune infiltration analysis is performed using the Cibersort method. This study has implications for understanding the underlying molecular mechanism of T2DM and provides potential targets for further research.

Comparative transcriptomic profiles of Paulownia catalpifolia under different degrees of chilling stress during the seedling stage.

BACKGROUND: Paulownia, an ecologically and economically valuable plant species native to China, is notable for its excellent timber quality and strong adaptability. Among them, Paulownia catalpifolia displays the ability to survive in cold climate, a trait associated with northern China. Yet, the molecular information for its cold-tolerance has not been explored. This study was to investigate the changes in physiological indices and transcript levels of P. catalpifolia following cold exposure, which could provide evidence for revealing whether there were differences in the genetic basis of inducing physiological perturbations between moderate low temperature (MLT) and extreme low temperature (ELT). RESULTS: The detection of physiological indices under diverse degrees of chilling stress showed similar patterns of alteration. Enhanced accumulation of osmoregulatory substances, such as soluble sugar and soluble protein, were more conducive under ELT compared to MLT in P. catalpifolia. Moreover, we observed leaf wilting symptoms distinctly after exposure to ELT for 48 h, while this effect was not obvious after MLT exposure for 48 h. Comparative transcriptomic analysis between MLT and ELT demonstrated 13,688 differentially expressed genes (DEGs), most of them appeared after 12 h and 48 h of treatment. GO and KEGG analyses elucidated prominent enrichment in aromatic-L-amino-acid decarboxylase activity term and carbohydrate metabolism pathways. Therefore, it was speculated that the DEGs involved in the above processes might be related to the difference in the contents of soluble protein and soluble sugar between MLT and ELT. Time series clustering analyses further highlighted several key genes engaged in the 'Glycosyltransferases', 'Galactose metabolism' and 'Starch and sucrose metabolism' pathways as well as the 'tyrosine decarboxylase activity' term. For instance, cellulose synthase-like A (CLSA2/9), raffinose synthase (RafS2), ß-amylase (BAM1) and tyrosine/DOPA decarboxylase (TYDC1/2/5) genes, diverging in their expression trends between MLT and ELT, might significantly affect the soluble sugar and soluble protein abundance within P. catalpifolia. CONCLUSION: Between MLT and ELT treatments, partial overlaps in response pathways of P. catalpifolia were identified, while several genes regulating the accumulation of osmotic adjustment substances had disparate expression patterns. These findings could provide a novel physiological and molecular perspective for P. catalpifolia to adapt to complex low temperature habitats.

Global analysis of DNA methylation changes during experimented lingual carcinogenesis.

OBJECTIVES: This study aims to assess the role of DNA methylation changes in tongue cancer through a comprehensive analysis of global DNA methylation alterations during experimental lingual carcinogenesis. METHODS: C57BL/6J mice were subjected to 16-week oral administration of 4-nitroquinoline-1-oxide (4NQO, 50 mg/L). Lingual mucosa samples, being representative of normal tissue (week 0) and early (week 12) and advanced (week 28) tumorigenesis, were harvested for microarray and methylated DNA immunoprecipitation sequencing (MeDIP-Seq). The mRNA and promoter methylation of transforming growth factor-beta-signaling protein 1 (SMAD1) were evaluated with real-time quantitative reverse transcription polymerase chain reaction and Massarray in human lingual mucosa and tongue cancer cell lines. RESULTS: The cytosine guanine island (CGI) methylation level observed at 28 weeks surpassed that of both 12 weeks and 0 weeks. The promoter methylation level at 12 weeks exceeded that at 0 weeks. Notably, 208 differentially expressed genes were negatively correlated to differential methylation in promoters among 0, 12, and 28 weeks. The mRNA of SMAD1 was upregulated, concurrent with a decrease in promoter methylation levels in cell lines compared to normal mucosa. CONCLUSIONS: DNA methylation changed during lingual carcinogenesis. Overexpression of SMAD1 was correlated to promoter hypomethylation in tongue cancer cell lines.

Transcriptional pathobiology and multi-omics predictors for Parkinson's disease.

Early diagnosis and biomarker discovery to bolster the therapeutic pipeline for Parkinson's disease (PD) are urgently needed. In this study, we leverage the large-scale whole-blood total RNA-seq dataset from the Accelerating Medicine Partnership in Parkinson's Disease (AMP PD) program to identify PD-associated RNAs, including both known genes and novel circular RNAs (circRNA) and enhancer RNAs (eRNAs). There were 1,111 significant marker RNAs, including 491 genes, 599 eRNAs, and 21 circRNAs, that were first discovered in the PPMI cohort (FDR < 0.05) and confirmed in the PDBP/BioFIND cohorts (nominal p < 0.05). Functional enrichment analysis showed that the PD-associated genes are involved in neutrophil activation and degranulation, as well as the TNF-alpha signaling pathway. We further compare the PD-associated genes in blood with those in post-mortem brain dopamine neurons in our BRAINcode cohort. 44 genes show significant changes with the same direction in both PD brain neurons and PD blood, including neuroinflammation-associated genes IKBIP, CXCR2, and NFKBIB. Finally, we built a novel multi-omics machine learning model to predict PD diagnosis with high performance (AUC = 0.89), which was superior to previous studies and might aid the decision-making for PD diagnosis in clinical practice. In summary, this study delineates a wide spectrum of the known and novel RNAs linked to PD and are detectable in circulating blood cells in a harmonized, large-scale dataset. It provides a generally useful computational framework for further biomarker development and early disease prediction.

Transcriptome Analysis Reveals the Role of Sucrose in the Production of Latilactobacillus sakei L3 Exopolysaccharide.

Latilactobacillus (L.) sakei is a species of lactic acid bacteria (LAB) mostly studied according to its application in food fermentation. Previously, L. sakei L3 was isolated by our laboratory and possessed the capability of high exopolysaccharide (EPS) yield during sucrose-added fermentation. However, the understanding of sucrose promoting EPS production is still limited. Here, we analyzed the growth characteristics of L. sakei L3 and alterations of its transcriptional profiles during sucrose-added fermentation. The results showed that L. sakei L3 could survive between pH 4.0 and pH 9.0, tolerant to NaCl (<10%, w/v) and urea (<6%, w/v). Meanwhile, transcriptomic analysis showed that a total of 426 differentially expressed genes and eight non-coding RNAs were identified. Genes associated with sucrose metabolism were significantly induced, so L. sakei L3 increased the utilization of sucrose to produce EPS, while genes related to uridine monophosphate (UMP), fatty acids and folate synthetic pathways were significantly inhibited, indicating that L. sakei L3 decreased self-growth, substance and energy metabolism to satisfy EPS production. Overall, transcriptome analysis provided valuable insights into the mechanisms by which L. sakei L3 utilizes sucrose for EPS biosynthesis. The study provided a theoretical foundation for the further application of functional EPS in the food industry.

Development and evaluation of a chronic kidney disease risk prediction model using random forest.

This research aims to advance the detection of Chronic Kidney Disease (CKD) through a novel gene-based predictive model, leveraging recent breakthroughs in gene sequencing. We sourced and merged gene expression profiles of CKD-affected renal tissues from the Gene Expression Omnibus (GEO) database, classifying them into two sets for training and validation in a 7:3 ratio. The training set included 141 CKD and 33 non-CKD specimens, while the validation set had 60 and 14, respectively. The disease risk prediction model was constructed using the training dataset, while the validation dataset confirmed the model's identification capabilities. The development of our predictive model began with evaluating differentially expressed genes (DEGs) between the two groups. We isolated six genes using Lasso and random forest (RF) methods-DUSP1, GADD45B, IFI44L, IFI30, ATF3, and LYZ-which are critical in differentiating CKD from non-CKD tissues. We refined our random forest (RF) model through 10-fold cross-validation, repeated five times, to optimize the mtry parameter. The performance of our model was robust, with an average AUC of 0.979 across the folds, translating to a 91.18% accuracy. Validation tests further confirmed its efficacy, with a 94.59% accuracy and an AUC of 0.990. External validation using dataset GSE180394 yielded an AUC of 0.913, 89.83% accuracy, and a sensitivity rate of 0.889, underscoring the model's reliability. In summary, the study identified critical genetic biomarkers and successfully developed a novel disease risk prediction model for CKD. This model can serve as a valuable tool for CKD disease risk assessment and contribute significantly to CKD identification.

YAP/TAZ, beta-catenin, and TGFb pathway activation in medical plasma-induced wound healing in diabetic mice.

INTRODUCTION: Hippo is a signaling pathway that is evolutionarily conserved and plays critical roles in wound healing and tissue regeneration. Disruption of the transcriptional activity of both Hippo-associated factors, the yes-associated protein (YAP), and the transcriptional co-activator with PDZ binding motif (TAZ) has been associated with cardiovascular diseases, fibrosis, and cancer. This makes the Hippo pathway an appealing target for therapeutic interventions. OBJECTIVES: Prior research has indicated that medical gas plasma promotes wound healing by delivering a combination of reactive species directly to the affected areas. However, the involvement of YAP/TAZ and other signaling pathways in diabetic wound healing remains unexplored. METHODS: To this extent, ear wounds were generated and treated with gas plasma in streptozotocin (STZ)-induced diabetic mice. Transcriptome profiling at two wound healing stages (days 9 and 20 post-wounding) was performed in female and male mice. Additionally, we employed gene and protein expression analyses, utilizing immunohistological and -chemical staining of various targets as well as quantitative PCR and Western blot analysis. RESULTS: Gas plasma treatment accelerated healing by increasing re-epithelialization and modifying extracellular matrix components. Transcriptomic profiling charting the major alterations in gene expression following plasma treatment was followed by a validation of several targets using transcriptional and translational quantification as well as localization analyses. CONCLUSION: Our study evaluated the cellular regulation of essential targets of the Hippo and related pathways such as YAP/TAZ, ß-catenin, tumor growth factor ß, and oxidative stress signaling after plasma treatment. The activation of genes, pathways, and their regulators is an attractive therapeutic aim for a therapeutic intervention in dermal skin repair in diabetic diseases using medical gas plasmas.

Bioinformatics analysis of the association between obesity and gastric cancer.

Background: Obesity and gastric cancer (GC) are prevalent diseases worldwide. In particular, the number of patients with obesity is increasing annually, while the incidence and mortality rates of GC are ranked high. Consequently, these conditions seriously affect the quality of life of individuals. While evidence suggests a strong association between these two conditions, the underlying mechanisms of this comorbidity remain unclear. Methods: We obtained the gene expression profiles of GSE94752 and GSE54129 from the Gene Expression Omnibus database. To investigate the associated biological processes, pathway enrichment analyses were conducted using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes for the shared differentially expressed genes in obesity and GC. A protein-protein interaction (PPI) network was subsequently established based on the Search Tool for the Retrieval of Interacting Genes (STRING) database, followed by the screening of the core modules and central genes in this network using Cytoscape plug-in MCODE. Furthermore, we scrutinized the co-expression network and the interplay network of transcription factors (TFs), miRNAs, and mRNAs linked to these central genes. Finally, we conducted further analyses using different datasets to validate the significance of the hub genes. Results: A total of 246 shared differentially expressed genes (209 upregulated and 37 downregulated) were selected for ensuing analyses. Functional analysis emphasized the pivotal role of inflammation and immune-associated pathways in these two diseases. Using the Cytoscape plug-in CytoHubba, nine hub genes were identified, namely, CXCR4, CXCL8, CXCL10, IL6, TNF, CCL4, CXCL2, CD4, and CCL2. IL6 and CCL4 were confirmed as the final hub genes through validation using different datasets. The TF-miRNA-mRNA regulatory network showed that the TFs primarily associated with the hub genes included RELA and NFKB1, while the predominantly associated miRNAs included has-miR-195-5p and has-miR-106a-5p. Conclusion: Using bioinformatics methods, we identified two hub genes from the Gene Expression Omnibus datasets for obesity and GC. In addition, we constructed a network of hub genes, TFs, and miRNAs, and identified the major related TFs and miRNAs. These factors may be involved in the common molecular mechanisms of obesity and GC.

RNA-Seq Reveals Pathways Responsible for Meat Quality Characteristic Differences between Two Yunnan Indigenous Chicken Breeds and Commercial Broilers.

Poultry is a source of meat that is in great demand in the world. The quality of meat is an imperative point for shoppers. To explore the genes controlling meat quality characteristics, the growth and meat quality traits and muscle transcriptome of two indigenous Yunnan chicken breeds, Wuding chickens (WDs) and Daweishan mini chickens (MCs), were compared with Cobb broilers (CBs). The growth and meat quality characteristics of these two indigenous breeds were found to differ from CB. In particular, the crude fat (CF), inosine monophosphate content, amino acid (AA), and total fatty acid (TFA) content of WDs were significantly higher than those of CBs and MCs. In addition, it was found that MC pectoralis had 420 differentially expressed genes (DEGs) relative to CBs, and WDs had 217 DEGs relative to CBs. Among them, 105 DEGs were shared. The results of 10 selected genes were also confirmed by qPCR. The differentially expressed genes were six enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathways including lysosomes, phagosomes, PPAR signaling pathways, cell adhesion molecules, cytokine-cytokine receptor interaction, and phagosome sphingolipid metabolism. Interestingly, four genes (LPL, GK, SCD, and FABP7) in the PPAR signal pathway related to fatty acid (FA) metabolism were elevated in WD muscles, which may account for higher CF, inosine monophosphate content, and AA and FA contents, key factors affecting meat quality. This work laid the foundation for improving the meat quality of Yunnan indigenous chickens, especially WD. In future molecular breeding, the genes in this study can be used as molecular screening markers and applied to the molecular breeding of chicken quality characteristics.

Visfatin (NAMPT) affects global gene expression in porcine anterior pituitary cells during the mid-luteal phase of the oestrous cycle.

BACKGROUND: The pituitary belongs to the most important endocrine glands involved in regulating reproductive functions. The proper functioning of this gland ensures the undisturbed course of the oestrous cycle and affects the female's reproductive potential. It is believed that visfatin, a hormone belonging to the adipokine family, may regulate reproductive functions in response to the female's metabolic state. Herein we verified the hypothesis that suggests a modulatory effect of visfatin on the anterior pituitary transcriptome during the mid-luteal phase of the oestrous cycle. RESULTS: RNA-seq analysis of the porcine anterior pituitary cells revealed changes in the expression of 202 genes (95 up-regulated and 107 down-regulated in the presence of visfatin, when compared to the non-treated controls), assigned to 318 gene ontology terms. We revealed changes in the frequency of alternative splicing events (235 cases), as well as long noncoding RNA expression (79 cases) in the presence of the adipokine. The identified genes were associated, among others, with reproductive system development, epithelial cell proliferation, positive regulation of cell development, gland morphogenesis and cell chemotaxis. CONCLUSIONS: The obtained results indicate a modulatory influence of visfatin on the regulation of the porcine transcriptome and, in consequence, pituitary physiology during the mid-luteal phase of the oestrous cycle.

Identification of the differentially expressed activated memory CD4+ T-cells-related genes and ceRNAs in oral lichen planus.

Background: Oral lichen planus (OLP) is a common chronic oral mucosal disease with 1.4 % malignant transformation rate, and its etiology especially immune pathogenesis remains unclear. This study was aimed at investigating the immune cells related molecular underlying the pathophysiology of OLP through bioinformatics analysis. Methods: The dataset GSE52130 obtained from the Gene Expression Omnibus (GEO) database was conducted a comprehensive analysis in this study. The CIBERSORTx was used for investigating immune cells infiltration. The gene set enrichment analysis (GSEA) and gene ontology (GO) enrichment were performed for exploring the biological functions and gene annotation. The protein-protein interactions (PPI) were constructed by STRING database and visualized by Cytoscape software. The cytohubba plugin was utilized for screening hub genes. The receiver operating characteristic (ROC) was performed for evaluating diagnostic value of hub genes. The miRNAs, lncRNAs and drugs were respectively predicted by NetworkAnalyst, miRTarbase, ENCORI, and DGIdb database. Results: This study identified 595 differentially expressed genes (DEGs). The GSEA indicated keratinization, innate immune system and biological oxidation were involved in OLP. GO analysis showed extracellular matrix and keratinocyte were mainly enriched. And we found the activated memory CD4+ T cells were lowly infiltrated in OLP. We identified 101 activated memory CD4+ T-cells-related DEGs. Three hub genes (APP, IL1B, TF) were selected. APP and IL1B were significantly up-regulated, whereas TF was down-regulated in OLP. The three hub genes show high diagnostic value in OLP. Additionally, they were involved in MAPK signal, NF-kappaB signal and iron metabolism in OLP. What's more, NEAT1/XIST - miR - 15a - 5p/miR - 155-5p - APP/IL1B signal axis was focused in competing endogenous RNA (ceRNA) network. In addition, 35 drugs were predicted for OLP. Conclusion: Three activated memory CD4+ T-cells-related DEGs were identified by integrative analysis. It may provide novel insight into the pathogenesis of OLP and suggest potential therapeutic targets for OLP.

Identification and role of differentially expressed genes/proteins between pulmonary tuberculosis patients and controls across lung tissues and blood samples.

BACKGROUND: Differentially expressed genes/proteins (DEGs/DEPs) play critical roles in pulmonary tuberculosis (PTB) diagnosis and treatment. However, there is a scarcity of reports on DEGs/DEPs in lung tissues and blood samples in PTB patients. OBJECTIVE: We aim to identify the DEGs/DEPs in lung tissues and blood samples of PTB patients and investigate their roles in PTB. MATERIALS AND METHODS: The lung granulomas and normal tissues were collected from PTB patients for proteomic and transcriptomic analyses. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses annotated the functions of DEGs/DEPs. The GSE107994 data set was downloaded to identify the DEGs/DEPs in peripheral blood. The common DEGs and DEPs were identified. A nomogram was established. Pearson correlation analysis was conducted. RESULTS: Eighty-three DEGs/DEPs were identified. These DEGs/DEPs were mainly enriched in the movement of cell or subcellular components, regulation of cellular component biogenesis, and actin filament-based process as well as in the pathways of inositol phosphate metabolism, adherens junction, phosphatidylinositol signaling system, leukocyte transendothelial migration, regulation of actin cytoskeleton, and tight junction. There were eight common DEGs/DEPs (TYMP, LAP3, ADGRL2, SIL1, LMO7, SULF 1, ANXA3, and PACSIN3) between the lung tissues and blood samples. They were effective in predicting tuberculosis. Moreover, the activated dendritic cells, macrophages, monocytes, neutrophils, and regulatory T cells were significantly positively correlated with TYMP (r > .50), LAP3 (r > .50), SIL1 (r > .50), ANXA3 (r > .5), and PACSIN3 (r < .50), while negatively correlated with LMO7 (r < -0.50) (p < .05). ADGRL2 and SULF1 did not have a significant correlation (p > .05). LIMITATIONS: The sample size was small. CONCLUSIONS: Eight common DEGs/DEPs of lung tissues and blood samples were identified. They were correlated with immune cells and demonstrated predictive value for PTB. Our data may facilitate the diagnosis and treatment of PTB.

Toxic effects of freshwater grouper (Acrossocheilus fasciatus) eggs on poultry: Morphological and transcriptomic insights into hepatic toxicity.

Fish egg poisoning is a serious and neglected public menace that kills hundreds of people and numerous poultry each year. Freshwater groupers (Acrossocheilus fasciatus) are common food fish in the southeastern regions of China. Their toxic eggs are regarded as a significant public health concern. The molecular mechanisms of egg-toxin toxicity in freshwater grouper to poisoned organisms are elusive. In this study, black-boned chicks were exposed to toxic eggs from freshwater grouper at a lethal dose. The hepatic morphology of the intoxicated chick was assessed. An analysis of the liver gene expression profile was conducted by comparing samples exposed to toxic eggs with control samples using RNA-Seq. The result revealed that an increase in vacuolation and congestion was observed in chicks with toxic eggs exposure. The transcriptome analysis revealed 5421 genes with differential expression, comprising 2810 up-regulated and 2611 down-regulated genes. The genes were primarily linked to energy metabolism, cell apoptosis, cell adhesion, exogenous microbial infection, and cell junction. The most strongly upregulated genes were cholecystokinin (CCK), cholecystokinin A receptor (CCKAR), and unc-80 homolog, NALCN activator (UNC80), and the most downregulated genes were glycine amidinotransferase (GATM), fatty acid desaturase 2 (FADS2), and hexokinase 2 (HKDC1). GO term with the highest enrichment of DEGs is nucleosome assembly. According to KEGG pathways, the three most significant metabolic pathways in the liver are DNA replication, retinol metabolism, and steroid biosynthesis. The results could be crucial for comprehending the negative biological impacts of egg-toxin and its toxic mechanisms. The outcome could provide potential biomarkers of egg-toxin exposure in hepatic, which might be useful for manufacturing an antidote to egg-toxin and providing valuable insights for ecotoxicity studies.

Identification and functionalization of thyrotropin receptor antibodies (TRAb) with different antigenic epitopes.

CONTEXT: One of the sensitive markers for autoimmune thyroid disease (AITD) clinical identification is TRAb. To quickly distinguish TRAb with distinct antigenic epitopes, a straightforward and uncomplicated technique has not yet been created. OBJECTIVE: To search for molecular diagnostic targets for different types of AITD (Graves' disease (GD), Graves' orbitopathy (GO), GD with III degree goiter (GD(3)), Hypothyroidism combined with positive TRAb (HT(TRAb+))) as molecular diagnostic targets. METHODS: Following action on thyroid cells, differential genes (DEGs) generated by TRAb with distinct antigenic epitopes were detected and identified by RNA-seq, bioinformatics analysis, and RT-qPCR in the serum of AITD patients. Using the EdU assay, the effect of co-culturing thyroid cells with different antigenic TRAb epitopes on the cells' capacity to proliferate was investigated. RESULTS: Bioinformatics analysis and RT-qPCR validation identified one GD key gene (AHSG), two GO key genes (ADRA1D and H2BC18), two GD(3) key genes (SOCS1 and CYBB), and one HT (TRAb+) key gene (MASP2). Correlation analysis and ROC curves showed that the above genes could be used as molecular diagnostic targets for different types of AITD. Finally, EdU results showed that TRAb inhibited thyroid cell proliferation in the HT (TRAb+) group compared with the normal control group, while the remaining three groups promoted thyroid cell proliferation, with a statistically significant difference (P < 0.05). CONCLUSION: We identified six key genes for different types of AITD, which have diagnostic value for different types of AITD. Meanwhile, we found that TRAb of different antigenic epitopes in AITD have different biological functions.

Transcriptome analysis of differentially expressed genes in rice seedling leaves under different nitrate treatments on resistance to bacterial leaf blight.

Nitrogen (N), as one of the most abundant mineral elements in rice, not only is the primary limiting factor for rice yield, but also impacts plant disease resistance by modulating plant morphology, regulating biochemical characteristics, as well as enhancing metabolic processes. Bacterial blight, a severe bacterial disease caused by Xanthomonas oryzae pv. oryzae (Xoo), significantly impairing rice yield and quality. Previous studies have shown that moderate application of nitrate nitrogen can improve plant disease resistance. However, further exploration is urgently required to investigate the involvement of the nitrate nitrogen signaling pathway in conferring resistance against bacterial leaf blight. In this study, we employed transcriptome sequencing to analyze the differentially expressed genes under various concentrations of nitrate supply duringrice bacterial blight infection. Our research reveals that nitrate nitrogen supply influences rice resistance to bacterial leaf blight. Through transcriptomic profiling of rice leaves inoculated under different nitrate nitrogen concentrations, we identified 4815 differentially expressed genes (DEGs) among four comparison groups, with notable differences in DEG enrichment between low and high nitrate nitrogen conditions, with some members of the NPF family implicated and we preliminarily elucidated the molecular regulatory network in which nitrate nitrogen participates in bacterial leaf blight resistance. Our findings provide a novel insight into a mechanism involving the nitrate nitrogen drive wider defense in rice.

Identification of key genes associated with cervical cancer based on bioinformatics analysis.

BACKGROUND: Cervical cancer has extremely high morbidity and mortality, and its pathogenesis is still in the exploratory stage. This study aimed to screen and identify differentially expressed genes (DEGs) related to cervical cancer through bioinformatics analysis. METHODS: GSE63514 and GSE67522 were selected from the GEO database to screen DEGs. Then GO and KEGG analysis were performed on DEGs. PPI network of DEGs was constructed through STRING website, and the hub genes were found through 12 algorithms of Cytoscape software. Meanwhile, GSE30656 was selected from the GEO database to screen DEMs. Target genes of DEMs were screened through TagetScan, miRTarBase and miRDB. Next, the hub genes screened from DEGs were merged with the target genes screened from DEMs. Finally, ROC curve and nomogram analysis were performed to assess the predictive capabilities of the hub genes. The expression of these hub genes were verified through TCGA, GEPIA, qRT-PCR, and immunohistochemistry. RESULTS: Six hub genes, TOP2A, AURKA, CCNA2, IVL, KRT1, and IGFBP5, were mined through the protein-protein interaction network. The expression of these hub genes were verified through TCGA, GEPIA, qRT-PCR, and immunohistochemistry, and it was found that TOP2A, AURKA as well as CCNA2 were overexpressed and IGFBP5 was low expression in cervical cancer. CONCLUSIONS: This study showed that TOP2A, AURKA, CCNA2 and IGFBP5 screened through bioinformatics analysis were significantly differentially expressed in cervical cancer samples compared with normal samples, which might be biomarkers of cervical cancer.