Current Issue : July-September Volume : 2026 Issue Number : 3 Articles : 5 Articles
Background: Crohn’s disease (CD) is a chronic, complex inflammatory condition that can affect the entire digestive tract, most commonly the terminal ileum. The exact cause of CD remains unknown. Bioinformatics was used in this study to identify the differentially expressed genes (DEGs) and microRNAs (miRNAs) that show potential as diagnostic and therapeutic agents in treating CD. Materials and Methods: Datasets were downloaded from the Gene Expression Omnibus database and filtered. DEGs between CD samples and healthy control samples were identified using the GEO2R tool (including GEOquery and Linear Models for Microarray Analysis), and Kyoto Encyclopedia of Genes and Genomes/Gene Ontology enrichment analyses were conducted as part of the study to gain deeper insights into the data. A network depicting protein–protein interactions was established and visualized using the STRING database and Cytoscape software, and hub genes were identified and extracted utilizing the cytoHubba program. Cytoscape and miRTarBase were used to construct the miRNA–hub gene regulatory network and predict the potential miRNAs associated with the DEGs. The hub genes were analyzed further using ROC curves and combined ROC curve analyses of the GSE179285, GSE186582, and GSE112366 datasets. A regularized LASSO regression model was constructed to reduce the risk of overfitting. Results: Three datasets (GSE179285, GSE186582, and GSE112366) were selected. A comprehensive analysis of the three datasets revealed 60 DEGs that showed significantly altered expression levels, including 44 upregulated genes and 16 downregulated genes. Ten different algorithms were randomly used, and three hub genes (CXCL1, CXCL2, and CXCR2) were identified. Based on the miRNA–hub gene regulatory network, hsa-miR-1-3p and hsa-miR-335-5p were recognized as potentially vital miRNAs. Conclusion: Three hub genes (CXCL1, CXCL2, and CXCR2) and two miRNAs (hsa-miR-1-3p and hsa-miR-335-5p) are postulated to play a role in the initiation and progression of CD, thereby offering potential as biomarkers for this condition....
Emerging studies focused on extrachromosomal circular DNA (eccDNA) due to its various functions and complex mechanisms. The main technique for eccDNA detection is using high‐throughput sequencing followed by bioinformatics analysis, but with shortcomings such as low accuracy and efficiency. To address these limitations, we developed ECCFP, a bioinformatics pipeline that detects eccDNAs from long‐read sequencing data with rolling circle amplification. ECCFP retains all consecutive full passes from individual reads, including those from ghost sequences, to obtain the candidate eccDNAs. Subsequently, ECCFP employs the Boyer–Moore majority voting algorithm to consolidate the multiple candidate eccDNAs to generate an accurate unique eccDNA and circular consensus sequence. By using multiple simulated datasets and real sequencing datasets with spike‐in eccDNAs or publicly available, we conducted comprehensive evaluations of ECCFP and compared it with three currently published pipelines that have demonstrated superior performance. The results indicate that ECCFP outperforms other pipelines in sensitivity, accuracy, and runtime efficiency. Furthermore, outward PCR amplification followed by Sanger sequencing validation confirmed that ECCFP detects more accurate eccDNA junction position than other pipelines. Conclusively, ECCFP is an efficient and accurate bioinformatic pipeline for eccDNA detection from long‐read sequencing data, which might provide a robust tool for eccDNA characterization in various biological samples....
The use of genomics offers substantial benefits to society by revolutionising approaches to healthcare and personalised medicine. It enables early detection of genetic predispositions to various diseases, allowing for proactive and tailored treatment plans, access to clinical trials, and improved health outcomes. Additionally, genomic testing plays an important role in focusing research activity by advancing our understanding and knowledge of molecular contributions to diseases and driving innovation in medical science. ‘Genetic testing’ is sometimes used interchangeably with ‘genomic testing’ but they have different meanings. Genetic testing examines the functioning and composition of single genes. Genomic testing can be defined as a more complex test that analyses or provides interpretation of information about a single gene or genes, RNA, or chromosomes, with the addition of other types of molecular testing. The use of the term ‘genomic testing’ is future proofing our use of this type of information, as we are moving from a single gene test (genetic testing) towards more complex and nuanced methods (genomic testing)....
Xin’anjiang water buffalo (XAJB) is crucial for meat production and agricultural activities in Anhui Province of China. To generate hypotheses regarding how DNA methylation might correlate with transcriptional differences in skeletal muscle, WGBS and RNA-seq were performed on three BF and three BM adult XAJB. The results revealed 31,333 differentially methylated cytosines (DMCs), 1961 differentially methylated regions (DMRs), and 230 differentially expressed genes (DEGs) in skeletal muscle between the two groups. The qRT-PCR results of ten DEGs (COL1A1, THBS1, SLITRK4, VIPR2, IGFBP6, WIF1, MMP16, LMOD3, NPR3 and MYLK4) enriched in protein digestion and absorption pathway, PPAR signaling pathway, ECM-receptor interaction pathway or PI3K-Akt signaling pathway were consistent with the RNA-seq results. Most methylation changes occurred in CG context, and sixteen genes were predicted as dual differential genes in both methylation and transcriptome. Moreover, CG methylation showed a significant negative correlation with gene expression within the 2 kb upstream region (rho = −0.42, p < 0.001). Given the limited number of animals examined, additional investigations with expanded cohorts are essential to verify the association between the methylome and transcriptome signatures underlying skeletal muscle in XAJB....
Canine hepatocellular carcinoma (HCC) requires further molecular characterization to identify diagnostic and therapeutic targets, and to establish whether dogs with this condition can model the human disease. Accordingly, we aimed to identify differentially expressed genes (DEGs) in canine HCC and evaluate cross‐species transcriptomic dysregulation in canine and human HCC. Liver tissue samples from three dogs with HCC and three healthy dogs were subjected to next‐generation sequencing, followed by RT‐qPCR validation. Identified DEGs were then targeted in bioinformatics analyses (pathway enrichment, protein‐protein interaction network, and hub gene analyses) for molecular characterization and comparison with human HCC datasets. We identified 975 DEGs (upregulated: 604; and downregulated: 371). Extracellular matrix‐receptor interaction, focal adhesion, cell adhesion molecule, PI3K/Akt signaling, and cytokine/chemokine‐related pathways were enriched. C1R, APOC3, C1QA, APOA1, C1QB, ACTG1, C1QC, CRP, ANXA5, and ANXA2 were identified as hub genes. Canine and human HCCs share 118 DEGs, highlighting conserved alterations in metabolic pathways, PI3K‐Akt signaling, focal adhesion, and PPAR signaling pathways. Based on human HCC data, SPP1, NQO1, RRM2, APOA1, APOC3, ALDOB, and IGF1 were identified as prognosticators indicating poor overall survival. This study presents the first cross‐species transcriptomic analysis of canine HCC, revealing significant molecular resemblances to human HCC, indicating it may be a promising comparative model for studying tumor biology, drug responses, and novel therapeutic interventions....
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