The rapid development of high-throughput chromatin conformation capture (Hi-C) technology provides rich genomic interaction data between chromosomal loci for chromatin structure analysis. However, existing methods for identifying topologically associated domains (TADs) based on Hi-C data suffer from low accuracy and sensitivity to parameters. In this context, a TAD identification method based on spatial density clustering was designed and implemented in this paper. The method preprocessed the raw Hi-C data to obtain normalized Hi-C contact matrix data. Then, it computed the distance matrix between loci, generated a reachability graph based on the core distance and reachability distance of loci, and extracted clustering clusters. Finally, it extracted TAD boundaries based on clustering results. This method could identify TAD structures with higher coherence, and TAD boundaries were enriched with more ChIP-seq factors. Experimental results demonstrate that our method has advantages such as higher accuracy and practical significance in TAD identification.
Chronic cerebral hypoperfusion (CCH) plays an important role in the occurrence and development of vascular dementia (VD). Recent studies have indicated that multiple stages of immune-inflammatory response are involved in the process of cerebral ischemia, drawing increasing attention to immune therapies for cerebral ischemia. This study aims to identify potential immune therapeutic targets for CCH using bioinformatics methods from an immunological perspective. We identified a total of 823 differentially expressed genes associated with CCH, and further screened for 9 core immune-related genes, namely RASGRP1, FGF12, SEMA7A, PAK6, EDN3, BPHL, FCGRT, HSPA1B and MLNR. Gene enrichment analysis showed that core genes were mainly involved in biological functions such as cell growth, neural projection extension, and mesenchymal stem cell migration. Biological signaling pathway analysis indicated that core genes were mainly involved in the regulation of T cell receptor, Ras and MAPK signaling pathways. Through LASSO regression, we identified RASGRP1 and BPHL as key immune-related core genes. Additionally, by integrating differential miRNAs and the miRwalk database, we identified miR-216b-5p as a key immune-related miRNA that regulates RASGRP1. In summary, the predicted miR-216b-5p/RASGRP1 signaling pathway plays a significant role in immune regulation during CCH, which may provide new targets for immune therapy in CCH.
Objective To investigate specific changes of T cell repertoire in convalescent patients infected by influenza A (H7N9) virus. Methods Peripheral blood samples from 8 convalescent patients infected by H7N9 virus and 10 healthy donors were collected. After extracting whole DNA from these samples, arm-PCR were performed and the products were submitted to Illumina HiSeq2000 platform to produce deep sequencing data of the nucleotide sequences of complementary determining region 3 of T cell receptor β chain (TRB). Differences were compared in TRB diversity and V-D-J gene usage and similarities of sequences between the patients and the healthy donors. Results Frequency of V-D-J gene usage was different between the H7N9 patient group and the healthy group, such as TRBV30, TRBV27, and TRBV18 (Student's t test, P < 05). Main component analysis showed V-J pairing pattern was significantly different between two groups, which may have potential in identifying patients from healthy people. A considerable number of shared CDR3s were found in patient-patient pairs and normal-normal pairs, while seldom were found in patient-normal pairs. The similarity between patients was also confirmed by overlap distance analysis. Indexes for assessing diversity of immune repertoires, Shannon-Weiner index and Simpson index, were both lower in the patients (Student's t test, P < 05), suggesting that the immune system of the patients had not recovered 6 months after H7N9 infection. Compared with the healthy donors, the number of hyper-expression clones increased in the patient group, and some of them showed similarity among patients. Conclusions TRB repertoires are less diverse in patients with increased hyper-expressed clones and identifiable V-J usage pattern, which is identifiable from normal population. These results suggest that there are H7N9-specific changes in TRB repertoires of H7N9 infected patients in convalescent phase, which have potential implication in diagnosis and therapeutic T cell development.
Objective To explore the expression of yes-associated protein 1 (YAP1), as a key protein of Hippo signal pathway, in rats with brain injury. Methods A total of 18 Sprague Dawley rats were randomly divided into three groups: normal group, sham operation group and brain injury group. The expression of YAP1 in rats with brain injury was detected by immunochemistry, quantitative polymerase chainreaction and Western blotting. Result Seventy-two hours after the brain injury, the expression level of YAP1 in protein and gene increased significantly in brain injury group, compared with those in the normal and sham operation group (P<0.05). Conclusion The expression of YAP1 increases in rats with brain injury, which maybe a new target for therapy.
ObjectiveTo investigate the significant genes in Mesio-temporal lobe epilepsy (MTLE) and explore the molecular mechanism of MTLE.MethodsThe microarray data of MTLE were downloaded from the Gene Expression Omnibus (GEO) database and analyzed by bioinformatics methods using GEO2R tool, Venny2.1.0, FUNRICH and Cytoscape software, DAVID and String databases.ResultsOf all the 331 differentially expressed genes(DEGs), 46 genes were down-regulated and 285 genes were up-regulated in dataset GSE88992; Furthermore, the core module genes were identified from those DEGs, which were expressed mostly in plasma membrane and extracellular space; The major molecular funtion were chemokine activity, cytokine activity and chemokine receptor binding; The main biological pathways involved neutrophil chemotaxis, inflammatory response and positive regulation of ERK1 and ERK2 cascade; The KEGG analysis showed DEGs enriched in Chemokine signaling pathway, Cytokine-cytokine receptor interaction and Complement and coagulation cascades. In addition, ten hub genes (Il6, Fos, Stat3, Ptgs2, Ccl2, Timp1, Cd44, Icam1, Atf3, Cxcl1) were found to significantly express in the MTLE.ConclusionThe pathogenesis of MTLE involves multiple genes, and multiple cell signaling pathways. Thus investigations of these genes may provide valuable insights into the mechanism of MTLE.
ObjectiveTo establish and validate the diagnostic model of ferroptosis genes for acute myocardial infarction (AMI) based on bioinformatics. MethodsFive AMI gene expression data were obtained from Gene Expression Omnibus (GEO), namely GSE66360, GSE48060, GSE60993, GSE83500, GSE34198. Among them, GSE66360 was used as the training set to perform differential analysis, and intersection of differential genes and ferroptosis genes was taken to obtain differentially expressed ferroptosis genes in AMI. GO and KEGG enrichment analysis was performed using Metascape website. Subsequently, random forest (RF) algorithm was used to screen out key genes with high classification performance according to the Keeny coefficient score, and artificial neural network (ANN) diagnostic model of AMI ferroptosis feature gene was constructed by model group GSE83500. The area under the receiver operating characteristic curve (AUC) of 10-fold cross-validation was used to evaluate the performance and generalization ability of the model, and 3 external independent datasets were used to verify the diagnostic performance of this model. The single sample gene setenrichment analysis was used to explore the difference in immune cell infiltration between infarcted myocardium and normal myocardium after AMI. In addition, correlation analysis between immune cells and key genes was also conducted. Finally, potential drugs that would prevent and treat AMI by regulating ferroptosis were screened out from the Coremin Medical platform. ResultsA total of 16 differentially expressed ferroptosis genes were obtained in the training set, GO enrichment analysis showed that they mainly participated in biological functions such as cellular response to biological stimuli and chemical stress, regulation of interleukin 17, etc. KEGG enrichment analysis showed that these genes were significantly enriched in NOD-like receptor signaling pathway, programmed cell necrosis, Leishmaniasis and other pathways. Four genes with good classification performance were screened out using RF algorithm, namely EPAS1, SLC7A5, FTH1, and ZFP36. The results of 10-fold cross-validation showed that the minimum AUC value was 0.746, the maximum value was 0.906, and the average value was 0.805. The AUC of the ANN model was 0.859, and the AUC values of the three independent validation sets were 0.763 (GSE48060), 0.673 (GSE60993), 0.698 (GSE34198). Immune cell infiltration found that macrophages, mast cells and monocytes were significantly active after AMI. Correlation analysis found that there were positive correlations between 4 key genes and activated dendritic cells, eosinophils and γδT cells. A total of 20 potential western medicines were predicted which could prevent and treat AMI by regulating ferroptosis, and the predicted potential Chinese medicine was mainly heat-clearing and detoxifying and blood-activating and removing blood stasis drugs. ConclusionThe identified AMI ferroptosis genes by bioinformatics method have certain diagnostic significance, which provides a reference for disease diagnosis and treatment.
Objective To investigate the expression levels of fatty acid metabolism-related genes in acute myeloid leukemia (AML) and construct a prognostic risk regression model for AML. Methods Gene expression data from control groups and AML patients were downloaded from the GTEx database and The Cancer Genome Atlas (TCGA) database, followed by screening for differentially expressed genes (DEGs) between AML patients and controls. Fatty acid metabolism-related genes were obtained from the MSigDB database. The intersection of DEGs and fatty acid metabolism-related genes yielded fatty acid metabolism-associated DEGs. A protein-protein interaction network was constructed using the STRING database. Hub genes were analyzed via random forest, Kaplan-Meier survival, and Cox proportional hazards regression based on TCGA clinical data to establish a prognostic model and evaluate their diagnostic and prognostic significance. Immune cell infiltration differences between high- and low-risk groups were assessed using CIBERSORT algorithms to explore immune microenvironment variations and correlations with risk scores. Results A total of 60 fatty acid metabolism-related DEGs were identified. Further screening revealed 15 hub genes, among which four genes (HPGDS, CYP4F2, ACSL1, and EHHADH) were selected via integrated random forest, Cox regression, and Kaplan-Meier analyses to construct an AML prognostic lipid metabolism gene signature. Heatmaps demonstrated statistically significant differences in tumor-infiltrating immune cell proportions between risk groups (P<0.05). Conclusion The constructed lipid metabolism gene prognostic model may serve as a biomarker for overall survival in AML patients and provide new insights for immunotherapy drug development.
ObjectiveTo lay a theoretical foundation for the research of regulation of Hyperpolarization activated cyclic nucleotide gated channel 1 (HCN1) gene expression and its involvement in the pathogenesis of Mesio-temporal lobe epilepsy (MTLE) and other related diseases, the bioinformatics methods were used to analyze sequence characteristic, transcription factors and their binding sites in the promoter region of human HCN1 gene, and the physicochemical properties, signal peptides, hydrophobicity, transmembrane regions, protein structure, interacting proteins and functions of HCN1 proteins.MethodBiological software and website, such as Protparam, Protscale, MHMM, SignalP 5.0, NetPhos 3.1, Swiss-Model, Promoter 2.0, AliBaba2.1 and EMBOSS were used to analyze and predict physicochemical properties, structural functions, localized expression, phylogenetic relationships and protein interactions with human HCN1 protein, and promoter, CpG island and transcription factor characteristics of HCN1 gene.ResultsThe evolutionary analysis of HCN1 protein showed that the genetic distance between human and Pongo abelii was the smallest, indicating the closest genetic relationship between human and Pongo abelii. Human HCN1 protein was an unstable hydrophilic protein located on the plasma membrane, which contained two transmembrane structure. However, the predicted results showed that there was no signal peptide and nuclear localization sequence in this protein. The secondary structure of HCN1 protein was mostly random coil and alpha helix, and it contained multiple potential phosphorylation sites. The ontology analysis results of HCN1 protein were showed as follows. The cellular component of HCN1 protein was located in the plasma membrane (GO:0005886); the molecular functionof HCN1 protein were cyclic adenosine monophosphate binding (GO:0030552) and voltage-gated ion channel activity (GO:0005244); the biological process of this protein were reacting to cAMP (GO:0071320) and transmembrane transport of potassium (GO:0071805). The analysis results of String database showed that the proteins that had close interaction with human HCN1 protein mainly included the ten proteins (HCN2, HCN4, PEX5L, MARCH7, KCTD3, GNAT3, SHKBP1, KCNQ2, FLNA and NEDD4L). These proteins were mainly involved in regulation of ion transport and transmembrane transport of potassium (GO:0071805). The HCN1 gene was located at 5p12 and contained 8 exons and 7 introns.There were at least three promoter regions in the nucleotide sequence of 2 000 bp from the upstream of the HCN1 gene to the 5 'flanks, and contained a 158 bp CpG island in the promoter region and one TATA boxes and one CAAT boxes in the 5' regulation region ofHCN1 gene; niceteen transcription factors, including NF-κB, NF-1, AP-1, TBP, IRF-1, c-Ets-1, Elf-1, HNF-3, HNF-1, YY1, GATA-1, RXR-α, GR, AP-2αA, ENKTF-1, C/EBPβ, C/EBPα, c-Fos and c-Jun, binding in the promoter region of the HCN1 gene were predicted by both softwares (AliBaba2.1 and PROMO2).ConclusionThe analysis results provide important information for further studies on the role of HCN1. Bioinformatics analysis of the promoter region can improve the research efficiency of gene promoters, and provide theoretical basis for subsequent experiments to construct expression vectors of HCN1 gene promoters and identify their functions.
Evidence-based medicine is the methodology of modern clinical research and plays an important role in guiding clinical practice. It has become an integral part of medical education. In the digital age, evidence-based medicine has evolved to incorporate innovative research models that utilize multimodal clinical big data and artificial intelligence methods. These advancements aim to address the challenges posed by diverse research questions, data methods, and evidence sources. However, the current teaching content in medical schools often fails to keep pace with the rapidly evolving disciplines, impeding students' comprehensive understanding of the discipline's knowledge system, cutting-edge theories, and development directions. In this regard, this article takes the opportunity of graduate curriculum reform to incorporate real-world data research, artificial intelligence, and bioinformatics into the existing evidence-based medicine curriculum, and explores the reform of evidence-based medicine teaching in the information age. The aim is to enable students to truly understand the role and value of evidence-based medicine in the development of medicine, while possessing a solid theoretical foundation, a broad international perspective, and a keen research sense, in order to cultivate talents for the development of the evidence-based medicine discipline.
Objective To study the expression of 4 circular RNA (circRNA) in peripheral blood mononuclear cells (PBMC) of patients with epilepsy and to predict its function by bioinformatics, so as to provide basis for exploring the pathogenesis of epilepsy. Methods From May 2020 to May 2021, 22 epilepsy patients were treated in the Department of Neurology of the First Affiliated Hospital of Baotou Medical College of Inner Mongolia University of Science and Technology, and 22 control group were selected. There were 13 males and 8 females in the epilepsy group, with an average age of (36.41±8.39)years. There were 11 males and 11 females in the control group, with an average age of (34.41±8.68) years. The expression levels of circRNA EFCAB2, C14orf159, PARG and TMEM39 in PBMC were detected by real-time fluorescence quantitative PCR, and their functions were predicted by bioinformatics. Results Compared with the control group, the relative expression of EFCAB2 and C14orf159 in PBMC of epileptic patients was 1.42±0.06 (t=29.41) and 1.31±0.03 (t=25.27), PARG and TMEM39 were not detected in peripheral blood PBMC. Bioinformatics analysis showed that three mirnas obtained by EFCAB2 were miR-6873-3p, miR-6739-3p and miR-7110-3p. Three mirnas were obtained by C14orf159: miR-1180-3p, miR-6501-3p, and miR-3622b-5p. The seizure-related genes were predicted by TargetScan database. EFCAB2: miR-6873-3p met the requirements of 11 downstream genes. A total of 7 downstream genes of miR-6739-3p met the requirements.A total of 14 downstream genes were eligible for miR-7110-3p and a total of 9 downstream genes were eligible for miR-6501-3p. A total of 14 downstream genes were eligible for miR-3622B-5p.miR-1180-3p has a total of 1 downstream genes that meet the requirements. Conclusions Studies have shown that two circrnas, EFCAB2 and C14orf159, may be important biological markers of epilepsy. Through bioinformatics analysis, these two circrnas may act as "molecular sponges" to regulate epilepsy. EFCAB2 has the potential to act as a "molecular sponge" for miR-6873-3p and miR-7110-3p, and it was found that miR-6873-3p and miR-7110-3 share a common downstream target gene MAP1B-which plays a role in epilepsy by regulating voltage-gated sodium channels. C14orf159 can act as a molecular sponge for miR-6501-3p to regulate the expression of CCL3 and play a role in epilepsy.