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.
Objective To explore the pathogenesis of acute respiratory disease syndrome (ARDS) by bioinformatics analysis of neutrophil gene expression profile in order to find new therapeutic targets. Methods The gene expression chips include ARDS patients and healthy volunteers were screened from the Gene Expression Omnibus (GEO) database. The differentially expressed genes were carried out through GEO2R, OmicsBean, STRING, and Cytoscape, then enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genomes (KEGG) pathways was conducted to investigate the biological processes involved in ARDS via DAVID website. Results Bioinformatics analysis showed 86 differential genes achieved through the GEO2R website. Eighty-one genes were included in the STRING website for protein interaction analysis. The results of the interaction were further analyzed by Cytoscape software to obtain 11 hub genes: AHSP, ALAS2, CD177, CLEC4D, EPB42, GPR84, HBD, HVCN1, KLF1, SLC4A1, and STOM. GO analysis showed that the differential gene was enriched in the cellular component, especially the integrity of the plasma membrane. KEGG analysis showed that multiple pathways especially the cytokine receptor pathway involved in the pathogenesis of ARDS. Conclusions A variety of genes and pathways have been involved in the pathogenesis of ARDS. Eleven hub genes are screened, which may be involved in the pathogenesis of ARDS and can be used in subsequent studies.
現已認識到免疫反應、轉錄因子核因子κB( NF-κB) 的激活、細胞因子、中性粒細胞的激活和肺泡滲入、凝血級聯反應、腎素-血管緊張素系統等多種因素構成的復雜網絡參與急性肺損傷/急性呼吸窘迫綜合征( ALI/ARDS) 的發病過程[ 1-5] 。雖然膿毒癥、創傷、肺炎等ALI/ARDS誘發因素很常見, 但僅有部分病人發生ALI/ARDS, 并且具有相似臨床特征的ALI/ARDS病人可有截然不同的結果, 這種異質性引起研究者對影響ALI/ARDS 易感性和預后的遺傳因子進行鑒別的濃厚興趣[ 6] 。由于數量龐大的表現型變異, 不完全的基因外顯率、復雜的基因-環境相互作用及高度可能的基因座不均一性而使ALI 遺傳學的研究受到挑戰[ 7] 。近年來基因組學技術被應用于ALI/ARDS 發病機制的研究, 加深了人們對ALI/ARDS的認識并有可能發展出新的治療策略以降低其發病率和病死率。
ObjectiveA competing endogenous RNA (ceRNA) regulatory network associated with long non-coding RNA (lncRNA) specific for lung adenocarcinoma (LUAD) was constructed based on bioinformatics methods, and the functional mechanism of actinfilament-associated protein 1-antisense RNA1 (AFAP1-AS1) in LUAD was analyzed, in order to provide a new direction for the study of LUAD therapeutic targets. MethodsThe gene chip of LUAD was downloaded from the Gene Expression Omnibus (GEO), and lncRNA and mRNA with differential expression between LUAD and normal tissues were screened using GEO2R online software, and their target genes were predicted by online databases to construct ceRNA networks and perform enrichment analysis. In cell experiments, AFAP1-AS1 was genetically knocked down and siRNA was constructed and transfected into LUAD cells A549 by cell transfection. CCK8, transwell, scratch assay and flow cytometry were used to detect the ability of cells to proliferate, invade, migrate and apoptosis. ResultsA total of 6 differentially expressed lncRNA and 494 differentially expressed mRNA were identified in the microarray of LUAD. The ceRNA network involved a total of 6 lncRNA, 22 miRNA, and 55 mRNA. Enrichment analysis revealed that mRNA was associated with cancer-related pathways. In cell assays, knockdown of AFAP1-AS1 inhibited cell proliferation, invasion, and migration, and AFAP1-AS1 promoted apoptosis. ConclusionIn this study, we construct a lncRNA-mediated ceRNA network, which may help to further investigate the mechanism of action of LUAD. In addition, through cellular experiments, AFAP1-AS1 is found to have potential as a therapeutic target for LUAD.
Objective To screen the differentially expressed genes and pathways involved in rosacea using bioinformatics analysis. Methods The GSE65914 gene chipset was collected from the Gene Expression Omnibus (up to July 12th, 2021). It was searched according to the keyword “rosacea”. The data was analyzed by GEO2R platform. The common differential genes of three subtypes of rosacea were screened out. The online DAVID analysis tool was used to perform the gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Protein-protein interaction networks of differentially expressed genes were made by String and Cytoscape. The key modules and genes were screened by Mcode and Cytohubba. Results A total of 957 common differential genes were identified, including 533 up-regulated genes and 424 down-regulated genes. GO enrichment analysis showed that these genes were mainly involved in immune response, inflammatory response, intercellular signal transduction, positive regulation of T cell proliferation, chemokine signaling pathways, cell surface receptor signaling pathways, cellular response to interferon-γ, and other biological processes. KEGG pathway enrichment analysis mainly included cytokine-cytokine receptor interaction, rheumatoid arthritis, chemokine signaling pathway, PPAR signaling pathway, Toll-like receptor signaling pathway, nuclear transcription factor-κB signaling pathway, tumor necrosis factor signaling pathway and other signaling pathways. Cytohubba analysis revealed 10 key genes, including PTPRC, MMP9, CCR5, IL1B, TLR2, STAT1, CXCR4, CXCL10, CCL5 and VCAM1. Conclusion The key genes and related pathways may play an important role in the pathogenesis of rosacea.
Circular RNA are one kind of non-coding RNA, charactered by covalently closed rings. They can influence biological functions such as cell transduction and protein synthesis. They are associated with pathogenesis of many diseases and become a novel family of biomarkers. Now we try to introduce the origin, structure, function of circular RNA and the involved research methodology. Furthermore, we primarily discuss their application in the tuberculosis research.
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.
ObjectiveTo analyze the expression profile changes of osteogenic-related genes during spontaneous calcification of rat bone marrow mesenchymal stem cells (BMSCs). MethodsBMSCs were isolated from 3-day-old healthy Sprague Dawley rats;cells at the 4th generation were used to establish the spontaneous calcification model in vitro. Spontaneous calcification process was recorded by inverted phase contrast microscope observation and alizarin red staining after 7 and 14 days of culture. For gene microarray analysis, cell samples were collected at 0, 7, and 14 days after culture; the differentially expressed genes were analyzed by bioinformatics methods and validated by real-time quantitative PCR (RT-qPCR) assay. ResultsRat BMSCs calcified spontaneously in vitro. When cultured for 7 days, the cells began to aggregate and were weakly positive for alizarin red staining. After 14 days of culture, obvious cellular aggregation and typical mineralized nodules were observed, the mineralized nodules were brightly positive for alizarin red staining. A total of 576 gene probe-sets expressed differentially during spontaneous calcification, corresponding 378 rat genes. Among them, 359 gene probe-sets expressed differentially between at 0 and 7 days, while only 13 gene probe-sets expressed differentially between at 7 and 14 days. The 378 differentially expressed genes were divided into 6 modes according to their expression profiles. Moreover, according to their biological functions, differentially expressed genes related to bone cell biology could be classified into 7 major groups:angiogenesis, apoptosis, bone-related genes, cell cycle, development, cell communication, and signal pathways related to osteogenic differentiation. In cell cycle group, 12 down-regulated genes were linked with each other functionally. Matrix metalloproteinase 13 (Mmp13), secreted phosphoprotein 1 (Spp1), Cxcl12, Mmp2, Mmp3, Apoe, and Itga7 had more functional connections with other genes. The results of genes Spp1, Mgp, Mmp13, Wnt inhibitory factor 1, Cxcl12, and cyclin A2 by RT-qPCR were consistent with that of gene microarray. ConclusionThe first 7 days after rat BMSCs were seeded are a key phase determining the fate of spontaneous calcification. Multiple genes related with cell communication, bone-related genes, cell cycle, transforming growth factor-β signaling pathway, mitogen-activated protein kinase signaling pathway, and Wnt signaling pathway are involved during spontaneous calcification.
ObjectiveTo conduct a bioinformatics analysis of gene expression profiles in frontal lobe of patients with Parkinson disease (PD), in order to explore the potential mechanism related to depression in PD.MethodsAll the bioinformatics data before March 20th 2019 were acquired from Gene Expression Omnibus (GEO) database, using " Parkinson disease” as the key word. The species was limited to human (Homo sapiens), and the detective method was limited to expression profiling by array. ImgGEO (Integrative Gene Expression Meta-Analysis from GEO database), DAVID (the Database for Annotation, Visualization and Integrated Discovery), STRING and Cytoscape 3.6.1 software were utilized for data analysis.ResultsTotally, 45 samples (24 PD cases and 21 healthy controls) were obtained from 2 datasets. We identified 236 differentially expressed genes (DEGs) in the post-mortem frontal lobe between PD cases and healthy controls, in which 146 genes were up-regulated and 90 genes were down-regulated. Based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis, the DEGs were mainly enriched in the structures of postsynaptic membrane, cell membrane component, postsynaptic membrane dense area, and myelin sheath, and were involved in the occurrence of PD, depression, and other diseases. These genes were involved in the biological processes of dopaminergic, glutamate-nergic, GABA-nergic synapses, and some other synapses, as well as several signaling pathways (e.g. mitogen- activated protein kinase signal pathway, p53 signal pathway, and Wnt signal pathway), which were associated with PD and depression pathogenesis. Besides, we found that NFKBIA, NRXN1, and RPL35A were the Hub proteins.ConclusionsGene expression in frontal lobe of patients with PD is associated with the pathogenesis of PD. This study provides a theoretical basis for understanding the mechanism of PD occurrence and progression, as well as the potential mechanism of depression in PD.
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.