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 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 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 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.
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.
ObjectiveTo explore the pathogenesis of tuberculosis and provide new ideas for its early diagnosis and treatment.MethodsGSE54992 gene expression profile was obtained from the gene expression database. Differentially expressed genes (DEGs) were screened using National Center forBiotechnology Information platform, and GO enrichment analysis, pathway analysis, pathway network analysis, gene network analysis, and co-expression analysis were performed to analyze the DEGs.ResultsCompared with the control group, a total of 3 492 genes were differentially expressed in tuberculosis. Among them, 1 686 genes were up-regulated and 1 806 genes were down-regulated. DEGs mainly involved small molecule metabolic processes, signal transduction, immune response, inflammatory response, and innate immune response. Pathway analysis revealed chemokine signaling pathway, tuberculosis, NF-Kappa B signaling pathway, cytokine-cytokine receptor interaction, and so on; gene signal network analysis found that the core genes were AKT3, PLCB1, MAPK8, and NFKB1; co-expression network analysis speculated that the core genes were PYCARD, TNFSF13, PHPT1, COMT, and GSTK1.ConclusionsAKT3, PYCARD, IRG1, CD36 and other genes and their related biological processes may be important participants in the occurrence and development of tuberculosis. Bioinformatics can help us to comprehensively study the mechanism of disease occurrence, which can provide potential targets for the diagnosis and treatment of tuberculosis.
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.