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 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.
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.
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 investigate the molecular pathogenesis of pulmonary fibrosis induced by bleomycin in a murine model,and provide novel insights for clinical diagnosis and treatment.
MethodsFrom Gene Expression Omnibus,we downloaded microarray data extracted from experiments of bleomycin induced pulmonary fibrosis in wild-type mice. With BRB-Array Tools,differentially expressed genes at different time points during disease development were screened,selected and analyzed by DAVID software.
ResultsBRB array analysis identified 45101 differentially expressed genes. After induction by bleomycin on 7th day,1164 genes and 735 genes were significantly up-regulated and down-regulated (P<0.05,fold change>2),respectively. On 14th day,731 genes and 390 genes were significantly up-regulated and down-regulated (P<0.05,fold change>2),respectively. DAVID analysis revealed that the up-regulated genes were significantly enriched in cell cycle,p53 signaling and chemokine signaling pathway,damaging reaction and collagen metabolism gene sets. While the down-regulated genes were enriched in the drug metabolism pathway gene set.
ConclusionsBioinformatics methodologies are able to efficiently analyze microarray data and extract its underlying information,provide novel insights for major molecular events and shift of cell signaling pathway during pulmonary fibrosis progression,and furthermore,finding molecular markers for early diagnosis and therapeutic targets.
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.
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.
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.
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.
