Project description:Deubiquitinating enzymes (DUBs) are divided into seven subgroups based on sequence and structure and perform the roles of mediating the deubiquitination of substrate proteins, regulating protein function, and participating in various cellular life activities. Among them, the ubiquitin-specific protease family (USP) is the DUB subtype with the most members and structural diversity discovered so far. USP48 is a member of the USP family of ubiquitin-specific proteases and has been found to promote glioblastoma by deubiquitinating the Gli1 transcription factor and to promote the progression of non-small-cell lung cancer through inhibition of the Wnt/β-catenin signaling pathway. We used microarrays to detail changes in gene expression regulated by USP48 overexpression in HCC cells.
Project description:Purpose: The purpose of this study was to find the differentially expressed genes in RBP4 and control treated cells by transcriptome analysis (RNA-seq) for subsequent mechanism study. Methods: Illumina Novaseq™ 6000 was used to sequencing RBP4 and control-treated human umbilical vein endothelial cells.Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.GO enrichment analysis provides all GO terms that significantly enriched in DEGs comparing to the genome background. Firstly all DEGs were mapped to GO terms in the Gene Ontology database (http://www.geneontology.org/), gene numbers were calculated for every term, significantly enriched GO terms in DEGs comparing to the genome background were defined by hypergeometric test. Results:The RNA-seq results showed that compared to the untreated HUVECs, RBP4 treatment resulted in significant changes in the gene expression, including 180 up-regulated and 53 down-regulated genes among a total number of 233 DEGs. GO enrichment were analyzed for relationships among all DEGs. Conclusions: Our study analyzed the mechanism of RBP4 on human umbilical vein endothelial cells and its possible pathway in detail by RNA-seq technique, and provided a basis for elucidating the damage of RBP4 on endothelial cells through large-scale gene screening.
Project description:An m1A enrichment analysis was conducted to investigate the epigenetic landscape and RNA modification profiles within SNU-668 Erastin-resistant gastric cancer cells following the experimental manipulation of ALKBH3 expression. Specifically, this analysis compared cells that had been stably transfected with a targeted shRNA construct designed to knock down ALKBH3 against control cells transfected with a non-targeting scramble shRNA sequence. The overarching goal was to assess and quantify the differential enrichment patterns of N1-methyladenosine (m1A) modifications across the transcriptome, thereby elucidating the potential regulatory role of the ALKBH3 demethylase in modulating the epitranscriptomic state underlying the acquired Erastin-resistant phenotype in this cellular model.
Project description:RNA transcriptome sequencing analysis was performed in SNU-668 Erastin-resistant cells and SNU-668 parental cells, SNU-484 RSL3-resistant cells and SNU-484 parental cells
Project description:Purpose: The goal of this experiment is to investigate the relative contributions of various types of cell death in NaIO3-treated RPE cells Methods: RPE cell mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. Results: According to the differential expressions of mRNA genes, among which 661 genes were upregulated and 637 genes were downregulated with significance after NaIO3 treatment . From the Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, it has been identified that ferroptosis ranked as the top pathway in comparison to other types of cell death (apoptosis, and necroptosis) upon NaIO3 treatment, which was additionally validated by the higher FPKM of main regulators in ferroptosis than that in apoptosis. Additionally, it was found that heme oxygenase-1 (HMOX1, also known as HO-1) as well as SLC7A11 (solute carrier family 7 member 11) mRNA were characterized as the most dramatically upregulated genes upon NaIO3 treatment against ARPE-19 cells Conclusions: Our study represented that ferroptosis serves as a predominant pathogenic factor involved in AMD pathological process.
Project description:purpose:To compare the enrichment of H3K27me3 on genes after treatment of control and α-KG. Method: Primary cardiomyocytes were treated with control (PBS) and α-KG for 24 h and precipitated with H3K27me3 antibody, then, the precipitated sequences were analysed by next generation RNA-seq. Results: There are significant differences between control and α-KG group. Conclusion:H3K27me3 ChIP-seq was used for analysing the enrichment of H3K27me3 on genes.
Project description:Purpose: The goals of this study are to compare the gene expression profile of Huh7 cells treated with different ectosomes or not and to evaluate the function of ectosomal Hexokianse 1 (HK1) derived from HSCs. Methods: Firstly, we treated different LX-2 HSCs with TGF-β (2 ng/mL) for 36 hours to activate HSCs, then ectosomes from LX-2 or HK1-KD LX-2 culture medium were isolated respectively by differential centrifugation processes. Secendly, Huh7 cells were preincubated with different ectosomes or not for 12 hours and then fresh medium for another 12 hours. Lastly, different groups of Huh7 cells were prepared for RNA-seq. Results: By Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the differentially expressed genes, a total of 124 pathways were found to be enriched in the ectosome-incubated Huh7 cells compared with the control Huh7 cells, while a total of 36 pathways were enriched in the ectosome-incubated Huh7 cells compared with the HK1-KD ectosome-incubated Huh7 cells.Gene set enrichment analysis (GSEA) also revealed enrichment of the N-glycosylation pathway in the ectosome-incubated Huh7 cells compared with the control Huh7 cells. Conversely, this pathway was negatively regulated in Huh7 cells incubated with HK1-KD HSC-derived ectosomes Conclusion: the transferal of HSC-derived ectosomal HK1 into HCC cells regulates the N-glycosylation level of Huh7.
