The cell line ontology-based representation, integration and analysis of cell lines used in China

Abstract Background The Chinese National Infrastructure of Cell Line stores and distributes cell lines for biomedical research in China. This study aims to represent and integrate the information of NICR cell lines into the community-based Cell Line Ontology (CLO). Results We have aligned, represented, and added all identified 2704 cell line cells in NICR to CLO. We also proposed new ontology design patterns to represent the usage of cell line cells as disease models by inducing tumor formation in model organisms, and the relations between cell line cells and their expressed or overexpressed genes or proteins. The resulting CLO-NICR ontology also includes the Chinese representation of the NICR cell line information. CLO-NICR was merged into the general CLO. To serve the cell research community in China, the Chinese version of CLO-NICR was also generated and deposited in the OntoChina ontology repository. The usage of CLO-NICR was demonstrated by DL query and knowledge extraction. Conclusions In summary, all identified cell lines from NICR are represented by the semantics framework of CLO and incorporated into CLO as a most recent update. We also generated a CLO-NICR and its Chinese view (CLO-NICR-Cv). The development of CLO-NICR and CLO-NIC-Cv allows the integration of the cell lines from NICR into the community-based CLO ontology and provides an integrative platform to support different applications of CLO in China.https://deepblue.lib.umich.edu/bitstream/2027.42/148821/1/12859_2019_Article_2724.pd

Analysis of genomic copy number variations in human hepatocellular carcinoma cell lines HepG2 and Huh7

Objective To explore the effect of copy number variation on the occurrence and development of hepatocellular carcinoma by using copy number variation and transcriptome experiment of hepatocellular carcinoma combined with public clinical data. Methods The copy number variation found in hepatoma cell lines HepG2 and Huh7 was identified by optical genome mapping. The function of the copy number variant genes in the two cell lines was analyzed, and the protein interaction network was mapped according to the enrichment pathway. Key genes in the core network of two cell lines were selected to analyze the relationship between copy number variation and gene expression in hepatocellular carcinoma. The relationship between gene expression and clinical survival was analyzed by GEPIA database. RNA-seq assay and public data were used to verify gene expression levels. Results HepG2 cells mainly showed increased copy number, and related genes were enriched in estrogen signaling pathway and Staphylococcus aureus infection pathway. Huh7 cells showed both increased and decreased copy number, and related genes mainly concentrated in olfactory conduction and cytokine-cytokine receptor interaction pathways. The copy number of key genes SRC, MAPK3 and MAP3K7 was proportional to gene expression, and survival was significantly reduced in patients with high expression of these genes (P＜0.05). Compared with HEK293T cell line, the expression of SRC and MAP3K7 genes in the two hepatocellular carcinoma lines was significantly increased(P＜0.001), suggesting the specific variation of hepatocellular carcinoma. MAPK3 had no difference. Conclusions The expression of copy number variant genes SRC and MAP3K7 in hepatocellular carcinoma is significantly correlated with the prognosis of patients, and may significantly affect the development and heterogeneity of hepatocellular carcinoma

Ubiquitin-Specific Peptidase USP22 Negatively Regulates the STAT Signaling Pathway by Deubiquitinating SIRT1

Background/Aims: The ubiquitin-specific peptidase USP22 mediates various cellular and organismal processes, such as cell growth, apoptosis, and tumor malignancy. However, the molecular mechanisms that regulate USP22 activity remain poorly understood. Here we identify STAT3 as a new USP22 interactor. Methods:· We used western blotting and RT-PCR to measure key protein, acetylated STAT3, and mRNA levels in HEK293 and colorectal cancer cell lines transfected with expression plasmids or specific siRNAs. Co-immunoprecipitation was used to demonstrate protein-protein interaction and protein complex composition. Results: USP22 overexpression down-regulated STAT3 acetylation by deubiquitinating SIRT1. The three proteins were found to be present in a single protein complex. SiRNA-mediated depletion of endogenous USP22 resulted in SIRT1 destabilization and elevated STAT3 acetylation. Consistent with this finding, USP22 also down-regulated the expression of two known STAT3 target genes, MMP9 and TWIST. Conclusion: We show that USP22 is a new regulator of the SIRT1-STAT3 signaling pathway and report a new mechanistic explanation for cross talk between USP22 and the SIRT1-STAT pathways

Protective Effects of α-Lipoic Acid and Chlorogenic Acid on Cadmium-Induced Liver Injury in Three-Yellow Chickens

Cadmium (Cd) is a type of noxious heavy metal that is distributed widely. It can severely injure the hepatocytes and cause liver dysfunction by inducing oxidative stress and mitochondrial damage. We evaluated the protective effects of α-lipoic acid (α-LA) or chlorogenic acid (CGA) and their combination on counteracting cadmium toxicity in vivo in three-yellow chickens. For three months, CdCl2 (50 mg/L) was administrated through their drinking water, α-LA (400 mg/kg) was added to feed and CGA (45 mg/kg) was employed by gavage. The administration of Cd led to variations in growth performance, biochemical markers (of the liver, kidney and heart), hematological parameters, liver histopathology (which suggested hepatic injury) and ultrastructure of hepatocytes. Some antioxidant enzymes and oxidative stress parameters showed significant differences in the Cd-exposure group when compared with the control group. The groups treated with Cd and administrated α-LA or CGA showed significant amelioration with inhibited mitochondrial pathway-induced apoptosis. Combining both drugs was the most effective in reducing Cd toxicity in the liver. In summary, the results demonstrated that α-LA and CGA may be beneficial in alleviating oxidative stress induced by oxygen free radicals and tissue injury resulting from Cd-triggered hepatotoxicity

Cloning and Expression of a Novel Target Fusion Protein and its Application in Anti-Tumor Therapy

Backgrounds: Epidermal growth factor (EGF) is a 53 amino acid polypeptide and its receptor EGFR is an established therapeutic target for anti-tumor therapy. Two major categories of EGFR-targeted drugs include monoclonal antibodies (mAbs) and small molecular tyrosine kinase inhibitors (TKIs). However, drug resistance occurs in a significant proportion of patients due to EGFR mutations. Since EGFR can maintain activation while abrogating the activity of mAbs or TKIs, or bypass signaling functions while successfully circumventing the EGF-EGFR switch, developing new mechanism-based inhibitors is necessary. Methods: In this study, based on the principle of tumor immunotherapy, a recombinant protein pLLO-hEGF was constructed. The N-terminal portion contains three immunodominant epitopes from listeriolysin O (LLO) and the C-terminal includes EGF. To use EGF as a target vector to recognize EGFR-expressing cancer cells, immunodominant epitopes could enhance immunogenicity of tumor cells for immune cell activation and attack. Results: Recombinant protein pLLO-hEGF was successfully expressed and showed strong affinity to cancer cells. Also, pLLO-hEGF could significantly stimulate human lymphocyte proliferation and the lymphocytes demonstrated enhanced killing potency in EGFR-expressing cancer cells in vitro and in vivo. Conclusion: This study can provide novel strategies and directions in tumor biotherapy