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      Role of Asxl2 in non-alcoholic steatohepatitis-related hepatocellular carcinoma developed from diabetes

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          Abstract

          The present study investigated the mechanism(s) of non-alcoholic steatohepatitis-related hepatocellular carcinoma (NASH-HCC) developed from diabetes. Streptozotocin and a high-fat diet (STZ-HFD) were used to induce NASH-HCC in ApoE −/− mice. Mouse liver functions were evaluated by H&E staining, liver/body weight and serum biochemical analysis. The expression levels of inflammation-associated factors were determined by RT-qPCR. Gene expression profiles related to molecular functions and pathways of NASH-HCC were examined by principal component analysis, heatmap, gene ontology and KEGG pathway enrichment analysis. Differentially expressed genes (DEGs) in tumor tissues were confirmed by RT-qPCR. The expression of Asxl2 in human NASH-HCC, other HCC tissues and HCC cells was measured by western blot (WB analysis) and RT-qPCR. For SNU-182 cells transfected with siAsxl2 or Hep3B cells with Asxl2 overexpression, cell proliferation, cell cycle, migration and invasion were respectively determined by CCK-8 assays, flow cytometry, wounding healing and Transwell assays. The expression levels of cell metastasis- and cycle-related proteins were determined by WB analysis and RT-qPCR. NASH-HCC model mice exhibited tumor protrusion with severe steatosis. The blood glucose concentration, serum levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST) and low-density lipoprotein (LDL), total bile acid (TBA) and the levels of interleukin (IL)-6, tumor necrosis factor (TNF)-α, glypican 3 (GPC3) and transforming growth factor (TGF)-β were all increased in NASH-HCC model mice. DEGs were mainly related to chromosome organization, the cell cycle and the mitogen-activated kinase (MAPK) pathway. Asxl2 was significantly downregulated in HCC tissues and cells, and this regulated cell growth, migration and invasion. The gene expression pattern, related molecular functions and signaling pathways of NASH-HCC differed from those of normal liver tissues. Additionally, the downregulation of Asxl2 may play a potential role in development of NASH-HCC in patients with diabetes.

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          Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

          The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data. Copyright 2001 Elsevier Science (USA).
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            edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

            Summary: It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability. Empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference. The methodology can be used even with the most minimal levels of replication, provided at least one phenotype or experimental condition is replicated. The software may have other applications beyond sequencing data, such as proteome peptide count data. Availability: The package is freely available under the LGPL licence from the Bioconductor web site (http://bioconductor.org). Contact: mrobinson@wehi.edu.au
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              featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.

              Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to each genomic feature, for example to each exon or each gene. The process of counting reads is called read summarization. Read summarization is required for a great variety of genomic analyses but has so far received relatively little attention in the literature. We present featureCounts, a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments. featureCounts implements highly efficient chromosome hashing and feature blocking techniques. It is considerably faster than existing methods (by an order of magnitude for gene-level summarization) and requires far less computer memory. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications. featureCounts is available under GNU General Public License as part of the Subread (http://subread.sourceforge.net) or Rsubread (http://www.bioconductor.org) software packages.
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                Author and article information

                Journal
                Int J Mol Med
                Int J Mol Med
                IJMM
                International Journal of Molecular Medicine
                D.A. Spandidos
                1107-3756
                1791-244X
                January 2021
                04 November 2020
                04 November 2020
                : 47
                : 1
                : 101-112
                Affiliations
                [1 ]Department of Hepatopancreatobiliary Surgery, Minhang Hospital, Fudan University
                [2 ]Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai 201199, P.R. China
                Author notes
                Correspondence to: Dr Qimeng Chang, Department of Hepatopancreatobiliary Surgery, Minhang Hospital, Fudan University, 170 Xinsong Road, Minhang, Shanghai 201199, P.R. China, E-mail: chqimeng_chqm@ 123456163.com
                [*]

                Contributed equally

                Article
                ijmm-47-01-0101
                10.3892/ijmm.2020.4782
                7723516
                33155659
                c05c2d67-a859-4327-9f2c-6c7e31fceeee
                Copyright: © Hu et al.

                This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

                History
                : 13 April 2020
                : 27 August 2020
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                diabetes,nash-hcc,mice administered stz-hfd,asxl2
                diabetes, nash-hcc, mice administered stz-hfd, asxl2

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