Integrated Analysis of Mutation Data from Various Sources Identifies Key Genes and Signaling Pathways in Hepatocellular Carcinoma

AbstractCrohn’s disease is a type of inflammatory bowel disease posing a significant threat to human health all over the world. Genome-wide gene expression profiles of mucosal colonic biopsies have provided some insight into the molecular mechanisms of Crohn’s disease. However, the exact pathogenesis is unclear. This study aimed to identify key genes and significant signaling pathways associated with Crohn’s disease by bioinformatics analysis. To identify key genes, an integrated analysis of gene expression signature was conducted using a robust rank aggregation approach. A total of 179 Crohn’s disease patients and 94 healthy controls from nine public microarray datasets were included. MMP1 and CLDN8 were two key genes screened from the differentially expressed genes. Connectivity Map predicted several small molecules as possible adjuvant drugs to treat CD. Besides, we used weighted gene co-expression network analysis to explore the co-expression modules associated with Crohn’s disease pathogenesis. Seven main functional modules were identified, of which black module showed the highest correlation with Crohn’s disease. The genes in black module mainly enriched in Interferon Signaling and defense response to virus. Blue module was another important module and enriched in several signaling pathways, including extracellular matrix organization, inflammatory response and blood vessel development. There were also several other meaningful functional modules which enriched in many biological processes. The present study identified a number of key genes and pathways correlated with Crohn’s disease and potential drugs to combat it, which might offer insights into Crohn’s disease pathogenesis and provide a clue to potential treatments.

Download Full-text

NF-κB, JNK, and TLR Signaling Pathways in Hepatocarcinogenesis

Gastroenterology Research and Practice ◽

10.1155/2010/367694 ◽

2010 ◽

Vol 2010 ◽

pp. 1-10 ◽

Cited By ~ 39

Author(s):

Shin Maeda

Keyword(s):

Hepatocellular Carcinoma ◽

Signaling Pathways ◽

Inflammatory Cell ◽

Prognostic Markers ◽

Tumor Promotion ◽

Neoplastic Cell ◽

Nuclear Factor ◽

Tlr Signaling ◽

The Third

Hepatocellular carcinoma (HCC) is the third largest cause of cancer deaths worldwide. The role of molecular changes in HCC have been used to identify prognostic markers and chemopreventive or therapeutic targets. It seems that toll-like receptors (TLRs) as well as the nuclear factor (NF)-κB, and JNK pathways are critical regulators for the production of the cytokines associated with tumor promotion. The cross-talk between an inflammatory cell and a neoplastic cell, which is instigated by the activation of NF-κB and JNKs, is critical for tumor organization. JNKs also regulate cell proliferation and act as oncogenes, making them the main tumor-promoting protein kinases. TLRs play roles in cytokine and hepatomitogen expression mainly in myeloid cells and may promote liver tumorigenesis. A better understanding of these signaling pathways in the liver will help us understand the mechanism of hepatocarcinogenesis and provide a new therapeutic target for HCC.

Download Full-text

MicroRNA-21 Plays Multiple Oncometabolic Roles in the Process of NAFLD-Related Hepatocellular Carcinoma via PI3K/AKT, TGF-β, and STAT3 Signaling

Cancers ◽

10.3390/cancers13050940 ◽

2021 ◽

Vol 13 (5) ◽

pp. 940

Author(s):

Chi-Yu Lai ◽

Kun-Yun Yeh ◽

Chiu-Ya Lin ◽

Yang-Wen Hsieh ◽

Hsin-Hung Lai ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Signaling Pathways ◽

Stellate Cell ◽

Human Cancer ◽

Tumor Formation ◽

Transgenic Zebrafish ◽

Zebrafish Model ◽

Lipid Metabolism Disorder ◽

Full Spectrum ◽

Stat3 Signaling

MicroRNA-21 (miR-21) is one of the most frequently upregulated miRNAs in liver diseases such as nonalcoholic fatty liver disease (NAFLD) and hepatocellular carcinoma (HCC). However, mechanistic pathways that connect NAFLD and HCC remain elusive. We developed a doxycycline (Dox)-inducible transgenic zebrafish model (LmiR21) which exhibited an upregulation of miR-21 in the liver, which in turn induced the full spectrum of NAFLD, including steatosis, inflammation, fibrosis, and HCC, in the LmiR21 fish. Diethylnitrosamine (DEN) treatment led to accelerated liver tumor formation and exacerbated their aggressiveness. Moreover, prolonged miR-21 expression for up to ten months induced nonalcoholic steatohepatitis (NASH)-related HCC (NAHCC). Immunoblotting and immunostaining confirmed the presence of miR-21 regulatory proteins (i.e., PTEN, SMAD7, p-AKT, p-SMAD3, and p-STAT3) in human nonviral HCC tissues and LmiR21 models. Thus, we demonstrated that miR-21 can induce NAHCC via at least three mechanisms: First, the occurrence of hepatic steatosis increases with the decrease of ptenb, pparaa, and activation of the PI3K/AKT pathway; second, miR-21 induces hepatic inflammation (or NASH) through an increase in inflammatory gene expression via STAT3 signaling pathways, and induces liver fibrosis through hepatic stellate cell (HSC) activation and collagen deposition via TGF-β/Smad3/Smad7 signaling pathways; finally, oncogenic activation of Smad3/Stat3 signaling pathways induces HCC. Our LmiR21 models showed similar molecular pathology to the human cancer samples in terms of initiation of lipid metabolism disorder, inflammation, fibrosis and activation of the PI3K/AKT, TGF-β/SMADs and STAT3 (PTS) oncogenic signaling pathways. Our findings indicate that miR-21 plays critical roles in the mechanistic perspectives of NAHCC development via the PTS signaling networks.

Download Full-text

Integrated analysis of methylation-driven genes and pretreatment prognostic factors in patients with hepatocellular carcinoma

BMC Cancer ◽

10.1186/s12885-021-08314-5 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Dongsheng He ◽

Shengyin Liao ◽

Lifang Cai ◽

Weiming Huang ◽

Xuehua Xie ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Prognostic Factors ◽

Risk Score ◽

Prognostic Model ◽

Cox Regression ◽

The Cancer Genome Atlas ◽

Integrated Analysis ◽

Calibration Plot ◽

Clinical Parameters ◽

T Stage

Abstract Background The potential reversibility of aberrant DNA methylation indicates an opportunity for oncotherapy. This study aimed to integrate methylation-driven genes and pretreatment prognostic factors and then construct a new individual prognostic model in hepatocellular carcinoma (HCC) patients. Methods The gene methylation, gene expression dataset and clinical information of HCC patients were downloaded from The Cancer Genome Atlas (TCGA) database. Methylation-driven genes were screened with a Pearson’s correlation coefficient less than − 0.3 and a P value less than 0.05. Univariable and multivariable Cox regression analyses were performed to construct a risk score model and identify independent prognostic factors from the clinical parameters of HCC patients. The least absolute shrinkage and selection operator (LASSO) technique was used to construct a nomogram that might act to predict an individual’s OS, and then C-index, ROC curve and calibration plot were used to test the practicability. The correlation between clinical parameters and core methylation-driven genes of HCC patients was explored with Student’s t-test. Results In this study, 44 methylation-driven genes were discovered, and three prognostic signatures (LCAT, RPS6KA6, and C5orf58) were screened to construct a prognostic risk model of HCC patients. Five clinical factors, including T stage, risk score, cancer status, surgical method and new tumor events, were identified from 13 clinical parameters as pretreatment-independent prognostic factors. To avoid overfitting, LASSO analysis was used to construct a nomogram that could be used to calculate the OS in HCC patients. The C-index was superior to that from previous studies (0.75 vs 0.717, 0.676). Furthermore, LCAT was found to be correlated with T stage and new tumor events, and RPS6KA6 was found to be correlated with T stage. Conclusion We identified novel therapeutic targets and constructed an individual prognostic model that can be used to guide personalized treatment in HCC patients.

Download Full-text

SMYD3 promotes hepatocellular carcinoma progression by methylating S1PR1 promoters

Cell Death and Disease ◽

10.1038/s41419-021-04009-8 ◽

2021 ◽

Vol 12 (8) ◽

Author(s):

Heyun Zhang ◽

Zhangyu Zheng ◽

Rongqin Zhang ◽

Yongcong Yan ◽

Yaorong Peng ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Signaling Pathways ◽

Histone Methylation ◽

Cell Growth And Migration ◽

Histone 3 ◽

Sphingosine 1 Phosphate ◽

And Migration ◽

Proliferation And Migration

AbstractHepatocellular carcinoma (HCC) is one of the most common malignancies worldwide. SET and MYND domain-containing protein 3 (SMYD3) has been shown to promote the progression of various types of human cancers, including liver cancer; however, the detailed molecular mechanism is still largely unknown. Here, we report that SMYD3 expression in HCC is an independent prognostic factor for survival and promotes the proliferation and migration of HCC cells. We observed that SMYD3 upregulated sphingosine-1-phosphate receptor 1 (S1PR1) promoter activity by methylating histone 3 (H3K4me3). S1PR1 was expressed at high levels in HCC samples, and high S1PR1 expression was associated with shorter survival. S1PR1 expression was also positively correlated with SMYD3 expression in HCC samples. We confirmed that SMYD3 promotes HCC cell growth and migration in vitro and in vivo by upregulating S1PR1 expression. Further investigations revealed that SMYD3 affects critical signaling pathways associated with the progression of HCC through S1PR1. These findings strongly suggest that SMYD3 has a crucial function in HCC progression that is partially mediated by histone methylation at the downstream gene S1PR1, which affects key signaling pathways associated with carcinogenesis and the progression of HCC.

Download Full-text

AB0005 IDENTIFICATION OF KEY GENES AND PATHWAYS FOR PSORIASIS BASED ON GEO DATABASES BY BIOINFORMATICS ANALYSIS

Annals of the Rheumatic Diseases ◽

10.1136/annrheumdis-2021-eular.1773 ◽

2021 ◽

Vol 80 (Suppl 1) ◽

pp. 1037.2-1038

Author(s):

X. Sun ◽

S. X. Zhang ◽

S. Song ◽

T. Kong ◽

C. Zheng ◽

...

Keyword(s):

Gene Expression ◽

Signaling Pathways ◽

Differentially Expressed Genes ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Shanxi Province ◽

Receptor Interaction ◽

Term Therapy ◽

Pathway Enrichment Analysis ◽

Key Genes

Background:Psoriasis is an immune-mediated, genetic disease manifesting in the skin or joints or both, and also has a strong genetic predisposition and autoimmune pathogenic traits1. The hallmark of psoriasis is sustained inflammation that leads to uncontrolled keratinocyte proliferation and dysfunctional differentiation. And it’s also a chronic relapsing disease, which often necessitates a long-term therapy2.Objectives:To investigate the molecular mechanisms of psoriasis and find the potential gene targets for diagnosis and treating psoriasis.Methods:Total 334 gene expression data of patients with psoriasis research (GSE13355 GSE14905 and GSE30999) were obtained from the Gene Expression Omnibus database. After data preprocessing and screening of differentially expressed genes (DEGs) by R software. Online toll Metascape3 was used to analyze Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs. Interactions of proteins encoded by DEGs were discovered by Protein-protein interaction network (PPI) using STRING online software. Cytoscape software was utilized to visualize PPI and the degree of each DEGs was obtained by analyzing the topological structure of the PPI network.Results:A total of 611 DEGs were found to be differentially expressed in psoriasis. GO analysis revealed that up-regulated DEGs were mostly associated with defense and response to external stimulus while down-regulated DEGs were mostly associated with metabolism and synthesis of lipids. KEGG enrichment analysis suggested they were mainly enriched in IL-17 signaling, Toll-like receptor signaling and PPAR signaling pathways, Cytokine-cytokine receptor interaction and lipid metabolism. In addition, top 9 key genes (CXCL10, OASL, IFIT1, IFIT3, RSAD2, MX1, OAS1, IFI44 and OAS2) were identified through Cytoscape.Conclusion:DEGs of psoriasis may play an essential role in disease development and may be potential pathogeneses of psoriasis.References:[1]Boehncke WH, Schon MP. Psoriasis. Lancet 2015;386(9997):983-94. doi: 10.1016/S0140-6736(14)61909-7 [published Online First: 2015/05/31].[2]Zhang YJ, Sun YZ, Gao XH, et al. Integrated bioinformatic analysis of differentially expressed genes and signaling pathways in plaque psoriasis. Mol Med Rep 2019;20(1):225-35. doi: 10.3892/mmr.2019.10241 [published Online First: 2019/05/23].[3]Zhou Y, Zhou B, Pache L, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun 2019;10(1):1523. doi: 10.1038/s41467-019-09234-6 [published Online First: 2019/04/05].Acknowledgements:This project was supported by National Science Foundation of China (82001740), Open Fund from the Key Laboratory of Cellular Physiology (Shanxi Medical University) (KLCP2019) and Innovation Plan for Postgraduate Education in Shanxi Province (2020BY078).Disclosure of Interests:None declared

Download Full-text