Potential biomarkers of HCC based on gene expression and DNA methylation profiles

Meng, Chao; Shen, Xiao-Min; Jiang, Wentao

doi:10.3892/ol.2018.9020

Cited by 12 publications

(13 citation statements)

References 48 publications

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“…The findings from this study suggest potential HCC biomarker roles for certain genes such as DTL, DUSP1, NFKBIA, and SOCS2 [160]. Similar to TCGA Research Network analyses mentioned above [157], these investigators also suggest that the tumor protein 'p53 signaling' and 'metabolic' pathways may serve important roles in the pathogenesis of HCC [160]. Other polymorphic variants serving as potential risk factors for HCC in highrisk patients infected with HBV/HCV have also been reported [161].…”

Section: The Genetics Of Hccsupporting

confidence: 77%

“…In another recent study, gene expression and DNA methylation profiles were screened to identify potential genetic biomarkers of HCC. The findings from this study suggest potential HCC biomarker roles for certain genes such as DTL, DUSP1, NFKBIA, and SOCS2 [160]. Similar to TCGA Research Network analyses mentioned above [157], these investigators also suggest that the tumor protein 'p53 signaling' and 'metabolic' pathways may serve important roles in the pathogenesis of HCC [160].…”

Section: The Genetics Of Hccsupporting

confidence: 75%

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The Rise in the Prevalence of Nonalcoholic Fatty Liver Disease and Hepatocellular Carcinoma

Sherif¹

2019

Nonalcoholic Fatty Liver Disease - An Update

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Nonalcoholic fatty liver disease (NAFLD) affects a third of the world's population and its rapid rise parallels the increase in hepatocellular carcinoma (HCC). NAFLD replacing hepatitis C virus (HCV) infection as a leading indicator for liver transplantation (LT) in the United States. NAFLD is a spectrum of disease ranging from simple steatosis (NAFL) to nonalcoholic steatohepatitis (NASH), which can progress to advanced fibrosis (AF) and cirrhosis, culminating in HCC. The main clinical concern of public health administrators is that many patients who are unaware of NAFLD remain undiagnosed and risk developing end-stage liver disease (ESLD). Clinicians overly rely on surrogate liver enzymes to identify patients with NAFLD, allowing for substantial liver disease to go unnoticed and untreated. Furthermore, according to epidemiological studies, in patients diagnosed with NAFLD, ethnicity plays a role in complications and treatment response, and ethnic correlations with NAFLD are thoroughly underreported. Although liver biopsy is the gold standard method for appropriately diagnosing and staging NAFLD, most patients can be effectively diagnosed non-invasively with imaging modalities and integrated tests that are routinely available in the clinic today. This chapter discusses the current global rise in the rates of NAFLD and HCC; the current key findings incidences and the recommended diagnostic approaches and in therapeutic methods.

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Section: The Genetics Of Hccsupporting

confidence: 77%

Section: The Genetics Of Hccsupporting

confidence: 75%

The Rise in the Prevalence of Nonalcoholic Fatty Liver Disease and Hepatocellular Carcinoma

Sherif¹

2019

Nonalcoholic Fatty Liver Disease - An Update

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“…A literature search was conducted to validate selected molecules, many of which were found to be extensively reported in relation to HCC. Several of these selected molecules are already identified as being either diagnostic (VSP45, TERT, EBF2, hsa-miR-324-5p, hsa-miR-130a-3p, hsa-miR-200a-3p, hsa-miR-106b-5p, hsa-21-5p, hsa-424-5p), prognostic (CAP2, TRMT6, MT1JP, hsa-miR-10b-5p, hsa-miR-139-3p, hsa-miR-101, hsa-miR-122-5p, hsa-miR-1285-3p, hsa-miR-203a-3p), recurrence-related (CD34, hsa-miR-183), or therapeutic (AKR1B10, SLC25A4, CYP2B7, FBXL18, hsa-miR-146a-5p, hsa-miR-34a, hsa-miR-122, hsa-miR-671-5p) biomarker candidates for HCC [23][24][25][26][27]. These molecules appear to be involved in molecular events relating to inflammation, tumor microenvironment, cell cycle, apoptosis, and metabolism.…”

Section: Dysregulation Of Mirna-mrna Pairs In Hccmentioning

confidence: 99%

Identification of miRNA-mRNA associations in hepatocellular carcinoma using hierarchical integrative model

et al. 2020

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Background: The established role miRNA-mRNA regulation of gene expression has in oncogenesis highlights the importance of integrating miRNA with downstream mRNA targets. These findings call for investigations aimed at identifying disease-associated miRNA-mRNA pairs. Hierarchical integrative models (HIM) offer the opportunity to uncover the relationships between disease and the levels of different molecules measured in multiple omic studies. Methods: The HIM model we formulated for analysis of mRNA-seq and miRNA-seq data can be specified with two levels: (1) a mechanistic submodel relating mRNAs to miRNAs, and (2) a clinical submodel relating disease status to mRNA and miRNA, while accounting for the mechanistic relationships in the first level. Results: mRNA-seq and miRNA-seq data were acquired by analysis of tumor and normal liver tissues from 30 patients with hepatocellular carcinoma (HCC). We analyzed the data using HIM and identified 157 significant miRNA-mRNA pairs in HCC. The majority of these molecules have already been independently identified as being either diagnostic, prognostic, or therapeutic biomarker candidates for HCC. These pairs appear to be involved in processes contributing to the pathogenesis of HCC involving inflammation, regulation of cell cycle, apoptosis, and metabolism. For further evaluation of our method, we analyzed miRNA-seq and mRNA-seq data from TCGA network. While some of the miRNA-mRNA pairs we identified by analyzing both our and TCGA data are previously reported in the literature and overlap in regulation and function, new pairs have been identified that may contribute to the discovery of novel targets. Conclusion: The results strongly support the hypothesis that miRNAs are important regulators of mRNAs in HCC. Furthermore, these results emphasize the biological relevance of studying miRNA-mRNA pairs.

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“…A literature search was conducted to validate selected molecules, many of which were found to be extensively reported in relation to HCC. Several of these selected molecules are already identified as being either diagnostic (VSP45, TERT, EBF2, hsa-miR-324-5p, hsa-miR-130a-3p, hsa-miR-200a-3p, hsa-miR-106b-5p, hsa-21-5p, hsa-424-5p,), prognostic (CAP2, TRMT6, MT1JP, hsa-miR-10b-5p, hsa-miR-139-3p, hsa-miR-101, hsa-miR-122-5p, hsa-miR-1285-3p, hsa-miR-203a-3p), recurrence-related (CD34, hsa-miR-183,), or therapeutic (AKR1B10, SLC25A4, CYP2B7, FBXL18, hsa-miR-146a-5p, hsa-miR-34a, hsa-miR-122, hsa-miR-671-5p) biomarker candidates for HCC [11][12][13][14][15]. These molecules appear to be involved in molecular events relating to inflammation, tumor microenvironment, cell cycle, apoptosis, and metabolism.…”

Section: Dysregulation Of Mirna-mrna Pairs In Hccmentioning

confidence: 99%

Identification of miRNA-mRNA associations in hepatocellular carcinoma using hierarchical integrative model

Varghese

Zhou

Barefoot

et al. 2019

Preprint

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Background : The established role miRNA-mRNA regulation of gene expression has in oncogenesis highlights the importance of integrating miRNA with downstream mRNA targets. These findings call for investigations aimed at identifying disease-associated miRNA-mRNA pairs. Hierarchical integrative models (HIM) offer the opportunity to uncover the relationships between disease and the levels of different molecules measured in multiple omic studies. Results: mRNA-seq and miRNA-seq data were acquired by analysis of tumor and normal liver tissues from 30 patients with hepatocellular carcinoma (HCC). We analyzed the data using HIM and identified 157 significant miRNA-mRNA pairs in HCC. The majority of these molecules have already been independently identified as being either diagnostic, prognostic, or therapeutic biomarker candidates for HCC. These pairs appear to be involved in processes contributing to the pathogenesis of HCC involving inflammation, regulation of cell cycle, apoptosis, and metabolism. For further evaluation of our method, we analyzed miRNA-seq and mRNA-seq data from TCGA network. While some of the miRNA-mRNA pairs we identified by analyzing both our and TCGA data are previously reported in the literature and overlap in regulation and function, new pairs have been identified that may contribute to the discovery of novel targets. Conclusion: The results strongly support the hypothesis that miRNAs are important regulators of mRNAs in HCC. Furthermore, these results emphasize the biological relevance of studying miRNA-mRNA pairs.

show abstract

Potential biomarkers of HCC based on gene expression and DNA methylation profiles

Cited by 12 publications

References 48 publications

The Rise in the Prevalence of Nonalcoholic Fatty Liver Disease and Hepatocellular Carcinoma

The Rise in the Prevalence of Nonalcoholic Fatty Liver Disease and Hepatocellular Carcinoma

Identification of miRNA-mRNA associations in hepatocellular carcinoma using hierarchical integrative model

Identification of miRNA-mRNA associations in hepatocellular carcinoma using hierarchical integrative model

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