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

MicroRNA-483-5p Inhibits Hepatocellular Carcinoma Cell Proliferation, Cell Steatosis, and Fibrosis by Targeting PPARα and TIMP2

MicroRNAs (miRNAs) are small non-coding RNA molecules that bind with the 3′ untranslated regions (UTRs) of genes to regulate expression. Downregulation of miR-483-5p (miR-483) is associated with the progression of hepatocellular carcinoma (HCC). However, the significant roles of miR-483 in nonalcoholic fatty liver disease (NAFLD), alcoholic fatty liver diseases (AFLD), and HCC remain elusive. In the current study, we investigated the biological significance of miR-483 in NAFLD, AFLD, and HCC in vitro and in vivo. The downregulation of miR-483 expression in HCC patients’ tumor samples was associated with Notch 3 upregulation. Overexpression of miR-483 in a human bipotent progenitor liver cell line HepaRG and HCC cells dysregulated Notch signaling, inhibited cell proliferation/migration, induced apoptosis, and increased sensitivity towards antineoplastic agents sorafenib/regorafenib. Interestingly, the inactivation of miR-483 upregulated cell steatosis and fibrosis signaling by modulation of lipogenic and fibrosis gene expression. Mechanistically, miR-483 targets PPARα and TIMP2 gene expression, which leads to the suppression of cell steatosis and fibrosis. The downregulation of miR-483 was observed in mice liver fed with a high-fat diet (HFD) or a standard Lieber-Decarli liquid diet containing 5% alcohol, leading to increased hepatic steatosis/fibrosis. Our data suggest that miR-483 inhibits cell steatosis and fibrogenic signaling and functions as a tumor suppressor in HCC. Therefore, miR-483 may be a novel therapeutic target for NAFLD/AFLD/HCC management in patients with fatty liver diseases and HCC.

A Bayesian two-step integrative procedure incorporating prior knowledge for the identification of miRNA-mRNAs involved in hepatocellular carcinoma

Recent studies have confirmed the role of miRNA regulation of gene expression in oncogenesis for various cancers. In parallel, prior knowledge about relationships between miRNA and mRNA have been accumulated from biological experiments or statistical analyses. Improved identification of disease-associated miRNA-mRNA pairs may be achieved by incorporating prior knowledge into integrative genomic analyses. In this study we focus on 39 patients with hepatocellular carcinoma (HCC) and 25 patients with liver cirrhosis and use a flexible Bayesian two-step integrative method. We found 66 significant miRNA-mRNA pairs, several of which contain molecules that have previously been identified as potential biomarkers. These results demonstrate the utility of the proposed approach in providing a better understanding of relationships between different biological levels, thereby giving insights into the biological mechanisms underlying the diseases, while providing a better selection of biomarkers that may serve as diagnostic, prognostic, or therapeutic biomarker candidates.

Cross-talk of four types of RNA modification writers defines the immune microenvironment in severe asthma

Adenine modifications, including m⁶ A, m¹ A, APA, and A-to-I modifications, are the most impactful RNA modifications. These modifications are primarily produced by enzymes called writers. The main purpose of this study was to explore the cross-talk and potential roles of these writers in severe asthma. We found 13 RNA writers potentially related to severe asthma and three RNA modification patterns. Cluster 3 showed predominant neutrophil infiltration and C-type lectin receptor signaling; cluster 1 showed predominant innate immune cell infiltration and ubiquitin-proteasome system activation; and cluster 2 did not show obvious immune infiltration characteristics. We found that RNA modification writers modified immune cell-related genes and led to both accumulation of different immune cells in the airways and activation of a series of biological processes, which ultimately leads to severe asthma. TRMT6, WTAP, and TRMT6A were included in a random forest model as predictors. Cromoglicic acid, thioperamide, and fluvastatin were potential drugs for clusters 1, 2, and 3, respectively. We found that cross-talk of RNA modifications is significant in severe asthma, which provides insight into severe asthma pathogenesis and possible treatment avenues.

Non-coding RNAs as biomarkers for hepatocellular carcinoma-A systematic review

Hepatocellular carcinoma (HCC) is the sixth most common malignancy in the world and the fourth leading cause of cancer-related death, and its incidence is increasing globally. Despite significant advances in treatment strategies for HCC, the prognosis is still poor due to its high recurrence rate. Therefore, there is an urgent need to understand the pathogenesis of HCC and further develop new therapies to improve the prognosis and quality of life of HCC patients. MicroRNAs (miRNAs, miRs) are small non-coding RNAs involved in post-transcriptional regulation of gene expression that is abnormally expressed in cancer-associated genomic regions or vulnerable sites. More and more findings have shown that miRNAs are important regulatory factors of mRNA expression in HCC, and they are receiving more and more attention as a possible key biomarker of HCC. This review mainly summarizes the potential applied value on miRNAs as diagnostic, drug resistant, prognostic, and therapeutic biomarkers in the diagnosis, therapy, and prognosis of HCC. Also, we summarize the research value of long non-coding RNA (lncRNAs), circular RNAs (circRNAs), and miRNAs network in HCC as novel biomarkers, aiming at providing some references for the therapy of HCC.

Integrative Analysis of DNA Methylation and microRNA Expression Reveals Mechanisms of Racial Heterogeneity in Hepatocellular Carcinoma

Pathologic alterations in epigenetic regulation have long been considered a hallmark of many cancers, including hepatocellular carcinoma (HCC). In a healthy individual, the relationship between DNA methylation and microRNA (miRNA) expression maintains a fine balance; however, disruptions in this harmony can aid in the genesis of cancer or the propagation of existing cancers. The balance between DNA methylation and microRNA expression and its potential disturbance in HCC can vary by race. There is emerging evidence linking epigenetic events including DNA methylation and miRNA expression to cancer disparities. In this paper, we evaluate the epigenetic mechanisms of racial heterogenity in HCC through an integrated analysis of DNA methylation, miRNA, and combined regulation of gene expression. Specifically, we generated DNA methylation, mRNA-seq, and miRNA-seq data through the analysis of tumor and adjacent non-tumor liver tissues from African Americans (AA) and European Americans (EA) with HCC. Using mixed ANOVA, we identified cytosine-phosphate-guanine (CpG) sites, mRNAs, and miRNAs that are significantly altered in HCC vs. adjacent non-tumor tissue in a race-specific manner. We observed that the methylome was drastically changed in EA with a significantly larger number of differentially methylated and differentially expressed genes than in AA. On the other hand, the miRNA expression was altered to a larger extent in AA than in EA. Pathway analysis functionally linked epigenetic regulation in EA to processes involved in immune cell maturation, inflammation, and vascular remodeling. In contrast, cellular proliferation, metabolism, and growth pathways are found to predominate in AA as a result of this epigenetic analysis. Furthermore, through integrative analysis, we identified significantly differentially expressed genes in HCC with disparate epigenetic regulation, associated with changes in miRNA expression for AA and DNA methylation for EA.