The mir-767-105 cluster: a crucial factor related to the poor prognosis of hepatocellular carcinoma

Hsa_circ_0052611 and mir-767-5p guide the warburg effect, migration, and invasion of BRCA cells through modulating SCAI

Noncoding RNAs are key regulators in the Warburg Effect, an emerging hallmark of cancer. We intended to investigate the role and mechanism of circular RNA hsa_circ_0052611 (circ_0052611) and microRNA (miR)-767-5p in breast cancer (BRCA) hallmarks, especially the Warburg Effect. Expression of circ_0052611 and SCAI was downregulated, and miR-767-5p was upregulated in human BRCA tissues and cells; moreover, circ_0052611 acted as a miR-767-5p sponge to modulate the expression of miR-767-5p-targeted SCAI. Functionally, re-expressing circ_0052611 suppressed migration, invasion, glucose uptake, lactate production, and extracellular acidification rate (ECAR) in BRCA cells, and promoted apoptotic rate. These effects were accompanied by decreased Vimentin, N-cadherin, Bcl-2, and LDHA, and increased E-cadherin and Bax. Consistently, exhausting miR-767-5p exerted similar effects in BRCA cells. High miR-767-5p could counteract the role of circ_0052611 overexpression, and low SCAI likewise blocked the role of miR-767-5p deletion. In vivo, upregulating circ_0052611 delayed tumor growth of BRCA cells by altering miR-767-5p and SCAI expression. circ_0052611/miR-767-5p/SCAI axis might boycott the malignancy of BRCA cells.

Diagnostic and prognostic potential clustered miRNAs in bladder cancer

At specific genomic loci, miRNAs are in clusters and their association with copy number variations (CNVs) may exhibit abnormal expression in several cancers. Hence, the current study aims to understand the expression of miRNA clusters residing within CNVs and the regulation of their target genes in bladder cancer. To achieve this, we used extensive bioinformatics resources and performed an integrated analysis of recurrent CNVs, clustered miRNA expression, gene expression, and drug–gene interaction datasets. The study identified nine upregulated miRNA clusters that are residing on CNV gain regions and three miRNA clusters (hsa-mir-200c/mir-141, hsa-mir-216a/mir-217, and hsa-mir-15b/mir-16-2) are correlated with patient survival. These clustered miRNAs targeted 89 genes that were downregulated in bladder cancer. Moreover, network and gene enrichment analysis displayed 10 hub genes (CCND2, ETS1, FGF2, FN1, JAK2, JUN, KDR, NOTCH1, PTEN, and ZEB1) which have significant potential for diagnosis and prognosis of bladder cancer patients. Interestingly, hsa-mir-200c/mir-141 and hsa-mir-15b/mir-16-2 cluster candidates showed significant differences in their expression in stage-specific manner during cancer progression. Downregulation of NOTCH1 by hsa-mir-200c/mir-141 may also sensitize tumors to methotrexate thus suggesting potential chemotherapeutic options for bladder cancer subjects. To overcome some computational challenges and reduce the complexity in multistep big data analysis, we developed an automated pipeline called CmiRClustFinder v1.0 (https://github.com/msls-bioinfo/CmiRClustFinder_v1.0), which can perform integrated data analysis of 35 TCGA cancer types.

Mir-4728 is a Valuable Biomarker for Diagnostic and Prognostic Assessment of HER2-Positive Breast Cancer

Breast cancer remains one of the most common malignancies in female cancer patients. The rapid and accurate diagnosis of human epidermal growth factor receptor 2 (HER2) status is indispensable for breast cancer patients. The pre-miR-4728 (mir-4728) is encoded within an intron of the HER2 gene. We showed here that mir-4728 was the most significantly upregulated pre-miRNA in HER2-positive breast cancer patients (fold-change: 4.37), and it could serve as a strong diagnostic factor for the HER2 status in breast cancer patients (p < 0.0001). Moreover, mir-4728 was positively correlated with tumor recurrence and appeared to be a critical independent risk factor of tumor recurrence in patients with high tumor burden (HR: 7.558, 95% CI:1.842-31.006, p = 0.005). Remarkably, HER2-positive patients with higher mir-4728 expression levels had better drug responses to targeted therapies. Furthermore, estrogen receptor (ESR), the predictive marker for endocrine therapies, was found to be the direct target of miR-4728-3p. Taken together, our results supported the potential role of mir-4728 in the diagnosis of HER2 status and the prognostic assessment of HER2-positive patients in response to targeted therapies.

Mechanosensitive pathways are regulated by mechanosensitive miRNA clusters in endothelial cells

Shear stress is known to affect many processes in (patho-) physiology through a complex, multi-molecular mechanism, termed mechanotransduction. The sheer complexity of the process has raised questions how mechanotransduction is regulated. Here, we comprehensively evaluate the literature about the role of small non-coding miRNA in the regulation of mechanotransduction. Regulation of mRNA by miRNA is rather complex, depending not only on the concentration of mRNA to miRNA, but also on the amount of mRNA competing for a single mRNA. The only mechanism to counteract the latter factor is through overarching structures of miRNA. Indeed, two overarching structures are present miRNA families and miRNA clusters, and both will be discussed in details, regarding the latest literature and a previous conducted study focussed on mechanotransduction. Both the literature and our own data support a new hypothesis that miRNA-clusters predominantly regulate mechanotransduction, affecting 65% of signalling pathways. In conclusion, a new and important mode of regulation of mechanotransduction is proposed, based on miRNA clusters. This finding implicates new avenues for treatment of mechanotransduction and atherosclerosis.

MOUSSE: Multi-Omics Using Subject-Specific SignaturEs

Simple Summary

Modern profiling technologies have led to relevant progress toward precision medicine and disease management. A new trend in patient classification is to integrate multiple data types for the same subjects to increase the chance of identifying meaningful phenotype groups. However, these methodologies are still in their infancy, with their performance varying widely depending on the biological conditions analyzed. We developed MOUSSE, a new unsupervised and normalization-free tool for multi-omics integration able to maintain good clustering performance across a wide range of omics data. We verified its efficiency in clustering patients based on survival for ten different cancer types. The results we obtained show a higher average score in classification performance than ten other state-of-the-art algorithms. We have further validated the method by identifying a list of biological features potentially involved in patient survival, finding a high degree of concordance with the literature.

Abstract

High-throughput technologies make it possible to produce a large amount of data representing different biological layers, examples of which are genomics, proteomics, metabolomics and transcriptomics. Omics data have been individually investigated to understand the molecular bases of various diseases, but this may not be sufficient to fully capture the molecular mechanisms and the multilayer regulatory processes underlying complex diseases, especially cancer. To overcome this problem, several multi-omics integration methods have been introduced but a commonly agreed standard of analysis is still lacking. In this paper, we present MOUSSE, a novel normalization-free pipeline for unsupervised multi-omics integration. The main innovations are the use of rank-based subject-specific signatures and the use of such signatures to derive subject similarity networks. A separate similarity network was derived for each omics, and the resulting networks were then carefully merged in a way that considered their informative content. We applied it to analyze survival in ten different types of cancer. We produced a meaningful clusterization of the subjects and obtained a higher average classification score than ten state-of-the-art algorithms tested on the same data. As further validation, we extracted from the subject-specific signatures a list of relevant features used for the clusterization and investigated their biological role in survival. We were able to verify that, according to the literature, these features are highly involved in cancer progression and differential survival.

Long Noncoding RNA PRR34-AS1 Aggravates the Progression of Hepatocellular Carcinoma by Adsorbing microRNA-498 and Thereby Upregulating FOXO3

Purpose

Long noncoding RNAs are differentially expressed in hepatocellular carcinoma (HCC) and have been validated as essential regulators in HCC. However, there is limited knowledge regarding the detailed roles and mechanisms of most lncRNAs in HCC cells. In this study, the expression profiles of PRR34 antisense RNA 1 (PRR34-AS1) in HCC tissues and cell lines were determined. In addition, the detailed roles and underlying mechanisms of PRR34-AS1 in HCC cells were comprehensively elucidated.

Methods

Reverse transcription-quantitative polymerase chain reaction (PCR) was performed to measure PRR34-AS1 expression in HCC cells. Cell proliferation, apoptosis, and migration and invasion were evaluated in vitro using the cell counting kit-8 (CCK-8) assay, flow cytometric analysis, and transwell cell migration and invasion assays, respectively. In vivo tumor growth was determined using tumor xenograft experiments. The potential miRNA targets of PRR34-AS1 were predicted via bioinformatic analysis and further confirmed using the luciferase reporter assay, RNA immunoprecipitation assay, and reverse transcription-quantitative PCR.

Results

PRR34-AS1 was highly expressed in HCC tissues and cell lines, and its interference suppressed HCC cell proliferation, migration, and invasion but promoted cell apoptosis in vitro. In addition, loss of PRR34-AS1 decreased tumor growth in HCC cells in vivo. Mechanistically, PRR34-AS1 functions as a miR-498 sponge and subsequently increases forkhead box O3 (FOXO3) expression in HCC cells. Rescue experiments revealed that the suppressive effects triggered by PRR34-AS1 knockdown on the malignant characteristics of HCC cells could be abrogated by inhibiting miR-498 or restoring FOXO3 expression.

Conclusion

The depletion of PRR34-AS1 suppresses the oncogenicity of HCC cells by targeting the miR-498/FOXO3 axis. Therefore, the PRR34-AS1/miR-498/FOXO3 pathway may offer a basis for HCC treatment.

Characterization of microRNA profiles in the mammary gland tissue of dairy goats at the late lactation, dry period and late gestation stages

MicroRNAs (miRNAs) play an important role in regulating mammary gland development and lactation. We previously analyzed miRNA expression profiles in Laoshan dairy goat mammary glands at the early (20 d postpartum), peak (90 d postpartum) and late lactation (210 d postpartum) stages. To further enrich and clarify the miRNA expression profiles during the lactation physiological cycle, we sequenced miRNAs in the mammary gland tissues of Laoshan dairy goats at three newly selected stages: the late lactation (240 d postpartum), dry period (300 d postpartum) and late gestation (140 d after mating) stages. We obtained 4038 miRNAs and 385 important miRNA families, including mir-10, let-7 and mir-9. We also identified 754 differentially expressed miRNAs in the mammary gland tissue at the 3 different stages and 6 groups of miRNA clusters that had unique expression patterns. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that GO terms such as mammary gland development (GO:0030879) and mammary gland morphogenesis (GO:0060443) and important signaling pathways, including the insulin signaling pathway (chx04910), hippo signaling pathway (chx04390) and estrogen signaling pathway (chx04915), were enriched. We screened miRNAs and potential target genes that may be involved in the regulation of lactation, mammary gland growth and differentiation, cell apoptosis, and substance transport and synthesis and detected the expression patterns of important genes at the three stages. These miRNAs and critical target genes may be important factors for mammary gland development and lactation regulation and potentially valuable molecular markers, which may provide a theoretical reference for further investigation of mammary gland physiology.