miRTissue ce: extending miRTissue web service with the analysis of ceRNA-ceRNA interactions

Systems Approaches to Cell Culture-Derived Extracellular Vesicles for Acute Kidney Injury Therapy: Prospects and Challenges

Acute kidney injury (AKI) is a heterogeneous syndrome, comprising diverse etiologies of kidney insults that result in high mortality and morbidity if not well managed. Although great efforts have been made to investigate underlying pathogenic mechanisms of AKI, there are limited therapeutic strategies available. Extracellular vesicles (EV) are membrane-bound vesicles secreted by various cell types, which can serve as cell-free therapy through transfer of bioactive molecules. In this review, we first overview the AKI syndrome and EV biology, with a particular focus on the technical aspects and therapeutic application of cell culture-derived EVs. Second, we illustrate how multi-omic approaches to EV miRNA, protein, and genomic cargo analysis can yield new insights into their mechanisms of action and address unresolved questions in the field. We then summarize major experimental evidence regarding the therapeutic potential of EVs in AKI, which we subdivide into stem cell and non-stem cell-derived EVs. Finally, we highlight the challenges and opportunities related to the clinical translation of animal studies into human patients.

RNA-RNA competitive interactions: a molecular civil war ruling cell physiology and diseases

The idea that proteins are the main determining factors in the functioning of cells and organisms, and their dysfunctions are the first cause of pathologies, has been predominant in biology and biomedicine until recently. This protein-centered view was too simplistic and failed to explain the physiological and pathological complexity of the cell. About 80% of the human genome is dynamically and pervasively transcribed, mostly as non-protein-coding RNAs (ncRNAs), which competitively interact with each other and with coding RNAs generating a complex RNA network regulating RNA processing, stability, and translation and, accordingly, fine-tuning the gene expression of the cells. Qualitative and quantitative dysregulations of RNA-RNA interaction networks are strongly involved in the onset and progression of many pathologies, including cancers and degenerative diseases. This review will summarize the RNA species involved in the competitive endogenous RNA network, their mechanisms of action, and involvement in pathological phenotypes. Moreover, it will give an overview of the most advanced experimental and computational methods to dissect and rebuild RNA networks.

Integrative competing endogenous RNA network analyses identify novel lncRNA and genes implicated in metastatic breast cancer

Competing endogenous RNAs (ceRNAs) have gained attention in cancer research owing to their involvement in microRNA-mediated gene regulation. Previous studies have identified ceRNA networks of individual cancers. Nevertheless, none of these studies has investigated different cancer stages. We identify stage-specific ceRNAs in breast cancer using the cancer genome atlas data. Moreover, we investigate the molecular functions and prognostic ability of ceRNAs involved in stage I-IV networks. We identified differentially expressed candidate ceRNAs using edgeR and limma R packages. A three-step analysis was used to identify statistically significant ceRNAs of each stage. Survival analysis and functional enrichment analysis were conducted to identify molecular functions and prognostic ability. We found five genes and one long non-coding RNA unique to the stage IV ceRNA network. These genes have been described in previous breast cancer studies. Genes acted as ceRNAs are enriched in cancer-associated pathways. Two, three, and three microRNAs from stages I, II, and III were prognostic from the Kaplan-Meier survival analysis. Our results reveal a set of unique ceRNAs in metastatic breast cancer. Further experimental work is required to evaluate their role in metastasis. Moreover, identifying stage-specific ceRNAs will improve the understanding of personalised therapeutics in breast cancer.

Competing endogenous RNA-networks reveal key regulatory microRNAs involved in the response of Atlantic salmon to a novel orthomyxovirus

One of the most intriguing discoveries of the genomic era is that only a small fraction of the genome is dedicated to protein coding. The remaining fraction of the genome contains, amongst other elements, a number of non-coding transcripts that regulate the transcription of protein coding genes. Here we used transcriptome sequencing data to explore these gene regulatory networks using RNA derived from gill tissue of Atlantic salmon (Salmo salar) infected with Pilchard orthomyxovirus (POMV), but showing no clinical signs of disease. We examined fish sampled early during the challenge trial (8-12 days after infection) to uncover potential biomarkers of early infection and innate immunity, and fish sampled late during the challenge trial (19 dpi) to elucidate potential markers of resistance to POMV. We analysed total RNA-sequencing data to find differentially expressed messenger RNAs (mRNA) and identify new long-noncoding RNAs (lncRNAs). We also evaluated small RNA sequencing data to find differentially transcribed microRNAs (miRNAs) and explore their role in gene regulatory networks. Whole-genome expression data (both coding and non-coding transcripts) were used to explore the crosstalk between RNA molecules by constructing competing endogenous RNA networks (ceRNA). The teleost specific miR-462/miR-731 cluster was strongly induced in POMV infected fish and deemed a potential biomarker of early infection. Gene networks also identified a selenoprotein (selja), downregulated in fish sampled late during the challenge, which may be associated to viral clearance and the return to homeostasis after infection. This study provides the basis for further investigations using molecular tools to overexpress or inhibit miRNAs to confirm the functional impact of the interactions presented here on gene expression and their potential application at commercial level.

Downregulation of ZC3H13 by miR-362-3p/miR-425-5p is associated with a poor prognosis and adverse outcomes in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is notorious for its poor prognosis. Previous studies identified several N6-methyladenosine (m6A)-related genes that play key roles in the initiation and progression of HCC patients. In particular, the N6-methyladenosine RNA methylation regulator ZC3H13 could be a candidate as a novel biomarker and therapeutic target for hepatocellular carcinoma. In HCC, low expression of ZC3H13 was reported, but the molecular reason is unclear. In this study, we performed pan cancer analysis for ZC3H13 expression and prognosis using The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) data and found that ZC3H13 might be a potential tumor suppressor gene in HCC. Subsequently, miRNAs contributing to ZC3H13 downregulation were identified by a series of in silico analyses, including expression analysis, correlation analysis, and survival analysis. Finally, the miR-362-3p/miR-425-5p-ZC3H13 axis was identified as the most likely upstream miRNA-related pathway of ZC3H13 in HCC. Additionally, miR-362-3p/miR-425-5p mimic and inhibitor results were detected by quantitative real-time PCR (qPCR) analysis and western blotting. We identified an upstream regulatory mechanism of ZC3H13 in HCC, namely, the miR-362-3p/miR-425-5p-ZC3H13 axis. Moreover, the ZC3H13 level was significantly positively associated with tumor immune cell infiltration, biomarkers of immune cells, and immune checkpoint expression. Collectively, our findings elucidated that ncRNA-mediated downregulation of ZC3H13 was correlated with a poor prognosis and tumor immune infiltration in HCC. In conclusion, this study demonstrates that ZC3H13 is a direct target of miR-362-3p/miR-425-5p in liver hepatocellular carcinoma (LIHC) that regulates immune modulation in the microenvironment of LIHC.

Classical and noncanonical functions of miRNAs in cancers

Alterations in microRNAs (miRNAs) expression are causative in the initiation and progression of human cancers. The molecular events responsible for the widespread differential expression of miRNAs in malignancy are exemplified by their location in cancer-associated genomic regions, epigenetic mechanisms, transcriptional dysregulation, chemical modifications and editing, and alterations in miRNA biogenesis proteins. The classical miRNA function is synonymous with post-transcriptional repression of target protein genes. However, several studies have reported miRNAs functioning outside this paradigm and some of these novel modes of regulation of gene expression have been implicated in cancers. Here, we summarize key aspects of miRNA involvement in cancer, with a special focus on these lesser-studied mechanisms of action.

Identifying Complex lncRNA/Pseudogene-miRNA-mRNA Crosstalk in Hormone-Dependent Cancers

Simple Summary

Competing endogenous RNAs (ceRNAs) have gained attention in cancer research owing to their involvement in microRNA-mediated gene regulation. Here, we identified a shared ceRNA network across five hormone-dependent (HD) cancers (prostate, breast, colon, rectal, and endometrial), that contain two long non-coding RNAs, nine mRNAs, and seventy-four microRNAs. Among them, two mRNAs and forty-one microRNAs were associated with at least one HD cancer survival. A similar analytical approach can be applied to identify shared ceRNAs across a group of related cancers, which will significantly contribute to understanding their shared disease biology.

Abstract

The discovery of microRNAs (miRNAs) has fundamentally transformed our understanding of gene regulation. The competing endogenous RNA (ceRNA) hypothesis postulates that messenger RNAs and other RNA transcripts, such as long non-coding RNAs and pseudogenes, can act as natural miRNA sponges. These RNAs influence each other’s expression levels by competing for the same pool of miRNAs through miRNA response elements on their target transcripts, thereby modulating gene expression and protein activity. In recent years, these ceRNA regulatory networks have gained considerable attention in cancer research. Several studies have identified cancer-specific ceRNA networks. Nevertheless, prior bioinformatic analyses have focused on long-non-coding RNA-associated ceRNA networks. Here, we identify an extended ceRNA network (including both long non-coding RNAs and pseudogenes) shared across a group of five hormone-dependent (HD) cancers, i.e., prostate, breast, colon, rectal, and endometrial cancers, using data from The Cancer Genome Atlas (TCGA). We performed a functional enrichment analysis for differentially expressed genes in the shared ceRNA network of HD cancers, followed by a survival analysis to determine their prognostic ability. We identified two long non-coding RNAs, nine genes, and seventy-four miRNAs in the shared ceRNA network across five HD cancers. Among them, two genes and forty-one miRNAs were associated with at least one HD cancer survival. This study is the first to investigate pseudogene-associated ceRNAs across a group of related cancers and highlights the value of this approach to understanding the shared molecular pathogenesis in a group of related diseases.

lncRNA AC007207.2 Promotes Malignant Properties of Osteosarcoma via the miR-1306-5p/SIRT7 Axis

Background

Long non-coding RNAs (lncRNAs) have been implicated in initiation and development of numerous cancers. In the present study, we explored the role of lncRNAs AC007207.2 in osteosarcoma (OS).

Methods

Gene expression data of OS tissues was downloaded from the TARGET database. All the experiments were repeated at least three times. Data were analyzed using Perl, R, SPSS v12.0 and GraphPad Prism 8 software.

Results

We found lncRNA AC007207.2 was over-expressed in OS tissues and cell lines, and this phenomenon was associated with the worse prognosis of OS. Moreover, we found that AC007207.2 promotes proliferation and metastasis of OS cells via the miR-1306-5p/SIRT7 axis. Meanwhile, we found miR-1306-5p remarkably inhibits the malignant behavior of OS cells.

Conclusion

lncRNA AC007207.2 promotes progression of OS by upregulating SIRT7 expression through miR-1306-5p sponging. Thus, lncRNA AC007207.2/miR-1306-5p/SIRT7 axis is a promising therapeutic target for OS treatment.

Time to infer miRNA sponge modules

Inferring competing endogenous RNA (ceRNA) or microRNA (miRNA) sponge modules is a challenging and meaningful task for revealing ceRNA regulation mechanism at the module level. Modules in this context refer to groups of miRNA sponges which have mutual competitions and act as functional units for achieving biological processes. The recent development of computational methods based on heterogeneous data provides a novel way to discern the competitive effects of miRNA sponges on human complex diseases. This article aims to provide a comprehensive perspective of miRNA sponge module discovery methods. We first review the publicly available databases of cancer-related miRNA sponges, as the miRNA sponges involved in human cancers contribute to the discovery of cancer-associated modules. Then we review the existing computational methods for inferring miRNA sponge modules. Furthermore, we conduct an assessment on the performance of the module discovery methods with the pan-cancer dataset, and the comparison study indicates that it is useful to infer biologically meaningful miRNA sponge modules by directly mapping heterogeneous data to the competitive modules. Finally, we discuss the future directions and associated challenges in developing in silico methods to infer miRNA sponge modules. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.

SPONGEdb: a pan-cancer resource for competing endogenous RNA interactions

microRNAs (miRNAs) are post-transcriptional regulators involved in many biological processes and human diseases, including cancer. The majority of transcripts compete over a limited pool of miRNAs, giving rise to a complex network of competing endogenous RNA (ceRNA) interactions. Currently, gene-regulatory networks focus mostly on transcription factor-mediated regulation, and dedicated efforts for charting ceRNA regulatory networks are scarce. Recently, it became possible to infer ceRNA interactions genome-wide from matched gene and miRNA expression data. Here, we inferred ceRNA regulatory networks for 22 cancer types and a pan-cancer ceRNA network based on data from The Cancer Genome Atlas. To make these networks accessible to the biomedical community, we present SPONGEdb, a database offering a user-friendly web interface to browse and visualize ceRNA interactions and an application programming interface accessible by accompanying R and Python packages. SPONGEdb allows researchers to identify potent ceRNA regulators via network centrality measures and to assess their potential as cancer biomarkers through survival, cancer hallmark and gene set enrichment analysis. In summary, SPONGEdb is a feature-rich web resource supporting the community in studying ceRNA regulation within and across cancer types.

BITS2019: the sixteenth annual meeting of the Italian society of bioinformatics

The 16th Annual Meeting of the Bioinformatics Italian Society was held in Palermo, Italy, on June 26-28, 2019. More than 80 scientific contributions were presented, including 4 keynote lectures, 31 oral communications and 49 posters. Also, three workshops were organised before and during the meeting. Full papers from some of the works presented in Palermo were submitted for this Supplement of BMC Bioinformatics. Here, we provide an overview of meeting aims and scope. We also shortly introduce selected papers that have been accepted for publication in this Supplement, for a complete presentation of the outcomes of the meeting.