Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction

microRNA-132 regulates gene expression programs involved in microglial homeostasis

microRNA-132 (miR-132), a known neuronal regulator, is one of the most robustly downregulated microRNAs (miRNAs) in the brain of Alzheimer's disease (AD) patients. Increasing miR-132 in AD mouse brain ameliorates amyloid and Tau pathologies, and also restores adult hippocampal neurogenesis and memory deficits. However, the functional pleiotropy of miRNAs requires in-depth analysis of the effects of miR-132 supplementation before it can be moved forward for AD therapy. We employ here miR-132 loss- and gain-of-function approaches using single-cell transcriptomics, proteomics, and in silico AGO-CLIP datasets to identify molecular pathways targeted by miR-132 in mouse hippocampus. We find that miR-132 modulation significantly affects the transition of microglia from a disease-associated to a homeostatic cell state. We confirm the regulatory role of miR-132 in shifting microglial cell states using human microglial cultures derived from induced pluripotent stem cells.

miRSCAPE - inferring miRNA expression from scRNA-seq data

Our understanding of miRNA activity at cellular resolution is thwarted by the inability of standard scRNA-seq protocols to capture miRNAs. We introduce a novel tool, miRSCAPE, to infer miRNA expression in a sample from its RNA-seq profile. We establish miRSCAPE's accuracy in 10 tumor and normal cohorts demonstrating its superiority over alternatives. miRSCAPE accurately infers cell type-specific miRNA activities (predicted versus observed fold-difference correlation ∼0.81) in two independent scRNA-seq datasets. We apply miRSCAPE to infer miRNA activities in scRNA clusters in pancreatic and lung adenocarcinomas, as well as in 56 cell types in the human cell landscape (HCL). In pancreatic and breast cancer scRNA-seq data, miRSCAPE recapitulates miRNAs associated with stemness and epithelial-mesenchymal transition (EMT) cell states, respectively. Overall, miRSCAPE recapitulates and refines miRNA biology at cellular resolution. miRSCAPE is freely available and is easily applicable to scRNA-seq data to infer miRNA activities at cellular resolution.

Prognostic Roles of ceRNA Network-Based Signatures in Gastrointestinal Cancers

Gastrointestinal cancers (GICs) are high-incidence malignant tumors that seriously threaten human health around the world. Their complexity and heterogeneity make the classic staging system insufficient to guide patient management. Recently, competing endogenous RNA (ceRNA) interactions that closely link the function of protein-coding RNAs with that of non-coding RNAs, such as long non-coding RNA (lncRNA) and circular RNA (circRNA), has emerged as a novel molecular mechanism influencing miRNA-mediated gene regulation. Especially, ceRNA networks have proven to be powerful tools for deciphering cancer mechanisms and predicting therapeutic responses at the system level. Moreover, abnormal gene expression is one of the critical breaking events that disturb the stability of ceRNA network, highlighting the role of molecular biomarkers in optimizing cancer management and treatment. Therefore, developing prognostic signatures based on cancer-specific ceRNA network is of great significance for predicting clinical outcome or chemotherapy benefits of GIC patients. We herein introduce the current frontiers of ceRNA crosstalk in relation to their pathological implications and translational potentials in GICs, review the current researches on the prognostic signatures based on lncRNA or circRNA-mediated ceRNA networks in GICs, and highlight the translational implications of ceRNA signatures for GICs management. Furthermore, we summarize the computational approaches for establishing ceRNA network-based prognostic signatures, providing important clues for deciphering GIC biomarkers.

EIF4A3-regulated circ_0087429 can reverse EMT and inhibit the progression of cervical cancer via miR-5003-3p-dependent upregulation of OGN expression

BACKGROUND

Circular RNAs (circRNAs) are noncoding RNAs with stable structures with high expression and tissue-specific expression. Studies have shown that circRNA dysregulation is closely related to the progression of tumours. However, the function and regulatory mechanism of most circRNAs in cervical cancer are still unclear.   METHODS: CircRNAs related to cervical cancer were screened through the Gene Expression Omnibus (GEO) database. qRT-PCR was used to verify the expression of circ_0087429 in cervical cancer tissues and cells. Then, in vivo and in vitro experiments were conducted to evaluate the role of circ_0087429 in the progression of cervical cancer. The role of the circ_0087429/miR-5003-3p/osteoglycin (OGN) axis in the epithelial to mesenchymal transition (EMT) was confirmed by rescue experiments, fluorescence in situ hybridization, luciferase reporter assays, immunofluorescence staining and western blotting. The inhibitory effect of Eukaryotic initiation factor 4A-III (EIF4A3) on the biogenesis of circ_0087429 was verified by RNA immunoprecipitation (RIP) assays and qRT-PCR.

RESULTS

circ_0087429 is significantly downregulated in cervical cancer tissues and cells and negatively correlated with International Federation of Gynecology and Obstetrics (FIGO) staging and lymphatic metastasis in cervical cancer patients. circ_0087429 can significantly inhibit the proliferation, migration, invasion and angiogenesis of cervical cancer in vitro and tumour growth and metastasis in vivo. OGN is significantly downregulated in cervical cancer tissues and cells. circ_0087429 can upregulate the expression of OGN by competitively binding with miR-5003-3p, thereby reversing EMT and inhibiting the progression of cervical cancer. EIF4A3 can inhibit circ_0087429 expression by binding to its flanking regions.

CONCLUSIONS

As a tumour suppressor, circ_0087429 regulated by EIF4A3 can reverse EMT and inhibit the progression of cervical cancer through the miR-5003-3p/OGN axis. It is expected to become a potential target for the treatment of cervical cancer.

Integrated analysis of expression profiles with meat quality traits in cattle

MicroRNAs (miRNAs) play a vital role in improving meat quality by binding to messenger RNAs (mRNAs). We performed an integrated analysis of miRNA and mRNA expression profiling between bulls and steers based on the differences in meat quality traits. Fat and fatty acids are the major phenotypic indices of meat quality traits to estimate between-group variance. In the present study, 90 differentially expressed mRNAs (DEGs) and 18 differentially expressed miRNAs (DEMs) were identified. Eighty-three potential DEG targets and 18 DEMs were used to structure a negative interaction network, and 75 matching target genes were shown in this network. Twenty-six target genes were designated as intersection genes, screened from 18 DEMs, and overlapped with the DEGs. Seventeen of these genes enriched to 19 terms involved in lipid metabolism. Subsequently, 13 DEGs and nine DEMs were validated using quantitative real-time PCR, and seven critical genes were selected to explore the influence of fat and fatty acids through hub genes and predict functional association. A dual-luciferase reporter and Western blot assays confirmed a predicted miRNA target (bta-miR-409a and PLIN5). These findings provide substantial evidence for molecular genetic controls and interaction among genes in cattle.

Network Approaches to Study Endogenous RNA Competition and Its Impact on Tissue-Specific microRNA Functions

microRNAs are small non-coding RNAs that play a key role in regulating gene expression. These molecules exert their function through sequence complementarity with microRNA responsive elements and are typically located in the 3' untranslated region of mRNAs, negatively regulating expression. Even though the relevant role of miRNA-dependent regulation is broadly recognized, the principles governing their ability to lead to specific functional outcomes in distinct cell types are still not well understood. In recent years, an intriguing hypothesis proposed that miRNA-responsive elements act as communication links between different RNA species, making the investigation of microRNA function even more complex than previously thought. The competing endogenous RNA hypothesis suggests the presence of a new level of regulation, whereby a specific RNA transcript can indirectly influence the abundance of other transcripts by limiting the availability of a common miRNA, acting as a "molecular sponge". Since this idea has been proposed, several studies have tried to pinpoint the interaction networks that have been established between different RNA species and whether they contribute to normal cell function and disease. The focus of this review is to highlight recent developments and achievements made towards the process of characterizing competing endogenous RNA networks and their role in cellular function.

Brain microRNAs are associated with variation in cognitive trajectory in advanced age

In advancing age, some individuals maintain a stable cognitive performance over time, while others experience a rapid decline. Such variation in cognitive trajectory is only partially explained by common neurodegenerative pathologies. Hence, we aimed to identify new molecular processes underlying variation in cognitive trajectory using brain microRNA profile followed by an integrative analysis with brain transcriptome and proteome. Individual cognitive trajectories were derived from longitudinally assessed cognitive-test scores of older-adult brain donors from four longitudinal cohorts. Postmortem brain microRNA profiles, transcriptomes, and proteomes were derived from the dorsolateral prefrontal cortex. The global microRNA association study of cognitive trajectory was performed in a discovery (n = 454) and replication cohort (n = 134), followed by a meta-analysis that identified 6 microRNAs. Among these, miR-132-3p and miR-29a-3p were most significantly associated with cognitive trajectory. They explain 18.2% and 2.0% of the variance of cognitive trajectory, respectively, and act independently of the eight measured neurodegenerative pathologies. Furthermore, integrative transcriptomic and proteomic analyses revealed that miR-132-3p was significantly associated with 24 of the 47 modules of co-expressed genes of the transcriptome, miR-29a-3p with 3 modules, and identified 84 and 214 downstream targets of miR-132-3p and miR-29a-3p, respectively, in cognitive trajectory. This is the first global microRNA study of cognitive trajectory to our knowledge. We identified miR-29a-3p and miR-132-3p as novel and robust contributors to cognitive trajectory independently of the eight known cerebral pathologies. Our findings lay a foundation for future studies investigating mechanisms and developing interventions to enhance cognitive stability in advanced age.

Role of microRNAs in the pathophysiology of addiction

Addiction is a chronic and relapsing brain disorder characterized by compulsive seeking despite adverse consequences. There are both heritable and epigenetic mechanisms underlying drug addiction. Emerging evidence suggests that non-coding RNAs (ncRNAs) such as microRNAs (miRNAs), long non-coding RNAs, and circular RNAs regulate synaptic plasticity and related behaviors caused by substances of abuse. These ncRNAs modify gene expression and may contribute to the behavioral phenotypes of addiction. Among the ncRNAs, the most widely researched and impactful are miRNAs. The goal in this systematic review is to provide a detailed account of recent research involving the role of miRNAs in addiction. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA in Disease and Development > RNA in Disease.

LncRNA Gas5 regulates Fn1 deposition via Creb5 in renal fibrosis

Aim: Although studies on lncRNAs in renal fibrosis have focused on target genes and functions of lncRNAs, a comprehensive interaction analysis of lncRNAs is lacking. Materials & methods: Differentially expressed genes in renal fibrosis were screened, and the interaction between lncRNAs and miRNAs was searched. Results: We constructed a ceRNA network associated with renal fibrosis, by which we found the transcription factor Creb5, a target gene of lncRNA Gas5 that might regulate extracellular Fn1 deposition. Conclusion: Our study not only provides a theoretical basis for the ceRNA regulation mechanism of Gas5 but also provides experimental evidence supporting the use of Gas5 targeting in the treatment of renal fibrosis.

Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells

Single-cell RNA sequencing studies on gene co-expression patterns could yield important regulatory and functional insights, but have so far been limited by the confounding effects of differentiation and cell cycle. We apply a tailored experimental design that eliminates these confounders, and report thousands of intrinsically covarying gene pairs in mouse embryonic stem cells. These covariations form a network with biological properties, outlining known and novel gene interactions. We provide the first evidence that miRNAs naturally induce transcriptome-wide covariations and compare the relative importance of nuclear organization, transcriptional and post-transcriptional regulation in defining covariations. We find that nuclear organization has the greatest impact, and that genes encoding for physically interacting proteins specifically tend to covary, suggesting importance for protein complex formation. Our results lend support to the concept of post-transcriptional RNA operons, but we further present evidence that nuclear proximity of genes may provide substantial functional regulation in mammalian single cells.

Gene expression covariation can be studied by single-cell RNA sequencing. Here the authors analyze intrinsically covarying gene pairs by eliminating the confounding effects in single-cell experiments and observe covariation of proximal genes and miRNA-induced covariation of target mRNAs.

LncRNA TTN-AS1 acts as sponge for miR-15b-5p to regulate FBXW7 expression in ovarian cancer

Emerging evidence showed that long noncoding RNA (lncRNA) plays crucial roles in regulating various cancer biological behaviors. Titin-antisense RNA1 (TTN-AS1) has been reported to have crucial roles in cancers but its role in ovarian cancer remains unknown. The levels of TTN-AS1, microNRA-15b-5p (miR-15b-5p), and F-box and WD repeat domain containing 7 (FBXW7) in ovarian cancer cells were measured by quantitative reverse-transcription PCR. Targets for TTN-AS1 and miR-15b-5p were predicted by bioinformatic tools, and validated by luciferase activity reporter assay. Cell proliferation, colony formation, and cell apoptosis were analyzed with cell counting kit-8 assay, colony formation assay, and flow cytometry. Correlation of TTN-AS1 and FBXW7 was analyzed at gene expression profiling interactive analysis. TTN-AS1 was found decreased expression in ovarian cancer tissues and cells. Dual-luciferase activity validated TTN-AS1 and FBXW7 shared binding site in miR-15b-5p. Functional assays showed TTN-AS1 overexpression inhibits ovarian cancer cell proliferation, colony formation but promotes apoptosis. Rescue experiments showed that knockdown of FBXW7 could partially counteracted the effects of TTN-AS1 overexpression on ovarian cancer cell behaviors. Our results indicated that the TTN-AS1/miR-15b-5p/FBXW7 axis identified in this work could help to identify treatment biomarkers for ovarian cancer.

microRNA-mediated noise processing in cells: A fight or a game?

In the past decades, microRNAs (miRNA) have much attracted the attention of researchers at the interface between life and theoretical sciences for their involvement in post-transcriptional regulation and related diseases. Thanks to the always more sophisticated experimental techniques, the role of miRNAs as "noise processing units" has been further elucidated and two main ways of miRNA noise-control have emerged by combinations of theoretical and experimental studies. While on one side miRNAs were thought to buffer gene expression noise, it has recently been suggested that miRNAs could also increase the cell-to-cell variability of their targets. In this Mini Review, we focus on the role of miRNAs in molecular noise processing and on the advantages as well as current limitations of theoretical modelling.

Methamphetamine Enhances HIV-1 Replication in CD4+ T-Cells via a Novel IL-1β Auto-Regulatory Loop

Methamphetamine (Meth) abuse is a worldwide public health problem and contributes to HIV-1 pathobiology and poor adherence to anti-retroviral therapies. Specifically, Meth is posited to alter molecular mechanisms to provide a more conducive environment for HIV-1 replication and spread. Enhanced expression of inflammatory cytokines, such as Interleukin-1β (IL-1β), has been shown to be important for HIV-1 pathobiology. In addition, microRNAs (miRNAs) play integral roles in fine-tuning the innate immune response. Notably, the effects of Meth abuse on miRNA expression are largely unknown. We studied the effects of Meth on IL-1β and miR-146a, a well-characterized member of the innate immune signaling network. We found that Meth induces miR-146a and triggers an IL-1β auto-regulatory loop to modulate innate immune signaling in CD4⁺ T-cells. We also found that Meth enhances HIV-1 replication via IL-1 signaling. Our results indicate that Meth activates an IL-1β feedback loop to alter innate immune pathways and favor HIV-1 replication. These observations offer a framework for designing targeted therapies in HIV-infected, Meth using hosts.

From Endogenous to Synthetic microRNA-Mediated Regulatory Circuits: An Overview

MicroRNAs are short non-coding RNAs that are evolutionarily conserved and are pivotal post-transcriptional mediators of gene regulation. Together with transcription factors and epigenetic regulators, they form a highly interconnected network whose building blocks can be classified depending on the number of molecular species involved and the type of interactions amongst them. Depending on their topology, these molecular circuits may carry out specific functions that years of studies have related to the processing of gene expression noise. In this review, we first present the different over-represented network motifs involving microRNAs and their specific role in implementing relevant biological functions, reviewing both theoretical and experimental studies. We then illustrate the recent advances in synthetic biology, such as the construction of artificially synthesised circuits, which provide a controlled tool to test experimentally the possible microRNA regulatory tasks and constitute a starting point for clinical applications.

Competing endogenous RNA crosstalk at system level

microRNAs (miRNAs) regulate gene expression at post-transcriptional level by repressing target RNA molecules. Competition to bind miRNAs tends in turn to correlate their targets, establishing effective RNA-RNA interactions that can influence expression levels, buffer fluctuations and promote signal propagation. Such a potential has been characterized mathematically for small motifs both at steady state and away from stationarity. Experimental evidence, on the other hand, suggests that competing endogenous RNA (ceRNA) crosstalk is rather weak. Extended miRNA-RNA networks could however favour the integration of many crosstalk interactions, leading to significant large-scale effects in spite of the weakness of individual links. To clarify the extent to which crosstalk is sustained by the miRNA interactome, we have studied its emergent systemic features in silico in large-scale miRNA-RNA network reconstructions. We show that, although generically weak, system-level crosstalk patterns (i) are enhanced by transcriptional heterogeneities, (ii) can achieve high-intensity even for RNAs that are not co-regulated, (iii) are robust to variability in transcription rates, and (iv) are significantly non-local, i.e. correlate weakly with miRNA-RNA interaction parameters. Furthermore, RNA levels are generically more stable when crosstalk is strongest. As some of these features appear to be encoded in the network's topology, crosstalk may functionally be favoured by natural selection. These results suggest that, besides their repressive role, miRNAs mediate a weak but resilient and context-independent network of cross-regulatory interactions that interconnect the transcriptome, stabilize expression levels and support system-level responses.

Large-scale inference of competing endogenous RNA networks with sparse partial correlation

MOTIVATION

MicroRNAs (miRNAs) are important non-coding post-transcriptional regulators that are involved in many biological processes and human diseases. Individual miRNAs may regulate hundreds of genes, giving rise to a complex gene regulatory network in which transcripts carrying miRNA binding sites act as competing endogenous RNAs (ceRNAs). Several methods for the analysis of ceRNA interactions exist, but these do often not adjust for statistical confounders or address the problem that more than one miRNA interacts with a target transcript.

RESULTS

We present SPONGE, a method for the fast construction of ceRNA networks. SPONGE uses 'multiple sensitivity correlation', a newly defined measure for which we can estimate a distribution under a null hypothesis. SPONGE can accurately quantify the contribution of multiple miRNAs to a ceRNA interaction with a probabilistic model that addresses previously neglected confounding factors and allows fast P-value calculation, thus outperforming existing approaches. We applied SPONGE to paired miRNA and gene expression data from The Cancer Genome Atlas for studying global effects of miRNA-mediated cross-talk. Our results highlight already established and novel protein-coding and non-coding ceRNAs which could serve as biomarkers in cancer.

AVAILABILITY AND IMPLEMENTATION

SPONGE is available as an R/Bioconductor package (doi: 10.18129/B9.bioc.SPONGE).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Single-Cell RNA Sequencing-Based Computational Analysis to Describe Disease Heterogeneity

The trillions of cells in the human body can be viewed as elementary but essential biological units that achieve different body states, but the low resolution of previous cell isolation and measurement approaches limits our understanding of the cell-specific molecular profiles. The recent establishment and rapid growth of single-cell sequencing technology has facilitated the identification of molecular profiles of heterogeneous cells, especially on the transcription level of single cells [single-cell RNA sequencing (scRNA-seq)]. As a novel method, the robustness of scRNA-seq under changing conditions will determine its practical potential in major research programs and clinical applications. In this review, we first briefly presented the scRNA-seq-related methods from the point of view of experiments and computation. Then, we compared several state-of-the-art scRNA-seq analysis frameworks mainly by analyzing their performance robustness on independent scRNA-seq datasets for the same complex disease. Finally, we elaborated on our hypothesis on consensus scRNA-seq analysis and summarized the potential indicative and predictive roles of individual cells in understanding disease heterogeneity by single-cell technologies.

Long non-coding RNA FLJ33360 participates in ovarian cancer progression by sponging miR-30b-3p

Background

Long noncoding RNAs (lncRNAs) have been reported to play a key role in the development and progression of human malignancies. FLJ33360 is an lncRNA with unknown functions. This study was designed to determine the clinical significance and mechanism of FLJ33360 in ovarian cancer.

Materials and methods

The clinical significance of FLJ33360 in ovarian cancer was determined using the Gene Expression Profiling Interactive Analysis (GEPIA) database, Kaplan-Meier Plotter database, quantitative reverse transcription polymerase chain reaction (qRT-PCR) and statistical analysis. The regulatory relationships between FLJ33360 and miR-30b-3p were explored through bioinformatics, the Gene Expression Omnibus (GEO) database, the ArrayExpress database and meta-analysis. The possible pathways were predicted using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. In addition, the key target genes were identified using a protein-protein interaction (PPI) network, the Cancer Genome Atlas (TCGA) database, and correlation analysis.

Results

FLJ33360 expression was significantly downregulated in ovarian cancer tissue (P=0.0011) and was closely associated with International Federation of Gynecology and Obstetrics (FIGO) stage (P=0.027) and recurrence (P=0.002). FLJ33360 may have potential value in detecting ovarian cancer (area under the curve =0.793). Function analysis demonstrated that FLJ33360 can act as a molecular sponge of miR-30b-3p to regulate the expression of target genes that are mainly involved in positive regulation of smooth muscle cell migration, the unsaturated fatty acid metabolic process, and positive regulation of the epithelial to mesenchymal transition. Among these target genes, BCL2 is the hub gene.

Conclusion

FLJ33360 is a potential biomarker for early diagnosis and prognostic assessment in ovarian cancer and may regulate the expression of genes by sponging miR-30b-3p and thus participate in the development of ovarian cancer.