miRNA Activity Research Articles

Transposons Acting as Competitive Endogenous RNAs: In-Silico Evidence from Datasets Characterised by L1 Overexpression.

LINE L1 are transposable elements that can replicate within the genome by passing through RNA intermediates. The vast majority of these element copies in the human genome are inactive and just between 100 and 150 copies are still able to mobilize. During evolution, they could have been positively selected for beneficial cellular functions. Nonetheless, L1 deregulation can be detrimental to the cell, causing diseases such as cancer. The activity of miRNAs represents a fundamental mechanism for controlling transcript levels in somatic cells. These are a class of small non-coding RNAs that cause degradation or translational inhibition of their target transcripts. Beyond this, competitive endogenous RNAs (ceRNAs), mostly made by circular and non-coding RNAs, have been seen to compete for the binding of the same set of miRNAs targeting protein coding genes. In this study, we have investigated whether autonomously transcribed L1s may act as ceRNAs by analyzing public dataset in-silico. We observed that genes sharing miRNA target sites with L1 have a tendency to be upregulated when L1 are overexpressed, suggesting the possibility that L1 might act as ceRNAs. This finding will help in the interpretation of transcriptomic responses in contexts characterized by the specific activation of transposons.

MiRNAs Participate in the Regulation of Oxidative Stress-Related Gene Expression in Endometrioid Endometrial Cancer.

Reactive oxygen species are formed as by-products of normal cell metabolism. They are needed to maintain cell homeostasis and signaling, which is possible due to defense systems. Disruption of this balance leads to oxidative stress that can induce cancer. Redox regulation by miRNAs may be a potential therapeutic target. The aim of the study was to assess the activity of genes associated with oxidative stress in endometrial cancer and to determine their relationship with miRNAs. The study included 45 patients with endometrioid endometrial cancer and 45 without neoplastic changes. The expression profile of genes associated with oxidative stress was determined with mRNA microarrays, RT-qPCR and ELISA. The miRNA prediction was performed based on the miRNA microarray experiment and the mirDB tool. PRDX2 and AQP1 showed overexpression that was probably not related to miRNA activity. A high level of PKD2 may be the result of a decrease in the activity of miR-195-3p, miR-20a, miR-134. A SOD3 level reduction can be caused by miR-328, miR-363. In addition, miR-363 can also regulate KLF2 expression. In the course of endometrial cancer, the phenomenon of oxidative stress is observed, the regulation of which may be influenced by miRNAs.

Human microRNA‐298 plays a vital role in maintaining APP and tau homeostasis and IL‐induced inflammation: Implication in Alzheimer’s disease.

AbstractBackgroundAlzheimer’s disease (AD) is marked by neurofibrillary tangles mainly composed of hyperphosphorylated microtubule‐associated protein tau; senile plaques comprising amyloid β (Aβ) peptides; and neuroinflammation. How these pathological changes are regulated remains unclear. Genetic, epigenetic, and environmental factors play important roles in disease progression. MicroRNA (miRNA), a group of small non‐coding RNAs, regulates multiple biological and pathological processes by binding to target mRNAs and altering translation levels. Disrupting this process could contribute to AD pathogenesis. We hypothesize that miR‐298 plays a vital role in maintaining APP and tau homeostasis and IL‐induced inflammation, particularly gliosis.MethodWe performed miR‐298 treatments and blockade by antisense‐miR298 (antagomiRs) in 3’UTR‐reporter clone‐transfected cultures and protein levels from target native mRNAs (Chopra et al‐Mol. Psychiatry‐2021). We transfected human astrocyte cells with miR‐298 mimics or antagomiRs. We analyzed culture media and lysates for protein and mRNA. We performed ELISA and real‐time‐qPCR assays to determine cytokines, APP and tau levels. We analyzed autopsy brain tissues from non‐cognitively impaired (NCI) and AD subjects by measuring levels of miR‐298, target mRNAs and proteins in cortical samples, as we described (Wang et al‐Mol. Psychiatry‐2022).ResultWe identified putative sites for miR‐298 in mRNAs encoding APP, BACE1, MAPT, IL1α, and IL6. Treatment by miR‐298 significantly increased production and secretion of multiple pro‐inflammatory cytokines, specifically IL‐1, IL‐6 and TNF‐α in human astrocyte cultures. Furthermore, treatment by miR‐298 reduced tau, APP and BACE1 protein and mRNA levels in astrocyte cultures. Levels of miR‐298 varied in postmortem human temporal lobe between AD patients and age‐matched NCI controls.ConclusionMiR‐298 induced a variety of pro‐inflammatory cytokines without administration of other challenges. Induction of multiple cytokines may be due to combinations of direct miRNA activity and regulation of upstream signaling pathways. MiR‐298 may play an important biological role in AD by reducing APP, BACE1 and tau expression while increasing the physiologic production of IL cytokines. This apparent paradox is resolved by noting that early‐stage (prodromal) gliosis may contribute to the clearance of toxic aggregates. We plan to test miR‐298 in AD animal models, including human tau‐overexpressing transgenic mice.We appreciate NIH‐NIA grants: (R01AG051086, R21AG056007, R56AG072810, P01AG014449, P30AG072976).

Identification of Novel miRNAs Involved in Cancer Progression and Metastasis in Clear Cell Renal Cell Carcinoma

MicroRNAs are non-coding molecules 21–23 nucleotides long that are involved in post-transcriptional regulation of gene expression by mRNA silencing. There is evidence that miRNA activity is associated with various types of human cancer, such as breast cancer, colorectal cancer, ovarian cancer and hepatocellular carcinoma, as well as with clear cell renal cell carcinoma. In 2020, the incidence of kidney cancer worldwide was 319,016. Clear cell renal cell carcinoma is associated with loss or mutation of the VHL gene. The aim of this study was to identify miRNAs that are expressed differently in samples of normal kidney tissue and tissue affected by clear cell renal cell carcinoma. For this study, a public miRNA dataset from ArrayExpress was obtained and post-processed. Mapping, identification of known and new microRNAs, and quantification were performed using the miRDeep2 computer program from the DESeq R/Bioconductor package. We performed target identification and functional load analysis using GeneCodis4. A total of 2656 miRNAs were found to be differentially expressed, of which 229 miRNAs were overexpressed and 302 were underexpressed. In this study, we identified five miRNAs that were already known from the literature to be significantly associated with clear cell renal cell carcinoma. In addition, we found a set of five microRNAs that had not previously associated with clear cell renal cell carcinoma.

One microRNA has the potential to target whole viral mRNAs in a given human coronavirus.

MicroRNAs (miRNAs) can repress viral replication by targeting viral messenger RNA (mRNA), which makes them potential antiviral agents. The antiviral effects of miRNAs on infectious viruses have been explored extensively; however, recent studies mainly considered the action modes of miRNAs, neglecting another key factor, the molecular biology of viruses, which may be particularly important in the study of miRNA actions against a given virus. In this paper, the action modes of miRNAs and the molecular biology of viruses are jointly considered for the first time and based on the reported roles of miRNAs on viruses and human coronaviruses (HCoVs) molecular biology, the general and specific interaction modes of miRNAs-HCoVs are systematically reviewed. It was found that HCoVs transcriptome is a nested set of subgenomic mRNAs, sharing the same 5' leader, 3' untranslated region (UTR) and open reading frame (ORF). For a given HCoV, one certain miRNA with a target site in the 5' leader or 3' UTR has the potential to target all viral mRNAs, indicating tremendous antiviral effects against HCoVs. However, for the shared ORFs, some parts are untranslatable attributed to the translation pattern of HCoVs mRNA, and it is unknown whether the base pairing between the untranslated ORFs and miRNAs plays a regulatory effect on the local mRNAs where the untranslated ORFs are located; therefore, the regulatory effects of miRNAs with targets within the shared ORFs are complicated and need to be confirmed. Collectively, miRNAs may bepromising antiviral agents against HCoVs due to their intrinsically nested set of mRNAs, and some gaps are waiting to be filled. In this review, insight is provided into the exploration of miRNAs that can interrupt HCoVs infection.

MicroRNAs modulate neuroinflammation after intracerebral hemorrhage: Prospects for new therapy.

Intracerebral hemorrhage (ICH) is the most common subtype of hemorrhagic stroke. After ICH, blood components extravasate from vessels into the brain, activating immune cells and causing them to release a series of inflammatory mediators. Immune cells, together with inflammatory mediators, lead to neuroinflammation in the perihematomal region and the whole brain, and neuroinflammation is closely related to secondary brain injury as well as functional recovery of the brain. Despite recent progress in understanding the pathophysiology of ICH, there is still no effective treatment for this disease. MicroRNAs (miRNAs) are non-coding RNAs 17-25 nucleotides in length that are generated naturally in the human body. They bind complementarily to messenger RNAs and suppress translation, thus regulating gene expression at the post-transcriptional level. They have been found to regulate the pathophysiological process of ICH, particularly the neuroinflammatory cascade. Multiple preclinical studies have shown that manipulating the expression and activity of miRNAs can modulate immune cell activities, influence neuroinflammatory responses, and ultimately affect neurological functions after ICH. This implicates the potentially crucial roles of miRNAs in post-ICH neuroinflammation and indicates the possibility of applying miRNA-based therapeutics for this disease. Thus, this review aims to address the pathophysiological roles and molecular underpinnings of miRNAs in the regulation of neuroinflammation after ICH. With a more sophisticated understanding of ICH and miRNAs, it is possible to translate these findings into new pharmacological therapies for ICH.

An miRISC-initiated DNA nanomachine for monitoring MicroRNA activity in living cells

MicroRNAs (miRNAs) play an important role in post-transcriptional regulation of gene expression. However, methods to accurately detect miRNA activity in living cells are still limited. Here we developed a DNA nanomachine initiated by a miRNA-induced silencing complex (miRISC) for imaging miRNA activity in living cells. miRISC-mediated RNA cleavage reaction activated the DNA nanomachine by the specific cleavage of an RNA strand on the machine, resulting in autonomous movement of the walking leg around the AuNP surface with the release of a large number of fluorescently labeled DNA strands. The DNA nanomachine was successfully applied to detect miR-21 activity in three cell lines with different miR-21 expression profiles. We also demonstrated that terminal uridylyltransferase Tut4 knockdown by siRNA significantly increased the activity of let-7b miRNA, which further verifies the versatility of our DNA nanomachine. This new nanomachine has distinct advantages compared with reported methods for detecting miRNA activity, including simple operating procedures, short analysis time and sensitive signal output. Collectively, this work not only expands the application of the DNA nanomachine in the detection of miRNA activity, but also provides a promising tool for basic research in cell biology and development of clinical biomedicine.

Genetically Encoded Light-Up RNA Amplifier Dissecting MicroRNA Activity in Live Cells.

Live cell dissection of microRNA activities is crucial for basic and translational medicine, but current hybridization-based strategies may fail to dissect surrounding-dependent activities. Here, we develop a genetically encoded miRNA-induced light-up RNA amplifier (iLAMP) that enables fast-activated, signal-amplified, fluorogenic imaging of miRNA activities in live cells. iLAMP responds to miRNA targets in the mode of "activation upon cleavage", in which the light-up RNA aptamer restores its fluorescence rapidly upon cleavage by the RNA-induced silencing complex. We demonstrate that iLAMP affords substantial signal amplification of ∼100-fold and high specificity in single nucleotide discrimination because of the miRNA-mediated cyclic cleavage. Combined with a Mango RNA aptamer reference module and a pseudoknot terminal stabilizer, iLAMP is shown for quantitative ratiometric imaging and dynamic monitoring of miRNA activities under exogenous stimulations. iLAMP is featured by a modular "plug and play" design and can be readily adapted to the detection of other miRNAs, highlighting its potential in tracking cell differentiation and screening miRNA therapeutics.

Mechanisms of action of cytoplasmic miRNAs. Part 4. Recruitment of the DCP1-DCP2 decapping complex. Mechanisms of final mRNA degradation

This scientific review deals with the mechanisms of action of cytoplasmic microRNAs, namely post-transcriptional silencing: recruitment of the DCP1-DCP2 decapping complex and disruption of the interaction of mRNA with ribosomes. To write the article, information was searched using Scopus, Web of Science, MedLine, PubMed, Google Scholar, EMBASE, Global Health, The Cochrane Library, CyberLeninka databases. The authors indicate that the key process that determines both mRNA stability and expression efficiency is the removal of the 5’-terminal cap. Decapping of mRNA is controlled by several direct and indirect regulators. The DCP1-DCP2 complex can be recruited directly to mRNA and indirectly with the help of several decapping enhancers: PAT1 directly interacts with DCP1 and the decapping stimulator; EDC, DDX6. It is known that the protein DCP2 (Nudt20) is a representative of the conserved subfamily of Nudix hydrolases, which catalyze the hydrolysis of small nucleotide substrates. It is presented that the DCP1 protein is a small molecule that contains the EVH1 (enabled/vasodilator-stimulated phosphoprotein homology 1) domain, which usually acts as a protein-protein interaction module, and a C-terminal trimerization domain. It is known that the DCP1-DCP2 complex exists in an open and closed conformation, with the closed conformation having catalytic activity. DCP2 protein and its enhancer and cofactor partners accumulate in P-bodies. The authors indicate that in P-bodies, 5’-monophosphorylated mRNA is finally cleaved under the action of 5’-3’-exoribonuclease XRN1. XRN exoribonucleases are vital enzymes whose gene deletion is accompanied by intraembryonic lethality against the background of various abnormalities in the development of organs and systems. Thus, recruitment of the DCP1-DCP2 decapping complex and disruption of the interaction of mRNA with ribosomes in the cytoplasm of the cell are mechanisms of post-transcriptional silencing. The stability of the mRNA and the efficiency of expression determines the removal of the 5’ end cap. Termination of translation is caused by mRNA. MicroRNA-mediated degradation of this mRNA can be carried out both in the 3’-5’ and 5’-3’ directions of the molecule.

Cardiovascular Diseases and their Novel Therapeutic Interventions: A Literature Review

Introduction: Cardiovascular diseases (CVD) are responsible for millions of deaths worldwide every year and remain one of the main causes of death in low- middle-income countries. Current methods of treating CVD involve the use of lipid- lowering drugs although these patients continue to suffer from atherosclerotic disease risk. Novel RNA therapeutic strategies are being brought to light with the advancement in our understanding of cellular mechanisms and communication, however, these need to be evaluated critically before their clinical use. Methods: Electronic literature databases such as PubMed and Google Scholar were used to access review papers and research studies done in the past 25 years. Studies most relevant to RNA cardiovascular therapeutics were used to study therapeutic interventions and their limitations. Results: MicroRNAs (miRNAs), a subset of non-coding RNAs play an important function in cell-cell communication and microenvironment remodeling due to their role in cellular processes such as differentiation, proliferation, and apoptosis. Dysregulation of miRNA synthesis has been shown to drive disease pathology. Administration of the miRNAs downregulated during disease or silencing the activity of pathogenic miRNA can be used to establish the genetic composition of a healthy individual. Exosomes are cell-derived bilipid layer extracellular vesicles, 40-150 nm in size, which conduct paracrine signaling by carrying a cargo of mRNAs, non-coding RNAs, and proteins. They could be used as an efficient delivery method for miRNAs. Gene silencing therapies targeting the ApoCIII gene have emerged as novel therapeutic interventions to treating CVD with genome-wide association studies demonstrating enhanced cardioprotective function with ApoCIII deficiency. Gene silencing through miRNA delivery and antisense oligonucleotides reveals new avenues of CVD treatment. Discussion: Novel therapeutics addressing miRNA dysregulation and gene expression regulation come with caveats that need to be addressed before they are prescribed. This review describes the role of the gene silencing interventions and the implementation barriers that delay their approval for use in treating heart disease. Conclusion: The treatments and limitations addressed in this review suggest more studies are needed to determine the pharmacokinetic aspects of RNA drugs prior to establishing the use of RNA therapeutics along with conventional cholesterol-lowering drugs to ameliorate CVD risk.

C-Jun-mediated miR-19b expression induces endothelial barrier dysfunction in an in vitro model of hemorrhagic shock

BackgroundOur previous data demonstrated that miR-19b expression was increased in human lung microvascular endothelial cells in-vitro-, in-vivo and in patients with hemorrhagic shock, leading to a decrease in syndecan-1 mRNA and protein and resulting in loss of endothelial barrier function. However, the mechanism underlying increased miR-19b expression remains unclear. The objective of the current study was to determine if c-Jun mediates the early responsive microRNA, miR-19b, to cause endothelial barrier dysfunction.MethodHuman lung microvascular endothelial cells (HLMEC) or HEK293T cells were transfected with c-Jun overexpressing vector, c-Jun siRNA, miR-19b promoter vector, miR-19b mutated promoter vector, miR-19b oligo inhibitor, then subjected to hypoxia/reoxygenation as in-vitro model of hemorrhagic shock. Levels of protein, miRNA, and luciferase activity were measured. Transwell permeability of endothelial monolayers were also determined. Plasma levels of c-Jun were measured in injured patients with hemorrhagic shock.ResultHypoxia/reoxygenation induced primary (pri-)miR-19b, mature miR-19b, and c-Jun expression over time in a comparable timeframe. c-Jun silencing by transfection with its specific siRNA reduced both pri-miR-19b and mature miR-19b levels. Conversely, c-Jun overexpression enhanced H/R-induced pri-miR-19b. Studies using a luciferase reporter assay revealed that in cells transfected with vectors containing the wild-type miR-19b promoter and luciferase reporter, c-Jun overexpression or hypoxia/ reoxygenation significantly increased luciferase activity. c-Jun knockdown reduced the luciferase activity in these cells, suggesting that the miR-19b promoter is directly activated by c-Jun. Further, chromatin immunoprecipitation assay confirmed that c-Jun directly bound to the promoter DNA of miR-19b and hypoxia/reoxygenation significantly increased this interaction. Additionally, c-Jun silencing prevented cell surface syndecan-1 loss and endothelial barrier dysfunction in HLMECs after hypoxia/reoxygenation. Lastly, c-Jun was significantly elevated in patients with hemorrhagic shock compared to healthy controls.ConclusionTranscription factor c-Jun is inducible by hypoxia/reoxygenation, binds to and activates the miR-19b promoter. Using an in-vitro model of hemorrhagic shock, our findings identified a novel cellular mechanism whereby hypoxia/ reoxygenation increases miR-19b transcription by inducing c-Jun and leads to syndecan-1 decrease and endothelial cell barrier dysfunction. This finding supports that miR-19b could be a potential therapeutic target for hemorrhage shock.

Efficacy of green tea extract on PC3 prostate cancer cells through upregulation of miR-195 expression and suppression of epithelial to mesenchymal transition.

To evaluate anticancer efficacy of green tea extract (GTE) on PC3 prostate cancer cells. By using quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot methods, the expression of miR-195 and the epithelial to mesenchymal transition (EMT) markers such as E-cadherin and vimentin was analyzed. Based on the results of 2D and 3D cell culture models, the inhibition of EMT and up regulation of miR-195 expression were detected. Our findings will be helpful to design anti-tumor regimens with natural product original, and more studies will be required to identify the related mechanisms involving anticancer activities of green tea miRNAs.

Whole blood microRNAs capture systemic reprogramming and have diagnostic potential in patients with biliary tract cancer.

Late diagnosis is a critical factor undermining clinical management of patients with biliary tract cancer (BTC). While biliary tumours display extensive inter-patient heterogeneity, the host immune response may be comparatively homogenous, providing diagnostic opportunities. Herein, we investigated whether cancer-associated systemic reprogramming could be detected non-invasively to improve diagnosis of BTC. In this prospective Danish study, whole blood (WB) microRNA (miRNA) profiling was performed in samples from 218 patients with BTC, 99 healthy participants, and 69 patients with differential diagnoses split into discovery (small RNA-sequencing) and validation (RT-qPCR) cohorts. miRNA expression and activity were further investigated in 119 and 660 BTC tissues, respectively. Four WB miRNAs (let-7a-3p, miR-92b-5p, miR-145-3p, miR-582-3p) were identified and validated as diagnostic of BTC on univariable analysis. Two diagnostic miRNA indexes were subsequently identified that were elevated in patients with BTC and in patients with differential diagnoses, compared to healthy participants. The combination of these miRNA indexes with serum CA 19-9 significantly improved the diagnostic performance of CA 19-9 alone, consistently achieving superior AUC values irrespective of clinical setting (minimum AUC >0.84) or tumour location (minimum AUC >0.87). The diagnostic information captured by miRNA indexes was not recapitulated by routine clinical measurements. Index miRNA expression in BTC tissues was associated with distinct pathobiological and immune features. WB miRNA profiles are altered in patients with BTC. Quantification of miRNA indexes in combination with serum CA 19-9 has the potential to improve early diagnosis of BTC, pending further validation. Surgery is currently the only curative intervention for patients with biliary tract cancer (BTC). However, resection is not possible for most patients who are diagnosed with late-stage disease. With the aim of identifying new early diagnostic opportunities, we analysed circulating microRNAs (small non-coding RNAs whose role in cancer is being increasingly recognised) in whole blood samples. We identified a microRNA signature that could distinguish patients with BTC from healthy participants. These miRNAs significantly improved the diagnostic potential of the routinely measured biomarker, CA 19-9, and were implicated in distinct immune processes in tumour tissues.

Mechanisms of action of cytoplasmic microRNAs. Part 3. TNRC6-associated mechanism of miRNA-mediated mRNA degradation

The scientific review presents the mechanisms of action of cytoplasmic miRNAs, namely posttranscriptional silencing: the TNRC6-associated mechanism of miRNA-mediated mRNA degradation. To write the article, information was searched using databases Scopus, Web of Science, MedLine, PubMed, Google Scholar, EMBASE, Global Health, The Cochrane Library, CyberLeninka. It is known that in the cytoplasm of cells in cases of short region, miRNA complementarities cause posttranscriptional silencing, using the first of the main molecular mechanisms: the TNRC6-associated mechanism of miRNA-mediated mRNA degradation. Mammalian AGO proteins have been shown to contain the conserved m7G-cap-binding protein motif (known as the MID domain), which is required to induce microRNA-mediated translation repression. After binding of this AGO motif to microRNAs, TNRC6 proteins (GW182) are recruited that, in turn, recruits various proteins (PABPC1, PAN3 and NOT1) involved in the induction of the target gene silencing. The authors state that tryptophan residues, which are placed in the hydrophobic pockets of TNRC6 protein partners, cause a high degree of affinity and specificity of interactions. Scientists believe that the TNRC6 protein when interacting with AGO proteins can simultaneously use three GW/WG repeats (motif 1, motif 2 and hook motif), which are located in the Argonaute-binding domain. Therefore, the TNRC6 protein can bind to three AGO molecules simultaneously. TNRC6 proteins are known to be PABP-interacting proteins whose interaction with PABP is mediated by conservative PABP-binding motif 2. TNRC6 proteins have been shown to interact with the cytoplasmic PABPC1 protein during mRNA translation and stabilization. It is shown that the CCR4-NOT protein complex is a highly conserved multifunctional multiprotein formation having 3’-5’-exoribonuclease activity, due to which it controls mRNA metabolism. Thus, the TNRC6-associated mechanism of miRNA-mediated mRNA degradation in the cytoplasm of the cell causes posttranscriptional silencing. In this mechanism, there is an interaction of TNRC6 with PABPC1 protein, recruitment of deadenylating complexes PAN2-PAN3 and CCR4-NOT by the TNRC6 proteins.

Mechanisms of action of cytoplasmic microRNAs. Part 2. MicroRNA-mediated post-translational silencing

The scientific review presents the mechanisms of action of cytoplasmic miRNAs, namely miRNA-mediated posttranslational silencing. To write the article, information was searched using Scopus, Web of Science, MedLine, PubMed, Google Scholar, EMBASE, Global Health, The Cochrane Library, CyberLeninka databases. It is stated that protein synthesis is a complex process which involved many regulators. It is known that the translation process consists of three main stages: initiation, elongation of the polypeptide chain and termination. It is presented that dozens of “basic” factors and numerous accessory proteins, both regulators and repressors of the process, take part in the translation initiation. The authors provide a kinetic model proposed by Christopher S. Fraser. According to this model, translation initiation is a ranked process. It is emphasized that subsequently the ribosome interacts with the beginning of the coding nucleotide sequence of mRNA. Modifications of nucleotides by elongation factors in the anticodon of tRNA regulate the dynamics of ribosome function and, thus, fine-tune the rate of protein synthesis. The authors state that translation termination is induced by the interaction of the decoding A-region of the ribosome with one of the three stop codons (UAA, UAG or UGA) of mRNA. “Termination factors” are also involved in the termination of translation. Scientists say that the main factors that regulate the functional activity of mRNA act on the cap and poly(A)tail, which protects mRNA from exonuclease action. Thus, various proteins surround mRNA molecule in the cell and support the existence and functional activity of mRNA. Each mRNA region interacts with a specific spectrum of RNA-binding proteins. The initiation of translation is a ranked process and is inextricably linked with mRNA degradation. It is widely believed that translation is largely controlled during the initiation period. The mechanism of silencing caused by mRNA degradation depends on the size of the complementary region.

ASCL1 regulates super-enhancer-associated miRNAs to define molecular subtypes of small cell lung cancer.

Small cell lung cancer (SCLC) is a highly aggressive neuroendocrine tumor with dismal prognosis. Recently, molecular subtypes of SCLC have been defined by the expression status of ASCL1, NEUROD1, YAP1, and POU2F3 transcription regulators. ASCL1 is essential for neuroendocrine differentiation and is expressed in the majority of SCLC. Although previous studies investigated ASCL1 target genes in SCLC cells, ASCL1-mediated regulation of miRNAs and its relationship to molecular subtypes remain poorly explored. Here, we performed genome-wide profiling of chromatin modifications (H3K27me3, H3K4me3, and H3K27ac) by CUT&Tag assay and ASCL1 knockdown followed by RNA sequencing and miRNA array analyses in SCLC cells. ASCL1 could preferentially regulate genes associated with super-enhancers (SEs) defined by enrichment of H3K27ac marking. Moreover, ASCL1 positively regulated several SE-associated miRNAs, such as miR-7, miR-375, miR-200b-3p, and miR-429, leading to repression of their targets, whereas ASCL1 suppressed miR-455-3p, an abundant miRNA in other molecular subtypes. We further elucidated unique patterns of SE-associated miRNAs in different SCLC molecular subtypes, highlighting subtype-specific miRNA networks with functional relevance. Notably, we found apparent de-repression of common target genes of different miRNAs following ASCL1 knockdown, suggesting combinatorial action of multiple miRNAs underlying molecular heterogeneity of SCLC (e.g., co-targeting of YAP1 by miR-9 and miR-375). Our comprehensive analyses provide novel insights into SCLC pathogenesis and a clue to understanding subtype-dependent phenotypic differences.

Functional high-throughput screen identifies microRNAs that promote butyrate-induced death in colorectal cancer cells

The gut fermentation product butyrate displays anti-cancer properties in the human proximal colon, including the ability to inhibit proliferation and induce apoptosis in colorectal cancer (CRC) cells. A natural histone deacetylase inhibitor (HDACi), butyrate can alter histone acetylation patterns in CRC cells, and thereby regulate global gene expression, including the non-coding transcriptome and microRNAs (miRNAs). Dysregulated miRNA expression affects CRC development and progression; however, the interplay between miRNA activity and butyrate response remains to be elucidated. A high-throughput functional screen was employed to identify miRNAs that can act as enhancers of the anti-cancer properties of butyrate. Validation studies confirmed that several miRNAs, including miR-125b, miR-181a, miR-593, and miR-1227, enhanced apoptosis, decreased proliferation, and promoted cell-cycle arrest in the presence of butyrate. Pathway analyses of predicted miRNA target genes highlighted their likely involvement in critical cancer-related growth pathways, including WNT and PI3K signaling. Several cancer-associated miRNA targets, including TRIM29, COX2, PIK3R3, CCND1, MET, EEF2K, DVL3, and NUP62 were synergistically regulated by the combination of cognate miRNAs and butyrate. Overall, this study has exposed the potential of miRNAs to act as enhancers of the anti-cancer effects of HDAC inhibition and identifies specific miRNAs that might be exploited for therapeutic benefit.

Influence of phytochromes on microRNA expression, phenotype, and photosynthetic activity in A. thaliana phy mutants under light with different spectral composition

Light-induced changes in miRNAs, morphogenesis, and photosynthetic processes in phytochrome-deficient mutant plants grown under different light qualities were studied. miRNA activity in many processes is regulated by phytochromes and phytochrome-interacting factors (PIFs). The reduced content of photoreceptors in phytochrome mutants affects the PIF-microRNA interaction. In plants grown under red light (RL) and white light (WL), the phenotype of phyb mutant was distorted; however, under blue light (BL) conditions, the phyb phenotype was normalized. The photosynthetic rates of both the mutants and wild type were higher under BL than under RL and WL. The expression of most studied miRNAs increased in phyaphyb mutants under BL conditions, which is probably one of the reasons for the normalization of the phenotype, the increase in PSII activity, and the photosynthetic rate. MicroRNAs under BL can partially improve photosynthesis and phenotype of the mutants, which indicates the conjugation of the functioning of phytochromes in miRNA formation.

The role of the circular RNAs in multiple sclerosis and other neuroimmune disorders

In recent years non-coding RNAs have received increasing attention as an important epigenetic mechanism, with particular role of micro RNAs. As the regulation of miRNA expression is highly dynamic and complex, growing evidence suggests the existence of another higher level of regulatory mechanism involved in miRNA activity – circular RNAs (circRNAs). circRNAs represent novel, unique class of endogenous ncRNAs controlling the expression and function of miRNA. They are called natural miRNA “sponges”. Accumulating evidence reveals circRNAs role in physiological and pathological processes including CNS and immune regulation. Previous studies implicated miRNAs in regulation of autoimmune demyelination in MS. Multiple sclerosis is a chronic neurological inflammatory demyelinating disorder of the central nervous system. While the etiology of MS is still not fully understood, accumulating evidence suggests that it is a multifactorial entity with significant involvement of autoimmune processes.

Mutational signatures representative transcriptomic perturbations in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is a primary malignancy with increasing incidence and poor prognosis. Heterogeneity originating from genomic instability is one of the critical reasons of poor outcomes. However, the studies of underlying mechanisms and pathways affected by mutations are still not intelligible. Currently, integrative molecular-level studies using multiomics approaches enable comprehensive analysis for cancers, which is pivotal for personalized therapy and mortality reduction. In this study, genomic and transcriptomic data of HCC are obtained from The Cancer Genome Atlas (TCGA) to investigate the affected coding and non-coding RNAs, as well as their regulatory network due to certain mutational signatures of HCC. Different types of RNAs have their specific enriched biological functions in mutational signature-specific HCCs, upregulated coding RNAs are predominantly associated with lipid metabolism-related pathways, and downregulated coding RNAs are enriched in axonogenesis for tumor microenvironment generation. Additionally, differentially expressed miRNAs are inclined to concentrate in cancer-related signaling pathways. Some of these RNAs also serve as prognostic factors that help predict the survival outcome of HCCs with certain mutational signatures. Furthermore, deregulation of competing endogenous RNA (ceRNA) regulatory network is identified, which suggests a potential therapy via interference of miRNA activity for mutational signature-specific HCC. This study proposes a projection approach to reduce therapeutic complexity from genomic mutations to transcriptomic alterations. Through this method, we identify genes and pathways critical for mutational signature-specific HCC and further discover a series of prognostic markers indicating patient survival outcome.