An estimate of the total number of true human miRNAs

Micro-RNAs targeting the estrogen receptor alpha involved in endocrine therapy resistance in breast cancer

Endocrine therapy resistance (ETR) in breast cancer (BC) is a multicausal phenomenon with diverse alterations in the tumor cell interactome. Within these alterations, non-coding RNAs (ncRNAs) such as micro-RNAs (miRNAs) modulate the expression of tumor suppressor genes and proto-oncogenes, such as the ESR1 gene encoding estrogen receptor alpha (ERα). This work aims to review the effects of miRNAs targeting ERα mRNA and their mechanisms related to ETR in BC. A thorough review of the literature and an in silico study were carried out to elucidate the involvement of each miRNA, thus contributing to the understanding of ETR in BC.

AhR Activation at the Air-Blood Barrier Alters Systemic microRNA Release After Inhalation of Particulate Matter Containing Environmentally Persistent Free Radicals

Particulate matter containing environmentally persistent free radicals (EPFRs) is formed when organic pollutants are incompletely burned and adsorb to the surface of particles containing redox-active metals. Our prior studies showed that in mice, EPFR inhalation impaired vascular relaxation in a dose- and endothelium-dependent manner. We also observed that activation of the aryl hydrocarbon receptor (AhR) in the alveolar type-II (AT-II) cells that form the air-blood interface stimulates the release of systemic factors that promote endothelial dysfunction in vessels peripheral to the lung. AhR is a recognized regulator of microRNA (miRNA) biogenesis, and miRNA control diverse signaling pathways. We thus hypothesized that systemic EPFR-induced vascular endothelial dysfunction is initiated via AhR activation in AT-II cells, resulting in a systemic release of miRNA. Using a combustion reactor, we generated EPFR of two free radical concentrations-EPFRlo (1016-17 radicals/g particles) and EPFR (1018-19 radicals/g)-and exposed mice by inhalation. EFPR inhalation resulted in changes in a distinct array of miRNA in the plasma, and these miRNAs are linked to multiple systemic effects, including cardiovascular diseases and dysregulation of cellular and molecular pathways associated with cardiovascular dysfunction. We identified 17 miRNA in plasma that were altered dependent upon both AhR activation in AT-II cells and ~ 280 ug/m3 EPFR exposure. Using Ingenuity Pathway Analysis, we found that 5 of these miRNAs have roles in modulating endothelin-1 and endothelial nitric oxide signaling, known regulators of endothelial function. Furthermore, EPFR exposure reduced the expression of lung adherens and gap junction proteins in control mice but not AT-II-AhR deficient mice, and reductions in barrier function may facilitate miRNA release from the lungs. In summary, our findings support that miRNA may be systemic mediators promoting endothelial dysfunction mediated via EPFR-induced AhR activation at the air-blood interface.

Chasing non-existent "microRNAs" in cancer

MicroRNAs (miRNAs) are important regulators of gene expression whose dysregulation is widely linked to tumourigenesis, tumour progression and Epithelial-Mesenchymal Transition (EMT), a developmental process that promotes metastasis when inappropriately activated. However, controversy has emerged regarding how many functional miRNAs are encoded in the genome, and to what extent non-regulatory products of RNA degradation have been mis-identified as miRNAs. Central to miRNA function is their capacity to associate with an Argonaute (AGO) protein and form an RNA-Induced Silencing Complex (RISC), which mediates target mRNA suppression. We report that numerous "miRNAs" previously reported in EMT and cancer contexts, are not incorporated into RISC and are not capable of endogenously silencing target genes, despite the fact that hundreds of publications in the cancer field describe their roles. Apparent function can be driven through the expression of artificial miRNA mimics which is not necessarily reflective of any endogenous gene regulatory function. We present biochemical and bioinformatic criteria that can be used to distinguish functional miRNAs from mistakenly annotated RNA fragments.

Exosomes and MicroRNAs: key modulators of macrophage polarization in sepsis pathophysiology

Sepsis is a highly dangerous and complex condition that can result in death. It is characterized by a strong reaction to an infection, causing dysfunction in multiple bodily systems and a high risk of mortality. The transformation of macrophages is a vital stage in the procedure as they possess the capability to interchange between two separate types: M1, which promotes inflammation, and M2, which inhibits inflammation. The choice greatly affects the immune response of the host. This analysis underscores the rapidly expanding roles of exosomes and microRNAs (miRNAs) in regulating the trajectory of macrophage polarization during episodes of sepsis. Exosomes, extremely small extracellular vesicles, facilitate cellular communication by transferring biologically active compounds, including miRNAs, proteins, and lipids. We investigate the impact of changes in exosome production and composition caused by sepsis on macrophage polarization and function. Unique microRNAs present in exosomes play a significant role in controlling crucial signaling pathways that govern the phenotype of macrophages. Through thorough examination of recent progress in this area, we clarify the ways in which miRNAs derived from exosomes can either aggravate or alleviate the inflammatory reactions that occur during sepsis. This revelation not only deepens our comprehension of the underlying mechanisms of sepsis, but it also reveals potential new biomarkers and targets for treatment. This assessment aims to amalgamate diverse research investigations and propose potential avenues for future investigations on the influence that exosomes and miRNAs have on macrophage polarization and the body's response to sepsis. These entities are essential for controlling the host's reaction to sepsis and hold important functions in this mechanism.

miR-126: a bridge between cancer and exercise

The microRNA miR-126 supports endothelial cells and blood vessel integrity. Recent research has shown that it also serves as a key link between exercise and cancer. This article delves into how exercise affects the expression of miR-126, impacting cardiovascular well-being and metabolic control. The article also examines the various contributions of miR-126 in cancer, acting as both a suppressor and an enhancer depending on the particular context. Regular aerobic exercises, including HIIT, consistently increase levels of miR-126, leading to enhanced angiogenesis, endothelial repair, and improved vascular function through mechanisms involving VEGF, HIF-1α, and EPC mobilization. Resistance training affects similar pathways, but does not cause a significant change in miR-126 levels.MiR-126 involves in cancer by suppressing tumor growth and controlling key pathways such as PI3K/Akt, ERK/MAPK, and EMT. Lower levels are associated with negative outcomes, later stages of the disease, and increased spread of different types of cancer like glioblastoma, CRC, ovarian, esophageal, gastric, and prostate cancer.The relationship between exercise and cancer suggests a possible therapeutic approach, where the regulation of miR-126 through exercise could help improve vascular function and slow tumor growth. Further studies should focus on understanding the specific molecular pathways through which miR-126 connects these areas, leading to potential interventions that utilize its regulatory network to promote cardiovascular well-being and enhance cancer treatment.

Critical analysis of descriptive microRNA data in the translational research on cardioprotection and cardiac repair: lost in the complexity of bioinformatics

The unsuccessful translation of cardiac regeneration and cardioprotection from animal experiments to clinical applications in humans has raised the question of whether microRNA bioinformatics can narrow the gap between animal and human research outputs. We reviewed the literature for the period between 2000 and 2024 and found 178 microRNAs involved in cardioprotection and cardiac regeneration. On analyzing the orthologs and annotations, as well as downstream regulation, we observed species-specific differences in the diverse regulation of the microRNAs and related genes and transcriptomes, the influence of the experimental setting on the microRNA-guided biological responses, and database-specific bioinformatics results. We concluded that, in addition to reducing the number of in vivo experiments, following the 3R animal experiment rules, the bioinformatics approach allows the prediction of several currently unknown interactions between pathways, coding and non-coding genes, proteins, and downstream regulatory elements. However, a comprehensive analysis of the miRNA-mRNA-protein networks needs a profound bioinformatics and mathematical education and training to appropriately design an experimental study, select the right bioinformatics tool with programming language skills and understand and display the bioinformatics output of the results to translate the research data into clinical practice. In addition, using in-silico approaches, a risk of deviating from the in vivo processes exists, with adverse consequences on the translational research.

MicroRNAs as Endocrine Modulators of Breast Cancer

Breast cancer is an aggressive disease of multiple subtypes with varying phenotypic, hormonal, and clinicopathological features, offering enhanced resistance to conventional therapeutic regimens. There is an unmet need for reliable molecular biomarkers capable of detecting the malignant transformation from the early stages of the disease to enhance diagnosis and treatment outcomes. A subset of small non-coding nucleic acid molecules, micro ribonucleic acids (microRNAs/miRNAs), have emerged as promising biomarkers due to their role in gene regulation and cancer pathogenesis. This review discusses, in detail, the different origins and hormone-like regulatory functionalities of miRNAs localized in tumor tissue and in the circulation, as well as their inherent stability and turnover that determines the utility of miRNAs as biomarkers for disease detection, monitoring, prognosis, and therapeutic targets.

Transcriptomic miRNA and mRNA signatures in primary prostate cancer that are associated with lymph-node invasion

BACKGROUND

Nomograms or comparable techniques can be used to determine which patients with prostate cancer (PCa) will benefit from extended pelvic lymph node dissection (ePLND). While nomograms help guide clinical decisions, ∼80% of the patients undergo unnecessary ePLND. This pilot study aims to identify both transcriptomic mRNA and microRNA (miR) signatures in primary PCa tumours that are associated with the presence of lymph node metastasis (LNM).

METHODS

Primary PCa tumours obtained from 88 patients (pathologically diagnosed as N0 [pN0, n = 44] or as N1 [pN1, n = 44]) were profiled using two different probe-based captured direct assays based on next-generation sequencing and targeting 19398 mRNA transcripts (human transcriptome panel [HTP] dataset) and 2083 miRs (miRs whole-transcriptome assay [WTA] dataset). The TCGA-PRAD (pN0 [n = 382] and pN1 [n = 70]) and GSE220095 (pN0 [n = 138] and pN1 [n = 17]) datasets were used for validation using bioinformatic analyses.

RESULTS

A four-mRNA signature (CHRNA2, NPR3, VGLL3 and PAH) was found in primary tumour tissue samples from pN1 PCa patients, and then it was validated using the TCGA-PRAD and GSE220095 datasets. Adding serum prostate-specific antigen (PSA) values to the four-gene signature increased the performance to identify pN1 (HTP [AUC = .8487, p = 2.18e-09], TCGA-PRAD [AUC = .7150, p = 8.66e-08] and GSE220095 datasets [AUC = .8772, p = 4.09e-07]). Paired miR analyses showed that eight miRs were significantly upregulated in primary PCa that were pN1 (p < .01). The eight-miR signature performance increased when adding PSA (WTA dataset [AUC = .8626, p = 4.66e-10]) or Grade group (WTA dataset [AUC = .8689, p = 2e-10]). When combining the miR/mRNA signatures (miR-663b, CHRNA2 and PAH) with PSA levels, it showed the best performance to distinguish pN1 from pN0 PCa patients.

CONCLUSION

This study found miR/mRNA signatures in primary PCa tumours that in combination with serum PSA levels may complement nomograms for better detection of PCa patients with LNM and triage patients into better surgical decision-making.

KEY POINTS

Primary prostate cancer (PCa) tumours from patients pathologically diagnosed as N0 (pN0) or N1 (pN1) were dually assessed for microRNA (miRs) and mRNA levels using an NGS-based assay. A four-mRNA and an eight-miRNA signature were found. The mRNA signatures were further validated using two datasets. The combination of serum prostate-specific antigen (PSA) levels or Grade Group with the miR/mRNA signatures separates pN1 from pN0 PCa patients.

Long Noncoding LINC00115 Facilitates Cell Growth and Inhibits Apoptosis by Regulating the miR-4701-5p/P4HB Axis in Bladder Cancer

Bladder cancer (BCa) is a prevalent urogenital malignancy, imposing a significant burden on health-care systems worldwide. Long noncoding RNAs (lncRNAs) are important regulators of carcinogenesis and affect BCa progression. In this study, the influence of lncRNA LINC00115 on malignant behavior of BCa cells were explored. Bioinformatics method was used for prediction of gene expression and downstream molecules of LIN00115. LINC00115 expression level in BCa cells was measured using RT-qPCR. After LINC00115 depletion, the proportion of viable, proliferative, and apoptotic BCa cells were calculated by methyl thiazolyl tetrazolium (MTT) assays, colony formation assays, and TUNEL staining, respectively. FISH was performed to verify the cellular distribution of LINC00115. The interaction between LINC00115 and miR-4701-5p and the binding between miR-4701-5p and P4HB were confirmed using RNA pulldown, RNA immunoprecipitation (RIP), and luciferase reporter assays. Experimental results showed that LINC00115 was highly expressed in BCa cells. The silencing of LINC00115 restrained BCa cell proliferation and stimulated apoptosis. LINC00115 could directly bind to miR-4701-5p and thus initiate P4HB upregulation in BCa cells. P4HB 3'untranslated region could be targeted by miR-4701-5p. Additionally, Amplification of P4HB expression offset the effects of LINC00115 knockdown on BCa cell proliferative and apoptotic behaviors. In conclusion, LINC00115 facilitates BCa cell growth and inhibits apoptosis via interaction with miR-4701-5p and upregulation of P4HB.

miR-6516-3p-mediated downregulation of the endogenous MMP-9 inhibitor RECK in mesangial cells might exacerbate lupus nephritis

BACKGROUND

MicroRNAs (miRNAs) regulate biological processes by inhibiting translation and causing mRNA degradation. In this study, we identified the miRNAs involved in the development and progression of lupus nephritis (LNs) and verified their roles.

METHODS

Total RNA, extracted from PBMCs collected from patients with LNs before and after treatment, was used for miRNA array analysis to identify miRNAs whose expression was significantly altered. The results of this analysis were confirmed using qRT-PCR. The identified miRNAs were transfected into normal human mesangial cells (NHMCs), human renal proximal tubule epithelial cells (RPTECs), human umbilical vein endothelial cells (HUVECs), and THP-1-derived macrophages (THP1-Mφ) to investigate their biological functions.

RESULTS

Three miRNAs were altered in PBMCs before and after treatment of LNs. Among these miRNAs, hsa-miR-6516-3p promoted TNF-α-induced expression of MMP-9 in NHMCs. Moreover, hsa-miR-6516-3p downregulated the expression of RECK, an endogenous inhibitor of MMP-9. However, in NHMCs, endogenous hsa-miR-6516-3p was not present in functional amounts under inflammatory environment; therefore, we performed analysis using an experimental system considering extracellular influences of mesangial cells under LNs. The expression of hsa-miR-6516-3p was increased in HUVECs under inflammatory conditions and in activated macrophages.

CONCLUSIONS

hsa-miR-6516-3p increases MMP9 expression by suppressing RECK, and might, thereby, exacerbate LNs.

Cellular Phenotypic Transformation During Atherosclerosis: The Potential Role of miRNAs as Biomarkers

Cellular phenotypic transformation is a key process that occurs during the development and progression of atherosclerosis. Within the arterial wall, endothelial cells, vascular smooth muscle cells, and macrophages undergo phenotypic changes that contribute to the pathogenesis of atherosclerosis. miRNAs have emerged as potential biomarkers for cellular phenotypic changes during atherosclerosis. Monitoring miR-155-5p, miR-210-3p, and miR-126-3p or 5p levels could provide valuable insights into disease progression, risk of complications, and response to therapeutic interventions. Moreover, miR-92a-3p's elevated levels in atherosclerotic plaques present opportunities for predicting disease progression and related complications. Baseline levels of miR-33a/b hold the potential for predicting responses to cholesterol-lowering therapies, such as statins, and the likelihood of dyslipidemia-related complications. Additionally, the assessment of miR-122-5p levels may offer insights into the efficacy of low-density-lipoprotein-lowering therapies. Understanding the specific miRNA-mediated regulatory mechanisms involved in cellular phenotypic transformations can provide valuable insights into the pathogenesis of atherosclerosis and potentially identify novel therapeutic targets.

Identifying Essential Hub Genes and circRNA-Regulated ceRNA Networks in Hepatocellular Carcinoma

Competitive endogenous RNAs (ceRNAs) absorb microRNAs and subsequently promote corresponding mRNA and long noncoding RNA (lncRNA) expression, which may alter cancer cell malignancy. Thus, dissecting ceRNA networks may reveal novel targets in cancer therapies. In this study, we analyzed differentially expressed genes (DEGs) of mRNAs and lncRNAs, and differentially expressed microRNAs (DE-miRNAs) and circular RNAs (DE-circRNAs) extracted from high-throughput sequencing datasets of hepatocellular carcinoma patients. Based on these data, we identified 26 gene modules using weighted gene co-expression network analysis (WGCNA), of which 5 were associated with tumor differentiation. In these modules, 269 genes were identified by GO and KEGG enrichment and patient's survival correlation analyses. Next, 40 DE-miRNAs, each of which potentially bound a pair of DE-circRNA and hub gene, were discovered. Together with 201 circRNAs and 24 hub genes potentially bound by these miRNAs, 1151 ceRNA networks were constructed. Among them, 75 ceRNA networks consisting of 24 circRNAs, 28 miRNAs and 17 hub genes showed a positive circRNA-hub gene correlation. For validation, we carried out experiments for 4 randomly selected circRNAs regulating 19 potential ceRNA networks and verified 5 of them. This study represents a powerful strategy to identify essential gene networks and provides insights into designing effective therapeutic strategies.

miRNA Library Preparation Optimisation for Low-Concentration and Low-Volume Paediatric Plasma Samples

Background: Analysing circulating miRNAs in paediatric plasma is challenging due to typically low sample volumes. The QIAseq miRNA UDI Library Kit (Qiagen, Hilden, Germany) was selected as it has a proven track record with a specific protocol for plasma and serum. The protocol, however, required optimisation for use with low-volume paediatric plasma samples before generating acceptable yields in our cohort. Methods: The miRNeasy Serum/Plasma kit (Qiagen) and the MagMAX miRVana Total Isolation kit (ThermoFisher Scientific, Waltham, MA, USA) were assessed following the manufacturer's instructions with 100 µL and 200 µL of paediatric plasma. Libraries were prepared using the QIAseq miRNA UDI Library Kit (Qiagen). Optimisations were made for the QIAseq miRNA UDI Library Kit (Qiagen) using total RNA extracted with the miRNeasy Serum/Plasma kit (Qiagen) from 100 µL of plasma. Results: Prior to optimisation, both RNA extraction kits underperformed with the QIAseq miRNA UDI Library kit, producing low miRNA library yields ranging between 0 and 1.42 ng/µL. Plasma input volumes of 100 µL and 200 µL demonstrated no significant differences. Adjusting the QIAseq protocol for low RNA concentrations improved miRNA library yields, an average of 5.6 ng/µL and a maximum of 24.3 ng/µL across 92 samples. The optimised protocol showed no age or gender biases with the QIAseq kit. Conclusions: Failure rates in miRNA library preparations are rarely reported, making it hard to gauge whether the 8.7% failure rate observed here is typical. However, given the challenges of using low-concentration, low-volume paediatric plasma, this represents a significant improvement over previous attempts, supporting further research in the field.

Chromato-kinetic fingerprinting enables multiomic digital counting of single disease biomarker molecules

Early and personalized intervention in complex diseases requires robust molecular diagnostics, yet the simultaneous detection of diverse biomarkers-microRNAs (miRNAs), mutant DNAs, and proteins-remains challenging due to low abundance and preprocessing incompatibilities. We present Biomarker Single-molecule Chromato-kinetic multi-Omics Profiling and Enumeration (Bio-SCOPE), a next-generation, triple-modality, multiplexed detection platform that integrates both chromatic and kinetic fingerprinting for molecular profiling through digital encoding. Bio-SCOPE achieves femtomolar sensitivity, single-base mismatch specificity, and minimal matrix interference, enabling precise, parallel quantification of up to six biomarkers in a single sample with single-molecule resolution. We demonstrate its versatility in accurately detecting low-abundance miRNA signatures from human tissues, identifying upregulated miRNAs in the plasma of prostate cancer patients, and measuring elevated interleukin-6 (IL-6) and hsa-miR-21 levels in cytokine release syndrome patients. By seamlessly integrating multiomic biomarker panels on a unified, high-precision platform, Bio-SCOPE provides a transformative tool for molecular diagnostics and precision medicine.

Stoichiometric constraints for detection of EV-borne biomarkers in blood

Stochiometric issues, encompassing both the quantity and heterogeneity of extracellular vesicles (EVs) derived from tumour or other tissues in blood, pose important challenges across various stages of biomarker discovery and detection, affecting the integrity of data, introducing losses and artifacts during blood processing, EV purification and analysis. These challenges shape the diagnostic utility of EVs especially within the framework of established and emerging methodologies. By addressing these challenges, we aim to delineate crucial parameters and requirements for tumour-specific EV detection, or more precisely, for tumour identification via EV based assays. Our endeavour involves a comprehensive examination of the layers that mask or confound the traceability of EV markers such as nucleic acids and proteins, and focus on 'low prevalence-low concentration' scenario. Finally, we evaluate the advantages versus limitations of single-particle analysers over more conventional bulk assays, suggesting that the combined use of both to capture and interpret the EV signals, in particular the EV surface displayed proteins, may ultimately provide quantitative information on their absolute abundance and distribution.

Altered expression of miRNA profile in peripheral blood mononuclear cells following the third dose of inactivated COVID-19 vaccine

COVID-19 vaccination is the most effective strategy for preventing severe disease and death. Inactivated vaccines are the most accessible type of COVID-19 vaccines in developing countries. Several studies, including work from our group, have demonstrated that the third dose (booster vaccination) of inactivated COVID-19 vaccine induces robust humoral and cellular immune responses. The present study aimed to examine miRNA expression profile in participants who received a homologous third dose of the CoronaVac vaccine. Samples of peripheral blood mononuclear cells (PBMCs) were collected from healthcare volunteers both before and 1-2 weeks after the booster dose. miRNA microarray analysis in a discovery cohort of six volunteers identified 67 miRNAs with differential expression. Subsequently, the expression of six miRNAs related to immune responses was examined in a validation cohort of 31 participants via qRT-PCR. Our results validated the differential expression of miR-25-5p, miR-34c-3p, and miR-206 post-booster, with a significant correlation to the receptor binding domain (RBD)-specific antibody. Bioinformatic analysis suggested that miR-25-5p, miR-34c-3p, and miR-206 may target multiple pathways involved in immune regulation and inflammation. Therefore, our study highlights miR-25-5p, miR-34c-3p, and miR-206 in PBMCs as promising biomarkers for assessing the immune response induced by the booster dose of the CoronaVac vaccine.

Dynamic Roles of RNA and RNA Epigenetics in HTLV-1 Biology

Since the discovery of RNA in the early 1900s, scientific understanding of RNA form and function has evolved beyond protein coding. Viruses, particularly retroviruses like human T-cell leukemia virus type 1 (HTLV-1), rely heavily on RNA and RNA post-transcriptional modifications to regulate the viral lifecycle, pathogenesis, and evasion of host immune responses. With the emergence of new sequencing technologies in the last decade, our ability to dissect the intricacies of RNA has flourished. The ability to study RNA epigenetic modifications and splice variants has become more feasible with the recent development of third-generation sequencing technologies, such as Oxford nanopore sequencing. This review will highlight the dynamic roles of known RNA and post-transcriptional RNA epigenetic modifications within HTLV-1 biology, including viral hbz, long noncoding RNAs, microRNAs (miRNAs), transfer RNAs (tRNAs), R-loops, N6-methyladenosine (m6A) modifications, and RNA-based therapeutics and vaccines.

MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models

We present a major update of MirGeneDB (3.0), the manually curated animal microRNA gene database. Beyond moving to a new server and the creation of a computational mirror, we have expanded the database with the addition of 33 invertebrate species, including representatives of 5 previously unsampled phyla, and 6 mammal species. MirGeneDB now contains entries for 21 822 microRNA genes (5160 of these from the new species) belonging to 1743 microRNA families. The inclusion of these new species allowed us to refine both the evolutionary node of appearance of a number of microRNA genes/families, as well as MirGeneDB's phylogenetically informed nomenclature system. Updated covariance models of all microRNA families, along with all smallRNA read data are now downloadable. These enhanced annotations will allow researchers to analyze microRNA properties such as secondary structure and features of their biogenesis within a robust phylogenetic context and without the database plagued with numerous false positives and false negatives. In light of these improvements, MirGeneDB 3.0 will assume the responsibility for naming conserved novel metazoan microRNAs. MirGeneDB is part of RNAcentral and Elixir Norway and is publicly and freely available at mirgenedb.org.

Harnessing DNA computing and nanopore decoding for practical applications: from informatics to microRNA-targeting diagnostics

DNA computing represents a subfield of molecular computing with the potential to become a significant area of next-generation computation due to the high programmability inherent in the sequence-dependent molecular behaviour of DNA. Recent studies in DNA computing have extended from mathematical informatics to biomedical applications, with a particular focus on diagnostics that exploit the biocompatibility of DNA molecules. The output of DNA computing devices is encoded in nucleic acid molecules, which must then be decoded into human-recognizable signals for practical applications. Nanopore technology, which utilizes an electrical and label-free decoding approach, provides a unique platform to bridge DNA and electronic computing for practical use. In this tutorial review, we summarise the fundamental knowledge, technologies, and methodologies of DNA computing (logic gates, circuits, neural networks, and non-DNA input circuity). We then focus on nanopore-based decoding, and highlight recent advances in medical diagnostics targeting microRNAs as biomarkers. Finally, we conclude with the potential and challenges for the practical implementation of these techniques. We hope that this tutorial will provide a comprehensive insight and enable the general reader to grasp the fundamental principles and diverse applications of DNA computing and nanopore decoding, and will inspire a wide range of scientists to explore and push the boundaries of these technologies.

Cancer Network Macromolecules

The members of the network (interactome) that controls cancer needs to be known. This network consists of proteins and non-coding, single-stranded RNAs, such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and transfer RNAs (tRNAs). miRNAs are 21-23 nucleotides-long, and degrade messenger RNAs (mRNAs) and lncRNAs. lncRNAs are longer than 200 nucleotides, and sponge (sequester) miRNAs.

Analysis of the Effects of Short-Term Pterostilbene Intake on Healthy Participants: A Pilot Study

Pterostilbene, a polyphenolic compound and an analog of resveratrol, exerts various biological activities and has higher bioavailability and metabolic stability than resveratrol. However, the effectiveness of pterostilbene intake in humans, particularly its effect on blood microRNA (miRNA) expression levels, has not been evaluated. Accordingly, this pilot study aimed to investigate the effects of pterostilbene on blood biochemistry and blood miRNA expression levels and the safety of continuous intake at doses of 10 or 100 mg/d over 12 wk. A double-blind, placebo-controlled parallel-arm comparison trial was conducted with 30 healthy men. In the analysis of blood miRNA expression levels, miR-34a and miR-193b showed very high increases at week 4 and after week 4 of intake, respectively, suggesting that the responders might be present among participants in the pterostilbene intake group. No adverse events were reported during the trial in any participant, and no abnormalities were observed upon examination by the responsible physician. Thus, pterostilbene intake would regulate blood miRNA expression levels, and the results can be utilized in human studies investigating miRNA expression levels with functional food ingredients.

Role of miRNAs in breast cancer development and progression: Current research

Breast cancer, a complex and heterogeneous ailment impacting numerous women worldwide, persists as a prominent cause of cancer-related fatalities. MicroRNAs (miRNAs), small non-coding RNAs, have garnered significant attention for their involvement in breast cancer's progression. These molecules post-transcriptionally regulate gene expression, influencing crucial cellular processes including proliferation, differentiation, and apoptosis. This review provides an overview of the current research on the role of miRNAs in breast cancer. It discusses the role of miRNAs in breast cancer, including the different subtypes of breast cancer, their molecular characteristics, and the mechanisms by which miRNAs regulate gene expression in breast cancer cells. Additionally, the review highlights recent studies identifying specific miRNAs that are dysregulated in breast cancer and their potential use as diagnostic and prognostic biomarkers. Furthermore, the review explores the therapeutic potential of miRNAs in breast cancer treatment. Preclinical studies have shown the effectiveness of miRNA-based therapies, such as antagomir and miRNA mimic therapies, in inhibiting tumor growth and metastasis. Emerging areas, including the application of artificial intelligence (AI) to advance miRNA research and the "One Health" approach that integrates human and animal cancer insights, are also discussed. However, challenges remain before these therapies can be fully translated into clinical practice. In conclusion, this review emphasizes the significance of miRNAs in breast cancer research and their potential as innovative diagnostic and therapeutic tools. A deeper understanding of miRNA dysregulation in breast cancer is essential for their successful application in clinical settings. With continued research, miRNA-based approaches hold promise for improving patient outcomes in this devastating disease.

The Role of Estrogen in Brain MicroRNAs Regulation

Purpose

This review aims to elucidate the role of estrogen-sensitive microRNAs (miRNAs) in modulating brain functions and disorders, highlighting the protective effects of estrogen on the central nervous system.

Methods

A comprehensive literature review was conducted, examining the relationship between estrogen, miRNAs, and cognitive health. The study focused on experimental data comparing cognitive impairments between genders and the mechanisms of estrogen's effects on brain function.

Results

Cognitive impairments are less prevalent in women of reproductive age compared to men, indicating estrogen's neuroprotective role. Estrogen modulates gene expression through specific receptors, while miRNAs regulate approximately 30% of protein-coding genes in mammals. These miRNAs play critical roles in synaptic plasticity and neuronal survival. The review identifies several estrogen-sensitive miRNAs and their potential involvement in brain disorders.

Conclusion

The interplay between estrogen and miRNAs offers valuable insights into the molecular mechanisms underlying cognitive health and disease. Understanding these relationships may lead to novel therapeutic strategies for addressing various brain disorders, particularly those associated with hormonal changes and aging.

Brain-Periphery Axes: The Potential Role of Extracellular Vesicles-Delivered miRNAs

Bidirectional communication between the central nervous system (CNS) and peripheral organs and tissue has been widely documented in physiological and pathological conditions. This communication relies on the bilateral transmission of signaling molecules and substances that circulate throughout the body and reach their target site(s) via the blood and other biological fluids (e.g., the cerebrospinal fluid, the lymph). One of the mechanisms by which these molecular messengers are exchanged is through the secretion of extracellular vesicles (EVs). EVs are known to mediate cell-to-cell communication by delivering biological molecules, including nucleic acids, proteins, lipids, and various other bioactive regulators. Moreover, EVs can cross the blood-brain barrier (BBB), enabling direct communication between the periphery and the brain. In particular, the delivery of microRNAs (miRNAs) can modulate the expression profiles of recipient cells, thereby influencing their functions. This review synthesizes current findings about the brain-periphery cross-talk mediated by EVs-delivered miRNAs. Although this mechanism has been definitively shown in a few cases, much evidence indirectly indicates that it could mediate brain-peripherical organs/tissue communication, especially in pathological conditions. Therefore, understanding this process could provide valuable insights for the treatment and management of neurological and systemic diseases.

Circulating microRNAs as Diagnostic Biomarkers to Detect Specific Stages of Ovarian Cancer: A Comprehensive Meta-Analysis

Ovarian cancer (OC) is one of the most common gynecological cancers [...].

Increased Levels of hsa-miR-199a-3p and hsa-miR-382-5p in Maternal and Neonatal Blood Plasma in the Case of Placenta Accreta Spectrum

Despite the increasing number of placenta accreta spectrum (PAS) cases in recent years, its impact on neonatal outcomes and respiratory morbidity, as well as the underlying pathogenetic mechanism, has not yet been extensively studied. Moreover, no study has yet demonstrated the effectiveness of antenatal corticosteroid therapy (CT) for the prevention of respiratory distress syndrome (RDS) in newborns of mothers with PAS at the molecular level. In this regard, microRNA (miRNA) profiling by small RNA deep sequencing and quantitative real-time PCR was performed on 160 blood plasma samples from preterm infants (gestational age: 33-36 weeks) and their mothers who had been diagnosed with or without PAS depending on the timing of the antenatal RDS prophylaxis. A significant increase in hsa-miR-199a-3p and hsa-miR-382-5p levels was observed in the blood plasma of the newborns from mothers with PAS compared to the control group. A clear trend toward the normalization of hsa-miR-199a-3p and hsa-miR-382-5p levels in the neonatal blood plasma of the PAS groups was observed when CT was administered within 14 days before delivery, but not beyond 14 days. Direct correlations were found among the hsa-miR-382-5p level in neonatal blood plasma and the hsa-miR-199a-3p level in the same sample (r = 0.49; p < 0.001), the oxygen requirements in the NICU (r = 0.41; p = 0.001), the duration of the NICU stay (r = 0.31; p = 0.019), and the severity of the newborn's condition based on the NEOMOD scale (r = 0.36; p = 0.005). Logistic regression models based on the maternal plasma levels of hsa-miR-199a-3p and hsa-miR-382-5p predicted the need for cardiotonic therapy, invasive mechanical ventilation, or high-frequency oscillatory ventilation in newborns during the early neonatal period, with a sensitivity of 95-100%. According to the literary data, these miRNAs regulate fetal organogenesis via IGF-1, the formation of proper lung tissue architecture, surfactant synthesis in alveolar cells, and vascular tone.

Protein Glycosylation Patterns Shaped By the IRE1-XBP1s Arm of the Unfolded Protein Response

The unfolded protein response (UPR) is a sensing and signaling pathway that surveys the endoplasmic reticulum (ER) for protein folding challenges and responds whenever issues are detected. UPR activation leads to upregulation of secretory pathway chaperones and quality control factors, as well as reduces the nascent protein load on the ER, thereby restoring and maintaining proteostasis. This paradigm-defining view of the role of the UPR is accurate, but it elides additional key functions of the UPR in cell biology. In particular, recent work has revealed that the UPR can shape the structure and function of N- and O-glycans installed on ER client proteins. This crosstalk between the UPR's response to protein misfolding and the regulation of glycosylation remains insufficiently understood. Still, emerging evidence makes it clear that the UPR, and particularly the IRE1-XBP1s arm of the UPR, may be a central regulator of protein glycosylation with important biological consequences. In this review, we discuss the crosstalk between proteostasis, the UPR, and glycosylation, present progress towards understanding biological functions of this crosstalk, and examine potential roles in diseases such as cancer.

miRNAs in ovarian disorders: Small but strong cast

PURPOSE

This research aimed to analyze alterations in microRNA expression in the diseases POF (Premature Ovarian Failure), PCOS (Polycystic Ovarian Syndrome), and ovarian cancer in order to understand the molecular changes associated with these conditions. The findings could potentially be utilized for diagnostic, therapeutic, predictive, and preventive purposes. Furthermore, the impact and role of microRNAs in each ailment, along with their functional pathways, were elucidated and examined.

METHODS

In this study, the genes involved in the disease were studied, and then the miRNAs that targeted these genes were evaluated, and finally the signaling and functional pathways of each of the miRNAs were assessed. In this process, genetic databases and previous studies were carefully assessed.

RESULTS

miRNAs are short nucleotide sequences that belong to the category of non-coding RNAs. They play a crucial role in various physiological activities, including cell division, growth, differentiation, and cell death (necrosis and apoptosis), miRNAs are involved in various physiological processes Such alterations are common in various diseases, including cancer. miRNAs are involved in various physiological processes, such as folliculogenesis and steroidogenesis, as well as in pathological conditions such as POF, PCOS, and ovarian cancer. They have powerful regulatory effects and controlling the most activities of normal and pathological cells. While microRNAs (miRNAs) play a significant role in normal ovarian functions, there are reports of their expression changes in PCOS, ovarian cancer, and POF.

CONCLUSIONS

miRNAs have been found to exert significant influence on both physiological and pathological cellular processes. Understanding the dynamic patterns of miRNA alterations can provide valuable insights for researchers and therapists, enabling them to utilize these biomarkers effectively in diagnostic, therapeutic, and preventive applications.

PRIMITI: A computational approach for accurate prediction of miRNA-target mRNA interaction

Current medical research has been demonstrating the roles of miRNAs in a variety of cellular mechanisms, lending credence to the association between miRNA dysregulation and multiple diseases. Understanding the mechanisms of miRNA is critical for developing effective diagnostic and therapeutic strategies. miRNA-mRNA interactions emerge as the most important mechanism to be understood despite their experimental validation constraints. Accordingly, several computational models have been developed to predict miRNA-mRNA interactions, albeit presenting limited predictive capabilities, poor characterisation of miRNA-mRNA interactions, and low usability. To address these drawbacks, we developed PRIMITI, a PRedictive model for the Identification of novel miRNA-Target mRNA Interactions. PRIMITI is a novel machine learning model that utilises CLIP-seq and expression data to characterise functional target sites in 3'-untranslated regions (3'-UTRs) and predict miRNA-target mRNA repression activity. The model was trained using a reliable negative sample selection approach and the robust extreme gradient boosting (XGBoost) model, which was coupled with newly introduced features, including sequence and genetic variation information. PRIMITI achieved an area under the receiver operating characteristic (ROC) curve (AUC) up to 0.96 for a prediction of functional miRNA-target site binding and 0.96 for a prediction of miRNA-target mRNA repression activity on cross-validation and an independent blind test. Additionally, the model outperformed state-of-the-art methods in recovering miRNA-target repressions in an unseen microarray dataset and in a collection of validated miRNA-mRNA interactions, highlighting its utility for preliminary screening. PRIMITI is available on a reliable, scalable, and user-friendly web server at https://biosig.lab.uq.edu.au/primiti.

microRNAs: critical targets for treating rheumatoid arthritis angiogenesis

Vascular neogenesis, an early event in the development of rheumatoid arthritis (RA) inflammation, is critical for the formation of synovial vascular networks and plays a key role in the progression and persistence of chronic RA inflammation. microRNAs (miRNAs), a class of single-stranded, non-coding RNAs with approximately 21-23 nucleotides in length, regulate gene expression by binding to the 3' untranslated region (3'-UTR) of specific mRNAs. Increasing evidence suggests that miRNAs are differently expressed in diseases associated with vascular neogenesis and play a crucial role in disease-related vascular neogenesis. However, current studies are not sufficient and further experimental studies are needed to validate and establish the relationship between miRNAs and diseases associated with vascular neogenesis, and to determine the specific role of miRNAs in vascular development pathways. To better treat vascular neogenesis in diseases such as RA, we need additional studies on the role of miRNAs and their target genes in vascular development, and to provide more strategic references. In addition, future studies can use modern biotechnological methods such as proteomics and transcriptomics to investigate the expression and regulatory mechanisms of miRNAs, providing a more comprehensive and in-depth research basis for the treatment of related diseases such as RA.

STK33 as the functional substrate of miR-454-3p for suppression and apoptosis in neuroblastoma

miR-454-3p has been reported to be a tumor-suppressive microRNA (miRNA) in multiple cancer types. We identified the kinase STK33 mRNA, which is a high-risk factor for survival in neuroblastoma (NB) patients, as being a substrate of miR-454-3p in NB. Even though STK33 is an attractive target for several cancers, the development of inhibitors of STK33 has been challenging. For the various cell lines tested, we demonstrated reduced growth and viability with the miR-454-3p mimic. From among the candidate NB-associated miRNAs, miR-454-3p mimic and its antagonist had the most profound effect on STK33 mRNA and protein-level changes. Under various conditions of growth and external stress for the cells, the RNA levels for miR-454-3p and STK33 also negatively correlated. Luciferase reporter assays demonstrated STK33 as a substrate for miR-454-3p, and recombinant versions of STK33 resistant to miR-454-3p significantly blunted the suppressive effect of the miR-454-3p and established STK33 as the major functional substrate of miR-454-3p. Overexpression of miR-454-3p or knockdown of STK33 mRNA promoted autophagy and at the same time, increased the apoptotic markers in the tested NB cells, indicating a mechanism for the suppressive effect of the agents. Given the difficult-to-drug targets such as STK33 and the recent successes in RNA delivery methods for cancer treatment, it is thought that targeting cancer cells with a suppressive miRNA such as miR-454-3p for STK33-dependent cancer types may be an alternative means of NB therapy.

miRNAs in HCC, pathogenesis, and targets

Liver cancer is the third leading cause of cancer-related mortality worldwide. HCC, the most common type of primary liver cancer, is driven by complex genetic, epigenetic, and environmental factors. MicroRNAs, a class of naturally occurring small noncoding RNAs, play crucial roles in HCC by simultaneously modulating the expression of multiple genes in a fine-tuning manner. Significant progress has been made in understanding how miRNAs influence key oncogenic pathways, including cell proliferation, apoptosis, angiogenesis, and epithelial-mesenchymal transition (EMT), as well as their role in modulating the immune microenvironment in HCC. Due to the unexpected stability of miRNAs in the blood and fixed HCC tumors, recent advancements also highlight their potential as noninvasive diagnostic tools. Restoring or inhibiting specific miRNAs has offered promising strategies for targeted HCC treatment by suppressing malignant hepatocyte growth and enhancing antitumor immunity. In this comprehensive review, we consolidate previous research and provide the latest insights into how miRNAs regulate HCC and their therapeutic and diagnostic potential. We delve into the dysregulation of miRNA biogenesis in HCC, the roles of miRNAs in the proliferation and apoptosis of malignant hepatocytes, angiogenesis and metastasis of HCC, the immune microenvironment in HCC, and drug resistance. We also discuss the therapeutic and diagnostic potential of miRNAs and delivery approaches of miRNA drugs to overcome the limitations of current HCC treatment options. By thoroughly summarizing the roles of miRNAs in HCC, our goal is to advance the development of effective therapeutic drugs with minimal adverse effects and to establish precise tools for early diagnosis of HCC.

The DLEU2-miR-15a-16-1 Cluster Is a Determinant of Bone Microarchitecture and Strength in Postmenopausal Women and Mice

This study explores how select microRNAs (miRNAs) influence bone structure in humans and in transgenic mice. In trabecular bone biopsies from 84 postmenopausal women (healthy, osteopenic, and osteoporotic), we demonstrate that DLEU2 (deleted in lymphocytic leukemia 2)-encoded miR-15a-5p is strongly positively associated with bone mineral density (BMD) at different skeletal sites. In bone transcriptome analyses, miR-15a-5p levels correlated positively with the osteocyte characteristic transcripts SOST (encoding sclerostin) and MEPE (Matrix Extracellular Phosphoglycoprotein), while the related miR-15b-5p showed a negative association with BMD and osteoblast markers. The data imply that these miRNAs have opposite roles in bone remodeling with distinct actions on bone cells. Expression quantitative trait loci (eQTL) variants confirmed earlier DLEU2 associations. Furthermore, a novel variant (rs12585295) showed high localization with transcriptionally active chromatin states in osteoblast primary cell cultures. The supposition that DLEU2-encoded miRNAs have an important regulatory role in bone remodeling was further confirmed in a transgenic mice model showing that miR-15a/16-1-deleted mice had significantly higher percentage bone volume and trabecular number than the wild type, possibly due to prenatal actions. However, the three-point mechanical break force test of mice femurs showed a positive correlation between strength and miR-15a-5p/miR-16-5p levels, indicating differential effects on cortical and trabecular bone. Moreover, these miRNAs appear to have distinct and complex actions in mice prenatally and in adult humans, impacting BMD and microstructure by regulating bone cell transcription. However, detailed interactions between these miRNAs and their downstream mechanisms in health and disease need further clarification.

Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21: A Machine-Learning-Aided Enhanced Sampling Study

MicroRNAs (miRs) are short, noncoding RNA strands that regulate the activity of mRNAs by affecting the repression of protein translation, and their dysregulation has been implicated in several pathologies. miR21 in particular has been implicated in tumorigenesis and anticancer drug resistance, making it a critical target for drug design. miR21 biogenesis involves precise biochemical pathways, including the cleavage of its precursor, pre-miR21, by the enzyme Dicer. The present work investigates the conformational dynamics of pre-miR21, focusing on the role of adenine29 in switching between Dicer-binding-prone and inactive states. We also investigated the effect of L50, a cyclic peptide binder of pre-miR21 and a weak inhibitor of its processing. Using time series data and our novel collective variable-based enhanced sampling technique, OneOPES, we simulated these conformational changes and assessed the effect of L50 on the conformational plasticity of pre-miR21. Our results provide insight into peptide-induced conformational changes and pave the way for the development of a computational platform for the screening of inhibitors of pre-miR21 processing that considers RNA flexibility, a stepping stone for effective structure-based drug design, with potentially broad applications in drug discovery.

Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues

The capability to spatially explore RNA biology in formalin-fixed paraffin-embedded (FFPE) tissues holds transformative potential for histopathology research. Here, we present pathology-compatible deterministic barcoding in tissue (Patho-DBiT) by combining in situ polyadenylation and computational innovation for spatial whole transcriptome sequencing, tailored to probe the diverse RNA species in clinically archived FFPE samples. It permits spatial co-profiling of gene expression and RNA processing, unveiling region-specific splicing isoforms, and high-sensitivity transcriptomic mapping of clinical tumor FFPE tissues stored for 5 years. Furthermore, genome-wide single-nucleotide RNA variants can be captured to distinguish malignant subclones from non-malignant cells in human lymphomas. Patho-DBiT also maps microRNA regulatory networks and RNA splicing dynamics, decoding their roles in spatial tumorigenesis. Single-cell level Patho-DBiT dissects the spatiotemporal cellular dynamics driving tumor clonal architecture and progression. Patho-DBiT stands poised as a valuable platform to unravel rich RNA biology in FFPE tissues to aid in clinical pathology evaluation.

It's about time: the heterochronic background for the 2024 Nobel Prize in Physiology or Medicine

The 2024 Nobel Prize in Physiology or Medicine has been awarded to Victor Ambros and Gary Ruvkun "for the discovery of microRNA and its role in post-transcriptional gene regulation". The award celebrates the discovery of small regulatory miRNAs and their mRNA targets, published over three decades ago. The groundwork for this discovery was laid during the early 1980s, when Ambros began studying mutations that caused heterochronic defects in the nematode Caenorhabditis elegans - or shifts in the temporal identities of cells. A major impetus to study the heterochronic genes of C. elegans was to gain mechanistic understanding of how developmental stages are specified - a fascinating question in basic and evolutionary biology. Asking fundamental biological questions with no immediate application to human health ultimately led to the discovery of a new type of RNA, which had broad implications for understanding and treating human disease.

Description Generation Using Variational Auto-Encoders for Precursor microRNA

Micro RNAs (miRNA) are a type of non-coding RNA involved in gene regulation and can be associated with diseases such as cancer, cardiovascular, and neurological diseases. As such, identifying the entire genome of miRNA can be of great relevance. Since experimental methods for novel precursor miRNA (pre-miRNA) detection are complex and expensive, computational detection using Machine Learning (ML) could be useful. Existing ML methods are often complex black boxes that do not create an interpretable structural description of pre-miRNA. In this paper, we propose a novel framework that makes use of generative modeling through Variational Auto-Encoders to uncover the generative factors of pre-miRNA. After training the VAE, the pre-miRNA description is developed using a decision tree on the lower dimensional latent space. Applying the framework to miRNA classification, we obtain a high reconstruction and classification performance while also developing an accurate miRNA description.

Quantitative design of cell type-specific mRNA stability from microRNA expression data

Limiting expression to target cell types is a longstanding goal in gene therapy, which could be met by sensing endogenous microRNA. However, an unclear association between microRNA expression and activity currently hampers such an approach. Here, we probe this relationship by measuring the stability of synthetic microRNA-responsive 3'UTRs across 10 cell lines in a library format. By systematically addressing biases in microRNA expression data and confounding factors such as microRNA crosstalk, we demonstrate that a straightforward model can quantitatively predict reporter stability purely from expression data. We use this model to design constructs with previously unattainable response patterns across our cell lines. The rules we derive for microRNA expression data selection and processing should apply to microRNA- responsive devices for any environment with available expression data.

Advancements in Research on Mesenchymal Stem-Cell-Derived Exosomal miRNAs: A Pivotal Insight into Aging and Age-Related Diseases

Mesenchymal stem cells (MSCs) are capable of differentiating into various cell types and play a crucial role in repairing aging tissues and diseased organs. Aging manifests as a gradual loss of cellular, tissue, and organ function, leading to the progression of pathologies. Exosomes (Exos) are extracellular vesicles secreted by cells, which maintain cellular homeostasis, clear cellular debris, and facilitate communication between cells and organs. This review provides a comprehensive summary of the mechanisms for the synthesis and sorting of MSC-Exo miRNAs and summarizes the current research status of MSCs-Exos in mitigating aging and age-related diseases. It delves into the underlying molecular mechanisms, which encompass antioxidative stress, anti-inflammatory response, and the promotion of angiogenesis. Additionally, this review also discusses potential challenges in and future strategies for advancing MSC-Exo miRNA-based therapies in the treatment of aging and age-related diseases.

Stage-specific expression patterns and co-targeting relationships among miRNAs in the developing mouse cerebral cortex

microRNAs are crucial regulators of brain development, however, miRNA regulatory networks are not sufficiently well characterized. By performing small RNA-seq of the mouse embryonic cortex at E14, E17, and P0 as well as in neural progenitor cells and neurons, here we detected clusters of miRNAs that were co-regulated at distinct developmental stages. miRNAs such as miR-92a/b acted as hubs during early, and miR-124 and miR-137 during late neurogenesis. Notably, validated targets of P0 hub miRNAs were enriched for downregulated genes related to stem cell proliferation, negative regulation of neuronal differentiation and RNA splicing, among others, suggesting that miRNAs are particularly important for modulating transcriptional programs of crucial factors that guide the switch to neuronal differentiation. As most genes contain binding sites for more than one miRNA, we furthermore constructed a co-targeting network where numerous miRNAs shared more targets than expected by chance. Using luciferase reporter assays, we demonstrated that simultaneous binding of miRNA pairs to neurodevelopmentally relevant genes exerted an enhanced transcriptional silencing effect compared to single miRNAs. Taken together, we provide a comprehensive resource of miRNA longitudinal expression changes during murine corticogenesis. Furthermore, we highlight several potential mechanisms through which miRNA regulatory networks can shape embryonic brain development.

Decoding biology with massively parallel reporter assays and machine learning

Massively parallel reporter assays (MPRAs) are powerful tools for quantifying the impacts of sequence variation on gene expression. Reading out molecular phenotypes with sequencing enables interrogating the impact of sequence variation beyond genome scale. Machine learning models integrate and codify information learned from MPRAs and enable generalization by predicting sequences outside the training data set. Models can provide a quantitative understanding of cis-regulatory codes controlling gene expression, enable variant stratification, and guide the design of synthetic regulatory elements for applications from synthetic biology to mRNA and gene therapy. This review focuses on cis-regulatory MPRAs, particularly those that interrogate cotranscriptional and post-transcriptional processes: alternative splicing, cleavage and polyadenylation, translation, and mRNA decay.

Epidrugs in the clinical management of atherosclerosis: Mechanisms, challenges and promises

Atherosclerosis is a complex and multigenic pathology associated with significant epigenetic reprogramming. Traditional factors (age, sex, obesity, hyperglycaemia, dyslipidaemia, hypertension) and non-traditional factors (foetal indices, microbiome alteration, clonal hematopoiesis, air pollution, sleep disorders) induce endothelial dysfunction, resulting in reduced vascular tone and increased vascular permeability, inflammation and shear stress. These factors induce paracrine and autocrine interactions between several cell types, including vascular smooth muscle cells, endothelial cells, monocytes/macrophages, dendritic cells and T cells. Such cellular interactions lead to tissue-specific epigenetic reprogramming regulated by DNA methylation, histone modifications and microRNAs, which manifests in atherosclerosis. Our review outlines epigenetic signatures during atherosclerosis, which are viewed as potential clinical biomarkers that may be adopted as new therapeutic targets. Additionally, we emphasize epigenetic modifiers referred to as 'epidrugs' as potential therapeutic molecules to correct gene expression patterns and restore vascular homeostasis during atherosclerosis. Further, we suggest nanomedicine-based strategies involving the use of epidrugs, which may selectively target cells in the atherosclerotic microenvironment and reduce off-target effects.

Epigenetic alteration in cervical cancer induced by human papillomavirus

The critical role of a subset of Human Papillomavirus in cervical cancer has been widely acknowledged and studied. Despite progress in our understanding of the viral molecular mechanisms of pathogenesis, knowledge of how infection with HPV oncogenic variants progresses from latent infection to incurable cancer has not been completely elucidated. In this paper we reviewed the relationship between HPV infection and epigenetic mechanisms such as histone acetylation and deacetylation, DNA methylation and non-coding RNAs associated with this infection and the carcinogenic process.

Duck plague virus-encoded microRNA dev-miR-D28-3p inhibits viral replication via targeting UL27

Herpesviruses-encoded microRNAs (miRNAs) have been discovered to be essential regulators in viral life cycle, participating in viral replication, latent or lytic infection, and immunological escape. However, the roles of miRNAs encoded by duck plague virus (DPV) are still unknown. Dev-miR-D28-3p is a miRNA uniquely encoded by DPV CHv strain. The aim of this study was to explore the effect of dev-miR-D28-3p on DPV replication and explore the potential mechanisms involved. Our findings demonstrated that transfection of dev-miR-D28-3p mimic into duck embryo fibroblasts (DEFs) effectively suppressed viral copies, viral titers and viral protein expressions during DPV infection, while the results above were reversed after transfection with dev-miR-D28-3p inhibitor. Subsequently, we further discovered that dev-miR-D28-3p specifically bound to DPV-encoded UL27 and inhibited its expression, suggesting that UL27 was the target gene of dev-miR-D28-3p. Finally, we investigated the role of UL27 in DPV replication and found the overexpression of UL27 increased viral copies, viral titers, and viral protein expressions; whereas the opposite results appear when knockdown of UL27. Our findings illustrated a novel mechanism that DPV regulated itself replication via dev-miR-D28-3p, paving the way for exploring the role of DPV-encoded miRNAs.

Paving the way to a neural fate - RNA signatures in naive and trans-differentiating mesenchymal stem cells

Mesenchymal Stem Cells (MSCs) derived from the embryonic mesoderm persist as a viable source of multipotent cells in adults and have a crucial role in tissue repair. One of the most promising aspects of MSCs is their ability to trans-differentiate into cell types outside of the mesodermal lineage, such as neurons. This characteristic positions MSCs as potential therapeutic tools for neurological disorders. However, the definition of a clear MSC signature is an ongoing topic of debate. Likewise, there is still a significant knowledge gap about functional alterations of MSCs during their transition to a neural fate. In this study, our focus is on the dynamic expression of RNA in MSCs as they undergo trans-differentiation compared to undifferentiated MSCs. To track and correlate changes in cellular signaling, we conducted high-throughput RNA expression profiling during the early time-course of human MSC neurogenic trans-differentiation. The expression of synapse maturation markers, including NLGN2 and NPTX1, increased during the first 24 h. The expression of neuron differentiation markers, such as GAP43 strongly increased during 48 h of trans-differentiation. Neural stem cell marker NES and neuron differentiation marker, including TUBB3 and ENO1, were highly expressed in mesenchymal stem cells and remained so during trans-differentiation. Pathways analyses revealed early changes in MSCs signaling that can be linked to the acquisition of neuronal features. Furthermore, we identified microRNAs (miRNAs) as potential drivers of the cellular trans-differentiation process. We also determined potential risk factors related to the neural trans-differentiation process. These factors include the persistence of stemness features and the expression of factors involved in neurofunctional abnormalities and tumorigenic processes. In conclusion, our findings contribute valuable insights into the intricate landscape of MSCs during neural trans-differentiation. These insights can pave the way for the development of safer treatments of neurological disorders.

Guidelines for mitochondrial RNA analysis

Mitochondria are the energy-producing organelles of mammalian cells with critical involvement in metabolism and signaling. Studying their regulation in pathological conditions may lead to the discovery of novel drugs to treat, for instance, cardiovascular or neurological diseases, which affect high-energy-consuming cells such as cardiomyocytes, hepatocytes, or neurons. Mitochondria possess both protein-coding and noncoding RNAs, such as microRNAs, long noncoding RNAs, circular RNAs, and piwi-interacting RNAs, encoded by the mitochondria or the nuclear genome. Mitochondrial RNAs are involved in anterograde-retrograde communication between the nucleus and mitochondria and play an important role in physiological and pathological conditions. Despite accumulating evidence on the presence and biogenesis of mitochondrial RNAs, their study continues to pose significant challenges. Currently, there are no standardized protocols and guidelines to conduct deep functional characterization and expression profiling of mitochondrial RNAs. To overcome major obstacles in this emerging field, the EU-CardioRNA and AtheroNET COST Action networks summarize currently available techniques and emphasize critical points that may constitute sources of variability and explain discrepancies between published results. Standardized methods and adherence to guidelines to quantify and study mitochondrial RNAs in normal and disease states will improve research outputs, their reproducibility, and translation potential to clinical application.

MiRNA-100 ameliorates diabetes mellitus-induced erectile dysfunction by modulating autophagy, anti-inflammatory, and antifibrotic effects

BACKGROUND

Diabetes mellitus-induced erectile dysfunction (DMED) has become a common disease in adult men that can seriously reduce the quality of life of patients, and new therapies are urgently needed. miRNA-100 has many targets and can induce autophagy and reduce fibrosis by inhibiting the mTOR pathway and the TGF-β pathway. However, no research has been conducted with miR-100 in the field of DMED, and the specific mechanism of action is still unclear.

OBJECTIVES

To ascertain the effects of miR-100 on corpus cavernosum tissue of DMED rats and vascular endothelial cells in a high glucose environment and to elucidate the relevant mechanisms in autophagy, fibrosis and inflammation to find a new approach for the DMED therapy.

METHODS

Thirty rats were divided into three groups: the control group, the DMED group, and the DMED + miR-100 group. Using intraperitoneal injections of streptozotocin, all rats except the control group were modeled with diabetes mellitus, which was verified using the apomorphine (APO) test. For rats in the DMED + miR-100 group, rno-miR-100-5p agomir (50 nmol/kg, every 2 days, 6 times in total) was injected via the tail vein. After 13 weeks, the erectile function of each rat was assessed using cavernous manometry, and the corpus cavernosum tissue was harvested for subsequent experiments. For cellular experiments, human coronary microartery endothelial cells (HCMEC) were divided into four groups: the control group, the high-glucose (HG, 40 mM) group, the HG + mimic group, and the HG + inhibitor group. The cells were cultured for 6 days and collected for subsequent experiments 2 days after transfection.

RESULTS

Diabetic modeling impaired the erectile function in rats, and miR-100 reversed this effect. By measuring autophagy-related proteins such as mTOR/Raptor/Beclin1/p62/LC3B, we found that miR-100 could suppress the expression of mTOR and induce autophagy. The analysis of the eNOS/NO/cGMP axis function indicated that impaired endothelial function was improved by miR-100. By evaluating the TGF-β1/CTGF/Smad2/3 and NF-κB/TNF-α pathways, we found that miR-100 could lower the level of inflammation and fibrosis, which contributed to the improvement of the erectile function. Cellular experiments can be used as supporting evidence for these findings.

CONCLUSION

MiR-100 can improve the erectile function by inhibiting mTOR and thus inducing autophagy, improving the endothelial function through the eNOS/NO/cGMP axis, and exerting antifibrotic and anti-inflammatory effects, which may provide new ideas and directions for the treatment of DMED.

MicroRNAs in Genitourinary Malignancies: An Exciting Frontier of Cancer Diagnostics and Therapeutics

Genitourinary (GU) malignancies, including prostate, urothelial, kidney, testicular, penile, and adrenocortical cancers, comprise a significant burden of cancers worldwide. While many practice-changing advances have been made in the management of GU malignancies in the last decade, there is still significant room for improvement. MicroRNAs (miRNAs) are noncoding RNAs that regulate post-transcription gene expression and which have been implicated in multiple mechanisms of carcinogenesis. Therefore, they have the potential to revolutionize personalized cancer therapy, with several ongoing preclinical and clinical studies underway to investigate their efficacy. In this review, we describe the current landscape of miRNAs as diagnostics, therapeutics, and biomarkers of response for GU malignancies, reflecting a novel frontier in cancer treatment.

MicroRNA signature of stromal-epithelial interactions in prostate and breast cancers

Stromal-epithelial communication is an absolute necessity when it comes to the morphogenesis and pathogenesis of solid tissues, including the prostate and breast. So far, signalling pathways of several growth factors have been investigated. Besides such chemical factors, non-coding RNAs such as miRNAs have recently gained much interest because of their variety and complexity of action. Prostate and breast tissues being highly responsive to steroid hormones such as androgen and estrogen, respectively, it is not surprising that a huge set of available literature critically investigated the interplay between such hormones and miRNAs, especially in carcinogenesis. This review showcases our effort to highlight hormonally-related miRNAs that also somehow perturb the regular stromal-epithelial interactions during carcinogenesis in the prostate and breast. In future, we look forward to exploring how hormonal changes in the tissue microenvironment bring about miRNA-mediated changes in stromal-epithelial interactome in carcinogenesis and cancer progression.