miRNA Interactions Research Articles

Exosome-Mediated Communication in Thyroid Cancer: Implications for Prognosis and Therapeutic Targets.

Thyroid cancer (THCA) is one of the most common malignancies of the endocrine system. Exosomes have significant value in performing molecular treatments, evaluating the diagnosis and determining tumor prognosis. Thus, the identification of exosome-related genes could be valuable for the diagnosis and potential treatment of THCA. In this study, we examined a set of exosome-related differentially expressed genes (DEGs) (BIRC5, POSTN, TGFBR1, DUSP1, BID, and FGFR2) by taking the intersection between the DEGs of the TCGA-THCA and GeneCards datasets. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of the exosome-related DEGs indicated that these genes were involved in certain biological functions and pathways. Protein‒protein interaction (PPI), mRNA‒miRNA, and mRNA-TF interaction networks were constructed using the 6 exosome-related DEGs as hub genes. Furthermore, we analyzed the correlation between the 6 exosome-related DEGs and immune infiltration. The Genomics of Drug Sensitivity in Cancer (GDSC), the Cancer Cell Line Encyclopedia (CCLE), and the CellMiner database were used to elucidate the relationship between the exosome-related DEGs and drug sensitivity. In addition, we verified that both POSTN and BID were upregulated in papillary thyroid cancer (PTC) patients and that their expression was correlated with cancer progression. The POSTN and BID protein expression levels were further examined in THCA cell lines. These findings provide insights into exosome-related clinical trials and drug development.

Identifying miRNA as biomarker for breast cancer subtyping using association rule

— This paper presents a comprehensive study focused on breast cancer subtyping, utilizing a multifaceted approach that integrates feature selection, machine learning classifiers, and miRNA regulatory networks. The feature selection process begins with the CFS algorithm, followed by the Apriori algorithm for association rule generation, resulting in the identification of significant features tailored to Luminal A, Luminal B, HER-2 enriched, and Basal-like subtypes. The subsequent application of Random Forest (RF) and Support Vector Machine (SVM) classifiers yielded promising results, with the SVM model achieving an overall accuracy of 76.60 % and the RF model demonstrating robust performance at 80.85 %. Detailed accuracy metrics revealed strengths and areas for refinement, emphasizing the potential for optimizing subtype-specific recall. To explore the regulatory landscape in depth, an analysis of selected miRNAs was conducted using MIENTURNET, a tool for visualizing miRNA-target interactions. While FDR analysis raised concerns for HER-2 and Basal-like subtypes, Luminal A and Luminal B subtypes showcased significant miRNA-gene interactions. Functional enrichment analysis for Luminal A highlighted the role of Ovarian steroidogenesis, implicating specific miRNAs such as hsa-let-7c-5p and hsa-miR-125b-5p as potential diagnostic biomarkers and regulators of Luminal A breast cancer. Luminal B analysis uncovered associations with the MAPK signaling pathway, with miRNAs like hsa-miR-203a-3p and hsa-miR-19a-3p exhibiting potential diagnostic and therapeutic significance. In conclusion, this integrative approach combines machine learning techniques with miRNA analysis to provide a holistic understanding of breast cancer subtypes. The identified miRNAs and associated pathways offer insights into potential diagnostic biomarkers and therapeutic targets, contributing to the ongoing efforts to improve breast cancer diagnostics and personalized treatment strategies.

Next-generation Sequencing of MicroRNA in Acquired Middle Ear Cholesteatoma.

The pathophysiology of cholesteatoma is not precisely understood, and research on the associated microRNAs (miRNAs) is also deficient. We demonstrated the expression of miRNA in normal skin and middle ear cholesteatoma by next-generation sequencing (NGS) technology. The profiles of miRNA and relevant molecular interaction pathways were investigated. Case-control experimental study. Middle ear cholesteatoma and post-auricular skin tissue specimens were collected from 13 adult patients. Total RNA was extracted, and miRNA expression profiles were analyzed by NGS technology. Functional gene classification to predict target genes and relevant biological pathways was performed using DIANA-microT-CDS and the Kyoto Encyclopedia Gene and Genome database (KEGG) pathways. The expression of 2588 miRNAs from middle ear cholesteatoma and skin tissue samples was analyzed. The expression of 76 upregulated and 128 downregulated miRNAs was identified in the cholesteatoma samples compared to normal skin (FC ≥2 and p < 0.05). Ninety-nine differentially expressed miRNAs (FC ≥4 and p < 0.05) were used to explore the biological pathways involved in the etiopathogenesis of cholesteatoma. The most predicted pathway in cholesteatoma in the upregulated miRNA group was the ErbB signaling pathway and it was extracellular matrix (ECM)-receptor interaction in the downregulated miRNA group. This was the first study investigating small miRNAs in human acquired cholesteatoma using NGS technique. We were able to identify new miRNAs and pathways related to cholesteatoma. The results of this study are expected to be helpful in revealing new pathophysiologies of cholesteatoma. N/A Laryngoscope, 134:4374-4382, 2024.

Identification and characterization of the CRK gene family in the wheat genome and analysis of their expression profile in response to high temperature-induced male sterility.

Cysteine-rich receptor-like kinases (CRKs) play many important roles during plant development, including defense responses under both biotic and abiotic stress, reactive oxygen species (ROS) homeostasis, callose deposition and programmed cell death (PCD). However, there are few studies on the involvement of the CRK family in male sterility due to heat stress in wheat (Triticum aestivum L.). In this study, a genome-wide characterization of the CRK family was performed to investigate the structural and functional attributes of the wheat CRKs in anther sterility caused by heat stress. A total of 95 CRK genes were unevenly distributed on 18 chromosomes, with the most genes distributed on chromosome 2B. Paralogous homologous genes with Ka/Ks ratios less than 1 may have undergone strong purifying selection during evolution and are more functionally conserved. The collinearity analysis results of CRK genes showed that wheat and Arabidopsis (A. thaliana), foxtail millet, Brachypodium distachyon (B. distachyon), and rice have three, 12, 15, and 11 pairs of orthologous genes, respectively. In addition, the results of the network interactions of genes and miRNAs showed that five miRNAs were in the hub of the interactions map, namely tae-miR9657b-5p, tae-miR9780, tae-miR9676-5p, tae-miR164, and tae-miR531. Furthermore, qRT-PCR validation of the six TaCRK genes showed that they play key roles in the development of the mononuclear stage anthers, as all six genes were expressed at highly significant levels in heat-stressed male sterile mononuclear stage anthers compared to normal anthers. We hypothesized that the TaCRK gene is significant in the process of high-temperature-induced sterility in wheat based on the combination of anther phenotypes, paraffin sections, and qRT-PCR data. These results improve our understanding of their relationship.

Functional Analysis of BRCA1 3'UTR Variants Predisposing to Breast Cancer.

Breast Cancer (BC) is the main female cancer diagnosed worldwide, and it has been described that few genes, such as BRCA1, have a high penetrance for this type of cancer. In this manuscript, we were interested in evaluating the effect of 3'UTR variants on BRCA1 expression. To accomplish this objective, Whole Exome Sequencing (WES) data of 400 patients with unselected BC was used to filter variants located in the region of interest of BRCA1 gene, finding two of them (c.*36C>G and c.*369_373del). miRGate and miRanda in silico tools were used to predict microRNA (miRNA) interaction. The two variants (c.*36C>G, c.*369_373del) were predicted to affect miRNA interaction. After cloning of BRCA1 3'UTR into pMIR-Report vector, the construct was transfected into two BC cell lines (MDA-MB-231 and MCF-7), and the variant c.*36C>G evidenced overexpression of reporter gene luciferase, showing that the transcript was not being degraded by the miRNA in MDA-MB-231 cells. The variant seems to protect against Triple Negative BC probably due to the expression level of miRNA in this particular cell line (MDA-MB-231). This is consistent with the clinical history of the patients who harbor BC Hormone Receptors positive (HR+).

Pathway analysis for functional characterization of microRNAs

DIANA-miRPath webserver enables the exploration of combined miRNA effects using predicted or experimentally supported miRNA interactions. Its latest version (DIANA-miRPath v4.0, http://www.microrna.gr/miRPathv4 ), introduces the capacity to tailor its target-based miRNA functional analysis engine towards specific biological/experimental contexts. Via a modular interface with rich interaction, annotation and parameterization options, users can perform enrichment analysis on Gene Ontology (GO) terms, KEGG and REACTOME pathways, gene sets from Molecular Signatures Database (MSigDB) and PFAM. Included miRNA interaction sets are derived from state-of-the-art resources of experimentally supported (DIANA-TarBase v8.0, miRTarBase and microCLIP cell-type-specific interactions) or from in silico miRNA-target interactions (DIANA-microT-2023 and TargetScan predictions). Bulk and single-cell expression datasets from The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression project (GTEx), as well as single-cell expression atlases can be used to assess expression change of targeted genes within terms, across a wide range of states. A discrete module to perform miRNA-tailored CRISPR knock-out screen analyses deems possible the investigation of selected miRNAs within conditions under study. Hellenic Foundation for Research and Innovation (HFRI) under the 1 st Call for HFRI Research Projects to Support Faculty Members &amp; Researchers and Procure High-Value Research Equipment grant (Project Number 2563). This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

In Vivo Imaging MicroRNA with Bright Fluorescent RNA Aptamer Through Target-Mediated Entropy-Driven Toehold Exchange.

MicroRNAs (miRNAs) play vital roles in biological activities, but their in vivo imaging is still challenging due to the low abundance and the lack of efficient fluorescent tools. RNA aptamers with high affinity and low background emerge for bioimaging yet suffering from low brightness. We introduce a rational design based on target-mediated entropy-driven toehold exchange (EDTE) to induce the release of RNA aptamer and subsequently light up corresponding fluorophore, which achieves selective imaging of miRNAs with good stability in both living cells and tumor-bearing mouse. Through tailoring recognition unit of the EDTE probes, highly sensitive imaging of different miRNAs including miRNA-125b and miRNA-21 is achieved, confirming its universal bioimaging applications. In comparison with the reported "one-to-one" model, the EDTE strategy shows a remarkable 4.6-time improvement in signal/noise ratio for intracellular imaging of the same miRNA. Particularly, it realizes sensitive imaging of miRNA in vivo, providing a promising tool in investigating functions and interactions of disease-associated miRNAs.

EGCG Disrupts the LIN28B/Let-7 Interaction and Reduces Neuroblastoma Aggressiveness.

Neuroblastoma (NB) is the most commonly diagnosed extracranial solid tumor in children, accounting for 15% of all childhood cancer deaths. Although the 5-year survival rate of patients with a high-risk disease has increased in recent decades, NB remains a challenge in pediatric oncology, and the identification of novel potential therapeutic targets and agents is an urgent clinical need. The RNA-binding protein LIN28B has been identified as an oncogene in NB and is associated with a poor prognosis. Given that LIN28B acts by negatively regulating the biogenesis of the tumor suppressor let-7 miRNAs, we reasoned that selective interference with the LIN28B/let-7 miRNA interaction would increase let-7 miRNA levels, ultimately leading to reduced NB aggressiveness. Here, we selected (-)-epigallocatechin 3-gallate (EGCG) out of 4959 molecules screened as the molecule with the best inhibitory activity on LIN28B/let-7 miRNA interaction and showed that treatment with PLC/PLGA-PEG nanoparticles containing EGCG (EGCG-NPs) led to an increase in mature let-7 miRNAs and a consequent inhibition of NB cell growth. In addition, EGCG-NP pretreatment reduced the tumorigenic potential of NB cells in vivo. These experiments suggest that the LIN28B/let-7 miRNA axis is a good therapeutic target in NB and that EGCG, which can interfere with this interaction, deserves further preclinical evaluation.

Comprehensive analysis of circRNA expression profiles in postmenopausal women differing in bone mineral density.

Postmenopausal osteoporosis (PMOP) seriously endangers the bone health of older women. Although there are currently indicators to diagnose PMOP, early diagnostic biomarkers are lacking. Circular ribonucleic acid (circRNA) has a stable structure, regulates gene expression, participates in the pathological process of disease, and has the potential to become a biomarker. The purpose of this study was to investigate circRNAs that could be used to predict patients with early PMOP. Ribonucleic acid (RNA) sequencing was performed on peripheral blood leukocytes from 15 female patients to identify differential circRNAs between different groups. Using bioinformatics analysis, enrichment analysis was performed to discover relevant functions and pathways. CircRNA-micro ribonucleic acid (miRNA) interaction analysis and messenger ribonucleic acid (mRNA) prediction and network construction help us to understand the relationship between circRNA, miRNA, and mRNA. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the gene expression of candidate circRNAs. We screened out 2 co-expressed differential circRNAs, namely hsa_circ_0060849 and hsa_circ_0001394. By analyzing the regulatory network, a total of 54 miRNAs and 57 osteoporosis-related mRNAs were identified, which, as potential downstream target genes of hsa_circ_0060849 and hsa_circ_0001394, may play a key role in the occurrence and development of PMOP. The occurrence and development of PMOP is regulated by circRNAs, and hsa_circ_0060849 and hsa_circ_0001394 can be used as new diagnostic markers and therapeutic targets for early PMOP.

Decoding dynamic miRNA:ceRNA interactions unveils therapeutic insights and targets across predominant cancer landscapes.

Competing endogenous RNAs play key roles in cellular molecular mechanisms through cross-talk in post-transcriptional interactions. Studies on ceRNA cross-talk, which is particularly dependent on the abundance of free transcripts, generally involve large- and small-scale studies involving the integration of transcriptomic data from tissues and correlation analyses. This abundance-dependent nature of ceRNA interactions suggests that tissue- and condition-specific ceRNA dynamics may fluctuate. However, there are no comprehensive studies investigating the ceRNA interactions in normal tissue, ceRNAs that are lost and/or appear in cancerous tissues or their interactions. In this study, we comprehensively analyzed the tumor-specific ceRNA fluctuations observed in the three highest-incidence cancers, LUAD, PRAD, and BRCA, compared to healthy lung, prostate, and breast tissues, respectively. Our observations pertaining to tumor-specific competing endogenous RNA (ceRNA) interactions revealed that, in the cases of lung adenocarcinoma (LUAD), prostate adenocarcinoma (PRAD), and breast invasive carcinoma (BRCA), 3,204, 1,233, and 406 ceRNAs, respectively, engage in post-transcriptional intercommunication within tumor tissues, in contrast to their absence in corresponding healthy samples. We also found that 90 ceRNAs are shared by the three cancer types and that these ceRNAs participate in ceRNA interactions in tumor tissues compared to those in normal tissues. Among the 90 ceRNAs that directly interact with miRNAs, we uncovered a core network of 165 miRNAs and 63 ceRNAs that should be considered in RNA-targeted and RNA-mediated approaches in future studies and could be used in these three aggressive cancer types. More specifically, in this core interaction network, ceRNAs such as GALNT7, KLF9, and DAB2 and miRNAs like miR-106a/b-5p, miR-20a-5p, and miR-519d-3p may have potential as common targets in the three critical cancers. In contrast to conventional methods that construct ceRNA networks using differentially expressed genes compared to normal tissues, our proposed approach identifies ceRNA players by considering their context within the ceRNA:miRNA interactions. Our results have the potential to reveal distinct and common ceRNA interactions in cancer types and to pinpoint critical RNAs, thereby paving the way for RNA-based strategies in the battle against cancer.

MiR-638 suppresses cervical cancer progression by inhibiting NCAPG2 under the treatment of Tetrandrine.

The interaction of microRNA with Chinese herbal medicines is a promising therapeutic approach for prevention of cervical cancer. Western blotting or qRT-PCR were carried out to identify the expression of NCAPG2 and miR-638. A tetrandrine (TET) cell model was used to explore the effects of miR-638 and its target gene NCAPG2 using CCK-8, transwell, wound healing, and western blot assays. Furthermore, luciferase activity assay was conducted to measure the interaction among TET, NCAPG2 and miR-638. Under TET treatment, Hela and SiHa cells exhibited repressed cell viability, migration, invasion, and epithelial-mesenchymal transition (EMT), and these effects were further enhanced by high expression of miR-638. In contrast, NCAPG2 expression was low in TET-treated cells and had an opposite effect to that of miR-638. We highlighted that miR-638 suppresses cervical cancer progression by inhibiting NCAPG2 under tetrandrine treatment.

Abstract 5172: miRNA lncRNA network associated with response to cemiplimab in cutaneous squamous cell carcinoma

Abstract Introduction: For advanced cSCC the use of immunological therapies relies on the biology of the tumor, characterized by high mutational burden. However, although the anti-PD1 cemiplimab showed to be a promising treatment option, future research focusing on the use of biomarkers to predict treatment response are needed. Since increasing number of studies has revealed the crucial roles of non-coding RNAs, such as miRNAs and lncRNAs in the development of SCC, the present study had the purpose to explore the lncRNA-miRNA-mRNA networks associated with response to anti-PD1. For this purpose the experimental procedure envisaged a preliminary in silico analysis followed by the investigation of identified miRNA and lncDNA in liquid biopsy. Methods: For the in silico study, GSE139505 RNA-sequencing raw data have been retrieved from SRA, including 7 Healthy Samples and 9 cSCC biopsies. Two matrices have been prepared, including coding genes and lncRNAs. Normalized coding gene matrix have been used as input to perform GSEA. Coexpression analysis between lncRNAs and Core enrichment genes resulting from GSEA was performed. Biological network including validated miRNA-gene interactions (TarBase) and lncRNA-miRNA interactions (lncBase) has been built-up through Cytoscape. MCODE analysis to identify subnetwork with the closest relationships was performed. The quantification of identified miRNAs (miR-125a, miR-125b, miR-148a, miR-148b) and lnc (AF131217.1, RP11-362F19.1, PVT1, LINC00665) was performed in pre-therapy plasma samples of 34 cSCC patients, categorized according to clinical response to cemiplimab, in responders and non-responders. miRNA-specific RT primers were used for reverse transcription by ddPCR. Results: The computational analysis revealed a significant enrichment of two gene sets related to immunotherapy, namely the Reactome_PD1_signaling and WP_Cancer_Immunotherapy_by_PD1_blockade. The coespression analyses highlighted more than 600 correlations gene-miRNA-lncRNA for the two above-mentioned genesets. CD4-miR-125a/b and AF131217.1/RP11-362F19.1 are strongly correlated for the first one; whilst, regarding the latter one, CD274/HLA-A with mir-148a/b and PVT1/LINC00665 and JUN with mir-125a/b and AF131217.1/RP11-362F19.1 were found. The validation in cSCC plasma samples evidenced the significant correlation between mir-148a/b and PVT1/LINC00665 and an higher expression of all miRNAs in responders respect to non-responders. The longitudinal study assessing the correlation between miRNA expression and response to cemiplimab is ongoing. Conclusion: Preliminary analysis in pre-therapy plasma samples of cSCC validated the in silico data highlighting the inverse correlation between miR-148a/b and lnc (PVT1 and LINC00665). Further investigation will confirm the role of miR125a/b and miR148a/b as predictors of cemiplimab response. Citation Format: Letizia Porcelli, Simona De Summa, Rossella Fasano, Michele Guida, Tommaso M. Marvulli, Tania Rafaschieri, Giuseppe De Palma, Simona Serratì, Roberta Di Fonte, Ivana De Risi, Sabino Strippoli, Stefania Tommasi, Amalia Azzariti. miRNA lncRNA network associated with response to cemiplimab in cutaneous squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5172.

Exogenous dsRNA sequence based on miR1917 downregulates its target gene related to ethylene signaling in tomato seedlings and fruit

The recent developments in application of RNA interference present a novel strategy for combating plant diseases by targeting pathogen genes. This study aimed to design, synthesize, and administer a double-stranded RNA (dsRNA) in tomato (var. Microtom) plants, drawing inspiration from the interaction between miR1917 and its target, the negative regulator of ethylene perception, Constitutive Triple Response 4 splicing variant 3 (CTR4sv3). An assessment of the potential endogenous effects stemming from the application of RNA molecules onto plant tissues was conducted, with a particular focus on observing resultant phenotypic changes. For seedling development analysis, seeds were soaked in a dsRNA solution for analysis, and they showed triple response phenotypic traits: reduction in root and hypocotyl length by up to 81 % and 60 % respectively, coupled with the noticeable development of hook. Furthermore, an 81 % decrease in CTR4sv3 expression was recorded, along with a 17-fold increase in the ethylene biosynthesis gene ACO1. Conversely, green-mature tomato fruit were subjected to dsRNA injections, resulting in a 43 % reduction in CTR4sv3 levels, accompanied by a more than 3-fold increase in ACO1 levels. Altogether, it is reported that the utilization of dsRNA based on miR1917 downregulates CTR4sv3, and the concomitant increase in ACO1 in both seedlings and fruit. With these findings, we propose that miRNA and target interactions can serve as a basis for RNA interference design and its application in plants to inhibit the plant's own mRNA can modify biosynthetic pathways, addressing both scientific inquiries and technological objectives.

MiRNA-miRNA interaction network in peripheral blood of patients with myocardial infarction: a gene expression meta-analysis

In recent years, investigations have revealed that microRNAs (miRNAs) can bind together and form a miRNA-miRNA-mRNA regulatory network that alters the consequence of miRNA-mRNA interaction. If we consider the miRNA that binds to mRNA as the primary miRNA and the miRNA that binds to the primary miRNA as the secondary one, secondry miRNAs can act as master regulators upstream of primary miRNAs and their target mRNAs. One of the distinguishing characteristics of secondary miRNAs as master regulators within a diverse set of differentially expressed genes is the absence of direct target mRNA for them. Instead, these master regulators exclusively govern the regulation of miRNAs that target specific mRNAs. Through in silico analysis, we identified 18 miRNAs among 385 differentially expressed miRNAs (DEmiRNAs) with no direct target mRNAs among 58 differentially expressed mRNAs (DEmRNAs) in peripheral blood of patients with myocardial infarction (MI). Instead, these secondary miRNAs targeted 9 primary miRNAs that had 36 direct targets among 58 DEmRNAs. We found that one primary miRNA might be regulated by more than one secondary miRNAs and each secondary miRNA can target more than one primary miRNAs. Among identified miRNA-miRNA-mRNA networks miR-188-5p/miR-299-3p/natural killer cell granule protein (NKG7), miR-200a-3p/miR-199b-5p/granzyme B (GZMB), and miR-377-3p/miR-581/oviductal glycoprotein 1 (OVGP1) exhibited higher scors in terms of expression levels (>2-fold increase or decrease) and strengh of interactions (ΔG < −5). Given the extensive network of miRNA interactions, focusing on master regulators opens up avenues for identifying key regulatory nodes for more effective therapeutic strategies.

Leaf Senescence Database v5.0: A Comprehensive Repository for Facilitating Plant Senescence Research

Through an extensive literature survey, we have upgraded the Leaf Senescence Database (LSD v5.0; https://ngdc.cncb.ac.cn/lsd/), a curated repository of comprehensive senescence-associated genes (SAGs) and their corresponding mutants. Since its inception in 2010, LSD undergoes frequent updates to encompass the latest advances in leaf senescence research and its current version comprises a high-quality collection of 31,740 SAGs and 1,209 mutants from 148 species, which were manually searched based on robust experimental evidence and further categorized according to their functions in leaf senescence. Furthermore, LSD was greatly enriched with comprehensive annotations for the SAGs through meticulous curation using both manual and computational methods. In addition, it was equipped with user-friendly web interfaces that facilitate text queries, BLAST searches, and convenient download of SAG sequences for localized analysis. Users can effortlessly navigate the database to access a plethora of information, including literature references, mutants, phenotypes, multi-omics data, miRNA interactions, homologs in other plants, and cross-links to various databases. Taken together, the upgraded version of LSD stands as the most comprehensive and informative plant senescence-related database to date, incorporating the largest collection of SAGs and thus bearing great utility for a wide range of studies related to plant senescence.

Tiny Guides, Big Impact: Focus on the Opportunities and Challenges of miR-Based Treatments for ARDS.

Acute Respiratory Distress Syndrome (ARDS) is characterized by lung inflammation and increased membrane permeability, which represents the leading cause of mortality in ICUs. Mechanical ventilation strategies are at the forefront of supportive approaches for ARDS. Recently, an increasing understanding of RNA biology, function, and regulation, as well as the success of RNA vaccines, has spurred enthusiasm for the emergence of novel RNA-based therapeutics. The most common types of RNA seen in development are silencing (si)RNAs, antisense oligonucleotide therapy (ASO), and messenger (m)RNAs that collectively account for 80% of the RNA therapeutics pipeline. These three RNA platforms are the most mature, with approved products and demonstrated commercial success. Most recently, miRNAs have emerged as pivotal regulators of gene expression. Their dysregulation in various clinical conditions offers insights into ARDS pathogenesis and offers the innovative possibility of using microRNAs as targeted therapy. This review synthesizes the current state of the literature to contextualize the therapeutic potential of miRNA modulation. It considers the potential for miR-based therapeutics as a nuanced approach that incorporates the complexity of ARDS pathophysiology and the multifaceted nature of miRNA interactions.

Integrated Analysis of a ceRNA (lncRNA-miRNA-mRNA) Regulatory Network for Prostate Cancer

Objective. This study was to construct a ceRNA (lncRNA-miRNA-mRNA) regulatory network for prostate cancer (PCa) and to explore the prognostic correlation, key biological functions, and pathways of core RNAs. Methods. Three subgene expression matrices (miRNA, lncRNA, and mRNA expression matrix) were taken from the TCGA database and used in this investigation. Differential expression analysis and differential expression miRNAs were carried out. Next, the ceRNA (lncRNA-miRNA-mRNA) regulatory complex was used to visualize our data and show how they interacted. Ultimately, the primary molecular roles and biological pathways of PCa were identified using enrichment analysis by the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO). An effect of AC016773.1 on prostate cancer cell proliferation was investigated by knocking out AC016773.1 in an animal model. The interrelationship between AC016773.1 and hsa-mir-25 was validated using RNA immunoprecipitation technology. Results. The lncRNA, miRNA, and mRNA expression matrices obtained from the TCGA database contain 16901, 1881, and 19962 transcripts, respectively. Through differential expression analysis, we obtained 2010 de lncRNA comparative information, 75 lncRNA and miRNA interaction pairs, and 31 targeted de mRNAs. Through the differential expression analysis of RNA nodes in the ceRNA regulatory network, we found that compared with the NP group, in the PCa group, there were 14 lncRNAs upregulated and 25 lncRNAs downregulated, 1 miRNA upregulated and 3 miRNA downregulated, and 10 mRNA upregulated and 21 mRNA downregulated. In KEGG enrichment analysis, the pathways identified by targeted DE-mRNAs were mainly related to calcium signaling pathway, EGFR tyrosine kinase inhibitor resistance, melanoma, PI3K−Akt signaling pathway, and proteoglycans in cancer. In animal models, it was found that knocking down AC016773.1 significantly reduced tumor volume and weight, indicating that AC016773.1 may promote the proliferation of PCa cells. The use of RNA immunoprecipitation technology indicates a direct binding between AC016773.1 and hsa-mir-25. Conclusion. We elucidated the network regulatory relationship of lncRNA-miRNA-mRNA in PCa and further explored the key molecular functions, biological pathways, and prognostic value of targeted DE-mRNAs.

MiR-23a-5p alleviates chronic obstructive pulmonary disease through targeted regulation of RAGE-ROS pathway

BackgroundChronic obstructive pulmonary disease (COPD) is a common respiratory disease and represents the third leading cause of death worldwide. This study aimed to investigate miRNA regulation of Receptor for Advanced Glycation End-products (RAGE), a causal receptor in the pathogenesis of cigarette smoke (CS)-related COPD, to guide development of therapeutic strategies.MethodsRAGE expression was quantified in lung tissue of COPD patients and healthy controls, and in mice with CS-induced COPD. RNA-sequencing of peripheral blood from COPD patients with binding site prediction was used to screen differentially expressed miRNAs that may interact with RAGE. Investigation of miR-23a-5p as a potential regulator of COPD progression was conducted with miR-23a-5p agomir in COPD mice in vivo using histology and SCIREQ functional assays, while miR-23a-5p mimics or RAGE inhibitor were applied in 16-HBE human bronchial epithelial cells in vitro. RNA-sequencing, ELISA, and standard molecular techniques were used to characterize downstream signaling pathways in COPD mice and 16-HBE cells treated with cigarette smoke extract (CSE).ResultsRAGE expression is significantly increased in lung tissue of COPD patients, COPD model mice, and CSE-treated 16-HBE cells, while inhibiting RAGE expression significantly reduces COPD severity in mice. RNA-seq analysis of peripheral blood from COPD patients identified miR-23a-5p as the most significant candidate miRNA interaction partner of RAGE, and miR-23a-5p is significantly downregulated in mice and cells treated with CS or CSE, respectively. Injection of miR-23a-5p agomir leads to significantly reduced airway inflammation and alleviation of symptoms in COPD mice, while overexpressing miR-23a-5p leads to improved lung function. RNA-seq with validation confirmed that reactive oxygen species (ROS) signaling is increased under CSE-induced aberrant upregulation of RAGE, and suppressed in CSE-stimulated cells treated with miR-23a-5p mimics or overexpression. ERK phosphorylation and subsequent cytokine production was also increased under RAGE activation, but inhibited by increasing miR-23a-5p levels, implying that the miR-23a-5p/RAGE/ROS axis mediates COPD pathogenesis via ERK activation.ConclusionsThis study identifies a miR-23a-5p/RAGE/ROS signaling axis required for pathogenesis of COPD. MiR-23a-5p functions as a negative regulator of RAGE and downstream activation of ROS signaling, and can inhibit COPD progression in vitro and in vivo, suggesting therapeutic targets to improve COPD treatment.Graphical

MiTDS: Uncovering miRNA-mRNA interactions with deep learning for functional target prediction

MicroRNAs (miRNAs) are vital in regulating gene expression through binding to specific target sites on messenger RNAs (mRNAs), a process closely tied to cancer pathogenesis. Identifying miRNA functional targets is essential but challenging, due to incomplete genome annotation and an emphasis on known miRNA-mRNA interactions, restricting predictions of unknown ones. To address those challenges, we have developed a deep learning model based on miRNA functional target identification, named miTDS, to investigate miRNA–mRNA interactions. miTDS first employs a scoring mechanism to eliminate unstable sequence pairs and then utilizes a dynamic word embedding model based on the transformer architecture, enabling a comprehensive analysis of miRNA-mRNA interaction sites by harnessing the global contextual associations of each nucleotide. On this basis, miTDS fuses extended seed alignment representations learned in the multi-scale attention mechanism module with dynamic semantic representations extracted in the RNA-based dual-path module, which can further elucidate and predict miRNA and mRNA functions and interactions. To validate the effectiveness of miTDS, we conducted a thorough comparison with state-of-the-art miRNA-mRNA functional target prediction methods. The evaluation, performed on a dataset cross-referenced with entries from MirTarbase and Diana-TarBase, revealed that miTDS surpasses current methods in accurately predicting functional targets. In addition, our model exhibited proficiency in identifying A-to-I RNA editing sites, which represents an aberrant interaction that yields valuable insights into the suppression of cancerous processes.

Key Genes in Olfactory Disorder in Experimental Autoimmune Encephalomyelitis Identified by Transcriptomic Analysis of the Olfactory Bulbs.

Experimental autoimmune encephalomyelitis (EAE) is an animal model of multiple sclerosis that shows demyelination in the central nervous system and functional deficits, including olfactory impairment. However, the genes related to olfactory impairment in EAE are unknown. We evaluated hub genes of the olfactory bulb in EAE mice. Differentially expressed genes (cut-offs, fold change > 2 and adjusted p < 0.05) and their related pathways in olfactory bulbs were subjected to gene ontology (GO) pathway analysis, gene set enrichment analysis (GSEA). Protein-protein interactions with selected genes were evaluated using the Search Tool for the Retrieval of Interacting Genes/Proteins. Gene regulatory networks (GRNs) which were constructed at the post-transcriptional level, including the genes-transcription factors (TFs) and gene-microRNAs (miRNAs) interaction networks. Twelve hub genes were found, three of which (Ctss, Itgb2, and Tlr2) were validated by RT-qPCR to be related to GO pathways such as immune response and regulation of immune response. GSEA showed that neuron-related genes-including Atp6v1g2, Egr1, and Gap43-and their pathways were significantly downregulated. GRNs analysis of six genes (Ctss, Itgb2, Tlr2, Atp6v1g2, Egr1, and Gap43) revealed 37 TFs and 84 miRNAs were identified as potential regulators of six genes, indicating significant interaction among six genes, TFs, and miRNAs. Collectively, these results suggest that transcriptomic analysis of the olfactory bulb of EAE mice can provide insight into olfactory dysfunction and reveal therapeutic targets for olfactory impairment.