miRNA Regulation Research Articles

The chromosome-level Elaeagnus mollis genome and transcriptomes provide insights into genome evolution, glycerolipid and vitamin E biosynthesis in seeds

Elaeagnus mollis, which has seeds with high lipid and vitamin E contents, is a valuable woody oil plant with potential for utilization. Currently, the biosynthesis and regulation mechanism of glycerolipids and vitamin E are still unknown in E. mollis. Here, we present the chromosome-level reference genome of E. mollis (scaffold N50: ~40.66Mbp, genome size: ~591.48Mbp) by integrating short-read, long-read, and Hi-C sequencing platforms. A total of 36,796 protein-coding sequences, mainly located on 14 proto-chromosomes, were predicted. Additionally, two whole genome duplication (WGD) events were suggested to have occurred ~54.07 and ~35.06 million years ago (MYA), with Elaeagnaceae plants probably experiencing both WGD events. Furthermore, the long terminal retrotransposons in E. mollis were active ~0.23MYA, and one of them was inferred to insert into coding sequence of the negative regulatory lipid synthesis gene, EMF2. Through transcriptomic and metabonomic analysis, key genes contributing to the high lipid and vitamin E levels of E. mollis seeds were identified, while miRNA regulation was also considered. This comprehensive work on the E. mollis genome not only provides a solid theoretical foundation and experimental basis for the efficient utilization of seed lipids and vitamin E, but also contributes to the exploration of new genetic resources.

Deciphering Immune-related Gene Signatures in Diabetic Retinopathy: Insights from In silico Analysis and In vitro Experiment.

Diabetes retinopathy (DR) is one of the most common microvascular consequences of diabetes, and the economic burden is increasing. Our aim is to decipher the relevant mechanisms of immune-related gene features in DR and explore biomarkers targeting DR. Provide a basis for the treatment and prevention of DR. The immune infiltration enrichment score of DR patients was evaluated from the single- cell RNA sequencing dataset, and the samples were divided into low immune subgroups and high immune subgroups based on this result. Through weighted gene correlation network analysis, differentially expressed genes (DEGs) between two subgroups were identified and crossed with genes with the strongest immune association, resulting in significant key genes. Then divide the DR individuals into two immune related differentially expressed gene (IDEG) clusters, A and B. Submit cross DEGs between two clusters through Gene Set Enrichment Analysis (GSEA) to further explore their functions. A protein-protein interaction (PPI) network of IDEG was established to further identify central genes associated with DR. Use the discovered central genes to predict the regulatory network involved in the pathogenesis of DR. Then, the role of the identified hub gene in the pathogenesis of DR was further studied through in vitro experiments. We found that the immune scores of DR and control groups were different, and 27 IDEGs were found in the DR subgroup. Compared with cluster A, the proportion of cytotoxic lymphocytes, B lineage, monocyte lineage, and fibroblasts in DR patients in cluster B is significantly enriched. GSEA indicates that these genes are associated with T cell activation, regulation of immune response processes, lymphocyte-mediated immunity, TNF signaling pathway, and other signaling pathways. The PPI network subsequently identified 10 hub genes in DR, including SIGLEC10, RGS10, PENK, FGD2, LILRA6, CIITA, EGR2, SIGLEC7, LILRB1, and CD300LB. The upstream regulatory network and lncRNA miRNA mRNA ceRNA network of these hub genes were ultimately constructed. The discovery and identification of these genes will provide biomarkers for targeted prediction and treatment of DR. By integrating bioinformatics analysis and in vitro experiments, we have identified a set of central genes, indicating that these genes can serve as potential biomarkers for DR, which may be promising targets for future DR immunotherapy interventions.

Exercise Alters FBF1-Regulated Novel-miRNA-1135 Associated with Hydrolethalus Syndrome 1 in Rheumatoid Arthritis: A Preliminary Study.

Hydrolethalus Syndrome 1 (HYDS1) is a rare disorder that occurs commonly in Finnish infants but originates from the mother. This autosomal recessive syn-drome is associated with the FBF1, which is usually expressed in the centriole. The FBF1 is an inheritable arthritis disease phenotype that includes rheumatoid arthritis. Several studies have investigated males with FBF1 mutation carriers also related to arthritis diseases, including those under rheumatoid arthritis conditions, which revealed the possibility of conferring the gene mutation to the next generation of offspring. Nonetheless, there are some complications of FBF1 mutation with target miRNAs that can be affected by exercise. The objective of this study was to evaluate the different exercises that can be utilized to suppress the FBF1 mutation targeted by Novel-rno-miRNAs-1135 as a biomarker and assess the effectiveness of exercise in mitigating the FBF1 mutation. Four exercise interventional groups were divided into exercise and non-exercise groups. One hundred microliter pristane-induced arthritis (PIA) was injected at the dorsal re-gion of the tails of rodents and introduced to the two PIA interventional groups. On day forty-five, all animals were euthanized, and total RNA was extracted from the blood samples of ro-dents, while polymerase chain reaction (PCR) was amplified by using 5-7 primers. Computeri-zation was used for miRNA regulation and analysis of target gene candidates. The novel-rno-miRNA-1135 was downregulated to FBF1 in exercise groups. The exercise was found to have no significant impact in terms of change in novel-rno-miRNA-1135 regulation of FBF1 expression. Exercise has no impact on novel-rno-miRNA-1135 targeted for FBF1 in autoso-mal recessive disease.

MiR-195-5p inhibits cisplatin resistance in lung adenocarcinoma by regulating DNA damage via targeting E2F7.

Lung adenocarcinoma (LUAD) emerges as one of the most lethal malignant tumors worldwide. Platinum-based combination chemotherapy remains one of the main methods for patients with advanced LUAD. Due to the resistance, the effect of this chemotherapy was not satisfactory. Therefore, studying the mechanism of cisplatin (DDP) resistance is essential for promoting the effect of this therapeutic strategy. Therefore, this work sought to probe the impact of E2F Transcription Factor 7 (E2F7) on LUAD resistance and the molecular regulatory mechanism. The mRNA expression level of the target gene E2F7 in LUAD was predicted by bioinformatics analysis, and regulatory miRNA upstream of the target gene was identified. The mRNA and protein expression of E2F7 in LUAD cells was detected through quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) and Western blot, respectively. The expression of miR-195-5p in LUAD cells was measured via qRT-PCR. E2F7 high and low expression groups underwent enrichment analysis by utilizing Gene Set Enrichment Analysis software. The targeting relationship of miR-195-5p and E2F7 was validated by conducting a dual-luciferase reporter assay. The cell viability was tested through cell counting kit-8. The cell cycle was examined by flow cytometry. DNA damage level was determined via Comet assay and Western blot assay. The findings indicated that the mRNA and protein levels of E2F7 were high in LUAD. MiR-195-5p was the regulatory miRNA upstream of E2F7, and lowly expressed in LUAD. The cell experiments suggested that E2F7 advanced the DDP resistance of LUAD cells by repressing DNA damage. Finally, the rescue assay manifested that miR-195-5p overexpression could abate inhibition of E2F7 overexpression on the DNA damage and the DDP sensitivity of LUAD cells. MiR-195-5p raised the DDP sensitivity of LUAD cells by advancing the DNA damage in LUAD cells via inhibition of E2F7.

A comprehensive study of genetic regulation and disease associations of plasma circulatory microRNAs using population-level data.

MicroRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate gene expression. Perturbations in plasma miRNA levels are known to impact disease risk and have potential as disease biomarkers. Exploring the genetic regulation of miRNAs may yield new insights into their important role in governing gene expression and disease mechanisms. We present genome-wide association studies of 2083 plasma circulating miRNAs in 2178 participants of the Rotterdam Study to identify miRNA-expression quantitative trait loci (miR-eQTLs). We identify 3292 associations between 1289 SNPs and 63 miRNAs, of which 65% are replicated in two independent cohorts. We demonstrate that plasma miR-eQTLs co-localise with gene expression, protein, and metabolite-QTLs, which help in identifying miRNA-regulated pathways. We investigate consequences of alteration in circulating miRNA levels on a wide range of clinical conditions in phenome-wide association studies and Mendelian randomisation using the UK Biobank data (N = 423,419), revealing the pleiotropic and causal effects of several miRNAs on various clinical conditions. In the Mendelian randomisation analysis, we find a protective causal effect of miR-1908-5p on the risk of benign colon neoplasm and show that this effect is independent of its host gene (FADS1). This study enriches our understanding of the genetic architecture of plasma miRNAs and explores the signatures of miRNAs across a wide range of clinical conditions. The integration of population-based genomics, other omics layers, and clinical data presents opportunities to unravel potential clinical significance of miRNAs and provides tools for novel miRNA-based therapeutic target discovery.

Association of SLC19A1 Gene Polymorphisms and Its Regulatory miRNAs with Methotrexate Toxicity in Children with Acute Lymphoblastic Leukemia.

Methotrexate (MTX) is an anti-folate chemotherapeutic agent that is considered to be a gold standard in Acute Lymphoblastic Leukemia (ALL) therapy. Nevertheless, toxicities induced mainly due to high doses of MTX are still a challenge for clinical practice. MTX pharmacogenetics implicate various genes as predictors of MTX toxicity, especially those that participate in MTX intake like solute carrier family 19 member 1 (SLC19A1). The aim of the present study was to evaluate the association between SLC19A1 polymorphisms and its regulatory miRNAs with MTX toxicity in children with ALL. A total of 86 children with ALL were included in this study and were all genotyped for rs2838958, rs1051266 and rs1131596 SLC19A1 polymorphisms as well as the rs56292801 polymorphism of miR-5189. Patients were followed up (48, 72 and 96 h) after treatment with MTX in order to evaluate the presence of MTX-associated adverse events. Our results indicate that there is a statistically significant correlation between the rs1131596 SLC19A1 polymorphism and the development of MTX-induced hepatotoxicity (p = 0.03), but there is no significant association between any of the studied polymorphisms and mucositis or other side effects, such as nausea, emesis, diarrhea, neutropenia, skin rash and infections. In addition, when genotype TT of rs1131596 and genotype AA of rs56292801 are both present in a patient then there is a higher risk of developing severe hepatotoxicity (p = 0.0104).

The effects of fumonisin B1 on intercellular communications and miRNA modulations: Non-genotoxic carcinogenesis mechanisms in human kidney cells

Fumonisin B1 (FB1), which is produced by Fusarium species, is one of the most prevalent mycotoxins known to exert several toxic effects, particularly nephrotoxicity. While its genotoxic carcinogenic mechanisms have been extensively studied, its influence on non-genotoxic pathways including intercellular communication and microRNA (miRNA) regulation remain underexplored. The present study investigates the effects of FB1 on gap junctions, miRNA expression profiles, and their relationship in human kidney cells (HK-2 and HEK293). Both cell lines showed increased apoptosis rates at 50 and 100 µM, while FB1 exposure significantly reduced gap junctional intercellular communication (GJIC) and decreased the expression levels of related genes, including Cx43, Cx45, e-cadherin, Cadherin-2, and β-catenin. After FB1 treatments alteration on the regulation of miRNAs including let-7a-5p, miR-125a-5p, miR-222–3p, miR-92a-3p, let-7b-5p, let-7e-5p, miR-21–5p, miR-155–5p, let-7i-5p, let-7d-5p, let-7f-5p, miR-181b-5p, miR-15b-5p, miR-23b-3p, miR-20b-5p, miR-196a-5p miRNAs have been shown. Let-7a-5p was selected among the altered miRNAs to elucidate the relationship between miRNAs and GJIC after FB1 exposure as it is one of the common miRNAs that changes in both cell lines and one of its target genes is Cx45, which is an important gene for GJIC. However, transfection analysis did not show any differences, resulting in Cx45 not being a direct target of let-7a-5p in HK-2 and HEK-293 cells. Through comprehensive analysis, we elucidated that FB1's impact on intercellular signaling cascades and its regulatory role on miRNA expression profiles, offering valuable insights into carcinogenesis beyond traditional genotoxic paradigms. Understanding these mechanisms is crucial for elucidating the mechanisms of FB1-induced toxicity.

Systems analysis of miR-199a/b-5p and multiple miR-199a/b-5p targets during chondrogenesis

Changes in chondrocyte gene expression can contribute to the development of osteoarthritis (OA), and so recognition of the regulative processes during chondrogenesis can lead to a better understanding of OA. microRNAs (miRNAs) are key regulators of gene expression in chondrocytes/OA, and we have used a combined experimental, bioinformatic, and systems biology approach to explore the multiple miRNA–mRNA interactions that regulate chondrogenesis. A longitudinal chondrogenesis bioinformatic analysis identified paralogues miR-199a-5p and miR-199b-5p as pro-chondrogenic regulators. Experimental work in human cells demonstrated alteration of miR-199a-5p or miR-199b-5p expression led to significant inverse modulation of key chondrogenic genes and extracellular matrix production. miR-199a/b-5p targets FZD6, ITGA3 and CAV1 were identified by inhibition experiments and verified as direct targets by luciferase assay. The experimental work was used to generate and parameterise a multi-miRNA 14-day chondrogenesis kinetic model to be used as a repository for the experimental work and as a resource for further investigation of this system. This is the first multi-miRNA model of a chondrogenesis-based system, and highlights the complex relationships between regulatory miRNAs, and their target mRNAs.

Genomic Analysis and Expression Dynamics of GH3 Genes Under Abiotic Stresses in Brassica rapa

ABSTRACTIn silico characterization of the Gretchen Hagen3 (GH3) gene family is required for understanding phytohormone regulation and stress responses in Brassica rapa to develop the improved stress‐tolerant cultivars. The main objective of this research was to identify the key BrGH3 genes under different abiotic stresses. Using bioinformatics tools, a total of 27 BrGH3 genes were identified in B. rapa for which phylogenetic relationship, syntenic pairing, conserved motifs, miRNA regulation, and cis‐regulatory elements of BrGH3s were also studied. BrGH3 gene expression has been examined in numerous tissues and under various abiotic and phytohormone stressors. Phylogenetic studies separated BrGH3 genes into three major classes and nine subclasses based on gene functional evolution. Collinearity analysis demonstrated that all BrGH3 genes had syntenic linkage with AtGH3, BnaGH3, and BolGH3, indicating that genome duplication mechanisms were crucial to BrGH3 gene evolution. The expression dynamics of BrGH3 under diverse phytohormonal stresses methyl jasmonate (MeJA), auxin (IAA), abscisic acid (ABA), gibberellic acid (GA), and salicylic acid (SA) at different time intervals suggest that BrGH3‐5.1 has a consistently greater expression than other BrGH3 genes. Under salt, drought, and low temperature stress, BrGH3‐1 and BrGH3‐4 genes expressed comparatively higher. The findings suggest that five genes (BrGH3‐5.1, BrGH3‐5.2, BrGH3‐15, BrGH3‐17.2, and BrGH3‐19) have a key role in inducing broad stress resilience. These results can be beneficial in developing stress‐tolerant varieties of Chinese cabbage.

5178 TNFα-dependent altered miRNA expression regulates endometrial stromal cell proliferation

Abstract Disclosure: I. Chowdhury: None. S. Banerjee: None. W. Xu: None. A. Driss: None. C. Nezhat: None. N. Sidell: None. R.N. Taylor: None. W.E. Thompson: None. Abstract: Aberrant upregulation of cytokines, including tumor necrosis factor α (TNFα) and activation of nuclear factor κB (NF-κB) with disbalance of microRNAs (miRNAs) are often found in endometrium of endometriosis subjects, which causes directly or indirectly pelvic inflammation, pain, and infertility, Although, the pathophysiology of endometriosis is not clearly established yet, inflammation is an essential feature. MicroRNAs are emerging as potential regulatory factors in cellular processes such as cell growth, survival, migration, and invasion. In the current study, we examined the direct effects of exogenous recombinant TNFα dependent regulation of miRNAs involved in proliferation in primary cultures of normal endometrial stromal cells (NESC) and compared with the untreated cells derived from endometriosis-ESC (EESC). NanoString nCounter-based assays and quantitative real-time polymerase chain reaction (RT-PCR) were used to identify and validate differentially expressed miRNAs linked to cell proliferation in EESC compared to NESC and TNFα treated NESCs. The expression level of miRNAs linked to cell cycle was downregulated significantly in EESCs compared to NESCs. Interestingly, a dose and time-dependent exogenous TNFα treatment in NESCs showed a similar cell cycle regulator miRNAs expression pattern with EESCs. In further studies, protein analysis by Western Blots of selective cell cycle regulators such as PCNA, Ki67, CDK2, CDK4, CDK6, p21, and p27, and cell proliferation assay demonstrated an inverse correlation between cell cycle regulators and miRNA expression pattern both in EESC and TNFα treated NESCs. These findings suggest that TNFα dependent dysregulation of miRNAs in EESCs may promote proliferation of endometriosis. Further research is needed to investigate the detailed mechanisms by which TNFα regulates miRNA expression and determine these findings' potential therapeutic implications. Acknowledgments: This study was supported in part by National Institutes of Health Grants 1SC3 GM113751, 1SC1 GM130544, U01 HD66439, 1R01HD057235, U54 CA118948, HD41749, S21MD000101, and G12-RR03034. This investigation was conducted in a facility constructed with support from Research Facilities Improvement Grant #C06 RR18386 from NIH/NCRR. Presentation: 6/2/2024

Shedding light on the DICER1 mutational spectrum of uncertain significance in malignant neoplasms.

The Dicer protein is an indispensable player in such fundamental cell pathways as miRNA biogenesis and regulation of protein expression in a cell. Most recently, both germline and somatic mutations in DICER1 have been identified in diverse types of cancers, which suggests Dicer mutations can lead to cancer progression. In addition to well-known hotspot mutations in RNAase III domains, DICER1 is characterized by a wide spectrum of variants in all the functional domains; most are of uncertain significance and unstated clinical effects. Moreover, various new somatic DICER1 mutations continuously appear in cancer genome sequencing. The latest contemporary methods of variant effect prediction utilize machine learning algorithms on bulk data, yielding suboptimal correlation with biological data. Consequently, such analysis should be conducted based on the functional and structural characteristics of each protein, using a well-grounded targeted dataset rather than relying on large amounts of unsupervised data. Domains are the functional and evolutionary units of a protein; the analysis of the whole protein should be based on separate and independent examinations of each domain by their evolutionary reconstruction. Dicer represents a hallmark example of a multidomain protein, and we confirmed the phylogenetic multidomain approach being beneficial for the clinical effect prediction of Dicer variants. Because Dicer was suggested to have a putative role in hematological malignancies, we examined variants of DICER1 occurring outside the well-known hotspots of the RNase III domain in this type of cancer using phylogenetic reconstruction of individual domain history. Examined substitutions might disrupt the Dicer function, which was demonstrated by molecular dynamic simulation, where distinct structural alterations were observed for each mutation. Our approach can be utilized to study other multidomain proteins and to improve clinical effect evaluation.

Cancer Pathways Targeted by Berberine: Role of microRNAs.

Cancer is a complex and heterogeneous malignant disease. Due to its multifactorial nature, including progressive changes in genetic, epigenetic, transcript, and protein levels, conventional therapeutics fail to save cancer patients. Evidence indicates that dysregulation of microRNA (miRNA) expression plays a crucial role in tumorigenesis, metastasis, cell proliferation, differentiation, metabolism, and signaling pathways. Moreover, miRNAs can be used as diagnostic and prognostic markers and therapeutic targets in cancer. Berberine, a naturally occurring plant alkaloid, has a wide spectrum of biological activities in different types of cancers. Inhibition of cell proliferation, metastasis, migration, invasion, and angiogenesis, as well as induction of cell cycle arrest and apoptosis in cancer cells, is reported by berberine. Recent studies suggested that berberine regulates many oncogenic and tumor suppressor miRNAs implicated in different phases of cancer. This review discussed how berberine inhibits cancer growth and propagation and regulates miRNAs in cancer cells. And how berberine-mediated miRNA regulation changes the landscape of transcripts and proteins that promote or suppress cancer progression. Overall, the underlying molecular pathways altered by berberine and miRNA influencing the tumor pathophysiology will enhance our understanding to combat the malignancy.

Peripheral Brain-Derived Neurotrophic Factor (BDNF) and Its Regulatory miRNAs as Biological Correlates of Impulsivity in Young Adults.

Background: Impulsivity assessment may serve as a valuable clinical tool in the stratification of suicide risk. Acting without forethought is a crucial feature in the psychopathology of many psychiatric disturbances and corresponds with suicidal ideations, behaviors, and attempts. Methods: We present data on biological and psychological correlates of impulsivity among young adults (n = 47). Psychological analysis included both the self-description questionnaire-Barratt Impulsiveness Scale (BIS-11)-and neuropsychological behavioral tests, including the Iowa Gambling Task (IGT), the Simple Response Time task (SRT), and the Continuous Performance Test (CPT). mRNA and micro-RNA were isolated from peripheral blood mononuclear cells (PBMC). Expression levels of Brain-Derived Neurotrophic Factor (BDNF) mRNA and its regulatory micro RNAs, mir-1-3p, mir-15a-5p, mir-26a-5p, mir-26b-5p, and mir-195-5p, were analyzed using the quantitative reverse transcription polymerase chain reaction (RT-qPCR) method. proBDNF and BDNF plasma protein levels were quantified using enzyme-linked immunosorbent assay (ELISA). Results: Significant correlations between BDNF mRNA and mir-15a-5p as well as proBDNF levels and mir-1-3p were detected. proBDNF protein levels correlated with motor and perseverance, while mir-26b correlated with cognitive complexity subdimensions of the BIS-11 scale. Correlations between BDNF, miRNAs, and the results of neuropsychological tests were also detected. Conclusions: The BDNF pathway shows a clinical potential in searching for biomarkers of impulse-control impairment. BDNF-regulatory micro-RNAs are detectable and related to clinical parameters in the studied population, which needs further research.

Scanning sample-specific miRNA regulation from bulk and single-cell RNA-sequencing data

BackgroundRNA-sequencing technology provides an effective tool for understanding miRNA regulation in complex human diseases, including cancers. A large number of computational methods have been developed to make use of bulk and single-cell RNA-sequencing data to identify miRNA regulations at the resolution of multiple samples (i.e. group of cells or tissues). However, due to the heterogeneity of individual samples, there is a strong need to infer miRNA regulation specific to individual samples to uncover miRNA regulation at the single-sample resolution level.ResultsHere, we develop a framework, Scan, for scanning sample-specific miRNA regulation. Since a single network inference method or strategy cannot perform well for all types of new data, Scan incorporates 27 network inference methods and two strategies to infer tissue-specific or cell-specific miRNA regulation from bulk or single-cell RNA-sequencing data. Results on bulk and single-cell RNA-sequencing data demonstrate the effectiveness of Scan in inferring sample-specific miRNA regulation. Moreover, we have found that incorporating the prior information of miRNA targets can generally improve the accuracy of miRNA target prediction. In addition, Scan can contribute to construct cell/tissue correlation networks and recover aggregate miRNA regulatory networks. Finally, the comparison results have shown that the performance of network inference methods is likely to be data-specific, and selecting optimal network inference methods is required for more accurate prediction of miRNA targets.ConclusionsScan provides a useful method to help infer sample-specific miRNA regulation for new data, benchmark new network inference methods and deepen the understanding of miRNA regulation at the resolution of individual samples.

EXPRESS:Molecular Mechanisms of Ferroptosis in Renal Ischemia-Reperfusion Injury Investigated via Bioinformatics Analysis and Animal Experiments.

Kidney transplantation is a pivotal treatment for end-stage renal disease (ESKD). However, renal ischemia-reperfusion injury (IRI) during surgery significantly impacts graft function. Despite unclear molecular mechanisms, no specific therapies or preventative measures are available. Gene expression profiles from renal biopsies before and after IRI were downloaded from public databases. Differentially expressed genes (DEGs) were identified using the Wilcoxon rank-sum test and weighted gene co-expression network analysis. Ferroptosis-associated genes were screened using the FerrDb database. The genes with the highest connectivity were identified via the PPI network, and upstream regulatory miRNAs were found through the gene-miRNA network. A mouse renal IRI model was constructed for transcriptome sequencing and qRT-PCR validation to elucidate the relationship between key ferroptosis genes and regulatory miRNAs in renal IRI. Differential analysis identified 15 ferroptosis-associated genes (TNFAIP3, IL6, KLF2, EGR1, JUN, ZFP36, GDF15, CDKN1A, HSPB1, BRD2, PDK4, DUSP1, SLC2A3, DDIT3, CXCL2) involved in renal IRI regulation. In animal experiments, ferroptosis-related genes were also upregulated in the model group. Enrichment analysis and H&E pathological staining suggested these genes are primarily involved in renal inflammatory responses. PPI network analysis revealed IL6 as the gene with the highest connectivity, and the gene-miRNA network indicated IL6 might be regulated by miR-let-7a. Animal experiments revealed decreased miR-let-7a and increased IL6 levels in the model group, identifying potential therapeutic targets. MiR-let-7a regulates ferroptosis in renal IRI by targeting IL6, highlighting IL6 as a crucial gene in the ferroptosis process of renal IRI.

Exogenous Janus Kinase 617 Codon Influences Small Noncoding RNAs and Gene Expression in Ba/F3 Cells.

Myeloproliferative neoplasms (MPNs) are blood cancers caused by mutations that originate from hematopoietic stem cells. More than 50%-90% of MPN patients had a dominant negative valine (V) to phenylalanine (F) mutation at the Janus kinase 617 codon (JAK2V617F) within the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling pathway; however, this mutation was also found in a high percentage of the general population, its penetrance varied, and its onset was shown to be polygenic. Consequently, it is still unknown what molecular mechanism underlies the MPN transformation produced by JAK2V617F. Patients with MPN have been shown to have dysregulation of noncoding RNAs, such as microRNA (miRNA) and PIWI-interacting RNA (piRNA), although there is not any concrete proof that JAK2V617F alone is responsible for the aberrant regulation of miRNA and piRNA. Human wild type versus V617F-mutated JAK2 are expressed in mouse Ba/F3 cells, and the expressed small and total RNAs were subjected to next generation sequencing analysis to determine the direct induction. Differentially expressed miRNAs, gene expression, and transcript and gene variations were found between exogenously expressed JAK2 and JAK2V617F in Ba/F3 cells. The differently expressed variations contained enriched transposable elements and piRNAs, indicating a rearranged epigenome. The results of the pathway analysis show that the transformation that self-validated the chosen sequencing target genes is impacted by the JAK-STAT pathway. The induction route is functionally conserved, according to exogenously produced miRNA and gene expression. These results may clarify how the JAK2V617F induces transformation.

MiR-24-3p inhibits lipid synthesis and progesterone secretion in chicken granulosa cells via ERK1/2 signaling pathway

Normal follicular development is the basis for ovulation in poultry. Our previous sequencing analysis revealed a high expression of miR-24-3p in chicken follicles from degenerated ovaries, suggesting that miR-24-3p may modulate follicular development. Hence, this study investigated the specific mechanisms of miR-24-3p in regulating chicken follicular development. The results revealed that the proliferation, lipid synthesis, and progesterone secretion were significantly inhibited after miR-24-3p overexpression in chicken granulosa cells, vice versa by miR-24-3p knockdown. Dual-specificity phosphatase 16 (DUSP16) and thousand and one amino acid kinase 1 (TAOK1) were identified as potential target genes of miR-24-3p. Further validation revealed that knockdown of DUSP16 and TAOK1 suppressed proliferation, lipid synthesis, and progesterone secretion in chicken granulosa cells. Moreover, we observed that miR-24-3p, along with knockdown of DUSP16 and TAOK1, increased the phosphorylation levels of extracellular signal-regulated kinases 1 and 2 (ERK1/2). Our previous study proved that activation of ERK1/2 inhibited lipid synthesis and progesterone secretion of chicken granulosa cells. In summary, we demonstrated that miR-24-3p targeting DUSP16 and TAOK1 disrupts lipid synthesis and progesterone secretion via ERK1/2 signaling pathway in chicken granulosa cells in vitro. These results may provide a new theoretical basis for resolving miRNAs regulation on reproductive performance of chickens.

MicroRNA and Rare Human Diseases

Background: The role of microRNAs (miRNAs) in the pathogenesis of rare genetic disorders has been gradually discovered. MiRNAs, a class of small non-coding RNAs, regulate gene expression by silencing target messenger RNAs (mRNAs). Their biogenesis involves transcription into primary miRNA (pri-miRNA), processing by the DROSHA–DGCR8 (DiGeorge syndrome critical region 8) complex, exportation to the cytoplasm, and further processing by DICER to generate mature miRNAs. These mature miRNAs are incorporated into the RNA-induced silencing complex (RISC), where they modulate gene expression. Methods/Results: The dysregulation of miRNAs is implicated in various Mendelian disorders and familial diseases, including DICER1 syndrome, neurodevelopmental disorders (NDDs), and conditions linked to mutations in miRNA-binding sites. We summarized a few mechanisms how miRNA processing and regulation abnormalities lead to rare genetic disorders. Examples of such genetic diseases include hearing loss associated with MIR96 mutations, eye disorders linked to MIR184 mutations, and skeletal dysplasia involving MIR140 mutations. Conclusions: Understanding these molecular mechanisms is crucial, as miRNA dysregulation is a key factor in the pathogenesis of these conditions, offering significant potential for the diagnosis and potential therapeutic intervention.

Non-Linear Relationship between MiRNA Regulatory Activity and Binding Site Counts on Target mRNAs

MicroRNAs (miRNA) exert regulatory actions via base pairing with their binding sites on target mRNAs. Cooperative binding, i.e., synergism, among binding sites on an mRNA is biochemically well characterized. We studied whether this synergism is reflected in the global relationship between miRNA-mediated regulatory activity and miRNA binding site count on the target mRNAs, i.e., leading to a non-linear relationship between the two. Recently, using our own and public datasets, we have enquired into miRNA regulatory actions: first, we analyzed the power-law distribution pattern of miRNA binding sites; second, we found that, strikingly, mRNAs for core miRNA regulatory apparatus proteins have extraordinarily high binding site counts, forming self-feedback-control loops; third, we revealed that tumor suppressor mRNAs generally have more sites than oncogene mRNAs; and fourth, we characterized enrichment of miRNA-targeted mRNAs in translationally less active polysomes relative to more active polysomes. In these four studies, we qualitatively observed obvious positive correlation between the extent to which an mRNA is miRNA-regulated and its binding site count. This paper summarizes the datasets used. We also quantitatively analyzed the correlation by comparative linear and non-linear regression analyses. Non-linear relationships, i.e., accelerating rise of regulatory activity as binding site count increases, fit the data much better, conceivably a transcriptome-level reflection of cooperative binding among miRNA binding sites on a target mRNA. This observation is potentially a guide for integrative quantitative modeling of the miRNA regulatory system.

Regulation of idiopathic pulmonary fibrosis: a cross-talk between TGF-β signaling and MicroRNAs.

Pulmonary fibrosis (PF) is a highly complex and challenging disease affecting the respiratory system. Patients with PF usually have an abbreviated survival period and a consequential high mortality rate after the diagnosis is confirmed, posing serious threats to human health. In clinical practice, PF is typically treated by antifibrotic agents, such as Pirfenidone and Nintedanib. However, these agents have been reported to correlate with substantial adverse effects, escalating costs, and insufficient efficacy. Moreover, it remains unclarified about the multifactorial pathology of PF. Therefore, there is an urgent demand for elucidating these underlying mechanisms and identifying safe, efficient, and targeted therapeutic strategies for PF treatment. The crucial role of the transforming growth factor-β (TGF-β) signaling pathway in PF development has been explored in many studies. MicroRNAs (miRNAs), which function as post-transcriptional regulators of gene expression, can significantly affect the development of PF by modulating TGF-β signaling. In turn, TGF-β signaling can regulate the expression and biogenesis of miRNAs, thereby substantially affecting the progression of PF. Hence, the therapeutic strategies that focus on the drug-targeted regulation of miRNAs, either by augmenting down-regulated miRNAs or inhibiting overexpressed miRNAs, may hinder the pathways related to TGF-β signaling. These strategies may contribute to the prevention and suppression of PF progression and may provide novel insights into the treatment of this disease.