Differential miRNA Research Articles

P0255 Predictive potential of microRNA expression for Juvenile Idiopathic Arthritis development in paediatric Inflammatory Bowel Disease

Abstract Background Children diagnosed with inflammatory bowel disease (IBD) often experience a more severe disease course than adults, and up to 50% develop extra-intestinal manifestations (EIMs).1 The most common EIM is juvenile idiopathic arthritis (JIA), affecting approximately 16–33% of paediatric patients with IBD, increasing risks of long-term complications such as uveitis, joint destruction, reduced physical activity, and psychological challenges.2 MicroRNAs (miRNAs) are small, non-coding RNA molecules that regulate gene expression and play key roles in immune and inflammatory processes. They hold potential as biomarkers and therapeutic targets in IBD, offering opportunities for advancements in early diagnosis and treatment.3 The aim of this study was to investigate whether miRNA expressed in intestinal biopsies can identify paediatric patients with IBD at risk of developing JIA. Methods Paediatric patients under 18 years of age diagnosed with IBD between 1 May 2021 and 1 May 2024, along with healthy controls from the Copenhagen IBD Inception Cohort, were enrolled.4 One mucosal biopsy from either the ileum or colon was collected from each patient during their index endoscopy. Additionally, biopsies from paediatric patients diagnosed with both IBD and JIA (IBD-JIA) prior to 1 May 2021 were retreived from the Department of Pathology at Copenhagen University Hospital, Hvidovre. Total RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue, and miRNA expression was analysed using the GeneChip™ microarray platform. Results The study included 62 biopsies from 62 patients (27 with IBD, 25 with both IBD and JIA (IBD-JIA), and 10 HC). Patient characteristics are shown in table 1. Analysis identified 532 significantly differentially expressed probe sets (adjusted p<0.05) among IBD, IBD-JIA, and HC (Figure 1). Among these, 123 probe sets, including miR-486-2, let-7b-5p, and miR-92a-3p, exhibited a more than two-fold change (adjusted p<0.001) between IBD and IBD-JIA, with 120 miRNAs upregulated and 3 downregulated in IBD-JIA compared to IBD. Conclusion This study provides the first evidence of differential miRNA expression in paediatric patients with IBD and co-occurring JIA. These miRNAs may serve as novel biomarkers for the early detection, aiding in timely diagnosis and better management of paediatric IBD patients.

Exploring the Mechanism of Acupuncture in Improving Ovarian Function in Rats with Poor Ovarian Response Using High-Throughput Sequencing.

This study aimed to investigate the possible mechanism through which acupuncture protects ovaries with Poor Ovarian Response (POR) in rats based on microRNA (miRNA). Thirty-six SPF SD female non-pregnant rats aged 8 weeks were randomly divided into the blank group, model group, and acupuncture group, with 12 rats in each group. According to the group, the rats were given gavage of Tripterygium wilfordii polyglycosides suspension for 14 days to establish the model of POR, and then the rats were treated with acupuncture for 2 weeks, once a day, for 20 minutes. Afterward, their hormone levels were measured, and HE staining was performed on the ovaries after the intervention. Three rats from each group were randomly selected for ovarian tissue miRNA sequencing, and differential miRNAs were subjected to Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway analysis, and Quantitative Polymerase Chain Reaction (QPCR) verification. By using TargetScan to predict the target genes of differential miRNAs, we validated the results with a dual luciferase reporter gene assay. Compared with the blank group, the estrus cycle of the model group was significantly prolonged (P<0.01). Anti-Müllerian Hormone (AMH) (P<0.01) and Estrogen (E2) were significantly decreased (P<0.05). Follicle-Stimulating Hormone (FSH)(P<0.05) and Luteinizing Hormone (LH) increased sharply (P<0.01). Compared with the model group, the estrus cycle was significantly shortened in the acupuncture group (P<0.01). AMH and E2 were markedly raised (P<0.05). FSH (P<0.05) and LH (P<0.01) were significantly declined. miRNA sequencing showed that there were 23 miRNAs significantly different between the model group and the blank group (P<0.05), and 30 miRNAs significantly different between the acupuncture group and the model group (P<0.05). GO demonstrated that the network was mainly involved in cellular components, cells, cellular metabolic processes, binding, and single biological processes; KEGG signaling pathway enrichment showed that it was mainly related to MAPK, adhesion junction, calcium signaling pathways, etc. Q-PCR results showed that after modeling, the expression rose, and after acupuncture, the expression of the following miRNA decreased: miR-154-5p (P<0.01), miR-300-5p (P < 0.05), miR-376c-5p (P<0.05). The dual luciferase reporter assay showed that the relative luciferase activity of the miR-300-5p mimics+MAP3K1-WT group was significantly lower than that of the NC+MAP3K1-WT group (P<0.01). HE results demonstrated that the number of primordial follicles and primary follicles in the model group was significantly lower than that in the blank group (P<0.05). Moreover, the morphology was poorer, and the granulosa cell layer was thinner. Compared with the model group, the number of primary follicles in the acupuncture group increased (P<0.05); the morphology and granulosa cell structure of the ovary were improved to different degrees, and mature follicles could be seen. Acupuncture may improve the ovarian responsiveness of POR rats by regulating miR-154- 5p,miR-300-5p, and miR-376c-5p. Furthermore, miR-300-5p can specifically bind to the 3'-UTR of MAP3K1, and MAP3K1 may be the target of miR-300-5p.

Differential expressions of exosomal miRNAs in patients with chronic heart failure and hyperuricemia: diagnostic values of miR-27a-5p and miR-139-3p.

To analyze the differentially expressed exosomal miRNAs in patients with chronic heart failure (CHF) complicated by hyperuricemia (HUA) and explore their potential as novel diagnostic molecular markers and their target genes. This study was conducted among 30 CHF patients with HUA (observation group) and 30 healthy volunteers (control group) enrolled between September, 2020 and September, 2023. Peripheral blood samples were collected from 6 CHF patients with HUA for analyzing exosomal miRNAs by high-throughput sequencing, and the results were validated in the remaining 24 patients using qRT-PCR. GO and KEGG enrichment analyses were performed to predict the the target genes of the identified differential miRNAs. We also validated the differentially expressed miRNAs by animal experiment. A total of 42 differentially expressed exosomal miRNAs were detected in observation group by high-throughput sequencing; among them, miR-27a-5p was significantly upregulated (P=0.000179), and miR-139-3p was significantly downregulated (P=0.000058). In the 24 patients with both CHF and PUA, qRT-PCR validated significant upregulation of miR-27a-5p (P=0.004) and downregulation of miR-139-3p (P=0.005) in serum exosomes. When combined, miR-27a-5p and miR-139-3p had a maximum area under the curve (AUC) of 0.899 (95% CI: 0812-0.987) for predicting CHF complicated by HUA. GO and KEGG enrichment analyses suggested that the differential expressions of miR-27a-5p and miR-139-3p was associated with the activation of the AMPK-mTOR signaling pathway to activate the autophagic response. We obtained the same conclusion from animal experiment. Upregulated exosomal miR-27a-5p combined with downregulated exosomal miR-139-3p expression can serve as a novel molecular marker for diagnosis of CHF complicated by HUA, and their differential expression may promote autophagy in cardiomyocytes by activating the AMPK-mTOR signaling pathway.

Inferring single-cell and spatial microRNA activity from transcriptomics data

The activity of miRNA varies across different cell populations and systems, as part of the mechanisms that distinguish cell types and roles in living organisms and in human health and disease. Typically, miRNA regulation drives changes in the composition and levels of protein-coding RNA and of lncRNA, with targets being down-regulated when miRNAs are active. The term “miRNA activity" is used to refer to this transcriptional effect of miRNAs. This study introduces miTEA-HiRes, a method designed to facilitate the evaluation of miRNA activity at high resolution. The method applies to single-cell transcriptomics, type-specific single-cell populations, and spatial transcriptomics data. By comparing different conditions, differential miRNA activity is inferred. For instance, miTEA-HiRes analysis of peripheral blood mononuclear cells comparing Multiple Sclerosis patients to control groups revealed differential activity of miR-20a-5p and others, consistent with the literature on miRNA underexpression in Multiple Sclerosis. We also show miR-519a-3p differential activity in specific cell populations.

Decorin-mediated dermal papilla cell-derived exosomes regulate hair follicle growth and development through miR-129-2-3p/SMAD3/TGF-β axis.

Decorin (DCN) is a member of the small leucine-rich proteoglycan family within the extracellular matrix, playing a role in the growth and development of hair follicle (HF). Exosomes serve as significant mediators of intercellular communication and are involved in the cyclic regeneration of HF. Exosomes derived from dermal papilla cells (DPC-Exos) are essential for the cycling and regrowth of HF. The present study demonstrated that DCN treatment significantly enhances the proliferation of DPCs, thereby promoting hair follicle growth. miRNA sequencing revealed 442 differentially expressed exosomal miRNAs. The regulatory mechanism of exosomal miR-129-2-3p, an up-regulated differential miRNA, was further investigated. The study identified its role in transporting DPCs to HFSCs through DPC-Exos. miR-129-2-3p has been shown to suppress the expression of genes associated with HF growth and development, lower the expression of genes and proteins downstream of the TGF-β signaling pathway, promote HFSC proliferation, and decrease HFSC apoptosis. Furthermore, miR-129-2-3p displayed an antagonistic effect on activating the TGF-β/SMAD3 signaling pathway induced by SRI-011381. The findings indicate that DCN-mediated DPC-Exos influence HF growth and development through the miR-129-2-3p/SMAD3/TGF-β regulatory axis. These results may facilitate novel strategies for the diagnosis and treatment of human hair disorders, in addition to enhancing industrial wool production.

Integration of miRNA expression analysis of purified leukocytes and whole blood reveals blood-borne candidate biomarkers for lung cancer

ABSTRACT Changes in leukocyte populations may confound the disease-associated miRNA signals in the blood of cancer patients. We aimed to develop a method to detect differentially expressed miRNAs from lung cancer whole blood samples that are not influenced by variations in leukocyte proportions. The Ref-miREO method identifies differential miRNAs unaffected by changes in leukocyte populations by comparing the within-sample relative expression orderings (REOs) of miRNAs from healthy leukocyte subtypes and those from lung cancer blood samples. Over 77% of the differential miRNAs observed between lung cancer and healthy blood samples overlapped with those between myeloid-derived and lymphoid-derived leukocytes, suggesting the potential impact of changes in leukocyte populations on miRNA profile. Ref-miREO identified 16 differential miRNAs that target 19 lung adenocarcinoma-related genes previously linked to leukocytes. These miRNAs showed enrichment in cancer-related pathways and demonstrated high potential as diagnostic biomarkers, with the LASSO regression models effectively distinguishing between healthy and lung cancer blood or serum samples (all AUC > 0.85). Additionally, 12 of these miRNAs exhibited significant prognostic correlations. The Ref-miREO method offers valuable candidates for circulating biomarker detection in cancer that are not affected by changes in leukocyte populations.

MicroRNA as an Important Mediator in the Regulation of Male Gallus gallus domesticus Reproduction: Current State of the Problem.

During all periods of male ontogenesis, physiological processes responsible for the correct functioning of reproductive organs and spermatogenesis are under the influence of various factors (neuro-humoral, genetic, and paratypical). Recently, the attention of researchers has increasingly turned to the study of epigenetic factors. In scientific publications, one can increasingly find references to the direct role of microRNAs, small non-coding RNAs involved in post-transcriptional regulation of gene expression, in the processes of development and functioning of reproductive organs. Although the role of microRNAs in the reproduction of mammals, including humans, has been intensively studied, this area of knowledge in birds remains under-researched and limited to single experiments. This is likely due to the unique features of embryogenesis and the structure of the avian reproductive system. This review summarizes the current state of knowledge on the role of microRNAs in avian reproduction. Insight into the molecular basis of spermatogenesis in Gallus gallus domesticus is provided. Data on the functions and mechanisms by which microRNAs influence the processes of growth, development, and formation of rooster germ cells that determine the necessary morphofunctional qualitative characteristics of mature spermatozoa are summarized. Particular attention is paid to miRNA biogenesis as an important step affecting the success of spermatogenesis, as well as the role of miRNAs in avian sex differentiation during early embryogenesis. The modern literature sources systematized in this review, revealing the questions about the role of miRNAs in the reproductive function of birds, create a theoretical basis and define new perspectives and directions for further research in this field.

Exploratory miRNA profiling from serum and bone tissue of mice with T1D-induced bone loss.

Type 1 diabetes (T1D) represents a significant health burden worldwide, with associated complications including bone fragility. Current clinical methods and biomarkers for assessing bone health and predicting fracture risk in T1D are limited and lack accuracy. MicroRNAs (miRNAs) have emerged as potential biomarkers for predicting T1D-induced bone loss, although comprehensive profiling studies are lacking. Previous investigations have indicated a link between dysregulated miRNA expression levels and impaired bone health in T1D. Therefore, in this study, we explored differential miRNA expression levels in serum and bone tissue of mice with T1D-induced bone loss using Next Generation Sequencing (NGS). T1D was induced using streptozotocin in male wild-type mice. Serum and bone tissues were analyzed at 14 weeks of age, following the prior characterization of bone loss in this mouse model. MiRNA profiling was conducted using two-independent NGS analyses and validated through quantitative RT-PCR. NGS profiling identified differential expression of miRNAs in serum and bone tissue of T1D mice compared to controls. The first NGS analysis revealed 24 differentially expressed miRNAs in serum and 13 in bone tissue. Especially, miR-136-3p was consistently downregulated in both serum and bone tissue. However, the second NGS analysis presented a distinct set of dysregulated miRNAs, with miR-206-3p overlapping in both tissues but exhibiting differential expression patterns. Surprisingly, miR-144-5p, miR-19a-3p, and miR-21a-5p displayed contrasting regulatory patterns between NGS and qPCR analyses. Finally, gene network analysis identified associations between dysregulated miRNAs and pathways involved in bone physiology, including TGF-beta, PI3-Akt signaling, and osteoclast differentiation in humans. In conclusion, our study offers initial insights into dysregulated miRNAs associated with T1D-induced bone loss, but also highlights the lack of consistency in the results obtained from miRNA sequencing in different cohorts. Thus, further investigation is needed to better understand the complexities of miRNA analyses before they can be established as reproducible biomarkers for predicting bone health in T1D.

Insights into pubertal development: a narrative review on the role of epigenetics.

Puberty is a key phase of growth and development, characterized by psychophysical transformations. It is driven by a combination of genetic, hormonal, and environmental variables. Epigenetic mechanisms, including histone post-translational modifications and chromatin remodeling, microRNAs, and DNA methylation, play important roles in orchestrating the developmental processes. We describe environmental factors that may interact with genetics, and factors influencing puberty onset, focusing in particular on epigenetic mechanisms that can help understand the timing and variations that lead to precocious or delayed puberty. We conducted a narrative review of associations between puberty and epigenetic mechanisms through a comprehensive search of PubMed, Scopus, and Web of Science databases. The chromatin landscape of genes as KISS1 has revealed dynamic changes in histone modifications as puberty approaches, influencing the stimulation or inhibition of gene expression critical for reproductive maturation. MiRNAs regulate gene expression, whereas DNA methylation affects activation or repression of gene transcription of genes involved in pubertal timing. Moreover, studies in animal models have provided insights into the role of DNA methylation and miRNAs in brain sexual differentiation, highlighting the active involvement of epigenetic mechanisms in shaping sexually dimorphic brain structures. This review highlights the importance of understanding the complex interplay between epigenetic regulation and pubertal development, which can lead to new therapeutic options and shed light on the fundamental processes driving reproductive maturation.

Expression profiles of microRNA-mRNA and their potential impact on anthocyanin accumulation in purple petals of Brassica napus

Rapeseed (Brassica napus L.) possesses substantial economic value as an oil, vegetable, and forage crop, while also exhibiting notable ornamental characteristics. Recent advances in flower colour breeding have significantly enhanced the visual appeal of rapeseed, with anthocyanins identified as the primary contributor to the development of red, purple, and pink flowers. However, the mechanisms underlying the synthesis and regulation of anthocyanins during petal coloration in rapeseed are still poorly understood. This research combined miRNA and mRNA expression data from four different color phases, along with degradome analysis, to discover important miRNA-mRNA modules responsible for controlling the accumulation of anthocyanin in purple-flowered rapeseed. In the process of petal development, a grand sum of 247 miRNAs (including 223 known and 24 novel miRNAs) were effectively detected, with 64 of them displaying differential expression patterns. Degradome sequencing was used to conduct a comprehensive analysis of 152 targets for the differential expression miRNAs. Out of these, 108 miRNA-mRNA modules exhibit contrasting expression patterns. Some miRNAs and their corresponding targets have additionally been discovered, potentially playing a role in governing the buildup of anthocyanin in purple-flowered rapeseed. The regulatory modules miR156-SPL9 and miR828-PAP2 composed of miR156b and miR828 and their targets may play a key role in this process. The results offer a thorough analysis of miRNAs linked to the regulation of anthocyanin in B. napus, offering valuable understanding into the regulatory processes that govern miRNA-mediated anthocyanin production in Brassica crops.

MicroRNA Screening Reveals Upregulation of FoxO-Signaling in Relapsed Acute Myeloid Leukemia Patients.

Background/Objectives: AML is an aggressive malignant disease characterized by aberrant proliferation and accumulation of immature blast cells in the patient's bone marrow. Chemotherapeutic treatment can effectively induce remission and re-establish functional hematopoiesis. However, many patients experience chemoresistance-associated relapse and disease progression with a poor prognosis. The identification of molecular determinants of chemoresistance that could serve as potential targets for the therapeutic restoration of chemosensitivity has proven to be challenging. Methods: To address this, we have analyzed longitudinal changes in the expression of microRNAs during disease progression in a small set of four AML patients, combined with gene ontology (GO) pathway analysis and evaluation of gene expression data in patient databases. Results: MicroRNA profiling of bone marrow samples at diagnosis and after relapse revealed significant differential expression of a large number of microRNAs between the two time points. Subsequent GO pathway analysis identified 11 signal transduction pathways likely to be affected by the differential miRNA signatures. Exemplary validation of the FoxO signaling pathway by gene expression analysis confirmed significant upregulation of FOXO1 and the target genes GADD45 and SOD2. Conclusions: Here, we show how a microRNA-based pathway prediction strategy can be used to identify differentially regulated signaling pathways that represent potential targets for therapeutic intervention.

Identification of pyroptosis-associated miRNAs in the immunoscape and prognosis of hepatocellular carcinoma

BackgroundHepatocellular carcinoma is one of the most prevalent types of liver malignancy and poses a severe threat to global health. Despite recent improvements in therapeutic approaches, treatment options for patients with advanced or recurrent HCC are still limited.Materials and methodsOur study analyzed miRNA differential expression using data from hepatocellular carcinoma patients in the Cancer Genome Atlas. Pyroptosis-related genes were identified from gene cards. Differential expression of miRNAs was analyzed using DESeq2 and visualized using ggplot2 and pheatmap. A prognostic risk model for pyroptosis-associated miRNAs was constructed using LASSO regression and validated by principal component analysis, Kaplan-Meier survival and ROC curve analysis. We also performed gene and pathway enrichment analysis. Immune cell infiltration and function in HCC were assessed using single-sample genomic enrichment analysis, and correlations with immune cells and function were explored. Also, CCK-8 assay as well as migration and invasion assays were performed after knockdown of miR-6844.ResultsWe have established and validated a prognostic risk model based on ten DEmiRNAs, which is important for the survival of HCC patients. Significant changes in immune cell infiltration and immune function were also found in high-risk patients. It also demonstrated that knockdown of miR-6844 inhibited HCC cell proliferation, migration and invasion, highlighting its role in HCC progression.ConclusionOur study reveals the implications of pyroptosis-associated differential miRNAs on the prognosis of patients with hepatocellular carcinoma and provides a foundation for novel HCC therapies, especially immunotherapy.

Profile of miRNAs induced during sheep fat tail development and roles of four key miRNAs in proliferation and differentiation of sheep preadipocytes.

The fat tail of sheep is an adaptive trait that facilitates their adaptation to harsh natural environments. MicroRNAs (miRNAs) have been demonstrated to play crucial roles in the regulation of tail fat deposition. In this study, miRNA-Seq was employed to investigate the expression profiles of miRNAs during different developmental stages of sheep fat tails and elucidate the functions of differentially expressed miRNAs (DE miRNAs). A total of 350 DE miRNAs were identified, among which 191, 60, 26, and 21 were significantly upregulated in tail fat tissues of fetal, lamb, hogget Altay sheep, and adult Xinjiang fine wool (XFW) sheep but downregulated in other stages. Furthermore, we predicted a set of candidate target genes (4,476) for the top 20 DE miRNAs. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that they involve in several adipogenesis-related pathways. Subsequent investigations indicated that four DE miRNAs, miR-433-3p, miR-485-3p, miR-409-3p, and miR-495-3p, could suppress the expression of peroxisome proliferator-activated receptor gamma (PPARγ) and phosphoinositide-3-kinase regulatory subunit 3 (PIK3R3) and regulate the preadipocyte development in sheep. Meanwhile, the lipid metabolism-related genes, fatty acid-binding protein (FABP3), perilipin 1 (PLIN1), adiponectin C1Q and collagen domain containing (ADIPOQ), and lipoprotein lipase (LPL), were significantly downregulated (p < 0.01). The expression patterns of miRNAs exhibited significant fluctuations during different development periods of the fat tail, and some of them may participate in the regulation of tail fat deposition by modulating the proliferation and differentiation of preadipocytes.

Impact of dcEF on microRNA profiles in glioblastoma and exosomes using a novel microfluidic bioreactor.

Glioblastoma multiforme, the most common type of highly aggressive primary brain tumor, is influenced by complex molecular signaling pathways, where microRNAs (miRNAs) play a critical regulatory role. Originating from glial cells, glioblastoma cells are affected by the physiological direct current electric field (dcEF) in the central nervous system. While dcEF has been shown to affect glioblastoma migration (electrotaxis), the specific impact on glioblastoma intercellular communication and miRNA expression in glioblastoma cells and their exosomes remains unclear. This study aims to fill this gap by investigating the differential expression of microRNAs in glioblastoma cells and exosomes under dcEF stimulation. We have developed a novel, reversibly sealed dcEF stimulation bioreactor that ensures uniform dcEF stimulation across a large cell culture area, specifically targeting glioblastoma cells and primary human astrocytes. Using microarray analysis, we examined differential miRNA profiles in both cellular and exosomal RNAs. Our study identified shared molecular targets and pathways affected by dcEF stimulation. Our findings reveal significant changes in miRNA expression due to dcEF stimulation, with specific miRNAs, such as hsa-miR-4440 being up-regulated and hsa-miR-3201 and hsa-mir-548g being down-regulated. Future research will focus on elucidating the molecular mechanisms of these miRNAs and their potential as diagnostic biomarkers. The developed platform offers high-quality dcEF stimulation and rapid sample recovery, with potential applications in tissue engineering and multi-omics molecular analysis.

GD-Net: An Integrated Multimodal Information Model Based on Deep Learning for Cancer Outcome Prediction and Informative Feature Selection.

Multimodal information provides valuable resources for cancer prognosis and survival prediction. However, the computational integration of this heterogeneous data information poses significant challenges due to the complex interactions between molecules from different biological modalities and the limited sample size. Here, we introduce GD-Net, a Graph Deep learning algorithm to enhance the accuracy of survival prediction with an average accuracy of 72% by early fusing of multimodal information, which includes an interpretable and lightweight XGBoost module to efficiently extract informative features. First, we applied GD-Net to eight cancer datasets and achieved superior performance compared to benchmarking methods, with an average 7.9% higher C-index value. The ablation experiments strongly supported that multi-modal integration could significantly improve accuracy over the single-modality model. In the deep case study of liver cancer, 319 differential genes, 15 differential miRNAs and 155 methylated differential genes based on the predicted risk subgroups are identified as the informative features, and then we have statistically and biologically validated the efficacy of these key molecules in internal and external test datasets. The comprehensive independent validations demonstrated that GD-Net is accurate and competitive in predicting different cancer outcomes in real-time, and it is an effective tool for identifying new multimodal prognosis biomarkers.

Differential expression profile of miRNAs in maternal amniotic fluid exosomes in fetuses with isolated ventriculomegaly

To investigate the role of miRNAs in maternal amniotic fluid exosomes in development of isolated ventriculomegaly (VM) in fetuses. Amniotic fluid samples were collected from 9 cases of moderate isolated VM and 8 normal control cases to extract exosomal miRNA, and miRNA sequencing technique was used to identify differentially expressed miRNAs between the two groups. Three miRNAs with significant differential expression between the two groups, whose high expression was associated with VM, were selected for verification with RT-qPCR. Dual luciferase reporter assays were used to verify the regulatory effect of miR-122-5p on its predicted target genes AKT3 and CCDC88C. Gene ontology (GO) and KEGG pathway analyses were performed to explore the possible roles of the top 40 significant differential miRNAs in the pathophysiology of VM. We identified a total of 272 differentially expressed miRNAs in VM cases, including 43 up-regulated and 229 down-regulated miRNAs. The target genes of these differential miRNAs were associated with DNA and transcription factor binding, transmembrane transporter and nucleic acid binding transcription factor activity, and cell developmental process. These miRNAs were mostly enriched in the MAPK, cGMP-PKG and Wnt signaling pathways. Verification with RT-qPCR showed that miR-122-5p expression level was significantly lower in VM group than in the control group (P < 0.05), which was consistent with miRNA sequencing results; let-7b-5p expression level was significantly lower in VM group, which was contrary to miRNA sequencing result. Dual luciferase reporter assays showed that miR-122-5p was not capable of regulating AKT3 or CCDC88C expressions. The highly abundant differentially expressed miRNAs in maternal amniotic fluid exosomes play important roles in the occurrence of fetal VM possibly by regulating the MAPK, PI3K-Akt, Wnt and cGMP-PKG signaling pathways.

DIFFERENTIALLY REGULATED MIRNAS BY TWIST1 IN TRIPLE NEGATIVE BREAST CANCER CELLS

Objective: Breast cancer (BC) is the most common cancer in women and the second leading cause of cancer-related deaths. MicroRNAs (miRNAs) are short, non-coding RNA molecules that regulate gene expression post-transcriptionally and play a central role in the dysregulation of gene expression associated with carcinogenesis, cancer cell proliferation and metastasis. Twist1 is a transcription factor that binds to E-box motifs and controls the transcriptional activity of genes as a positive or negative regulator decisive in the cellular mechanisms. Accordingly, Twist1 also regulates the expression of miRNAs that are associated with cancer progression. In present study, we aimed to investigate the expressional changes of possible miRNAs directly regulated by Twist1 in triple negative breast cancer MDA-MB-231 cells. Materials and Methods: In this study, a total of 43 miRNA genes were evaluated that predicted might be associated with triple negative breast cancer. To determine the Twist1-targeted miRNA genes, endogenous high level Twist1 expression was suppressed through the antisense oligonucleotides in MDA-MB-231 TNBC cells. Differential miRNA expression levels were analyzed by real time PCR analysis in Twist1-suppressed cells compare to control. Results: Twist1 suppression leads to an increase in miR-1-1 and miR-210-3p expression, while a decrease in miR-193b-3p, miR-181b-5p, and miR-148a-3p expression. Conclusion: This study shows that the expression levels of certain miRNAs linked to invasion, metastasis, and apoptosis are controlled by Twist1 in triple negative breast cancer cells.

Exploring differential miRNA expression profiles in muscular and visceral adipose tissue of patients with severe obesity.

This study aims to investigate the differential miRNA expression profile between the visceral white adipose tissue and the skeletal muscle of people with obesity undergoing bariatric surgery. Skeletal muscle and visceral adipose tissue samples of 10 controls and 38 people with obesity (50% also with type 2 diabetes) undergoing bariatric surgery were collected. miRNA expression profiles were analyzed using Next-Generation Sequencing and subsequently validated using RT-PCR. Approximately 69% of miRNAs showed similar expression in both tissues, however, 55 miRNAs were preferentially expressed in visceral adipose tissue and 53 in skeletal muscle. miR-122b-5p was uniquely identified in skeletal muscle, while miR-1-3p and miR-206 were upregulated in skeletal muscle. Conversely, miR-224-5p and miR-335-3p exhibited upregulation in visceral adipose tissue. Notably, distinctions related to the presence of type 2 diabetes were observed solely in the expression of miR-1-3p and miR-206 in visceral adipose tissue. This is the first study unveiling distinct miRNA expression profiles in paired samples of visceral adipose tissue and skeletal muscle in humans. The identification of obesity-specific miRNAs in these tissues opens up promising avenues for research into potential biomarkers for obesity diagnosis and treatment.

Plasma exosomes may mediate the development of lupus nephritis in patients with systemic lupus erythematosus.

Lupus nephritis (LN) is the most serious complication of systemic lupus erythematosus (SLE), and plasma exosomes may serve as a bridge. MicroRNAs (miRNAs) are abundant in exosomes, so this study aimed to explore the role of exosome-derived miRNA in the development of LN. The publicly available data containing plasma exosomal miRNAs in SLE patients and healthy controls were researched, and differential expression and functional enrichment analysis of exosomal miRNA was conducted. Then, plasma exosomes from SLE patients were extracted, and the accuracy of differential expression and functional enrichment analysis was preliminarily verified. PKH26 dye was used to label exosomes to detect whether exosomes can enter HK2 cells. Evaluation of plasma exosomes impact on cell viability was done by utilizing CCK-8 assay. Flow cytometry was used to measure cell apoptosis. Plasma exosomes were successfully extracted and identified. Through differential expression analysis of the pulbilic data and subsequent qPCR validation, we observed that miR-20b-5p is overexpressed in plasma exosomes of SLE patients, whereas miR-181a-2-3p is downregulated. Then functional enrichment analysis revealed that these differential miRNAs primarily regulate processes such as apoptosis, autophagy, and inflammation. Then, flow cytometry analysis conducted after co-incubation of plasma exosomes and peripheral blood mononuclear cells confirmed that exosomes can indeed regulate apoptosis. And plasma exosomes can successfully enter HK2 cells without affecting cell activity. In addition, plasma exosomes promote HK2 cell apoptosis and autophagy. Overexpression of miR-181a-2-3p could inhibit HK2 cells apoptosis and upregulate the expression of bcl2, and beclin1. At the same time, a trend towards increased apoptosis rates was observed in HK2 overexpressed miR-20b-5p, although the difference did not reach statistical significance. And miR-20b-5p can enhance the expression of caspase3 and becin1 while suppressing the expression of bcl2 and LC3β. Our research indicates that the abundant presence of miR-20b-5p and the depletion of miR-181a-2-3p in plasma exosomes of SLE patients may mediate the promotion of apoptosis and autophagy in HK2 cells, thereby causing kidney damage and the development of LN.

Discovery of a blood-based miRNA signature that can predict onset of active tuberculosis among household contacts of TB patients

BackgroundNon-sputum based predictive biomarkers capable of identifying individuals with high risk of progression to active tuberculosis (TB) are critical for global TB control. MicroRNAs (miRNAs) are significant regulators involved in TB pathogenesis and hence we aimed to identify a miRNA signature capable of predicting progression to TB disease.MethodsWe compared the differential miRNA expression profile of QuantiFERON supernatants of TB Progressors, defined as healthy household contacts (HHCs) of TB patients, who developed active TB disease during a 2-year follow-up period, and Non-progressors defined as HHCs from the same longitudinal cohort who did not develop TB disease during the entire follow-up period, using the nanostring nCounter platform. Receiver Operator Characteristic (ROC) analysis was performed to evaluate the diagnostic accuracy of the identified miRNA biomarkers, followed by random forest analysis to determine the best predictive model.ResultsWe identified 30 differentially regulated miRNAs between the two groups. Of these, hsa-miR-585-3p and hsa-miR-92a-3p were up-regulated with a maximum fold change of 1.74 and 1.71 respectively, while hsa-miR-223-3p and hsa-miR-451a were down-regulated by −2.05 and −2.04 fold respectively. Random forest analysis revealed that hsa-miR-181a-5p, hsa-miR-204-5p, hsa-miR-197-3p, hsa-miR-92a-3p, hsa-miR-451a, hsa-miR-24-3p, and hsa-miR-487a-3p exhibited 100% accuracy in identifying Progressors. This panel of 7 miRNAs demonstrated excellent diagnostic performance characteristics with 100% sensitivity and specificity.ConclusionWe propose that the identified miRNA signature has the potential to serve as a very useful tool for early identification of individuals who bear the highest risk of progression to TB, so that they can be targeted for timely intervention.