Changes In miRNA Expression Research Articles

Whole transcriptome sequencing identifies key lncRNAs, circRNAs and miRNAs in sepsis-associated acute lung injury

Purpose: In this study, we identified differentially expressed genes (DEGs) and signaling pathways to gain insight into the pathogenesis of acute lung injury (ALI). Methods: C57BL/6 mice were intravenously injected with lipopolysaccharide (LPS) to establish a sepsis-induced ALI model. Hematoxylin-eosin (H&E) and enzyme-linked immunosorbent assays (ELISAs) were used to evaluate the model. Whole transcriptome sequencing was performed to identify the expression changes in lncRNAs, circRNAs, miRNAs and mRNAs in lung tissues. The crucial RNAs and the biological function of the target genes were confirmed and annotated based on bioinformatics analysis. Real-time quantitative reverse transcription-polymerase chain reaction (qRT–PCR) was employed to verify the expression levels of key lncRNAs, circRNAs, miRNAs and mRNAs in the lung tissues and human bronchoalveolar lavage (BALF). Results: A total of 3304 (1632 upregulated and 1672 downregulated) differentially expressed mRNAs, 794 (397 up and 397 down) differentially expressed lncRNAs, 89 (58 up and 31 down) differentially expressed circRNAs, and 14 (11 up and 3 down) differentially expressed miRNAs were identified between the control and LPS lung tissues. The lncRNA ceRNA subnetwork and circRNA ceRNA subnetwork were constructed based on the observed interaction and co-expression among the differentially expressed RNAs. An analysis of the protein–protein interaction (PPI) network and hub genes revealed crucial mRNAs for circRNA-Tcf20. The lncRNA-Snhg12, Edn1, Stat1, miR-212-3p and miR-223-3p were upregulated in sepsis ARDS patients. CircRNA-Tcf20, Col1a1, Col1a2 and Flt3 were significantly downregulated in sepsis ARDS patients. The biological function analysis indicated that these genes were enriched in the TNF signaling pathway, Necroptosis signaling pathway and the PI3K-Akt signaling pathway. Conclusions: Our findings suggest that circRNA-Tcf20, miR-212-3p, miR-223-3p, Col1a1, Col1a2 and Flt3 may be new regulatory factors that participate in the pathogenesis of sepsis-related acute lung injury. CircRNA-Tcf20, lncRNA-Snhg12 and all the other RNAs may be potential biomarkers for septic ALI/ARDS.

MicroRNA expression profiling in the adult offspring of rats with periodontal disease

ObjectiveThe present study investigated the relationship between maternal periodontal disease, insulin resistance, activation of inflammatory pathways and epigenetic modifications in adult offspring. DesignTherefore, female Wistar rats were divided into control and experimental groups. Seven days after the induction of periodontal disease, female rats from both groups were mated with healthy male rats. After weaning, male offspring were divided into control offspring (CN-o) and periodontal disease offspring (PED-o) groups. Body weight was measured at 0–75 days of age. At day 75, the following were measured in the offspring: insulin resistance by the HOMA-IR index; global miRNAs by microtranscriptome array; validation of the selected miRNAs by quantitative real-time PCR expression; interleukin 1 receptor associated kinase 1 (IRAK1) and tumor necrosis factor receptor-associated factor 6 (TRAF6) content in the gastrocnemius muscle tissue (GSM) by western blotting. ResultsMaternal periodontal disease leads to low birth weight (LBW) in the offspring and insulin resistance in adulthood; changes in global miRNA expression (5 miRNAs upregulated and 6 downregulated); and increased protein expression of IRAK1 and TRAF6 in GSM. ConclusionsThese findings demonstrate that maternal periodontal disease causes LBW, insulin resistance, activation of inflammatory pathways, and changes in global miRNA expression.

Granzyme mRNA-miRNA interaction and its implication to functional impact.

Granzyme activity can affect the processing and stability of miRNAs within target cells. They also could induce changes in miRNA expression that impact apoptotic signaling. Granzyme-induced apoptosis might result in changes to the miRNA profile, which can further influence the apoptosis and inflammation processes. The aim of this study was to bioinformatically analyze which miRNAs and transcription factors bind to the CDS and UTR regions of the granzyme family to regulate gene expression in relation to granzyme evolution and their association with human cancer diseases. The expression patterns of granzyme genes were analyzed in various human tissues. MiRNAs binding to the CDS and UTR of the granzyme family were examined, and the transcription factors binding to these miRNAs binding sites were also analyzed. Cytoscape program was used to visualize and analyze the networks of interactions between granzyme mRNA and miRNAs. Additionally, the evolutionary patterns of the granzyme family in relation to miRNAs and transcription factors binding were investigated. Analysis of the expression patterns of the granzyme family in various human tissues shows that GZMA and GZMK are strongly expressed in lymph nodes. GZMB exhibits strong expression in the bone marrow, while GZMA is prominently expressed in the spleen. Twenty-two miRNAs bind to both GZMK and GZMB mRNA, while six miRNAs bind to both GZMK and GZMM mRNA. The only miRNA that binds to GZMK, GZMB, GZMM, and GZMA mRNA is hsa-miR-146a-5p. Transcription factors JUND, FOS, and JUN are distinctly interconnected with has-miR-5696 and GZMK. Association data between the granzyme family and cancers showed that various miRNAs were consistently implicated and exhibited either upregulation or downregulation. Although the granzyme family possesses distinct genetic information, it shows relatively high expression levels in the lymph node, spleen, and bone marrow. Many miRNAs specifically regulate granzyme gene expression, and various transcription factors are involved. Analyzing the granzyme genes-miRNAs-transcription factors-related network will provide crucial insights into the mechanisms of cancer development and suppression.

Construction and integrative analysis of miRNA-mRNA response to salinity stress in Oreochromis mossambicus cells

This study investigated the genetic response of tilapia (Oreochromis mossambicus) brain cells to hypertonic stress, focusing on miRNAs regulation. Three hundred and thirty-one known miRNAs and 163 novel miRNAs which responded to hypertonic stress were identified by high-throughput sequencing in tilapia brain cells. Differential expression analysis revealed that 16 miRNAs were significantly upregulated, while 11 miRNAs were significantly downregulated. These differentially expressed miRNAs are closely related to metabolism, immune response, and neural regulation. The target genes of these miRNAs are implicated in neurotrophic and synaptic signaling pathways, potentially affecting metabolic and apoptotic processes. GO and KEGG enrichment analyses provided insights into the biological processes and pathways affected by hypertonic stress. Furthermore, correlation analysis between mRNA and miRNA highlighted miRNA-mRNA interactions related to cell cycle and apoptosis regulation. These results indicated significant changes of miRNA expression under hypertonic stress and their crucial role in osmotic pressure regulation. This study offers a basis for further exploration of miRNA functions and molecular mechanisms in tilapia, potentially informing practices for aquaculture in challenging environments such as saline-alkaline waters.

Recent Advances in DNA-Based Nanoprobes for In vivo MiRNA Imaging.

As a post transcriptional regulator of gene expression, microRNAs (miRNA) is closely related to many major human diseases, especially cancer. Therefore, its precise detection is very important for disease diagnosis and treatment. With the advancement of fluorescent dye and imaging technology, the focus has shifted from in vitro miRNA detection to in vivo miRNA imaging. This concept review summarizes signal amplification strategies including DNAzyme catalytic reaction, hybrid chain reaction (HCR), catalytic hairpin assembly (CHA) to enhance detection signal of lowly expressed miRNAs; external stimuli of ultraviolet (UV) light or near-infrared region (NIR) light, and internal stimuli such as adenosine triphosphate (ATP), glutathione (GSH), protease and cell membrane protein to prevent nonspecific activation for the avoidance of false positive signal; and the development of fluorescent probes with emission in NIR for in vivo miRNA imaging; as well as rare earth nanoparticle based the second near-infrared window (NIR-II) nanoprobes with excellent tissue penetration and depth for in vivo miRNA imaging. The concept review also indicated current challenges for in vivo miRNA imaging including the dynamic monitoring of miRNA expression change and simultaneous in vivo imaging of multiple miRNAs.

Validation of gene polymorphisms (rs2682818 and rs2043556) in has-miR-618 and has-miR-605 with the breast cancer susceptibility

BackgroundBreast cancer (BC) is one of the most frequent types of cancer and the second leading cause of cancer-affiliate death among ladies. BC is a heterogeneous sickness that is impacted by environment and genetic elements. Diagnosis in the early stages impacts treatment and patient survival rate. miRNA can play a vital role in BC's early stages of tumorigenesis. Single nucleotide polymorphism (SNP) can cause changes in miRNA expression and function, which are related to the risk of several cancers. AimThe goal of this examination is to assess the affiliation among two has-miR-605 (rs2043556A > G) and has-miR-618 (rs2682818 C > A) gene polymorphisms with the risk of BC in the Iranian ladies. MethodsOur case-control examination assessed two hundred whole blood samples of one hundred ladies with BC and one hundred healthy ladies. Hence, to assess the connection between the presence of SNP miRNA genes and the risk of BC, genotyping was done by the usage of the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method, then the usage of the Chi-square test of SPSS software statistically analyzed the acquired result. ResultsOur findings confirmed a statistically substantial distinction within the genotype frequency of the has-miR-618 gene polymorphism among the groups (P = 0.043), whereas no statistically substantial distinction inside the genotype frequency of the has-miR-605 gene polymorphism among the control and case (P = 0.183). In addition, the allelic frequency of two polymorphisms, (rs2043556 A > G) G allele (OR = 2.163, CI 95 % = 1.56–2.988, P = 0.022) and (rs2682818 C > A) A allele (OR = 3.997, CI 95 % = 1.584–10.081, P = 0.002) substantially enhance the risk of BC. ConclusionThe results show that the G allele of rs2043556 and the A allele of rs2682818 increase the risk of BC in the women population of East Azerbaijan province.

Expression of microRNA-21 in acute ischemic stroke: relationship with inflammatory cytokines, clinical severity, and clinical outcome

Background When the brain is deprived of oxygen and nutrients due to stenosis or arterial rupture, neurons in the affected area suffer irreversible damage and cellular death. MicroRNA has been shown to regulate target genes implicated in arterial hypertension, atherosclerosis, and diabetes mellitus, all of which influence the risk of ischemic stroke through inflammation, oxidative stress, cell proliferation, and apoptosis. The study aims to determine the changes in miRNA expression, namely miRNA-21, between acute ischemic stroke patients and controls and their relationship to proinflammatory cytokines, clinical severity, and outcome. Methods Serum samples from tertiary hospitals and controls were used to evaluate miRNA-21 expression as well as cytokines TNF-α, IL-10, ICAM-1, and CCL5 levels within 7 days of stroke onset. The 30-day clinical severity and outcome were assessed using the National Institute of Health Stroke Scale (NIHSS) and modified Rankin Scale (mRS), respectively. Result A total of 64 acute ischemic stroke patients and 22 age-matched controls were recruited, with median ages of 56 and 55.5 years old, respectively. There were more male subjects than females (35 to 29). A statistically significant difference was observed in miRNA-21 expression between patients and controls (p<0.001). This finding implies that miRNA-21 expression may have a contribution in acute stroke patients. This was followed by an increase in proinflammatory markers TNF-α, IL-10, ICAM-1, and CCL5. However, no association was found between miRNA-21 and any pro-inflammatory cytokine. There was no significant correlation between miRNA-21 or cytokines markers with clinical severity or prognosis. Conclusion Our study demonstrated increased miRNA-21 expression and proinflammatory cytokine expression in acute ischemic stroke patients relative to controls. However, this was not related to clinical severity or clinical outcomes.

Fasciola hepatica Excretory-Secretory Products (Fh-ES) Either Do Not Affect miRNA Expression Profile in THP-1 Macrophages or the Changes Are Undetectable by a Microarray Technique.

Fasciola hepatica is a liver fluke that resides in the bile ducts of various mammals. The parasitosis leads to economic losses in animal production estimated at USD 3.2 billion annually. It is also considered a zoonosis of great significance and a problem for public health affecting 2.4 million people worldwide. Nevertheless, besides the negative aspects of infestation, the antigens released by the fluke, F. hepatica Excretory-Secretory Products (Fh-ES) contain several immunomodulatory molecules that may be beneficial during the course of type I diabetes, multiple sclerosis, ulcerative colitis, or septic shock. This phenomenon is based on the natural abilities of adult F. hepatica to suppress proinflammatory responses. To underline the molecular basis of these mechanisms and determine the role of microRNA (miRNA) in the process, lipopolysaccharide (LPS)-activated THP-1 macrophages were stimulated with Fh-ES, followed by miRNA microarray analyses. Surprisingly, no results indicating changes in the miRNA expression profile were noted (p < 0.05). We discuss potential reasons for these results, which may be due to insufficient sensitivity to detect slight changes in miRNA expression or the possibility that these changes are not regulated by miRNA. Despite the negative data, this work may contribute to the future planning of experiments by other researchers.

Preliminary Evidence Supports that Long-Term Consumption of Higher-Protein Breakfast Promotes Higher Expression of Select miRNA Associated with Cardiometabolic Health in Adolescents

BackgroundIncreased dietary protein at breakfast promotes cardiometabolic health; however, whether these improvements occur at the molecular level is unknown. ObjectivesThe objective was to examine whether long-term consumption of breakfast, varying in protein quantity, alters the expression of circulating microRNAs (miRNAs) associated with cardiometabolic health in “breakfast-skipping” adolescents. MethodsThirty adolescents (age: 19 ± 1 y; body mass index: 25.4 ± 3 kg/m2) completed a 6-mo tightly controlled breakfast trial in which participants consumed 350 kcal normal-protein (NP, 10 g protein) or higher-protein (HP, 30 g protein) breakfasts or continued to BS for 6 mo. Fasting blood samples were collected at baseline (PRE) and 6 mo (POST) for assessment of 12 a priori circulating plasma miRNA expression levels (real-time quantitative polymerase chain reaction), glucose, insulin, IL-6, and C-reactive protein. ResultsNo main effects of group were observed for any miRNAs; however, a time-by-group interaction was detected for the expression of miR-126-3p (P = 0.05). HP breakfast tended to increase miR-126-3p expression throughout the study (POST-PRE, P = 0.09) leading to greater expression at POST compared with BS (P = 0.03), whereas NP breakfast did not. Additionally, several miRNAs predicted fasting concentrations of IL-6: miR-320a-3p, -146a-5p, -150-5p, -423-5p, -122-5p, glucose: miR-24-3p, -126-3p; insulin: miR-24-3p, -126-3p, -15b-5p; insulin sensitivity: miR-24-3p, -126-3p, -199a-5p, -15b-5p; and β-cell function: miR-15b-5p (R2 between 0.2 and 0.39; P < 0.05) from PRE and POST samples across groups. ConclusionsThese data support the daily consumption of a HP breakfast to promote cardiometabolic health, potentially through changes in miRNA expression, in a sensitive life-stage where early intervention strategies are critical to reduce the risk of adult-onset chronic disease. Trial registration numberNCT03146442.

A pilot study of precision treatment for patients with lung cancer pain by Longteng Tongluo recipe using serum genomics.

To investigate the efficacy of Longteng Tongluo recipe (, LTTL) combined with three-step analgesia for the treatment of lung cancer pain, and the changes in serum miRNA expressions before- and after treatment with LTTL and its correlation with lung cancer pain. The possible mechanism underlying LTTL effects on the treatment of lung cancer pain was conducted. The pilot study was conducted at the oncology ward of the Yueyang Hospital and the Longhua Hospital between March 2018 and October 2019. A prospective, single-blind, placebo controlled, randomized clinical trial of LTTL or placebo combined with three-step analgesia treatments were administered to 24 cancer pain patients diagnosed with lung cancer. Analgesic efficacy was investigated as the primary outcome. Equivalent morphine consumption and numerical rating scale (NRS) scores were used as the secondary outcome. In the present study, we utilized deep sequencing techniques to compare the differential miRNA expressions in serum samples obtained from two groups: the lung cancer pain treatment group (LTTL + three-step analgesia) and the control group (placebo + three-step analgesia). Next, we employed the target prediction database to investigate the target genes for differential miRNA expressions and Gene Ontology (GO) analysis along with Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis to examine the roles and the major biochemical and signaling pathways related to the differentially expressed target genes, respectively. LTTL treatment significantly reduces the NRS score (P = 0.021) as compared to those before treatment, along with significant reductions in the total morphine equivalent consumption (P = 0.007) and the average daily equivalent morphine consumption (P = 0.003) as opposed to the control group. The expressions of 31 miRNAs differed considerably between the two groups of patients (≥ 2 times up-modulated or down-regulated between these groups, P<0.05). For instance, the miRNAs expression levels for patients before treatment (has-miR-2110 and has-miR-7d-3p) were significantly enhanced as compared to the healthy people, after LTTL treatment, the expressions of miR-2110 and miR-7d-3p in patients with lung cancer pain reduced significantly. Studies show that the above two miRNAs were significantly associated with lung cancer pain, which could mediate lung cancer pain. Furthermore, we identified 355 genes as potential targets of the 31 differentially expressed miRNAs. Pathway enrichment analyses using KEGG and GO analysis indicated that these target genes may play a crucial role in the development and modulation of lung cancer pain. LTTL demonstrated a discernible impact on alleviating lung cancer pain and its mechanism of action may be related to the downregulation of has-miR-2110 and has-miR-7d-3p expressions. This pilot study provides support for further exploration of LTTL in patients with lung cancer pain.

Significant Impact of let-7d MicroRNA on Breast Cancer Cell Lines Post-Radiation Treatment

Introduction: Radiotherapy is a common treatment for breast cancer treatment, that induces DNA damage. These DNA damages are addressed through various repair pathways, which regulate the DNA repair systems and confer radio-resistance. Non-coding RNAs are a big proportion of genome transcripts without the potential to encode proteins. Related studies demonstrated that radiation affects the expression of non-coding RNAs. Let-7d, a tumor suppressor in numerous cancers, has some target genes that play a role in the DNA repair system. Materials and Methods: Human breast cancer cell lines MDA-MB-231 and MCF-7 were cultured in a Dulbecco's Modified Eagle Medium. The exponentially growing cells were treated with some doses of X-rays. After radiation treatment and cell harvesting, RNA was extracted, and cDNA synthesis was done. The let-7d miRNA expression changes were calculated with real-time quantitative reverse transcription polymerase chain reaction. Results: The results implied that radiation caused increased let-7d expression in breast cancer cell lines after radiation treatment. In addition, the results showed that 24 h after radiation, the expression of let-7d in the radioresistant cell line was higher than the radiosensitive one; 48 h after radiation, the expression of let-7d in the radiosensitive cell line was higher than the other one. Conclusions: The results demonstrated that radiation treatment increased let-7d miRNA expression in both radiosensitive and radio-resistant breast cancer cell lines. Therefore, let-7d might be involved in the radiosensitivity of breast cancer.

Expression changes of miRNAs and EMT-related genes in human mesothelial cells induced by long-term exposure to asbestos

Objective: To investigate the effects of long-term exposure to chrysotile and crocidolite on miRNAs and epithelial mesenchymal transformation (EMT) -related gene expression in human pleural mesothelial cells. Methods: In November 2020, fluorescence quantitative polymerase chain reaction (RT-qPCR) was used to detect the expressions of EMT-related genes in human pleural mesothelioma cells (NCl-H2052 cells, NCl-H2452 cells) and human normal mesothelial cells (Met-5A cells). MiRNAs with abnormal expression in human pleural mesothelioma cells were screened out from the previous miRNA chip data of research group, and target genes of differentially expressed miRNAs were predicted using miRWalk database (http: //mirwalk.umm.uni-heidelberg.de). RT-qPCR was used to verify the abnormal expression of EMT-related miRNAs in cell lines. Met-5A cells were treated with 5μg/cm(2) chrysotile and crocidolite respectively for 48 h a time, once a week and a total of 10 times. Chrysotile group, crocidolite group and control group were set up. And the control group was added with the same volume of PBS. The expression changes of EMT-related genes and abnormal expression miRNAs in each group were detected by RT-qPCR. The differences among the groups were compared by one-way ANOVA, and the differences between the control group and the experimental group were compared by dunnet-t test. Results: Compared with Met-5A cells, the expression levels of Vimentin and Twist genes were increased, and the expression level of E-cadherin genes was decreased in NCl-H2052 cells and NCl-H2452 cells (P<0.001). Target genes of miRNAs with abnormal expression in miRNA chip were predicted, and the results showed four abnormally expressed miRNAs associated with EMT and verified the expression of these four miRNAs in the cell lines. Compared with Met-5A cells, the expression level of hsa-miR-155-5p was increased in NCl-H2052 cells and NCl-H2452 cells, the expression levels of hsa-miR-34b-5p, hsa-miR-34c-5p and hsa-miR-28-5p were decreased in NCl-H2052 cells and NCl-H2452 cells (P<0.001), which was consistent with the results of chip analysis. After exposure of Met-5A cells, it was found that compared with the control group, the expression levels of Vimentin and Twist genes, hsa-miR-155-5p, hsa-miR-34b-5p and hsa-miR-34c-5p in the crocidolite group were increased, while the expression level of E-cadherin gene was decreased (P<0.05). Compared with the control group, the expression levels of Vimentin, Twist and E-cadherin genes in chrysotile group were increased, while the expression levels of hsa-miR-34b-5p, hsa-miR-34c-5p and hsa-miR-28-5p were decreased (P<0.05) . Conclusion: Long-term exposure to chrysotile and crocidolite could cause Met-5A cells to produce miRNAs and EMT-related gene expression changes similar to mesothelioma cells.

Cardioprotective microRNAs (protectomiRs) in a pig model of acute myocardial infarction and cardioprotection by ischaemic conditioning: MiR-450a.

Cardioprotective miRNAs (protectomiRs) are promising therapeutic tools. Here, we aimed to identify protectomiRs in a translational porcine model of acute myocardial infarction (AMI) and to validate their cardiocytoprotective effect. ProtectomiR candidates were selected after systematic analysis of miRNA expression changes in cardiac tissue samples from a closed-chest AMI model in pigs subjected to sham operation, AMI and ischaemic preconditioning, postconditioning or remote preconditioning, respectively. Cross-species orthologue protectomiR candidates were validated in simulated ischaemia-reperfusion injury (sI/R) model of isolated rat ocardiomyocytes and in human AC16 cells as well. For miR-450a, we performed target prediction and analysed the potential mechanisms of action by GO enrichment and KEGG pathway analysis. Out of the 220 detected miRNAs, four were up-regulated and 10 were down-regulated due to all three conditionings versus AMI. MiR-450a and miR-451 mimics at 25 nM were protective in rat cardiomyocytes, and miR-450a showed protection in human cardiomyocytes as well. MiR-450a has 3987 predicted mRNA targets in pigs, 4279 in rats and 8328 in humans. Of these, 607 genes are expressed in all three species. A total of 421 common enriched GO terms were identified in all three species, whereas KEGG pathway analysis revealed 13 common pathways. This is the first demonstration that miR-450a is associated with cardioprotection by ischaemic conditioning in a clinically relevant porcine model and shows cardiocytoprotective effect in human cardiomyocytes, making it a promising drug candidate. The mechanism of action of miR-450a involves multiple cardioprotective pathways.

Comparison of miRNA Profiles of Primary Tumors and Metastatic Tumors of Salivary Gland Tumors and Their Role in Prognosis: A Systematic Review.

MicroRNAs (miRNAs) are implicated in several biological processes, such as control of tissue homeostasis, cell signaling, differentiation, proliferation, neoplastic transformation, and activation/inhibition of apoptotic mechanisms. In this systematic review, we evaluated the changes in the expression pattern of miRNAs in salivary gland tumors (SGTs). A comprehensive search was conducted in PubMed, and Scopus with no language and date restrictions in Feb 2023. All the studies on SGTs that evaluated miRNA profiling were included. Relevant data regarding the overexpression and down-regulation of the miRNAs were extracted. The quality of the included studies was evaluated with Newcastle-Ottawa checklist. The altered expression of miRNAs was evaluated between SGTs and normal cases, benign and malignant tumors, and primary and high-grade tumors. Thirteen studies were included in this systematic review. There were considerable differences between malignant and benign tumors regarding the miRNAs expression level. In the five studies, the miRNA profile of the primary tumors was compared with metastatic tumors to reveal the involvement of the miRNA in the prognosis of the salivary tumors. The miRNAs expression changes were correlated with tumor size, stage, recurrence, and occurrence of solid components. Perineural invasion and lymph node metastasis were also reported in ACCLM cell line and recurrence of adenoid cystic carcinoma (ACC) tissues. The miRNA profiling confirms their prognostic value in salivary gland tumors. Significant alternations of the miRNAs expression are useful for distinguishing different types of salivary tumors and malignant tumors from benign types. The miRNA expression changes also affect the prognosis of salivary tumors.

Expression Changes of miRNAs in Humans and Animal Models of Amyotrophic Lateral Sclerosis and Their Potential Application for Clinical Diagnosis.

Amyotrophic lateral sclerosis (ALS) is a severe motor neuron disease. Current detection methods can only confirm the diagnosis at the onset of the disease, missing the critical window for early treatment. Recent studies using animal models have found that detecting changes in miRNA sites can predict the onset and severity of the disease in its early stages, facilitating early diagnosis and treatment. miRNAs show expression changes in motor neurons that connect the brain, spinal cord, and brain stem, as well as in the skeletal muscle in mouse models of ALS. Clinically, expression changes in some miRNAs in patients align with those in mouse models, such as the upregulation of miR-29b in the brain and the upregulation of miR-206 in the skeletal muscle. This study provides an overview of some miRNA study findings in humans as well as in animal models, including SOD1, FUS, TDP-43, and C9orf72 transgenic mice and wobbler mice, highlighting the potential of miRNAs as diagnostic markers for ALS. miR-21 and miR-206 are aberrantly expressed in both mouse model and patient samples, positioning them as key potential diagnostic markers in ALS. Additionally, miR-29a, miR-29b, miR-181a, and miR-142-3p have shown aberrant expression in both types of samples and show promise as clinical targets for ALS. Finally, miR-1197 and miR-486b-5p have been recently identified as aberrantly expressed miRNAs in mouse models for ALS, although further studies are needed to determine their viability as diagnostic targets.

Expression of microRNA induced by postoperative delirium-like behavior is associated with long-term default mode network disruption: Sequencing and a secondary analysis of resting-state fMRI data.

Resting state functional magnetic resonance imaging (rs-fMRI) has been widely used in studying default mode network (DMN) changes in postoperative delirium (POD). Reproducibility and interpretability of the analyzing results remain insufficiently studied. Delirium-like behavior was induced by tibial fixation surgery under isoflurane anesthesia. Firstly, we evaluated delirium-like behavior and inflammatory responses in hippocampus and systemic level. Then the expressions of microRNA (miRNA) and target gene were sequenced and validated. Afterwards the functional connectivity (FC) in DMN was analyzed. Finally, results were correlated with DMN changes. POD-like behavior caused significant changes of miR-34b-5p, miR-328-5p, and miR-3505 in miRNA level and Nos1, Tubb3, and Gys1 in the gene level. The FC in left and right hippocampus (L-Hip and R-Hip) and right auditory cortex (R-AC) was found significantly changed. Significant correlations were found in FCL-Hip/R-AC and FCR-Hip/R-AC for miR-34b-5p and miR-3505, as well as Nos1 and Tubb3. For miR-328-5p, no significant correlations were found. Our study demonstrates that POD-like behavior induced significant miRNA and gene expression changes were associated with hippocampus related long-term FC disruption in DMN. The results increased reproducibility and interpretability for standardized rs-fMRI data analysis, as well as providing potential targets for postoperative delirium treatment.

The association between toenail metals and extracellular MicroRNAs (ex-miRNAs) among the participants of the Normative Aging study (NAS)

BackgroundMechanistic studies of the effects of environmental risk factors have been exploring the potential role of microRNA(miRNAs) as a possible pathway to clinical disease. In this study we examine whether levels of toenail metals are associated with changes in extracellular miRNA(ex-miRNA) expression. MethodsWe used data derived from the Normative Aging Study from 1996 to 2014 to conduct our analyses. We looked at associations between measured toenail metals: arsenic, cadmium, lead, manganese, and mercury and 282 ex-miRNAs in this population using canonical correlation analyses (CCAs) and longitudinal median regression. We adjusted for covariates such as age, education, body mass index, drinking and smoking behaviors, diabetes, and where available, seafood consumption. The p-values obtained from regression analyses were corrected for multiple comparisons. Ex-miRNAs identified to be associated with toenail metal levels were further examined using pathway analyses. ResultsOur dataset included 937 observations from 589 men with an average age of 72.9 years at baseline. Both our correlation and regression analyses identified lead and cadmium as exposures most strongly associated with ex-miRNA expression. Numerous ex-miRNAs were identified as being associated with toenail metal levels. miR-27b-3p, in particular, was found to have high correlation with the first canonical dimension in the CCA and was significantly associated with cadmium in the regression analysis. Pathway analyses revealed messenger RNA (mRNA) targets for the ex-miRNAs that were associated with a number of clinical disorders including cancer, cardiovascular disease, and neurological disorders, etc. ConclusionToenail metals were associated with changes in ex-miRNA levels in both correlational and regression analyses. The ex-miRNAs identified can be linked to a variety of clinical disorders. Further studies are required to validate these findings.

MicroRNA Analysis of In Vitro Differentiation of Spermatogonial Stem Cells Using a 3D Human Testis Organoid System.

Spermatogenesis produces male gametes from spermatogonial stem cells (SSC), beginning at puberty. Modern-day laboratory techniques allow for the long-term culture of SSC and in vitro spermatogenesis. The specific biochemical processes that occur during spermatogenesis remain poorly understood. One particular element of spermatogenesis that has yet to be characterized is the role of microRNAs (miRNA), short, non-transcribed RNAs that act as post-translational regulators of gene activity. In this study, we seek to describe the presence of miRNA in a two-dimensional (2D) SSC culture and a 3D human testis organoid (HTO) system. Testicular cells were isolated from the frozen tissue of three brain-dead subjects, propagated in cultures for four to five weeks, and used to form 3D HTOs. Following organoid formation, differentiation of testicular cells was induced. RNA was isolated from the whole testis tissue (WT) showing in vivo conditions, HTO Day Zero (2D SSC culture), Day 2 HTOs, and Day 23 differentiated HTOs, then analyzed for changes in miRNA expression using the Nanostring nCounter miRNA panel. One hundred ninety-five miRNAs met the criteria for expression in WT, 186 in 2D culture, 190 in Day 2 HTOs, and 187 in differentiated HTOs. One hundred thirty-three miRNAs were common across all conditions, and 41, 17, 6, and 11 miRNAs were unique for WT, 2D culture, Day 2 HTOs, and differentiated HTOs, respectively. Twenty-two miRNAs were similar between WT and differentiated HTOS. We evaluated the miRNA expression profiles of progressively complex stages of testicular cell culture, culminating in a 3D organoid model capable of meiotic differentiation, and compared these to WT. We identified a great variance between the native tissue and the culture system; however, some miRNAs are preserved. These data may provide avenues for deeper understanding of spermatogenesis and the ability to improve this process in the laboratory. Research on miRNA continues to be an essential avenue for understanding human spermatogenesis.

Analyzing the defense response mechanism of Atractylodes macrocephala to Fusarium oxysporum through small RNA and degradome sequencing.

Fusarium oxysporum is a significant soil-borne fungal pathogen that affects over 100 plant species, including crucial crops like tomatoes, bananas, cotton, cucumbers, and watermelons, leading to wilting, yellowing, growth inhibition, and ultimately plant death. The root rot disease of A. macrocephala, caused by F. oxysporum, is one of the most serious diseases in continuous cropping, which seriously affects its sustainable development. In this study, we explored the interaction between A. macrocephala and F. oxysporum through integrated small RNA (sRNA) and degradome sequencing to uncover the microRNA (miRNA)-mediated defense mechanisms. We identified colonization of F. oxysporum in A. macrocephala roots on day 6. Nine sRNA samples were sequenced to examine the dynamic changes in miRNA expression in A. macrocephala infected by F. oxysporum at 0, 6, and 12 days after inoculation. Furthermore, we using degradome sequencing and quantitative real-time PCR (qRT-PCR), validated four miRNA/target regulatory units involved in A. macrocephala-F. oxysporum interactions. This study provides new insights into the molecular mechanisms underlying A. macrocephala's early defense against F. oxysporum infection, suggesting directions for enhancing resistance against this pathogen.

Analysis of Carcinogenic Involvement of MicroRNA Pattern in Peripheral Non-Cancerous Tissues and Chronic Viral Liver Injury.

Risk factors for hepatocarcinogenesis include chronic inflammation due to viral infection, liver fibrosis, and aging. In this study, we separated carcinogenic and non-carcinogenic cases due to hepatitis C virus (HCV) infection, aiming to comprehensively analyze miRNA expression in liver tissues by age, and identify factors that contribute to carcinogenesis. Total RNA was extracted from 360 chronic hepatitis C (CH), 43 HCV infected hepatocellular carcinoma (HCC), and surrounding non-tumor (SNT) tissues. MicroRNA (miRNA) expression patterns were analyzed using microarray. Using machine learning, we extracted characteristic miRNA expression patterns for each disease and age. There were no age-dependent changes in miRNA expression in the disease-specific comparisons; however, miRNA expression differed among the age groups of 50, 60, and 70 years of age between CH and SNT. The expression of miRNA was different between SNT and HCC only in patients in their 70s. Of the 55 miRNAs with significant differences in expression between CH and SNT, 34 miRNAs showed significant differences in expression even in the degree of liver fibrosis. The observation that miRNAs involved in hepatocarcinogenesis differ at different ages suggests that the mechanisms of carcinogenesis differ by age group as well. We also found that many miRNAs whose expression did not affect liver fibrosis were involved in carcinogenesis. These findings are expected to define biomarkers for detection of HCC at early stage, and develop novel therapeutic targets for HCC.