Analysis Of Target Genes Research Articles

Highly expressed miR-210 in the peripheral blood is closely associated with asphyxiated neonates.

In the present study, we aimed to detect microRNA-210 (miR-210) expression in the peripheral blood of neonates with asphyxia and determine the correlation between miR-210 and clinical manifestations and indicators related to pathological changes. Further, we performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of the potential target genes of miR-210 to examine their related diseases and network interactions. In total, 27 neonates with asphyxia were included in the asphyxia group and 26 healthy neonates were included in the normal group. Quantitative real-time polymerase chain reaction was performed to measure miR-210 expression in the peripheral blood. Furthermore, the correlation between miR-210 expression and asphyxia-related clinical indicators was determined, and the receiver operating characteristic curve analysis of miR-210 was conducted. Moreover, GO and KEGG analyses were conducted to identify the target genes of miR-210. Lastly, the association between miR-210 target genes and autism and epilepsy was elucidated and network interaction analysis was performed to determine the involvement of the target genes of miR-210 in neurological or cardiovascular diseases. miR-210 was highly expressed in the peripheral blood of neonates with asphyxia. Furthermore, the mode of normal delivery, cord potential of hydrogen, and Apgar scores were elevated in these neonates. Additionally, we identified 142 miR-210 target genes, which were associated with both neurodevelopmental and cardiovascular diseases. These genes were associated with the metabolic, cancer, and phosphatidylinositol3-kinase/serine/threonine kinase and mitogen-activated kinase-like protein pathways. Furthermore, 102 miR-210 target genes were associated with autism and epilepsy. High miR-210 expression in the peripheral blood of neonates with asphyxia may be associated with anoxic cerebral injury. The miR-210 target genes are associated with neurodevelopmental and cardiovascular diseases and autism and epilepsy.

EXOSOME MIRNAS PROFILING IN SERUM AND PROGNOSTIC EVALUATION IN PATIENTS WITH MULTIPLE MYELOMA

Introduction: Multiple Myeloma (MM) is an incurable hematological malignancy. Tightly crosstalk through microRNAs (miRNAs) carried by exosomes between the bone marrow microenvironment and MM cells plays pivotal roles in MM. Our study aimed to identify the expression profile of exosomal miRNAs (exo-miRNAs) in the serum of MM patients and investigate the regulation network and their potential functions. Methods: Exosomes in serum from 19 newly diagnosed multiple myeloma patients and 9 healthy donors were isolated and the miRNA profile was investigated by small RNA sequencing. Differential expression of exo-miRNAs was calculated and target genes of miRNAs were predicted. CytoHubba was applied to identify the hub miRNAs and core target genes. The LASSO Cox regression model was utilized to develop the prognostic model, and the ESTIMATE immune score was calculated to investigate the correlation between the model and immune status in MM patients. Results: Our study clarified 313 differentially expressed serum exo-miRNAs between MM patients and HD. GO analysis of target genes of differential miRNAs showed that these target genes are mainly involved in the critical biological processes related to MM pathogenesis such as proteasome-mediated ubiquitin-dependent protein catabolic process, indicating the indispensable roles of these miRNAs in MM pathogenesis. Top six hub differentially expressed serum exo-miRNAs (hsa-miR-4728-5p, hsa-miR-455-3p, hsa-miR-6779-5p, hsa-miR-124-3p, hsa-miR-615-3p, and hsa-miR-7106-5p) were identified. 513 target genes of six hub exo-miRNAs were confirmed to be differentially expressed in MM cells in Zhan Myeloma microarray dataset. Functional enrichment analysis indicated that these target genes mainly involved mRNA splicing, cellular response to stress, and deubiquitination. Thirteen core exo-miRNA target genes were applied to create a novel prognostic signature to facilitate the risk stratification of MM patients, and two groups of MM patients with diverse outcomes were recognized (Figure 1A). The high-score patients identified by thirteen core genes signature displayed a higher 70 high-risk gene set (UAMS-70) score and the 56 drug-resistance genes set score, which might partly explain their inferior outcomes (Figure 1B–C). Additionally, our results suggest that the thirteen core genes signature model was highly correlated with the status of the immune microenvironment, and patients in the low-score group had higher immune cell infiltration levels (Figure 1D). Besides, patients in the high-risk group displayed lower HLA family gene expression (Figure 1E). Encore Abstract - previously submitted to EHA 2023 Keywords: Bioinformatics, Computational and Systems Biology, Diagnostic and Prognostic Biomarkers, Risk Models No conflicts of interests pertinent to the abstract.

Urinary microRNAs in sepsis function as a novel prognostic marker.

Renal dysfunction is a common complication of sepsis. Early diagnosis and prompt treatment of sepsis with renal insufficiency are crucial for improving patient outcomes. Diagnostic markers can help identify patients at risk for sepsis and AKI, allowing for early intervention and potentially preventing the development of severe complications. The aim of the present study was to investigate the expression difference of urinary microRNAs (miRNAs/miRs) in elderly patients with sepsis and secondary renal insufficiency, and to evaluate their diagnostic value in these patients. In the present study, RNA was extracted from urine samples of elderly sepsis-related acute renal damage patients and the expression profiles of several miRNAs were analyzed. In order to evaluate the expression profile of several miRNAs, urine samples from elderly patients with acute renal damage brought on by sepsis were obtained. RNA extraction and sequencing were then performed on the samples. Furthermore, multiple bioinformatics methods were used to analyze miRNA profiles, including differential expression analysis, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis of different miRNA target genes, to further explore miRNAs that are suitable for utilization as biomarkers. A total of four miRNAs, including hsa-miR-31-5p, hsa-miR-151a-3p, hsa-miR-142-5p and hsa-miR-16-5p, were identified as potential biological markers and were further confirmed in sepsis using reverse transcription-quantitative PCR. The results of the present study demonstrated that the four urinary miRNAs were differentially expressed and may serve as specific markers for prediction of secondary acute kidney injury in elderly patients with sepsis.

Whole genome sequencing in the 100,000 Genomes project identifies a RYR2 variant associating with dilated cardiomyopathy and sudden unexpected death in the young

Abstract Funding Acknowledgements Type of funding sources: None. Background Previous studies have shown genetic testing in sudden unexpected death in the young (SUDY) cases identify a pathogenic variant in 13-27% of cases. This diagnostic yield increased up to 39% when genetic testing was combined with family evaluation. The 100,000 Genomes Project was launched to investigate the role of whole genome sequencing (WGS) as a diagnostic tool for cancers and rare diseases in a national health care system. Young sudden death victims with no finding on postmortem testing were enrolled to the SUDY cohort. Purpose We aimed to analyse WGS data in the SUDY cohort of 100,000 Genomes Project with panel analysis and trio studies in order to examine the yield of WGS in this population. Methods Sudden death victims, aged 40 or younger, without pre-existing condition that would explain the event and with no diagnosis established on postmortem examination were enrolled between 2017 and 2019 at different Genomic Medicine Centres (GMCs) across the UK. Parents were recruited in all paediatric cases. DNA sequencing was performed by Illumina. The platform's automated pipeline was used for variant calling. Panel based and hypothesis free approaches were used for data analysis. Variant analysis was performed with focus on variants with combined annotation-dependent depletion (CADD) score >15 and American College of Medical Genetics and Genomics (ACMG) classification of pathogenic (P), likely pathogenic (LP), or variant of unknown significance (VUS). Results A total of 15 participants, including 6 trios, were included in the study. Participants had a median age of 18 [IQR 1-29.5] and two thirds were male. Following assessment of all protein coding and intronic variants identified, only the missense variant RYR2:c.10046C>T (p.Ser3349Leu) was thought to be suitable for investigation for upgrade to likely pathogenic, giving a diagnostic yield of 6.67% for WGS in SUDY cases. This variant was detected in a 24-year-old sudden death victim. Family evaluation led to the diagnosis of dilated cardiomyopathy (DCM) in four family members and segregation testing confirmed affected family members harboured the variant. Further investigation in 100,000 Genomes Project, laboratory data, and our inherited cardiac conditions database as well as previous publications, identified additional cases of this variant in association with DCM and sudden cardiac death (see table and figure). Conclusion WGS with targeted gene analysis can be an effective diagnostic tool for SUDY. The study’s findings show the importance of large population databases and collaboration in the research community, allowing reclassification of a RYR2 VUS as a LP variant, the strongest genetic data so far to associate a missense variant with familial DCM and the risk for SCD. This research was made possible through access to the data and findings generated by the 100,000 Genomes Project.

Effect of hypoxia on the expression of microRNA in extracellular vesicles of human umbilical cord stem cells in vitro.

Mesenchymal stem cells (MSCs) derived extracellular vesicles, which have been shown to possess therapeutic effects for many diseases. However, how hypoxic conditions would affect exosomal microRNA expression in human umbilical cord MSCs (hUC-MSCs) is currently not investigated. This study aims to investigate the potential function of in vitro microRNAs of hUC-MSC cultured under normoxic and hypoxic conditions. Extracellular vesicles secreted from hUC-MSCs cultured in normoxic (21% O2) and hypoxic (5% O2) conditions were collected for microRNA identification. Zeta View Laser Scattering and transmission electron microscopy were used to observe the size and morphology of extracellular vesicles. qRT-PCR was performed to measure the expression of related microRNAs. The Gene Ontology and KEGG pathway were used to predict the function of microRNAs. Finally, the effects of hypoxia on the expression of related mRNAs and cellular activity were examined. This study identified 35 upregulated and 8 downregulated microRNAs in the hypoxia group. We performed target genes analysis to explore the potential function of these microRNA upregulated in the hypoxia group. Significant enrichment of the cell proliferation, pluripotency of stem cells, MAPK, Wnt, and adherens junction pathways were observed in the GO and KEGG pathways. Under hypoxic conditions, the expression levels of 7 target genes were lower than that of the normal environment. In conclusion, this study demonstrated for the first time that microRNA expression in extracellular vesicles of human umbilical vein stem cells cultured under hypoxia is different from that under normal conditions, and these microRNAs may be markers for detecting hypoxia.

Indoleamine 2,3-dioxygenase 1 promotes osteosarcoma progression by regulating tumor-derived exosomal miRNA hsa-miR-23a-3p.

Background: Osteosarcoma (OS) is the most common primary malignant tumor originating in bone. Immunosuppressive enzyme indoleamine 2,3-dioxygenase 1 (IDO1) participates in tumor immune tolerance and promotes tumor progression, while the study of IDO1 in OS is limited. Methods: Immunohistochemistry analysis was performed to test the expression of IDO1 and Ki67. The relationship between IDO1 or Ki67 positive count and clinical stage of the patient was analyzed. Laboratory test indexes including serum alkaline phosphatase (ALP), lactate dehydrogenase (LDH), white blood cell (WBC) count and C-reactive protein (CRP) at diagnosis of OS patients were collected. The relationship between positive count of IDO1 and Ki67 or laboratory test indexes was analyzed by Pearson's correlation analysis. IDO1 stably overexpressed cell lines of these cells (MG63 OE, 143B OE and hFOB1.19 OE) were constructed and validated by Western blot and Elisa. Exosomes were isolated from conditioned culture media of these cells and were identified by Zetaview nanoparticle tracking analyzer. Next-generation sequencing was conducted to identify miRNAs enriched in exosomes. Differentially expressed miRNAs (DE miRNAs) were verified in clinical samples and cell lines by qPCR. Biological processes and cell components analysis of DE miRNAs was conducted by GO enrichment analysis using the protein interaction network database. Results: Immunosuppressive enzyme IDO1 was highly expressed in tumor tissues. 66.7% (6/9) of the tissues showed moderately or strongly positive immunostaining signal of IDO1, and 33.3% (3/9) were weakly positive. The expression of IDO1 was positively related to Ki67 and associated with prognostic-related clinical features of OS patients. Overexpression of IDO1 significantly affected the exosome-derived miRNA subsets from MG63, 143B and hFOB1.19 cells. A total of 1244 DE miRNAs were identified, and hsa-miR-23a-3p was further screened as key DE miRNA involved in the progression of OS. GO analysis of target genes of the DE miRNA results showed that target enrichment in the functions of immune regulation and tumor progression. Discussion: Our results indicate that IDO1 has the potential to promote the progression of OS that is related to miRNAs mediated tumor immunity. Targeting IDO1-mediated hsa-miR-23a-3p may be a potential therapeutic strategy for OS treatment.

Bone marrow mesenchymal stem cell-derived exosomes loaded with miR-26a through the novel immunomodulatory peptide DP7-C can promote osteogenesis.

As small bioactive molecules, exosomes can deliver osteogenesis-related miRNAs to target cells and promote osteogenesis. This study aimed to investigate miR-26a as a therapeutic cargo to be loaded into bone marrow stromal cell exosomes through a novel immunomodulatory peptide (DP7-C). After transfecting BMSCs with DP7-C as a transfection agent, exosomes were extracted by ultracentrifugation from the culture supernatant of miR-26a-modified BMSCs. We then characterized and identified the engineered exosomes. The effect of the engineered exosomes on osteogenesis was then evaluated in vitro and in vivo, including transwell, wound healing, modified alizarin red staining, western blot, real-time quantitative PCR, and experimental periodontitis assays. Bioinformatics and data analyses were conducted to investigate the role of miR-26a in bone regeneration. The DP7-C/miR-26a complex successfully transfected miR-26a into BMSCs and stimulated them to release more than 300 times the amount of exosomes overexpressing miR-26a compared with the ExoNC group. Furthermore, exosomes loaded with miR-26a could enhance proliferation, migration, and osteogenic differentiation of BMSCs in vitro compared with the ExoNC and blank groups. In vivo, the ExomiR-26a group inhibited the destruction of periodontitis compared with the ExoNC and blank groups, as revealed by HE staining. Micro-CT indicated that treatment of ExomiR-26a increased the percent bone volume and the bone mineral density compared with those of the ExoNC (P < 0.05) and blank groups (P < 0.001). Target gene analysis indicated that the osteogenic effect of miR-26a is related to the mTOR pathway. miR-26a can be encapsulated into exosomes through DP7-C. Exosomes loaded with miR-26a can promote osteogenesis and inhibit bone loss in experimental periodontitis and serve as the foundation for a novel treatment strategy.

Vitamin D inhibits osteosarcoma by reprogramming nonsense-mediated RNA decay and SNAI2-mediated epithelial-to-mesenchymal transition.

Osteosarcomas are immune-resistant and metastatic as a result of elevated nonsense-mediated RNA decay (NMD), reactive oxygen species (ROS), and epithelial-to-mesenchymal transition (EMT). Although vitamin D has anti-cancer effects, its effectiveness and mechanism of action against osteosarcomas are poorly understood. In this study, we assessed the impact of vitamin D and its receptor (VDR) on NMD-ROS-EMT signaling in in vitro and in vivo osteosarcoma animal models. Initiation of VDR signaling facilitated the enrichment of EMT pathway genes, after which 1,25(OH)2D, the active vitamin D derivative, inhibited the EMT pathway in osteosarcoma subtypes. The ligand-bound VDR directly downregulated the EMT inducer SNAI2, differentiating highly metastatic from low metastatic subtypes and 1,25(OH)2D sensitivity. Moreover, epigenome-wide motif and putative target gene analysis revealed the VDR's integration with NMD tumorigenic and immunogenic pathways. In an autoregulatory manner, 1,25(OH)2D inhibited NMD machinery genes and upregulated NMD target genes implicated in anti-oncogenic activity, immunorecognition, and cell-to-cell adhesion. Dicer substrate siRNA knockdown of SNAI2 revealed superoxide dismutase 2 (SOD2)-mediated antioxidative responses and 1,25(OH)2D sensitization via non-canonical SOD2 nuclear-to-mitochondrial translocalization leading to overall ROS suppression. In a mouse xenograft metastasis model, the therapeutically relevant vitamin D derivative calcipotriol inhibited osteosarcoma metastasis and tumor growth shown for the first time. Our results uncover novel osteosarcoma-inhibiting mechanisms for vitamin D and calcipotriol that may be translated to human patients.

A Tumor and Immune-Related Micro-RNA Signature Predicts Relapse-Free Survival of Melanoma Patients Treated with Ipilimumab.

Despite the unprecedented advances in the treatment of melanoma with immunotherapy, there continues to be a major need for biomarkers of clinical benefits and immune resistance associated with immune checkpoint inhibitors; microRNA could play a vital role in these efforts. This study planned to identify differentially expressed miRNA molecules that may have prognostic value for clinical benefits. Patients with surgically operable regionally advanced melanoma were treated with neoadjuvant ipilimumab (10 mg/kg intravenously every 3 weeks × two doses) bracketing surgery. Tumor biospecimens were obtained at baseline and surgery, and microRNA (miRNA) expression profiling was performed on the tumor biopsies. We found that an expression profile consisting of a 4-miRNA signature was significantly associated with improved relapse-free survival (RFS). The signature consisted of biologically relevant molecules previously reported to have prognostic value in melanoma and other malignancies, including miR-34c, miR-711, miR-641, and miR-22. Functional annotation analysis of target genes for the 4-miRNA signature was significantly enriched for various cancer-related pathways, including cell proliferation regulation, apoptosis, the MAPK signaling pathway, and the positive regulation of T cell activation. Our results presented miRNAs as potential biomarkers that can guide the treatment of melanoma with immune checkpoint inhibitors. These findings warrant further investigation in relation to CTLA4 blockade and other immune checkpoint inhibitors. ClinicalTrials.gov NCT00972933.

Elucidating the material basis and potential mechanisms of Myricaria germanica acting on rheumatoid arthritis by UPLC-Q-TOF-MS /MS and network pharmacology

ObjectiveThis study used the UPLC-Q-TOF-MS/MS technique, network pharmacology, and molecular docking technology to elucidate the molecular mechanism of action of Myricaria germanica against rheumatoid arthritis. MethodsThe UPLC-Q-TOF MS/MS technique and Swiss Target Prediction databases were used to select active compounds for Myricaria germanica and to predict relevant targets, respectively. The targets of rheumatoid arthritis were obtained from the TTD and GeneCards databases. Constructing protein interaction networks utilizing the String database, GO functional enrichment analysis, and KEGG pathway enrichment analysis of target genes utilizing the DAVID database, constructing "component-potential target-pathway" networks utilizing Cytoscape 3.9.1 software, and finally performing molecular docking utilizing Autodock Vina and other software. ResultsMyricaria germanica screened 47 chemical components and 302 component targets, obtaining 4017 disease targets, and 32 intersection targets of chemical component targets and disease targets using the Veen diagram. PPI results demonstrate the greatest impact on TNF, VEGFA, ALB, etc. The GO enrichment analysis of 32 targets associated with rheumatoid arthritis reveals that all of these targets are associated with 129 biological processes, including the process of collagen degeneration and the positive regulation of the RNA polymerase II promoter. KEGG enrichment analysis reveals that 87 signaling pathways are involved in these rheumatoid arthritis-related targets, with the IL-17, Relaxin, and TNF signaling pathways being the most significant. As deduced from the network diagram of ingredient-potential target-pathway, the key ingredients for the treatment of rheumatoid arthritis in Myricaria germanica are Apigenin, Quillaic Acid, and Isorhamnetin, and the associated targets are MMP9, PTGS2, and TNF, with a binding energy of less than -4.25 kcal/mol. ConclusionMyricaria germanica may act on potential core targets such as TNF, PTGS2, and MMP9 through key active ingredients such as Apigenin, Quillaic Acid, and Isorhamnetin to regulate signaling pathways such as IL-17, TNF, and Relaxin to exert therapeutic effects on rheumatoid arthritis.

Small RNA-seq and hormones in the testes of dwarf hamsters (Cricetulus barabensis) reveal the potential pathways in photoperiod regulated reproduction

Photoperiod regulates the functions and development of gonadal organs of seasonally breeding animals, resulting in breeding peaks in specific seasons. miRNA plays an important role in the regulation of testicular physiological functions. However, the relationship between photoperiods and miRNA levels in testes has yet to be conclusively determined. We investigated testicular miRNA of striped dwarf hamster (Cricetulus barabensis) responses to different photoperiods (long daylength [LD], moderate daylength [MD], and short daylength [SD]) and the potential pathways involved in photoperiod regulated reproduction. Testicular weights and reproductive hormone levels were measured in each of photoperiod treatments after 30 days. The concentrations of testosterone (T) and dihydrogen testosterone (DHT) in testes and Gonadotropin-releasing hormone (GnRH), follicle-stimulating hormone (FSH), and luteinizing hormone (LH) in serum were higher in MD than in the other two groups. Testicular weights were heaviest in MD. Small RNA-seq was performed for the testes of hamsters in three groups. A total of 769 miRNAs were identified, of which 83 were differentially expressed between LD, MD, and SD. GO and KEGG analysis of target genes revealed that some miRNAs influence testicular activities by regulating the pathways related to cell apoptosis and metabolism. Gene expression pattern analysis showed that the MAPK signaling pathway may be the core pathway for photoperiodic regulation of reproduction. These results suggest that moderate daylength is more suitable for hamster reproduction while long daylength and short daylength may regulate reproduction through different molecular pathways.

Genome-wide analyses of LATERAL ORGAN BOUNDARIES in cassava reveal the role of LBD47 in defence against bacterial blight.

The Arabidopsis thaliana ASYMMETRIC LEAVES2 (AS2) gene is responsible for the development of flat, symmetric, and extended leaf laminae and their veins. The AS2 gene belongs to the plant-specific AS2-LIKE/LATERAL ORGAN BOUNDARIES (LOB)-domain (ASL/LBD), which consists of 42 proteins in Arabidopsis with a conserved amino-terminal domain known as the AS2/LOB domain, and a variable carboxyl-terminal region. AS2/LOB domain consists of an amino-terminal (N-terminal) that contains a cysteine repeat (the C-motif), a conserved glycine residue, and a leucine-zipper-like. AS2/LOB domain has been characterised in plants such as A. thaliana, Zea mays, and Oryza sativum. Nevertheless, it remains uncharacterised in cassava (Manihot esculenta). Characterisation and identification of cassava ASL/LBD genes using the computational algorithms, hidden Markov model profiles (PF03195), determined 55 ASL/LBD genes (MeASLBD1 to MeASLBD55). The gene structure and motif composition were conserved in MeASLBDs, while the expression profiles of these genes were highly diverse, implying that they are associated with diverse functions. Weighted gene co-expression network analysis (WGCNA) of target genes and promoter analysis suggest that these MeASLBDs may be involved in hormone and stress responses. Furthermore, the analysis of cis-regulatory elements in promoter regions suggested that MeASLBDs may be involved in the plant phytohormone signal response. The transcriptome data of cassava under biotic and abiotic stresses revealed that MeASLBD46 and MeASLBD47 greatly respond to disease and drought. The MeASLBD47 gene was selected for functional analysis. The result indicated that MeASLBD47 significantly mitigated the virulence of cassava bacterial blight (XamCHN11) through Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) and Virus-induced gene silencing (VIGS). These findings provided a comprehensive analysis of ASL/LBD genes and laid the groundwork for future research to understand ASL/LBD genes.

Identification of MicroRNAs Regulating Clostridium perfringens Type C Infection in the Spleen of Diarrheic Piglets

Clostridium perfringens (C. perfringens) type C is one of the common bacteria in piglet diarrhea, which seriously affects the swine industry's development. The spleen plays crucial roles in the resistance and elimination of pathogenic microorganisms, and miRNAs play important roles in regulating piglet diarrhea caused by pathogens. However, the mechanism by which miRNAs in the spleen are involved in regulating C. perfringens type C causing diarrhea in piglets remains unclear. The expression profiles of the spleen miRNAs of 7-day-old piglets challenged by C. perfringens type C were studied using small RNA-sequencing in control (SC), susceptible (SS), and resistant (SR) groups. Eight-eight differentially expressed miRNAs were screened. The KEGG pathway analysis of target genes revealed that the miRNAs were involved in the MAPK, p53, and ECM-receptor interaction signaling pathways. NFATC4 was determined to be a direct target of miR-532-3p and miR-133b using a dual-luciferase reporter assay. Thus, miR-133b and miR-532-3p targeted to NFATC4 were likely involved to piglet resistance to C. perfringens type C. This paper provides the valuable resources to deeply understand the genetic basis of C. perfringens type C resistance in piglets and a solid foundation to identify novel markers of C. perfringens type C resistance.

Characterization of microRNAs and Target Genes in Musa acuminata subsp. burmannicoides, var. Calcutta 4 during Interaction with Pseudocercospora musae

Endogenous microRNAs (miRNAs) are small non-coding RNAs that perform post-transcriptional regulatory roles across diverse cellular processes, including defence responses to biotic stresses. Pseudocercospora musae, the causal agent of Sigatoka leaf spot disease in banana (Musa spp.), is an important fungal pathogen of the plant. Illumina HiSeq 2500 sequencing of small RNA libraries derived from leaf material in Musa acuminata subsp. burmannicoides, var. Calcutta 4 (resistant) after inoculation with fungal conidiospores and equivalent non-inoculated controls revealed 202 conserved miRNAs from 30 miR-families together with 24 predicted novel miRNAs. Conserved members included those from families miRNA156, miRNA166, miRNA171, miRNA396, miRNA167, miRNA172, miRNA160, miRNA164, miRNA168, miRNA159, miRNA169, miRNA393, miRNA535, miRNA482, miRNA2118, and miRNA397, all known to be involved in plant immune responses. Gene ontology (GO) analysis of gene targets indicated molecular activity terms related to defence responses that included nucleotide binding, oxidoreductase activity, and protein kinase activity. Biological process terms associated with defence included response to hormone and response to oxidative stress. DNA binding and transcription factor activity also indicated the involvement of miRNA target genes in the regulation of gene expression during defence responses. sRNA-seq expression data for miRNAs and RNAseq data for target genes were validated using stem-loop quantitative real-time PCR (qRT-PCR). For the 11 conserved miRNAs selected based on family abundance and known involvement in plant defence responses, the data revealed a frequent negative correlation of expression between miRNAs and target host genes. This examination provides novel information on miRNA-mediated host defence responses, applicable in genetic engineering for the control of Sigatoka leaf spot disease.

RBFOX2 modulates a metastatic signature of alternative splicing in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDA) is characterized by aggressive local invasion and metastatic spread, leading to high lethality. Although driver gene mutations during PDA progression are conserved, no specific mutation is correlated with the dissemination of metastases1–3. Here we analysed RNA splicing data of a large cohort of primary and metastatic PDA tumours to identify differentially spliced events that correlate with PDA progression. De novo motif analysis of these events detected enrichment of motifs with high similarity to the RBFOX2 motif. Overexpression of RBFOX2 in a patient-derived xenograft (PDX) metastatic PDA cell line drastically reduced the metastatic potential of these cells in vitro and in vivo, whereas depletion of RBFOX2 in primary pancreatic tumour cell lines increased the metastatic potential of these cells. These findings support the role of RBFOX2 as a potent metastatic suppressor in PDA. RNA-sequencing and splicing analysis of RBFOX2 target genes revealed enrichment of genes in the RHO GTPase pathways, suggesting a role of RBFOX2 splicing activity in cytoskeletal organization and focal adhesion formation. Modulation of RBFOX2-regulated splicing events, such as via myosin phosphatase RHO-interacting protein (MPRIP), is associated with PDA metastases, altered cytoskeletal organization and the induction of focal adhesion formation. Our results implicate the splicing-regulatory function of RBFOX2 as a tumour suppressor in PDA and suggest a therapeutic approach for metastatic PDA.

RNA sequencing-based exploration of the effects of far-red light on microRNAs involved in the shade-avoidance response of D. officinale.

Dendrobium officinale (D. officinale) has remarkable medicinal functions and high economic value. The shade-avoidance response to far-red light importantly affects the D. officinale productivity. However, the regulatory mechanism of miRNAs involved in the far-red light-avoidance response is unknown. Previous studies have found that, in D. officinale, 730 nm (far-red) light can promote the accumulation of plant metabolites, increase leaf area, and accelerate stem elongation. Here, the effects of far-red light on D. officinale were analysed via RNA-seq. KEGG analysis of miRNA target genes revealed various far-red light response pathways, among which the following played central roles: the one-carbon pool by folate; ascorbate and aldarate; cutin, suberine and wax biosynthesis; and sulfur metabolism. Cytoscape analysis of DE miRNA targets showed that novel_miR_484 and novel_miR_36 were most likely involved in the effects of far-red light on the D. officinale shade avoidance. Content verification revealed that far-red light promotes the accumulation of one-carbon compounds and ascorbic acid. Combined with qPCR validation results, the results showed that miR395b, novel_miR_36, novel_miR_159, novel_miR_178, novel_miR_405, and novel_miR_435 may participate in the far-red light signalling network through target genes, regulating the D. officinale shade avoidance. These findings provide new ideas for the efficient production of D. officinale.

Foxm1 regulates cardiomyocyte proliferation in adult zebrafish after cardiac injury.

The regenerative capacity of the mammalian heart is poor, with one potential reason being that adult cardiomyocytes cannot proliferate at sufficient levels to replace lost tissue. During development and neonatal stages, cardiomyocytes can successfully divide under injury conditions; however, as these cells mature their ability to proliferate is lost. Therefore, understanding the regulatory programs that can induce post-mitotic cardiomyocytes into a proliferative state is essential to enhance cardiac regeneration. Here, we report that the forkhead transcription factor Foxm1 is required for cardiomyocyte proliferation after injury through transcriptional regulation of cell cycle genes. Transcriptomic analysis of injured zebrafish hearts revealed that foxm1 expression is increased in border zone cardiomyocytes. Decreased cardiomyocyte proliferation and expression of cell cycle genes in foxm1 mutant hearts was observed, suggesting it is required for cell cycle checkpoints. Subsequent analysis of a candidate Foxm1 target gene, cenpf, revealed that this microtubule and kinetochore binding protein is also required for cardiac regeneration. Moreover, cenpf mutants show increased cardiomyocyte binucleation. Thus, foxm1 and cenpf are required for cardiomyocytes to complete mitosis during zebrafish cardiac regeneration.

A NETWORK PHARMACOLOGICAL INVESTIGATION INTO THE TREATMENT OF PERIMENOPAUSAL DEPRESSION WITH A WARMING AND TONIFYING KIDNEY-YANG RECIPE

We examine the mechanism of warming and tonifying kidney-yang recipe (WTKYR) in treating perimenopausal depression (PMD) using a network pharmacological approach. We identified the active ingredients and targets of WTKYR using the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. PMD targets were extracted from the Online Mendelian Inheritance in Man (OMIM), DisGeNET, and GeneCards databases. Venn diagrams were created with Venny to identify common WTKYR and PMD targets. A network diagram of WTKYR targets in PMD was created with Cytoscape to examine its core active ingredients. A protein–protein interaction (PPI) network of WTKYR’s targets was constructed using the STRING database, and its primary targets were evaluated using Network Analyzer and MCODE. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of essential WTKYR target genes were performed with Bioconductor. The LibDock program was applied to molecularly dock the core active ingredients of the WTKYR and the critical targets of PMD. The core WTKYR components for PMD identified were as oleic acid, beta-sitosterol, and phytodolor. The core WTKYR targets identified were the Jun proto-oncogene AP-1 transcription factor subunit (JUN), peroxisome proliferator-activated receptor gamma (PPARG), brain-derived neurotrophic factor (BDNF), caspase 3 (CASP3), and estrogen receptor 1 (ESR1) proteins and the neurotrophin, estrogen, serotonergic synapse, and cyclic adenosine monophosphate (cAMP) signaling pathways. The primary functions of these pathways include extensive neuroprotective and regenerative effects, regulation of 5-hydroxytryptamine (5-HT) metabolism, and participation in regulating the physiological functions of endogenous substances. These improve synaptic sensitivity, promote neuronal cell excitability, and enhance persistent firing in the medial and lateral entorhinal cortex. Molecular docking results show good affinity between the core active ingredients of WTKYR and the critical targets of PMD. This study predicted the essential WTKYR components and its primary targets and pathways for PMD treatment, and found that improving synaptic plasticity, participating in neuroelectrophysiological processes, and regulating related signaling pathways enhance PMD, which require confirmation by future cell or animal validation experiments.

Astragaloside IV inhibits angiotensin II-induced aortic dissection formation by regulating miR-320a/matrix metallopeptidase 9 axis

This study explored the role of miR-320a and Matrix metallopeptidase 9 (MMP-9) in aortic dissection (AD) formation. Aortic tissue diameter (LD) and medial thickness (MT) were measured after the AD model was established. Aortic smooth muscle cells (VSMCs) were assigned into blank group, Astragaloside IV (AS-IV), which was treated with 100, 150 or 200 μg/mL and AngII group. Cells in the AngII group were added with MMP9 inhibitor (MMP9 inhibitor group) and mimics (MMP9 mimics group), followed by analysis of cell proliferation, apoptosis, and target gene for miR-320a. Aortic tissue diameter(LD) from the AD group was significantly higher and MT was lower than in the control group (p&lt;0.05). VSMCs proliferative activity in the AS-IV group and AngII group was increased significantly (p &lt;0.05), with lower activity in the AS-IV group than AngII group (p &lt; 0.05). After transfection, the VSMCs apoptosis in the AngII group was decreased (p &lt;0.05). In addition, cell migration in the AS-IV and AngII groups increased (p &lt;0.05), with lower ability in the AS-IV group than in the AngII group (p &lt;0.05). Alpha smooth muscle Actin (α-SMA) expression was elevated after AngII stimulation and decreased after AS-IV treatment (p &lt;0.05). After AngII stimulation, miR-320a and MMP9 were upregulated (p &lt;0.05) and downregulated by AS-IV (p &lt;0.05). MMP9 is a target gene for miR-320a. miR-320a and MMP9 expressions in the AS-IV group were significantly decreased, with lowest levels in the AS-IV-200 μg/mL group. In addition, MMP9 overexpression reduced the AngII expression. The expression of miR-320a/MMP9 axis was low in the AD, and activity were increased after AngII stimulation. In conclusion, As-IV can relieve the occurrence of AD via regulation of miR-320a/MMP9 axis.

Metabolic pathways of potential miRNA biomarkers derived from liquid biopsy in epithelial ovarian cancer.

Epithelial ovarian cancer (EOC) is the type of OC with the highest mortality rate. Due to the asymptomatic nature of the disease and few available diagnostic tests, it is mostly diagnosed at the advanced stage. Therefore, the present study aimed to discover predictive and/or early diagnostic novel circulating microRNAs (miRNAs or miRs) for EOC. Firstly, microarray analysis of miRNA expression levels was performed on 32 samples of female individuals: Eight plasma samples from patients with pathologically confirmed EOC (mean age, 45 (30-54) years), eight plasma samples from matched healthy individuals (HIs) (mean age, 44 (30-65) years), eight EOC tissue samples (mean age, 45 (30-54) years) and eight benign ovarian (mean age, 35 (17-70) years) neoplastic tissue samples A total of 31 significantly dysregulated miRNAs in serum and three miRNAs in tissue were identified by microarray. The results were validated using reverse transcription-quantitative PCR on samples from 10 patients with pathologically confirmed EOC (mean age, 47(30-54) years), 10 matched His (mean age, 40(26-65) years], 10 EOC tissue samples (mean age, 47(30-54) years) and 10 benign ovarian neoplastic tissue samples (mean age, 40(17-70) years). The 'Kyoto Encyclopedia of Genes and Genomes' (KEGG) database was used for target gene and pathway analysis. A total of three miRNAs from EOC serum (hsa-miR-1909-5p, hsa-miR-885-5p and hsa-let-7d-3p) and one microRNA from tissue samples (hsa-miR-200c-3p) were validated as significant to distinguish patients with EOC from HIs. KEGG pathway enrichment analysis showed seven significant pathways, which included 'prion diseases', 'proteoglycans in cancer', 'oxytocin signaling pathway', 'hippo signaling pathway', 'adrenergic signaling in cardiomyocytes', 'oocyte meiosis' and 'thyroid hormone signaling pathway', in which the validated miRNAs served a role. This supports the hypothesis that four validated miRNAs, have the potential to be a biomarker of EOC diagnosis and target for treatment.