Predicted Target Genes Research Articles

The expression profile analysis and functional prediction of lncRNAs in peripheral blood mononuclear cells in maintenance hemodialysis patients developing heart failure

Heart failure (HF) is the leading cause of death in patients with maintenance hemodialysis (MHD). Biomarkers has an important guiding role in the early diagnosis, risk stratification, and prognostic assessment of HF. Increasing studies have indicated that long non-coding RNAs (lncRNAs) have played an indispensable role in the regulatory network of HF. This study was aiming to explore the expression profiles of lncRNAs in patients treated with MHD developing heart failure. Peripheral blood mononuclear cells were isolated from 4 hemodialysis patients with reduced ejection fraction (HFrEF) and 4 hemodialysis patients with preserved ejection fraction (HFpEF), respectively. The expression profile analysis of lncRNAs was performed by using Illumina Novaseq 6000 sequencer. Quantitative real time polymerase chain reaction (qRT-PCR) was used to verify the expression of representative differentially expressed lncRNAs. Based on lncRNA-miRNA-mRNA-KEGG network analysis, the potential role of candidate lncRNAs and their association with the severity of HF were further evaluated. In total, 1,429 differentially expressed lncRNAs were found between patients with HFrEF and patients with HFpEF, of which 613 were up-regulated and 816 were down-regulated (P < 0.05). Five candidate lncRNAs were screened out by a series of bioinformatic analyses. After being compared with miRBase, ENST00000561762, one of the 5 candidates, was considered the most likely lncRNA to be serving as a precursor for miRNA. Nine predicted target genes were found by further lncRNA-miRNA-mRNA-KEGG network analysis, and among which ITGB5 was enriched in the actin dynamics signaling pathway. In another cohort of hemodialysis patients, the expression of lncRNA ENST00000561762 was verified by qRT-PCR. Further analysis revealed that there was a strong correlation between left ventricular ejection fraction and ENST00000561762, proBNP, and 6-minute walk distance, respectively. LncRNAs expression profile was remarkably different in hemodialysis patients with HFrEF compared to those with HFpEF. Among which, lncRNA ENST00000561762 was considered as a promising biomarker for patients with HFrEF as it was predicted to be a miRNA precursor to regulate the actin dynamics signaling pathway.

Identification of miRNAs Involved in Lipid Metabolism and Tuber Development in Cyperus esculentus L.

Tiger nut (Cyperus esculentus L.) is recognized for its high oil and oleic acid content in underground tubers. However, the molecular mechanisms governing growth, development, and fatty acid accumulation in these tubers are not well understood. This study employed gas chromatography–mass spectrometry (GC–MS) and small RNA sequencing on tiger nut tubers across five developmental stages. The findings indicate that the critical period for accumulating dry matter and oils, particularly oleic acid, occurs between 35 and 75 days after tuber formation. A total of 183 microRNAs (miRNAs) were identified, comprising 31 known and 152 novel miRNAs. Approximately half of these miRNAs (such as ces-miR156b-3p and ces-miR166a-3p) exhibited differential expression during and around the key periods of metabolite synthesis. The predicted target genes of these miRNAs were significantly enriched in glycerate 3-phosphate metabolism and cell growth processes. Furthermore, 13 miRNA–mRNA interaction modules related to oil accumulation and tuber growth were identified, and these target genes’ expression levels showed significant differences during the tuber developmental stages. These findings advance the understanding of the molecular mechanisms underlying tuber development and oil accumulation in tiger nut.

A machine learning model revealed that exosome small RNAs may participate in the development of breast cancer through the chemokine signaling pathway

BackgroundExosome small RNAs are believed to be involved in the pathogenesis of cancer, but their role in breast cancer is still unclear. This study utilized machine learning models to screen for key exosome small RNAs and analyzed and validated them.MethodPeripheral blood samples from breast cancer screening positive and negative people were used for small RNA sequencing of plasma exosomes. The differences in the expression of small RNAs between the two groups were compared. We used machine learning algorithms to analyze small RNAs with significant differences between the two groups, fit the model through training sets, and optimize the model through testing sets. We recruited new research subjects as validation samples and used PCR-based quantitative detection to validate the key small RNAs screened by the machine learning model. Finally, target gene prediction and functional enrichment analysis were performed on these key RNAs.ResultsThe machine learning model incorporates six small RNAs: piR-36,340, piR-33,161, miR-484, miR-548ah-5p, miR-4282, and miR-6853-3p. The area under the ROC curve (AUC) of the machine learning model in the training set was 0.985 (95% CI = 0.948-1), while the AUC in the test set was 0.972 (95% CI = 0.882–0.995). RT-qPCR was used to detect the expression levels of these key small RNAs in the validation samples, and the results revealed that their expression levels were significantly different between the two groups (P < 0.05). Through target gene prediction and functional enrichment analysis, it was found that the functions of the target genes were enriched mainly in the chemokine signaling pathway.ConclusionThe combination of six plasma exosome small RNAs has good prognostic value for women with positive breast cancer by imaging screening. The chemokine signaling pathway may be involved in the early stage of breast cancer. It is worth further exploring whether small RNAs mediate chemokine signaling pathways in the pathogenesis of breast cancer through the delivery of exosomes.

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.

Transcriptome profiling of maize transcription factor mutants to probe gene regulatory network predictions.

Transcription factors (TFs) play important roles in regulation of gene expression and phenotype. A variety of approaches have been utilized to develop gene-regulatory networks (GRNs) to predict the regulatory targets for each TF, such as yeast-one-hybrid (Y1H) screens and gene co-expression network (GCN) analysis. Here we identified potential TF targets and used a reverse genetics approach to test the predictions of several GRNs in maize. Loss-of-function mutant alleles were isolated for 22 maize TFs. These mutants did not exhibit obvious morphological phenotypes. However, transcriptomic profiling identified differentially expressed genes in each of the mutant genotypes, and targeted metabolic profiling indicated variable phenolic accumulation in some mutants. An analysis of expression levels for predicted target genes based on Y1H screens identified a small subset of predicted targets that exhibit altered expression levels. The analysis of predicted targets from GCN-based methods found significant enrichments for prediction sets of some TFs, but most predicted targets did not exhibit altered expression. This could result from false-positive GCN predictions, a TF with a secondary regulatory role resulting in minor effects on gene regulation, or redundant gene regulation by other TFs. Collectively, these findings suggest that loss-of-function for single uncharacterized TFs might have limited phenotypic impacts but can reveal subsets of GRN predicted targets with altered expression.

Plasma-derived exosomes of Edwardsiella piscicida challenged olive flounder (Paralichthys olivaceus): Characterization and miRNA profiling for potential biomarkers screening

Exosomes are released from multiple cell types as part of their normal physiology as well as during acquired abnormalities. In this study, we investigated the effect of pathogenic Edwardsiella piscicida infection on olive flounder (Paralichthys olivaceus) exosomes at morphometric, physicochemical, and molecular levels. Unique cup-shaped exosomes were isolated from the plasma of non-infected (PBS-Exo) and E. piscicida experimentally challenged (Ep-Exo) olive flounder using ultracentrifugation. The average particle size, concentration, and zeta potential were 150.9 ± 6.9 nm, 5.67 × 1010 particles/mL, and −25.6 ± 1.36 mV for PBS-Exo while 138.7 ± 1.9 nm, 1.22 × 1011 particles/mL, and −35 ± 1.82 mV for Ep-Exo, respectively. Expression of tetraspanin markers (CD81, CD9, and CD63) confirmed the presence of olive flounder exosomes. Differentially expressed (DE) known (9) and novel (29) miRNAs (log2 fold change ≥1; p < 0.05) were identified in the Ep-Exo that could be potential as diagnostic biomarkers for the infection. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that the predicted target genes of the DE miRNAs were highly enriched in metabolic and immune roles. Both PBS-Exo and Ep-Exo were non-toxic in vitro (up to 100 μg/mL) and in vivo (up to 400 μg/mL). Compared to the vehicle, PBS-Exo at 50 μg/mL induced Nf-kB (>1.50-fold) while at 100 μg/mL, Il8, Il10, Nf-kB, P53, and Inf were induced (>1.50-fold) in fathead minnow cells (FHMs). This suggests that the PBS-Exo contains molecules that moderately stimulate gene expression. In the future, validating the exact olive flounder immune response target genes that interact with DE miRNAs in Ep-Exo will be crucial for investigating the host-pathogen interactions, immune defense mechanisms, and therapeutic targets for olive flounder against E. piscicida infection.

Mechanism of MiR-145a-3p/Runx2 pathway in dexamethasone impairment of MC3T3-E1 osteogenic capacity in mice.

In this experiment, we screened key miRNAs involved in the dexamethasone-induced decrease in osteogenic capacity of mouse precursor osteoblasts MC3T3-E1 over and investigated their specific regulatory mechanisms. In this experiment, cell counting kit assay was utilized to act on MC3T3-E1 cells at 0, 5μM, 10μM, 15μM concentrations of dexamethasone for 24h, 48h and 72h to observe the changes in cell viability in order to select the appropriate dexamethasone concentration. Apoptosis and reactive oxygen species were detected by flow cytometry. The transcription of osteogenesis-related genes (Runx2, ALP, OCN, OPN, OPG, COL1A1) and protein expression levels (Runx2, ALP, OCN, OPN) were detected by Western Blot and qRT-PCR to validate the changes in cellular osteogenesis. The differentially expressed miRNAs related to MC3T3-E1 osteogenic differentiation after dexamethasone action were screened out. The expression levels of selected target miRNAs were verified in the experimental group and the control group by qRT-PCR. The miRNA inhibitor was transfected to knock down miRNA in dexamethasone-induced MC3T3-E1 injury. Alkaline phosphatase staining and flow cytometry were performed to detect apoptosis and reactive oxygen species changes. transcript and protein expression levels of osteogenesis-related genes in mouse MC3T3-E1 were detected by qRT-PCR and Western blot experiments. By miRNA target gene prediction, luciferase reporter gene experiments, qRT-PCR and Western blot experiments were used to verify whether the selected target miRNAs targeted the target gene. First, it was determined that 10μM dexamethasone solution was effective in inducing a decrease in osteogenic function in mouse MC3T3-E1 by CCK8 experiments, which showed a significant decrease in alkaline phosphatase activity, a decrease in calcium nodules as shown by alizarin red staining, an increase in apoptosis and reactive oxygen species as detected by flow cytometry, as well as a decrease in the expression of osteogenesis-related genes and proteins. Five target miRNAs were identified: miR-706, miR-296-3p, miR-7011-5p, miR-145a-3p, and miR-149-3p. miR-145a-3p, which had the most pronounced and stable expression trend and was the most highly expressed miRNA, was chosen as the target of this experiment by qRT-PCR analysis. -145a-3p, as the subject of this experiment. Knockdown of miR-145a-3p in MC3T3-E1 cells after dexamethasone action significantly improved the expression of their impaired osteogenic indicators. It was shown that after knocking down the target miRNA, alkaline phosphatase staining was significantly increased compared with the dexamethasone-stimulated group and approached the level of the blank control group. Meanwhile, the expression of osteogenic function-related proteins and genes also increased in the dexamethasone-stimulated group after knocking down miR-145a-3p, and approached the level of the blank control group. A direct targeting relationship between miR-145a-3p and Runx2 was indeed confirmed by luciferase reporter gene assays, qRT-PCR and Western blot experiments. The results indicated that dexamethasone impaired the osteogenic differentiation ability of MC3T3-E1 cells by inducing the up-regulation of miR-145a-3p expression. MiR-145a-3p inhibited the osteogenic differentiation ability of MC3T3-E1 cells by targeting and suppressing the expression level of Runx2 protein. Inhibition of miR-145a-3p levels significantly improved the osteogenic differentiation ability of MC3T3-E1 cells.

Bio-characteristics, tissue expression of miR-375 in hypothalamic-pituitary-ovarian axis and its regulation in reproduction-related diseases

Our study concentrated on the expression of miRNA-375 in the hypothalamic-pituitary-gonadal axis of female Hu sheep. The investigation involved cloning the precursor sequence of miR-NA-375, followed by comparison with database entries and subsequent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. In our approach, we obtained ovaries, thalamus, cerebellum, brain, uterus, pituitary gland, hypothalamus, and pineal gland from fertile but nonpregnant Hu ewes. MiRNA extraction kit was used to extract miRNA from the above eight tissues. Real-time fluorescent quantitative polymerase chain reaction was used to evaluate the role of miR-375 in the hy-pothalamic-pituitary-gonadal axis. The results of miR-375 precursor sequence cloning were compared with those of Anopheles gambiae, Apis mellifera, Bos taurus, Drosophila melanogaster, Danio rerio, Fugu rubripes, Gallus gallus, Homo sapiens, Monodelphis domestica, Macaca mulatta, Mus musculus, Pan troglodytes, Rattus norvegicus, Tetraodon nigroviridis, Xenopus tropicalis miR-375 in miRBase database. It was found that oar-miR-375 was highly conserved. Notably, miR-375 expression in the pineal gland was significantly higher (p < 0.01) than that in the ovaries, thalamus, cerebellum, brain, uterus, pituitary gland, hypothalamus. The study also involved predicting miR-375 target genes. GO and KEGG enrichment analyses of these predicted target genes revealed that miR-375 is involved in 182 biological processes, affects 186 cellular components, and participates in 184 molecular functions. In terms of pathway enrichment, miR-375 was linked to nine pathways, including the Hippo, Wnt, and mTOR signaling pathways. This study has validated the interaction between miR-375 and its target gene FZD4, which can be recognized and bound to produce effects. These findings lead to the inference that miR-375 may play a crucial regulatory role in sheep reproduction through the Hippo pathway and Wnt pathway, laying a foundation for further exploration of miR-375’s role in this domain.

Extracellular vesicle transfer of miR-1 to adipose tissue modifies lipolytic pathways following resistance exercise.

Extracellular vesicles (EVs) have emerged as important mediators of intertissue signaling and exercise adaptations. In this human study, we provide evidence that muscle-specific microRNA-1 (miR-1) was transferred to adipose tissue via EVs following an acute bout of resistance exercise. Using a multimodel machine learning automation tool, we discovered muscle primary miR-1 transcript and CD63+ EV count in circulation as top explanatory features for changes in adipose miR-1 levels in response to resistance exercise. RNA-Seq and in-silico prediction of miR-1 target genes identified caveolin 2 (CAV2) and tripartite motif containing 6 (TRIM6) as miR-1 target genes downregulated in the adipose tissue of a subset of participants with the highest increases in miR-1 levels following resistance exercise. Overexpression of miR-1 in differentiated human adipocyte-derived stem cells downregulated these miR-1 targets and enhanced catecholamine-induced lipolysis. These data identify a potential EV-mediated mechanism by which skeletal muscle communicates with adipose tissue and modulates lipolysis via miR-1.

Validation of Interaction Between Sugarcane miR167d and Predicted Target Gene ScPUM1 and Analysis of Their Expression Under Cold Stress: A Novel Mechanism of miR167d

Validation of Interaction Between Sugarcane miR167d and Predicted Target Gene ScPUM1 and Analysis of Their Expression Under Cold Stress: A Novel Mechanism of miR167d

MiR-193b-5p and miR-374b-5p Are Aberrantly Expressed in Endometriosis and Suppress Endometrial Cell Migration In Vitro.

(1) Background: Endometriosis is a highly prevalent gynecological disease affecting 10% of women of reproductive age worldwide. miRNAs may play a role in endometriosis, though their exact function remains unclear. This study aimed to identify differentially expressed miRNAs in endometriosis and study their functions in the disease. (2) Methods: Endometrial tissue was collected from women with endometriosis (n = 15) and non-endometriosis controls (n = 17). Dysregulated miRNAs were identified through small RNA-sequencing, and their biological significance was explored by target gene prediction and pathway analysis. Selected miRNAs were examined in paired ectopic endometriomas and eutopic endometrium (n = 10) using qRT-PCR. Their roles in cell migration and proliferation were further examined in vitro using functional assays. To identify potential target genes, we performed mRNA sequencing on transfected cells and the endometrioma cohort. (3) Results: We identified 14 dysregulated miRNAs in the eutopic endometrium of women with endometriosis compared to endometrial tissue from women without endometriosis. Pathway analysis indicated enrichment in cell migration and proliferation-associated pathways. Further ex vivo studies of miR-193b-5p and miR-374b-5p showed that both miRNAs were upregulated in endometrioma. Overexpression of these two miRNAs in vitro inhibited cell migration, and mRNA sequencing revealed several migration-related genes that are targeted by these miRNAs. (4) Conclusions: Our study identified two key endometrial miRNAs that may be involved in the pathogenesis of endometriosis by regulating cell migration.

MicroRNA profiling yields immune response and metabolic changes in juvenile largemouth bass (Micropterus salmoides) infected with LMBV

The largemouth bass virus (LMBV) exhibits high pathogenicity in both adult and juvenile largemouth bass, causing substantial economic losses within the aquaculture industry. MicroRNAs (miRNAs) are crucial in controlling viral infections and the host’s immune responses, making them significantly valuable in the treatment and diagnosis of diseases. Nevertheless, research on miRNA expression profiles associated with LMBV infection in largemouth bass is currently insufficient. This research attempts to investigate the roles and molecular mechanisms of miRNAs in the potential immune response and metabolic alterations triggered by LMBV infection in largemouth bass using miRNA sequencing. Following quality screening, the infection group and control group yielded a combined total of 142.73 million clean reads, with lengths predominantly at 22 nt. 1,718 known miRNAs were identified, including 238 differentially expressed miRNAs (DEMs). In addition, 400 novel miRNAs were predicted, 36 of which were DEMs. To gain further insight into the immune and metabolic related biological functions of DEMs, target gene prediction was conducted. KEGG pathway analysis revealed that LMBV impacted pathways such as Endocytosis, Purine metabolism, Phosphatidylinositol, Fatty acid Biosynthesis, and Phagosome signaling systems, highlighting the vital role of miRNAs in immune responses and metabolic alterations. Furthermore, the miRNA-mRNA interaction network revealed crucial miRNAs and their corresponding target genes involved in conferring resistance against viral infections by utilizing metabolic and immune related pathways as the foundation. Ten DEMs were selected at random for real-time quantitative PCR (qRT-PCR), and results exhibited expression patterns that were consistent with sequencing data. These findings validate the immune and metabolic regulatory function of miRNAs against LMBV in largemouth bass, offering valuable perspectives for the prevention and management of illnesses linked to iridoviruses.

Inhibition of miR-92a normalizes vascular gene expression and prevents diastolic dysfunction in heart failure with preserved ejection fraction

Heart failure with preserved ejection fraction (HFpEF) remains a major public health burden with increasing prevalence but only few effective therapies. Endothelial dysfunction and inflammation are identified as pathophysiological drivers of HFpEF disease progression. MicroRNAs are increasingly recognized as key regulators of these pathological processes, while antimiR-based therapies have been emerged as promising therapeutics in mice and humans. Therefore, we tested whether targeting miR-92a-3p inhibition is a promising therapeutic intervention to target HFpEF in vivo.By injection of locked nucleic acid (LNA)-based antimiR (LNA-92a) weekly, we demonstrate that inhibition of miR-92a-3p attenuates the development of diastolic dysfunction and left atrial dilation following experimental induction of HFpEF in mice. Indeed, LNA-92a depleted miR-92a-3p expression in the myocardium and peripheral blood, and derepressed predicted target genes in a cell type-specific manner. Furthermore, cell-type specific efficacy of LNA-92a treatment was assessed by single-nuclear RNA sequencing of HFpEF hearts either treated with LNA-92a or LNA-Control. Endothelial cells of LNA-92a treated mice showed normalized vascular gene expression and reduced gene signatures associated with endothelial-mesenchymal transition. ConclusionThis study demonstrates that LNA-based antimiR-92a is an effective therapeutic strategy to target diastolic dysfunction and left atrial dilation in HFpEF.

Assessing the antiproliferative properties of various teas against the DU-145 prostate cancer cell line: A combined in vitro and in silico investigation

BackgroundPhytotherapy emerges as a promising solution to the challenges posed by cancer treatment. Black, green, and purple teas, renowned for their antioxidant properties, exhibit efficacy against various cancers, including prostate cancer. Study DesignThis was an experimental study conducted from the Kenya Medical Research Institute (KEMRI). Aim of the Studythe present study aimed to evaluate the Cytotoxic effect of black, green and purple teas against prostate cancer cell line DU-145 and in silico prediction of Tea catechins interaction with prostate cancer proteins such as 3D-crystal structures of Androgen-receptor(5T8E) and Human p38 MAPK(1KV2). MethodsThe study started by quantifying tea catechins (Epigallocatechin gallate (EGCG), Epigallocatechin EGC, Epicatechin gallate (ECG) and Epicatechin (EC) with high-liquid chromatography (HPLC), cytotoxicity analysis of black, green and purple tea crude extracts against DU-145 cell line at 24hr and 48 hrs by Resazurin assay and molecular docking was performed with Autodock Vina 1.1.2 software. ResultsEGCG appeared the most predominant catechin with 552.2 ± 10.61 (mg g-1 DW) while EC was the lowest detected with 118.08 ± 9.45 (mg g-1 DW). Purple tea extract exhibited high antiproliferative activity with IC50 of 98.69±1.99 µg/ml at 24hr and 91.21±6.91 µg/ml at 48hr, green tea followed with 121 ± 5.97µg/ml at 24hr and 107.1 ± 2.03 µg/ml at 48hr IC50; black tea was the least effective tea at both 24hr and 48hr with IC50 of 290.8 ± 2.46µg/ml and 237.8 ± 5.59µg/ml respectively. Prediction of catechin target genes and Prostate cancer (Pca)-related genes discovered 121 catechin target genes and 34,926 Pca-related genes. EGC exhibited high binding interaction to 5T8E with the lowest affinity of -9.1Kcal/mol followed by EGCG at -8.4 (Kcal/mol then EC with -8.2 (Kcal/mol) and EGC at -8.1 (Kcal/mol). Catechins interaction with 1KV2 was in the following order EGCG (-9.4 Kcal/mol) ˃ECG (-8.2 Kcal/mol) ˃EC (-8.2 Kcal/mol) ˃EGC (-8.1 Kcal/mol). ConclusionIn vitro experiment detected a very significant antiproliferative activity of black, green and purple tea crude extracts against the DU-145 cell line; furthermore, in silico analysis revealed a strong binding interaction with proteins associated with prostate cancer, indicating that black, green, and purple teas, along with catechins, hold promise as potential herbal remedies for combating prostate cancer.

Integrated Analysis of microRNAs and Transcription Factor Targets in Floral Transition of Pleioblastus pygmaeus.

Bamboo plants have erratic flowering habits with a long vegetative growth and an uncertain flowering cycle. The process of floral transition has always been one of the hot and intriguing topics in bamboo developmental biology. As master modulators of gene expression at the post-transcriptional level, miRNAs play a crucial role in regulating reproductive growth, especially in floral transition of flowering plants. Pleioblastus pygmaeus is a kind of excellent ground cover ornamental bamboo species. In this study, we performed miRNA expression profiling of the shoot buds and flower buds from the bamboo species, to investigate flowering-related miRNAs in bamboo plants. A total of 179 mature miRNAs were identified from P. pygmaeus, including 120 known miRNAs and 59 novel miRNAs, of which 96 (61 known miRNAs and 35 novel miRNAs) were differentially expressed in the shoots at different growth stages. Based on target gene (TG) prediction, a total of 2099 transcription factors (TFs) were annotated to be TGs of the 96 differentially expressed miRNAs (DEMs), corresponding to 839 recordings of DEM-TF pairs. In addition, we identified 23 known DEMs involved in flowering and six known miRNAs related to floral organ development based on previous reports. Among these, there were 11 significantly differentially expressed miRNAs, with 124 TF targets corresponding to 132 DEM-TF pairs in P. pygmaeus. In particular, we focused on the identification of miR156a-SPL (SQUAMOSA Promoter-Binding protein-Like) modules in the age pathway, which are well-known to regulate the vegetative-to-reproductive phase transition in flowering plants. A total of 36 TF targets of miR156a were identified, among which there were 11 SPLs. The Dual-Luciferase transient expression assay indicated miR156a mediated the repression of the PpSPL targets in P. pygmaeus. The integrated analysis of miRNAs and TGs at genome scale in this study provides insight into the essential roles of individual miRNAs in modulating flowering transition through regulating TF targets in bamboo plants.

The implantation of a left ventricular assist device causes changes in the aortic miRNome and proteome - an integrative analysis

Abstract Background Left ventricular assist devices (LVAD) have been widely used and accepted to treat patients with end-stage heart failure. LVAD non-physiological blood flow velocity, wall shear stress distribution, vorticity current intensity, and vorticity flow generation affect the pathophysiology of vascular changes in aortic tissue. Purpose In this study, we performed multi-omics-based analysis of the aorta to identify molecular markers that could clarify vascular remodeling during LVAD support. Methods Aortic specimens from 48 patients (pair matched samples N=96) were excised during implantation and explantation of LVAD. Small RNA-Seq screening using Next Generation Sequencing and proteomic profile using Data-Independent Acquisition mass spectroscopy were conducted. Experimental and computational approaches, proteomics and transcriptomics data, were integrated and bioinformatics analyses were performed. Results The principal component analysis of miRNome and permutational multivariate analysis of variance of proteomic profile clearly segregated samples before and after LVAD support. We identified a total of 113 differently expressed (DE) miRNAs (61 up-regulated; Padj&amp;lt;0.05 and log2 fold change&amp;gt;|0.5|) after long-term LVAD support. Proteomic analysis identified in total 93 protein significantly changed (47 increased; Padj&amp;lt;0.05 and log2 fold change&amp;gt;|0.5|). Correlation analysis identified strong association between 270 proteins and 66 DE-miRNAs (Padj&amp;lt;0.05 and correlation coefficient&amp;gt;|0.7|). Gene Set Enrichment Analysis revealed, that predicted target genes of DE-miRNAs were mainly engaged in axon guidance, regulation of actin cytoskeleton, endocytosis, and MAP signaling pathway (Padj&amp;lt;0.05). DE-proteins participated mainly in ECM-receptor interaction, focal adhesion, and platelet activation (Padj&amp;lt;0.05). Conclusion Our study presents a network-based method of integrating microRNAs and proteome data and reveals molecular signatures that reflects aortic vascular remodeling due to LVAD treatment.PCA of miRNA DESeq2PCA of protemic profile

Transcriptome analysis of liver and ileum reveals potential regulation of long non-coding RNA in pigs with divergent feed efficiency.

LncRNA plays a significant role in regulating feed efficiency. This study aims to explore the key long non-coding RNAs, associated genes, and pathways in pigs with extreme feed efficiencies. We screened pigs with extremely high and low RFI through a 12-week animal growth trial and then conducted transcriptome analysis on their liver and ileum tissues. We analyzed the differential expressed lncRNAs, miRNAs, and mRNAs through target gene prediction and functional analysis. And we identified key lncRNAs and their potential regulatory genes associated with feed efficiency through the construction of competitive endogenous RNA network. Differentially expressed lncRNAs were pinpointed in the liver, revealing 23 crucial target genes primarily associated with GTP metabolism and glycolipid biosynthesis. In the ileum, a screening identified 92 pivotal target genes, mainly linked to lipid and small molecule metabolism. Moreover, LOC106504303 and LOC102160805 emerged as potentially significant lncRNAs respectively, playing roles in mitochondrial oxidative phosphorylation in the liver, and lipid and cholesterol metabolism in the ileum. The lncRNAs regulate energy metabolism and biosynthesis in the liver, and the digestive absorption capacity in the small intestine, affecting the feed efficiency of pigs.

Pre-eclampsia intronic polyadenylation enriched in VEGFA-VEGFR2 signaling pathway

AimsThis study aims to reveal transcriptome-wide intronic polyadenylation (IPA) events associated with Pre-eclampsia (PE). BackgroundPre-eclampsia (PE) is a potentially life-threatening complication of pregnancy, affecting both maternal and fetal health. However, our understanding of the underlying molecular mechanisms of PE remains limited. ObjectiveIn this study, we conducted a transcriptome-wide analysis of gene expression levels and intronic polyadenylation (IPA) events in samples of patients with PE. We also conducted motif analysis and scanned the microRNA targeting IPA network. MethodWe collected 90 PE-related samples from GEO database. IPA events were analyzed using IPAfinder software from hg38 alignment files from STAR. Miranda software was used to perform miRNA target gene prediction. Differentially expressed genes (DEG) were evaluated using edgeR with log2 fold change >1 and adjusted p-value <0.05. Function enrichment was performed through Clusterprofiler. ResultOur analysis revealed that genes in the VEGFA-VEGFR2 signaling pathway were functionally enriched with IPA events related to PE. We observed a negative correlation between gene expression levels and IPA events in VEGFA-VEGFR2 pathway. We identified LIN28B and AGO2 as the most significantly binding motifs to IPA sites. Furthermore, our analysis of miRNA binding sites associated with these IPA events revealed the central regulatory roles of miR-193b and miR-365a in IPA genes. ConclusionOur findings suggest that transcriptome data-mining might be a useful approach in future studies aimed at identifying potential biomarkers for PE.

RettDb: the Rett syndrome omics database to navigate the Rett syndrome genomic landscape.

Rett syndrome (RTT) is a neurodevelopmental disorder occurring almost exclusively in females and leading to a variety of impairments and disabilities from mild to severe. In >95% cases, RTT is due to mutations in the X-linked gene MECP2, but the molecular mechanisms determining RTT are unknown at present, and the complexity of the system is challenging. To facilitate and provide guidance to the unraveling of those mechanisms, we developed a database resource for the visualization and analysis of the genomic landscape in the context of wild-type or mutated Mecp2 gene in the mouse model. Our resource allows for the exploration of differential dynamics of gene expression and the prediction of new potential MECP2 target genes to decipher the RTT disorder molecular mechanisms. Database URL: https://biomedinfo.di.unipi.it/rett-database/.

The usefulness of evaluating PTEN expression for accurate grading of phyllodes tumors

Phyllodes tumors (PTs) are classified as benign, borderline, or malignant based on histologic characteristics. However, because histological criteria are subjective and diagnosis requires integrating multiple findings, discrepancies often occur between observers. Therefore, it is necessary to discover biomarkers based on the molecular characteristics of PTs. This study aimed to identify dysregulated microRNAs (miRNAs) in PTs through miRNA profiling and determine whether expression of their target genes could be useful as PT biomarkers. MiRNA profiling was performed on 13 PTs (three malignant, three borderline, seven benign) and six fibroadenomas, and predicted target genes of dysregulated miRNAs were selected using three computation algorithms. The expression of two miRNAs, miR-155 and miR-200c, was 1.69-fold and 1.61-fold higher, respectively, in borderline and malignant PT groups than in the benign PT group (p < 0.05). KEGG pathway analysis revealed that the 374 target genes of these two miRNAs (miR-155 and miR200c) participated in several signaling pathways, adherens junction, cell cycle, and pathway in cancer. Immunohistochemical staining for PTEN, one of candidate target genes of miR-200c, was performed on whole slides of PT tissue classified as malignant (n = 9), borderline (n = 12), or benign (n = 21). Stromal tumor cells of high-grade PTs (borderline and malignant) had significantly lower PTEN expression than those of low-grade PTs (benign) (p-value ≤0.001). Semiquantitative analysis of PTEN expression, score 0–8, revealed that it correlated with histologic findings. Low PTEN expression (s-score of 6 or less) was used as a diagnostic criterion for high-grade PTs, it showed 100 % sensitivity and 95.2 % specificity in 42 cases of PTs. Currently, PT grading based solely on subjective histologic findings is challenging, but semiquantitative PTEN expression analysis could provide a more accurate and objective way to grade PTs.