Putative Target Genes Research Articles

LncRNA Malat1 regulates iPSC-derived β-cell differentiation by targeting the miR-15b-5p/Ihh axis

BackgroundDifferentiation of induced pluripotent stem cells (iPSCs)-derived β-like cells is a novel strategy for treatment of type 1 diabetes. Elucidation of the regulatory mechanisms of long noncoding RNAs (lncRNAs) in β-like cells derived from iPSCs is important for understanding the development of the pancreas and pancreatic β-cells and may improve the quality of β-like cells for stem cell therapy. Methodsβ-like cells were derived from iPSCs in a three-step protocol. RNA sequencing and bioinformatics analysis were carried out to screen the differentially expressed lncRNAs and identify the putative target genes separately. LncRNA Malat1 was chosen for further research. Series of loss and gain of functions experiments were performed to study the biological function of LncRNA Malat1. Quantitative real-time PCR (qRT-PCR), Western blot (WB) analysis and immunofluorescence (IF) staining were carried out to separately detect the functions of pancreatic β-cells at the mRNA and protein levels. Cytoplasmic and nuclear RNA fractionation and fluorescence in situ hybridization (FISH) were used to determine the subcellar location of lncRNA Malat1 in β-like cells. Enzyme-linked immunosorbent assays (ELISAs) were performed to examine the differentiation and insulin secretion of β-like cells after stimulation with different glucose concentrations. Structural interactions between lncRNA Malat1 and miR-15b-5p and between miR-15b-5p/Ihh were detected by dual luciferase reporter assays (LRAs). ResultsWe found that the expression of lncRNA Malat1 declined during differentiation, and overexpression (OE) of lncRNA Malat1 notably impaired the differentiation and maturation of β-like cells derived from iPSCs in vitro and in vivo. Most importantly, lncRNA Malat1 could function as a competing endogenous RNA (ceRNA) of miR-15b-5p to regulate the expression of Ihh according to bioinformatics prediction, mechanistic analysis and downstream experiments. ConclusionThis study established an unreported regulatory network of lncRNA Malat1 and the miR-15b-5p/Ihh axis during the differentiation of iPSCs into β-like cells. In addition to acting as an oncogene promoting tumorigenesis, lncRNA Malat1 may be an effective and novel target for treatment of diabetes in the future.

Knockdown of Chronophage in the nervous system mimics features of neurodevelopmental disorders caused by BCL11A/B variants

Neurodevelopmental disorders (NDD) are a group of disorders that include intellectual disability. Although several genes have been implicated in NDD, the molecular mechanisms underlying its pathogenesis remain unclear. Therefore, it is important to develop novel models to analyze the functions of NDD-causing genes in vivo. Recently, rare pathogenic variants of the B-cell lymphoma/leukemia11A/B (BCL11A/B) gene have been identified in several patients with NDD. Drosophila carries the Chronophage (Cph) gene, which has been predicted to be a homolog of BCL11A/B based on the conservation of the amino acid sequence. In the present study, we investigated whether nervous system-specific knockdown of Cph mimics NDD phenotypes in Drosophila. Nervous system-specific knockdown of Cph induced learning and locomotor defects in larvae and epilepsy-like behaviors in adults. The number of synaptic branches was also elevated in the larval neuromuscular junction without a corresponding increase in the number of boutons. Furthermore, the expression levels of putative target genes that are Drosophila homologs of the mammalian BCL11 target genes were decreased in Cph knockdown flies. These results suggest that Cph knockdown flies are a promising model for investigating the pathology of NDD-induced BCL11A/B dysfunction.

Comparative analyses of salivary exosomal miRNAs for patients with or without lung cancer.

Introduction: Lung cancer is the most frequent cause of cancer-related deaths worldwide. Exosomes are involved in different types of cancer, including lung cancer. Methods: We collected saliva from patients with (LC) or without (NC) lung cancer and successfully isolated salivary exosomes by ultracentrifugation. MiRNA sequencing was implemented for the exosome samples from NC and LC groups, dgeR was used to determine differentially expressed miRNAs (DE miRNAs), and quantitative real-time polymerase chain reaction (qPCR) was used to verify three differentially expressed microRNAs (miRNAs). Results: A total of 372 miRNAs were identified based on the sequencing results. Subsequently, 15 DE miRNAs were identified in LC vs. NC, including eight upregulated miRNAs and seven downregulated miRNAs. Some DE miRNAs were validated via qPCR. A total of 488 putative target genes of the upregulated DE miRNAs were found, and the functional analyses indicated that numerous target genes were enriched in the pathways associated with cancer. Discussion: This suggests that miRNAs of salivary exosomes might have the potential to be used as biomarkers for prediction and diagnosis of lung cancer.

Recombinant Human Erythropoietin Combined with All-Trans Retinoic Acid and Testosterone Undecanoate in the Treatment of Anemia in Patients with Lower-Risk Myelodysplastic Syndromes: Updated Results of a Multicenter, Single-Arm, Prospective Trial

[Background] More than 90% of low-risk MDS face refractory anemia and blood transfusion dependence for a long time. At present, recombinant human erythropoietin (EPO) is the main treatment, but the effective rate of single agent is 30%-40%, which seriously affects the quality of life of patients. Previous studies had shown that testosterone undecanoate could promote erythroid hematopoiesis and all-trans retinoic acid (ATRA) had the function of promoting blood cell differentiation in vitro. We previously reported that EPO combined with ATRA and testosterone undecanoate in the treatment of patients with low-risk MDS and demonstrated promising efficacy and safety in a prospective trial (Chen et al, ASH 2022). Here we present an updated analysis of efficacy and safety results in the ongoing study. [Methods] In this multicenter, single-arm trial, patients with newly diagnosed lower-risk MDS based on the 2016 WHO classification and the Revised International Prognostic Scoring System (IPSS-R) from 3 different tertiary medical centers in China were included. Patients were received EPO (10000IU/day) plus ATRA (25mg/m 2/day) and testosterone undecanoate (80mg twice daily) for 3 months. The primary endpoint was overall hemoglobin response rate, defined as an increase in hemoglobin levels of ≥ 1.5g/dL from baseline in 2 or more consecutive assessments (2 weeks apart) and no red blood cell transfusions during this period. Response was assessed after completion of 3months. The data cut-off date was July 25, 2023. [Results] As of July 2023, a total of 43 patients were enrolled, with a median age of 65 years, 24 males and 19 females, with median hemoglobin of 63 g/L, EPO concentration > 500 IU/L in 18 patients, and the overall hemoglobin response rate of 65.1% (28/43). The hemoglobin response rates were 61.1% (11/18) in patients with EPO concentrations greater than > 500 IU/L and 68.0% (17/25) in patients with EPO concentrations ≤ 500, which were not statistically different. Among them, 112 known or putative mutational gene targets in hematologic malignancy were examined for mutations in 32 patients using a custom targeted next-generation sequencing (NGS) gene panel. The most frequent mutations were SF3B1 (15/32, 46.8%) and ASXL1 (8/32, 25.0%). The hemoglobin response rate was 80.0% (12/15) in patients with SF3B1 mutation and 37.5% (3/8) in patients with ASXL1 mutation, respectively. Among 43 patients evaluable for safety analysis, the most common non-hematological adverse events were dry skin (17/43, 39.5%) and fatigue (12/43, 27.9%). No patients had disease progression during the treatment period. [Conclusion]: This study showed that EPO combined with tretinoin and testosterone undecanoate regimen can effectively improve the anemia of lower risk MDS in approximately 65.1% of patients and is not affected by EPO concentration. It has the better efficacy in patients with SF3B1 mutation, but has worse efficacy in patients with ASXL1 mutation. It is worthy of further randomized controlled studies to verify the efficacy.

Revisiting the role of endogenous STAT3 in HPV-positive cervical cancer cells.

Novel treatment options for human papillomavirus (HPV)-induced cancers are urgently required. The oncogenic transcription factor signal transducer and activator of transcription 3 (STAT3) is considered to be constitutively active in HPV-positive cervical cancer cells and essential for their proliferation. Moreover, STAT3 was reported to undergo mutually stimulatory interactions with the HPV E6/E7 oncogenes. Thus, inhibiting STAT3 in HPV-positive cancer cells is under discussion to provide a powerful novel therapeutic strategy. We here show that the antifungal drug ciclopirox destabilizes the STAT3 protein by acting as an iron chelator. However, by exploring the functional consequences of STAT3 inhibition in HPV-positive cancer cells, we obtained several unexpected results. Chemical STAT3 inhibitors heterogeneously affect cervical cancer cell proliferation and those which act antiproliferative also block the growth of STAT3 knockout cells, indicating induction of off-target effects. In contrast to several chemical inhibitors, genetic inhibition of STAT3 expression by either RNA interference or the CRISPR/Cas9 method does not appreciably affect cervical cancer cell proliferation. Transcriptome analyses indicate that blocking STAT3 expression in HPV-positive cancer cells has very limited effects on putative STAT3 target genes. Although the targeted inhibition of specific growth-promoting signaling pathways leads to a feedback activation of STAT3 in cervical cancer cells via Janus kinase1/2, this does not lead to treatment resistance. Moreover, we did not obtain experimental evidence for a STAT3-linked activation of HPV E6/E7 oncogene expression or, vice versa, an E6/E7-dependent activation of STAT3, at endogenous conditions in cervical cancer cells. Collectively, these findings question the essential role of STAT3 in cervical cancer cell proliferation and the strategy to inhibit STAT3 in these cells for therapeutic purposes.

Rapeseed NTL4 transcription factor positively regulates leaf senescence and resistance against bacterial pathogen via controlling transcription of ROS and SA biosynthetic genes

Rapeseed (Brassica napus L.) is widely planted for both edible oil and biodiesel. However, its growth is frequently affected by adverse environmental factors such as pathogens. Moreover, rapeseed shows significant falling of leaves during the whole growth period, making it important to control leaf senescence for better nutrient utilization efficiency and improved growth. Membrane-tethered transcription factors (MTTF) constitute a special group of proteins, which facilitate rapid response to adverse conditions. However, the role of MTTFs in rapeseed has seldomly been reported. Here BnaNTL4 was functionally characterized to transcriptionally regulate leaf senescence and resistance towards a bacterial pathogen in rapeseed. BnaNTL4 encodes a member-associated transcription factor and its expression was induced by several stimuli including salicylic acid and hydrogen peroxide. Both stable and transient expression demonstrated BnaNTL4 could induce reactive oxygen species (ROS) production and leaf chlorosis. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assay of differentially expressed genes in BnaNTL4 overexpression lines and control plants uncovered that several genes related to programmed cell death (γVPE, BFN1), ROS production (RbohF), salicylic acid (SA) synthesis (PBS3) and senescence (SEN4) were induced by BnaNTL4 overexpression. Further, a dual luciferase reporter assay revealed BnaNTL4 transactivated the activities of the promoters of putative target genes. At last, an electrophoretic mobility shift assay discovered that BnaNTL4 directly bound to promoters of BnaRbohF, BnaPBS3 and BnaSEN4. Overexpression of BnaNTL4 also enhances resistance towards a bacterial pathogen Pseudomonas syringae DC3000. Thus, the results uncovered a dual role of BnaNTL4 in leaf senescence and disease resistance in rapeseed.

Identification of microRNAs Derived from Transposable Elements in the Macaca mulatta (Rhesus Monkey) Genome.

Transposable elements (TEs) are mobile DNA entities that can move within the host genome. Over long periods of evolutionary time, TEs are typically silenced via the accumulation of mutations in the genome, ultimately resulting in their immobilization. However, they still play an important role in the host genome by acting as regulatory elements. They influence host transcription in various ways, one of which as the origin of the generation of microRNAs (miRNAs), which are so-called miRNAs derived from TEs (MDTEs). miRNAs are small non-coding RNAs that are involved in many biological processes by regulating gene expression at the post-transcriptional level. Here, we identified MDTEs in the Macaca mulatta (rhesus monkey) genome, which is phylogenetically close species to humans, based on the genome coordinates of miRNAs and TEs. The expression of 5 out of 17 MDTEs that were exclusively registered in M. mulatta from the miRBase database (v22) was examined via quantitative polymerase chain reaction (qPCR). Moreover, Gene Ontology analysis was performed to examine the functional implications of the putative target genes of the five MDTEs.

Maize GOLDEN2-LIKE proteins enhance drought tolerance in rice by promoting stomatal closure.

Drought has become one of the most severe abiotic stresses experienced in agricultural production across the world. Plants respond to water deficit via stomatal movements in the leaves, which are mainly regulated by abscisic acid (ABA). A previous study from our lab showed that constitutive expression of maize (Zea mays L.) GOLDEN2-LIKE (GLK) transcription factors in rice (Oryza sativa L.) can improve stomatal conductance and plant photosynthetic capacity under field conditions. In the present study, we uncovered a function of ZmGLK regulation of stomatal movement in rice during drought stress. We found that elevated drought tolerance in rice plants overexpressing ZmGLK1 or GOLDEN2 (ZmG2) was conferred by rapid ABA-mediated stomatal closure. Comparative analysis of RNA-sequencing (RNA-seq) data from the rice leaves and DNA affinity purification sequencing (DAP-seq) results obtained in vitro revealed that ZmGLKs played roles in regulating ABA-related and stress-responsive pathways. Four upregulated genes closely functioning in abiotic stress tolerance with strong binding peaks in the DAP-seq data were identified as putative target genes of ZmGLK1 and ZmG2 in rice. These results demonstrated that maize GLKs play an important role in regulating stomatal movements to coordinate photosynthesis and stress tolerance. This trait is a valuable target for breeding drought-tolerant crop plants without compromising photosynthetic capacity.

Elongation of very long chain fatty acids-3 (Elovl3) is activated by ZHX2 and is a regulator of cell cycle progression.

Zinc fingers and homeoboxes 2 (Zhx2) are transcriptional regulators of liver gene expression with key functions in embryonic development as well as tissue regeneration in response to damage and disease, presumably through its control of target genes. Previous microarray data suggested that elongation of very long chain fatty acids-3 (Elovl3), a member of the ELOVL family of enzymes that synthesize very long chain fatty acids (VLCFAs), is a putative Zhx2 target gene. VLCFAs are core component of ceramides and other bioactive sphingolipids that are often dysregulated in diseases and regulate key cellular processes including proliferation. Since several previously identified Zhx2 targets become dysregulated in liver damage, we investigated the relationship between Zhx2 and Elovl3 in liver development, damage, and regeneration. Here, using mouse and cell models, we demonstrate that Zhx2 positively regulates Elovl3 expression in the liver and that male-biased hepatic Elovl3 expression is established between 4 and 8 wk of age in mice. Elovl3 is dramatically repressed in mouse models of liver regeneration, and the reduced Elovl3 levels in the regenerating liver are associated with changes in hepatic VLCFAs. Human hepatoma cell lines with forced Elovl3 expression have lower rates of cell growth; analysis of synchronized cells indicates that this reduced proliferation correlates with cells stalling in S-phase and lower mRNA levels of cell cyclins. Taken together, these data indicate that Elovl3 expression helps regulate cellular proliferation during liver development and regeneration, possibly through control of VLCFAs.NEW & NOTEWORTHY Numerous targets of the transcription factor Zhx2 are dysregulated in liver disease. We show that the elongase Elovl3 is a novel Zhx2 target. Elovl3 and Zhx2 expression change during liver regeneration, which is associated with changes in very long chain fatty acids. Forced Elovl3 expression reduces cell growth and blocks cell cycle progression. This suggests that Elovl3 may account, at least in part, for the relationship between Zhx2 and proliferation during liver development and disease.

Fibromodulin overexpression drives oral squamous cell carcinoma via activating downstream EGFR signaling

Accumulating evidence has shown that fibromodulin (FMOD) plays a pivotal role in tumorigenesis and metastasis. However, the biological function of FMOD in oral squamous cell carcinoma (OSCC) remains largely unclear to date. In this study, we confirmed that FMOD was overexpressed and showed a significant association with malignant progression and lymph node metastasis in OSCC. Depletion of FMOD inhibited OSCC proliferation and metastasis invitro and invivo. RNA sequencing, western blotting, and rescue assays verified that FMOD exerted oncogenic roles in OSCC via activation of EGFR signaling. In addition, FMOD was proved to be a putative target gene of miR-338-3p. Taken together, FMOD overexpression due to the reduced level of miR-338-3p promotes OSCC by activating EGFR signaling. Our findings provide direct evidence that targeting FMOD could be a promising therapeutic strategy for OSCC patients.

Isolated loss of the AUTS2 long isoform, brain-wide or targeted to Calbindin-lineage cells, generates a specific suite of brain, behavioral, and molecular pathologies.

Rearrangements within the AUTS2 region are associated with a rare syndromic disorder with intellectual disability, developmental delay, and behavioral abnormalities as core features. In addition, smaller regional variants are linked to wide range of neuropsychiatric disorders, underscoring the gene's essential role in brain development. Like many essential neurodevelopmental genes, AUTS2 is large and complex, generating distinct long (AUTS2-l) and short (AUTS2-s) protein isoforms from alternative promoters. Although evidence suggests unique isoform functions, the contributions of each isoform to specific AUTS2-linked phenotypes have not been clearly resolved. Furthermore, Auts2 is widely expressed across the developing brain, but cell populations most central to disease presentation have not been determined. In this study, we focused on the specific roles of AUTS2-l in brain development, behavior, and postnatal brain gene expression, showing that brain-wide AUTS2-l ablation leads to specific subsets of the recessive pathologies associated with mutations in 3' exons (exons 8-19) that disrupt both major isoforms. We identify downstream genes that could explain expressed phenotypes including hundreds of putative direct AUTS2-l target genes. Furthermore, in contrast to 3' Auts2 mutations which lead to dominant hypoactivity, AUTS2-l loss-of-function is associated with dominant hyperactivity and repetitive behaviors, phenotypes exhibited by many human patients. Finally, we show that AUTS2-l ablation in Calbindin 1-expressing cell lineages is sufficient to yield learning/memory deficits and hyperactivity with abnormal dentate gyrus granule cell maturation, but not other phenotypic effects. These data provide new clues to in vivo AUTS2-l functions and novel information relevant to genotype-phenotype correlations in the human AUTS2 region.

A peptide encoded by a highly conserved gene belonging to the genus Streptomyces shows antimicrobial activity against plant pathogens.

The genus Streptomyces has been unceasingly highlighted for the versatility and diversity of the antimicrobial agents they produce. Moreover, it is a heavily sequenced taxon in the phylum Actinobacteria. In this study, 47 sequence profiles were identified as proteins highly conserved within the genus Streptomyces. Significant hits to the 38 profiles were found in more than 2000 Streptomyces genomes, 11 of which were further conserved in more than 90% of Actinobacterial genomes analyzed. Only a few genes corresponding to these sequence profiles were functionally characterized, which play regulatory roles in the morphology and biosynthesis of antibiotics. Here a highly conserved sequence, namely, SHC-AMP (Streptomyces highly conserved antimicrobial peptide), which exhibited antimicrobial activity against bacterial and fungal plant pathogens, was reported. In particular, Arabidopsis thaliana was effectively protected against infection with Pseudomonas syringae pv. tomato DC3000 by treatment with this peptide. Results indicated the potential application of this peptide as an antimicrobial agent for control of plant diseases. Our results suggest putative target genes for controlling Streptomyces spp., including the one exhibiting antimicrobial activity against a wide range of phytopathogens.

Possible molecular exploration of herbal pair Haizao-Kunbu in the treatment of Graves' disease by network pharmacology, molecular docking, and molecular dynamic analysis.

To promote the development and therapeutic application of new medications, it is crucial to conduct a thorough investigation into the mechanism by which the traditional Chinese herb pair of Haizao-Kunbu (HK) treats Graves' disease (GD). Chemical ingredients of HK, putative target genes, and GD-associated genes were retrieved from online public databases. Using Cytoscape 3.9.1, a compound-gene target network was established to explore the association between prosperous ingredients and targets. STRING, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathway analyses visualized core targets and disease pathways. Additionally, we conducted a refined analysis of the binding interactions between active ingredients and their respective targets. To visualize these findings, we employed precise molecular docking techniques. Furthermore, we carried out molecular dynamics simulations to gain insights into the formation of more tightly bound complexes. We found that there were nine key active ingredients in HK, which mainly acted on 21 targets. These targets primarily regulated several biological processes such as cell population proliferation, protein phosphorylation, and regulation of kinase activity, and acted on PI3K-AKT and MAPK pathways to treat GD. Analysis of the molecular interaction simulation under computer technology revealed that the key targets exhibited strong binding activity to active ingredients, and Fucosterol-AKT1 and Isofucosterol-AKT1 complexes were highly stable in humans. This study demonstrates that HK exerts therapeutic effects on GD in a multi-component, multi-target, and multi-pathway manner by regulating cell proliferation, differentiation, inflammation, and immunomodulatory-related targets. This study provides a theoretical foundation for further investigation into GD.

Double-stranded RNA mediated knockdown of sucrase gene induced mortality and reduced offspring production in Aphis gossypii.

The importance of gut sucrase in maintaining osmotic equilibrium and utilizing phloem contents as a carbon source has been widely investigated and proven in sap-sucking insects. In the present study, silencing of Aphis gossypii sucrase1 (Agsuc1) was carried out by double-stranded RNA (dsRNA), which would be lethal to it due to disruption of osmotic balance. The dsRNA corresponding to Agsuc1 was synthesized by two methods, i.e., in vitro synthesis using T7/SP6 RNA polymerase and in vivo synthesis by bacterial expression, i.e., Escherichia coli strain HT115 transformed with the L4440 vector system. Oral delivery of double-stranded Agsuc1 synthesized in vitro (dsAgsuc1) and in vivo (HT115Agsuc1) induced around 50% mortality in nymphs of A. gossypii. Moreover, the number of offspring produced by the survived aphids decreased by 39-43%. Parthenogenetic reproduction of the aphids is the critical factor for their fast population build-up, leading to yield losses of economic significance. Thus, the present study demonstrated that the silencing of the Agsuc1 gene reduced the aphid population by killing it and inhibited the population buildup by reducing the number of offspring produced by the survived aphids, likely to result in a significant reduction in crop damage. The production of dsRNA by bacterial expression is a cost-effective method. It has the potential to be used as a biopesticide. The sucrase gene is an excellent putative target gene for RNAi against A. gossypii. It could be used to develop a transgenic plant that produces dsAgsuc1 to keep A. gossypii populations below the economic threshold level.

Computational tools for inferring transcription factor activity.

Transcription factors (TFs) are essential players in orchestrating the regulatory landscape in cells. Still, their exact modes of action and dependencies on other regulatory aspects remain elusive. Since TFs act cell type-specific and each TF has its own characteristics, untangling their regulatory interactions from an experimental point of view is laborious and convoluted. Thus, there is an ongoing development of computational tools that estimate transcription factor activity (TFA) from a variety of data modalities, either based on a mapping of TFs to their putative target genes or in a genome-wide, gene-unspecific fashion. These tools can help to gain insights into TF regulation and to prioritize candidates for experimental validation. We want to give an overview of available computational tools that estimate TFA, illustrate examples of their application, debate common result validation strategies, and discuss assumptions and concomitant limitations.

CUL4B-DDB1-COP1-mediated UTX downregulation promotes colorectal cancer progression

BackgroundUTX (encoded by KDM6A), a histone demethylase for H3K27me2/3, is frequently mutated in human cancers. However, its functional and regulatory mechanisms in colorectal cancer (CRC) remain unclear.MethodsImmunohistochemistry staining was used to investigate the clinical relevance of UTX in CRC. Additionally, we generated a spontaneous mouse CRC model with conditional Utx knockout to explore the role of UTX in the colorectal tumorigenesis. Post-translational regulation of UTX was determined by co-immunoprecipitation and immunoblot analyses.ResultsHerein, we identify that downregulation of UTX, mediated by the Cullin 4B-DNA Damage Binding Protein-1-Constitutive Photomorphogenesis Protein 1 (CUL4B-DDB1-COP1) complex, promotes CRC progression. Utx deletion in intestinal epithelial cells enhanced the susceptibility to tumorigenesis in AOM/DSS-induced spontaneous mouse CRC model. However, this effect is primarily alleviated by GSK126, an inhibitor of histone methyltransferase EZH2. Mechanistically, EMP1 and AUTS2 are identified as putative UTX target genes mediating UTX functions in limiting intestinal tumorigenesis. Notably, the CUL4B-DDB1-COP1 complex is identified as the functional E3 ligase responsible for targeting UTX for degradation in CRC cells. Thus, Cop1 deficiency in mouse intestinal tissue results in UTX accumulation and restricts tumorigenesis. Furthermore, patient cohort analysis reveals that UTX expression is negatively correlated with clinical stage, favorable disease outcomes, and COP1 expression.ConclusionsIn the current study, the tumor suppressor function and regulation of UTX in CRC provide a molecular basis and the rationale to target EZH2 in UTX-deficient CRC.

Effects of Biological Nitrogen Metabolism on Glufosinate-Susceptible and -Resistant Goosegrass (Eleusine indica L.).

Glufosinate is a broad-spectrum herbicide used to control most weeds in agriculture worldwide. Goosegrass (Eleusine indica L.) is one of the top ten malignant weeds across the world, showing high tolerance to glufosinate via different mechanisms that are not yet fully understood. This study revealed that nitrogen metabolism could be a target-resistant site, providing clues to finally clarify the mechanism of glufosinate resistance in resistant goosegrass populations. Compared to susceptible goosegrass (NX), the resistant goosegrass (AUS and CS) regarding the stress of glufosinate showed stronger resistance with lower ammonia contents, higher target enzyme GS (glutamine synthetase) activity, and lower GOGAT (glutamine 2-oxoglutarate aminotransferase) activity. The GDH (glutamate dehydrogenase) activity of another pathway increased, but its gene expression was downregulated in resistant goosegrass (AUS). Analyzing the transcriptome and proteome data of goosegrass under glufosinate stress at 36 h showed that the KEGG pathway of the nitrogen metabolism was enriched in glufosinate-susceptible goosegrass (NX), but not in glufosinate-resistant goosegrass (CS and AUS). Several putative target genes involved in glufosinate stress countermeasures were identified. This study provides specific insights into the nitrogen metabolism of resistant goosegrass, and gives a basis for future functional verification of glufosinate-tolerance genes in plants.

Computational discovery of a miRNA and its putative target genes in Ziziphus jujuba using genome-wide expressed sequence tags

Computational discovery of a miRNA and its putative target genes in Ziziphus jujuba using genome-wide expressed sequence tags

Elucidating the Molecular Targets and Mechanisms of Chlorogenic Acid Against Alzheimer’s Disease via Network Pharmacology and Molecular Docking

Background: Chlorogenic acid (CGA), a polyphenolic substance extracted from many traditional Chinese medicines, exerts a mitigative effect in dementia, including Alzheimer’s disease (AD). However, the pathological mechanisms of CGA against AD remain obscure. Objective: To elucidate the core targets, functional characteristics, and underlying mechanisms of CGA against AD using network pharmacology approaches and molecular docking technologies. Methods: GEO database was used to identify the differentially expressed genes (DEGs) in AD. PharmMpper, TargetNet, and SwissTargetPrediction predicted the CGA-related targets. STRING and Cytoscape were employed to construct and analyze the PPI network. Moreover, the Metascape platform was used to perform the GO biological processes and KEGG pathways enrichment. Molecular docking was performed using Autodock Vina software. Results: A total of 5437 targets related to AD were identified with |log2Fold Change (FC)| ≥ 1 and P < 0.05. Based on public databases, 193 putative target genes of CGA were screened. Using the Venn diagram, we found 137 co-targets between CGA and AD. According to the PPI network, 23 core targets for CGA to treat AD were obtained. KEGG enrichment displayed that the PI3K-Akt signaling pathway, MAPK signaling pathway, apoptosis, and NOD-like receptor signaling pathway were several important signaling pathways involved in CGA against AD. SRC, EGFR, HSP90AA1, MAPK1, RHOA, and PIK3R1 were hub targets associated with the activities of CGA against AD. Molecular docking analysis revealed a good binding affinity between CGA and these targets through hydrogen bonds. Conclusion: CGA might exert therapeutic effects in AD by regulating multiple targets and signaling pathways. However, further in vitro and in vivo experiments are required to thoroughly confirm the detailed targets and mechanisms of CGA against AD.

IL-13–induced STAT3-dependent signaling networks regulate esophageal epithelial proliferation in eosinophilic esophagitis

Basal zone hyperplasia (BZH) and dilated intercellular spaces (DISs) are thought to contribute to the clinical manifestations of eosinophilic esophagitis (EoE); however, the molecular pathways that drive BZH remain largely unexplored. We sought to define the role of IL-13-induced transcriptional programs in esophageal epithelial proliferation in EoE. We performed RNA sequencing, bioinformatics, Western blot, reverse transcriptase quantitative PCR, and histologic analyses on esophageal biopsies from healthy control and patients with EoE, primary esophageal cells derived from patients with EoE, and IL-13-stimulated esophageal epithelial keratinocytes grown at the air-liquid interface (EPC2-ALI). Genetic (shRNA) and pharmacologic (proteolysis-targeting chimera degrader) approaches and invivo model of IL-13-induced esophageal epithelial remodeling (Krt5-rtTA x tetO-IL-13Tg) were used to define the role of signal transducer and activator of transcription 3 (STAT3) and STAT6 and secreted frizzled-related protein 1 (SFRP1) in esophageal epithelial proliferation. RNA-sequencing analysis of esophageal biopsies (healthy control vs EoE) and EPC2-ALI revealed 82 common differentially expressed genes that were enriched for putative STAT3 target genes. Invitro and invivo analyses revealed a link between IL-13-induced STAT3 and STAT6 phosphorylation, SFRP1 mRNA expression, and esophageal epithelial proliferation. Invitro studies showed that IL-13-induced esophageal epithelial proliferation was STAT3-dependent and regulated by the STAT3 target SFRP1. SFRP1 mRNA is increased in esophageal biopsies from patients with active EoE compared with healthy controls or patients in remission and identifies an esophageal suprabasal epithelial cell subpopulation that uniquely expressed the core EoE proinflammatory transcriptome genes (CCL26, ALOX15, CAPN14, ANO1, and TNFAIP6). These studies identify SFRP1 as a key regulator of IL-13-induced and STAT3-dependent esophageal proliferation and BZH in EoE and link SFRP1+ esophageal epithelial cells with the proinflammatory and epithelial remodeling response in EoE.