Suppress Gene Expression Research Articles

Sustainable natural bioresources in crop protection: antimicrobial hydroxycoumarins induce membrane depolarization-associated changes in the transcriptome of Ralstonia solanacearum.

Ralstonia solanacearum is one of the most devastating pathogens affecting crop production worldwide. The hydroxycoumarins (umbelliferone, esculetin and daphnetin) represent sustainable natural bioresources on controlling plant bacterial wilt. However, the antibacterial mechanism of hydroxycoumarins against plant pathogens still remains poorly understood. Here we characterized the effect of three hydroxycoumarins on the transcriptome of R. solanacearum. All three hydroxycoumarins were able to kill R. solanacearum, but their antibacterial activity impacted differently the bacterial transcriptome, indicating that their modes of action might be different. Treatment of R. solanacearum cultures with hydroxycoumarins resulted in a large number of differentially expressed genes (DEGs), involved in basic cellular functions and metabolic process, such as down-regulation of genes involved in fatty acid synthesis, lipopolysaccharides biosynthesis, RNA modification, ribosomal submits, oxidative phosphorylation and electrontransport, as well as up-regulation of genes involved in transcriptional regulators, drug efflux, and oxidative stress responses. Future studies based on in vitro experiments are proposed to investigate lipopolysaccharides biosynthesis pathway leading to R. solanacearum cell death caused by hydroxycoumarins. Deletion of lpxB substantially inhibited the growth of R. solanacearum, and reduced virulence of pathogen on tobacco plants. Our transcriptomic analyses show that specific hydroxycoumarins suppressed gene expression involved in fatty acid synthesis, RNA modification, ribosomal submits, oxidative phosphorylation and electrontransport. These findings provide evidence that hydroxycoumarins inhibit R. solanacearum growth through multi-target effect. Hydroxycoumarins could serve as sustainable natural bioresources against plant bacterial wilt through membrane destruction targeting the lipopolysaccharides biosynthesis pathway.

Spatial transcriptomics analysis of uterine gene expression in enhancer of zeste homolog 2 conditional knockout mice†.

Histone proteins undergo various modifications that alter chromatin structure, including addition of methyl groups. Enhancer of zeste homolog 2 (EZH2) is a histone methyltransferase that methylates lysine residue 27, and thereby suppresses gene expression. EZH2 plays integral roles in the uterus and other reproductive organs. We have previously shown that conditional deletion of uterine EZH2 results in increased proliferation of luminal and glandular epithelial cells, and RNA-seq analyses reveal several uterine transcriptomic changes in Ezh2 conditional (c) knockout (KO) mice that can affect estrogen signaling pathways. To pinpoint the origin of such gene expression changes, we used the recently developed spatial transcriptomics (ST) method with the hypotheses that Ezh2cKO mice would predominantly demonstrate changes in epithelial cells and/or ablation of this gene would disrupt normal epithelial/stromal gene expression patterns. Uteri were collected from ovariectomized adult WT and Ezh2cKO mice and analyzed by ST. Asb4, Cxcl14, Dio2, and Igfbp5 were increased, Sult1d1, Mt3, and Lcn2 were reduced in Ezh2cKO uterine epithelium vs. WT epithelium. For Ezh2cKO uterine stroma, differentially expressed key hub genes included Cald1, Fbln1, Myh11, Acta2, and Tagln. Conditional loss of uterine Ezh2 also appears to shift the balance of gene expression profiles in epithelial vs. stromal tissue toward uterine epithelial cell and gland development and proliferation, consistent with uterine gland hyperplasia in these mice. Current findings provide further insight into how EZH2 may selectively affect uterine epithelial and stromal compartments. Additionally, these transcriptome data might provide mechanistic understanding and valuable biomarkers for human endometrial disorders with epigenetic underpinnings.

Receptor Tyrosine Kinase Inhibitor Sunitinib as Novel Immunotherapy to Inhibit Myeloid-Derived Suppressor Cells for Treatment of Endometriosis.

Endometriosis is a common, benign, and hormone-dependent gynaecological disorder that displays altered immunoinflammatory profiles. Myeloid-derived suppressor cells (MDSCs) suppressed immunosurveillance in endometriosis in human and mouse model. Receptor tyrosine kinase inhibitor Sunitinib can induce MDSC apoptosis and suppress the progression of cancer. However, the effects of Sunitinib on MDSCs in endometriosis and the underlying mechanism are not clear. In this study, we employed an animal study of the endometriosis model in mice for treatment of Sunitinib. After syngeneic endometrium transplantation and treatment, endometriotic lesion volume, weight, and histology were compared. Peritoneal fluid, peripheral blood, and bone marrow MDSC subsets and their molecular signaling were monitored by flow cytometry. Peritoneal cytokines were assayed by ELISA. The gene expression profiles of isolated CD11b+Ly6G+Ly6Clo cells were studied by RNA sequencing. We found that Sunitinib significantly decreased the endometriotic lesion size and weight after 1 and 3 weeks, and decreased p-STAT3 activation in MDSCs after 1 week of treatment. In the first week, Sunitinib specifically increased the G-MDSC population in peritoneal fluid but the isolated CD11b+Ly6G+Ly6Clo MDSCs after Sunitinib treatment were presented as mature polynuclear MDSCs, while the control group had immature mononuclear MDSCs. Importantly, we found Sunitinib differentially suppressed gene expressions of immunosuppressive function and differentiation in peritoneal G-MDSCs. Apelin signaling pathway associated genes and inflammation related genes were upregulated, and amino acid metabolism regulator genes were downregulated in bone marrow G-MDSCs. For endometriotic lesions, the PPARG gene governing glucose metabolism and fatty acid storage, which is important for the development of endometriosis was upregulated. In conclusion, Sunitinib inhibited endometriotic lesions, by promoting peritoneal fluid MDSCs maturation and inhibiting the immunosuppressive function. These findings suggest that Sunitinib changed the immune microenvironment and inhibited the development of endometriosis, which has potential therapeutic effects as novel immunotherapy to promote MDSCs maturation, differentiation, and metabolism for the treatment of endometriosis.

RETRACTED: Precise editing of FGFR3-TACC3 fusion genes with CRISPR-Cas13a in glioblastoma

FGFR3-TACC3 (F3-T3) gene fusions are regarded as a "low-hanging fruit" paradigm for precision therapy in human glioblastoma (GBM). Small molecules designed to target the kinase in FGFR currently serve as one form of potential treatment but cause off-target effects and toxicity. Here, CRISPR-Cas13a, which is known to directly suppress gene expression at the transcriptional level and induce a collateral effect in eukaryotes, was leveraged as a possible precision therapy in cancer cells harboring F3-T3 fusion genes. A library consisting of crRNAs targeting the junction site of F3-T3 was designed, and an in silico simulation scheme was created to select the optimal crRNA candidates. An optimal crRNA, crRNA1, showed efficiency and specificity in inducing the collateral effect in only U87 cells expressing F3-T3 (U87-F3-T3). Expression profiles obtained with microarray analysis were consistent with induction of the collateral effect by the CRISPR-Cas13a system. Tumor cell proliferation and colony formation were decreased in U87-F3-T3 cells expressing the Cas13a-based tool, and tumor growth was suppressed in an orthotopic tumor model in mice. These findings demonstrate that the CRISPR-Cas13a system induces the collateral damage effect in cancer cells and provides a viable strategy for precision tumor therapy based on the customized design of a CRISPR-Cas13a-based tool against F3-T3 fusion genes.

A quinazoline-based bromodomain inhibitor, CN210, ameliorates indomethacin-induced ileitis in mice by inhibiting inflammatory cytokine expression.

Inhibitors of bromodomain and extra-terminal motif (BET) proteins are emerging epigenetic therapeutics that suppress gene expressions that drive cancer and inflammation. The present study examined anti-inflammatory effects of a quinazoline-based BET inhibitor, CN210, in a murine ileitis model. CN210 was given orally 30 min before and 24 h after a subcutaneous administration of indomethacin. Macroscopic and histological evidences of ileitis, mucosal myeloperoxidase (MPO) activity and cytokine expressions were evaluated 48 h after the indomethacin administration. To further characterize the anti-inflammatory pathways modulated by CN210, its effects on RAW264 cells treated with lipopolysaccharide (LPS) were investigated. Competitive ligand binding and docking studies of CN210 to CREB-binding protein (CBP) and p300 were also performed. Oral administration of CN210 significantly reduced the severity of ileitis, normalized both proinflammatory MPO activity and concomitant cytokine expressions induced by indomethacin administration. Furthermore, CN210 attenuated the expression of cytokines and reversed the activation of nuclear factor κB (NF-κB) and mitogen-activated protein kinases (MAPK) induced by LPS. Competitive ligand binding assays showed that CN210 bound to the bromodomains of two paralogous histone acetyltransferases, CBP and p300, in addition to the bromodomains of BET proteins. Docking studies of CN210 to the bromodomains of CBP and p300 showed a similarity to the binding mode of SGC-CBP30, a specific CBP/p300 inhibitor. CN210 ameliorates indomethacin-induced ileitis by inhibiting the expression of inflammatory cytokines through the attenuation of NF-κB and MAPK pathways. CN210 thus represents a new mode of therapy for non-steroidal anti-inflammatory drug-induced ileitis and inflammatory bowel disease.

Transcriptome analysis of the toxic mechanism of nanoplastics on growth, photosynthesis and oxidative stress of microalga Chlorella pyrenoidosa during chronic exposure

The toxicity of nanoplastics to aquatic organisms has been widely studied in terms of biochemical indicators. However, there is little discussion about the underlying toxic mechanism of nanoplastics on microalgae. Therefore, the chronic effect of polystyrene (PS) nanoplastics (80 nm) on Chlorella pyrenoidosa was investigated, in terms of responses at the biochemical and molecular/omic level. It was surprising that both inhibitory and promoting effects of nanoplastcis on C. pyrenoidosa were found during chronic exposure. Before 13 days, the maximum growth inhibition rate was 7.55% during 10 mg/L PS nanoplastics treatment at 9 d. However, the inhibitory effect gradually weakened with the prolongation of exposure time. Interestingly, algal growth was promoted for 1–5 mg/L nanoplastics during 15–21 d exposure. Transcriptomic analysis explained that the inhibitory effect of nanoplastics could be attributed to suppressed gene expression of aminoacyl-tRNA synthetase that resulted in the reduced synthesis of related enzymes. The promotion phenomenon may be due to that C. pyrenoidosa defended against nanoplastics stress by promoting cell proliferation, regulating intracellular osmotic pressure, and accelerating the degradation of damaged proteins and organs. This study is conducive to provide theoretical basis for evaluating the actual hazard of nanoplastics to aquatic organisms.

Increased miR‑187‑3p expression after cerebral ischemia/reperfusion induces apoptosis via initiation of endoplasmic reticulum stress

Ischemia/reperfusion (I/R) injury induces activation of the endoplasmic reticulum stress (ERS) pathway, accompanied by an increase in apoptosis. Multiple microRNAs (miRNAs/miRs) are dysregulated during I/R and contribute to I/R-induced injury. miRNAs act as suppressors of gene expression and negatively regulate gene expression by targeting the protein-coding sequence (CDS) of specific target mRNAs. Seipin is an endoplasmic reticulum protein that has recently been associated with ERS. We previously reported that seipin is the target gene of miR‑187‑3p. Therefore, we explored the involvement of miR-187-3p in I/R-induced ERS via the regulation of seipin. A rat MCAO/R model was established by 1 h of occlusion and 24 h reperfusion. Neurological deficits and infarction area were examined. PC12 cells were exposed to oxygen‑glucose deprivation/reoxygenation (OGD/R) to model I/R. Expression levels of miR-187-3p and proteins related to ERS and apoptosis were measured using RT-PCR, western blotting, immunofluorescence, and immunohistochemistry, respectively. TUNEL staining was used to assay apoptosis. MCAO/R-induced morphological changes were analyzed with Nissl staining and Hematoxylin-eosin staining. I/R-induced ERS was closely associated with an increase in miR-1873p and a decrease in seipin expression. miR-187-3p agomir further activated the ERS pathway and promoted apoptosis but decreased seipin expression levels; these effects were reversed by miR-187-3p antagomir. Moreover, seipin knockdown aggravated ERS in PC12 cells after OGD/R, and this change was rescued by seipin overexpression. miR-187-3p antagomir did not suppress ERS and apoptosis in seipin knockdown PC12 cells after OGD/R. Our findings demonstrate that the inhibition of miR‑187‑3p attenuated I/R‑induced cerebral injury by regulating seipin-mediated ERS.

Beet (Beta vulgaris) Suppressed Gene Expression and Serum Fatty Acid Synthase in High Fat and Fructose-induced Rats

BACKGROUND: The expression and activity of fatty acid synthase (FAS) enzymes determine de novo fatty acid synthesis, which can be enhanced by a high-fat and high fructose diet or inhibited by some bioactive compound diets. Beets are a great source of therapeutic compounds that have the potential to improve health and prevent disease. AIM: This study examined the effects of beets on liver FAS gene expression and FAS levels. METHODS: A total of 25 male Wistar rats divided into five groups: (1) Standard diet (n); (2) high fat and fructose diet (HFFD); (3) HFFD have given beet 6%-contained standard diet (B1); (4) HFFD have given beet 9%-contained standard diet (B2), and (5) HFFD have given beet 12%-contained standard diet (B3). The HFFD was given to rats in the 2, 3, 4, and 5 group diets for 8 weeks? and then 3, 4, and 5 groups received beet-contained standard diet for 6 weeks. At the end of the intervention, FAS levels were measured (please specify where it was measured from) using the ELISA method, liver FAS gene expression was analyzed by quantitative polymerase chain reaction, and triglyceride (TG) levels were determined by the colorimetric method. RESULTS: The beet-substituted diet significantly suppressed the hepatic FAS gene expression and decreased the serum FAS levels in rats previously given HFFD (p < 0.05). The expression of the FAS gene showed a significant positive correlation with the levels of FAS serum (p < 0.05), and also with the hepatic TG levels but not significant (p > 0.05). Substitution of beet 9% in diet gives the best effect in hepatic FAS gene expression and the serum FAS levels. CONCLUSIONS: The diet contained beet 9% was seen as a necessary physiological dose to improve the effects of high-fat and diet fructose diet through suppressing FAS gene expression and a decreased serum FAS levels.

The overexpression of insect endogenous microRNA in transgenic rice inhibits the pupation of Chilo suppressalis and Cnaphalocrocis medinalis.

Chilo suppressalis and Cnaphalocrocis medinalis are destructive rice pests co-occurring in major rice-growing areas in China. RNA interference (RNAi)-based insect-resistant genetically engineered (IRGE) crops provide a promising approach for pest management by suppressing gene expression or translation. A microRNA (miRNA)-mediated IRGE rice line expressing endogenous Chilo suppressalis miRNA Csu-novel-260, showing significant resistance against Chilo suppressalis, provides an attractive control strategy for Chilo suppressalis by suppressing the expression of the disembodied (dib) gene expression. However, whether this transgenic line also shows the resistance against Cnaphalocrocis medinalis remains unknown. A spatiotemporal expression analysis of Csu-novel-260 in the transgenic rice line was performed by quantitative reverse transcription polymerase chain reaction (qRT-PCR) to determine the paddy field pest exposure dose. In diet feeding assays, a chemically synthesized Csu-novel-260 agomir at 200 fmol g-1 significantly inhibited Chilo suppressalis pupation. However, larval development, survival and pupal weight were not significantly affected. Additionally, the transgenic line significantly affected Cnaphalocrocis medinalis pupation but not larval survival. The qRT-PCR showed that Csdib and Cmdib expression levels were significantly suppressed when the two pests fed on the transgenic line. Additionally, the transgenic line significantly decreased Cry1C-resistant and Cry1C-susceptible Chilo suppressalis larval survival in detached rice tissue feeding assays, indicating that Cry1C-resistant Chilo suppressalis was not cross-resistant to Csu-novel-260 expressed in miRNA-mediated IRGE rice. Our study demonstrated that miRNA-mediated IRGE rice significantly inhibited Chilo suppressalis and Cnaphalocrocis medinalis pupation. The results provide a new viewpoint for the application of RNAi-based plants and the inspiration for environmental risk assessment.

A Timely Review of Cross-Kingdom Regulation of Plant-Derived MicroRNAs.

MicroRNAs (miRNAs) belong to a class of non-coding RNAs that suppress gene expression by complementary oligonucleotide binding to the sites in target messenger RNAs. Numerous studies have demonstrated that miRNAs play crucial role in virtually all cellular processes of both plants and animals, such as cell growth, cell division, differentiation, proliferation and apoptosis. The study of rice MIR168a has demonstrated for the first time that exogenous plant MIR168a influences cholesterol transport in mice by inhibiting low-density lipoprotein receptor adapter protein 1 expression. Inspired by this finding, the cross-kingdom regulation of plant-derived miRNAs has drawn a lot of attention because of its capability to provide novel therapeutic agents in the treatment of miRNA deregulation-related diseases. Notably, unlike mRNA, some plant miRNAs are robust because of their 3′ end modification, high G, C content, and the protection by microvesicles, miRNAs protein cofactors or plant ingredients. The stability of these small molecules guarantees the reliability of plant miRNAs in clinical application. Although the function of endogenous miRNAs has been widely investigated, the cross-kingdom regulation of plant-derived miRNAs is still in its infancy. Herein, this review summarizes the current knowledge regarding the anti-virus, anti-tumor, anti-inflammatory, anti-apoptosis, immune modulation, and intestinal function regulation effects of plant-derived miRNAs in mammals. It is expected that exploring the versatile role of plant-derived miRNAs may lay the foundation for further study and application of these newly recognized, non-toxic, and inexpensive plant active ingredients.

Antisense Oligonucleotides as a Novel Therapy for Cushing’s Disease

Background: Cushing’s disease (CD) is caused by high levels of blood cortisol resulting from excess secretion of ACTH from a corticotroph adenoma in the anterior pituitary gland. Clinical features include hypertension, diabetes, osteoporosis, and depression. If untreated CD has an increased mortality of five-fold owing to cardiovascular comorbidities, stroke or raised vulnerability to infection. Transsphenoidal surgery is considered the first-line treatment but remission is achieved in only 65% of cases and the relapse rate is high. Furthermore, medical treatments are often accompanied by unpleasant side-effects. Antisense therapy is a technique for suppressing gene expression at the level of translation using antisense oligonucleotides (ASOs) against the mRNA of interest. Aims: To investigate antisense therapy as a treatment for CD by targeting ASOs against ACTH-encoding POMC mRNA thereby reducing secretion of the hormone. To transfect mouse AtT20 cells (cells that secrete high levels of ACTH) with ASOs against POMC at varying doses to determine which is the most effective at reducing ACTH secretion. Methods: AtT-20 cells that secrete high levels of ACTH were used as the model system. ASOs were designed to specifically target exon 3 of the POMC gene. Transfection of AtT-20 was carried out using Lipofectamine. FACS was used to determine transfection efficiency. ACTH levels secreted by AtT-20 cells were determined by immunoassay. Statistical analysis was done using ANOVA with P values < 0.05 considered significant. Results: ASOs that targeted POMC exon 3 (ASO-2 and ASO-3) were transfected into AtT-20 cells at 10 and 100 nM. Control ASOs were ASO-1 (matched to POMC sense strand) and ASO-4 (a scrambled version of ASO-3). Experiments included untreated AtT-20 cells and AtT-20 cells treated with transfection reagent or ASOs alone. The results of six experiments indicated that ACTH secretion from AtT-20 cells was reduced after transfection with ASO-2 and ASO-3 at 100 nM (ANOVA, P = < 0.05) and 10 nM (ANOVA, P < 0.05) when compared with untreated AtT20 cells. ASO-1 and ASO-4 had no effect on ACTH secretion by AtT-20 cells (ANOVA, P > 0.05). Conclusions: Initial experiments have shown that ASOs against POMC can reduce ACTH secretion from AtT-20 cells and may be useful as a novel therapy for CD.

AR Is Not an Independent Marker for TNBC: The Lesson We Learn From Two PDX Models

Extensive efforts, through cell line-based models, have been made to characterize the androgen receptor (AR) signaling pathway in triple-negative breast cancer (TNBC). However, these efforts have not yet reached a consensus with regards to the mechanism of AR in TNBC. On the other hand, patient-derived xenografts (PDXs) are generally considered more appropriate than cell line-based models for recapitulating the structural and molecular features of a patient’s tumor, but only a few have been reported to be AR-positive TNBC. In our study, we identified and molecularly characterized two new, AR-positive TNBC PDX models and assessed the impacts of AR agonist (DHT) and antagonist (enzalutamide) on tumor growth and gene expression profiles by utilizing immunohistochemistry (IHC), western blots, and RNA-Seq and TNBC subtyping analyses. Two PDX models, termed TN1 and TN2, were derived from two grade 3 TNBC tumors, each containing 1~5% of AR positive tumor cells. DHT activated AR in both PDX tumors by increasing AR nuclear localization and protein levels. However, the endpoint tumor volume of DHT-treated TN1 was 3-folds smaller than that of non-treated TN1 tumors. Conversely, the endpoint tumor volume of DHT-treated TN2 was 2-folds larger than that of non-treated TN2. Moreover, enzalutamide failed to antagonize DHT-induced tumor growth in TN2. The RNA-Seq analyses revealed that DHT suppressed gene expression in TN1 (961 down-regulated genes versus 149 up-regulated genes), while the DHT promoted gene expression in TN2 (673 up-regulated genes versus192 down-regulated genes). TNBC subtyping analyses based on RNA-Seq data predicted distinct molecular subtypes of TN1 and TN2: TN1 correlated to a basal-like 1 (BL1) subtype, and TN2 correlated to a basal-like 2 (BL2) subtype. These analyses suggest that TN1 and TN2, which both express functional AR, are two molecularly distinct PDX models that expand our current knowledge of AR-positive TNBC. Our results do not support that AR is a suitable therapeutic target in TNBC. To our best knowledge, the molecular mechanisms of AR in TNBC are equivocal and should be evaluated using clinically relevant models, considering both the heterogeneous expression of AR in TNBC and the general complexities of AR signaling.

Moringa oleifera Lam. leaf extract mitigates carbon tetrachloride-mediated hepatic inflammation and apoptosis via targeting oxidative stress and toll-like receptor 4/nuclear factor kappa B pathway in mice

Carbon tetrachloride (CCl4) is a hepatotoxin that triggers liver damage. This study aimed to evaluate the protective effect of phytochemicals detected in Moringa oleifera Lam. leaf extract (MOLE) on CCl4-induced hepatotoxicity in mice. Phytochemicals, total phenolics, and total flavonoids were detected in MOLE. MOLE markedly decreased the elevation of serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) in consistence with the ameliorating effect on CCl4-induced histopathological abnormalities. Moreover, MOLE significantly alleviated the decrease in the antioxidant defense mechanism induced by CCl4. The suppressing effect of MOLE on the boosted inflammatory pathway triggered by CCl4 was detected by measuring the protein levels of nuclear factor kappa-light-chain-enhancer of activated B-cells (NF-κB-p65), toll-like receptor 4 (TLR4), tumor necrosis factor-α (TNF-α), interleukin (IL)-6, IL-1β, and IL-8 as well as the relative expressions of nuclear factor kappa B (NF-κB), TNF-α, IL-1β, and TLR4 genes. Apoptosis and genotoxicity induced by CCl4 were significantly alleviated by MOLE. MOLE co-administration modulated TLR4/NF-κB pathway as presented by the suppressed gene expression of TLR4 and NF-κB as well as by the reduced protein expression of TLR4 and NF-κB-p65. In conclusion, MOLE has a multifarious protective role against hepatotoxicity through control of oxidative stress and modulation of TLR4/NF-κB.

Identification of dicyclohexyl phthalate as a glucocorticoid receptor antagonist by molecular docking and multiple in vitro methods.

The potential activities of phthalate esters (PAEs) that interfere with the endocrine system have been focused recently. However, information on modulating the glucocorticoid receptor (GR) of PAEs is scarce. Our aim was to evaluate the agonistic / antagonistic properties of PAEs on human GR. Luciferase reporter gene assay revealed that the tested chemicals displayed no agonistic effects but dicyclohexyl phthalate (DCHP) exerted antagonistic activity in a dose-responsive manner for GR in HeLa cells. The effects of DCHP on dexamethasone (DEX)-induced GR nuclear translocation and gene expression of glucocorticoid-responsive gene expression (G6Pase, PEPCK, FAS, GILZ and MKP-1), as well as protein expression of G6Pase and PEPCK were further examined by RT-qPCR and western blot analysis. DCHP antagonized DEX-induced GR nuclear translocation and suppressed gene expression in both mRNA and protein levels. Furthermore, the results of molecular docking and molecular dynamics simulation showed that DCHP could bind to GR and exhibited potential regulation on this target protein. Collectively, we demonstrate that DCHP may act as a GR antagonist in vitro and is considered to exert endocrine effects via human GR.

Identification of miR-17, miR-21, miR-27a, miR-106b and miR-222 as endoplasmic reticulum stress-related potential biomarkers in circulation of patients with atherosclerosis.

Atherosclerosis and related cardiovascular diseases are among the most commoncauses of death worldwide. Unfolded protein response, also known as Endoplasmic reticulum stress, has a critical role in many diseases including atherosclerosis. Small non-coding microRNAs (miRNA), which generally suppress gene expression, regulate UPR signalling and they may also be involved in the progression of atherosclerosis. We aim to investigate the expression levels of miR-17, miR-21, miR-27a, miR-106b, miR-222 and CHOP gene in circulation of atherosclerosis patients compared to healthy controls to establish a link between ERstress and atherosclerosis. miRNAcontaining whole RNAwasisolated from blood samples of25patientswith atherosclerosis and 26healthy controls.Expression levels of miRNAs andCHOP were measured via Real Time PCR method. miR-17and miR-106b were significantly increased whilemiR-21, miR-27a, and miR-222 weresignificantly decreasedin patients compared to controls. CHOP gene wasalso dramaticallyand significantlyinducedin patientsamples. miR-17, miR-21, miR-27a, miR-106b,miR-222and CHOPwere significantly differentially expressed in patients with atherosclerosis. EachmiRNAand CHOPmight regulate atherosclerotic plaque progression andthey canbe used as a biomarker in the diagnosis and follow-up of atherosclerosis-related cardiovascular diseases.

Inchworm-type PNA-PEG conjugate regulates gene expression based on single nucleotide recognition

In order to detect single nucleotide mutations and suppress gene expression, we synthesized an artificial nucleic acid, an inchworm-type PNA-PEG conjugate (i-PPc), that possessed a chemical structure in which 8 residues of peptide nucleic acid (PNA) were linked to both ends of a polyethylene glycol molecule. I-PPc_T7FM, which forms a complementary strand with the T7 promoter region of luciferase-expressing mRNA, failed to suppress the amount of luciferase produced via gene expression. However, 10 μM of i-PPc_ATGFM, targeting the start codon of luciferase (Luc+), suppressed approximately 85% of Luc+ production compared to that of the control in the cell-free protein synthesis system. Moreover, i-PPc_ATGMM (i-PPc_ATGFM with a single base mutation) only suppressed the amount of luciferase produced by approximately 15%, and such suppression of luciferase expression has not been achieved with block-type PPc or PNA oligos. The thermodynamic parameters suggested that the difference in stability of each PNA segment of the i-PPc contributed to single nucleotide recognition. These results indicate that the i-PPc could be used in antisense therapy to target single nucleotide polymorphisms (SNP).

Detection of H3K4me3 Identifies NeuroHIV Signatures, Genomic Effects of Methamphetamine and Addiction Pathways in Postmortem HIV+ Brain Specimens that Are Not Amenable to Transcriptome Analysis.

Human postmortem specimens are extremely valuable resources for investigating translational hypotheses. Tissue repositories collect clinically assessed specimens from people with and without HIV, including age, viral load, treatments, substance use patterns and cognitive functions. One challenge is the limited number of specimens suitable for transcriptional studies, mainly due to poor RNA quality resulting from long postmortem intervals. We hypothesized that epigenomic signatures would be more stable than RNA for assessing global changes associated with outcomes of interest. We found that H3K27Ac or RNA Polymerase (Pol) were not consistently detected by Chromatin Immunoprecipitation (ChIP), while the enhancer H3K4me3 histone modification was abundant and stable up to the 72 h postmortem. We tested our ability to use H3K4me3 in human prefrontal cortex from HIV+ individuals meeting criteria for methamphetamine use disorder or not (Meth +/−) which exhibited poor RNA quality and were not suitable for transcriptional profiling. Systems strategies that are typically used in transcriptional metadata were applied to H3K4me3 peaks revealing consistent genomic activity differences in regions where addiction and neuronal synapses pathway genes are represented, including genes of the dopaminergic system, as well as inflammatory pathways. The resulting comparisons mirrored previously observed effects of Meth on suppressing gene expression and provided insights on neurological processes affected by Meth. The results suggested that H3K4me3 detection in chromatin may reflect transcriptional patterns, thus providing opportunities for analysis of larger numbers of specimens from cases with substance use and neurological deficits. In conclusion, the detection of H3K4me3 in isolated chromatin can be an alternative to transcriptome strategies to increase the power of association using specimens with long postmortem intervals and low RNA quality.

Cytoplasmic delivery of small interfering RNA by photoresponsive non-cationic liposomes

Small interfering RNA (siRNA) can specifically suppress gene expression by cleaving mRNA in the cytoplasm, termed RNA interference (RNAi). Although a nanoparticle-based siRNA delivery system has been approved for clinical use, the efficiency of cytoplasmic delivery of siRNA is still low. Recently, our group has established a highly efficient siRNA encapsulation method using non-cationic liposomes (LPs), which are more biocompatible than conventional cationic LPs. While non-cationic LPs containing siRNA were taken up by cells in vitro, the cytoplasmic release of siRNA and subsequent phenomena involving RNAi were not observed. It was considered that cytoplasmic delivery of siRNA, and siRNA release from LPs, should occur sequentially. We utilized amphiphilic photosensitizer Al (III) phthalocyanine chloride disulfonic acid (AlPcS2a), which can generate singlet oxygen under exposure to red light. When SK-HEP-1 cells expressing luciferase were treated with non-cationic LPs containing both siRNA and AlPcS2a, RNAi could be observed upon red light exposure, suggesting that singlet oxygen efficiently disrupts the membranous structures of endo/lysosomes and LPs. Thus, the combined use of AlPcS2a and red light is effective for utilizing non-cationic LPs for cytoplasmic delivery of siRNA.

Malonic acid suppresses lipopolysaccharide-induced BV2 microglia cell activation by inhibiting the p38 MAPK/NF-κB pathway

ABSTRACT An inflammatory reaction caused by the activation of microglia in the brain can lead to neurodegeneration and cause diseases, such as Alzheimer’s and Parkinson’s disease. The regulation of inflammation can aid in preventing the development of neurodegenerative disease. Malonic acid has a variety of biological activity. The effects of malonic acid on microglia are not currently well known. Therefore, in this study, we investigate the effects of inflammation of malonic acid in BV2 microglia cells. As a result, we demonstrated that malonic acid on LPS-treated microglia decreased pro-inflammatory responses and mechanisms of the p38 MAPK/NF-κB pathway. Inflammatory mediators significantly decreased the LPS-induced production of nitric oxide and reactive oxygen species. Pro-inflammatory cytokines of IL-6 suppressed gene expression. In addition, the protein expression of NF-κB decreased at the nucleus, as did the protein expression of activated phosphorylated IκB-α, which is an NF-κB regulator-related protein. The expression of phosphorylated p38, a mediator of inflammatory cytokines, was regulated. Therefore, our results indicate that malonic acid has anti-inflammatory effects and may be a potential therapeutic candidate for neuroinflammatory diseases.

Genome-wide analysis identifies critical DNA methylations within NTRKs genes in colorectal cancer

BackgroundNeurotrophic tropomyosin receptor kinases (NTRKs) are a gene family function as oncogene or tumor suppressor gene in distinct cancers. We aimed to investigate the methylation and expression profiles and prognostic value of NTRKs gene in colorectal cancer (CRC).MethodsAn analysis of DNA methylation and expression profiles in CRC patients was performed to explore the critical methylations within NTRKs genes. The methylation marker was validated in a retrospectively collected cohort of 229 CRC patients and tested in other tumor types from TCGA. DNA methylation status was determined by quantitative methylation-specific PCR (QMSP).ResultsThe profiles in six CRC cohorts showed that NTRKs gene promoter was more frequently methylated in CRC compared to normal mucosa, which was associated with suppressed gene expression. We identified a specific methylated region within NTRK3 promoter targeted by cg27034819 and cg11525479 that best predicted survival outcome in CRC. NTRK3 promoter methylation showed independently predictive value for survival outcome in the validation cohort (P = 0.004, HR 2.688, 95% CI [1.355, 5.333]). Based on this, a nomogram predicting survival outcome was developed with a C-index of 0.705. Furthermore, the addition of NTRK3 promoter methylation improved the performance of currently-used prognostic model (AIC: 516.49 vs 513.91; LR: 39.06 vs 43.64, P = 0.032). Finally, NTRK3 promoter methylation also predicted survival in other tumors, including pancreatic cancer, glioblastoma and stomach adenocarcinoma.ConclusionsThis study highlights the essential value of NTRK3 methylation in prognostic evaluation and the potential to improve current prognostic models in CRC and other tumors.