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Background and Aim: The macrophage receptor with collagenous structure (MARCO) belongs to the scavenger receptor family; however, few studies have assessed their potentials in modulating inflammatory signaling other than the typical function of pattern recognition and phagocytic clearance. Interestingly, RNA-Seq analyses of hepatocellular carcinoma (HCC) have identified MARCO as one of the top 30 differentially expressed genes between cancerous and adjacent noncancerous tissues. However, no research has been performed to study MARCO in liver cancer., Methods: MARCO protein expression was evaluated by immunostaining liver tissue specimens collected from 88 HCC patients, 10 liver cirrhosis patients, 6 metastatic patients, and 5 healthy controls. All sections were reviewed by blinded observers followed by the interpretation of integral optical density per area as a measure of protein intensity., Results: We observed significantly decreased expression of MARCO in intratumoral tissues of HCC compared with expression in peritumoral tissues. The expression of MARCO declined progressively as the disease condition was aggravated, with the highest expression found in healthy controls and the lowest found in patients with HCC metastasis. Furthermore, MARCO expression decreased along with tumor progression. MARCO + cells co-localized with CD68 + cells, indicating predominant expression on macrophages. The overall survival rate was significantly increased in patients with high intratumoral MARCO expression compared with that of patients with low intratumoral MARCO expression., Conclusions: Our study is the first to demonstrate an association between MARCO expression and the progression and prognosis of HCC., (© 2016 Journal of Gastroenterology and Hepatology Foundation and John Wiley & Sons Australia, Ltd.)

Quantitative real-time polymerase chain reaction (qRT-PCR) is a valuable tool for estimating gene expression; however, the validity is largely dependent on the selection of stable reference genes. The suitability of various reference genes for qRT-PCR analysis was evaluated in, Chilo suppressalis (Walker). The ΔCt method, geNorm, NormFinder, and BestKeeper were used to evaluate the suitability of nine candidate reference genes for normalizing gene expression in larval tissues and organs and during high and low temperature stress. The ΔCt method, geNorm, and NormFinder produced similar stability rankings; H3, UBI, and EF1 were the most stable reference genes for monitoring gene expression in larval tissue and organs, and EF1, TUB, and AK were the optimal genes for thermal stress. However, for thermal stress, RPS11 was the most stable gene based on BestKeeper. To validate these recommendations, the expression profile of the gene encoding heat shock protein 60 (Hsp60) was investigated. Hsp60 transcript levels showed significant differences when normalized to the most versus least stable reference genes. These results further confirm the importance of testing reference genes using the selected experimental parameters. The reference genes identified in the present study will improve the quality of gene expression data obtained for C. suppressalis and will facilitate future studies aimed at understanding the biology of this important insect pest., (© The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Growing evidence suggests that the brain, in particular the hypothalamus, directly senses hormones and nutrients to initiate feeding behavior and metabolic responses in the control of energy homeostasis. However, the molecular mechanisms underlying this important process have remained largely unknown. Our study provides the evidence for the role of Abelson helper integration site 1 (Ahi1) protein as a sensor of insulin signaling in the hypothalamus. We found that fasting increased the expression of hypothalamic Ahi1 which was accompanied by lower levels of circulating insulin compared with satiated mice, while re-feeding decreased the expression of hypothalamic Ahi1 which was accompanied by higher levels of circulating insulin. We also found the up-regulated expression of hypothalamic Ahi1 in high-fat induced obese mice, db/db mice, and streptozotocin induced diabetic mice. In addition, we demonstrated that insulin could decrease the expression of Ahi1 in neuroblastoma cell line N18TG2. Taken together, our results indicate that hypothalamic Ahi1 functions as a sensor of insulin signaling.

TmGUSI, a gene identical to that encoding a thermostable β-glucuronidase in the hyperthermophilic anaerobe Thermotoga maritima, has been synthesized using a PCR-based two-step DNA synthesis and codon optimization for plants, and expressed in both Escherichia coli and Arabidopsis thaliana. TmGUSI expressed in transformed E. coli cells exhibited maximum hydrolytic activity at 65 °C and pH 6.5 and retained more than 80% activity after incubation at 85 °C for 30 min. TmGUSI activity in transgenic A. thaliana plants containing TmGUSI was also stable over the temperature range 65-80 °C. Our data suggest that β-glucuronidase from T. maritima can serve as a useful thermostable marker in higher plants.

In plants, anthocyanins often appear at specific developmental stages, but are also induced by a number of environmental factors. The coordinated expression of genes encoding the anthocyanin biosynthetic pathway enzymes is controlled at the transcriptional level usually by an R2R3Myb transcription factor. However, little is known about the effects of R2R3-Myb on plant resistance to environmental stresses. In this study, we introduced an R2R3Myb transcription factor gene Mdmyb10, a regulatory gene of anthocyanin biosynthesis in apple fruit, into Arabidopsis and analyzed its function to osmotic stress in transgenic plants. Under high osmotic stress, the Mdmyb10 over-expressing plants exhibited growth better than wild-type plants. The elevated tolerance of the transgenic plants to osmotic stress was confirmed by the changes of flavonoids, chlorophyll, malondialdehyde and proline contents. These results preliminarily showed that the Mdmyb10 can possibly be used to enhance the high osmotic-tolerant ability of plants.

Background: TaqMan low density array (LDA) is promising for high throughput screening in functional genomics by simultaneously measuring mRNA expression of multiple genes. However, the reproducibility and reliability remain to be explored., Methods: We applied LDA to detect mRNA expression of 95 gastrointestinal differentiation associated genes in 27 colorectal cancers with individual-matched normal mucosa. Conventional Q-PCR assay was done to detect 18 differentially expressed genes in additional 22 colorectal cancers., Results: A total of 97.2% (11,520/11,844) gene samples were successfully amplified by LDA. There was a perfect agreement between intra-LDA assays in all gene samples (CCC=0.952, p<0.0001). Seventy-nine genes showed perfect or substantial agreement between intra-LDA tests (CCC>0.713). Genes with low Ct values (<30 cycles) had more genes showing perfect agreement, less showing moderate agreement, and lower DeltaCt variances between intra-plate assays than that with high Ct values (>30 cycles) (p<0.01). All 18 genes showed the same directional changes in colorectal cancers versus normal mucosa by both SYBR Green and LDA approaches., Conclusions: LDA is a roughly robust method for gene quantification in colorectal cancer, but its reproducibility decreased in low copy genes. Hence, we strongly recommend caution when analyzing LDA results of those low copy genes.

The trefoil factors (TFFs) are pleiotropic factors involved in organization and homeostasis of the gastrointestinal tract, estrogen responsiveness, inflammatory disorders, and carcinogenesis. In an earlier study using cDNA array technologies to identify new genes expressed in irradiated cell survivors, we isolated a cDNA clone corresponding to the reported human TFF1 gene (E. K. Balcer-Kubiczek et al., Int. J. Radiat. Biol., 75: 529-541, 1999). To determine whether expression of other TFFs is altered by ionizing radiation, we quantified changes in expression of TFF3 as well as TFF1 in RNA samples obtained from irradiated and control human tumor breast, colon, and gastric tumor cells and examined expression kinetics up to 2 weeks after irradiation. X-ray-induced TFF1 and TFF3 expression profiles were compared with those induced by hydrogen peroxide (H2O2) or 17beta-estradiol (ES). The results revealed that TFF1 and TFF3 mRNA are coinduced by X-irradiation in a subset of the lines, but substantial heterogeneity in their responses was observed in cells derived from a single cell type. TFF1 and TFF3 transcriptional response to X-irradiation differed from that to H2O2 or ES in the timing of their induction as well as tissue-type dependence, i.e., their induction pattern after X-irradiation was late and sustained, whereas their induction by H2O2 or ES was early and transient. TFF1 mRNA, protein production in the cytoplasm, and secretion in the culture supernatant were coordinately regulated after X-irradiation. There was no requirement for TP53 in this induction. These results demonstrate the existence of a novel class of radiation-responsive genes that might be involved in bystander effects.

Human papillomavirus (HPV) infection is a major contributor to cervical cancer. Persistent HPV infection can trigger the expression of IL-32, yet the precise role of IL-32 in the occurrence and development of cervical cancer remains elusive. To investigate this, qRT‒PCR and western blotting were utilized to measure the mRNA and protein expression levels; bioinformatics analysis was used to screen differentially expressed miRNAs; wound healing and transwell assays were conducted to evaluate cell migration and invasion capabilities. Comparative analysis revealed significantly elevated IL-32 expression in cervical cancer tissues and cell lines compared to control groups. In SiHa and/or HeLa, overexpression of IL-32 and IL-32 exposure markedly upregulated miR-205, whereas its knockdown resulted in a substantial downregulation of miR-205. Furthermore, miR-205 also could significantly regulate the expression of IL-32 in HeLa and SiHa cells. Upregulation and downregulation of IL-32 led to a significant increase or decrease in NFκB expression, respectively. Treatment with BAY11-7082 (an NFκB inhibitor) notably decreased miR-205 expression but had no effect on IL-32 levels. qRT‒PCR and western blotting analyses demonstrated that both overexpression and underexpression of IL-32 and miR-205 significantly enhanced or reduced MMP2 and MMP9 expression in cervical cancer cells, respectively. Knockdown of IL-32 significantly inhibited the migration and invasion of HeLa and SiHa; conversely, treatment with rIL-32α and rIL-32γ notably promoted their migration and invasion. In brief, IL-32 is highly expressed via the formation of a positive regulatory loop with NFκB/miR-205, contributing to the persistence of inflammation and promoting the progression of cervical cancer. [ABSTRACT FROM AUTHOR]

Background: Schistosomiasis is a relatively neglected parasitic disease that afflicts more than 250 million people worldwide, for which the control strategy relies mainly on mass treatment with the only available drug, praziquantel (PZQ). This approach is not sustainable and is a priority for developing novel drug candidates for the treatment and control of schistosomiasis. Methodologys/Principal findings: In our previous study, we found that DW-3-15, a kind of PZQ derivative, could significantly downregulate the expression of the histone acetyltransferase of Schistosoma japonicum (SjHAT). In this study, several commercially available HAT inhibitors, A485, C646 and curcumin were screened in vitro to verify their antischistosomal activities against S. japonicum juveniles and adults. Parasitological studies and scanning electron microscopy were used to study the primary action characteristics of HAT inhibitors in vitro. Quantitative real-time PCR was employed to detect the mRNA level of SjHAT after treatment with different HAT inhibitors. Our results demonstrated that curcumin was the most effective inhibitor against both juveniles and adults of S. japonicum, and its schistosomicidal effects were time- and dose dependent. However, A485 and C646 had limited antischistosomal activity. Scanning electron microscopy demonstrated that in comparison with DW-3-15, curcumin caused similar tegumental changes in male adult worms. Furthermore, both curcumin and DW-3-15 significantly decreased the SjHAT mRNA level, and curcumin dose-dependently reduced the SjHAT expression level in female, male and juvenile worms. Conclusions: Among the three commercially available HATs, curcumin was the most potent against schistosomes. Both curcumin and our patent compound DW-3-15 markedly downregulated the expression of SjHAT, indicating that SjHAT may be a potential therapeutic target for developing novel antischistosomal drug candidates. Author summary: Schistosomiasis is a zoonotic parasitic disease caused by Schistosoma spp. infection. Due to the lack of effective vaccines for schistosomiasis, PZQ is the only available drug chosen for the treatment and control of schistosomiasis in most developing countries. Drug resistance due to long-term, large-scale and single-agent use has been a great concern. Therefore, there is an urgent need for new therapies. In our previous study, we developed the patented compound DW-3-15 (patent no. ZL201110142538.2), which has significant and stable antiparasitic activity, and can significantly decrease the expression of S. japonicum histone acetyltransferase (SjHAT). As we known, HATs are a class of epigenetic enzymes that are crucial for chromatin restructuring and transcriptional regulation in mammals and in parasitic development, and are thus promising targets for antischistosomal therapeutic development. In this study, we assessed three commercial HATs, including two selective p300/CBP inhibitors A485 and C646, and one natural compound, curcumin. Our results demonstrated that curcumin had the most potent worm-killing efficacy against S. japonicum juveniles and adults. In contrast, A485 and C646 displayed no effects on adult worms or mild effects on juveniles. Moreover, curcumin caused severe damage to the tegument of male worms, and the damage was similar to that of DW-3-15. Coincidentally, both curcumin and DW-3-15 significantly downregulated the expression of SjHAT, indicating that SjHAT might be an effective target for the development of novel therapeutic drugs. The screening and identification of selective HAT inhibitors may be a promising strategy for developing novel antischistosomal agents. [ABSTRACT FROM AUTHOR]

SUMMARY: Gibberellins (GAs) play crucial roles in regulating plant architecture and grain yield of crops. In rice, the inactivation of endogenous bioactive GAs and their precursors by GA 2‐oxidases (GA2oxs) regulates stem elongation and reproductive development. However, the regulatory mechanisms of GA2ox gene expression, especially in rice reproductive organs, are unknown. The BEL1‐like homeodomain protein OsBLH4, a negative regulatory factor for the rice OsGA2ox1 gene, was identified in this study. Loss of OsBLH4 function results in decreased bioactive GA levels and pleiotropic phenotypes, including reduced plant height, decreased grain number per panicle, and delayed heading date, as also observed in OsGA2ox1‐overexpressing plants. Consistent with the mutant phenotype, OsBLH4 was predominantly expressed in shoots and young spikelets; its encoded protein was exclusively localized in the nucleus. Molecular analysis demonstrated that OsBLH4 directly bound to the promoter region of OsGA2ox1 to repress its expression. Genetic assays revealed that OsBLH4 acts upstream of OsGA2ox1 to control rice plant height, grain number, and heading date. Taken together, these results indicate a crucial role for OsBLH4 in regulating rice plant architecture and yield potential via regulation of bioactive GA levels, and provide a potential strategy for genetic improvements of rice. Significance Statement: GA 2‐oxidases (GA2oxs) play crucial roles in regulating plant architecture and yield by inactivating endogenous bioactive GAs and their precursors, but the regulatory mechanisms of GA2ox gene expression remain unclear. This study identifies that OsBLH4, a member of the BEL1‐like homeodomain proteins, acts upstream of OsGA2ox1, modulates endogenous bioactive GA levels, and regulates stem elongation and reproductive development in rice. [ABSTRACT FROM AUTHOR]

Reconstructing functional gene regulatory networks (GRNs) is a primary prerequisite for understanding pathogenic mechanisms and curing diseases in animals, and it also provides an important foundation for cultivating vegetable and fruit varieties that are resistant to diseases and corrosion in plants. Many computational methods have been developed to infer GRNs, but most of the regulatory relationships between genes obtained by these methods are biased. Eliminating indirect effects in GRNs remains a significant challenge for researchers. In this work, we propose a novel approach for inferring functional GRNs, named EIEPCF (eliminating indirect effects produced by confounding factors), which eliminates indirect effects caused by confounding factors. This method eliminates the influence of confounding factors on regulatory factors and target genes by measuring the similarity between their residuals. The validation results of the EIEPCF method on simulation studies, the gold-standard networks provided by the DREAM3 Challenge and the real gene networks of Escherichia coli demonstrate that it achieves significantly higher accuracy compared to other popular computational methods for inferring GRNs. As a case study, we utilized the EIEPCF method to reconstruct the cold-resistant specific GRN from gene expression data of cold-resistant in Arabidopsis thaliana. The source code and data are available at https://github.com/zhanglab-wbgcas/EIEPCF. [ABSTRACT FROM AUTHOR]

Diabetic cardiomyopathy (DCM) is a common cardiovascular complication of diabetes, which may threaten the quality of life and shorten life expectancy in the diabetic population. However, the molecular mechanisms underlying the diabetes cardiomyopathy are not fully elucidated. We analyzed two datasets from Gene Expression Omnibus (GEO). Differentially expressed and weighted gene correlation network analysis (WGCNA) was used to screen key genes and molecules. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and protein–protein interaction (PPI) network analysis were constructed to identify hub genes. The diagnostic value of the hub gene was evaluated using the receiver operating characteristic (ROC). Quantitative real-time PCR (RT-qPCR) was used to validate the hub genes. A total of 13 differentially co-expressed modules were selected by WGCNA and differential expression analysis. KEGG and GO analysis showed these DEGs were mainly enriched in lipid metabolism and myocardial hypertrophy pathway, cytomembrane, and mitochondrion. As a result, six genes were identified as hub genes. Finally, five genes (Pdk4, Lipe, Serpine1, Igf1r, and Bcl2l1) were found significantly changed in both the validation dataset and experimental mice with DCM. In conclusion, the present study identified five genes that may help provide novel targets for diagnosing and treating DCM. [ABSTRACT FROM AUTHOR]

Background: Circular RNAs (circRNAs) play important roles in cancer progression and metastasis. However, the expression profiles and biological roles of circRNAs in non-small cell lung cancer (NSCLC) remain unclear. Methods: In this study, we identified a novel circRNA, hsa_circ_0006834 (termed circ6834), in NSCLC by RNA-seq and investigated the biological role of circ6834 in NSCLC progression in vitro and in vivo. Finally, the molecular mechanism of circ6834 was revealed by tagged RNA affinity purification (TRAP), western blot, RNA immunoprecipitation, dual luciferase reporter gene assays and rescue experiments. Results: Our results showed that circ6834 was downregulated in NSCLC tumor tissues and cell lines. Circ6834 overexpression inhibited NSCLC cell growth and metastasis both in vitro and in vivo, while circ6834 knockdown had the opposite effect. We found that TGF-β treatment decreased circ6834 expression, which was associated with the QKI reduction in NSCLC cells and circ6834 antagonized TGF-β-induced EMT and metastasis in NSCLC cells. Mechanistically, circ6834 bound to AHNAK protein, a key regulator of TGF-β/Smad signaling, and inhibited its stability by enhancing TRIM25-mediated ubiquitination and degradation. In addition, circ6834 acted as a miRNA sponge for miR-873-5p and upregulated TXNIP gene expression, which together inactivated the TGF-β/Smad signaling pathway in NSCLC cells. Conclusion: In conclusion, circ6834 is a tumor-suppressive circRNA that inhibits NSCLC progression by forming a negative regulatory feedback loop with the TGF-β/Smad signaling pathway and represents a novel therapeutic target for NSCLC. [ABSTRACT FROM AUTHOR]

Background: Dendrobium officinale Kimura et Migo, a renowned traditional Chinese orchid herb esteemed for its significant horticultural and medicinal value, thrives in adverse habitats and contends with various abiotic or biotic stresses. Acid invertases (AINV) are widely considered enzymes involved in regulating sucrose metabolism and have been revealed to participate in plant responses to environmental stress. Although members of AINV gene family have been identified and characterized in multiple plant genomes, detailed information regarding this gene family and its expression patterns remains unknown in D. officinale, despite their significance in polysaccharide biosynthesis. Results: This study systematically analyzed the D. officinale genome and identified four DoAINV genes, which were classified into two subfamilies based on subcellular prediction and phylogenetic analysis. Comparison of gene structures and conserved motifs in DoAINV genes indicated a high-level conservation during their evolution history. The conserved amino acids and domains of DoAINV proteins were identified as pivotal for their functional roles. Additionally, cis-elements associated with responses to abiotic and biotic stress were found to be the most prevalent motif in all DoAINV genes, indicating their responsiveness to stress. Furthermore, bioinformatics analysis of transcriptome data, validated by quantitative real-time reverse transcription PCR (qRT-PCR), revealed distinct organ-specific expression patterns of DoAINV genes across various tissues and in response to abiotic stress. Examination of soluble sugar content and interaction networks provided insights into stress release and sucrose metabolism. Conclusions: DoAINV genes are implicated in various activities including growth and development, stress response, and polysaccharide biosynthesis. These findings provide valuable insights into the AINV gene amily of D. officinale and will aid in further elucidating the functions of DoAINV genes. [ABSTRACT FROM AUTHOR]

Summary: MicroRNA482/2118 (miR482/2118) is a 22‐nt miRNA superfamily, with conserved functions in disease resistance and plant development. It usually instigates the production of phased small interfering RNAs (phasiRNAs) from its targets to expand or reinforce its silencing effect. Using a new high‐quality reference genome sequence and comprehensive small RNA profiling, we characterized a newly evolved regulatory pathway of miR482/2118 in litchi. In this pathway, miR482/2118 cleaved a novel noncoding trans‐acting gene (LcTASL1) and triggered phasiRNAs to regulate the expression of gibberellin (GA) receptor gene GIBBERELLIN INSENSITIVE DWARF1 (GID1) in trans; another trans‐acting gene LcTASL2, targeted by LcTASL1‐derived phasiRNAs, produced phasiRNAs as well to target LcGID1 to reinforce the silencing effect of LcTASL1. We found this miR482/2118‐TASL‐GID1 pathway was likely involved in fruit development, especially the seed development in litchi. In vivo construction of the miR482a‐TASL‐GID1 pathway in Arabidopsis could lead to defects in flower and silique development, analogous to the phenotype of gid1 mutants. Finally, we found that a GA‐responsive transcription factor, LcGAMYB33, could regulate LcMIR482/2118 as a feedback mechanism of the sRNA‐silencing pathway. Our results deciphered a lineage‐specifically evolved regulatory module of miR482/2118, demonstrating the high dynamics of miR482/2118 function in plants. [ABSTRACT FROM AUTHOR]

Background: Sanguinarine chloride (S.C) is a benzophenanthrine alkaloid derived from the root of sanguinaria canadensis and other poppy-fumaria species. Studies have reported that S.C exhibits antioxidant, anti-inflammatory, proapoptotic, and growth inhibitory effects, which contribute to its anti-cancer properties. Recent studies suggested that the antitumor effect of S.C through inducing ferroptosis in some cancers. Nevertheless, the precise mechanism underlying the regulation of ferroptosis by S.C remains poorly understood. Methods: A small molecule library was constructed based on FDA and CFDA approved small molecular drugs. CCK-8 assay was applied to evaluate the effects of the small molecule compound on tumor cell viability. Prostate cancer cells were treated with S.C and then the cell viability and migration ability were assessed using CCK8, colony formation and wound healing assay. Reactive oxygen species (ROS) and iron accumulation were quantified through flow cytometry analysis. The levels of malondialdehyde (MDA) and total glutathione (GSH) were measured using commercially available kits. RNA-seq analysis was performed to identify differentially expressed genes (DEGs) among the treatment groups. Western blotting and qPCR were utilized to investigate the expression of relevant proteins and genes. In vivo experiments employed a xenograft mice model to evaluate the anti-cancer efficacy of S.C. Results: Our study demonstrated that S.C effectively inhibited the viability of various prostate cancer cells. Notably, S.C exhibited the ability to enhance the cytotoxicity of docetaxel in DU145 cells. We found that S.C-induced cell death partially relied on the induction of ferroptosis, which was mediated through up-regulation of HMOX1 protein. Additionally, our investigation revealed that S.C treatment decreased the stability of BACH1 protein, which contributed to HMOX1expression. We further identified that S.C-induced ROS caused BACH1 instability by suppressing USP47expression. Moreover, In DU145 xenograft model, we found S.C significantly inhibited prostate cancer growth, highlighting its potential as a therapeutic strategy. Collectively, these findings provide evidence that S.C could induce regulated cell death (RCD) in prostate cancer cells and effectively inhibit tumor growth via triggering ferroptosis. This study provides evidence that S.C effectively suppresses tumor progression and induces ferroptosis in prostate cancer cells by targeting ROS/USP47/BACH1/HMOX1 axis. Conclusion: This study provides evidence that S.C effectively suppresses tumor progression and induces ferroptosis in prostate cancer cells by targeting the ROS/USP47/BACH1/HMOX1 axis. These findings offer novel insights into the underlying mechanism by which S.C inhibits the progression of prostate cancer. Furthermore, leveraging the potential of S.C in targeting ferroptosis may present a new therapeutic opportunity for prostate cancer. This study found that S.C induces ferroptosis by targeting the ROS/USP47/BACH1/HMOX1 axis in prostate cancer cells. [ABSTRACT FROM AUTHOR]

Studies have shown that the occurrence and development of endometriosis are closely linked to long-term psychological stress. The specific contribution of chronic stress to the metabolic adaptations in patients with endometriosis is still unknown. Lesions were removed from ten endometriosis patients during an operation, and the participants were divided into two groups using a psychological questionnaire. An mRNA Human Gene Expression Microarray analysis was applied to compare the mRNA expression profiles between the chronic stress group and the control group. In addition, the reliability of the mRNA Human Gene Expression Microarray analysis was verified by using research on metabolites based on both the liquid chromatography (LC-MS/MS) technique and quantitative reverse transcription polymerase chain reaction (RT–PCR). A microarray analysis of significantly up-regulated, differentially expressed genes between the chronic stress and the control groups showed genes that were principally related to metabolism-related processes and immune-related processes, such as the immune response process, negative regulation of T cell proliferation, the leucine metabolic process, and the L-cysteine metabolic process (p < 0.05). LC-MS showed that the differential metabolites were primarily concerned with arginine and proline metabolism, D-glutamine and D-glutamate metabolism, aspartate metabolism, glycine, serine metabolism, and tyrosine metabolism (p < 0.05). The possibility of chronic stress blocks the endometriosis immune response through metabolic reprogramming. Chronic stress reduces the supply of energy substrates such as arginine and serine, down-regulates T immune cell activation, and affects the anti-tumor immune response, thereby promoting the migration and invasion of endometriosis lesions in patients with chronic stress. [ABSTRACT FROM AUTHOR]

Castration-resistant prostate cancer (CRPC) represents one type of advanced prostate cancer (PCa) with a median survival time of 1–2 years. Currently, there is a lack of reliable gene panels in predicting hormone treatment (HT) responses due to limited knowledge of CRPC-specific tumor-microenvironment (TME) characteristics. In this study, we first screened for up-regulated genes in CRPC samples using bulk-sequencing data retrieved from TCGA online database, and further investigated the expression status of these genes in four sets of downloaded single-cell RNA sequencing (scRNAseq) data: GSE117403 containing 16 normal human prostate samples; GSE141445 containing 13 PCa samples; GSE176031 containing 11 PCa samples and GSE137829 containing 6 CRPC samples. We identified a series of CRPC-specific TME characteristics including an enriched number of PEG10+ neuroendocrine cells, elevated expression of PPIB/CCDC74A/GAPDH/AR genes in tumor cells, increased expression of FAP/TGFB1 in cancer-associated fibroblasts (CAFs), suppressed immune environment featured by enhanced M2 macrophage polarization, T cell exhaustion and increased number of regulatory B cells. We further established a 12-gene panel using these characteristics and showed that this panel could separate CRPC samples from PCa samples (AUC of 0.78), and CRPC patients with higher panel scores tended to have treatment failure or progression (R = −0.47, p = 0.019). Based on these unique TME characteristics of CRPC, we established a prediction tool for estimating the duration of HT responses in PCa treatment. Our results suggest mechanisms by which prostate cancer becomes castrate resistant. Further study of PEG10 (and/or others) to evaluate therapeutic efficacy should be considered. Increased number of PEG10+ neuroendocrine cells is associated with recurrence of HT PCa patients A 12-gene panel could be used to predict duration of HT responses in PCa treatment [ABSTRACT FROM AUTHOR]

MicroRNA exerts an important regulatory role in almost all the biological process, including hair follicle development in Liaoning Cashmere goat. In order to improve the Cashmere performance of goat, the regulatory role of microRNA in hair follicle cycle has drawn hotspot attention. However, the molecular mechanisms of miRNA-1-3p involved in hair follicle development are poorly understood. In this study, we found that miRNA-1-3p was less expressed in anagen stage of hair follicle cycle of Cashmere goat than that in telogen stage by using RT-qPCR and immunoblotting analysis, in contrast to the expression pattern of FGF14. The Dual-Luciferase reporter assay was employed to verify the relationship between miRNA-1-3p and FGF14. The results showed that miRNA-1-3p specifically binds to the 3′UTR of FGF14 mRNA, and FGF14 is the target gene of miR-1-3p. In conclusion, this study shows that miRNA-1-3p may regulate hair follicle development in Liaoning Cashmere goats by targeting FGF14. [ABSTRACT FROM AUTHOR]

Background: Investigate the AMPK (protein kinase AMP-activated catalytic subunit alpha 1)/YAP (Yes1 associated transcriptional regulator)/NLRP3 (NLR family pyrin domain containing 3) signaling pathway's role in ankylosing spondylitis (AS) development using public database analysis, in vitro and in vivo experiments. Methods: Retrieve AS dataset, analyze differential gene expression in R, conduct functional enrichment analysis, collect 30 AS patient and 30 normal control samples, and construct a mouse model. ELISA, IP, and knockdown experiments were performed to detect expression changes. Results: NLRP3 was identified as a significant AS-related gene. Caspase-1, IL-1β, IL-17A, IL-18, IL-23, YAP, and NLRP3 were upregulated in AS patients. Overexpressing AMPK inhibited YAP's blockade on NLRP3 ubiquitination, reducing ossification in fibroblasts. Inhibiting AMPK exacerbated AS symptoms in AS mice. Conclusion: AMPK may suppress YAP expression, leading to NLRP3 inflammasome inhibition and AS alleviation. [ABSTRACT FROM AUTHOR]

Skin cutaneous melanoma (SKCM) has a low early detection rate and a high mortality rate. There are many problems such as side effects and drug resistance in existing therapeutic drugs. Current studies have confirmed that SKCM pathogenesis-related genes promote the invasion and metastasis of cutaneous melanoma, but their roles in the tumor microenvironment (TME) remain unclear. Network pharmacology provides new opportunities for drug repurposing and repositioning, and is a fast, safe, and inexpensive drug discovery method to find new drugs for the treatment of SKCM. In this study, based on 3 databases (KEGG, OMIM, and Genotype) to obtain SKCM-related genes, and TCGA SKCM dataset, SKCM differential genes in GSE3189 and GSE46517 were intersected to identify SKCM pathogenesis-related differential genes, and the differential genes were immune infiltration and analysis, For survival analysis, a prognostic nomogram risk model was constructed based on the results of multivariate Cox regression analysis for risk stratification and prognosis prediction, then focused on the differential expression of ZC3H12A and its effect on TME. Finally, the protein interaction network method was used to quantify the similarity between 684 drug targets and skin melanoma, and to screen out drugs similar to skin melanoma. Based on 3 databases of KEGG, OMIM, and Genotype, 294 SKCM-related genes and 18 SKCM pathogenesis-related differential genes were obtained, and 18 SKCM pathogenesis-related differential genes were significantly correlated with TME. The constructed prognostic nomogram risk model predicted performance better and provided valuable information for immunotherapy. Multivariate Cox regression analysis and K-M analysis showed that ZC3H12A was a differentially expressed gene affecting the prognosis of SKCM and promoted the infiltration of anti-tumor immune cells CD8 + T cells, B cells, and DC cells. Based on the analysis of the protein interaction network method, 43 drugs were found to have high potential in the treatment of SKCM, and the literature search of these 43 drugs was carried out, and 21 drugs were found to have experimental verification for the treatment of SKCM. Taken together, the differential genes associated with the pathogenesis of SKCM have important roles in the tumor immune microenvironment, clinicopathological features, and prognosis, especially ZC3H12A has a potential role in identifying early SKCM patients. At the same time, it provides a new strategy for the drug development of SKCM and provides a basis for the reuse of SKCM drugs. [ABSTRACT FROM AUTHOR]

The main component of donkey meat is skeletal muscle, and different muscle fibers have been found to be associated with meat quality. However, RNA-seq technology has yet to be used to profile the transcriptomic changes of different muscles of the donkey. In this study, the characterizations of different muscles on the gene expression profiles of Dezhou donkey were obtained, the aim was to identify the important genes in donkey muscles, and aid in improving donkey meat quality via RNA-seq. In the donkey gluteus (DG) and donkey longissimus dorsi (DL) group, GO enrichment indicated that DEGs were mainly involved in the biological regulation and metabolic process, and KEGG analysis shows that a total of 427 DEGs were mapped to 216 KEGG pathways and 23 KEGG pathways were significantly enriched such as the ribosome, glycolysis/gluconeogenesis, glucagon signaling pathway and biosynthesis of amino acids pathways. Meanwhile, 504 DEGs were mapped to 223 KEGG pathways, in which 17 were significantly enriched including cardiac muscle contraction and oxytocin signaling pathway in donkey hamstring muscles (DH) and DL group. In addition, the tenderness in donkey meat might involve muscle fiber type and glucose metabolism, which might profit from the DEGs including MYH1, MYH7, TNNC1, TNNI3, TPM3, ALDOA, ENO3, and PGK1. The genes found in this study will provide some ideas for further understanding the molecular mechanism of donkey meat quality. [ABSTRACT FROM AUTHOR]

Astragalus sinicus is an important winter-growing cover crop. It is widely utilized, not only as a cover crop for its benefits in fertilizing the soil but also as a landscape ground cover plant. Anthocyanins are involved in the pigmentation of plants in leaves and flowers, which is a crucial characteristic trait for A. sinicus. The formation of anthocyanins depends significantly on the enzyme chalcone isomerase (CHI). However, research on the CHI gene of A. sinicus remains unexplored. The rapid amplification of cDNA ends (RACE) approach was used in this research to clone the CHI sequence from A. sinicus (AsiCHI). The expression profiles of the AsiCHI gene in multiple tissues of A. sinicus were subsequently examined by qRT-PCR (Quantitative Real-Time PCR). Furthermore, the function of the AsiCHI was identified by the performance of ectopic expression in Arabidopsis (Arabidopsis thaliana). The outcomes revealed that the full-length cDNA of the AsiCHI gene (GeneBank: OQ870547) measured 972 bp in length and included an open reading frame of 660 bp. The encoded protein contains 219 amino acids with a molecular weight of 24.14 kDa and a theoretical isoelectric point of 5.11. In addition, the remarkable similarity between the AsiCHI protein and the CHI proteins of other Astragalus species was demonstrated by the sequence alignment and phylogenetic analysis. Moreover, the highest expression level of AsiCHI was observed in leaves and showed a positive correlation with anthocyanin content. The functional analysis further revealed that the overexpression of AsiCHI enhanced the anthocyanidin accumulation in the transgenic lines. This study provided a better understanding of AsiCHI and elucidated its role in anthocyanin production. [ABSTRACT FROM AUTHOR]

Resistance to epidermal growth factor tyrosine kinase inhibitors (EGFR-TKI) remains one of the major challenges in lung adenocarcinoma (LUAD) therapy. Here, we find an increased frequency of the L12_16 amino acid deletion mutation in the signal peptide region of NOTCH4 (NOTCH4ΔL12_16) in EGFR-TKI-sensitive patients. Functionally, exogenous induction of NOTCH4ΔL12_16 in EGFR-TKI -resistant LUAD cells sensitizes them to EGFR-TKIs. This process is mainly mediated by the reduction of the intracellular domain of NOTCH4 (NICD4) caused by the NOTCH4ΔL12_16 mutation, which results in a lower localization of NOTCH4 in the plasma membrane. Mechanistically, NICD4 transcriptionally upregulates the expression of HES1 by competitively binding to the gene promoter relative to p-STAT3. Because p-STAT3 can downregulate the expression of HES1 in EGFR-TKI-resistant LUAD cells, the reduction of NICD4 induced by NOTCH4ΔL12_16 mutation leads to a decrease in HES1. Moreover, inhibition of the NOTCH4-HES1 pathway using inhibitors and siRNAs abolishes the resistance of EGFR-TKI. Overall, we report that the NOTCH4ΔL12_16 mutation sensitizes LUAD patients to EGFR-TKIs through transcriptional down-regulation of HES1 and that targeted blockade of this signaling cohort could reverse EGFR-TKI -resistance in LUAD, providing a potential approach to overcome resistance to EGFR-TKI -therapy. Patients with lung adenocarcinoma (LUAD) patients carrying EGFR mutations are often treated with EGFR-tyrosine kinase inhibitors (EGFR-TKIs), but sensitivity to the therapy varies. Here, using 3D printed patient derived xenograft models, the authors identify a NOTCH mutation as an indicator of favourable response to EGFR-TKI in LUAD. [ABSTRACT FROM AUTHOR]

Motivation: Single-cell RNA-sequencing (scRNA-seq) technologies provide an opportunity to infer cell-specific gene regulatory networks (GRNs), which is an important challenge in systems biology. Although numerous methods have been developed for inferring GRNs from scRNA-seq data, it is still a challenge to deal with cellular heterogeneity. Results: To address this challenge, we developed an interpretable transformer-based method namely STGRNS for inferring GRNs from scRNA-seq data. In this algorithm, gene expression motif technique was proposed to convert gene pairs into contiguous sub-vectors, which can be used as input for the transformer encoder. By avoiding missing phase-specific regulations in a network, gene expression motif can improve the accuracy of GRN inference for different types of scRNA-seq data. To assess the performance of STGRNS, we implemented the comparative experiments with some popular methods on extensive benchmark datasets including 21 static and 27 time-series scRNA-seq dataset. All the results show that STGRNS is superior to other comparative methods. In addition, STGRNS was also proved to be more interpretable than "black box" deep learning methods, which are well-known for the difficulty to explain the predictions clearly. Availability and implementation: The source code and data are available at https://github.com/zhanglab-wbgcas/STGRNS. [ABSTRACT FROM AUTHOR]

Immune system has been reported to play a key role in the development of ischaemic stroke (IS). Nevertheless, its exact immune‐related mechanism has not yet been fully revealed. Gene expression data of IS and healthy control samples was downloaded from Gene Expression Omnibus database and differentially expressed genes (DEGs) was obtained. Immune‐related genes (IRGs) data was downloaded from the ImmPort database. The molecular subtypes of IS were identified based on IRGs and weighted co‐expression network analysis (WGCNA). 827 DEGs and 1142 IRGs were obtained in IS. Based on 1142 IRGs, 128 IS samples were clustered into two molecular subtypes: clusterA and clusterB. Based on the WGCNA, the authors found that the blue module had the highest correlation with IS. In the blue module, 90 genes were screened as candidate genes. The top 55 genes were selected as the central nodes according to gene degree in protein–protein interactions network of all genes in blue module. Through taking overlap, nine real hub genes were obtained that might distinguish between clusterA subtype and clusterB subtype of IS. The real hub genes (IL7R, ITK, SOD1, CD3D, LEF1, FBL, MAF, DNMT1, and SLAMF1) may be associated with molecular subtypes and immune regulation of IS. [ABSTRACT FROM AUTHOR]

In recent years, microRNAs (miRNAs) derived from exosomes have been attracting attention as novel clinical biomarkers in a variety of cancers. In this study, plasma samples from 60 gastric cancer (GC) patients and 63 healthy individuals were collected, and the exosomal microRNAs (ex-miRNAs) were isolated. We determined the specific ex-miRNAs through miRNA microarray and a database of differentially expressed miRNAs called dbDEMC. Then, the expression levels of exosomal miR-31, miR-192, and miR-375 were analyzed by quantitative polymerase chain reaction (qRT-PCR). Compared to the matched controls, exosomal miR-31, miR-375, and miR-192 were significantly upregulated in GC patients. Also, they were found to be associated with gender, with miR-192 being significantly upregulated in male GC patients. Kaplan–Meier analysis indicated that high expressions of exosomal miR-31, miR-375, and miR-192 were positively correlated with poor clinical outcomes of GC patients. Cox univariate and multivariate analysis found that ex-miR-375 expression and TNM stage were independent prognostic factors of overall survival (OS). Our findings revealed that exosomal miR-31, miR-192, and miR-375 might serve as noninvasive, sensitive, and specific biomarkers for the diagnosis and prognosis of GC patients. [ABSTRACT FROM AUTHOR]

Pulmonary inflammation involves complex changes of the immune cells, in which macrophages play important roles and their function might be influenced by metabolism. Slc38a6 acts as a carrier of nutrient for macrophages (Mφ) to exert the function. In this study, pneumonia patient blood was found up-regulated SLC38A6 expression, which correlated with monocytes number and white blood cell number. The similar result was also shown in LPS induced sepsis mice. To reveal the key role of Slc38a6, we used systemic and conditional knock-out mice. Either systemic or LyzCRE specific knock-out could alleviate the severity of sepsis mice, reduce the proinflammatory cytokine TNF-α and IL-1β expression in serum and decrease the monocytes number in bronchial alveolar lavage and peritoneal lavage via flow cytometry. In order to reveal the signal of up-regulated Slc38a6, the Tlr4 signal inhibitor TAK242 and TLR4 knock-out mice were used. By blocking Tlr4 signal in macrophages via TAK242, the expression of Slc38a6 was down-regulated synchronously, and the same results were also found in Tlr4 knock-out macrophages. However, in the overexpressed Slc38a6 macrophages, blocking Tlr4 signal via TAK242, 20% of the mRNA expression of IL-1β still could be expressed, indicating that up-regulated Slc38a6 participates in IL-1β expression process. Collectively, it is the first time showed that an amino acid transporter SLC38A6 up-regulated in monocytes/macrophages promotes activation in pulmonary inflammation. SLC38A6 might be a promising target molecule for pulmonary inflammation treatment. [ABSTRACT FROM AUTHOR]

Background: Ulcerative colitis (UC) is a form of chronic inflammatory bowel disease of nonspecific origin. This study used an RNA-Sequencing (RNA-Seq) approach to evaluate the transcriptomic landscape of a well-stratified treatment-naïve pediatric UC patient population by comparing them with healthy control children. The data were analyzed to evaluate the mechanisms driving UC-related intestinal inflammation and fibrosis. Methods: Intestinal mucosal samples from five pediatric UC patients and five healthy controls were analyzed by RNA-Seq, and results were verified by qPCR. A CRISPR/Cas9 approach was used to knock out the expression of HLA-DRB5, and molecular biology techniques were used for additional mechanistic studies. Results: In these analyses, 2290 genes were found to be differentially expressed between the UC and control samples, of which 1258 and 1032 were upregulated and downregulated, respectively. Gene Ontology analysis showed that these genes were enriched in extracellular matrix (ECM)-related processes and that 7 of 8 differentially expressed genes of interest (PIK3CD, IL1β, IL1α, TIMP1, MMP1, MMP12, COL6A3, and HLADRB5) were upregulated and involved in ECM-receptor interaction and inflammatory bowel disease-related pathways. Increased HLA-DRB5 expression driven by intestinal bacteria was found to promote IL-1α secretion, leading to intestinal inflammation and fibrosis, suggesting a possible target for the treatment of UC. Conclusion: These data suggest that intestinal inflammation is present in pediatric UC patients for extended periods before the onset of symptoms, and intestinal fibrosis begins even during the early stages of UC. Intestinal bacteria were also found to trigger intestinal inflammation and fibrosis, with HLA-DRB5 playing a central role in this process. [ABSTRACT FROM AUTHOR]

Unintended effects of gene edit crops may pose safety issues. Omics is a useful tool for researchers to evaluate these unexpected effects. Transcriptome and proteomics analyses were performed for two gene editors, CRISPR-Cas9 and adenine base editor (ABE) gene edit rice, as well as corresponding wild-type plants (Nipponbare). Transcriptome revealed 520 and 566 rice differentially expressed genes (DEGs) in the Cas9/Nip and ABE/Nip comparisons, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that most DEGs participated in metabolism of terpenoids and polyketones, plant–pathogen interactions, and plant signal transduction. It mainly belongs to environmental adaptation. Proteomics revealed 298 and 54 rice differentially expressed proteins (DEPs) in the Cas9/Nip and ABE/Nip comparisons, respectively. KEGG pathway enrichment analysis showed that most DEPs participated in the biosynthesis of secondary metabolite and metabolic pathways. According to integrated transcriptomes and proteomics analysis, the results showed that no newly generated genes were identified as new transcripts of these differentially expressed genes, and gene edit tools had little effect on rice transcription levels and no new proteins were generated in the gene-edited rice. [ABSTRACT FROM AUTHOR]

Myocardial ischemia/reperfusion (I/R) injury seriously threats the health and life of patients with ischemia heart disease. Herein, we probed the potential influence of myosin 1b (myo1b) on hypoxia/reoxygenation- (H/R-) stimulated cardiomyocyte H9c2 cell apoptosis and autophagy. After H/R stimulation, the myo1b mRNA level in H9c2 cells was tested via qRT-PCR. Myo1b overexpression plasmid (OE-myo1b) and small interfering RNA (siRNA) targeting myo1b (si-myo1b) were transfected into H9c2 cells to alter myo1b expression in H9c2 cells. Following H/R stimulation and/or OE-myo1b (or si-myo1b) transfection, H9c2 cell apoptosis, proliferation, and autophagy were detected, respectively. We found that H/R stimulation reduced the mRNA level of myo1b in H9c2 cells and resulted in H9c2 cell apoptosis, proliferation inhibition, and autophagy. Overexpression of myo1b reversed the H/R-resulted H9c2 cell apoptosis, proliferation inhibition, and autophagy. Silence of myo1b had opposite effects, which promoted H9c2 cell apoptosis, reduced cell proliferation, and accelerated cell autophagy. Taken together, Myo1b took part in the modulation of H/R-stimulated cardiomyocyte apoptosis and autophagy, which might be serve as a potential endogenous target for prevention and therapy of I/R injury. [ABSTRACT FROM AUTHOR]

Background: Production of vitamin C has been traditionally based on the Reichstein process and the two-step process. However, the two processes share a common disadvantage: vitamin C cannot be directly synthesized from D-glucose. Therefore, significant effort has been made to develop a one-step vitamin C fermentation process. While, 2-KLG, not vitamin C, is synthesized from nearly all current one-step fermentation processes. Vitamin C is naturally synthesized from glucose in Arabidopsis thaliana via a ten-step reaction pathway that is encoded by ten genes. The main objective of this study was to directly produce vitamin C from D-glucose in Escherichia coli by expression of the genes from the A. thaliana vitamin C biosynthetic pathway. Results: Therefore, the ten genes of whole vitamin C synthesis pathway of A. thaliana were chemically synthesized, and an engineered strain harboring these genes was constructed in this study. The direct production of vitamin C from D-glucose based on one-step fermentation was achieved using this engineered strain and at least 1.53 mg/L vitamin C was produced in shaking flasks. Conclusions: The study demonstrates the feasibility of one-step fermentation for the production of vitamin C from D-glucose. Importantly, the one-step process has significant advantages compared with the currently used fermentation process: it can save multiple physical and chemical steps needed to convert D-glucose to D-sorbitol; it also does not involve the associated down-streaming steps required to convert 2-KLG into vitamin C. [ABSTRACT FROM AUTHOR]

Biofilm cells exhibit higher resistance than their planktonic counterparts to commonly used disinfectants in food industry. Phenolic acids are promising substitute offering less selective pressure than traditional antibiotics. This study aims to evaluate the inhibitory effects of ferulic acid (FA) and p-coumaric acid (p-CA) on Salmonella Enteritidis biofilm formation and explore the underlying inhibitory mechanisms. The minimal inhibitory concentration (MIC) of FA and p-CA were 1.0 and 0.5 mg/ml, respectively. The sub-inhibitory concentration (1/8 MIC) significantly decreased biofilm formation without growth inhibitory effects. The biomass and extracellular polymeric substances (EPS) of S. Enteritidis biofilm as well as the bacterial swimming and chemotaxis abilities were significantly decreased when exposed to sub-MIC concentrations of FA and p-CA. These two phenolic acids showed high affinity to proteins involved in flagella motility and repressed the S. Enteritidis biofilm formation-related gene expressions. Furthermore, these two phenolic acids maintained high antibiofilm efficiency in simulated food processing conditions. This study provided valuable information of multiple phenotypic and molecular responses of S. Enteritidis to these two phenolic acids. [ABSTRACT FROM AUTHOR]

Melanoma has become the most severe sort of skin cancer, deriving from the pigment-producing melanocytes. Existing research has validated that long noncoding RNAs (lncRNAs) have critical function in the progression of cancers. LINC00518 has been studied in cutaneous melanoma; however, the molecular mechanism of LINC00518 in melanoma needs in-depth investigation. In our study, LINC00518 was revealed to be upregulated in melanoma tissues and cells, and melanoma patients in high LINC00518 expression group had poorer prognosis as depicted in GEPIA database. Functional assays revealed that LINC00518 depletion inhibited cell proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT). Furthermore, MITF was confirmed to be upregulated in melanoma tissues and cells, and melanoma patients in high MITF expression group had poorer prognosis as displayed in GEPIA database. MITF expression was positively connected to LINC00518 expression. Additionally, results of mechanism assays uncovered EIF4A3 could bind with LINC00518 and MITF, and LINC00518 recruited EIF4A3 to stabilize MITF mRNA. Finally, it was demonstrated that upregulation of MITF could partially abrogate the inhibitory impact of LINC00518 knockdown on melanoma cell malignant behaviors. To summarize, LINC00518 promotes the malignant processes of melanoma cells through targeting EIF4A3/MITF axis, which might provide novel potential biomarkers for melanoma prognosis. [ABSTRACT FROM AUTHOR]

Background: As a novel form of programmed cell death, necroptosis is related to multiple tumor types and their immune microenvironments. However, its association with glioma has not been clarified. Methods: Necroptosis genes were obtained from the Gene Set Enrichment Analysis (GSEA) database. RNA-seq and clinical data were downloaded from TCGA and CGGA databases. A necroptosis gene signature was constructed based on univariate and multivariate Cox regression analyses. Next, survival analysis, independent prognostic analysis, and nomogram were performed to assess and verify the model. Subsequently, we analyzed the tumor microenvironment (TME) and immune cell infiltration via ESTIMATE and CIBERSORTx algorithms. Finally, the response of glioma patients in the TCGA database to immune checkpoint inhibitor (ICI) therapy was predicted using the Tumor Immune Dysfunction and Exclusion (TIDE) database. Results: Of the seven prognostic necroptosis genes, RIPK1, RIPK3, FAS, and FADD were used to construct the risk signature that accurately predicts the prognosis of glioma patients. Functional enrichment results suggest that necroptosis is correlated with immune response and angiogenesis. Immune analysis revealed that necroptosis can boost inflammatory activity and attract immunosuppressive cell infiltration to form a chronic inflammatory microenvironment, promoting glioma growth. Additionally, glioma patients in the TCGA cohort with high necroptosis gene expression exhibited a better response to ICI therapy predicted by the TIDE algorithm. Conclusion: We constructed a necroptosis gene signature, which has the potential for use as a biomarker for predicting glioma patients' prognosis, revealing the association between necroptosis and the immune microenvironment, and serving as a reference for immune therapy. [ABSTRACT FROM AUTHOR]

Understanding the impact of arbuscular mycorrhizal fungi (AMF) upon the nitrogen (N) uptake of tomato (Lycopersicum esculentum L.) plants is crucial for effectively utilizing these beneficial microorganisms in industrial hydroponic tomato production. Yet it remains unknown whether, besides fungal delivery, the AMF also affects N uptake via altered plant root growth or whether, together with changed N transporters expression of hosts, this impact is isolate-specific. We investigated tomato root architecture and the expression of LeAMT1.1, LeAMT1.2, and LeNRT2.3 genes in roots inoculated with five isolates of Funneliformis mosseae, these collected from different geographical locations, under greenhouse conditions with nutritional solution in coconut coir production. Our results revealed that isolate-specific AMF inoculation strongly increased the root biomass, total root length, surface area, and volume. Linear relationships were found between the total root length and N accumulation in plants. Furthermore, expression levels of LeAMT1.1, LeAMT1.2, and LeNRT2.3 were significantly up-regulated by inoculation with F. mosseae with isolate-specific. These results implied N uptake greater than predicted by root growth, and N transporters up-regulated by AMF symbiosis in an isolate-specific manner. Thus, an overlap in root biomass, architecture and expression of N transporters increase N acquisition in tomato plants in the symbiosis. [ABSTRACT FROM AUTHOR]

Purpose: To explore the function and regulatory mechanism of IFITM3 in mouse neural retinal progenitor cells (mNRPCs), which was found to be very important not only in the development of the retina in embryos but also in NRPCs after birth. Methods: Published single-cell sequencing data were used to analyze IFITM3 expression in mNRPCs. RNA interference was used to knock down the expression of IFITM3. CCK-8 assays were used to analyze cell viability. RNA-seq was used to assess mRNA expression, as confirmed by real-time quantitative PCR, and immunofluorescence assays and western blots were used to validate the levels of relative proteins, and autophagy flux assay. Lysosomal trackers were used to track the organelle changes. Results: The results of single-cell sequencing data showed that IFITM3 is highly expressed in the embryo, and after birth, RNA-seq showed high IFITM3 expression in mNRPCs. Proliferation and cell viability were greatly reduced after IFITM3 was knocked down. The cell membrane system and lysosomes were dramatically changed, and lysosomes were activated and evidently agglomerated in RAMP-treated cells. The expression of LAMP1 was significantly increased with lysosome agglomeration after treatment with rapamycin (RAMP). Further detection showed that SQSTM1/P62, HSC70 and LAMP-2A were upregulated, while no significant difference in LC3A/B expression was observed; no autophagic flux was generated. Conclusion: IFITM3 regulates mNRPC viability and proliferation mainly through chaperone-mediated autophagy (CMA) but not macroautophagy (MA). IFITM3 plays a significant role in maintaining the homeostasis of progenitor cell self-renewal by sustaining low-level activation of CMA to eliminate deleterious factors in cells. [ABSTRACT FROM AUTHOR]

• Acupuncture upregulates A 3 R of superficial fascia of acupoint areas in CFA rats. • Acupuncture inhibits inflammatory signaling molecules. • Acupuncture has analgesic effects by inhibiting inflammation via A 3 R. Adenosine A 3 receptor (A 3 R) exerts analgesic, anti-inflammatory, and anti-nociceptive effects. In this study, we determined the analgesic mechanism of manual acupuncture (MA) in rats with complete Freund's adjuvant (CFA)-induced arthritis and explored whether MA ameliorates inflammation in these rats by upregulating A 3 R. Sixty Sprague Dawley (SD) rats were randomly divided into the following groups: Control, CFA, CFA + MA, CFA + sham MA, CFA + MA + DMSO, CFA + MA + IB-MECA, and CFA + MA + Reversine groups. The arthritis rat model was induced by injecting CFA into the left ankle joints. Thereafter, the rats were subjected to MA (ST36 acupoint) for 3 days. The clinical indicators paw withdrawal latency (PWL), paw withdrawal threshold (PWT), and open field test (OFT) were used to determine the analgesic effect of MA. In addition, to explore the effect of A 3 R on inflammation after subjecting arthritis rats to MA, IB-MECA (A 3 R agonist) and Reversine (A 3 R antagonist) were injected into ST36 before MA. MA ameliorated the pathological symptoms of CFA-induced arthritis, including the pain indicators PWL and PWT, number of rearing, total ambulatory distance, and activity trajectory. Furthermore, after MA, the mRNA and protein expression of A 3 R was upregulated in CFA-induced arthritis rats. In contrast, the protein levels of TNF-α, IL-1β, Rap1, and p-p65 were downregulated after MA. Interestingly, the A 3 R agonist and antagonist further downregulated and upregulated inflammatory cytokine expression, respectively, after MA. Furthermore, the A 3 R antagonist increased the degree of ankle swelling after MA. MA can alleviate inflammatory pain by inhibiting the NF-κB signaling pathway via upregulating A 3 R expression of the superficial fascia of the ST36 acupoint site in CFA-induced arthritis rats. [ABSTRACT FROM AUTHOR]

Embryonic stem cells (ESCs) exhibit a metabolic preference for glycolysis over oxidative phosphorylation to meet their substantial adenosine triphosphate (ATP) demands during self-renewal. This metabolic choice inherently maintains low mitochondrial activity and minimal reactive oxygen species (ROS) generation. Nonetheless, the intricate molecular mechanisms governing the restraint of ROS production and the mitigation of cellular damage remain incompletely elucidated. In this study, we reveal the pivotal role of RNA-binding motif protein 46 (RBM46) in ESCs, acting as a direct post transcriptional regulator of ROS levels by modulating BCL2/adenovirus E1B 19 kDa protein-interacting protein 3 (Bnip3) mRNA expression. Rbm46 knockout lead to diminished mitochondrial autophagy, culminating in elevated ROS within ESCs, disrupting the delicate balance required for healthy self-renewal. These findings provide insights into a novel mechanism governing ROS regulation in ESCs. RBM46 binds to and facilitates the translation of Bnip3 mRNA. Once translated into protein, BNIP3 is translocated to mitochondria, where it initiates the engulfment of mitochondria by autophagosomes. Following RBM46 knockout, the expression of BNIP3 protein decreases, hampering mitochondrial autophagy. Consequently, this disruption leads to an elevation in the number of mitochondria and an increase in intracellular ROS levels. [Display omitted] • Rbm46 is crucial for mouse embryonic stem cell self-renewal and survival. • Knockout of Rbm46 increases reactive oxygen species levels and induces apoptosis. • Rbm46 directly binds to Bnip3 mRNA and regulates mitophagy in mouse embryonic stem cells. [ABSTRACT FROM AUTHOR]

Background: In the present study, we used a computational method to identify Guillain–Barré syndrome (GBS) related genes based on (i) a gene expression profile, and (ii) the shortest path analysis in a protein–protein interaction (PPI) network. Materials and Methods: mRNA Microarray analyses were performed on the peripheral blood mononuclear cells (PBMCs) of four GBS patients and four age- and gender-matched healthy controls. Results: Totally 30 GBS-related genes were screened out, in which 20 were retrieved from PPI analysis of upregulated expressed genes and 23 were from downregulated expressed genes (13 overlap genes). Gene ontology (GO) enrichment and KEGG enrichment analysis were performed, respectively. Results showed that there were some overlap GO terms and KEGG pathway terms in both upregulated and downregulated analysis, including positive regulation of macromolecule metabolic process, intracellular signaling cascade, cell surface receptor linked signal transduction, intracellular non-membrane-bounded organelle, non-membrane-bounded organelle, plasma membrane, ErbB signaling pathway, focal adhesion, neurotrophin signaling pathway and Wnt signaling pathway, which indicated these terms may play a critical role during GBS process. Discussion: These results provided basic information about the genetic and molecular pathogenesis of GBS disease, which may improve the development of effective genetic strategies for GBS treatment in the future. [ABSTRACT FROM AUTHOR]

This study was carried out to demonstrate the prognostic value of CD274 (PD-L1 promoter gene) methylation in bladder cancer patients. UCSC Xena database was searched for relevant information on PD-L1 (CD274) methylation and PD-L1 mRNA expression in bladder cancer. 407 bladder patients were included in our analyses. Multivariate analysis revealed that PD-L1 methylation was an independent predictor for OS (P = 0.037). Moreover, PD-L1 methylation might be a prognostic biomarker for immunotherapy response. However, PD-L1 methylation and PD-L1 mRNA expression was not statistically associated with chemotherapy response. In conclusion, PD-L1 methylation was an independent prognostic factor for bladder cancer patients. [ABSTRACT FROM AUTHOR]