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The Vitreoscilla hemoglobin (VHb) gene was expressed in Ganoderma lucidum to enhance antitumor ganoderic acid (GA) production. The effects of VHb expression on the accumulation of GAs and lanosterol (intermediate) and the transcription of GA biosynthesis genes were also investigated. In VHb-expressing G. lucidum, the maximum concentrations of four individual GAs (GA-S, GA-T, GA-Mk and GA-Me) were 19.1±1.8, 34.6±2.1, 191.5±13.1 and 45.2±2.8μg/100mg dry weight, respectively, which were 1.4-, 2.2, 1.9- and 2.0-fold higher than those obtained in the wild-type strain. Moreover, the maximum lanosterol concentration in the strain expressing VHb was 1.28-fold lower than that in the wild-type strain. The transcription levels of 3-hydroxy-3-methylglutaryl coenzyme A reductase, squalene synthase, and lanosterol synthase genes were up-regulated by 1.6-, 1.5-, and 1.6-fold, respectively, in the strain expressing VHb. This work is beneficial in developing an efficient fermentation process for the hyperproduction of GAs., (Copyright © 2016 Elsevier B.V. All rights reserved.)

We report the construction of a plasmid, pJW-EXP, designed for the expression of homologous and heterologous genes in Ganoderma lucidum. pJW-EXP was generated from the plasmid pMD19-T by inserting the G. lucidum glyceraldehyde-3-phosphate dehydrogenase gene promoter, the G. lucidum iron-sulfur protein subunit of succinate dehydrogenase gene terminator and the homologous carboxin-resistance gene as selection marker. This expression plasmid can be efficiently transformed into Ganoderma through polyethylene glycol-mediated protoplast transformation. Southern blot analysis showed that most of the integrated DNA appeared as multiple copies in the genome. The applicability of the constructed plasmid was tested by expression of the truncated G. lucidum 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) gene that encodes the catalytic domain of HMGR. Overexpression of the truncated HMGR gene, which is a key gene in the biosynthetic pathway of the antitumor compounds, ganoderic acids, increased the transcription of the HMGR gene and enhanced ganoderic acid accumulation. pJW-EXP can serve as a useful tool in the genetic improvement and metabolic engineering of Ganoderma.

Bronchopulmonary dysplasia (BPD) is the most common sequela of prematurity and is characterized by alveolar simplification and lung angiogenesis failure. The aim of this study was to explore the immune signatures of BPD. Differentially expressed gene analysis and immune infiltration analysis were conducted to identify key immune cell types and related genes by using the mRNA-seq dataset GSE25286. The expression patterns of key genes were validated in the scRNA-seq dataset GSE209664 and in experiments. The cell–cell crosstalk of key immune cells was explored with CellChat. We found that differentially expressed genes between BPD mice and controls were mostly enriched in leukocyte migration and M1 macrophages were highly enriched in BPD lungs. Hub genes (Cybb, Papss2, F7 and Fpr2) were validated at the single-cell level, among which the downregulation of Cybb was most closely related to macrophage infiltration. The reduced mRNA and protein levels of Cybb were further validated in animal experiments. Colocalization analysis of Cybb and macrophage markers demonstrated a significant decrease of Cybb in M1 macrophages. Cell–cell crosstalk found that alveolar epithelial cells interacted actively with macrophages through MIF-(CD74 + CD44) signalling. In conclusion, M1 macrophages played important roles in promoting BPD-like lung injury, which was correlated with a specific reduction of Cybb in macrophages and the potential activation of MIF signalling. [ABSTRACT FROM AUTHOR]

Small intestine damage caused by diclofenac is called diclofenac enteropathy. Berberine (BBR), a class of isoquinoline alkaloids derived from Berberis vulgaris and Phellodendron amurense, is widely used in intestinal diseases. The present study evaluated the protective effect of BBR on the intestinal mucosal mechanical barrier in diclofenac enteropathy and its possible action mechanism. The in vitro animal experiment revealed that BBR downregulated the expression of long non-coding RNA H19 (lncRNA H19) in the small intestine and exosomes. In the co-culture experiment involving exosomes and intestinal epithelial cell-6 (IEC-6) cells, the results of qRT-PCR, western blotting, and immunofluorescence assays demonstrated that the elevated expression of lncRNA H19 in the small intestine, conveyed via exosomes derived from the diclofenac group, suppressed the expression levels of autophagy-associated protein 5 (Atg 5) and light chain 3 (LC 3), as well as and the tight junction (TJ) proteins zonula occludens-1 (ZO-1), claudin-1, and occluding, relative to the control group. BBR treatment attenuated exosomal lncRNA H19 levels, upregulated the expression of Atg5 and LC3 expression, enhanced TJ protein expression, and increased the light chain 3 (LC3)-II/LC3-I ratio. These findings significantly elucidated that BBR promoted the restoration of autophagy in IECs by inhibiting exosomal lncRNA H19, thereby mitigating the impairment of the intestinal mucosal mechanical barrier function in diclofenac enteropathy. The process involving exosomal lncRNA H19 regulating autophagy, thereby affecting the intestinal mucosal mechanical barrier, offers a novel perspective for the application of BBR in the treatment of diclofenac enteropathy. [ABSTRACT FROM AUTHOR]

The circadian clock plays multiple functions in the regulation of plant growth, development and response to various abiotic stress. Here, we showed that the core oscillator component late elongated hypocotyl (LHY) was involved in rice response to salt stress. The mutations of OsLHY gene led to reduced salt tolerance in rice. Transcriptomic analyses revealed that the OsLHY gene regulates the expression of genes related to ion homeostasis and the abscisic acid (ABA) signalling pathway, including genes encoded High‐affinity K+ transporters (OsHKTs) and the stress‐activated protein kinases (OsSAPKs). We demonstrated that OsLHY directly binds the promoters of OsHKT1;1, OsHKT1;4 and OsSAPK9 to regulate their expression. Moreover, the ossapk9 mutants exhibited salt tolerance under salt stress. Taken together, our findings revealed that OsLHY integrates ion homeostasis and the ABA pathway to regulate salt tolerance in rice, providing insights into our understanding of how the circadian clock controls rice response to salt stress. Summary statement: The expression of rice core component circadian clock gene LATE ELONGATED HYPOCOTYL can be induced under salt stress, which alters the expression of Na+ and K+ transporter related genes and genes in the ABA signalling pathway to positively regulate salt stress tolerance in rice. [ABSTRACT FROM AUTHOR]

Background: The La-related proteins (LARPs) are a superfamily of RNA-binding proteins associated with regulation of gene expression. Evidence points to an important role for post-transcriptional control of gene expression in germinating pollen tubes, which could be aided by RNA-binding proteins. Results: In this study, a genome-wide investigation of the LARP proteins in eight plant species was performed. The LARP proteins were classified into three families based on a phylogenetic analysis. The gene structure, conserved motifs, cis-acting elements in the promoter, and gene expression profiles were investigated to provide a comprehensive overview of the evolutionary history and potential functions of ZmLARP genes in maize. Moreover, ZmLARP6c1 was specifically expressed in pollen and ZmLARP6c1 was localized to the nucleus and cytoplasm in maize protoplasts. Overexpression of ZmLARP6c1 enhanced the percentage pollen germination compared with that of wild-type pollen. In addition, transcriptome profiling analysis revealed that differentially expressed genes included PABP homologous genes and genes involved in jasmonic acid and abscisic acid biosynthesis, metabolism, signaling pathways and response in a Zmlarp6c1::Ds mutant and ZmLARP6c1-overexpression line compared with the corresponding wild type. Conclusions: The findings provide a basis for further evolutionary and functional analyses, and provide insight into the critical regulatory function of ZmLARP6c1 in maize pollen germination. [ABSTRACT FROM AUTHOR]

Ovarian cancer is a common, highly lethal tumor. Herein, we reported that S-phase kinase-associated protein 2 (Skp2) is essential for the growth and aerobic glycolysis of ovarian cancer cells. Skp2 was upregulated in ovarian cancer tissues and associated with poor clinical outcomes. Using a customized natural product library screening, we found that xanthohumol inhibited aerobic glycolysis and cell viability of ovarian cancer cells. Xanthohumol facilitated the interaction between E3 ligase Cdh1 and Skp2 and promoted the Ub-K48-linked polyubiquitination of Skp2 and degradation. Cdh1 depletion reversed xanthohumol-induced Skp2 downregulation, enhancing HK2 expression and glycolysis in ovarian cancer cells. Finally, a xenograft tumor model was employed to examine the antitumor efficacy of xanthohumol in vivo. Collectively, we discovered that xanthohumol promotes the binding between Skp2 and Cdh1 to suppress the Skp2/AKT/HK2 signal pathway and exhibits potential antitumor activity for ovarian cancer cells. [ABSTRACT FROM AUTHOR]

Wing dimorphism is a life‐historical trait of insects which indicates the developmental trend of populations, going as migrants or staying as residents. The alternative wing morph enhances adaptability of insects to changing environments. However, the underlying mechanism for maintaining wing dimorphism remains vague. The brown planthoppers Nilaparvata lugens, a serious pest of rice, are either short‐winged or long‐winged. The shift between two wing morphs is determined by two insulin receptors. So, this pest is a better model organism to explore the mechanism of wing dimorphism. Here, the short‐ and long‐winged strains of N. lugens were selected. Rates of a selected wing morph were linearly increased in populations, and the selection response of the short‐winged morph was stronger than that of the long‐winged. Selection enhanced the migratory or resident propensity. Directional selection for the long‐winged morph resulted in longer and lighter forewings, while selection for the short‐winged morph generated shorter and thicker wings and higher fecundity. Relative expression levels of wing development genes InR1, InR2 and Foxo were positively correlated with the short‐winged rate in the short‐winged strain, while they were negatively correlated with the long‐winged rate in the long‐winged strain at specific stages. The change rate of expression levels was approximately two times as high as that of the wing morph rates in populations, indicating a high threshold‐dependent gene expressed regulation of wing morph. A partial assortative mating behavior occurred between the nearly pure‐bred lineages of short‐ and long‐winged strains. The short‐winged males preferred to mate with short‐winged females while the long‐winged males mated with the short‐ and long‐winged females equally. The threshold‐dependent mode may be more flexible to adjust wing morphs according to environmental conditions and the partial assortative mating promotes the genetic exchange between two wing morphs which drive the maintenance of wing dimorphism. [ABSTRACT FROM AUTHOR]

Background: Lymph node (LN) status is vital to evaluate the curative potential of relatively early gastric cancer (GC; T1–T2) treatment (endoscopic or surgery). Currently, there is a lack of robust and convenient methods to identify LN metastasis before therapeutic decision-making. Methods: Genome-wide expression profiles of long noncoding RNA (lncRNA) in primary T1 gastric cancer data from The Cancer Genome Atlas (TCGA) was used to identify lncRNA expression signature capable of detecting LN metastasis of GC and establish a 10-lncRNA risk-prediction model based on deep learning. The performance of the lncRNA panel in diagnosing LN metastasis was evaluated both in silico and clinical validation methods. In silico validation was conducted using TCGA and Asian Cancer Research Group (ACRG) datasets. Clinical validation was performed on T1 and T2 patients, and the panel's efficacy was compared with that of traditional tumor markers and computed tomography (CT) scans. Results: Profiling of genome-wide RNA expression identified a panel of lncRNA to predict LN metastasis in T1 stage gastric cancer (AUC = 0.961). A 10-lncRNA risk-prediction model was then constructed, which was validated successfully in T1 and T2 datasets (TCGA, AUC = 0.852; ACRG, AUC = 0.834). Thereafter, the clinical performance of the lncRNA panel was validated in clinical cohorts (T1, AUC = 0.812; T2, AUC = 0.805; T1 + T2, AUC = 0.764). Notably, the panel demonstrated significantly better performance compared with CT and traditional tumor markers. Conclusions: The novel 10-lncRNA could diagnose LN metastasis robustly in relatively early gastric cancer (T1–T2), with promising clinical potential. [ABSTRACT FROM AUTHOR]

How cells adapt their gene expression to nutritional changes remains poorly understood. Histone H3T11 is phosphorylated by pyruvate kinase to repress gene transcription. Here, we identify the protein phosphatase 1 (PP1), Glc7 as the enzyme that specifically dephosphorylates H3T11. We also characterize two novel Glc7-containing complexes and reveal their roles in regulating gene expression upon glucose starvation. Specifically, the Glc7–Sen1 complex dephosphorylates H3T11 to activate the transcription of autophagy-related genes. The Glc7–Rif1–Rap1 complex dephosphorylates H3T11 to derepress the transcription of telomere-proximal genes. Upon glucose starvation, Glc7 expression is up-regulated and more Glc7 translocates into the nucleus to dephosphorylate H3T11, leading to induction of autophagy and derepressed transcription of telomere-proximal genes. Furthermore, the functions of PP1/Glc7 and the two Glc7-containing complexes are conserved in mammals to regulate autophagy and telomere structure. Collectively, our results reveal a novel mechanism that regulate gene expression and chromatin structure in response to glucose availability. [ABSTRACT FROM AUTHOR]

Simple Summary: Glioblastoma is the deadliest primary brain tumor. Current treatment strategies for glioblastoma are not effective, and patients exhibit poor survival rates. Emerging studies implicated glioma stem cells (GSCs) in tumor initiation, progression, and therapy resistance. There is an unmet need to identify new therapeutic candidates for glioblastoma. Our study showed that reticulocalbin 3 (RCN3), an ER lumen residing Ca2+ binding protein, is overexpressed in glioblastoma and associated with poor survival rates. The reduction in RCN3 expression using shRNA or gRNA resulted in reduced proliferation and self-renewal of GSCs. The RNA-seq results showed that RCN3 knockdown altered the expression of several genes related to translation, ribosome, stem cell differentiation, and extracellular matrix. In silico analysis of glioblastoma patient datasets demonstrated a positive correlation of RCN3 with ribosomal pathway genes. Importantly knockdown of RCN3 significantly enhanced the survival of tumor-bearing mice. Our study suggests that RCN3 could be a potential therapeutic target in glioblastoma. Glioblastoma is the most common malignant primary brain tumor. Molecular mechanisms underlying the pathobiology of glioblastoma are incompletely understood, emphasizing an unmet need for the identification of new therapeutic candidates. Reticulocalbin 3 (RCN3), an ER lumen-residing Ca2+ binding protein, plays an essential role in protein biosynthesis processes via the secretory pathway. Emerging studies demonstrated that RCN3 is a target for therapeutic intervention in various diseases. However, a knowledge gap exists about whether RCN3 plays a role in glioblastoma. Publicly available datasets suggest RCN3 is overexpressed in glioblastoma and portends poor survival rates. The knockdown or knockout of RCN3 using shRNA or CRISPR/Cas9 gRNA, respectively, significantly reduced proliferation, neurosphere formation, and self-renewal of GSCs. The RNA-seq studies showed downregulation of genes related to translation, ribosome, and cytokine signaling and upregulation of genes related to immune response, stem cell differentiation, and extracellular matrix (ECM) in RCN3 knockdown cells. Mechanistic studies using qRT-PCR showed decreased expression of ribosomal and increased expression of ER stress genes. Further, in silico analysis of glioblastoma patient datasets showed RCN3 expression correlated with the ribosome, ECM, and immune response pathway genes. Importantly, the knockdown of RCN3 using shRNA significantly enhanced the survival of tumor-bearing mice in orthotopic glioblastoma models. Our study suggests that RCN3 could be a potential target for the development of a therapeutic intervention in glioblastoma. [ABSTRACT FROM AUTHOR]

Leaf‐form ferredoxin‐NADP+ oxidoreductases (LFNRs) function in the last step of the photosynthetic electron transport chain, exist as soluble proteins in the chloroplast stroma and are weakly associated with thylakoids or tightly anchored to chloroplast membranes. Arabidopsis thaliana has two LFNRs, and the chloroplast proteins AtTROL and AtTIC62 participate in anchoring AtLFNRs to the thylakoid membrane. By contrast, the membrane anchoring mechanism of rice (Oryza sativa) LFNRs has not been elucidated. Here, we investigated the membrane‐anchoring mechanism of LFNRs and its physiological roles in rice. We characterized the rice protein OsTROL1 based on its homology to AtTROL. We determined that OsTROL1 is also a thylakoid membrane anchor and its loss leads to a compensatory increase in OsTIC62. OsLFNR1 attachment through a membrane anchor depends on OsLFNR2, unlike the Arabidopsis counterparts. In addition, OsTIC62 was more highly expressed in the dark than under light conditions, consistent with the increased membrane binding of OsLFNR in the dark. Moreover, we observed reciprocal stabilization between OsLFNRs and their membrane anchors. In addition, unlike in Arabidopsis, the loss of LFNR membrane anchor affects photosynthesis in rice. Overall, our study sheds light on the mechanisms anchoring LFNRs to membranes in rice and highlights differences with Arabidopsis. Summary statement: Leaf‐form ferredoxin‐NADP+ oxidoreductases (LFNRs) play an important role in regulating ferredoxin (FD)‐dependent electron partitioning in the chloroplast, acting at the branch of photosynthetic electron transfer and reductive metabolism. However, the membrane‐anchoring mechanism of LFNRs and its physiological roles in rice remains largely elusive. Here, we compared the growth phenotype, fresh weight, chlorophyll content, photosynthetic rate, and electron transfer rate among the wild‐type (WT), Oslfnr1‐1, Oslfnr2‐1, Ostic62, Ostrol1‐1 mutants, and Ostrol1‐1 and Ostic62 double mutant. The results showed that mutation of OsLFNRs and their putative anchor partners affects plant growth and photosynthesis. We found that OsTIC62 is necessary for thylakoid‐bound high‐molecular‐weight LFNR complexes, as low‐molecular‐weight LFNR complexes on OsTROL1 and medium‐molecular‐weight complexes are likely a mixture of OsTROL2‒OsLFNR and OsTIC62‒OsLFNR. OsLFNR tightly bind to the thylakoid membrane through OsTIC62 and OsTROL1, this binding stabilizes OsLFNR; also, OsLFNR and its membrane anchors reciprocally stabilize each other. What is more, loss of OsTROL1 leads to a compensatory increase in OsTIC62. In Oslfnr2 mutants, we could not find any OsLFNR complexes in the thylakoid membrane, whereas the Oslfnr1 mutant still had many OsLFNR complexes, which suggested that OsLFNR2 is required for the binding of OsLFNRs to the thylakoid membrane. As the expression pattern of membrane anchors under diurnal conditions has not been reported, we investigated the expression pattern of OsTIC62 under diurnal condition. Gene expression and protein levels suggested that OsTIC62 is highly expressed under dark than in daylight at both the transcript and protein levels, which means that OsTIC62 expression have day‒night rhythm. [ABSTRACT FROM AUTHOR]

Fusarium head blight (FHB) is primarily caused by Fusarium graminearum and severely reduces wheat yield, causing mycotoxin contamination in grains and derived products. F. graminearum-secreted chemical toxins stably accumulate in plant cells, disturbing host metabolic homeostasis. We determined the potential mechanisms underlying FHB resistance and susceptibility in wheat. Three representative wheat varieties (Sumai 3, Yangmai 158, and Annong 8455) were inoculated with F. graminearum and their metabolite changes were assessed and compared. In total, 365 differentiated metabolites were successfully identified. Amino acids and derivatives, carbohydrates, flavonoids, hydroxycinnamate derivatives, lipids, and nucleotides constituted the major changes in response to fungal infection. Changes in defense-associated metabolites, such as flavonoids and hydroxycinnamate derivatives, were dynamic and differed among the varieties. Nucleotide and amino acid metabolism and the tricarboxylic acid cycle were more active in the highly and moderately resistant varieties than in the highly susceptible variety. We demonstrated that two plant-derived metabolites, phenylalanine and malate, significantly suppressed F. graminearum growth. The genes encoding the biosynthetic enzymes for these two metabolites were upregulated in wheat spike during F. graminearum infection. Thus, our findings uncovered the metabolic basis of resistance and susceptibility of wheat to F. graminearum and provided insights into engineering metabolic pathways to enhance FHB resistance in wheat. [ABSTRACT FROM AUTHOR]

Background: It has been proved that mutations in the PADI6 gene can cause early embryo arrest. This study describes a newly discovered mutation in PADI6 that expands the genetic spectrum of early embryo arrest. Methods: Peripheral blood of a patient diagnosed with early embryo arrest was collected for whole-exome sequencing. Sanger sequencing was performed to confirm this mutation. The effects of the variant were investigated in human embryonic kidney 293T (HEK293T) cells using western blotting, real-time quantitative polymerase chain reaction, and immunofluorescence. Results: A novel homozygous mutation in PADI6 was identified in the proband. The patient carried a frameshift insertion mutation c.558dupA (p.Thr187Asnfs*48), which was located in the protein arginine deiminase middle domain. The variant destroyed PADI6 protein expression and reduced PADI6 mRNA expression in HEK293T cells. Conclusions: The newly identified mutation in PADI6 accounts for early embryo arrest. It expands the spectrum of genetic causes and phenotypes of infertility in humans. These findings also provide an additional possible diagnostic marker for patients with recurrent in vitro fertilization/intracytoplasmic sperm injection failure. Plain Language Summary: Some infertile patients experience multiple in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI) failure owing to recurrent early embryo arrest. However, the underlying mechanisms remain largely unknown. Due to the development of whole-exome sequencing, early embryo arrest has been confirmed as a type of Mendelian disease. This study aimed to identify the genetic cause of early embryo arrest in patients and to expand the genetic spectrum. Furthermore, it can help doctors offer better suggestions to such patients and prevent patients from suffering from multiple IVF/ICSI failures. [ABSTRACT FROM AUTHOR]

Wall-associated kinases (WAKs) are important receptor-like proteins that play major roles in plant defense against pathogens. Fusarium head blight (FHB), one of the most widespread and devastating crop diseases, reduces wheat yield and leads to quality deterioration. Although WAK gene families have been studied in many plants, systematic research on bread wheat (Triticum aestivum) and its role in FHB resistance, in particular, is lacking. In this study, we identified and characterized 320 genes of the TaWAK family in wheat distributed across all chromosomes except 4B and divided them into three phylogenetic groups. Duplication and synteny analyses provided valuable information on the evolutionary characteristics of the TaWAK genes. The gene expression pattern analysis suggested that TaWAK genes play diverse roles in plant biological processes and that at least 30 genes may be involved in the response to Fusarium infection in wheat spikes, with most of the genes contributing to pectin- and chitin-induced defense pathways. Furthermore, 45 TaWAK genes were identified within 17 hcmQTLs that are related to wheat FHB resistance. Our findings provide potential candidate genes for improving FHB resistance and insights into the future functional analysis of TaWAK genes in wheat. [ABSTRACT FROM AUTHOR]

Simple Summary: LncRNA JPX acts as an oncogenic regulator in various types of cancer. Here, we present insights into the mechanistic evidence for the function of JPX in ESCC progression. To clarify the potential role of JPX in ESCC, JPX was upregulated or downregulated in ESCC cells, and in a xenograft model. We showed that JPX promoted ESCC cell proliferation, migration, and invasion via the miR-516b-5p/VEGFA pathway. Our study revealed the importance of JPX as a promising biomarker for ESCC diagnosis and therapeutic target for ESCC in clinic. Long non-coding RNAs (lncRNAs) are reported act as important regulators in various types of cancer. LncRNA JPX was identified as an oncogenic regulator in lung cancer. However, the function of JPX in the progression of esophageal squamous cell carcinoma (ESCC) remains unclear. In the present study, we found JPX was highly expressed in esophageal tissue from ESCC patients. Functional assays demonstrated that JPX promoted ESCC cell proliferation, migration, and invasion in vitro, and accelerated tumor growth in vivo. Mechanistically, the results showed that JPX functioned as a sponge of miR-516b-5p, which targeted vascular endothelial growth factor A (VEGFA) in ESCC cells. Interactions between miR-516b-5p and JPX or VEGFA were confirmed by luciferase reporter assays. Inhibition of JPX significantly attenuated the cell growth and mobility ability of ESCC cells in vitro. In addition, overexpression of miR-516b-5p abrogated JPX-enhanced proliferation, migration, invasion, and angiogenesis of ESCC cells. Our study demonstrated that JPX played an important role in promoting ESCC progression via the miR-516b-5p/VEGFA pathway, which might serve as a promising novel diagnostic biomarker and therapeutic target for ESCC in clinic. [ABSTRACT FROM AUTHOR]

Objective: To determine the role of gasdermin E (GSDME)–mediated pyroptosis in the pathogenesis and progression of rheumatoid arthritis (RA), and to explore the potential of GSDME as a therapeutic target in RA. Methods: The expression and activation of caspase 3 and GSDME in the synovium, macrophages, and monocytes of RA patients were determined by immunohistochemistry, immunofluorescence, and Western blot analysis. The correlation of activated GSDME with RA disease activity was evaluated. The pyroptotic ability of monocytes from RA patients was tested, and the effect of tumor necrosis factor (TNF) on caspase 3/GSDME‐mediated pyroptosis of monocytes and macrophages was investigated. In addition, collagen‐induced arthritis (CIA) was induced in mice lacking Gsdme, and the incidence and severity of arthritis were assessed. Results: Compared to cells from healthy controls, monocytes and synovial macrophages from RA patients showed increased expression of activated caspase 3, GSDME, and the N‐terminal fragment of GSDME (GSDME‐N). The expression of GSDME‐N in monocytes from RA patients correlated positively with disease activity. Monocytes from RA patients with higher GSDME levels were more susceptible to pyroptosis. Furthermore, TNF induced pyroptosis in monocytes and macrophages by activating the caspase 3/GSDME pathway. The use of a caspase 3 inhibitor and silencing of GSDME significantly blocked TNF‐induced pyroptosis. Gsdme deficiency effectively alleviated arthritis in a mouse model of CIA. Conclusion: These results support the notion of a pathogenic role of GSDME in RA and provide an alternative mechanism for RA pathogenesis involving TNF, which activates GSDME‐mediated pyroptosis of monocytes and macrophages in RA. In addition, targeting GSDME might be a potential therapeutic approach for RA. [ABSTRACT FROM AUTHOR]

Background: To explore the clinicopathological significance and prognostic value of thiopurine methyltransferase (TPMT) in patients with colon cancer by bioinformatics analysis. Materials and Methods: The clinicopathological information and TPMT expression data were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Wilcoxon signed-rank test was used to evaluate the relationship between TPMT mRNA expression levels and clinicopathological characteristics in patients with colon cancer. Then, the prognostic value of TPMT mRNA expression for disease-free survival (DFS) and overall survival (OS) in patients with colon cancer was assessed by Kaplan–Meier and Cox regression analyses. Additionally, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to explore potential functions of TPMT in patients with colon cancer. Results: TPMT mRNA was significantly downregulated in colon cancer compared with normal tissues (P < 0.05). Wilcoxon analysis revealed that lower TPMT mRNA expression was remarkably associated with lymph node metastasis (P = 0.008), distant metastasis (P = 0.012) and advanced pathological stage (P = 0.010). Besides, the high TPMT mRNA level was also correlated with a favorable DFS and OS in colon cancer patients (both P < 0.05). Moreover, GO enrichment analysis indicated that the co-expressed genes of TPMT function as extracellular matrix (ECM) structural constituent, insulin-like growth factor binding, cell adhesion molecule binding and growth factor binding. KEGG enrichment analysis suggested that the co-expressed genes of TPMT were particularly enriched in amino sugar and nucleotide sugar metabolism, ECM-receptor interaction and focal adhesion. Conclusion: TPMT mRNA level might be a novel prognostic biomarker for patients with colon cancer. [ABSTRACT FROM AUTHOR]

Background. Activating transcription factor 6 (ATF6) and receptor-interacting protein 3 (RIP3) are important signaling proteins in endoplasmic reticulum (ER) stress and necroptosis, respectively. However, their regulatory relationship and clinical significance are unknown. We investigate the impact of ATF6 on RIP3 expression, and its role in hepatocyte necroptosis in an acute liver injury model. Methods. In vivo and in vitro experiments were carried out. LO2 cells were treated with thapsigargin (TG). In vivo, male BALB/c mice were treated with carbon tetrachloride (CCl4, 1 mL/kg) or tunicamycin (TM, 2 mg/kg). Then, the impact of ATF6 or RIP3 silencing on liver injury, hepatocyte necroptosis, and ER stress-related protein expression was examined. Results. TG induced ER stress and necroptosis and ATF6 and RIP3 expression in LO2 cells. The knockdown of ATF6 significantly decreased RIP3 expression (p < 0.05) and increased ER stress and necroptosis. The downregulation of RIP3 significantly reduced necroptosis and ER stress (p < 0.05). Similar results were observed in CCl4 or the TM-induced mouse model. The knockdown of ATF6 significantly decreased CCl4-induced RIP3 expression and increased liver injury, necroptosis, and ER stress in mice livers (p < 0.05). In contrast, the downregulation of RIP3 significantly reduced liver injury, hepatocyte necroptosis, and ER stress. Conclusions. Hepatocyte ATF6 has multiple roles in acute liver injury. It reduces hepatocyte necroptosis via negative feedback regulation of ER stress. In addition, ATF6 can upregulate the expression of RIP3, which is not helpful to the recovery process. However, downregulating RIP3 reduces hepatocyte necroptosis by promoting the alleviation of ER stress. The findings suggest that RIP3 could be a plausible target for the treatment of liver injury. [ABSTRACT FROM AUTHOR]

MicroRNA is a small noncoding RNA that plays a role in regulating gene expression. miR-1271 is a tumor suppressor microRNA, which is related to the biological changes of many cancers. miR-1271 is considered a biomarker with a potential prognosis and high therapeutic value in tumors. Besides, the expression of miR-1271 is also regulated by many factors. In this study, we summarize the role of miR-1271 in tumors, focusing on the molecular mechanisms of the target genes of miR-1271. Our review will provide a comprehensive understanding of miR-1271 in tumors, as well as ideas for subsequent tumor research related to miR-1271. [ABSTRACT FROM AUTHOR]

Lung adenocarcinoma (LUAD) is one of the most malignant tumors with high morbidity and mortality worldwide due to the lack of reliable methods for early diagnosis and effective treatment. It's imperative to study the mechanism of its development and explore new biomarkers for early detection of LUAD. In this study, the Gene Expression Omnibus (GEO) dataset GSE43458 and The Cancer Genome Atlas (TCGA) were used to explore the differential co-expressed genes between LUAD and normal samples. Three hundred sixity-six co-expressed genes were identified by differential gene expression analysis and Weighted Gene Co-expression Network Analysis (WGCNA) method. Those genes were mainly enriched in ameboidal-type cell migration (biological process), collagen-containing extracellular matrix (cell component), and extracellular matrix structure constituent (molecular function). The protein-protein network (PPI) was constructed and 10 hub genes were identified, including IL6, VWF, CDH5, PECAM1, EDN1, BDNF, CAV1, SPP1, TEK, and SELE. The expression level of hub genes was validated in the GEPIA database, compared with normal tissues, VWF is lowly expressed and SPP1 is upregulated in LUAD tissues. The survival analysis showed increased expression of SPP1 indicated unfavorable prognosis whereas high expression of VWF suggested favorable prognosis in LUAD (p < 0.05). Based on the immune infiltration analysis, the relationship between SPP1 and VWF expression and macrophage, neutrophil, and dendritic cell infiltration was weak in LUAD. Quantitative real-time PCR (qRT-PCR) and western blotting were used to validate the expression of VWF and SPP1 in normal human bronchial epithelial (HBE) cell and three LUAD cell lines, H1299, H1975, and A549. Immunohistochemistry (IHC) was further performed to detect the expression of VWF in 10 cases LUAD samples and matched normal tissues. In summary, the data suggest that VWF is a potential novel biomarker for prognosis of LUAD. [ABSTRACT FROM AUTHOR]

Cholangiocarcinoma (CCA) still has a very unfavorable prognosis with a very high mortality, which is complicated by a lack of prognostic biomarkers. In this study, CCA patients in the Gene Expression Omnibus (GEO) cohort were categorized into two subtypes. Differentially expressed and methylated genes were identified, and the impact of DNA methylation in the trans‐regulation of gene expression was investigated. Finally, a CIMP‐related methylation signature specific for CCA (CMSC) was trained in GEO and validated in the Tongji cohort. A subset of patients with CIMP‐H was identified, which was correlated with an unfavorable prognosis. Gene enrichment analysis implied the potential mechanism of CIMP as a promoter of carcinogenesis by regulating proliferation. The trans‐regulation among differentially methylated CpG sites and genes with the same change trends was positively correlated, while the converse situation showed a negative correlation. Notably, CMSC based on four genes could significantly classify CCA patients into low‐ and high‐risk groups in the GEO cohort, and the robustness of CMSC was validated in the Tongji cohort. The results of receiver operating characteristic analysis further indicated that CMSC was capable of highly sensitive and specific prediction of the patient outcomes in CCA. In conclusion, our work highlights the clinical significance of CMSC in the prognosis of CCA. [ABSTRACT FROM AUTHOR]

Lung adenocarcinoma (LUAD) is a major pathological type of lung cancer. Understanding the mechanism of LUAD at the molecular level is important for a clinical decision. In this study, we use bioinformatic analysis to explore the prognostic value of P4HA1 in lung adenocarcinoma (LUAD) and the relationship with prognosis and tumor-infiltrating immune cells (TIICs). The results showed that the expression of P4HA1 was significantly higher in tumor tissues than in normal tissues for LUAD patients. Upregulated P4HA1 was related to stage and T classification. Kaplan-Meier analysis indicated that upregulation of P4HA1 was significantly related to worse overall survival (OS). Univariate and multivariate Cox analysis indicated P4HA1 remained to be an independent prognostic factor. GSEA showed that several cancer-related and immune-related signaling pathways exhibited prominently differential enrichment in P4HA1-high expression phenotype. In addition, the expression of P4HA1 was significantly correlated with proportion of several TIICs, particularly B cells and CD4+ T cells. In conclusion, our study confirmed that P4HA1 is a promising biomarker of poor prognosis and relates to immune infiltrates in LUAD. [ABSTRACT FROM AUTHOR]

Super-enhancers (SEs) refer to large clusters of enhancers that drive gene expressions. Recent data has provided novel insights in elucidating the roles of SEs in many diseases, including cancer. Many mechanisms involved in tumorigenesis and progression, ranging from internal gene mutation and rearrangement to external damage and inducement, have been demonstrated to be highly associated with SEs. Moreover, translocation, formation, deletion, or duplication of SEs themselves could lead to tumor development. It has been reported that various oncogenic molecules and pathways are tightly regulated by SEs. Moreover, several clinical trials on novel SEs blockers, such as BET inhibitor and CDK7i, have indicated the potential roles of SEs in cancer therapy. In this review, we highlighted the underlying mechanism of action of SEs in cancer development and the corresponding novel potential therapeutic strategies. It is speculated that targeting SEs could complement the traditional approaches and lead to more effective treatment for cancer patients. [ABSTRACT FROM AUTHOR]

Aim: Examine the effects of dipeptidyl peptidase‐4 (DPP4) inhibitor Sitagliptin on the transforming growth factor‐β1 (TGF‐β1) signal transduction pathway in polycystic ovary syndrome (PCOS) rats with ovarian fibrosis. Methods: Thirty rats were divided randomly into the PCOS model group, Sitagliptin treatment group and blank control group. Dehydroepiandrosterone was administered to the model group and treatment group to establish the models. Then, the phenotype of rats was recorded, and the serum sex hormone levels were measured. The pathological structures of the rat ovaries were observed. The protein and mRNA expression levels of DPP4, connective tissue growth factor (CTGF), TGF‐β1 and Smad2/3 in the ovaries were analyzed. Results: There was no statistically difference in fasting body weight and blood glucose among the three groups before Sitagliptin treatment (P > 0.05). The fasting blood glucose level was significantly decreased after the administration of Sitagliptin (P < 0.05). The level of testosterone in the model group was reduced remarkably after Sitagliptin treatment (P < 0.001). The protein expression levels of DPP4, CTGF and TGF‐β1 in the ovarian stroma were lower in the treatment group than in the model group (P < 0.01, P < 0.001, P < 0.05). The mRNA levels of DPP4, CTGF and TGF‐β1 in the model group also greatly declined after Sitagliptin treatment (P < 0.05, P < 0.001, P < 0.01). Conclusion: The DPP4 inhibitor Sitagliptin lowers fasting blood glucose, relieves the high androgen state of PCOS rats and delays the process of ovarian fibrosis, which may be related to reducing the levels of factors related to the TGF‐β1/Smad2/3 signaling pathway. [ABSTRACT FROM AUTHOR]

Background/Aims: Pulmonary fibrosis is a common outcome of various interstitial lung diseases. Prodigiosin (PG) is a series of red pigment with methoxypyrrole ring. This studyinvestigates therole of prodigiosin in pulmonary fibrosis and its underlying mechanisms. Methods: A pulmonary fibrosis rat model was established by intra-trachealinjection ofbleomycin A5. Rats were divided into 4 groups: Normal group, pulmonary fibrosis Model group, Prodigiosin treatment group and hydrocortisone treatmentgroup. HE and Masson staining were carried outto evaluate histopathological changes. The content of hydroxyproline in lung tissue was determined by alkaline hydrolysis. The expression of PICP and PIIINP was examined by ELISA. The mRNA expression of miR-410, TGF-β1 and ADAMTS1 in lung homogenate were detected by RT-PCR. The bronchoalveolar lavage fluid (BALF) and lung tissues of rats were collected and analyzed. Human embryonic pulmonary fibroblast (HEPF) was used for study in vitro. A dual-luciferase reporter assay was conducted to examine the effect of miR-410 on ADAMTS1 expression. Cell transfection was conducted to inhibit miR-410. MTT assay was performed to investigate cell proliferation. The expressions of miR-410, TGF-β1, ADAMTS1and other fibrosis related biomarkers (Col I, Col III, and α-SMA) wereexamined by RT-PCR and Western Blot. Results: HE and Masson staining showed thickened alveolar septum, hyperplasticcapillaries, and large areas of collagen fiber deposition in pulmonary fibrosis model rats. Rats in prodigiosin and hydrocortisone treatment groups had alleviated symptoms. There was high hydroxyproline expression in model rats, whereas the expression of hydroxyproline reduced after prodigiosin or hydrocortisone treatments. RT-PCR results showed high miR-410,high TGF-β1 and low ADAMTS1 in lung tissue of model rats. The expression of PICP and PIIINP werehigher in BALF of model group than in treatment groups. Prodigiosin and hydrocortisone treatment significantly reduced PICP and PIIINP content. RT-PCR and Western Blot analysis showed that prodigiosin inhibited expression of miR-410 and TGF-β1, but up-regulated ADAMTS1 expression. MTT assay indicated that prodigiosin inhibited HEPF proliferation induced by miR-410 overexpression. Conclusion: Prodigiosin down-regulates the expression of miR-410 and TGF-β1, up-regulates ADAMTS1, leading to decrease accumulation of fibrotic proteins. It could be used in alleviating pulmonary fibrosis. [ABSTRACT FROM AUTHOR]

Prostate cancer (PCa) is the most commonly diagnosed cancer in males worldwide. MicroRNAs (miRNAs/miRs) are small non-coding RNAs that participate in the regulation of various biological processes by regulating post-transcriptional gene expression. However, whether dysregulation of miRNA expression may be associated with the carcinogenesis of PCa remains to be elucidated. The present study identified differentially expressed miRNAs in PCa by analyzing two publicly available gene expression datasets, GSE14857 and GSE21036. The results demonstrated that miR-512-3p was significantly upregulated in PCa. Furthermore, the present study explored the molecular functions of miR-512-3p in PCa, and demonstrated that overexpression of miR-512-3p promoted PCa cell proliferation and reduced G1 phase cell cycle arrest in PCa. These results indicated that miR-512-3p may act as an oncogene in PCa. To the best of our knowledge, this is the first study revealed the molecular functions of miR-512-3p in PCa. To obtain valuable insights into the potential mechanisms of miR-512-3p, bioinformatics analyses were performed to identify the targets of miR-512-3p. Kyoto Encyclopedia of Genes and Genomes pathway and Gene Ontology category analyses revealed that miR-512-3p may be associated with the mitogen-activated protein kinase signaling pathway and numerous biological processes, including cell adhesion, cell proliferation, cell cycle and apoptosis. These results suggested that miR-512-3p may be considered a potential diagnostic and therapeutic target of PCa. [ABSTRACT FROM AUTHOR]

The intra-articular injection of adipose-derived stem cells ( ASCs) is a novel potential therapy for patients with osteoarthritis ( OA). However, the efficacy of ASCs from different regions of the body remains unknown. This study investigated whether ASCs from subcutaneous or visceral adipose tissue provide the same improvement of OA. Mouse and human subcutaneous and visceral adipose tissue were excised for ASC isolation. Morphology, proliferation, surface markers and adipocyte differentiation of subcutaneous ASCs (S- ASCs) and visceral ASCs (V- ASCs) were analysed. A surgically induced rat model of OA was established, and 4 weeks after the operation, S- ASCs, V- ASCs or phosphate-buffered saline ( PBS, control) were injected into the articular cavity. Histology, immunohistochemistry and gene expression analyses were performed 6 weeks after ASC injection. The ability of ASCs to differentiate into chondrocytes was assessed by in vitro chondrogenesis, and the immunosuppressive activity of ASCs was evaluated by co-culturing with macrophages. The proliferation of V- ASCs was significantly greater than that of S- ASCs, but S- ASCs had the greater adipogenic capacity than V- ASCs. In addition, the infracted cartilage treated with S- ASCs showed significantly greater improvement than cartilage treated with PBS or V- ASCs. Moreover, S- ASCs showed better chondrogenic potential and immunosuppression in vitro. Subcutaneous adipose tissue is an effective cell source for cell therapy of OA as it promotes stem cell differentiation into chondrocytes and inhibits immunological reactions. [ABSTRACT FROM AUTHOR]

Transcription regulation emerged to be one of the key mechanisms in regulating autophagy. Inhibitors of H3K9 methylation activates the expression of LC3B, as well as other autophagy-related genes, and promotes autophagy process. However, the detailed mechanisms of autophagy regulated by nuclear factors remain elusive. In this study, we performed a drug screen of SMYD2-/- cells and discovered that SMYD2 deficiency enhanced the cell death induced by BIX01294, an inhibitor of histone H3K9 methylation. BIX-01294 induces accumulation of LC3 II and autophagy-related cell death, but not caspase-dependent apoptosis. We profiled the global gene expression pattern after treatment with BIX-01294, in comparison with rapamycin. BIX-01294 selectively activates the downstream genes of p53 signaling, such as p21 and DOR, but not PUMA, a typical p53 target gene inducing apoptosis. BIX-01294 also induces other autophagy-related genes, such as ATG4A and ATG9A. SMYD2 is a methyltransferase for p53 and regulates its transcription activity. Its deficiency enhances the BIX-01294-induced autophagy-related cell death through transcriptionally promoting the expression of p53 target genes. Taken together, our data suggest BIX-01294 induces autophagy-related cell death and selectively activates p53 target genes, which is repressed by SMYD2 methyltransferase. [ABSTRACT FROM AUTHOR]

Spermiogenesis is the terminal differentiation process during which the round spermatid develops into the tadpole-shaped spermatozoon undergoing morphological changes, including the condensation of spermatid nucleus, the formation of acrosome and tail, the elimination of residual body and the transient appearance of manchette. Recently, with the development and application of new bio-techniques such as gene knockout, gene expression as well as gene functional analysis, many spermiogenesis-related genes and proteins have been unveiled. Some of those proteins were proved to play crucial roles in spermiogenesis. Herein, we reviewed the research advances in spermiogenesis -related proteins, including Golgi apparatus proteins, flagellum-related proteins and residual body-related proteins. [ABSTRACT FROM AUTHOR]

Highlights: [•] The expression of reference genes (RGs) in rat nigrostriatal dopaminergic system can be altered by methamphetamine (MA). [•] Temporal and spatial changes in RGs expression were found after MA administration. [•] Selection of an unstable gene for reference altered the significance of TH mRNA expression after MA administration. [•] The impact of MA on RGs stability should be evaluated before determining gene expression in nigra and striatum. [ABSTRACT FROM AUTHOR]

Abstract: PPPDE peptidase domain 1 (PPPDE1) is a recently identified gene; however, its expression regulation and biological function are unclear. Previous studies have indicated that PPPDE1 is involved in embryogenesis, apoptosis induction and cell cycle regulation. In the present study, we first used an anti-PPPDE1 antibody to determine that endogenous PPPDE1 is located in the Golgi apparatus. Immunohistochemistry (IHC) of mouse embryos indicated that PPPDE1 was markedly distributed in liver, skin, intestinal villi, and muscles, whereas Western blot analysis of mouse mature organs revealed its ubiquitous expression, without an appreciable distinction in protein abundance. Surprisingly, another potential isoform of PPPDE1 with a molecular weight of 18 kD (rather than its predicted molecular weight of 21 kD) was detected in the mouse kidney, testis, and intestine. Moreover, microarrays that were derived from twelve tumor types revealed that PPPDE1 expression was significantly lower in pancreas, stomach, and skin tumors compared with normal tissue from these organs. We specifically and extensively analyzed PPPDE1 expression in clinical samples and observed strong associations between PPPDE1 expression and (i) differentiation grade in pancreatic ductal adenocarcinoma and (ii) T stage in skin squamous cell carcinoma. Our data are the first to reveal the expression profile of PPPDE1 protein and its implications in cancer. These results will contribute to the understanding of the expression regulation and biological functions of PPPDE1 in development and carcinogenesis. [Copyright &y& Elsevier]

Aim: The present study describes the ability of a newly developed N-terminal pro-peptides of type IV collagen 7S domain (P4NP 7S) competitive enzyme-linked immunosorbent assay (ELISA) for describing liver fibrosis. The assay applies a monoclonal antibody specific for a PIVNP 7S epitope 100% homologous in the human, rat, and mouse species. Methods: Monoclonal antibodies were raised against selected P4NP 7S specific sequences. Antibodies were screened and a competitive ELISA assay was developed using a selected antibody. The assay was evaluated in relation to technical performance, and in two preclinical liver fibrosis models; the bile duct ligation model (BDL) and the carbon tetrachloride model (CCL4) both performed in rats. Results: A technically robust P4NP 7S ELISA assay using a monoclonal antibody was produced. In the BDL and CCL4 liver fibrosis models it was observed that the P4NP 7S levels were significantly elevated in rat with liver fibrosis as seen by histology (CCL4: 283% elevated in the highest quartile of total hepatic collagen compared with controls, P = 0.001; BDL: 183% elevated at week 4 compared with sham, P < 0.001) and correlated to the amount of hepatic type IV collagen expression in BDL rats (r = 0.49, P < 0.05) in contrast to sham (r = −0.12). P4NP 7S also correlated to total collagen in CCL4 treated livers ( P < 0.001, r = 0.67), however, not in controls (r = 0.04). Conclusions: This newly developed serum assay specific for P4NP 7S was highly related to liver fibrosis and correlated to extent of hepatic fibrosis. This assay may improve fibrosis quantification. [ABSTRACT FROM AUTHOR]

We have previously isolated ypt3-i5 mutant and showed that Ypt3 GTPase functions in the fission yeast secretory pathway. Here, the same genetic screen led to the isolation of ryh1-i6, a mutant allele of the ryh1+ gene encoding a homolog of Rab6. The ryh1-i6 mutant showed phenotypes that support its role in retrograde traffic from endosome to the Golgi. Interestingly, ryh1+ gene deletion was synthetically lethal with ypt3-i5 mutation. Consistently, the over-expression of the GDP-conformational mutant, Ryh1T25 N, inhibited the growth of ypt3-i5 mutant but had no effect on that of wild-type cells. Furthermore, the over-expression of the Ryh1T25N mutant inhibited the acid phosphatase glycosylation and exacerbated the cell wall integrity of ypt3-i5 mutant, but had no effect on those of wild-type cells. GFP-Ryh1 and GFP-Ypt3 both localized at the Golgi/endosome, but showed distinct subcellular localizations. The localization of GFP-Ryh1 in ypt3-i5 mutant and that of GFP-Ypt3 in ryh1-i6 mutant were distinct from those in wild-type cells. In addition, Ryh1 as well as Ypt3 were shown to be involved in acid phosphatase secretion. These results suggest that Ryh1 is involved in the secretory pathway and may have a potential overlapping function with Ypt3 in addition to its role in recycling. [ABSTRACT FROM AUTHOR]

Carotenoids are the principal pigments in the loquat. Although the metabolic pathway of plant carotenoids has been extensively investigated, few studies have been explored the regulatory mechanisms of loquat carotenoids because knowledge of the loquat genome is incomplete. The chromoplast-specific lycopene β-cyclase gene (CYC-B) could catalyze cyclization of lycopene to β-carotene. In this study, the differential accumulation patterns of loquat with different colors were analyzed and virus-induced gene silencing (VIGS) was utilized in order to verify CYC-B gene function. Using a cloning strategy of homologous genes, a CYC-B gene orthologue was successfully identified from the loquat. At a later stage of maturation, CYC-B gene expression and carotenoids concentrations in the 'Dawuxing' variety were higher than in 'Chuannong 1-5-9′, possibly leading to the difference in pulp coloration of loquat. Interference of CYC-B gene expression in the loquat demonstrated clear visual changes. The green color in negative control fruits became yellow, while TRV2-CYC-B silenced fruits remained green. CYC-B gene expression and total carotenoid content in the pulp decreased by 32.5% and 44.1%, respectively. Furthermore, multiple key genes in the carotenoid metabolic pathway synergistically responded to downregulation of CYC-B gene expression. In summary, we provide direct evidences that CYC-B gene is involved in carotenoid accumulation and coloration in the loquat. [ABSTRACT FROM AUTHOR]

Autism spectrum disorder (ASD) is not a single disease but a set of disorders. To find clues of ASD pathogenesis in transcriptomic data, we performed an integrated transcriptomic analysis of ASD. After screening based on several standards in Gene Expression Omnibus (GEO) database, we obtained 11 series of transcriptomic data of different human tissues of ASD patients and healthy controls. Multidimensional scaling analysis revealed that datasets from the same tissue had bigger similarity than from different tissues. Functional enrichment analysis demonstrated that differential expressed genes were significantly enriched in inflammation/immune response, mitochondrion-related function and oxidative phosphorylation. Interestingly, genes enriched in inflammation/immune response were up-regulated in the brain tissues and down-regulated in the blood. In addition, drug prediction provided several compounds which might reverse gene expression profiles of ASD patients. And we also replicated the methods and criteria of transcriptomic analysis with datasets of ASD animal models and healthy controls, the results from animal models consolidated the results of transcriptomic analysis of ASD human tissues. In general, the results of our study may provide researchers a new sight of understanding the etiology of ASD and clinicians the possibilities of developing medical therapies. [ABSTRACT FROM AUTHOR]

Background: This study explored the possible mechanism of flavones from Vitis vinifera L. (VTF) on neurotransmitters, synaptic transmission and related learning and memory in rats with Alzheimer disease (AD). Methods: The researchers injected amyloid-β(25–35) into the hippocampus to establish AD model rats. The Sprague-Dawley (SD) rats were divided into a control group, a donepezil group, an AD model group, a VTF low-dose group, a VTF medium-dose group and a VTF high-dose group. The researchers detected the activity of choline acetyltransferase (ChAT) and acetylcholinesterase (AChE) according to kit instructions. The protein expression of brain-derived neurotrophic factor (BDNF), synaptotagmin-1 (SYT1) and cyclic adenosine monophosphate response element binding protein (CREB) in the rats' hippocampi was detected by immunohistochemistry and Western blot, and the gene expression of cAMP-regulated enhancer (CRE) was detected by real-time quantitative polymerase chain reaction (PCR). Results: VTF may enhance the protein expression of p-CREB, BDNF and SYT1 in rat hippocampi, depending on dose. The messenger RNA (mRNA) level of CREB was significantly higher in the VTF high-dose group than in the model group, which was consistent with the results of Western blotting. VTF may reduce the activity of AChE and increase that of ChAT in rat hippocampi. Finally, VTF effectively improved the learning and memory abilities of AD rats. Conclusions: VTF can promote synaptic plasticity and indirectly affect the expression of cholinergic neurotransmitters, which may be one mechanism of VTF protection in AD rats. [ABSTRACT FROM AUTHOR]

To investigate the role and mechanisms of methyltransferase-like 3 (METTL3) in the pathogenesis of lipopolysaccharide (LPS)-induced acute lung injury (ALI). LPS intratracheally instillation was applied in alveolar epithelial cell METTL3 conditional knockout (METTL3-CKO) mice and their wild-type littermates. In addition, METTL3 inhibitor STM2457 was used. LPS treatment on mouse lung epithelial 12 (MLE-12) cell was applied to establish an in vitro model of LPS-induced ALI. H&E staining, lung wet-to-dry ratio, and total broncho-alveolar lavage fluid (BALF) concentrations were used to evaluate lung injury. Overall, the m6A level was determined with the m6A RNA Methylation Quantification Kit and dot blot assay. Expression of METTL3 and neprilysin were measured with immunohistochemistry, immunofluorescence, immunofluorescence-fluorescence in situ hybridization, and western blot. Apoptosis was detected with TUNEL, western blot, and flow cytometry. The interaction of METTL3 and neprilysin was determined with RIP-qPCR and MeRIP. METTL3 expression and apoptosis were increased in alveolar epithelial cells of mice treated with LPS, and METTL3-CKO or METTL3 inhibitor STM2457 could alleviate apoptosis and LPS-induced ALI. In MLE-12 cells, LPS-Induced METTL3 expression and apoptosis. Knockdown of METTL3 alleviated, while overexpression of METTL3 exacerbated LPS-induced apoptosis. LPS treatment reduced neprilysin expression, the intervention of neprilysin expression negatively regulated apoptosis without affecting METTL3 expression, and mitigated the promoting effect of METTL3 on LPS-induced apoptosis. Additionally, METTL3 could bind to the mRNA of neprilysin, and reduce its expression. Our findings revealed that inhibition of METTL3 could exert anti-apoptosis and ALI-protective effects via restoring neprilysin expression. [ABSTRACT FROM AUTHOR]

Ovarian cancer (OCa) is the most lethal gynecologic cancer. Emerging data indicates that estrogen receptor beta (ERβ) functions as a tumor suppressor in OCa. Lysine-specific histone demethylase 1A (KDM1A) is an epigenetic modifier that acts as a coregulator for steroid hormone receptors. However, it remain unknown if KDM1A interacts with ERβ and regulates its expression/functions in OCa. Analysis of TCGA data sets indicated KDM1A and ERβ expression showed an inverse relationship in OCa. Knockout (KO), knockdown (KD), or inhibition of KDM1A increased ERβ isoform 1 expression in established and patient-derived OCa cells. Further, KDM1A interacts with and functions as a corepressor of ERβ, and its inhibition enhances ERβ target gene expression via alterations of histone methylation marks at their promoters. Importantly, KDM1A-KO or -KD enhanced the efficacy of ERβ agonist LY500307, and the combination of KDM1A inhibitor (KDM1Ai) NCD38 with ERβ agonist synergistically reduced the cell viability, colony formation, and invasion of OCa cells. RNA-seq and DIA mass spectrometry analyses showed that KDM1A-KO resulted in enhanced ERβ signaling and that genes altered by KDM1A-KO and ERβ agonist were related to apoptosis, cell cycle, and EMT. Moreover, combination treatment significantly reduced the tumor growth in OCa orthotopic, syngeneic, and patient-derived xenograft models and proliferation in patient-derived explant models. Our results demonstrate that KDM1A regulates ERβ expression/functions, and its inhibition improves ERβ mediated tumor suppression. Overall, our findings suggest that KDM1Ai and ERβ agonist combination therapy is a promising strategy for OCa. • KDM1A knockdown/inhibition increased tumor suppressor ERβ expression via alteration of histone methylation marks. • KDM1A interacts with, and functions as a corepressor of ERβ, and KDM1A knockout enhanced the ERβ agonist-mediated transcriptome. • KDM1A knockdown/inhibition and ERβ agonist combination treatment significantly reduced oncogenic functions of ovarian cancer cells. • KDM1A inhibitor and ERβ agonist combination significantly reduced ovarian tumor growth in mouse xenograft models. [ABSTRACT FROM AUTHOR]

Mucin 2 (MUC2) is a mucin molecule aberrantly expressed by ovarian cancer cells. Previous in vitro studies have indicated that MUC2 promotes cancer growth and metastasis through a tumor-associated macrophage (TAM)-dependent mechanism. However, this mechanism has never been linked to clinical oncology, and its prognostic significance needed to be clarified. Here, we collected 102 consecutive ovarian cancer specimens and used the multiple immuno-histo-chemical/-fluorescent technique to determine the correlations between the MUC2 expression status, the ratio of M1/M2 TAMs and the densities of cyclooxygenase-2 (COX-2)+ TAMs and COX-2+ cancer cells. The Kaplan-Meier survival analysis and multivariate Cox regression analysis were used to evaluate the prognostic influences of these parameters. As a result, we found that the MUC2 overexpression (immunostaining ++/+++) was significantly correlated with a reduced ratio of M1/M2 TAMs (p<0.001), an increased density of COX-2+ TAMs (p<0.001) and an increased density of COX-2+ cancer cells (p=0.017). Moreover, most of the M2 TAMs (93%-100%) and COX-2+ TAMs (63%-89%) overlapped; and the COX-2+ cancer cells were frequently observed near the COX-2+ TAMs. In the Cox regression analysis, MUC2 overexpression was found to be an independent prognostic factor for ovarian cancer patients, of which the hazard ratio (HR) was 2.354 (95% confidence interval (CI): 1.031-10.707, p=0.005). Also, the reduced ratio of M1/M2 TAMs and the increased densities of COX-2+ TAMs and COX-2+ cancer cells were demonstrated to be the predictors of poor prognosis, among which the reduced M1/M2 ratio possessed the highest HR (1.767, 95% CI: 1.061-6.957, p=0.019). All these findings revealed that MUC2 can concurrently exert M2-polarizing and COX-2-inducing effects on TAMs, by which it causes an imbalanced TAM M1-/M2-polarization pattern and induces local PGE2 synthesis (in both TAMs and cancer cells). The positive feedback between local PGE2 synthesis and TAM M2-polarization accelerates ovarian cancer progression. [ABSTRACT FROM AUTHOR]

This SERS biosensor was developed by employing miRNA 21-triggered DNA nanomaterials to facilitate the release of the Raman signal molecule Cy3 from a catalytic hairpin assembly. The cyclic amplification of catalyzed hairpin amplification (CHA) allowed for the selective enrichment of Cy3 within the localized hot spot region on the substrate thereby facilitating robust generation of surface-enhanced Raman scattering (SERS) signals for precise quantification of miRNA 21. The unidirectional enrichment of Cy3 to Au nanocubes (Au NCs) was achieved by using MiRNA 21 as a trigger chain to trigger the CHA cycle between H1 (tagged Raman probe Cy3) and H2 functionalized Fe 3 O 4 and Au NCs. Finally, a substantial quantity of Au NCs enriched with Cy3 was obtained. By achieving the formation of a densely packed and two-dimensional array of gold nan water-cyclohexane interface, Cy3 is effectively concentrated within the hotspot region, leading to amplified and stable SERS signals. The synergetic combination of CHA, Fe 3 O 4 , and Au NCs facilitated the unidirectional transfer of Raman molecules from Fe 3 O 4 to Au NCs, thereby enhancing the capacity of the Cy3 substrate hot spot region. The sensor utilized Au NCs to form highly stable and well-ordered two-dimensional arrays at the water-cyclohexane interface, demonstrating exceptional stability, and reproducibility. [Display omitted] • The unidirectional enrichment of Cy3 significantly intensified its concentration in the hotspot of Au NCs, enhancing detection capabilities. • The self-assembled Au NCs array exhibited consistent, uniform, and long-lasting surface enhancement, guaranteeing stability and reliability. • The SERS biosensor achieved remarkable sensitivity, detecting miRNA 21 down to 0.81 fM, with a broad detection range from 1 − 1 × 106 fM. The involvement of microRNA (miRNA) in the transcriptional and regulatory processes of gene expression in organisms, along with its aberrant expression patterns in various malignant diseases such as tumors, underscores its significance. Surface-enhanced Raman scattering (SERS) biosensing technology offers distinct advantages for miRNA detection, including simplified procedures, non-destructive analysis, fingerprint spectroscopy capabilities, and rapid detection times. This study presents the development of a novel SERS-based biosensor utilizing miRNA-21 stimulated-responsive DNA-functionalized nanomaterials. The DNA structure within the the catalyzed hairpin amplification (CHA) was utilized to modify Fe 3 O 4 and Au nanocubes (Au NCs), and subsequently, miRNA21 served as a key to trigger the CHA reaction between these two materials. Notably, during this process, the signal probe Cy3 underwent directed migration and accumulation from Fe 3 O 4 to Au NCs, resulting in the unidirectional enrichment of beacon probe from Fe 3 O 4 to Au NCs, which was facilitated by the progression of the CHA cycle. This facilitated robust generation of SERS signals for precise quantification of miRNA-21. The sensor utilized Au NCs enriched with Cy3 to form highly stable and well-ordered two-dimensional arrays at the water-cyclohexane interface, demonstrating exceptional stability and reproducibility. It achieved an impressive detection limit of 0.81 fM across a dynamic range from 1 to 1 × 10⁶ fM. This work advances practical methods for amplification analysis in the sensing field, demonstrating significant potential for clinical medicine and early cancer diagnosis. [ABSTRACT FROM AUTHOR]

Wild tomatoes, which are the natural ancestors of the tomato genus, exhibit a wide range of genetic diversity and adaptability. They possess unique characteristics in terms of their ability to withstand cold stress, which sets them apart from cultivated tomatoes. However, the specific mechanisms underlying the differences in cold tolerance between wild and cultivated tomatoes remain unclear. Studies have shown that the expression of SAMDC2 , a gene involved in the synthesis of spermidine (Spd), significantly increases in both wild tomato (S. habrochaites) LA1777 and cultivated tomato (S. lycopersicum) AC after exposure to cold stress. Additionally, the content of Spd also increases significantly in these materials, particularly in wild tomato LA1777. Further analysis, involving the use of exogenous Spd and the polyamine synthesis inhibitor MGBG under cold stress conditions, has revealed that the application of exogenous Spd enhances the plant's cold tolerance by increasing the endogenous Spd content, while the use of MGBG inhibits Spd accumulation and reduces the plant's cold tolerance. By comparing the cis -acting regulatory elements in the SAMDC2 promoter of both materials, we discovered that wild tomato LA1777 possesses an extra W-box compared to cultivated tomato AC. Through yeast one-hybrid, EMSA, and dual-luciferase assays, we demonstrated that ShWRKY55 can target the promoter of ShSAMDC2 and regulate its upregulation expression. Our study suggests that the stronger cold resistance observed in wild tomato LA1777, as compared to cultivated tomato AC, can be attributed to the regulation of ShSAMDC2 expression through ShWRKY55 after exposure to cold stress, which leads to higher Spd accumulation. However, this regulatory mechanism is absent in cultivated tomatoes. This research contributes to our understanding of the distinct adaptation mechanisms of wild and cultivated tomatoes to cold stress and provides novel insights and strategies for improving the cold tolerance of cultivated tomatoes. • The expression of SAMDC2 , significantly increases in LA1777 and AC after exposure to cold stress. • The content of Spd also increases significantly, particularly in wild tomato LA1777. • By comparing the promoter of SAMDC2 , discovered that LA1777 possesses an extra W-box compared to AC. • In LA1777, ShWRKY55 can target the promoter of ShSAMDC2 and regulate its upregulation expression. This regulatory mechanism is absent in AC. [ABSTRACT FROM AUTHOR]

Both lipid metabolism reprogramming and lncRNAs exert effects on tumor development. We aimed to predict the prognosis of head and neck squamous cell carcinoma (HNSCC) based on lipid metabolism-related (LR)-lncRNAs. LR-lncRNAs were determined from the RNA-ref profiles of HNSCC samples in The Cancer Genome Atlas (TCGA). The prognostic model was established by univariate Cox and Lasso regression analysis. Clinical relevance and predictive accuracy were investigated, and external validation was also performed in the Gene Expression Omnibus (GEO) cohort. Tumor immune infiltration and relevant functional analysis, including the association of autophagy with prognostic signatures, were conducted through single-sample gene set enrichment analysis (ssGSEA). The regulatory network of candidate LR-lncRNAs was investigated via coexpression, ceRNA and cis/trans acting interactions. Potential genes were selected through qRT–PCR analysis, and their effects on tumor biological activities and autophagic activity were explored after gene knockdown. A total of 222 LR-lncRNAs were identified. Among the 41 genes with prognostic significance, 17 lncRNAs were eligible for the risk model. Patients in the high-risk group had a poorer prognosis than those in the low-risk group, and the risk score was found to be positively associated with tumor microenvironment infiltration via multiple algorithms. Furthermore, improved prognosis was found in patients with high autophagic scores and low risk scores, and autophagy-related genes such as PINK1 and CCL2 showed significantly lower expression in the low-risk group. The expression of immune checkpoint genes such as CD28, CTLA4 and PDCD1 decreased dramatically in the high-risk group. The target genes of candidate lncRNAs were confirmed, such as ENO2 and PPAR-gamma. Furthermore, MIR4435-2HG was the most significantly overexpressed lncRNA in HNSCC cell lines and tumor samples, which could promote proliferation and migration and inhibit apoptosis. Additionally, MIR4435-2HG silencing activated autophagy by increasing LC3B expression. This study constructed an LR-lncRNA prognostic signature for HNSCC and indicated its relationships with tumor immunity and autophagy, which provides a promising future for LR-lncRNA-oriented prognostic tools and therapeutic targets. • A risk model was established based on lipid metabolism-related lncRNAs (LR-lncRNAs) based on TCGA database. • This risk model was associated with the prognosis of HNSCC patients and well verified in the external validation. • This risk model was related to immune response, autophagy activation and drug sensitivity. • Potential hub genes and regulatory mechanism were screened from interaction networks of LR-lncRNAs. • MiR4435-2HG expressed higher in tumor and showed capacities of promoting tumor growth and inhibiting autophagy. [ABSTRACT FROM AUTHOR]