Search

The prevalence of papillary thyroid cancer (PTC) has been rising in recent years. Despite its relatively low mortality, PTC frequently metastasizes to lymph nodes and often recurs, posing significant health and economic burdens. The role of iodine in the pathogenesis and advancement of thyroid cancer remains poorly understood. Circular RNAs (circRNAs) are recognized to function as competing endogenous RNAs (ceRNAs) that modulate gene expression and play a role in various cancer stages. Consequently, this research aimed to elucidate the mechanism by which circRNA influences the impact of iodine on PTC. Our research indicates that high iodine levels can exacerbate the malignancy of PTC via the circ_0004851/miR-296-3p/FGF11 axis. These insights into iodine's biological role in PTC and the association of circRNA with the disease could pave the way for novel biomarkers and potentially effective therapeutic strategies to mitigate PTC progression. [ABSTRACT FROM AUTHOR]

In experiments, the distributions of mRNA or protein numbers in single cells are often fitted to the random telegraph model which includes synthesis and decay of mRNA or protein, and switching of the gene between active and inactive states. While commonly used, this model does not describe how fluctuations are influenced by crucial biological mechanisms such as feedback regulation, non-exponential gene inactivation durations, and multiple gene activation pathways. Here we investigate the dynamical properties of four relatively complex gene expression models by fitting their steady-state mRNA or protein number distributions to the simple telegraph model. We show that despite the underlying complex biological mechanisms, the telegraph model with three effective parameters can accurately capture the steady-state gene product distributions, as well as the conditional distributions in the active gene state, of the complex models. Some effective parameters are reliable and can reflect realistic dynamic behaviors of the complex models, while others may deviate significantly from their real values in the complex models. The effective parameters can also be applied to characterize the capability for a complex model to exhibit multimodality. Using additional information such as single-cell data at multiple time points, we provide an effective method of distinguishing the complex models from the telegraph model. Furthermore, using measurements under varying experimental conditions, we show that fitting the mRNA or protein number distributions to the telegraph model may even reveal the underlying gene regulation mechanisms of the complex models. The effectiveness of these methods is confirmed by analysis of single-cell data for E. coli and mammalian cells. All these results are robust with respect to cooperative transcriptional regulation and extrinsic noise. In particular, we find that faster relaxation speed to the steady state results in more precise parameter inference under large extrinsic noise. Author summary: Over the past decade, significant progress has been made in the theory and experiments of single-cell stochastic gene expression dynamics. The most well studied and widely used stochastic gene expression model is the two-state telegraph model. However, the conventional telegraph model is too simple and limited in its predictive power because it lacks a description of some important biological mechanisms, such as feedback regulation, multiple gene activation steps, and multiple gene activation pathways. This raises a important question: what can we learn when fitting a complex gene expression model to a simple telegraph model? In this paper, we investigate four complex gene expression models by fitting their steady-state mRNA or protein number distributions to the telegraph model and then obtain estimates of the effective parameters. We show that while the estimated values of the parameters in the "artificial" telegraph model are not always accurate, they are still sometimes reliable and can also reveal important dynamical properties of the complex models such as the ability for a complex model to produce bimodality. Moreover, we provide an effective method of distinguishing the complex models from the telegraph model by using additional information such as gene expression data at multiple time points. Finally, we show that fitting the mRNA or protein number distributions to the telegraph model may even reveal the underlying gene regulation mechanism of a complex model by using measurements under varying experimental conditions. The effectiveness of these methods is well confirmed by analysis of single-cell gene expression data for E. coli and mammalian cells. [ABSTRACT FROM AUTHOR]

Objective To investigate the effect of MAPK on intestinal obstruction during pregnancy. Methods A total of 105 SPF Wistar rats (female = 70 and male = 35) were selected. After placing all the rats in the same cage, 33 female rats were pregnant, and 8 rats were assigned to the control group and the other 25 rats were used to established bowel obstruction model. A total of 24 rats were successfully modelled, which were divided into model group (n = 8), up-regulation group (n = 8), and down-regulation group (n = 8). Results Compared with the model group, MAPK expression, VIP, GAS, TNF-α, IL-6 levels, TLR4, Myd88, NF-κB mRNA were increased and MOT, IL-4, IL-10 levels were decreased in up-regulation group; MAPK expression, VIP, GAS, TNF-α, IL-6 levels, TLR4, Myd88, NF-κB mRNA were decreased and MOT, IL-4, IL-10 levels were increased in down-regulation group (P < 0.05). Conclusion MAPK down-regulation reduced inflammatory response and improved bowel obstruction in pregnancy, and the mechanism may be related to the inhibition of TLR4/Myd88/NF-κB pathway. [ABSTRACT FROM AUTHOR]

Post-transcriptional regulation by small RNAs and post-translational modifications (PTM) such as lysine acetylation play fundamental roles in physiological circuits, offering rapid responses to environmental signals with low energy consumption. Yet, the interplay between these regulatory systems remains underexplored. Here, we unveil the cross-talk between sRNAs and lysine acetylation in Streptococcus mutans, a primary cariogenic pathogen known for its potent acidogenic virulence. Through systematic overexpression of sRNAs in S. mutans, we identified sRNA SmsR1 as a critical player in modulating acidogenicity, a key cariogenic virulence feature in S. mutans. Furthermore, combined with the analysis of predicted target mRNA and transcriptome results, potential target genes were identified and experimentally verified. A direct interaction between SmsR1 and 5'-UTR region of pdhC gene was determined by in vitro binding assays. Importantly, we found that overexpression of SmsR1 reduced the expression of pdhC mRNA and increased the intracellular concentration of acetyl-CoA, resulting in global changes in protein acetylation levels. This was verified by acetyl-proteomics in S. mutans, along with an increase in acetylation level and decreased activity of LDH. Our study unravels a novel regulatory paradigm where sRNA bridges post-transcriptional regulation with post-translational modification, underscoring bacterial adeptness in fine-tuning responses to environmental stress. Author summary: Post-transcriptional regulation and post-translational modification are widely present in physiological circuits due to their low energy consumption and rapid response to the environment. sRNA is an important post-transcriptional regulatory factor in bacterial response to environmental stress, and bacteria also use sRNA as a key signal to control multicellular behaviors such as biofilm formation and quorum sensing to regulate virulence. S. mutans is an intractable cariogenic pathogen, but the role of sRNA in S. mutans is poorly understood. Here, we elucidated the virulence regulation and mechanism of sRNA SmsR1 in S. mutans by means of transcriptomics, acetyl-proteomics and animal models, and found its relationship with protein acetylation (post-translational modification), and a new role of sRNA physiological regulatory network was shown. This study presents an innovative perspective that a sRNA in S. mutans is involved in the correlation between post-transcriptional regulation and post-translational modification. [ABSTRACT FROM AUTHOR]

Aeromonas hydrophila and A. veronii are widespread and important critical pathogenic bacteria in the aquaculture industry and cause severe economic damage. At present, magnolol has been proved to be a broad‐spectrum antibacterial activity, such as A. hydrophila, Staphylococcus aureus and Streptococcus mutans. In order to explore the cause of in vivo disease resistance of magnolol and promote its safe application in aquaculture, the pathological detection and changes in immune indicators of fish after feeding with magnolol were conducted in this paper. Results showed that the diets supplemented with magnolol (3 g magnolol/kg commercial feed) significantly increase the expression level of anti‐inflammatory cytokines (IL‐10, TGF‐β and IL‐4) in the liver of goldfish (p <.05). Additionally, the expression levels of proinflammatory cytokines (IL‐1β, IL‐8 and IFN‐γ) did not increase significantly. Subsequently, this study investigated the resistance of goldfish to A. hydrophila and A. veronii infection after feeding with magnolol. The results showed that the survival rates of treatment groups fed 3 g magnolol/kg commercial feed daily increased by 23.1% and 38.5% after 10 days post A. hydrophila and A. veronii (p =.0351) infection, respectively. Meanwhile, growth performance (body weight and length), major internal organs (liver, spleen, kidney and intestine) and the serum biochemistry indicators (ATL and AST) all exhibited no significant adverse effects after the goldfish fed with magnolol for 30 days. TP showed an increasing concentration in the treatment group (p <.05). Results of the mRNA expression of stress response indicated that the expression level of cyp1a and hsp70 was significantly down‐regulated after a 30‐day treatment (p <.05), and the two genes recovered to the similar level as the control group after a commercial feed diet. In brief, the diets supplemented with magnolol protected the host from the excessive immune response caused by A. hydrophila and A. veronii via enhancing its anti‐inflammatory capacity and had no adverse effects with feeding. [ABSTRACT FROM AUTHOR]

Peripheral blood mononuclear cell (PBMC) genes reflect the host immune status and could be suitable for evaluating the prognosis of patients with hepatocellular carcinoma (HCC), for which a reliable biomarker is unavailable and the host immune responses to cancer cells. This study aimed to investigate prognostically relevant genes in HCC PBMCs and assessed whether their expression represents tumor immune infiltration. Gene expression in PBMCs from patients with advanced or terminal HCC who had survived or died was examined. Correlations among FAT atypical cadherin 4 (FAT4) expression, cancer immune characteristics, and infiltrated immune cell gene marker sets were analyzed. FAT4 expression was lower in the PBMCs of patients with advanced or terminal HCC who had died than that in patients who survived. Kaplan–Meier analysis indicated that FAT4 downregulation was associated with a relatively poor prognosis while overexpression was positively correlated with immune cell infiltration, several immune cell markers, and immune checkpoint expression. Hsa-miR-93-5p represented the most probable upstream microRNA of FAT4. Thus, upregulated FAT4 in PBMCs and HCC tissues might indicate a favorable prognosis and increased immune cell infiltration, while miRNA-93-5p could be a modulator of FAT4 expression. Collectively, these findings suggest novel immunotherapy targets for HCC. [ABSTRACT FROM AUTHOR]

Globally, gastric cancer (GC) is a major cause of cancer death. This study is aimed at investigating the biological functions of activating transcription factor 2 (ATF2) and the underlying mechanism in GC. In the present work, GEPIA, UALCAN, Human Protein Atlas and StarBase databases were adopted to analyze ATF2 expression characteristics in GC tissues and normal gastric tissues, and its relationships with tumor grade and patients' survival time. Quantitative real‐time polymerase chain reaction (qRT‐PCR) method was employed to examine ATF2 mRNA expression in normal gastric tissues, GC tissues, and GC cell lines. Cell counting kit‐8 (CCK‐8) and EdU assays were utilized for detecting GC cell proliferation. Cell apoptosis was detected by flow cytometry. PROMO database was applied to predict the binding site of ATF2 with the METTL3 promoter region. The binding relationship between ATF2 and the METTL3 promoter region was verified through dual‐luciferase reporter gene assay and chromatin immunoprecipitation‐quantitative PCR (ChIP‐qPCR) assay. Western blot was performed to evaluate the effect of ATF2 on METTL3 expression. METTL3‐related signaling pathways were predicted using Gene Set Enrichment Analysis (GSEA) in the LinkedOmics database. It was found that, ATF2 level was elevated in GC tissues and cell lines in comparison with normal tissues and correlated with short patients' survival time. ATF2 overexpression facilitated GC cell growth and suppressed the apoptosis, whereas ATF2 knockdown suppressed GC cell proliferation and facilitated the apoptosis. ATF2 bound to the METTL3 promoter region, and ATF2 overexpression promoted the transcription of METTL3, and ATF2 knockdown restrained the transcription of METTL3. METTL3 was associated with cell cycle progression, and ATF2 overexpression enhanced cyclin D1 expression, and METTL3 knockdown reduced cyclin D1 expression. In summary, ATF2 facilitates GC cell proliferation and suppresses the apoptosis via activating the METTL3/cyclin D1 signaling pathway, and ATF2 is promising to be an anti‐drug target for GC. [ABSTRACT FROM AUTHOR]

Influenza A virus (IAV) is a leading cause of human respiratory infections and poses a major public health concern. IAV replication can affect the expression of DNA methyltransferases (DNMTs), and the subsequent changes in DNA methylation regulate gene expression and may lead to abnormal gene transcription and translation, yet the underlying mechanisms of virus-induced epigenetic changes from DNA methylation and its role in virus–host interactions remain elusive. Here in this paper, we showed that DNMT1 expression could be suppressed following the inhibition of miR-142-5p or the PI3K/AKT signaling pathway during IAV infection, resulting in demethylation of the promotor region of the 2′-5′-oligoadenylate synthetase-like (OASL) protein and promotion of its expression in A549 cells. OASL expression enhanced RIG-I-mediated interferon induction and then suppressed replication of IAV. Our study elucidated an innate immunity mechanism by which up-regulation of OASL contributes to host antiviral responses via epigenetic modifications in IAV infection, which could provide important insights into the understanding of viral pathogenesis and host antiviral defense. [ABSTRACT FROM AUTHOR]

Minichromosome maintenance complex component 6 (MCM6), a member of the MCM family, plays a pivotal role in DNA replication initiation and genome duplication of proliferating cells. MCM6 is upregulated in multiple malignancies and is considered a novel diagnostic biomarker. However, the functional contributions and prognostic value of MCM6 in intrahepatic cholangiocarcinoma (ICC) remain unexplored. In this study, we investigated the molecular function of MCM6 in ICC. Data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO, GSE107943) indicated an upregulation of MCM6 in tumor tissues. Immunohistochemical analysis performed on 115 cases of ICC samples confirmed the upregulation of MCM6 and further suggested that a high level of MCM6 expression predicted shorter overall and disease-free survival in ICC patients. Functional studies suggested that MCM6 knockdown significantly suppressed cell viability, blocked cell cycle progression and inhibited metastasis, while the enhancement of MCM6 expression promoted the proliferation and migration of ICC cells both in vitro and in vivo. Mechanistically, Gene Set Enrichment Analysis (GSEA) suggested that the epithelial–mesenchymal transition (EMT) and E2F1-correlated genes were enriched in ICC tissues with high MCM6 expression. Further verification indicated that MCM6 promoted the EMT of ICC cells via upregulating E2F1. In addition, E2F1 knockdown partially blocked the pro-malignant effects of MCM6 overexpression. In summary, MCM6 was found to be a novel prognostic and predictive marker for ICC. MCM6 promoted ICC progression via activation of E2F1-mediated EMT. [ABSTRACT FROM AUTHOR]

Hypertension (HTN) is associated with gut dysbiosis and the depletion of butyrate-producing bacteria in animal models and people. Furthermore, fecal material transfer from donor hypertensive patients increases blood pressure in normotensive recipient animals and ameliorates HTN-associated pathophysiology. These observations have implications in the impaired interactions between the gut and gut microbiota in HTN. Although this concept is supported in animal models, little is known about human HTN. Therefore, our objective for this study was to compare gene expression with transcriptomics and its potential to influence microbiota in subjects with normal and high blood pressure (HBP). Colon samples from reference subjects with normal blood pressure (REF) and HBP were used for RNA-seq to analyze their transcriptomes. We observed the significant downregulation of gene sets governing immune responses (e.g., SGK1 and OASL), gut epithelial function (e.g., KRT20 and SLC9A3R1), gut microbiota (e.g., PPARG and CIDEC) and genes associated with cardiovascular and gut diseases (e.g., PLAUR and NLN) in HBP subjects; the expression of genes within these pathways correlated with blood pressure. Potential drug targets in the gut epithelium were identified using the Drug Gene International Database for possible use in HTN. They include peroxisome proliferator-activated receptor gamma (PPRG), active serum/glucocorticoid regulated kinase 1 (SGK1) and 3 beta-hydroxysteroid isomerase type II inhibitor (HSD3B). Finally, butyrate, a microbiota-derived short-chain fatty acid, restored the disrupted expression of certain functional genes in colonic organoids from HBP subjects. Patients with HBP exhibit a unique transcriptome that could underlie impaired gut–microbiota interactions. Targeting these interactions could provide a promising new therapeutic intervention for hypertension management. [ABSTRACT FROM AUTHOR]

Barley (Hordeum vulgare L.) grass has been recognized as a functional food with a wide spectrum of health-promoting properties. Supplementation with barley grass has the potential to prevent chronic diseases, such as cancer. Here, we investigated whether barley grass could protect against hepatocellular carcinoma (HCC). Our data showed that administration of barley grass juice attenuates tumor development in a hydrodynamic gene delivery-induced model of HCC. The expression levels of the immune cell markers Ptprc and Adgre1 were upregulated in the barley grass juice-treated and normal groups, compared to those in the vehicle group in the HCC model. Immune cells (CD45+, F4/80+, and CLEC4F + iNOS + cells) infiltration in the liver increased following barley grass juice administration. Our results indicate that barley grass could be beneficial for HCC alleviation, partly by regulating immune cell infiltration. The ingredients of barley grass affect immune cell infiltration in HCC, and the detailed mechanism requires further study. [ABSTRACT FROM AUTHOR]

G protein-coupled receptors play important roles in mediating signal transformation and physiological processes. As a new type of insecticide target, GPCRs have attracted much attention in recent years. However, GPCRs have not yet been identified in Aphis gossypii. In the present study, a total of 87 GPCRs were identified from A. gossypii , including 65 Family A, 12 Family B, 7 Family C, and 3 Family F receptors. Most of the GPCRs in A. gossypii showed considerable sequence identity, and all of them have conserved transformmembrane domains. Newly identified GPCR genes were differentially expressed in different developmental stages and tissues. Moreover, we found that 34 GPCR genes were highly overexpressed in a sulfoxaflor-resistant strain, 4 and 10 of them were highly induced by LC 15 and LC 50 of sulfoxaflor, respectively. Furthermore, silencing of two highly overexpressed GPCRs by RNAi indicated that suppression the expression of AgoGPCR48 and AgoGPCR53 significantly increased the susceptibility of A. gossypii to sulfoxaflor, suggesting that these GPCR genes may be associated with sulfoxaflor resistance in A. gossypii. Our results imply that the overexpression of GPCR genes contribute to the sulfoxaflor resistance development in A. gossypii and provide useful targets for developing novel insecticides to manage this pest. • A total of 87 GPCR genes were identified from A. gossypii. • Identified GPCR genes differentially expressed at different developmental stages and tissues. • Overexpression of GPCR genes could be involved in the resistance of A. gossypii to sulfoxaflor. [ABSTRACT FROM AUTHOR]

Sheng Mai Yin (SMY) has therapeutic effects on myocardial infarction (MI), heart failure (HF), diabetic cardiomyopathy (DCM), and myocarditis. To study whether SMY can relieve pyroptosis and play a protective role in diabetic cardiomyopathy, a molecular docking technique was used to predict the possible mechanism of SMY against DCM. Then, a DCM rat model was induced by intraperitoneal injection of streptozotocin (STZ), divided into 5 groups: the DM group (model), SMY-L group (2.7 mL/kg SMY), SMY-M group (5.4 mL/kg SMY), SMY-H group (10.8 mL/kg SMY), and Met group (120 mg/kg metformin). Rats in the CTL group (control) and DM group were given normal saline. After 8 weeks, the levels of blood glucose, lipids, and myocardial enzymes were detected according to the kit instructions. Cardiac function was detected by echocardiography. HE and Masson were used to observing the pathological changes, collagen deposition, and collagen volume fraction (CVF). The apoptosis rate of cardiomyocytes was determined by Tunel. The IL-1β level was determined by ELISA and RT-PCR. The expressions of NLRP3, caspase-1, and GSDMD were measured using RT-PCR and Western blotting. The docking results suggested that SMY may act on NLRP3 and its downstream signal pathway. The in vivo results showed that SMY could reduce blood glucose and lipid levels, improve heart function, improve histopathological changes and myocardial enzymes, and alleviate cardiomyocyte apoptosis and myocardial fibrosis. SMY inhibited the mRNA and protein expressions of NLRP3, ASC, Caspase-1, and GSDMD and IL-1β production. SMY can reduce DCM by regulating the NLRP3/caspase-1 signaling pathway, providing a new research direction for the treatment of DCM. [ABSTRACT FROM AUTHOR]

Roselle (Hibiscus sabdariffa L.) is an annual herbaceous plant of the genus Hibiscus in family Malvaceae. Roselle calyxes are rich in anthocyanins, which play important roles in human health. However, limited information is available on anthocyanin biosynthesis in the roselle calyx. In this study, transcriptomic and metabolomic analyses were performed to identify the key genes involved in anthocyanin biosynthesis in the roselle calyx. Three roselle cultivars with different calyx colors, including FZ-72 (red calyx, R), Baitao K (green calyx, G), and MG5 (stripped calyx, S), were used for metabolomic analyses with UPLC-Q-TOF/MS and RNA-seq. Forty-one compounds were quantified, including six flavonoids and 35 anthocyanins. The calyx of FZ-72 (red calyx) had the highest contents of anthocyanin derivatives such as delphinidin-3-O-sambubioside (955.11 μg/g) and cyanidin-3-O-sambubioside (531.37 μg/g), which were responsible for calyx color, followed by those in MG5 (stripped calyx) (851.97 and 330.06 μg/g, respectively). Baitao K (green calyx) had the lowest levels of these compounds. Furthermore, RNA-seq analysis revealed 114,415 differentially expressed genes (DEGs) in the calyxes at 30 days after flowering (DAF) for the corresponding cultivars FZ-72 (R), Baitao K (G), and MG5(S). The gene expression levels in the calyxes of the three cultivars were compared at different flowering stages, revealing 11,555, 11,949, and 7177 DEGs in R vs. G, R vs. S, and G vs. S, respectively. Phenylpropanoid and flavonoid biosynthesis pathways were found to be enriched. In the flavonoid pathway, 29, 28, and 27 genes were identified in G vs. R, G vs. S, and S vs. R, respectively. In the anthocyanin synthesis pathway, two, two, and one differential genes were identified in the three combinations; these differential genes belonged to the UFGT gene family. After joint analysis of the anthocyanin content in roselle calyxes, nine key genes belonging to the CHS, CHI, UFGT, FLS, ANR, DFR, CCoAOMT, SAT, and HST gene families were identified as strongly related to anthocyanin synthesis. These nine genes were verified using qRT-PCR, and the results were consistent with the transcriptome data. Overall, this study presents the first report on anthocyanin biosynthesis in roselle, laying a foundation for breeding roselle cultivars with high anthocyanin content. [ABSTRACT FROM AUTHOR]

Background: The repair of cranio-maxillofacial bone defects remains a formidable clinical challenge. The Ets variant 2 (ETV2) transcription factor, which belongs to the E26 transformation-specific (ETS) family, has been reported to play a key role in neovascularization. However, the role of ETV2 in the osteogenesis of human dental pulp stem cells (hDPSCs) remains unexplored. Methods: Transgenic overexpression of ETV2 was achieved using a lentiviral vector, based on a Dox-inducible system. The effects of Dox-induced overexpression of ETV2 on the osteogenesis of hDPSCs were evaluated by quantitative real-time polymerase chain reaction (qRT-PCR), western blot, immunofluorescence staining, alkaline phosphatase (ALP) staining, and Alizarin Red S (ARS) staining. Additionally, RNA-sequencing (RNA-Seq) analysis was performed to analyze the underlying mechanisms of ETV2-induced osteogenesis. Additionally, the role of ETV2 overexpression in bone formation in vivo was validated by animal studies with a rat calvarial defect model and a nude mice model. Results: Our results demonstrated that ETV2 overexpression significantly upregulated the mRNA and protein expression levels of osteogenic markers, markedly enhanced ALP activity, and promoted matrix mineralization of hDPSCs. Moreover, the results of RNA-Seq analysis and western blot showed that the ERK/MAPK and PI3K-Akt signaling pathways were activated upon transgenic overexpression of ETV2. The enhanced osteogenic differentiation of hDPSCs due to ETV2 overexpression was partially reversed by treatment with inhibitors of ERK/MAPK or PI3K-AKT signaling. Furthermore, the results of in vivo studies demonstrated that ETV2 overexpression improved bone healing in a rat calvarial defect model and increased ectopic bone formation in nude mice. Conclusions: Collectively, our results indicated that ETV2 overexpression exerted positive effects on the osteogenesis of hDPSCs, at least partially via the ERK/MAPK and PI3K/AKT signaling pathways. [ABSTRACT FROM AUTHOR]

Cadmium (Cd) is one of the toxic heavy metals found widely in the environment. Skin is an important target organ of Cd exposure. However, the adverse effects of Cd on human skin are still not well known. In this study, normal human skin keratinocytes (HaCaT cells) were studied for changes in cell viability, morphology, DNA damage, cycle, apoptosis, and the expression of endoplasmic reticulum (ER) stress-related genes (XBP-1, BiP, ATF-4, and CHOP) after exposure to Cd for 24 h. We found that Cd decreased cell viability in a concentration-dependent manner, with a median lethal concentration (LC50) of 11 µM. DNA damage induction was evidenced by upregulation of the level of γ-H2AX. Furthermore, Cd induced G0/G1 phase cell cycle arrest and apoptosis in a dose-dependent manner and upregulated the mRNA levels of ER stress biomarker genes (XBP-1, BiP, ATF4, and CHOP). Taken together, our results showed that Cd induced cytotoxicity and DNA damage in HaCaT cells, eventually resulting in cell cycle arrest in the G0/G1 phase and apoptosis. In addition, ER stress may be involved in Cd-induced HaCaT apoptosis. Our data imply the importance of reducing Cd pollution in the environment to reduce its adverse impacts on human skin. [ABSTRACT FROM AUTHOR]

The ZIP protein (ZRT, the IRT-like protein) is an important metal transporter that transports Zn, Fe, and other divalent metal ions in plants. In this study, we identified 20 ZIP genes in lettuce (Lactuca sativa L.). We used bioinformatics methods and renamed them according to their E value in hmmsearch. We also analyzed their gene structure, chromosomal location, constructed a phylogenetic tree, conserved motifs, performed synonymous analysis and responses to abiotic stresses. The results show that these LsZIP genes have 3–11 exons and were distributed unequally on 8 of the 9 chromosomes in lettuce. Based on phylogenetic analyses, the LsZIP gene family can be divided into three subfamilies, and the LsZIP genes within the same subfamily shared similar gene structure. The LsZIP genes contain 12 Motifs, of which Motif1 to Motif8 are widely distributed in group Ⅰ. Furthermore, the LsZIP gene contains numerous hormones and anti-stress response elements. Real-time quantitative PCR demonstrated that most LsZIP genes is up-regulated under the elemental stress in this experiment, indicating that they are positively regulated. But different elemental stressors can induce the expression of LsZIP gene to varying degrees. The LsZIP genes also change in response to different elemental stresses. The present study serves as a basic foundation for future functional studies on the lettuce ZIP family. [ABSTRACT FROM AUTHOR]

The development of high-throughput omics technologies has enabled the quantification of vast amounts of genes and gene products in the whole genome. Pathway enrichment analysis (PEA) provides an intuitive solution for extracting biological insights from massive amounts of data. Topology-based pathway analysis (TPA) represents the latest generation of PEA methods, which exploit pathway topology in addition to lists of differentially expressed genes and their expression profiles. A subset of these TPA methods, such as BPA, BNrich, and PROPS, reconstruct pathway structures by training Bayesian networks (BNs) from canonical biological pathways, providing superior representations that explain causal relationships between genes. However, these methods have never been compared for their differences in the PEA and their different topology reconstruction strategies. In this study, we aim to compare the BN reconstruction strategies of the BPA, BNrich, PROPS, Clipper, and Ensemble methods and their PEA and performance on tumor and non-tumor classification based on gene expression data. Our results indicate that they performed equally well in distinguishing tumor and non-tumor samples (AUC > 0.95) yet with a varying ranking of pathways, which can be attributed to the different BN structures resulting from the different cyclic structure removal strategies. This can be clearly seen from the reconstructed JAK-STAT networks by different strategies. In a nutshell, BNrich, which relies on expert intervention to remove loops and cyclic structures, produces BNs that best fit the biological facts. The plausibility of the Clipper strategy can also be partially explained by intuitive biological rules and theorems. Our results may offer an informed reference for the proper method for a given data analysis task. [ABSTRACT FROM AUTHOR]

Trichoderma atroviride SS003 is a mycoparasite of Cronartium ribicola, and it has a significant destructive effect on rust aeciospores. Based on transcriptome sequencing results and qPCR validation, the expression of a chitinase gene named CHI10 was upregulated after induction for 24, 72 and 120 h. A 1.3‐kb cDNA of CHI10 was obtained by RT‐PCR from SS003 mycelium co‐cultured with the cell walls of the aeciospores for 24 h. After the prokaryotic expression of CHI10 gene in Escherichia coli, a recombinant 46.0 kD protein was obtained, and the target fusion protein was partially purified, which was shown to have destructive effects on the cell wall of aeciospores at 40–55°C. This chitinase may be associated with the mycoparasitism of T. atroviride on aeciospores of C. ribicola. [ABSTRACT FROM AUTHOR]

Aim. Chlorogenic acid (CGA) is a natural polyphenolic compound found in human dietary products. Previous studies have confirmed that CGA has many biological activities, such as regulating glucose and lipid metabolism and improving insulin resistance. However, its underlying mechanisms of action remains unclear. Here, we demonstrate the protective effects and molecular mechanisms of action of CGA in reducing weight gain and hyperlipidemia in mice fed with a high-fat diet (HFD). Methods and Results. C57BL/6 mice were fed with normal chow or HFD; half of the mice in each group received CGA treatment by oral gavage for 16 weeks. CGA treatment was found to significantly inhibit HFD-induced weight gain and hyperlipidemia and increased energy expenditure by promoting the expression of genes involved in thermogenesis and mitochondrial biogenesis. Furthermore, CGA was shown to inhibit the enterohepatic farnesoid X receptor (FXR) fibroblast growth factor 15 (FGF15) pathway and changes serum bile acid (BA) pool, thereby contributing to the increased expression of cholesterol 7 α-hydroxylase (CYP7A1). Conclusions. CGA increases the metabolic elimination of cholesterol by inhibiting the enterohepatic FXR/FGF15 pathway. [ABSTRACT FROM AUTHOR]

Background: Epidemiological studies have confirmed that abnormal circadian rhythms are associated with tumorigenesis in breast cancer. However, few studies have investigated the pathological roles of rhythm genes in breast cancer progression. In this study, we aimed to evaluate the aberrant expression of 32 rhythm genes in breast cancer and detect the pathological roles and molecular mechanisms of the altered rhythm gene in regulating the progression of triple negative breast cancer (TNBC). Methods: The aberrant expression of rhythm genes in breast cancer was screened by searching the GEPIA database and validated by using qRT-PCR and immunohistochemistry staining. Bioinformatics analysis combined with luciferase reporter experiment and chromatinimmunopercitation (ChIP) were used to investigate the molecular mechanism about aberrant expression of identified rhythm gene in breast cancer. The pathological roles of identified rhythm gene in TNBC progression was evaluated by colony formation assay, wound healing experiment, transwell assay, subcutaneous tumor formation and the mouse tail vein injection model through gain-of-function and loss-of-function strategies respectively. mRNA array, bioinformatics analysis, luciferase reporter experiment, ChIP and immunoflurescence assay were employed to investigate the key molecules and signaling pathways by which the identified rhythm gene regulating TNBC progression. Results: We identified that nuclear factor interleukin 3 regulated (NFIL3) expression is significantly altered in TNBC compared with both normal breast tissues and other subtypes of breast cancer. We found that NFIL3 inhibits its own transcription, and thus, downregulated NFIL3 mRNA indicates high expression of NFIL3 protein in breast cancer. We demonstrated that NFIL3 promotes the proliferation and metastasis of TNBC cells in vitro and in vivo, and higher expression of NFIL3 is associated with poor prognosis of patients with TNBC. We further demonstrated that NFIL3 enhances the activity of NF-κB signaling. Mechanistically, we revealed that NFIL3 directly suppresses the transcription of NFKBIA, which blocks the activation of NF-κB and inhibits the progression of TNBC cells in vitro and in vivo. Moreover, we showed that enhancing NF-κB activity by repressing NFKBIA largely mimics the oncogenic effect of NFIL3 in TNBC, and anti-inflammatory strategies targeting NF-κB activity block the oncogenic roles of NFIL3 in TNBC. Conclusion: NFIL3 promotes the progression of TNBC by suppressing NFKBIA transcription and then enhancing NF-κB signaling-mediated cancer-associated inflammation. This study may provide a new target for TNBC prevention and therapy. [ABSTRACT FROM AUTHOR]

Background. The interleukin-1 receptor-associated kinases (IRAK) family genes, indispensable mediators of interleukin-1 receptor (IL1R) and Toll-like receptor (TLR)-inflammatory signaling, may be involved in the biological function of human cancers due to the crucial roles of inflammation in tumor development. Though a little research has demonstrated the function of individual IRAK family members in specific tumors, comprehensive analysis is still lacking in pan-cancer. Methods. We analyzed the mRNA expression landscape, mutation, and prognosis value of IRAK genes based on The Cancer Genome Atlas (TCGA), cBioPortal, GlioVis, and Rembrandt databases. The correlation between the expression of IRAK genes and tumor microenvironment (TME), Stemness score, and immune subtypes was explored. Western blot, cell proliferation, apoptosis, migration assays, and xenograft models were utilized in this study. Results. We found that the expression of IRAK genes extensively changed and was related to patient survival in pan-cancer. Besides, IRAK family genes were correlated with TME, Stemness score, and immune subtypes in most cases. Given that high expression of all IRAK family members predicted poor prognosis in low-grade glioma (LGG), the oncogenic function of the highest expressed IRAK1 in LGG has been confirmed in vitro and in vivo. IRAK1 was uncovered to inhibit cell apoptosis and augment malignancy of LGG in vitro and in vivo. Conclusion. These findings revealed the potential targets of IRAK family genes in pan-cancer and provided insights for further investigation of IRAK1 as a novel oncogenic gene in LGG. [ABSTRACT FROM AUTHOR]

It is uncertain whether Bmi-1 deficiency could lead to skin aging by redox imbalance and DNA damage. In this study, we first confirmed that Bmi-1 had a relatively high expression level in the skin and Bmi-1 expression levels gradually decreased with age. Then, we studied the role of Bmi-1 in the skin using a Bmi-1-/- mouse model. Bmi-1-/- mice were supplemented with or without pyrroloquinoline quinone (PQQ) for 5 weeks, and their skin phenotypes were compared with Bmi1-/- and wild-type littermates. Our results showed that Bmi-1-/- mice displayed decreased vertical thickness of skin, sparse hair follicles, and thinner and more irregular collagen bundles. Mechanistically, increased oxidative stress with reducing antioxidant capacity and induced DNA damage occurred in Bmi-1-/- mice. Subsequently, this would lead to reduced cell proliferation, increased cell senescence and matrix metalloproteinases (MMPs), and the degradation of fibroblast function and further reduce collagen synthesis. All pathological alterations in the skin of Bmi-1-/- mice were alleviated by PQQ supplementation. These results demonstrated that Bmi-1 might play a key role in protection from skin aging by maintaining redox balance and inhibiting DNA damage response and will be a novel and potential target for preventing skin aging. [ABSTRACT FROM AUTHOR]

Objectives: This study aimed to investigate the gene expression of angiogenic marker in surgically treated jawbones and femur on a rat model administrated with zoledronic acid. Results: No soft tissue fenestration or bone exposure was found in femur. Delayed soft tissue healing was found in both ZA group (3 in mandible, 4 in maxilla) and control group (1 in mandible, 2 in maxilla), while exposed bone was found only in the ZA group (1 in maxilla, 2 in mandible). RT-PCR analysis demonstrated no significant difference in gene expression of angiogenetic markers between ZA-treated and control groups in femur and mandible. In the maxilla, the expression of VEGFA and VEGFR-2 in medium-term ZA group was significantly down-regulated compared with that in the control. The ZA treatment does not change significantly the expression of the angiogenic factors in femur and mandible, but significantly downregulates the expression in maxilla in this rat model. The angiogenesis inhibition may contribute to the development of MRONJ but does not play a key role. [ABSTRACT FROM AUTHOR]

• Tissue-Specific Expression: ADAR1 in liver cancer (LIHC) and kidney cancers (KICH, KIRC, KIRP) informs tissue-specific roles. • ADAR1 Prognostic Correlation: KIRC - Higher expression, better prognosis; KIRP, LIHC - Lower expression, better prognosis. • Tumor Microenvironment Influence: Contrasting effects of ADAR1 on tumor microenvironment in KIRC and LIHC. • Stromal-Specific Cell Type Associations: ADAR1 is linked to blood and lymphatic endothelial cells. • Therapeutic Implications: Insights into the tumor microenvironment advance immunotherapy and precision medicine. Adenosine deaminase acting on RNA 1 (ADAR1) is an RNA-editing enzyme that significantly impacts cancer progression and various biological processes. The expression of ADAR1 mRNA has been examined in multiple cancer types using The Cancer Genome Atlas (TCGA) dataset, revealing distinct patterns in kidney chromophobe (KICH), kidney renal clear cell carcinoma (KIRC), kidney renal papillary cell carcinoma (KIRP), and liver hepatocellular carcinoma (LIHC) compared to normal controls. However, the reasons for these differential expressions remain unclear. In this study, we performed RT-PCR and western blotting (WB) to validate ADAR1 expression patterns in clinical tissue samples. Survival analysis and immune microenvironment analysis (including immune score and stromal score) were conducted using TCGA data to determine the specific cell types associated with ADAR1, as well as the key genes in those cell types. The relationship between ADAR1 and specific cell types' key genes was verified by immunohistochemistry (IHC), using clinical liver and kidney cancer samples. Our validation analysis revealed that ADAR1 expression was downregulated in KICH, KIRC, and KIRP, while upregulated in LIHC compared to normal tissues. Notably, a significant correlation was found between ADAR1 mRNA expression and patient prognosis, particularly in KIRC, KIRP, and LIHC. Interestingly, we observed a positive correlation between ADAR1 expression and stromal scores in KIRC, whereas a negative correlation was observed in LIHC. Cell type analysis highlighted distinct relationships between ADAR1 expression and the two stromal cell types, blood endothelial cells (BECs) and lymphatic endothelial cells (LECs), and further determined the signature gene claudin-5 (CLDN5), in KIRC and LIHC. Moreover, ADAR1 was inversely related with CLDN5 in KIRC (n = 26) and LIHC (n = 30) samples, verified via IHC. ADAR1 plays contrasting roles in LIHC and KIRC, associated with the enrichment of BECs and LECs within tumors. This study sheds light on the significant roles of stromal cells within the complex tumor microenvironment (TME) and provides new insights for future research in tumor immunotherapy and precision medicine. [ABSTRACT FROM AUTHOR]

• Electro-acupuncture at Shuigou (GV 26) can promote the multiplication of hemal endothelial cells, induce angiogenesis, treatment of cerebral infarction. • Shh induces the downstream factors to promote angiogenesis via the Gli2 pathway. • Electro-acupuncture at Shuigou (GV 26) can upregulate the expression of the Shh signaling pathway factors Shh, Ptch, Smo, and Gli2 mRNA and proteins. To study the factors of the Sonic Hedgehog (Shh) signaling pathway after permanent cerebral ischemic and the effects by acupuncture. Male Wistar rats were divided into Electro-acupuncture (EA) group, Model Control (MC) group, and blank control (Control) group. EA and MC were divided into 9 phases, namely 1 h, 3 h, 6 h, 9 h, 12 h, 24 h, 3 d, 7 d, and 12 d after the operation. The neurological deficits and permanent cerebral ischemic volume were observed. The immunofluorescence method was used to examine the angiogenesis. (Polymerase Chain Reaction) PCR and (Immunohistochemistry) IHC were used to test the changes in Shh, Ptch, Smo, and Gli2 mRNA and proteins. The neurological severity scores (NSS) of the Control was 0, the score of the EA group was less than that of the MC. The cerebral permanent ischemic volume of the Control was 0 %, and the EA group's was smaller than that of the MC. The expression of copositive cells in the EA group was higher than the MC's from 12 h to 12 d, and the EA group had more peripheral blood vessels. The rat brain expressions of Shh, Ptch, Smo and Gli2 mRNA and proteins in the MC was higher than that of the Control, the rat brain expression of the EA group was higher than that of the MC. EA can upregulate the expression of the Shh signaling pathway factors, thereby promoting angiogenesis. [ABSTRACT FROM AUTHOR]

The WRKY family of transcription factors (TFs) is an important gene family involved in abiotic stress responses. Although the roles of WRKY TFs in plant abiotic stress responses are well studied, little is known about the stress-induced changes in WRKY family in Platycodon grandiflorus. 42 PgWRKY genes in seven subgroups were identified in the P. grandiflorus genome. The content of eight platycodins in P. grandiflorus was investigated under cold, heat, and drought stresses. Platycodin D levels significantly increased under three abiotic stresses, while the content changes of other platycodins varied. Transcriptome analysis showed that different WRKY family members exhibited varied expression patterns under different abiotic stresses. PgWRKY20 , PgWRKY26 , and PgWRKY39 were identified as three key candidates for temperature and drought stress responses, and were cloned and analysed for sequence characteristics, gene structure, subcellular localisation, and expression patterns. The RT-qPCR results showed that PgWRKY26 expression significantly increased after heat stress for 48 h, cold stress for 6 h, and drought stress for 2 d (DS_2 d). The PgWRKY39 expression level significantly increased at DS_2 d. This study provides a theoretical basis for clarifying the molecular mechanism of the abiotic stress responses of the WRKY gene family in P. grandiflorus. • We firstly carried out the genome-wide identification of WRKY family in Platycodon grandiflorus. • Three WRKY genes were identified as key candidates for temperature and drought stresses. • PgWRKY26 is vital for the response to temperature and drought stresses, and PgWRKY39 is important in responsing to drought stress. [ABSTRACT FROM AUTHOR]

Sophorae Flavescentis Radix (Kushen) is the primary herb component of Compound Kushen Injection (CKI), an approved clinical treatment for tumors. Despite CKI's widespread use, the underlying mechanisms of Kushen regarding microRNA-target and pathway remain unclear in non-small cell lung cancer (NSCLC). This study aimed to elucidate the crucial miRNAs-targets and pathways responsible for the Kushen's impact on NSCLC. CCK8, colony formation, and apoptosis assays were performed to assess the effects of Kushen on NSCLC cells. Subsequently, we treated the A549 cell line with varying concentrations of Kushen to obtain mRNA and miRNA expression profiles. A DE (differentially expressed) miRNAs-DEGs network was then constructed to identify the critical miRNA-mRNA interaction influenced by Kushen. Furthermore, we performed clinical significance and prognosis analyses of hub genes to narrow down key genes and their corresponding miRNAs. Finally, the effects of Kushen on critical miRNA-mRNA interaction and related pathway were verified by in vitro and in vivo experiments. In this study, we initially demonstrated that Kushen significantly inhibited cell proliferation, suppressed colony formation, and induced apoptosis in the A549 cells, PC9 cells, and the A549 zebrafish xenograft model. Through expression profile analysis, a DE miRs-DEGs network was constructed with 16 DE miRs and 68 DEGs. Through the network analysis and expression validation, we found Kushen could significantly down-regulate miR-183-5p expression and up-regulate EGR1 expression. Additionally, Kushen affected the PTEN/Akt pathway, increasing PTEN expression and decreasing pAkt expression. Finally, matrine, the essential active compound of Kushen, also inhibited cell growth, induced apoptosis, and regulated miR-183-5p/EGR1 and PTEN/AKT pathway. Altogether, these findings supported the critical role of miR-183-5p/EGR1 and the PTEN/AKT pathway in the beneficial effects of Kushen on NSCLC, highlighting the therapeutic potential of Kushen in NSCLC treatment. [Display omitted] • Kushen inhibited NSCLC cell proliferation and induced apoptosis in vitro and in vivo. • Kushen regulated miR-183-5p/EGR1 and PTEN/AKT pathway in NSCLC. • Matrine inhibited NSCLC cell proliferation and induced apoptosis in vitro and in vivo. • Matrine regulated miR-183-5p/EGR1 and PTEN/AKT pathway in NSCLC. • Multi-omic data analysis revealed the molecular mechanism of Kushen treating NSCLC. [ABSTRACT FROM AUTHOR]

Chromatin remodeling proteins modulate nucleosome dynamic to affect global gene expression and other cellular processes. Their roles in the regulation of plant growth and development have been widely reported, but their roles in plant stress resistance, especially disease resistance, have not been extensively investigated. Here, we show that the Arabidopsis Immunity Switch (ISWI) chromatin-remodeling factors CHR11 and CHR17, are negative regulators of plant disease resistance. The loss of both CHR11 and CHR17 function led to upregulation of a large set of defense response genes in the absence of pathogen infection. The chr11 single mutant showed enhanced resistance against a virulent pathogen Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). Further analysis revealed that mutation of Phytoalexin Deficient4 (PAD4) reduced the upregulation of defense gene expression as well as resistance against Pst DC3000 in the chr11 chr17 double mutant. However, mutation of PAD4 does not rescue the growth defects of chr11 chr17. Together, our study revealed a function of ISWI in repressing defense response under non-pathogenic conditions and indicates distinct target genes of ISWI in regulating plant growth and plant immunity. • ISWI represses defense response gene expression under normal growth condition. • ISWI negatively regulate resistance to bacterial pathogen in Arabidopsis. • The ISWI-regulated plant immunity is partially dependent on PAD4. [ABSTRACT FROM AUTHOR]

This study aimed to analyze the role of the FcepsilonRI (FcεRI) signaling pathway in the pathogenesis of benign lymphoepithelial lesion of lacrimal gland (LGBLEL). Transcriptomic analysis was performed on LGBLEL and orbital cavernous hemangioma (CH) patients diagnosed via histopathology in Beijing Tongren Hospital, Capital Medical University, between July 2010 and October 2013. Four LGBLEL and three orbital CH patients, diagnosed between October 2018 and August 2019, were randomly selected as experimental and control groups, respectively. RT-PCR, immunohistochemical staining, and western blotting were used to verify genes and proteins related to the FcεRI signaling pathway. Transcriptomic analysis showed that the FcεRI signaling pathway was upregulated in the LGBLEL compared with the CH group. The mRNA expression levels of important genes including SYK, p38, JNK, PI3K, and ERK were significantly increased in the LGBLEL group (P = 0.0066, P = 0.0002, P = 0.0003, P < 0.0001, P < 0.0001, respectively). Immunohistochemical staining results showed that SYK, p38, and ERK were positively expressed in LGBLEL, while JNK and PI3K were not. The protein contents of P-SYK, P-p38, P-JNK, P-PI3K, and P-ERK were significantly higher in the LGBLEL than in the CH group (P = 0.0169, P = 0.0074, P = 0.0046, P = 0.0157, P = 0.0156, respectively). The FcεRI signaling pathway participates in the pathogenesis of LGBLEL. [ABSTRACT FROM AUTHOR]

Background: Human cytomegalovirus (HCMV) infection in utero is very common during pregnancy, which can lead to adverse outcomes in both pregnancy and progeny, but its pathogenesis has not been fully clarified. The decrease of extravillous cytotrophoblasts (EVT) invasion is an essential pathophysiological process of some pregnancy complications. Hippo-YAP signaling pathway plays an important role in regulating cell proliferation and apoptosis. However, whether YAP is involved in HCMV uterine infection remains to be studied. Methods: The primary EVT was cultured and infected by the HCMV strain AD169 virus in vitro. Immunofluorescence staining of HCMVpp65 antigen was conducted afterward to confirm the establishment of an infection model. The optimal virus infection dose was determined by the EVT proliferation status in vitro. Real-time PCR was performed to examine the mRNA level of major genes involved in the Hippo pathway in EVT after HCMV infection. The effect of HCMV on the expression of YAP protein in EVT was evaluated by Immunofluorescence staining and Western blot. An in vitro cell invasion assay was carried out to analyze the influence of HCMV on EVT invasion. The changes of EVT invasion was accessed by establishing YAP silencing and over-expression models using YAP1 specific siRNA and plasmid pcDH. Results: The optimal HCMV infection dose was 282.5TCID50/ml. Compared to the control group, the infection of HCMV significantly reduced the mRNA expression of Mst1, Mst2, SAV, Lats1, Lats2, Mob1, YAP1, TAZ, TEAD1-4 genes and YAP protein expression in the Hippo-YAP pathway. HCMV infection also decreased the EVT invasion. In non-infected EVT, the number of transmembrane EVT cells was significantly reduced when YAP1 gene was silenced, while it was significantly increased when YAP1 gene was over-expressed. In the HCMV-infected EVT, the number of transmembrane EVT cells significantly increased when over-expressed and eventually recovered to the level of NC. Conclusions: HCMV may decrease EVT invasion by inhibiting the expression of mRNA and protein of YAP in the Hippo-YAP signaling pathway. HCMV eventually reduces the invasion ability of EVT by inhibiting multiple genes in the Hippo-YAP signaling pathway, especially inhibiting YAP which serves as the downstream effector. [ABSTRACT FROM AUTHOR]

Primary aldosteronism is the most common form of secondary hypertension, and aldosteronoma makes up a significant proportion of primary aldosteronism cases. Aldosteronoma is also called aldosterone-producing adenoma (APA). Although there have been many studies about APA, the pathogenesis of this disease is not yet fully understood. In this study, we aimed to find out the difference of gene expression patterns between APA and nonfunctional adrenocortical adenoma (NFAA) using a weighted gene coexpression network (WGCNA) and differentially expressed gene (DEG) analysis; only the genes that meet the corresponding standards of both methods were defined as real hub genes and then used for further analysis. Twenty-nine real hub genes were found out, most of which were enriched in the phospholipid metabolic process. WISP2, S100A10, SSTR5-AS1, SLC29A1, APOC1, and SLITRK4 are six real hub genes with the same gene expression pattern between the combined and validation datasets, three of which indirectly or directly participate in lipid metabolism including WISP2, S100A10, and APOC1. According to the gene expression pattern of DEGs, we speculated five candidate drugs with potential therapeutic value for APA, one of which is cycloheximide, an inhibitor for phospholipid biosynthesis. All the evidence suggests that phospholipid metabolism may be an important pathophysiological mechanism for APA. Our study provides a new perspective regarding the pathophysiological mechanism of APA and offers some small molecules that may possibly be effective drugs against APA. [ABSTRACT FROM AUTHOR]

Inflammation response is an important reason for disc cell senescence during disc degeneration. Recently, melatonin is suggested to protect against disc degeneration. However, the effects of melatonin on annulus fibrosus (AF) cell senescence are not fully studied. The main purpose of this study was to investigate the effects of melatonin on AF cell senescence in an inflammatory environment and the underlying mechanism. Rat disc AF cells were cultured in a medium with tumor necrosis factor-α (TNF-α). Melatonin was added along with the medium to observe its protective effects. Compared with the control AF cells, TNF-α significantly declined cell proliferation potency and telomerase activity, elevated senescence-associated β-galactosidase (SA-β-Gal) activity, upregulated protein expression of senescence markers (p16 and p53), and increased reactive oxygen species (ROS) content and activity of the NF-κB pathway. However, when the TNF-α-treated AF cells were incubated with melatonin, ROS content and activity of the NF-κB pathway were decreased, and those parameters reflecting cell senescence indicated that AF cell senescence was also partly alleviated. Together, melatonin suppresses AF cell senescence through regulating the ROS/NF-κB pathway in an inflammatory environment. This study sheds a new light that melatonin may be promising to retard inflammation-caused disc degeneration. [ABSTRACT FROM AUTHOR]

Dichomitus squalens is an efficient white-rot fungus that generates a wide range of extracellular enzymes to degrade lignocellulose in nature. Although a protoplast-mediated transformation method for D. squalens has been developed, the transformation efficiency remains low. Here, we established a highly efficient Agrobacterium tumefaciens -mediated transformation (ATMT) procedure for D. squalens by transferring a binary vector harboring the neomycin phosphotransferase II (nptII) resistance gene fused with DsRed-Express2 , under the control of the native glyceraldehyde-3-phosphate dehydrogenase (GPD) gene promoter. Key factors affecting the efficiency of transformation were tested. A. tumefaciens EHA105 strain with a cell density of 0.4 OD 600nm and 96 h co-cultivation resulted in the highest transformation efficiency, with an average of 98 ± 11 transformants per co-cultivation plate. Besides, the strong expression of DsRed-Express2 indicates the effectiveness of the DsGPD promoter in driving gene expression in D. squalens. This ATMT system of D. squalens would be beneficial for its molecular genetic studies. • Establishment and optimization of the Agrobacterium tumefaciens –mediated transformation method for Dichomitus squalens. • An average of 98 ± 11 transformants per co-cultivation plate was obtained. • Homologous promoter of DsGPD efficiently drives the expression of the nptII - DsRed Express2 fusion gene. • Transgenes were expressed stably in D. squalens. [ABSTRACT FROM AUTHOR]

Cardiovascular diseases have been closely linked to abnormal epigenetic regulation. In the context of epigenetic regulation, BRG1, a pivotal SWI/SNF chromatin remodeling enzyme, emerges as a key epigenetic regulator with significant impact on the development and progression of cardiovascular disorders. From the perspective of epigenetic regulation of cardiovascular diseases, BRG1 emerges as a pivotal SWI/SNF chromatin remodeling enzyme, functioning as a key epigenetic regulator. It exerts substantial influence on the development and progression of cardiovascular disorders by exerting precise control over gene expression and protein levels. Therefore, a comprehensive understanding of BRG1's epigenetic regulatory role in cardiovascular disease is essential for unraveling its underlying pathophysiological mechanisms. This paper summarizes and discusses the function of BRG1 in the epigenetic regulation of cardiovascular diseases. [ABSTRACT FROM AUTHOR]

Polymerase chain reaction (PCR) is a widely used technique in gene expression analysis, diagnostics, and various molecular biology applications. However, the accuracy and sensitivity of PCR can be compromised by primer–template mismatches, potentially leading to erroneous results. In this study, we strategically designed 111 primer–template combinations with varying numbers, types, and locations of mismatches to meticulously assess their impact on qPCR performance while two distinctly different types of DNA polymerases were used. Notably, when a single-nucleotide mismatch occurred at the 3' end of the primer, we observed significant decreases in the analytical sensitivity (0–4%) with Invitrogen™ Platinum™ Taq DNA Polymerase High Fidelity, while the analytical sensitivity remained unchanged with Takara Ex Taq Hot Start Version DNA Polymerase. Leveraging these findings, we designed a highly specific PCR to amplify Babesia while effectively avoiding the genetically close Theileria. Through elucidating the critical interplay between types of DNA polymerases and primer–template mismatches, this research provides valuable insights for improving PCR accuracy and performance. These findings have important implications for researchers aiming to achieve robust qPCR results in various molecular biology applications. [ABSTRACT FROM AUTHOR]

Heart failure (HF) is a global pandemic cardiovascular disease with increasing prevalence, but the pathogenesis remains to be elucidated. The present study aimed to investigate the underlying mechanism in heart failure (HF) using bioinformatics and experimental validation. A HF-associated dataset GSE84796 was downloaded from the Gene Expression Omnibus database and differentially expressed genes (DEGs) were screened for using Bayes method in the Limma package. Kyoto Encyclopedia of Genes and Genomes pathway analysis was used to perform pathway enrichment analysis of these DEGs using The Database for Annotation, Visualization and Integrated Discovery. A protein-protein interaction (PPI) network of DEG-encoded proteins was subsequently constructed using the Search tool for the Retrieval of Interacting Genes/Proteins, and a transcription factor (TF)/miRNA-target network was constructed according to the WEB-based Gene SeT AnaLysis Tookit. The expression levels of microRNA (miRNA/miR)-155, G-protein coupled receptor 18 (GRP18) and E26 transformation-specific transcription factor 2 (ETS2) were analyzed in clinical HF samples, and functional validations were performed in H9c2 (2-1) cells. A total of 419 DEGs were identified, including 366 upregulated genes and 53 downregulated genes. The upregulated DEGs were significantly enriched in the pathways of 'cytokine-cytokine receptor interaction', 'natural killer cell mediated cytotoxicity' and 'primary immunodeficiency'. A total of two functional modules were identified in the PPI network: Module A was enriched in 3 KEGG pathways and module B was enriched in 15 KEGG pathways. Furthermore, a total of three miRNAs and eight TFs were identified in the TF/miRNA-target network. Specifically, GPR18 was discovered to be targeted by both ETS2 and miR-155. Clinical validation revealed that the expression levels of miR-155 were significantly decreased in the HF samples, whereas the expression levels of ETS2 and GPR18 were significantly increased in HF samples. In conclusion, the present study suggested that GPR18 may be a target of ETS2 and miR-155, and miR-155 may regulate cell viability and apoptosis in H9c2 (2-1) cells through targeting and regulating GPR18. [ABSTRACT FROM AUTHOR]

Background: Histological grade (HG) is commonly adopted as a prognostic factor for ER-positive breast cancer patients. However, HG evaluation methods, such as the pathological Nottingham grading system, are highly subjective with only 50–85% inter-observer agreements. Specifically, the subjectivity in the pathological assignment of the intermediate grade (HG2) breast cancers, comprising of about half of breast cancer cases, results in uncertain disease outcomes prediction. Here, we developed a qualitative transcriptional signature, based on within-sample relative expression orderings (REOs) of gene pairs, to define HG1 and HG3 and reclassify pathologically-determined HG2 (denoted as pHG2) breast cancer patients. Results: From the gene pairs with significantly stable REOs in pathologically-determined HG1 (denoted as pHG1) samples and reversely stable REOs in pathologically-determined HG3 (denoted as pHG3) samples, concordantly identified from seven datasets, we extracted a signature which could determine the HG state of samples through evaluating whether the within-sample REOs match with the patterns of the pHG1 REOs or pHG3 REOs. A sample was classified into the HG3 group if at least a half of the REOs of the 10 gene pairs signature within this sample voted for HG3; otherwise, HG1. Using four datasets including samples of early stage (I–II) ER-positive breast cancer patients who accepted surgery only, we validated that this signature was able to reclassify pHG2 patients into HG1 and HG3 groups with significantly different survival time. For the original pHG1 and pHG3 patients, the signature could also more accurately and objectively stratify them into distinct prognostic groups. And the up-regulated and down down-regulated genes in HG1 compared with HG3 involved in cell proliferation and extracellular signal transduction pathways respectively. By comparing with existing signatures, 10-GPS was with prognostic significance and was more aligned with survival of patients especially for pHG2 samples. Conclusions: The transcriptional qualitative signature can provide an objective assessment of HG states of ER-positive breast cancer patients, especially for reclassifying patients with pHG2, to assist decision making on clinical therapy. [ABSTRACT FROM AUTHOR]

In this study, the mineral-weathering bacterium Pseudomonas azotoformans F77, which was isolated from the soil of a debris flow area, was evaluated for its weathering activity under direct contact with biotite or without contact. Then, biotite-weathering behaviors of strain F77, mutants that had been created by deleting the gcd and adh genes (which are involved in gluconic acid metabolism and pilus formation, respectively), and the double mutant F77ΔgcdΔadh were compared. The relative gene expression levels of F77 and its mutants F77Δgcd and F77Δadh were also analyzed in the presence of biotite. Direct contact with biotite increased Fe and Al release from the mineral in the presence of F77. All strains had similar abilities to release Fe and Al from the mineral except for F77Δgcd and F77Δadh. Mobilized Fe and Al concentrations were decreased by up to 72, 26, and 87% in the presence of F77Δgcd, F77Δadh, and F77ΔgcdΔadh, respectively, compared to levels observed in the presence of F77 during the mineral-weathering process. Gluconic acid production was decreased for F77Δgcd and F77ΔgcdΔadh, while decreased cell attachment on the mineral surface was observed for F77Δadh, compared to findings for F77. The F77 genes involved in pilus formation and gluconic acid metabolism showed increased expression levels in the presence of biotite. The results of this study showed important roles for the genes involved in gluconic acid metabolism and pilus formation in mineral weathering by F77 and demonstrated the distinctive effect of these genes on mineral weathering by F77. [ABSTRACT FROM AUTHOR]

Background: Preimplantation embryo development is a highly ordered sequence of processes and it requires a precise temporal and spatial control of gene expression. Alternative splicing (AS) is a crucial process that changes the genomic instructions into functional proteins, playing a critical role in the regulation of gene expression. Therefore, studies of AS can significantly improve our understanding of transcription and splicing events in preimplantation embryo development. Results: To study signatures of AS in embryo development, we firstly identified the critical stage for gene transcription during the preimplantation embryo development. By analyzing single cells RNA-seq (scRNA-seq) data, we found that the two-cell stage is a critical stage for gene transcription in preimplantation embryo development. Further study showed that AS was widespread in preimplantation embryo development, especially at the two-cell stage. In combination with high-throughput chromosome conformation (Hi-C) data, we demonstrated that AS genes were highly enriched in TAD boundaries, while they had no relationship with the A/B compartment and TAD. Conclusion: Our results provide new insight into the relationship among AS, gene transcription and chromatin structure in preimplantation embryo development. [ABSTRACT FROM AUTHOR]

Oil palm (Elaeis guineensis Jacq.) is a representative tropical oil crop that is sensitive to low temperature. Oil palm can experience cold damage when exposed to low temperatures for a long period. During these unfavorable conditions, a series of gene induction/repression and physico-chemical changes occur in oil palm. To better understand the link between these events, we investigated the expression levels of various genes (including COR410, COR413, CBF1, CBF2, CBF3, ICE1-1, ICE1-2, ICE1-4, SIZ1-1, SIZ1-2, ZAT10, ZAT12) and the accumulation of osmolytes (proline, malondialdehyde and sucrose). Likewise, the activity of superoxide dismutase (SOD) in oil palm under cold stress (4°C, 8°C and 12°C) was examined. The results showed a clear link among the expression of CBFs (especially CBF1 and CBF3) and the all genes examined under cold stress (12°C). The expression of CBF1 and CBF2 also exhibited a positive link with the accumulation of sucrose and proline under cold stress in oil palm. At 4°C, the proline content exhibited a very significant correlation with electrolyte leakage in oil palm. The results of this study provide necessary information regarding the mechanism of the response and adaption of oil palm to cold stress. Additionally, they offer clues for the selection or development of cold-tolerant cultivars from the available germplasms of oil palm. [ABSTRACT FROM AUTHOR]

Ogawa and Inaba are two main serotypes of O1 V. cholerae and alternate among cholera epidemics. The rfbT gene encodes a methyltransferase and is required for Ogawa serotype. The Inaba serotype is the consequence of genetic alterations in rfbT gene which results in loss-of-function enzyme product. However, the expression and regulation of rfbT has not been understood yet. Here we demonstrated that a global regulator, cAMP receptor protein (CRP), positively regulates rfbT transcription through a non-canonical CRP binding site (CBS) in its promoter region. This finding is supported by the analyses of rfbT mRNA abundance, rfbT – lacZ fusions and electrophoretic mobility shift assay (EMSA). The analyses of rfbT mRNA level in wild type (WT), Δ crp , and lower or higher level of cAMP backgrounds revealed that CRP is required for rfbT expression in response to intracellular cAMP level. Subsequent rfbT – lacZ fusions and EMSA collectively displayed that cAMP-CRP complex transcriptionally activates rfbT through directly binding to CBS in rfbT promoter region. Consistently, serological microagglutination test showed that crp deletion resulted in at least 4-fold decrease in titer of Ogawa serum compared to its WT. These results expanded our knowledge of understanding the genetic determinants and probable regulatory mechanism of V. cholerae O1 serotype shift between Ogawa and Inaba. • CRP up-regulates serotype-shifting gene rfbT expression at transcriptional level in V. cholerae O1. • CRP directly binds to a non-canonical cis -acting element in rfbT promoter region. • CRP participates in the maintenance of Ogawa specific serological phenotype of V. cholerae O1. [ABSTRACT FROM AUTHOR]

Omega-3 has been proposed as an antitumor substance that suppresses the growth and metastasis of multiple types of tumor cells, including lung cancer, but the specific mechanisms involved remain obscure. Our previous studies showed that the expression of chemokine ligand 18 was related to the migration and metastasis of non-small cell lung cancer. Here, we aim to explore whether omega-3 inhibits invasion and metastasis of NSCLC by regulating the expression of CCL18. The expression of CCL18, metastasis- and epithelial-mesenchymal transition (EMT)-related genes at mRNA and protein levels in NSCLC cell lines were detected by RT-qPCR and Western blot, respectively. The metastatic and invasive capability of NSCLC cells were evaluated by scratch wound healing and Transwell assays, respectively. Our results showed that the level of CCL18 is positively associated with metastatic ability of NSCLC cells. Docosahexaenoic acid, an important long-chain, polyunsaturated omega-3 (n−3) fatty acid, significantly inhibited invasion and metastasis of NSCLC cells, and concomitantly downregulated the expression of metastasis- and EMT-related genes and p-STAT3 signaling pathway. Additionally, we found that DHA inhibited CCL18 expression in lung cancer cells, while overexpression of CCL18 effectively reversed DHA-mediated downregulation in the expression of metastasis- and EMT-related genes and p-STAT3 signaling as well as DHA-mediated inhibitory effect on metastasis and invasion of NSCLC cells. DHA inhibits NSCLC cell invasion and metastasis possibly through targeted inhibition of CCL18/ STAT3 signaling pathway and EMT process. [ABSTRACT FROM AUTHOR]

DNA methylation is an important epigenetic mechanism for phenotypic diversification in all forms of life. We previously described remarkable cell-to-cell heterogeneity in epigenetic pattern within a clonal population of Streptococcus pneumoniae, a leading human pathogen. We here report that the epigenetic diversity is caused by extensive DNA inversions among hsdSA , hsdSB , and hsdSC, three methyltransferase hsdS genes in the Spn556II type-I restriction modification (R-M) locus. Because hsdSA encodes the sequence recognition subunit of this type-I R-M DNA methyltransferase, these site-specific recombinations generate pneumococcal cells with variable HsdSA alleles and thereby diverse genome methylation patterns. Most importantly, the DNA methylation pattern specified by the HsdSA1 allele leads to the formation of opaque colonies, whereas the pneumococci lacking HsdSA1 produce transparent colonies. Furthermore, this HsdSA1-dependent phase variation requires intact DNA methylase activity encoded by hsdM in the Spn556II (renamed olony pacity eterminant or cod) locus. Thus, the DNA inversion-driven ON/OFF switch of the hsdSA1 allele in the cod locus and resulting epigenetic switch dictate the phase variation between the opaque and transparent phenotypes. Phase variation has been well documented for its importance in pneumococcal carriage and invasive infection, but its molecular basis remains unclear. Our work has discovered a novel epigenetic cause for this significant pathobiology phenomenon in S. pneumoniae. Lastly, our findings broadly represents a significant advancement in our understanding of bacterial R-M systems and their potential in shaping epigenetic and phenotypic diversity of the prokaryotic organisms because similar site-specific recombination systems widely exist in many archaeal and bacterial species. [ABSTRACT FROM AUTHOR]

The human solute carrier 26 (SLC26) gene family of anion transporters consists of 10 members (SLC26A1–A11, A10 being a pseudogene) that encode membrane glycoproteins with 14 transmembrane segments and a C-terminal cytoplasmic sulfate transporter anti-sigma antagonist domain. Thus far, mutations in eight members of the SLC26 family (A1–A6, A8, and A9) have been linked to diseases in humans. Our goal is to characterize the role of N-glycosylation and the effect of mutations in SLC26A2 and A3 proteins on their functional expression in transfected HEK-293 cells. We found that certain mutants were retained in the endoplamic reticulum via an interaction with the lectin chaperone calnexin. Some could escape protein quality control and traffic to the cell surface upon removal of the N-glycosylation sites. Furthermore, we found that loss of N-glycosylation reduced expression of SLC26A2 at the cell surface. Loss of N-glycosylation had no effect on the stability of SLC26A3, yet resulted in a profound decrease in transport activity. Thus, N-glycosylation plays three roles in the functional expression of SLC26 proteins: (1) to retain misfolded proteins in the endoplamic reticulum, (2) to stabilize the protein at the cell surface, and (3) to maintain the transport protein in a functional state. [ABSTRACT FROM AUTHOR]

Head and neck squamous cell carcinoma (HNSC) is one of most common types of cancer worldwide, and mRNAs and long non-coding RNAs (lncRNAs) have been identified as prognostic biomarkers in HNSC. In the present study, using gene expression datasets from multiple platforms, survival-associated genes in HNSC were identified. Subsequently, a combination of 17 genes (14 mRNAs and 3 lncRNA) was optimized using random forest variable hunting and a risk score model for HNSC prognosis was developed using a cohort from The Cancer Genome Atlas. Patients with high-risk scores tend to have earlier disease recurrence and lower survival rates, compared with those with low-risk scores. This observation was further validated in three independent datasets (GSE41613, GSE10300 and E-MTAB-302). Association analysis revealed that the risk score is independent of other clinicopathological observations. On the basis of the results depicted in the nomogram, the risk score performs better in 3-year survival rate prediction than other clinical observations. In summary, the lncRNA-mRNA signature-based risk score successfully predicts the survival of HNSC and serves as an indicator of prognosis. [ABSTRACT FROM AUTHOR]

Abstract Cell cycle dysregulation is typical in human cancers, and CDK4/6 inhibitors targeting cell cycle have potential antiapoptosis effect. The aim of this work is to identify the regulatory effect of Palbociclib on apoptosis of H9c2 cells induced by high glucose (HG) and to elucidate the fundamental mechanisms. It was observed that Palbociclib decreased intracellular ROS production, augmented mitochondrial membrane potential and hindered apoptosis of H9c2 cells. Palbociclib increased the Bcl-2/Bax ratio, diminished the expressions of Bax and cleaved-caspase-3, and affected the RB phosphorylation and p53 expression. Altogether, the anti-apoptotic efficacy of Palbociclib could be attributed in part to the modulation of the mitochondria apoptotic pathway. Highlights • CDK4/6 inhibitor Palbociclib protects high glucose-induced apoptosis in H9c2 cells. • Palbociclib decreased intracellular ROS production, augmented mitochondrial membrane potential of H9c2 cells. • RB phosphorylation and p53 are involved the protection effect of Palbociclib. [ABSTRACT FROM AUTHOR]

Background: Capn4 and ZEB1 play important roles in the metastasis of several types of cancer. However, the roles and relationship of Capn4 and ZEB1 in esophageal squamous cell carcinoma (ESCC) remain unclear. Methods: ESCC tumor tissues and corresponding normal esophageal epithelial tissues were obtained from 86 patients undergoing resection surgery at the Department of General Surgery, First Affiliated Hospital of Chinese PLA General Hospital from 2012 to 2017. Cell migration and invasion were examined via quantitative real‐time PCR and Western blot assay. Results: Our results indicate that both Capn4 and ZEB1 are significantly upregulated in ESCC tissues compared to corresponding adjacent tissues, and a positive correlation between expression and associated malignant characteristics was found. Silencing of Capn4 expression markedly inhibited ESCC invasion and metastasis in vitro and in vivo, and was accompanied by decreased ZEB1 expression. Furthermore, the anti‐metastasis role of Capn4 silencing was reversed by ZEB1 overexpression, whereas knockdown of ZEB1 decreased ESCC metastasis driven by the upregulation of Capn4. Mechanistically, Capn4 regulated ZEB1 expression via activation of the Wnt/β‐catenin signaling pathway in ESCC cells. Conclusion: Overall, our results show that enhanced Capn4 expression activates the Wnt/β‐catenin signaling pathway, resulting in increased ZEB1 expression and the promotion of ESCC cell metastasis. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • ZjDREB1.4 is belongs to a DREB1 branch in the grass family that is more highly represented in warm-season species. • The over-expression of ZjDREB1.4 in Arabidopsis induced the expression of multiple genes including a subset of the CBF regulon. • Plants over-expressing ZjDREB1.4 showed enhanced tolerance to high and freezing temperature stresses with only a few days delay in bolting. Abstract The DREB (dehydration-responsive element binding) protein family comprises transcription factors that can increase the survivability of a plant under abiotic stresses by regulating expression of multiple genes and altering downstream metabolism at the cost of growth retardation and developmental delay. In this study, a gene for the DREB1-type transcription factor, designated ZjDREB1.4 , was isolated from zoysiagrass (Zoysia japonica Steud.), a popular warm-season turfgrass. This gene contains a conserved AP2/ERF DNA-binding domain flanking the signature sequence of DREB1 and belongs to a DREB1 branch in the grass family that expands in the warm-season species. The expression of ZjDREB1.4 was significantly induced by chilling stress (4–15 °C), moderately induced by salt stress, and only slightly induced by drought stress. The product of ZjDREB1.4 was targeted to the nucleus and showed strong transactivation activity but weak binding to the DRE with ACCGAC as the core sequence. The ZjDREB1.4 protein bound to GCCGAC more preferentially than to ACCGAC. Overexpression of ZjDREB1.4 in Arabidopsis induced the expression of multiple genes including a part of the CBF-regulon, and moderately increased the levels of proline and soluble sugars under normal growth conditions. The transgenic Arabidopsis plants showed an increase in tolerance to high and freezing temperature stresses without obvious growth inhibition and with only a few days delay in bolting. ZjDREB1.4 is potentially useful for producing transgenic plants that are tolerant to high temperature and/or cold stresses with few negative effects. [ABSTRACT FROM AUTHOR]

Highlights • UVC induced naringin/neoeriocitrin accumulation and synthetic gene expression in D. roosii. • The inducing effects of UVC depended on irradiation dosage in separate new and old rhizomes. • Modular organization analysis revealed specific naringin/neoeriocitrin related gene expression. • WGCNA identified the hub naringin/neoeriocitrin synthetic genes in response to UVC. Abstract Drynaria roosii is a traditional medicinal fern, whose rhizome is particularly valued for its effective flavonoid components of naringin/neoeriocitrin. UV irradiation can induce flavonoid accumulation in plants, however the molecular mechanism of UVC-mediated naringin/neoeriocitrin synthesis in D. roosii has never been reported. Our HPLC-tandem mass spectrometry (MS/MS) results showed that UVC irradiation increased naringin/neoeriocitrin contents (NNCs) based on irradiation dosage in D. roosii. According to the NGS data, DEG-based heat map analysis revealed up-regulation of naringin/neoeriocitrin synthetic genes was more obvious in 12h UVC irradiation (UV dose = 81.648 kJ m−2) when compared with 24h (UV dose = 163.296 kJ m−2), especially for PAL , C 3' H and HCT in old rhizomes. Through systems biology method of modular organization analysis, we clustered 15,678 DEGs into 19 modules, and calculated correlation coefficients between modules and samples, as well as modules and NNCs. Four significant naringin-related modules were achieved and displayed high correlations with specific samples. Moreover, weighted gene co-expression network analysis results discovered that 4CL , CHS and HCT , C3H acted as the hub responsive genes to UVC irradiation involved in naringin and neoeriocitrin synthesis respectively, and presented high co-expression with MYB/bHLH-regulated DEGs. Overall, we demonstrated that UVC irradiation up-regulated the naringin/neoeriocitrin related gene expression in separate new and old rhizomes to enhance NNCs in a dose-dependent manner. Hormetic UVC dose ranges improving NNCs in D. roosii were established for the first time. Our work also provided new insights into the study of secondary metabolites in medicinal plants. [ABSTRACT FROM AUTHOR]