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Abstract Increased GP73 expression in hepatocytes from patients with acute hepatitis, through disease progression to cirrhosis and chronic liver disease suggests that progressive tissue remodeling and fibrogenesis are driving forces for GP73 upregulation. Nevertheless, details about regulation of GP73 expression and its biological functions remain elusive and await further characterization. In this study, we demonstrate that GP73 is a direct target of TGF-β1 transcriptional regulation. Its induced expression inhibits TGF-β-Smad mediated growth suppression. On the other hand, elevated GP73 results in upregulation of ERK/Akt signaling induced by TGF-β1. Mechanistically, upregulation of lipid raft and caveolae-1 induced by GP73 overexpression mediates its regulatory effect on TGF-β1 signaling. Notably, lipid raft expression is elevated in HCC tumors and tissues with higher GP73 expression yield more intensive Flotillin staining. Our results establish the linkage between GP73 and TGF-β signaling, indicating that GP73 may promote HCC tumorigenesis by selectively regulating TGF-β signaling through lipid raft modulation. Highlights • GP73 expression induced by TGF-β1 transcriptional regulation inhibits TGF-β-Smad mediated growth suppression. • Elevated GP73 results in upregulation of extracellular signal-regulated kinases (ERK) signaling. • Lipid raft and caveolae upregulation induced by GP73 overexpression mediates its regulatory effect on TGF-β signaling. • Lipid raft expression is elevated in HCC tumors, tissues with higher GP73 expression yield more intensive Flotillin staining. • GP73 may selectively regulate TGF-β signaling via lipid raft modulation and probably promotes HCC tumorigenesis. [ABSTRACT FROM AUTHOR]

Background: Osteoarthritis (OA) is a kind of chronic osteoarthropathy and degenerative joint disease. Epigenetic regulation in the gene expression dynamics has become increasingly important in OA. We performed a combined analysis of two types of microarray datasets (gene expression and DNA methylation) to identify methylation‐based key biomarkers to provide a better understanding of molecular biological mechanisms of OA. Methods: We obtained two expression profiling datasets (GSE55235, GSE55457) and one DNA methylation profiling data set (GSE63695) from the Gene Expression Omnibus. First, differentially expressed genes (DEGs) between patients with OA and controls were identified using the Limma package in R(v3.4.4). Then, function enrichment analysis of DEGs was performed using a DAVID database. For DNA methylation datasets, ChAMP methylation analysis package was used to identify differential methylation genes (DMGs). Finally, a comprehensive analysis of DEGs and DMGs was conducted to identify genes that exhibited differential expression and methylation simultaneously. Results: We identified 112 DEGs and 2,896 DMGs in patients with OA compared with controls. Functional analysis of DEGs obtained that inflammatory responses, immune responses, and positive regulation of apoptosis, tumor necrosis factor (TNF) signaling pathway, and osteoclast differentiation may be involved in the pathogenesis of OA. Cross‐analysis revealed 26 genes that exhibited differential expression and methylation in OA. Among them, ADAMTS9, FKBP5, and PFKBF3 were identified as valuable methylation‐based biomarkers for OA. Conclusion: In summary, our study identified different molecular features between patients with OA and controls. This may provide new clues for clarifying the pathogenetic mechanisms of OA. We performed the combined analysis of two types of microarray datasets (gene expression and DNA methylation) to identify methylation‐based key biomarkers to provide a better understanding of molecular biological mechanisms of osteoarthritis (OA). We identified different molecular features between patients with OA and controls and identified ADAMTS9, FKBP5, and PFKBF3 as valuable methylation‐based biomarkers for OA. [ABSTRACT FROM AUTHOR]

Background. Excessive activation of the nod-like receptor family pyrin domain containing 3(NLRP3) inflammasome plays a significant role in the progression of cardiac injury. In China, it has been well recognized that Chinese herbal medicine is markedly effective in treating cardiovascular diseases (CVDs). LuQi Formula (LQF) has been used clinically for more than 10 years and confirmed to be effective in improving cardiac function and inhibiting apoptosis. However, the specific mechanisms underlying its efficacy are mostly unknown. This study aimed to evaluate whether LQF could alleviate cardiac injury and apoptosis by regulating the NLRP3 inflammasome and the caspase-3/Bax pathway. Purpose. In this study, we investigated the effects of LQF on cardiac remodeling in a mouse model of myocardial infarction (MI) in vivo. Methods. Forty male C57BL/6 mice were randomly divided into four groups: the sham group, the model group, the LQF group, and the perindopril group, with a sample size (n) of 10 mice in each group. Except the sham group, the other groups received left anterior descending (LAD) coronary artery ligation to induce MI and then treated with LQF, perindopril, or saline. Six weeks after MI, echocardiography was used to evaluate cardiac structure and function. Myocardial tissue morphology was observed by haematoxylin and eosin (H&E) staining, and heart samples were stained with Masson's trichrome to analyse myocardial fibrosis. Myocardial hypertrophy was observed by fluorescent wheat germ agglutinin (WGA) staining. The expressions of NLRP3, ASC, Cle-caspase-1, IL-1β, TXNIP, Cle-caspase-3, Bcl-2, and Bax in heart tissues were assessed by western blot analysis. mRNA expressions of ANP and BNP in heart tissues were measured by RT-PCR. The expression of reactive oxygen species in myocardial tissue was detected by using a DCFH-DA probe. Results. Echocardiographic analysis showed that compared with the model group, the left ventricular ejection fraction (LVEF) and left ventricular fractional shortening (LVFS) in the LQF and perindopril group were increased (P < 0.05), left ventricular internal diameter end diastole (LVIDd) and left ventricular internal diameter end-systole (LVIDs) were reduced (P < 0.05), and H&E and Masson's trichrome staining of cardiac tissues showed that LQF and perindopril could partially reverse ventricular remodeling and alleviate myocardial fibrosis (P < 0.05). WGA fluorescence results showed that compared with the model group, myocardial hypertrophy was significantly reduced in the LQF and perindopril group. We also found that LQF and perindopril reduce the oxidative stress response in the heart of MI mice. The protein expression of NLRP3, ASC, Cle-caspase-1, IL-1β, TXNIP, Cle-caspase-3, and Bax was downregulated in the LHF and perindopril treatment group, and Bcl-2 expression was upregulated. Conclusion. LQF and perindopril significantly attenuated cardiac injury and apoptosis in the MI model. In addition, we found that LQF effectively inhibited the activation of the NLRP3/ASC/caspase-1/IL-1β cascade, decreased inflammatory infiltration, delayed ventricular remodeling, and downregulated caspase-3/Bax signaling, which can effectively reduce the apoptosis of cardiomyocytes. Perindopril showed the same mechanism. [ABSTRACT FROM AUTHOR]

Kashin–Beck disease (KBD) is a complex endemic osteoarthropathy, which mainly occurs in the northeast to southwest China. Iodothyronine deiodinases 3 (DIO3) is one of the selenoproteins, which is closely related to bone metabolism and unclear to KBD. This study aims to investigate the role and associated mechanisms of methylation and expression of DIO3 with disease severity in patients with KBD. We performed a bioinformatics analysis first to identify the biological mechanisms involved in selenoproteins. The methylation status of the DIO3 gene and DIO3 gene expression, as well as DIO3‐related regulatory genes in patients with KBD, were analyzed. We found that 15 CpG sites of six selenoproteins were hypomethylated with 5‐azacytidine treatment. DIO3 hypermethylation was associated with an increased risk of KBD and may lead to downregulation of DIO3 gene expression as well as be an indicator of the severity of KBD, which may provide a new insight for gene–environment correlations and interactions in etiology and pathogenesis of KBD. [ABSTRACT FROM AUTHOR]

Rheumatoid arthritis (RA) is a multi-systemic inflammatory autoimmune disease involving peripheral joints, and the pathogenesis is not clear. Studies showed that DNA methylation and expression might also be involved in the pathogenesis of RA. This study integrated three expression profile datasets (GSE55235, GSE12021, and GSE55457) and one methylation profile dataset GSE111942 to elucidate the potential essential candidate genes and pathways in RA. Differentially expressed genes (DEGs) and differentially methylation genes (DMGs) were identified by R programming software, using Limma package and ChAMP package, respectively. DAVID performed gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs. Functional annotation and construction of a protein–protein interaction (PPI) network and the Molecular Complex Detection Algorithm (MCODE) were analysed by STRING and Cystoscope, respectively. Then the connection analysis of DEGs and DMGs was carried out, and further to analyse the relationship between methylation and gene expression, aiming to screen out the potential genes. In this study, 288 DEGs and 228 DMGs were identified, and the majority of DEGs were up-regulated. Enrichment analysis represented that DEGs mainly involved immune response and participated in the Cytokine–cytokine receptor interaction signal pathway. 282 nodes were identified from DEGs PPI network and MCODE, filtering the most significant 2 modules, 23 core node genes were identified and most of them are involved in the T cell receptor signalling pathway and chemokine-mediated signalling pathway. Cross-analysis revealed 4 genes [KNTC1 (cg 01277763), LRRC8D (cg 07600884), DHRS9 (cg 05961700), and UCP2 (cg 05205664)] that exhibited differential expression and methylation in RA simultaneously. Therefore, the four genes could be used as the target for RA. [ABSTRACT FROM AUTHOR]

Highlights • A promoter trap system using two reporter genes was developed in P. polymyxa SC2-M1. • Some novel and native promoters of P. polymyxa were identified and characterized. • An XI was expressed in P. polymyxa SC2-M1 to improve the xylose metabolic capacity. Abstract Paenibacillus polymyxa is a rhizobacterium that has attracted substantial attention due to its ability to produce functional metabolites and promote plant growth. Metabolic and genetic improvements in this species will benefit research and other applications of the bacterium. However, a suitable gene expression system has not been established in this species. In this study, a promoter trap system based on a green fluorescent protein and a chloramphenicol-resistance gene was developed to isolate native promoters of P. polymyxa SC2-M1 to regulate gene expression. Through high-throughput screening, the novel promoter P LH-77 was identified, sequenced, and subsequently characterized. Promoter P LH-77 is a strong, continuous expression system containing the typical -10 and -35 motifs regions. Its effective sequence was evaluated and then cascaded to improve the promotion efficiency. To further verify the existence of P LH-77 , a heterogenous xylose isomerase was expressed by P LH-77 in P. polymyxa SC2-M1. In the resulting strain, the amount of xylose consumed was increased by 2.5 g/L during the 78 h fermentation period. Meanwhile, the production levels of lactate and acetate increased. It was confirmed that promoter P LH-77 could effectively mediate gene expression in P. polymyxa SC2-M1 and will further benefit the quantitative monitoring of gene expression in P. polymyxa. [ABSTRACT FROM AUTHOR]

Diabetic nephropathy is a major cause of chronic kidney disease and end-stage kidney disease. However, so little is known about alterations of the glycopatterns in urine with the development of diabetic nephropathy. Presently, we interrogated glycopatterns in urine specimens using a lectin microarray. The results showed that expression levels of Siaα2-6Gal/GalNAc recognized by SNA exhibited significantly increased tendency with the development of diabetic nephropathy; moreover, SNA blotting indicated glycoproteins (90 kDa, 70 kDa, and 40 kDa) in urine may contribute to this alteration. Furthermore, the glycopatterns of (GlcNAc)2–4 recognized by STL exhibited difference between diabetic and nondiabetic nephropathy. The results of urinary protein microarray fabricated by another 48 urine specimens also indicated (GlcNAc)2–4 is a potential indictor to differentiate the patients with diabetic nephropathy from nondiabetic nephropathy. Furtherly, STL blotting showed that the 50 kDa glycoproteins were correlated with this alteration. In conclusion, our data provide pivotal information to monitor the development of diabetic nephropathy and distinguish between diabetic nephropathy and nondiabetic renal disease based on precise alterations of glycopatterns in urinary proteins, but further studies are needed in this regard. [ABSTRACT FROM AUTHOR]