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Primary cilia are essential cellular antennae that transmit external signals into intracellular responses. These sensory organelles perform crucial tasks in triggering intracellular signaling pathways, including those initiated by G protein-coupled receptors (GPCRs). Given the involvement of GPCRs in serum-induced signaling, we investigated the contribution of ciliary proteins in mitogen perception and cell proliferation. We found that depletion of cilia via IFT88 silencing impaired cell growth and repressed YAP activation against serum and its mitogenic constituents, namely lysophosphatidic acid (LPA) and sphingosine 1-phosphate (S1P). To identify the key player of serum mitogen signaling, a mutant cell line library with 30 ablated individual ciliary proteins was established and screened based on YAP dephosphorylation and target gene induction. While 9 of them had altered signaling, ablation of IFT38 or IFT144 led to a particularly robust repression of YAP activation upon LPA and S1P. The deficiency of IFT38 and IFT144 attenuated cell proliferation, as corroborated in either 2-dimensional cultures or tumor spheroids. In subcutaneous skin melanoma patients, expression of IFT38 and IFT144 was associated with unfavorable outcomes in overall survival. In conclusion, our study demonstrates the involvement of ciliary proteins in mitogen signaling and identifies the regulatory roles of IFT38 and IFT144 in serum-mediated Hippo pathway signaling and cellular growth. • Cellular sensitivity to serum mitogens is controlled by primary cilia. • Functional comparison of ciliary proteins was done using CRISPRi cell line library. • IFT38 and IFT144 were identified as crucial components for serum mitogen perception. • Silencing IFT38 and IFT144 leads to reduced tumor spheroid growth. [ABSTRACT FROM AUTHOR]

The NFκB family of transcription factors is crucial for innate or adaptive immunity, inflammation, and diseases including cancer. The two NFκB signaling pathways (canonical and non-canonical) differ from each other in extracellular signals, membrane receptors, signaling adaptors, and dimer subunits. The p52 (NFκB2) subunit, which participates in the non-canonical pathway, is generated by ubiquitin-mediated processing of the p100 precursor. Here, we found that NFκB2 processing and activation were mediated by mitogen-activated protein kinase kinase-4 (MKK4) and its substrate c-Jun N-terminal kinase (JNK). In MKK4-null mouse embryonic fibroblasts (MEFs), serum- and lymphotoxin β receptor (LTβR) antibody-induced processing of p100 and nuclear translocation of p52 were found to be defective. Serum and LTβR antibody activated the MKK4-JNK signaling pathway, and SP600125, a JNK inhibitor, blocked p100 processing. Cellular senescence, one of the responses regulated by the non-canonical NFκB pathway, was observed more frequently in MKK4-null MEFs than in wildtype cells. These results suggest that the MKK4/JNK-dependent pathway regulates NFκB2 processing/activation and, through this mechanism, MKK4 and NFκB2 control cellular growth and senescence. [ABSTRACT FROM AUTHOR]

Abstract: Nitroreductases comprise a group of FMN- or FAD-dependent enzymes that reduce nitrosubstituted compounds by using NAD(P)H, and are found in bacterial species and yeast. Although there is little information on the biological functions of nitroreductases, some studies suggest their possible involvement in oxidative stress responses. In the yeast Saccharomyces cerevisiae, a putative nitroreductase protein, Frm2, has been identified based on its sequence similarity with known bacterial nitroreductases. Frm2 has been reported to function in the lipid signaling pathway. To study the functions of Frm2, we measured the nitroreductase activity of purified Frm2 on 4-nitroquinoline-N-oxide (4-NQO) using NADH. LC-MS analysis of the reaction products revealed that Frm2 reduced NQO into 4-aminoquinoline-N-oxide (4-AQO) via 4-hydroxyaminoquinoline (4-HAQO). An Frm2 deletion mutant exhibited growth inhibition in the presence of 4-NQO. Thus, in this study, we demonstrate a novel nitroreductase activity of Frm2 and its involvement in the oxidative stress defense system. [Copyright &y& Elsevier]

Abstract: Hypoxia-inducible factor (HIF)-1 has been established as a master regulator of vascular responses to hypoxia and ischemia by driving transcriptional activation of angiogenic factors. Oxygen- and 2-oxoglutarate (2-OG)-dependent, iron(II) containing HIF-specific prolyl-4-hydroxylases (PHDs) and factor inhibiting HIF-1α (FIH-1) catalyze the hydroxylation of the specific proline and asparagine residues of HIF-1α, thereby controlling the level of HIF-1α and ultimately the HIF response. Here, we unveil a new action of hinokitiol, an iron chelator found in natural plants, on stabilization of HIF-1α in cell cultures in a dose-dependent manner. In vitro PHD2 and FIH activity assays based on fluorescence polarization reveal that such HIF-1α stabilization is likely medicated by inhibitory effects of hinokitiol on prolyl and asparaginyl hydroxylation of HIF-1α. In addition, the inhibition of PHD2 by hinokitiol is reversed by the addition of 2-OG and iron(II), suggesting that the underlying inhibitory mechanism involves displacement of 2-OG and a chelate formation with iron(II) at the enzyme active site by hinokitiol. Furthermore, hinokitiol treated cells show increased transcription of vascular endothelial growth factor, providing the therapeutic potential in the treatment of ischemic diseases. [Copyright &y& Elsevier]

Abstract: Neovascularization in the eye is the most common cause of blindness in all age groups; retinopathy of prematurity (ROP), diabetic retinopathy, and age-related macular degeneration. Despite current advances in surgical treatments, ROP remains as the most serious problem of vision loss in children. Here, we report that homoisoflavanone, a natural product from Cremastra appendiculata, significantly reduces retinal neovascularization in a mouse model of ROP. Homoisoflavanone inhibited the cell growth of HUVECs, but its cytotoxic effect was not observed in a concentration range of 1–20μM. HUVECs population gradually increased in G2/M phase and reduced in G0/G1 and S phases after exposure to the compound. Homoisoflavanone decreased the level of cdc2 expression whereas the level of p21WAF1 expression was increased in a dose-dependent manner. These data demonstrate that homoisoflavanone could inhibit retinal neovascularization and be applied in the treatment of other vasoproliferative retinopathies. [Copyright &y& Elsevier]

Abstract: Few studies have examined in detail the combined effects of vascular endothelial growth factor (VEGF) and basic fibroblast growth factor (bFGF) gene delivery on collateral development. Here, we evaluated the potential synergism of naked DNA vectors encoding VEGF and bFGF using a skeletal-muscle based ex vivo angiogenesis assay and compared tissue perfusion and limb loss in a murine model of hindlimb ischemia. In the ex vivo angiogenesis assay, the VEGF+bFGF combination group had a larger capillary sprouting area than those of the LacZ, VEGF, and bFGF groups. Consistent with these results, regional blood flow recovery on day 14 was also highest in the VEGF+bFGF combination group, followed by the bFGF, VEGF, and LacZ groups. The limb loss frequency was 0% in the combination group, whereas the limb loss frequencies of the other groups were 7–29%. The ischemic muscles of the combination group revealed evidence of increased angiogenesis and arteriogenesis and the upregulated expression of genes that may be associated with arteriogenesis, such as those for cardiac ankyrin repeat protein, early growth response factor-1, and transforming growth factor-β1. Our study has implications for the development of a combined gene therapy for the vascular occlusive diseases. [Copyright &y& Elsevier]

Abstract: T cell activation signals induced by altered peptide ligands (APLs) are different from those induced by the original agonistic peptide. The characteristics of the former are partial phosphorylation of TCR-ζ and no tyrosine-phosphorylation of ζ-associated protein-70 (ZAP-70). To analyze further those signaling pathways, we introduced a dominant negative (DN) form of ZAP-70 into a human CD4+ T cell clone in which fully and partially agonistic peptide ligands have been well characterized. We found that some over-expressed partially agonistic ligands (OPALs) induced T cell responses without tyrosine-phosphorylation and kinase activation of ZAP-70. However, those responses were inhibited in T cells expressing DN ZAP-70, which could associate with partially phosphorylated TCR-ζ. In OPAL-stimulated T cells, PLC-γ1 was phosphorylated and it was suppressed by DN ZAP-70 expression, suggesting that the ZAP-70-TCR-ζ association mediates the activation of PLC-γ1 leading to T cell responses even in the absence of kinase activation of ZAP-70. [Copyright &y& Elsevier]

We report that fullerene inhibits strongly the amyloid peptide aggregation at the early stage. It specifically binds to the central hydrophobic motif, KLVFF, of Aβ peptides. The IC50 value has been measured as 9 μM for both Aβ11–25 and Aβ1–40. On the other hand, a control experiment shows melatonin rather specifically binds to the C-terminus region. The IC50 value of fullerene appears to be at least four times larger for Aβ1–40, compared with melatonin, and 15 times larger for Aβ11–25. This work shows that fullerene can be a promising candidate in search of AD therapeutics because it has the very high IC50 value for Aβ aggregation. [Copyright &y& Elsevier]

Phytochromes are photoreceptors that regulate plant growth and development in response to the solar radiation environment. Recent studies reveal how phytochrome-mediated light signals can be transduced to the cells for their responses. The possible signal transduction pathways of phytochromes include: (a) direct regulation of gene transcription and (b) typical kinase-involved signaling pathways and its regulation by phosphorylation, dephosphorylation, and proteolytic degradation. This review highlights some of the recent findings. [Copyright &y& Elsevier]

Transforming growth factor-β (TGF-β) plays a crucial role in the development of epithelial to mesenchymal transition (EMT) and fibrosis, particularly in an ocular disorder such as proliferative vitreoretinopathy (PVR). However, the key molecular mechanism underlying its pathogenesis remains unknown. In the present study, using cultured ARPE-19 cells, we determined that TGF-β initiates a signaling pathway through extracellular signal-regulated kinase (ERK)-mammalian target of rapamycin complex 1 (mTORC1) that stimulates trans-differentiation and fibrosis of retinal pigment epithelium. Blocking this pathway by a TGF-βRI, ERK or mTORC1 inhibitor protected cells from EMT and fibrotic protein expression. TGF-β1 treatment increased reactive oxygen species (ROS) via NOX4 upregulation, which acts downstream of ERK and mTORC1, as the ROS scavenger N-acetylcysteine and a pan-NADPH oxidase (NOX) inhibitor DPI dissipated excess ROS generation. TGF-β1-induced oxidative stress resulted in EMT and fibrotic changes, as NAC and DPI prevented α-SMA, Col4α3 expression and cell migration. All these inhibitors blocked the downstream pathway activation in addition to clearly preventing the activation of its upstream molecules, indicating the presence of a feedback loop system that may boost the upstream events. Furthermore, the FDA-approved drug trametinib (10 nM) blunted TGF-β1-induced mTORC1 activation and downstream pathogenic alterations through ERK1/2 inhibition, which opens a therapeutic avenue for the treatment of PVR in the future. • TGF-β induces EMT and fibrosis in retinal pigment epithelial cells via ERK1/2-mTORC1-NOX4 axis. • TGF-β1 increases both cytosolic and mitochondrial ROS production through NOX4 upregulation. • Scavenging oxidative stress or NOX inhibition successfully prevents TGF-β-induced EMT and fibrosis. • FDA-approved drug trametinib effectively prevents EMT and fibrosis by inhibition of ERK-mTOR signaling. [ABSTRACT FROM AUTHOR]

The tRNA methyltransferase J (TrmJ) and D (TrmD) catalyze the transferring reaction of a methyl group to the tRNA anticodon loop. They commonly have the N-terminal domain (NTD) and the C-terminal domain (CTD). Whereas two monomeric CTDs symmetrically interact with a dimeric NTD in TrmD, a CTD dimer has exhibited an asymmetric interaction with the NTD dimer in the presence of a product. The elucidated apo-structure of the full-length TrmJ from Zymomonas mobilis ZM4 shows a dimeric CTD that asymmetrically interacts with the NTD dimer, thereby distributing non-symmetrical potential charge on the both side of the protein surface. Comparison with the product-bound structures reveals a local re-orientation of the two arginine-containing loop at the active site, which interacts with the product. Further, the CTD dimers have diverse orientations compared to the NTD dimers, suggesting their flexibility. These data indicate that an asymmetric interaction between the NTD dimer and the CTD dimer is a common structural feature among TrmJ proteins, regardless of the presence of a substrate or a product. [ABSTRACT FROM AUTHOR]

8-Chloro-cyclic AMP (8-Cl-cAMP) is a cyclic AMP analog that induces growth inhibition and apoptosis in a broad spectrum of cancer cells. Previously, we found that 8-Cl-cAMP-induced growth inhibition is mediated by AMP-activated protein kinase (AMPK) as well as p38 mitogen-activated protein kinase (p38 MAPK). To identify downstream mediators of the 8-Cl-cAMP signaling, we performed co-immunoprecipitation combined with mass spectrometry using the anti-AMPK or p38 MAPK antibodies. Through this approach, SHC1 was identified as one of the binding partners of p38 MAPK. SHC1 phosphorylation was suppressed by 8-Cl-cAMP in HeLa and MCF7 cancer cells, which was mediated by its metabolites, 8-Cl-adenosine and 8-Cl-ATP; however, 8-Cl-cAMP showed no effect on SHC1 phosphorylation in normal human fibroblasts. SHC1 siRNA induced AMPK and p38 MAPK phosphorylation and growth inhibition in cancer cells, and SHC1 overexpression re-sensitized human foreskin fibroblasts to the 8-Cl-cAMP treatment. SHC1 phosphorylation was unaffected by Compound C (an AMPK inhibitor) and SB203580 (a p38 MAPK inhibitor), which suggests that SHC1 is upstream of AMPK and p38 MAPK in the 8-Cl-cAMP-stimulated signaling cascade. On the basis of these findings, we conclude that SHC1 functions as a sensor during the 8-Cl-cAMP-induced growth inhibition in SHC1-overexpressing cancer cells. [ABSTRACT FROM AUTHOR]

Highlights: [•] The crystal structure of one cbbF from Zymomonas mobilis was revealed. [•] Scores of residues form two secondary structures with a non-polar protruded residue. [•] It exists as a dimeric form in solution. [ABSTRACT FROM AUTHOR]

Apoptosis plays an essential role in maintaining cellular homeostasis and preventing cancer progression. Bcl-xL, an anti-apoptotic protein, is an important modulator of the mitochondrial apoptosis pathway and is a promising target for anticancer therapy. In this study, we identified octenidine as a novel Bcl-xL inhibitor through structural feature-based deep learning and molecular docking from a library of approved drugs. The NMR experiments demonstrated that octenidine binds to the Bcl-2 homology 3 (BH3) domain-binding hydrophobic region that consists of the BH1, BH2, and BH3 domains in Bcl-xL. A structural model of the Bcl-xL/octenidine complex revealed that octenidine binds to Bcl-xL in a similar manner to that of the well-known Bcl-2 family protein antagonist ABT-737. Using the NanoBiT protein–protein interaction system, we confirmed that the interaction between Bcl-xL and Bak-BH3 domains within cells was inhibited by octenidine. Furthermore, octenidine inhibited the proliferation of MCF-7 breast and H1299 lung cancer cells by promoting apoptosis. Taken together, our results shed light on a novel mechanism in which octenidine directly targets anti-apoptotic Bcl-xL to trigger mitochondrial apoptosis in cancer cells. • Artificial intelligence-based identification of a novel Bcl-xL inhibitor. • Octenidine directly binds to the BH3 domain-binding site in Bcl-xL. • Octenidine inhibits Bcl-xL/Bak interaction to induce apoptosis. • Octenidine inhibits the proliferation of breast and lung cancer cells. • A novel action mechanism of octenidine for cancer therapy. [ABSTRACT FROM AUTHOR]

Abstract: Although total UBA1 levels were unchanged, after oxidation for 60min, we observed dramatic changes in the levels of BIAM-labeled UBA1 in both the membrane and cytosol fractions that suggested oxidative stress induces translocation of UBA1 from the cytosol to the membrane. Notably, in PrdxII−/− oxRBCs, ubiquitination levels were reduced about 75% in the membrane fraction after 90min, even though UBA1 levels were increased. These results suggest ubiquitination levels are determined by UBA1 activity, not the level of UBA1 protein. Levels of ubiquitin conjugate (denoted ∼Ub) in HEK293T and CMT93 cells transfected with UBA1(C278S) or UBA1(C632S) were lower than in cells expressing UBA1(WT) or another cysteine mutant. During the reaction, UBA1(WT)∼Ub was nearly completely eliminated within 30min, whereas UBA1(C278S)∼Ub and UBA1(C632S)∼Ub persisted. Within UBA1(C278S)∼Ub, the catalytic cysteine (Cys-632) remained intact; nonetheless, migration of UBA1(C278S)∼Ub and UBA1(C632S)∼Ub were similar. These data suggest that Cys-278 can affect Ub charging through a change in the structural conformation of UBA1, not through direct interaction at the UBA1–Ub interface. [Copyright &y& Elsevier]

Abstract: Twist1 is a transcription factor that is involved in epithelial–mesenchymal transition by suppressing intercellular adhesion. In this study, we aimed to determine the role of Twist1 in the regulation of claudin-4 expression and investigate its specific mechanisms and clinical implications using human esophageal carcinoma cell lines and tissues. As a result, up-regulation of Twist1 decreased both gene and protein expression levels of endogenous claudin-4 and the suppression was mediated by direct binding of Twist1 to the canonical E-box in the promoter region of claudin-4. In addition, there was a significant inverse correlation of claudin-4 with Twist1 in esophageal cancer tissues. High Twist1 and low claudin-4 expression was associated with the poorest prognosis and was more highly correlated with adverse outcome than any other subgroup with statistical significance (p =0.001). Our results indicate that Twist1 induces the repression of claudin-4 expression during the epithelial–mesenchymal transition in esophageal carcinoma. [Copyright &y& Elsevier]

Abstract: PKM2 is an isoenzyme of the glycolytic enzyme pyruvate kinase that promotes aerobic glycolysis. Here, we describe an important role for PKM2 in regulating the survival of gastric cancer (GC) cells. We showed that PKM2 was overexpressed in gastric tumor tissues compared to normal tissues and its expression level was associated with poor survival of gastric cancer patients. We also showed that PKM2 affected cell survival by regulating Bcl-xL at the transcriptional level. PKM2 knockdown partially affected the stability of NF-kB subunit p65, suggesting that post-translational regulation of p65 by PKM2 is one of plausible mechanisms for the increased cell growth. Therefore, PKM2 may function as an upstream molecule that regulates p65 function and thus enhances the growth of tumor cells. [Copyright &y& Elsevier]

Abstract: Humanization of nonhuman antibodies (Abs) has been carried out mainly for Abs which bind to antigen without catalytic activity. Here we report humanization of mouse-originated 3D8 (m3D8) mAbs (scFv, VH, and VL) with DNA hydrolyzing catalytic activity by grafting the complementarity determining regions (CDRs) into the corresponding regions of a fixed human framework scaffold, generating humanized 3D8 (h3D8) Abs in the respective format of scFv, VH, and VL. h3D8 Abs retained comparable DNA binding and hydrolyzing activities to those of the corresponding m3D8 Abs. Our results suggest that CDRs of anti-DNA hydrolyzing Abs might possess the intrinsic properties of DNA binding and hydrolyzing activities. [Copyright &y& Elsevier]

Abstract: Recent finding has shown that LIMS2 (also known as PINCH2) functions as a natural regulator of the LIMS1–ILK–parvin complex formation and is associated with cell spreading and migration via integrins at focal adhesions. Here, we report for the first time the epigenetic silencing of LIMS2 in gastric tumors. Downregulation of LIMS2 was detected in 91% (10 of 11) of gastric cancer cell lines by real-time quantitative RT-PCR and 80% (8 of 10) of the LIMS2-downregulated cell lines were associated with CpG island hypermethylation at a 5′-upstream region of LIMS2. Furthermore, LIMS2 was restored in its non-expressing cell lines after treatment with 5-Aza-dC and/or trichostatin A. Loss of expression of LIMS2 was also detected in 53% (51 of 96) of primary gastric tumors. This decrease in expression level significantly correlated with an increase of the CpG island hypermethylation. In addition, the methylation status in any normal-appearing gastric tissues was gradually increased in an age-dependent manner, suggesting that the positive methylation in normal-appearing gastric mucosa can be due to ‘field cancerization effect’ as an early event in gastric carcinogenesis. Moreover, the transient transfection of LIMS2-siRNA significantly stimulated cell migration in gastric cancer cells but had no effects on cell growth. These results suggest that the frequent inactivation of LIMS2 by epigenetic alteration in gastric cancer may be important in tumor progression events, such as invasion and metastasis. Thus, LIMS2 may be useful as a molecular biomarker and a therapeutic target by increasing its expression and activity in gastric cancer. [Copyright &y& Elsevier]

Osteoarthritis (OA) is an incurable joint disease affecting 240 million elderly population, and major unmet medical needs exist for better therapeutic options for OA. During skeletal development, Nkx3.2 has been shown to promote chondrocyte differentiation and survival, but to suppress cartilage hypertrophy and blood vessel invasion. Here we show that Nkx3.2 plays a key role in osteoarthritis (OA) pathogenesis. Marked reduction of Nkx3.2 expression was observed in three different murine OA models. Consistent with these findings, analyses of surgery-induced and age-driven OA models revealed that cartilage-specific post-natal induction of Nkx3.2 can suppress OA progression in mice. These results suggest that Nkx3.2 may serve as a promising target for OA drug development. [Display omitted] • Nkx3.2 expression is found to be reduced in multiple osteoarthritis (OA) models. • Nkx3.2 can alleviate disease severity in both traumatic and degenerative OA models. • Nkx3.2 can protect articular cartilages from osteoarthritic destruction. • Nkx3.2 can attenuate osteophyte maturation facilitated by aging. • Nkx3.2 may serve as a promising target for OA drug development. [ABSTRACT FROM AUTHOR]

Baeyer-Villiger monooxygenase (BVMO) catalyzes insertion of an oxygen atom into aliphatic or cyclic ketones with high regioselectivity. The BVMOs from Parvibaculum lavamentivorans (BVMO Parvi) and Oceanicola batsensis (BVMO Ocean) are interesting because of their homologies, with >40% sequence identity, and reaction with the same cyclic ketones with a methyl moiety to give different products. The revealed BVMO Parvi structure shows that BVMO Parvi forms a two-domain structure like other BVMOs. It has two inserted residues, compared with BVMO Ocean , that form a bulge near the bound flavin adenine dinucleotide in the active site. Furthermore, this bulge is linked to a nearby α-helix via a disulfide bond, probably restricting access of the bulky methyl group of the substrate to this bulge. Another sequence motif at the entrance of the active site (Ala-Ser in BVMO Parvi and Ser-Thr in BVMO Ocean) allows a large volume in BVMO Parvi. These minute differences may discriminate a substrate orientation in both BVMOs from the initial substrate binding pocket to the final oxygenation site, resulting in the inserted oxygen atom being in different positions of the same substrate. • Crystal structure of Parvibaculum BVMO was determined as a NADPH complex form. • Parvibaculum BVMO has a rigid bulge at the oxygenase site. • Parvibaculum BVMO has a large pocket at the initial substrate binding site. [ABSTRACT FROM AUTHOR]

Inner and rosette leaves of Chinese cabbage ( Brassica rapa ) have different characteristics in terms of nutritional value, appearance, taste, color and texture. Many researchers have utilized differentially expressed genes for exploring the difference between inner and rosette leaves of Brassica rapa . The functional characteristics of a gene, however, is determined by complex interactions between genes. Hence, a noble network approach is required for elucidating such functional difference that is not captured by gene expression profiles alone. In this study, we measured gene expression in the standard cabbage genome by RNA-Sequencing and constructed rosette and inner leaf networks based on the gene expression profiles. Furthermore, we compared the topological and functional characteristics of these networks. We found significant functional difference between the rosette and inner leaf networks. Specifically, we found that the genes in the rosette leaf network were associated with homeostasis and response to external stimuli whereas the genes in the inner leaf network were mainly related to the glutamine biosynthesis processes and developmental processes with hormones. Overall, the network approach provides an insight into the functional difference of the two leaves. [ABSTRACT FROM AUTHOR]

In order to discover the common characteristics of various cell types in the human body, many researches have been conducted to find the set of genes commonly expressed in various cell types and tissues. However, the functional characteristics of a cell is determined by the complex regulatory relationships among the genes rather than by expressed genes themselves. Therefore, it is more important to identify and analyze a core regulatory network where all regulatory relationship between genes are active across all cell types to uncover the common features of various cell types. Here, based on hundreds of tissue-specific gene regulatory networks constructed by recent genome-wide experimental data, we constructed the core regulatory network. Interestingly, we found that the core regulatory network is organized by simple cascade and has few complex regulations such as feedback or feed-forward loops. Moreover, we discovered that the regulatory links from genes in the core regulatory network to genes in the peripheral regulatory network are much more abundant than the reverse direction links. These results suggest that the core regulatory network locates at the top of regulatory network and plays a role as a 'hub' in terms of information flow, and the information that is common to all cells can be modified to achieve the tissue-specific characteristics through various types of feedback and feed-forward loops in the peripheral regulatory networks. We also found that the genes in the core regulatory network are evolutionary conserved, essential and non-disease, non-druggable genes compared to the peripheral genes. Overall, our study provides an insight into how all human cells share a common function and generate tissue-specific functional traits by transmitting and processing information through regulatory network. [ABSTRACT FROM AUTHOR]

Although the ubiquitin–proteasome system is believed to play an important role in the pathogenesis of familial amyotrophic lateral sclerosis (FALS), caused by mutations in Cu/Zn-superoxide dismutase 1 (SOD1), the mechanism of how mutant SOD1 protein is regulated in cells is still poorly understood. Here we have demonstrated that cellular inhibitor of apoptosis proteins (cIAPs) are specifically associated with FALS-linked mutant SOD1 (mSOD1) and that this interaction promotes the ubiquitin-dependent proteasomal degradation of mutant SOD1. By utilizing cumate inducible SOD1 cells, we also showed that knock-down or pharmacologic depletion of cIAPs leads to H 2 O 2 induced cytotoxicity in mSOD1 expressing cells. Altogether, our results reveal a novel role of cIAPs in FALS-associated mutant SOD1 regulation. [ABSTRACT FROM AUTHOR]

Aurora A is involved in regulating multiple steps of mitosis. Over-expression of Aurora A is related to tumorigenesis and poor prognosis. KRC-108 is a novel multi-kinase inhibitor which has anti-tumor activity in vivo . In this study, we identified the inhibitory effects of KRC-108 on Aurora A kinase and growth-inhibitory characteristics of KRC-108. The in vitro kinase activity assay, immunoblot, and immunofluorescence analyses demonstrated that KRC-108 inhibited Aurora A activity. KRC-108 exhibited cytotoxicity against human colorectal cancer cell line HT-29. Colony formation assays showed that KRC-108 reduced the colony growth of HT-29 cells. KRC-108 also inhibited migration of HT-29 cells. The expression levels of cyclin B1 and CDC2 were decreased by KRC-108 in HT-29 cells. Cell cycle analysis and flow cytometry indicated that the inhibitory effects of KRC-108 on cell growth are due to induction of G 2 /M arrest and apoptosis by inhibition of Aurora A. KRC-108 induces cell-cycle arrest and apoptosis in colorectal cancer cell line by Aurora A inhibition. The reported in vivo anti-tumor effects of KRC-108 might partly be due to anti-Aurora A effects. This study suggests that KRC-108 has potential for development as an anti-tumor agent, although further studies are needed. [ABSTRACT FROM AUTHOR]

Viral protein genome-linked (VPg) proteins play a critical role in the life cycle of vertebrate and plant positive-sense RNA viruses by acting as a protein primer for genome replication and as a protein cap for translation initiation. Here we report the solution structure of the porcine sapovirus VPg core (VPg C ) determined by multi-dimensional NMR spectroscopy. The structure of VPg C is composed of three α-helices stabilized by several conserved hydrophobic residues that form a helical bundle core similar to that of feline calicivirus VPg. The putative nucleotide acceptor Tyr956 within the first helix of the core is completely exposed to solvent accessible surface to facilitate nucleotidylation by viral RNA polymerase. Comparison of VPg structures suggests that the surface for nucleotidylation site is highly conserved among the Caliciviridae family, whereas the backbone core structures are different. These structural features suggest that caliciviruses share common mechanisms of VPg-dependent viral replication and translation. [ABSTRACT FROM AUTHOR]

Fibulin-3 (FBLN-3) has been postulated to be either a tumor suppressor or promoter depending on the cell type, and hypermethylation of the FBLN-3 promoter is often associated with human disease, especially cancer. We report that the promoter region of the FBLN-3 was significantly methylated (>95%) in some pancreatic cancer cell lines and thus FBLN-3 was poorly expressed in pancreatic cancer cell lines such as AsPC-1 and MiaPaCa-2. FBLN-3 overexpression significantly down-regulated the cellular level of c-MET and inhibited hepatocyte growth factor-induced c-MET activation, which were closely associated with γ-radiation resistance of cancer cells. Moreover, we also showed that c-MET suppression or inactivation decreased the cellular level of ALDH1 isozymes (ALDH1A1 or ALDH1A3), which serve as cancer stem cell markers, and subsequently induced inhibition of cell growth in pancreatic cancer cells. Therefore, forced overexpression of FBLN-3 sensitized cells to cytotoxic agents such as γ-radiation and strongly inhibited the stemness and epithelial to mesenchymal transition (EMT) property of pancreatic cancer cells. On the other hand, if FBLN3 was suppressed in FBLN-3 -expressing BxPC3 cells, the results were opposite. This study provides the first demonstration that the FBLN-3/c-MET/ALDH1 axis in pancreatic cancer cells partially modulates stemness and EMT as well as sensitization of cells to the detrimental effects of γ-radiation. [ABSTRACT FROM AUTHOR]

Highlights: [•] Suppression of PKC ζ effectively attenuated vascular leakage in diabetic retina. [•] Inhibition of PKC ζ prevented tight junction protein decrease on retinal vessels. [•] PKC ζ inhibition prevented tight junction loss in HRMECs under diabetic condition. [Copyright &y& Elsevier]

Highlights: [•] DKK1 was expressed differently among non-small-cell lung cancer cell lines. [•] DKK1 negatively regulated ROMO1 gene expression. [•] Disturbance of DKK1 level induced the imbalance of cellular ROS. [•] DKK1/ROMO1-induced ROS imbalance is involved in cell survival in NSCLC. [ABSTRACT FROM AUTHOR]

Highlights: [•] The crystal structure of Cas1 from Archaeoglobus fulgidus was revealed. [•] It has insertion of five residues into the loop around the active site. [•] It has a metal-dependent nucleolytic activity against double-stranded DNA. [ABSTRACT FROM AUTHOR]

Abstract: p-Coumaric acid (3-[4-hydroxyphenyl]-2-propenoic acid) is a ubiquitous plant metabolite with antioxidant, anti-inflammatory, and anticancer properties. In this study, we examined whether p-coumaric acid modulates glucose and lipid metabolism via AMP-activated protein kinase (AMPK) in L6 skeletal muscle cells. p-Coumaric acid increased the phosphorylation of AMPK in a dose-dependent manner in differentiated L6 skeletal muscle cells. It also increased the phosphorylation of acetyl-CoA carboxylase (ACC) and the expression of CPT-1 mRNA and PPARα, suggesting that it promotes the β-oxidation of fatty acids. Also, it suppressed oleic acid-induced triglyceride accumulation, and enhanced 2-NBDG uptake in differentiated L6 muscle cells. Pretreatment with compound C inhibited AMPK activation, reduced ACC phosphorylation and 2-NBDG uptake, and increased triglyceride accumulation. However, p-coumaric acid counterbalanced the inhibitory effects of compound C. Taken together, these results suggest that p-coumaric acid modulates glucose and lipid metabolism via AMPK activation in L6 skeletal muscle cells and that it has potentially beneficial effects in improving or treating metabolic disorders. [Copyright &y& Elsevier]

Abstract: The angiogenic aspect of neurotrophins and their receptors rather than the neuroscientific aspect has been focused. However, their role in retinal vascular development is underdiscovered. The purpose of this study is to understand the role of neurotrophin receptors in retinal vascular development and the mechanisms of their action. To identify the expression of tropomyosin receptor kinase receptor (Trk) in developing retina, tissues of 4, 8, 12, 16 and 26day-old mice were prepared for experiments. Immunohistochemistry and immunofluorescence double staining against glial fibrillary acidic protein and type IV collagen were performed. TrkA was expressed mainly along the vessel structure in inner part of retina, especially in retinal astrocyte. In cultured primary astrocyte, recombinant nerve growth factor (NGF) was used to activate TrkA. NGF induced the phosphorylation of TrkA, and it also enhanced the level of activated Akt and vascular endothelial growth factor (VEGF) mRNA. Inhibition of phosphoinositide 3-kinase (PI3K) reversed the NGF-induced activation of these two molecules. This study demonstrated that TrkA activation on NGF leads to VEGF elevation by PI3K-Akt pathway and therefore suggested that TrkA could be a stimulator of retinal vascular development. [Copyright &y& Elsevier]

Abstract: Anterior Gradient 2 (AGR2), an ER stress-inducible protein, has been reported to be localized in endoplasmic reticulum (ER) and its level is elevated in numerous metastatic cancers. Recently, it has been demonstrated that AGR2 is involved in the control of ER homeostasis. However, the molecular mechanism how AGR2 regulates ER stress response remains unclear. Herein we show that AGR2 homo-dimerizes through an intermolecular disulfide bond. Moreover, dimerization of AGR2 attenuates ER stress-induced cell death through the association with BiP/GRP78. Thus, these results suggest that dimerization of AGR2 is crucial in mediating the ER stress signaling pathway. [Copyright &y& Elsevier]

Abstract: The LAMB3 and LAMC2 genes encode the laminin-5 β3 and γ2 chains, respectively, which are parts of laminin-5, one of the major components of the basement membrane zone. Here, we report the frequent up-regulation of LAMB3 and LAMC2 by promoter demethylation in gastric cancer. Gene expression data analysis showed that LAMB3 and LAMC2 were up-regulated in various tumor tissues. Combined analyses of DNA methylation and gene expression of both genes in gastric cancer cell lines and tissues showed that DNA hypomethylation was associated with the up-regulation of both genes. Treatment with a methylation inhibitor induced LAMB3 and LAMC2 expression in gastric cancer cell lines in which both genes were silenced. By chromatin immunoprecipitation assay, we showed the activation histone mark H3K4me3 was associated with the expression of both genes. The expression level of LAMB3 affected multiple malignant phenotypes in gastric cancer cell lines. These results suggest that epigenetic activation of LAMB3 and LAMC2 may play an important role in gastric carcinogenesis. [Copyright &y& Elsevier]

Abstract: Dihydroavenanthramide D (DHAvD) is a synthetic analog to naturally occurring avenanthramide, which is the active component of oat. Previous study demonstrates that DHAvD strongly inhibits activation of nuclear factor-kappa B (NF-κB), which is a major component in cancer cell invasion. The present study investigated whether DHAvD can modulate MMP-9 expression and cell invasion in MCF-7 human breast cancer cells. MMP-9 expression and cell invasion in response to 12-O-tetradecanoylphorbol-13-acetate (TPA) was increased, whereas these inductions were muted by DHAvD. DHAvD also suppressed activation of mitogen-activated protein kinase (MAPK), and MAPK-mediated nuclear factor-kappa B (NF-κB) and activator protein-1 (AP-1) activations in TPA-treated MCF-7 cells. The results indicate that DHAvD-mediated inhibition of TPA-induced MMP-9 expression and cell invasion involves the suppression of the MAPK/NF-κB and MAPK/AP-1 pathways in MCF-7 cells. DHAvD may have potential value in breast cancer metastasis. [Copyright &y& Elsevier]

Abstract: Fluorescent proteins that can be useful as indicators or reporters must have rapid maturation time, high quantum yield and photobleaching stability. A red fluorescent protein DsRed that has a high quantum yield and photostability has an innately slow maturation time when compared to other fluorescence proteins. In this study, we combined a functional salvage screen (FSS) and elongation mutagenesis to obtain a DsRed variant that maintained structural features closely linked with a high quantum yield and photostability and evolved to have a rapid maturation time. It is expected that the variant generated here, FmRed (fast maturating red fluorescent protein), will be widely used as an indicator or reporter because it maintained traits superior to that of the wild-type protein and also matured rapidly. [Copyright &y& Elsevier]

Abstract: Gingival fibroblast cells (rGF) from aged rats have an age-related decline in proliferative capacity compared with young rats. We investigated G1 phase cell cycle regulation and MMP-9 expression in both young and aged rGF. G1 cell cycle protein levels and activity were significantly reduced in response to interleukin-1β (IL-1β) stimulation with increasing in vitro age. Tumor necrosis factor-α (TNF-α)-induced matrix metalloproteinase-9 (MMP-9) expression was also decreased in aged rGF in comparison with young rGF. Mutational analysis and gel shift assays demonstrated that the lower MMP-9 expression in aged rGF is associated with lower activities of transcription factors NF-κB and AP-1. These results suggest that cell cycle dysregulation and down-regulation of MMP-9 expression in rGF may play a role in gingival remodeling during in vitro aging. [Copyright &y& Elsevier]

Abstract: Changes in cardiac osmolarity occur in myocardial infarction. Osmoregulatory mechanisms may, therefore, play a crucial role in cardiomyocyte survival. Tonicity-responsive enhancer binding protein (TonEBP) is a key transcription factor participating in the adaptation of cells to increases in tonicity. However, it is unknown whether cardiac TonEBP is activated by tonicity. Hypertonicity activated transcriptional activity of TonEBP, increased the amounts of both TonEBP mRNA and protein, and induced both the mRNA and protein of TonEBP target genes (aldose reductase and heat shock protein-70). Hypotonicity decreased the amount of TonEBP protein indicating bidirectional osmoregulation of this transcription factor. Adenoviral expression of a dominant negative TonEBP suppressed the hypertonicity-dependent increase of aldose reductase protein. These results indicated that TonEBP controls osmoregulatory mechanisms in cardiomyocytes. [Copyright &y& Elsevier]

Abstract: AMP-activated protein kinase (AMPK) is an energy-sensing enzyme that is implicated as a key factor in controlling whole body homeostasis, including fatty acid oxidation and glucose uptake. We report that a synthetic structural isomer of dihydrocapsiate, isodihydrocapsiate (8-methylnonanoic acid 3-hydroxy-4-methoxy benzyl ester) improves type 2 diabetes by activating AMPK through the LKB1 pathway. In L6 myotube cells, phosphorylation of AMPK and acetyl-CoA carboxylase (ACC) and glucose uptake were significantly increased, whereas these effects were attenuated by an AMPK inhibitor, compound C. In addition, increased phosphorylation of AMPK and ACC by isodihydrocapsiate was significantly reduced by radicicol, an LKB1 destabilizer, suggesting that increased glucose uptake in L6 cells with isodihydrocapsiate treatment is predominantly accomplished by a LKB1-mediated AMPK activation pathway. Oral administration of isodihydrocapsiate to diabetic (db/db) mice reduced blood glucose levels by 40% after a 4-week treatment period. Our results support the development of isodihydrocapsiate as a potential therapeutic agent to target AMPK in type 2 diabetes. [Copyright &y& Elsevier]

Abstract: Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), existing as homotrimer in solution, contains a unique zinc-binding site coordinated by three Cys230 residues at the tip of trimeric interface. TRAIL mutant with replacements of Cys230 with Ala (TRAILC230A) negligibly formed trimeric structure and showed no apoptotic activity. Here, to elucidate the relationship between the trimeric stability and the apoptotic activity of TRAILC230A, we rationally designed mutations to induce homotrimerization of TRAILC230A by substituting for the three residues involved in hydrogen bonding (Tyr183 and Tyr243) and putative repulsive electrostatic (Arg227) interactions at the buried trimeric interface into hydrophobic residues, like Y183F, Y243F, and R227I. The TRAILC230A-derived mutants exhibited enhanced homotrimerization, but only the mutants containing R227I exhibited significant apoptosis-inducing activity in cancer cells. These results, together with the induction of rigid local structure around the zinc-binding region by R227I in TRAILC230A, suggest that ordered, rigid structure around the zinc-binding region is critical for the homotrimerization and apoptotic activity of TRAIL. [Copyright &y& Elsevier]

Abstract: The IRS-1 PH and PTB domains are essential for insulin-stimulated IRS-1 Tyr phosphorylation and insulin signaling, while Ser/Thr phosphorylation of IRS-1 disrupts these signaling events. To investigate consensus PKC phosphorylation sites in the PH-PTB domains of human IRS-1, we changed Ser24, Ser58, and Thr191 to Ala (3A) or Glu (3E), to block or mimic phosphorylation, respectively. The 3A mutant abrogated the inhibitory effect of PKCδ on insulin-stimulated IRS-1 Tyr phosphorylation, while reductions in insulin-stimulated IRS-1 Tyr phosphorylation, cellular proliferation, and Akt activation were observed with the 3E mutant. When single Glu mutants were tested, the Ser24 to Glu mutant had the greatest inhibitory effect on insulin-stimulated IRS-1 Tyr phosphorylation. PKCδ-mediated IRS-1 Ser24 phosphorylation was confirmed in cells with PKCδ catalytic domain mutants and by an RNAi method. Mechanistic studies revealed that IRS-1 with Ala and Glu point mutations at Ser24 impaired phosphatidylinositol-4,5-bisphosphate binding. In summary, our data are consistent with the hypothesis that Ser24 is a negative regulatory phosphorylation site in IRS-1. [Copyright &y& Elsevier]

Abstract: Lymphocytes from eight individuals out of 60 healthy donors, whose plasmas showed relatively higher antibody titer for a target antigen of death receptor 5 (DR5), were selected for the source of antibody genes to construct so called an anti-DR5 pseudo-immune human single-chain fragment variable (scFv) library on the yeast cell surface (∼2×106 diversity). Compared with a large nonimmune human scFv library (∼1×109 diversity), the repertoire of the pseudo-immune scFv library was significantly biased toward the target antigen, which facilitated rapid enrichments of the target-specific high affinity scFvs during selections by fluorescence activated cell sortings. Isolated scFvs, HW5 and HW6, from the pseudo-immune library showed much higher specificity and affinity for the targeted antigen than those from the nonimmune library. Our results suggest that a pseudo-immune antibody library is very efficient to isolate target-specific high affinity antibody from a relatively small sized library. [Copyright &y& Elsevier]

Abstract: Intrahepatic cholangiocarcinoma (ICC), a malignant tumor derived from the bile duct epithelium, is one of the leading causes of death from cancer, worldwide. However, the mechanisms related to it remain largely unknown. In this study, an analysis of the gene expression profiles for ICC was done using the frequency of the ESTs obtained from nine cDNA libraries that constructed from 4 ICC cell lines and 4 normal liver tissues. One hundred and thirty-seven genes were identified as being either up- or down-regulated in human ICC cells. Thirty genes were randomly selected to confirm their differential expression in 4 human ICC cell lines and 5 ICC tissues compared to normal liver tissues by semi-quantitative RT-PCR. Among these genes, ANXA1, ANXA2, AMBP, and SERPINC1 were further verified by immunohistochemical analyses. In conclusion, these identified genes represent potential biomarkers for ICC and represent potential targets for elucidating the molecular mechanisms that are associated with ICC. [Copyright &y& Elsevier]

C-reactive protein (CRP), a predictor of future cardiovascular diseases, has been reported to damage the vascular wall by inducing endothelial dysfunction and inflammation. This proatherogenic CRP was speculated to have a role in attenuating angiogenic functions of human endothelial progenitor cells (EPCs), possibly impairing vascular regeneration and increasing cardiovascular vulnerability to ischemic injury. Herein, we investigated the direct effect of CRP on angiogenic activity and gene expression in human EPCs. Incubation of EPCs with human recombinant CRP significantly inhibited EPC migration in response to vascular endothelial growth factor, possibly by decreasing the expression of endothelial nitric oxide synthase and subsequent nitric oxide production. In addition, CRP-treated EPCs showed the reduced adhesiveness onto an endothelial cell monolayer. When assayed for the gene expression of arteriogenic chemo-cytokines, CRP substantially decreased their expression levels in EPC, in part due to the upregulation of suppressors of cytokine signaling proteins. These results suggest that CRP directly attenuates the angiogenic and possibly arteriogenic functions of EPCs. This CRP-induced EPC dysfunction may impair the vascular regenerative capacity of EPCs, thereby leading to increased risk of cardiovascular diseases. [Copyright &y& Elsevier]

The low density lipoprotein receptor (LDLR)-related protein (LRP) is a multifunctional receptor which mediates the endocytic uptake of several ligands implicated in Alzheimer’s disease pathophysiology. Although LRP, as a member of the LDLR family, is likely to be regulated in response to various cellular stresses, this regulation has not been fully understood yet. In the present study we studied the regulation of LRP expression in primary cultured rat astrocytes in response to serum deprivation as a general cellular stress. A significant increase in LRP expression was detected after serum deprivation and this increase was blocked by treatment of U0126, an inhibitor of MAP kinase. This serum deprivation action was partially reversed by either serum or d-glucose supplementation, but further augmented by glutamine. This result contrasted with a finding that glutamine suppressed gadd153 protein induced by serum deprivation. Taken together, the present data suggest that serum deprivation induces dramatically LRP expression in astrocytes partly by MAPK signaling pathways and by signaling pathways apparently distinct from gadd153 induction. [Copyright &y& Elsevier]

The phytopathogenic bacterium Pectobacteium chrysanthemi PY35 secretes Cel5Z endoglucanase belonging to the glycoside hydrolase family 5 of EC 3.2.1.4. The mutation of cel5Z::Ω gene was constructed by cloning the 2.0-kb SmaI fragment containing the streptomycin/spectinomycin-resistance gene of pHP45Ω into the BalI site of pPY100. The insertion of Ω fragment generated a new stop codon, removing the Ser/Thr-rich linker region and the cellulose binding domain (CBD) in the C-terminal region of cel5Z gene. By subsequent subcloning from this 4.9-kb fragment (pPY1001), a 1.0-kb (pPY1002) fragment was obtained and designated as cel5Z::Ω. The cel5Z::Ω gene had an open reading frame (ORF) of 1011 bp, encoding 336 amino acids, starting with an ATG codon and ending with a new TGA stop codon. The molecular mass of the Cel5Z::Ω protein in E. coli transformant appeared to be 32 kDa by SDS–PAGE analysis in the presence of carboxymethyl-cellulose (CMC). The Cel5Z::Ω protein hydrolyzed CMC with 1.7-fold higher activity than the intact Cel5Z cellulase. [Copyright &y& Elsevier]