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1.
J Adv Res ; 2024 May 10.
Article in English | MEDLINE | ID: mdl-38735388

ABSTRACT

INTRODUCTION: Hepatic ischemia-reperfusion injury (IRI) is an inevitable adverse event following liver surgery, leading to liver damage and potential organ failure. Despite advancements, effective interventions for hepatic IRI remain elusive, posing a significant clinical challenge. The innate immune response significantly contributes to the pathogenesis of hepatic IRI by promoting an inflammatory cytotoxic cycle. We have reported that blocking GSDMD-induced pyroptosis in innate immunity cells protected hepatic IRI from inflammatory injury. However, the search for effective pyroptosis inhibitors continues. OBJECTIVES: This study aims to evaluate whether quercetin, a natural flavonoid, can inhibit GSDMD-induced pyroptosis and mitigate hepatic IRI. METHODS: We established the hepatic IRI murine model and cellular pyroptosis model to evaluate the efficacy of quercetin. RESULTS: Quercetin effectively alleviated hepatic IRI-induced tissue necrosis and inflammation. We found that during hepatic IRI, the cleavage of GSDMD occurred in hepatic macrophages, but not in other non-parenchymal cells. Quercetin inhibited the cleavage of GSDMD in macrophages. Moreover, we found that quercetin blocked the ASC assembly to inhibit the formation of NLRP3 inflammasomes and AIM2 inflammasomes, suppressing macrophage pyroptosis. Co-immunoprecipitation experiments confirmed that quercetin inhibited the interaction between ASC and Caspase-8, which is the mechanism of ASC complex and inflammasome formation. Overexpression of Caspase-8 abolished the anti-pyroptosis effect of quercetin in NLRP3 and AIM2 inflammasome signaling. Furthermore, we found that the hepatoprotective activity of quercetin was reduced in myelocytic GSDMD-deficient mice. CONCLUSION: Our findings suggest that quercetin has beneficial effects on hepatic IRI. Quercetin could attenuate hepatic IRI and target inhibition of macrophage pyroptosis via blocking Caspase-8/ASC interaction. We recommend that quercetin might serve as a targeted approach for the prevention and personalized treatment of hepatic IRI in perioperative patients.

2.
Mol Cancer Ther ; 22(4): 539-550, 2023 04 03.
Article in English | MEDLINE | ID: mdl-36696581

ABSTRACT

Antibodies targeting insulin-like growth factor 1 receptor (IGF-1R) induce objective responses in only 5% to 15% of children with sarcoma. Understanding the mechanisms of resistance may identify combination therapies that optimize efficacy of IGF-1R-targeted antibodies. Sensitivity to the IGF-1R-targeting antibody TZ-1 was determined in rhabdomyosarcoma and Ewing sarcoma cell lines. Acquired resistance to TZ-1 was developed and characterized in sensitive Rh41 cells. The BRD4 inhibitor, JQ1, was evaluated as an agent to prevent acquired TZ-1 resistance in Rh41 cells. The phosphorylation status of receptor tyrosine kinases (RTK) was assessed. Sensitivity to TZ-1 in vivo was determined in Rh41 parental and TZ-1-resistant xenografts. Of 20 sarcoma cell lines, only Rh41 was sensitive to TZ-1. Cells intrinsically resistant to TZ-1 expressed multiple (>10) activated RTKs or a relatively less complex set of activated RTKs (∼5). TZ-1 decreased the phosphorylation of IGF-1R but had little effect on other phosphorylated RTKs in all resistant lines. TZ-1 rapidly induced activation of RTKs in Rh41 that was partially abrogated by knockdown of SOX18 and JQ1. Rh41/TZ-1 cells selected for acquired resistance to TZ-1 constitutively expressed multiple activated RTKs. TZ-1 treatment caused complete regressions in Rh41 xenografts and was significantly less effective against the Rh41/TZ-1 xenograft. Intrinsic resistance is a consequence of redundant signaling in pediatric sarcoma cell lines. Acquired resistance in Rh41 cells is associated with rapid induction of multiple RTKs, indicating a dynamic response to IGF-1R blockade and rapid development of resistance. The TZ-1 antibody had greater antitumor activity against Rh41 xenografts compared with other IGF-1R-targeted antibodies tested against this model.


Subject(s)
Nuclear Proteins , Sarcoma , Child , Humans , Transcription Factors , Receptor, IGF Type 1 , Sarcoma/drug therapy , Receptors, Somatomedin , Antibodies, Monoclonal/pharmacology , Cell Line, Tumor , Cell Cycle Proteins , SOXF Transcription Factors
3.
Clin Cancer Res ; 28(17): 3836-3849, 2022 09 01.
Article in English | MEDLINE | ID: mdl-35797217

ABSTRACT

PURPOSE: We investigated why three patient-derived xenograft (PDX) childhood BRAFV600E-mutant brain tumor models are highly sensitive to trametinib. Mechanisms of acquired resistance selected in situ, and approaches to prevent resistance were also examined, which may translate to both low-grade glioma (LGG) molecular subtypes. EXPERIMENTAL DESIGN: Sensitivity to trametinib [MEK inhibitor (MEKi)] alone or in combination with rapamycin (TORC1 inhibitor), was evaluated in pediatric PDX models. The effect of combined treatment of trametinib with rapamycin on development of trametinib resistance in vivo was examined. PDX tissue and tumor cells from trametinib-resistant xenografts were characterized. RESULTS: In pediatric models TORC1 is activated through ERK-mediated inactivation of the tuberous sclerosis complex (TSC): consequently inhibition of MEK also suppressed TORC1 signaling. Trametinib-induced tumor regression correlated with dual inhibition of MAPK/TORC1 signaling, and decoupling TORC1 regulation from BRAF/MAPK control conferred trametinib resistance. In mice, acquired resistance to trametinib developed within three cycles of therapy in all three PDX models. Resistance to trametinib developed in situ is tumor-cell-intrinsic and the mechanism was tumor line specific. Rapamycin retarded or blocked development of resistance. CONCLUSIONS: In these three pediatric BRAF-mutant brain tumors, TORC1 signaling is controlled by the MAPK cascade. Trametinib suppressed both MAPK/TORC1 pathways leading to tumor regression. While low-dose intermittent rapamycin to enhance inhibition of TORC1 only modestly enhanced the antitumor activity of trametinib, it prevented or retarded development of trametinib resistance, suggesting future therapeutic approaches using rapamycin analogs in combination with MEKis that may be therapeutically beneficial in both KIAA1549::BRAF- and BRAFV600E-driven gliomas.


Subject(s)
Brain Neoplasms , Glioma , Mechanistic Target of Rapamycin Complex 1 , Pyridones , Pyrimidinones , Animals , Brain Neoplasms/drug therapy , Brain Neoplasms/genetics , Cell Line, Tumor , Disease Models, Animal , Glioma/drug therapy , Glioma/genetics , Glioma/metabolism , Humans , Mechanistic Target of Rapamycin Complex 1/genetics , Mice , Mitogen-Activated Protein Kinase Kinases , Mutation , Protein Kinase Inhibitors/pharmacology , Protein Kinase Inhibitors/therapeutic use , Proto-Oncogene Proteins B-raf/genetics , Pyridones/therapeutic use , Pyrimidinones/therapeutic use , Sirolimus
4.
Cell Oncol (Dordr) ; 45(1): 19-40, 2022 Feb.
Article in English | MEDLINE | ID: mdl-34997546

ABSTRACT

BACKGROUND: The EWSR1/FLI1 gene fusion is the most common rearrangement leading to cell transformation in Ewing sarcoma (ES). Previous studies have indicated that expression at the cellular level is heterogeneous, and that levels of expression may oscillate, conferring different cellular characteristics. In ES the role of EWSR1/FLI1 in regulating subpopulation dynamics is currently unknown. METHODS: We used siRNA to transiently suppress EWSR1/FLI1 expression and followed population dynamics using both single cell expression profiling, CyTOF and functional assays to define characteristics of exponentially growing ES cells and of ES cells in which EWSR1/FLI1 had been downregulated. Novel transcriptional states with distinct features were assigned using random forest feature selection in combination with machine learning. Cells isolated from ES xenografts in immune-deficient mice were interrogated to determine whether characteristics of specific subpopulations of cells in vitro could be identified. Stem-like characteristics were assessed by primary and secondary spheroid formation in vitro, and invasion/motility was determined for each identified subpopulation. Autophagy was determined by expression profiling, cell sorting and immunohistochemical staining. RESULTS: We defined a workflow to study EWSR1/FLI1 driven transcriptional states and phenotypes. We tracked EWSR1/FLI1 dependent proliferative activity over time to discover sources of intra-tumoral diversity. Single-cell RNA profiling was used to compare expression profiles in exponentially growing populations (si-Control) or in two dormant populations (D1, D2) in which EWSR1/FLI1 had been suppressed. Three distinct transcriptional states were uncovered contributing to ES intra-heterogeneity. Our predictive model identified ~1% cells in a dormant-like state and ~ 2-4% cells with stem-like and neural stem-like features in an exponentially proliferating ES cell line and in ES xenografts. Following EWSR1/FLI1 knockdown, cells re-entering the proliferative cycle exhibited greater stem-like properties, whereas for those cells remaining quiescent, FAM134B-dependent dormancy may provide a survival mechanism. CONCLUSIONS: We show that time-dependent changes induced by suppression of oncogenic EWSR1/FLI1 expression induces dormancy, with different subpopulation dynamics. Cells re-entering the proliferative cycle show enhanced stem-like characteristics, whereas those remaining dormant for prolonged periods appear to survive through autophagy. Cells with these characteristics identified in exponentially growing cell populations and in tumor xenografts may confer drug resistance and could potentially contribute to metastasis.


Subject(s)
Sarcoma, Ewing , Animals , Carcinogenesis , Cell Line, Tumor , Down-Regulation/genetics , Humans , Mice , Oncogene Proteins, Fusion/genetics , RNA , RNA-Binding Protein EWS/genetics , RNA-Binding Protein EWS/metabolism , Sarcoma, Ewing/genetics , Sarcoma, Ewing/metabolism , Sarcoma, Ewing/pathology
5.
Sensors (Basel) ; 21(24)2021 Dec 17.
Article in English | MEDLINE | ID: mdl-34960537

ABSTRACT

This paper presents a method for measuring aircraft landing gear angles based on a monocular camera and the CAD aircraft model. Condition monitoring of the aircraft landing gear is a prerequisite for the safe landing of the aircraft. Traditional manual observation has an intense subjectivity. In recent years, target detection models dependent on deep learning and pose estimation methods relying on a single RGB image have made significant progress. Based on these advanced algorithms, this paper proposes a method for measuring the actual angles of landing gears in two-dimensional images. A single RGB image of an aircraft is inputted to the target detection module to obtain the key points of landing gears. The vector field network votes the key points of the fuselage after extraction and scale normalization of the pixels inside the aircraft prediction box. Knowing the pixel position of the key points and the constraints on the aircraft, the angle between the landing gear and fuselage plane can be calculated even without depth information. The vector field loss function is improved based on the distance between pixels and key points, and synthetic datasets of aircraft with different angle landing gears are created to verify the validity of the proposed algorithm. The experimental results show that the mean error of the proposed algorithm for the landing gears is less than 5 degrees on the light-varying dataset.

6.
Sensors (Basel) ; 21(22)2021 Nov 12.
Article in English | MEDLINE | ID: mdl-34833608

ABSTRACT

Ranking-oriented cross-project defect prediction (ROCPDP), which ranks software modules of a new target industrial project based on the predicted defect number or density, has been suggested in the literature. A major concern of ROCPDP is the distribution difference between the source project (aka. within-project) data and target project (aka. cross-project) data, which evidently degrades prediction performance. To investigate the impacts of training data selection methods on the performances of ROCPDP models, we examined the practical effects of nine training data selection methods, including a global filter, which does not filter out any cross-project data. Additionally, the prediction performances of ROCPDP models trained on the filtered cross-project data using the training data selection methods were compared with those of ranking-oriented within-project defect prediction (ROWPDP) models trained on sufficient and limited within-project data. Eleven available defect datasets from the industrial projects were considered and evaluated using two ranking performance measures, i.e., FPA and Norm(Popt). The results showed no statistically significant differences among these nine training data selection methods in terms of FPA and Norm(Popt). The performances of ROCPDP models trained on filtered cross-project data were not comparable with those of ROWPDP models trained on sufficient historical within-project data. However, ROCPDP models trained on filtered cross-project data achieved better performance values than ROWPDP models trained on limited historical within-project data. Therefore, we recommended that software quality teams exploit other project datasets to perform ROCPDP when there is no or limited within-project data.


Subject(s)
Machine Learning , Software , Empirical Research
7.
Food Res Int ; 142: 110222, 2021 04.
Article in English | MEDLINE | ID: mdl-33773696

ABSTRACT

Chinese dry-cured hams have unique aroma characteristics appreciated by local consumers. The volatile organic compounds (VOCs) of six selected Chinese dry-cured hams (Mianning, Nuodeng, Saba, Sanchuan, Wanhua, and Xuanen) were analyzed by solvent assisted flavor evaporation (SAFE) combined with GC × GC-ToF-MS and head-space (HS) injection combined with GC-IMS. To visualize VOCs and differentiate samples, principal component analysis (PCA) and multiple factor analysis (MFA) were performed. GC × GC-ToF-MS resulted in over five times more VOCs (265) than GC-IMS (45). However, PCA and MFA indicated similar results using GC-IMS or GC × GC-ToF-MS data, suggesting HS-GC-IMS as a good choice to differentiate dry-cured hams from different regions. Xuanen ham from Yunnan Province having smoky aroma was significantly different from other hams, likely due to its unique process. Many aldehydes (heptanal, nonanal, etc.) played an important role in Sanchuan ham. Ketones were related to other four dry-cured hams, though they came from different regions. This study provides valuable analytical data to characterize and discriminate the flavor profile of Chinese dry-cured hams.


Subject(s)
Meat Products , Pork Meat , Volatile Organic Compounds , China , Gas Chromatography-Mass Spectrometry , Meat Products/analysis , Volatile Organic Compounds/analysis
8.
J Mol Model ; 26(11): 331, 2020 Nov 04.
Article in English | MEDLINE | ID: mdl-33150494

ABSTRACT

A series of interatomic interactions interpretable as halogen bonds involving I…I, I…O, and I…C(π), as well as the noncovalent interactions I…H and O…O, were observed in the crystal structures of trans-1,2-diiodoolefins dimers according to ab initio calculations and the quantum theory of "atoms in molecules" (QTAIM) method. The interplay between each type of halogen bond and other noncovalent interactions was studied systematically in terms of bond length, electrostatic potential, and interaction energy, which are calculated via ab initio methods at the B3LYP-D3/6-311++G(d,p) and B3LYP-D3/def2-TZVP levels of theory. Characteristics and nature of the halogen bonds and other noncovalent interactions, including the topological properties of the electron density, the charge transfer, and their strengthening or weakening, were analyzed by means of both QTAIM and "natural bond order" (NBO). These computational methods provide additional insight into observed intermolecular interactions and are utilized to explain the differences seen in the crystal structures. Graphical abstract The contour map presents the regions of electronic concentration and depletion along each bond in one dimer. The blue points denote the BCPs. The blue lines denote positive Laplacian of electron density, which indicate the ionic interactions, van der Waals or intermolecular interactions, and the red lines denote negative Laplacian of electron density which indicate the covalent bonds.

9.
Nat Struct Mol Biol ; 26(3): 155-163, 2019 03.
Article in English | MEDLINE | ID: mdl-30778235

ABSTRACT

Ribonucleoside monophosphates (rNMPs) mis-incorporated during DNA replication are removed by RNase H2-dependent excision repair or by topoisomerase I (Top1)-catalyzed cleavage. The cleavage of rNMPs by Top1 produces 3' ends harboring terminal adducts, such as 2',3'-cyclic phosphate or Top1 cleavage complex (Top1cc), and leads to frequent mutagenesis and DNA damage checkpoint induction. We surveyed a range of candidate enzymes from Saccharomyces cerevisiae for potential roles in Top1-dependent genomic rNMP removal. Genetic and biochemical analyses reveal that Apn2 resolves phosphotyrosine-DNA conjugates, terminal 2',3'-cyclic phosphates, and their hydrolyzed products. APN2 also suppresses 2-base pair (bp) slippage mutagenesis in RNH201-deficient cells. Our results define additional activities of Apn2 in resolving a wide range of 3' end blocks and identify a role for Apn2 in maintaining genome integrity during rNMP repair.


Subject(s)
Base Pairing/genetics , DNA Repair/genetics , DNA Replication/genetics , DNA-(Apurinic or Apyrimidinic Site) Lyase/genetics , Ribonucleotides/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae/genetics , 3' Untranslated Regions/genetics , DNA Topoisomerases, Type I/metabolism , DNA, Fungal/genetics , DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism , Genome, Fungal/genetics , Mutagenesis/genetics , Ribonucleases/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/metabolism
10.
Int Immunopharmacol ; 64: 326-332, 2018 Nov.
Article in English | MEDLINE | ID: mdl-30243068

ABSTRACT

Rheumatoid arthritis (RA) is an autoimmune disease characterized by chronic inflammatory synovitis, bone atrophy, and subsequent progressive destruction of articular tissue. Targeted inhibition of receptor activator of NF-kB ligand (RANKL) has been highly successful in preventing RA-mediated bone erosion in animal models and patients, suggesting that development of a RANKL vaccine might be of therapeutic value. Our previous study has shown that the recombinant RANKL vaccine Y234pNO2Phe, generated by replacement of a single tyrosine residue (Tyr234) in murine RANKL (mRANKL) with p-nitrophenylalanine (pNO2Phe), induces a high titer antibody response and prevents ovariectomy (OVX)-induced bone loss in mice. This aim of this study was to further evaluate the vaccine's preventive effects in a murine model of collagen-induced arthritis. The results of this study showed that Y234pNO2Phe not only induced a high titer antibody response and inhibited osteoclastogenesis but also significantly prevented bone erosion and ameliorated the severity of a collagen-induced arthritis (CIA) model in mice. Moreover, use of the vaccine improved the clinical situations of the CIA mice. These results suggest a potential application of an anti-RANKL vaccine in the treatment of RA-induced bone erosion.


Subject(s)
Arthritis, Experimental/prevention & control , RANK Ligand/immunology , Animals , Cell Differentiation , Disease Models, Animal , Female , Immunization , Male , Mice , Mice, Inbred C57BL , Mice, Inbred DBA , Osteoclasts/cytology , Osteoprotegerin/blood , RANK Ligand/blood , Vaccines, Synthetic/immunology
11.
Nat Commun ; 9(1): 2025, 2018 05 23.
Article in English | MEDLINE | ID: mdl-29795289

ABSTRACT

Yeast Rad1-Rad10 (XPF-ERCC1 in mammals) incises UV, oxidation, and cross-linking agent-induced DNA lesions, and contributes to multiple DNA repair pathways. To determine how Rad1-Rad10 catalyzes inter-strand crosslink repair (ICLR), we examined sensitivity to ICLs from yeast deleted for SAW1 and SLX4, which encode proteins that interact physically with Rad1-Rad10 and bind stalled replication forks. Saw1, Slx1, and Slx4 are critical for replication-coupled ICLR in mus81 deficient cells. Two rad1 mutations that disrupt interactions between Rpa1 and Rad1-Rad10 selectively disable non-nucleotide excision repair (NER) function, but retain UV lesion repair. Mutations in the analogous region of XPF also compromised XPF interactions with Rpa1 and Slx4, and are proficient in NER but deficient in ICLR and direct repeat recombination. We propose that Rad1-Rad10 makes distinct contributions to ICLR depending on cell cycle phase: in G1, Rad1-Rad10 removes ICL via NER, whereas in S/G2, Rad1-Rad10 facilitates NER-independent replication-coupled ICLR.


Subject(s)
DNA Damage/genetics , DNA Repair Enzymes/metabolism , DNA Repair/physiology , DNA-Binding Proteins/metabolism , Endonucleases/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Single-Strand Specific DNA and RNA Endonucleases/metabolism , Animals , CHO Cells , Cell Cycle/genetics , Cricetulus , Cross-Linking Reagents/toxicity , DNA Damage/drug effects , DNA Damage/radiation effects , DNA Repair Enzymes/genetics , DNA-Binding Proteins/genetics , Endonucleases/genetics , Intravital Microscopy , Mutagenesis, Site-Directed , Mutation , Saccharomyces cerevisiae Proteins/genetics , Single-Strand Specific DNA and RNA Endonucleases/genetics , Ultraviolet Rays/adverse effects
12.
Biochem Biophys Res Commun ; 499(3): 648-654, 2018 05 15.
Article in English | MEDLINE | ID: mdl-29604276

ABSTRACT

Bone homeostasis is maintained by a dynamic balance between osteoblastic bone formation and osteoclastic bone resorption. The receptor activator of nuclear-κB ligand (RANKL) is essential for the function of the bone-resorbing osteoclasts, and targeting RANKL has been proved highly successful in osteoporosis patients. This study aimed to design a novel vaccine targeting RANKL and evaluate its therapeutic effects in OVX-induced bone loss model. Anti-RANKL vaccine was generated by incorporating the unnatural amino acid p-nitrophenylalanine (pNO2Phe) into selected sites in the murine RANKL (mRANKL) molecule. Specifically, mutation of a single tyrosine residue Tyr234 (Y234) or Tyr240 (Y240) of mRANKL to pNO2Phe (thereafter named as Y234pNO2Phe or Y240pNO2Phe) induced a high titer antibody response in mice, whereas no significant antibody response was observed for the wild type mRANKL (WT mRANKL). The antiserum induced by Y234pNO2Phe or Y240pNO2Phe could efficiently prevent osteoclastogenesis in vitro. Moreover, immunization with Y234pNO2Phe or Y240pNO2Phe could also prevent OVX-induced bone loss in mice, suggesting that selected pNO2Phe-substituted mRANKL may pave the way for creating a novel vaccine to treat osteoporosis.


Subject(s)
Bone Resorption/immunology , Bone Resorption/prevention & control , Ovariectomy/adverse effects , Phenylalanine/analogs & derivatives , RANK Ligand/chemistry , Vaccines/immunology , Amino Acid Sequence , Animals , Bone Resorption/etiology , Bone Resorption/pathology , Cell Differentiation , Female , Immunization , Immunoglobulin G/metabolism , Mice, Inbred C57BL , Osteoclasts/metabolism , Phenylalanine/chemistry
13.
Sci Rep ; 7(1): 6131, 2017 07 21.
Article in English | MEDLINE | ID: mdl-28733675

ABSTRACT

The Surface Evolver is used to minimize the surface energy of two ordered structures for bilayer monodisperse wet foams with arbitrary liquid fraction. Previous researchers have found a reversible structural transition in bilayer monodisperse foams by changing the foam liquid fraction in a physical experiment. We simulated this phenomenon by analyzing the interfacial energy of two bilayer foam systems with varying liquid fractions. The calculations reported here show that the Tóth structure is energy minimizing when the liquid fraction is below a critical value, around 2.26%, above which point the honeycomb structure becomes preferable, although the Tóth structure remains metastable.

14.
PLoS Genet ; 13(4): e1006714, 2017 04.
Article in English | MEDLINE | ID: mdl-28419093

ABSTRACT

Microhomology (MH) flanking a DNA double-strand break (DSB) drives chromosomal rearrangements but its role in mutagenesis has not yet been analyzed. Here we determined the mutation frequency of a URA3 reporter gene placed at multiple locations distal to a DSB, which is flanked by different sizes (15-, 18-, or 203-bp) of direct repeat sequences for efficient repair in budding yeast. Induction of a DSB accumulates mutations in the reporter gene situated up to 14-kb distal to the 15-bp MH, but more modestly to those carrying 18- and 203-bp or no homology. Increased mutagenesis in MH-mediated end joining (MMEJ) appears coupled to its slower repair kinetics and the extensive resection occurring at flanking DNA. Chromosomal translocations via MMEJ also elevate mutagenesis of the flanking DNA sequences 7.1 kb distal to the breakpoint junction as compared to those without MH. The results suggest that MMEJ could destabilize genomes by triggering structural alterations and increasing mutation burden.


Subject(s)
DNA End-Joining Repair/genetics , DNA/genetics , Mutagenesis/genetics , Saccharomyces cerevisiae Proteins/genetics , Chromosomes/genetics , DNA Breaks, Double-Stranded/drug effects , DNA-Binding Proteins/genetics , Galactose/genetics , Kinetics , Mutagenesis/drug effects , Mutagenesis, Insertional , Saccharomyces cerevisiae , Translocation, Genetic/drug effects , Translocation, Genetic/genetics
15.
EMBO J ; 35(7): 743-58, 2016 Apr 01.
Article in English | MEDLINE | ID: mdl-26717941

ABSTRACT

ATP-dependent DNA end recognition and nucleolytic processing are central functions of the Mre11/Rad50 (MR) complex in DNA double-strand break repair. However, it is still unclear how ATP binding and hydrolysis primes the MR function and regulates repair pathway choice in cells. Here,Methanococcus jannaschii MR-ATPγS-DNA structure reveals that the partly deformed DNA runs symmetrically across central groove between two ATPγS-bound Rad50 nucleotide-binding domains. Duplex DNA cannot access the Mre11 active site in the ATP-free full-length MR complex. ATP hydrolysis drives rotation of the nucleotide-binding domain and induces the DNA melting so that the substrate DNA can access Mre11. Our findings suggest that the ATP hydrolysis-driven conformational changes in both DNA and the MR complex coordinate the melting and endonuclease activity.


Subject(s)
Adenosine Triphosphate/metabolism , Archaeal Proteins/metabolism , DNA/metabolism , Methanococcus/metabolism , Amino Acid Sequence , Archaeal Proteins/chemistry , DNA/chemistry , Molecular Sequence Data , Sequence Homology, Amino Acid
16.
EMBO J ; 33(20): 2422-35, 2014 Oct 16.
Article in English | MEDLINE | ID: mdl-25107472

ABSTRACT

The Mre11-Rad50-Nbs1 (MRN) complex plays important roles in sensing DNA damage, as well as in resecting and tethering DNA ends, and thus participates in double-strand break repair. An earlier structure of Mre11 bound to a short duplex DNA molecule suggested that each Mre11 in a dimer recognizes one DNA duplex to bridge two DNA ends at a short distance. Here, we provide an alternative DNA recognition model based on the structures of Methanococcus jannaschii Mre11 (MjMre11) bound to longer DNA molecules, which may more accurately reflect a broken chromosome. An extended stretch of B-form DNA asymmetrically runs across the whole dimer, with each end of this DNA molecule being recognized by an individual Mre11 monomer. DNA binding induces rigid-body rotation of the Mre11 dimer, which could facilitate melting of the DNA end and its juxtaposition to an active site of Mre11. The identified Mre11 interface binding DNA duplex ends is structurally conserved and shown to functionally contribute to efficient resection, non-homologous end joining, and tolerance to DNA-damaging agents when other resection enzymes are absent. Together, the structural, biochemical, and genetic findings presented here offer new insights into how Mre11 recognizes damaged DNA and facilitates DNA repair.


Subject(s)
Archaeal Proteins/chemistry , DNA Breaks, Double-Stranded , DNA End-Joining Repair , Endodeoxyribonucleases/chemistry , Exodeoxyribonucleases/chemistry , Methanocaldococcus/enzymology , Models, Molecular , Amino Acid Sequence , Archaeal Proteins/genetics , Archaeal Proteins/metabolism , Crystallography, X-Ray , DNA Mutational Analysis , DNA, Archaeal/genetics , DNA, Archaeal/metabolism , Dimerization , Endodeoxyribonucleases/genetics , Endodeoxyribonucleases/metabolism , Exodeoxyribonucleases/genetics , Exodeoxyribonucleases/metabolism , Methanocaldococcus/chemistry , Methanocaldococcus/genetics , Models, Structural , Molecular Sequence Data , Protein Binding , Sequence Alignment
17.
EMBO J ; 32(3): 461-72, 2013 Feb 06.
Article in English | MEDLINE | ID: mdl-23299942

ABSTRACT

The Saccharomyces cerevisiae Rad1/Rad10 complex is a multifunctional, structure-specific endonuclease that processes UV-induced DNA lesions, recombination intermediates, and inter-strand DNA crosslinks. However, we do not know how Rad1/Rad10 recognizes these structurally distinct target molecules or how it is incorporated into the protein complexes capable of incising divergent substrates. Here, we have determined the order and hierarchy of assembly of the Rad1/Rad10 complex, Saw1, Slx4, and Msh2/Msh3 complex at a 3' tailed recombination intermediate. We found that Saw1 is a structure-specific DNA binding protein with high affinity for splayed arm and 3'-flap DNAs. By physical interaction, Saw1 facilitates targeting of Rad1 at 3' tailed substrates in vivo and in vitro, and enhances 3' tail cleavage by Rad1/Rad10 in a purified system in vitro. Our results allow us to formulate a model of Rad1/Rad10/Saw1 nuclease complex assembly and 3' tail removal in recombination.


Subject(s)
DNA Repair Enzymes/metabolism , DNA Repair/genetics , DNA-Binding Proteins/metabolism , Endonucleases/metabolism , Multiprotein Complexes/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Single-Strand Specific DNA and RNA Endonucleases/metabolism , Chromatin Immunoprecipitation , DNA Primers/genetics , DNA Repair/physiology , DNA-Binding Proteins/genetics , Electrophoretic Mobility Shift Assay , Gene Expression Profiling , Mutagenesis , Recombination, Genetic/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/genetics
18.
Curr Eye Res ; 36(9): 838-49, 2011 Sep.
Article in English | MEDLINE | ID: mdl-21851170

ABSTRACT

PURPOSE: Choroidal neovascularization (CNV) is a major cause of vision loss in patients with age-related macular degeneration (AMD). Stromal cell-derived factor-1 (SDF-1)/CXC chemokine receptor 4 (CXCR4) plays a critical role in homing of bone marrow-derived cells (BMCs) to choroidal neovascularization (CNV). In this study, we investigated the contribution of hypoxia specific HIF-1α-induced SDF-1 expression in retinal pigment epithelium (RPE) cells and the potential role of SDF-1 in CNV formation. MATERIALS AND METHODS: Green fluorescent protein (GFP) chimeric mice were developed by transplanting bone marrow cells of gfp(+/+) transgenic mice to sublethally irradiated C57BL/6J mice. CNV was induced by laser photocoagulation. Ocular tissue was processed for immunofluorescence to detect HIF-1α and SDF-1 expression, and cell surface markers such as CXCR4, CD34 and CD31 and so on during CNV formation. In vitro, adult human RPE (hRPE) cells were cultured under conditions of chemical hypoxia using CoCl2 administration. And RNAi technique was used to knock down HIF-1α gene to observe the expression of HIF-1α and SDF-1 in hRPE cells. RESULTS: BMCs trafficked around laser lesion adjacent to RPE layer 4 h after laser photocoagulation, where SDF-1 expression was relatively higher. With increasing expression of SDF-1, more BMCs were infiltrated into laser lesion to participate in CNV, and both reached peak at 3 d (p < 0.05). About 81% BMCs involved in CNV were CXCR4+. Many of them acquired the surface marker of endothelial precursor cells (CD34+) and endothelial cells (CD31+). The constituent ratio of CD34+ and CD31+ BMCs increased with SDF-1 expression. In vitro, we proved that hypoxia specific-HIF-1α influenced SDF-1 expression in hRPE cells. CONCLUSIONS: These findings suggested that hypoxia-induced SDF-1 expression in RPE might be a critical initiator for recruitment of BMCs in CNV. SDF-1 might be another important factor in BMCs' differentiation into endothelial cells to participate in the CNV.


Subject(s)
Chemokine CXCL12/genetics , Choroidal Neovascularization/genetics , DNA/genetics , Gene Expression Regulation , Macrophages/pathology , Retinal Pigment Epithelium/metabolism , Adult , Animals , Blotting, Western , Cells, Cultured , Chemokine CXCL12/biosynthesis , Choroidal Neovascularization/metabolism , Choroidal Neovascularization/pathology , Disease Models, Animal , Enzyme-Linked Immunosorbent Assay , Humans , Lasers/adverse effects , Macrophages/metabolism , Mice , Mice, Inbred C57BL , Real-Time Polymerase Chain Reaction , Retinal Pigment Epithelium/pathology
19.
Appl Biochem Biotechnol ; 152(2): 306-15, 2009 Feb.
Article in English | MEDLINE | ID: mdl-18758694

ABSTRACT

The full-length hNdrg2 cDNA-coded 357 amino acids was cloned and expressed in Escherichia coli strain DH5alpha as a 6x His-tagged protein. The purified 6x His-fusion protein was used to immunize mice for preparing monoclonal antibodies (mAb) against N-myc downstream-regulated gene 2 (Ndrg2). A hybridoma secreting a monoclonal antibody against Ndrg2 was obtained and named FMU-Ndrg2.3. Western blot analysis confirmed that this mAb is specific only to Ndrg2 but not to Ndrg1, Ndrg3, and Ndrg4-B. Some tissue distribution features of Ndrg2 proteins, such as thyroid, kidney, testis, prostate, and pancreas islets, were present by immunohistochemistry.


Subject(s)
Antibodies, Monoclonal/immunology , Tumor Suppressor Proteins/immunology , Animals , Antibody Specificity , Blotting, Western , Cattle , Escherichia coli/genetics , Female , Humans , Hybridomas/immunology , Immunohistochemistry , Mice , Recombinant Fusion Proteins/analysis , Recombinant Fusion Proteins/immunology , Recombinant Fusion Proteins/metabolism , Recombinant Fusion Proteins/pharmacokinetics , Staining and Labeling , Tissue Distribution , Tumor Suppressor Proteins/analysis , Tumor Suppressor Proteins/metabolism , Tumor Suppressor Proteins/pharmacokinetics
20.
Eur J Pharmacol ; 591(1-3): 252-8, 2008 Sep 04.
Article in English | MEDLINE | ID: mdl-18619958

ABSTRACT

This study is the first to investigate Calebin-A, a natural compound present in Curcuma longa, which inhibits cell growth and induce apoptosis in SGC7901/VINCRISTINE cells, a multidrug resistant (MDR) human gastric adenocarcinoma cell line. Our data suggest the drug efflux function of P-glycoprotein was inhibited by Calebin-A treatment, while the expression level of P-glycoprotein was not affected. Additionally, co-treatment of Calebin-A and vincristine resulted in a remarkable reduction in S phase and G2/M phase arrest in SGC7901/VINCRISTINE cells. Calebin-A was also found to modulate the activities of mitogen-activated protein kinase (MAPK) family members, which includes decreased c-Jun N-terminal kinase (JNK), extracellular signal-regulated kinase (ERK) and increased protein kinase of 38 kDa (p38) activity. These results suggest that Calebin-A might be an effective compound for the treatment of human gastric and other MDR cancers.


Subject(s)
Antineoplastic Agents, Phytogenic/pharmacology , Cinnamates/pharmacology , Mitogen-Activated Protein Kinases/drug effects , Monoterpenes/pharmacology , Stomach Neoplasms/drug therapy , ATP Binding Cassette Transporter, Subfamily B, Member 1/drug effects , ATP Binding Cassette Transporter, Subfamily B, Member 1/metabolism , Adenocarcinoma/drug therapy , Adenocarcinoma/pathology , Apoptosis/drug effects , Cell Cycle/drug effects , Cell Line, Tumor , Curcuma/chemistry , Drug Resistance, Multiple , Drug Resistance, Neoplasm , Drug Therapy, Combination , Gene Expression Regulation, Neoplastic/drug effects , Humans , Mitogen-Activated Protein Kinases/metabolism , Stomach Neoplasms/pathology , Vincristine/pharmacology
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