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1.
Parasit Vectors ; 14(1): 386, 2021 Aug 04.
Article in English | MEDLINE | ID: mdl-34348769

ABSTRACT

BACKGROUND: The salivary glands of female ticks degenerate rapidly by apoptosis and autophagy after feeding. Bcl-2 family proteins play an important role in the apoptosis pathways, but the functions of these proteins in ticks are unclear. We studied Bcl-2 and Bax homologs from Rhipicephalus haemaphysaloides and determined their functions in the degeneration of the salivary glands. METHODS: Two molecules containing conserved BH (Bcl-2 family homology) domains were identified and named RhBcl-2 and RhBax. After protein purification and mouse immunization, specific polyclonal antibodies (PcAb) were created in response to the recombinant proteins. Reverse transcription quantitative PCR (RT-qPCR) and western blot were used to detect the presence of RhBcl-2 and RhBax in ticks. TUNEL assays were used to determine the level of apoptosis in the salivary glands of female ticks at different feeding times after gene silencing. Co-transfection and GST pull-down assays were used to identify interactions between RhBcl-2 and RhBax. RESULTS: The RT-qPCR assay revealed that RhBax gene transcription increased significantly during feeding at all tick developmental stages (engorged larvae, nymphs, and adult females). Transcriptional levels of RhBcl-2 and RhBax increased more significantly in the female salivary glands than in other tissues post engorgement. RhBcl-2 silencing significantly inhibited tick feeding. In contrast, RhBax interference had no effect on tick feeding. TUNEL staining showed that apoptosis levels were significantly reduced after interference with RhBcl-2 expression. Co-transfection and GST pull-down assays showed that RhBcl-2 and RhBax could interact but not combine in the absence of the BH3 domain. CONCLUSIONS: This study identified the roles of RhBcl-2 and RhBax in tick salivary gland degeneration and finds that the BH3 domain is a key factor in their interactions.


Subject(s)
Proto-Oncogene Proteins/isolation & purification , Rhipicephalus/metabolism , bcl-2-Associated X Protein/isolation & purification , Animals , Apoptosis , Female , In Situ Nick-End Labeling , Mice , Proto-Oncogene Proteins/physiology , Salivary Glands/metabolism , Salivary Glands/pathology , bcl-2-Associated X Protein/physiology
2.
Methods Mol Biol ; 2272: 225-237, 2021.
Article in English | MEDLINE | ID: mdl-34009617

ABSTRACT

The 5-methylcytosine (5mC) oxidation pathway mediated by TET proteins involves step-wise oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC and 5caC can be removed from DNA by base excision repair and the completion of this pathway results in "demethylation" of 5mC by converting the modified base back into cytosine. In vitro studies with TET proteins aimed at analyzing their DNA substrate specificities and their activity within defined chromatin templates are relatively limited. Here we describe purification methods for mammalian TET proteins based on expression in insect cells or in 293T cells. We also briefly summarize a method that can be used to monitor 5-methylcytosine oxidase activity of the purified TET proteins in vitro.


Subject(s)
5-Methylcytosine/analogs & derivatives , 5-Methylcytosine/chemistry , DNA Methylation , DNA/analysis , Mixed Function Oxygenases/isolation & purification , Mixed Function Oxygenases/metabolism , Proto-Oncogene Proteins/isolation & purification , Proto-Oncogene Proteins/metabolism , DNA/chemistry , DNA/genetics , Humans , Mixed Function Oxygenases/genetics , Oxidation-Reduction , Proto-Oncogene Proteins/genetics , Substrate Specificity
3.
Theranostics ; 10(23): 10769-10790, 2020.
Article in English | MEDLINE | ID: mdl-32929379

ABSTRACT

Rationale: A number of guanine nucleotide exchange factors (GEFs) including epithelial cell transforming factor ECT2 are believed to drive carcinogenesis through activating distinct oncogenic GTPases. Yet, whether GEF-independent activity of ECT2 also plays a role in tumorigenesis remains unclear. Methods: Immunohistochemical (IHC) staining, colony formation and xenograft assays were used to examine the role of ECT2 in breast carcinogenesis. Co-immunoprecipitation, immunofluorescent stainings, in vivo deubiquitination and in vitro deubiquitination experiments were performed to examine the physical and functional interaction between ECT2 and ubiquitin-specific protease USP7. High-throughput RNA sequencing, quantitative reverse transcription-PCR and Western blotting were employed to investigate the biological significance of the interplay between ECT2 and USP7. Results: We report that ECT2 plays a tumor-promoting role in breast cancer, and GEF activity-deficient ECT2 is able to alleviate ECT2 depletion associated growth defects in breast cancer cells. Mechanistically, we demonstrated that ECT2 physically interacts with ubiquitin-specific protease USP7 and functionally facilitates USP7 intermolecular self-association, -deubiquitination and -stabilization in a GEF activity-independent manner. USP7 in turn, deubiquitinates and stabilizes ECT2, resulting in a feedforward regulatory circuit that ultimately sustains the expression of oncogenic protein MDM2. Conclusion: Our study uncovers a GEF-independent role of ECT2 in promoting survival of breast cancer cells, provides a molecular insight for the reciprocal regulation of ECT2 and USP7, and supports the pursuit of ECT2/USP7 as potential targets for breast cancer intervention.


Subject(s)
Breast Neoplasms/genetics , Carcinogenesis/genetics , Proto-Oncogene Proteins c-mdm2/genetics , Proto-Oncogene Proteins/metabolism , Ubiquitin-Specific Peptidase 7/metabolism , Animals , Breast Neoplasms/pathology , Cell Line, Tumor , Cell Survival/genetics , Enzyme Assays , Feedback, Physiological , Female , Gene Expression Regulation, Neoplastic , Gene Knockdown Techniques , Gene Knockout Techniques , HEK293 Cells , Humans , Mice , Protein Binding/genetics , Protein Stability , Proto-Oncogene Proteins/genetics , Proto-Oncogene Proteins/isolation & purification , RNA-Seq , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Ubiquitin-Specific Peptidase 7/genetics , Ubiquitin-Specific Peptidase 7/isolation & purification , Ubiquitination , Xenograft Model Antitumor Assays
4.
Oncoimmunology ; 9(1): 1758003, 2020 05 06.
Article in English | MEDLINE | ID: mdl-32923114

ABSTRACT

Introduction: Despite some of the oncogenic driver mutations that have been associated with increased expression of programmed death-ligand 1 (PD-L1), the correlation between PD-L1 expression and ROS1 fusion in NSCLC cells, especially for those with Crizotinib resistance has not been fully addressed. Materials and Methods: The expression of PD-L1 in 30 primary NSCLC tumors with/without ROS1-fusion protein was evaluated by immunohistochemical (IHC) analysis. To assess the correlation between ROS1 fusion and PD-L1 expression, we down-regulated ROS1 with RNA interference or specific inhibitor (Crizotinib) in ROS1-fusion positive NSCLC cell line HCC78; or up-regulate ROS1-fusion gene in an immortalized human bronchial epithelial cell line (HBE). Mouse xenograft models were also used to determine the effect of ROS1 expression on PD-L1 expression in vivo. Crizotinib-resistant cell line was generated for measuring the association between Crizotinib resistance and PD-L1 expression. Results: ROS1-rearrangement in primary NSCLC tumor was significantly associated with up-regulated PD-L1 expression. PD-L1 expression was significantly up-regulated in bronchial epithelial cells after forced expression of ROS1 fusion and was eliminated when HCC78 xenograft mouse models were treated with Crizotinib. We found PD-L1 expression was modulated by MEK-ERK pathway signaling in both parental and Crizotinib-resistant NSCLC cells with ROS1 fusion. Conclusions: The correlation between ROS1-fusion and PD-L1 overexpression suggested that PD-L1/PD-1 blockade could be the second-line treatment option for the Crizotinib-resistant NSCLC with ROS1 rearrangement.


Subject(s)
B7-H1 Antigen , Carcinoma, Non-Small-Cell Lung , Lung Neoplasms , MAP Kinase Signaling System , Oncogene Proteins, Fusion , Protein-Tyrosine Kinases , Proto-Oncogene Proteins , Animals , B7-H1 Antigen/biosynthesis , B7-H1 Antigen/genetics , B7-H1 Antigen/immunology , Carcinoma, Non-Small-Cell Lung/drug therapy , Heterografts , Humans , Lung Neoplasms/drug therapy , Mice , Mitogen-Activated Protein Kinase Kinases/metabolism , Protein-Tyrosine Kinases/genetics , Protein-Tyrosine Kinases/isolation & purification , Proto-Oncogene Proteins/genetics , Proto-Oncogene Proteins/isolation & purification
5.
Protein Expr Purif ; 165: 105499, 2020 01.
Article in English | MEDLINE | ID: mdl-31541685

ABSTRACT

The protein ALL1 fused from chromosome 1q (AF1q) is overexpressed in a variety of cancers and acts to activate several signaling pathways that lead to oncogenesis. For example, AF1q has been shown to interact with T-cell Factor 7 (TCF7; also known as TCF1) from the Wnt/ß-catenin pathway resulting in the transcriptional activation of the CD44 and the enhancement of breast cancer metastasis. Despite the importance of AF1q in facilitating oncogenesis and metastasis, the structural and biophysical properties of AF1q remain largely unexplored due to the absence of a viable method for producing recombinant protein. Here, we report the overexpression of AF1q in E. coli as a fusion to a N-terminal His6-tag, which forms inclusion bodies (IBs) during expression. The AF1q protein was purified from IBs under denaturing conditions by immobilized metal affinity chromatography followed by a successful one-step dialysis refolding. Refolded AF1q was further purified to homogeneity by gel filtration chromatography resulting in an overall yield of 35 mg/L culture. Our nuclear magnetic resonance (NMR) and analytical ultracentrifugation (AUC) measurements reveal AF1q interacts with TCF7, specifically with TCF7's high-mobility group (HMG) domain (residues 154-237), which is, to our knowledge, the first biophysical characterization of the AF1q and TCF7 interaction.


Subject(s)
Neoplasm Proteins/genetics , Proto-Oncogene Proteins/genetics , Recombinant Proteins/genetics , T Cell Transcription Factor 1/metabolism , Amino Acid Sequence , Base Sequence , Binding Sites , Chromatography, Affinity , Cloning, Molecular , Escherichia coli , Gene Expression Regulation, Bacterial , Humans , Magnetic Resonance Spectroscopy , Neoplasm Proteins/isolation & purification , Neoplasm Proteins/metabolism , Protein Binding , Protein Conformation , Proto-Oncogene Proteins/isolation & purification , Proto-Oncogene Proteins/metabolism , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Ultracentrifugation
6.
J Vis Exp ; (140)2018 10 15.
Article in English | MEDLINE | ID: mdl-30371677

ABSTRACT

The epigenetic transcription regulation mediated by 5-methylcytosine (5mC) has played a critical role in eukaryotic development. Demethylation of these epigenetic marks is accomplished by sequential oxidation by ten-eleven translocation dioxygenases (TET1-3), followed by the thymine-DNA glycosylase-dependent base excision repair. Inactivation of the TET2 gene due to genetic mutations or by other epigenetic mechanisms is associated with a poor prognosis in patients with diverse cancers, especially hematopoietic malignancies. Here, we describe an efficient single step purification of enzymatically active untagged human TET2 dioxygenase using cation exchange chromatography. We further provide a liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach that can separate and quantify the four normal DNA bases (A, T, G, and C), as well as the four modified cytosine bases (5-methyl, 5-hydroxymethyl, 5-formyl, and 5-carboxyl). This assay can be used to evaluate the activity of wild type and mutant TET2 dioxygenases.


Subject(s)
Chromatography, Liquid , DNA-Binding Proteins/isolation & purification , DNA-Binding Proteins/metabolism , Enzyme Assays/methods , Proto-Oncogene Proteins/isolation & purification , Proto-Oncogene Proteins/metabolism , Tandem Mass Spectrometry , 5-Methylcytosine/analysis , 5-Methylcytosine/metabolism , Cytosine/analogs & derivatives , Cytosine/analysis , DNA/chemistry , DNA Demethylation , Dioxygenases , Humans
7.
Protein Expr Purif ; 132: 143-151, 2017 04.
Article in English | MEDLINE | ID: mdl-28188826

ABSTRACT

5-Methylcytosine within CpG islands in DNA plays a crucial role in epigenetic transcriptional regulation during metazoan development. Recently, it has been established that the Ten-Eleven Translocation (TET) family, Fe(II)- and 2-oxoglutarate (2OG/αKG)-dependent oxygenases initiate 5-methylcytosine demethylation by iterative oxidation reactions. Mutations in the TET2 gene are frequently detected in patients with myeloid malignancies. Here, we describe the cloning of untagged human TET2 demethylase using Gateway technology and its efficient expression in E. coli. The untagged TET2 enzyme was purified using cation exchange and heparin sepharose chromatography. In addition, a reliable quantitative liquid chromatography-tandem mass spectrometry-based assay was utilized to analyze the activity of TET2 oxygenase. This assay was further used to analyze the activity of a number of clinical TET2 variants with mutations in the 2OG binding sites. Our results demonstrate that the activity of one TET2 mutant, TET2-R1896S, can be restored using an excess of 2OG in the reaction mixture. These studies suggest that dietary 2OG supplements, which are commonly used for several other conditions, may be used to treat some patients with myeloid malignancies harboring TET2-R1896S mutation. Results described in this paper serve as a foundation for better characterization of wild type as well as mutant TET2 demethylases.


Subject(s)
DNA-Binding Proteins , Gene Expression , Oxidoreductases , Proto-Oncogene Proteins , Chromatography, Liquid , DNA-Binding Proteins/biosynthesis , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/genetics , DNA-Binding Proteins/isolation & purification , Dioxygenases , Escherichia coli/genetics , Escherichia coli/metabolism , Humans , Mass Spectrometry , Oxidoreductases/biosynthesis , Oxidoreductases/chemistry , Oxidoreductases/genetics , Oxidoreductases/isolation & purification , Proto-Oncogene Proteins/biosynthesis , Proto-Oncogene Proteins/chemistry , Proto-Oncogene Proteins/genetics , Proto-Oncogene Proteins/isolation & purification , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification
8.
Methods Mol Biol ; 1515: 37-53, 2017.
Article in English | MEDLINE | ID: mdl-27797072

ABSTRACT

During the cell cycle, duplicated sister chromatids become physically connected during S phase through a process called sister-chromatid cohesion. Cohesion is terminated during the metaphase-to-anaphase transition to trigger sister-chromatid segregation. The establishment and dissolution of cohesion are highly regulated by the cohesin complex and its multitude of regulators. In particular, the cohesin regulator Wapl promotes the release of cohesin from chromosomes during both interphase and mitosis. Here, we describe in vitro protein binding assays between Wapl and a cohesin subcomplex, and cellular assays in human cells that probe the functions of Wapl in cohesin release.


Subject(s)
Carrier Proteins/isolation & purification , Cell Cycle Proteins/isolation & purification , Chromosomal Proteins, Non-Histone/isolation & purification , Chromosome Segregation/genetics , Molecular Biology/methods , Nuclear Proteins/isolation & purification , Proto-Oncogene Proteins/isolation & purification , Carrier Proteins/genetics , Cell Cycle Proteins/genetics , Chromatids/genetics , Chromosomal Proteins, Non-Histone/genetics , Humans , Mitosis/genetics , Nuclear Proteins/genetics , Proto-Oncogene Proteins/genetics , Saccharomyces cerevisiae/genetics , Cohesins
9.
Mol Cell Biochem ; 418(1-2): 119-35, 2016 Jul.
Article in English | MEDLINE | ID: mdl-27334754

ABSTRACT

The Wnt signaling pathway plays a predominant role in aberrant proliferation in myriad of cancers. In non-cancerous cells, Wnts are blocked by the secreted frizzled-related proteins (sFRPs) that are generally downregulated in cancer cells. We have purified and characterized bacterially expressed glutathione S-transferase-tagged SFRP4 from a novel clone generated from human cell origin. Cervical cancer (HeLa) and lung cancer (A549) cells, in which Wnt and associated genes were found to be expressed, were treated with the purified recombinant sFRP4, which revealed a significant dose-dependent cell growth inhibition up to 40 %. The current investigation on functionality of this bacterially produced recombinant sFRP4 in arresting cancer cell proliferation is the first of its kind, where G2/M phase arrest and early apoptosis were evident. Increase in phosphorylated ß-catenin in sFRP4 treatment indicated inhibition of Wnt pathway, which was further confirmed by downregulation of pro-proliferative genes, namely cyclin D1, c-myc, and survivin. Functional activity of recombinant sFRP4 was further exploited in co-therapy module with chemotherapeutic drugs to decipher molecular events. Collectively, our study on purified recombinant sFRP4 from bacterial host holds great promise in targeting Wnt signaling for exploring new strategies to combat cancer.


Subject(s)
Antineoplastic Agents , Cell Division/drug effects , G2 Phase/drug effects , Neoplasms/drug therapy , Proto-Oncogene Proteins , Wnt Signaling Pathway/drug effects , Antineoplastic Agents/chemistry , Antineoplastic Agents/isolation & purification , Antineoplastic Agents/pharmacology , Escherichia coli , HEK293 Cells , HeLa Cells , Humans , Neoplasm Proteins/biosynthesis , Neoplasms/metabolism , Neoplasms/pathology , Proto-Oncogene Proteins/biosynthesis , Proto-Oncogene Proteins/chemistry , Proto-Oncogene Proteins/isolation & purification , Proto-Oncogene Proteins/pharmacology , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Recombinant Proteins/pharmacology
10.
Protein Expr Purif ; 118: 105-12, 2016 Feb.
Article in English | MEDLINE | ID: mdl-26518367

ABSTRACT

Human neutrophil gelatinase associated lipocalin (NGAL) is a secretory glycoprotein initially isolated from neutrophils. It is thought to be involved in the incidence and development of immunological diseases and cancers. Urinary and serum levels of NGAL have been investigated as a new biomarker of acute kidney injury (AKI), for an earlier and more accurate detection method than with creatinine level. However, expressing high-quality recombinant NGAL is difficult both in Escherichia coli and mammalian cells for the low yield. Here, we cloned and fused NGAL to the C-terminus of signal peptides of human NGAL, human interleukin-2 (IL2), gaussia luciferase (Gluc), human serum albumin preproprotein (HSA) or an hidden Markov model-generated signal sequence (HMM38) respectively for transient expression in Expi293F suspension cells to screen for their ability to improve the secretory expression of recombinant NGAL. The best results were obtained with signal peptide derived from HSA. The secretory recombinant protein could react specifically with NGAL antibody. For scaled production, we used HSA signal peptide to establish stable Chinese hamster ovary cell lines. Then we developed a convenient colony-selection system to select high-expression, stable cell lines. Moreover, we purified the NGAL with Ni-Sepharose column. The recombinant human NGAL displayed full biological activity. We provide a method to enhance the secretory expression of recombinant human NGAL by using the HSA signal peptide and produce the glycoprotein in mammalian cells.


Subject(s)
Acute-Phase Proteins/genetics , Lipocalins/genetics , Protein Engineering , Proto-Oncogene Proteins/genetics , Acute-Phase Proteins/chemistry , Acute-Phase Proteins/isolation & purification , Acute-Phase Proteins/metabolism , Animals , CHO Cells , Cricetinae , Cricetulus , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Humans , Lipocalin-2 , Lipocalins/chemistry , Lipocalins/isolation & purification , Lipocalins/metabolism , Lysobacter/genetics , Lysobacter/metabolism , Protein Folding , Protein Sorting Signals , Proto-Oncogene Proteins/chemistry , Proto-Oncogene Proteins/isolation & purification , Proto-Oncogene Proteins/metabolism , Serum Albumin/chemistry , Serum Albumin/genetics
11.
Chembiochem ; 17(8): 759-67, 2016 Apr 15.
Article in English | MEDLINE | ID: mdl-26634982

ABSTRACT

Polo-like kinase 1 (Plk1), a validated cancer target, harbors a protein-protein interaction domain referred to as the polo-box domain (PBD), in addition to its enzymatic domain. Although functional inhibition either of the enzymatic domain or of the PBD has been shown to inhibit Plk1, so far there have been no reports of bifunctional agents with the potential to target both protein domains. Here we report the development of Plk1 inhibitors that incorporate both an ATP-competitive ligand of the enzymatic domain, derived from BI 2536, and a functional inhibitor of the PBD, based either on the small molecule poloxin-2 or on a PBD-binding peptide. Although these bifunctional agents do not seem to bind both protein domains simultaneously, the most potent compound displays low-nanomolar activity against the Plk1 PBD, with excellent selectivity over the PBDs of Plk2 and Plk3. Our data provide insights into challenges and opportunities relating to the optimization of Plk1 PBD ligands as potent Plk1 inhibitors.


Subject(s)
Cell Cycle Proteins/antagonists & inhibitors , Peptides/pharmacology , Protein Kinase Inhibitors/pharmacology , Protein Serine-Threonine Kinases/antagonists & inhibitors , Proto-Oncogene Proteins/antagonists & inhibitors , Cell Cycle Proteins/isolation & purification , Cell Cycle Proteins/metabolism , Dose-Response Relationship, Drug , Fluorescence Polarization , Humans , Molecular Structure , Peptides/chemical synthesis , Peptides/chemistry , Protein Kinase Inhibitors/chemistry , Protein Serine-Threonine Kinases/isolation & purification , Protein Serine-Threonine Kinases/metabolism , Proto-Oncogene Proteins/isolation & purification , Proto-Oncogene Proteins/metabolism , Structure-Activity Relationship , Polo-Like Kinase 1
12.
Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi ; 31(7): 933-6, 2015 Jul.
Article in Chinese | MEDLINE | ID: mdl-26146065

ABSTRACT

OBJECTIVE: To construct a prokaryotic expression vector of human neutrophil gelatinase associated lipocalin (NGAL) and identify the bioactivity of the fusion protein. METHODS: The cDNA of human NGAL obtained from GenBank was linked to a cloning vector to construct the prokaryotic expression vector pCold-NGAL. Then the vector was transformed into E.coli BL21(DE3) plysS. Under the optimal induction condition, the recombinant NGAL (rNGAL) was expressed and purified by Ni Sepharose 6 Fast Flow affinity chromatography. The purity and activity of the rNGAL were respectively identified by SDS-PAGE and Western blotting combined with NGAL reagent (Latex enhanced immunoturbidimetry). RESULTS: Restriction enzyme digestion and nucleotide sequencing proved that the expression vector pCold-NGAL was successfully constructed. Under the optimal induction condition that we determined, the rNGAL was expressed in soluble form in E.coli BL21(DE3) plysS. The relative molecular mass of the rNGAL was 25 000, and its purity was more than 98.0%. Furthermore, Western blotting and immunoturbidimetry indicated that the rNGAL reacted with NGAL mAb specifically. CONCLUSION: Human rNGAL of high purity and bioactivity was successfully constructed in E.coli BL21(DE3) plysS using the expression vector pCold-NGAL.


Subject(s)
Acute-Phase Proteins/genetics , Acute-Phase Proteins/immunology , Escherichia coli/genetics , Genetic Engineering/methods , Lipocalins/genetics , Lipocalins/immunology , Proto-Oncogene Proteins/genetics , Proto-Oncogene Proteins/immunology , Acute-Phase Proteins/isolation & purification , Cloning, Molecular , Gene Expression , Genetic Vectors/genetics , Humans , Lipocalin-2 , Lipocalins/isolation & purification , Proto-Oncogene Proteins/isolation & purification , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/immunology , Recombinant Fusion Proteins/isolation & purification
13.
Methods Cell Biol ; 129: 369-382, 2015.
Article in English | MEDLINE | ID: mdl-26175448

ABSTRACT

Centrosomes are major microtubule-organizing centers in eukaryotic cells and play a critical role in embryonic development and asymmetric cell division. Centrosomes comprise a pair of centrioles surrounded by an amorphous proteinaceous meshwork called the pericentriolar material (PCM). Robust deposition of PCM around the centrioles is essential for a centrosome to achieve full microtubule nucleating potential. Despite the wealth of information on PCM composition and function, the mechanism and regulation of PCM assembly have been difficult to ascertain, due in part to the lack of an in vitro system. Here, we describe methods to establish an in vitro system to study PCM assembly in Caenorhabditis elegans. Specifically, we describe (1) how to express and purify the C. elegans PCM proteins SPD-5, SPD-2, and PLK-1 from baculovirus-infected insect cells, (2) how to assemble these proteins into PCM-like structures in vitro, and (3) how to quantify this assembly process in a semiautomated fashion.


Subject(s)
Caenorhabditis elegans Proteins/chemistry , Cell Cycle Proteins/chemistry , Centrioles/chemistry , Animals , Caenorhabditis elegans Proteins/isolation & purification , Cell Cycle Proteins/isolation & purification , Chromatography, Affinity , Drosophila Proteins/chemistry , Drosophila Proteins/isolation & purification , Green Fluorescent Proteins/chemistry , Microscopy, Fluorescence , Protein Multimerization , Protein Serine-Threonine Kinases/chemistry , Protein Serine-Threonine Kinases/isolation & purification , Proto-Oncogene Proteins/chemistry , Proto-Oncogene Proteins/isolation & purification , Sf9 Cells , Polo-Like Kinase 1
14.
Mol Cell Biol ; 33(10): 2067-77, 2013 May.
Article in English | MEDLINE | ID: mdl-23508102

ABSTRACT

Methylation of lysine 4 on histone H3 (H3K4) at promoters is tightly linked to transcriptional regulation in human cells. At least six different COMPASS-like multisubunit (SET1/MLL) complexes that contain methyltransferase activity for H3K4 have been described, but a comprehensive and quantitative analysis of these SET1/MLL complexes is lacking. We applied label-free quantitative mass spectrometry to determine the subunit composition and stoichiometry of the human SET1/MLL complexes. We identified both known and novel, unique and shared interactors and determined their distribution and stoichiometry over the different SET1/MLL complexes. In addition to being a core COMPASS subunit, the Dpy30 protein is a genuine subunit of the NURF chromatin remodeling complex. Furthermore, we identified the Bod1 protein as a discriminator between the SET1B and SET1A complexes, and we show that the H3K36me-interactor Psip1 preferentially binds to the MLL2 complex. Finally, absolute protein quantification in crude lysates mirrors many of the observed SET1/MLL complex stoichiometries. Our findings provide a molecular framework for understanding the diversity and abundance of the different SET1/MLL complexes, which together establish the H3K4 methylation landscape in human cells.


Subject(s)
DNA-Binding Proteins/metabolism , Histone-Lysine N-Methyltransferase/metabolism , Neoplasm Proteins/metabolism , Protein Subunits/metabolism , Adaptor Proteins, Signal Transducing/isolation & purification , Adaptor Proteins, Signal Transducing/metabolism , Cell Cycle Proteins/isolation & purification , Cell Cycle Proteins/metabolism , Cell Nucleus/metabolism , Chromatography, Affinity , DNA-Binding Proteins/isolation & purification , HeLa Cells , Histone-Lysine N-Methyltransferase/isolation & purification , Humans , Intracellular Signaling Peptides and Proteins , Myeloid-Lymphoid Leukemia Protein/isolation & purification , Myeloid-Lymphoid Leukemia Protein/metabolism , Neoplasm Proteins/isolation & purification , Nuclear Proteins/isolation & purification , Nuclear Proteins/metabolism , Protein Interaction Mapping , Protein Subunits/isolation & purification , Proto-Oncogene Proteins/isolation & purification , Proto-Oncogene Proteins/metabolism , Transcription Factors/isolation & purification , Transcription Factors/metabolism
15.
Mol Cell ; 49(4): 645-56, 2013 Feb 21.
Article in English | MEDLINE | ID: mdl-23352454

ABSTRACT

O-linked N-acetylglucosamine (O-GlcNAc) transferase (Ogt) activity is essential for embryonic stem cell (ESC) viability and mouse development. Ogt is present both in the cytoplasm and the nucleus of different cell types and catalyzes serine and threonine glycosylation. We have characterized the biochemical features of nuclear Ogt and identified the ten-eleven translocation (TET) proteins Tet1 and Tet2 as stable partners of Ogt in the nucleus of ESCs. We show at a genome-wide level that Ogt preferentially associates with Tet1 to genes promoters in close proximity of CpG-rich transcription start sites. These regions are characterized by low levels of DNA modification, suggesting a link between Tet1 and Ogt activities in regulating CpG island methylation. Finally, we show that Tet1 is required for binding of Ogt to chromatin affecting Tet1 activity. Taken together, our data characterize how O-GlcNAcylation is recruited to chromatin and interacts with the activity of 5-methylcytosine hydroxylases.


Subject(s)
DNA-Binding Proteins/metabolism , Embryonic Stem Cells/enzymology , N-Acetylglucosaminyltransferases/metabolism , Proto-Oncogene Proteins/metabolism , Animals , Binding Sites , Cell Nucleus/metabolism , Cells, Cultured , Chromatin , CpG Islands , DNA-Binding Proteins/isolation & purification , Dioxygenases , Embryonic Stem Cells/metabolism , Gene Expression Regulation , Immunoprecipitation , Metabolic Networks and Pathways/genetics , Mice , N-Acetylglucosaminyltransferases/isolation & purification , Promoter Regions, Genetic , Protein Binding , Protein Transport , Proto-Oncogene Proteins/isolation & purification , Signal Transduction/genetics , Transcription Initiation Site
16.
Methods Enzymol ; 512: 93-105, 2012.
Article in English | MEDLINE | ID: mdl-22910204

ABSTRACT

One of the most exciting recent advances in the epigenetic field is the discovery that 5-methylcytosine (5mC) in DNA can be iteratively oxidized by a family of proteins known as Tet proteins to generate 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). These 5mC derivatives can be further processed by thymine-DNA glycosylase (TDG) followed by base excision repair or by replication-dependent dilution leading to DNA demethylation. Given the similarity between 5mC and its oxidation derivatives, many of the conventional techniques used for 5mC analysis cannot distinguish between 5mC and 5hmC/5fC/5caC. Here, we describe 2D-TLC and mass spectrometry methods that we have successfully used in differentiating 5mC from its oxidative derivatives as well as in characterizing the enzymatic activity of Tet proteins both in vitro and in vivo.


Subject(s)
5-Methylcytosine/chemistry , DNA Methylation , DNA-Binding Proteins/chemistry , Enzyme Assays , Proto-Oncogene Proteins/chemistry , 5-Methylcytosine/isolation & purification , Animals , Base Sequence , Chromatography, Thin Layer , DNA/chemistry , DNA-Binding Proteins/biosynthesis , DNA-Binding Proteins/isolation & purification , Dioxygenases , HEK293 Cells , Humans , Mice , Oxidation-Reduction , Proto-Oncogene Proteins/biosynthesis , Proto-Oncogene Proteins/isolation & purification , Spectrometry, Mass, Electrospray Ionization , Tandem Mass Spectrometry
17.
J Proteome Res ; 11(7): 3908-13, 2012 Jul 06.
Article in English | MEDLINE | ID: mdl-22671702

ABSTRACT

Tumor-derived mutant KRAS (v-Ki-ras-2 Kirsten rat sarcoma viral oncogene) oncoprotein is a critical driver of cancer phenotypes and a potential biomarker for many epithelial cancers. Targeted mass spectrometry analysis by multiple reaction monitoring (MRM) enables selective detection and quantitation of wild-type and mutant KRAS proteins in complex biological samples. A recently described immunoprecipitation approach (Proc. Nat. Acad. Sci.2011, 108, 2444-2449) can be used to enrich KRAS for MRM analysis, but requires large protein inputs (2-4 mg). Here, we describe sodium dodecyl sulfate-polyacrylamide gel electrophoresis-based enrichment of KRAS in a low molecular weight (20-25 kDa) protein fraction prior to MRM analysis (GeLC-MRM). This approach reduces background proteome complexity, thus, allowing mutant KRAS to be reliably quantified in low protein inputs (5-50 µg). GeLC-MRM detected KRAS mutant variants (G12D, G13D, G12V, G12S) in a panel of cancer cell lines. GeLC-MRM analysis of wild-type and mutant was linear with respect to protein input and showed low variability across process replicates (CV = 14%). Concomitant analysis of a peptide from the highly similar HRAS and NRAS proteins enabled correction of KRAS-targeted measurements for contributions from these other proteins. KRAS peptides were also quantified in fluid from benign pancreatic cysts and pancreatic cancers at concentrations from 0.08 to 1.1 fmol/µg protein. GeLC-MRM provides a robust, sensitive approach to quantitation of mutant proteins in complex biological samples.


Subject(s)
Mutant Proteins/metabolism , Pancreatic Cyst/metabolism , Proto-Oncogene Proteins/metabolism , ras Proteins/metabolism , Cell Line, Tumor , Electrophoresis, Polyacrylamide Gel , Humans , Mutant Proteins/chemistry , Mutant Proteins/genetics , Mutant Proteins/isolation & purification , Peptide Fragments/chemistry , Proteolysis , Proto-Oncogene Proteins/chemistry , Proto-Oncogene Proteins/genetics , Proto-Oncogene Proteins/isolation & purification , Proto-Oncogene Proteins p21(ras) , Reference Standards , Tandem Mass Spectrometry/standards , ras Proteins/chemistry , ras Proteins/genetics , ras Proteins/isolation & purification
18.
J Proteome Res ; 11(8): 4052-64, 2012 Aug 03.
Article in English | MEDLINE | ID: mdl-22694338

ABSTRACT

Activation of hepatic stellate cells (HSCs) and subsequent uncontrolled accumulation of altered extracellular matrix (ECM) underpin liver fibrosis, a wound healing response to chronic injury, which can lead to organ failure and death. We sought to catalogue the components of fibrotic liver ECM to obtain insights into disease etiology and aid identification of new biomarkers. Cell-derived ECM was isolated from the HSC line LX-2, an in vitro model of liver fibrosis, and compared to ECM from human foreskin fibroblasts (HFFs) as a control. Mass spectrometry analyses of cell-derived ECMs identified, with ≥99% confidence, 61 structural ECM or secreted proteins (48 and 31 proteins for LX-2 and HFF, respectively). Gene ontology enrichment analysis confirmed the enrichment of ECM proteins, and hierarchical clustering coupled with protein-protein interaction network analysis revealed a subset of proteins enriched to fibrotic ECM, highlighting the existence of cell type-specific ECM niches. Thirty-six proteins were enriched to LX-2 ECM as compared to HFF ECM, of which Wnt-5a and CYR61 were validated by immunohistochemistry in human and murine fibrotic liver tissue. Future studies will determine if these and other components may play a role in the etiology of hepatic fibrosis, serve as novel disease biomarkers, or open up new avenues for drug discovery.


Subject(s)
Cysteine-Rich Protein 61/metabolism , Extracellular Matrix/metabolism , Hepatic Stellate Cells/metabolism , Liver Cirrhosis/metabolism , Proteome/metabolism , Proto-Oncogene Proteins/metabolism , Wnt Proteins/metabolism , Animals , Cell Line , Cluster Analysis , Cysteine-Rich Protein 61/isolation & purification , Fibroblasts/metabolism , Humans , Mice , Mice, Inbred C57BL , Protein Interaction Mapping , Protein Interaction Maps , Proteome/isolation & purification , Proteomics , Proto-Oncogene Proteins/isolation & purification , Wnt Proteins/isolation & purification , Wnt-5a Protein
19.
Biosens Bioelectron ; 36(1): 89-94, 2012.
Article in English | MEDLINE | ID: mdl-22534103

ABSTRACT

Herein we report a new strategy for highly sensitive and selective colorimatric assay for genotyping of single-nucleotide polymorphisms (SNPs). It is based on the use of a specific gap ligation reaction, horseradish peroxidase (HRP) for signal amplification, and magnetic beads for the easy separation of the ligated product. Briefly, oligonucleotide capture probe functionalized magnetic beads are first hybridized to a target DNA. Biotinylated oligonucleotide detection probes are then allowed to hybridize to the already captured target DNA. A subsequent ligation at the mutation point joins the two probes together. The introduction of streptavidin-conjugated HRP and a simple magnetic separation allow colorimetric genotyping of SNPs. The assay is able to discriminate one copy of mutant in 1000 copies of wild-type KRAS oncogene at 30 picomolar. The detection limit of the assay is further improved to 1 femtomolar by incorporating a ligation chain reaction amplification step, offering an excellent opportunity for the development of a simple and highly sensitive diagnostic tool.


Subject(s)
Biosensing Techniques/methods , Colorimetry/methods , Genotyping Techniques/methods , Proto-Oncogene Proteins , ras Proteins , Biotin/chemistry , Humans , Limit of Detection , Magnets/chemistry , Mutation , Oligonucleotide Probes/chemistry , Polymorphism, Single Nucleotide , Proto-Oncogene Proteins/genetics , Proto-Oncogene Proteins/isolation & purification , Proto-Oncogene Proteins p21(ras) , ras Proteins/genetics , ras Proteins/isolation & purification
20.
Hybridoma (Larchmt) ; 30(5): 433-43, 2011 Oct.
Article in English | MEDLINE | ID: mdl-22008070

ABSTRACT

The chromosomal translocation t(8;21) often found in acute myeloid leukemia generates an oncogenic fusion protein AML1-ETO. This chimeric oncoprotein disrupts wild-type AML1 function and dysregulates genes important for normal myelopoiesis. Monoclonal antibodies that can capture and detect the AML1-ETO fusion protein would help with early diagnosis and treatment prognosis of acute myeloid leukemia. We report the development of murine monoclonal antibodies (MAbs) that specifically bind epitopes encoded by either AML1 or ETO. Since alignment to the human ETO protein indicated almost 100% homology to the mouse ortholog, a strategy was needed to instruct humoral immunity in mice to focus and respond to self-epitopes. Our strategy to develop capture/detector reagents involved producing MAbs that would bind to epitopes within the non-fused myelopic protein (i.e., either AML1 or ETO). This included a process to select antibodies for their ability to also recognize the translocated chromosomal AML1-ETO fusion protein and to identify complementary capture/detector antibody pairs. Construction of a peptide hapten-carrier complex and use of a rapid immunization protocol resulted in IgM-IgG ETO specific MAbs. These MAbs bound specifically to a recombinant form of AML1-ETO fusion protein expressed in HEK and to an endogenous AML1-ETO form of the fusion protein expressed in Kasumi-1. We report the development of murine hybridoma MAbs derived from immunizations with a peptide "self-epitope." Our findings provide a potential strategy to instruct humoral immunity in mice to focus and respond to self-epitopes. This strategy has been validated with the oncogenic fusion protein AML1-ETO involved in acute myeloid leukemia.


Subject(s)
Antibodies, Monoclonal, Murine-Derived/biosynthesis , Core Binding Factor Alpha 2 Subunit/immunology , Proto-Oncogene Proteins/immunology , Recombinant Fusion Proteins/immunology , Transcription Factors/immunology , Amino Acid Sequence , Animals , Antibody Affinity , Antibody Specificity , Cloning, Molecular , Core Binding Factor Alpha 2 Subunit/isolation & purification , Enzyme-Linked Immunosorbent Assay , Female , HEK293 Cells , Humans , Hybridomas/metabolism , Mice , Mice, Inbred BALB C , Molecular Sequence Data , Proto-Oncogene Proteins/isolation & purification , RUNX1 Translocation Partner 1 Protein , Recombinant Fusion Proteins/isolation & purification , Sequence Homology, Amino Acid , Transcription Factors/isolation & purification
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