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Lin TY, Hua WJ, Yeh H, Tseng AJ. Functional proteomic analysis reveals that fungal immunomodulatory protein reduced expressions of heat shock proteins correlates to apoptosis in lung cancer cells. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2021; 80:153384. [PMID: 33113507 DOI: 10.1016/j.phymed.2020.153384] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Ling Zhi-8 (LZ-8) and GMI are two fungal immunomodulatory proteins (FIPs) with a similar structure and amino acid sequence and are respectively obtained from the medicinal mushroom Ganoderma lucidum and Ganoderma microsporum. They present the anti-cancer progression and metastasis. We previously demonstrated that LZ-8 reduces the tumor progression in lung cancer LLC1 cell-bearing mouse. However, it is unclear whether these FIPs induce changes in the protein expression profile in cancer cells and the mechanism for such a process is not defined. PURPOSE This study determines the changes in the proteomic profile for tumor lesions of LLC1 cell-bearing mouse received with LZ-8 and the potential mechanism for FIPs in anti-lung cancer cells. METHODS The proteomic profile of tumor lesions was determined using two-dimensional electrophoresis and a LTQ-OrbitrapXL mass spectrometer (LC-MS/MS). The biological processes and the signaling pathway enrichment analysis were performed using Ingenuity Pathway Analysis (IPA). The differentially expressed proteins were verified by Western blot. Cell viability was determined by MTT assay. Cell morphology was characterized using electron microscopy. Migration was detected using the Transwell assay. The apoptotic response was determined using Western blot and flow cytometry. RESULTS Obtained results showed that 21 proteins in the tumor lesions exhibited differential (2-fold change, p < 0.05) expression between PBS and LZ-8 treatment groups. LZ-8-induced changes in the proteomic profile that may relate to protein degradation pathways. Specifically, three heat shock proteins (HSPs), HSP60, 70 and 90, were significantly downregulated in tumor lesions of LLC1-bearing mouse received with LZ-8. Both LZ-8 and GMI reduced the protein levels for these HSPs in lung cancer cells. Functional studies showed that they inhibited cell migration but effectively induced apoptotic response in LLC1 cells in vitro. In addition, the inhibitors of HSP60 and HSP70 effectively inhibited cell migration and decreased cell viability of LLC1 cells. CONCLUSIONS LZ-8 induced changes in the proteomic profile of tumor lesions which may regulate the HSPs-related cell viability. Moreover, inhibition of HSPs may be related to the anti-lung cancer activity.
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Affiliation(s)
- Tung-Yi Lin
- Institute of Traditional Medicine, National Yang-Ming University, Taipei, Taiwan; Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan.
| | - Wei-Jyun Hua
- Institute of Traditional Medicine, National Yang-Ming University, Taipei, Taiwan; Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan
| | - Hsin Yeh
- Institute of Traditional Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Ai-Jung Tseng
- Institute of Traditional Medicine, National Yang-Ming University, Taipei, Taiwan
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2
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Chen HM, Lee LC, Hu KY, Tsai WJ, Huang C, Tsay HJ, Liu HK. The application of post-translational modification oriented serum proteomics to assess experimental diabetes with complications. PLoS One 2018; 13:e0206509. [PMID: 30395577 PMCID: PMC6218044 DOI: 10.1371/journal.pone.0206509] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/14/2018] [Indexed: 01/01/2023] Open
Abstract
Proteome analysis of serum from type 2 diabetics with complications may lead to the discovery of diagnostic or prognostic biomarkers. To circumvent the principal barrier of serum proteomics, our investigation aimed to evaluate whether a study of post-translational modification enriched serum proteins could be valuable for the discovery of biomarkers or metabolic pathways related to type 2 diabetes pathogenesis. Type 2 diabetes was induced from high-fat diet fed Sprague Dawley rats with streptozotocin injection. Once diabetic status was confirmed, serum samples from either fasted healthy or diabetic rats were pooled and profiled by two-dimensional difference gel electrophoresis or comparative 2D electrophoresis after protein enrichments using immobilized metal ion, concanavalin A, and lentil affinity chromatography, respectively. Differential expressed proteins were identified and the associated networks were established by an Ingenuity Pathway Analysis. As a result, induced rats became severe diabetic and accompanied by hyperlipidemia, fatty liver, and glomerular hypertrophy. There were 3 total, 14 phosphorylated and 23 glycosylated protein targets differentially expressed. Proteins could be linked to HNF4A, HNF1A, and NFκB transcriptional factors and antigen presentation, humoral immune response, and inflammatory response pathways. Predicted organ toxicity in kidney, heart, and liver matched with our histopathological results. In conclusion, post-translational modification based serum protein enrichment could be a valuable approach to enhance the resolution of serum proteomics without depleting potentially valuable abundant proteins. Our results also indicated the potential association of the hepatic secretome and hepatocyte nuclear factors in the pathogenesis of type 2 diabetes and its complications.
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Affiliation(s)
- Han-Min Chen
- Department of Life Science, Fu Jen Catholic University, New Taipei city, Taiwan, ROC
| | - Lin-Chien Lee
- Department of Physical Medicine and Rehabilitation, Cheng Hsin General Hospital, Taipei, Taiwan, ROC
| | - Kuang-Yu Hu
- Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Wei-Jern Tsai
- Division of Chinese Medicine Literature and Informatics, National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei, Taiwan, ROC
| | - Cheng Huang
- Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei, Taiwan, ROC
- Department of Earth and Life Sciences, University of Taipei, Taipei, Taiwan, ROC
| | - Hui-Jen Tsay
- Institute of Neuroscience, Brain Research Center, school of life science, National Yang-Ming University, Taipei, Taiwan, ROC
- * E-mail: (HKL); (THJ)
| | - Hui-Kang Liu
- Division of Basic Chinese Medicine, National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei, Taiwan, ROC
- Ph.D. Program in Clinical Drug Development of Chinese Herbal Medicine, Taipei Medical University, Taipei, Taiwan, ROC
- * E-mail: (HKL); (THJ)
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3
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Curcumin/Turmeric as an Environment-Friendly Protein Gel Stain. Methods Mol Biol 2018. [PMID: 30097937 DOI: 10.1007/978-1-4939-8745-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
Curcumin, the main curcuminoid in food spice turmeric, is insoluble in water at room temperature. We showed that curcumin can be solubilized in water with the application of heat (100 °C). Here we demonstrate that heat-solubilized curcumin can serve as a nontoxic and environment-friendly fluorescent/colorimetric reversible protein stain. Curcumin, the yellow pigment found in the rhizomes of the perennial herb Curcuma longa (turmeric), is insoluble in aqueous solvents. However, heat solubilization in water renders 1.5% of curcumin soluble. Curcumin solubilized by ethanol or alkali is ineffective in staining proteins. Heat-solubilized curry spice turmeric also stains proteins. Staining is achieved in 30 min, with a sensitivity almost equaling that of Coomassie Brilliant Blue (CBB). Destaining is not required and excess curcumin/turmeric can be discarded into the sink. Binding of proteins by silver inhibits curcumin binding, suggesting similarity of protein binding by silver and curcumin. It costs $1.5-2.0 to stain a mini-gel with curcumin, while turmeric costs less than 0.005 cent. CBB staining/destaining costs about two cents. Curcumin/turmeric, thus, can serve as an ideal nontoxic protein stain.
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4
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Heat/Pressure Treatment with Detergents Significantly Increases Curcumin Solubility and Stability: Its Use as an Environment-Friendly Protein Gel Stain. Methods Mol Biol 2018. [PMID: 30097949 DOI: 10.1007/978-1-4939-8745-0_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
Curcumin, the principal curcuminoid in the food spice turmeric, is insoluble in water at room temperature. We have previously solubilized curcumin in water with the application of heat (100 °C) and found that this solubilized curcumin could be used as a gel protein stain. However, heat solubilization in water solubilized only a small fraction of the curcuminoid (1.5%), making it relatively expensive to stain one gel ($1.5-2 per gel). Heat/pressure solubilization (121 °C/15 psi) helps increase the solubility of curcumin in water to only 5%. Therefore, we ventured into increasing curcumin solubility further by using detergents (Tween 20, Tween 80, or Triton X-100) combined with heat/pressure treatment. Curcumin solubilized with Tween 20, Tween 80 or Triton X-100 stained proteins efficiently as before. We could dramatically increase the solubility of curcumin by solubilizing in detergents such that we had to dilute the solubilized curcumin 1:100 with water to stain proteins. However, we had to use the soluble curcumin (extracted with heat/pressure alone) straight without dilution. Thus, the amount of curcumin solubilized with detergents was at least 100-fold, with 0.5% Tween 80 being the most efficient. Staining can be carried out in 30 min, and sensitivity of staining is similar or better than that obtained with Coomassie Brilliant Blue (CBB). It is unnecessary to destain the gel, and excess curcumin can be discarded into the sink, unlike CBB. Curcumin solubilized in Tween 20 has been found to be stable for a period of over 4 years. Therefore, curcumin solubilized in Tween 80 or Triton X-100 can serve as an efficient nontoxic and environment-friendly protein stain. Tween 80 has been used in cough syrups to make a colloidal suspension, and also in foods. Solubilizing curcumin with Tween 80 would be a useful alternative to increase curcumin bioavailability in clinical studies.
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Abstract
Imidazole-zinc reverse stain (ZN stain) is known for high sensitivity, ease of use, and cost-effective feature. ZN stain is compatible to many experiments of which those are proteomics-related in particular. Here, we describe the ZN staining procedures and the subsequent procedures incorporated in detail, along with the improvements of setup in aspects of visualization and documentation for postprocessing ZN stained gel images.
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Affiliation(s)
- Han-Min Chen
- Department of Life Science, Catholic Fu-Jen University, New Taipei City, Taiwan.
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6
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Sodium polyanethol sulfonate (SPS) falsifies protein staining and quantification and how to solve this problem. J Microbiol Methods 2015; 118:176-81. [DOI: 10.1016/j.mimet.2015.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 10/05/2015] [Accepted: 10/05/2015] [Indexed: 11/18/2022]
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7
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Young GH, Lin JT, Cheng YF, Huang CF, Chao CY, Nong JY, Chen PK, Chen HM. Identification of adenine modulating AMPK activation in NIH/3T3 cells by proteomic approach. J Proteomics 2015; 120:204-14. [DOI: 10.1016/j.jprot.2015.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/28/2015] [Accepted: 03/12/2015] [Indexed: 02/08/2023]
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8
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Chen Y, Lin PX, Hsieh CL, Peng CC, Peng RY. The proteomic and genomic teratogenicity elicited by valproic acid is preventable with resveratrol and α-tocopherol. PLoS One 2014; 9:e116534. [PMID: 25551574 PMCID: PMC4281235 DOI: 10.1371/journal.pone.0116534] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/28/2014] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Previously, we reported that valproic acid (VPA), a common antiepileptic drug and a potent teratogenic, dowregulates RBP4 in chicken embryo model (CEM) when induced by VPA. Whether such teratogenicity is associated with more advanced proteomic and genomic alterations, we further performed this present study. METHODOLOGY/PRINCIPAL FINDINGS VPA (60 µM) was applied to 36 chicken embryos at HH stage 10 (day-1.5). Resveratrol (RV) and vitamin E (vit E) (each at 0.2 and 2.0 µM) were applied simultaneously to explore the alleviation effect. The proteins in the cervical muscles of the day-1 chicks were analyzed using 2D-electrophoresis and LC/MS/MS. While the genomics associated with each specific protein alteration was examined with RT-PCR and qPCR. At earlier embryonic stage, VPA downregulated PEBP1 and BHMT genes and at the same time upregulated MYL1, ALB and FLNC genes significantly (p<0.05) without affecting PKM2 gene. Alternatively, VPA directly inhibited the folate-independent (or the betaine-dependent) remethylation pathway. These features were effectively alleviated by RV and vit E. CONCLUSIONS VPA alters the expression of PEBP1, BHMT, MYL1, ALB and FLNC that are closely related with metabolic myopathies, myogenesis, albumin gene expression, and haemolytic anemia. On the other hand, VPA directly inhibits the betaine-dependent remethylation pathway. Taken together, VPA elicits hemorrhagic myoliposis via these action mechanisms, and RV and vit E are effective for alleviation of such adverse effects.
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Affiliation(s)
- Yeh Chen
- Research Institute of Biotechnology, Hungkuang University, 34 Chung-Chie Rd., Shalu County, Taichung Hsien, Taiwan 43302
| | - Ping-Xiao Lin
- Graduate Institute of Biotechnology, Changhua University of Education, 1 Jin-De Rd., Changhua, Taiwan 50007
| | - Chiu-Lan Hsieh
- Graduate Institute of Biotechnology, Changhua University of Education, 1 Jin-De Rd., Changhua, Taiwan 50007
| | - Chiung-Chi Peng
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, 250 Wu-Shing St., Taipei, Taiwan 11031
| | - Robert Y. Peng
- Research Institute of Biotechnology, Hungkuang University, 34 Chung-Chie Rd., Shalu County, Taichung Hsien, Taiwan 43302
- Research Institute of Medicinal Sciences, College of Medicine, Taipei Medical University, 250 Wu-Xing St., Taipei, Taiwan 11031
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9
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Chen LC, Wu JC, Tuan YF, Tseng YK, Hseu YC, Chen SC. Molecular mechanisms of 3,3'-dichlorobenzidine-mediated toxicity in HepG2 cells. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2014; 55:407-420. [PMID: 24604609 DOI: 10.1002/em.21858] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 01/29/2014] [Accepted: 01/29/2014] [Indexed: 06/03/2023]
Abstract
3,3'-Dichlorobenzidine (DCB) (CAS 91-94-1), a synthetic, chlorinated, primary aromatic amine, is typically used as an intermediate in the manufacturing of pigments for printing inks, textiles, paints, and plastics. In this study, we found that DCB could significantly inhibit the cell viability of HepG2 cells in a concentration-dependent manner. Flow cytometry revealed that DCB induced G2/M-phase arrest and apoptosis in HepG2 cells. DCB treatment dramatically induced the dissipation of mitochondrial membrane potential (Δψm ) and enhanced the enzymatic activities of caspase-9 and caspase-3 whilst hardly affecting caspase-8 activity. Furthermore, Western blotting indicated that DCB-induced apoptosis was accompanied by the down-regulation of Bcl-2/Bax ratio. These results suggested that DCB led to cytotoxicity involving activation of mitochondrial-dependent apoptosis through Bax/Bcl-2 pathways in HepG2 cells. Furthermore, HepG2 cells treated with DCB showed significant DNA damage as supported by the concentration-dependent increase in olive tail moments as determined by the comet assay and by concentration- and time-dependent increase in histone H2AX phosphorylation (γ-H2AX). Two-dimensional-difference gel electrophoresis (2D-DIGE), combined with mass spectrometry (MS), was used to unveil the differences in protein expression between cells exposed to 25 µM or 100 µM of DCB for 24 hr and the control cells. Twenty-seven differentially expressed proteins involved in DNA repair, unfolded protein response, metabolism, cell signaling, and apoptosis were identified. Among these, 14-3-3 theta, CGI-46, and heat-shock 70 protein 4 were confirmed using Western blot assay. Taken together, these data suggest that DCB is capable of inducing DNA damage and some cellular stress responses in HepG2 cells, thus eventually leading to cell death by apoptosis.
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MESH Headings
- 3,3'-Dichlorobenzidine/adverse effects
- Apoptosis/drug effects
- Biomarkers, Tumor/metabolism
- Blotting, Western
- Carcinogens/pharmacology
- Carcinoma, Hepatocellular/drug therapy
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/pathology
- Caspase 3/metabolism
- Caspase 8/metabolism
- Caspase 9/metabolism
- Cell Cycle/drug effects
- Cell Proliferation/drug effects
- Electrophoresis, Gel, Two-Dimensional
- Humans
- Liver Neoplasms/drug therapy
- Liver Neoplasms/metabolism
- Liver Neoplasms/pathology
- Membrane Potential, Mitochondrial/drug effects
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Tumor Cells, Cultured
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Affiliation(s)
- Lei-Chin Chen
- Department of Nutrition, I-Shou University, Kaohsiung City, Taiwan, Republic of China
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10
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Wang X, Li F, Song G, Guo S, Liu H, Chen G, Li Z. Broad-spectrum four-dimensional orthogonal electrophoresis: a novel comprehensively feasible system for protein complexomics investigation. Mol Cell Proteomics 2012; 11:786-99. [PMID: 22375076 DOI: 10.1074/mcp.m111.012450] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The major challenge of "protein complexomics" is to separate intact protein complexes or interactional proteins without dissociation or denaturation from complex biological samples and to characterize structural subunits of protein complexes. To address these issues, we developed a novel approach termed "broad-spectrum four-dimensional orthogonal electrophoresis (BS4-DE) system," which is composed of a nondenaturing part I and denaturing part II. Here we developed a mild acidic-native-PAGE to constitute part I, together with native-thin-layer-IEF and basic-native-PAGE, widening the range of BS4-DE system application for extremely basic proteins with the range of pI from about 8 to 11 (there are obviously 1000 kinds of proteins in this interval), and also speculated on the mechanism of separating. We first proposed ammonium hydroxide-ultrasonic protein extractive strategy as a seamless connection between part I and part II, and also speculated on the extractive mechanism. More than 4000 protein complexes could be theoretically solved by this system. Using this approach, we focus on blood rich in protein complexes which make it challenging to sera/plasma proteome study. Our results indicated that the BS4-DE system could be applied to blood protein complexomics investigation, providing a comprehensively feasible approach for disease proteomics.
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Affiliation(s)
- Xiaodong Wang
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
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11
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Revisit of imidazole-zinc reverse stain for protein polyacrylamide gel electrophoresis. Methods Mol Biol 2012; 869:487-95. [PMID: 22585514 DOI: 10.1007/978-1-61779-821-4_43] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Imidazole-zinc reverse stain (ZN stain) is known for its high sensitivity, ease of use, and cost-effective feature. ZN stain is compatible to many experiments of which those are proteomics-related in particular. Here, we describe the ZN staining procedures and the subsequent procedures incorporated in detail, along with the improvements of setup in aspects of visualization and documentation for post-processing ZN-stained gel images.
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12
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Kurien BT, Dorri Y, Scofield RH. Spicy SDS-PAGE gels: curcumin/turmeric as an environment-friendly protein stain. Methods Mol Biol 2012; 869:567-78. [PMID: 22585522 DOI: 10.1007/978-1-61779-821-4_51] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Gel proteins are commonly stained with calorimetric/fluorescent dyes. Here, we demonstrate that heat-solubilized curcumin can serve as a nontoxic and environment-friendly fluorescent/colorimetric reversible protein stain. Curcumin, the yellow pigment found in the rhizomes of the perennial herb Curcuma longa (turmeric), is insoluble in aqueous solvents. However, heat (100°C) solubilization in water renders 1.5% of curcumin soluble. Curcumin solubilized by ethanol or alkali is ineffective in staining proteins. Heat solubilized curry spice turmeric stains proteins similarly. Staining is achieved in 30 min, with a sensitivity almost equaling that of Coomassie Brilliant Blue (CBB). Destaining is not required, and excess curcumin/turmeric can be discarded into the sink. Binding of proteins by silver inhibits curcumin binding, suggesting similarity of protein binding by silver and curcumin. It costs $1.5-2.0 to stain a mini-gel with curcumin, while turmeric costs less than 0.005 cent. CBB staining/destaining costs about 2 cents. However, CBB is toxic and its use necessitates specialized disposal efforts. Curcumin/turmeric, thus, can serve as an ideal nontoxic protein stain.
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Affiliation(s)
- Biji T Kurien
- Department of Veterans Affairs, University of Oklahoma Health Sciences Center, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.
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13
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Tsai YY, Huang YH, Chao YL, Hu KY, Chin LT, Chou SH, Hour AL, Yao YD, Tu CS, Liang YJ, Tsai CY, Wu HY, Tan SW, Chen HM. Identification of the nanogold particle-induced endoplasmic reticulum stress by omic techniques and systems biology analysis. ACS NANO 2011; 5:9354-9369. [PMID: 22107733 DOI: 10.1021/nn2027775] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Growth inhibition and apoptotic/necrotic phenotype was observed in nanogold particle (AuNP)-treated human chronic myelogenous leukemia cells. To elucidate the underlying cellular mechanisms, proteomic techniques including two-dimensional electrophoresis/mass spectrometry and protein microarrays were utilized to study the differentially expressed proteome and phosphoproteome, respectively. Systems biology analysis of the proteomic data revealed that unfolded protein-associated endoplasmic reticulum (ER) stress response was the predominant event. Concomitant with transcriptomic analysis using mRNA expression, microarrays show ER stress response in the AuNP-treated cells. The ER stress protein markers' expression assay unveiled AuNPs as an efficient cellular ER stress elicitor. Upon ER stress, cellular responses, including reactive oxygen species increase, mitochondrial cytochrome c release, and mitochondria damage, chronologically occurred in the AuNP-treated cells. Conclusively, this study demonstrates that AuNPs cause cell death through induction of unmanageable ER stress.
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Affiliation(s)
- Yen-Yin Tsai
- Department of Life-Science, Fu-Jen Catholic University, Taipei, Taiwan
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Chiu CD, Chen TY, Chin LT, Shen CC, Huo J, Ma SY, Chen HM, Chu CH. Investigation of the effect of hyperglycemia on intracerebral hemorrhage by proteomic approaches. Proteomics 2011; 12:113-23. [DOI: 10.1002/pmic.201100256] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 08/18/2011] [Accepted: 10/25/2011] [Indexed: 12/20/2022]
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15
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Gauci VJ, Wright EP, Coorssen JR. Quantitative proteomics: assessing the spectrum of in-gel protein detection methods. J Chem Biol 2011; 4:3-29. [PMID: 21686332 PMCID: PMC3022124 DOI: 10.1007/s12154-010-0043-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 06/02/2010] [Indexed: 11/28/2022] Open
Abstract
Proteomics research relies heavily on visualization methods for detection of proteins separated by polyacrylamide gel electrophoresis. Commonly used staining approaches involve colorimetric dyes such as Coomassie Brilliant Blue, fluorescent dyes including Sypro Ruby, newly developed reactive fluorophores, as well as a plethora of others. The most desired characteristic in selecting one stain over another is sensitivity, but this is far from the only important parameter. This review evaluates protein detection methods in terms of their quantitative attributes, including limit of detection (i.e., sensitivity), linear dynamic range, inter-protein variability, capacity for spot detection after 2D gel electrophoresis, and compatibility with subsequent mass spectrometric analyses. Unfortunately, many of these quantitative criteria are not routinely or consistently addressed by most of the studies published to date. We would urge more rigorous routine characterization of stains and detection methodologies as a critical approach to systematically improving these critically important tools for quantitative proteomics. In addition, substantial improvements in detection technology, particularly over the last decade or so, emphasize the need to consider renewed characterization of existing stains; the quantitative stains we need, or at least the chemistries required for their future development, may well already exist.
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Affiliation(s)
- Victoria J. Gauci
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
| | - Elise P. Wright
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
| | - Jens R. Coorssen
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
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Wu HC, Chen TN, Kao SH, Shui HA, Chen WJ, Lin HJ, Chen HM. Isoelectric focusing management: an investigation for salt interference and an algorithm for optimization. J Proteome Res 2010; 9:5542-56. [PMID: 20883018 DOI: 10.1021/pr1008256] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two-dimensional electrophoresis (2-DE) has evolved into a robust separation technique in proteomic research. However, one of the major challenges in 2-DE experiments, the reproducibility of the first dimensional electrophoresis (IEF), has remained unsolved. It is well-known that the quality of IEF experiments is significantly affected by the salt interference. Nevertheless, the interference mechanisms of salts in IEF have never been systematically investigated. In this study, we comprehensively investigated the interference effects in IEF due to various kinds of simple and buffer salts in protein samples. Two interference schemes were proposed accordingly to elucidate the interference mechanisms of salts in IEF. Furthermore, to increase the reproducibility of IEF, we proposed that conductivity measurement is a feasible method to assess the salt content of 2-DE samples and developed an algorithm to predict the optimal total volt-hours (Vh) required for protein focusing in IEF. The developed algorithm had been evaluated under various IEF conditions for a variety of 2-DE samples and proven to be a reliable guide. In sum, information disclosed in this study should be of use for increasing the reproducibility and thus the applicability of 2-DE in current proteomics.
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Affiliation(s)
- Hui-Chung Wu
- Department of Biotechnology, Ming-Chuan University, Taoyuan, Taiwan
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17
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Chin LT, Huang PR, Hu KY, Huang NK, Chiu CD, Hour AL, Shui HA, Chu CH, Chen HM. A Proteomics-Based Translational Approach Reveals an Antifolate Resistance Inherent in Human Plasma Derived from Blood Donation. J Proteome Res 2010; 9:3091-102. [DOI: 10.1021/pr100005u] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Li-Te Chin
- Department of Microbiology and Immunology, National Chiayi University, Chiayi, Taiwan, Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Department of Life-Science, Catholic Fu-Jen University, Taipei, Taiwan, Institute of Applied Science and Engineering, Catholic Fu-Jen University, Taipei, Taiwan, Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan, Division of Basic Chinese Medicine, National Research Institute of Chinese Medicine, Taipei,
| | - Pei-Ru Huang
- Department of Microbiology and Immunology, National Chiayi University, Chiayi, Taiwan, Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Department of Life-Science, Catholic Fu-Jen University, Taipei, Taiwan, Institute of Applied Science and Engineering, Catholic Fu-Jen University, Taipei, Taiwan, Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan, Division of Basic Chinese Medicine, National Research Institute of Chinese Medicine, Taipei,
| | - Kuang-Yu Hu
- Department of Microbiology and Immunology, National Chiayi University, Chiayi, Taiwan, Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Department of Life-Science, Catholic Fu-Jen University, Taipei, Taiwan, Institute of Applied Science and Engineering, Catholic Fu-Jen University, Taipei, Taiwan, Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan, Division of Basic Chinese Medicine, National Research Institute of Chinese Medicine, Taipei,
| | - Nai-Kuei Huang
- Department of Microbiology and Immunology, National Chiayi University, Chiayi, Taiwan, Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Department of Life-Science, Catholic Fu-Jen University, Taipei, Taiwan, Institute of Applied Science and Engineering, Catholic Fu-Jen University, Taipei, Taiwan, Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan, Division of Basic Chinese Medicine, National Research Institute of Chinese Medicine, Taipei,
| | - Cheng-Di Chiu
- Department of Microbiology and Immunology, National Chiayi University, Chiayi, Taiwan, Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Department of Life-Science, Catholic Fu-Jen University, Taipei, Taiwan, Institute of Applied Science and Engineering, Catholic Fu-Jen University, Taipei, Taiwan, Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan, Division of Basic Chinese Medicine, National Research Institute of Chinese Medicine, Taipei,
| | - Ai-Ling Hour
- Department of Microbiology and Immunology, National Chiayi University, Chiayi, Taiwan, Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Department of Life-Science, Catholic Fu-Jen University, Taipei, Taiwan, Institute of Applied Science and Engineering, Catholic Fu-Jen University, Taipei, Taiwan, Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan, Division of Basic Chinese Medicine, National Research Institute of Chinese Medicine, Taipei,
| | - Hao-Ai Shui
- Department of Microbiology and Immunology, National Chiayi University, Chiayi, Taiwan, Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Department of Life-Science, Catholic Fu-Jen University, Taipei, Taiwan, Institute of Applied Science and Engineering, Catholic Fu-Jen University, Taipei, Taiwan, Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan, Division of Basic Chinese Medicine, National Research Institute of Chinese Medicine, Taipei,
| | - Chi-Hong Chu
- Department of Microbiology and Immunology, National Chiayi University, Chiayi, Taiwan, Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Department of Life-Science, Catholic Fu-Jen University, Taipei, Taiwan, Institute of Applied Science and Engineering, Catholic Fu-Jen University, Taipei, Taiwan, Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan, Division of Basic Chinese Medicine, National Research Institute of Chinese Medicine, Taipei,
| | - Han-Min Chen
- Department of Microbiology and Immunology, National Chiayi University, Chiayi, Taiwan, Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Department of Life-Science, Catholic Fu-Jen University, Taipei, Taiwan, Institute of Applied Science and Engineering, Catholic Fu-Jen University, Taipei, Taiwan, Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan, Division of Basic Chinese Medicine, National Research Institute of Chinese Medicine, Taipei,
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A red line not to cross: evaluating the limitation and properness of gel image tuning procedures. Anal Biochem 2010; 396:42-50. [PMID: 19733146 DOI: 10.1016/j.ab.2009.08.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Revised: 08/31/2009] [Accepted: 08/31/2009] [Indexed: 11/24/2022]
Abstract
Currently, results of gel electrophoresis are commonly documented in digital formats by image acquisition instruments. In this study, gel images tuned by a common image processing software package, Photoshop, were assessed to understand the transforming algorithms and their impacts on quantitative analysis. TotalLab 100, an electrophoresis gel image analysis software package, was applied for image quantitation and evaluation. The three most frequently used image tuning functions-adjustments of the brightness, contrast, and grayscale span (level) of images-were investigated using both data generated from a standard grayscale tablet and an actual electrophoresis gel image. The influences of these procedures were analyzed for the grayscale transformation between the input and output images. Although all three procedures differentially improved the visualization of the input image, adjusting the contrast of images disrupted the quantitative information because of its nonlinear transforming algorithm. Under certain conditions, adjusting the brightness or the level of images could preserve the quantitative information because of the linear transforming algorithms. It was found that when the minimum and maximum grayscales of a gel image were recognized, using a commercial software package to maximally stretch the level may significantly improve the quality of a gel image without jeopardizing quantitative analysis.
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Chen G, Liu H, Wang X, Li Z. In vitro methylation by methanol: proteomic screening and prevalence investigation. Anal Chim Acta 2009; 661:67-75. [PMID: 20113717 DOI: 10.1016/j.aca.2009.12.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 11/21/2009] [Accepted: 12/10/2009] [Indexed: 11/17/2022]
Abstract
It is assumed that much more functional importance for protein activity than expected may be granted by methylation that occurs at the side-chain of aspartate or glutamate residue. In vitro methylation mainly comes from the use of methanol in sample preparation prior to MS analysis. In this study, we first performed the methylation site-directed proteomic screening of bovine serum albumin, ovalbumin and 20S proteasome for gel staining using a meaningfully indicative MS-pattern of peak tag (termed as 4P tag) and manual inspection for mass spectral data. As a result, there were 17 proteolytic peptides with 20 modified sites confirmed to be in vitro methylated. Subsequently, the prevalence investigation was performed, focusing on the reaction kinetic behavior of in vitro methylation. This study provided a simple and robust approach for confirmation of in vitro methylation by methanol, as well as the precautious guide for the use of methanol in proteomic study.
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Affiliation(s)
- Guoqiang Chen
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
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