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Ghosh S, Garige M, Haggerty PR, Norris A, Chou CK, Wu WW, Shen RF, Sourbier C. Impact of sunitinib resistance on clear cell renal cell carcinoma therapeutic sensitivity in vitro. Cell Cycle 2024; 23:43-55. [PMID: 38263737 PMCID: PMC11005810 DOI: 10.1080/15384101.2024.2306760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/01/2022] [Indexed: 01/25/2024] Open
Abstract
Sunitinib resistance creates a major clinical challenge for the treatment of advanced clear cell renal cell carcinoma (ccRCC) and functional and metabolic changes linked to sunitinib resistance are not fully understood. We sought to characterize the molecular and metabolic changes induced by the development of sunitinib resistance in ccRCC by developing and characterizing two human ccRCC cell lines resistant to sunitinib. Consistent with the literature, sunitinib-resistant ccRCC cell lines presented an aberrant overexpression of Axl and PD-L1, as well as a metabolic rewiring characterized by enhanced OXPHOS and glutamine metabolism. Therapeutic challenges of sunitinib-resistant ccRCC cell lines in vitro using small molecule inhibitors targeting Axl, AMPK and p38, as well as using PD-L1 blocking therapeutic antibodies, showed limited CTL-mediated cytotoxicity in a co-culture model. However, the AMPK activator metformin appears to sensitize the effect of PD-L1 blocking therapeutic antibodies and to enhance CTLs' cytotoxic effects on ccRCC cells. These effects were not broadly observed with the Axl and the p38 inhibitors. Taken together, these data suggest that targeting certain pathways aberrantly activated by sunitinib resistance such as the AMPK/PDL1 axis might sensitize ccRCC to immunotherapies as a second-line therapeutic approach.
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Affiliation(s)
- Susmita Ghosh
- Division of Biotechnology Review and Research 1, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Mamatha Garige
- Division of Biotechnology Review and Research 1, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Patrick R. Haggerty
- Division of Biotechnology Review and Research 1, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Alexis Norris
- Division of Animal Bioengineering and Cellular Therapies, Office of New Animal Drug Evaluation, Center for Veterinary Medicine, U.S. Food and Drug Administration, Rockville, MD, USA
| | - Chao-Kai Chou
- Facility for Biotechnology Resources, Center for Biologicals Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Wells W. Wu
- Facility for Biotechnology Resources, Center for Biologicals Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, Center for Biologicals Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Carole Sourbier
- Division of Biotechnology Review and Research 1, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
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2
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Choy C, Chen J, Li J, Gallagher DT, Lu J, Wu D, Zou A, Hemani H, Baptiste BA, Wichmann E, Yang Q, Ciffelo J, Yin R, McKelvy J, Melvin D, Wallace T, Dunn C, Nguyen C, Chia CW, Fan J, Ruffolo J, Zukley L, Shi G, Amano T, An Y, Meirelles O, Wu WW, Chou CK, Shen RF, Willis RA, Ko MSH, Liu YT, De S, Pierce BG, Ferrucci L, Egan J, Mariuzza R, Weng NP. SARS-CoV-2 infection establishes a stable and age-independent CD8 + T cell response against a dominant nucleocapsid epitope using restricted T cell receptors. Nat Commun 2023; 14:6725. [PMID: 37872153 PMCID: PMC10593757 DOI: 10.1038/s41467-023-42430-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023] Open
Abstract
The resolution of SARS-CoV-2 replication hinges on cell-mediated immunity, wherein CD8+ T cells play a vital role. Nonetheless, the characterization of the specificity and TCR composition of CD8+ T cells targeting non-spike protein of SARS-CoV-2 before and after infection remains incomplete. Here, we analyzed CD8+ T cells recognizing six epitopes from the SARS-CoV-2 nucleocapsid (N) protein and found that SARS-CoV-2 infection slightly increased the frequencies of N-recognizing CD8+ T cells but significantly enhanced activation-induced proliferation compared to that of the uninfected donors. The frequencies of N-specific CD8+ T cells and their proliferative response to stimulation did not decrease over one year. We identified the N222-230 peptide (LLLDRLNQL, referred to as LLL thereafter) as a dominant epitope that elicited the greatest proliferative response from both convalescent and uninfected donors. Single-cell sequencing of T cell receptors (TCR) from LLL-specific CD8+ T cells revealed highly restricted Vα gene usage (TRAV12-2) with limited CDR3α motifs, supported by structural characterization of the TCR-LLL-HLA-A2 complex. Lastly, transcriptome analysis of LLL-specific CD8+ T cells from donors who had expansion (expanders) or no expansion (non-expanders) after in vitro stimulation identified increased chromatin modification and innate immune functions of CD8+ T cells in non-expanders. These results suggests that SARS-CoV-2 infection induces LLL-specific CD8+ T cell responses with a restricted TCR repertoire.
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Affiliation(s)
- Cecily Choy
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Joseph Chen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Jiangyuan Li
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - D Travis Gallagher
- National Institute of Standards and Technology (NIST), Gaithersburg, MD, USA
| | - Jian Lu
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Daichao Wu
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Ainslee Zou
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Humza Hemani
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Beverly A Baptiste
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Emily Wichmann
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Qian Yang
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Jeffrey Ciffelo
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Rui Yin
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Julia McKelvy
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Denise Melvin
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Tonya Wallace
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Christopher Dunn
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Cuong Nguyen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Chee W Chia
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Jinshui Fan
- Computational Biology and Genomics Core, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Jeannie Ruffolo
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Linda Zukley
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | | | | | - Yang An
- Laboratory of Behavioral Neuroscience, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Osorio Meirelles
- Laboratory of Epidemiology & Population Sciences, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Wells W Wu
- Facility for Biotechnology Resources, CBER, Food and Drug Administration, Silver Spring, MD, USA
| | - Chao-Kai Chou
- Facility for Biotechnology Resources, CBER, Food and Drug Administration, Silver Spring, MD, USA
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, CBER, Food and Drug Administration, Silver Spring, MD, USA
| | - Richard A Willis
- NIH Tetramer Core Facility at Emory University, Atlanta, GA, USA
| | | | | | - Supriyo De
- Computational Biology and Genomics Core, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Brian G Pierce
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Josephine Egan
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Roy Mariuzza
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Nan-Ping Weng
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA.
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3
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Garige M, Poncet S, Norris A, Chou CK, Wu WW, Shen RF, Greenberg JW, Krane LS, Sourbier C. Extended Opioid Exposure Modulates the Molecular Metabolism of Clear Cell Renal Cell Carcinoma. Life (Basel) 2023; 13:life13051196. [PMID: 37240841 DOI: 10.3390/life13051196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/06/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Opioids are commonly prescribed for extended periods of time to patients with advanced clear cell renal cell carcinoma to assist with pain management. Because extended opioid exposure has been shown to affect the vasculature and to be immunosuppressive, we investigated how it may affect the metabolism and physiology of clear cell renal cell carcinoma. RNA sequencing of a limited number of archived patients' specimens with extended opioid exposure or non-opioid exposure was performed. Immune infiltration and changes in the microenvironment were evaluated using CIBERSORT. A significant decrease in M1 macrophages and T cells CD4 memory resting immune subsets was observed in opioid-exposed tumors, whereas the changes observed in other immune cells were not statistically significant. Further RNA sequencing data analysis showed that differential expression of KEGG signaling pathways was significant between non-opioid-exposed specimens and opioid-exposed specimens, with a shift from a gene signature consistent with aerobic glycolysis to a gene signature consistent with the TCA cycle, nicotinate metabolism, and the cAMP signaling pathway. Together, these data suggest that extended opioid exposure changes the cellular metabolism and immune homeostasis of ccRCC, which might impact the response to therapy of these patients, especially if the therapy is targeting the microenvironment or metabolism of ccRCC tumors.
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Affiliation(s)
- Mamatha Garige
- Division of Biotechnology Review and Research 1, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Sarah Poncet
- Division of Biotechnology Review and Research 1, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Alexis Norris
- Division of Animal Bioengineering and Cellular Therapies, Office of New Animal Drug Evaluation, Center for Veterinary Medicine, U.S. Food and Drug Administration, Rockville, MD 20852, USA
| | - Chao-Kai Chou
- Facility for Biotechnology Resources, Center for Biologicals Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Wells W Wu
- Facility for Biotechnology Resources, Center for Biologicals Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, Center for Biologicals Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Jacob W Greenberg
- Department of Urology, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Louis Spencer Krane
- Department of Urology, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Carole Sourbier
- Division of Biotechnology Review and Research 1, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA
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4
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Wang Q, Wang T, Wu WW, Lin CY, Yang S, Yang G, Jankowska E, Hu Y, Shen RF, Betenbaugh MJ, Cipollo JF. Comprehensive N- and O-Glycoproteomic Analysis of Multiple Chinese Hamster Ovary Host Cell Lines. J Proteome Res 2022; 21:2341-2355. [PMID: 36129246 DOI: 10.1021/acs.jproteome.2c00207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glycoproteomic analysis of three Chinese hamster ovary (CHO) suspension host cell lines (CHO-K1, CHO-S, and CHO-Pro5) commonly utilized in biopharmaceutical settings for recombinant protein production is reported. Intracellular and secreted glycoproteins were examined. We utilized an immobilization and chemoenzymatic strategy in our analysis. Glycoproteins or glycopeptides were first immobilized through reductive amination, and the sialyl moieties were amidated for protection. The desired N- or O-glycans and glycopeptides were released from the immobilization resin by enzymatic or chemical digestion. Glycopeptides were studied by Orbitrap Liquid chromatography-mass spectrometry (LC/MS), and the released glycans were analyzed by Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF). Differences were detected in the relative abundances of N- and O-glycopeptide types, their resident and released glycans, and their glycoprotein complexity. Ontogeny analysis revealed key differences in features, such as general metabolic and biosynthetic pathways, including glycosylation systems, as well as distributions in cellular compartments. Host cell lines and subfraction differences were observed in both N- and O-glycan and glycoprotein pools. Differences were observed in sialyl and fucosyl glycan distributions. Key differences were also observed among glycoproteins that are problematic contaminants in recombinant antibody production. The differences revealed in this study should inform the choice of cell lines best suited for a particular bioproduction application.
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Affiliation(s)
- Qiong Wang
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993, United States.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21210, United States
| | - Tiexin Wang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21210, United States
| | - Wells W Wu
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Chang-Yi Lin
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Shuang Yang
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993, United States.,Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Ganglong Yang
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21287, United States.,Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ewa Jankowska
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Yifeng Hu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21210, United States
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21210, United States
| | - John F Cipollo
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993, United States
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5
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Sun X, Nguyen T, Achour A, Ko A, Cifello J, Ling C, Sharma J, Hiroi T, Zhang Y, Chia CW, Wood Iii W, Wu WW, Zukley L, Phue JN, Becker KG, Shen RF, Ferrucci L, Weng NP. Longitudinal analysis reveals age-related changes in the T cell receptor repertoire of human T cell subsets. J Clin Invest 2022; 132:158122. [PMID: 35708913 PMCID: PMC9433102 DOI: 10.1172/jci158122] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 06/14/2022] [Indexed: 11/17/2022] Open
Abstract
A diverse T cell receptor (TCR) repertoire is essential for protection against a variety of pathogens, and TCR repertoire size is believed to decline with age. However, the precise size of human TCR repertoires, in both total and subsets of T cells, as well as their changes with age, are not fully characterized. We conducted a longitudinal analysis of the human blood TCRα and TCRβ repertoire of CD4+ and CD8+ T cell subsets using a unique molecular identifier–based (UMI-based) RNA-seq method. Thorough analysis of 1.9 × 108 T cells yielded the lower estimate of TCR repertoire richness in an adult at 3.8 × 108. Alterations of the TCR repertoire with age were observed in all 4 subsets of T cells. The greatest reduction was observed in naive CD8+ T cells, while the greatest clonal expansion was in memory CD8+ T cells, and the highest increased retention of TCR sequences was in memory CD8+ T cells. Our results demonstrated that age-related TCR repertoire attrition is subset specific and more profound for CD8+ than CD4+ T cells, suggesting that aging has a more profound effect on cytotoxic as opposed to helper T cell functions. This may explain the increased susceptibility of older adults to novel infections.
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Affiliation(s)
- Xiaoping Sun
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, United States of America
| | - Thomas Nguyen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, United States of America
| | - Achouak Achour
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, United States of America
| | - Annette Ko
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, United States of America
| | - Jeffrey Cifello
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, United States of America
| | - Chen Ling
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, United States of America
| | - Jay Sharma
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, United States of America
| | - Toyoko Hiroi
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, United States of America
| | - Yongqing Zhang
- Gene expression and Genomics Unit, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, United States of America
| | - Chee W Chia
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, United States of America
| | - William Wood Iii
- Gene expression and Genomics Unit, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, United States of America
| | - Wells W Wu
- Facility for Biotechnology Resources, Food and Drug Administration, Silver Spring, United States of America
| | - Linda Zukley
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, United States of America
| | - Je-Nie Phue
- Facility for Biotechnology Resources, Food and Drug Administration, Silver Spring, United States of America
| | - Kevin G Becker
- Gene expression and Genomics Unit, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, United States of America
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, Food and Drug Administration, Silver Spring, United States of America
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, United States of America
| | - Nan-Ping Weng
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, United States of America
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6
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Garige M, Ghosh S, Norris A, Li G, Poncet S, Chou CK, Wu WW, Shen RF, Sourbier C. PD-L1 Mediates IFNγ-Regulation of Glucose but Not of Tryptophan Metabolism in Clear Cell Renal Cell Carcinoma. Front Oncol 2022; 12:858379. [PMID: 35656514 PMCID: PMC9152103 DOI: 10.3389/fonc.2022.858379] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/13/2022] [Indexed: 12/21/2022] Open
Abstract
The immune checkpoint programmed death-ligand 1 (PD-L1) is expressed on the cell surface of tumor cells and is key for maintaining an immunosuppressive microenvironment through its interaction with the programmed death 1 (PD-1). Clear cell renal cell carcinoma (ccRCC) is a highly immunogenic cancer characterized by an aberrant aerobic glycolytic metabolism and is known to overexpress PD-L1. Multiple immunotherapies have been approved for the treatment of ccRCC, including cytokines and immune checkpoint inhibitors. Recently the intrinsic role of PD-L1 and interferon gamma (IFNγ) signaling have been studied in several types of tumor cells, yet it remains unclear how they affect the metabolism and signaling pathways of ccRCC. Using metabolomics, metabolic assays and RNAseq, we showed that IFNγ enhanced aerobic glycolysis and tryptophan metabolism in ccRCC cells in vitro and induced the transcriptional expression of signaling pathways related to inflammation, cell proliferation and cellular energetics. These metabolic and transcriptional effects were partially reversed following transient PD-L1 silencing. Aerobic glycolysis, as well as signaling pathways related to inflammation, were not induced by IFNγ when PD-L1 was silenced, however, tryptophan metabolism and activation of Jak2 and STAT1 were maintained. Our data demonstrate that PD-L1 expression is required to mediate some of IFNγ's effect in ccRCC cells and highlight the importance of PD-L1 signaling in regulating the metabolism of ccRCC cells in response to inflammatory signals.
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Affiliation(s)
- Mamatha Garige
- Division of Biotechnology Review and Research 1, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, United States
| | - Susmita Ghosh
- Division of Biotechnology Review and Research 1, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, United States
| | - Alexis Norris
- Division of Animal Bioengineering and Cellular Therapies, Office of New Animal Drug Evaluation, Center for Veterinary Medicine, United States Food and Drug Administration, Rockville, MD, United States
| | - Guangyuan Li
- Division of Biotechnology Review and Research 1, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, United States
| | - Sarah Poncet
- Division of Biotechnology Review and Research 1, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, United States
| | - Chao-Kai Chou
- Facility for Biotechnology Resources, Center for Biologicals Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, United States
| | - Wells W Wu
- Facility for Biotechnology Resources, Center for Biologicals Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, United States
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, Center for Biologicals Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, United States
| | - Carole Sourbier
- Division of Biotechnology Review and Research 1, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, United States
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7
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Mascia F, Mazo I, Alterovitz WL, Karagiannis K, Wu WW, Shen RF, Beaver JA, Rao VA. In search of autophagy biomarkers in breast cancer: Receptor status and drug agnostic transcriptional changes during autophagy flux in cell lines. PLoS One 2022; 17:e0262134. [PMID: 34990474 PMCID: PMC8735604 DOI: 10.1371/journal.pone.0262134] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/18/2021] [Indexed: 12/15/2022] Open
Abstract
Autophagy drives drug resistance and drug-induced cancer cell cytotoxicity. Targeting the autophagy process could greatly improve chemotherapy outcomes. The discovery of specific inhibitors or activators has been hindered by challenges with reliably measuring autophagy levels in a clinical setting. We investigated drug-induced autophagy in breast cancer cell lines with differing ER/PR/Her2 receptor status by exposing them to known but divergent autophagy inducers each with a unique molecular target, tamoxifen, trastuzumab, bortezomib or rapamycin. Differential gene expression analysis from total RNA extracted during the earliest sign of autophagy flux showed both cell- and drug-specific changes. We analyzed the list of differentially expressed genes to find a common, cell- and drug-agnostic autophagy signature. Twelve mRNAs were significantly modulated by all the drugs and 11 were orthogonally verified with Q-RT-PCR (Klhl24, Hbp1, Crebrf, Ypel2, Fbxo32, Gdf15, Cdc25a, Ddit4, Psat1, Cd22, Ypel3). The drug agnostic mRNA signature was similarly induced by a mitochondrially targeted agent, MitoQ. In-silico analysis on the KM-plotter cancer database showed that the levels of these mRNAs are detectable in human samples and associated with breast cancer prognosis outcomes of Relapse-Free Survival in all patients (RSF), Overall Survival in all patients (OS), and Relapse-Free Survival in ER+ Patients (RSF ER+). High levels of Klhl24, Hbp1, Crebrf, Ypel2, CD22 and Ypel3 were correlated with better outcomes, whereas lower levels of Gdf15, Cdc25a, Ddit4 and Psat1 were associated with better prognosis in breast cancer patients. This gene signature uncovers candidate autophagy biomarkers that could be tested during preclinical and clinical studies to monitor the autophagy process.
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Affiliation(s)
- Francesca Mascia
- Laboratory of Applied Biochemistry, Division of Biotechnology Review and Research III, Office of Biotechnology Products, CDER, FDA, Silver Spring, Maryland, United States of America
| | - Ilya Mazo
- HIVE Bioinformatics Group, Office of Biostatistics and Epidemiology, CBER, FDA, Silver Spring, Maryland, United States of America
| | - Wei-Lun Alterovitz
- HIVE Bioinformatics Group, Office of Biostatistics and Epidemiology, CBER, FDA, Silver Spring, Maryland, United States of America
| | - Konstantinos Karagiannis
- HIVE Bioinformatics Group, Office of Biostatistics and Epidemiology, CBER, FDA, Silver Spring, Maryland, United States of America
| | - Wells W. Wu
- Facility for Biotechnology Resource CBER, FDA, Silver Spring, Maryland, United States of America
| | - Rong-Fong Shen
- Facility for Biotechnology Resource CBER, FDA, Silver Spring, Maryland, United States of America
| | - Julia A. Beaver
- Oncology Center of Excellence, FDA, Silver Spring, Maryland, United States of America
| | - V. Ashutosh Rao
- Laboratory of Applied Biochemistry, Division of Biotechnology Review and Research III, Office of Biotechnology Products, CDER, FDA, Silver Spring, Maryland, United States of America
- * E-mail:
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8
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Chun H, Pettersson JR, Shestopal SA, Wu WW, Marakasova ES, Olivares P, Surov SS, Ovanesov MV, Shen RF, Sarafanov AG. Characterization of protein unable to bind von Willebrand factor in recombinant factor VIII products. J Thromb Haemost 2021; 19:954-966. [PMID: 33527662 DOI: 10.1111/jth.15257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 11/26/2020] [Accepted: 12/01/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Therapeutic products with coagulation factor VIII (FVIII) have a wide range of specific activities, implying presence of protein with altered structure. Previous studies showed that recombinant FVIII products (rFVIII) contain a fraction (FVIIIFT ) unable to bind von Willebrand factor (VWF) and reported to lack activity. Because of loss of function(s), FVIIIFT can be defined as a product-related impurity, whose properties and levels in rFVIII products should be investigated. OBJECTIVE To isolate and characterize the FVIIIFT fraction in rFVIII products. METHODS Protein fractions unable (FVIIIFT ) and able (FVIIIEL ) to bind VWF were isolated from rFVIII products using immobilized VWF affinity chromatography (IVAC) and characterized by gel electrophoresis, immunoblotting, FVIII activity test, surface plasmon resonance, mass spectrometry, and for plasma clearance in mice. RESULTS AND CONCLUSIONS A robust IVAC methodology was developed and applied for analysis of 10 rFVIII products marketed in the United States. FVIIIFT was found at various contents (0.4%-21.5%) in all products. Compared with FVIIIEL , FVIIIFT had similar patterns of polypeptide bands by gel electrophoresis, but lower functional activity. In several representative products, FVIIIFT was found to have reduced sulfation at Tyr1680, important for VWF binding, decreased interaction with a low-density lipoprotein receptor-related protein 1 fragment, and faster plasma clearance in mice. These findings provide basic characterization of FVIIIFT and demonstrate a potential for IVAC to control this impurity in rFVIII products to improve their efficacy in therapy of hemophilia A.
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Affiliation(s)
- Haarin Chun
- Center for Biologics Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - John R Pettersson
- Center for Biologics Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Svetlana A Shestopal
- Center for Biologics Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Wells W Wu
- Center for Biologics Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Ekaterina S Marakasova
- Center for Biologics Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Philip Olivares
- Center for Biologics Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Stepan S Surov
- Center for Biologics Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Mikhail V Ovanesov
- Center for Biologics Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Rong-Fong Shen
- Center for Biologics Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Andrey G Sarafanov
- Center for Biologics Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
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9
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Bozza WP, Takeda K, Alterovitz WL, Chou CK, Shen RF, Zhang B. Anthracycline-Induced Cardiotoxicity: Molecular Insights Obtained from Human-Induced Pluripotent Stem Cell-Derived Cardiomyocytes (hiPSC-CMs). AAPS J 2021; 23:44. [PMID: 33719006 PMCID: PMC7956936 DOI: 10.1208/s12248-021-00576-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 02/24/2021] [Indexed: 01/18/2023]
Abstract
Anthracyclines are a class of chemotherapy drugs that are highly effective for the treatment of human cancers, but their clinical use is limited by associated dose-dependent cardiotoxicity. The precise mechanisms by which individual anthracycline induces cardiotoxicity are not fully understood. Human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) are emerging as a physiologically relevant model to assess drugs cardiotoxicity. Here, we describe an assay platform by coupling hiPSC-CMs and impedance measurement, which allows real-time monitoring of cardiomyocyte cellular index, beating amplitude, and beating rate. Using this approach, we have performed comparative studies on a panel of four anthracycline drugs (doxorubicin, epirubicin, idarubicin, and daunorubicin) which share a high degree of structural similarity but are associated with distinct cardiotoxicity profiles and maximum cumulative dose limits. Notably, results from our hiPSC-CMs impedance model (dose-dependent responses and EC50 values) agree well with the recommended clinical dose limits for these drugs. Using time-lapse imaging and RNAseq, we found that the differences in anthracycline cardiotoxicity are closely linked to extent of cardiomyocyte uptake and magnitude of activation/inhibition of several cellular pathways such as death receptor signaling, ROS production, and dysregulation of calcium signaling. The results provide molecular insights into anthracycline cardiac interactions and offer a novel assay system to more robustly assess potential cardiotoxicity during drug development.
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Affiliation(s)
- William P Bozza
- Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA
| | - Kazuyo Takeda
- Microscopy and Imaging Core Facility, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA
| | - Wei-Lun Alterovitz
- High-performance Integrated Virtual Environment, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA
| | - Chao-Kai Chou
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA
| | - Baolin Zhang
- Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA.
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10
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Wang Q, Wang T, Yang S, Sha S, Wu WW, Chen Y, Paul JT, Shen RF, Cipollo JF, Betenbaugh MJ. Metabolic engineering challenges of extending N-glycan pathways in Chinese hamster ovary cells. Metab Eng 2020; 61:301-314. [PMID: 32663509 DOI: 10.1016/j.ymben.2020.06.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/28/2020] [Accepted: 06/11/2020] [Indexed: 12/22/2022]
Abstract
In mammalian cells, N-glycans may include multiple N-acetyllactosamine (poly-LacNAc) units that can play roles in various cellular functions and properties of therapeutic recombinant proteins. Previous studies indicated that β-1,3-N-acetylglucosaminyltransferase 2 (B3GNT2) and β-1,4-galactotransferase 1 (B4GALT1) are two of the primary glycosyltransferases involved in generating LacNAc units. In the current study, knocking out sialyltransferase genes slightly enhanced the LacNAc content (≥4 repeats per glycan) on recombinant EPO protein. Next, the role of single and dual-overexpression of B3GNT2 and B4GALT1 was explored in recombinant EPO-expressing Chinese hamster ovary (CHO) cells. While overexpression of B4GALT1 slightly enhanced the levels of large glycans on recombinant EPO, overexpression of B3GNT2 in EPO-expressing CHO cells significantly decreased the recombinant EPO LacNAc content, resulting in N-glycans terminating primarily with GlcNAc structures, a limited number of Gals, and nearly undetectable sialylation, which was also observed in sialyltransferases knock-out-B3GNT2 overexpression cell lines. Considering the nature of the binding domain motifs present on B3GNT2, which evolved from β1,3-galactosyltransferases, its overexpression may have competed and inhibited endogenous β1,4-galactosyltransferases for exposed GlcNAc residues on the N-glycans, resulting in premature termination of many N-glycans at GlcNAc. Furthermore, B3GNT2 overexpression enhanced intracellular UDP-GlcNAc and CMP-Neu5Ac content while slightly lowering UDP-Gal content. The presence of a sink for UDP-GlcNAc in the form of B3GNT2 with no disposition may have also elevated the intracellular levels of this nucleotide as well as its downstream product, CMP-Neu5Ac. Furthermore, we were unable to overexpress B4GALT1 at either the transcriptional or translational levels following initial B3GNT2 expression. Expression of B3GNT2 following initial expression of B4GALT1 was also problematic in that transcriptional and translational analysis indicated the accumulation of truncated B3GNT2 missing a section of the B3GNT2 trans-Golgi lumen domain while transmembrane and cytoplasmic domains were present. Given that glycosylation is a very complex intra-network process, the addition of one or more recombinant glycosyltransferases may have an unexpected influence on the expression and activities of glycosyltransferases, which can disrupt the nucleotide sugar levels and lead to unexpected modifications of the resulting N-glycan patterns.
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Affiliation(s)
- Qiong Wang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Tiexin Wang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Shuang Yang
- Laboratory for Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products (DBPAP), Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Sha Sha
- Center for Biomedical Innovation, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
| | - Wells W Wu
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Yiqun Chen
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jackson T Paul
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - John F Cipollo
- Laboratory for Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products (DBPAP), Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
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11
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Xu L, Pelosof L, Wang R, McFarland HI, Wu WW, Phue JN, Lee CT, Shen RF, Juhl H, Wu LH, Alterovitz WL, Petricon E, Rosenberg AS. NGS Evaluation of Colorectal Cancer Reveals Interferon Gamma Dependent Expression of Immune Checkpoint Genes and Identification of Novel IFNγ Induced Genes. Front Immunol 2020; 11:224. [PMID: 32265897 PMCID: PMC7103651 DOI: 10.3389/fimmu.2020.00224] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/28/2020] [Indexed: 12/28/2022] Open
Abstract
To evaluate the expression of immune checkpoint genes, their concordance with expression of IFNγ, and to identify potential novel ICP related genes (ICPRG) in colorectal cancer (CRC), the biological connectivity of six well documented ("classical") ICPs (CTLA4, PD1, PDL1, Tim3, IDO1, and LAG3) with IFNγ and its co-expressed genes was examined by NGS in 79 CRC/healthy colon tissue pairs. Identification of novel IFNγ- induced molecules with potential ICP activity was also sought. In our study, the six classical ICPs were statistically upregulated and correlated with IFNγ, CD8A, CD8B, CD4, and 180 additional immunologically related genes in IFNγ positive (FPKM > 1) tumors. By ICP co-expression analysis, we also identified three IFNγ-induced genes [(IFNγ-inducible lysosomal thiol reductase (IFI30), guanylate binding protein1 (GBP1), and guanylate binding protein 4 (GBP4)] as potential novel ICPRGs. These three genes were upregulated in tumor compared to normal tissues in IFNγ positive tumors, co-expressed with CD8A and had relatively high abundance (average FPKM = 362, 51, and 25, respectively), compared to the abundance of the 5 well-defined ICPs (Tim3, LAG3, PDL1, CTLA4, PD1; average FPKM = 10, 9, 6, 6, and 2, respectively), although IDO1 is expressed at comparably high levels (FPKM = 39). We extended our evaluation by querying the TCGA database which revealed the commonality of IFNγ dependent expression of the three potential ICPRGs in 638 CRCs, 103 skin cutaneous melanomas (SKCM), 1105 breast cancers (BC), 184 esophageal cancers (ESC), 416 stomach cancers (STC), and 501 lung squamous carcinomas (LUSC). In terms of prognosis, based on Pathology Atlas data, correlation of GBP1 and GBP4, but not IFI30, with 5-year survival rate was favorable in CRC, BC, SKCM, and STC. Thus, further studies defining the role of IFI30, GBP1, and GBP4 in CRC are warranted.
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Affiliation(s)
- Lai Xu
- Office of Oncologic Diseases, Center for Drug Evaluation and Research (CDER), FDA, Silver Spring, MD, United States
| | - Lorraine Pelosof
- Office of Oncologic Diseases, Center for Drug Evaluation and Research (CDER), FDA, Silver Spring, MD, United States
| | - Rong Wang
- Office of Biotechnology Products, Division of Biotechnology Review and Research III (DBRRIII), Office of Pharmaceutical Quality (OPQ), Center for Drug Evaluation and Research (CDER), FDA, Silver Spring, MD, United States
| | - Hugh I. McFarland
- Office of Biotechnology Products, Division of Biotechnology Review and Research III (DBRRIII), Office of Pharmaceutical Quality (OPQ), Center for Drug Evaluation and Research (CDER), FDA, Silver Spring, MD, United States
| | - Wells W. Wu
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, United States
| | - Je-Nie Phue
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, United States
| | - Chun-Ting Lee
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, United States
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, United States
| | | | - Lei-Hong Wu
- Division of Bioinformatics and Biostatistics (DBB), National Center for Toxicological Research (NCTR), FDA, Jefferson, AR, United States
| | - Wei-Lun Alterovitz
- HIVE, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, United States
| | - Emanuel Petricon
- Center for Applied Proteomics and Molecular Medicine (CAPMM), George Mason University, Fairfax, VA, United States
| | - Amy S. Rosenberg
- Office of Biotechnology Products, Division of Biotechnology Review and Research III (DBRRIII), Office of Pharmaceutical Quality (OPQ), Center for Drug Evaluation and Research (CDER), FDA, Silver Spring, MD, United States
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12
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Wan H, Gao J, Yang H, Yang S, Harvey R, Chen YQ, Zheng NY, Chang J, Carney PJ, Li X, Plant E, Jiang L, Couzens L, Wang C, Strohmeier S, Wu WW, Shen RF, Krammer F, Cipollo JF, Wilson PC, Stevens J, Wan XF, Eichelberger MC, Ye Z. The neuraminidase of A(H3N2) influenza viruses circulating since 2016 is antigenically distinct from the A/Hong Kong/4801/2014 vaccine strain. Nat Microbiol 2019; 4:2216-2225. [PMID: 31406333 PMCID: PMC6879794 DOI: 10.1038/s41564-019-0522-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 06/24/2019] [Indexed: 11/08/2022]
Abstract
A(H3N2) virus predominated recent influenza seasons, which has resulted in the rigorous investigation of haemagglutinin, but whether neuraminidase (NA) has undergone antigenic change and contributed to the predominance of A(H3N2) virus is unknown. Here, we show that the NA of the circulating A(H3N2) viruses has experienced significant antigenic drift since 2016 compared with the A/Hong Kong/4801/2014 vaccine strain. This antigenic drift was mainly caused by amino acid mutations at NA residues 245, 247 (S245N/S247T; introducing an N-linked glycosylation site at residue 245) and 468. As a result, the binding of the NA of A(H3N2) virus by some human monoclonal antibodies, including those that have broad reactivity to the NA of the 1957 A(H2N2) and 1968 A(H3N2) reference pandemic viruses as well as contemporary A(H3N2) strains, was reduced or abolished. This antigenic drift also reduced NA-antibody-based protection against in vivo virus challenge. X-ray crystallography showed that the glycosylation site at residue 245 is within a conserved epitope that overlaps the NA active site, explaining why it impacts antibody binding. Our findings suggest that NA antigenic drift impacts protection against influenza virus infection, thus highlighting the importance of including NA antigenicity for consideration in the optimization of influenza vaccines.
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MESH Headings
- Animals
- Antibodies, Monoclonal
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Catalytic Domain
- Crystallography, X-Ray
- Disease Models, Animal
- Genes, Viral/genetics
- Glycosylation
- Hong Kong
- Humans
- Immunogenicity, Vaccine
- Influenza A Virus, H3N2 Subtype/enzymology
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza Vaccines/immunology
- Influenza, Human/prevention & control
- Mice
- Models, Molecular
- Mutation
- Neuraminidase/chemistry
- Neuraminidase/genetics
- Neuraminidase/immunology
- Orthomyxoviridae Infections/immunology
- Protein Conformation
- Sequence Analysis, Protein
- Viral Proteins/chemistry
- Viral Proteins/genetics
- Viral Proteins/immunology
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Affiliation(s)
- Hongquan Wan
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
| | - Jin Gao
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Hua Yang
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shuang Yang
- Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Ruth Harvey
- National Institute for Biological Standards and Control, Potters Bar, UK
| | - Yao-Qing Chen
- Department of Medicine, Section of Rheumatology, The University of Chicago, Chicago, IL, USA
| | - Nai-Ying Zheng
- Department of Medicine, Section of Rheumatology, The University of Chicago, Chicago, IL, USA
| | - Jessie Chang
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Paul J Carney
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Xing Li
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Ewan Plant
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Lianlian Jiang
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Laura Couzens
- Division of Biological Standards and Quantity Control, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Carol Wang
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Shirin Strohmeier
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wells W Wu
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John F Cipollo
- Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Patrick C Wilson
- Department of Medicine, Section of Rheumatology, The University of Chicago, Chicago, IL, USA
| | - James Stevens
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Xiu-Feng Wan
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS, USA
| | - Maryna C Eichelberger
- Division of Biological Standards and Quantity Control, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Zhiping Ye
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
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13
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Liu F, Endo Y, Romantseva T, Wu WW, Akue A, Shen RF, Golding H, Zaitseva M. T cell-derived soluble glycoprotein GPIbα mediates PGE 2 production in human monocytes activated with the vaccine adjuvant MDP. Sci Signal 2019; 12:12/602/eaat6023. [PMID: 31594856 DOI: 10.1126/scisignal.aat6023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Vaccine adjuvants containing analogs of microbial products activate pattern recognition receptors (PRRs) on antigen-presenting cells, including monocytes and macrophages, which can cause prostaglandin E2 (PGE2) release and consequently undesired inflammatory responses and fever in vaccine recipients. Here, we studied the mechanism of PGE2 production by human monocytes activated with muramyl dipeptide (MDP) adjuvant, which activates cytosolic nucleotide-binding oligomerization domain 2 (NOD2). In rabbits, administration of MDP elicited an early increase in PGE2 followed by fever. In human monocytes, MDP alone did not induce PGE2 production. However, high amounts of PGE2 and the proinflammatory cytokines IL-1β and IL-6 were secreted by monocytes activated with MDP in the presence of conditioned medium obtained from CD3 bead-isolated T cells (Tc CM) but not from those isolated without CD3 beads. Mass spectrometry and immunoblotting revealed that the costimulatory factor in Tc CM was glycoprotein Ib α (GPIbα). Antibody-mediated blockade of GPIbα or of its receptor, Mac-1 integrin, inhibited the secretion of PGE2, IL-1β, and IL-6 in MDP + Tc CM-activated monocytes, whereas recombinant GPIbα protein increased PGE2 production by MDP-treated monocytes. In vivo, COX2 mRNA abundance was reduced in the liver and spleen of Mac-1 KO mice after administration of MDP compared with that of treated wild-type mice. Our findings suggest that the production of PGE2 and proinflammatory cytokines by MDP-activated monocytes is mediated by cooperation between two signaling pathways: one delivered by MDP through NOD2 and a second through activation of Mac-1 by T cell-derived GPIbα.
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Affiliation(s)
- Fengjie Liu
- Division of Viral Products, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Yukinori Endo
- Division of Viral Products, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Tatiana Romantseva
- Division of Viral Products, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Wells W Wu
- Facility for Biotechnology Resources, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Adovi Akue
- Flow Cytometry Core, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Hana Golding
- Division of Viral Products, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Marina Zaitseva
- Division of Viral Products, Food and Drug Administration, Silver Spring, MD 20993, USA.
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14
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Xu L, Luo H, Wang R, Wu WW, Phue JN, Shen RF, Juhl H, Wu L, Alterovitz WL, Simonyan V, Pelosof L, Rosenberg AS. Novel reference genes in colorectal cancer identify a distinct subset of high stage tumors and their associated histologically normal colonic tissues. BMC Med Genet 2019; 20:138. [PMID: 31409279 PMCID: PMC6693228 DOI: 10.1186/s12881-019-0867-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 07/29/2019] [Indexed: 12/20/2022]
Abstract
Background Reference genes are often interchangeably called housekeeping genes due to 1) the essential cellular functions their proteins provide and 2) their constitutive expression across a range of normal and pathophysiological conditions. However, given the proliferative drive of malignant cells, many reference genes such as beta-actin (ACTB) and glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) which play critical roles in cell membrane organization and glycolysis, may be dysregulated in tumors versus their corresponding normal controls Methods Because Next Generation Sequencing (NGS) technology has several advantages over hybridization-based technologies, such as independent detection and quantitation of transcription levels, greater sensitivity, and increased dynamic range, we evaluated colorectal cancers (CRC) and their histologically normal tissue counterparts by NGS to evaluate the expression of 21 “classical” reference genes used as normalization standards for PCR based methods. Seventy-nine paired tissue samples of CRC and their patient matched healthy colonic tissues were subjected to NGS analysis of their mRNAs. Results We affirmed that 17 out of 21 classical reference genes had upregulated expression in tumors compared to normal colonic epithelial tissue and dramatically so in some cases. Indeed, tumors were distinguished from normal controls in both unsupervised hierarchical clustering analyses (HCA) and principal component analyses (PCA). We then identified 42 novel potential reference genes with minimal coefficients of variation (CV) across 79 CRC tumor pairs. Though largely consistently expressed across tumors and normal control tissues, a subset of high stage tumors (HSTs) as well as some normal tissue samples (HSNs) located adjacent to these HSTs demonstrated dysregulated expression, thus identifying a subset of tumors with a potentially distinct and aggressive biological profile. Conclusion While classical CRC reference genes were found to be differentially expressed between tumors and normal controls, novel reference genes, identified via NGS, were more consistently expressed across malignant and normal colonic tissues. Nonetheless, a subset of HST had profound dysregulation of such genes as did many of the histologically normal tissues adjacent to such HSTs, indicating that the HSTs so distinguished may have unique biological properties and that their histologically normal tissues likely harbor a small population of microscopically undetected but metabolically active tumors. Electronic supplementary material The online version of this article (10.1186/s12881-019-0867-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lai Xu
- OBP/DBRR-III, CDER, FDA, Silver Spring, MD, 20993, USA. .,Office of Hematology and Oncology Products CDER, FDA, Silver Spring, MD, 20993, USA. .,, Silver Spring, USA.
| | - Helen Luo
- OBP/DBRR-III, CDER, FDA, Silver Spring, MD, 20993, USA
| | - Rong Wang
- OBP/DBRR-III, CDER, FDA, Silver Spring, MD, 20993, USA
| | - Wells W Wu
- Facility for Biotechnology Resources CBER, FDA, Silver Spring, MD, 20993, USA
| | - Je-Nie Phue
- Facility for Biotechnology Resources CBER, FDA, Silver Spring, MD, 20993, USA
| | - Rong-Fong Shen
- Facility for Biotechnology Resources CBER, FDA, Silver Spring, MD, 20993, USA
| | | | - Leihong Wu
- OCS/NCTR/DBB, FDA, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | | | | | - Lorraine Pelosof
- Office of Hematology and Oncology Products CDER, FDA, Silver Spring, MD, 20993, USA
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15
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Mascia F, Karagiannis K, Wu WW, Shen RF, Rao A. Abstract 2093: Drug induced autophagy and transcriptional gene expression signatures in breast cancer cell lines. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-2093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cancer cells can bypass the desired cell death response to chemotherapy through cytoprotective autophagy. In support of this hypothesis, drug resistant clones display higher basal autophagy than the correspondent drug sensitive cell lines. Autophagy therefore represents a potential target to reduce drug resistance and to enhance drug efficacy. We induced autophagy in several breast cancer cell lines with differing ER/PR/Her2 status by exposing them to tamoxifen (MCF-7/ER positive cells), trastuzumab (SKBR3/Her2 positive cells), bortezomib and rapamycin (MDA-MB-231 triple negative cells) in the presence and absence of an autophagy inhibitor such as hydroxychloroquine. While the ongoing autophagy flux process was confirmed by the amount of LC3II at the lipidated protein level, total RNA was extracted at the same time to perform RNA sequencing analysis. We performed differential expression analysis between all the drug treatments and the relative basal level of each cell type obtaining a cell and drug-specific gene list. We then compared all the gene lists to find a common, cell and drug-independent signature. Bioinformatic analysis was performed using the software IPA (Ingenuity Pathway Analysis) and setting a threshold of 0.01 for the p value. This analysis suggested a set of canonical pathways that are significantly and commonly affected in all the samples tested. The top canonical pathways disrupted in all the gene sets were the one identified as tRNA charging, CHK proteins in cell cycle check point control, hypoxia signaling and unfolded protein response. We plan to further identify the smallest gene list that is associated with the disruption of all these pathways across all the cells. This signature may help to uncover a consistent biomarker of autophagy that can be used during preclinical and clinical drug development aiming to reduce or eliminate drug resistance and improve cancer treatment outcomes.
Citation Format: Francesca Mascia, Kostantinos Karagiannis, Wells W. Wu, Rong-Fong Shen, Ashutosh Rao. Drug induced autophagy and transcriptional gene expression signatures in breast cancer cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2093.
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Silva G, Marins M, Chaichanasak N, Yoon Y, Fachin AL, Pinhanelli VC, Regasini LO, dos Santos MB, Ayusso GM, Marques BDC, Wu WW, Phue JN, Shen RF, Baek SJ. Trans-chalcone increases p53 activity via DNAJB1/HSP40 induction and CRM1 inhibition. PLoS One 2018; 13:e0202263. [PMID: 30118500 PMCID: PMC6097677 DOI: 10.1371/journal.pone.0202263] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/31/2018] [Indexed: 11/19/2022] Open
Abstract
Naturally-occurring chalcones and synthetic chalcone analogues have been demonstrated to have many biological effects, including anti-inflammatory, anti-malarial, anti-fungal, and anti-oxidant/anti-cancerous activities. Compared to other chalcones, trans-chalcone exhibits superior inhibitory activity in cancer cell growth as shown via in vitro assays, and exerts anti-cancerous effects via the activation of the p53 tumor suppressor protein. Thus, characterization of the specific mechanisms, by which trans-chalcone activates p53, can aid development of new chemotherapeutic drugs that can be used individually or synergistically with other drugs. In this report, we found that trans-chalcone modulates many p53 target genes, HSP40 being the most induced gene in the RNA-Seq data using trans-chalcone-treated cells. CRM1 is also inhibited by trans-chalcone, resulting in the accumulation of p53 and other tumor suppressor proteins in the nucleus. Similar effects were seen using trans-chalcone derivatives. Overall, trans-chalcone could provide a strong foundation for the development of chalcone-based anti-cancer drugs.
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Affiliation(s)
- Gabriel Silva
- Biotechnology Unit, University of Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Mozart Marins
- Biotechnology Unit, University of Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
- Medicine School, University of Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Nadda Chaichanasak
- Laboratory of Signal Transduction, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | - Yongdae Yoon
- Laboratory of Signal Transduction, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | - Ana Lúcia Fachin
- Biotechnology Unit, University of Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
- Medicine School, University of Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | | | - Luis Octávio Regasini
- Department of Chemistry and Environmental Chemistry, São Paulo State University (UNESP), São Paulo, Brazil
| | - Mariana Bastos dos Santos
- Department of Chemistry and Environmental Chemistry, São Paulo State University (UNESP), São Paulo, Brazil
| | - Gabriela Miranda Ayusso
- Department of Chemistry and Environmental Chemistry, São Paulo State University (UNESP), São Paulo, Brazil
| | | | - Wells W. Wu
- Facility for Biotechnology Resources, CBER, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Je-Nie Phue
- Facility for Biotechnology Resources, CBER, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, CBER, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Seung Joon Baek
- Laboratory of Signal Transduction, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea
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Yang S, Onigman P, Wu WW, Sjogren J, Nyhlen H, Shen RF, Cipollo J. Deciphering Protein O-Glycosylation: Solid-Phase Chemoenzymatic Cleavage and Enrichment. Anal Chem 2018; 90:8261-8269. [DOI: 10.1021/acs.analchem.8b01834] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Shuang Yang
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Philip Onigman
- Genovis Inc., Cambridge, Massachusetts 02142, United States
| | - Wells W. Wu
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | | | | | - Rong-Fong Shen
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - John Cipollo
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993, United States
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Yang S, Wu WW, Shen RF, Bern M, Cipollo J. Identification of Sialic Acid Linkages on Intact Glycopeptides via Differential Chemical Modification Using IntactGIG-HILIC. J Am Soc Mass Spectrom 2018; 29:1273-1283. [PMID: 29651731 PMCID: PMC6744383 DOI: 10.1007/s13361-018-1931-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/15/2018] [Accepted: 02/16/2018] [Indexed: 05/20/2023]
Abstract
Mass spectrometric analysis of intact glycopeptides can reveal detailed information about glycosite, glycan structural features, and their heterogeneity. Sialyl glycopeptides can be positively, negatively, or neutrally charged depending on pH of their buffer solution and ionization conditions. To detect sialoglycopeptides, a negative-ion mode mass spectrometry may be applied with a minimal loss of sialic acids, although the positively charged or neutral glycopeptides may be excluded. Alternatively, the sialyl glycopeptides can be identified using positive-ion mode analysis by doping a high concentration of sodium salts to the analytes. Although manipulation of unmodified sialoglycopeptides can be useful for analysis of samples, less than optimal ionization, facile loss of sialyl and unfavorable ionization of accompanying non-sialyl peptides make such strategies suboptimal. Currently available chemical derivatization methods, while stabilizing for sialic acid, mask sialic acid linkage configuration. Here, we report the development of a novel approach to neutralize sialic acids via sequentially chemical modification that also reveals their linkage configuration, often an important determinant in biological function. This method utilizes several components to facilitate glycopeptide identification. These include the following: solid phase derivatization, enhanced ionization of sialoglycopeptides, differentiation of sialic acid linkage, and enrichment of the modified glycopeptides by hydrophilic interaction liquid chromatography. This technology can be used as a tool for quantitative analysis of protein sialylation in diseases with determination of sialic acid linkage configuration. Graphical Abstract ᅟ.
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Affiliation(s)
- Shuang Yang
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, G614, Bldg 75, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA.
| | - Wells W Wu
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Marshall Bern
- Protein Metrics Inc., 1622 San Carlos Ave, Suite C, San Carlos, CA, 94070, USA
| | - John Cipollo
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, G637, Bldg 52/72, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA.
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Wu WW, Phue JN, Lee CT, Lin C, Xu L, Wang R, Zhang Y, Shen RF. Robust Sub-nanomolar Library Preparation for High Throughput Next Generation Sequencing. BMC Genomics 2018; 19:326. [PMID: 29728062 PMCID: PMC5935984 DOI: 10.1186/s12864-018-4677-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 04/16/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Current library preparation protocols for Illumina HiSeq and MiSeq DNA sequencers require ≥2 nM initial library for subsequent loading of denatured cDNA onto flow cells. Such amounts are not always attainable from samples having a relatively low DNA or RNA input; or those for which a limited number of PCR amplification cycles is preferred (less PCR bias and/or more even coverage). A well-tested sub-nanomolar library preparation protocol for Illumina sequencers has however not been reported. The aim of this study is to provide a much needed working protocol for sub-nanomolar libraries to achieve outcomes as informative as those obtained with the higher library input (≥ 2 nM) recommended by Illumina's protocols. RESULTS Extensive studies were conducted to validate a robust sub-nanomolar (initial library of 100 pM) protocol using PhiX DNA (as a control), genomic DNA (Bordetella bronchiseptica and microbial mock community B for 16S rRNA gene sequencing), messenger RNA, microRNA, and other small noncoding RNA samples. The utility of our protocol was further explored for PhiX library concentrations as low as 25 pM, which generated only slightly fewer than 50% of the reads achieved under the standard Illumina protocol starting with > 2 nM. CONCLUSIONS A sub-nanomolar library preparation protocol (100 pM) could generate next generation sequencing (NGS) results as robust as the standard Illumina protocol. Following the sub-nanomolar protocol, libraries with initial concentrations as low as 25 pM could also be sequenced to yield satisfactory and reproducible sequencing results.
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Affiliation(s)
- Wells W Wu
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA
| | - Je-Nie Phue
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA
| | - Chun-Ting Lee
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA
| | - Changyi Lin
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA
| | - Lai Xu
- OBP/DBRR-III, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Rong Wang
- OBP/DBRR-III, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Yaqin Zhang
- OBP/DBRR-III, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA.
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Lee CT, Bendriem RM, Wu WW, Shen RF. 3D brain Organoids derived from pluripotent stem cells: promising experimental models for brain development and neurodegenerative disorders. J Biomed Sci 2017; 24:59. [PMID: 28822354 PMCID: PMC5563385 DOI: 10.1186/s12929-017-0362-8] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/09/2017] [Indexed: 02/07/2023] Open
Abstract
Three-dimensional (3D) brain organoids derived from human pluripotent stem cells (hPSCs), including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), appear to recapitulate the brain's 3D cytoarchitectural arrangement and provide new opportunities to explore disease pathogenesis in the human brain. Human iPSC (hiPSC) reprogramming methods, combined with 3D brain organoid tools, may allow patient-derived organoids to serve as a preclinical platform to bridge the translational gap between animal models and human clinical trials. Studies using patient-derived brain organoids have already revealed novel insights into molecular and genetic mechanisms of certain complex human neurological disorders such as microcephaly, autism, and Alzheimer's disease. Furthermore, the combination of hiPSC technology and small-molecule high-throughput screening (HTS) facilitates the development of novel pharmacotherapeutic strategies, while transcriptome sequencing enables the transcriptional profiling of patient-derived brain organoids. Finally, the addition of CRISPR/Cas9 genome editing provides incredible potential for personalized cell replacement therapy with genetically corrected hiPSCs. This review describes the history and current state of 3D brain organoid differentiation strategies, a survey of applications of organoids towards studies of neurodevelopmental and neurodegenerative disorders, and the challenges associated with their use as in vitro models of neurological disorders.
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Affiliation(s)
- Chun-Ting Lee
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, FDA, Silver Spring, MD, 20993, USA. .,Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Building 52, Rm 1121, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA.
| | - Raphael M Bendriem
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Wells W Wu
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, FDA, Silver Spring, MD, 20993, USA
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, FDA, Silver Spring, MD, 20993, USA
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Xu L, Wang R, Ziegelbauer J, Wu WW, Shen RF, Juhl H, Zhang Y, Pelosof L, Rosenberg AS. Transcriptome analysis of human colorectal cancer biopsies reveals extensive expression correlations among genes related to cell proliferation, lipid metabolism, immune response and collagen catabolism. Oncotarget 2017; 8:74703-74719. [PMID: 29088818 PMCID: PMC5650373 DOI: 10.18632/oncotarget.20345] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 07/12/2017] [Indexed: 12/12/2022] Open
Abstract
Precise characterization of biological processes critical to proliferation and metastasis of colorectal cancer should facilitate the development of diagnostic and prognostic biomarkers as well as novel treatments. Using mRNA-Seq, we examined the protein coding messenger RNA (mRNA) expression profiles across different histologically defined stages of primary colon cancers and compared them to their patient matched normal tissue controls. In comparing 79 colorectal cancers to their matched normal mucosa, tumors were distinguished from normal non-malignant tissues not only in the upregulation of biological processes pertaining to cell proliferation, inflammation, and tissue remodeling, but even more strikingly, in downregulated biological processes including fatty acid beta oxidization for ATP production and epithelial cell differentiation and function. A network analysis of deregulated genes revealed newly described cancer networks and putative hub genes. Taken together, our findings suggest that, within an inflammatory microenvironment, invasive, dedifferentiated and rapidly dividing tumor cells divert the oxidation of fatty acids and lipids from energy production into lipid components of cell membranes and organelles to support tumor proliferation. A gene co-expression network analysis provides a clear and broad picture of biological pathways in tumors that may significantly enhance or supplant current histopathologic studies.
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Affiliation(s)
- Lai Xu
- Office of Biotechnology Products, CDER, FDA, Silver Spring, MD 20993, USA
| | - Rong Wang
- Office of Biotechnology Products, CDER, FDA, Silver Spring, MD 20993, USA
| | | | - Wells W Wu
- Facility for Biotechnology Resources, CBER, FDA, Silver Spring, MD 20993, USA
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, CBER, FDA, Silver Spring, MD 20993, USA
| | | | - Yaqin Zhang
- Office of Biotechnology Products, CDER, FDA, Silver Spring, MD 20993, USA
| | - Lorraine Pelosof
- Office of Hematology and Oncology Products, CDER, FDA, Silver Spring, MD 20993, USA
| | - Amy S Rosenberg
- Office of Biotechnology Products, CDER, FDA, Silver Spring, MD 20993, USA
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Abstract
Clostridium tetani and Clostridium botulinum produce two of the most potent neurotoxins known, tetanus neurotoxin and botulinum neurotoxin, respectively. Extensive biochemical and genetic investigation has been devoted to identifying and characterizing various C. botulinum strains. Less effort has been focused on studying C. tetani likely because recently sequenced strains of C. tetani show much less genetic diversity than C. botulinum strains and because widespread vaccination efforts have reduced the public health threat from tetanus. Our aim was to acquire genomic data on the U.S. vaccine strain of C. tetani to better understand its genetic relationship to previously published genomic data from European vaccine strains. We performed high throughput genomic sequence analysis on two wild-type and two vaccine C. tetani strains. Comparative genomic analysis was performed using these and previously published genomic data for seven other C. tetani strains. Our analysis focused on single nucleotide polymorphisms (SNP) and four distinct constituents of the mobile genome (mobilome): a hypervariable flagellar glycosylation island region, five conserved bacteriophage insertion regions, variations in three CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems, and a single plasmid. Intact type IA and IB CRISPR/Cas systems were within 10 of 11 strains. A type IIIA CRISPR/Cas system was present in two strains. Phage infection histories derived from CRISPR-Cas sequences indicate C. tetani encounters phages common among commensal gut bacteria and soil-borne organisms consistent with C. tetani distribution in nature. All vaccine strains form a clade distinct from currently sequenced wild type strains when considering variations in these mobile elements. SNP, flagellar glycosylation island, prophage content and CRISPR/Cas phylogenic histories provide tentative evidence suggesting vaccine and wild type strains share a common ancestor.
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Affiliation(s)
- Jonathan E. Cohen
- Laboratory of Respiratory and Special Pathogens, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Rong Wang
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Wells W. Wu
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - James E. Keller
- Laboratory of Respiratory and Special Pathogens, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
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Jiang B, Shen RF, Bi J, Tian XS, Hinchliffe T, Xia Y. Catalpol: a potential therapeutic for neurodegenerative diseases. Curr Med Chem 2016; 22:1278-91. [PMID: 25620103 DOI: 10.2174/0929867322666150114151720] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 01/05/2015] [Accepted: 01/08/2015] [Indexed: 11/22/2022]
Abstract
Neurodegenerative disorders, e.g., Alzheimer's disease (AD) and Parkinson's disease (PD) are characterized by the progressive loss of neurons and subsequent cognitive decline. They are mainly found in older populations. Due to increasing life expectancies, the toll inflicted upon society by these disorders continues to become heavier and more prominent. Despite extensive research, however, the exact etiology of these disorders is still unknown, though the pathophysiological mechanisms have been attributed to oxidative, inflammatory and apoptotic injury in the brain. Moreover, there is currently no promising therapeutic agent against these neurodegenerative changes. Catalpol, an iridoid glucoside contained richly in the roots of the small flowering plant species Rehmannia glutinosa Libosch, has been shown to have antioxidation, anti-inflammation, anti-apoptosis and other neuroprotective properties and plays a role in neuroprotection against hypoxic/ischemic injury, AD and PD in both in vivo and in vitro models. It may therefore represent a potential therapeutical agent for the treatment of hypoxic/ischemic injury and neurodegenerative diseases. Based on our studies and those of others in the literature, here we comprehensively review the role of Catalpol in neuroprotection against pathological conditions, especially in neurodegenerative states and the potential mechanisms involved.
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Affiliation(s)
- B Jiang
- School of Biological Science & Technology, Dalian University of Technology, Dalian, Liaoning 116024, China.
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Xu L, Ziegelbauer J, Wang R, Wu WW, Shen RF, Juhl H, Zhang Y, Rosenberg A. Distinct Profiles for Mitochondrial t-RNAs and Small Nucleolar RNAs in Locally Invasive and Metastatic Colorectal Cancer. Clin Cancer Res 2015; 22:773-84. [PMID: 26384739 DOI: 10.1158/1078-0432.ccr-15-0737] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 09/02/2015] [Indexed: 01/01/2023]
Abstract
PURPOSE To gain insight into factors involved in tumor progression and metastasis, we examined the role of noncoding RNAs in the biologic characteristics of colorectal carcinoma, in paired samples of tumor together with normal mucosa from the same colorectal carcinoma patient. The tumor and healthy tissue samples were collected and stored under stringent conditions, thereby minimizing warm ischemic time. EXPERIMENTAL DESIGN We focused particularly on distinctions among high-stage tumors and tumors with known metastases, performing RNA-Seq analysis that quantifies transcript abundance and identifies novel transcripts. RESULTS In comparing 35 colorectal carcinomas, including 9 metastatic tumors (metastases to lymph nodes and lymphatic vessels), with their matched healthy control mucosa, we found a distinct signature of mitochondrial transfer RNAs (MT-tRNA) and small nucleolar RNAs (snoRNA) for metastatic and high-stage colorectal carcinoma. We also found the following: (i) MT-TF (phenylalanine) and snord12B expression correlated with a substantial number of miRNAs and mRNAs in 14 colorectal carcinomas examined; (ii) an miRNA signature of oxidative stress, hypoxia, and a shift to glycolytic metabolism in 14 colorectal carcinomas, regardless of grade and stage; and (iii) heterogeneous MT-tRNA/snoRNA fingerprints for 35 pairs. CONCLUSIONS These findings could potentially assist in more accurate and predictive staging of colorectal carcinoma, including identification of those colorectal carcinomas likely to metastasize.
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Affiliation(s)
- Lai Xu
- OBP/DBRR-III, CDER, FDA, Silver Spring, Maryland
| | | | - Rong Wang
- OBP/DBRR-III, CDER, FDA, Silver Spring, Maryland
| | - Wells W Wu
- Facility for Biotechnology Resources, CBER, FDA, Silver Spring, Maryland
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, CBER, FDA, Silver Spring, Maryland
| | | | - Yaqin Zhang
- OBP/DBRR-III, CDER, FDA, Silver Spring, Maryland
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Huang IH, Hsiao CT, Wu JC, Shen RF, Liu CY, Wang YK, Chen YC, Huang CM, del Álamo JC, Chang ZF, Tang MJ, Khoo KH, Kuo JC. GEF-H1 controls focal adhesion signaling that regulates mesenchymal stem cell lineage commitment. Development 2014. [DOI: 10.1242/dev.117994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Huang IH, Hsiao CT, Wu JC, Shen RF, Liu CY, Wang YK, Chen YC, Huang CM, del Álamo JC, Chang ZF, Tang MJ, Khoo KH, Kuo JC. GEF-H1 controls focal adhesion signaling that regulates mesenchymal stem cell lineage commitment. J Cell Sci 2014; 127:4186-200. [PMID: 25107365 PMCID: PMC4179489 DOI: 10.1242/jcs.150227] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Focal adhesions (FAs) undergo maturation that culminates in size and composition changes that modulate adhesion, cytoskeleton remodeling and differentiation. Although it is well recognized that stimuli for osteogenesis of mesenchymal stem cells (MSCs) drive FA maturation, actin organization and stress fiber polarization, the extent to which FA-mediated signals regulated by the FA protein composition specifies MSC commitment remains largely unknown. Here, we demonstrate that, upon dexamethasone (osteogenic induction) treatment, guanine nucleotide exchange factor H1 (GEF-H1, also known as Rho guanine nucleotide exchange factor 2, encoded by ARHGEF2) is significantly enriched in FAs. Perturbation of GEF-H1 inhibits FA formation, anisotropic stress fiber orientation and MSC osteogenesis in an actomyosin-contractility-independent manner. To determine the role of GEF-H1 in MSC osteogenesis, we explore the GEF-H1-modulated FA proteome that reveals non-muscle myosin-II heavy chain-B (NMIIB, also known as myosin-10, encoded by MYH10) as a target of GEF-H1 in FAs. Inhibition of targeting NMIIB into FAs suppresses FA formation, stress fiber polarization, cell stiffness and osteogenic commitments in MSCs. Our data demonstrate a role for FA signaling in specifying MSC commitment.
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Affiliation(s)
- I-Husan Huang
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Cheng-Te Hsiao
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Jui-Chung Wu
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Rong-Fong Shen
- Proteomics and Analytical Biochemistry Unit, Research Resources Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Ching-Yi Liu
- Institute of Basic Medical Sciences, National Cheng Kung University, Tainan 70101, Taiwan Department of Physiology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Yang-Kao Wang
- Department of Cell Biology and Anatomy, National Cheng Kung University, Tainan 70101, Taiwan Center for Neurotrauma and Neuroregeneration, Taipei Medical University, Taipei 11031, Taiwan
| | - Yu-Chen Chen
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Chi-Ming Huang
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Juan C del Álamo
- Institute of Engineering in Medicine, University of California at San Diego, La Jolla, CA 92093, USA Department of Mechanical and Aerospace Engineering, University of California at San Diego, La Jolla, CA 92093, USA
| | - Zee-Fen Chang
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Ming-Jer Tang
- Institute of Basic Medical Sciences, National Cheng Kung University, Tainan 70101, Taiwan Department of Physiology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Kay-Hooi Khoo
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Jean-Cheng Kuo
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan
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Laslo M, Sun X, Hsiao CT, Wu WW, Shen RF, Zou S. A botanical containing freeze dried açai pulp promotes healthy aging and reduces oxidative damage in sod1 knockdown flies. Age (Dordr) 2013; 35:1117-32. [PMID: 22639178 PMCID: PMC3705126 DOI: 10.1007/s11357-012-9437-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 05/16/2012] [Indexed: 05/10/2023]
Abstract
Superoxide dismutase 1 (SOD1), a critical enzyme against oxidative stress, is implicated in aging and degenerative diseases. We previously showed that a nutraceutical containing freeze-dried açai pulp promotes survival of flies fed a high-fat diet or sod1 knockdown flies fed a standard diet. Here, we investigated the effect of açai supplementation initiated at the early or late young adulthood on lifespan, physiological function, and oxidative damage in sod1 knockdown flies. We found that Açai supplementation extended lifespan even when started at the age of 10 days, which is the time shortly before the mortality rate of flies accelerated. Life-long açai supplementation increased lifetime reproductive output in sod1 knockdown flies. Our molecular studies indicate that açai supplementation reduced the protein levels of genes involved in oxidative stress response, cellular growth, and nutrient metabolism. Açai supplementation also affected the protein levels of ribosomal proteins. In addition, açai supplementation decreased the transcript levels of genes involved in oxidative stress response and gluconeogenesis, while increasing the transcript levels of mitochondrial biogenesis genes. Moreover, açai supplementation reduced the level of 4-hydroxynonenal-protein adducts, a lipid peroxidation marker. Our findings suggest that açai supplementation promotes healthy aging in sod1-deficient flies partly through reducing oxidative damage, and modulating nutrient metabolism and oxidative stress response pathways. Our findings provide a foundation to further evaluate the viability of using açai as an effective dietary intervention to promote healthy aging and alleviate symptoms of diseases with a high level of oxidative stress.
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Affiliation(s)
- Mara Laslo
- />Laboratory of Experimental Gerontology, National Institute on Aging, 251 Bayview Blvd., Suite #100, Baltimore, MD 21224 USA
| | - Xiaoping Sun
- />Laboratory of Experimental Gerontology, National Institute on Aging, 251 Bayview Blvd., Suite #100, Baltimore, MD 21224 USA
| | - Cheng-Te Hsiao
- />Laboratory of Experimental Gerontology, National Institute on Aging, 251 Bayview Blvd., Suite #100, Baltimore, MD 21224 USA
| | - Wells W. Wu
- />Laboratory of Clinical Investigation, National Institute on Aging, Baltimore, MD 21224 USA
| | - Rong-Fong Shen
- />Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20892 USA
| | - Sige Zou
- />Laboratory of Experimental Gerontology, National Institute on Aging, 251 Bayview Blvd., Suite #100, Baltimore, MD 21224 USA
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Obolensky OI, Wu WW, Shen RF, Yu YK. Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptides. II. Results for hexapeptides with non-polar side chains. Rapid Commun Mass Spectrom 2013; 27:152-156. [PMID: 23239328 PMCID: PMC3856442 DOI: 10.1002/rcm.6451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 10/12/2012] [Accepted: 10/14/2012] [Indexed: 06/01/2023]
Abstract
RATIONALE The hypothesis that dissociation energies can serve as a predictor of observability of b- and y-peaks is tested for seven hexapeptides. If the hypothesis holds true for large classes of peptides, one would be able to improve the scoring accuracy of peptide identification tools by excluding theoretical peaks that cannot be observed in practical product ion spectra due to various physical, chemical or thermodynamic considerations. METHODS Product ion m/z spectra of hexapeptides AAAAAA, AAAFAA, AAAVAA, AAFAAA, AAVAAA, AAFFAA and AAVVAA have been acquired on a Finnigan LTQ XL mass spectrometer in the collision-induced dissociation (CID) activation mode on a grid of activation times 0.05 to 100 ms and normalized collision energy 10 to 35%. Dissociation energies were calculated for all fragmentation channels leading to b- and y-fragments at the TPSS/6-31G(d,p) level of the density functional theory. RESULTS It was demonstrated that the m/z peaks observed in the product ion spectra correspond to the fragmentation channels with dissociation energies below a certain threshold value. However, there is no direct correlation between the most intense m/z peaks and the lowest dissociation energies. Using the dissociation energies, it was predicted that out of 63 theoretically possible peaks in the b- and y-series of the seven hexapeptides, 19 should not be observable in practical spectra. In the experiments, 24 peaks were not observed, including all 19 predicted. CONCLUSIONS Dissociation energies alone are not sufficient for predicting ion intensity relationships in product ion m/z spectra. Nevertheless, the present data suggest that dissociation energies appear to be good predictors of observability of b- and y-peaks and potentially very useful for filtering theoretical peaks of each candidate peptide in peptide identification tools. Published 2012. This article is a US Government work and is in the public domain in the USA.
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Affiliation(s)
- O. I. Obolensky
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Wells W. Wu
- National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Rong-Fong Shen
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Bethesda, MD, USA
| | - Yi-Kuo Yu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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Abstract
PURPOSE Our study aims to establish a plasma biomarker analysis workflow, with fewer fractionation steps, for enhanced identification of plasma biomarkers by precursor ion exclusion (PIE). EXPERIMENTAL DESIGN Plasma samples were depleted for highly abundant proteins, then further fractionated by molecular weight (MW), before trypsinization for LTQ-Orbitrap mass analysis. Data-dependent acquisition (DDA) was used for baseline analysis. PIE involves the re-injection of samples with exclusion of the previously identified peptides. We compared analyses using multiple PIE iterations, compared to DDA, for plasma interrogation RESULTS A higher percentage of unique plasma peptides was identified with PIE, compared to DDA. The first PIE iteration reveals an increase of 75-112% more peptides than the DDA method alone. PIE can interrogate complex plasma samples with the percentage of peptides identified successively increasing with even ≥4 iterations. The total number of peptides identified increases rapidly across the first three PIE iterations and then continues more slowly up to nine iterations. CONCLUSIONS AND CLINICAL RELEVANCE Iterative injections with PIE resulted in many more peptide identifications in plasma samples of varying degrees of complexity, compared to re-injections using similar DDA parameters. PIE methods may therefore expand our ability to recover plasma peptides for plasma biomarker discovery.
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Affiliation(s)
- Wells W Wu
- Metabolism Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
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Park SS, Wu WW, Zhou Y, Shen RF, Martin B, Maudsley S. Effective correction of experimental errors in quantitative proteomics using stable isotope labeling by amino acids in cell culture (SILAC). J Proteomics 2012; 75:3720-32. [PMID: 22575385 DOI: 10.1016/j.jprot.2012.04.035] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 03/29/2012] [Accepted: 04/24/2012] [Indexed: 12/22/2022]
Abstract
Accurate and reliable quantitative proteomics in cell culture has been considerably facilitated by the introduction of the stable isotope labeling by amino acids in cell culture (SILAC), combined with high resolution mass spectrometry. There are however several major sources of quantification errors that commonly occur with SILAC techniques, i.e. incomplete incorporation of isotopic amino acids, arginine-to-proline conversion, and experimental errors in final sample mixing. Dataset normalization is a widely adopted solution to such errors, however this may not completely prevent introducing incorrect expression ratios. Here we demonstrate that a label-swap replication of SILAC experiments was able to effectively correct experimental errors by averaging ratios measured in individual replicates using quantitative proteomics and phosphoproteomics of ligand treatment of neural cell cultures. Furthermore, this strategy was successfully applied to a SILAC triplet experiment, which presents a much more complicated experimental matrix, affected by both incomplete labeling and arginine-to-proline conversion. Based on our results, we suggest that SILAC experiments should be designed to incorporate label-swap replications for enhanced reliability in expression ratios.
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Affiliation(s)
- Sung-Soo Park
- Receptor Pharmacology Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
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31
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Obolensky OI, Wu WW, Shen RF, Yu YK. Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptides. Rapid Commun Mass Spectrom 2012; 26:915-20. [PMID: 22396027 PMCID: PMC3468955 DOI: 10.1002/rcm.6180] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
RATIONALE Peptide identification reliability can be improved by excluding from analysis those m/z peaks of candidate peptides which cannot be observed in practice due to various physical, chemical or thermodynamic considerations. We propose using dissociation energies (as opposed to proton affinities) as a predictor of observability of different m/z peaks in spectra of short peptides. METHODS Mass spectra of the tetrapeptides AAAA, AAFA, AAVA, AFAA, AVAA, AFFA, and AVVA were measured in the collision-induced dissociation (CID) activation mode on a grid of activation times 0.05 to 100 ms and normalized collision energy 10 to 35%. The lowest energy geometries and vibrational spectra were calculated for the precursor ions and their charged and neutral fragments using density functional theory (DFT) at the TPSS/6-31G(d,p) level. Dissociation energies were calculated for all fragmentation channels leading to b- or y-fragments. RESULTS It is demonstrated that m/z peaks observed in the mass spectra correspond to the fragmentation channels with the lowest dissociation energies. Using 50 kcal/mol as the cut-off value of dissociation energy, it was predicted that 28 out of 42 possible peaks in the b- and y-series of the seven tetrapeptides can be observed in mass spectra. In the experiments, 26 b- or y-peaks were observed, all of which are among the 28 predicted ones. CONCLUSIONS The use of dissociation energies generalizes the use of proton affinities for semi-quantitative predictions of relative intensities of different m/z peaks of short peptides. Further advances in this direction will pave the way for reliable quantitative predictions and, hence, for a significant improvement in robustness and accuracy of peptide and protein identification tools.
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Affiliation(s)
- O I Obolensky
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
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32
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Khositseth S, Somparn P, Thippamon N, Uawithya P, Shen RF, Chen SH. Quantitative phosphoproteomics of hypercalcemia induced nephrogenic diabetes insipidus. FASEB J 2012. [DOI: 10.1096/fasebj.26.1_supplement.1100.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sookkasem Khositseth
- Department of PediatricsFaculty of MedicineThammasat UniversityPatumthaneeThailand
| | - Poorichaya Somparn
- Department of PediatricsFaculty of MedicineThammasat UniversityPatumthaneeThailand
| | - Nattakarn Thippamon
- Department of PediatricsFaculty of MedicineThammasat UniversityPatumthaneeThailand
| | - Panapat Uawithya
- Department of PhysiologyFaculty of MedicineSiriraj HospitalBangkokThailand
| | - Rong-Fong Shen
- Center for Biologics Evaluation and ResearchFDABethesdaMD
| | - Shu-Hui Chen
- Department of ChemistryNational Cheng Kung UniversityTainanTaiwan
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LI CHUNCHUN, Shen X, Aponte A, Shen RF, Billings EM, Moss J, Vaughan M. BIG2, an ARF guanine nucleotide‐exchange protein, regulates cell migration via effects integrin β1 cycling and actin cytoskeleton remodeling. FASEB J 2012. [DOI: 10.1096/fasebj.26.1_supplement.782.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- CHUN-CHUN LI
- Cardiovascular and Pulmonary BranchNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMD
| | - Xiaoyan Shen
- Cardiovascular and Pulmonary BranchNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMD
| | - Angel Aponte
- Proteomics Core FacilityNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMD
| | - Rong-Fong Shen
- Proteomics Core FacilityNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMD
| | - Eric M Billings
- Proteomics Core FacilityNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMD
| | - Joel Moss
- Cardiovascular and Pulmonary BranchNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMD
| | - Martha Vaughan
- Cardiovascular and Pulmonary BranchNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMD
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Wu WW, Wang G, Insel PA, Hsiao CT, Zou S, Martin B, Maudsley S, Shen RF. Discovery- and target-based protein quantification using iTRAQ and pulsed Q collision induced dissociation (PQD). J Proteomics 2012; 75:2480-7. [PMID: 22397766 DOI: 10.1016/j.jprot.2012.02.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 02/07/2012] [Accepted: 02/20/2012] [Indexed: 12/27/2022]
Abstract
Pulsed Q collision-induced dissociation (PQD) was developed in part to facilitate detection of low-mass reporter ions using labeling reagents (e.g. iTRAQ) on LTQ platforms. It has generally been recognized that the scan speed and sensitivity of an LTQ are superior than those of an Orbitrap using the higher-energy collisional dissociation (HCD). However, the use of PQD in quantitative proteomics is limited, primarily due to the meager reproducibility of reporter ion ratios. Optimizations of PQD for iTRAQ quantification using LTQ have been reported, but a universally applicable strategy for quantifying the less abundant proteins has not been fully established. Adjustments of the AGC target, μscan, or scan speed offer only incremental improvements in reproducibility. From our experience, however, satisfactory coefficients of variation (CVs) of reporter ion ratios were difficult to achieve using the discovery-based approach. As an alternative, we implemented a target-based approach that obviates data dependency to allow repetitive data acquisitions across chromatographic peaks. Such a strategy generates enough data points for more reliable quantification. Using cAMP treatment in S49 cell lysates and this target-based approach, we were able to validate differentially expressed proteins, which were initially identified as potential candidates using the discovery-based PQD. The target-based strategy also yielded results comparable to those obtained from HCD in an Orbitrap. Our findings should aid LTQ users who desire to explore iTRAQ quantitative proteomics but have limited access to the more costly Orbitrap or other instruments.
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Affiliation(s)
- Wells W Wu
- Metabolism Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
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35
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Wu WW, Wang G, Insel PA, Hsiao CT, Zou S, Maudsley S, Martin B, Shen RF. Identification of proteins and phosphoproteins using pulsed Q collision induced dissociation (PQD). J Am Soc Mass Spectrom 2011; 22:1753-1762. [PMID: 21952889 PMCID: PMC3183836 DOI: 10.1007/s13361-011-0197-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 06/14/2011] [Accepted: 06/14/2011] [Indexed: 05/31/2023]
Abstract
Pulsed Q collision induced dissociation (PQD) was developed to facilitate detection of low-mass reporter ions from labeling reagents (e.g., iTRΑQ) in peptide quantification using an LTQ mass spectrometer (MS). Despite the large number of linear ion traps worldwide, the use and optimization of PQD for protein identification have been limited, in part due to less effective ion fragmentation relative to the collision induced dissociation (CID). PQD expands the m/z coverage of fragment ions to the lower m/z range by circumventing the typical low mass cut-off of an ion trap MS. Since database searching relies on the matching between theoretical and observed spectra, it is not clear how ion intensity and peak number might affect the outcomes of a database search. In this report, we systematically evaluated the attributes of PQD mass spectra, performed intensity optimization, and assessed the benefits of using PQD on the identification of peptides and phosphopeptides from an LTQ. Based on head-to-head comparisons between CID (higher intensity) and PQD (better m/z coverage), peptides identified using PQD generally have Xcorr scores lower than those using CID. Such score differences were considerably diminished by the use of 0.1% m-nitrobenzyl alcohol (m-NBA) in mobile phases. The ion intensities of both CID and PQD were adversely affected by increasing m/z of the precursor, with PQD more sensitive than CID. In addition to negating the 1/3 rule, PQD enhances direct bond cleavage and generates patterns of fragment ions different from those of CID, particularly for peptides with a labile functional group (e.g., phosphopeptides). The higher energy fragmentation pathway of PQD on peptide fragmentation was further compared to those of CID and the quadrupole-type activation in parallel experiments.
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Affiliation(s)
- Wells W. Wu
- Laboratory of Clinical Investigation, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Guanghui Wang
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Paul A. Insel
- Department of Pharmacology and Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Cheng-Te Hsiao
- Laboratory of Experimental Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Sige Zou
- Laboratory of Experimental Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Stuart Maudsley
- Receptor Pharmacology Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Bronwen Martin
- Laboratory of Clinical Investigation, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Rong-Fong Shen
- Laboratory of Clinical Investigation, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
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36
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Li T, Santockyte R, Yu S, Shen RF, Tekle E, Lee CGL, Yang DCH, Chock PB. FAT10 modifies p53 and upregulates its transcriptional activity. Arch Biochem Biophys 2011; 509:164-9. [PMID: 21396347 DOI: 10.1016/j.abb.2011.02.017] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 02/16/2011] [Accepted: 02/18/2011] [Indexed: 10/18/2022]
Abstract
FAT10, also known as diubiquitin, has been implicated in the regulation of diverse cellular processes, including mitosis, immune response, and apoptosis. We seek to identify FAT10-targeted proteins, an essential step in elucidating the physiological function of FAT10. To this end, human FAT10 or its non-conjugatable derivative, FAT10ΔGG, was overexpressed in HEK293 cells. We observed a number of high molecular weight FAT10 conjugates in cells expressing wild-type FAT10, but not in FAT10ΔGG. The FAT10 conjugates are inducible by TNF-α and accumulated significantly when cells were treated with proteasome inhibitor, MG132. Among them, tumor suppressor p53 was found to be FATylated. The p53 transcriptional activity was found to be substantially enhanced in FAT10-overexpressing cells. In addition, overexpressing FAT10 in HEK293 cells also reduced the population of p53 which cross reacted with monoclonal anti-p53 antibody, PAB240, known to recognize only the transcriptionally inactive p53. FAT10 in the nucleus was found co-localized with p53 and altered its subcellular compartmentalization. Furthermore, overexpressing FAT10 led to a reduction in the size of promyelocytic leukemia nuclear bodies (PML-NBs) and altered their distribution in the nucleus. Based on these observations, a potential mechanism which correlates FATylation of p53 to its translocation and transcriptional activation is discussed.
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Affiliation(s)
- Tianwei Li
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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37
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Zhou Y, Yi T, Park SS, Chadwick W, Shen RF, Wu WW, Martin B, Maudsley S. Rapid and enhanced proteolytic digestion using electric-field-oriented enzyme reactor. J Proteomics 2011; 74:1030-5. [PMID: 21338726 DOI: 10.1016/j.jprot.2011.02.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 01/25/2011] [Accepted: 02/06/2011] [Indexed: 01/26/2023]
Abstract
We have created a novel enzyme reactor using electric field-mediated orientation and immobilization of proteolytic enzymes (trypsin/chymotrypsin) on biocompatible PVDF membranes in a continuous flow-through chamber. Using less than 5min, this reactor in various enzyme combinations can produce enhanced rapid digestion for standardized prototypic proteins, hydrophilic proteins and hydrophobic transmembrane proteins when compared to in-solution techniques. With improved digestive efficiency, our reactor improved the overall functional analysis of lipid raft proteomes by identifying more closely functionally linked proteins and elucidated a richer set of biological processes and pathways linked to the proteins than traditional in-solution methods.
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Affiliation(s)
- Yu Zhou
- Receptor Pharmacology Unit, Laboratory of Neuroscience, National Institute on Aging, Biomedical Research Center, Baltimore, MD, USA
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38
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Abstract
Glycomic analysis is an increasingly important field in biological and biomedical research as glycosylation is one of the most important protein post-translational modifications. We have developed a new technique to detect carbohydrates using surface enhanced Raman spectroscopy (SERS) by designing and applying a Rhodamine B derivative as the SERS tag. Using a reductive amination reaction, the Rhodamine-based tag (RT) was successfully conjugated to three model carbohydrates (glucose, lactose, and glucuronic acid). SERS detection limits obtained with a 633 nm HeNe laser were ∼1 nM in concentration for all the RT-carbohydrate conjugates and ∼10 fmol in total sample consumption. The dynamic range of the SERS method is about 4 orders of magnitude, spanning from 1 nM to 5 μM. Ratiometric SERS quantification using isotope-substituted SERS internal references allows comparative quantifications of carbohydrates labeled with RT and deuterium/hydrogen substituted RT tags, respectively. In addition to enhancing the SERS detection of the tagged carbohydrates, the Rhodamine tagging facilitates fluorescence and mass spectrometric detection of carbohydrates. Current fluorescence sensitivity of RT-carbohydrates is ∼3 nM in concentration while the mass spectrometry (MS) sensitivity is about 1 fmol, achieved with a linear ion trap electrospray ionization (ESI)-MS instrument. Potential applications that take advantage of the high SERS, fluorescence, and MS sensitivity of this SERS tagging strategy are discussed for practical glycomic analysis where carbohydrates may be quantified with a fluorescence and SERS technique and then identified with ESI-MS techniques.
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Affiliation(s)
| | - Michael Yanney
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762
| | - Cheng-Te Hsiao
- Laboratory of Experimental Gerontology, National Institute on Aging, NIH, Baltimore, MD 21224
| | - Wells W. Wu
- Proteomics and Analytical Biochemistry Unit, National Institute on Aging, NIH, Baltimore, MD 21224
| | - Rong-Fong Shen
- Proteomics and Analytical Biochemistry Unit, National Institute on Aging, NIH, Baltimore, MD 21224
| | - Sige Zou
- Laboratory of Experimental Gerontology, National Institute on Aging, NIH, Baltimore, MD 21224
| | - Andrzej Sygula
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762
| | - Dongmao Zhang
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762
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Kunin M, Dmitrieva NI, Gallazzini M, Shen RF, Wang G, Burg MB, Ferraris JD. Mediator of DNA damage checkpoint 1 (MDC1) contributes to high NaCl-induced activation of the osmoprotective transcription factor TonEBP/OREBP. PLoS One 2010; 5:e12108. [PMID: 20711462 PMCID: PMC2920327 DOI: 10.1371/journal.pone.0012108] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 07/12/2010] [Indexed: 01/17/2023] Open
Abstract
Background Hypertonicity, such as induced by high NaCl, increases the activity of the transcription factor TonEBP/OREBP whose target genes increase osmoprotective organic osmolytes and heat shock proteins. Methodology We used mass spectrometry to analyze proteins that coimmunoprecipitate with TonEBP/OREBP in order to identify ones that might contribute to its high NaCl-induced activation. Principal Findings We identified 20 unique peptides from Mediator of DNA Damage Checkpoint 1 (MDC1) with high probability. The identification was confirmed by Western analysis. We used small interfering RNA knockdown of MDC1 to characterize its osmotic function. Knocking down MDC1 reduces high NaCl-induced increases in TonEBP/OREBP transcriptional and transactivating activity, but has no significant effect on its nuclear localization. We confirm six previously known phosphorylation sites in MDC1, but do not find evidence that high NaCl increases phosphorylation of MDC1. It is suggestive that MDC1 acts as a DNA damage response protein since hypertonicity reversibly increases DNA breaks, and other DNA damage response proteins, like ATM, also associate with TonEBP/OREBP and contribute to its activation by hypertonicity. Conclusions/Significance MDC1 associates with TonEBP/OREBP and contributes to high NaCl-induced increase of that factor's transcriptional activity.
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Affiliation(s)
- Margarita Kunin
- Laboratory of Kidney and Electrolyte Metabolism, National Heart, Lung and Blood Institute, Bethesda, Maryland, United States of America
| | - Natalia I. Dmitrieva
- Laboratory of Kidney and Electrolyte Metabolism, National Heart, Lung and Blood Institute, Bethesda, Maryland, United States of America
| | - Morgan Gallazzini
- Laboratory of Kidney and Electrolyte Metabolism, National Heart, Lung and Blood Institute, Bethesda, Maryland, United States of America
| | - Rong-Fong Shen
- Proteomics Core Facility, National Heart, Lung and Blood Institute, Bethesda, Maryland, United States of America
| | - Guanghui Wang
- Proteomics Core Facility, National Heart, Lung and Blood Institute, Bethesda, Maryland, United States of America
| | - Maurice B. Burg
- Laboratory of Kidney and Electrolyte Metabolism, National Heart, Lung and Blood Institute, Bethesda, Maryland, United States of America
- * E-mail:
| | - Joan D. Ferraris
- Laboratory of Kidney and Electrolyte Metabolism, National Heart, Lung and Blood Institute, Bethesda, Maryland, United States of America
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40
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Eyster CA, Higginson JD, Huebner R, Porat-Shliom N, Weigert R, Wu WW, Shen RF, Donaldson JG. Discovery of new cargo proteins that enter cells through clathrin-independent endocytosis. Traffic 2010; 10:590-9. [PMID: 19302270 DOI: 10.1111/j.1600-0854.2009.00894.x] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Clathrin-independent endocytosis (CIE) allows internalization of plasma membrane proteins lacking clathrin-targeting sequences, such as the major histocompatibility complex class I protein (MHCI), into cells. After internalization, vesicles containing MHCI fuse with transferrin-containing endosomes generated from clathrin-dependent endocytosis. In HeLa cells, MHCI is subsequently routed to late endosomes or recycled back out to the plasma membrane (PM) in distinctive tubular carriers. Arf6 is associated with endosomal membranes carrying CIE cargo and expression of an active form of Arf6 leads to the generation of vacuolar structures that trap CIE cargo immediately after endocytosis, blocking the convergence with transferrin-containing endosomes. We isolated these trapped vacuolar structures and analyzed their protein composition by mass spectrometry. Here we identify and validate six new endogenous cargo proteins (CD44, CD55, CD98, CD147, Glut1, and ICAM1) that use CIE to enter cells. CD55 and Glut1 appear to closely parallel the trafficking of MHCI, merging with transferrin endosomes before entering the recycling tubules. In contrast, CD44, CD98, and CD147 appear to directly enter the recycling tubules and by-pass the merge with EEA1-positive, transferrin-containing endosomes. This divergent itinerary suggests that sorting may occur along this CIE pathway. Furthermore, the identification of new cargo proteins will assist others studying CIE in different cell types and tissues.
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Affiliation(s)
- Craig A Eyster
- Laboratory of Cell Biology, NHLBI, National Institutes of Health, Bethesda, Maryland 20892, USA
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Wang G, Wu WW, Zhang Z, Masilamani S, Shen RF. Decoy methods for assessing false positives and false discovery rates in shotgun proteomics. Anal Chem 2009; 81:146-59. [PMID: 19061407 DOI: 10.1021/ac801664q] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The potential of getting a significant number of false positives (FPs) in peptide-spectrum matches (PSMs) obtained by proteomic database search has been well-recognized. Among the attempts to assess FPs, the concomitant use of target and decoy databases is widely practiced. By adjusting filtering criteria, FPs and false discovery rate (FDR) can be controlled at a desired level. Although the target-decoy approach is gaining in popularity, subtle differences in decoy construction (e.g., reversing vs stochastic methods), rate calculation (e.g., total vs unique PSMs), or searching (separate vs composite) do exist among various implementations. In the present study, we evaluated the effects of these differences on FP and FDR estimations using a rat kidney protein sample and the SEQUEST search engine as an example. On the effects of decoy construction, we found that, when a single scoring filter (XCorr) was used, stochastic methods generated a higher estimation of FPs and FDR than sequence reversing methods, likely due to an increase in unique peptides. This higher estimation could largely be attenuated by creating decoy databases similar in effective size but not by a simple normalization with a unique-peptide coefficient. When multiple filters were applied, the differences seen between reversing and stochastic methods significantly diminished, suggesting multiple filterings reduce the dependency on how a decoy is constructed. For a fixed set of filtering criteria, FDR and FPs estimated by using unique PSMs were almost twice those using total PSMs. The higher estimation seemed to be dependent on data acquisition setup. As to the differences between performing separate or composite searches, in general, FDR estimated from the separate search was about three times that from the composite search. The degree of difference gradually decreased as the filtering criteria became more stringent. Paradoxically, the estimated true positives in separate search were higher when multiple filters were used. By analyzing a standard protein mixture, we demonstrated that the higher estimation of FDR and FPs in the separate search likely reflected an overestimation, which could be corrected with a simple merging procedure. Our study illustrates the relative merits of different implementations of the target-decoy strategy, which should be worth contemplating when large-scale proteomic biomarker discovery is to be attempted.
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Affiliation(s)
- Guanghui Wang
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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Looze C, Yui D, Leung L, Ingham M, Kaler M, Yao X, Wu WW, Shen RF, Daniels MP, Levine SJ. Proteomic profiling of human plasma exosomes identifies PPARgamma as an exosome-associated protein. Biochem Biophys Res Commun 2008; 378:433-8. [PMID: 19028452 DOI: 10.1016/j.bbrc.2008.11.050] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Accepted: 11/06/2008] [Indexed: 11/25/2022]
Abstract
Exosomes are nanovesicles that are released from cells as a mechanism of cell-free intercellular communication. Only a limited number of proteins have been identified from the plasma exosome proteome. Here, we developed a multi-step fractionation scheme incorporating gel exclusion chromatography, rate zonal centrifugation through continuous sucrose gradients, and high-speed centrifugation to purify exosomes from human plasma. Exosome-associated proteins were separated by SDS-PAGE and 66 proteins were identified by LC-MS/MS, which included both cellular and extracellular proteins. Furthermore, we identified and characterized peroxisome proliferator-activated receptor-gamma (PPARgamma), a nuclear receptor that regulates adipocyte differentiation and proliferation, as well as immune and inflammatory cell functions, as a novel component of plasma-derived exosomes. Given the important role of exosomes as intercellular messengers, the discovery of PPARgamma as a component of human plasma exosomes identifies a potential new pathway for the paracrine transfer of nuclear receptors.
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Affiliation(s)
- Christopher Looze
- Pulmonary and Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Building, Room 6D03, MSC 1590, Bethesda, MD 20892, USA
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Yu MJ, Pisitkun T, Wang G, Aranda JF, Gonzales PA, Tchapyjnikov D, Shen RF, Alonso MA, Knepper MA. Large-scale quantitative LC-MS/MS analysis of detergent-resistant membrane proteins from rat renal collecting duct. Am J Physiol Cell Physiol 2008; 295:C661-78. [PMID: 18596208 PMCID: PMC2544440 DOI: 10.1152/ajpcell.90650.2007] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2007] [Accepted: 07/02/2008] [Indexed: 11/22/2022]
Abstract
In the renal collecting duct, vasopressin controls transport of water and solutes via regulation of membrane transporters such as aquaporin-2 (AQP2) and the epithelial urea transporter UT-A. To discover proteins potentially involved in vasopressin action in rat kidney collecting ducts, we enriched membrane "raft" proteins by harvesting detergent-resistant membranes (DRMs) of the inner medullary collecting duct (IMCD) cells. Proteins were identified and quantified with LC-MS/MS. A total of 814 proteins were identified in the DRM fractions. Of these, 186, including several characteristic raft proteins, were enriched in the DRMs. Immunoblotting confirmed DRM enrichment of representative proteins. Immunofluorescence confocal microscopy of rat IMCDs with antibodies to DRM proteins demonstrated heterogeneity of raft subdomains: MAL2 (apical region), RalA (predominant basolateral labeling), caveolin-2 (punctate labeling distributed throughout the cells), and flotillin-1 (discrete labeling of large intracellular structures). The DRM proteome included GPI-anchored, doubly acylated, singly acylated, cholesterol-binding, and integral membrane proteins (IMPs). The IMPs were, on average, much smaller and more hydrophobic than IMPs identified in non-DRM-enriched IMCD. The content of serine 256-phosphorylated AQP2 was greater in DRM than in non-DRM fractions. Vasopressin did not change the DRM-to-non-DRM ratio of most proteins, whether quantified by tandem mass spectrometry (LC-MS/MS, n=22) or immunoblotting (n=6). However, Rab7 and annexin-2 showed small increases in the DRM fraction in response to vasopressin. In accord with the long-term goal of creating a systems-level analysis of transport regulation, this study has identified a large number of membrane-associated proteins expressed in the IMCD that have potential roles in vasopressin action.
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Affiliation(s)
- Ming-Jiun Yu
- Laboratory of Kidney and Electrolyte Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892-1603, USA
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Alves G, Ogurtsov AY, Kwok S, Wu WW, Wang G, Shen RF, Yu YK. Detection of co-eluted peptides using database search methods. Biol Direct 2008; 3:27. [PMID: 18597684 PMCID: PMC2483259 DOI: 10.1186/1745-6150-3-27] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Accepted: 07/02/2008] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Current experimental techniques, especially those applying liquid chromatography mass spectrometry, have made high-throughput proteomic studies possible. The increase in throughput however also raises concerns on the accuracy of identification or quantification. Most experimental procedures select in a given MS scan only a few relatively most intense parent ions, each to be fragmented (MS2) separately, and most other minor co-eluted peptides that have similar chromatographic retention times are ignored and their information lost. RESULTS We have computationally investigated the possibility of enhancing the information retrieval during a given LC/MS experiment by selecting the two or three most intense parent ions for simultaneous fragmentation. A set of spectra is created via superimposing a number of MS2 spectra, each can be identified by all search methods tested with high confidence, to mimick the spectra of co-eluted peptides. The generated convoluted spectra were used to evaluate the capability of several database search methods - SEQUEST, Mascot, X!Tandem, OMSSA, and RAId_DbS - in identifying true peptides from superimposed spectra of co-eluted peptides. We show that using these simulated spectra, all the database search methods will gain eventually in the number of true peptides identified by using the compound spectra of co-eluted peptides. OPEN PEER REVIEW Reviewed by Vlad Petyuk (nominated by Arcady Mushegian), King Jordan and Shamil Sunyaev. For the full reviews, please go to the Reviewers' comments section.
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Affiliation(s)
- Gelio Alves
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20894, USA
| | - Aleksey Y Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20894, USA
| | - Siwei Kwok
- Department of Mathematics, University of Maryland, College Park, MD, 20742, USA
| | - Wells W Wu
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, 20892, USA
| | - Guanghui Wang
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, 20892, USA
| | - Rong-Fong Shen
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, 20892, USA
| | - Yi-Kuo Yu
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20894, USA
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Abstract
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Confident peptide identification is one of the most important components in mass-spectrometry-based proteomics. We propose a method to properly combine the results from different database search methods to enhance the accuracy of peptide identifications. The database search methods included in our analysis are SEQUEST (v27 rev12), ProbID (v1.0), InsPecT (v20060505), Mascot (v2.1), X! Tandem (v2007.07.01.2), OMSSA (v2.0) and RAId_DbS. Using two data sets, one collected in profile mode and one collected in centroid mode, we tested the search performance of all 21 combinations of two search methods as well as all 35 possible combinations of three search methods. The results obtained from our study suggest that properly combining search methods does improve retrieval accuracy. In addition to performance results, we also describe the theoretical framework which in principle allows one to combine many independent scoring methods including de novo sequencing and spectral library searches. The correlations among different methods are also investigated in terms of common true positives, common false positives, and a global analysis. We find that the average correlation strength, between any pairwise combination of the seven methods studied, is usually smaller than the associated standard error. This indicates only weak correlation may be present among different methods and validates our approach in combining the search results. The usefulness of our approach is further confirmed by showing that the average cumulative number of false positive peptides agrees reasonably well with the combined E-value. The data related to this study are freely available upon request. Properly combining the results from different database search methods will enhance the accuracy of peptide identifications. This nevertheless requires, among different search methods, a common statistical standard, which can be achieved by statistical calibration of E-values. After transforming E-values into database P-values, we use the well-established Fisher’s formula to combine different P-values. Our protocol provides a statistically sound method for integration of search results.
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Affiliation(s)
- Gelio Alves
- National Center for Biotechnology Information, Library of Medicine, NIH, Bethesda, MD 20894, USA
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Hao JJ, Wang G, Pisitkun T, Patino-Lopez G, Nagashima K, Knepper MA, Shen RF, Shaw S. Enrichment of distinct microfilament-associated and GTP-binding-proteins in membrane/microvilli fractions from lymphoid cells. J Proteome Res 2008; 7:2911-27. [PMID: 18505283 DOI: 10.1021/pr800016a] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Lymphocyte microvilli mediate initial adhesion to endothelium during lymphocyte transition from blood into tissue but their molecular organization is incompletely understood. We modified a shear-based procedure to prepare biochemical fractions enriched for membrane/microvilli (MMV) from both human peripheral blood T-lymphocytes (PBT) and a mouse pre-B lymphocyte line (300.19). Enrichment of proteins in MMV relative to post nuclear lysate was determined by LC/MS/MS analysis and label-free quantitation. Subsequent analysis emphasized the 291 proteins shared by PBT and 300.19 and estimated by MS peak area to be highest abundance. Validity of the label-free quantitation was confirmed by many internal consistencies and by comparison with Western blot analyses. The MMV fraction was enriched primarily for subsets of cytoskeletal proteins, transmembrane proteins and G-proteins, with similar patterns in both lymphoid cell types. The most enriched cytoskeletal proteins were microfilament-related proteins NHERF1, Ezrin/Radixin/Moesin (ERMs), ADF/cofilin and Myosin1G. Other microfilament proteins such as talin, gelsolin, myosin II and profilin were markedly reduced in MMV, as were intermediate filament- and microtubule-related proteins. Heterotrimeric G-proteins and some small G-proteins (especially Ras and Rap1) were enriched in the MMV preparation. Two notable general observations also emerged. There was less overlap between the two cells in their transmembrane proteins than in other classes of proteins, consistent with a special role of plasma membrane proteins in differentiation. Second, unstimulated primary T-lymphocytes have an unusually high concentration of actin and other microfilament related proteins, consistent with the singular role of actin-mediated motility in the immunological surveillance performed by these primary cells.
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Affiliation(s)
- Jian-Jiang Hao
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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47
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Wu WW, Wang G, Liang XJ, Park JK, Shen RF. Covalent modification of stathmin by CCNU determined by FTMS analysis of modified proteins and tryptic peptides. Biochem Biophys Res Commun 2008; 367:7-13. [PMID: 18162179 PMCID: PMC2266066 DOI: 10.1016/j.bbrc.2007.12.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Accepted: 12/07/2007] [Indexed: 05/25/2023]
Abstract
Chemical modification of proteins is often carried out to generate protein-small molecule conjugates for various applications. The high resolution and mass accuracy of a Fourier transform mass spectrometer is particularly useful for assessing the extent or sites of covalent modifications. As protein-small molecule reactions often produce products with variable numbers of the compound incorporated at different sites, a direct mass analysis of the reaction products at times yields mass spectra hard to interpret. Chromatographic separation at protein level could reduce the complexity of a sample, thus allowing more accurate mass spectrometric analysis. In this report, we demonstrate the utility of reversed-phase protein chromatography and FT-ICR mass spectrometry in analyzing CCNU (lomustine, 1-(2-chloroethyl)-3-cyclohexyl-1-nitroso-urea, MW: 233.7Da) modification of stathmin. With this combined approach, we determined the stoichiometry as well as sites of CCNU incorporation into the protein, demonstrating differential reactivity of several lysyl residues to CCNU alkylation.
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Affiliation(s)
- Wells W. Wu
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Guanghui Wang
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Xing-Jie Liang
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892
| | - John K. Park
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892
| | - Rong-Fong Shen
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
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Choi SJ, Song IS, Ryu OH, Choi SW, Suzanne Hart P, Wu WW, Shen RF, Hart TC. A 4 bp deletion mutation in DLX3 enhances osteoblastic differentiation and bone formation in vitro. Bone 2008; 42:162-71. [PMID: 17950683 PMCID: PMC2253671 DOI: 10.1016/j.bone.2007.08.047] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2007] [Revised: 08/02/2007] [Accepted: 08/31/2007] [Indexed: 12/29/2022]
Abstract
A 4 base-pair deletion mutation in the Distal-less 3 (DLX3) gene is etiologic for Tricho-Dento-Osseous syndrome (TDO). A cardinal feature of TDO is an increased thickness and density of bone. We tested the effects of the DLX3 gene mutation responsible for TDO on the osteoblastic differentiation of preosteoblastic MC3T3E1 cells and multipontent mesenchymal C2C12 cells. Differential expression analysis of C2C12 cells transfected with wild type DLX3 or mutant DLX3 was performed and desmin gene expression, an early myoblastic differentiation marker in mesenchymal cells, was evaluated by RT-PCR, western blot analysis, and desmin promoter transcriptional activity. Transfection of wild type DLX3 into MC3T3E1 and C2C12 cells increased alkaline phosphatase-2 activity, mineral deposition, and promoter activities of the osteocalcin and type 1 collagen genes compared to empty vector transfected cells. Transfection of mutant DLX3 into these cells further enhanced alkaline phosphatase activity, mineral deposition, and osteocalcin promoter activities, but did not further enhance type 1 collagen promoter activity. Transfection of mutant DLX3 into C2C12 cells markedly down regulated desmin gene expression, and protein expression of desmin and MyoD, while increasing protein expression of osterix and Runx2. These results demonstrate that the DLX3 deletion mutation associated with TDO enhances mesenchymal cell differentiation to an osteoblastic lineage rather than a myoblastic lineage by changing the fate of mesenchymal cells. This DLX3 mutation also accelerates the differentiation of osteoprogenitor cells to osteoblasts at later stages of osteogenesis.
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Affiliation(s)
- Sun Jin Choi
- Human Craniofacial Genetics Section, National Institute of Dental and Craniofacial Research, National Institutes of Health
| | - In Sun Song
- Human Craniofacial Genetics Section, National Institute of Dental and Craniofacial Research, National Institutes of Health
| | - Ok Hee Ryu
- Human Craniofacial Genetics Section, National Institute of Dental and Craniofacial Research, National Institutes of Health
| | - Sung Won Choi
- Human Craniofacial Genetics Section, National Institute of Dental and Craniofacial Research, National Institutes of Health
| | - P. Suzanne Hart
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health
| | - Wells W. Wu
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health
| | - Rong-Fong Shen
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health
| | - Thomas C. Hart
- Human Craniofacial Genetics Section, National Institute of Dental and Craniofacial Research, National Institutes of Health
- *Corresponding author; Thomas C Hart, 10 Center Drive, Building 10, Room 5-2531, Bethesda, MD, 20892. Tel. 301-402-1706, Fax: 1-301-480-4455, E-mail address:
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Alves G, Ogurtsov AY, Wu WW, Wang G, Shen RF, Yu YK. Calibrating E-values for MS2 database search methods. Biol Direct 2007; 2:26. [PMID: 17983478 PMCID: PMC2206012 DOI: 10.1186/1745-6150-2-26] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Accepted: 11/05/2007] [Indexed: 11/25/2022] Open
Abstract
Background The key to mass-spectrometry-based proteomics is peptide identification, which relies on software analysis of tandem mass spectra. Although each search engine has its strength, combining the strengths of various search engines is not yet realizable largely due to the lack of a unified statistical framework that is applicable to any method. Results We have developed a universal scheme for statistical calibration of peptide identifications. The protocol can be used for both de novo approaches as well as database search methods. We demonstrate the protocol using only the database search methods. Among seven methods -SEQUEST (v27 rev12), ProbID (v1.0), InsPecT (v20060505), Mascot (v2.1), X!Tandem (v1.0), OMSSA (v2.0) and RAId_DbS – calibrated, except for X!Tandem and RAId_DbS most methods require a rescaling according to the database size searched. We demonstrate that our calibration protocol indeed produces unified statistics both in terms of average number of false positives and in terms of the probability for a peptide hit to be a true positive. Although both the protocols for calibration and the statistics thus calibrated are universal, the calibration formulas obtained from one laboratory with data collected using either centroid or profile format may not be directly usable by the other laboratories. Thus each laboratory is encouraged to calibrate the search methods it intends to use. We also address the importance of using spectrum-specific statistics and possible improvement on the current calibration protocol. The spectra used for statistical (E-value) calibration are freely available upon request. Open peer review Reviewed by Dongxiao Zhu (nominated by Arcady Mushegian), Alexey Nesvizhskii (nominated by King Jordan) and Vineet Bafna. For the full reviews, please go to the Reviewers' comments section.
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Affiliation(s)
- Gelio Alves
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA.
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Sun J, Morgan M, Shen RF, Steenbergen C, Murphy E. Preconditioning results in S-nitrosylation of proteins involved in regulation of mitochondrial energetics and calcium transport. Circ Res 2007; 101:1155-63. [PMID: 17916778 DOI: 10.1161/circresaha.107.155879] [Citation(s) in RCA: 303] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Nitric oxide has been shown to be an important signaling messenger in ischemic preconditioning (IPC). Accordingly, we investigated whether protein S-nitrosylation occurs in IPC hearts and whether S-nitrosoglutathione (GSNO) elicits similar effects on S-nitrosylation and cardioprotection. Preceding 20 minutes of no-flow ischemia and reperfusion, hearts from C57BL/6J mice were perfused in the Langendorff mode and subjected to the following conditions: (1) control perfusion; (2) IPC; or (3) 0.1 mmol/L GSNO treatment. Compared with control, IPC and GSNO significantly improved postischemic recovery of left ventricular developed pressure and reduced infarct size. IPC and GSNO both significantly increased S-nitrosothiol contents and S-nitrosylation levels of the L-type Ca2+ channel alpha1 subunit in heart membrane fractions. We identified several candidate S-nitrosylated proteins by proteomic analysis following the biotin switch method, including the cardiac sarcoplasmic reticulum Ca2+-ATPase, alpha-ketoglutarate dehydrogenase, and the mitochondrial F1-ATPase alpha1 subunit. The activities of these enzymes were altered in a concentration-dependent manner by GSNO treatment. We further developed a 2D DyLight fluorescence difference gel electrophoresis proteomic method that used DyLight fluors and a modified biotin switch method to identify S-nitrosylated proteins. IPC and GSNO produced a similar pattern of S-nitrosylation modification and cardiac protection against ischemia/reperfusion injury, suggesting that protein S-nitrosylation may play an important cardioprotective role in heart.
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Affiliation(s)
- Junhui Sun
- NHLBI, NIH, Vascular Medicine Branch, Bethesda, MD 20892, USA
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