1
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Maurer J, Grouzmann E, Eugster PJ. Tutorial review for peptide assays: An ounce of pre-analytics is worth a pound of cure. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1229:123904. [PMID: 37832388 DOI: 10.1016/j.jchromb.2023.123904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Abstract
The recent increase in peptidomimetic-based medications and the growing interest in peptide hormones has brought new attention to the quantification of peptides for diagnostic purposes. Indeed, the circulating concentrations of peptide hormones in the blood provide a snapshot of the state of the body and could eventually lead to detecting a particular health condition. Although extremely useful, the quantification of such molecules, preferably by liquid chromatography coupled to mass spectrometry, might be quite tricky. First, peptides are subjected to hydrolysis, oxidation, and other post-translational modifications, and, most importantly, they are substrates of specific and nonspecific proteases in biological matrixes. All these events might continue after sampling, changing the peptide hormone concentrations. Second, because they include positively and negatively charged groups and hydrophilic and hydrophobic residues, they interact with their environment; these interactions might lead to a local change in the measured concentrations. A phenomenon such as nonspecific adsorption to lab glassware or materials has often a tremendous effect on the concentration and needs to be controlled with particular care. Finally, the circulating levels of peptides might be low (pico- or femtomolar range), increasing the impact of the aforementioned effects and inducing the need for highly sensitive instruments and well-optimized methods. Thus, despite the extreme diversity of these peptides and their matrixes, there is a common challenge for all the assays: the need to keep concentrations unchanged from sampling to analysis. While significant efforts are often placed on optimizing the analysis, few studies consider in depth the impact of pre-analytical steps on the results. By working through practical examples, this solution-oriented tutorial review addresses typical pre-analytical challenges encountered during the development of a peptide assay from the standpoint of a clinical laboratory. We provide tips and tricks to avoid pitfalls as well as strategies to guide all new developments. Our ultimate goal is to increase pre-analytical awareness to ensure that newly developed peptide assays produce robust and accurate results.
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Affiliation(s)
- Jonathan Maurer
- Service of Clinical Pharmacology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Eric Grouzmann
- Service of Clinical Pharmacology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Philippe J Eugster
- Service of Clinical Pharmacology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
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2
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Patterson KL, Arul AB, Choi MJ, Oliver NC, Whitaker MD, Bodrick AC, Libby JB, Hansen S, Dumitrescu L, Gifford KA, Jefferson AL, Hohman TJ, Robinson RAS. Establishing Quality Control Procedures for Large-Scale Plasma Proteomics Analyses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37163770 DOI: 10.1021/jasms.3c00050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Proteomics research has been transformed due to high-throughput liquid chromatography (LC-MS/MS) tandem mass spectrometry instruments combined with highly sophisticated automated sample preparation and multiplexing workflows. However, scaling proteomics experiments to large sample cohorts (hundreds to thousands) requires thoughtful quality control (QC) protocols. Robust QC protocols can help with reproducibility, quantitative accuracy, and provide opportunities for more decisive troubleshooting. Our laboratory conducted a plasma proteomics study of a cohort of N = 335 patient samples using tandem mass tag (TMTpro) 16-plex batches. Over the course of a 10-month data acquisition period for this cohort we collected 271 pooled QC LC-MS/MS result files obtained from MS/MS analysis of a patient-derived pooled plasma sample, representative of the entire cohort population. This sample was tagged with TMTzero or TMTpro reagents and used to inform the daily performance of the LC-MS/MS instruments and to allow within and across sample batch normalization. Analytical variability of a number of instrumental and data analysis metrics including protein and peptide identifications, peptide spectral matches (PSMs), number of obtained MS/MS spectra, average peptide abundance, percent of peptides with a Δ m/z between ±0.003 Da, percent of MS/MS spectra obtained at the maximum injection time, and the retention time of selected tracking peptides were evaluated to help inform the design of a robust LC-MS/MS QC workflow for use in future cohort studies. This study also led to general tips for using selected metrics to inform real-time troubleshooting of LC-MS/MS performance issues with daily QC checks.
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Affiliation(s)
- Khiry L Patterson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Albert B Arul
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Min Ji Choi
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Nekesa C Oliver
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Marsalas D Whitaker
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Angel C Bodrick
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Cancer Biology, Neuroscience, and Pharmacology, Meharry Medical College, Nashville, Tennessee 37208, United States
| | - Julia B Libby
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Shania Hansen
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
| | - Logan Dumitrescu
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Katherine A Gifford
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
| | - Angela L Jefferson
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Timothy J Hohman
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
- Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
- Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
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3
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Kobayashi Y, Yokoi A, Hashimura M, Oguri Y, Konno R, Matsumoto T, Tochimoto M, Nakagawa M, Ishibashi Y, Ito T, Ohhigata K, Harada Y, Fukagawa N, Kodera Y, Saegusa M. Nucleobindin-2 mediates TGF-β1-driven phenotypes in ZEB1-high uterine carcinosarcoma. THE AMERICAN JOURNAL OF PATHOLOGY 2023:S0002-9440(23)00168-2. [PMID: 37169340 DOI: 10.1016/j.ajpath.2023.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/31/2023] [Accepted: 04/26/2023] [Indexed: 05/13/2023]
Abstract
Epithelial-mesenchymal transition (EMT) is a hallmark of uterine carcinosarcoma (UCS). Here, we used shotgun proteomics analysis to identify biomarkers associated with blebbistatin-mediated EMT in UCS, and found upregulation of nucleobindin-2 (NUCB2) in endometrial carcinoma (Em Ca) cells. Expression of N-cadherin, Snail, Slug, and ZEB1, was reduced in NUCB2 knockout Em Ca cells, whereas ZEB1, Twist1, and vimentin were upregulated in NUCB2-overexpressing Em Ca cells. NUCB2 knockout reduced cell proliferation and migration, whereas NUCB2 overexpression had the opposite effect. Treatment of Em Ca cells with TGF-β1 dramatically altered morphology toward a fibroblastic appearance; concomitantly, expression of NUCB2 and ZEB1 increased. The NUCB2 promoter was also activated by transfection of Smad2. In UCS tissues, NUCB2 expression was significantly higher in sarcomatous as compared to carcinomatous components; this was consistent with increased TGF-β1 mRNA expression in stromal and sarcomatous components as compared to carcinomatous components. In addition, NUCB2 score correlated positively with ZEB1 and vimentin scores, whereas ZEB1 score correlated positively with Slug and vimentin scores and inversely with the E-cadherin score. We therefore suggest that TGF-β-dependent upregulation of NUCB2 and ZEB1 contributes to the phenotypic characteristics of sarcomatous components in UCS.
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Affiliation(s)
- Yui Kobayashi
- Department of Pathology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan
| | - Ako Yokoi
- Department of Pathology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan
| | - Miki Hashimura
- Department of Pathology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan
| | - Yasuko Oguri
- Department of Pathology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan
| | - Ryo Konno
- Center for Disease Proteomics, School of Science, Kitasato University, Sagamihara, Kanagawa 252-0374, Japan
| | - Toshihide Matsumoto
- Department of Pathology, Kitasato University School of Allied Health Science,1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan
| | - Masataka Tochimoto
- Department of Pathology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan
| | - Mayu Nakagawa
- Department of Pathology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan
| | - Yu Ishibashi
- Department of Pathology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan
| | - Takashi Ito
- Department of Pathology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan
| | - Kensuke Ohhigata
- Department of Pathology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan
| | - Yohei Harada
- Department of Pathology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan
| | - Naomi Fukagawa
- Department of Pathology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan
| | - Yoshio Kodera
- Center for Disease Proteomics, School of Science, Kitasato University, Sagamihara, Kanagawa 252-0374, Japan
| | - Makoto Saegusa
- Department of Pathology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan.
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4
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Nie S, O'Brien Johnson R, Livson Y, Greer T, Zheng X, Li N. Maximizing hydrophobic peptide recovery in proteomics and antibody development using a mass spectrometry compatible surfactant. Anal Biochem 2022; 658:114924. [PMID: 36162445 DOI: 10.1016/j.ab.2022.114924] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/18/2022] [Indexed: 11/01/2022]
Abstract
Peptide loss due to surface absorption can happen at any step in a protein analysis workflow and is sometimes especially deleterious for hydrophobic peptides. In this study, we found the LC-MS compatible surfactant, n-Dodecyl-β-D-maltoside (DDM), can maximize hydrophobic peptide recovery in various samples including single cell digests, mAb clinical PK samples, and mAb peptide mapping samples. In HeLa single cell proteomics analysis, more than half of all unique peptides identified were found only in DDM prepared samples, most of which had significantly higher hydrophobicities compared to peptides in control samples. In clinical PK studies, DDM enhanced hydrophobic complementarity-determining region (CDR) peptide signals significantly. The fold change of CDR peptides' intensity enhancement in DDM added samples compared to controls correlate with peptide retention time and hydrophobicity, providing guidance for surrogate peptide selection and peptide standard handling in PK studies. For peptide mapping analysis of mAbs, DDM can improve hydrophobic peptide signal and solution stability over 48 h in an autosampler at 4 °C, which can aid method qualification and transfer during drug development. Lastly, maximizing hydrophobic peptide recovery from samples dried in vacuo was achieved by DDM reconstitution, which provided higher signal for later eluting peaks and higher proteome coverage overall.
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Affiliation(s)
- Song Nie
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591-6707, United States.
| | - Reid O'Brien Johnson
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591-6707, United States
| | - Yuliya Livson
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591-6707, United States
| | - Tyler Greer
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591-6707, United States
| | - Xiaojing Zheng
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591-6707, United States.
| | - Ning Li
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591-6707, United States
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5
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Kruszewska J, Zajda J, Matczuk M. How to effectively prepare a sample for bottom-up proteomic analysis of nanoparticle protein corona? A critical review. Talanta 2021; 226:122153. [PMID: 33676702 DOI: 10.1016/j.talanta.2021.122153] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 02/08/2023]
Abstract
Since the interest in the biomedical applications of inorganic nanoparticles (NPs) has rapidly grown over the last decades, there is a need for a thorough characterization of bio-nano interactions. NPs introduced to the body (mostly intravenously) encounter plasma proteins, that instantly create a so-called "protein corona" on the NPs surface, giving the nanomaterial a new biological identity. Type of the proteins that interact with NPs may affect the in vivo fate of NPs. For that reason, it is particularly important to establish analytical methods capable of corona protein identification. Bottom-up proteomics is most often used for that purpose. A crucial part of the experiment is sample preparation, as it is already proven that different protocols may lead to distinct results. This review is aimed at providing a characterization of two main stages of sample preparation: separation of NPs with protein corona from the unbound proteins and the digestion of corona proteins. Separation techniques such as centrifugation, magnetic separation, and chromatography and three digestion methods (in-gel, in-solution, and on-particle) are described with special emphasis paid on their advantages and disadvantages as well as their influence on the result of identification. This paper also indicates the need for standardization of protein corona identification protocols, as some of the proteins may be preferentially detected while applying a particular digestion procedure.
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Affiliation(s)
- Joanna Kruszewska
- Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664, Warsaw, Poland
| | - Joanna Zajda
- Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664, Warsaw, Poland
| | - Magdalena Matczuk
- Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664, Warsaw, Poland.
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6
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Taguchi T, Kodera Y, Oba K, Saito T, Nakagawa Y, Kawashima Y, Shichiri M. Suprabasin-derived bioactive peptides identified by plasma peptidomics. Sci Rep 2021; 11:1047. [PMID: 33441610 PMCID: PMC7806982 DOI: 10.1038/s41598-020-79353-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/08/2020] [Indexed: 01/29/2023] Open
Abstract
Identification of low-abundance, low-molecular-weight native peptides using non-tryptic plasma has long remained an unmet challenge, leaving potential bioactive/biomarker peptides undiscovered. We have succeeded in efficiently removing high-abundance plasma proteins to enrich and comprehensively identify low-molecular-weight native peptides using mass spectrometry. Native peptide sequences were chemically synthesized and subsequent functional analyses resulted in the discovery of three novel bioactive polypeptides derived from an epidermal differentiation marker protein, suprabasin. SBSN_HUMAN[279-295] potently suppressed food/water intake and induced locomotor activity when injected intraperitoneally, while SBSN_HUMAN[225-237] and SBSN_HUMAN[243-259] stimulated the expression of proinflammatory cytokines via activation of NF-κB signaling in vascular cells. SBSN_HUMAN[225-237] and SBSN_HUMAN[279-295] immunoreactivities were present in almost all human organs analyzed, while immunoreactive SBSN_HUMAN[243-259] was abundant in the liver and pancreas. Human macrophages expressed the three suprabasin-derived peptides. This study illustrates a new approach for discovering unknown bioactive peptides in plasma via the generation of peptide libraries using a novel peptidomic strategy.
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Affiliation(s)
- Tomomi Taguchi
- grid.410786.c0000 0000 9206 2938Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374 Japan
| | - Yoshio Kodera
- grid.410786.c0000 0000 9206 2938Department of Physics, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373 Japan ,grid.410786.c0000 0000 9206 2938Center for Disease Proteomics, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373 Japan
| | - Kazuhito Oba
- grid.410786.c0000 0000 9206 2938Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374 Japan
| | - Tatsuya Saito
- grid.410786.c0000 0000 9206 2938Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374 Japan ,grid.410786.c0000 0000 9206 2938Department of Physics, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373 Japan
| | - Yuzuru Nakagawa
- grid.410786.c0000 0000 9206 2938Department of Physics, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373 Japan
| | - Yusuke Kawashima
- grid.410786.c0000 0000 9206 2938Department of Physics, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373 Japan
| | - Masayoshi Shichiri
- grid.410786.c0000 0000 9206 2938Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374 Japan
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7
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Dong Y, Lee Y, Cui K, He M, Wang B, Bhattacharjee S, Zhu B, Yago T, Zhang K, Deng L, Ouyang K, Wen A, Cowan DB, Song K, Yu L, Brophy ML, Liu X, Wylie-Sears J, Wu H, Wong S, Cui G, Kawashima Y, Matsumoto H, Kodera Y, Wojcikiewicz RJH, Srivastava S, Bischoff J, Wang DZ, Ley K, Chen H. Epsin-mediated degradation of IP3R1 fuels atherosclerosis. Nat Commun 2020; 11:3984. [PMID: 32770009 PMCID: PMC7414107 DOI: 10.1038/s41467-020-17848-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 07/15/2020] [Indexed: 12/18/2022] Open
Abstract
The epsin family of endocytic adapter proteins are widely expressed, and interact with both proteins and lipids to regulate a variety of cell functions. However, the role of epsins in atherosclerosis is poorly understood. Here, we show that deletion of endothelial epsin proteins reduces inflammation and attenuates atherosclerosis using both cell culture and mouse models of this disease. In atherogenic cholesterol-treated murine aortic endothelial cells, epsins interact with the ubiquitinated endoplasmic reticulum protein inositol 1,4,5-trisphosphate receptor type 1 (IP3R1), which triggers proteasomal degradation of this calcium release channel. Epsins potentiate its degradation via this interaction. Genetic reduction of endothelial IP3R1 accelerates atherosclerosis, whereas deletion of endothelial epsins stabilizes IP3R1 and mitigates inflammation. Reduction of IP3R1 in epsin-deficient mice restores atherosclerotic progression. Taken together, epsin-mediated degradation of IP3R1 represents a previously undiscovered biological role for epsin proteins and may provide new therapeutic targets for the treatment of atherosclerosis and other diseases. Endothelial cell (EC) dysfunction and inflammation contribute to plaque destabilization in atherosclerosis, increasing the risk of thrombotic events. Here, the authors show that epsin promotes EC inflammation via a mechanism involving IP3R1 degradation, and that deletion of epsin in the endothelium prevents EC dysfunctoin and atherosclerosis in mice.
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Affiliation(s)
- Yunzhou Dong
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Yang Lee
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kui Cui
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Ming He
- Department of Medicine, University of California, San Diego, San Diego, CA, 92093, USA
| | - Beibei Wang
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Sudarshan Bhattacharjee
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Bo Zhu
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Tadayuki Yago
- Cardiovascular Biology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Kun Zhang
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Lin Deng
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Kunfu Ouyang
- Department of Medicine, University of California, San Diego, San Diego, CA, 92093, USA
| | - Aiyun Wen
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Douglas B Cowan
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kai Song
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Lili Yu
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Megan L Brophy
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Xiaolei Liu
- Center for Vascular and Developmental Biology, Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Jill Wylie-Sears
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Hao Wu
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Scott Wong
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Guanglin Cui
- Department of Nutrition and Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Yusuke Kawashima
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.,Center for Disease Proteomics, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Hiroyuki Matsumoto
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Yoshio Kodera
- Center for Disease Proteomics, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | | | - Sanjay Srivastava
- Department of Medicine, Division of Cardiovascular Medicine, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Joyce Bischoff
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Da-Zhi Wang
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Klaus Ley
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - Hong Chen
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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8
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Tochimoto M, Oguri Y, Hashimura M, Konno R, Matsumoto T, Yokoi A, Kodera Y, Saegusa M. S100A4/non-muscle myosin II signaling regulates epithelial-mesenchymal transition and stemness in uterine carcinosarcoma. J Transl Med 2020; 100:682-695. [PMID: 31857700 DOI: 10.1038/s41374-019-0359-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/05/2019] [Accepted: 11/09/2019] [Indexed: 11/09/2022] Open
Abstract
Uterine carcinosarcoma (UCS) represents a true example of cancer associated with epithelial-mesenchymal transition (EMT), which exhibits cancer stem cell (CSC)-like traits. Although S100A4 is an inducer of EMT, little is known about its involvement in UCS tumorigenesis. Herein, we focused on the functional role of S100A4 during development of UCS. Expression of S100A4 and molecules associated with its function were also examined in 35 UCS cases. In endometrial carcinoma cell lines, S100A4 promoter activity and mRNA levels were significantly increased by the transfection of NF-κB/p65, independent of a putative κB-binding site in the promoter. Cells stably overexpressing S100A4 showed enhancement of CSC properties, along with decreased cell proliferation and acceleration of cell migration. These phenotypes were abrogated in S100A4-knockdown cells. A combination of S100A4 antibody-mediated co-immunoprecipitation and shotgun proteomics analysis revealed that S100A4 strongly interacted with non-muscle myosin II (NMII) heavy chains, including myosin 9 and myosin 14. Specific inhibition of NMII by blebbistatin phenocopied S100A4 overexpression and induced a fibroblast-like morphology. In clinical samples, S100A4 score was significantly higher in sarcomatous as compared with carcinomatous components of UCS, and was positively correlated with ALDH1, Slug, and vimentin scores, and inversely with Ki-67 labeling indices. These findings suggest that an S100A4/NMII-related signaling cascade may contribute to the establishment and maintenance of EMT/CSC properties, along with changes in cell proliferation and migration capability. These events may be initiated in carcinomatous components in UCS and lead to divergent sarcomatous differentiation.
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Affiliation(s)
- Masataka Tochimoto
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Kanagawa, 252-0374, Japan
| | - Yasuko Oguri
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Kanagawa, 252-0374, Japan
| | - Miki Hashimura
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Kanagawa, 252-0374, Japan
| | - Ryo Konno
- Center for Disease Proteomics, School of Science, Kitasato University, Sagamihara, Kanagawa, 252-0374, Japan
| | - Toshihide Matsumoto
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Kanagawa, 252-0374, Japan
| | - Ako Yokoi
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Kanagawa, 252-0374, Japan
| | - Yoshio Kodera
- Center for Disease Proteomics, School of Science, Kitasato University, Sagamihara, Kanagawa, 252-0374, Japan
| | - Makoto Saegusa
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Kanagawa, 252-0374, Japan.
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9
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Kong MS, Hashimoto-Tane A, Kawashima Y, Sakuma M, Yokosuka T, Kometani K, Onishi R, Carpino N, Ohara O, Kurosaki T, Phua KK, Saito T. Inhibition of T cell activation and function by the adaptor protein CIN85. Sci Signal 2019; 12:12/567/eaav4373. [PMID: 30723173 DOI: 10.1126/scisignal.aav4373] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
T cell activation is initiated by signaling molecules downstream of the T cell receptor (TCR) that are organized by adaptor proteins. CIN85 (Cbl-interacting protein of 85 kDa) is one such adaptor protein. Here, we showed that CIN85 limited T cell responses to TCR stimulation. Compared to activated wild-type (WT) T cells, those that lacked CIN85 produced more IL-2 and exhibited greater proliferation. After stimulation of WT T cells with their cognate antigen, CIN85 was recruited to the TCR signaling complex. Early TCR signaling events, such as phosphorylation of ζ-chain-associated protein kinase 70 (Zap70), Src homology 2 (SH2) domain-containing leukocyte protein of 76 kDa (SLP76), and extracellular signal-regulated kinase (Erk), were enhanced in CIN85-deficient T cells. The inhibitory function of CIN85 required the SH3 and PR regions of the adaptor, which associated with the phosphatase suppressor of TCR signaling-2 (Sts-2) after TCR stimulation. Together, our data suggest that CIN85 is recruited to the TCR signaling complex and mediates inhibition of T cell activation through its association with Sts-2.
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Affiliation(s)
- Mei Suen Kong
- Laboratory for Cell Signaling, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,Institute for Research in Molecular Medicine, Main Campus, Universiti Sains Malaysia, 11800 Pulau Pinang, Malaysia
| | - Akiko Hashimoto-Tane
- Laboratory for Cell Signaling, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yusuke Kawashima
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Machie Sakuma
- Laboratory for Cell Signaling, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Tadashi Yokosuka
- Laboratory for Cell Signaling, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Kohei Kometani
- Laboratory for Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Reiko Onishi
- Laboratory for Cell Signaling, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Nick Carpino
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794-8434, USA
| | - Osamu Ohara
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Tomohiro Kurosaki
- Laboratory for Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,Lymphocyte Differentiation, Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kia Kien Phua
- Institute for Research in Molecular Medicine, Main Campus, Universiti Sains Malaysia, 11800 Pulau Pinang, Malaysia
| | - Takashi Saito
- Laboratory for Cell Signaling, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan. .,Cell Signaling, Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
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10
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Shichiri M, Nonaka D, Lee LJ, Tanaka K. Identification of the salusin-β receptor using proteoliposomes embedded with endogenous membrane proteins. Sci Rep 2018; 8:17865. [PMID: 30552345 PMCID: PMC6294790 DOI: 10.1038/s41598-018-35740-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 10/31/2018] [Indexed: 01/02/2023] Open
Abstract
Although orphan G protein-coupled receptors (GPCRs) have been used as targets to discover unidentified natural ligands, increasing numbers of non-GPCRs have been found to mediate important biological functions. Bioinformatics of genome and cDNA resources predict putative bioactive peptides, demanding an alternative approach to efficiently unravel cell surface targets. In silico analysis of a full-length cDNA library previously allowed us to identify salusin-β, a parasympathomimetic/pro-atherosclerotic peptide with unique physicochemical properties. Here, we show that the β-chain of ATP synthase is a cell surface receptor for salusin-β by utilizing artificial liposomes embedded with endogenous membrane proteins directly transferred from animal tissues while retaining the ligand-binding capability. Conventional techniques using detergents identified a β-actin-profilin complex as membrane-associated salusin-β-binding proteins, but failed to identify the cell surface receptor. Since the α-chain of ATP synthase is a principal cell surface target for angiostatin, a potent endogenous angiogenesis inhibitor, we investigated whether salusin-β modulates angiogenesis. Salusin-β inhibited cell surface ATP synthase activity and prevented sarcoma cell-induced angiogenesis in an in vivo mouse air sac model. Therefore, salusin-β binds to membrane-bound ATP synthase and acts as an angiogenesis inhibitor. The current methodology allows the identification of novel cell surface targets, irrespective of the receptor structure.
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Affiliation(s)
- Masayoshi Shichiri
- Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0374, Japan.
| | - Daisuke Nonaka
- Protosera Inc., 4-3-22 Nishinakajima, Yodogawa-ku, Osaka, 532-0011, Japan
| | - Lyang-Ja Lee
- Protosera Inc., 4-3-22 Nishinakajima, Yodogawa-ku, Osaka, 532-0011, Japan
| | - Kenji Tanaka
- Protosera Inc., 4-3-22 Nishinakajima, Yodogawa-ku, Osaka, 532-0011, Japan
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11
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Thinon E, Fernandez JP, Molina H, Hang HC. Selective Enrichment and Direct Analysis of Protein S-Palmitoylation Sites. J Proteome Res 2018; 17:1907-1922. [PMID: 29575903 PMCID: PMC6104640 DOI: 10.1021/acs.jproteome.8b00002] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
S-Fatty-acylation is the covalent attachment of long chain fatty acids, predominately palmitate (C16:0, S-palmitoylation), to cysteine (Cys) residues via a thioester linkage on proteins. This post-translational and reversible lipid modification regulates protein function and localization in eukaryotes and is important in mammalian physiology and human diseases. While chemical labeling methods have improved the detection and enrichment of S-fatty-acylated proteins, mapping sites of modification and characterizing the endogenously attached fatty acids are still challenging. Here, we describe the integration and optimization of fatty acid chemical reporter labeling with hydroxylamine-mediated enrichment of S-fatty-acylated proteins and direct tagging of modified Cys residues to selectively map lipid modification sites. This afforded improved enrichment and direct identification of many protein S-fatty-acylation sites compared to previously described methods. Notably, we directly identified the S-fatty-acylation sites of IFITM3, an important interferon-stimulated inhibitor of virus entry, and we further demonstrated that the highly conserved Cys residues are primarily modified by palmitic acid. The methods described here should facilitate the direct analysis of protein S-fatty-acylation sites and their endogenously attached fatty acids in diverse cell types and activation states important for mammalian physiology and diseases.
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Affiliation(s)
- Emmanuelle Thinon
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY 10065, USA
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, UK
| | - Joseph P. Fernandez
- Proteomics Resource Center, The Rockefeller University, New York, New York, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, New York, USA
| | - Howard C. Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY 10065, USA
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12
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Fujimoto K, Hayashi A, Kodera Y, Saito T, Toki T, Ogawa A, Kamata Y, Takano K, Katakami H, Shichiri M. Identification and quantification of plasma free salusin-β, an endogenous parasympathomimetic peptide. Sci Rep 2017; 7:8275. [PMID: 28811505 PMCID: PMC5557946 DOI: 10.1038/s41598-017-08288-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 07/10/2017] [Indexed: 11/10/2022] Open
Abstract
Salusin-β is an endogenous parasympathomimetic proatherosclerotic peptide. Salusin-β was initially predicted from bioinformatic analyses and later immunologically detected in human biofluids. However, elucidation of salusin-β bioactivity has faced enormous challenges because of its unique physicochemical characteristics that cause it to strongly adhere to laboratory apparatus materials. In the strictest sense, the discovery of bioactive peptides is not complete until their exact native sequences have been confirmed in the peripheral circulation. In this study, we determined the plasma molecular form and levels of free salusin-β to determine its pathophysiological significance. Ultra-high-yield enrichment and preseparation of non-tryptic human plasma was followed by LC-MS/MS, and full-length salusin-β and seven different endogenous fragment sequences were identified. We established a new ELISA that specifically detects plasma free salusin-β without cross-reacting with any of its identified endogenous fragments. Free salusin-β levels exhibited a profound early morning nadir and rapidly decreased in response to parasympathetic nervous augmentation. Our technical advance in plasma native peptide analysis successfully identified a hard-to-detect bioactive peptide, salusin-β, together with its formerly unrecognized fragments, and further suggests that conventional immunological measurements of target peptides may not be fully representative.
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Affiliation(s)
- Kazumi Fujimoto
- Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0374, Japan
| | - Akinori Hayashi
- Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0374, Japan
| | - Yoshio Kodera
- Department of Physics, Laboratory of Biophysics, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan.,Center for Disease Proteomics, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Tatsuya Saito
- Department of Physics, Laboratory of Biophysics, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan.,Center for Disease Proteomics, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Takuya Toki
- Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0374, Japan
| | - Akifumi Ogawa
- Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0374, Japan
| | - Yuji Kamata
- Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0374, Japan
| | - Koji Takano
- Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0374, Japan
| | - Hideki Katakami
- Teikyo University Chiba Medical Center, 3426-3 Anesaki, Ichihara, Chiba, 299-0111, Japan
| | - Masayoshi Shichiri
- Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0374, Japan.
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13
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Akiya M, Yamazaki M, Matsumoto T, Kawashima Y, Oguri Y, Kajita S, Kijima D, Chiba R, Yokoi A, Takahashi H, Kodera Y, Saegusa M. Identification of LEFTY as a molecular marker for ovarian clear cell carcinoma. Oncotarget 2017; 8:63646-63664. [PMID: 28969018 PMCID: PMC5609950 DOI: 10.18632/oncotarget.18882] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 06/11/2017] [Indexed: 01/16/2023] Open
Abstract
To identify proteins involved in ovarian clear cell carcinoma (OCCCa), shotgun proteomics analysis was applied using formalin-fixed and paraffin-embedded samples of ovarian carcinoma. Analysis of 1521 proteins revealed that 52 were differentially expressed between four OCCCa and 12 non-OCCCa samples. Of the highly expressed proteins in OCCCa, we focused on left-right determination factor (LEFTY), a novel member of the transforming growth factor-β superfamily. In 143 cases of ovarian epithelial carcinoma including 99 OCCCas and 44 non-OCCCas, LEFTY expression at both mRNA and protein levels was significantly higher in OCCCas compared with non-OCCCas, with the mRNA expression of LEFTY1 being predominant compared to that of LEFTY2. OCCCa cells stably overexpressing LEFTY1 showed reduced cell proliferation, along with decreased pSmad2 expression, and also either displayed an activated p53/p21waf1 pathway or increased p27kip1 expression, directly or indirectly. Moreover, the treatment of stable cell lines with cisplatin led to increased apoptotic cells, together with the inhibition of protein expression of a pSmad2-mediated X-linked inhibitor of apoptosis and a decreased bcl2/bax ratio. Blocking LEFTY1 expression with a specific short hairpin RNA inhibited cisplatin-induced apoptosis, probably through the increased expression of both XIAP and bcl2, but not bax. In clinical samples, a significantly higher number of apoptotic cells and lower Ki-67 labeling indices were observed in OCCCas with a high LEFTY score relative to those with a low score. These findings suggest that LEFTY may be an excellent OCCCa-specific molecular marker, which has anti-tumor effects in altering cell proliferation and cellular susceptibility to apoptosis.
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Affiliation(s)
- Masashi Akiya
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Kanagawa 252-0374, Japan
| | - Masaaki Yamazaki
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Kanagawa 252-0374, Japan
| | - Toshihide Matsumoto
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Kanagawa 252-0374, Japan
| | - Yusuke Kawashima
- Center for Disease Proteomics, School of Science, Kitasato University, Sagamihara, Kanagawa 252-0374, Japan
| | - Yasuko Oguri
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Kanagawa 252-0374, Japan
| | - Sabine Kajita
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Kanagawa 252-0374, Japan
| | - Daiki Kijima
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Kanagawa 252-0374, Japan
| | - Risako Chiba
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Kanagawa 252-0374, Japan
| | - Ako Yokoi
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Kanagawa 252-0374, Japan
| | - Hiroyuki Takahashi
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Kanagawa 252-0374, Japan
| | - Yoshio Kodera
- Center for Disease Proteomics, School of Science, Kitasato University, Sagamihara, Kanagawa 252-0374, Japan
| | - Makoto Saegusa
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Kanagawa 252-0374, Japan
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14
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Xiao M, Yang J, Feng Y, Zhu Y, Chai X, Wang Y. Metaproteomic strategies and applications for gut microbial research. Appl Microbiol Biotechnol 2017; 101:3077-3088. [PMID: 28293710 DOI: 10.1007/s00253-017-8215-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 02/28/2017] [Accepted: 03/04/2017] [Indexed: 01/16/2023]
Abstract
The human intestine hosts various complex microbial communities that are closely associated with multiple health and disease processes. Determining the composition and function of these microbial communities is critical to unveil disease mechanisms and promote human health. Recently, meta-omic strategies have been developed that use high-throughput techniques to provide a wealth of information, thus accelerating the study of gut microbes. Metaproteomics is a newly emerged analytical approach that aims to identify proteins on a large scale in complex environmental microbial communities (e.g., the gut microbiota). This review introduces the recent analytical strategies and applications of metaproteomics, with a focus on advances in gut microbiota research, including a discussion of the limitations and challenges of these approaches.
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Affiliation(s)
- Mingming Xiao
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China
| | - Junjun Yang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China
| | - Yuxin Feng
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China
| | - Yan Zhu
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China
| | - Xin Chai
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China
| | - Yuefei Wang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China. .,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China.
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15
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Methionine sulfoxides in serum proteins as potential clinical biomarkers of oxidative stress. Sci Rep 2016; 6:38299. [PMID: 27929071 PMCID: PMC5144094 DOI: 10.1038/srep38299] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 11/07/2016] [Indexed: 02/02/2023] Open
Abstract
Oxidative stress contributes to the pathophysiology of a variety of diseases, and circulating biomarkers of its severity remains a topic of great interest for researchers. Our peptidomic strategy enables accurate and reproducible analysis of circulating proteins/peptides with or without post-translational modifications. Conventional wisdom holds that hydrophobic methionines exposed to an aqueous environment or experimental handling procedures are vulnerable to oxidation. However, we show that the mass spectra intensity ratio of oxidized to non-oxidized methionine residues in serum tryptic proteins can be accurately quantified using a single drop of human serum and give stable and reproducible results. Our data demonstrate that two methionine residues in serum albumin (Met-111 and Met-147) are highly oxidized to methionine sulfoxide in patients with diabetes and renal failure and in healthy smokers versus non-smoker controls. This label-free mass spectrometry approach to quantify redox changes in methionine residues should facilitate the identification of additional circulating biomarkers suitable for predicting the development or progression of human diseases.
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16
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Holman SW, McLean L, Eyers CE. RePLiCal: A QconCAT Protein for Retention Time Standardization in Proteomics Studies. J Proteome Res 2016; 15:1090-102. [PMID: 26775667 DOI: 10.1021/acs.jproteome.5b00988] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This study introduces a new reversed-phase liquid chromatography retention time (RT) standard, RePLiCal (Reversed-phase liquid chromatography calibrant), produced using QconCAT technology. The synthetic protein contains 27 lysine-terminating calibrant peptides, meaning that the same complement of standards can be generated using either Lys-C or trypsin-based digestion protocols. RePLiCal was designed such that each constituent peptide is unique with respect to all eukaryotic proteomes, thereby enabling integration into a wide range of proteomic analyses. RePLiCal has been benchmarked against three commercially available peptide RT standard kits and outperforms all in terms of LC gradient coverage. RePLiCal also provides a higher number of calibrant points for chromatographic retention time standardization and normalization. The standard provides stable RTs over long analysis times and can be readily transferred between different LC gradients and nUHPLC instruments. Moreover, RePLiCal can be used to predict RTs for other peptides in a timely manner. Furthermore, it is shown that RePLiCal can be used effectively to evaluate trapping column performance for nUHPLC instruments using trap-elute configurations, to optimize gradients to maximize peptide and protein identification rates, and to recalibrate the m/z scale of mass spectrometry data post-acquisition.
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Affiliation(s)
- Stephen W Holman
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Lynn McLean
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Claire E Eyers
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Crown Street, Liverpool L69 7ZB, United Kingdom
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17
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Scheerlinck E, Dhaenens M, Van Soom A, Peelman L, De Sutter P, Van Steendam K, Deforce D. Minimizing technical variation during sample preparation prior to label-free quantitative mass spectrometry. Anal Biochem 2015; 490:14-9. [PMID: 26302362 DOI: 10.1016/j.ab.2015.08.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 07/01/2015] [Accepted: 08/13/2015] [Indexed: 11/18/2022]
Abstract
Sample preparation is the crucial starting point to obtain high-quality mass spectrometry data and can be divided into two main steps in a bottom-up proteomics approach: cell/tissue lysis with or without detergents and a(n) (in-solution) digest comprising denaturation, reduction, alkylation, and digesting of the proteins. Here, some important considerations, among others, are that the reagents used for sample preparation can inhibit the digestion enzyme (e.g., 0.1% sodium dodecyl sulfate [SDS] and 0.5 M guanidine HCl), give rise to ion suppression (e.g., polyethylene glycol [PEG]), be incompatible with liquid chromatography-tandem mass spectrometry (LC-MS/MS) (e.g., SDS), and can induce additional modifications (e.g., urea). Taken together, all of these irreproducible effects are gradually becoming a problem when label-free quantitation of the samples is envisioned such as during the increasingly popular high-definition mass spectrometry (HDMS(E)) and sequential window acquisition of all theoretical fragment ion spectra (SWATH) data-independent acquisition strategies. Here, we describe the detailed validation of a reproducible method with sufficient protein yield for sample preparation without any known LC-MS/MS interfering substances by using 1% sodium deoxycholate (SDC) during both cell lysis and in-solution digest.
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Affiliation(s)
- E Scheerlinck
- Laboratory for Pharmaceutical Biotechnology, Ghent University, B-9000 Ghent, Belgium
| | - M Dhaenens
- Laboratory for Pharmaceutical Biotechnology, Ghent University, B-9000 Ghent, Belgium
| | - A Van Soom
- Department of Reproduction, Obstetrics, and Herd Health, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - L Peelman
- Department of Nutrition, Genetics, and Ethology, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - P De Sutter
- Department of Reproductive Medicine, Ghent University Hospital, B-9000 Ghent, Belgium
| | - K Van Steendam
- Laboratory for Pharmaceutical Biotechnology, Ghent University, B-9000 Ghent, Belgium
| | - D Deforce
- Laboratory for Pharmaceutical Biotechnology, Ghent University, B-9000 Ghent, Belgium.
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