Total cellular glycomics allows characterizing cells and streamlining the discovery process for cellular biomarkers
Although many of the frequently used pluripotency biomarkers are glycoconjugates, a glycoconjugate-based exploration of novel cellular biomarkers has proven difficult due to technical difficulties. This study reports a unique approach for the systematic overview of all major classes of oligosacchari...
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Veröffentlicht in: | Proceedings of the National Academy of Sciences - PNAS 2013-02, Vol.110 (6), p.2105-2110 |
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creator | Fujitani, Naoki Furukawa, Jun-ichi Araki, Kayo Fujioka, Tsuyoshi Takegawa, Yasuhiro Piao, Jinhua Nishioka, Taiki Tamura, Tomohiro Nikaido, Toshio Ito, Makoto Nakamura, Yukio Shinohara, Yasuro |
description | Although many of the frequently used pluripotency biomarkers are glycoconjugates, a glycoconjugate-based exploration of novel cellular biomarkers has proven difficult due to technical difficulties. This study reports a unique approach for the systematic overview of all major classes of oligosaccharides in the cellular glycome. The proposed method enabled mass spectrometry–based structurally intensive analyses, both qualitatively and quantitatively, of cellular N - and O -linked glycans derived from glycoproteins, glycosaminoglycans, and glycosphingolipids, as well as free oligosaccharides of human embryonic stem cells (hESCs), induced pluripotent stem cells (hiPSCs), and various human cells derived from normal and carcinoma cells. Cellular total glycomes were found to be highly cell specific, demonstrating their utility as unique cellular descriptors. Structures of glycans of all classes specifically observed in hESCs and hiPSCs tended to be immature in general, suggesting the presence of stem cell–specific glycosylation spectra. The current analysis revealed the high similarity of the total cellular glycome between hESCs and hiPSCs, although it was suggested that hESCs are more homogeneous than hiPSCs from a glycomic standpoint. Notably, this study enabled a priori identification of known pluripotency biomarkers such as SSEA-3, -4, and -5 and Tra-1–60/81, as well as a panel of glycans specifically expressed by hESCs and hiPSCs. |
doi_str_mv | 10.1073/pnas.1214233110 |
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This study reports a unique approach for the systematic overview of all major classes of oligosaccharides in the cellular glycome. The proposed method enabled mass spectrometry–based structurally intensive analyses, both qualitatively and quantitatively, of cellular N - and O -linked glycans derived from glycoproteins, glycosaminoglycans, and glycosphingolipids, as well as free oligosaccharides of human embryonic stem cells (hESCs), induced pluripotent stem cells (hiPSCs), and various human cells derived from normal and carcinoma cells. Cellular total glycomes were found to be highly cell specific, demonstrating their utility as unique cellular descriptors. Structures of glycans of all classes specifically observed in hESCs and hiPSCs tended to be immature in general, suggesting the presence of stem cell–specific glycosylation spectra. The current analysis revealed the high similarity of the total cellular glycome between hESCs and hiPSCs, although it was suggested that hESCs are more homogeneous than hiPSCs from a glycomic standpoint. Notably, this study enabled a priori identification of known pluripotency biomarkers such as SSEA-3, -4, and -5 and Tra-1–60/81, as well as a panel of glycans specifically expressed by hESCs and hiPSCs.</description><identifier>ISSN: 0027-8424</identifier><identifier>EISSN: 1091-6490</identifier><identifier>DOI: 10.1073/pnas.1214233110</identifier><identifier>PMID: 23345451</identifier><language>eng</language><publisher>United States: National Academy of Sciences</publisher><subject>Animals ; Biological markers ; Biological Sciences ; Biomarkers ; Biomarkers - chemistry ; Biomarkers - metabolism ; Caco 2 cells ; Carbohydrate Metabolism ; Cell Line ; Cell Line, Tumor ; Cell lines ; Chromatography, High Pressure Liquid ; Cricetinae ; Embryonic stem cells ; Embryonic Stem Cells - metabolism ; Glycomics - methods ; glycoproteins ; glycosaminoglycans ; glycosphingolipids ; Glycosylation ; HEK293 cells ; Hepatocytes ; Humans ; induced pluripotent stem cells ; Induced Pluripotent Stem Cells - metabolism ; Kidney cells ; Lipids ; Mass spectrometry ; Metabolome ; Molecular Structure ; neoplasm cells ; oligosaccharides ; Oligosaccharides - chemistry ; Oligosaccharides - metabolism ; Pluripotent stem cells ; Polysaccharides ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Stem cells</subject><ispartof>Proceedings of the National Academy of Sciences - PNAS, 2013-02, Vol.110 (6), p.2105-2110</ispartof><rights>copyright © 1993-2008 National Academy of Sciences of the United States of America</rights><rights>Copyright National Academy of Sciences Feb 5, 2013</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c633t-82f9e1bf5eef2e5568997b668e721e9f52e7dcb01e9deed01ebf0fc329d135bc3</citedby><cites>FETCH-LOGICAL-c633t-82f9e1bf5eef2e5568997b668e721e9f52e7dcb01e9deed01ebf0fc329d135bc3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Uhttp://www.pnas.org/content/110/6.cover.gif</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/41992187$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/41992187$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>230,314,723,776,780,799,881,27901,27902,53766,53768,57992,58225</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23345451$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Fujitani, Naoki</creatorcontrib><creatorcontrib>Furukawa, Jun-ichi</creatorcontrib><creatorcontrib>Araki, Kayo</creatorcontrib><creatorcontrib>Fujioka, Tsuyoshi</creatorcontrib><creatorcontrib>Takegawa, Yasuhiro</creatorcontrib><creatorcontrib>Piao, Jinhua</creatorcontrib><creatorcontrib>Nishioka, Taiki</creatorcontrib><creatorcontrib>Tamura, Tomohiro</creatorcontrib><creatorcontrib>Nikaido, Toshio</creatorcontrib><creatorcontrib>Ito, Makoto</creatorcontrib><creatorcontrib>Nakamura, Yukio</creatorcontrib><creatorcontrib>Shinohara, Yasuro</creatorcontrib><title>Total cellular glycomics allows characterizing cells and streamlining the discovery process for cellular biomarkers</title><title>Proceedings of the National Academy of Sciences - PNAS</title><addtitle>Proc Natl Acad Sci U S A</addtitle><description>Although many of the frequently used pluripotency biomarkers are glycoconjugates, a glycoconjugate-based exploration of novel cellular biomarkers has proven difficult due to technical difficulties. This study reports a unique approach for the systematic overview of all major classes of oligosaccharides in the cellular glycome. The proposed method enabled mass spectrometry–based structurally intensive analyses, both qualitatively and quantitatively, of cellular N - and O -linked glycans derived from glycoproteins, glycosaminoglycans, and glycosphingolipids, as well as free oligosaccharides of human embryonic stem cells (hESCs), induced pluripotent stem cells (hiPSCs), and various human cells derived from normal and carcinoma cells. Cellular total glycomes were found to be highly cell specific, demonstrating their utility as unique cellular descriptors. Structures of glycans of all classes specifically observed in hESCs and hiPSCs tended to be immature in general, suggesting the presence of stem cell–specific glycosylation spectra. The current analysis revealed the high similarity of the total cellular glycome between hESCs and hiPSCs, although it was suggested that hESCs are more homogeneous than hiPSCs from a glycomic standpoint. Notably, this study enabled a priori identification of known pluripotency biomarkers such as SSEA-3, -4, and -5 and Tra-1–60/81, as well as a panel of glycans specifically expressed by hESCs and hiPSCs.</description><subject>Animals</subject><subject>Biological markers</subject><subject>Biological Sciences</subject><subject>Biomarkers</subject><subject>Biomarkers - chemistry</subject><subject>Biomarkers - metabolism</subject><subject>Caco 2 cells</subject><subject>Carbohydrate Metabolism</subject><subject>Cell Line</subject><subject>Cell Line, Tumor</subject><subject>Cell lines</subject><subject>Chromatography, High Pressure Liquid</subject><subject>Cricetinae</subject><subject>Embryonic stem cells</subject><subject>Embryonic Stem Cells - metabolism</subject><subject>Glycomics - methods</subject><subject>glycoproteins</subject><subject>glycosaminoglycans</subject><subject>glycosphingolipids</subject><subject>Glycosylation</subject><subject>HEK293 cells</subject><subject>Hepatocytes</subject><subject>Humans</subject><subject>induced pluripotent stem cells</subject><subject>Induced Pluripotent Stem Cells - metabolism</subject><subject>Kidney cells</subject><subject>Lipids</subject><subject>Mass spectrometry</subject><subject>Metabolome</subject><subject>Molecular Structure</subject><subject>neoplasm cells</subject><subject>oligosaccharides</subject><subject>Oligosaccharides - chemistry</subject><subject>Oligosaccharides - metabolism</subject><subject>Pluripotent stem cells</subject><subject>Polysaccharides</subject><subject>Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization</subject><subject>Stem cells</subject><issn>0027-8424</issn><issn>1091-6490</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkU1v1DAQhiMEokvhzAmIxIVL2hk7TuwLEqr4kipxoD1bjjPezZLEi50ULb8ehy3bwoXTWJ5n3vl4s-w5whlCzc93o4lnyLBknCPCg2yFoLCoSgUPsxUAqwtZsvIkexLjFgCUkPA4O0l0KUqBqyxe-cn0uaW-n3sT8nW_t37obMxN3_sfMbcbE4ydKHQ_u3H9G0y5sc3jFMgMfTcu39OG8raL1t9Q2Oe74C3FmDsf7pSbzg8mfKMQn2aPnOkjPbuNp9n1h_dXF5-Kyy8fP1-8uyxsxflUSOYUYeMEkWMkRCWVqpuqklQzJOUEo7q1DaR3S9Sm2DhwljPVIheN5afZ24Pubm4Gai2NUzC93oUuDbLX3nT678zYbfTa32ieevG6TgJvbgWC_z5TnPSQdkwLmZH8HDVKSFevpcL_o0wKkKXEKqGv_0G3fg5jusRClVJWNSyC5wfKBh9jIHecG0Ev3uvFe33nfap4eX_dI__H7HvAUnmUS3qVZggiAS8OwDZOPhyJEpViKJd7vDrknfHarEMX9fVXBlgBYAlKcf4LCnnK1Q</recordid><startdate>20130205</startdate><enddate>20130205</enddate><creator>Fujitani, Naoki</creator><creator>Furukawa, Jun-ichi</creator><creator>Araki, Kayo</creator><creator>Fujioka, Tsuyoshi</creator><creator>Takegawa, Yasuhiro</creator><creator>Piao, Jinhua</creator><creator>Nishioka, Taiki</creator><creator>Tamura, Tomohiro</creator><creator>Nikaido, Toshio</creator><creator>Ito, Makoto</creator><creator>Nakamura, Yukio</creator><creator>Shinohara, Yasuro</creator><general>National Academy of Sciences</general><general>National Acad Sciences</general><scope>FBQ</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QG</scope><scope>7QL</scope><scope>7QP</scope><scope>7QR</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TK</scope><scope>7TM</scope><scope>7TO</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>7S9</scope><scope>L.6</scope><scope>5PM</scope></search><sort><creationdate>20130205</creationdate><title>Total cellular glycomics allows characterizing cells and streamlining the discovery process for cellular biomarkers</title><author>Fujitani, Naoki ; Furukawa, Jun-ichi ; Araki, Kayo ; Fujioka, Tsuyoshi ; Takegawa, Yasuhiro ; Piao, Jinhua ; Nishioka, Taiki ; Tamura, Tomohiro ; Nikaido, Toshio ; Ito, Makoto ; Nakamura, Yukio ; Shinohara, Yasuro</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c633t-82f9e1bf5eef2e5568997b668e721e9f52e7dcb01e9deed01ebf0fc329d135bc3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Animals</topic><topic>Biological markers</topic><topic>Biological Sciences</topic><topic>Biomarkers</topic><topic>Biomarkers - 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This study reports a unique approach for the systematic overview of all major classes of oligosaccharides in the cellular glycome. The proposed method enabled mass spectrometry–based structurally intensive analyses, both qualitatively and quantitatively, of cellular N - and O -linked glycans derived from glycoproteins, glycosaminoglycans, and glycosphingolipids, as well as free oligosaccharides of human embryonic stem cells (hESCs), induced pluripotent stem cells (hiPSCs), and various human cells derived from normal and carcinoma cells. Cellular total glycomes were found to be highly cell specific, demonstrating their utility as unique cellular descriptors. Structures of glycans of all classes specifically observed in hESCs and hiPSCs tended to be immature in general, suggesting the presence of stem cell–specific glycosylation spectra. The current analysis revealed the high similarity of the total cellular glycome between hESCs and hiPSCs, although it was suggested that hESCs are more homogeneous than hiPSCs from a glycomic standpoint. Notably, this study enabled a priori identification of known pluripotency biomarkers such as SSEA-3, -4, and -5 and Tra-1–60/81, as well as a panel of glycans specifically expressed by hESCs and hiPSCs.</abstract><cop>United States</cop><pub>National Academy of Sciences</pub><pmid>23345451</pmid><doi>10.1073/pnas.1214233110</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Animals Biological markers Biological Sciences Biomarkers Biomarkers - chemistry Biomarkers - metabolism Caco 2 cells Carbohydrate Metabolism Cell Line Cell Line, Tumor Cell lines Chromatography, High Pressure Liquid Cricetinae Embryonic stem cells Embryonic Stem Cells - metabolism Glycomics - methods glycoproteins glycosaminoglycans glycosphingolipids Glycosylation HEK293 cells Hepatocytes Humans induced pluripotent stem cells Induced Pluripotent Stem Cells - metabolism Kidney cells Lipids Mass spectrometry Metabolome Molecular Structure neoplasm cells oligosaccharides Oligosaccharides - chemistry Oligosaccharides - metabolism Pluripotent stem cells Polysaccharides Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization Stem cells |
title | Total cellular glycomics allows characterizing cells and streamlining the discovery process for cellular biomarkers |
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