Sensitive profiling of cell surface proteome by using an optimized biotinylation method

2019 ◽  
Vol 196 ◽  
pp. 33-41 ◽  
Author(s):  
Yanan Li ◽  
Yan Wang ◽  
Jiawei Mao ◽  
Yating Yao ◽  
Keyun Wang ◽  
...  
Keyword(s):  
Cell Surface ◽  
Surface Proteome ◽  
Cell Surface Proteome

scholarly journals CIRFESS: An interactive resource for querying the set of theoretically detectable peptides for cell surface and extracellular enrichment proteomic studies

2020 ◽  
Author(s):  
Matthew Waas ◽  
Jack Littrell ◽  
Rebekah L. Gundry
Keyword(s):  
Cell Surface ◽  
Critical Role ◽  
Affinity Reagents ◽  
Extracellular Proteome ◽  
Online Resource ◽  
Health And Disease ◽  
Limited Mass ◽  
Multiple Prediction ◽  
Surface Proteome ◽  
Cell Surface Proteome

AbstractCell surface transmembrane, extracellular, and secreted proteins are high value targets for immunophenotyping, drug development, and studies related to intercellular communication in health and disease. As the number of specific and validated affinity reagents that target this subproteome are limited, mass spectrometry (MS)-based approaches will continue to play a critical role in enabling discovery and quantitation of these molecules. Given the technical considerations that make MS-based cell surface proteome studies uniquely challenging, it can be difficult to select an appropriate experimental approach. To this end, we have integrated multiple prediction strategies and annotations into a single online resource, Compiled Interactive Resource for Extracellular and Surface Studies (CIRFESS). CIRFESS enables rapid interrogation of the human proteome to reveal the cell surface proteome theoretically detectable by current approaches and highlights where current prediction strategies provide concordant and discordant information. We applied CIRFESS to identify the percentage of various subsets of the proteome which are expected to be captured by targeted enrichment strategies, including two established methods and one that is possible but not yet demonstrated. These results will inform the selection of available proteomic strategies and development of new strategies to enhance coverage of the cell surface and extracellular proteome. CIRFESS is available at www.cellsurfer.net/cirfess.

scholarly journals Cell Surface Proteome of Dental Pulp Stem Cells Identified by Label-Free Mass Spectrometry

PLoS ONE ◽  
2016 ◽  
Vol 11 (8) ◽  
pp. e0159824 ◽  
Author(s):  
Christian Niehage ◽  
Jana Karbanová ◽  
Charlotte Steenblock ◽  
Denis Corbeil ◽  
Bernard Hoflack
Keyword(s):  
Mass Spectrometry ◽  
Stem Cells ◽  
Cell Surface ◽  
Dental Pulp ◽  
Dental Pulp Stem Cells ◽  
Label Free ◽  
Surface Proteome ◽  
Cell Surface Proteome

Distinct cell surface proteome profiling by biotin labeling and glycoprotein capturing

2011 ◽  
Vol 74 (10) ◽  
pp. 1985-1993 ◽  
Author(s):  
Kohji Nagano ◽  
Takashi Shinkawa ◽  
Kuniyasu Kato ◽  
Noriyuki Inomata ◽  
Nami Yabuki ◽  
...  
Keyword(s):  
Cell Surface ◽  
Proteome Profiling ◽  
Distinct Cell ◽  
Biotin Labeling ◽  
Surface Proteome ◽  
Cell Surface Proteome

Mapping and comprehensive analysis of the extracellular and cell surface proteome of the human pathogenCorynebacterium diphtheriae

PROTEOMICS ◽  
2006 ◽  
Vol 6 (8) ◽  
pp. 2465-2476 ◽  
Author(s):  
Nicole Hansmeier ◽  
Tzu-Chiao Chao ◽  
Jörn Kalinowski ◽  
Alfred Pühler ◽  
Andreas Tauch
Keyword(s):  
Cell Surface ◽  
Comprehensive Analysis ◽  
Surface Proteome ◽  
Cell Surface Proteome

scholarly journals Global Profiling of the Cell Surface Proteome of Cancer Cells Uncovers an Abundance of Proteins with Chaperone Function

2002 ◽  
Vol 278 (9) ◽  
pp. 7607-7616 ◽  
Author(s):  
Bong Kyung Shin ◽  
Hong Wang ◽  
Anne Marie Yim ◽  
Francois Le Naour ◽  
Franck Brichory ◽  
...  
Keyword(s):  
Cell Surface ◽  
Cancer Cells ◽  
Chaperone Function ◽  
Surface Proteome ◽  
Cell Surface Proteome

scholarly journals Multi-omics analysis of AML cells treated with azacitidine reveals highly variable cell surface proteome remodeling

2018 ◽  
Author(s):  
Kevin K Leung ◽  
Aaron Nguyen ◽  
Tao Shi ◽  
Lin Tang ◽  
Xiaochun Ni ◽  
...  
Keyword(s):  
Cell Surface ◽  
Cell Lines ◽  
Protein Level ◽  
Dna Methyltransferase ◽  
Immune Defense ◽  
Surface Proteins ◽  
Gene Set Enrichment Analysis ◽  
Surface Proteome ◽  
The Impact ◽  
Cell Surface Proteome

AbstractMyelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) are diseases of abnormal hematopoietic differentiation with aberrant epigenetic alterations. Azacitidine (AZA) is a DNA methyltransferase inhibitor (DNMTi) widely used to treat MDS and AML, yet the impact of AZA on the cell surface proteome has not been defined. To identify potential therapeutic targets for use in combination with AZA in AML patients, we investigated the effects of AZA treatment on four AML cell lines (KG1a, HL60, HNT34, and AML193), representing different stages of differentiation. The effect of AZA treatment on these cell lines was characterized at three levels: the DNA methylome (methylation array), the transcriptome (gene expression array), and the cell surface proteome (glycoprotein capture with SILAC labeling). Untreated AML cell lines showed substantial overlap in their methylomes, transcriptomes, and cell surface proteomes. AZA treatment globally reduced DNA methylation in all cell lines, but changes in the transcriptome and surface proteome were subtle and differed among the cell lines. Transcriptome analysis identified five commonly up-regulated coding genes upon AZA treatment in all four cell lines, TRPM4 being the only gene encoding a surface protein, and surface proteomics analysis found no commonly regulated proteins. Gene Set Enrichment Analysis (GSEA) of differentially-regulated RNA and surface proteins showed a decrease in metabolism pathways and an increase in immune defense response pathways. As such, AZA treatment in four AML cell lines had diverse effects at the individual gene and protein level, but converged to regulation of metabolism and immune response at the pathway level. Given the heterogeneous response of AZA in the four cell lines at the gene and protein level, we discuss potential therapeutic strategies for combinations with AZA.

scholarly journals The regulation of the cell surface proteome by amp-activated protein kinase

2021 ◽  
Author(s):  
Eden Ross
Keyword(s):  
Protein Kinase ◽  
Cell Surface ◽  
Metabolic Regulation ◽  
Cultured Cells ◽  
Cellular Adhesion ◽  
Ampk Activation ◽  
And Migration ◽  
Surface Proteome ◽  
Amp Activated Protein Kinase ◽  
Cell Surface Proteome

The cell-surface proteome controls numerous cellular functions and is dynamically controlled by endocytosis and recycling under different cellular conditions. Energy stress is a state in which a cell must engage adaptive responses to ensure survival, including remodelling of the cell-surface proteome. AMP-activated protein kinase (AMPK) is an important metabolic regulator in the cell. Recent studies suggest AMPK activation may alter the endocytosis of a few specific proteins. How increased AMPK activity globally regulates the cell surface proteome is not known. I have developed a method to isolate the cell surface proteome from cultured cells. Coupling this method to quantitative mass spectrometry has allowed systematic identification of changes in the cell-surface proteome upon metabolic regulation. I found that activation of AMPK results in robust changes in the cell surface proteome, including cell adhesion and migration proteins. I confirmed that AMPK activation elicits a decrease in the cell surface abundance of the adhesion and migration protein β1-integrin, and that this is correlated with altered function of the endocytosis protein Dab2. Thus, my research furthers our understanding of how AMPK regulates the cell surface proteome and the specific mechanism by which AMPK regulates cellular adhesion and migration.

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