Bioinformatics construction of the human cell surfaceome
J. P. C. da Cunha,Pedro A. F. Galante,J. E. de Souza,R. F. de Souza,P. M. Carvalho,Daniel T. Ohara,Ricardo Pereira de Moura,S. M. Oba-Shinja,Suely Kazue Nagahashi Marie,Wilson A. Silva,Rodrigo Oliva Perez,Beatriz Stransky,Martin Pieprzyk,Jordan Moore,Otavia L. Caballero,Joaquim Gama-Rodrigues,Angelita Habr-Gama,Winston Patrick Kuo,A. J. G. Simpson,Anamaria A. Camargo,Lloyd J. Old,S J de Souza +21 more
TLDR
The genetic diversity of the human cell surfaceome at different levels is explored, including the distribution of polymorphisms, conservation among eukaryotic species, and patterns of gene expression, by integrating expression information from a variety of sources.Abstract:
Cell surface proteins are excellent targets for diagnostic and therapeutic interventions. By using bioinformatics tools, we generated a catalog of 3,702 transmembrane proteins located at the surface of human cells (human cell surfaceome). We explored the genetic diversity of the human cell surfaceome at different levels, including the distribution of polymorphisms, conservation among eukaryotic species, and patterns of gene expression. By integrating expression information from a variety of sources, we were able to identify surfaceome genes with a restricted expression in normal tissues and/or differential expression in tumors, important characteristics for putative tumor targets. A high-throughput and efficient quantitative real-time PCR approach was used to validate 593 surfaceome genes selected on the basis of their expression pattern in normal and tumor samples. A number of candidates were identified as potential diagnostic and therapeutic targets for colorectal tumors and glioblastoma. Several candidate genes were also identified as coding for cell surface cancer/testis antigens. The human cell surfaceome will serve as a reference for further studies aimed at characterizing tumor targets at the surface of human cells.read more
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Journal ArticleDOI
A Mass Spectrometric-Derived Cell Surface Protein Atlas
Damaris Bausch-Fluck,Andreas Hofmann,Thomas Bock,Andreas P. Frei,Ferdinando Cerciello,Andrea Jacobs,Hansjoerg Moest,Ulrich Omasits,Rebekah L. Gundry,Charles Yoon,Ralph Schiess,Alexander Schmidt,Paulina Mirkowska,Anetta Härtlova,Jennifer E. Van Eyk,Jean-Pierre Bourquin,Ruedi Aebersold,Kenneth R. Boheler,Kenneth R. Boheler,Peter W. Zandstra,Bernd Wollscheid +20 more
TL;DR: In this paper, the authors applied the Cell Surface Capture (CSC) technology to 41 human and 31 mouse cell types to generate a mass-spectrometry derived Cell Surface Protein Atlas (CSPA) providing cellular surfaceome snapshots at high resolution.
Journal ArticleDOI
Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome
Ulrike Kusebauch,David S. Campbell,Eric W. Deutsch,Caroline S. Chu,Douglas A. Spicer,Mi-Youn Brusniak,Joseph Slagel,Zhi Sun,Jeffrey Stevens,Barbara Grimes,David Shteynberg,Michael R. Hoopmann,Peter Blattmann,Alexander V. Ratushny,Oliver Rinner,Paola Picotti,Christine Carapito,Chung-Ying Huang,Meghan Kapousouz,Henry H N Lam,Tommy Tran,Emek Demir,John D. Aitchison,John D. Aitchison,Chris Sander,Leroy Hood,Ruedi Aebersold,Ruedi Aebersold,Robert L. Moritz +28 more
TL;DR: The generation and verification of a compendium of highly specific assays that enable quantification of 99.7% of the 20,277 annotated human proteins by the widely accessible, sensitive, and robust targeted mass spectrometric method selected reaction monitoring, SRM are described.
Journal ArticleDOI
The in silico human surfaceome.
Damaris Bausch-Fluck,Ulrich Goldmann,Sebastian Müller,Marc van Oostrum,Maik Müller,Olga T. Schubert,Bernd Wollscheid +6 more
TL;DR: The surfaceome diversity depends on cell type and appears to be more dynamic than the nonsurface proteome, and the in silico surfaceome enables the filtering of data generated by multiomics screens and supports the elucidation of the surfaceome nanoscale organization.
Journal ArticleDOI
An Extracellular Interactome of Immunoglobulin and LRR Proteins Reveals Receptor-Ligand Networks
Engin Özkan,Robert A. Carrillo,Catharine L. Eastman,Richard Weiszmann,Deepa Waghray,Karl G. Johnson,Kai Zinn,Susan E. Celniker,K. Christopher Garcia +8 more
TL;DR: In this paper, a set of 202 proteins composed of the Drosophila melanogaster immunoglobulin superfamily (IgSF), fibronectin type III (FnIII), and leucine-rich repeat (LRR) families were probed for extracellular interactions.
PatentDOI
High-resolution transcriptome of human macrophages
TL;DR: In this paper, the finding of specific surface markers for M1-like and M2-like macrophages was proposed for the identification, characterization and isolation of M1 -like and m2 -like macophages based on the abundance of surface markers.
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TL;DR: The interim integrative analysis of DNA copy number, gene expression and DNA methylation aberrations in 206 glioblastomas reveals a link between MGMT promoter methylation and a hypermutator phenotype consequent to mismatch repair deficiency in treated gliobeasts, demonstrating that it can rapidly expand knowledge of the molecular basis of cancer.
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