title: Bioinformatics construction of the human cell surfaceome.
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.
authors.affiliation: São Paulo Branch, Ludwig Institute for Cancer Research, 01323-903 São Paulo, Brazil.
authors.forename: J P C
authors.initials: JP
authors.lastname: da Cunha
authors.forename: P A F
authors.initials: PA
authors.lastname: Galante
authors.forename: J E
authors.initials: JE
authors.lastname: de Souza
authors.forename: R F
authors.initials: RF
authors.lastname: de Souza
authors.forename: P M
authors.initials: PM
authors.lastname: Carvalho
authors.forename: D T
authors.initials: DT
authors.lastname: Ohara
authors.forename: R P
authors.initials: RP
authors.lastname: Moura
authors.forename: S M
authors.initials: SM
authors.lastname: Oba-Shinja
authors.forename: S K N
authors.initials: SK
authors.lastname: Marie
authors.forename: W A
authors.initials: WA
authors.lastname: Silva
authors.forename: R O
authors.initials: RO
authors.lastname: Perez
authors.forename: B
authors.initials: B
authors.lastname: Stransky
authors.forename: M
authors.initials: M
authors.lastname: Pieprzyk
authors.forename: J
authors.initials: J
authors.lastname: Moore
authors.forename: O
authors.initials: O
authors.lastname: Caballero
authors.forename: J
authors.initials: J
authors.lastname: Gama-Rodrigues
authors.forename: A
authors.initials: A
authors.lastname: Habr-Gama
authors.forename: W P
authors.initials: WP
authors.lastname: Kuo
authors.forename: A J
authors.initials: AJ
authors.lastname: Simpson
authors.forename: A A
authors.initials: AA
authors.lastname: Camargo
authors.forename: Lloyd J
authors.initials: LJ
authors.lastname: Old
authors.forename: S J
authors.initials: SJ
authors.lastname: de Souza
mesh_terms: D000954:Antigens, Surface / Q000235:genetics; D014408:Biomarkers, Tumor / Q000235:genetics / Q000378:metabolism; D045744:Cell Line, Tumor; D015179:Colorectal Neoplasms / Q000235:genetics; D019295:Computational Biology; D030541:Databases, Genetic; D044127:Epigenesis, Genetic; D014644:Genetic Variation; D005909:Glioblastoma / Q000235:genetics; D006801:Humans; D008565:Membrane Proteins / Q000235:genetics* / Q000378:metabolism
chemical_list: D000954:Antigens, Surface; D014408:Biomarkers, Tumor; D008565:Membrane Proteins