title: Gene expression profiling-based identification of cell-surface targets for developing multimeric ligands in pancreatic cancer.
abstract: Multimeric ligands are ligands that contain multiple binding domains that simultaneously target multiple cell-surface proteins. Due to cooperative binding, multimeric ligands can have high avidity for cells (tumor) expressing all targeting proteins and only show minimal binding to cells (normal tissues) expressing none or only some of the targets. Identifying combinations of targets that concurrently express in tumor cells but not in normal cells is a challenging task. Here, we describe a novel approach for identifying such combinations using genome-wide gene expression profiling followed by immunohistochemistry. We first generated a database of mRNA gene expression profiles for 28 pancreatic cancer specimens and 103 normal tissue samples representing 28 unique tissue/cell types using DNA microarrays. The expression data for genes that encode proteins with cell-surface epitopes were then extracted from the database and analyzed using a novel multivariate rule-based computational approach to identify gene combinations that are expressed at an efficient binding level in tumors but not in normal tissues. These combinations were further ranked according to the proportion of tumor samples that expressed the sets at efficient levels. Protein expression of the genes contained in the top ranked combinations was confirmed using immunohistochemistry on a pancreatic tumor tissue and normal tissue microarrays. Coexpression of targets was further validated by their combined expression in pancreatic cancer cell lines using immunocytochemistry. These validated gene combinations thus encompass a list of cell-surface targets that can be used to develop multimeric ligands for the imaging and treatment of pancreatic cancer.
authors.affiliation: Translational Genomics Research Institute, 445 North Fifth Street, Phoenix, AZ 85004, USA.
authors.forename: Yoganand
authors.initials: Y
authors.lastname: Balagurunathan
authors.forename: David L
authors.initials: DL
authors.lastname: Morse
authors.forename: Galen
authors.initials: G
authors.lastname: Hostetter
authors.forename: Vijayalakshmi
authors.initials: V
authors.lastname: Shanmugam
authors.forename: Phillip
authors.initials: P
authors.lastname: Stafford
authors.forename: Sonsoles
authors.initials: S
authors.lastname: Shack
authors.forename: John
authors.initials: J
authors.lastname: Pearson
authors.forename: Maria
authors.initials: M
authors.lastname: Trissal
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Demeure
authors.forename: Daniel D
authors.initials: DD
authors.lastname: Von Hoff
authors.forename: Victor J
authors.initials: VJ
authors.lastname: Hruby
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Gillies
authors.forename: Haiyong
authors.initials: H
authors.lastname: Han