Developing and applying a gene functional association network for anti-angiogenic kinase inhibitor activity assessment in an angiogenesis co-culture model.
BACKGROUND
Tumor angiogenesis is a highly regulated process involving intercellular communication as well as the interactions of multiple downstream signal transduction pathways. Disrupting one or even a few angiogenesis pathways is often insufficient to achieve sustained therapeutic benefits due to the complexity of angiogenesis. Targeting multiple angiogenic pathways has been increasingly recognized as a viable strategy. However, translation of the polypharmacology of a given compound to its antiangiogenic efficacy remains a major technical challenge. Developing a global functional association network among angiogenesis-related genes is much needed to facilitate holistic understanding of angiogenesis and to aid the development of more effective anti-angiogenesis therapeutics.


RESULTS
We constructed a comprehensive gene functional association network or interactome by transcript profiling an in vitro angiogenesis model, in which human umbilical vein endothelial cells (HUVECs) formed capillary structures when co-cultured with normal human dermal fibroblasts (NHDFs). HUVEC competence and NHDF supportiveness of cord formation were found to be highly cell-passage dependent. An enrichment test of Biological Processes (BP) of differentially expressed genes (DEG) revealed that angiogenesis related BP categories significantly changed with cell passages. Built upon 2012 DEGs identified from two microarray studies, the resulting interactome captured 17226 functional gene associations and displayed characteristics of a scale-free network. The interactome includes the involvement of oncogenes and tumor suppressor genes in angiogenesis. We developed a network walking algorithm to extract connectivity information from the interactome and applied it to simulate the level of network perturbation by three multi-targeted anti-angiogenic kinase inhibitors. Simulated network perturbation correlated with observed anti-angiogenesis activity in a cord formation bioassay.


CONCLUSIONS
We established a comprehensive gene functional association network to model in vitro angiogenesis regulation. The present study provided a proof-of-concept pilot of applying network perturbation analysis to drug phenotypic activity assessment.
Chen
Yuefeng
Y
Angiogenesis and Tumor Microenvironment Biology, Lilly Research Laboratories, Indianapolis, IN 46285, USA. chenyu@lilly.com
Wei
Tao
T
Yan
Lei
L
Lawrence
Frank
F
Qian
Hui-Rong
HR
Burkholder
Timothy P
TP
Starling
James J
JJ
Yingling
Jonathan M
JM
Shou
Jianyong
J
D000465:Algorithms; D020533:Angiogenesis Inhibitors / Q000494:pharmacology*; D001681:Biological Assay; D002450:Cell Communication / Q000235:genetics; D018920:Coculture Techniques; D020405:Dermis / Q000166:cytology; D042783:Endothelial Cells / Q000166:cytology; D005347:Fibroblasts / Q000166:cytology; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D006801:Humans; D008954:Models, Biological; D009389:Neovascularization, Pathologic / Q000188:drug therapy / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D009857:Oncogenes; D010641:Phenotype; D047428:Protein Kinase Inhibitors / Q000494:pharmacology*; D014471:Umbilical Veins / Q000166:cytology
D020533:Angiogenesis Inhibitors; D047428:Protein Kinase Inhibitors