Functional genomics and proteomics approaches to study the ERBB network in cancer

A systematic understanding of signaling by ErbB2 in cancer using phosphoproteomics

ErbB2 is an important receptor tyrosine kinase and a member of the ErbB family. Although it does not have a specific ligand, it transmits signals downstream by heterodimerization with other receptors in the family. It plays a major role in a variety of cellular responses like proliferation, differentiation, and adhesion. ErbB2 is amplified at the DNA level in breast cancer (20%–30%) and gastric cancer (10%–20%), and trastuzumab is effective as a therapeutic antibody. This review is a critical analysis of the currently published data on the signaling pathways of ErbB2 and the interacting proteins. It also focuses on the techniques that are currently available to evaluate the entire phosphoproteome following activation of ErbB2. Identification of new and relevant phosphoproteins can not only serve as new therapeutic targets but also as a surrogate marker in patients to assess the activity of compounds that inhibit ErbB2. Overall, such analysis will improve understanding of signaling by ErbB2.

Brain cancer immunoediting: novel examples provided by immunotherapy of malignant gliomas

A number of studies in murine models have suggested that the immune system may edit different tumors by forcing their expression profiles so that they escape immune reactions and proliferate. Glioblastoma (GB), the most frequent and aggressive primary brain tumor, provides a good example of this, thanks to the production of numerous immunosuppressive molecules (with TGF-β being of paramount importance), downregulation of the MHC complex and deregulation of the potential for antigen presentation by the surrounding microglia. Given that surgery, radiotherapy and chemotherapy with available protocols have limited effects on the survival of GB patients, different immunotherapy strategies have been developed, based on the use of dendritic cells, antibodies and peptide vaccination. Presently, bevacizumab, a humanized anti-VEGF antibody, provides the most successful example for immune-based treatment of GB, however, its action is limited in time, as the often tumor relapses due to still undefined immunoediting mechanisms. Altered function of EGF receptor-driven pathways is common in GB and is most frequently due to the presence of a deleted form named EGFRvIII, providing a unique cancer epitope that has been targeted by immunotherapy. A recent trial of GB immunotherapy based on vaccination with the EGFRvIII peptide has shown clinical benefit: interestingly most GBs at relapse were negative for EGFRvIII expression, a relevant, direct example of cancer immunoediting. Investigations on the mechanisms of GB immunoediting will lead to an increased understanding of the biology of this malignancy and hopefully provide novel therapeutic targets.

Genomic screening with RNAi: results and challenges

RNA interference (RNAi) is an effective tool for genome-scale, high-throughput analysis of gene function. In the past five years, a number of genome-scale RNAi high-throughput screens (HTSs) have been done in both Drosophila and mammalian cultured cells to study diverse biological processes, including signal transduction, cancer biology, and host cell responses to infection. Results from these screens have led to the identification of new components of these processes and, importantly, have also provided insights into the complexity of biological systems, forcing new and innovative approaches to understanding functional networks in cells. Here, we review the main findings that have emerged from RNAi HTS and discuss technical issues that remain to be improved, in particular the verification of RNAi results and validation of their biological relevance. Furthermore, we discuss the importance of multiplexed and integrated experimental data analysis pipelines to RNAi HTS.