Executive Summary The applicant proposes to establish a multidisciplinary team to employ proteomics and molecular approaches in the identification and characterization of novel biomarkers on cancer stem cells (CSC), with the ultimate aim to develop targeted therapy for breast cancer. Recent research implicates cancer stem cells in the origin, progression and relapse of malignant disease. Failure to fully eradicate CSC by conventional chemotherapy is believed to be a source of therapeutic resistance. The proposal is focused on a highly significant disease, breast cancer, and has as its goal the development of a targeted therapy for this disease. However, the reviewers’ enthusiasm was limited by the fact that the proposal relies on a specific phenotype for the isolation of the cancer stem cell. This subclass of cells is very likely to be a heterogeneous population, which may reduce the likelihood of finding appropriate molecular targets through proteomic and chemical approaches described in the proposal. If the emphasis of the proposal is more on the fractionation and characterization of CSC, improved enrichment would greatly facilitate the biological and chemical approaches described in the application. Further, it was pointed out that even if specific molecular targets are identified, planning clinical studies may be a challenge as therapy for breast cancer is progressively improving, and incorporating new agents into accepted treatment protocols may not be straightforward. The PI is an experienced and respected senior investigator in cancer research. However, reviewers raised some concern over the PI’s lack of clinical experience, which reviewers felt was an important perspective for leading this team. Reviewers agree that the planning approach has been well thought out and appropriate experts are included in the team. However, the absence of a defined population of breast CSCs, which may differ between different subtypes of disease and may reduce the likelihood of success in identifying suitable target for therapy diminished reviewers’ overall enthusiasm for the proposal. Reviewer Synopsis This planning application, submitted by the PI, an established cancer biologist, centers on the characterization and development of targeted therapies for breast cancer. The overall plan is to focus on stem cell-like cells (SCLC) or cancer stem cells and develop novel small molecule or antibody-mediated therapies. The team will include a Clinical Team, a Discovery Team, Biomolecular Characteization Team and an Evaluation Team that will concentrate on aspects of this proposal. The Discovery and Clinical Teams will work together to isolate and characterize putative CSCs from primary breast material. The Biomolecular Characterization Team will perform proteomics approaches, mass spectrometry and phage escape technology to identify proteins specifically expressed in CSCs. Additional work will provide gene expression and epigenetic signatures of CSCs. The Evaluation Team will use xenograft and syngeneic mouse models to test mechanisms. A Steering Committee and SAB are proposed to advice the group. Reviewer Comments Concept: The hypothesis underlying this proposal is that CSCs may not be adequately treated by conventional chemotherapeutic approaches and that specific characterization of CSCs will permit identification of new molecular targets for therapy. The problem is significant, though it is uncertain as yet whether the clinical impact will be great. A potential problem with the proposed approach is the reliance on the CD44+/CD24- phenotype to isolate breast CSCs. Although this has been reported as the phenotype of breast CSCs in the initial reports, there is not uniform agreement within the field and it is evident that even if CD44+CD24- includes CSCs it is a very heterogeneous population. Such heterogeneity may reduce the likelihood of finding appropriate targets through proteomic and molecular approaches. Emphasis might be increased on the fractionation and characterization of CSCs, as improved enrichment would greatly facilitate the biological and chemical approaches that have been described. Principal Investigator: The PI is an experienced and respected senior investigator in cancer research. Although not a clinician he has assembled an appropriate group of collaborators in this consortium at the Scripps Institute. He is well suited to serve as the leader of the planning group. Planning Approach: The planning approach is described briefly in this application. Highlighting different teams to develop each aspect of the work is logical. The proposal will necessitate strong collaboration between bench scientists and clinicians. This seems to be in place. A potential difficulty noted above is that the “maturity” of the field in terms of defining breast CSCs, which may differ between different subtypes of disease, may reduce the likelihood of success in identifying suitable targets for therapy. Once targets are identified, planning clinical studies will be a challenge as therapy for breast cancer is progressively improving and incorporating new agents into accepted therapies will not be straightforward.