NSBCC Research Summary
The Nanosystems Biology Cancer Center (NSBCC) is organized to take advantage of the state-of-the-art in chemistry, materials, and physics of nanotechnology science and engineering, the state-of-the-art in systems biology approach to health and disease, and the state-of-the-art in the science, technology, and clinical applications of cancer biology. The NSBCC is Directed by Professor James R. Heath (Caltech) and co-directed by Dr. Leroy Hood (Institute for Systems Biology [Seattle, WA]) and Professor Michael Phelps (UCLA Geffen School of Medicine and Department of Molecular & Medical Pharmacology). The NSBCC is also aligned with UCLA’s Jonsson Comprehensive Cancer Center.
The concept behind the NSBCC is that measurement and analysis needs of systems approaches to cancer, ranging from cancer biology to clinical oncololgy, should drive the nature and direction technology development. Specific cancer projects within the center are focused around prostate and ovarian cancers, melanoma, and glioblastoma, but the technologies being developed to help understand and treat these cancers are intended to serve as a general class of technologies for all cancers. The goals of early detection of ovarian and prostate cancers will be achieved through (1) the identification of a panel of organ-specific, secreted biomarkers that serve as sentinels for reporting the health status of the diseased organs; (2) the development of relatively small molecule, high affinity protein capture agents as probes against those secreted proteins; and (3) the development of high throughput, real time, label-free nanoelectronic/microfluidics sensor arrays for quantitating those protein levels through serum analysis , diagnostic approaches for following the positive and adverse responses of therapy. For melanoma, a project directed by Professor Owen Witte (UCLA and Professor Michael Roukes (Caltech) is aimed at cancer immunotherapy by using novel chemical and chip-based techniques to select, sort, and analyze rare CD8+ T-cells as agents for fighting the cancer. The use of nanotech tools to analyze the heterogeneity of glioblastoma tissues at the level of a few cells, and to utilize that analysis to direct therapies, is a project directed by Professor Paul Mischel (UCLA), Hood, and Heath. Following the responses of cancer development and therapeutic response in oncogene and suppressor gene mouse models of prostate and ovarian cancer constitutes a projected directed by Professors Charles Sawyers and Hong Wu (UCLA) and Heath and Hood. The goal is to utilize a systems biology analysis to generate a predictive network hypothesis of that disease, and to utilize that hypothesis to identify the most promising biomarkers (e.g. a set of independent variables) for diagnosing the disease and analyzing the response of the disease to emerging molecular therapies. Finally, Professors Phelps, Hartmuth Kolb (Siemens and UCLA) and Professor Mark Davis (Caltech) are developing in vivo diagnostic strategies based upon the development of high-affinity, radiolabeled molecular imaging probes against specific cancer targets, using a technology called in situ click chemistry. Those probes are prepared using an integrated microfluidics technology called chemical reaction circuits that allows for the ultra-rapid and high efficiency preparation of human-level doses of radiopharmaceuticals on chip. Professor Robert Grubbs (Caltech, Nobel Laureate in Chemistry 2005) is developing novel elastomeric materials to enable the application of these chemical reaction circuits within a diverse range of chemical environments.
More detailed descriptions of the individual projects are given below. The NSBCC external advisory board is headed by Professor Judith Gasson (Director of the Jonsson Comprehensive Cancer Center) and includes Hamilton Jordan and Roy Doumani. Companies allied with the NSBCC include Homestead Clinical Corporation (Seattle), MoB, Inc. (LA), Siemens Biomarker Solutions (LA) and Materia (LA).
Project 1: Leroy Hood, MD, PhD—Institute for Systems, Biology, Seattle, Washington
The systems approach to biology and medicine pioneered by the Institute for Systems Biology promises to transform the practice of oncology over the next 2-15 years moving it from a reactive discipline (responding after the patient is sick) to a predictive, preventive and personalize modes. This will be, in part, achieved by using the blood as a window into health and disease. The idea is that biology is mediated by networks of proteins and other molecules that operate within the cell to execute normal functions through the regulation of gene expression. In disease, one or more of these networks becomes perturbed (genetically or environmentally) and the altered patterns of gene expression mediate the disease. These disease-perturbed networks change dynamically with the progression of the diseases as do their patterns of gene expression. We have identified by computational analyses organ-specific transcripts in the prostate and ovary and again by computational analyses some of these appear to be secreted. Our hypothesis is that at least some of these molecules are secreted into the blood at detectable levels and hence constitute a molecular fingerprint for each organ whose protein components change individually in their levels of expression as one shifts from the normal to a diseased state and as one progresses through the disease state. The power of these proposed organ-specific blood markers is that they let one focus on the changes that occur in just a single organ and that the blood baths all organs and tissues and hence receives secreted protein fingerprints from each. Hence we plan to test the hypothesis that these blood fingerprints become a multiparameter panel of proteins capable of identifying particular diseases and the state of progression of these diseases—and will do using blood proteomics techniques for three different cancers: prostate, ovarian and glioblastoma. We will also test the idea that these blood tests will allow cancer to be detected at a very early stage. The need to extend these blood diagnostic techniques in the future to millions of patients means that new measuring techniques will have to be developed which are ultimately capable of making perhaps 1000 quantitative protein measurements—and doing so rapidly, cheaply, on very small samples and fully automatically. Hence in this project we will also begin to develop blood-protein measuring devices using microfluidic and nanotechnology approaches that will begin to acquire these features.
Project 2: Owen Witte, MD, UCLA
Immunotherapy approaches for cancer can result in occasional long term remissions of advanced metastatic cancers resistant to conventional modes of therapy. Development of more effective approaches requires a detailed analysis of the immunobiology of these antitumor responses. However, existing technologies for the study of immune responses have proven to have limited ability to fully characterize this complex process, mainly due to the fact that the cells that orchestrate these responses, the tumor antigen-specific CD8+ cytotoxic T lymphocytes (CTL) are rare cells in peripheral circulation. We plan to develop a modular technology to allow for the design, production and validation of functional components for the enumeration of tumor-specific CD8+ CTL using limiting samples, eventually allowing to quantitate and functionally characterize tumor-infiltrating CD8+ CTL. We propose to use capture MHC tetramers loaded with tumor antigens (the specific ligands for CD8+ CTL) to develop murine and human micro-Immunochip (mIC) modules with digitally controlled, individually accessible microfluidic chambers to capture, sort, quantitate and incubate tumor-specific T-cells. Next, we will develop individual modules for quantifying surface, intracellular and secreted proteins, from very small numbers of anti-tumor specific T cells (even single cells), and a module for quantifying mRNA signatures from small numbers of cells (in collaboration with Fluidigm). Finally, the different modules will be integrated and tested, first using defined populations of tumor-specific CD8+ CTL, followed by samples of increasing complexity obtained from mouse models of immunotherapy, and eventually human tumor-specific CD8+ CTL obtained from patients participating in clinical trials of cancer immunotherapy being conducted at UCLA.
Project 3: Michael E. Phelps, MD, UCLA
Positron Emission Tomography (PET), using 2-deoxy-2-[F-18]fluoro-D-glucose (FDG) as the imaging probe, has been proven to be a valuable tool for the early detection, staging, and restaging of cancer. However, despite the clear value of PET imaging, limitations do exist, since current imaging probes may lack specificity or have inadequate signal to background characteristics in vivo. Additional biomarkers are needed that show a very high affinity to and specificity for tumor targets to support cancer drug development and to provide health care providers with better diagnostic tools. Such high-affinity imaging probes could dramatically improve the apparent spatial resolution of the PET scanner, allowing smaller tumors and lower concentration disease targets to be detected. We will address this need by creating a generalizable technology platform based on the fragment-based in situ click chemistry approach in combination with microfluidics technologies to identify high-affinity PET probes that target cancer-related proteins. For platform development and validation, we will employ the cancer-related kinase Akt. The UCLA/CalTech/MTI team is an international leader in the PET field and in the development of click chemistry and microfluidics integrated chemical reaction circuits (CRCs), as well as novel chemical-resistant polymers. The team will develop new CRCs that accelerate the discovery of high-affinity protein ligands through in situ click chemistry, as well as CRCs that allow the production of research quantities of radioactive [F-18]-containing PET probes targeting Akt. The specific aims are as follows: (1) Develop microfluidics CRCs for in situ click chemistry screening, including the interface with mass spectrometry instruments. (2) Develop high-affinity ligands for the oncogenic kinase Akt through in situ click chemistry using fragments that carry [F-19] as part of their design in order to facilitate later introduction of the PET radionuclide [F-18]. (3) Develop microfluidics CRCs for probe synthesis and produce [F-18]-labeled high-affinity kinase ligands.
Project 4: Charles Sawyers, MD, UCLA
Clinical evaluation of targeted cancer therapy is currently hampered by the difficulty in matching a new molecularly targeted agent to the appropriate molecular-defined patient. The solution requires the use of molecularly-based biomarkers to guide patient selection, optimize drug dosage and assess response to treatment. This project will use two well-annotated, genetically-defined mouse models of human prostate cancer to discover biomarkers that define disease progression, the initiating oncogenic lesion and response to therapy. The molecular profiles of these mouse models closely resemble human prostate cancers, giving us confidence in their utility for discovery of human tumor biomarkers. In addition, we have already demonstrated that dominant molecular signatures of disease stage and the initiating molecular lesion are easily detected in both models. Aim 1 of this project will use existing mRNA and proteomics datasets to define the optimal mRNA signatures from tumor tissue and protein signatures from serum to determine disease stage, molecular lesion and response to therapy (in collaboration with the Hood lab). We will then develop nanodevices for measuring these mRNA signatures from small numbers of cells (in collaboration with Fluidigm) and Si-based nanodevices for measuring serum protein signatures (in collaboration with the Heath lab). We will then evaluate and optimize the performance of these nanodevices in mice (Aim 2) and in patients (Aim 3) treated with two different kinase inhibitors as well as using more conventional blood proteomics analyses for these studies (in collaboration with Hood lab). Success in the project will provide proof-of-concept for detailed molecular evaluation of cancer patients before and during therapy using highly accurate, cost-effective and minimally invasive technologies.
Project 5: Project 5--Paul Mischel, PhD, UCLA
An emerging set of molecular and nanotechnologies are being developed that promise to revolutionize pathologic analysis of cancer samples. Microfluidics integrated nanoelectronic sensors facilitate the separation, manipulation, and multi-parameter measurement of genes and proteins in large numbers of cancer cells from tissue samples, thus providing a more complete characterization of its pathologic state, including intratumor molecular heterogeneity. These technologies have the potential to rapidly and reproducibly identify predictive molecular signatures that can be used to guide patient therapy. Although technical challenges remain, these technologies are now ready to be tested in biologically and clinically relevant cancer models. Our NSBCC team is an international leader in the development of microfluidics integrated nanoelectronic sensors. The UCLA pathology team has recently identified a predictive molecular signature that is significantly, and reproducibly, associated with glioblastoma patient response to EGFR kinase inhibitor therapy. Taking advantage of this synergy between technological and clinical expertise, this project will optimize and validate microfluidics integrated nanoelectronic sensors as a diagnostic tool for cancer. We will first optimize preparation of human glioblastoma patient samples, the intratumor molecular heterogeneity in these clinical samples will be measured and the ability of microfluidic integrated nanoelectronic sensors to perform multiparameter measurements of single cancer cells in tumor tissue will be validated. Next, the utility of microfluidics integrated nanoelectronic sensors to guide therapy decisions will be determined. Finally, new materials for improved multiparameter quantitative analysis of cancer cells using microfluidics integrated nanoelectronic sensors will be developed and validated.
All projects have received any necessary IACUC and/or IRB approvals.
These projects are designed for the development of biomarker panels and technologies that can enable the early detection of cancer (and thus their cures by conventional therapies, the stratification of cancers, the ability to follow cancer progression, the ability to stratify patients as responders or non-responders to therapy and the ability to monitor in vivo cancer biology and therapeutic responses. It will also build an oncology community that is receptive to co-developing and taking advantage of state-of-the-art technologies that can prove enabling weapons for fighting the war on cancer.