We explore the roles and mechanisms of enzymes, receptors, and membrane proteins in complex biological processes using a vast, cross-disciplinary toolset, and we develop technologies to facilitate these studies.
Researchers in the Craik Lab are intensely focused on using antibody-based technologies and protease-related targets to tackle challenging problems relating to oncology, infectious disease, and neuro-degenerative and neuro-developmental disorders. This work is highly translational in nature, and practical applications are an integral part of our projects. The team is led by Charles S. Craik, PhD, a faculty member in the Department of Pharmaceutical Chemistry in the UCSF School of Pharmacy and director of the Quantitative Biosciences Consortium, a consortium of five UCSF PhD degree programs.
Leading and innovative research
Our work has enabled critical advances in:
Accurately detecting pancreatic cancer
Due to the lack of accurate, non-invasive diagnostics for pancreatic cancer, many healthy patients undergo unnecessary surgery of benign pancreatic lesions, which is costly and potentially harmful due to high complication rates. The Craik Lab has developed a simple and direct tool that uses enzymatic activity to discern cancerous lesions from those that are benign and do not require surgery. This tool is highly sensitive and nearly 100% accurate, vastly outperforming existing diagnostics.
Monitoring response to cancer therapy and potential treatment
Not only is prostate cancer a serious and often fatal disease, but it also is challenging to treat due to difficulties in assessing patients’ responses to therapy. A majority of patients show a good response to therapy early on, but many go on to relapse, leading to castration-resistant prostate cancer. Non-invasive imaging would enable physicians to find cancerous lesions and measure cancer cell viability, and moreover help patients accurately follow their own therapeutic response. The Craik Lab has engineered an antibody into a molecular tool that first recognizes and enters prostate cancer cells, and then delivers a dye that reveals tumor cells and how they are affected by therapy. Thanks to its novel mechanism of entering specific cancer cells, our tool has the potential to serve as both a diagnostic and a therapeutic agent.
Breast cancer is the most common malignant cancer in Western women, with metastases to distant sites being the main cause of death. By targeting the protein and cellular marker, urokinase plasminogen activator receptor (uPAR), with our preclinical antibody platform, the Craik Lab has generated and validated fully human antibodies against uPAR in breast cancer cell lines and xenograft models. Antibody-based uPAR imaging probes accurately detect small disseminated lesions in tumor metastasis models, complementing the current clinical imaging standard, PET imaging with 18F-fluorodeoxyglucose, at detecting non-glucose-avid metastatic lesions. The antagonistic antibodies result in a significant decrease in tumor growth in xenograft models of cancer in both monotherapy and radioimmunotherapy studies. These results offer a preclinical proof of concept for uPAR targeting as a strategy for breast cancer diagnosis and therapy.
A preclinical probe specific for the measurement of a biomarker for stage II colon cancer was developed using an active site-specific, recombinant human antibody for matriptase. We found that the selective targeting of active matriptase can be used to visualize the tumorigenic epithelium and that the probe localized only to cancer cell lines with active matriptase on the surface. Labeling of the active form of matriptase in vivo was measured in human colon cancer xenografts and in a patient-derived xenograft model using near-infrared and single-photon emission computed tomography imaging, suggesting that emergent active matriptase is a functional biomarker of the transformed epithelium and that its proteolytic activity can be exploited to noninvasively evaluate tumorigenesis in vivo.
Macromolecular recognition for substrate and inhibitor design
Determining the substrate specificity of enzymes that modify the proteome, referred to as post-translational modifying (PTM) enzymes that are central regulators of cellular signaling, is a critical step in unraveling their biological functions both in normal physiological processes and in disease states. The Craik Lab has developed a technology, known as multiplex substrate profiling by mass spectrometry (MSP-MS), to globally profile the substrate specificity of PTM enzymes. This assay uses a rationally designed, physicochemically diverse library of tetradecapeptides to provide maximum coverage of sequence space. This method has been applied to PTM enzymes to uncover biological function and guide substrate and inhibitor design with proteases and kinases from diverse sources and myriad compositions.
Novel methods for antiviral treatments
The Craik Lab has identified the protease encoded by Kaposi’s sarcoma herpes virus, a virus associated with the most common neoplasia of AIDS patients. This enzyme is a dimer that undergoes a disorder-to-order transition upon dimerization, and the lab has characterized a concentration-dependent mechanism for enzyme activation. The protease appears to engage in a concentration-dependent timing mechanism that regulates viral assembly of a human pathogen. Crystal structure and NMR solution structural studies have provided an atomic level understanding of the conformational changes that regulate the activity of the protease. Using this approach, the lab was able to localize this conformational change to an oligomerization-induced helical switch of enzyme activity. We were then able to target this switch, located at the dimer interface, with small molecule dimerization disruptors to reveal a new target for enzyme inhibition.
Located in Genentech Hall at the dynamic Mission Bay campus of UC San Francisco, the Craik Lab is part of a flourishing scientific community exclusively focused on excellence in health science. Curious researchers from all over the globe join our lab as students and postdocs, bringing expertise from a variety of scientific backgrounds. We share facilities with the James Lab, Burlingame Lab, Gross Lab, Kirkwood Lab, and Miller Lab, and we contribute expertise and resources to several interdisciplinary research programs. This allowed us to adopt new breakthrough technologies like cryo-electron microscopy and CRISPR gene editing as fast as they became available. Because of the immediate need for the diagnostic tools under development in the Craik Lab, a highly collaborative network is essential to translate our ideas into practical applications. For example, our tool for early detection of pancreatic cancer could not have been developed without our collaboration with clinicians in the Kirkwood Lab, who routinely perform resection of pancreatic cysts.
Our work supports multiple aims of the School of Pharmacy mission by generating new knowledge through innovation, delivering a unique education to our students, and sharing our expertise with others. Our work also supports the UCSF mission of advancing health worldwide®.
Our standard of medical treatment is rapidly evolving towards patient-centric, personalized medicine. Tailoring treatment to complex medical needs requires precision tools for patient profiling and drug delivery. Our lab is developing precision diagnostics, delivery platforms for novel therapeutic approaches, and a new generation of intelligent drugs that can discern between health and diseased tissue targets.
Image credits: Craik: © Majed; Genentech Hall: Frank Farm