Frank McCormick - US grants

[unreadable] DESCRIPTION (provided by applicant): The University of California San Francisco Comprehensive Cancer Center is an NCI-designed matrix center conducting a wide range of inter-disciplinary research in the areas of laboratory, clinical and population sciences integrating the activities of 223 members working at 4 major campus and hospital locations. Its goals are to: (1) support cancer research of the highest possible quality, in the areas of laboratory, clinical and population sciences; (2) develop patient outreach and education programs to increase the value of the Center to the local community; (3) promote and develop first-class care for cancer patient in our affiliated hospitals; and (4) create an integrated community of investigators dedicated to the shared goal of translating innovative science into improved clinical care. These goals are accomplished through the following 11 Programs and 12 Shared Resources: [unreadable] [unreadable] Programs Shared Resources [unreadable] Breast Cancer Laboratory for Cell Analysis [unreadable] Neurologic Oncology Genome Analysis [unreadable] Cancer & Immunity Array [unreadable] Prostate Cancer Tissue [unreadable] Society, Diversity & Disparities Immunohistochemistry and Molecular Pathology [unreadable] Pancreas Cancer Transgenic/Targeted Mutagenesis [unreadable] Hematopoietic Malignancies Informatics [unreadable] Pediatric Malignancies Mouse Pathology [unreadable] Cell Cycling and Signaling Preclinical Therapeutics [unreadable] Cancer Genetics Mass Spectrometry [unreadable] Tobacco Control Biostatistics [unreadable] Clinical Research Support Services [unreadable]

Affinity Chromatography; CRISP; Cells; Cellular Expansion; Cellular Growth; Chromatography, Affinity; Colon Cancer; Colon Carcinoma; Colonic Carcinoma; Complex; Computer Retrieval of Information on Scientific Projects Database; Coomassie blue; Family; Funding; GTP Binding; GTP Phosphohydrolases; GTPases; Grant; Guanosine Triphosphate Phosphohydrolases; Guanosinetriphosphatases; Institution; Investigators; Malignant Cell; Mass Spectrum; Mass Spectrum Analysis; Method LOINC Axis 6; Methodology; NIH; National Institutes of Health; National Institutes of Health (U.S.); Oncogenesis; Photometry/Spectrum Analysis, Mass; Play; Proteins; Ras Signaling Pathway; Research; Research Personnel; Research Resources; Researchers; Resources; Role; Sequence Homology; Source; Spectrometry, Mass; Spectroscopy, Mass; Spectrum Analyses, Mass; Spectrum Analysis, Mass; Staining method; Stainings; Stains; United States National Institutes of Health; affinity purification; base; cancer cell; cell growth; gel electrophoresis; gene product; guanosinetriphosphatase; homology (molecular); insight; member; social role; tumorigenesis

The Cancer Center is requesting funding for partial salary support for Staff Investigators who perform as liaisons for its Executive Committee. An internal advisory committee, the Executive Committee is chaired by the Director of the Cancer Center and includes the Cancer Center's Deputy Directors, Associate Directors, liaisons, and key administrators. The liaisons interact with Bay Area hospitals, universities, medical centers, and UCSF departments to coordinate research efforts, share information, promote cooperation, and increase the Cancer Center's value to the local community. The eight liaisons and development representative were chosen for their expertise and leadership qualities.

The Senior Leadership of the Cancer Center is responsible for all major decision-making and activities within the Center. The Cancer Center Director, his Deputy Director, five Associate Directors, and the Director of Scientific Programs Administration (described in Section 7.6) make up the top leadership group, the Directors Group. The Assistant Directors join this group at the quarterly Cancer Center Leadership Retreat. Funding is requested for salary support for each senior leader commensurate with his/her role within the Cancer Center.

Adenoviridae; Adenoviridae Infections; Adenovirus Infections; Adenoviruses; Binding; Binding (Molecular Function); CI-1042; CI1042; CRISP; Complex; Computer Retrieval of Information on Scientific Projects Database; Funding; Grant; Institution; Investigators; Mammalian Cell; Mediating; Molecular Interaction; NIH; National Institutes of Health; National Institutes of Health (U.S.); Normal Cell; ONYX-015; ONYX-015 (E1B-Attenuated Adenovirus); ONYX015; Oncolytic; Peptide Biosynthesis, Ribosomal; Process; Protein Biosynthesis; Protein Biosynthesis, Ribosomal; Protein Synthesis, Ribosomal; Proteins; RNA Binding; Regulation; Research; Research Personnel; Research Resources; Researchers; Resources; Source; Translation Initiation; Translations; Tumor Cell; United States National Institutes of Health; Viral; Virus; Viruses, General; Work; design; designing; gene product; insight; mutant; neoplastic cell; novel; oncolytic vector; prevent; preventing; protein function; protein synthesis; prototype; tool

Funding is requested to support a salary percentage for each Program Leader. Details included in each Program section.

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The mitotic spindle assembly checkpoint (SAC) is the only known checkpoint in mitosis. The SAC is composed of complex multi-signal transduction pathways that promote the proper segregation of chromosomes during cell division. As such, defects in the SAC result in chromosome instability (CIN), a hallmark of cancer. Of clinical importance, apoptosis caused by mitotic catastrophe depends on the activation of SAC. However, our knowledge of SAC signaling is far from complete, and the functional cross-talk between SAC activation and the induction of mitotic apoptosis is poorly understood. This makes it difficult to explain the mechanism by which cancer cells respond or become refractory to anti-mitotic drugs, e.g. taxol, that induced spindle-damage or mitotic catastrophe. Therefore, it is highly important to understand both the molecular mechanism by which SAC (i) controls proper chromosome segregation to maintain chromosome stability during cell division and (ii) elicits an apoptotic response in mitosis to anti-mitotic cancer therapeutic drugs. Specific Aims 1. Determine the molecular mechanisms by which the SAC-machinery controls SAC signaling and SAC-mediated mitotic cell death. a. Identify the protein components in the SAC machinery that are required for SAC-dependent mitotic cell death. b. Identify the signaling proteins that interact with the protein components in the SAC machinery that are required for SAC-dependent mitotic cell death. c. Identify the mechanism by which these signaling proteins control SAC signaling and elicit mitotic cell death.

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Spredl, Sprouty related with an ENA VASP homology domain, appears to be an antagonist of the Ras/MAPK pathway, although how it inhibits the pathway is uncertain. Completing a tandem affinity purification of Spredl, followed by mass spectrometry, will allow us to uncover novel binding partners of Spredl that may play a role in the inhibition of the Ras/MAPK pathway.

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. CD133 is a pentaspan membrane glycoprotein with homology to mouse Prominin. It was initially identified as a stem cell marker on a subset of CD34+ cells by the monoclonal antibody AC133. CD133 is over-expressed in glioblastoma, leukemia, prostate and colon cancers. The mechanism by which CD133 confers tumorigenesis is not understood. The open reading frame of human Prominin-1 predicted a protein of 865 amino acids with a molecular weight of 96.8 KD. The antibody, however, recognizes a 120KD single band on an SDS gel consistent with protein glycosylation. The CD133 transcript is expressed in a variety of tissues, with the highest expression being in kidney, pancreas and placenta. A single nucleotide deletion at position 1878 of human Prominin-1 which results in premature truncation of the protein, has been identified in human retinal degeneration, an autosomal recessive disorder (Maw, et. al. 2000). The localization of CD133 in the protrusions of plasma membrane suggests a role in cell polarity, migration, and interaction of stem cells with neighboring cells and/or extra-cellular matrix. Using Tandem Affinity Purification (TAP) and mass spectroscopy, we hope to identify binding partners of CD133 in order to understand signaling events downstream of CD133.

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Work in our lab involves using adenovirus as a potential oncolytic agent, as well as a tool to study regulation of translation in mammalian cells. The prototype of adenoviral oncolytic therapy is a mutant adenovirus -ONYX-015- which was designed to replicate in tumor cells but not in normal cells. However, in certain tumor cells, 0NYX-015 fails to replicate and this was shown to be because it fails to express the L4 100K protein, which is involved in inhibition of host protein synthesis and specific translation of late viral messages, a process which is critical for a productive adenovirus infection. Therefore, I study the mechanism by which L4-100k is regulated, and how this protein mediates host protein synthesis shutoff. It is a multifunctional protein, has RNA binding activity and is known to bind to the Translation initiation complex and prevent cap-dependent translation of cellular messages, thus promoting virus-specific translation which can occur in a cap-independent manner. This part of the project, which involves TAP purification and Mass spec, aims at identifying novel cellular partners of 100k, which is key to understanding the function of this protein and should give us more insights into how to design more effective oncolytic vectors, and may provide insights into the mechanism of translational control in mammalian cells.

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The Ras signaling pathway plays a crucial role in regulating cell growth and tumorigenesis. Ras is a member of a sub-family of related GTPases that functions by regulating a variety of downstream targets of effectors. Based on sequence homologies in the Ras Association domain, we have identified serveral new Ras family GTPase effectors and confirmed that these new proteins can interact with Ras when in its active, GTP-bound state. Very little, if anything, is known about these new Ras effectors. As a way of getting some insight into their function and mechanism of action, we are trying to identify the proteins they interact with within the cell. We have used the Tandem Affinity Purification (TAP) methodology to express and purify from colon cancer cells TAP-tagged versions of these new Ras effectors. After separation of the protein complexes by gel electrophoresis and coomassie blue staining, we can visualize several co-purifying protein bands that we would now like to identify by mass spectrometry.

Program Planning and Evaluation helps Cancer Center Leadership chart the course of the Cancer Center, making it an integral part of meeting the Cancer Center's primary objectives. Program Planning and Evaluation funds are used to support the Cancer Center's External Advisory Board, individual Program Retreats and quarterly Cancer Center Leadership Retreats. The advisory boards and committees provide key input on all matters regarding research and management, including the development of new Cores, the strengthening of affiliations with other research institutions, and the facilitation of minority and community outreach efforts. Recent accomplishments of the External Advisory Board include providing a review of the Investigational Trials Resource and Translational Informatics Initiative, and evaluating and making recommendations relating to the Center's Programs. By building partnerships that address the needs of communities in Northern California, the Community Advisory Board has recommended initiatives that challenge cancer care-related barriers and reduce cancer-related disparities. Cancer Center Leadership Retreats help integrate the Cancer Center's community of investigators by providing forums for information sharing and idea exchange. Through the retreats, the Cancer Center has identified current strengths, scientific areas that could be developed, and potential new collaborations.

The Neurologic Oncology Program (Program) is a collection of 17 basic scientists, neuro-oncologists, and neurosurgeons who take a team approach to the improvement of brain cancer therapy. The Program, which has been in existence since the inception of the Helen Diller Family Comprehensive Cancer Center (Center), has as its three programmatic themes: to better understand the underlying biology of brain tumors, to use that information to better predict disease occurrence and outcome, and most importantly, to improve brain tumor therapy. The 17 members of the Neurologic Oncology Program are drawn from seven different UCSF departments, and represent a truly interdisciplinary team. The NCI and other peer-reviewed support for this group of investigators for the 2010-2011 academic year totaled over $23,377,244, including funds to support a P01, T32, and SPORE grants, all specifically designed to pursue and encourage translational brain tumor research. This group of investigators is both highly productive and interactive, as witnessed by the 437 publications of the group in the previous funding period; the multiple publications of the group in leading journals such as Nature, Science, Cancer Cell, Nature Medicine, Nature Genetics, and Neuron; and the high percentage of intra-programmatic (32%) and inter-programmatic (31%) publications. The clinical portion of the Program has been successful developing early phase investigator initiated therapeutic studies and bringing these to the clinic for testing, with particular emphasis on SPORE related clinical trials. The broad range of publications covering population science, cell signaling, genomics, imaging, and clinical science, as well as the high percentage of intra- and inter-programmatic publications, are the result of a strategically Integrated, highly interactive, diverse, and productive Program that continues to make significant progress in reaching its stated goals.

The goal of the Pediatric Malignancies Program (Program) is to improve, the outcome for children with cancer through basic and clinical translational research. Pediatric cancers are unique in their morphology, tissues of origin, and behavior. They provide an opportunity to understand the link between normal development and the aberrant signaling networks of childhood malignancy; to discover through these genetic networks new therapeutic targets; and then integrate these into innovative clinical trials. The molecular studies will also lead to new understanding of the interactions of genetics and environment in cancer development and the late effects of treatment, thus improving the outcome for survivors of pediatric cancer. Our integrated research program provides a forum through which insights into childhood cancer can inform trainees, health care professionals, patients and the public. The main research themes of the Program focus particularly on the common childhood tumors, neuroblastoma, brain tumors, leukemias, and sarcomas; and translating our molecular and genomic studies into developmental therapeutics in these cancers (prioritizing PISK, RAS and MAPK signaling as areas where we have strong collective expertise), and understanding the late effects and epidemiology of childhood cancer in order to improve survival and quality of life. The Program has 18 members from six different departments. The Program is enhanced by close synergy with Helen Diller Family Comprehensive Cancer Center (Center) Programs such as Hematopoietic Malignancies, Neurologic Oncology, Developmental Therapeutics, Cancer Disparities, and Tobacco Control, as well as many interactions with scientists in basic science programs, such as Cancer Genetics and Cancer, Immunity, and the Microenvironment, and with essential use of the Center Cores such as Clinical Research Support Office, Laboratory for Cell Analysis, Preclinical Therapeutics, and Genome Analysis. The Program has $8,789,236 total peer reviewed support for the last budget year. The Program has 20% intra-programmatic and 36% inter-programmatic publications.

DESCRIPTION (provided by applicant): Currently, enormous volumes of data are being generated by the comprehensive molecular characterization of a number of human tumors. The ability to effectively and efficiently use RNAi to assess the biologic consequences of gene target inhibition is of critical importance to understanding gene function and to uncover tumor-specific vulnerabilities. The identification of tumor-specific vulnerabilities provides rationale for the development of biologically-based targeted therapies. RNAi screening is a powerful technology for high- throughput gene function discovery that has been used to identify tumor-specific vulnerabilities. However there are significant limitations to the RNAi screening resources that are currently available. The RNAi screening tools used to date do not efficiently target the full compendium of cancer relevant genes due to technological limitations in genome coverage and RNAi gene knockdown efficacy. These technological limitations also lead to false-positive and false-negative screen hits. Thus, currently available RNAi screening platforms are not cost-effective for performing high-throughput screens for most labs. Here we present technologies and resources that overcome these limitations, dramatically improving RNAi screening capabilities. We take advantage of statistically-based analyses and the power of new deep sequencing technologies that are being rapidly democratized. Our new approaches will greatly facilitate the development of cancer polytherapies, opening a new paradigm for rationally-based cancer therapeutics that fully capitalize on genomic profiling of human tumors. In order to design effective combination cancer therapies (polytherapies) we must first identify the signaling pathways that act synergistically to promote tumor growth or therapeutic resistance. This knowledge then enables the design of therapies that target these key cancer driver pathways. A major obstacle to the development of therapies that preclude or overcome resistance to targeted cancer therapy is that there is no systematic means by which to identify pathways that functionally cooperate and synergize to drive tumor growth or therapeutic resistance. Therefore, the search for effective cancer polytherapies has been done largely in an ad hoc manner exploring only a very limited number of potential combinations. The key to rationally designing an optimal combination of therapies lies in the systematic identification of pathways that when targeted, lead to specific and synergistic destruction of cancer cells. Our new approaches can determine simultaneously and rapidly (within 1-3 weeks) high precision measures of functional genetic interactions between large numbers (typically 100,000) pairs of shRNAs that target genes of interest in the context of any cancer. This represents a transformative technology in terms of our ability to systematically uncover cancer- relevant gene interaction networks that drive tumor growth and that potentially can be exploited as rational, tumor-specific polytherapies.

The Preclinical Therapeutics Core (Core) provides in vivo services to UCSF Helen Diller Family Comprehensive Cancer Center (Center) investigators. Offering a variety of tumor engraftment-based cancer models for use in preclinical oncology trials, the Core provides a complete set of services that include consultation regarding experimental design, tumor cell culture and implantation in mice, administration of experimental agents, monitoring of tumor burden and response to therapy, and interpretation of study results. The Core maintains a cryorepository of commonly used human cancer cell lines derived from multiple tumor types along with data regarding their in vivo growth characteristics, as well as a collection of patient-derived tumor xenograft models. The Core's offerings also include pharmacological analysis and optimization of novel agents such as compound formulation, pharmacokinetics (PK), pharmacodynamics (PD), and safety-toxicity analyses. The Core is also a resource of expertise in small animal survival surgery, and is available to provide training in these techniques on a recharge basis. Although the Core primarily functions to test experimental anti-cancer agents in vivo, it also provides animal models of human cancer for use in novel diagnostic, tumor imaging, and basic mechanistic research. The Core oversees, maintains, and provides as a service a number of small animal imaging technologies housed within the barrier facility. The availability of centralized cell and animal resources, together with personnel with expertise in conducting preclinical studies, ensures appropriate experimental design and reproducibility, compliance with local and federal regulatory guidelines for tumor-bearing animals, and maximum resource utilization through coordinated animal purchasing and housing.

The Prostate Cancer Program (Program) of the UCSF Helen Diller Family Comprehensive Cancer (Center) is a multidisciplinary group of investigators focused on understanding the core biology that drives the clinical behavior of prostate cancer across the full spectrum of the disease. The Prostate Cancer Program comprises 25 basic and clinical scientists from nine departments working together to translate research into advances in the epidemiology, prevention, staging, and treatment of prostate cancer. Program faculty represent membership in five graduate programs: Program in Biological Sciences (PIBS); Biomedical Sciences (BMS); Bioengineering, Pharmaceutical Sciences and Pharmacogenomics (PSPG); and Chemical Biology. The goals of the Program are to promote interdisciplinary research that will allow a better understanding ofthe biology of prostate cancer from the biologic and environmental factors associated with carcinogenesis, through the early detection and disease progression to prognostication, and the biologic basis of disease progression. The ultimate goal is the development of novel intervention strategies that will improve the lives of men who carry a diagnosis of prostate cancer or who are at risk of developing prostate cancer. The Prostate Cancer Program pursues these goals through ongoing work in four major thematic areas: (1) Risk and Oncogenesis; (2) Prognosis and Progression; (3) Biology and Therapeutic Targets; and (4) Disparities, Health Related Quality of Life (HRQOL), and Outcomes. The Program has $9,667,568 in total peer reviewed support for the last grant year. The Program has 16% intra-programmatic and 13% inter-programmatic publications.

The Protocol Review and Monitoring System consists of two main elements: the Program Site Committees and the Protocol Review Committee (PRC). Funding is requested for salary support for the Protocol Review Committee Chair, the PRMS & Policy Administrator and the Protocol Review Committee Administrator.

Protocol-Specific Research Support funds are requested to cover salary support for a core group of research nurses and data managers for conduct of high priority, innovative, feasibility and phase I institutional clinical research protocols. Staffing for pilot, feasibility, phase I studies is based on the complexity of the study itself and the increased regulatory requirements for reporting of adverse events.

The UCSF Helen Diller Family Comprehensive Cancer Center is requesting funding for partial salary support for Staff Investigators who lead key research initiatives within the Center that are not reflected elsewhere within the programmatic structure. The five Staff Investigators (Coordinators) were chosen for their expertise and leadership qualities. Our Coordinators join the rest of the Center leadership in our quarterly Center Leadership retreats.

The Tissue Core (the Core) provides both tissue collection and analytic services, and sets the standards for the use of human tissue across all research programs at the UCSF Helen Diller Family Comprehensive Cancer Center (Center), including those that have separately managed tissue-collection efforts. In this latter function. Tissue Core provides oversight and guidance for common issues including tissue consent, standard operating procedures, databases, and quality control (QC). The Core provides tissue-banking services, partially supported by recharge to user programs, including procurement, annotation, processing, storage, tracking, and distribution. Several programs provide direct financial support for Core staff for this purpose. The Core acts as the central hub for the collection of fresh surgical tissue from the hospitals at the Mt. Zion and Moffitt-Long (Parnassus) campuses for those programs without their own tissue- collection efforts. The Core supports the processing, storage, and distribution of blood from patients at UCSF and other sites. In addition, the Core collects, and manages solid tissue from patients at hospitals offsite for several clinical efforts. The Core offers routine histology services, including sectioning, staining, histologic interpretation, and tissue microarray preparation. Distribution of banked material requires approval by the Institutional Review Board (IRB), and by the appropriate programmatic Tissue Utilization Committee.

The Tobacco Control Program (Program) is the focal point for University of California, San Francisco (UCSF) scientists in disciplines ranging from the molecular biology of nicotine addiction through political science. These scientists combine their efforts to eradicate the use of tobacco and tobacco-induced cancer and other diseases worldwide. A strong theme is that science-driven policy and public health interventions are key to ending the tobacco epidemic, as well as biological and clinical science. The role of the tobacco industry has been an important focus. The specific scientific goals are to conduct clinical and laboratory investigations of the mechanisms of nicotine addiction; to further understand the effects of tobacco use and exposure to second-hand tobacco smoke, including genetic studies and investigations of racial and ethnic differences in measures of tobacco exposure and tobacco-related diseases; to develop and test innovative interventions for tobacco users, especially those in high-risk populations, including youth, individuals co-morbid with mental and substance abuse disorders, chronic smokers, and ethnic minorities; to provide estimates of the economic costs of tobacco use to society and the corresponding benefits of tobacco control programs; to conduct research on tobacco related policy and to continue to study the effects of the tobacco industry, both nationally and internationally, on tobacco use; and to better describe populations with high smoking rates, both in this country and internationally. Rather than being distinct areas of work, these investigations often interact with, and benefit from each other, spanning multiple disciplines. The expertise inherent of the Program membership supports the accomplishment of these goals. Tobacco Control Program work is grouped into five themes: (1) studies of nicotine and tobacco effects, metabolism and biomarkers, including second hand smoke; (2) clinical interventions; (3) the economics of tobacco control; (4) the tobacco industry; and (5) descriptive and epidemiological studies. Since the last competitive review of the Helen Diller Family Comprehensive Cancer Center (Center), the productivity of the Program has increased, new faculty have been mentored and added to the roster, and collaboration across disciplines is increasingly evident. The Program has 20% intra-programmatic and 10% inter-programmatic publications.

The aim of the Translational Informatics (Tl) core is to provide the Informatics infrastructure, and to develop, deploy and maintain data systems and applications that optimize the translation of basic scientific discoveries into clinical applications. Tl members are made up of experienced informaticians and clinical research support specialists and analysts with backgrounds in clinical data coordination, biomedical research, molecular biology, computer science, software engineering, and application architecture. The Tl core develops data systems that span a range of users, from individual investigators, to individual programs within the Cancer Center, and to the Cancer Center as a whole. Tl works with researchers, other Cores, and Cancer Center administration to fulfill its goals with the ability to provide customizable informatics solutions for all data needs. Over the next five years, Tl will continue to provide the Cancer Center members with Informatics and computational support for an array of activities, including continued participation in grant applications and expanding efforts as needed to respond to changing needs of funded grants. Tl priorities are to: 1) Access, training, and management of Clinical and Biomedical Software Tools 2) Provide access to Clinical and Biomedical Data for Research 3) Research Data Management Solutions including access to High Performance Compute Cluster and allocated software. Pathway analysis tools (IPA), and design of Data Collection Models 4) Biospecimen Data Management 5) Custom Research Software Development including user interfaces 6) Oversee and provide guidance for Research Data Privacy, Security, and Quality Control 7) Standardize and Harmonize Data Collection Vocabularies and Common Data Elements 8) Maintenance of databases. Patient centric data-warehouse, and associated web sites 9) Custom data services involving specific programming expertise for specialized databases

The Laboratory for Cell Analysis (LCA) is a core facility that provides cytometric support to the UCSF Helen Diller Family Comprehensive Cancer Center (Center). The LCA provides: ¿ access to flow and image cytometers, including cell sorters, confocal microscopes, digital pathology and laser microdissection systems, as well as technical support needed to make use of these instruments. ¿ education and hands-on training for students, staff, and faculty in cytometry technology and applications. ¿ expertise for the development of new cytometric assays, analytic software, and new instrumentation; as well as the interpretation and presentation of results. Instruments currently operated by the LCA include: four Becton-Dickinson (BD) FACS Aria systems with high-speed cell sorting, with minimally four laser excitation, ten detectors and single-cell cloning; two BD LSRII flow cytometers; a FACS Canto II; three bench-top flow cytometers; one Zeiss 510 Confocal Laser Scanning Microscope, with multi-photon lasers, spectral emission detection and live cell scanning capability; one Zeiss Spinning Disc Confocal system with TIRF; four digital video fluorescent microscopes with high resolution CCD cameras; a Nuance Spectral imaging system; a Zeiss PALM Laser Micro Dissection microscope consisting of a robotic cutting system with non-contact sample collection. A variety of computer software packages and platforms are available to collect and analyze acquired data along with links to offline databases and statistical processing routines for more advance processing. In addition, the staff of the LCA offers their expertise in the use of this technology as it applies to instrument support and biological applications for CC members. The LCA website is http://cancer.ucsf.edu/lca/index.php.

Cancer Center Administration provides the administrative management required to support the research operations of the Cancer Center. It is responsible for the following: ¿ Managing Cancer Center finances, including grants, contracts, institutional support, and philanthropic funds. ¿ Managing Cancer Center Support Grant programs and governance activities. ¿ Planning, evaluating and managing Cancer Center shared resources. Managing and allocating space, facilities and equipment. ¿ Providing decision support analysis and recommendations for strategic planning. ¿ Providing communications services, including public affairs, education and programmatic communications. ¿ Supporting the membership application and review process. ¿ Managing the Cancer Center administrative support staff. Funding is requested to cover salary and supply costs for this effort.

The Biostatistics and Computational Biology Core of the Cancer Center was established in 1994 with the goal of assuring appropriate biostatistical support to cancer-related research at UCSF. In 2011, at the suggestion of an external advisory board, the Core was split into two separate cores: 1) Biostatistics Core and 2) Computational Biology Core. This division was undertaken as a reflection of the distinct needs of projects focusing on clinical and laboratory studies involving standard statistical approaches and those involving genomics and requiring high performance computing services. Because some projects may require both types of support, the Cores are closely coordinated. There is no overlap of services provided by each core, and funding is not duplicated for the same services in two cores. The major functions of the Biostatistics Core include: (1) Consultation services for experimental design and data analysis for clinical, epidemiological and laboratory studies conducted through the Cancer Center; (2) grant development services, including experimental design, sample size planning, preliminary data analyses and writing; (3) support for protocol review and data safety monitoring for proposed and ongoing studies through PRMS and DSMC; and (4) education, in both formal and informal settings. The Core provides partial support to nine statisticians (seven UCSF faculty, two are UCSF staff) who provide the extensive breadth of expertise required for Cancer Center projects. CCSG support pays for consulting and grant development services provided to Cancer Center researchers, protocol review services in PRMS and DSMC. CCSG support provides from 25 - 30% salary support for the faculty statisticians. Each statistician has the remainder of their support provided through scientific collaborations with other Cancer Center investigators, from grants for their own research, and from direct support from the Departments in which they work.

The Breast Oncology Program (Program) is comprised of 39 Program Members from 13 different UCSF departments. The Program supports and stimulates basic, clinical, and population research in breast cancer and facilitates the translation of these findings into improved cancer management and control. The Program's themes are as follows: (1) epidemiology and etiology; (2) cancer prevention, risk models, and early detection; (3) genetics and biology of cancer progression; (4) new therapeutic targets and approaches; and (5) outreach, clinical care delivery, and outcomes. Research in the Program is supported by the Bay Area Breast Cancer SPORE, eight large multi-disciplinary, multi-institutional projects that support work in one or more themes, a multi-campus University of California Office of the President sponsored ATHENA Breast Health Network integrating clinical care and research by numerous individual investigator-initiated grants. Since the last competitive renewal much effort has been dedicated towards investigator initiated therapeutic trials, innovative companion diagnostic clinical trials, testing new radiation oncology treatment delivery systems including correlative science, as well as establishing a CLIA-compliant testing laboratory and an integrative bioinformatics and IT infrastructure. The Program has become more cohesive, has a high level of interaction that has led to new grant funding with joint program and project leaders and co-investigators across disciplines. Interactions between Program members are encouraged in several discussion forums, including a weekly multidisciplinary seminar, an annual retreat, a weekly tumor board, a bi-weekly breast site study review meeting, a monthly community forum, and a patient-physician management discussion series. The Program has $22,189,900 total peer-reviewed support for the last budget year. The Program has 17% intra-programmatic and 17% inter-programmatic publications.

The goal of the Cancer Disparities Program (CD) is to foster and sustain an integrated transdisciplinary environment for dedicated multi-level and multi-ethnic cancer disparities research that studies mechanisms and interventions from prevention through survivorship. The Program research emphasizes disparities affecting the region's largest ethnic populations, Latinos and Asians, engages intensively with the African American community, and includes other groups that are affected by disparities such as those who have limited English proficiency. Based on a shared understanding of the multi-level nature of these disparities and the interventions to reverse their course, the Program themes are: (A) Biologic determinants of cancer disparities; (B) Individual behavioral/psychological factors, emphasizing culture, language, and social context; and (C) healthcare and other systems factors, including interventions for systems change to reduce cancer disparities. CD is led by Dr. Rena Pasick, whose career has been dedicated to conducting social and behavioral research in cancer disparities among multi-ethnic populations, and to training a diverse cadre of cancer disparities population scientists; and Dr. Tung Nguyen, a clinician researcher with scientific expertise in Asian American cancer disparities and community-based participatory research. The Program has 24 members who have published 399 peer-reviewed papers in the past five years; 15% were intra- and 16% were inter-programmatic publications. Annual extramural funding (total costs, 2010) is $10,476,370 in peer-reviewed support, nearly double the amount at the last review; total non-peer reviewed support is $1,631,255. The Program also adds value to the Helen Diller Family Comprehensive Cancer Center (Center) by bringing expertise in diverse populations to clinical programs; by connecting community members and clinicians; by fostering the intra-programmatic and inter-programmatic collaborations that advance knowledge in cancer disparities; and by conducting significant and successful training programs to increase the number of researchers who are under-represented minorities. Future directions include expansion of the Program via new and continuing multi-component grants, addition of members through recruitment and advancement of junior faculty, increased collaboration with clinical programs, and development of a multi-cultural communication shared resource.

Cancer is a complex disease with a range of genetic, genomic, and environmental factors that can impact disease development, progression, and response to therapy. These factors exhibit broad heterogeneity: large variations are seen between individuals in germline DNA sequence, tumor genetics, or histological subtypes, and environmental exposures. A high level of complexity is seen in the patterns of inherited genetic variants (SNPs) in the normal host DNA, and in the combinations of somatic genetic events and gene expression changes in tumors. In addition, complex interactions exist between the genetics of the host and environmental exposures that contribute to tumor susceptibility. The overall goal of the Cancer Genetics Program (Program) is to elucidate the genetics of tumor susceptibility, tumorigenesis, and progression; and to use this information clinically to improve cancer management. The central themes of the Program that we aim to further develop in the next five years are: (1) Genetics of Cancer Susceptibility, Progression, and Response; (2) Cancer Genome and Epigenome; (S) Functional Genomics; and (4) Systems Genetics of Cancer. The Program brings together experts in the application of advanced genomic and genetic analysis tools to identify abnormalities that contribute to cancer genesis and progression by utilizing the outstanding mouse and human genetic resources at UCSF. There are 24 members in the Program, and they represent 12 Departments from the Schools of Medicine and Pharmacy at UCSF. The NCI and other peer-reviewed support among Program members during the last budget year was $13,592,313, in total. Since 2007, 492 total papers were published by members of the Program, with 12 percent intra- and 33 percent interprogrammatic. Program members are fully integrated into the organ site-specific programs, and participate broadly in seminars, and discussion groups organized by the Program; and in conjunction with other research programs (e.g., the Cancer Genetics Risk Program, and the Human Genetics Program). Ultimately the Program aims to encourage and support cross-cutting research that encompasses both germline and somatic approaches to deciphering the genetic basis of cancer.

Cancers are composed of multiple cell types, including fibroblasts and epithelial cells; innate and adaptive immune cells; and cells forming blood and lymphatic vasculature; as well as specialized mesenchymal cell-types unique to each tissue microenvironment. While tissue homeostasis is maintained by collaborative interactions between these diverse cell types, cancer development is enhanced when genetically altered initiated cells harness these collaborative capabilities to favor their own survival and, in so doing, hijack or exploit normal physiological processes typically involved in maintaining tissue homeostasis. While previously supporting research programs focused solely on cancer and immunity, the expanded Cancer, Immunity, and the Microenvironment Program (Program) now supports research programs revealing insights into the interactions between evolving neoplastic cells with activated non-neoplastic host cells, and with soluble or insoluble components of extracellular matrix, as well as studies based on these interactions that foster development of novel cellular or molecular-based strategies to combat cancer. Specific scientific goals of the Program include: (1) to explore the relationship between neoplastic cells and stromal cells (i.e., immune, vascular, and mesenchymal) in mouse models of cancer to gain insights into the ability of stromal cells in the tumor microenvironment to promote or deter tumorigenesis; (2) to identify molecules and pathways in the tumor microenvironment that regulate anti-tumor activity; (3) to study the relationship between viral infections and malignancy, particularly in immunodeficient patients with HIV infection, and to develop new approaches for the prevention and treatment of malignancy in this population; and (4) to provide the basic scientific foundation and support for the application of new immune- or microenvironment-based therapeutics in cancer in conjunction with the organ-based Helen Diller Family Comprehensive Cancer Center (Center) Programs. With these expanded goals, the retooled Program grew to 27 faculty representing 13 departments in the School of Medicine. Faculty in the new Cancer, Immunity, and the Microenvironment Program are supported by $16,323,690 in NCI and other peer-reviewed grants per year, and published 612 scientific articles in the previous funding cycle. The Program has 6% intra-programmatic and 21% inter-programmatic publications.

The specific objectives of the Clinical Research Support Office (CRSO) are to: ¿ provide streamlined protocol development, activation and implementation, and reduce the time to protocol activation ¿ increase the quality and quantity of investigator-initiated clinical trials and facilitate the translational research efforts of the Center by providing assistance in protocol development, implementation and data capture ¿ provide infrastructure for the conduct of early phase clinical trials ¿ provide a central core of personnel with expertise in all types of clinical trials management including protocol development and trial design, regulatory, compliance, and financial management ¿ provide central oversight of research personnel (clinical research coordinators and data managers), including initial and ongoing training, education, monitoring, and mentorship ¿ serve as the central office of record for all clinical trials conducted at the HDFCCC ¿ increase the participation of volunteer subjects in clinical trials with an emphasis on diversity ¿ seamlessly integrate informatics and biostatistical support provided by the Biostatistics and Translational Informatics Cores, including ensuring access to and training for a web-based protocol, data capture, and management system managed by the Translational Informatics Core The Clinical Research Support Office serves as the Office of Record and comprises several units, including the Early Phase Clinical Trials Unit, the Finance Unit, the Protocol Development and Regulatory Unit, and the Research Personnel Unit. These units work together to provide oversight, infrastructure support and quality control for the Center's entire clinical trials effort.

The Biostatistics and Computational Biology Core of the Cancer Center was established in 1994 with the goal of assuring biostatistical and computational biology support to cancer-related research at UCSF. In 2011, at the suggestion of an external advisory board, the Biostatistics and Computational Biology Core was split into two separate cores: 1) Biostatistics Core and 2) Computational Biology Core. This division was undertaken as a reflection of the distinct needs of projects focusing on clinical and laboratory studies involving standard statistical approaches and those involving genomics and requiring high performance computing services. Because some projects may require both types of support, the Cores are closely coordinated. There is no overlap of services provided by each core, and funding is not duplicated for the same services in two cores. The Computational Biology Core provides partial support to six computational biologists, biostatisticians, and programmers, half of whom are UCSF faculty, who together cover the extensive breadth of expertise required for Cancer Center projects. The Core has the expertise to support genomics, proteomics, and all other types of omics, as well as network and pathway analysis. The core works with many types of data including microarray data, second generation sequencing data, and other types of high-throughput data. The Core provides services on a charge back basis, as collaborators on grants, or without charge when developing research projects for grant funding. One major goal of the Core is to assure that novel analytical approaches developed in one project are rapidly available to all Cancer Center investigators. The five major functions of the Computational Biology Core within the Cancer Center are: (1) scientific consultation for problems relating to computational biology; (2) data analysis for such projects; (3) grant development, including design of experiments, initial data analyses and writing; (4) education, in both formal and informal settings; and (5) software development and training. Core personnel also perform computational biology research within the context of Cancer Center projects, or on projects for which they have obtained independent funding.

Data and Safety Monitoring at the Helen Diller Family Comprehensive Cancer Center is overseen by a Data and Safety Monitoring Committee (DSMC), and conducted by a group of monitors and auditors within the Center. The DSMC and monitors are responsible for several activities related to the implementation of the Center's NCI-approved Data and Safety Monitoring Plan (DSMP). Data and Safety and Monitoring functions within the HDFCCC include 1) the conduct of internal audits of protocols; 2) evaluation of the results of both internal and external audits of protocols, including those conducted by the NCI Cooperative Groups, other consortia, and CTEP; 3) review and approval of any cohort dose escalation decisions on UCSF Institutional Phase I studies; 4) review of interim analyses for institutional studies; 5) evaluation and addressing of any concerns with regards to safety, or related study design and stopping rules, raised by principal investigators, site committees, the Protocol Review Committee (PRC), or Institutional Review Board (IRB); 6) oversight of toxicity and Serious Adverse Events (SAEs) reported by each site committee; 7) development and updating of the DSMP and guidelines for its use; 8) communication of findings and recommendations with key stakeholders, including the PRC, IRB, and leadership of the Center; and 9) closure of studies for noncompliance or safety issues.

The Cancer Center is requesting Development Funds to support recruitment, pilot projects, and two developing Cores. The projects and Cores will strengthen the Cancer Center by addressing specific research needs, increasing its value to the local community, and promoting collaboration among investigators. ¿ Recruitment: We are requesting funds to facilitate key appointments in collaboration with departments over the next five years. ¿ Pilot Projects: We are requesting funds to support a multi-investigator pilot project award on an annual basis. ¿ Developing Cores: We are requesting funds to support two developing cores: Investigational Pharmacy and Pharmacogenomics.

The Developmental Therapeutics Program evolved from the more basic Cell Cycling and Signaling Program, which scored Outstanding in prior renewal cycles ofthis Helen Diller Family Comprehensive Cancer Center support grant. The research themes ofthe Cell Cycling and Signaling Program were related to identification and validation of therapeutic targets. Many of these targets have subsequently moved into preclinical testing or are ready to be explored in early-stage clinical trials. The new Eariy Phase Clinical Trials Unit has created an ideal opportunity to translate these themes effectively, through the design and analysis of innovative research protocols. The Program comprises 32 members involving 13 different departments and brings together basic cancer biologists and physician scientists with the common goal of discovering and testing novel compounds and treatment strategies for cancer The Program themes are: 1) Targeting signal transduction pathways (RTKs, RAS, RAF/MAPK, Pl 3' kinase, and wnt) 2) Targeting DNA replication and genome integrity (cell cycle, telomerase, HDAC) 3) Angiogenesis 4) Apoptosis 5) Genetic determinants of sensitivity and resistance The wide range of expertise ofthe Program members will mutually enrich and complement the discoveries of individual investigators with the overall Program goal being to accelerate the transition from drug discovery to the approval of more effective and less toxic drugs for patients with cancer. Research in the Program spans from drug discovery, cell signaling, molecular pathology and bioimaging to pharmacogenomics, as well as clinical and population science with recent high impact publications in Nature, Nature Medicine, Nature Genetics, New England Journal of Medicine, Journal of Clinical Oncology, Journal of Biological Chemistry, JAMA, Proceedings of the National Academy of Science of the United States, and The Lancet. The Program has a sizable and increasing percentage of intra- and inter-programmatic publications, which reflect the thematic breadth of the work and the emerging efforts of strategic integration of its members. The Program had $7,271,609 total peer-reviewed support for the last budget year. The Program has 12% intra-programmatic and 13% inter-programmatic publications.

The Genome Analysis Core (GAC or the Core) provides services, advice, and instrumentation for genotyping, gene expression, and epigenetic (methylation) analysis. Using two main platforms, the Sequenom MassArray and the AB 7900HT Real-Time QPCR instrument, the Core provides a variety of services at the low- to medium-throughput level important for understanding the genetics of cancer. Genotyping and mutation analyses of single nucleotide polymorphisms (SNPs) using the Sequenom MassArray are instrumental in helping scientists determine causative mutations in the germline or somatic genes, which lead to certain cancers or human diseases. Methylation analyses provided by the Sequenom MassArray assist in understanding the control of gene expression in tumor progression. A major focus of the Core's services is the use of quantitative real-time PCR (QPCR) on the 7900HT platform. Using a repository of TaqMan assays, the Core provides services for DNA copy number measurements, mRNA and miRNA expression analyses, plus training courses for members of the Helen Diller Family Comprehensive Cancer Center (Center) to learn QPCR techniques. Besides full-service options, most instrumentation is available for independent use by investigators The Center GAC works to improve access by Center members to genetic and genomic technologies. The services we offer, or propose to develop, are actively coordinated with the other UCSF genomics core facilities to avoid detrimental duplication of capacity. For example. Center members have access to extensive high throughput gene expression, genotyping, and sequencing technologies (Affymetrix and Illumina) through Core facilities at UCSF's Parnassus and Mission Bay campuses.

The Hematopoietic Malignancies Program of the UCSF Helen Diller Family Comprehensive Cancer Center includes 18 members from eight academic departments. The Program is built upon extraordinary institutional strengths in basic and population sciences, outstanding clinical programs for the care of patients with leukemia, lymphoma, and myeloma; and a tradition of cross-disciplinary collaborations in scientific investigations. The Program activities comprise two broad themes: (1) Hematopoiesis and Myeloid Leukemogenesis; and (2) Lymphoid Growth Control and Lymphoid Malignancies. Within these major themes the Program has established a highly interactive interdisciplinary approach that includes efforts directed at: gene discovery; modeling leukemia and lymphoma-associated genetic lesions in the mouse; characterizing signal transduction pathways that are crucial for cellular growth control; testing experimental therapeutics with molecular analysis to ascertain mechanisms of drug action and drug resistance; and defining environmental risk factors that contribute to the development of hematologic cancers. The NCI and other peer-reviewed support for this group of investigators for the 2010-2011 academic year totaled $4,541,421. The Program has 9% intra-programmatic and 12.5% inter-programmatic publications.

The Mission of the Immunohistochemistry and Molecular Pathology Core (the Core) is to facilitate education, development, and application of immunohistochemistry, immunofluorescence, and molecular pathology tools for the UCSF Helen Diller Family Comprehensive Cancer Center (Center) members. The Core will: 1. Develop immunohistochemistry (IHC), immunofluorescence (IMF) and in situ hybridization (FISH) based assays for new antibodies and genetic loci in collaboration with Center members. 2. Perform routine immunohistochemical analyses of animal and human tissue sections and cell lines. 3. Perform IHC and IMF analysis of tissue arrays produced by the Center's Tissue Core. 4. Perform FISH analyses for DNA copy number in cell lines, animal models, and human tumors. 5. Collaborate with Center members in microdissection, and extraction of DNA and RNA from tumor sections. 6. Perform genomic mapping onto metaphase chromosomes of human and mouse DNA clones The Core will work closely with other Cores (particularly the Tissue, Genome Analysis, and the Laboratory for Cell Analysis Cores) to allow research protocols to take advantage of the resources and expertise offered within each Core.

The mission of the Mouse Pathology Core (the Core) is to provide histologic and hematopoietic research support services to UCSF Helen Diller Family Comprehensive Cancer Center (Center) investigators studying the pathogenesis and treatment of organ and hematologic malignancies in mouse models of human cancer. This facility provides services for members of many of the Center's programs. Histology services performed by the manager and staff include processing, embedding, and histologic sectioning of murine tissues in paraffin and frozen blocks (with re-embedding of tissue as necessary); routine histochemical staining (hematoxylin and eosin); and other special histochemical stains. In addition to providing both training on and access to the equipment utilized for pathologic analysis of murine tissues, the Core also conducts a mouse pathology workshop that provides training in necropsy, dissection, tissue trimming, and sectioning techniques. Furthermore, the Core provides expertise in murine hematology. Complete blood counts are provided for investigators, including preparation of blood smears for analysis of white blood cell, red blood cell, and platelet morphology. Another service provided by the Core is access to outside veterinary laboratory testing (e.g., serum chemistry assays). The Core also facilitates pathologic consultation for researchers provided by the Co-Directors, Drs. Coussens and Kogan. Offering consultation with the Co- Directors makes available the same expertise an in-house murine pathologist would provide, including aid in planning experiments, and expertise in data analysis at a greatly reduced cost to the organization. The Core was used by laboratory personnel representing approximately 50 different investigators at the Center, providing a total of 8533 units of service during the most recent 12 month period (January 2010 through December 2010). Investigators in many of the Center programs have relied upon the Core not only for direct services, but also for training of their personnel. Demonstration of the utility and expertise of the Core is evident by extensive publications reflecting use of mouse models of human cancer by investigators that utilize this service.

DESCRIPTION (provided by applicant): The 2009 Tobacco Control Act Tobacco gave the Food and Drug Administration (FDA) regulatory authority over tobacco products. One of the first actions of the FDA, under this law, was to develop graphic warnings to appear on cigarette packaging. Tobacco companies challenged the new warnings as a violation of their first amendment rights, and the court ruled for tobacco in R.J. Reynolds v. FDA. The ruling found that available research did not show that graphic warnings placed on cigarette packs were associated with changes in tobacco use behavior. This is because, in part, experimental research to date has relied on onetime exposure to graphic labels, and these paradigms are too brief to measure change in tobacco use behavior. This application develops and tests an experimental approach that simulates real-world and prolonged exposure to FDA graphic warnings. In collaboration with a large community-based behavioral health provider, smokers are recruited from three residential addiction treatment programs. Key features of residential treatment are: a concentration of smokers, daily patient contact in which experimental labels can be affixed to the patient's own cigarette packs, ability to observe changes in smoking behavior. The project creates the 9 approved FDA warnings using adherence paper and measures behavioral and communication impacts associated with prolonged exposure to the warnings. The design is a sequence of off-on-off-on recruitment periods, each lasting 4 months, during which participants are either exposed to transparent labels (attention control condition) or to graphic warnings (experimental condition) on their own cigarette packs. 450 smokers will be enrolled, evenly distributed across conditions. For each participant there is a baseline interview, a 30 day exposure period (to transparent or graphic labels) and a follow up interview. Behavioral measures include intent to quit, quit attempts, cigarettes per day, and initiation of cessation services. Communication measures include tobacco risk perception, impacts of cigarette pack warnings, and thoughts about abstinence. The general hypothesis is that persons exposed to graphic labels, compared to those in an attention control condition, are more likely to change smoking behavior. The short term goal is to test an original experimental approach that will improve understanding of how graphic labels affect smoking-related behavior. The long term goal is to provide scientific information in support of the FDA regulatory mission.

? DESCRIPTION (provided by applicant): We propose three related area of research, each focused on a major aspect of Ras signaling. The first attempts to solve an important question relating to the NF1 gene, now recognized as a major tumor suppressor in human cancer as well as genetic basis for neurofibromatosis, a disease that affects 1 in 3500 people worldwide. Using biochemical approaches as well as cell-based screens, we will try and identify proteins or other cellular factors that regulate neurofibromin's ability to regulate Ras. Recently, we identified the first bone fide neurofibromin binding proteins other than Ras, the Spred proteins that are essential for neurofibromin's activity. We will build on this discovery to determine how the neurofibromin/Spred complex is assembled and regulated, and, in addition, we will perform unbiased screens for factors that regulate Ras through neurofibromin, or regulate Ras-independent functions of this highly conserved protein. Second, we will analyze individual mutants of K-Ras for their requirement for upstream signaling, and for the specific activation of downstream pathways. We will do this, as in the previous section, by combining analysis of biochemical properties of the proteins themselves, and analysis of downstream pathways. We will focus on known pathways that are clearly activated differently by different oncogenic forms of Ras, such as the Raf MAPK pathway, and unbiased analysis of signaling differences that are revealed by analysis of individual proteins in a clean, isogenic background. Finally, we have discovered that K-Ras promotes a stem-cell like phenotype in cancer cells that enables them to form tumors very efficiently from small numbers of cells, to metastasize and to become drug resistant. These phenotypes are caused by K-Ras binding to calmodulin and suppressing non-canonical wnt signaling, while increasing transcription from beta-catenin and other factors involved in stem-cell signaling. One of these factors that is produced by K-Ras cancers and plays a major role in the stem-cell phenotype is Leukemia Inhibitory Factor (LIF). We have found that neutralizing LIF prevents tumor initiation in vivo and sensitizes pancreatic tumor cells to gemcitabine, so that established tumors can be completely eradicated. We propose to undertake pre-clinical analysis of humanized anti-LIF monoclonal antibodies, using several models of pancreatic cancer, with the intention of moving these antibodies into clinical testing based on the results of these experiments. Binding of K-Ras to calmodulin is prevented by phosphorylation on serine-181, by PKC. The non-tumor promoting natural product, prostratin, activates PKC in vivo and disrupts K-Ras-calmodulin interaction. Oral administration of prostratin prevents development of pancreatic cancers in mouse models, with no obvious side effects. Several analogs of prostratin have been synthesized: we will test all of these, and make more. We will identify which form of PKC is involved in K-Ras phosphorylation and perform thorough preclinical testing for safety and efficacy of the most promising analogs, so that, if successful, we will advance one of these towards clinical testing.

The relationship between protein structure and function is fundamental for understanding the biological mechanisms that contribute to disease pathogenesis. Proteins are dynamic molecules that are capable of changing their shape, or conformation, in response to changes in their environment and upon ligand binding. Many important therapeutic protein targets undergo conformational change as part of their molecular mechanism of action. Recent drug development strategies have been focused on understanding the effects of small molecules on protein conformation, prompting efforts to rationally design specific and potent conformation-disrupting inhibitors. Thus, tools that can measure conformational changes induced by low- molecular weight modulators are necessary to accelerate the pace of basic research and the drug discovery process. We propose to acquire a Biodesy Delta system to complement the protein structure and characterization equipment that is currently available to investigators in the San Francisco Bay Area Region. The Biodesy Delta platform is based on an optical phenomenon called Second Harmonic Generation (SHG) which can be used to very precisely measure protein conformational changes in real-time following analyte binding or exposure to environmental stimuli. The system can work with any protein target, regardless of size, and a wide variety of ligands, including small molecules, fragments, proteins and mixtures. This high-throughput, automated method can be utilized to analyze thousands of wells per day, as opposed to standard methods that are low-throughput and labor intensive. The SHG conformational signatures provide a high-resolution means of mapping compound structures to function (e.g., activity data) via protein conformation. As a result, the Biodesy platform can be used to enhance primary screening and follow-up work, including protein structure-activity relationship (SAR) studies. Preliminary data that was generated by the major users demonstrates the utility of the SHG method for conducting initial library screening, as well as dose-response measurements, washout experiments, and real-time kinetics for hit triage. The proposed research will be conducted by 4 major PIs who oversee 16 NIH-funded grants. Additionally, 9 minor users will employ the technology in their current research projects. By obtaining the technology proposed in this grant, San Francisco Bay Area regional researchers will be uniquely positioned to accelerate protein characterization and drug discovery efforts. This tool will help revolutionize the understanding of the complex ligand-protein interactions that affect disease pathways which should ultimately lead to discovery of new therapeutics to improve human health.

Biological research collections are most typically appreciated as resources for taxonomic and evolutionary research and some of these collections may even be made available for public viewing through local or national museums. Regionally focused collections can serve these purposes, but they have an even greater potential to play important roles in long-term, high-impact, ecological and environmental research. This workshop will bring together fish biologists, who, in addition to being researchers, also serve as the custodians of specimens and data in the largest regional fish collections in the U.S. Participants in the workshop will include ecologists who use stable isotopes to understand how environmental change is impacting freshwater aquatic ecosystems and scientists from national ecological monitoring infrastructure and environmental forecasting centers, who manage and interpret long-term datasets on environmental trends. A primary goal of the workshop is to bring together these groups of scientists to understand the practices of each group and then develop a program that will allow the best use of and synthesis for understanding fish response to changing environmental conditions.

The ecological and environmental researchers will learn from the fish biologists who curate these collections about sampling and preservation methods of the represented regional fish collections, along with the spatial and temporal breadth of the collections, specimen lot sizes and repetitiveness of sampling, and examples of past research that ecological and environmental researchers have done involving the collections. Participating fish collection curators will learn how isotope geochemistry can be used to understand food web dynamics and ecosystem change. Participants will learn about and explore how stable isotope studies involving specimens from biodiversity collections are performed and issues that must be considered when using these specimens. The wealth of environmental data that can be related to fish-specimen data will also be discussed (e.g., climate, hydrology, land use). Workshop participants will work together to synthesize a program of ecological research involving specimens from regional fish collections.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.