James Richard Heath - US grants

In this NSF Young Investigator Award in the Physical Chemistry Program of the Chemistry Division, James R. Heath will focus on understanding and controlling the chemistry and physics of size and shape on a nanometer-length scale, with emphasis on Group IV and III-V quantum crystals. The physics of size and shape is probed through a variety of single-particle and time- and frequency-resolved spectroscopies. Silicon and germanium quantum dots, atomically straight Ge quantum wires, and atomically flat Ge quantum wells have all been synthesized and are candidates for study. Ordered, complex structures over three dimensions will be prepared by coupling wires, dots, and platelets together. Self-assembly techniques are also investigated. Biological systems are also being examined as templates on which to fabricate tiny superconducting metal wires. %%% The synthetic methods developed and investigated under this award offer the promise for substantially better size resolution than state-of-the-art lithographic techniques. The challenge in this program is to learn how to assemble nanometer-size structures over two dimensions with regularity. Such nano-scale structures are important in the fabrication of miniaturized electronic devices which could help form the microchips for future applications.

This project is developing a laboratory to house the junior/senior level physical chemistry, instrumental analysis, and polymer science labs. These labs are being developed in concert with other aspects of curriculum revision. The concept for these labs is unique. Laboratory experiments are being grouped into clusters, with each cluster stressing a particular chemical theme and individual experiments stressing a fundamental principle. Students are learning basic chemistry, and yet their experiments will build on each other from one week to the next, and even from one lab course to the next. The flexibility to continuously introduce or phase out experiments and experimental clusters is built into the program.

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Heath

This proposal is to support a workshop that will be designed to explore issues related to the future of nano-scale and molecular electronics. In particular, issues related to computer architectures for molecular and nano-electronics, chemical self-assembly as a fabrication technology, and the expected scientific challenges associated with making molecular electronics a reality will be discussed. The meeting will include presentations by leading practitioners in the fields of computer architecture and design as well as physical scientists working in the areas of nanoscale systems and molecular electronics. Of potential interest to both of these groups is the field of neuroscience, and a small number of participants (and a corresponding few scientific presentations) will be from that field. The goal of this workshop will be to explore the common ground that exists between computer architecture, molecular and nano-scale electronics, and neuroscience. The result will be a document that can assist the NSF in developing a strategy for funding these various areas. The workshop is being co-funded by NSF Divisions: ECS/ENG, CTS/ENG, DMR/MPS, DBI/BIO AND EIA/CISE.
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Under the influence of light, electricity, or chemical reagents, certain interlocked molecules, known as catenanes and rotaxanes-which comprise appropriately matched ring and dumbbell-shaped components-will perform motions (e.g., rotary and linear) at a molecular level reminiscent of the moving parts of macroscopic machines. Such molecular motors hold promise as the intelligent" building blocks for the construction of devices and machines. A team of chemists and engineers from two different institutions (UCLA and nearby CALTECH) will address the fundamental scientific issues surrounding the relationships between controllable molecular machines, nanoscate devices, and the predictable movements of machine components at a macroscopic level.

The aims of this collaborative project-which focuses on the NSE RESEARCH THEME of Nanoscale Devices and System Architecture-are to (I) develop the template-directed synthesis (self-assembly) of interlocked molecules (switchable catenanes and rotaxanes) and interpenetrating supermolecules (addressable pseudorotaxanes) as a forerunner to (2) attaching them covalently to frameworks (e.g., silica, alumina) whose (3) synthesis (self-organization) must be established prior to (4) demonstrating the abilities of these machine-like (super)molecules to express different kinds of coherent movements (mainly linear but also possibly rotary ones) characteristic of macroscopic machines when (5) they are activated by chemicals (acids/bases or oxidizing/reducing agents) or electrons or light (redox and electron transfer processes) as a prelude to (6) transducing and amplifying the coherent molecular level movements into macroscopic motions.

The specific objectives of the team are to demonstrate transduction of force and motion from the relative mechanical movements of the components present in catenanes, rotaxanes and pseudorotaxanes through the development-on the nanoscale level-of actuating materials and devices reminiscent of (1) engines, (2) levers, (3) muscles, and (4) valves.

In thc first instance, we envisage constructing supramolecular two-stroke engines based on two-station pseudorotaxanes with the ring component lodged covalently in appropriately-sized silica pores, leaving the semi-dumbbell-shaped component to act as the piston. In the second example, we propose to design mechanical levers to amplify nanometer motions generated by suitable molecular or supramolecular machines. In the third instance, we propose to graft the ring and thread components of pseudorotaxanes onto separate carbon nanotubes using an aromatic polymer which we have demonstrated wraps itself helically around carbon nanotubes in order to realize artificial muscles and actuators. And, in the final example, we intend to develop molecular valves at the necks of suitably-sized silica pores, lined with pseudorotaxanes that can be induced to associate and dissociate (rings from threads) such that guest molecules located within the pores are, respectively, trapped or free to escape.

The anticipated outcome of the proposed program of research includes (I) the synthesis of new molecular motors capable of operating as machines, (2) the synthesis of integrated power supplies for the machines, (3) a bottom-up and top-down integration of frameworks for the machines, (4) new fundamental understanding of forces, friction, etc., on the nanoscale, and (5) a group of students with both broad perspectives and individual expertise in nanoscicnce.

With chemists and engineers working side-by-side, this highly integrated project seeks to transform molecular machines from being scientific curiosities into functioning nanosystems with technological potential, to enrich the education of both graduate and undergraduate students, and to promote the public awareness of nano-science and technology through community outreach.

This Nanoscale Interdisciplinary Research Team (NIRT) project is designed to develop a flexible, targetable nanocapsule by exploiting a naturally occurring nanoscale structure, the vault. Vaults are large (13 MDa) ribonucleoprotein particles composed of multiple copies of three proteins and an RNA, found in nearly all eucaryotic cells. The vault particle is a nanocapsule honed by millions of years of evolution with incredible potential for compound encapsulation, protection, and delivery. The vault nanocapsule can assemble from multiple copies of a few subunits into a stable structure that adheres to and is transported along skeletal networks in the cell, and is likely to open and close in response to cellular signals. Understanding how such a capsule can be manipulated will allow encapsulation of small molecules (drugs, sensors, enzymes, toxins etc.) and targeting the engineered nanostructures to specific tissues, cells, or organelles.

This team plans to modify the vault using a cell-based protein production system and test the concept that vaults can have a broad nanosystems application as malleable nanocapsules. Seven research groups at the University of California, Los Angeles, and other locations (California Institute of Technology; Vanderbilt University), organized by Dr. Leonard Rome, will direct their attention to engineered vault nanocapsules produced in a core production laboratory. Modified vaults will be examined with molecular imaging techniques including negative-stain, cryo-EM single particle reconstruction, atomic force microscopy, and X-ray crystallography. This structural characterization of the vault is an essential first step in designing new vault-based nanocapsules.

Vault nanocapsules will be produced with sequestered metal binding sites and assessed for functional consequences of metal sequestration; for example, cells expressing the engineered particle will be examined to determine whether they have increased resistance to metal toxicity. In other studies, particles will be imbued with functional properties of light emission and magnetic properties to allow the particles to be manipulated in a magnetic field and to probe physiological properties of the vault, i.e., the inflow and outflow of large and small molecules. The ability to manipulate biological nanoparticles in these and other ways offers an opportunity to assemble these particles into structures that may have significant future applications. Spectroscopic techniques will be applied to the engineered particles to allow assessment of the interconversion of opened and closed forms. These studies will lay the groundwork to enable the control of entrapment and release of specific encapsulated materials.

The participants of this team are founding members of the California Nanosystems Institute (CNSI), established to bring together scientists and engineers across disciplines and across institutional boundaries in order to push forward in the area of nanotechnologies. In partnership with the CNSI, the team will establish an educational program designed to advance the field of nanosystems research and technology. This will include training of future researchers and decision-makers and creation of multidisciplinary courses, to enrich school and community resources and influence the technical capabilities of industrial scientists and engineers. In addition, the PI and co-PIs will be involved in research mentoring of undergraduate, graduate and postdoctoral students, curriculum planning, and lecturing. A vault website (www.vaults.arc.ucla.edu) will be maintained and expanded to disseminate information about vaults and vault nanocapsule development. This centralized source of information will include links to published materials and lists of materials and reagents available for sharing.

Funding for this interdisciplinary project is provided through collaborative contributions from the Directorate for Biological Sciences (Division of Molecular and Cellular Biosciences), the Directorate for Engineering (Divisions of Bioengineering & Environmental Systems and Chemical & Transport Systems), and the Directorate for Mathematics & Physical Sciences (Divisions of Physics and Chemistry).

[unreadable] DESCRIPTION (provided by the applicant): 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 grant we will also begin to develop blood-protein measuring devices using microfluidic and nanotechnology approaches that will begin to acquire these features. [unreadable] [unreadable] [unreadable]

Project Summary In 2004,the 90 nm node for CMOS-based Si integrated circuits was commercialized.90
nm refers to the 'half-pitch ' between the most closely spaced metal lines the actual pitch of those lines is 180 nm..Assuming that the current scaling trends continue,technology nodes within the 10-15 nm range would be commercialized around the timeframe 2020 or so.It has previously not been possible to even explore circuitry at these dimensions,since no patterning method for creating such ultra-high density semiconductor circuitry existed.However,the SNAP (superlattice nanowire pattern transfer)method has been recently demonstrated as capable of producing relatively large scale,highly conducting Si nanowire circuits at these dimensions.
The work proposed herewill utilize these circuits,and will focus on addressing some of the most fundamental,chemical,and materials issues that are associated with scaling semiconductor computational circuitry to near molecular dimensions.The intellectual merit of this work will be to establish whether or not it is even possible to scale CMOS circuitry to such extremes.The broader impact is that,regardless of what computational paradigm follows the current one,a high levelof manufacturing perfection at the atomic scale is likely to be necessary.
The work described in this proposal will lay much of the foundation for achieving such perfection.
In the spirit of the RFA,certain approaches described here require manufacturing at a near atomic level of
control,although parallel fabrication approaches for achieving such perfection are proposed,rather than atom by atom assembly approaches.Also,in the spirit of the RFA,architectural approaches for novel omputational schemes,such as those that can take advantage of highly regular circuit structures,or that can bridge length scales from the nano-scale of the logic circuits to the sub-micron scale of standard lithography,will be exploited.
In fabricating and utilizing ultra-dense silicon circuitry,several chemical and materials issues become im-
portant.For example, as Si wire widths are reduced to a few nm,the role that surface states play in the conductivity characteristics of the nanowires becomes increasingly important.Since oxide passivation of Si reduces the mobility of charge carriers near the surface,we want to replace the oxide with an atomically perfect (and very thin)surface passivant.We propose to explore the use of methyl termination of Si(111)for applications to these circuits,an alternative that has been demonstrated to be air-stable with atomically complete passivation that dramatically reduces the surface charge carrier recombination velocities.
Silicon conductors with a thin,high-k gate dielectrics and metal gate electrodes are envisioned to become
important by decade 's end.Equally important for more extreme scaling,will be low-k dielectrics that serve to electronically isolate one nanowire from its nearest neighbor,so that the field-gating can be localized to individual nanowires within a high density logic circuit.These issues will be addressed by combining theoretical modeling to determine effective dielectric constants of ultra-thin materials and molecular films with experimental studies incorporating atomic-layer deposition of high-k gate dielectrics (i.e.HfO2)coupled with the incorporating low-k dielectrics for separating the Si nanowire conductors.
Finally,ultra-high density patterning methods will likely be limited in terms of the physical complexity
achievable in a circuit design.This requires the incorporation of novel approaches for bridging the length scales between the sub-micron world of lithography and the nanometer world of ultra-high density circuits.It also requires novel architectural concepts to take advantage of highly-or quasi-regular patterning methods.Architectural approaches that solve these issues will provide a driver for much of the fundamental science described herein.

This Core Resource has three components. The Noyes Nanofabrication facility, the Nanomaterials Preparation and Characterization Facility, and the Materials &Surface Imaging Facility. These facilities support all of the nano µfabrication aspects of the NSBCC projects. In the rare cases where very high end fabrication resources are needed, the Kavli Nanofabrication Facility (opened in 2007) is available. For all resources, training is available to all NSBCC investigators and, for those trained researchers, the highest demand equipment is available for use by signing for time on a web-based scheduler, while the rest of the equipment is available on a first-come-first serve basis.

Administrative approaches and leveraged resources for NSBCC Pilot Projects and Trans Alliance Challenges is described. The goal of the Pilot Projects program is to further the vision of the NSBCC at two levels - broaden our impact and influence with the local oncology community, and accelerate our Project goals. The goal of our Trans-Alliance activities programs are to assemble the best possible teams for meeting trans-Alliance challenges - whether meeting those challenges involves a competition or a cooperation with other CCNEs. For pilot projects, the NSBCC is partnering with the Broad Center for Regenerative l\/ledicine and Stem Cell Research (Broad CRM), and with the Jonsson Comprehensive Cancer Center (JCCC), to develop a pilot project program that is designed to outreach to the broader, local community of cancer researchers and clinical oncologists. The Broad CRM and JCCC are providing at least $60,000 direct costs to match the $70,000 direct costs committed from CCNE funding, and are providing assistance in pilot project solicitations, selection, and oversight. Criteria for the selection of pilot projects are outlined. For trans-Alliance challenges and related activities, an administrative program is outlined for deciding how the NSBCC will respond to specific challenges. All NSBCC investigators, by choosing to be a part of the NSBCC, are committed towards working towards successfully executing of trans Alliance challenges, and so, depending upon the nature of the challenge, our approach is to put together the best team possible to meet that challenge. NSBCC director Heath, in consultation with co-Directors Dr. Phelps and Dr. Hood, as well as the NSBCC Internal Review Council, provide for oversight and administration of the Pilot Projects and Trans-Aliance Activities. The NSBCC External Advisory Board provides review expertise on the success of our programs.

Biology; Cancer Center; nanosystems;

NSBCC education & training programs are designed to bring cancer researchers together with physical scientists and technologists in order to expedite the develoment of new and effective tools for fighting cancer. Our goal is to have student and postdoctoral researchers who understand the cancer biology or clinical oncology problem, can participate in technology invention, development, and validation, and then can demonstrate the value of the technology in pre-clinical settings and hopefully via participation in human studies. We describe one-on-one mentorship programs within our individual projects designed to bothfacilitate such training, but also catalyze the collaboratory effort. We also describe three NSBCC short courses, taught at each of the participating institutions, that are designed to teach our researchers key fundamental aspects associated with NSBCC-developed technologies, as well as NSBCC ongoing projects. These courses, designed for non-specialists, are complemented with in depth courses designed for more specialist students that are offered at the participating institutions. We also describe internal educational activities that include student and postdoc participation in our annual retreat, biweekly NSBCC Project meetings, site reviews and national CCNE meetings. Mechanisms to facilitate intra- and inter-CCNE collaborations. The educational programs are overseen by our Internal Review Council and annually reviewed by our External Advisory Board. Outreach programs to the local oncology community are enabled via our IMED Core, and additional outreach programs to underrepresented minority students and industry are described. Finally, we describe our outreach to the global community via public data base sharing, publication, and public communication forums.

DESCRIPTION (provided by applicant): Cancer immunotherapy encompasses classes of treatments designed to attack cancer via activating or suppressing the tumor-associated immune response. Immunotherapies range from adoptive cell transfer (ACT) therapies to administered immuno-modulators such as IL-2 or anti-CTLA-4. Significant progress has been made in demonstrating the efficacy of immunotherapies for some patients, but responses are often transient, and pre-selecting likely responders, or modifying immunotherapies to improve response durabilities, is challenging. For many immunotherapies, traditional molecular or cellular biomarker assays rarely provide correlates with clinical outcomes. This situation will likely be further exacerbated as the field towards trials in which multiple immunotherapies are combined. We propose to address PQ20 through the use of advanced immune monitoring techniques that will initially be deployed retrospectively, and then integrated into well-designed immunotherapy clinical trials. Our specific focus is on late-stage melanoma patients participating in a variety of ACT trials. Our hypothesis is more general: We hypothesize that a comprehensive functional analysis of key, tumor-associated compartments of the immune system, measured across an immunotherapy regimen, can help answer PQ20. To test this hypothesis, we bring together three recently developed, highly multiplex immune monitoring tools to permit an unprecedented level of analysis of cancer patient immune system function: (1) The Single Cell Barcode Chip (SCBC) is designed to quantitate a panel of ~20 functional proteins from single cells, with >103-104 cells profiled in parallel, thus permitting a full functinal analysis of, for example, key T cell phenotypes associated with a given immunotherapy. (2) Nucleic Acid Cell Sorting (NACS), is a tetramer library approach for quantitating the populations of ~50 antigen specific T cells. (3) DNA-encoded antibody libraries (DEAL) integrated onto microfluidic chips; permit the quantitation of a large panel of blood-based biomarker proteins for surveying immune system functions and tumor markers. These assay results, plus additional (traditional) assays, patient demographics, etc., will be incorporated into algorithms for the analysis, dimensional reduction, integration, and visualization of the resultant data, which we anticipate will lead to a resolution of PQ20. We describe the recent application of our technologies towards analyzing the time-dependent responses of late-stage metastatic melanoma patients participating in an engineered T Cell Receptor (TCR) ACT immunotherapy trial. That trial involves multiple immunotherapies, including lymphodepletion of the host immune system, engineered TCR lymphocytes, dendritic cell vaccines, and IL-2. Traditional molecular diagnostic results did not correlate with clinical outcomes. However, application of the new immune monitoring tools yielded clear insights that strongly correlated with clinical outcomes, and those results have informed a clear direction for designing the proposed program.

Shared Resources Cores. NanoSystems Biology Cancer Center Nano/micro Fabrication and Materials (NM2) Core ABSTRACT: The Nano/micro fabrication and Materials (NM2) Core is a custom-designed Core Resource of the NSBCC. By distilling out the research needs of the individual Project Specific Aims, we identified a set of research tools that were needed by least 3 out of the 4 projects, or which were heavily used by at least 2 projects. These tools beak down into (1) resources for micro/nano fabrication of microchip-based platforms and the execution of the associated assays; (2) resources for nanoparticle characterization; and, (3) resources for peptide and biomolecular preparation, modification, and purification. We view these common research needs as an opportunity to increase the cost-efficiency of our Projects, while also accelerating progress by promoting cross- fertilization of ideas, knowledge, and researchers between the projects. Under the direction of Core Director Dr. Jim Heath (Caltech) and co-director Dr. Young Shik Shin (UCLA) these research needs, and the resultant educational and scientific opportunities, inform the composition and administrative structure of a centrally managed NM2 core, with locations at both Caltech and UCLA.

Nanosystems Biology Cancer Center DEVELOPMENTAL PROGRAMS ABSTRACT As specified in the RFA, we are setting aside $70k in direct costs for the Developmental NSBCC Program, and devoting those full resources towards the support of one or, more likely, two pilot projects. Each pilot project will be funded for a one year period, so that the proposed NSBCC will support between 5 and 10 such projects during the 5 year funding cycle. Pilot project proposals will be solicited from the broader Caltech and UCLA communities in the form of a brief (1-2 pages) format that will include a specific Aim, the proposed work plan, and a budget. The resources for these pilot projects are very limited, and so we will encourage submissions that leverage existing NSBCC research projects and core resources, but also have the scientific merit to potentially evolve into separately funded projects. Pilot Projects are refereed by the NSBCC executive council (please see Administrative Core). As described in the Administrative Core, the NSBCC is led by Jim Heath from Caltech and Michael Phelps from UCLA, with the Executive Council (EC) serving as a governing body. The Executive Council is comprised of the PI's from each of the Projects and Cores, and meets once a month, following a regularly scheduled NSBCC-wide scientific forum. The Pilot Program is overseen by the EC. Starting with positive announcement of center funding, we will convene an NSBCC EC meeting, and one of the major items on the agenda will be to solicit Pilot Project proposals. This will initiate a sequence of events that will occur over a 3 month period, with the monthly EC meetings providing the reference for this timeline. In month 1, pilot projects are solicited and received. In month 2, pilot projects are refereed. In month 3, pilot projects are awarded.

PROJECT 3: Tools for Capturing Immune Cell/Cancer Cell Interactions in Cancer Immunotherapies and Combination Immunotherapies. ABSTRACT: Cancer Immunotherapy was Science Breakthrough of the Year 2013[1], with tremendous promise and excitement surrounding two immunotherapy classes. Class 1 is comprised of immune checkpoint inhibitors[2, 3], such as for Programmed Death (PD)-1/L1 blockade. These drugs can increase the susceptibility of cancer cells to immune system attack. The clinical testing of PD-1/L1 blockade in multiple cancers, but led by work in melanoma[4], has demonstrated a new era in cancer treatment[5, 6]. Therapy Class 2 is Adoptive Cell Transfer (ACT)[7, 8], which seeks to strengthen the anti-tumor immune system function. Technologies to support these cancer immunotherapies have been an NSBCC theme [9-13], and our immune monitoring tools are used in several trials and patient studies. Recent immunotherapy successes have raised patient expectations. We propose technologies to advance the science to bring this promise to more patients. We will interrogate how tumor models and patients with cancer respond or become resistant to single and combination immunotherapies, with anticipated implications for all cancer patients receiving immunotherapies. We focus on measuring, in vivo and in vitro, the interactions between the cancer cells and tumor infiltrating lymphocytes (TILs). Such interactions can yield tumor cell killing, but can also promote the activation of tumor cell resistance to such killing. This theme is central for improving both ACT and checkpoint inhibitor therapies.

Project 4. A Discovery-Level Functional Proteomics/Metabolomics Platform for Resolving the Heterogeneity of GBM Tumors and Identifying Effective Therapy Combinations. ABSTRACT: Molecular profiling of glioblastoma (GBM) - one of the most lethal of all cancers - has revealed a molecular landscape of altered signal transduction cascades that cluster along a set of druggable core pathways. Yet, drugs designed to target these pathways have failed in the clinic, presumably due to the genetic and functional heterogeneity of the tumor. Single cell analyses may resolve the heterogeneity of GBM in a manner that can point to rationale combination therapies for treating the disease and suppressing resistance. So far, those analyses have been limited to two classes. The first is single-cell genome and transcriptome analysis, which is a discovery-level analysis, but is also noisy and contains limited functional information. The second is single- cell functional proteomic analysis of the altered signaling networks from which drug targets emerge. This tool can provide powerful new ways to look at known biology, but it does not permit discovery. In principle, one wants to know, for each single cell, the molecular code of the cell (the genome), the functionality of that cell (the proteome and metabolome), and the connection between the two ? the transcriptome. This requires single cell discovery science that extends from genomics to biological function. We hypothesize that such a deep and multi-level analysis can unveil how GBM tumors adapt or evolve to develop resistance against targeted therapies, thus guiding the design of successful combination therapies for GBM patients. Our specific aims are:

SHARED RESOURCE CORE CRUMP PRECLINICAL IMAGING TECHNOLOGY CENTER ABSTRACT: The Crump Preclinical Imaging Technology Center will provide comprehensive support for the in vivo imaging studies carried out in the NSBCC projects. Under the direction of Core Director Dr. Michael Phelps, the Imaging Center is comprised of two other faculty, Dr. Arion Hadjioannou and Dr. Jason Lee, and one full-time staff member. All faculty members have extensive experience and recognition in preclinical molecular imaging. The Imaging Center will provide all radio-labeled probes, perform all microPET and CT studies, and data analysis. In addition, they will provide support and training to investigators, including animal preparation and monitoring, quality control and the strictest safety measures. The goal of the Shared Resource Core is to provide advanced molecular imaging support to assess the kinetics of tumor metabolism and therapeutic outcome in response to therapeutic intervention. These experiments will consist of highly-controlled, serially- acquired PET and CT scans for both functional and anatomical assessment, respectively. Since the PET radio- labeled probe used is also widely available in the clinic, the preclinical imaging data acquired by the Shared Resource Core can be translated as biomarkers for evaluation of treatment response in patients.

Project Summary/Abstract Cellular transitions are fundamental to many steps of carcinogenesis and tumor progression. Such transitions are broadly studied, but general models have been historically limited to qualitative descriptions. This contrasts with phase transitions in physical systems, which are well characterized within the context of the physico- chemical laws, and can be partially understood, in a predictive capacity, using simple, precise models such as the Ising model. Such models are based upon a system of interacting lattice sites. A parameter (e.g. Temperature) is varied, and the fluctuations of the lattice sites are analyzed as the system approaches and passes through a critical point. All critical system-specific details are captured in the interactions between the lattice sites, and the models can yield specific, experimentally verifiable predictions. Ising-like in silico models have guided theoretical studies of transitions in various gene or protein regulatory networks, although resultant predictions can be challenging to experimentally test. We seek a general approach where the experimental input is a statistically large number of single cell measurements, with many protein and metabolite analytes quantitatively measured per cell. From this data we capture the fluctuations and thereby determine the analyte-analyte correlations. In an Ising model analogy, such measurements define the site interactions. These inputs permit straightforward theoretic models for resolving cellular steady states, transitions between steady states, and for making testable predictions. Studies of the chemically-induced-carcinogenesis transition provide preliminary data/proof of concept. For Aim 1 we develop a picture of cancer cell steady states using integrated metabolic and proteomic single cell assays on cancer models of Glioblastoma Multiforme and Melanoma. In Aims 2 and 3 we expand this approach to two apparent cellular transitions associated with resistance against targeted therapies: the adaptation of heterogeneous brain cancers to certain targeted inhibitors, and a drug-induced cellular de-differentiation observed in melanomas and other tumors in response to immunotherapy and targeted inhibitors. All aims are joint experiment/theory aims. Aims 2-3 involve in vivo testing of predictions, as well as exome sequencing and global RNA-seq kinetic studies to complement the single cell kinetic analyses. Anticipated outcomes of the work include a general, quantitative approach towards describing cellular transitions associated with cancer. Further, we propose to mine those descriptions of cellular transitions to identify therapy combinations that are designed to hit targets that drive tumor growth, as well as those that drive the transition (and thus promote resistance) Preliminary data to support of this goal is provided. Additionally, guidance for non-continuous therapy dosing (e.g. metronomic or pulsatile regimens) that exploit knowledge of the kinetics, barriers, and reversibility of the transition to resistance is anticipated