Research Grant Abstracts 2012
Memorial Sloan Kettering Cancer Center
New York, NY
Work in this laboratory led to the surprising discovery that a proportion of tumor blood vessels within gliomas are neoplastic in origin (Nature 468:829, 2010). More recently, unpublished data from the same lab shows that under certain conditions glioblastoma cells can transition from epithelial to highly motile and invasive mesenchymal cells. This work opens the door to an entirely new concept in tumor cell biology: that tumors function as a consortium of cell subpopulations capable of switching their fate to different lineages in order to adapt to and modify microenvironmental conditions and stressors. Using a combination of genetic fate mapping, confocal time lapse microphotography, and laser microdissection, the research team aims to capture cells undergoing phenotypic transition into blood vessel or mesenchymal cells in a large set of patient-derived tumors. The cells will be subject to single cell analysis and genomic, transcriptomal, and epigenetic profiling. Efforts will be made to determine the mechanisms underlying lineage reprogramming and to identify molecules that can modulate this process. The team seeks to establish tumor cell plasticity as a fundamental component of cancer and, in doing so, transform our understanding of the cell biology of solid tumors.
University of California, Berkeley
David Schaffer, Mikhail Shapiro, Arash Komeili, Steven Conolly
Genetically encoded optical reporters such as the green fluorescent protein (GFP) have revolutionized biology by making it possible to directly observe cellular processes such as gene expression. However, because light does not penetrate whole animals, fluorescent reporters have limited utility for the study of many of today's key biomedical questions, such as how tumors spread, how immune cells find pathogens, or how brain cells degenerate. Magnetic resonance imaging (MRI) can image whole organisms non-invasively, but at present there are no sensitive genetically encoded MRI reporters analogous to GFP. The team proposes to develop a "magnetic GFP" by borrowing genes from magnetotactic bacteria—organisms that use the Earth's magnetic field to navigate their environment. Magnetotactic bacteria contain iron nanoparticles known as magnetosomes that can be sensitively detected with MRI. Their unique multi-disciplinary team will isolate a set of genes from these bacteria that are responsible for magnetosome formation, then transfer them into mammalian cells and animals to enable MRI of specific cellular processes. The resulting technology could transform biomedicine by opening a broad range of biological questions being studied in whole animals, thereby enabling fundamentally new studies in cancer, immunology, neuroscience and many other areas.
University of Michigan
Ann Arbor, MI
One of the most fundamental mysteries in biology concerns how a fertilized egg becomes an organism with hundreds of different cell types, despite having only a single set of genes. To explain this mystery, epigenetics proposes that the genome is marked in a way that results in specific gene expression patterns unique to each cell type. However, no study has answered the question of when and how such distinct gene expression patterns, or epigenomes, are created. By utilizing a unique and novel application of CO-FISH (chromosome oriented¬ fluorescent in situ hybridization), the investigators discovered that Drosophila male germline stem cells retain the template copy of sister chromatid of X and Y chromosomes. This is the first demonstration that cells are capable of distinguishing sister chromatids and segregating them non-randomly. This non-random segregation of sister chromatid may explain how cells can divide "asymmetrically" by inheriting distinctively marked epigenomes, adopting distinct cell fates. Building upon their initial discovery, the research team proposes to investigate the molecular mechanism and the biological relevance of this novel, unanticipated phenomenon.
University of North Carolina, Chapel Hill
Chapel Hill, NC
The DNA in our cells encodes all the information necessary to specify every aspect of our growth and development. However, a second layer of information — epigenetic information in the form of methylation (a type of molecular tag) of DNA and DNA-associated proteins — is key to accessing the information encoded by DNA. Recent insights show that a wide range of proteins encoded by our genes are methylated, and studies suggest this methylation may be linked to a wide range of diseases, including cancer. However, because of the lack of appropriate tools, we currently know little about the total number of proteins methylated, how aberrant protein methylation contributes to human disease, or how the enzymes that establish this methylation are influenced by other chemical modifications they encounter in the methylation process. The investigators propose to develop new chemical tools for the detection of protein methylation that circumvent the limitations of currently available biological tools. These reagents will be applied to address the fundamental questions raised above, and will lay the foundation for a comprehensive understanding of the role protein methylation plays in human biology and disease.
Broad Institute Inc.
Neuropsychiatric diseases arise from a combination of genetic and environmental factors that influence the molecular, morphological and physiological properties of neurons and glia in the brain. Elucidation and treatment of these diseases will benefit from understanding how specific brain cell types connect and signal in neural circuits, and how genetic factors affect their cellular function. Transgenic techniques have been widely used to target specific cell populations with fluorescent reporter (e.g. GFP) and modulator (e.g. channelrhodopsin-2) genes to probe their role in disease mechanisms. However these conventional gene targeting strategies depend on the identification of unique molecular markers and promoters and are largely limited to the mouse, whereas other animal models that are commonly used for neuroscience and disease studies (e.g. rats and primates) are still mostly inaccessible. Additionally, since many non-rodent animal models have long reproductive cycles, fundamentally new approaches for cell-type specific gene targeting are highly desirable. The researchers propose to develop and apply a generalizable genetic circuit for detecting endogenous transcription states to enable conditional genetic manipulation of specific cell types. The proposed technology could have broad applications for both disease research as well future therapeutic interventions.
J. David Gladstone Institutes
Sheng Ding, Steve Finkbeiner, Shinya Yamanaka
San Francisco, CA
The human brain can carry out more operations per second than the most powerful computer. It also has capacities no computer is likely to ever have, such as consciousness and self- awareness. Thanks to human induced pluripotent stem cells and other induced neural precursor cells, scientists can now make, in theory, any type of brain cell from adult skin cells. Still, only a few types of human brain cells have been made, and the process for making them remains inefficient. The investigators propose to establish an interdisciplinary program to understand how cells that are reprogrammed to pluripotency can be instructed to generate each type of cell in the brain. They have assembled a team that can create, in the laboratory, a number of cell types that compose the brain. In this project they propose to make certain brain cells (e.g., von Economo neurons that are thought to confer unique abilities, such as emotional and social salience, to the human brain) that do not exist in standard laboratory animals. This work could lay the foundation for both the development of cellular therapies to treat neurological diseases and for a greater understanding of what makes us unique as humans.
Oregon Health & Science University
This project will initiate development of image-based approaches that will allow architectural analysis of the nanoscale molecular assemblies that regulate information flow in cells. The team will coordinately develop multi-scale imaging, labeling chemistry and computer science to visualize specific molecular assemblies in cells and to localize these relative to cellular ultrastructural features using a new integrated light and electron microscope (iLEM) to analyze the signaling architecture. The iLEM consists of a custom-designed fluorescent microscope mounted on the side port of a transmission electron microscope. The project team will develop the technologies to enable the detection of the molecular structures that regulate information flow within cells and learn how these structures assemble, integrate signals from multiple sources, and shuttle the information to action centers in cells that control activities such as growth, death and movement. The research team expects that their iLEM analysis approaches eventually will be broadly applicable to studies of regulatory signal networks in normal and diseased tissues.
University of California, San Diego
Steven Dowdy, Yitzhak Tor
San Diego, CA
The discovery of RNA interference (RNAi), a natural gene silencing mechanism with exquisite selectivity for all 23,000 human mRNAs, opened the door to a global therapeutic approach that can be tailored to keep evolutionary pace with pandemic viral outbreaks or for personalized medicine. However, use of RNAi as a therapeutic is severely hindered by the negatively charged phosphate backbone: it simply cannot enter cells on its own. Current RNAi delivery approaches utilize nanoparticles that are 5,000-fold larger than the actual RNAi cargo, which due to this size, have inherently poor pharmacological properties. Using an interdisciplinary chemistry and molecular approach, we seek funds to build a paradigm shifting RNAi technology that radically shrinks the delivery size to the smallest possible, self delivering monomeric RNAi-inducing molecule via synthesis of neutral, bioreversible phosphotriester RiboNucleic Neutrals. Once inside cells, cytoplasmic enzymes unmask the phosphate groups and convert them into negatively charged, active RNAi molecules. Although the technology has broad applicability, the team will establish efficacy of this delivery system in mouse models of cancer.
University of Wisconsin, Madison
Aseem Ansari, Parameswaran Ramanathan, Jennifer Reed, David C. Schwartz
The ability to compose or “program” genomes to perform desired functions will yield insights into how gene networks govern life and will stimulate innovation in many disciplines that interface with biology. The current approach to synthetic genomes involves copying an existing small genome via time-intensive and cost-prohibitive methods. The UW team of engineers, chemists and biologists seeks to create a multifaceted system – a genome foundry – that permits rapid, inexpensive fabrication of de novo designed genomes. The interdisciplinary team, will develop an integrated system to enable design-to-fabricated genome production. The proposed “genome foundries” will comprise an inter-locking suite of computational tools, nanofluidic instrumentation, hardware fabrication languages, and custom-designed synthetic gene switches. The new technology envisioned could enable widespread invention of genome-aided solutions to fundamental and applied problems and the ability to compose and automate the synthesis of large DNA molecules could spur innovations in DNA-based nano-device fabrication and DNA computing.