1993 — 2001 |
Kingsley, David M |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Genetic Analysis of Bone Morphogenetic Proteins
The long term goal of this research is to define the molecular mechanisms that control the growth and patterning of skeletal tissue. This is a general problem in the development of higher animals, and is of particular relevance to the diagnosis and treatment of human skeletal diseases and bone fractures. The studies are particularly directed to understanding the role of bone morphogenetic proteins (BMPs) in normal development. BMPs were originally isolated based on their ability to induce cartilage and bone formation when implanted under the skin of animals. Combinations of BMPs and a carrier matrix are sufficient to induce a complex cascade of chemotactic and differentiation events that ultimately results in the formation of a marrow filled bony ossicle at ectopic body sites. The presence of these proteins in mature bones, and their ability to stimulate new bone formation, suggests that they may be the natural mediators of bone growth and modeling during embryonic development and repair of bone fractures. Cloning studies have shown that most BMPs are members of a family of secreted signaling molecules that have structural homology to transforming growth factor beta. The BMPs are strikingly conserved in evolution, with close relatives present in organisms such as the fruit fly Drosophila. BMP-like proteins have thus existed for at least a half billion years, and must predate the evolutionary invention of bone and cartilage. Mutations in a Drosophila homolog of a BMP gene disrupt early dorsal/ventral patterning of the embryo and are lethal. These findings, together with data showing that mammalian BMPs are expressed in many different tissues during mouse development, suggest that the BMPs may play diverse roles in higher animals as well. Until recently, no mutations have been available to test the function of BMPs in vertebrates. However, this laboratory has recently shown that a BMP gene called Bmp-5 is defective in mice carrying mutations at the short ear locus. Complete loss of the gene is compatible with full viability and fertility of mice, but is associated with a specific syndrome of skeletal abnormalities including reduction of the external ear, loss of one pair of ribs, alterations in the size and shape of many bones, defects in repair of bone fractures, and a number of soft tissue abnormalities. This important mouse mutation provides the first genetic model for defining the roles of BMPs in the development of higher organisms. The proposed studies will determine how the expression pattern of Bmp-5 is related to the phenotypes seen in mutant mice, which domains of BMP molecules are most important for normal function, and what roles BMPs play outside the skeleton. Cis-acting sequences will be defined that control when and where the Bmp-5 osteoinductive signal is expressed during normal development. Finally, short ear mice will be used to test a new genetic approach for correcting skeletal defects using cloned BMP genes.
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1996 — 2001 |
Kingsley, David |
P01Activity Code Description: For the support of a broadly based, multidisciplinary, often long-term research program which has a specific major objective or a basic theme. A program project generally involves the organized efforts of relatively large groups, members of which are conducting research projects designed to elucidate the various aspects or components of this objective. Each research project is usually under the leadership of an established investigator. The grant can provide support for certain basic resources used by these groups in the program, including clinical components, the sharing of which facilitates the total research effort. A program project is directed toward a range of problems having a central research focus, in contrast to the usually narrower thrust of the traditional research project. Each project supported through this mechanism should contribute or be directly related to the common theme of the total research effort. These scientifically meritorious projects should demonstrate an essential element of unity and interdependence, i.e., a system of research activities and projects directed toward a well-defined research program goal. |
Gli3 and Gdf5 Response Genes
The long-term goal of the proposed research is to understand how transcription factors control cell fate and cell death in higher animals. In the last ten years, a number of transcription factors have been found that play an important role in both development and oncogenesis. Many of these genes are highly conserved in evolution, and control a variety of different developmental events in both vertebrates and invertebrates. The GLI3 gene is a Zn-finger transcription factor that was originally isolated because of its close homology to an oncogene amplified in human gliomas (GLI). Highly related genes are present in Drosophila and C. elegans, and play a key role in patterning or set determination in these different organisms. In mammals, mutations in the GLI3 gene alter patterns of programmed cell death and lead to overgrowth of both neural and limb tissue. The normal targets of GLI-like genes are largely unknown, although candidate genes have been identified in both Drosophila and mice. Here we propose to carry out a direct search for target genes that mediate GLI3 functions during limb development. We will focus on the developing digits for two reasons. First, an association between GLI3 and programmed cell death is particularly clear in this region. GLI3 is expressed in the regions where cells are known to die, and defects in GLI3 alter the patterns of cell death both between and inside the digits. Second, a candidate gene has already been identified whose expression pattern and mutant phenotype suggest that it may be a target of GLI3. The candidate gene, growth/differentiation factor 5 (GDF5), encodes a secreted signalling molecule that is structurally related to suspected targets of GLI-like genes in Drosophila. GDF5 is also expressed in digit regions where cells undergo programmed cell death, and mutations in GDF5 produce phenotypes that resemble those of GLI3 in the digit region. Here we propose to examine the possible regulatory relationships between these genes using null mutations available in mice, and an organ culture system that recapitulates many of the developmental events in the digit region. Potential target genes for GLI3 and GDF5 will be isolated by screening for genes that are differentially expressed in limb buds of GLI3 and GDF5 mutants, or in organ cultures directly exposed to the GDF5 gene product. A yeast screen will be carried out to identify genes that contain direct GLI3 response elements. Candidate target genes will be sequenced, surveyed for their expression in digits and other tissues, and tested for their effects on programmed cell death in cultured cell lines. The results of the study should provide a new understanding of the molecular events that control cell fate and cell death decisions in response to GLI3. The nature of the target genes may suggest new tests or treatments for human cancers that are caused by abnormal expression of master regulatory transcription factors.
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2002 — 2011 |
Kingsley, David M |
R37Activity Code Description: To provide long-term grant support to investigators whose research competence and productivity are distinctly superior and who are highly likely to continue to perform in an outstanding manner. Investigators may not apply for a MERIT award. Program staff and/or members of the cognizant National Advisory Council/Board will identify candidates for the MERIT award during the course of review of competing research grant applications prepared and submitted in accordance with regular PHS requirements. |
Genetic Analysis of Bone Morphogenic Proteins
[unreadable] DESCRIPTION (provided by applicant): Bone morphogenetic proteins (BMPs) are key signalling molecules that control many different steps in development. A large number of studies suggest that BMPs are the endogenous signals used by vertebrates to induce formation of cartilage and bone during embryonic development, and to stimulate repair of bone fractures in adults. More recent studies suggest that some BMP family members also play an important role in joint formation, and that BMP signalling may be required to maintain articular cartilage after birth. The remarkable ability of these proteins to induce the formation of new skeletal tissues when implanted at ectopic sites raises the possibility that they may form the basis of important new clinical treatments for fracture repair, spinal fusion, increased bone strength, and maintenance of articular cartilage. Despite the importance of BMPs in skeletal biology, very little is known about the molecular mechanisms that control where and when they are normally expressed. Increased understanding of this area may suggest new ways of manipulating BMP expression at particular sites and stages of development, or to inhibit BMP expression in diseases of ectopic bone formation. We are carrying out a detailed genetic, genomic, and functional study of the regulatory sequences that control expression of 3 different BMP genes during normal development. These studies have already shown that the regulatory sequences that control BMP expression are distributed over enormous distances around the coding sequences. The overall patterns of BMP expression are built up from a number of modular elements, each responsible for controlling expression in a small anatomical subset of the overall skeleton. We will use a combination of comparative sequencing, clone scanning, and functional tests in transgenic mice to identify minimal control elements responsible for BMP expression in the key proliferative layer that surrounds growing skeletal elements, and in interzones that mark the sites of joint formation. Transcription factors that act through these elements will be identified by a combination of expression screening and biochemical interaction with wild-type and mutant control elements. The isolated control elements will also be used to test the functional role of BMP signalling in controlling the size, shape, and curvature of ribs. Finally, joint specific control elements will be used to develop a general system for studying the role of other genes in joints.
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2007 — 2011 |
Kingsley, David M |
P50Activity Code Description: To support any part of the full range of research and development from very basic to clinical; may involve ancillary supportive activities such as protracted patient care necessary to the primary research or R&D effort. The spectrum of activities comprises a multidisciplinary attack on a specific disease entity or biomedical problem area. These grants differ from program project grants in that they are usually developed in response to an announcement of the programmatic needs of an Institute or Division and subsequently receive continuous attention from its staff. Centers may also serve as regional or national resources for special research purposes. |
Genomic Basis of Vertebrate Diversity
DESCRIPTION: The long-term goal of this project is to understand the genomic mechanisms that generate phenotypic diversity in vertebrates. Rapid progress in genomics has provided nearly complete sequences for several organisms. Comparative analysis suggests many fundamental pathways and gene networks are conserved between organisms. And yet, the morphology, physiology, and behavior of different species are obviously and profoundly different. What are the mechanisms that generate these key differences? Are unique traits controlled by few or many genetic changes? What kinds of changes? Are there particular genes and mechanisms that are used repeatedly when organisms adapt to new environments? Can better understanding of these mechanisms help explain dramatic differences in disease susceptibility that also exist between groups? The Stanford CEGS will use an innovative combination of approaches in fish, mice, and humans to identify the molecular basis of major phenotypic change in natural populations of vertebrates. Specific aims include: 1) cross stickleback fish and develop a genome wide map of the chromosomes, genes, and mutations that control a broad range of new morphological, physiological, and behavioral traits in natural environments;2) test which population genetic measures provide the most reliable "signatures of selection" surrounding genes that are known to have served as the basis of parallel adaptive change in many different natural populations around the world;3) assemble the stickleback proto Y chromosome and test whether either sex or autosomal rearrangements play an important role in generating phenotypic diversity, or are enriched in genomic regions that control phenotypic change;4) test whether particular genes and mechanisms are used repeatedly to control phenotypic change in many different vertebrates. Preliminary data suggests that mechanisms identified as the basis of adaptive change in natural fish populations may be broadly predictive of adaptive mechanisms across a surprisingly large range of animals, including humans. Genetic regions hypothesized to be under selection in humans will be compared to genetic regions under selection in fish. Regions predicted to play an important role in natural human variation and disease susceptibility will be modeled in mice, generating new model systems for confirming functional variants predicted from human population genetics and comparative genomics.
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2013 — 2020 |
Brunet, Anne [⬀] Kingsley, David M |
T32Activity Code Description: To enable institutions to make National Research Service Awards to individuals selected by them for predoctoral and postdoctoral research training in specified shortage areas. |
Genetics and Developmental Biology Training Program
? DESCRIPTION (provided by applicant): This is a competitive renewal of a training program in Genetics and Developmental Biology at Stanford University. The grant currently supports 10 students who train among 57 distinguished faculty from two highly interactive departments. The faculty and trainees have a remarkable record of landmark contributions to the fields of genetics, genomics, and developmental biology. These include: the invention of recombinant DNA methods; the first molecular studies of developmental mutations in flies; the discovery and elucidation of the homeobox, Wnt, BMP, and hedgehog signaling pathways; the mechanistic study of RNAi pathways; the large- scale mapping and sequencing of microbial, fish, and mammalian genomes; the application of genome-wide expression analysis in bacteria, yeast, worms, flies, and humans, and the purification of many kinds of stem cells. We have also pioneered the development of several new model organisms for studying key problems in biology, including mechanisms of cellular asymmetry, vertebrate evolution, plant and animal domestication, and the control of lifespan in natural species. In each case, major progress has depended on combining genetic, genomic, and developmental approaches. In the current era, we believe that similar interdisciplinary training is more important than ever. High-throughput sequencing and massive studies of genetic variation are currently transforming much of biomedical research. However, connecting DNA sequence to traits remains a key challenge for researchers in all fields. Our training program directly addresses the problem of mapping genotypes to phenotypes by offering combined training in genetics and genomics, as well as experimental methods for examining gene function in a wide range of both model and non-model organisms. This grant has led to the development of many special features that are now hallmarks of graduate student training in our program, including: coordinated admissions, a joint training camp combining computational and experimental methods, core courses, joint teaching, flexible research rotations during the first year, joint advising, joint journal clubs and research seminars, and major curricular innovations now underway to encourage interdisciplinary training. By all measures, the program has been highly successful. We receive an exceptional number of applicants for the limited number of positions available, can accept only 4% of applicants, and have successfully enrolled over 70% of accepted students in the last two years. Over 90% of admitted students successfully progress to the Ph.D., and our average time to graduation has been falling in response to a renewed focus on career preparation and timely completion of thesis research. Impressively, the 215 Ph.D. students who have completed their training in the last 10 years have produced nearly 800 publications in leading journals. Most importantly, our trainees are embracing a full range of genetic, genomic, computational, and experimental approaches, often combining techniques from different disciplines to make major research advances, while at the same time bringing the benefits of these advances to applications in the clinical realm.
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