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Overall PGA Program
Brief Description of this PGA:
This PGA is centered at the Massachusetts General Hospital, Harvard Medical School, with bioinformatics participation from the Boston University Biomedical Engineering Department and the Genetics Department at Harvard Medical School.
The investigators in the program propose to identify and characterize gene networks activated by pro-inflammatory, metabolic, and pathogen stresses affecting the cardiovascular system and the lung. Stress-activated pathways play central roles in the pathophysiology of some of the most important diseases addressed by the National Heart, Lung and Blood Institute, including atherosclerosis, pulmonary infection, cystic fibrosis, and heart failure. The exploration of these pathways is likely to result in the generation of fundamentally new insights into these disorders.
To fully exploit the opportunities offered by emerging genomics technologies, and to capitalize on the imminent completion of the sequencing of the human and mouse genomes, an integrated, multi-disciplinary research team has been assembled.
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There are 5 components in the program:
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Microarray and Sequencing Center
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Education and Training Center
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Proteomics and Molecular Biology Center
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Human Tissue and Animal Model Center
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Bioinformatics Center.
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Each of the component directors also serves as the PI of a research project, with the exception of the Bioinformatics directors. The research projects are interrelated in order to produce synergies between research teams as well as between component technologies.
- The research projects are entitled:
- Genetic dissection of signal transduction
- Host-Pathogen interactions: Pseudomonas and cystic fibrosis
- Definition of Protein networks using RNA display
- Macrophage activation by metabolic and pathogen stresses disorders
Resources to be developed by this PGA:
- Microarrays:
- Indexed cDNA libraries from mouse and human sources
- Our center will produce some specialty arrays as well as arrays arising from cDNA clones available from a variety of public sources
- Proposed specialty arrays include: cytokine gene arrays, macrophage-specific gene arrays, other arrays representing components of inflammatory and stress induced, and signal transduction pathways
- cDNA libraries:
- We will make expression cDNA libraries We anticipate making two general versions of such libraries, truncation libraries, in which cDNAs are inserted downstream of a consensus translational initiation sequence and oligopeptide tag, and full-length libraries. We have found that truncation of sequences is a powerful complementary approach to full-length library screens, and turns up many candidate dominant negative protein fragments. As an outgrowth of the initial success of this approach to identify genes that induce apoptosis, we intend to systematically create libraries that represent protein fragments and express them in mammalian cells
- Available cDNA libraries will be listed through a web resource page
- Protocols for the use of the libraries will be made available in print and web-based formats
- Pseudomonas tagged mutant collection:
- The transposon-mutagenized P. aeruginosa collection, consisting of approximately 4800 nonredundant gene knockout mutants, will be made available for research purposes to any interested academic investigator
- RNA display tools:
- The tools to construct RNA displays will be made available to requesting investigators. These include expression vectors required to generate the bait proteins and to support subsequent subcloning and sequencing of candidate interactors. RNA-based libraries from various tissue sources will also be provided to interested investigators. Protocols for the use of the materials will be provided in print and web format
- RNA samples:
- RNA will be prepared from human tissues including cystic fibrosis and normal lungs, cardiomyopathic hearts, hearts affected by diffuse coronary artery disease, vascular tissues, including carotid, aortic and ilio-femoral artery samples, and coronary atherectomy specimens. As limited material can be obtained from some of these tissue sources, it may not be possible to share all specimens
- Animal and human tissue resources:
- Tissue samples (when sufficient material is available) cardiomyopathic heart tissue, cystic fibrosis lung tissue, and atherosclerotic vascular tissues
- A collection of knockout mice back-bred into the C57BL6 background is being generated
- Null animals include those lacking SR-A, CD36, CD14, apo E, and the LDL receptor. Intercrosses of these animals are also now in progress. The animals themselves or their tissues and nucleic acid by-products will be shared as outlined for the human tissues above, if not already available from Jackson labs
- Array data:
- The array data that arises from all experiments conducted under the purview of the PGA will be shared on our website
Email Contact for this PGA:
Updated: September 19, 2007
