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NHLBI Proteomics Center
> Abstract
Abstract from Yale/NHLBI Proteomics Center
Contract PI: Kenneth R. Williams
The tenet of this proposal is that rapidly evolving advances in mass
spectrometry (MS) instrumentation and methodologies have brought us to the very
promising threshold of being able to quantify accurately the relative levels of
expression of thousands of proteins that make up the human proteome and that
crossing this threshold will enable biomedical researchers to diagnose,
molecularly classify, understand, and develop more effective therapeutic
treatments for a very wide range of heart, lung, and blood diseases. Building on
the considerable biotechnological strengths of Yale faculty and of the Keck
Laboratory, we propose a multidisciplinary and well coordinated program to
further develop and implement MS-based analysis of protein expression and
protein phosphorylation at the "genome" level as we also investigate new
proteomic technologies. Quantitative analysis of protein expression will be
based initially on very high resolution/mass accuracy analysis of tryptic
digests of protein extracts using the innovative, isotope-coded affinity tag
approach (ICAT) of Gygi et al (Nature Biotech. 17, 994 (1999)). Currently, no
other biotechnology seems to offer as much promise for quantitative analysis of
protein expression - with the profiling of 491 differentiation-induced human
proteins providing a glimpse of the future (Nature Biotech. 19, 946 (2001)).
Together with a similar strategy for quantifying the phosphoproteome, we propose
to quantitatively define changes in the relative levels of protein expression
that underlie, define, and result from pathophysiologies in three biomedically
important areas where Yale has well established and highly regarded NHLBI
-funded programs: vascular biology, hematopoiesis, and hypertension. To assist
with analyzing the enormous amounts of protein expression data that will be
produced and to archive this data so it can be analyzed, queried, and
disseminated via web interface by any NHLBI-supported investigator, we will
design and institute the NHLBI/Yale Expression Database. This database will be
effectively linked and cross-correlated with mRNA expression data in the Yale
Microarray Database and with functional and other bioinformatics databases. To
take full advantage of the ability of protein profiling to uncover proteins that
play key roles in pathophysiologies of interest will require that equally
effective biotechnologies be developed for modulating the in vivo activities of
these protein targets. Hence, we propose also a tightly coordinated program for
improving and then utilizing cell permeable synthetic delivery systems to block
specific protein:protein interactions and protein post-translational
modifications. Since both biotechnologies may be applied equally well to a wide
spectrum of diseases, the value of the proposed research will be substantially
and positively leveraged by bringing it to bear initially on several important
areas of biomedical research.
The strengths of this proposal are manifold and
include the multidisciplinary and exceptionally talented team of 23 key
personnel who are ready to go forward; the demonstrated ability of the PI, who
is the founder and Director of the Keck Laboratory (which has been referred to
by NIH Study Panels as "the premier biotechnology resource center in the world")
to direct and interact effectively with large multi-disciplinary groups of
investigators and to bring sophisticated MS technologies to bear on biomedical
research; the outstanding success of preliminary research at Yale U. that has
been directed at developing cell permeable synthetic biomolecule delivery
systems; the very strong support of Yale U. for proteomics and for providing
newly renovated laboratory space to allow substantial expansion of this program;
the rapid progress of the Keck Microarray Resource - which provides an excellent
opportunity to correlate mRNA versus protein expression analysis; and the
extensive infrastructure which is in place to ensure the success of the proposed
research. This infrastructure ranges from the MS, protein chemistry, and
separation science technology expertise needed to fully implement protein
expression analysis to the bioinformatic, computer science, biostatistical, and
database expertise needed to ensure the resulting data is properly interpreted,
archived, and made available to others. The 65 current NHLBI awards to 59 Yale
Faculty and the presence of the Keck Laboratory ensures that as the proposed
biotechnologies are developed and then adopted also by the Keck Laboratory, they
will be rapidly applied to a wide range of important NHLBI-funded research at
Yale and will be made available also to the 1,060 principal investigators at 193
institutions who used state-of-the-art biotechnologies provided by the Keck
Laboratory in fiscal year 2001. We believe that a NHLBI Proteomics Center at
Yale U. would make a major and lasting contribution to heart, lung and blood
research that would extend far beyond the individual biomedical applications
described in this application. |
