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IMAT: Support for New and First-Time Investigators

As part of its commitment to bring together a diverse group of investigators from traditionally disparate fields in order to focus their efforts on innovative cancer-relevant technology development, the IMAT Program has continued to support the development of technologies from young, up-and-coming investigators. A significant percentage of applications submitted to the IMAT Program in recent fiscal years have, in fact, originated from new or first-time applicants. In FY 2005, for instance, the IMAT Program provided 14 awards to new or first-time investigators. Such awards were followed by 12 additional awards to new or first-time investigators in FY 2006 and 11 additional awards in 2007. As of calendar year 2008, the program continues to experience growth in both the number and quality of first-time investigators from a variety of scientific and technical disciplines.

New Investigator

Some representative profiles of new or first-time investigators to the program follow:

Sequence Enrichment Using Droplet-Based Microfluidics

Dr. Darren R. LinkInvestigator's Background. Dr. Darren R. Link is Cofounder and Vice President of Research and Development at RainDance Technologies, Inc. He received a Ph.D. degree in physics from the University of Colorado in 1998 and then continued his research on the electro-optical properties of liquid crystals as a postdoctoral scientist at Tokyo Institute of Technology. In 2001 he returned to Harvard University as a postdoctoral scientist and developed electrical techniques for manipulating droplets in microfluidic channels. This work at Harvard, in 2004, led to the founding of RainDance Technologies, a company dedicated to commercializing the use of droplets to perform bioassays in pico-liter volumes. Dr. Link has coauthored more than 55 peer-reviewed articles and 10 patent applications and is a member of the industrial advisory board for the Vanderbilt Institute for Integrative Biosystems Research & Education.

Project Summary. High-throughput sequencing of genomic DNA has gained increasing acceptance as a means to identify the genetic origins of disease. However, whole-genome sequencing of thousands of patients in large cancer studies is not yet practical. Targeted sequencing of specific exons is more practical, but there is a lack of good tools to selectively enrich target DNA sequence from a preponderance of off-target DNA. Current tools for enriching target DNA sequence result in the absence of some target regions, the inclusion of off-target sequence, and the introduction of a bias in the way target loci are enriched. These shortcomings limit the amount of information that can be obtained from sequencing samples prepared with current tools and largely offset the anticipated cost savings.

RainDance Technologies is developing a microfluidic tool for sequence enrichment that enables highly uniform amplification of target loci without the introduction of off-target sequence. The key to this technology is a library of PCR primer droplets that encapsulate individual primer pairs in 10 pico-liter droplets. These droplets are then combined with 15 pico-liter template droplets to amplify a unique target in a 25 pico-liter reaction volume using conventional laboratory thermocyclers. With processing rates of thousands of droplets per second, large numbers of individual reactions are used to amplify target loci in a simple, robust manner that is uniform across multiple loci and provides a practical, economic solution for sequence enrichment.

See article on RainDance Technologies Inc., published by The Boston Globe on August 31, 2008 (page 36 of this report).

IMAT Award: R21 CA 125693-01

Isolation of Circulating Tumor Cells From Blood Using Microbubbles

Dr. Dmitri SimbergInvestigator's Background. Dr. Dmitri Simberg received his Ph.D. degree in biochemistry from the Hebrew University of Jerusalem, Israel, where he researched the mechanisms of transfection using cationic liposomes and membranes. During his graduate studies, he developed transfection reagents that are now sold commercially. Dr. Simberg received postdoctoral training in the laboratory of Dr. Erkki Ruoslahti at the Burnham Institute on targeting tumors with nanoparticles for imaging and treatment of cancers, and additional training in the laboratory of Dr. Mattrey, where he developed targeted ultrasound contrast reagents and conceived the idea of microbubble-assisted cell separation. He currently holds a position of Project Scientist at the NanoTumor Center at University of California , San Diego .

Project Summary. In cancer, malignant cells are shed into blood (1-3). These extremely rare cells (few cells/mL blood) could be isolated and analyzed to provide invaluable information for diagnosis and prognosis of cancer patients. However, because of low concentration in blood, the isolation of circulating tumor cells (CTCs) is a laborious and expensive process.

Immunomagnetic separation is the currently used method for CTC isolation from blood samples of cancer patients. This method is very sensitive (1 CTC/mL blood or lower) but produces significant contamination of nonspecific cells in the isolated sample; it is laborious and is practically limited to small volumes of sample.

SchemeIn order to address the existing problems of CTC isolation from blood, Dr. Simberg and his team propose to develop a cell isolation technique based on capture of rare cells in blood by gas-filled microbubbles (µbubbles). The µbubbles coated with tumor-targeting ligands will selectively bind tumor cells in a blood sample. Because of the buoyancy of the µbubbles, they will drag bound CTCs upwards, while the rest of the cells will sediment to the bottom (see Scheme). The µbubbles will be concentrated, and tumor cells will be detected and counted.

To prove that µbubbles could selectively bind and separate the cells in whole blood, Dr. Simberg first attached a specific antibody to µbubbles in order to detect chemically modified red blood cells. Indeed, the specific antibody-coated µbubbles bound and separated the modified erythrocytes from blood. Next, he used an antibody that can recognize tumor cells; µbubbles coated with this antibody efficiently bound tumor cells that were blended with normal blood.

The ultimate goal of this project is to develop a technology for quick and efficient isolation of rare cells from large volumes of biological samples. This technology could open new possibilities for diagnostics and treatment of cancers. If successful, the technique can be used for efficient large-scale isolation of tumor cells and biomarkers as well as depletion of cells from blood and other tissues.

References

1. Fehm T, Sagalowsky A, Clifford E, Beitsch P, Saboorian H, Euhus D, Meng S, Morrison L, Tucker T, Lane N, Ghadimi BM, Heselmeyer-Haddad K, Ried T, Rao C, Uhr J. Clin Cancer Res 8:2073-84, 2002.

2. Steeg PS. Nat Med 12:895-904, 2006.

3. Pantel K, Brakenhoff RH. Nat Rev Cancer 4:448-56, 2004.

IMAT Award: R21 CA 137721-01