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2005 Scientific Report

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Laboratory of

Laboratory of Analytical, Cellular, and Molecular Microscopy and Laboratory of Microarray Technology and Molecular Diagnostics James H. Resau, Ph.D. Dr. Resau received his Ph.D. from the University of Maryland School of Medicine in 1985. He has been involved in clinical and basic science imaging and pathologyrelated research since 1972. Between 1968 and 1994, he was in the U.S. Army (active duty and reserve) and served in Vietnam. From 1985 until 1992, Dr. Resau was a tenured faculty member at the University of Maryland School of Medicine, Department of Pathology. Dr. Resau was the Director of the Analytical, Cellular and Molecular Microscopy Laboratory in the Advanced BioScience Laboratories–Basic Research Program at the National Cancer Institute–Frederick Cancer Research and Development Center, Maryland, from 1992 to 1999. He joined VARI as a Special Program Senior Scientific Investigator in June 1999 and in 2003 was promoted to Deputy Director. In 2004, Dr. Resau assumed as well the direction of the Laboratory of Microarray Technology to consolidate the imaging and quantification of clinical samples in a CLIA-type research laboratory program. Staff Eric Kort, M.S. Bree Berghuis, B.S., HTL (ASCP), QIHC Pete Haak, B.S. Eric Hudson, B.S. Paul Norton, B.S. J.C. Goolsby Laboratory Members Consulting Veterinarian Robert Sigler, D.V.M., Ph.D. Students Hien Dang Brandon Leeser Amy Percival Huang Tran Research Interests T he Laboratory of Analytical, Cellular, and Molecular Microscopy (ACMM) and the Laboratory of Microarray Technology and Molecular Diagnostics (MTMD) are organized and equipped to produce highresolution images, genomic arrays, and bioinformatics data that support the cellular and molecular biology programs of the Institute. Our laboratories collaborate with the investigators to improve the understanding, diagnosis, and characterization of disease, injury, and differentiation. Although we primarily study cancer, we work with investigators in and out of the Institute on a variety of diseases and processes. As examples, during the past year, we have used our microscopes to produce intravital images of the Met protein in living cells and animals; localized and quantified a unique transcriptional protein in human cells; worked closely with VARI’s Bart Williams to characterize the phenotypic changes in transgenic mice expressing mutations related to Wnt and the Lrp5/Lrp6 genes; began to image Art Alberts’ small GTPase proteins in living cells; and collaborated in studies of the expression of c-Met in a series of primary human breast cancers. During 2004, we added two significant instruments to the ACMM laboratory. The first is the Aperio Scanscope, which enables us to digitize a 1 × 3-inch microscope slide in full color such that it can be analyzed, quantified, and shared throughout the digital network. The second is the Ventana automated immunostainer, which can carry out FISH, ISH, IHC, and array spotting in a programmed, specific, and accurate fashion. These two instruments have allowed us to increase our productivity, shorten our turnaround time, and improve the quality of our preparations without any increase in personnel. In the last calendar year, we processed 403 requests for histopathologic services that required 4,100 blocks and more than 31,600 glass slides. Using the Scanscope during December 2004, we scanned over 300 cases in high resolution for inclusion in the VATR database. We anticipate generating digital Scanscope files for 3,000–4,000 cases in 2005 that will be available on network servers. The MTMD laboratory is preparing gene expression data from cells and tissues and is correlating that with histology, tissue volume, and nuclear density to determine an effective and accurate 38

screen for applications in molecular diagnostic assays. We have developed a QC and QA protocol for evaluating specimens for array analysis. During the past year we have prepared 1,500 cDNA arrays for 20 collaborators from both in and outside the Institute. Our laboratories are primarily responsible for the archived clinical histopathology program called the Van Andel Tissue Repository (VATR). This program allows investigators to use existing human clinical samples to assess the expression of proteins. We also use these blocks to prepare a wide variety of tissue microarrays for research. We have increased the number of specimens in VATR to nearly 200,000 tissue samples. We are continuously entering data from the 200,000 blocks and now have 54,473 reports that further explain and describe the archives. The reports are not directly linked to any personal identifiers or names and meet all HIPAA/CLIA regulations. During this year we have begun the process of imaging representative blocks from the cases and adding demographic data. The material from future years will have digital information on age, sex, and diagnosis and will be linked to image files. These samples will be used in cellular and molecular protocols approved by our Institutional Review Board. Since its inception, the VATR program has been used by 24 registered users who have submitted 534 requests for searches and 101 subsequent tissue requests. In collaboration with Rick Hay, we have augmented the VATR program with freshly frozen tissues from the tissue acquisition program. This HIPAA-compliant program involves the active cooperation of patients, surgeons, and pathologists from area hospitals, and the surgical tissues collected are used primarily in cDNA and Affymetrix gene expression studies. This collection also provides the participating physicians with access to research collaborations, with the aim of facilitating the translation of research results into clinical practice. The goal of this project is to develop genetics-based diagnostic classification of human disease. There is a Scientific Advisory Board for this project comprising members of VARI and of the Spectrum Health pathology, surgical and medical oncology, and surgery departments. Original research within our labs focuses on quantification of images or arrays and the development of objective measurable data from images. A recent paper by Rozenblatt-Rosen et al. used a program written by Eric Kort for determining the co-localization of pixels that express unique fluorescent properties as well as the number of lumens or vessels in IHC-stained preparations. This is a direct extension of our Cytometry paper of 2003. We have recently obtained funding to advance our understanding of breast cancer in collaboration with Ilan Tsarfaty, George Vande Woude, and Craig Webb. We have begun molecular imaging of breast cancer and correlation of the findings with Affymetrix gene expression. Other collaborations within VARI involve Met and HGF/SF in cells and tissues; the location of gene-targeted proteins in rodents; and the evaluation of monoclonal antibodies as diagnostic reagents. We have been funded by the Michigan Technology Tri-Corridor to develop the commercialization of diagnostic gene expression (collaboration with Bin Teh), imaging of primary tumors (Rick Hay), and expression of mRNA in human sperm as an indicator of fertility or sterility (Stephen Krawetz). We are in the early stages of developing a program in neuropathology with a concentration on Parkinson’s disease, starting with the morphological and genomic characterization of human adult stem-cell populations of specific neurons. This year we have a student from Bath University in the U.K. The Bridges to the Baccalaureate program is a collaboration to support the recruitment of women and minorities into science careers; Dr. Resau is a coinvestigator and the VAI site coordinator for the program. In addition this year, we partnered with the Grand Rapids Area Pre-College Engineering Program (GRAPCEP) to build a school within a school for science education and instruction in Creston High School of the Grand Rapids Public School system. Our GRAPCEP mentorship program continues to be funded by Pfizer for a fifth year. Seven high school students have trained in the laboratory and are now in baccalaureate programs. 39

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