My laboratory has initiated a functional genomics program here at AECOM. Usually we associate the study of gene expression and function with one or at most a few genes. We are now capable of simultaneously and quantitatively studying thousands of genes at once using DNA microarray chip technology. To do this we have built a robot to deposit thousands of PCR products of cDNA clones on small glass slides. Current generation chips contain 28,000 genes. We have always been interested in embryonic gene expression, lineage commitment and developmental biology. We have been using microarray technology to study cardiac myocyte differentiation from stem cell models in cell culture (see publications below).
Our goals are to determine all of the gene expression changes associated with lineage commitment and then terminal differentiation. We are in the process of examining the contributions of individual transcription factors and signaling systems by reintroducing estrogen receptor fusions of key transcription factors back into cells, activating the factors one at a time with estrogen and profiling downstream events with microarrays. In addition an SiRNA approach is being used for “loss of function” analysis followed by microarray comparisons. In this systematic way, we hope to develop a hierarchy of events that result in neural or cardiac myocyte differentiation. We are also using in vivo approaches in mice that combine BAC transgenics expressing florescent protein from individual cardiac and vascular promoters (Nkx2.5, Gata4, Mef2A) with laser capture microscopy and microarrays.
In this way, we can for the first time purify embryonic cells of interest and use high throughput expression analysis. Squamous cell carcinomas of the head and neck are particularly difficult to classify using histological methods. The tumors arise at different anatomical locations and the prognosis of patients’ tumors originating at different sites is difficult to ascertain. My laboratory is collaborating with Drs. Prystowsky (chairman of Pathology) and Belbin to examine the gene expression profiles from a series of clinical samples using cDNA microarrays.
We have developed statistical and clustering methods to ask if gene expression patterns correlate with clinical observations. A set of about 400 genes was identified whose pattern of expression could be correlated with the patient outcome. Thus, we have established for this disease model the hope that gene expression profiles can be used as a diagnostic tool to assist the physician in determining the course of treatment. Using these methods, we hope to develop molecular markers for accurate diagnosis and to identify candidate proteins for new drug targets. We have recently begun a very large prospective study of patients containing squamous cell carcinomas. In addition, we are in the process of obtaining additional sets of patient material where the response to chemotherapy and radiation will be known.
We will attempt to correlate gene expression patterns with future sensitivity and resistance to these agents.
Cheung, V.G., Morley, M., Aguilar, F., Massimi, A., Kucherlapati, R., and Childs, G. (1999). Making and reading microarrays. Nature Genetics 21, 15-19.
Harris, T.M., Massimi, A., and Childs, G. (2000). Injecting new ideas into microarray printing. Nat. Biotech. 18, 384-385.
Gonzalez, J., Harris, T.M., Childs, G., and Prystowsky, M. (2001). Rapamycin blocks IL2-driven T cell cycle progression while preserving T cell survival. Blood Cells, Molecules, and Diseases, 27, 572-585.
Belbin, T., Singh, B., Barber, I., Socci, N., Wenig, B., Smith, R., Prystowsky, M., and Childs, G. (2002). Molecular classification of head and neck squamous cell carcinoma using cDNA microarrays. Cancer Research 62, 1184-1190.
Childs, G., DeRisi, J., Harris, T., Holloway, A., Hou, BH, Massimi, A., Murphy, M., Somerville, S. Printing Spotted Glass Microarrays. In Molecular Cloning a Laboratory Manual Volume IV: DNA Microarrays. Sambrook and Bowtell editors, Cold Spring Harbor Press, (2002) Section 2, 61-100.
Wei, Yi, Harris, T.M. and Childs, G. (2002). Global expression patterns during neural differentiation of P19 embryonic carcinoma cells. Differentiation, 70, 204-219.
Harris, T.M. and Childs, G. Global gene expression patterns during differentiation of F9 embryonal carcinoma cells into parietal endoderm. (2002) Functional and Integrative Genomics, Aug;2(3):105-119.
Peng, C.F., Wei, Y., Levsky, J.M., McDonald, T.V., Childs, G., and Kitsis, R.N. (2002) Microarray analysis of global gene expression patterns during cardiac myocyte differentiation in P19clone6 cells. Physiological Genomics, 9(3):145-55.
Shin, C.H., Liu, Z.-P., Passier, R., Zhang, C.-L., Wang, D.-Z., Harris, T.M., Yamagishi, H., Richardson, J.A., Childs, G. and Olson, E.N. (2002) Modulation of cardiac development by HOP, an unusual homeodomain protein. Cell, 110, 725-735.
Sanchez-Carbayo, M., Socci, N., Charitonovicz, E., Lu, M., Prystowski, M., Childs, G., and Cordon-Cardo, C. (2002). Molecular profiling of bladder cancer cell lines using cDNA microarrays: defining histogenesis and biological phenotypes. Cancer Research 62, 6973-6980.
Sanchez-Carbayo, M., Belbin, T., Scotto, K., Scotlandi, K., Prystowsky, M., Baldini, N., Childs, G., Cordon-Cardo, C. (2003). Expression Profiling of Osteosarcoma Cells Transfected with MDR1 and NEO Genes: Regulation of Cell Adhesion, Apoptosis, and Tumor Suppression-Related Genes. Lab Invest. 2003 Apr;83(4):507-17.
Sanchez-Carbayo M, Socci ND, Lozano JJ, Li W, Charytonowicz E, Belbin TJ, Prystowsky MB, Ortiz AR, Childs G, Cordon-Cardo C. (2003) Gene Discovery in Bladder Cancer Progression using cDNA Microarrays. Am J Pathol. 2003 Aug;163(2):505-16.
Belbin, T.J., Gaspar, J., Haigentz, M., Perez-Soler, R., Keller, S.M., Prystowsky, M.B., Childs, G., and Socci, N.D. (2004) Indirect Measurements of Differential Gene Expression with cDNA microarrays. Biotechniques 36, 310-315.
Birge, R.B., Wadsworth, S., Akakura, R., Abeysinghe, H., Kanojia, R., Macielag, M., Desbarats, J., Escalante, M., Singh, K., Sundarababu, S., Parris, K., Childs, G., August, A., Siekierka, J. and Weinstein, D.E. (2004) A role for Schwann cells in the neuroregenerative effects of a non-immunosuppressive FK506 derivative, JNJ460. Neuroscience 124, 351-366.
Wreesmann, V.B., Sieczka, E.M., Socci, N.D., Hezel, M., Belbin, T.J., Childs, G., Patel, S.G., Patel, K.N., Tallini, G., Prystowsky, M., Shaha, A.R., Kraus, D., Shah, J.P., Rao, P.H., Ghossein, R. and Singh, B. (2004) Genome-wide profiling of papillary thyroid cancer identifies MUC1 as an independent prognostic marker. Cancer Res. 64, 3780-3789.
Cao, J.Q., Belbin, T., Socci, N., Balan, R., Prystowsky, M.B., Childs, G. and Jones, J.G. (2004) Distinctive gene expression profiles in human endometroid and serous carcinomas of the uterus of cDNA microarrays. Intl. J. Gyn. Pathol. 23(4), 321-329.
Belbin TJ, Singh B, Wreesmann V, Socci N, Masterson J, Smith R, Cordone Cardo C, Sanchez-Carbayo M, Prystowsky MB, Childs G. (2004) Molecular Profiling of Tumor Progression In Head and Neck Squamous Cell Carcinoma. Archives of Otolaryngology- Head and Neck Surgery- in press.
H. Liu ,Thomas M Harris, T.M., H., Kim, H.H., and Childs, G. Identification of Nkx2.5 and Cripto Target Genes During Cardiac Myocyte Differentiation of P19 Clone6 Cells (2004) submitted for publication.
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