Development of Tumor Specific Transcript Panels

Project: Research project


DESCRIPTION (provided by applicant): Human tumors have numerous genetic and epigenetic alterations that produce complex downstream changes in the expression levels of many genes. While some of these changes are necessary for the maintenance of the malignant phenotype, many others are sporadic or non-essential. One of the main challenges in new drug development for cancer is the identification of relevant therapeutic targets among a substantial number of these spurious background changes. Ideally, such a target would be tumor specific, present in a majority of tumors and necessary for tumor cell survival. The central hypothesis in this proposal is that tumors that appear different based on genetic changes alone, share converging downstream tumor specific pathways. The short-term objective of this proposal is to develop laboratory tools that are necessary to find these convergent pathways. The long-term objective is to validate our laboratory findings in primary human tumor samples and a broad cell line panel. The specific aims of the project are: 1.) Establishing a panel of human tumor cell lines by ectopic expression of different transforming gene sets. 2.) Identification of the mRNAs expression pattern changes common to multiple transformation pathways and cellular backgrounds. 3.) Organization of the individual tumor specific changes into common pathways. The significance of this project is that the tools that are developed in the short-term will have broad applications for all human tumor types, and in the long-term, the results will have the potential to lead to new cancer treatment strategies. The experimental design will take advantage of unique tumorigenic human cell lines expressing defined transforming genes. These cells were recently developed by the laboratory in which these studies will be performed. Suppression subtractive hybridization (SSH) will be used to compare cell lines with different genetic backgrounds, in order to progressively eliminate all the genes that are non-essential for the tumorigenic phenotype. This tumor restricted gene panel will be used to profile primary human tumor samples. The pre-selection process will simplify data collection and interpretation. The priority of this project will be the development of the tumor restricted gene panel as a tool, rather than large scale expression profiling. The candidate, Dr. Tan A. Ince, will work at the Whitehead Institute for Biomedical Research, under the mentorship of Dr. Robert Weinberg and with the long-term goal of establishing an independent research career.
Effective start/end date8/13/016/30/08


  • National Institutes of Health: $139,320.00
  • National Institutes of Health: $69,660.00
  • National Institutes of Health: $69,660.00
  • National Institutes of Health: $139,320.00
  • National Institutes of Health: $139,320.00
  • National Institutes of Health: $139,320.00


Cell Line
Essential Genes
Tumor Cell Line
Biomedical Research
Cell Survival
Research Design
Messenger RNA
Pharmaceutical Preparations


  • Medicine(all)