Cherry trees
University of Washington
Department of Biochemistry
The Morris Lab

$1.3 M GO grant funded by NCI

Title:Application of RiboTag-seq to Exploration of Tumor Microenvironments

PI: David Morris, Department of Biochemistry

CoPI: Pete Nelson, FHCRC

CoPI: Jay Shendure, Department of Genome Sciences



This is a proposal to seize the opportunity of the co-existence of two paradigm-shifting technologies at the University of Washington and, by adding a third, bring them together to address one of the major challenges in biomedical research – quantitative descriptions of intricate developmental, physiological and pathological relationships in expression patterns between multiple cell types in complex tissues.  Dr. Morris is a biochemist/molecular biologist who has developed the “RiboTag mouse”, which enables isolation and analysis of ribosome-associated transcriptomes of individual cell types in a tissue without prior cell separations.  Dr. Shendure is a genome scientist who pioneered the development of one of the first next-generation sequencing platforms and has extensive expertise in developing new technologies for second-generation sequencing and analysis of large-scale genomic data, including RNA-Seq.  The new hybrid technology – RiboTag-seq – will not only provide highly quantitative measurements of transcript levels in individual cell types, but will yield robust estimates of the translation of individual proteins by mapping the numbers and positions of ribosomes engaged with transcriptomes of interest.   Drs. Morris and Shendure are teaming with Dr. Nelson, who is at the Fred Hutchinson Cancer Research Center and an expert in tumor-microenvironment interaction, to apply RiboTag-seq to analyzing reciprocal interactions between a tumor and its adjacent cellular milieu, i.e. the tumor microenvironment.   In this instance, prostatic epithelial and stromal transcriptomes will be analyzed during the course of carcinogenesis in a well-defined mouse model.  The results from RiboTag-seq will be compared with those from expression arrays performed in parallel and the strengths and weaknesses of the two approaches evaluated.  The outcome of this analysis of prostate cancer in situ will lead to evaluation of two commonly used models of neoplasia – tumor xenografts in nude mice and co-culture in vitro of tumor cells and stromal fibroblasts.  When completed, the project will provide the basis for more expansive studies of tumor microenvironment and, more significantly, allow extension of the RiboTag-seq technology to examination of any other complex tissue of interest.