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Identification of post-transcriptionally regulated targets by TrIP-Chip/Seq

Keywords: colon cancer, stem cells, post-transcriptional regulation of mRNA, miRNA, Translational Immunoprecipitation-Microarray Analysis (TrIP-Chip), Next-gen sequencing, multi-dimensional protein identification technology (MudPIT), miR-215, thymidylate synthase, dihydrofolate reductase.

Contact: Jingfang Ju
Phone: (631) 444-2176
E-mail: jingfang.ju@stonybrookmedicine.edu
State University New York at Stony Brook

DESCRIPTION (provided by applicant): Resistance to chemotherapy is one of the major reasons for the failure of cancer treatment. Post- transcriptional and translational control plays an important role in chemoresistance. Currently there is no available high throughput approach to investigate post-transcriptional and translational control mediated by RNA binding proteins or non-coding microRNAs from a small number of cells. Our primary objective in the proposed project is to apply our newly developed Translational Immunoprecipitation-Microarray Analysis (TrIP-Chip) (1) to discover post-transcriptionally regulated mRNA targets mediated by miR-215 from a small number of colon cancer stem cells. Our recent studies revealed that miR-215 is involved in regulating some key anticancer targets, e.g. thymidylate synthase and dihydrofolate reductase. Thymidylate synthase (TS) is a folate-dependent enzyme that catalyzes the reductive methylation of dUMP by 5,10-methylenetetrahydrofolate to form dTMP and dihydrofolate. Because the TS-catalyzed enzymatic reaction provides the sole intracellular de novo source of thymidylate, an essential precursor for DNA biosynthesis, TS has been an important target for cancer chemotherapy for over 50 years. The enzyme dihydrofolate reductase (DHFR) catalyzes the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate. This reaction provides the key intermediate in one-carbon transfer reactions. DHFR plays a critical role in folate homeostasis, and is required for the de novo synthesis of purines, thymidylate and certain amino acids. Therefore, DHFR has served as a critical target in cancer chemotherapy. The mRNAs regulated post-transcriptionally by miR-215 will be validated at the protein level by a sensitive, high throughput shotgun proteomic analysis based on multi-dimensional protein identification technology (MudPIT). We will further develop a TrIP-Seq approach to increase both the coverage and sensitivity to detecting rare transcripts potentially at the single cell level. Three specific aims are proposed: Specific Aim 1. Identify post-transcriptionally and translationally regulated mRNA targets of miR-215 using TrIP-Chip approach. Specific Aim 2. Validate miR-215 mediated targets by high throughput proteomic analysis. Specific Aim 3. We will further develop the TrIP-Chip approach by integrating next generation sequencing based expression analysis (TrIP-Seq) to increase coverage and detection sensitivity from a small number of cells. PUBLIC HEALTH RELEVANCE: Currently, there is a lack of high throughput approach to study post- transcriptional and translational control with a small number of cells. We have developed a novel Translational Immunoprecipitation-Array Gene expression analysis (TrIP-Chip) technology that allow us to investigating post-transcriptional and translational regulated genes from as few as 500 cells. We believe with the improvement of the dynamic range of the next generation deep sequencing platform (e.g. Illumina Instrument), we can potentially analyze translational control from a single cell. The proposed project will develop and apply this new approach to discover miR-215 mediated targets and functional significance in colon cancer and colon cancer stem like cells. The technology will have a broad application not only in cancer but other human diseases as well.

Kudo et al, Translational control analysis by tranlationally active RNA capture/microarray analysis (TrIP-Chip), Nucleic Acids Res, Jan 2010

CA147966-01A1

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