We like to explore, understand and utilize the role of different species of RNAs in various biological contexts. Our interest ranges from understanding how the RNA levels are regulated in the cells under various physiological states to developing RNA based diagnostic tools for early and sensitive detection of various diseases.
The recent focus of lab is to understand the role of non coding RNAs and transcriptional regulation of pediatric cancer Ewing's Sarcoma. We are a very collaborative group and we active seek new avenues to inquire the whereabouts and association of different RNA species at single molecule resolution.
Some of our recently completed and ongoing adventures :
Fusion-FISH: Imaging gene fusion products at single molecule resolution
We have developed Fusion-FISH, a novel assay for single molecule resolution imaging of RNA products of gene fusions that are leading cause of many cancers including Chronic Myeloid Leukemia (CML) and Ewing's Sarcoma (ES). This technology can be used to detect gene fusion transcripts products of any translocation and thus can be developed into a diagnostic assay.
Currently we are working to understand gene expression regulation and role of non coding RNAs in Ewing's Sarcoma.
Gene expression regulation at the level of RNA: understanding transcriptional signature of individual cells
We utilize single molecule RNA imaging to understand the transcriptioanl signature of malignant cells. We used Chronic Lymphocytic Leukemia (CLL) as a model system to identify the differential expression of key regulatory RNAs in mouse models and engineered murine cell lines in order to understand the initiation of Chronic lymphocytic leukemia (CLL).This work contributed significantly to the quest of finding the cell of origin of CLL and hence provides significant leads into the role of microRNA during early B cell development and regulating the balance between B1 and B2 populations.
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We are now further exploring the transcriptional signature of therapy resistant cells and also the role of other non codingRNAs in early B cell development that lead to CLL.
RNA localization and processing: taking snapshots of RNA in action
RNA splicing is a major step in regulating gene expression. It has been lately appreciated that although most of the splicing occur co transcriptionally, a fraction of transcripts actually undergo post transcriptional splicing. We utilized smFISH to image the phenomenon of post transcriptional splicing and to understand the factors that lead to uncoupling of splicing and transcription.
Currently we are utilizing this methodology to understand the alternative splicing in Ewing's Sarcoma.
Understanding mRNA localization in neurons
To understand the molecular events that take place when neurons form connections with other neurons in the hippocampus, a region of the brain that is believed to be the storehouse of acquired memories, we explored the transport of dendritically localized mRNAs in hippocampal neurons. RNA transport granules are believed to deliver translationally repressed mRNAs to synaptic sites in dendrites, where synaptic activity promotes their localized translation. Imaging nine different dendritically localized mRNA species with single-molecule sensitivity and sub-diffraction-limit resolution in cultured hippocampal neurons, we found that there is just one molecule of mRNA in each RNA granule. These results support a model in which mRNA molecules are transported to distal reaches of dendrites singly, and independent of other mRNAs, thereby enabling a finer control of mRNAontent within synapses.
Currently we are developing genetically encodable probes to image neuronal mRNA dynamics in live cells