Nathan Ocampo

Nathan Ocampo, senior biomedical engineering at Columbia University, characterized ITGB1 and SLC39A9 mutations in cancer cell lines as well as developed novel organoid for use in further characterization.

The BSRP program and my mentor helped me develop both strong skills in research, but also science communication. The cohort was unforgettable and all the BSRP staff helped make this experience extremely impactful in my path towards my future career goals.Utilizing in vitro 2D cancer screens, researchers have uncovered many cancer dependencies, however, the shortcomings of relying on this approach alone are unknown. To generate more physiologically relevant screening modalities, we created a pipeline for the discovery of novel cancer dependencies using engineered organoid models and in vivo intracardiac injection xenograft murine models of metastasis. Further, we characterized in vivo cancer dependencies that arose from our screens that were not seen in parallel 2D screens. Specifically, we investigated integrin beta 1 (ITGB1), a transmembrane protein that connects to the extracellular matrix (ECM), and Zip9 (SLC39A9), a zinc transporter protein. To study both dependencies, we developed organoid models that can be perturbed with CRISPR/enCas12a gene knockout and gene overexpression with CRISPRa, working towards unbiased characterization of these phenotypes with convolutional neural networks and immunofluorescent microscopy images. ITGB1 will continue to be characterized in multiple organ-mimicking ECMs to see the effect on cell state and viability, and SLC39A9 will be characterized in zinc deprived environments. Because of the lack of characterization, we also investigated the localization of Zip9 within all our models to contextualize the mechanism of a zinc transporter dependency. We plan to analyze differential gene expression to determine the transcriptional profile of cancer cell lines with these dependencies and identify associated genes. These novel assays for assessing cancer dependencies in organoids will help to generate a more relevant picture of both dependencies than traditional studies in 2D models. Characterizing these dependencies should provide a more complete understanding of the complex requirements of cancer cells in the tumor microenvironment.

Project: Characterization of ITGB1 & SLC39A9 in Organoid Models

Mentor: Dean Procter, MIDAS Team, Golub Lab, Cancer Program