Determining the cell fate programs of mammalian retina development

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Project Summary/Abstract The overarching goal of this proposal is to understand how the stereotypical structure of retina forms during embryonic development. Towards this goal, this proposal seeks to develop novel molecular recording technologies that allow the reconstruction of lineage history based on endpoint measurements. This method leverages genome editing techniques to stochastically create heritable mutations within synthetic barcode arrays that accumulate edits over time. Because readout of these arrays is compatible with spatial transcriptomics technologies, these methods when combined will allow the simultaneous capturing of transcriptional cell state, lineage relationships, and spatial position of single cells within retina tissue. The resulting lineage tree datasets will then be analyzed using a novel statistical tool termed Lineage Motif Analysis, a computational approach to identify all significantly over- or under-represented cellular patterns. This approach systematically enumerates all possible arrangements of observed fates on progressively larger subtrees and then compares their frequencies to those expected in a null model based on uncorrelated cell fate between cell divisions. Lineage trees will reveal how birth-order of cell types is regulated on the clonal level and lineage motifs will reveal the extent to which lineage in the retina is stochastic or preprogrammed. Furthermore, lineage motifs represent direct insight into the “rules” that govern how the retina forms during development, and provide a way to describe how such “rules” change in different contexts like disease or pharmacological perturbation. The datasets and analysis proposed here will inform the development of new therapeutic strategies for regenerative medicine to treat retinal diseases that lead to blindness. My training program outlined here will equip me with the necessary tools and knowledge to (1) carry out the aims of this proposal and gain novel biological understanding, and (2) advance me towards my career goal of leading a research team focused on studying the fundamental principles that underlie embryonic development and disease progression. I will work with Dr. Long Cai, a pioneer in spatial transcriptomics, to learn imaging and image processing techniques, as well as Dr. Carlos Lois, an expert in neurobiology, to learn mouse manipulation and surgical procedures. Dr. Elowitz and I will meet regularly to discuss my research progress, writing plans for paper publications and grants, teaching/mentoring students, and opportunities to present my research at Caltech and national conferences. As a PhD student at Caltech, I will have access to leaders well-versed in applying quantitative approaches to study developmental biology, state-of-the-art core facilities, and cutting-edge coursework in both biology and statistics. By funding the rest of my PhD research, this fellowship will enable me to uncover the fundamental principles that underlie retina development and set me up for independence as I transition towards becoming an independent investigator in my later career.