Abstract
The long term goal of this project is to describe how the intricate structure of mammalian retina is made during
development. To achieve this goal, this proposal focuses on developing novel molecular recording
technologies that enable reconstruction of cell lineage and molecular history based on in situ endpoint
measurements. These methods leverage recent advances in genome editing technology to make targeted
mutations in synthetic barcode arrays that make a permanent and inheritable record of history of individual
cells in their genome. Importantly, the methods developed here are compatible with imaging based readout of
information and can be combined with in situ transcriptional profiling to provide a unified view of the current
state, past history, and spatial context of individual cells. By applying these methods, I will map the clonal
structure of the mouse retina, investigate the extent to which local signals affect cell fate decisions, reveal the
stochastic versus pre-programmed aspects of retinal lineage, and reconstruct the single cell trajectory of retinal
progenitor cells as they proceed through different competence states. Together, these experiments provide
fundamental new insight into cell fate specification process in mammalian retina and, therefore, will aid the
future efforts in regenerative medicine to remedy conditions in which misspecification or degeneration of retinal
neurons lead to blindness.
My career goal is to run an academic lab that studies how cells acquire and maintain different identities during
development, using molecular recording and synthetic biology approaches. The proposed experiments will
provide me with further training in retina biology, multiplexed sequential FISH technology, and single cell
genomics that are required for this goal. I have developed a detailed training plan with my mentor, Dr. Michael
Elowitz, to help me transition to independence. I will meet regularly with Dr. Elowitz to discuss research
progress, strategies for grant writing, student mentorship and lab management. To practice my mentorship
skills, I will oversee the work of a graduate student and a technician in the lab. To broaden my scientific
network, I will present my work at 2-3 international meetings per year. To seek out additional mentorship, in
areas critical to the success of this project, I will collaborate with and receive guidance from Dr. Connie Cepko,
expert in retina biology, Dr. Long Cai, pioneer in sequential FISH methods, and Dr. Jay Shendure, expert in
single cell genomics. As a member of Caltech Division of Biology and Biological Engineering, I will have
access to leaders in synthetic as well as developmental biology, cutting-edge courses and training programs,
and state-of-the-art core facilities. The Pathway to Independence Award will provide the time and resources
required to initiate an ambitious research program on the reconstruction of developmental history of
mammalian retina.