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Synthetic recording and in situ readout of cell lineage and molecular history in mammalian retina

Award Number: R00EY031782
ORGANIZATION: NATIONAL EYE INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 09/30/2020
PERIOD OF PERFORMANCE END DATE: 11/30/2024

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Synthetic recording and in situ readout of cell lineage and molecular history in mammalian retina - 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.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2025 ( Subtotal = -$1 )
2025	2024	UNIVERSITY OF CALIFORNIA, LOS ANGELES	10889 WILSHIRE BLVD STE 700	LOS ANGELES	CA	90024	LOS ANGELES	USA	Vision Research	000	5	4/11/2025	NON-COMPETING CONTINUATION	-$1
														Subtotal = -$1

Issue Date FY: 2024 ( Subtotal = $249,000 )
2024	2024	UNIVERSITY OF CALIFORNIA, LOS ANGELES	10889 WILSHIRE BLVD STE 700	LOS ANGELES	CA	90024	LOS ANGELES	USA	Vision Research	000	5	12/5/2023	NON-COMPETING CONTINUATION	$249,000
														Subtotal = $249,000

Issue Date FY: 2023 ( Subtotal = $249,000 )
2023	2023	UNIVERSITY OF CALIFORNIA, LOS ANGELES	10889 WILSHIRE BLVD STE 700	LOS ANGELES	CA	90024	LOS ANGELES	USA	Vision Research	000	4	12/8/2022	NON-COMPETING CONTINUATION	$249,000
														Subtotal = $249,000

Issue Date FY: 2022 ( Subtotal = $263,971 )
2022	2022	UNIVERSITY OF CALIFORNIA, LOS ANGELES	10889 WILSHIRE BLVD STE 700	LOS ANGELES	CA	90024	LOS ANGELES	USA	Vision Research	001	3	3/29/2022	EXTENSION WITH OR WITHOUT FUNDS	$14,970
2022	2022	UNIVERSITY OF CALIFORNIA, LOS ANGELES	10889 WILSHIRE BLVD STE 700	LOS ANGELES	CA	90024	LOS ANGELES	USA	Vision Research	002	3	8/11/2022	EXTENSION WITH OR WITHOUT FUNDS	$0
2022	2022	UNIVERSITY OF CALIFORNIA, LOS ANGELES	10889 WILSHIRE BLVD STE 700	LOS ANGELES	CA	90024	LOS ANGELES	USA	Vision Research	000	3	1/31/2022	EXTENSION WITH OR WITHOUT FUNDS	$249,001
														Subtotal = $263,971

Grand Total All Awards = $761,971

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Synthetic recording and in situ readout of cell lineage and molecular history in mammalian retina

Award Number: R00EY031782

ORGANIZATION: NATIONAL EYE INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 09/30/2020

PERIOD OF PERFORMANCE END DATE: 11/30/2024

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