Dissertations, Theses, and Capstone Projects
Date of Degree
9-2025
Document Type
Doctoral Dissertation
Degree Name
Doctor of Philosophy
Program
Biology
Advisor
Mark Emerson
Committee Members
Andreas Kottmann
Daniel Weinstein
Bo Chen
Andrea Viczian
Subject Categories
Cell Biology | Developmental Biology | Genetics | Genomics
Keywords
Photoreceptors, sequencing, genetics, vision, development
Abstract
The vertebrate retina is a complex tissue made up of seven major cell subtypes which during development must differentiate and localize into a highly organized structure. These neuronal cells do not regenerate if damaged or diseased, and the progressive deterioration of cone photoreceptor cells is the leading cause of age related blindness. Currently there are no cures for this disease, but one promising therapeutic avenue is cell transplantation research. If we can further elucidate the gene regulatory networks that define cone cell development, this knowledge could be applied to the generation of healthy cone cells in clinically relevant models.
The rod dominant mouse retina is specifically amenable during development to in vivo gain and loss-of-function assays which can upregulate cone photoreceptor signals more readily observable against the mostly rod background. In this dissertation I investigated whether the use of a cis-regulatory element from the Crx gene can increase the targeting of developing photoreceptors. This research characterizes the in vivo activity of this element for the first time, and explores its use as a tool for gain-of-function and loss-of-function experiments.
I further investigated several developmental stages during which the progenitors or developing precursor cells which give rise to photoreceptors can be targeted. I then used previous research from our lab on early cone transcriptomics to prioritize a list of genes which may be able to initiate the cone fate when overexpressed during development, and then tested these genes in my optimized gain-of-function assay. Given our initial results we focused on the Onecut1 gain-of-function experiments, in which we observed the most potent initiation of cone gene upregulation. I implemented a specific cell sorting strategy based on these results and performed multimodal single cell sequencing on the precursor enriched population for both control and gain-of-function conditions. The analysis elucidates the gene regulation of normal rod development, as well as the extent of photoreceptor reprogramming in the Onecut1 induced cells.
Recommended Citation
Patierno, Brendon M., "Retinal Precursor Cell Enriched Multiomic and Pseudo-Time Analysis of Developing and Reprogrammed Photoreceptors" (2025). CUNY Academic Works.
https://academicworks.cuny.edu/gc_etds/6424
