Large-scale identification of CIS-regulatory modules for targeting retinal cell types in primates

The National Institutes of Health National Eye Institute awarded a $1.792 million Cooperative Agreement to the University of California, Los Angeles on September 1, 2026, under the Vision Research program (CFDA 93.867). The award funds development of adeno-associated virus vectors incorporating cell-type-specific cis-regulatory modules to target 23 distinct retinal cell types in primates, enabling precise labeling and functional manipulation of specific cells. The project aims to dissect cellular and circuit principles of early visual processing and to develop cell-type-specific therapeutic targeting for blinding conditions in humans. Work will be performed in Los Angeles, California, with a period of performance extending through June 30, 2031. The recipient will use existing human retinal cell atlases and newly generated single-cell RNA sequencing and single-cell ATAC sequencing datasets from marmoset and human retina to systematically identify and synthesize cis-regulatory modules enriched in the 23 retinal cell types. Novel modules will be packaged in adeno-associated virus capsids to generate screening libraries, with active vectors identified through high-throughput sequencing following injection in marmosets. Selected vectors will be validated for cell-type specificity in marmoset and human retinal explants.

Abstract

Primates, including humans, possess a remarkable and highly specialized visual system that enables intricate perception of fine detail, color, and motion. This specialization begins in the retina, with a diversity of cell types, each with distinct morphology and physiology, that form a complex neural circuit for processing visual signals. How each of these cell types contributes to vision remains largely unknown due to the lack of cell-type specific tools in primates. The lack of tools also poses a barrier to developing treatments for blinding diseases. Notably, the molecular signatures of retinal cells are poorly conserved across non-primate species and thus, their translatability is assured only if they are developed in primates. To address this unmet need, we aim to develop adeno-associated virus (AAV) vectors incorporating cell-type-specific CIS-regulatory modules (crms) to specifically target 23 retinal cell types in primates. These viral tools will enable precise labeling and functional manipulation of specific cell types and facilitate two subsequent goals: (1) to dissect the cellular and circuit principles of early visual processing and (2) to develop cell-type specific targeting of therapeutics to treat blinding conditions in humans. In aim 1, we will use existing human retinal cell atlases and our newly generated scrna-SEQ and scatac-SEQ datasets from marmoset and human retina to systematically identify and synthesize CIS-regulatory modules (crms) enriched in the 23 distinct retinal cell types in primates. These novel crms will be packaged in state of the art AAV capsids to generate AAV-crms screening libraries. Active AAV-crms will be identified via high-throughput scrna-SEQ following injection in marmosets. In aim 2, we will validate selected AAV-crms for their cell-type specificity in marmoset and human retinal explants. Specificity will be confirmed via morphology and gene expression. In aim 3, we will establish the ability of AAV-crms to produce functional changes in the retina and develop a web-based catalog for broad dissemination. AAV-crms driving the fluorescent calcium indicator GCAMP8 or the optogenetic tool reachr will be used to measure or manipulate the activity of targeted cell types and verify their morphologies. This information will be catalogued along with prior information learned in the screening of AAV-crms and all data curated in a web-based atlas. The AAV-crms will be maintained and packaged for the smooth transfer of these resources to brain initiative funded dissemination facilities for use across the neuroscience and vision science communities. Successful completion of our studies will enable forward momentum in both the basic and applied sciences. We will not only transform the basic study of visual perception in primates at the level of individual cells and circuits but also advance clinical applications aimed at curing blindness. As such, this proposal meets key significance criteria for the brain initiative armamentarium project. Development of these tools by academia (rather than industry) will ensure the availability and sharing of resources with the broader scientific community.