Abstract
Purpose :
The optic nerve is crucial in various visual disorders that lead to blindness, such as glaucoma, toxic amblyopia, and optic nerve atrophy. Our goal is to develop a single-cell atlas of the optic nerve and optic nerve head. Utilizing single-nucleus ATAC sequencing (sn-ATAC-seq) and single-nucleus RNA sequencing (sn-RNA-seq), we aim to compile a comprehensive list of cell types in these tissues and to elucidate and compare gene expressions and regulatory mechanisms across different genders and ages.
Methods :
Samples from the human optic nerve and optic nerve head were collected, dissected, and processed into single nuclei suspensions. 10X Genomics capture and library preparation followed the manufacturer's guidelines using v3 chemistry kits. Counts were mapped to the human genome reference (GRCh38-2020-A) using CellRanger v. 7.1.0.
Results :
A total of 588,824 and 691,671 nuclei from 72 donors of diverse ancestry, including 32% White, 32% Black, 27% Hispanic, and 9% Asian, were profiled with sc-ATAC-seq and sn-RNA-seq, respectively. The donors span a wide age range of 10–90 years, with an average age of 55.75 years. Upon clustering, a total of 40 cell types were identified, including Astrocytes, B cells, T cells, macrophages, fibroblasts, oligodendrocytes and their precursor cells, pericytes, vascular endothelial cells, and Schwann cells. Gene set enrichment analysis reveals an enrichment of genes associated with glaucoma and optic nerve injury in various cell types of the optic nerve and optic nerve head. Some of these genes exhibit cell-type-specific expression. For instance, Foxc1, which is associated with childhood glaucoma, is exclusively expressed in optic nerve clusters. Furthermore, integrative multi-omics analysis has identified key transcription factors and gene regulatory networks that are important for defining each cell type and their functions. To facilitate public access to these datasets, we have created web browsers for the optic nerve (https://u247700.shinyapps.io/opticnerve/) and the optic nerve head (https://u247700.shinyapps.io/opticnerveheadatlas/).
Conclusions :
We have successfully developed a multi-omics single-cell atlas of the optic nerve and optic nerve head. This comprehensive atlas is a foundational resource for a deeper understanding of the cell types, transcriptome, and epigenome profiles in these critical regions
This abstract was presented at the 2024 ARVO Annual Meeting, held in Seattle, WA, May 5-9, 2024.