Fresh Human Retinal scRNA-seq Atlas Reveals a Novel Cone Subtype and Cellular Diversity

Abstract

The human retina has a remarkable diversity of cell types, which is crucial for understanding the mechanisms underpinning visual development and function. While single-cell RNA sequencing (scRNA-seq) has advanced our understanding of retinal biology, most studies have relied on postmortem or frozen samples, potentially missing important transcriptional information. The aim of this study was to create the first comprehensive scRNA-seq atlas of fresh human retinal samples from living donors and recently deceased individuals using scRNA-seq technology. A total of 106,829 cells were analyzed, which were collected from nine retinal samples using standardized scRNA-seq workflow. Our findings identified several novel subtypes of known retinal cells, including new subgroups of cones and amacrine cells (ACs), each characterized by distinct gene expression profiles. Notably, we discovered a novel cone subtype, the ELF1-Cone, which shows a clear developmental trajectory from mlCone precursors. This subtype exhibits unique functional properties and metabolic profiles, regulated by key transcription factors ELF1 and PRKAA1. We also identified five distinct AC subtypes, including three GABAergic ACs, each with unique gene expression profiles and functional characteristics. Our study highlights the critical importance of using fresh human retinal tissue for accurate cellular mapping and trajectory inference. Significant differences were observed between fresh and postmortem retinal samples in terms of pseudo time analysis such as RNA velocity. We also performed a comparative analysis of diabetic without retinopathy, diabetic retinopathy, and non-diabetic samples, suggesting diabetes-related transcriptional variation. In conclusion, we present a comprehensive human retina atlas using fresh samples that contribute to existing knowledge of retinal cell diversity, function, and transcriptional profiles. Our study is a milestone for future studies that will improve understanding of retinal biology and disease mechanisms.