First single-cell atlas of the human eye constructed

Scientists from the Agency for Science, Technology and Research (A*STAR)’s Institute of Molecular and Cell Biology (IMCB) have constructed the world’s first single-cell atlas of the human and porcine eyes. This has allowed them to create a disease map of genes involved in eye disorders across the different cell types, as well as the key switches which control cell specialisation of individual ocular tissues. The work would help to provide new insights about human eye diseases and age-related eye disorders, and potentially pave the way for regenerative medicine and cell replacement therapies for eye diseases.

The research team, led by IMCB, consisted of researchers from the National University of Singapore (NUS), Nanyang Technological University (NTU), Singapore Eye Research Institute (SERI), Mayo Clinic, Icahn School of Medicine at Mount Sinai, University of Melbourne, and Shenzhen Eye Hospital.

The human eye comprises different cell types from different developmental origins and functional roles. In order to decipher this diversity of cellular functions using single cell RNA sequencing, the research team catalogued over 50,000 cells in human and porcine eyes, and developed a cell atlas of these eyes that distinguishes individual cells by the activity of their genes.

As certain eye disorders are associated with mutations in the human genes, the atlas which profiles disease-causing genes across all cell types of the eye, could aid understanding of how cell types are affected by such disorders. A map of cell surface proteins that can act as viral entry receptors in the human eye could shed light on how infections could travel through ocular route. The research showed that ACE2 and TMPRSS2, the primary cell surface proteins responsible for entry of SARS-CoV-2 into human, are expressed in the conjunctival cells of eye. Similar observations have been reported from different research groups, suggesting an infection from ocular route is likely.

 Single-cell transcriptome atlas from non-retina cells in the human eye

Fig. 3

a tSNE plot visualisation of cells obtained from scleral and choroid layers of the eye. Five transcriptionally distinct clusters were observed. b tSNE plot visualisation of cells obtained from the cornea of the eye. Seven transcriptionally distinct clusters were observed. c tSNE plot visualisation of cells obtained from iris pigmented epithelium, iris muscle, and stromal region of iris. Seventeen transcriptionally distinct clusters were observed in the iris region of the eye. d Selecting highly variable interacting pairs that exhibited high cell type-to-cell type variation in the dataset. e Hierarchical clustering of similar cell–cell signalling probability scores and visualised on a tSNE plot. f Global cell–cell interaction map across cell type of the eye. Edge weights represent the probability of signalling between cell clusters.

“It is fascinating to observe the cross-talk of ocular cells through the interaction of signalling molecules with receptors. This will help us to understand how individual cell responds to external factors like injury,” said Mr Pradeep Gautam, PhD scholar at IMCB, A*STAR, who is the co-first author of the paper.

Eye diseases such as glaucoma, which is the leading cause of blindness globally, is caused by the degeneration of retinal ganglion cells (RGCs). Using embryonic stem cells as a platform for differentiation, the research team generated RGC progenitor cells in culture and validated that a switch KLF7 could accelerate RGC generation, opening up opportunities for the cultivation of lab grown RGCs to replace damaged RGCs as a potential therapy.

“This study paves the way to create mature retinal ganglion cells in the lab, which could be harnessed for the development of new approaches to reverse vision loss that results from optic nerve degeneration, including glaucoma,” said Dr Jonathan Loh Yuin-Han, Research Director at A*STAR’s IMCB and lead researcher of the study.

Moving forward, the research team hopes to use RGCs for cell therapies in patients and is working further to validate the KLF7-derived RGCs for preclinical studies. With the understanding of key molecular switches and ability to engineer cell types in culture, lab grown cells provide a key to therapy.

SourceAgency for Science, Technology and Research (A*STAR)

Gautam P, Hamashima K, Chen Y, Zeng Y, Makovoz B, Parikh BH, Lee HY, Lau KA, Su X, Wong RCB, Chan WK, Li H, Blenkinsop TA, Loh YH. (2021) Multi-species single-cell transcriptomic analysis of ocular compartment regulons. Nat Commun 12(1):5675. [article]

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