Multi-species single-cell transcriptomic analysis of ocular compartment regulons

Pradeep Gautam, Kiyofumi Hamashima, Ying Chen, Yingying Zeng, Bar Makovoz, Bhav Harshad Parikh, Hsin Yee Lee, Katherine Anne Lau, Xinyi Su, Raymond C.B. Wong, Woon Khiong Chan, Hu Li, Timothy A. Blenkinsop, Yuin Han Loh

Research output: Contribution to journalArticlepeer-review

40 Scopus citations


The retina is a widely profiled tissue in multiple species by single-cell RNA sequencing studies. However, integrative research of the retina across species is lacking. Here, we construct the first single-cell atlas of the human and porcine ocular compartments and study inter-species differences in the retina. In addition to that, we identify putative adult stem cells present in the iris tissue. We also create a disease map of genes involved in eye disorders across compartments of the eye. Furthermore, we probe the regulons of different cell populations, which include transcription factors and receptor-ligand interactions and reveal unique directional signalling between ocular cell types. In addition, we study conservation of regulons across vertebrates and zebrafish to identify common core factors. Here, we show perturbation of KLF7 gene expression during retinal ganglion cells differentiation and conclude that it plays a significant role in the maturation of retinal ganglion cells.

Original languageEnglish
Article number5675
JournalNature Communications
Issue number1
StatePublished - 1 Dec 2021


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