TY - JOUR
T1 - Multi-species single-cell transcriptomic analysis of ocular compartment regulons
AU - Gautam, Pradeep
AU - Hamashima, Kiyofumi
AU - Chen, Ying
AU - Zeng, Yingying
AU - Makovoz, Bar
AU - Parikh, Bhav Harshad
AU - Lee, Hsin Yee
AU - Lau, Katherine Anne
AU - Su, Xinyi
AU - Wong, Raymond C.B.
AU - Chan, Woon Khiong
AU - Li, Hu
AU - Blenkinsop, Timothy A.
AU - Loh, Yuin Han
N1 - Funding Information:
We thank the donors and their families for whom this work could not have been possible. We are grateful to Chadi El Farran and Haofei Wang for their helpful contributions to productive discussions. We also thank Vanessa Lorraine Chea for her help in editing the manuscript. We also thank the Spatial and Single Cell Genomics Platform at Genome Institute of Singapore for providing a single-cell RNA sequencing facility. We are thankful to Central Imaging Facility at IMCB for providing microscope resources. HLL is supported by the Glenn Foundation for Medical Research, the Mayo Clinic Centre for Biomedical Discovery and the Mayo Clinic Cancer Centre. Y.-H.L. is supported by the [NRF Investigatorship award—NRFI2018-02] and [JCO Development Programme Grant—1534n00153] grants. The work was supported by NIH/NEI grants EY029736 and EY030215. Finally, we are grateful to the Biomedical Research Council, Agency for Science, Technology and Research, Singapore, for research funding.
Publisher Copyright:
© 2021, The Author(s).
PY - 2021/12/1
Y1 - 2021/12/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85115999099&partnerID=8YFLogxK
U2 - 10.1038/s41467-021-25968-8
DO - 10.1038/s41467-021-25968-8
M3 - Article
C2 - 34584087
AN - SCOPUS:85115999099
SN - 2041-1723
VL - 12
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 5675
ER -