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

Author

Listed:
  • Pradeep Gautam

    (Cell Fate Engineering and Therapeutics Laboratory, A*STAR Institute of Molecular and Cell Biology
    National University of Singapore)

  • Kiyofumi Hamashima

    (Cell Fate Engineering and Therapeutics Laboratory, A*STAR Institute of Molecular and Cell Biology)

  • Ying Chen

    (Cell Fate Engineering and Therapeutics Laboratory, A*STAR Institute of Molecular and Cell Biology
    National University of Singapore
    National University of Singapore)

  • Yingying Zeng

    (Cell Fate Engineering and Therapeutics Laboratory, A*STAR Institute of Molecular and Cell Biology
    School of Biological Sciences, Nanyang Technological University)

  • Bar Makovoz

    (Icahn School of Medicine at Mount Sinai)

  • Bhav Harshad Parikh

    (Yong Loo Lin School of Medicine, National University of Singapore
    Translational Retinal Research Laboratory, A*STAR Institute of Molecular and Cell Biology)

  • Hsin Yee Lee

    (Cell Fate Engineering and Therapeutics Laboratory, A*STAR Institute of Molecular and Cell Biology)

  • Katherine Anne Lau

    (Cell Fate Engineering and Therapeutics Laboratory, A*STAR Institute of Molecular and Cell Biology)

  • Xinyi Su

    (Yong Loo Lin School of Medicine, National University of Singapore
    Translational Retinal Research Laboratory, A*STAR Institute of Molecular and Cell Biology
    Singapore Eye Research Institute)

  • Raymond C. B. Wong

    (Centre for Eye Research Australia
    University of Melbourne
    Shenzhen Eye Hospital, Shenzhen University School of Medicine)

  • Woon-Khiong Chan

    (National University of Singapore
    National University of Singapore)

  • Hu Li

    (Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic)

  • Timothy A. Blenkinsop

    (Icahn School of Medicine at Mount Sinai)

  • Yuin-Han Loh

    (Cell Fate Engineering and Therapeutics Laboratory, A*STAR Institute of Molecular and Cell Biology
    National University of Singapore
    National University of Singapore
    Yong Loo Lin School of Medicine, National University of Singapore)

Abstract

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.

Suggested Citation

  • 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 & Tim, 2021. "Multi-species single-cell transcriptomic analysis of ocular compartment regulons," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-25968-8
    DOI: 10.1038/s41467-021-25968-8
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    Cited by:

    1. Ka Wai Wong & Yingying Zeng & Edison Tay & Jia Hao Jackie Teo & Nadia Omega Cipta & Kiyofumi Hamashima & Yao Yi & Haijun Liu & Tushar Warrier & Minh T. N. Le & Soon Chye Ng & Qi-Jing Li & Hu Li & Yuin, 2024. "Nuclear receptor-SINE B1 network modulates expanded pluripotency in blastoids and blastocysts," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    2. Mingsen Li & Huizhen Guo & Bofeng Wang & Zhuo Han & Siqi Wu & Jiafeng Liu & Huaxing Huang & Jin Zhu & Fengjiao An & Zesong Lin & Kunlun Mo & Jieying Tan & Chunqiao Liu & Li Wang & Xin Deng & Guigang L, 2024. "The single-cell transcriptomic atlas and RORA-mediated 3D epigenomic remodeling in driving corneal epithelial differentiation," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    3. Birthe Dorgau & Joseph Collin & Agata Rozanska & Darin Zerti & Adrienne Unsworth & Moira Crosier & Rafiqul Hussain & Jonathan Coxhead & Tamil Dhanaseelan & Aara Patel & Jane C. Sowden & David R. FitzP, 2024. "Single-cell analyses reveal transient retinal progenitor cells in the ciliary margin of developing human retina," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    4. Jian Yuan & You-Yuan Zhuang & Xiaoyu Liu & Yue Zhang & Kai Li & Zhen Ji Chen & Dandan Li & He Chen & Jiacheng Liang & Yinghao Yao & Xiangyi Yu & Ran Zhuo & Fei Zhao & Xiangtian Zhou & Xiaoguang Yu & J, 2024. "Exome-wide association study identifies KDELR3 mutations in extreme myopia," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    5. James R. Tribble & Melissa Jöe & Carmine Varricchio & Amin Otmani & Alessio Canovai & Baninia Habchi & Evangelia Daskalakis & Romanas Chaleckis & Andrea Loreto & Jonathan Gilley & Craig E. Wheelock & , 2024. "NMNAT2 is a druggable target to drive neuronal NAD production," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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