Molecular and spatial analysis of ganglion cells on retinal flatmounts identifies perivascular neurons resilient to glaucoma

Kushal Nimkar¹, Nicole Y Tsai², Mengya Zhao², Yujuan Yi², Matthew R Lum², Tavita R Garrett³, Yixiao Wang², Kenichi Toma², Franklin Caval-Holme⁴, Nikhil Reddy¹, Aliza T Ehrlich⁵, Arnold R Kriegstein⁶, Michael Tri H Do⁴, Yang Hu⁷, Benjamin Sivyer³, Karthik Shekhar⁸, Xin Duan⁹

Affiliations

¹ Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA.
² Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA, USA.
³ Casey Eye Institute, Oregon Health and Science University, Portland, OR, USA.
⁴ Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
⁵ Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, USA.
⁶ Department of Neurology, The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
⁷ Department of Ophthalmology, Spencer Center for Vision Research, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA, USA.
⁸ Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA; Helen Wills Neuroscience Institute, Vision Sciences Graduate Program, Center for Computational Biology, Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA, USA. Electronic address: kshekhar@berkeley.edu.
⁹ Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Physiology, Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, USA. Electronic address: xin.duan@ucsf.edu.

PMID: 40840447
DOI: 10.1016/j.neuron.2025.07.025

Free article

Molecular and spatial analysis of ganglion cells on retinal flatmounts identifies perivascular neurons resilient to glaucoma

Kushal Nimkar et al. Neuron. 2025.

Free article

. 2025 Aug 19:S0896-6273(25)00552-5.

doi: 10.1016/j.neuron.2025.07.025. Online ahead of print.

Authors

Affiliations

¹ Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA.
² Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA, USA.
³ Casey Eye Institute, Oregon Health and Science University, Portland, OR, USA.
⁴ Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
⁵ Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, USA.
⁶ Department of Neurology, The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
⁷ Department of Ophthalmology, Spencer Center for Vision Research, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA, USA.
⁸ Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA; Helen Wills Neuroscience Institute, Vision Sciences Graduate Program, Center for Computational Biology, Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA, USA. Electronic address: kshekhar@berkeley.edu.
⁹ Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Physiology, Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, USA. Electronic address: xin.duan@ucsf.edu.

PMID: 40840447
DOI: 10.1016/j.neuron.2025.07.025

Abstract

Recent transcriptomic studies have categorized mouse retinal ganglion cells (RGCs) into 45 types; however, little is known about their spatial distributions on the two-dimensional retinal surface and how their local microenvironments impact their functions. Here, we optimized a workflow combining imaging-based spatial transcriptomics (multiplexed-error robust fluorescent in situ hybridization [MERFISH]) and immunostaining on retinal flatmounts. We computationally registered the somata distributions of all RGCs and found that 34/45 molecularly defined types exhibited non-uniform distributions. We analyzed local neighborhoods for each cell and identified seven RGC types enriched in the perivascular niche, including direction-selective RGC (DSGC) and intrinsically photosensitive RGC (ipRGC) types. We further examined an experimental glaucoma model and found that surviving RGCs are enriched in the perivascular niche. Perivascular DSGCs and M1 ipRGCs were especially resilient, suggesting that proximity to vasculatures confers mTOR-independent, cell-extrinsic neuroprotection. Together, our work provides a comprehensive spatial atlas of RGC types and links their microenvironment to differential vulnerability in neurodegeneration.

Keywords: MERFISH; glaucoma; neurodegeneration; neuronal types; neuroprotection; perivascular neurons; retinal ganglion cells; spatial patterning; spatial transcriptomics.

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Conflict of interest statement

Declaration of interests The authors declare no competing interests.

Update of

Molecular and spatial analysis of ganglion cells on retinal flatmounts: diversity, topography, and perivascularity.
Tsai NY, Nimkar K, Zhao M, Lum MR, Yi Y, Garrett TR, Wang Y, Toma K, Caval-Holme F, Reddy N, Ehrlich AT, Kriegstein AR, Do MTH, Sivyer B, Shekhar K, Duan X. Tsai NY, et al. bioRxiv [Preprint]. 2024 Dec 17:2024.12.15.628587. doi: 10.1101/2024.12.15.628587. bioRxiv. 2024. Update in: Neuron. 2025 Aug 19:S0896-6273(25)00552-5. doi: 10.1016/j.neuron.2025.07.025. PMID: 39763751 Free PMC article. Updated. Preprint.

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Molecular and spatial analysis of ganglion cells on retinal flatmounts identifies perivascular neurons resilient to glaucoma

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Molecular and spatial analysis of ganglion cells on retinal flatmounts identifies perivascular neurons resilient to glaucoma

Authors

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Abstract

Conflict of interest statement

Update of

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