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Identification of ligand–receptor pairs that drive human astrocyte development

Nature Neuroscience volume 26, pages 1339–1351 (2023)Cite this article

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Abstract

Extrinsic signaling between diverse cell types is crucial for nervous system development. Ligand binding is a key driver of developmental processes. Nevertheless, it remains a significant challenge to disentangle which and how extrinsic signals act cooperatively to affect changes in recipient cells. In the developing human brain, cortical progenitors transition from neurogenesis to gliogenesis in a stereotyped sequence that is in part influenced by extrinsic ligands. Here we used published transcriptomic data to identify and functionally test five ligand–receptor pairs that synergistically drive human astrogenesis. We validate the synergistic contributions of TGFβ2, NLGN1, TSLP, DKK1 and BMP4 ligands on astrocyte development in both hCOs and primary fetal tissue. We confirm that the cooperative capabilities of these five ligands are greater than their individual capacities. Additionally, we discovered that their combinatorial effects converge in part on the mTORC1 signaling pathway, resulting in transcriptomic and morphological features of astrocyte development. Our data-driven framework can leverage single-cell and bulk genomic data to generate and test functional hypotheses surrounding cell–cell communication regulating neurodevelopmental processes.

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Fig. 1: Computational identification of candidate gliogenic signals.
Fig. 2: Exposure to five ligand cocktails induces astrocyte gene expression.
Fig. 3: Ligand activity depends on the hCO developmental stage.
Fig. 4: Synergistic and individual contributions of ligands.
Fig. 5: Impact of candidate ligand exposures on human fetal cells.
Fig. 6: Impact of candidate ligand exposures on neural stem cell fate.
Fig. 7: Phosphoproteomic changes in ligand-treated hCOs.

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Data availability

All data generated in this work are available through GEO accession number (GSE213245). All scripts generated are available without restrictions upon request and at GitHub site below. Source data are provided with this paper.

Code availability

https://github.com/sloanlab-emory/voss-and-lanjewar-et-al-2023

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Acknowledgements

We would like to thank the Sloan Laboratory for helpful discussion and A. Erwood (Emory Department of Neurosurgery) for his contributions to early ligand identification. We would also like to thank J. Lee for his support with AWS management and usage. This study was supported by the National Institute of Health under grants R01MH125956 and R01NS123562 (to S.A.S.), and Brain and Behavior NARSAD Young Investigator Award. A.V. is supported by the Barry Goldwater Scholarship and the Emory IMSD program.

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Author notes

  1. These authors contributed equally: Anna J. Voss, Samantha N. Lanjewar.

Authors and Affiliations

  1. Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA

    Anna J. Voss, Samantha N. Lanjewar, Maureen M. Sampson, Alexia King, Emily J. Hill, Anson Sing, Caitlin Sojka, Tarun N. Bhatia & Steven A. Sloan

  2. Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA, USA

    Jennifer M. Spangle

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Contributions

A.J.V. and S.A.S. designed all experiments and performed NicheNet analysis. A.J.V. and S.N.L. performed ligand exposures. A.J.V., S.N.L., A.K. and A.S. performed hiPSC cultures, organoid formation and maintenance. A.J.V., S.N.L., M.M.S., E.H. and C.S. assisted with fetal tissue preparations and experimental procedures. S.N.L. designed and performed immunoblotting assays with input from T.N.B. and J.M.S. Bioinformatic processing was performed by A.J.V. and S.N.L. A.J.V., S.N.L. and S.A.S. wrote the manuscript with input from all contributing authors.

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Correspondence to Steven A. Sloan.

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Nature Neuroscience thanks Omer Ali Bayraktar and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–8 and Supplementary Note.

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Supplementary Tables

Supplementary Table 1: List of human astrocyte genes. Supplementary Table 2: List of candidate ligands. Supplementary Table 3: Concentration of candidate ligands. Supplementary Table 4: Targeted RNA-seq gene panel. Supplementary Table 5: List of neuronal and astrocyte signature genes.

Supplementary Data 1

Statistical supporting data for Supplementary Fig. 5.

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Voss, A.J., Lanjewar, S.N., Sampson, M.M. et al. Identification of ligand–receptor pairs that drive human astrocyte development. Nat Neurosci 26, 1339–1351 (2023). https://doi.org/10.1038/s41593-023-01375-8

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