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Characterization of the responses of brain macrophages to focused ultrasound-mediated blood–brain barrier opening

Nature Biomedical Engineering (2023)Cite this article

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Abstract

The opening of the blood–brain barrier (BBB) by focused ultrasound (FUS) coupled with intravenously injected microbubbles can be leveraged as a form of immunotherapy for the treatment of neurodegenerative disorders. However, how FUS BBB opening affects brain macrophages is not well understood. Here by using single-cell sequencing to characterize the distinct responses of microglia and central nervous system-associated macrophages (CAMs) to FUS-mediated BBB opening in mice, we show that the treatment remodels the immune landscape via the recruitment of CAMs and the proliferation of microglia and via population size increases in disease-associated microglia. Both microglia and CAMs showed early and late increases in population sizes, yet only the proliferation of microglia increased at both timepoints. The population of disease-associated microglia also increased, accompanied by the upregulation of genes associated with gliogenesis and phagocytosis, with the depletion of brain macrophages significantly decreasing the duration of BBB opening.

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Fig. 1: scRNA-seq identifies distinct microglia and CAM clusters.
Fig. 2: Treatment with FUS BBB opening promotes microglia proliferation.
Fig. 3: DAM population increases in size and exhibits an inflammatory signature in response to FUS BBB opening.
Fig. 4: Treatment with FUS BBB opening promotes central nervous system-associated macrophage migration to the area and inflammatory signature.
Fig. 5: Protein analysis confirms brain-macrophage changes.
Fig. 6: Macrophage depletion increases BBB opening volume and duration.
Fig. 7: FUS BBB opening remodels the immune landscape.

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Data availability

All sequencing data is available in both raw FASTQ and processed-table form on Gene Expression Omnibus via the accession code 22573264. The GRCm38 genome dataset is publicly available at https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.20.

Code availability

All custom code for analysis is available at https://github.com/ark2173/Seq1-2022.

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Acknowledgements

This research was funded by the National Institutes of Health R01AG038961 (EEK), R01NS095803 (SGK) and National Science Foundation DGE-2036197 (RLN).

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Author notes

  1. These authors contributed equally: Alina R. Kline-Schoder, Sana Chintamen, Alec J. Batts, Nancy Kwon, Steven G. Kernie, Elisa E. Konofagou.

Authors and Affiliations

  1. Department of Biomedical Engineering, Columbia University, New York, NY, USA

    Alina R. Kline-Schoder, Melody R. DiBenedetto, Rebecca L. Noel, Alec J. Batts, Nancy Kwon & Elisa E. Konofagou

  2. Department of Neurobiology and Behaviour, Columbia University, New York, NY, USA

    Sana Chintamen

  3. Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA

    Moshe J. Willner

  4. Department of Pediatrics, Columbia University, New York, NY, USA

    Stergios Zacharoulis, Cheng-Chia Wu & Steven G. Kernie

  5. Department of Neurology, Columbia University, New York, NY, USA

    Vilas Menon

  6. Department of Radiology, Columbia University, New York, NY, USA

    Elisa E. Konofagou

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Contributions

The original scRNA-seq experiments were executed, designed and performed by A.R.K.-S., S.C., S.G.K. and E.E.K., with input from V.M. Bioinformatics analyses were performed by A.R.K.-S. and S.C., with input from V.M. and oversight from E.E.K. S.G.K. and E.E.K. performed the data interpretation. IHC validation experiments were performed by A.R.K.-S., with support from M.J.W., M.R.D., R.L.N., A.J.B. and N.K. Flow cytometry validation experiments were performed by A.R.K.-S., M.J.W. and M.R.D. Manuscript preparation was performed by A.R.K.-S., with input and editing from V.M., S.G.K. and E.E.K. E.E.K., S.Z., S.G.K. and C.-C.W. obtained funding for this work.

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Correspondence to Elisa E. Konofagou.

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Nature Biomedical Engineering thanks Evandro Fang, Jurgen Gotz, Rao P. Gullapalli, Kazuyuki Takata and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Kline-Schoder, A.R., Chintamen, S., Willner, M.J. et al. Characterization of the responses of brain macrophages to focused ultrasound-mediated blood–brain barrier opening. Nat. Biomed. Eng (2023). https://doi.org/10.1038/s41551-023-01107-0

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