Single-cell analysis of microglia and monocyte dynamics uncovers distinct TNF-driven neuroimmune signatures in humans after intracerebral hemorrhage.

Overview

1. Department of Neurology, Yale School of Medicine, New Haven, CT, USA
2. School of Clinical Medicine, University of Cambridge, Cambridge, UK
3. Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
4. Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
5. Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
6. Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
7. Department of Neurosurgery, University of California–Davis, Sacramento, CA, USA

Abstract

Innate immune cells contribute to both secondary brain injury and repair following intracerebral hemorrhage (ICH). However, the signaling pathways governing initial inflammatory and subsequent reparative myeloid programs in living patients remain poorly understood. To better characterize mononuclear phagocyte cell changes over time, we generated a single-cell transcriptomic dataset of paired hematoma clot evacuates and peripheral blood samples from 10 patients following ICH (5–290 h). We identified distinct populations of activated and TNF-low microglia, as well as a highly activated population of CD14+ monocytes in the hematoma. Perturbation analysis identified TNF signaling as the primary driver of hematoma monocyte activation. Custom temporal trajectory analysis using single-cell foundation model embeddings found that this TNF response in monocytes was transient, peaking early after hemorrhage and decreasing over the following 48 h as monocytes shifted to reparative transcriptional programs. Transiently activated microglia emerged as the likely acute source of TNF among analyzed populations, signaling through monocyte TNFR2. Surprisingly, acute TNF signaling in CD14+ monocytes was also associated with better severity-adjusted neurological outcomes both in our cohort and an independent validation cohort. These findings suggest acute TNF signaling between activated microglia and hematoma-associated monocytes, particularly through TNFR2, may contribute to recovery following ICH.

Reproduced under the paper's license (CC BY-NC), from the paper cited above.

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Data

Datasets cited

• geo:GSE333172 — at NCBI GEO; found in “Data availability”

Data availability

Raw sequencing files and metadata are available at GSE333172 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE333172). Codes used for custom trajectory analysis is available at https://github.com/lucascamillomd/brain-hematoma.

Reproduced under the paper's license (CC BY-NC), from the paper cited above.

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Version 1, 27 September 2026: the first record

Recorded: type, language, journal, pages, dates, 12 authors, 5 keywords, 4 funders, 75 references.

Cite

This paper

Kawamura, Y., Johnson, C. W., DeLong, J., de Lima Camillo, L. P., Velazquez, S. E., Takahashi, M., Beatty, H. E., Hebert, R., Cord, B. J., Matouk, C., Askenase, M. H., & Sansing, L. H. (2026). Single-cell analysis of microglia and monocyte dynamics uncovers distinct TNF-driven neuroimmune signatures in humans after intracerebral hemorrhage. Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism, 0271678X261471282. https://doi.org/10.1177/0271678x261471282

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