Genome Medicine · Published 2026-06-10 · DOI 10.1186/s13073-026-01687-x · PMID: 42271455 · PMC · Cited by 3 (Crossref)
Hongli Ma, Nicolas Hugues, Kirsten Voice, Joshua Peter, Aleksandr Taranov, Christina Thapa, Krishna Roskin, Yu Luo
Abstract Background Ischemic stroke elicits a strong neuroinflammatory response characterized by activation of microglia and infiltration of monocytes-derived macrophages (iMM), which have been speculated to have differential functions in stroke. However, because the gene expression profiles of microglia and iMM overlap in the injured brain, distinguishing these two cell populations has posed a challenge for the field. Methods Using a recently characterized microglia-specific TMEM119 CreER -Ai14 tdTomato reporter mouse model and single cell RNA sequencing (scRNA-seq) analysis, we prelabeled microglia in the brain prior to stroke, enabling detailed characterization of the transcriptomic and spatial distributions of microglia vs. iMM across different stages of post-stroke. ScRNA-seq findings were validated through immunohistochemistry, RNAscope, and animal models. Results Here, we report that microglia and iMM are enriched at distinct locations and exhibit differential temporal dynamics in the stroke brain. Our genetic tracing data reveals that iMM does not survive in the chronic stroke brain past 30 days in our model. Additionally, scRNA-seq further revealed distinct transcriptomic states between microglia and iMM at D7 and D14 in the stroke brain. Genetic tracing also allowed us to identify novel markers for activated microglia vs. iMM in the acute stroke brain such as Gm21188. Finally, our data also showed that Igf1 is up-regulated in both microglia and iMM after stroke. Cx3cr1 ERT2 Igf1 fl/fl mediated myeloid-specific Igf1 gene deletion at 5–9 Days after stroke lead to decreased CD8+ T-cell infiltration in the stroke brain. Functionally, myeloid specific Igf1 iKO mice show expedited sensorimotor function recovery but worsened anxiety-like behavior. Conclusions In summary, Tmem119 CreER -Ai14 tdTomato reporter mouse line is a useful tool for the field to clearly delineate the cellular dynamics and transcriptomic profiles of microglia vs. iMM in a variety of central nervous system pathological conditions, which could have broad implications beyond stroke studies. Moreover, we have characterized novel subtypes and markers for activated microglia and iMM, as well as a possible novel role for myeloid cell-derived IGF-1 in driving T-cell infiltration and/or survival in the post-stroke brain. This study provides valuable insights for future investigations aimed at modulating microglia vs. iMM to promote stroke resolution and functional recovery in vivo.
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Ma, H., Hugues, N., Voice, K., et al. (2026). Infiltrating monocyte-derived macrophages does not survive long term in stroke brain despite their dominance in the acute ischemic core and myeloid derived IGF-1 play dichotomous roles in stroke recovery. Genome Medicine. https://doi.org/10.1186/s13073-026-01687-x