Early microglial priming in Alzheimer's disease revealed by ME-seq

Zhu, B.; Ghosh, A.; Wang, Z.; Liao, Z.; Appiah, M.; Li, J.; Zhang, M.; Tullio, F. D.; Kurowski, A.; Fullard, J.; Wagenblast, E.; Walsh, M. J.; Goate, A. M.; Roussos, P.; Cheung, K. l.; Yang, N.; Ma, S.

doi:10.64898/2026.01.30.702946

bioRxiv · 10.64898/2026.01.30.702946

Early microglial priming in Alzheimer's disease revealed by ME-seq

Zhu, B.·Ghosh, A.·Wang, Z.·Liao, Z.·Appiah, M.·Li, J.·Zhang, M.·Tullio, F. D.·Kurowski, A.·Fullard, J.·Wagenblast, E.·Walsh, M. J.·Goate, A. M.·Roussos, P.·Cheung, K. l.·Yang, N.·Ma, S.

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Abstract

Epigenetic modifications, particularly DNA methylation, change dynamically with aging and are implicated in Alzheimers Disease (AD), yet how methylation interfaces with transcriptional and chromatin regulation at single-cell resolution remains poorly understood. Progress has been limited by a lack of scalable technologies capable of jointly profiling these regulatory layers. Here, we present ME-seq, a highly scalable technologies capable of simultaneously profiling DNA methylation, gene expression, and chromatin accessibility, while achieving a 100-fold reduction in cost. We generated over 400,000 single-nucleus trimodal profiles from the aging and AD mouse brain across ages, producing the first such atlas of neurodegeneration. We found AD progression triggers pronounced, disease-specific shifts in cellular composition, characterized by accelerated epigenetic aging and the expansion of disease-associated microglia (DAM). Integrative analyses, including aging clocks, revealed that DNA methylation acts as an early priming layer preceding transcriptional activation with IRF1 identified as a methylation-sensitive transcription factor serving as a gatekeeper for DAM activation. Our results establish ME-seq as a transformative tool for large-scale epigenomic dissection, revealing DNA methylation as a primary coordinator of cell-state transitions in the aging brain. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=195 HEIGHT=200 SRC="FIGDIR/small/702946v1_ufig1.gif" ALT="Figure 1"> View larger version (70K): org.highwire.dtl.DTLVardef@67435dorg.highwire.dtl.DTLVardef@177c22aorg.highwire.dtl.DTLVardef@16c6fd9org.highwire.dtl.DTLVardef@231b92_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Zhu, B., Ghosh, A., Wang, Z., Liao, Z., Appiah, M., Li, J., Zhang, M., Tullio, F. D., Kurowski, A., Fullard, J., Wagenblast, E., Walsh, M. J., Goate, A. M., Roussos, P., Cheung, K. l., Yang, N., Ma, S.. 2026-02-02. Early microglial priming in Alzheimer's disease revealed by ME-seq. https://doi.org/10.64898/2026.01.30.702946

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