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. Author manuscript; available in PMC: 2025 Apr 17.
Published in final edited form as: Neuron. 2024 Feb 9;112(8):1235–1248.e5. doi: 10.1016/j.neuron.2024.01.013

Figure 3. Epigenetic changes to NF-κB signaling molecules in peripheral AD monocytes.

Figure 3.

(A) Scatterplots showing AD vs. HC DARs intersecting DEGs by fold change in CD14 and CD16 monocytes. (B) Transcription factor motif scanning analysis showing enrichment of REL and RELA binding sites in AD monocytes, where transcription factors are ranked by product of log(p-value) and log2(fold-change). (C) maxATAC analysis of TFBS in the NFκB2 gene indicating an AD-specific RELA binding site. (D) Chromatin track of the NFκB2 gene demonstrating the location of the AD-specific RELA binding site. The RELA binding site (red) is adjacent to an NFκB2 DAR (light blue). (E) Pathway analyses of upregulated DEGs of AD versus HC CD14 and CD16 monocytes indicating enrichment of NFκB signaling. ATAC-seq assay: HC monocytes = 9763, median (IQR) = 311 (163.25 – 451.75), AD monocytes = 7162, median (IQR) = 242.5 (112.5 – 397.75). RNA-seq assay: HC CD14 monocytes = 4414, median (IQR) = 105 (55 – 254.25), AD CD14 monocytes = 3455, median (IQR) = 61.5 (11 – 148), HC CD16 monocytes = 1837, median (IQR) = 42 (5 – 108), AD CD16 monocytes = 899, median (IQR) = 13 (4 – 41.25).