Fig. 3: Transcriptomic analysis reveals an abundance of downregulated genes across the disease spectrum of hippocampal vulnerability in AD.

a, b Venn diagram depicting the number of genes that were downregulated (a) or upregulated (b) in the representative phenotype (black) or extreme phenotype (purple). There was no overlap in upregulated genes. c Waterfall plot of the top ten upregulated or downregulated genes from each phenotype. d, e Process networks in the representative phenotype (black [d]) and extreme phenotype (purple [e]) reveal non-overlapping functions. f, g Examples of genes selected from the literature that exhibit monotonic directionality. SIRT1 is monotonically upregulated (f) while PSEN2 is monotonically downregulated (statistical values can be found in Supplementary Fig. 2) (g). h–j Digital pathology examples of immunohistochemistry and burden analysis markup using h CP13, i Ab39, and j 33.1.1 antibodies in CA1 subsector of the hippocampus of typical AD brains. Digital pathology measures were performed in those with sufficient tissue for serial immunohistochemical staining (n = 54/55 for RNA-Seq cohort and n = 170/182 for NanoString cohort). k, l Volcano plots showing fold change versus significance in the representative phenotype (k) and the extreme phenotype (l). Volcano plots reveal number of differentially expressed genes out of the total number of genes and subsequently show each step of our prioritization process: Step 1, literature-based genes (dark orange); Step 2a, differentially expressed genes (tan); Step 2b, bioinformatic prioritization of differentially expressed genes (orange); Step 3, process networks (magenta); and Step 4, translational neuropathology approach to identify NanoString validation genes (blue outline). AD, Alzheimer’s disease; IHC, immunohistochemistry; RNA-Seq, RNA sequencing; Sig Transd, signal transduction. Note: Box plots in f, g are derived from n = 55 independent samples. Box plots are displayed at the 25th and 75th percentiles with the median line. Whiskers are drawn to the largest and smallest values that are within 1.5 times the interquartile range from the upper or lower quartile. For observations larger or smaller than this distance, they are shown as observations outside the whiskers.