Journal: iScience

Article Title: An Alzheimer’s disease-associated common regulatory variant in a PTK2B intron alters microglial function

doi: 10.1016/j.isci.2026.115688

Figure Lengend Snippet: Isogenic edited cell lines show that rs28834970 affects chromatin accessibility and CEBPβ binding at the intronic enhancer in hiPSC-derived macrophages and microglia, but only modestly decreases PTK2B expression (A) Coverage tracks of cells with T/T (orange) and C/C (blue) allele at rs28834970. The tracks are: ATAC-seq in macrophages (upper track), ATAC-seq in microglia (second track), CUT&RUN for CEBPβ in microglia (third track), and IgG negative control for CUT&RUN (bottom track). Normalized read counts per basepair are plotted, and the rs28834970 variant in PTK2B intron is highlighted in yellow. (B) Effect of rs28834970 SNP on transcription factor binding probability. Position probability matrices are shown for CEBPβ (top) and CEBPα (middle) as well as the position of the binding motifs on the PTK2B sequence (bottom). The plot was generated using motifbreakerR. (C) Volcano plot shows fold changes of CEBPβ binding between microglia harboring the C/C and the T/T allele for all detectable peaks, measured by CUT&RUN. Blue dots indicate peaks with no significant change, while red dots represent significantly increased peaks (log2FC > 1 and adjusted p < 0.05). The only significantly increased CEBPβ peak found spans the rs28834970 variant in the PTK2B intron. (D) Boxplots show PTK2B expression in macrophages harboring the T/T or C/C allele at rs28834970 measured by RNA-seq (top) and droplet digital q-PCR (ddqPCR) (bottom). Top plot: TPM = transcripts per million. Bottom plot: Relative concentration = copies/ul relative to housekeeping gene (SDHA), n = 3 and ∗ p < 0.05, unpaired t test. Boxplot shows median expression and interquartile range. (E) Boxplots show PTK2B expression in microglia harboring the T/T or C/C allele at rs28834970 measured by RNA-seq (top) and droplet digital q-PCR (ddqPCR) (bottom). Top plot: TPM = transcripts per million. Bottom plot: Relative concentration = copies/ul relative to housekeeping gene (TBP), n = 3, and ns = non-significant, unpaired t test. Boxplot shows median expression and interquartile range. See also and , , , , and .

Article Snippet: 1 μg of C/EBP beta Antibody (H-7; Santa Cruz Biotechnology, Cat# sc-7962) was used per sample; a parallel negative control was treated with 1 μL of CUTANA Rabbit IgG CUT&RUN Negative Control Antibody (EpiCypher).

Techniques: Binding Assay, Derivative Assay, Expressing, Negative Control, Variant Assay, Sequencing, Generated, RNA Sequencing, Concentration Assay