Fig. 4: The LOAD-risk allele of PICALM dysregulates lipid gene pathways in iMGs.
From: PICALM Alzheimer’s risk allele causes aberrant lipid droplets in microglia
a, Principal component analysis (PCA) of RNA-seq samples of iMGs derived from CRISPR-engineered iPS cell lines carrying the PICALM risk or non-risk alleles. Samples are from 2 experiments each with 2–3 wells of differentiations for CD04 and CD09 lines, 1 clone per line. Expression of 13,947 genes was used for PCA. The sample labels describe the cell line, clone number, replicates, and batch number in sequential order, divided by the hyphen (-) symbol. b, DEGs in iMGs carrying the LOAD-risk allele. FC, fold change. c, Enriched Ingenuity canonical pathways for all DEGs (FDR < 0.05). Significantly enriched pathways (one-sided Fisher’s exact test, FDR < 0.05) are ranked by their activated or inactivated (inact.) z scores. TH1, T helper type 1. d, Significant correlation (Pearson’s R2) of the expression changes (−log2[fold change]) in iMGs carrying PICALM risk (versus non-risk) allele and in previously reported LD accumulated microglia (LDAM) of the ageing mouse10. Plotted are 56 DEGs (FDR < 0.1) in both RNA-seq datasets.
