Extended Data Fig. 7: LOAD risk-allele of PICALM causes LD accumulation in iMG.

(a) IF filipin staining in day-25 iMG (TREM2⁺) carrying the LOAD risk or non-risk allele of rs10792832. (b) Quantification of filipin fluorescence intensity in (a). PI, propidium iodide for nucleus staining. Scale bar, 50 µm. Each datapoint represents a single-well measurement field of view (FOV) of one experiment; for each condition (risk and non-risk), data are from two donor lines (CD04 and CD09), collected from one experiment with two wells of differentiations each with 2-3 FOV (n = 12 for risk group and n = 8 for non-risk group). (c) and (d) Quantification of LD staining shows increased LD (BODIPY⁺) size and fluorescence intensity in LOAD risk-allele iMG (vs. non-risk), respectively. (e) Fluorescence staining of LD (BODIPY⁺) and ROS (CellRox⁺) with or without pretreatment of Triacsin C (TrC) in iMG carrying risk or non-risk allele. Scale bar, 50 µm. (f) to (i) Quantification of (e) shows increased LD and CellRox density and area in iMG carrying LOAD risk-allele (vs. non-risk). Each datapoint represents a single well measurement (FOV) from one experiment; data are from a single clone of CD04 line, collected from one experiment with 2 wells of differentiations each with 4 FOV (n = 8). One-way ANOVA with Tukey’s correction. (j) Representative histogram of flow cytometry analysis of LD (BODIPY+) in iMG. Gating strategy is shown in Supplementary Fig. 10. (k) Quantification of the proportion of BODIPY+ cells from (j). Each datapoint represents a single-well measurement from one experiment; for each donor line (CD04 and CD09) and each condition (risk and non-risk), data are from single clone, collected from 3 experiments (n = 3). (l) Representative fluorescence images of LD staining with PLIN2. Scale bar, 50 µm. (m) and (n) Quantification of PLIN2+ LD area per iMG and LD fluorescence intensity per iMG, respectively. For (c), (d), (m), and (n), each datapoint represents a single-well measurement from one experiment; for each donor line (CD04 and CD09) and each condition (risk and non-risk), data are from 2 clones, collected from 2 independent experiments each with 3 wells of differentiations (n = 12). LMM was used to test the fixed effect of genotype (risk vs. non-risk), with clone identify and experimental rounds as the random factors; two-sided test, nominal P-values. For (b) and (k), two-sided unpaired Student’s t-test was used. For all comparisons, * P < 0.05, ** P < 0.01, ***, P < 0.001; mean ± s.e.m.