Fig. 7: Brain organoid-derived microglia gene expression is altered in ATXN2-ALS. | Nature Communications

Fig. 7: Brain organoid-derived microglia gene expression is altered in ATXN2-ALS.

From: ATAXIN-2 intermediate-length polyglutamine expansions elicit ALS-associated metabolic and immune phenotypes

Fig. 7

A Summary of the protocol used to generate microglia-containing cerebral organoids65. B Immunohistochemistry for MAP2 and CTIP2 in cryosections of DIV60 cerebral organoids from control (CTL) and ATXN2-ALS iPSC lines. Scale bar is 100 µm. C Immunohistochemistry for ATXN2, IBA1 and MAP2 in cryosections of DIV60 cerebral organoids from control (CTL) and ATXN2-ALS iPSC lines. Arrowheads indicate ATXN2+IBA1+ cells. Scale bar is 25 µm. D Immunohistochemistry for IBA1 in DIV60 cerebral organoids showing 3 distinct microglial morphologies used for quantification in E. Scale bar is 10 µm. E Semi-quantitative analysis of organoid microglia morphology using 3 pre-defined categories (ramified, rod-like and ameboid) using 2 CTL (CTL_1, CTL_7) and 2 ATXN2-ALS (ALS_A, ALS_B) iPSC lines. n = 100 cells per line from 1 experimental replicate, n ≥ 3 organoids. Data are mean ± SD. F qRT-PCR for homeostatic (P2Y12) and disease-associated genes (APOE, SPP1, ATPV1E1, TREM2) in microglia isolated from DIV60 cerebral organoids from 3 CTL (CTL_1, CTL_7, CTL_4) and 2 ATXN-ALS (ALS_A, ALS_B) iPSC lines (n = 3 independent experimental replicates per line, except n = 2 for ALS_A in ATPV1E1 plot). Two-tailed upaired t test (*P = 0.0102 for APOE, *P = 0.0148 for SPP1, **P = 0.0094 for ATPV1E1). Data are mean ± SD. G qRT-PCR for homeostatic (P2Y12) and disease-associated genes (APOE, SPP1, ATPV1E1, TREM2) in microglia isolated from DIV60 cerebral organoids from 4 CTL (CTL_1, CTL_7, NL1, NL2.1) and 4 C9-ALS (ND06769, ND10689, CS29, ND12099) iPSC lines (P2Y12/TREM2 – n = 5 for CTL_1, n = 7 for CTL_3, n = 2 for NL1, n = 3 for NL2, n = 6 for ND06769, n = 5 for ND12099, n = 4 for ND10689, n = 2 for CS29; APOE/SPP1/ATPV1E1 – n = 4 for CTL_1, n = 4 for CTL_3, n = 2 for NL1, n = 3 for NL2, n = 4 for ND06769 (except n = 3 in SPP1 plot), n = 4 for ND10689, n = 3 for ND12099, n = 2 for CS29). *P = 0.0046 for TREM2 (two-tailed upaired t test). Data are mean ± SD. F, G Individual datapoints correspond to an experimental replicate of one iPSC line. Source data are provided as a Source Data file for E–G. A was created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license.

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