Figure 11.
Gene deregulation in SCA7 cerebellum. A, MA plot of transcriptomic dataset between SCA7140Q/5Q and WT mice cerebellum at 40 weeks of age. Red points represent 676 genes deregulated in SCA7140Q/5Q (p < 0.05). B, Functional annotations of the deregulated genes performed using IPA. The most significantly affected pathways (p ≤ 0.0002) in SCA7140Q/5Q are indicated (for additional information, see Extended Data Fig. 11-1). C, The STRING version 10.5 software was used to generate the protein network based on known functional partnerships and interactions: light blue represents curated databases; pink represents experimentally determined; light green represents text mining; black represents coexpression. The assigned GO Biological Processes of upregulated genes are indicated and show significant enrichment in immune response and interferon signaling pathways, with IRF7, STAT1, and JUN at the center a large network of 189 edges. D, Cerebellar cell-type distribution of the genes deregulated in SCA7140Q/5Q mice based on curated dataset of Doyle et al. (2008) (for additional information, see Extended Data Fig. 11-2). E, Cell-type classification of upregulated and downregulated genes indicates PCs as the predominant cell type affected by gene downregulation in SCA7 cerebellum. Common means genes deregulated in more than one cell type. F, G, qRT-PCR analyses of SCA7140Q/5Q and WT cerebella point out the downregulation of Purkinje specific genes Pcp4, Rgs8, and Fam107b at presymptomatic stage and Grid2, Rora, Calb1, and Fam21 at symptomatic stage in SCA7 mice (n = 3 WT and 3 SCA7 mice per age) (F). qRT-PCR analyses confirm that two Purkinje-specific genes nonderegulated in RNA-seq (Orai2, Foxp4) have the same expression level in SCA7 and WT cerebella at 36 weeks (G). All data are normalized to the 36B4 level and are expressed as mean ± SEM. *p < 0.05; **p < 0.01; ***p < 0.001; two-tailed Student's t test. H, Western blot analyses of SCA7140Q/5Q and WT cerebella show the strong decreased level of IP3R1, RGS8, and FAM107B in SCA7 mice at 26 weeks, while the CALB1 is not affected. Tubulin (TUBB) and histone H3 protein levels are used as loading controls.