Fig. 6: RNA sequencing analyses following hippocampal knockdown of Ska2 identify transcriptional signatures associated with increased activity of secretory autophagy (SA) and cell death processes.

Deconvolution analysis of the RNA sequencing data (n = 8 per group) at 2 weeks (A) and 4 weeks (B) following hippocampal Ska2 knockdown reveals altered estimated cell proportions in the hippocampus (main cell types shown) (2-way ANOVA: 2 weeks: condition × cell type interaction F_5,84 = 23.44, p < 0.0001, Bonferroni’s post hoc test: neuron, p < 0.0001, microglia, p < 0.0001, astrocyte, p = 0.0320, n = 8 per group; 4 weeks: condition × cell type interaction F_5,84 = 115.2, p < 0.0001, Bonferroni’s post hoc test: neuron, p < 0.0001, microglia, p < 0.0001, n = 8 per group). * = p < 0.05; **** = p < 0.0001; Data are presented as mean + SEM. Differential gene expression analysis 2 (C) and 4 weeks (D) following hippocampal Ska2 knockdown after correction for changes in the proportion in cell types. Differentially expressed genes (DEGs) (p < 0.05 adjusted with Bonferroni correction) are depicted in dark green (absolute Log₂FC < 2) or light green (absolute Log₂FC > 2). Magenta data points depict significant differentially expressed interleukins, while orange data points show chemokines and blue data points illustrate cathepsins. Gray data points are not significant (39 data points at 2 weeks and 25 data points at 4 weeks are outside the axis limits; for full list of all DEGs see Supplementary Data 1, 2). Gene expression changes of some known SA cargo proteins at 2 weeks are depicted in the table. E Gene ontology (GO) enrichment analysis with DEGs at 2 weeks. Selected enriched GO terms relevant to SA are depicted (for full list of all GO terms see Supplementary Data 3). Circle size is proportional to the number of genes. BP biological process, CC cellular component, MF molecular function. F Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis with DEGs at 2 weeks. Circle size is proportional to the number of genes. Source data are provided as a Source Data file.