Fig 2: Promoters of downregulated genes in aged Hdac1 cKO mice are enriched for guanine-rich motifs and 8-oxoG lesions.a Enriched GO terms of DEGs from 13M animals were annotated using MSigDB31,32. b FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values of DEGs identified in 13M Hdac1 cKO mice function in ion transport, aging process, PKC pathway, protein chaperone, and antioxidant response. Cell cycle-related genes were unaltered. c Known motifs identified by HOMER program40 within upstream and downstream (±) 500 base pairs (bp) from TSS (transcriptional start site) of DEGs. d ChIP-qPCR analysis indicates the enrichment of 8-oxoG at gene promoters (500 bp upstream of TSS). At least five animals were analyzed from two independent experiments. e, f Representative images and quantification plots of the alkaline and FPG-modified comet assay using hippocampal homogenates from 13M control and Hdac1 cKO mice. e, f Nuclei analyzed (three mice/group) were: alkaline, 1928 (13M control), 1412 (13M Hdac1 cKO); FPG + alkaline, 1872 (13M control) and 1500 (13M Hdac1 cKO). g Representative images of 13M control and Hdac1 cKO mice stained for 8-oxoG (green), NeuN (red), and GFAP (magenta). h Quantification plots showing the 8-oxoG intensity. g, h Four mice were analyzed (two sections/mouse). Cells analyzed were: NeuN+ cells, 1585 (13M control), 2306 (13M Hdac1 cKO); GFAP+ cells, 191 (13M control), 164 (13M Hdac1 cKO). All values are shown as mean ± SEM. Statistical analysis: a weighted Kolmogorov–Smirnov-like test followed by multiple hypothesis testing; c cumulative binomial distributions; d, f one-way ANOVA with Tukey’s post hoc test; h two-tailed Student’s t test. Source data are provided as a Source Data file.

Fig 3: Hdac1 cKO mice exhibit age-associated impairments.a Representative images of control and Hdac1 cKO mice at the age of 3 months (3M) and 13 months (13M) stained for GFAP (red) and nuclei Hoechst (blue) in the hippocampal region. b Analysis of GFAP+ cells. a, b Three mice were analyzed in each group (two sections/mouse). Cells analyzed for cell volume were: 144 (3M control), 168 (3M Hdac1 cKO), 181 (13M control), and 227 (13M Hdac1 cKO). c, d Representative images and quantification of the comet assay using hippocampal homogenates. c, d Nuclei analyzed (three mice/group) were: 1356 (3M control), 1268 (3M Hdac1 cKO), 1898 (13M control), and 1944 (13M Hdac1 cKO). e Analysis of freezing behavior during contextual fear conditioning test. Animals analyzed were: 13 (3M control), 10 (3M Hdac1 cKO), 14 (13M control), and 22 (13M Hdac1 cKO). f, g Control and Hdac1 cKO mice were subjected to the Morris water maze (MWM) test. Shown are the latencies to hidden platform during training and time spent in each quadrant during the probe trial. Images show the location of each quadrant and swim trace of mouse during the probe trial. T = target, O = opposite, R = right, L = left. Animals analyzed were: 9 (3M control), 7 (3M Hdac1 cKO), 7 (17M control), and 11 (17M Hdac1 cKO). h, i Hippocampal LTP induction in control and Hdac1 cKO mice. Animals/slices analyzed were: 3/6 (2M control), 3/7 (2M Hdac1 cKO), 4/8 (6M control), and 5/8 (6M Hdac1 cKO). Overlay of the representative field excitatory post-synaptic potential slope (fEPSPs) before (black trace) and after (red trace) LTP induction. Theta-burst stimulation (TBS). All values are shown as mean ± SEM. Statistical analysis: b, d one-way ANOVA with Tukey’s post hoc test; e, h, i two-tailed Student’s t test; f, g two-way repeated-measures ANOVA with Bonferroni’s post hoc test for acquisition phase; two-way ANOVA with Bonferroni’s post hoc test for probe trial. Source data are provided as a Source Data file.

Fig 4: Tumors show lineage expansion and stem cell marker expression.a Feature plot of Sox2 and Yfp on the t-SNE projection of Fig. 2a. b Representative flow cytometry studies, plotting GFAP expression of each cell versus DENDRA2 expression, with thresholds for positivity indicated by solid lines, and with the fraction of GFAP+ cells in the DENDRA2+ cerebellar or tumor populations of replicate mice of indicated genotypes. c Bar plot showing the proportions of Sox2+ cells expressing indicated markers in each of the five vehicle-treated tumors. Error bars are SEM. d t-SNE projection of Sox2+ cells from the five vehicle-treated tumors, directed by ICA, with feature plots of Sox10 and Aqp4. e Oligodendrocytic clusters of the t-SNE projection in d, with feature plots of Pdgfra, Mbp1, Plp1, Mog and Yfp. f Astrocytic clusters of the t-SNE projection in d, with feature plots of Olig1 and Yfp. p Value in b determined by two-sided Student’s t-test and in e and f, by Fisher’s exact test.

Fig 5: Lipopolysaccharides (LPS) shifts ratio of stem cells, glial cells and neuron. Flow cytometry (A) demonstrated that cultivation without additional growth factors (–GF) for 24 hrs (DIV1; red profile) drastically limited the adhesion and proliferation of isolated glial fibrillary acidic protein (GFAP) cells (DIV0; grey profile). Under stimulation with LPS, a higher number of cells with increased expression level of GFAP was detected in both DIV1 and DIV6 cells deprived of growth factors (red profile) compared with corresponding samples cultured under standard conditions (blue profile). On x axis is shown fluorescence intensity and on y axis the number of positive cells. Data were expressed as percentage of positive cells compared to isotypic control. Moreover, the mean fluorescence intensities (MFI) relative to isotypic controls and GFAP samples were reported. qPCRs were performed after 6-day stimulation with different LPS concentrations (500 pg/ml–50 μg/ml; B). Investigated genes: βIII-tubulin, GFAP, neurofilament heavy (NF-H), medium (NF-M) and light (NF-L; n = 3). Significance levels: ≥2 significantly up-regulated; ≤0.4 significantly down-regulated, which is indicated by lines. βIII-tubulin expression was increased in the colon, but not in small intestine. GFAP expression was not influenced in the small intestine, while expression in colon is increased. The expression of NF-H, NH-M and NF-L was also not influenced except of NF-H expression in the colon. Western blot analysis indicated the presence of βIII-tubulin, GFAP and neurofilament in the small intestine, as well as in the colon in control and LPS-treated cultures (C). Immunofluorescence staining against DAPI (blue), nestin (green), GFAP (rot) and βIII-tubulin (green) after inducing differentiation of stimulated cells (D). Quantification indicated no difference in whole cell number, whereas the amount of nestin and GFAP-positive cells significantly increased after LPS stimulation. The number of βIII-tubulin-positive cells decreased by LPS treatment (n = 3). Significance compared to control; **P ≤ 0.01; bar: 50 μm.