FIGURE

Fig. 8

ID

ZDB-FIG-220818-11

Publication

Volpatti et al., 2022 - X-linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition

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Fig. 8

DNA methylation changes and 1-carbon metabolites in Mtm1 KO mice. a Volcano plot of CpGs differentially methylated between Mtm1 KO mice and WTs, assayed using RRBS. CpGs in light blue met a statistical threshold of 10% mean methylation difference between groups and FDR corrected **p value?<?0.01. 27 CpGs in dark blue were significant on RRBS and were located within 1 kb of a significant CpGs on the mouse array. b Heatmap of the 2,424 CpGs identified using RRBS. Samples (n?=?3 Mtm1 KO mice and n?=?3 WT) are ordered by hierarchical clustering, which shows two main clusters corresponding to genotype. c Density plot of all mouse array CpGs averaged across WT and Mtm1 KO (n?=?4 per genotype). WT distribution shows lower peak at methylated CpGs and higher peak at unmethylated CpGs, consistent with a global increase in DNA methylation in KO mice. d Schematic of 1-carbon metabolism and related DNA (hydroxy)methylation processes. e 5-methylcytosine (5mC) based ELISA shows an increase in global DNA methylation in untreated KO mouse muscle and similar levels in WT vs KO muscle treated with VPA. Values are Mean?�?SEM, n?=?4 per group. WT?+?PBS vs Mtm1 KO?+?PBS, 3.2?�?0.47, 4.47?�?0.14, *p?<?0.05 by Student?s T test. WT?+?VPA 4.93?�?0.71 and KO?+?VPA 4.65?�?0.7, one-way ANOVA followed by ?�d�k's multiple comparisons test. Values are relative to WT?+?PBS controls. f 5-hydroxymethycytosine (5-hmC) based ELSA shows increased 5-hmC% in hamstring muscle of Mtm1 KO compared to WT mice that is ameliorated with VPA treatment. Values are Mean?�?SEM relative to WT?+?PBS controls. n?=?6 per group. WT?+?PBS vs KO?+?PBS, 1.0?�?0.12, 1.87?�?0.44, *p?<?0.05 by one-way ANOVA followed by ?�d�k's multiple comparisons test. WT?+?VPA 0.77?�?.0.06 and KO?+?VPA 0.85?�?0.16 are not different from WT?+?PBS controls. g Total DNMT enzymatic activity is not significantly increased in hamstring muscle of Mtm1 KO?+?PBS compared to WT?+?PBS mice. Values are Mean?�?SEM relative to WT?+?PBS controls n?=?6 per group. WT?+?PBS vs KO?+?PBS, 1.0?�?0.23, 2.06?�?0.43, p?=?0.0736 by one-way ANOVA followed by Dunnett?s post-hoc test. WT?+?VPA 1.95?�?.14 and KO?+?VPA 1.24?�?0.39. h 10 CpGs with highest p-values, identified by modelling an interaction between genotype and VPA treatment (160 CpGs total nominal p value?<?0.01 and methylation difference?>?5%), in mouse array data. Most sites exhibiting hypermethylation in KOs are corrected by VPA treatment. i 1-carbon metabolites measured in muscle of 35 day old WT vs Mtm1 KO mice. Mtm1 KO mice have lower concentrations of betaine, higher concentration of SAM, and a higher SAM/SAH ratio. Values are Mean?�?SEM, n?=?2?3 per group. WT vs Mtm1 KO, Betaine 259?�?24, 128.8?�?10.9, *p?<?0.05; SAM 25.53?�?3.88, 39.23?�?0.76; SAH 3.83?�?0.27, 3.53?�?0.14; SAM:SAH 6.33?�?1.59, 11.13?�?0.50, *p?<?0.05; Cystathionine 2.2?�?0.14, 3.8?�?0.39, *p?<?0.05. Significance detected by Student?s T test

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Acknowledgments

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