Additional file 1 of Sex differences in muscle protein expression and DNA methylation in response to exercise training
Creators: name: Landen, Shanie
name: Jacques, Macsue
name: Hiam, Danielle
name: Alvarez-Romero, Javier
name: Schittenhelm, Ralf B.
name: Shah, Anup D.
name: Huang, Cheng
name: Steele, Joel R.
name: Harvey, Nicholas R.
name: Haupt, Larisa M.
name: Griffiths, Lyn R.
name: Ashton, Kevin J.
name: Lamon, Séverine
name: Voisin, Sarah
name: Eynon, Nir
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Histogram of p-values for DNA methylation and protein expression for all tested CpGs and proteins. DNA methylation (meta-analysis) histograms are A-F; proteomics (Gene SMART) histograms are G-K. (A) P-value histogram for the effect of training, model DNAm ~ sex + timepoint + batch (Gene SMART) + lean/obese (E-MTAB-11282) + age + baseline VO2. (B) P-value histogram for the interaction of sex and the training, model DNAm ~ sex * timepoint + batch (Gene SMART) + lean/obese (E-MTAB-11282) + age + baseline VO2. (C) P-value histogram for the interaction of baseline VO2 (CRF) and training, model DNAm ~ sex + batch (Gene SMART) + lean/obese (E-MTAB-11282) + age + baseline VO2 * timepoint. (D) P-value histogram for the interaction of sex and baseline VO2 (CRF), model DNAm ~ timepoint + batch + age + baseline VO2 * sex. (E) P-value histogram for baseline VO2 (CRF), model DNAm ~ timepoint + batch + age + baseline VO2 + sex. (F) P-value histogram for the control time point (“CON”; one month control period) relative to the PRE time point (Gene SMART only, before starting the HIIT intervention), model DNAm ~ sex + timepoint + batch + age + baseline VO2. (G) P-value histogram for the effect of training, model protein expression ~ sex + timepoint + age + baseline VO2. (H) P-value histogram for the interaction of sex and the training, model protein expression ~ sex * timepoint + age + baseline VO2. (I) P-value histogram for the interaction of baseline VO2 (CRF) and training, model protein expression ~ sex + age + baseline VO2 * timepoint. (J) P-value histogram for the interaction of sex and baseline VO2 (CRF), model protein expression ~ timepoint + age + baseline VO2 * sex. (K) P-value histogram for baseline VO2 (CRF), model protein expression ~ timepoint + age + baseline VO2 + sex. Figure S2. Volcano plots for proteomics and DNA methylation associations with training regardless of sex, sex, and cardiorespiratory fitness (CRF) regardless of sex. (A) Volcano plot of DNA methylome association with training, irrespective of sex. Red dots denote differentially methylated positions (DMPs) whose methylation increased with training; blue dots denote DMPs whose methylation decreased with training; black dots denote insignificant CpGs. Boxplots are the methylation levels (beta values residuals for batch) of the DMP pointed to, before and after training in the Gene SMART cohort. (B) Volcano plot of DNA methylome association with CRF, irrespective of sex. Red dots denote differentially methylated positions (DMPs) whose methylation increased with baseline VO2max (CRF); blue dots denote DMPs whose methylation decreased with baseline VO2max (CRF); black dots denote insignificant CpGs. Scatterplots are the methylation levels of the DMP pointed to (beta values residuals for batch), plotted against baseline VO2max in the Gene SMART cohort. (C) Volcano plot of proteome association with training in the Gene SMART cohort, irrespective of sex. Red dots denote differentially expressed proteins whose expression increased with training; blue dots denote proteins whose expression decreased with training; black dots denote insignificant proteins. Boxplots are the protein levels of the protein pointed to, before and after training. (D) Volcano plot of proteome association with CRF, irrespective of sex in the Gene SMART cohort. Black dots denote insignificant proteins. Figure S3. Correlation plots of residuals from the chi2 test for baseline fitness-DMPs enriched among the differing (A) Roadmap Epigenome project chromatin states and (B) CpG island locations. Blue denotes enrichment and red denotes depletion. Figure S4. Proteomics data before and after normalisation and plex correction. Log2 intensities (A) before and (B) after normalisation. (C) PCA plot of all samples in Gene SMART cohort after VSN normalisation and plex correction, each colour denotes a plex. Samples used in the manuscript were subsetted from a larger proteomics study. Figure S5 Sensitivity analyses for DNA methylation analysis. (A) Sensitivity analysis for using all covariates in one linear model or using a separate linear model (original) to detect delicate interaction between CRF and sex. 2D plot of effect sizes of each CpG for sex:CRF when comparing using one model (~ timepoint*sex + age + batch + baselineVO2*sex) vs a separate model (~ timepoint + age + batch + baselineVO2*sex). (B) Sensitivity analysis for using all covariates in one linear model or using a separate linear model (original) to detect delicate interaction between training and sex. 2D plot of effect sizes of each CpG for sex:training when comparing using one model (~ timepoint*sex + age + batch + baselineVO2*sex) vs a separate model (~ timepoint*sex + age + batch + baselineVO2). (C/D) Sensitivity analysis to ensure that a potential batch effect was not influencing our main findings, as one of the two batches in the Gene SMART data contained only males. We limited our analysis to only batch 2 in the Gene SMART study, which contained both males and females. We compared the effect sizes for coefficients of (C) sex:training and (D) sex:CRF (baseline VO2max) for all Gene SMART data (original) vs batch 2 of Gene SMART data at all CpGs. (E/F) Sensitivity analysis for effect of CRF on the DNA methylome by comparing to PRE-training samples only. 2D plot of effect sizes of (E) each CpG and (F) DMPs (FDR &lt; 0.005) for effect of CRF on the DNA methylome, regardless of sex in Gene SMART cohort in all samples vs the Gene SMART cohort limited to PRE samples. Effect sizes are of beta values, FDR from M values.