Additional file 2 of Distinct CSF biomarker-associated DNA methylation in Alzheimer’s disease and cognitively normal subjects
Creators: name: Zhang, Wei
name: Young, Juan I.
name: Gomez, Lissette
name: Schmidt, Michael A.
name: Lukacsovich, David
name: Varma, Achintya
name: Chen, X. Steven
name: Martin, Eden R.
name: Wang, Lily
Publisher: name: figshare
Year: 2024
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Mental Health
subject: Hematology

description: Additional file 2: Supplementary Figure 1. The estimated blood cell-type proportions from pre-mortem DNA methylation samples are not significantly associated with Braak scores measured on postmortem brain samples in the London dataset. Supplementary Figure 2. Overlap between significant individual CpGs (A) and significant DMRs (B) in the analysis of samples from AD subjects and cognitively normal subjects. Abbreviations: AD = Alzheimer's disease, CN = cognitivelynormal. Supplementary Figure 3. Overlap between significant individual CpGs (P &lt; 10-5) and CpGs in significant DMRs (Sidak adjusted P &lt; 0.05) associated with CSF biomarkers in (A) Alzheimer's disease subjects and (B) cognitively normal subjects. Supplementary Figure 4. The correlations of estimated effect sizes for CpG-to-CSF biomarker associations in cognitively normal (CN) subjects vs. those in Alzheimer's disease (AD) subjects are modest and non-significant. Supplementary Figure 5. The P-values for pathway enrichment of CSF biomarker-associated DNA methylation in cognitively normal (CN) samples are independent of those in Alzheimer's disease (AD) samples. Shown are 95 pathways (Supplementary Table 9) that reached FDR &lt; 0.25 in either CN sample analysis or AD sample analysis. Abbreviations: R = Spearman correlation, p = P-value. Supplementary Figure 6. Immune cell type proportions estimated using the EpiDISH (PMID: 28193155) and the IDOL (labeled as "estimateCell") (PMID: 29843789) algorithms are highly concordant. Supplementary Figure 7.  A subset of CpGs located in DMR chr7: 27183946 – 27184668 at HOXA5 geneshowed both (A) Significant association with Braak stage in London dataset (information extracted fromSupplementary Table 18). (B) Significant correlation between brain DNAm and blood DNAm. Supplementary Figure 8. DNA methylation (DNAm) at the DMR chr7:27183946 - 27184668 is significantly correlated with HOXA5 gene expression. The ADNI dataset with matched gene expression and DNAm measured on 263 subjects was used for this analysis. Residuals were obtained by adjusting DNAm and gene expression separately by age, sex, immune cell-type proportions, batch effect, number of APOE4 alleles, smoking and years of education. Methylation level for the DMR was estimated by median methylation level over all CpGs mapped within the DMR. Supplementary Figure 9. DNA methylation at the CpG cg06171420 is significantly associated with CSF total tau (TAU) in cognitively normal samples in the ADNI dataset. To remove confounding effects from covariate variables, residuals were obtained by fitting model log CSF total tau ~ age + methylation plate + sex + APOE4 + years of education + smoking history + immune cell-type proportions. Supplementary Figure 10. Aβ42-associated DMR on chromosome 3. The highlighted CpG next to purple line / purple dot is the most significant CpG in the DMR. Supplementary Figure 11. DNA methylation at the CpG cg24037493 is significantly associated with CSF Aβ42 in Alzheimer's disease subjects in the ADNI dataset. To remove confounding effects from covariate variables, residuals were obtained by fitting model log CSF Aβ42 ~ age + methylation plate + sex + APOE4 + years of education + smoking history + immune cell-type proportions. *An outlier sample with beta value of 0.5, log abeta residual of 0.04 was omitted to improve resolution of the figure for all other data points. The fitted line represents estimated linear model applied to all data points, including the omitted outlier. Robust linear model, which is often used to model data with outlier, showed similar P-value for this CpG cg24037493 (P-value = 8.79 x 10-7) as the P-value in linear regression (P-value = 1.81 x 10-9). Supplementary Figure 12. DNA methylation at the CpG cg03037740 is significantly associated with CSF pTau181 in Alzheimer's disease subjects in the ADNI dataset. To remove confounding effects from covariate variables, residuals were obtained by fitting model log CSF pTau181 ~ age + methylation plate + sex + APOE4 + years of education + smoking history + immune cell-type proportions. Supplementary Figure 13. The Aβ42-associated DMR on chromosome 16. The highlighted CpG next to purple line / purple dot is the most significant CpG in the DMR. Supplementary Figure 14. The pTau181-associated DMR on chromosome 9. The highlighted CpG next to purple line / purple dot is the most significant CpG in the DMR. Supplementary Figure 15. The pTau181-associated DMR at chr7: 27183946 - 27184668 in the ADNI dataset. The highlighted CpG next to purple line / purple dot is the most significant CpG in the DMR.