Journal: Nature Communications

Article Title: DNA methylation signatures of Alzheimer’s disease neuropathology in the cortex are primarily driven by variation in non-neuronal cell-types

doi: 10.1038/s41467-022-33394-7

Figure Lengend Snippet: Characteristics of the BDR samples profiled in this study

Article Snippet: Briefly, following tissue homogenization and nuclei purification using sucrose gradient centrifugation we used a FACS Aria III cell sorter (BD Biosciences) to simultaneously collect populations of NeuN+ (neuronal-enriched) (R&D systems, Cat No: NL2864R, dilution: 1:10) and SOX10+ (oligodendrocyte-enriched) (Millipore, Cat No: MAB377X, dilution: 1:1000) immunolabeled populations from bulk DLPFC tissue prior to genomic profiling, with the double-negative fraction and an aliquot of the “total” nuclei fraction (analogous to “bulk” cortex) also being collected from each tissue sample (Supplementary Fig. ).

Techniques: Purification

Journal: Nature Communications

Article Title: DNA methylation signatures of Alzheimer’s disease neuropathology in the cortex are primarily driven by variation in non-neuronal cell-types

doi: 10.1038/s41467-022-33394-7

Figure Lengend Snippet: Using linear regression models controlling for major covariates (see Methods) we show that a levels of tau pathology (measured using Braak NFT stage) are significantly associated with the proportion of NeuN+ cells (effect size = −2.74, SE = 0.705, P = 1.15E–04), SOX10+ cells (effect size = 1.60, SE = 0.423, P = 1.72E–04) and NeuN–/SOX10– cells (effect size = −2.00, SE = 0.687, P = 0.004) in the DLPFC ( N = 597 donors) using cell proportion estimates derived from “bulk” DNA methylation data. b In contrast no associations ( P > 0.008) between levels of tau pathology and cell proportion estimates derived from “bulk” DNA methylation data were observed in the OCC ( N = 598 donors). Boxplots of the estimated proportion of each cell-type across Braak NFT stages are shown, where the middle box represents the interquartile range (IQR), the middle line represents the median, and the whisker lines represent the minimum (quartile 1 –1.5 × IQR) and the maximum (quartile 3 + 1.5 × IQR). Tau pathology (Braak NFT stage) is shown on the x- axis split by cell-type and estimated cell proportions are shown on the y -axis. A similar pattern of results was found for levels of amyloid pathology as shown in Supplementary Fig. .

Article Snippet: Briefly, following tissue homogenization and nuclei purification using sucrose gradient centrifugation we used a FACS Aria III cell sorter (BD Biosciences) to simultaneously collect populations of NeuN+ (neuronal-enriched) (R&D systems, Cat No: NL2864R, dilution: 1:10) and SOX10+ (oligodendrocyte-enriched) (Millipore, Cat No: MAB377X, dilution: 1:1000) immunolabeled populations from bulk DLPFC tissue prior to genomic profiling, with the double-negative fraction and an aliquot of the “total” nuclei fraction (analogous to “bulk” cortex) also being collected from each tissue sample (Supplementary Fig. ).

Techniques: Derivative Assay, DNA Methylation Assay, Whisker Assay

Journal: Nature Communications

Article Title: DNA methylation signatures of Alzheimer’s disease neuropathology in the cortex are primarily driven by variation in non-neuronal cell-types

doi: 10.1038/s41467-022-33394-7

Figure Lengend Snippet: We compared effect sizes for the 334 overlapping tau-associated DMPs identified in our “bulk” cortex meta-analysis with those at the same sites in an analysis of purified DLPFC nuclei populations from low (Braak NFT stage 0 to II) and high (Braak NFT stage >V) tau-pathology donors. Shown is a comparison of effect sizes between the meta-analysis (bulk, N = 2013 individuals]) and the a total nuclei (bulk) nuclei fraction ( N = 26) (direction of effect = 87% concordant, sign-test P = 7.24E–46); b NeuN+ (neuron-enriched) nuclei fraction ( N = 27) (direction of effect = 60% concordant, sign-test P = 7.59E–05), c SOX10+ (oligodendrocyte-enriched) nuclei fraction ( N = 28) (direction of effect = 67% concordant, sign-test P = 2.15E–10), and d double-negative (microglia- and astrocyte-enriched) nuclei population ( N = 21) (direction of effect = 96% concordant, sign-test P = 1.2E–75). The x- axis shows effect sizes from the bulk cortex meta-analysis and the y -axis shows effect sizes for those same DMPs in each purified nuclei population. Gray dashed line represents y = x . e Bar-plots of the mean absolute relative effect sizes in each purified nuclei population compared to the bulk cortex across the 334 tau-associated DMPs, with error bars denoting the 95% confidence intervals.

Article Snippet: Briefly, following tissue homogenization and nuclei purification using sucrose gradient centrifugation we used a FACS Aria III cell sorter (BD Biosciences) to simultaneously collect populations of NeuN+ (neuronal-enriched) (R&D systems, Cat No: NL2864R, dilution: 1:10) and SOX10+ (oligodendrocyte-enriched) (Millipore, Cat No: MAB377X, dilution: 1:1000) immunolabeled populations from bulk DLPFC tissue prior to genomic profiling, with the double-negative fraction and an aliquot of the “total” nuclei fraction (analogous to “bulk” cortex) also being collected from each tissue sample (Supplementary Fig. ).

Techniques: Purification, Comparison