Single-Cell Multi-Regional Atlas of DNA Methylation and 3D Chromatin Conformation in the AD-Affected Brain

By Stuart P. Atkinson

Overall methylation levels in AD cases and controls, across brain regions and selected cell types. From figure 2 of Wang et al..

Studying Selective Vulnerability to Alzheimers Disease Beyond Chromatin Accessibility

While Alzheimers disease (AD) represents a globally prevalent neurodegenerative disorder, we know relatively little regarding the molecular mechanisms underlying its region and cell-type-specific pathogenesis. Recent investigations into why AD displays selective vulnerability across brain regions and cell types have focused on chromatin accessibility (Xiong et al. and Liu et al.), describing a loss of regulatory fidelity and neuronal identity due to the progressive erosion of cell-type-specific chromatin accessibility landscapes (epigenome erosion). However, DNA methylation and 3D chromatin conformation also mediate the interplay between genetic and environmental risk factors (Wang et al.) and can contribute to disease initiation and progression (Wen et al. and Wang et al.).

To fill this gaping knowledge gap, researchers from the laboratories of Bradley T. Hyman (Massachusetts General Hospital) and Joseph R. Ecker (Salk Institute for Biological Studies) generated a large-scale, single-cell multi-omic atlas that integrated two levels of epigenetic information DNA methylation and 3D chromatin conformation from cells isolated from brain regions that display distinct vulnerabilities to AD pathology. As reported in a bioRxiv preprint, this new region-resolved, single-cell multi-omic atlas reveals how DNA methylation and 3D chromatin conformation profiles differ across brain regions and cell types in post-mortem AD brain samples; thus, this advance offers mechanistic insights and provides a framework for the development of novel targeted therapeutic strategies (Wang et al.).

The single-cell epigenetic analyses of AD-affected human brain samples/cells have shifted focus from chromatin accessibility to DNA methylation and chromatin conformation; will histone modification profiles represent the next step? Paired-Tag technology from Epigenome Technologies, which generates joint epigenetic and transcriptomic profiles at single-cell resolution and detects histone modifications and RNA transcripts in individual nuclei with efficiency comparable to single-nucleus RNA-seq/ChIP-seq assays, could represent an efficient means of exploring this exciting concept.

Disease-associated cell types and pathways across regions and selected cell types. From figure 2 of Wang et al..

A Single-cell, Multi-regional Atlas of DNA methylation and 3D Chromatin Conformation of the AD Brain

To comprehensively map the regulatory landscape of AD at cellular resolution, the authors generated a large-scale, single-cell, multi-regional atlas of DNA methylation and 3D chromatin conformation from post-mortem brain tissue of AD patients and normal controls using single-nucleus methyl-3C sequencing (snm3C-seq) (Lee et al.). A yet-to-be-published companion study using the same samples measured chromatin accessibility and gene expression by applying the 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression (10x multiome) assay. The brain tissues involved - the temporal cortex (severely), prefrontal cortex (intermediate), and visual cortex (mildly) all display distinct vulnerabilities to AD pathology. Overall, the dataset comprised more than 230,000 individual cells and included significant neuronal and glial populations, providing a high-resolution view of epigenomic regulation.

Analysis of this atlas demonstrated the existence of widespread alterations to DNA methylation patterns and marked reorganization of 3D chromatin conformation (including alterations in A/B compartments, topologically associating domains, and chromatin loops) when comparing AD to normal patient samples. However, the authors also highlighted robust region-specific alterations in AD patients; for example, the severely affected temporal cortex displayed DNA hypermethylation, transcriptional downregulation, and elevated boundary density, while the less affected primary visual cortex showed an opposing trend with global DNA hypomethylation, and the intermediately affected prefrontal cortex showed an intermediate profile. Overall, the authors believe that these features will provide important clues for prevention strategies aimed at vulnerable brain regions. Notably, the study also identified AD-associated glial and neuronal states shared across cell types, which consistently exhibited increased putative genomic deletions near telomeres, a higher density of topologically associating domain boundaries, and broad gene expression repression.

High-dimensional changes in chromatin conformation indicate widespread epigenetic changes in AD compared to control. From figure 3 of Wang et al..

Single-Cell Epigenetic Analyses Of AD-Affected Human Brain: Where to Next?

DNA methylation and 3D chromatin conformation .

Paired-Tag technology from Epigenome Technologies, which generates joint epigenetic and transcriptomic profiles at single-cell resolution and detects histone modifications and RNA transcripts in individual nuclei with efficiency comparable to single-nucleus RNA-seq/ChIP-seq assays, could represent the tool that takes the single-cell epigenetic analyses of AD-affected human brain samples/cells to the next level.