Paired-Tag: Single-cell Joint Epigenetic and Gene Expression Profiling
Applying "Paired-Tag" (parallel analysis of individual cells for RNA expression and DNA from targeted tagmentation by sequencing) for joint epigenetic and gene expression profiling at single-cell resolution can improve our understanding of the epigenetic underpinnings of disease-affected tissues. Research has linked dysregulated gene expression to the development of conditions such as Alzheimer's disease, and evidence suggests that epigenetic factors play a significant potentially targetable role in developing and maintaining disease-associated transcriptomic profiles.
A series of introductory articles have described the development and applications of i) Paired-Tag, first described in a Nature Methods article by Bing Ren at the University of California San Diego, and ii) Droplet Paired-Tag - a fast, accessible methodology – as described in a Nature Structural & Molecular Biology article from the same team.
Epigenome Technologies now provides optimized Paired-Tag kits and services to researchers in the epigenetics field under an exclusive license from the Ludwig Institute for Cancer Research. Paired-Tag remains the only commercially available technology for joint epigenetic and gene expression profiling in single cells.
Can this technology define the dynamic, cell-type-specific epigenomic landscapes of complex tissues and diseases and identify potential therapeutic targets? A recent application in the brains of Alzheimer's disease patients, described in this fourth introductory article, suggests that Paired-Tag technology can open a world of possibilities.
Demonstrating the Power of Droplet Paired-Tag: Single-cell Epigenome Analysis of Alzheimer's Disease Brains
A recent application of Paired-Tag sought to identify the main cell types involved in Alzheimer's disease pathology and understand the molecular mechanisms underlying this devastating disease. Establishing Paired-Tag technology as fit-for-purpose in single-cell epigenetic/transcriptomic studies of Alzheimer's disease represented the primary goal of this study, which involved demonstrating agreement with previous single-cell results, identifying differential histone modification dynamics within cell types, linking Alzheimer's disease risk mutations to epigenetic states, and exploring the functional enrichment of Alzheimer's disease risk in cell-specific epigenetic states.
The findings of this exciting study (as summarized below) confirmed these objectives and highlighted Paired-Tag's potential to advance Alzheimer's disease research by identifying epigenetic regulators of pathological or pathogenic cell states.
Making Advancements and Optimizing Applications of Paired-Tag Technology in Alzheimer's Disease
· This study involved improving Paired-Tag technology to support an in-depth understanding of Alzheimer's disease:
Revision of chemistry and oligonucleotide design
The implementation of lectin beads improved the nuclei recovery rate while redesigned combinatorial oligonucleotides improved DNA library complexity
Paired-Tag profiling of Alzheimer's disease and healthy control cortices
Generation of libraries employed over one million nuclei across twenty post-mortem human brains (10 disease/10 controls; matched for age, sex, and APOE status), while sequencing sufficient libraries supported a study of over 500,000 tagmented nuclei
Application of droplet Paired-Tag to Alzheimer's disease brain
The microfluidic-compatible Droplet Paired-Tag protocol applied the newly developed oligonucleotides to three post-mortem brains, which demonstrated improved RNA library complexity and high concordance with Split&Pool Paired-Tag
Generation of a pilot Alzheimer's disease cellular epigenetics resource
Paired-Tag analysis of the Alzheimer's disease brain facilitated the creation of a human parietal cortex cellular transcriptomic and epigenetic atlas, which represents a potentially instrumental resource in Alzheimer's disease research
Paired-Tag: Providing New Scientific Insight Relevant to Alzheimer's Disease
Analysis of the Paired-Tag data revealed significant findings in Alzheimer's disease research:
Recapitulation of frontal cortex disease signatures in the parietal cortex
The thousands of differentially expressed genes identified across multiple cell types included 420 in astrocytes and 1334 in specific excitatory neurons
The scREAD database of Alzheimer's disease single-cell differential gene expression verified that cellular differential expression signatures display preservation between the frontal and parietal cortex
Identification of chromatin state shifts in Alzheimer's disease within cell types
Applying ChromHMM to aggregated signals within Alzheimer's disease and healthy control brain cells identified signatures of weak and robust transcription, bivalency, and repression
Microglial enhancers as a mediator of Alzheimer's disease risk
Application of linkage disequilibrium score regression to histone modification maps determined enrichment for both strongly- and weakly-active regions in microglia, suggesting that epigenetic determinants of enhancer states contribute to Alzheimer's disease risk
Annotation of genome-wide association study variants revealed regions in the MS4A locus that shift from strong bivalency in microglia into a repressed state in Alzheimer's disease patients
Alleles associated with MS4A downregulation correlate with lower sTREM2 and earlier onset of Alzheimer's disease
Epigenetic erosion in excitatory neurons via aberrant acetylation
The hundreds of differentially active peaks identified across cell types included 76 in excitatory neurons
Comparing region activity in terms of H3K27ac deposition via repressed regions from ENCODE cortical and cell line samples identified a signature of aberrant activation in excitatory neurons in Alzheimer's disease absent in other cell types
Bring The Power of Paired-Tag to Your Research
Paired-Tag from Epigenome Technologies represents an exciting and commercially available means for joint epigenetic and gene expression profiling at single-cell resolution and detects histone modifications and RNA transcripts in individual nuclei. Overall, Paired-Tag methodology may enable quantum leaps forward in our understanding of development and significantly improve disease management.
Here, Paired-Tag generated detailed insights into the molecular mechanisms of Alzheimer's disease through joint epigenetic and gene expression profiling at the single-cell level. This advancement marks a significant step forward and may open new avenues for therapeutic interventions by targeting epigenetic remodeling complexes or de-repressed genes.
By Stuart P. Atkinson
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