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Updated: Jul 24, 2025
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Determination of Immune Cell Identity and Purity Using Epigenetic-Based Quantitative PCR
Published on: February 19, 2020
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Genetics and Environment Distinctively Shape the Human Immune Cell Epigenome
Wenliang Wang1, Manoj Hariharan1, Wubin Ding1
1Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA.
Biorxiv : the Preprint Server for Biology
|July 10, 2023
Summary
Environmental exposures and genetic variations significantly alter the immune cell epigenome. This study reveals how these factors influence DNA methylation and chromatin accessibility, impacting immune cell function in health and disease.
Area of Science:
- Immunology
- Epigenetics
- Genomics
Background:
- The epigenomic landscape of human immune cells is influenced by genetic and environmental factors.
- The precise contributions of genetic variation versus environmental exposures to immune cell epigenomic regulation remain unclear.
Purpose of the Study:
- To systematically investigate how pathogen and chemical exposures, alongside genetic variation, shape the immune cell epigenome.
- To differentiate the regulatory roles of environmental exposures and genetic factors on DNA methylation and chromatin accessibility.
Main Methods:
- Single-nucleus methylation sequencing and ATAC-seq were utilized to analyze immune cell epigenomes.
- Identification of exposure-associated differentially methylated regions (eDMRs) and genotype-associated DMRs (gDMRs).
- Analysis of correlations between DNA methylation changes and chromatin accessibility, and colocalization of SNPs with meQTLs.
Main Results:
- Distinct eDMRs were identified for specific pathogen and chemical exposures, demonstrating environmental remodeling of the methylome and transcription factor binding.
- A strong correlation was observed between DNA methylation changes and chromatin accessibility, indicating a coordinated epigenetic response.
- gDMRs were preferentially located in gene bodies, contrasting with eDMRs enriched in regulatory regions, suggesting differential regulatory control.
- Disease-associated single nucleotide polymorphisms (SNPs) frequently colocalized with methylation quantitative trait loci (meQTLs), offering cell-type-specific genetic insights into disease.
Conclusions:
- Genetic and environmental factors intricately interact to shape the immune cell epigenome.
- Environmental exposures and genetic variations exert distinct regulatory controls on immune cell epigenomic states.
- Findings provide novel cell-type-specific insights into the genetic underpinnings of immune-related diseases and immune cell regulation.
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