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DNA-based immune profiling in murine blood with methylation cytometry deconvolution

ABSTRACT: Cell-type-specific patterns of DNA methylation have been leveraged to develop methods for accurate and reproducible DNA-based cell typing in human blood and other biospecimens. Recently developed and standardized genome -scale DNA methylation arrays for mus musculus offer an instrument for quantifying cellular composition with epigenetic signatures specific to each cell type. We present a novel murine immune cell deconvolution tool that leverages DNA methylation profiles FlowSorted.Blood.IlluminaMouseMethylation. Separately from BALB/c and C57BL/6 mice, we used flow cytometry to purify polymorphonuclear neutrophil (PMN), monocyte, B-lymphocyte, natural killer, and CD4+ and CD8+ T-cells. Genome-scale DNA methylation was measured with the Illumina MouseMethylation BeadChip array at >285,000 CpG loci in purified cells for reference profile development. For testing and validation, DNA methylation was measured in both eye bleed and terminal blood whole blood samples from four mouse strains. To benchmark and determine accuracy of reference libraries for DNA methylation cell type deconvolution, flow cytometry of independent whole blood samples from four mouse strains was used. The Identifying Optimal Libraries (IDOL) algorithm identified an optimal reference library of 300 CpGs for deconvolution with RMSE values across testing and validation samples of <1.7 for all cell types except B lymphocytes (RMSE<2.75). This methylation cytometry tool for mice offers the ability to conduct DNA-based immune profiling in archival samples and reduce confounding from cell type heterogeneity in molecular studies of whole blood samples.

ORGANISM(S): Mus musculus

PROVIDER: GSE284254 | GEO | 2026/05/14

REPOSITORIES: GEO

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