Leukocyte Counts Based on DNA Methylation at Individual Cytosines

Frobel, Joana; Božić, Tanja; Lenz, Michael; Uciechowski, Peter; Han, Yang; Herwartz, Reinhild; Strathmann, Klaus; Isfort, Susanne; Panse, Jens; Esser, André; Birkhofer, Carina; Gerstenmaier, Uwe; Kraus, Thomas; Rink, Lothar; Koschmieder, Steffen; Wagner, Wolfgang

doi:10.1373/clinchem.2017.279935

Cited by 23 publications

(28 citation statements)

References 52 publications

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“…We demonstrate that age-associated DNAm changes occur in multiple tissues in our three CpGs albeit they were initially identified in blood ( Petkovich et al, 2017 ). Furthermore, DNAm levels may vary between different hematopoietic subsets ( Frobel et al, 2018 ; Houseman et al, 2014 ). In the future, sorted subsets should be analyzed to determine how the three CpG signature is affected by blood counts.…”

Section: Discussionmentioning

confidence: 99%

Epigenetic age-predictor for mice based on three CpG sites

Han

Eipel

Franzen

et al. 2018

eLife

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Epigenetic clocks for mice were generated based on deep-sequencing analysis of the methylome. Here, we demonstrate that site-specific analysis of DNA methylation levels by pyrosequencing at only three CG dinucleotides (CpGs) in the genes Prima1, Hsf4, and Kcns1 facilitates precise estimation of chronological age in murine blood samples, too. DBA/2 mice revealed accelerated epigenetic aging as compared to C57BL6 mice, which is in line with their shorter life-expectancy. The three-CpG-predictor provides a simple and cost-effective biomarker to determine biological age in large intervention studies with mice.

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Section: Discussionmentioning

confidence: 99%

Epigenetic age-predictor for mice based on three CpG sites

Han

Eipel

Franzen

et al. 2018

eLife

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“…The cellular composition of hematopoietic subsets can be estimated based on DNAm patterns by deconvolution algorithms (Frobel et al, 2017;Houseman et al, 2012). When we applied the algorithm of Houseman et al on DNAm profiles of HuMice the estimated relative cell counts were overall in line with immunophenotypic assessment (Fig.…”

Section: Resultsmentioning

confidence: 77%

“…To better understand if DNAm patterns of normal human B cells are generally acquired in HuMice, we filtered for B cell-specific CpG sites (Frobel et al, 2017). The vast majority of these CpGs were hypomethylated in B cells and most of these were also hypomethylated in HuMice.…”

Section: Resultsmentioning

confidence: 99%

“…For selection of B cell-specific CpGs we filtered for CpGs with a difference in mean β-value of > 0.7 or < -0.7 in B cells (GSE35069) compared to other mature hematopoietic cell types isolated from peripheral blood (granulocytes, neutrophils, eosinophils, CD4 + T cells, CD8 + T cells, NK cells, and monocytes; GSE35069). Furthermore, only CpG sites with a standard deviation (SD) < 0.1 within the respective cell type(s) were considered as described before (Frobel et al, 2017). Using this selection strategy, 330 B cell-specific CpG sites were identified.…”

Section: Bioinformaticsmentioning

confidence: 99%

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Epigenetic aging of human hematopoietic cells is not accelerated upon transplantation into mice

Frobel

Rahmig

Franzen

et al. 2018

Preprint

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Transplantation of human hematopoietic stem cells into immunodeficient mice provides a powerful in vivo model system to gain functional insights into hematopoietic differentiation. So far, it remains unclear if epigenetic changes of normal human hematopoiesis are recapitulated upon engraftment into such "humanized mice". Mice have a much shorter life expectancy than men, and therefore we hypothesized that the xenogeneic environment might greatly accelerate the epigenetic clock. We demonstrate that genome-wide DNA methylation patterns of normal human hematopoietic development are indeed recapitulated upon engraftment in miceparticularly those of normal early B cell progenitor cells. Furthermore, we tested three epigenetic aging signatures and none of them indicated that the murine environment accelerated ageassociated DNA methylation changes. These results demonstrate that the murine transplantation model overall recapitulates epigenetic changes of human hematopoietic development, whereas epigenetic aging seems to occur cell intrinsically.

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“…Using the cell type specific CpGs previously selected for classification and their mean methylation value (for each cell type) on the training dataset as our reference matrix, we applied a reference-based non-negative least-squares (NNLS) algorithm (16,23). An application for cell type deconvolution is provided as separate Excel tool (Supplemental Table S3) and as the DeconvolutionApp, https://costalab.ukaachen.de/shiny/tmaie/deconapp/ (accessed 24 th July 2020).…”

Section: Deconvolution Of Cell Type Proportionsmentioning

confidence: 99%

Deconvolution of cellular subsets in human tissue based on targeted DNA methylation analysis at individual CpG sites

Schmidt

Maié

Dahl

et al. 2020

Preprint

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BackgroundThe complex composition of different cell types within a tissue can be estimated by deconvolution of omics datasets. For example, DNA methylation (DNAm) profiles have been used to establish an atlas for multiple human tissues and cell types. In this study, we investigated if deconvolution is also feasible with individual cell-type-specific CG dinucleotides (CpG sites), which can be addressed by targeted analysis, such as pyrosequencing.ResultsWe compiled and curated a dataset of 579 samples from Illumina 450k BeadChip technology that comprised 14 different purified and characterized human cell types. A training and validation strategy was applied to identify and test cell-type-specific CpGs. Initially, the amount of fibroblasts was estimated using two CpGs that were either hypermethylated or hypomethylated in fibroblasts. This FibroScore correlated with the state of fibrosis and was associated with overall survival in various types of cancer. Furthermore, we identified hypomethylated CpGs for leukocytes, endothelial cells, epithelial cells, hepatocytes, glia, neurons, fibroblasts and induced pluripotent stem cells. Using previously published BeadChip datasets with cell mixtures the accuracy of this eight CpG signature was comparable to previously published signatures based on several thousand CpGs. Finally, we established and validated pyrosequencing assays for the relevant CpGs that can be utilized for classification and deconvolution of cell types.ConclusionThis proof of concept study demonstrates that DNAm analysis at individual CpGs reflects the cellular composition of cellular mixtures and different tissues. Targeted analysis of these genomic regions facilitates robust methods for application in basic research and clinical settings.

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Leukocyte Counts Based on DNA Methylation at Individual Cytosines

Abstract: White blood cell counts can be reliably determined by site-specific DNAm analysis. This approach is applicable to very small blood volumes and frozen samples, and it allows for more standardized and cost-effective analysis in clinical application.

Cited by 23 publications

References 52 publications

Epigenetic age-predictor for mice based on three CpG sites

Epigenetic age-predictor for mice based on three CpG sites

Epigenetic aging of human hematopoietic cells is not accelerated upon transplantation into mice

Deconvolution of cellular subsets in human tissue based on targeted DNA methylation analysis at individual CpG sites

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