ArticleNature methods2022
A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution.
Article in Nature methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers, 4 of them syntheses that pooled it.
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Who cites it
69 citing papers in PubMed, 4 syntheses or guidelines pooled it, 106 citations in OpenAlex.
- A cell-type-resolved meta-analysis reveals glial DNA methylation changes associated with aging and Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Pooled it
- Schizophrenia is associated with altered DNA methylation variance.Molecular psychiatry · 2025Pooled it
- Exercise is associated with younger methylome and transcriptome profiles in human skeletal muscle.Aging cell · 2024Pooled it
- A meta-analysis of immune-cell fractions at high resolution reveals novel associations with common phenotypes and health outcomes.Genome medicine · 2023Pooled it
- A Phase II Trial of Guadecitabine plus Atezolizumab in Metastatic Urothelial Carcinoma Progressing after Initial Immune Checkpoint Inhibitor Therapy.Clinical cancer research : an official journal of the American Association for Cancer Research · 2023Trial
- Sellar region neurocytomas exhibit a CIMP and neuroendocrine-like epigenetic signature distinct from other intra-axial neurocytomas.Acta neuropathologica · 2026Article
- The Impact of Nutrition on DNA Methylation: Methodological Challenges in Understanding Cause and Effect.Nutrients · 2026Review
- DNA methylation-based classification of hematolymphoid neoplasms.Blood advances · 2026Article
- Single-Cell and Spatial Transcriptomics Reframe the Immunosuppressive Microenvironment of Neuroendocrine Neoplasms.Cancers · 2026Review
- Population epigenetics: deciphering DNA methylation diversity and its implications for health, disease, and evolution.Molecular biology and evolution · 2026Review
- Integrating DNA methylation and clinical features to predict prostate cancer prognosis.BMC cancer · 2026Article
- Human DNA levels in feces reflect gut inflammation and associate with presence of gut species in IBD patients across the age spectrum.Microbiome · 2026Article
- Guidelines on optimizing DNA methylation reference panels for cell-type deconvolution.Communications biology · 2026Article
- Genome-wide extraction of differentially methylated DNA regions using adapter-anchored proximity primers.Nucleic acids research · 2026Article
- Evolution of Cancer Metastases via Lineage Trans-Differentiation.Research (Washington, D.C.) · 2026Article
- Epigenetic Signatures of Social Defeat Stress Varying Duration.International journal of molecular sciences · 2025Article
- Cell type inference in cell-free nucleic acid liquid biopsy.Nature biotechnology · 2025Review
- Early-stage lung adenocarcinoma affects DNA methylation and gene expression in adjacent tissues.EMBO reports · 2025Article
- Whole-genome profiling of age- and sex-associated DNA methylation signatures in human plasma cell-free DNA.Communications medicine · 2025Article
- DNA methylation and machine learning: challenges and perspective toward enhanced clinical diagnostics.Clinical epigenetics · 2025Review
9 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 8 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bulk-tissue DNA methylomes represent an average over many different cell types, hampering our understanding of cell-type-specific contributions to disease development. As single-cell methylomics is not scalable to large cohorts of individuals, cost-effective computational solutions are needed, yet current methods are limited to tissues such as blood. Here we leverage the high-resolution nature of tissue-specific single-cell RNA-sequencing datasets to construct a DNA methylation atlas defined for 13 solid tissue types and 40 cell types. We comprehensively validate this atlas in independent bulk and single-nucleus DNA methylation datasets. We demonstrate that it correctly predicts the cell of origin of diverse cancer types and discovers new prognostic associations in olfactory neuroblastoma and stage 2 melanoma. In brain, the atlas predicts a neuronal origin for schizophrenia, with neuron-specific differential DNA methylation enriched for corresponding genome-wide association study risk loci. In summary, the DNA methylation atlas enables the decomposition of 13 different human tissue types at a high cellular resolution, paving the way for an improved interpretation of epigenetic data.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.