ArticleClinical epigenetics2015
Nucleated red blood cells impact DNA methylation and expression analyses of cord blood hematopoietic cells.
Article in Clinical epigenetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers, 3 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
45 citing papers in PubMed, 3 syntheses or guidelines pooled it, 67 citations in OpenAlex.
- Accelerated epigenetic age at birth and child emotional and behavioura development in early childhood: a meta-analysis of four prospective cohort studies in ECHO.Epigenetics · 2023Pooled it
- Maternal anxiety during pregnancy and newborn epigenome-wide DNA methylation.Molecular psychiatry · 2021Pooled it
- Maternal BMI at the start of pregnancy and offspring epigenome-wide DNA methylation: findings from the pregnancy and childhood epigenetics (PACE) consortium.Human molecular genetics · 2017Pooled it
- Identification of prognostic biomarkers and immunotherapy response predictors in lung adenocarcinoma: integrative Mendelian randomization and machine learning analysis.Translational lung cancer research · 2026Article
- Genomic interplay between deployment exposures and Gulf War illness in Million Veteran Program participants.Human genomics · 2026Article
- Unified high-resolution immune cell fraction estimation in blood tissue from birth to old age.Genome medicine · 2025Article
- Simulation-guided pan-cancer analysis identifies a novel regulator of CpG island hypermethylation heterogeneity.Briefings in bioinformatics · 2025Article
- Breaking rules: the complex relationship between DNA methylation and X-chromosome inactivation in the human placenta.Biology of sex differences · 2025Article
- DNA methylation differences between cord and adult white blood cells reflect postnatal immune cell maturation.Communications biology · 2025Article
- Decoding bronchopulmonary dysplasia in premature infants through an epigenetic lens.Frontiers in medicine · 2025Review
- Neural-net-based cell deconvolution from DNA methylation reveals tumor microenvironment associated with cancer prognosis.NAR cancer · 2024Article
- Epigenomic signature of major congenital heart defects in newborns with Down syndrome.Human genomics · 2023Article
- CimpleG: finding simple CpG methylation signatures.Genome biology · 2023Article
- Epigenomic signature of major congenital heart defects in newborns with Down syndrome.medRxiv : the preprint server for health sciences · 2023Article
- A robust mean and variance test with application to high-dimensional phenotypes.European journal of epidemiology · 2022Review
- DNA methylation signatures in human neonatal blood following maternal antenatal corticosteroid treatment.Translational psychiatry · 2022Article
- DNA methylation patterns in juvenile systemic sclerosis and localized scleroderma.Clinical immunology (Orlando, Fla.) · 2021Article
- Crosstalk between microRNA expression and DNA methylation drives the hormone-dependent phenotype of breast cancer.Genome medicine · 2021Article
- Prenatal lead exposure and cord blood DNA methylation in PROGRESS: an epigenome-wide association study.Environmental epigenetics · 2020Article
- 5-Hydroxymethylcytosine in cord blood and associations of DNA methylation with sex in newborns.Mutagenesis · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenome-wide DNA methylation (DNAm) studies have proven extremely useful to understand human hematopoiesis. Due to their active DNA content, nucleated red blood cells (nRBCs) contribute to epigenetic and transcriptomic studies derived from whole cord blood. Genomic studies of cord blood hematopoietic cells isolated by fluorescence-activated cell sorting (FACS) may be significantly altered by heterotopic interactions with nRBCs during conventional cell sorting.
resultsWe report that cord blood T cells, and to a lesser extent monocytes and B cells, physically engage with nRBCs during FACS. These heterotopic interactions resulted in significant cross-contamination of genome-wide epigenetic and transcriptomic data. Formal exclusion of erythroid lineage-specific markers yielded DNAm profiles (measured by the Illumina 450K array) of cord blood CD4 and CD8 T lymphocytes, B lymphocytes, natural killer (NK) cells, granulocytes, monocytes, and nRBCs that were more consistent with expected hematopoietic lineage relationships. Additionally, we identified eight highly differentially methylated CpG sites in nRBCs (false detection rate <5 %, |Δβ| >0.50) that can be used to detect nRBC contamination of purified hematopoietic cells or to assess the impact of nRBCs on whole cord blood DNAm profiles. Several of these erythroid markers are located in or near genes involved in erythropoiesis (ZFPM1, HDAC4) or immune function (MAP3K14, IFIT1B), reinforcing a possible immune regulatory role for nRBCs in early life.
conclusionsHeterotopic interactions between erythroid cells and white blood cells can result in contaminated cell populations if not properly excluded during cell sorting. Cord blood nRBCs have a distinct DNAm profile that can significantly skew epigenetic studies. Our findings have major implications for the design and interpretation of genome-wide epigenetic and transcriptomic studies using human cord blood.
Identifiers
What OpenQuestion holds
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.