Impact of red blood cells on genome-wide DNA methylation and expression analyses of cord blood hematopoietic cells

Genome-wide DNA methylation (DNAm) studies have been extremely useful to understand hematopoiesis in humans. For cell-specific epigenetic studies, fluorescence-activated cell sorting (FACS) is the gold standard technique to isolate homogeneous cell populations of interest. However, in cord blood, the DNAm signature of isolated hematopoietic cells may be significantly altered by heterotopic interactions with nucleated red blood cells (nRBCs) that go undetected during conventional cell sorting. Using the Illumina 450K array, genome-wide DNAm profiles of the following cell types were obtained: (1) T lymphocytes, monocytes, and nRBCs isolated using a “standard” strategy lacking exclusion for erythroid lineage markers; and (2) CD4 and CD8 T lymphocytes, B lymphocytes, Natural Killer (NK) cells, granulocytes, monocytes, and nRBCs isolated using a “stringent” strategy formally excluding erythroid lineage-specific markers. DNAm profiles of cord blood cells isolated by the standard sorting strategy showed significant heterotopic cross-contamination between cell populations, whereas the cord blood cells sorted by the stringent strategy displayed DNAm profiles more consistent with their expected hematopoietic lineage relationships. Bisulphite-converted DNA from 15 cord blood cell populations sorted by a standard FACS protocol with no erythroid exclusion (T cells, monocytes, and nucleated RBCs collected from 5 cord blood samples) and from 48 cord blood cell populations sorted by a stringent FACS protocol formally excluding erythroid lineage-specific marker CD235 (B cells, CD4 and CD8 T cells, granulocytes, monocytes, NK cells, and nucleated RBCs collected from 7 cord blood samples; CD8 T cells were not collected from one sample) were hybridized to the Illumina Infinium HumanMethylation450 BeadChip.