Gene expression profiles of cryopreserved CD34(+) human umbilical cord blood cells are related to their bone marrow reconstitution abilities in mouse xenografts

Transcriptomic analysis of functional diversity of human umbilical cord blood hematopoietic stem/progenitor cells in erythroid differentiation

Hematopoietic stem cells (HSC) give rise to all types of blood lineages, including red blood cells (RBC). Hematopoietic stem/progenitor cells (HSPC) are known to be functionally diverse in terms of their self-renewal potential and lineage output. Consequently, investigation of molecular heterogeneity in the differentiation potential of HSPC is vital to identify novel regulators that affect generation of specific cell types, especially RBC. Here, we compared the erythroid potential of CD34⁺ hematopoietic stem and progenitor cells from 50 different umbilical cord blood (UCB) donors and discovered that those donors gave rise to diverse frequencies of Glycophorin-A⁺ erythroid cells after in vitro differentiation, despite having similar frequencies of phenotypic HSC initially. RNA sequencing revealed that genes involved in G protein-coupled receptor (GPCR) signaling were significantly up-regulated in the high-erythroid output donors. When we chemically modified two main signaling elements in this pathway, adenylyl cyclase (AC) and phosphodiesterase (PDE), we observed that inhibition of PDE led to 10 times higher yield of Glycophorin-A⁺ cells than activation of AC. Our findings suggest that GPCR signaling, and particularly the cAMP-related pathway, contributes to the diversity of erythroid potential among UCB donors.

CTCF and CohesinSA-1 Mark Active Promoters and Boundaries of Repressive Chromatin Domains in Primary Human Erythroid Cells

Background

CTCF and cohesin^SA-1 are regulatory proteins involved in a number of critical cellular processes including transcription, maintenance of chromatin domain architecture, and insulator function. To assess changes in the CTCF and cohesin^SA-1 interactomes during erythropoiesis, chromatin immunoprecipitation coupled with high throughput sequencing and mRNA transcriptome analyses via RNA-seq were performed in primary human hematopoietic stem and progenitor cells (HSPC) and primary human erythroid cells from single donors.

Results

Sites of CTCF and cohesin^SA-1 co-occupancy were enriched in gene promoters in HSPC and erythroid cells compared to single CTCF or cohesin sites. Cell type-specific CTCF sites in erythroid cells were linked to highly expressed genes, with the opposite pattern observed in HSPCs. Chromatin domains were identified by ChIP-seq with antibodies against trimethylated lysine 27 histone H3, a modification associated with repressive chromatin. Repressive chromatin domains increased in both number and size during hematopoiesis, with many more repressive domains in erythroid cells than HSPCs. CTCF and cohesin^SA-1 marked the boundaries of these repressive chromatin domains in a cell-type specific manner.

Conclusion

These genome wide data, changes in sites of protein occupancy, chromatin architecture, and related gene expression, support the hypothesis that CTCF and cohesin^SA-1 have multiple roles in the regulation of gene expression during erythropoiesis including transcriptional regulation at gene promoters and maintenance of chromatin architecture. These data from primary human erythroid cells provide a resource for studies of normal and perturbed erythropoiesis.