Deciphering of single-cell chromatin accessibility and transcriptome reveals the discrepancy for ex vivo human erythropoiesis

Erythroid cells can be generated from hematopoietic stem and progenitor cells (HSPC) derived from various sources; however, few studies decode ex vivo human erythropoiesis for the discrepancies at single-cell multi-omics resolution and uncover the underlying restraints for erythrocyte regeneration.

Results

We deciphered ex vivo human erythropoiesis at two differentiation states from three sources at single-cell chromatin accessibility and transcriptomes level. We identified detrimental myeloid differentiation tendencies during early differentiation. These tendencies were linked to low glutamine activity in cord blood- and iPSC-derived erythropoiesis. The erythroid progenitor differentiation is restricted by cell cycle and hypoxia signaling deficiencies, which are pronounced in the iPSC-derived erythropoiesis. We delineated the erythroid differentiation trajectory of various ex vivo erythropoiesis systems, and revealed a distinct roadmap from HSC to orthochromatic erythroblast with unprecedented resolution. The integrative analysis of single-cell chromatin accessibility and transcriptome across developmental stages uncovered a dynamic coordination, and highlighted the pivotal role of chromatin accessibility and associated enhancers in regulating ex vivo erythropoiesis. Cell–cell communications in the ex vivo erythropoiesis system were not as well established as those in the BM, suggesting that modulating cell-cell communication signals in distinct ex vivo erythropoiesis system may facilitate erythrocyte regeneration.

Conclusions

This study comprehensively characterized the discrepancies and constraints in ex vivo human erythropoiesis at single-cell multi-omics resolution, offering novel strategies to overcome these constraints. These insights are critical for advancing functional erythrocyte generation and have significant implications for clinical applications.