Single Cell Analysis Elucidates the Maturation of Human Stem and Progenitor Cell Function from Fetal through Adult Hematopoiesis

• Published in: Blood 2021-11, Vol.138 (Supplement 1), p.1079-1079
• Main Authors: Li, Hojun, Ezike, Jideofor, Afanassiev, Anton, Greenstreet, Laura, Zhang, Stephen, Whangbo, Jennifer S., Butty, Vincent, Moiso, Enrico, Connelly, Guinevere, Morris, Vivian, Wang, Dahai, Daley, George Q., Garg, Salil, Chou, Stella T., Regev, Aviv, Lummertz da Rocha, Edroaldo, Schiebinger, Geoffrey, Rowe, R. Grant
• Format: Article
• Language: English
• ISSN: 0006-4971; 1528-0020
• DOI: 10.1182/blood-2021-151090

Hematopoiesis continually replenishes the supply of circulating blood cells from embryonic development through the entirety of human lifespan. Although all hematopoietic lineages are produced throughout life, biases in lineage output occur at various stages, including lymphoid bias in childhood and myeloid bias in adulthood. Furthermore, many blood disorders demonstrate marked biases in age of onset, such as bone marrow failure disorders, clonal hematopoiesis of indeterminate potential, and numerous hematologic malignancies. A lack of insight into the normal physiologic changes occurring in the hematopoietic stem and progenitor cell (HSPC) compartments during development and maturation fundamentally limits our understanding of how age biased blood disorders arise. Two major unresolved questions are: (1) what changes in the molecular regulation of hematopoietic lineage commitment occur over the course of human life? And (2) are certain HSPC states present only during specific ages of life, and if so, do age-specific HSPCs have distinct biology? To address these questions we performed single cell RNA sequencing (scRNAseq) on human HSPCs from first and second trimester fetal liver hematopoiesis, and bone marrow hematopoiesis spanning childhood into mature adulthood. In total, HSPC samples were obtained from 14 distinct human donors. Dimensionality reduction and marker gene analysis identified uncommitted hematopoietic stem cells (HSCs) and the developmental trajectories of each lineage emanating from multipotent HSCs. We then identified the genes activated upon commitment to each hematopoietic lineage during fetal, childhood, and mature adult hematopoiesis using the Population Balance Analysis and Stationary Optimal Transport algorithms, followed by Elastic Net gene regression. For each lineage we determined the putative transcription factor network that is consistently active in driving commitment to that lineage throughout life, but surprisingly also found the existence of adjunctive transcription factor networks that only drove lineage commitment at specific ages. We next used unbiased clustering of scRNAseq data to identify 21 distinct subtypes in the HSPC compartment across human life. Using marker gene analysis and singleCellNet algorithm comparisons to an existing human adult bone marrow scRNAseq data set, we hierarchically ordered and annotated these HSPC subtypes ranging from uncommitted HSCs to lineage committed progenitor cells. We found that cellu