Single-Cell Multiomics Reveals Distinct Cell States at the Top of the Human Hematopoietic Hierarchy

Abstract

The advent of single cell (Sc) genomics has challenged the dogma of haematopoiesis as a tree-like structure of stepwise lineage commitment through distinct and increasingly restricted progenitor populations. Instead, analysis of ScRNA-seq has proposed that the earliest events in human hematopoietic stem cell (HSC) differentiation are characterized by only subtle molecular changes, with hematopoietic stem and progenitor cells (HSPCs) existing as a continuum of low-primed cell-states that gradually transition into a specific lineage (CLOUD-HSPCs). Here, we combine ScRNA-seq, ScATAC-seq and cell surface proteomics to dissect the heterogeneity of CLOUD-HSPCs at different stages of human life. Within CLOUD-HSPCs, pseudotime ordering of both mRNA and chromatin data revealed a bifurcation of megakaryocyte/erythroid and lympho/myeloid trajectories immediately downstream a subpopulation with an HSC-specific enhancer signature. Importantly, both HSCs and lineage-restricted progenitor populations could be prospectively isolated based on correlation of their molecular signatures with CD35 and CD11A expression, respectively. Moreover, we describe the changes that occur in this heterogeneity as hematopoiesis develops from neonatal to aged bone marrow, including an increase of HSCs and depletion of lympho-myeloid biased MPPs. Thus, this study dissects the heterogeneity of human CLOUD-HSPCs revealing distinct HSPC-states of relevance in homeostatic settings such as ageing.

A Combined Immunophenotypic And Transcriptional Single-Cell Map Of First Trimester Human Fetal Liver Hematopoiesis

“…This also applies for the lymphoid surface markers, where CD10, mainly captured the lympho-myeloid cluster Ly-I, whereas our data revealed that IL7R in combination with CD38 and CD45RA could capture the Ly-II cell state with high purity in the embryo. This was opposite as to what was seen in adult where the population captured by CD10 comprised 70% Ly-II cells vs 43% when using IL7R ( data not shown and (Sommarin et al, 2021)). Thus, CITE-seq detects molecular heterogeneity within immunophenotypic progenitors, but also identifies surface markers that are preserved throughout development.…”

“…Next, the fetal cells were directly compared with our adult BM data set of HSPCs, analyzed with CITE-seq in a similar way and using the same platform as the fetal cells (Sommarin et al, 2021) ( Figure 3a and Sup Figure 2a ). First, the pseudo-bulked immunophenotypic gated populations from fetal and adult were compared using PCA.…”

“…Furthermore, MPP-I, which represents about 17% of the CS22 FL cells, were hardly detectable in the BM sample (2% of total cells). To narrow down the time window in development when these changes in cell states occurred, CB from the same data set as the adult BM, was analyzed, generating similar results as adult BM ( Figure 3b-c) ((Sommarin et al, 2021). Next, two more embryonic time-points were analyzed from first trimester; CS16, and 9pcw (143 and 1139 cells analyzed respectively, each stage two donors).…”

“…Samples were stored at −150°C until day of experiment. CB and adult BM (20-30 years old) data set were from (Sommarin et al, 2021).…”

“…a) UMAP of LIN - CD45 + CD34 + adult BM cells with cluster annotations from (Sommarin et al, 2021) b) PCA of pseudo-bulked immunophenotypic populations from FL CS22 and adult BM of 500 top variably expressed genes. PC1 vs PC2 left and PC2 vs PC3 right plot.…”