Single-cell RNA-sequencing uncovers transcriptional states and fate decisions in haematopoiesis

Abstract

The success of marker-based approaches for dissecting haematopoiesis in mouse and human is reliant on the presence of well-defined cell surface markers specific for diverse progenitor populations. An inherent problem with this approach is that the presence of specific cell surface markers does not directly reflect the transcriptional state of a cell. Here, we used a marker-free approach to computationally reconstruct the blood lineage tree in zebrafish and order cells along their differentiation trajectory, based on their global transcriptional differences. Within the population of transcriptionally similar stem and progenitor cells, our analysis reveals considerable cell-to-cell differences in their probability to transition to another committed state. Once fate decision is executed, the suppression of transcription of ribosomal genes and upregulation of lineage-specific factors coordinately controls lineage differentiation. Evolutionary analysis further demonstrates that this haematopoietic programme is highly conserved between zebrafish and higher vertebrates.

Dissecting intratumoral myeloid cell plasticity by single cell RNA‐seq

“…To quantitatively track myeloid reprogramming between adjacent normal and tumor states, we applied the Monocle2 trajectory analysis method to the myeloid cells from each patient (Figure ; P1‐P4). Each T‐N trajectory is composed of a lower “root”, referring to the monocytes from adjacent normal tissues, and “branches” (annotated as AT1 or AT2) that reflect the monocyte differentiation toward M1‐like macrophage, M2‐like macrophage, or dendritic cell fates.…”

Analysis of factor V in zebrafish demonstrates minimal levels needed for early hemostasis

“…Another limitation is that the model does not currently take into account the FV platelet (thrombocytes in zebrafish) pool, or tissue factor pathway inhibitor levels. Although zebrafish thrombocytes do express FV, 59 the ubi promoter drives ubiquitous expression, so we are unable to differentiate between effects within the plasma and platelet pools. However, for these studies, thrombocytes are not relevant as they do not appear until 5 to 6 dpf of life, whereas our studies of hemostasis were largely performed at 3 dpf.…”

Single-cell biology: resolving biological complexity, one cell at a time

“…The computationally generated lineage tree highlighted a continuous differentiation path of haematopoietic cells. Interestingly, the population of HSCs and progenitor cells within similar transcriptional profiles showed considerable variation in the probability of differentiating into distinct cell types (Athanasiadis et al, 2017).…”