Retracing the in vivo haematopoietic tree using single‐cell methods

Abstract

The dynamic process by which self-renewing stem cells and their offspring proliferate and differentiate to create the erythroid, myeloid and lymphoid lineages of the blood system has long since been an important topic of study. A range of recent single cell and family tracing methodologies such as massively parallel single-cell RNA-sequencing, mass cytometry, integration site barcoding, cellular barcoding and transposon barcoding are enabling unprecedented analysis, dissection and re-evaluation of the haematopoietic tree. In addition to the substantial experimental advances, these new techniques have required significant theoretical development in order to make biological deductions from their data. Here, we review these approaches from both an experimental and inferential point of view, considering their discoveries to date, their capabilities, limitations and opportunities for further development.

Simultaneous tracking of division and differentiation from individual hematopoietic stem and progenitor cells reveals within-family homogeneity despite population heterogeneity

“…The generation of a diversity of cell types is presently assumed to result from a diversification within a family, and methods for inferring differentiation trajectories using single cell RNA sequencing data from snapshot data assume that cells all behave independently [41,42]. Consistent with previous observations of early lineages decisions [22,43,44], our findings establish that familial dependencies that are currently unmeasured exist within the population, and call for a revision of that assumption and subsequent analysis. Ancestral cell surface expression of markers used for phenotyping serve as correlates that partially predict some of these familial properties, but, in particular, a correlate that explains the highly heritable division progression of ST-HSC and MPP families is not contained within them.…”

“…Those data suggest that HSCs are a heterogeneous population, where each one of them may be committed to the production of only a few lineages, possibly through lineage priming or externally through instruction from a niche. Similarly, transplanted barcoded MPPs have been reported to produce heterogeneous patterns of restricted cell types [21], suggesting that lineage restriction may occur early in the hematopoietic tree, in the pool of HSCs and MPPs [22].…”

The Human Cell Atlas

“…Various alternative approaches have been developed (Kretzschmar and Watt, 2012). In mice, cells can be genetically marked with different colors (Barker et al, 2007) or DNA barcodes (Lu et al, 2011;Naik et al, 2013;Perie and Duffy, 2016), and their offspring traced during development. Recent work has used iterative CRISPR-based genome editing to generate random genetic scars in the fetal genome and use them to reconstruct lineages in the adult animal (McKenna et al, 2016).…”

Tree-ensemble analysis tests for presence of multifurcations in single cell data

“…The protein abundances were saved at 100 uniformly placed time points from t=0 to t=150. 1 Here we mean cutting in the sense used regarding hierarchical clustering, and not in the sense previously used for trees.…”