Computational modelling of T-cell formation kinetics: output regulated by initial proliferation-linked deferral of developmental competence

Abstract

Bone-marrow-derived progenitors must continually enter the thymus of an adult mouse to sustain T-cell homeostasis, yet only a few input cells per day are sufficient to support a yield of 5 Â 10 7 immature T-cells per dayand an eventual output of 1-2 Â 10 6 mature cells per day. While substantial progress has been made to delineate the developmental pathway of T-cell lineage commitment, still little is known about the relationship between differentiation competence and the remarkable expansion of the earliest (DN1 stage) T-cell progenitors. To address this question, we developed computational models where the probability to progress to the next stage (DN2) is related to division number. To satisfy differentiation kinetics and overall cell yield data, our models require that adult DN1 cells divide multiple times before becoming competent to progress into DN2 stage. Our findings were subsequently tested by in vitro experiments, where putative early and later-stage DN1 progenitors from the thymus were purified and their progression into DN2 was measured. These experiments showed that the two DN1 sub-populations divided with similar rates, but progressed to the DN2 stage with different rates, thus providing experimental evidence that DN1 cells increase their commitment probability in a cell-intrinsic manner as they undergo cell division. Proliferation-linked shifts in eligibility of DN1 cells to undergo specification thus control kinetics of T-cell generation.

Regulation of early T-lineage gene expression and developmental progression by the progenitor cell transcription factor PU.1

“…Normally, proliferation accelerates between the ETP/DN1 and DN2 stages ( Fig. 2B; Manesso et al 2013), but this acceleration did not occur in PU.1-deficient cells. Instead, PU.1 knockout DN2 cells proliferated significantly less than their wild-type counterparts on both day 2 and day 3 of culture ( Fig.…”

Developmental gene networks: a triathlon on the course to T cell identity

“…However, in these early stages TCR-independent proliferation from any given immigrant can be extensive, spanning more than 10 cell cycles before commitment 7, 51 , and this proliferative expansion could be a major function supported by the legacy progenitor network . Many of the transcription factors that are expressed only in phase 1 ETP and/or DN2a cells have roles in the proliferation, survival, and self-renewal of other hematopoietic cells and leukemias, where the genes that encode them are functionally implicated as proto-oncogenes (see below; Table 2).…”

Cytokines, Transcription Factors, and the Initiation of T-Cell Development

“…This proliferation is driven first by a KITL-predominant microenvironment and then by an IL-7-predominant environment (Buono et al 2016), matching the shifts in the ratio of KIT to IL-7R as the cells progress from ETP to DN2a cells. However, computational modeling suggests that the largest part of the proliferation may take place in the ETP stage (Manesso et al 2013), before the cells activate strong expression of IL-7 receptors. This suggests that the earliest proliferative expansion could be a major function that depends not only on KIT signaling but also on another regulatory input in place of IL-7R, and one possibility is that this is supplied by the phase 1 specific transcription factors.…”

“…However, in the adult thymus, the specific transition from ETP to DN2 is disproportionately slower than in the fetus. In steady state, postnatal mouse ETPs take at least 7–10 days before they shift to the DN2(a) stage, although progression to subsequent stages may require only ∼2 days per step (Porritt et al 2003; Manesso et al 2013). By contrast, the ETP to DN2a transition takes no more than 1–2 days in the fetus.…”