Deep sequencing as a probe of normal stem cell fate and preneoplasia in human epidermis.

Using deep sequencing technology, methods based on the sporadic acquisition of somatic DNA mutations in human tissues have been used to trace the clonal evolution of progenitor cells in diseased states. However, the potential of these approaches to explore cell fate behavior of normal tissues and the initiation of preneoplasia remain underexploited. Focusing on the results of a recent deep sequencing study of eyelid epidermis, we show that the quantitative analysis of mutant clone size provides a general method to resolve the pattern of normal stem cell fate and to detect and characterize the mutational signature of rare field transformations in human tissues, with implications for the early detection of preneoplasia.We are indebted to Peter Campbell, Phil Jones and Inigo Martincorena for sharing information on the sizes of the biopsies used in their study, and for making their sequencing data publically available. We are also grateful to Trevor Graham, Philip Greulich and Anna Philpott for valuable discussions, and we acknowledge the financial support of the Wellcome Trust (grant number 098357/Z/12/Z).This is the author accepted manuscript. The final version is available from PNAS via http://dx.doi.org/10.1073/pnas.151612311

Dynamic stem cell heterogeneity.

Recent lineage-tracing studies based on inducible genetic labelling have emphasized a crucial role for stochasticity in the maintenance and regeneration of cycling adult tissues. These studies have revealed that stem cells are frequently lost through differentiation and that this is compensated for by the duplication of neighbours, leading to the consolidation of clonal diversity. Through the combination of long-term lineage-tracing assays with short-term in vivo live imaging, the cellular basis of this stochastic stem cell loss and replacement has begun to be resolved. With a focus on mammalian spermatogenesis, intestinal maintenance and the hair cycle, we review the role of dynamic heterogeneity in the regulation of adult stem cell populations.B.D.S. acknowledges the financial support of the Wellcome Trust [098357/Z/12/Z] as well as core grants from the Wellcome Trust [092096] and Cancer Research UK [C6946/A14492].This is the author accepted manuscript. The final version is available via The Company of Biologists at http://dev.biologists.org/content/142/8/1396.abstract

Multiscale dynamics of branching morphogenesis.

Branching morphogenesis is a prototypical example of complex three-dimensional organ sculpting, required in multiple developmental settings to maximize the area of exchange surfaces. It requires, in particular, the coordinated growth of different cell types together with complex patterning to lead to robust macroscopic outputs. In recent years, novel multiscale quantitative biology approaches, together with biophysical modelling, have begun to shed new light of this topic. Here, we wish to review some of these recent developments, highlighting the generic design principles that can be abstracted across different branched organs, as well as the implications for the broader fields of stem cell, developmental and systems biology.wellcome trust royal societ

Dynamic heterogeneity as a strategy of stem cell self-renewal.

To maintain cycling adult tissue in homeostasis the balance between proliferation and differentiation of stem cells needs to be precisely regulated. To investigate how stem cells achieve perfect self-renewal, emphasis has been placed on models in which stem cells progress sequentially through a one-way proliferative hierarchy. However, investigations of tissue regeneration have revealed a surprising degree of flexibility, with cells normally committed to differentiation able to recover stem cell competence following injury. Here, we investigate whether the reversible transfer of cells between states poised for proliferation or differentiation may provide a viable mechanism for a heterogeneous stem cell population to maintain homeostasis even under normal physiological conditions. By addressing the clonal dynamics, we show that such models of "dynamic heterogeneity" may be equally capable of describing the results of recent lineage tracing assays involving epithelial tissues. Moreover, together with competition for limited niche access, such models may provide a mechanism to render tissue homeostasis robust. In particular, in 2D epithelial layers, we show that the mechanism of dynamic heterogeneity avoids some pathological dependencies that undermine models based on a hierarchical stem/progenitor organization.Engineering and Physical Sciences Research CouncilThis is the author accepted manuscript. It is currently under an indefinite embargo pending publication by the National Academy of Sciences

Tracing cellular dynamics in tissue development, maintenance and disease.

The coordination of cell proliferation and differentiation is central to the development and maintenance of tissues, while its dysregulation underlies the transition to diseased states. By combining lineage tracing with transcriptional profiling and marker-based assays, statistical methods are delivering insights into the dynamics of stem cells and their developmental precursors. These studies have provided evidence for molecular heterogeneity and fate priming, and have revealed a role for stochasticity in stem cell fate, refocusing the search for regulatory mechanisms. At the same time, they present a quantitative platform to study the initiation and progression of disease. Here, we review how quantitative lineage tracing strategies are shaping our understanding of the cellular mechanisms of tissue development, maintenance and disease

Statistical theory of branching morphogenesis

Branching morphogenesis remains a subject of abiding interest. Although much is known about the gene regulatory programs and signaling pathways that operate at the cellular scale, it has remained unclear how the macroscopic features of branched organs, including their size, network topology and spatial patterning, are encoded. Lately, it has been proposed that, these features can be explained quantitatively in several organs within a single unifying framework. Based on large- scale organ recon - structions and cell lineage tracing, it has been argued that morphogenesis follows from the collective dynamics of sublineage- restricted self- renewing progenitor cells, localized at ductal tips, that act cooperatively to drive a serial process of ductal elon - gation and stochastic tip bifurcation. By correlating differentiation or cell cycle exit with proximity to maturing ducts, this dynamic results in the specification of a com- plex network of defined density and statistical organization. These results suggest that, for several mammalian tissues, branched epithelial structures develop as a self- organized process, reliant upon a strikingly simple, but generic, set of local rules, without recourse to a rigid and deterministic sequence of genetically programmed events. Here, we review the basis of these findings and discuss their implications

The developmental origin of brain tumours: a cellular and molecular framework.

The development of the nervous system relies on the coordinated regulation of stem cell self-renewal and differentiation. The discovery that brain tumours contain a subpopulation of cells with stem/progenitor characteristics that are capable of sustaining tumour growth has emphasized the importance of understanding the cellular dynamics and the molecular pathways regulating neural stem cell behaviour. By focusing on recent work on glioma and medulloblastoma, we review how lineage tracing contributed to dissecting the embryonic origin of brain tumours and how lineage-specific mechanisms that regulate stem cell behaviour in the embryo may be subverted in cancer to achieve uncontrolled proliferation and suppression of differentiation.This work was funded by MRC Research Grants (MR/K018329/1 (AP/RA), MR/L021129/1 (AP) and Neuroblastoma UK (AP), a Wellcome Trust Senior Investigator Award (098357/Z/12/Z (BDS/RA) and received core support from Wellcome Trust and MRC Cambridge Stem Cell Institute and the Cancer Research UK Cambridge Institute. We are grateful to members of the Philpott and Simons labs for useful discussions

The Independent Probabilistic Firing of Transcription Factors: A Paradigm for Clonal Variability in the Zebrafish Retina.

Early retinal progenitor cells (RPCs) in vertebrates produce lineages that vary greatly both in terms of cell number and fate composition, yet how this variability is achieved remains unknown. One possibility is that these RPCs are individually distinct and that each gives rise to a unique lineage. Another is that stochastic mechanisms play upon the determinative machinery of equipotent early RPCs to drive clonal variability. Here we show that a simple model, based on the independent firing of key fate-influencing transcription factors, can quantitatively account for the intrinsic clonal variance in the zebrafish retina and predict the distributions of neuronal cell types in clones where one or more of these fates are made unavailable.BDS and SR acknowledge the support of the Wellcome Trust (098357/Z/12/Z). WAH and HB also acknowledge the support of the Wellcome Trust (100329/Z/12/Z). HB was also supported by the Swedish Research Council (2011-7054).This is the final version of the article. It first appeared from Elsevier via http://dx.doi.org/10.1016/j.devcel.2015.08.01

Uncovering the Number and Clonal Dynamics of Mesp1 Progenitors during Heart Morphogenesis.

The heart arises from distinct sources of cardiac progenitors that independently express Mesp1 during gastrulation. The precise number of Mesp1 progenitors that are specified during the early stage of gastrulation, and their clonal behavior during heart morphogenesis, is currently unknown. Here, we used clonal and mosaic tracing of Mesp1-expressing cells combined with quantitative biophysical analysis of the clonal data to define the number of cardiac progenitors and their mode of growth during heart development. Our data indicate that the myocardial layer of the heart derive from ∼250 Mesp1-expressing cardiac progenitors born during gastrulation. Despite arising at different time points and contributing to different heart regions, the temporally distinct cardiac progenitors present very similar clonal dynamics. These results provide insights into the number of cardiac progenitors and their mode of growth and open up avenues to decipher the clonal dynamics of progenitors in other organs and tissues.S.C. and N.M. are supported by fellowship of the FRS/FRIA. F.L has been supported by the EMBO longterm fellowship. B.D.S. and S.R. are supported by Wellcome Trust (grant number 098357/Z/12/Z). C.B. is an investigator of WELBIO. This work was supported by the FNRS, the ULB foundation, the European Research Council (ERC), and the foundation Bettencourt Schueller (C.B. and F.L.).This is the final version of the article. It first appeared from Elsevier/Cell Press via http://dx.doi.org/10.1016/j.celrep.2015.12.01