Lineage dynamics of murine pancreatic development at single-cell resolution.

Organogenesis requires the complex interactions of multiple cell lineages that coordinate their expansion, differentiation, and maturation over time. Here, we profile the cell types within the epithelial and mesenchymal compartments of the murine pancreas across developmental time using a combination of single-cell RNA sequencing, immunofluorescence, in situ hybridization, and genetic lineage tracing. We identify previously underappreciated cellular heterogeneity of the developing mesenchyme and reconstruct potential lineage relationships among the pancreatic mesothelium and mesenchymal cell types. Within the epithelium, we find a previously undescribed endocrine progenitor population, as well as an analogous population in both human fetal tissue and human embryonic stem cells differentiating toward a pancreatic beta cell fate. Further, we identify candidate transcriptional regulators along the differentiation trajectory of this population toward the alpha or beta cell lineages. This work establishes a roadmap of pancreatic development and demonstrates the broad utility of this approach for understanding lineage dynamics in developing organs

Functional, metabolic and transcriptional maturation of human pancreatic islets derived from stem cells

Transplantation of pancreatic islet cells derived from human pluripotent stem cells is a promising treatment for diabetes. Despite progress in the generation of stem-cell-derived islets (SC-islets), no detailed characterization of their functional properties has been conducted. Here, we generated functionally mature SC-islets using an optimized protocol and benchmarked them comprehensively against primary adult islets. Biphasic glucose-stimulated insulin secretion developed during in vitro maturation, associated with cytoarchitectural reorganization and the increasing presence of alpha cells. Electrophysiology, signaling and exocytosis of SC-islets were similar to those of adult islets. Glucose-responsive insulin secretion was achieved despite differences in glycolytic and mitochondrial glucose metabolism. Single-cell transcriptomics of SC-islets in vitro and throughout 6 months of engraftment in mice revealed a continuous maturation trajectory culminating in a transcriptional landscape closely resembling that of primary islets. Our thorough evaluation of SC-islet maturation highlights their advanced degree of functionality and supports their use in further efforts to understand and combat diabetes. Pancreatic islets derived from stem cells are benchmarked against primary cells.Peer reviewe

Functionally heterogeneous human satellite cells identified by single cell RNA sequencing.

Although heterogeneity is recognized within the murine satellite cell pool, a comprehensive understanding of distinct subpopulations and their functional relevance in human satellite cells is lacking. We used a combination of single cell RNA sequencing and flow cytometry to identify, distinguish, and physically separate novel subpopulations of human PAX7+ satellite cells (Hu-MuSCs) from normal muscles. We found that, although relatively homogeneous compared to activated satellite cells and committed progenitors, the Hu-MuSC pool contains clusters of transcriptionally distinct cells with consistency across human individuals. New surface marker combinations were enriched in transcriptional subclusters, including a subpopulation of Hu-MuSCs marked by CXCR4/CD29/CD56/CAV1 (CAV1+). In vitro, CAV1+ Hu-MuSCs are morphologically distinct, and characterized by resistance to activation compared to CAV1- Hu-MuSCs. In vivo, CAV1+ Hu-MuSCs demonstrated increased engraftment after transplantation. Our findings provide a comprehensive transcriptional view of normal Hu-MuSCs and describe new heterogeneity, enabling separation of functionally distinct human satellite cell subpopulations

Mapping cellular diversity and lineage dynamics within the developing murine and human pancreas

The pancreas is a highly branched, compound gland whose development requires the diversification of many distinct cell lineages. Cells in exocrine compartment of the pancreas synthesize and secrete digestive enzymes required for food digestion, whereas cells in the endocrine compartment are responsible for maintaining glucose homeostasis through the production of various hormones. In this work, we sought to characterize the diversity of cell types present in the developing pancreas and chart their differentiation through multiple developmental stages. We start in Chapter 2 by identifying novel and known cell populations within the mesenchymal and epithelial compartments of the developing murine pancreas and mapping their developmental progress across multiple embryonic stages using single-cell RNA-sequencing. We uncover significant cellular diversity within the mesenchymal compartment and utilize single-cell transcriptomic data to reconstruct lineage relationships among the developing pancreatic mesothelium and several previously uncharacterized mesenchymal populations in mouse pancreatic development. In the epithelial compartment, we uncover a novel endocrine progenitor stage defined by high expression of a transcription factor named Fev. Through genetic lineage tracing, we demonstrate that this Fev+ progenitor population is derived from Ngn3+ endocrine progenitors and that all hormone-expressing endocrine lineages of the murine pancreas transit through a Fev-expressing cell stage. Through in silico reconstruction of endocrine lineages, we identify candidate regulators of alpha and beta lineage allocation expressed during this novel Fev+ progenitor stage. In Chapter 3, we apply our findings of endocrine lineage dynamics in murine pancreatic development to that of human and uncover similar FEV-expressing endocrine progenitor populations in human pancreatic development. We map the transcriptional dynamics of human endocrine cell differentiation and identify novel candidate lineage regulators of human alpha and beta lineage allocation. We subsequently identify major disparities between the developmental paths that human endocrine cells follow in vivo versus in vitro during directed differentiation of hESCs towards the beta lineage. Our analysis reveals a lineage that may be mis-differentiated as hESC-derived progenitors differentiate towards a beta cell fate. Blocking the generation of this mis-differentiated lineage during in vitro beta cell differentiation represents a powerful solution in making in vitro beta cell differentiation more robust. Finally, given that FEV+ progenitors constitute a major stage in human endocrine cell differentiation, we have generated novel tools to study both the function of FEV and FEV-expressing cells in in vitro beta cell differentiation. Our work forms a foundation on which improvements to in vitro beta cell differentiation can be made to more closely reflect proper endocrine cell development in vivo, thereby increasing beta cell yield at the end of this process and generating beta cells that are functional

Tracing tumorigenesis in a solid tumor model at single-cell resolution

Characterizing the complex composition of solid tumors is fundamental for understanding tumor initiation, progression and metastasis. While patient-derived samples provide valuable insight, they are heterogeneous on multiple molecular levels, and often originate from advanced tumor stages. Here, we use single-cell transcriptome and epitope profiling together with pathway and lineage analyses to study tumorigenesis from a developmental perspective in a mouse model of salivary gland squamous cell carcinoma. We provide a comprehensive cell atlas and characterize tumor-specific cells. We find that these cells are connected along a reproducible developmental trajectory: initiated in basal cells exhibiting an epithelial-to-mesenchymal transition signature, tumorigenesis proceeds through Wnt-differential cancer stem cell-like subpopulations before differentiating into luminal-like cells. Our work provides unbiased insights into tumor-specific cellular identities in a whole tissue environment, and emphasizes the power of using defined genetic model systems

Defining Lineage Potential and Fate Behaviour of Progenitors During Pancreas Development

The studentship and some of the consumables used to generate data for this thesis were funded by Medical Research Counci

Identification of dynamic undifferentiated cell states within the male germline

The role of stem cells in tissue maintenance is appreciated and hierarchical models of stem cell self-renewal and differentiation often proposed. Stem cell activity in the male germline is restricted to undifferentiated A-type spermatogonia (A(undiff)); however, only a fraction of this population act as stem cells in undisturbed testis and A(undiff) hierarchy remains contentious. Through newly developed compound reporter mice, here we define molecular signatures of self-renewing and differentiation-primed adult Aundiff fractions and dissect A(undiff) heterogeneity by single-cell analysis. We uncover an unappreciated population within the self-renewing Aundiff fraction marked by expression of embryonic patterning genes and homeodomain transcription factor PDX1. Importantly, we find that PDX1 marks a population with potent stem cell capacity unique to mature, homeostatic testis and demonstrate dynamic interconversion between PDX1+ and PDX1-(Aundiff) states upon transplant and culture. We conclude that Aundiff exist in a series of dynamic cell states with distinct function and provide evidence that stability of such states is dictated by niche-derived cues

Lgr5+ stem and progenitor cells reside at the apex of a heterogeneous embryonic hepatoblast pool.

During mouse embryogenesis, progenitors within the liver known as hepatoblasts give rise to adult hepatocytes and cholangiocytes. Hepatoblasts, which are specified at E8.5-E9.0, have been regarded as a homogeneous progenitor population that initiate differentiation from E13.5. Recently, scRNA-seq analysis has identified sub-populations of transcriptionally distinct hepatoblasts at E11.5. Here, we show that hepatoblasts are not only transcriptionally but also functionally heterogeneous, and that a subpopulation of E9.5-E10.0 hepatoblasts exhibit a previously unidentified early commitment to cholangiocyte fate. Importantly, we also identify a subpopulation constituting 2% of E9.5-E10.0 hepatoblasts that express the adult stem cell marker Lgr5, and generate both hepatocyte and cholangiocyte progeny that persist for the lifespan of the mouse. Combining lineage tracing and scRNA-seq, we show that Lgr5 marks E9.5-E10.0 bipotent liver progenitors residing at the apex of a hepatoblast hierarchy. Furthermore, isolated Lgr5+ hepatoblasts can be clonally expanded in vitro into embryonic liver organoids, which can commit to either hepatocyte or cholangiocyte fates. Our study demonstrates functional heterogeneity within E9.5 hepatoblasts and identifies Lgr5 as a marker for a subpopulation of bipotent liver progenitors.M.H. is a Wellcome Trust Sir Henry Dale Fellow and is jointly funded by the Wellcome Trust and the Royal Society (104151/Z/14/Z); M.H. and N.P. are funded by a Horizon 2020 grant (LSFM4LIFE). C.H. was funded by a Cambridge Stem Cell Institute Seed funding for interdisciplinary research awarded to M.H. and B.D.S., B.D.S acknowledges funding from the Royal Society E.P. Abraham Research Professorship (RP\R1\180165) and Wellcome Trust (098357/Z/12/Z). W.L. and B.G. were supported by programmatic funding from the Wellcome Trust, CRUK and Bloodwise, core infrastructure support from the Wellcome and MRC to the Wellcome & MRC Cambridge Stem Cell Institute, and an MRC Clinical Research Infrastructure grant supporting single cell molecular analysis. S.R. was funded on a Herchel-Smith Fellowship. The authors acknowledge core funding to the Gurdon Institute from the Wellcome Trust (092096) and CRUK (C6946/A14492)

Heterogeneity of Islet Cells during Embryogenesis and Differentiation

Diabetes is caused by insufficient insulin secretion due to β-cell dysfunction and/or β-cell loss. Therefore, the restoration of functional β-cells by the induction of β-cell differentiation from embryonic stem (ES) and induced-pluripotent stem (iPS) cells, or from somatic non-β-cells, may be a promising curative therapy. To establish an efficient and feasible method for generating functional insulin-producing cells, comprehensive knowledge of pancreas development and β-cell differentiation, including the mechanisms driving cell fate decisions and endocrine cell maturation is crucial. Recent advances in single-cell RNA sequencing (scRNA-seq) technologies have opened a new era in pancreas development and diabetes research, leading to clarification of the detailed transcriptomes of individual insulin-producing cells. Such extensive high-resolution data enables the inference of developmental trajectories during cell transitions and gene regulatory networks. Additionally, advancements in stem cell research have not only enabled their immediate clinical application, but also has made it possible to observe the genetic dynamics of human cell development and maturation in a dish. In this review, we provide an overview of the heterogeneity of islet cells during embryogenesis and differentiation as demonstrated by scRNA-seq studies on the developing and adult pancreata, with implications for the future application of regenerative medicine for diabetes

Gene dynamics of maturation in endogenous and pluripotent stem cell-derived cardiomyocytes

A primary limitation in the clinical application of pluripotent stem cell-derived cardiomyocytes (PSC-CMs) is the failure of these cells to achieve full functional maturity. In vivo, cardiomyocytes undergo numerous adaptive changes during perinatal maturation. By contrast, PSC-CMs fail to fully undergo these developmental processes, instead remaining arrested at an embryonic stage of maturation. To date, however, the precise mechanisms by which directed differentiation differs from endogenous development, leading to consequent PSC-CM maturation arrest, are unknown. The advent of single cell RNA-sequencing (scRNA-seq) has offered great opportunities for studying CM maturation at single cell resolution. However, postnatal cardiac scRNA-seq has been limited owing to technical difficulties in the isolation of single CMs. Additionally, cross-study comparison is limited by dataset specific batch effects. In this dissertation, I first established large particle fluorescence-activated cell sorting (LP-FACS) for isolation of viable single adult CMs. I secondly developed transcriptomic entropy as a robust, batch effect-resistant approach to quantifying CM maturation. With these and other computational tools, I investigated gene expression trends in endogenous and PSC-derived CMs. I first generated an scRNA-seq reference of mouse in vivo CM maturation with extensive sampling of perinatal time periods. I subsequently generated isogenic embryonic stem cells and created an in vitro scRNA-seq reference of PSC-CM directed differentiation. Through computational analysis, I identified a perinatal iimaturation program in endogenous CMs that is poorly recapitulated in vitro. By comparison of these trajectories with previously published human datasets, I identified a network of nine transcription factors (TFs) whose targets are consistently dysregulated in PSC-CMs across species. Notably, I demonstrated that these TFs are only partially activated in common ex vivo approaches to engineer PSC-CM maturation. This dissertation represents the first direct comparison of CM maturation in vivo and in vitro at the single cell level. Moreover, the findings and tools developed here can be leveraged towards improving the clinical viability of PSC-CMs