Single cell RNA-seq identifies developing corneal cell fates in the human cornea organoid

The cornea is a protective and refractive barrier in the eye crucial for vision. Understanding the human cornea in health, disease and cell-based treatments can be greatly advanced with cornea organoids developed in culture from induced pluripotent stem cells. While a limited number of studies have investigated the single-cell transcriptomic composition of the human cornea, its organoids have not been examined similarly. Here we elucidated the transcriptomic cell fate map of 4 month-old human cornea organoids and the central cornea from three donors. The organoids harbor cell clusters representing corneal epithelium, stroma and endothelium with sub populations that capture signatures of early developmental states. Unlike the adult cornea where the largest cell population is stromal, the organoids develop almost equal proportion of the three major cell types. These corneal organoids offer a three-dimensional platform to model corneal diseases and integrated responses of the different cell types to treatments.

Duplication of spiralian-specific TALE genes and evolution of the blastomere specification mechanism in the bivalve lineage

Background Despite the conserved pattern of the cell-fate map among spiralians, bivalves display several modified characteristics during their early development, including early specification of the D blastomere by the cytoplasmic content, as well as the distinctive fate of the 2d blastomere. However, it is unclear what changes in gene regulatory mechanisms led to such changes in cell specification patterns. Spiralian-TALE (SPILE) genes are a group of spiralian-specific transcription factors that play a role in specifying blastomere cell fates during early development in limpets. We hypothesised that the expansion of SPILE gene repertoires influenced the evolution of the specification pattern of blastomere cell fates. Results We performed a transcriptome analysis of early development in the purplish bifurcate mussel and identified 13 SPILE genes. Phylogenetic analysis of the SPILE gene in molluscs suggested that duplications of SPILE genes occurred in the bivalve lineage. We examined the expression patterns of the SPILE gene in mussels and found that some SPILE genes were expressed in quartet-specific patterns, as observed in limpets. Furthermore, we found that several SPILE genes that had undergone gene duplication were specifically expressed in the D quadrant, C and D quadrants or the 2d blastomere. These expression patterns were distinct from the expression patterns of SPILE in their limpet counterparts. Conclusions These results suggest that, in addition to their ancestral role in quartet specification, certain SPILE genes in mussels contribute to the specification of the C and D quadrants. We suggest that the expansion of SPILE genes in the bivalve lineage contributed to the evolution of a unique cell fate specification pattern in bivalves.

Duplication of Spiralian-Specific TALE Genes And Evolution of The Blastomere Specification Mechanism In The Bivalve Lineage

Background Despite the conserved pattern of the cell-fate map among spiralians, bivalves display several modified characteristics during their early development, including early specification of the D blastomere by the cytoplasmic content, as well as the distinctive fate of the 2d blastomere. However, it is unclear what changes in gene regulatory mechanisms led to such changes in cell specification patterns. Spiralian-TALE (SPILE) genes are a group of spiralian-specific transcription factors that play a role in specifying blastomere cell fates during early development in limpets. We hypothesised that the expansion of SPILE gene repertoires influenced the evolution of the specification pattern of blastomere cell fates.Results We performed a transcriptome analysis of early development in the purplish bifurcate mussel and identified 13 SPILE genes. Phylogenetic analysis of the SPILE gene in bivalves and limpets suggested that extra duplications of SPILE genes occurred in the bivalve lineage. We examined the expression patterns of the SPILE gene in mussels and found that some SPILE genes were expressed in quartet-specific patterns, as observed in limpets. Furthermore, we found that several SPILE genes that had undergone gene duplication were specifically expressed in the D quadrant, C and D quadrants or the 2d blastomere. These expression patterns were distinct from the expression patterns of SPILE in their limpet counterparts. Conclusions These results suggest that, in addition to their ancestral role in quartet specification, bivalve SPILE genes contributed to the specification of C and D quadrants. We propose that the expansion of SPILE genes in the bivalve lineage created extra SPILE genes that underwent expression pattern and functional divergence, thereby resulting in the evolution of a unique cell-fate specification pattern in bivalves.

A single-cell–resolution fate map of endoderm reveals demarcation of pancreatic progenitors by cell cycle

A progenitor cell could generate a certain type or multiple types of descendant cells during embryonic development. To make all the descendant cell types and developmental trajectories of every single progenitor cell clear remains an ultimate goal in developmental biology. Characterizations of descendant cells produced by each uncommitted progenitor for a full germ layer represent a big step toward the goal. Here, we focus on early foregut endoderm, which generates foregut digestive organs, including the pancreas, liver, foregut, and ductal system, through distinct lineages. Using unbiased single-cell labeling techniques, we label every individual zebrafish foregut endodermal progenitor cell out of 216 cells to visibly trace the distribution and number of their descendant cells. Hence, single-cell–resolution fate and proliferation maps of early foregut endoderm are established, in which progenitor regions of each foregut digestive organ are precisely demarcated. The maps indicate that the pancreatic endocrine progenitors are featured by a cell cycle state with a long G1 phase. Manipulating durations of the G1 phase modulates pancreatic progenitor populations. This study illustrates foregut endodermal progenitor cell fate at single-cell resolution, precisely demarcates different progenitor populations, and sheds light on mechanistic insights into pancreatic fate determination.

Cellular fate of intersex differentiation

Infertile ovotestis (mixture of ovary and testis) often occurs in intersex individuals under certain pathological and physiological conditions. However, how ovotestis is formed remains largely unknown. Here, we report the first comprehensive single-cell developmental atlas of the model ovotestis. We provide an overview of cell identities and a roadmap of germline, niche, and stem cell development in ovotestis by cell lineage reconstruction and a uniform manifold approximation and projection. We identify common progenitors of germline stem cells with two states, which reveal their bipotential nature to differentiate into both spermatogonial stem cells and female germline stem cells. Moreover, we found that ovotestis infertility was caused by degradation of female germline cells via liquid–liquid phase separation of the proteasomes in the nucleus, and impaired histone-to-protamine replacement in spermatid differentiation. Notably, signaling pathways in gonadal niche cells and their interaction with germlines synergistically determined distinct cell fate of both male and female germlines. Overall, we reveal a cellular fate map of germline and niche cell development that shapes cell differentiation direction of ovotestis, and provide novel insights into ovotestis development.

Unraveling the embryonic fate map through the mechanical signature of cells and their trajectories

Digital cell lineages reconstructed from 3D+time imaging data of the developing zebrafish embryo are used to uncover mechanical cues and their role in morphogenesis. A continuous approximation of cell displacements obtained from cell lineages is used to assess tissue deformation during gastrulation. At this stage, embryonic tissues display multi-scale compressible fluid-like properties. The deformation rate at the mesoscopic level of the cell’s immediate surroundings appears noisy, in both space and time. The patterns identified by clustering the cells, according to the cumulative deformation rate along their trajectory throughout gastrulation, lead to a robust, ordered and coherent biomechanical map. The timing and amplitude of the biomechanical deformations provide a measurement of the phenotypic variability in small cohorts of specimens. We show that the biomechanical map matches the embryonic fate map of the zebrafish presumptive forebrain, in both wild type and Nodal pathway mutants (zoeptz57/tz57), where it reveals the biomechanical defects that lead to cyclopia.. The comparison of biomechanical patterns and the expression pattern of a transgenic reporter for the transcription factor goosecoid (gsc), supports the hypothesis that embryonic cells acquire, at an early developmental stage, a biomechanical signature that contributes to defining their fate.

In Situ Fate Mapping of Native and Stress Myelopoiesis Reveals a Unique Niche for Mono- and Dendritic Cell -Poiesis

In contrast to virtually all other tissues in the body the anatomy of differentiation in the bone marrow remains unknown. This is due to the lack of strategies to examine blood cell production in situ, which are required to better understand differentiation, lineage commitment decisions, and to define how spatial organizing cues inform tissue function. We developed approaches to image and fate map -using confetti mice- myelopoiesis in situ and generated 3D atlases of granulocyte and monocyte/dendritic cell differentiation during homeostasis and after emergency myelopoiesis induced by infection with Listeria monocytogenes. Figure 1 shows stepwise differentiation during myelopoiesis. We have found that -in imaging studies- CD11b-Ly6C-CD117+CD115+ cells are MDP; Lin-CD117+CD16/32+CD115- cells are GMP; CD11b-Ly6C+CD117+CD115+ are MOP; CD11b-CD117+CD115-Ly6C+ are GP; CD11b+CD115+Ly6Chi and CD11b+CD115+Ly6Clo cells are Ly6Chi and Ly6Clo monocytes; and MHCIIhi reticular cells are dendritic cells (DC). We used these markers to map every myeloid cell in the sternum and assessed the relationships between myeloid progenitors, their offspring and candidate niches in situ with single cell resolution. To test whether the interactions observed were specific we obtained the X, Y and Z coordinates for every hematopoietic cell in the sternum (detected using αCD45 and αTer119). We then used these coordinates to randomly place each type of myeloid cell, at the same frequencies found in vivo, through the BM to generate random distributions for each myeloid cell type. We found that myeloid progenitors do not localize with HSC indicating that they leave the HSC niche during differentiation. In the steady-state GP, MOP, and MDP are found as single cells that do not associate with each other indicating that granulo-, mono-, and dendritic cell-poiesis take place in different location. Myeloid progenitors are specifically recruited to sinusoids but are depleted near endosteum and arterioles (e.g. mean MDP distance to sinusoids, arterioles, and endosteum observed 5, 134, and 105μm vs 9, 86, and 69µm in the random simulation). GP form clusters with preneutrophils and immature neutrophils, in situ fate mapping demonstrated that these clusters are oligoclonal and that additional GP are serially recruited to the cluster as the old ones differentiate. Ly6Clo monocytes and dendritic cells are selectively enriched near MDP (2.0 DC and 4.4 Ly6Clo monocytes observed within 50µm of an MDP vs 0.9 DC and 1.8 Ly6Clo monocytes in the random simulation p=0.02 and p<0.0001). Fate mapping experiments demonstrated that the monocytes around MOP and monocytes and dendritic cells around the MDP are oligoclonal but are not the derived from the MOP/MDP they associate with. These indicate that Ly6Clo monocytes and DC are produced elsewhere but are then selectively recruited to regions enriched in MDP. The results above suggest that different sinusoids might be responsible for supporting different myeloid lineages. We found that dendritic cells localize to a unique subset (8% of all vessels) of colony stimulating factor 1 (CSF1, the major regulator of monopoiesis) -expressing sinusoids. Csf1 deletion in the vasculature disrupted MDP interaction with sinusoids, leading to reduced MDP numbers and differentiation ability, with subsequent loss of Ly6Clo monocytes and dendritic cells. L. monocytogenes infection dramatically changed the architecture of myelopoiesis and caused massive expansion of myeloid progenitors leading to the formation of monoclonal GP clusters and oligoclonal MOP clusters whereas MDP are still found as single cells associated with dendritic cells. Even after this massive insult granulopoiesis and mono/DC poiesis remained spatially segregated to different sinusoids. Csf1 deletion in the vasculature prevented generation of MDP and dendritic cells in response to infection. In summary we have developed strategies to image and fate map myelopoiesis in situ; revealed spatial segregation of -and distinct clonal architectures for- granulopoiesis and mono/DCpoiesis; and identified rare CSF1+ sinusoids that maintain mono/DCpoiesis in the steady-state and after infection. These data indicate that there is a specific spatial organization of definitive hematopoiesis and that local cues produced by distinct blood vessels are responsible for this organization. Figure Disclosures No relevant conflicts of interest to declare.

Unravelling the Biology of Adult Cardiac Stem Cell-Derived Exosomes to Foster Endogenous Cardiac Regeneration and Repair

Cardiac remuscularization has been the stated goal of the field of regenerative cardiology since its inception. Along with the refreshment of lost and dysfunctional cardiac muscle cells, the field of cell therapy has expanded in scope encompassing also the potential of the injected cells as cardioprotective and cardio-reparative agents for cardiovascular diseases. The latter has been the result of the findings that cell therapies so far tested in clinical trials exert their beneficial effects through paracrine mechanisms acting on the endogenous myocardial reparative/regenerative potential. The endogenous regenerative potential of the adult heart is still highly debated. While it has been widely accepted that adult cardiomyocytes (CMs) are renewed throughout life either in response to wear and tear and after injury, the rate and origin of this phenomenon are yet to be clarified. The adult heart harbors resident cardiac/stem progenitor cells (CSCs/CPCs), whose discovery and characterization were initially sufficient to explain CM renewal in response to physiological and pathological stresses, when also considering that adult CMs are terminally differentiated cells. The role of CSCs in CM formation in the adult heart has been however questioned by some recent genetic fate map studies, which have been proved to have serious limitations. Nevertheless, uncontested evidence shows that clonal CSCs are effective transplantable regenerative agents either for their direct myogenic differentiation and for their paracrine effects in the allogeneic setting. In particular, the paracrine potential of CSCs has been the focus of the recent investigation, whereby CSC-derived exosomes appear to harbor relevant regenerative and reparative signals underlying the beneficial effects of CSC transplantation. This review focuses on recent advances in our knowledge about the biological role of exosomes in heart tissue homeostasis and repair with the idea to use them as tools for new therapeutic biotechnologies for “cell-less” effective cardiac regeneration approaches.

Neonatal annulus fibrosus regeneration occurs via recruitment and proliferation of Scleraxis-lineage cells

Intervertebral disc (IVD) injuries are a cause of degenerative changes in adults which can lead to back pain, a leading cause of disability. We developed a model of neonatal IVD regeneration with full functional restoration and investigate the cellular dynamics underlying this unique healing response. We employed genetic lineage tracing in mice using Scleraxis (Scx) and Sonic hedgehog (Shh) to fate-map annulus fibrosus (AF) and nucleus pulposus (NP) cells, respectively. Results indicate functional AF regeneration after severe herniation injury occurs in neonates and not adults. AF regeneration is mediated by Scx-lineage cells that lose ScxGFP expression and adopt a stem/progenitor phenotype (Sca-1, days 3–14), proliferate, and then redifferentiate towards type I collagen producing, ScxGFP+ annulocytes at day 56. Non Scx-lineage cells were also transiently observed during neonatal repair, including Shh-lineage cells, macrophages, and myofibroblasts; however, these populations were no longer detected by day 56 when annulocytes redifferentiate. Overall, repair did not occur in adults. These results identify an exciting cellular mechanism of neonatal AF regeneration that is predominantly driven by Scx-lineage annulocytes.

Fate-mapping post-hypoxic tumor cells reveals a ROS-resistant phenotype that promotes metastasis

Hypoxia is known to be detrimental in cancer and contributes to its development. In this work, we present an approach to fate-map hypoxic cells in vivo in order to determine their cellular response to physiological O2 gradients as well as to quantify their contribution to metastatic spread. We demonstrate the ability of the system to fate-map hypoxic cells in 2D, and in 3D spheroids and organoids. We identify distinct gene expression patterns in cells that experienced intratumoral hypoxia in vivo compared to cells exposed to hypoxia in vitro. The intratumoral hypoxia gene-signature is a better prognostic indicator for distant metastasis-free survival. Post-hypoxic tumor cells have an ROS-resistant phenotype that provides a survival advantage in the bloodstream and promotes their ability to establish overt metastasis. Post-hypoxic cells retain an increase in the expression of a subset of hypoxia-inducible genes at the metastatic site, suggesting the possibility of a ‘hypoxic memory.’