In vivo clonal tracking reveals evidence of haemangioblast and haematomesoblast contribution to yolk sac haematopoiesis

Organoid Vascularization: Strategies and Applications

Organoids provide 3D structures that replicate native tissues in biomedical research. The development of vascular networks within organoids enables oxygen and nutrient delivery while facilitating metabolic waste removal, which supports organoid growth and maturation. Recent studies demonstrate that vascularized organoid models offer insights into tissue interactions and promote tissue regeneration. However, the current limitations in establishing functional vascular networks affect organoid growth, viability, and clinical translation potential. This review examines the development of vascularized organoids, including the mechanisms of angiogenesis and vasculogenesis, construction strategies, and biomedical applications. The approaches are categorized into in vivo and in vitro methods, with analysis of their specific advantages and limitations. The review also discusses emerging techniques such as bioprinting and gene editing for improving vascularization and functional integration in organoid-based therapies. Current developments in organoid vascularization indicate potential applications in modeling human diseases and developing therapeutic strategies, contributing to advances in translational research.

The zebrafish ETS transcription factor Fli1b functions upstream of Scl/Tal1 during embryonic hematopoiesis

During embryonic development, vascular endothelial and hematopoietic cells are thought to originate from a common precursor, the hemangioblast. The evolutionarily conserved ETS transcription factor FLI1 has been previously implicated in hemangioblast formation and hematopoietic and vascular development. However, its role in regulating the hemangioblast transition into hematovascular lineages is still incompletely understood. Its zebrafish paralog Fli1b (also known as Fli1rs) functions partially redundantly with the ETS transcription factor Etv2 (also known as Etsrp) during vasculogenesis and angiogenesis. However, its role in embryonic hematopoiesis has not been previously investigated. Here, we show that zebrafish fli1b mutants have a reduced formation of primitive erythrocytes and hematopoietic stem and progenitor cells, and display reduced expression of key regulators of hematopoiesis, including scl (also known as tal1), gata1a and runx1. Expression of scl was sufficient to partially rescue defects in erythroid differentiation in fli1b mutants, arguing that scl functions downstream of fli1b during primitive erythropoiesis. In addition, myelopoiesis was strongly misregulated in fli1b mutants. Although the formation of the earliest myeloid progenitors - neutrophils and macrophages - was greatly reduced in fli1b mutants, this was compensated by the increased emergence of myeloid cells from the alternative hematopoietic site - the endocardium. Intriguingly, myeloid cells in fli1b mutants retained vascular endothelial marker expression, suggesting that they are present in a hemangioblast-like state. In summary, our results demonstrate a novel role of fli1b transcription factor in regulating embryonic hematopoiesis.

Unravelling early hematoendothelial development through the chick model: Insights and future perspectives

The chicken embryo has been an important model in advancing our understanding of early hematoendothelial development, particularly in the formation of hematopoietic stem cells (HSCs) and the endothelial-to-hematopoietic transition (EHT). The accessibility and ease of manipulation of chicken embryos have made them an invaluable tool for researching development of blood and endothelial cells. Early research using this model provided pivotal insights, demonstrating that intra-embryonic regions, such as the dorsal aorta (DA), are primary sources of HSCs, rather than the yolk sac (YS), as previously believed. The identification of intra-aortic hematopoietic clusters (IAHCs) and the process of EHT in the chicken embryo laid the foundation for similar discoveries in other vertebrate species, including mice and zebrafish. Recent advances in genetic tools, such as transgenic chickens expressing fluorescent proteins, have further enhanced the precision of cell lineage tracing and real-time imaging of dynamic cellular processes. This review highlights both historical contributions and contemporary advancements facilitated by the chicken model, underscoring its continued relevance in developmental biology. By examining key findings and methodological innovations, we aim to demonstrate the importance of the chicken embryo as a model system for understanding hematoendothelial development and its potential for informing therapeutic applications in regenerative medicine and blood disorders. Finally, we will underscore potential applications of the chicken model for comparative and omics-level studies in conjunction with other model systems and what future directions lie ahead.

Bloodhounds chasing the origin of blood cells

The generation of blood cells during embryonic development involves a process resembling lineage reprogramming, where specialized cells within the vasculature become blood forming, or hemogenic. These hemogenic cells undergo rapid transcriptional and morphological changes as they appear to switch from an endothelial to blood identity. What controls this process and the exact nature of the hemogenic cells remains debated, with evidence supporting several hypotheses. In this opinion, we synthesize current knowledge and propose a model reconciling conflicting observations, integrating evolutionary and mechanistic insights into blood cell emergence.

Impaired primitive erythropoiesis and defective vascular development in Trim71-KO embryos

The transition of an embryo from gastrulation to organogenesis requires precisely coordinated changes in gene expression, but the underlying mechanisms remain unclear. The RNA-binding protein Trim71 is essential for development and serves as a potent regulator of post-transcriptional gene expression. Here, we show that global deficiency of Trim71 induces severe defects in mesoderm-derived cells at the onset of organogenesis. Murine Trim71-KO embryos displayed impaired primitive erythropoiesis, yolk sac vasculature, heart function, and circulation, explaining the embryonic lethality of these mice. Tie2 Cre Trim71 conditional knockout did not induce strong defects, showing that Trim71 expression in endothelial cells and their immediate progenitors is dispensable for embryonic survival. scRNA-seq of E7.5 global Trim71-KO embryos revealed that transcriptomic changes arise already at gastrulation, showing a strong up-regulation of the mesodermal pioneer transcription factor Eomes. We identify Eomes as a direct target of Trim71-mediated mRNA repression via the NHL domain, demonstrating a functional link between these important regulatory genes. Taken together, our data suggest that Trim71-dependent control of gene expression at gastrulation establishes a framework for proper development during organogenesis.

Recording Lineage History with Cellular Barcodes in the Mammary Epithelium and in Breast Cancer

Lineage tracing methods have extensively advanced our understanding of physiological cell behaviour in vivo and in situ and have vastly contributed to decipher the phylogeny and cellular hierarchies during normal and tumour development. In recent years, increasingly complex systems have been developed to track thousands of cells within a given tissue or even entire organisms. Cellular barcoding comprises all techniques designed to genetically label single cells with unique DNA sequences or with a combination of fluorescent proteins, in order to trace their history and lineage production in space and time. We distinguish these two types of cellular barcoding as genetic or optical barcodes. Furthermore, transcribed cellular barcodes can integrate the lineage information with single-cell profiling of each barcoded cell. This enables the potential identification of specific markers or signalling pathways defining distinct stem cell states during development, but also signals promoting tumour growth and metastasis or conferring therapy resistance.In this chapter, we describe recent advances in cellular barcoding technologies and outline experimental and computational challenges. We discuss the biological questions that can be addressed using single-cell dynamic lineage tracing, with a focus on the study of cellular hierarchies in the mammary epithelium and in breast cancer.

Endothelial heterogeneity in bone marrow: insights across development, adult life and leukemia

The central role of the endothelial microenvironment in orchestrating bone marrow (BM) homeostasis and hematopoietic support has been confirmed at various developmental stages and in adult life. The BM vasculature is crucial in mediating communication between BM parenchyma and circulating blood, displaying remarkable heterogeneity in structure and function. While vascular cell diversity in other tissues has long been recognized, the molecular basis of this phenomenon in BM is just now emerging. Over the past decade, single-cell approaches and microscopic observations have expanded our understanding of BM vasculature. While solely characterized for their paracrine properties in the past, recent advances have revolutionized our perception of endothelial function, revealing distinct anatomical locations associated with diverse endothelial cell states. The identification of phenotypic differences between normal and pathological conditions has therefore deepened our understanding of vascular dynamics and their impact on hematopoiesis in health and disease. In this review, we highlight key milestones and recent advances in understanding vascular heterogeneity within BM microenvironment during development, adulthood and aging. We also explore how leukemia affects this heterogeneity and how we can take this knowledge forward to improve clinical practices. By synthesizing existing literature, we aim to address unresolved questions and outline future research directions.

A Pax3 lineage gives rise to transient haematopoietic progenitors

During embryonic development, muscle tissues, skin, and a subset of vascular endothelial cells arise from Pax3-expressing embryonic progenitors defined as paraxial mesoderm. By contrast, haemogenic potential is well established for extra-embryonic mesoderm and intra-embryonic lateral plate mesoderm, which do not express Pax3. To date, it is not known whether the haematopoietic system also contains Pax3 lineage cells. Here, we show that the mouse foetal liver and foetal circulation contain a transient population of Pax3 lineage cells with hallmarks of haematopoietic progenitors and the potential to generate both myeloid and erythroid cells. We propose that Pax3 lineage haematopoietic cells should be investigated to better understand normal haematopoietic development from different mesodermal derivatives. Further, genetic alterations of Pax3 lineage haematopoietic cells should be investigated for their potential to cause haematopoietic malignancies.

Molecular Characterization of Subdomain Specification of Cochlear Duct Based on Foxg1 and Gata3

The inner ear is one of the sensory organs of vertebrates and is largely composed of the vestibule, which controls balance, and the cochlea, which is responsible for hearing. In particular, a problem in cochlear development can lead to hearing loss. Although numerous studies have been conducted on genes involved in the development of the cochlea, many areas still need to be discovered regarding factors that control the patterning of the early cochlear duct. Herein, based on the dynamic expression pattern of FOXG1 in the apical and basal regions of the E13.5 cochlear duct, we identified detailed expression regions through an open-source analysis of single-cell RNA analysis data and demonstrated a clinical correlation with hearing loss. The distinct expression patterns of FOXG1 and GATA3 during the patterning process of the cochlear duct provide important clues to understanding how the fates of the apical and basal regions are divided. These results are expected to be extremely important not only for understanding the molecular mechanisms involved in the early development of the cochlear duct, but also for identifying potential genes that cause hearing loss.

Implementing distinct spatial proteogenomic technologies: opportunities, challenges, and key considerations

Our ability to understand the cellular complexity of tissues has been revolutionized in recent years with significant advances in proteogenomic technologies including those enabling spatial analyses. This has led to numerous consortium efforts, such as the human cell atlas initiative which aims to profile all cells in the human body in healthy and diseased contexts. The availability of such information will subsequently lead to the identification of novel biomarkers of disease and of course therapeutic avenues. However, before such an atlas of any given healthy or diseased tissue can be generated, several factors should be considered including which specific techniques are optimal for the biological question at hand. In this review, we aim to highlight some of the considerations we believe to be important in the experimental design and analysis process, with the goal of helping to navigate the rapidly changing landscape of technologies available.

Hematopoietic cluster formation: an essential prelude to blood cell genesis

Adult blood cells are produced in the bone marrow by hematopoietic stem cells (HSCs), the origin of which can be traced back to fetal developmental stages. Indeed, during mouse development, at days 10-11 of gestation, the aorta-gonad-mesonephros (AGM) region is a primary site of HSC production, with characteristic cell clusters related to stem cell genesis observed in the dorsal aorta. Similar clusters linked with hematopoiesis are also observed in the other sites such as the yolk sac and placenta. In this review, I outline the formation and function of these clusters, focusing on the well-characterized intra-aortic hematopoietic clusters (IAHCs).

Advances and challenges in investigating B-cells via single-cell transcriptomics

Single-cell RNA sequencing (scRNAseq) and Variable, Diversity, Joining (VDJ) profiling have improved our understanding of B-cells. Recent scRNAseq-based approaches have led to the discovery of intermediate B-cell states, including preplasma cells and pregerminal centre B-cells, as well as unveiling protective roles for B-cells within tertiary lymphoid structures in respiratory infections and cancers. These studies have improved our understanding of transcriptional and epigenetic control of B-cell development and of atypical and memory B-cell differentiation. Advancements in temporal profiling in parallel with transcriptomic and VDJ sequencing have consolidated our understanding of the trajectory of B-cell clones over the course of infection and vaccination. Challenges remain in studying B-cell states across tissues in humans, in relating spatial location with B-cell phenotype and function, in examining antibody isotype switching events, and in unequivocal determination of clonal relationships. Nevertheless, ongoing multiomic assessments and studies of cellular interactions within tissues promise new avenues for improving humoral immunity and combatting autoimmune conditions.

Single-cell lineage tracing approaches to track kidney cell development and maintenance

The kidney is a complex organ consisting of various cell types. Previous studies have aimed to elucidate the cellular relationships among these cell types in developing and mature kidneys using Cre-loxP-based lineage tracing. However, this methodology falls short of fully capturing the heterogeneous nature of the kidney, making it less than ideal for comprehensively tracing cellular progression during kidney development and maintenance. Recent technological advancements in single-cell genomics have revolutionized lineage tracing methods. Single-cell lineage tracing enables the simultaneous tracing of multiple cell types within complex tissues and their transcriptomic profiles, thereby allowing the reconstruction of their lineage tree with cell state information. Although single-cell lineage tracing has been successfully applied to investigate cellular hierarchies in various organs and tissues, its application in kidney research is currently lacking. This review comprehensively consolidates the single-cell lineage tracing methods, divided into 4 categories (clustered regularly interspaced short palindromic repeat [CRISPR]/CRISPR-associated protein 9 [Cas9]-based, transposon-based, Polylox-based, and native barcoding methods), and outlines their technical advantages and disadvantages. Furthermore, we propose potential future research topics in kidney research that could benefit from single-cell lineage tracing and suggest suitable technical strategies to apply to these topics.

Developmental regulation of primitive erythropoiesis

PURPOSE OF REVIEW

In this review, we present an overview of recent studies of primitive erythropoiesis, focusing on advances in deciphering its embryonic origin, defining species-specific differences in its developmental regulation, and better understanding the molecular and metabolic pathways involved in terminal differentiation.

RECENT FINDINGS

Single-cell transcriptomics combined with state-of-the-art lineage tracing approaches in unperturbed murine embryos have yielded new insights concerning the origin of the first (primitive) erythroid cells that arise from mesoderm-derived progenitors. Moreover, studies examining primitive erythropoiesis in rare early human embryo samples reveal an overall conservation of primitive erythroid ontogeny in mammals, albeit with some interesting differences such as localization of erythropoietin (EPO) production in the early embryo. Mechanistically, the repertoire of transcription factors that critically regulate primitive erythropoiesis has been expanded to include regulators of transcription elongation, as well as epigenetic modifiers such as the histone methyltransferase DOT1L. For the latter, noncanonical roles aside from enzymatic activity are being uncovered. Lastly, detailed surveys of the metabolic and proteomic landscape of primitive erythroid precursors reveal the activation of key metabolic pathways such as pentose phosphate pathway that are paralleled by a striking loss of mRNA translation machinery.

SUMMARY

The ability to interrogate single cells in vivo continues to yield new insights into the birth of the first essential organ system of the developing embryo. A comparison of the regulation of primitive and definitive erythropoiesis, as well as the interplay of the different layers of regulation - transcriptional, epigenetic, and metabolic - will be critical in achieving the goal of faithfully generating erythroid cells in vitro for therapeutic purposes.

A risk-reward examination of sample multiplexing reagents for single cell RNA-Seq

Single-cell RNA sequencing (scRNA-Seq) has emerged as a powerful tool for understanding cellular heterogeneity and function. However the choice of sample multiplexing reagents can impact data quality and experimental outcomes. In this study, we compared various multiplexing reagents, including MULTI-Seq, Hashtag antibody, and CellPlex, across diverse sample types such as human peripheral blood mononuclear cells (PBMCs), mouse embryonic brain and patient-derived xenografts (PDXs). We found that all multiplexing reagents worked well in cell types robust to ex vivo manipulation but suffered from signal-to-noise issues in more delicate sample types. We compared multiple demultiplexing algorithms which differed in performance depending on data quality. We find that minor improvements to laboratory workflows such as titration and rapid processing are critical to optimal performance. We also compared the performance of fixed scRNA-Seq kits and highlight the advantages of the Parse Biosciences kit for fragile samples. Highly multiplexed scRNA-Seq experiments require more sequencing resources, therefore we evaluated CRISPR-based destruction of non-informative genes to enhance sequencing value. Our comprehensive analysis provides insights into the selection of appropriate sample multiplexing reagents and protocols for scRNA-Seq experiments, facilitating more accurate and cost-effective studies.

Reconstructing cell lineage trees with genomic barcoding: approaches and applications

In multicellular organisms, developmental history of cell divisions and functional annotation of terminal cells can be organized into a cell lineage tree (CLT). The reconstruction of the CLT has long been a major goal in developmental biology and other related fields. Recent technological advancements, especially those in editable genomic barcodes and single-cell high-throughput sequencing, have sparked a new wave of experimental methods for reconstructing CLTs. Here we review the existing experimental approaches to the reconstruction of CLT, which are broadly categorized as either image-based or DNA barcode-based methods. In addition, we present a summary of the related literature based on the biological insight provided by the obtained CLTs. Moreover, we discuss the challenges that will arise as more and better CLT data become available in the near future. Genomic barcoding-based CLT reconstructions and analyses, due to their wide applicability and high scalability, offer the potential for novel biological discoveries, especially those related to general and systemic properties of the developmental process.

The evolving views of hematopoiesis: from embryo to adulthood and from in vivo to in vitro

The hematopoietic system composed of hematopoietic stem and progenitor cells (HSPCs) and their differentiated lineages serves as an ideal model to uncover generic principles of cell fate transitions. From gastrulation onwards, there successively emerge primitive hematopoiesis (that produces specialized hematopoietic cells), pro-definitive hematopoiesis (that produces lineage-restricted progenitor cells), and definitive hematopoiesis (that produces multipotent HSPCs). These nascent lineages develop in several transient hematopoietic sites and finally colonize into lifelong hematopoietic sites. The development and maintenance of hematopoietic lineages are orchestrated by cell-intrinsic gene regulatory networks and cell-extrinsic microenvironmental cues. Owing to the progressive methodology (e.g., high-throughput lineage tracing and single-cell functional and omics analyses), our understanding of the developmental origin of hematopoietic lineages and functional properties of certain hematopoietic organs has been updated; meanwhile, new paradigms to characterize rare cell types, cell heterogeneity and its causes, and comprehensive regulatory landscapes have been provided. Here, we review the evolving views of HSPC biology during developmental and postnatal hematopoiesis. Moreover, we discuss recent advances in the in vitro induction and expansion of HSPCs, with a focus on the implications for clinical applications.

Erythroid Krüppel-Like Factor (KLF1): A Surprisingly Versatile Regulator of Erythroid Differentiation

Erythroid Krüppel-like factor (KLF1), first discovered in 1992, is an erythroid-restricted transcription factor (TF) that is essential for terminal differentiation of erythroid progenitors. At face value, KLF1 is a rather inconspicuous member of the 26-strong SP/KLF TF family. However, 30 years of research have revealed that KLF1 is a jack of all trades in the molecular control of erythropoiesis. Initially described as a one-trick pony required for high-level transcription of the adult HBB gene, we now know that it orchestrates the entire erythroid differentiation program. It does so not only as an activator but also as a repressor. In addition, KLF1 was the first TF shown to be directly involved in enhancer/promoter loop formation. KLF1 variants underlie a wide range of erythroid phenotypes in the human population, varying from very mild conditions such as hereditary persistence of fetal hemoglobin and the In(Lu) blood type in the case of haploinsufficiency, to much more serious non-spherocytic hemolytic anemias in the case of compound heterozygosity, to dominant congenital dyserythropoietic anemia type IV invariably caused by a de novo variant in a highly conserved amino acid in the KLF1 DNA-binding domain. In this chapter, we present an overview of the past and present of KLF1 research and discuss the significance of human KLF1 variants.