Regulation of the embryonic erythropoietic niche: a future perspective

RNA Editors Sculpt the Transcriptome During Terminal Erythropoiesis

Selective RNA degradation during terminal erythropoiesis results in a globin-rich transcriptome in mature erythrocytes, but the specific RNA decay pathways remain unknown. We found that deficiency of the terminal uridylyl transferase enzyme Zcchc6 and the 3'-5' exoribonuclease Dis3l2 in mouse models led to fetal and perinatal reticulocytosis, an accumulation of RNA-rich precursors of terminal erythroid cells, suggesting their crucial roles in terminal red cell differentiation. Notably, knockout embryos exhibited persistent high-level expression of Hbb-bh1 globin, the ortholog of human fetal γ-globin. Perturbation of the Zcchc6-Dis3l2 pathway in mice engineered to express the human b-globin locus likewise increased γ-globin levels in fetal erythroid cells, suggesting that globin switching entails post-transcriptional mechanisms of mRNA destabilization in addition to transcriptional down-regulation. We cultured human hematopoietic stem and progenitor cells (HSPCs), performed CRISPR/Cas9-mediated knockout of ZCCHC6 and DIS3L2, and observed accumulation of RNA and elevated γ-globin levels in terminal erythroid cells. Our findings reveal a conserved role for the ZCCHC6/DIS3L2 RNA editors in terminal erythropoiesis and demonstrate a post-transcriptional mechanism for γ-globin gene switching, advancing research into in vitro erythrocyte generation and γ-globin stabilization to ameliorate hemoglobinopathies.

RNA Editors Sculpt the Transcriptome During Terminal Erythropoiesis

Selective RNA degradation during terminal erythropoiesis results in a globin-rich transcriptome in mature erythrocytes, but the specific RNA decay pathways remain unknown. We found that deficiency of the terminal uridylyl transferase enzyme Zcchc6 and the 3'-5' exoribonuclease Dis3l2 in mouse models led to fetal and perinatal reticulocytosis, an accumulation of RNA-rich precursors of terminal erythroid cells, suggesting their crucial roles in terminal red cell differentiation. Notably, knockout embryos exhibited persistent high-level expression of Hbb-bh1 globin, the ortholog of human fetal γ- globin. Perturbation of the Zcchc6-Dis3l2 pathway in mice engineered to express the human β-globin locus likewise increased γ -globin levels in fetal erythroid cells, suggesting that globin switching entails post-transcriptional mechanisms of mRNA destabilization in addition to transcriptional down-regulation. We cultured human hematopoietic stem and progenitor cells (HSPCs), performed CRISPR/Cas9-mediated knockout of ZCCHC6 and DIS3L2, and observed accumulation of RNA and elevated γ-globin levels in terminal erythroid cells. Our findings reveal a conserved role for the ZCCHC6/DIS3L2 RNA editors in terminal erythropoiesis and demonstrate a post-transcriptional mechanism for γ- globin gene switching, advancing research into in vitro erythrocyte generation and γ- globin stabilization to ameliorate hemoglobinopathies.

Smoothie: Efficient Inference of Spatial Co-expression Networks from Denoised Spatial Transcriptomics Data

Finding correlations in spatial gene expression is fundamental in spatial transcriptomics, as co-expressed genes within a tissue are linked by regulation, function, pathway, or cell type. Yet, sparsity and noise in spatial transcriptomics data pose significant analytical challenges. Here, we introduce Smoothie, a method that denoises spatial transcriptomics data with Gaussian smoothing and constructs and integrates genome-wide co-expression networks. Utilizing implicit and explicit parallelization, Smoothie scales to datasets exceeding 100 million spatially resolved spots with fast run times and low memory usage. We demonstrate how co-expression networks measured by Smoothie enable precise gene module detection, functional annotation of uncharacterized genes, linkage of gene expression to genome architecture, and multi-sample comparisons to assess stable or dynamic gene expression patterns across tissues, conditions, and time points. Overall, Smoothie provides a scalable and versatile framework for extracting deep biological insights from high-resolution spatial transcriptomics data.

Comparative in situ characterization of erythroid cells found throughout the developing tongue tissue, circulation, and liver of fetal mice

BACKGROUND

Erythroid cells contribute to embryonic organ development and adult tissue repair supplying oxygen to tissues. During mouse development, the primitive erythroid cells produced in the extraembryonic blood islands of the yolk sac begin to circulate as immature and nucleated erythroblasts with the onset of cardiac contractions around embryonic day 9.5 (E9.5). On the other hand, the definitive erythroid progenitors derived from the yolk sac and arterial vessels colonize the fetal liver, where they mature into small, enucleated definitive erythrocytes that are released into circulation at E11.5. In many cases, however, erythroblasts are also generated in situ during the development of tissue vasculature. We hypothesized that the properties of erythroid cells generated by peripheral tissue hematopoiesis may differ from those of contemporaneously circulating erythroid cells because hematopoiesis is spatiotemporally distinct from typical primitive and definitive hematopoiesis.

METHODS

Comparative in situ protein expression analyses of erythroid cells in developing tongue, circulation, and liver of fetal mice were performed at E12.5 and E14.5, using immunofluorescence staining of several marker proteins for erythroid and endothelial cells.

RESULTS

At E12.5, irregularly elongated immature vascular endothelial cells, many of which were in contact with nucleated erythroblasts, were distributed in the developing tongue. In the three fetal locations examined (tongue, circulation, and liver), most erythroid cells at E12.5 expressed CD31, which is involved in cell-cell interactions; however, the expression was downregulated by E14.5. Interestingly, at E12.5, several erythroblasts strongly expressing CD31 were found in the tongue, but less abundant in the circulation and fetal liver. Nearly all erythroblasts in E12.5 fetuses expressed primitive erythroid cell-specific βH1-globin; however, those strongly expressing the embryonic globin were scattered, particularly in the tongue, fewer in the circulation and fetal liver. On the contrary, erythroid cells expressing adult β1-globin were scarcely found in the tongue, which is in stark contrast to those in the circulation and fetal liver, where nearly all erythroid cells weakly expressed β1-globin at the embryonic stage. At E14.5, the number of βH1-globin-expressing cells drastically decreased; however, it was still significantly higher in the tongue than in the circulation and fetal liver. In all three locations, β1-globin accumulation and the enucleation of erythroid cells progressed uniformly and rapidly from E12.5 to E14.5.

CONCLUSION

The results indicate that primitive erythroblasts in the tongue highly express CD31, mature more slowly, and are replaced by definitive erythroid cells more slowly than those in the circulation and fetal liver. Primitive erythroblasts produced together with immature vascular endothelial cells during vasculogenesis in the developing tongue may perform functions other than oxygen supply, such as regulating vascular remodeling.

New insights into the mechanisms of red blood cell enucleation: From basics to clinical applications

Background

Red blood cell (RBC) enucleation is a crucial step in the process of erythropoiesis. By removing the nucleus, RBCs gain greater flexibility, enabling them to traverse narrow capillaries with ease, thereby enhancing the efficiency of oxygen and carbon dioxide transport. This transformation underscores the intricate balance between cellular structure and function essential for maintaining homeostasis.

Topic

This review delves into the multifaceted enucleation process, outlining its complex steps that encompass protein sorting, vesicle trafficking, cytoskeletal remodeling, and apoptosis regulation, while also exploring the potential of enhancing the enucleation rate of RBCs in vitro. We emphasize the intricate regulation of this process, which is orchestrated by multiple factors. This includes transcription factors that meticulously guide protein synthesis and sorting through the modulation of gene expression, as well as non-coding RNAs that play a pivotal role in post-transcriptional regulation during various stages of RBC enucleation. Additionally, macrophages participate in the enucleation process by engulfing and clearing the extruded nuclei, further ensuring the proper development of RBCs. Although many studies have deeply explored the molecular mechanisms of enucleation, the roles of apoptosis and anti-apoptotic processes in RBC enucleation remain incompletely understood.

Implication

In this review, we aim to comprehensively summarize the RBC enucleation process and explore the progress made in ex vivo RBC generation. In the future, a deeper understanding of the enucleation process could provide significant benefits to patients suffering from anemia and other related conditions.

Interpretable spatially aware dimension reduction of spatial transcriptomics with STAMP

Spatial transcriptomics produces high-dimensional gene expression measurements with spatial context. Obtaining a biologically meaningful low-dimensional representation of such data is crucial for effective interpretation and downstream analysis. Here, we present Spatial Transcriptomics Analysis with topic Modeling to uncover spatial Patterns (STAMP), an interpretable spatially aware dimension reduction method built on a deep generative model that returns biologically relevant, low-dimensional spatial topics and associated gene modules. STAMP can analyze data ranging from a single section to multiple sections and from different technologies to time-series data, returning topics matching known biological domains and associated gene modules containing established markers highly ranked within. In a lung cancer sample, STAMP delineated cell states with supporting markers at a higher resolution than the original annotation and uncovered cancer-associated fibroblasts concentrated on the tumor edge's exterior. In time-series data of mouse embryonic development, STAMP disentangled the erythro-myeloid hematopoiesis and hepatocytes developmental trajectories within the liver. STAMP is highly scalable and can handle more than 500,000 cells.

Regulation of erythropoiesis: emerging concepts and therapeutic implications

The process of erythropoiesis is complex and involves the transfer of cells from the yolk sac to the fetal hepar and, ultimately, to the bone marrow during embryonic development. Within the bone marrow, erythroid progenitor cells undergo several stages to generate reticulocytes that enter the bloodstream. Erythropoiesis is regulated by various factors, with erythropoietin (EPO) synthesized by the kidney being the promoting factor and hepcidin synthesized by the hepar inhibiting iron mobilization. Transcription factors, such as GATA and KLF, also play a crucial role in erythropoiesis. Disruption of any of these factors can lead to abnormal erythropoiesis, resulting in red cell excess, red cell deficiency, or abnormal morphological function. This review provides a general description of erythropoiesis, as well as its regulation, highlighting the significance of understanding the process for the diagnosis and treatment of various hematological disorders.

Lectin-based carbohydrate profile of megakaryocytes in murine fetal liver during development

Hematopoiesis is the process by which blood cells are generated. During embryonic development, these cells migrate through different organs until they reach the bone marrow, their definitive place in adulthood. Around E10.5, the fetal liver starts budding from the gut, where first hematopoietic cells arrive and expand. Hematopoietic cell migration occurs through cytokine stimulation, receptor expression, and glycosylation patterns on the cell surface. In addition, carbohydrates can modulate different cell activation states. For this reason, we aimed to characterize and quantify fetal megakaryocytic cells in mouse fetal liver according to their glycan residues at different gestational ages through lectins. Mouse fetuses between E11.5 and E18.5 were formalin-fixed and, paraffin-embedded, for immunofluorescence analysis using confocal microscopy. The results showed that the following sugar residues were expressed in proliferating and differentiating megakaryocytes in the fetal liver at different gestational ages: α-mannose, α-glucose, galactose, GlcNAc, and two types of complex oligosaccharides. Megakaryocytes also showed three proliferation waves during liver development at E12.5, E14.5, and E18.5. Additionally, the lectins that exhibited high and specific pattern intensities at liver capsules and vessels were shown to be a less time-consuming and robust alternative alternative to conventional antibodies for displaying liver structures such as capsules and vessels, as well as for megakaryocyte differentiation in the fetal liver.

Macrophages Derived From Human Induced Pluripotent Stem Cells: The Diversity of Protocols, Future Prospects, and Outstanding Questions

Macrophages (Mφ) derived from induced pluripotent stem cells (iMphs) represent a novel and promising model for studying human Mφ function and differentiation and developing new therapeutic strategies based on or oriented at Mφs. iMphs have several advantages over the traditionally used human Mφ models, such as immortalized cell lines and monocyte-derived Mφs. The advantages include the possibility of obtaining genetically identical and editable cells in a potentially scalable way. Various applications of iMphs are being developed, and their number is rapidly growing. However, the protocols of iMph differentiation that are currently used vary substantially, which may lead to differences in iMph differentiation trajectories and properties. Standardization of the protocols and identification of minimum required conditions that would allow obtaining iMphs in a large-scale, inexpensive, and clinically suitable mode are needed for future iMph applications. As a first step in this direction, the current review discusses the fundamental basis for the generation of human iMphs, performs a detailed analysis of the generalities and the differences between iMph differentiation protocols currently employed, and discusses the prospects of iMph applications.

The in vitro effects of hepatoblastoma cells on the growth and differentiation of blasts in transient abnormal myelopoiesis associated with Down syndrome

Transient abnormal myelopoiesis (TAM) in neonates with Down syndrome, which spontaneously resolves within several weeks or months after birth, may represent a special form of leukemia developing in the fetal liver (FL). To explore the role of hepatoblasts, one of the major constituents of the FL hematopoietic microenvironment, in the pathogenesis of TAM, we investigated the influence of a human hepatoblastoma cell line, HUH-6, on the in vitro growth and differentiation of TAM blasts. In a coculture system with membrane filters, which hinders cell-to-cell contact between TAM blasts and HUH-6 cells, the growth and megakaryocytic differentiation of TAM blast progenitors were increased in the presence of HUH-6 cells. The culture supernatant of HUH-6 cells contained hematopoietic growth factors, including stem cell factor (SCF) and thrombopoietin (TPO). The neutralizing antibody against SCF abrogated the growth-stimulating activity of the culture supernatant of HUH-6 cells, demonstrating that, among the growth factors produced by HUH-6 cells, SCF may be the major growth stimulator and that TPO may be involved in megakaryocytic differentiation, rather than growth, of TAM blasts. This suggests that hepatoblasts function in the regulation of the growth and differentiation of TAM blasts in the FL through the production of hematopoietic growth factors, including SCF and TPO, and are involved in the leukemogenesis of TAM.

A human cell atlas of fetal gene expression

The gene expression program underlying the specification of human cell types is of fundamental interest. We generated human cell atlases of gene expression and chromatin accessibility in fetal tissues. For gene expression, we applied three-level combinatorial indexing to >110 samples representing 15 organs, ultimately profiling ~4 million single cells. We leveraged the literature and other atlases to identify and annotate hundreds of cell types and subtypes, both within and across tissues. Our analyses focused on organ-specific specializations of broadly distributed cell types (such as blood, endothelial, and epithelial), sites of fetal erythropoiesis (which notably included the adrenal gland), and integration with mouse developmental atlases (such as conserved specification of blood cells). These data represent a rich resource for the exploration of in vivo human gene expression in diverse tissues and cell types.

Heat shock protein 60 regulates yolk sac erythropoiesis in mice

The yolk sac is the first site of blood-cell production during embryonic development in both murine and human. Heat shock proteins (HSPs), including HSP70 and HSP27, have been shown to play regulatory roles during erythropoiesis. However, it remains unknown whether HSP60, a molecular chaperone that resides mainly in mitochondria, could also regulate early erythropoiesis. In this study, we used Tie2-Cre to deactivate the Hspd1 gene in both hematopoietic and vascular endothelial cells, and found that Tie2-Cre⁺Hspd1^f/f (HSP60^CKO) mice were embryonic lethal between the embryonic day 10.5 (E10.5) and E11.5, exhibiting growth retardation, anemia, and vascular defects. Of these, anemia was observed first, independently of vascular and growth phenotypes. Reduced numbers of erythrocytes, as well as an increase in cell apoptosis, were found in the HSP60^CKO yolk sac as early as E9.0, indicating that deletion of HSP60 led to abnormality in yolk sac erythropoiesis. Deletion of HSP60 was also able to reduce mitochondrial membrane potential and the expression of the voltage-dependent anion channel (VDAC) in yolk sac erythrocytes. Furthermore, cyclosporine A (CsA), which is a well-recognized modulator in regulating the opening of the mitochondrial permeability transition pore (mPTP) by interacting with Cyclophilin D (CypD), could significantly decrease cell apoptosis and partially restore VDAC expression in mutant yolk sac erythrocytes. Taken together, we demonstrated an essential role of HSP60 in regulating yolk sac cell survival partially via a mPTP-dependent mechanism.

Pro-inflammatory Aorta-Associated Macrophages Are Involved in Embryonic Development of Hematopoietic Stem Cells

Hematopoietic stem cells (HSCs) are generated from specialized endothelial cells of the embryonic aorta. Inflammatory factors are implicated in regulating mouse HSC development, but which cells in the aorta-gonad-mesonephros (AGM) microenvironment produce these factors is unknown. In the adult, macrophages play both pro- and anti-inflammatory roles. We sought to examine whether macrophages or other hematopoietic cells found in the embryo prior to HSC generation were involved in the AGM HSC-generative microenvironment. CyTOF analysis of CD45⁺ AGM cells revealed predominance of two hematopoietic cell types, mannose-receptor positive macrophages and mannose-receptor negative myeloid cells. We show here that macrophage appearance in the AGM was dependent on the chemokine receptor Cx3cr1. These macrophages expressed a pro-inflammatory signature, localized to the aorta, and dynamically interacted with nascent and emerging intra-aortic hematopoietic cells (IAHCs). Importantly, upon macrophage depletion, no adult-repopulating HSCs were detected, thus implicating a role for pro-inflammatory AGM-associated macrophages in regulating the development of HSCs.

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Yolk-sac-derived macrophages are the most abundant hematopoietic cells in the AGM

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Cx3cr1 mediates yolk-sac macrophage progenitor recruitment to the AGM niche

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AGM macrophages dynamically interact with emerging intra-aortic hematopoietic cells

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Pro-inflammatory AGM macrophages are positive regulators of HSC generation

Retinoids in Stellate Cells: Development, Repair, and Regeneration

Stellate cells, either hepatic (HSCs) or pancreatic (PSCs), are a type of interstitial cells characterized by their ability to store retinoids in lipid vesicles. In pathological conditions both HSCs and PSCs lose their retinoid content and transform into fibroblast-like cells, contributing to the fibrogenic response. HSCs also participate in other functions including vasoregulation, drug detoxification, immunotolerance, and maintenance of the hepatocyte population. PSCs maintain pancreatic tissue architecture and regulate pancreatic exocrine function. Recently, PSCs have attracted the attention of researchers due to their interactions with pancreatic ductal adenocarcinoma cells. PSCs promote tumour growth and angiogenesis, and their fibrotic activity increases the resistance of pancreatic cancer to chemotherapy and radiation. We are reviewing the current literature concerning the role played by retinoids in the physiology and pathophysiology of the stellate cells, paying attention to their developmental aspects as well as the function of stellate cells in tissue repair and organ regeneration.