High-throughput single-cell fate potential assay of murine hematopoietic progenitors in vitro

In Vivo Tracking of Hematopoietic Stem and Progenitor Cell Ontogeny by Cellular Barcoding

Cellular barcoding is a powerful technique that allows for high-throughput mapping of the fate of single cells, notably hematopoietic stem and progenitor cells (HSPCs) after transplantation. Unique artificial DNA fragments, termed barcodes, are stably inserted into HSPCs using lentiviral transduction, making sure that each individual cell receives a single unique barcode. Barcoded HSPCs are transplanted into sublethally irradiated mice where they reconstitute the hematopoietic system through proliferation and differentiation. During this process, the barcode of each HSPC is inherited by all of its daughter cells and their subsequent mature hematopoietic cell progeny. After sorting mature hematopoietic cell subsets, their barcodes can be retrieved from genomic DNA through nested PCR and sequencing. Analysis of barcode sequencing results allows for determination of clonal relationships between the mature cells, that is, which cell types were produced by a single barcoded HSPC, as well as the heterogeneity of the initial HSPC population. Here, we give a detailed protocol of a complete HSPC cellular barcoding experiment, starting with barcode lentivirus production, isolation, transduction, and transplantation of HSPCs, isolation of target cells followed by PCR amplification and sequencing of DNA barcodes. Finally, we describe the basic filtering and analysis steps of barcode sequencing data to ensure high-quality results.

Mild anemia as a single independent predictor of mortality in patients with COVID-19

The coronavirus disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to an unprecedented international health crisis. COVID-19 clinical presentations cover a wide range from asymptomatic to severe illness and death. Given the limited therapeutic resources and unexpected clinical features of the disease, readily accessible predictive biomarkers are urgently needed to improve patient care and management. We asked the degree to which anemia may influence the outcome of patients with COVID-19. To this end, we identified 3777 patients who were positively diagnosed with COVID-19 between March 1 and April 1 2020 in New York City. We evaluated 2,562 patients with available red blood cell, hemoglobin, and related laboratory values. Multivariable cox proportional hazards regression showed that anemia was a significant independent predictor of mortality (hazard ratio (HR): 1.26, 95% Confidence Interval [CI]: 1.06-1.51), independent of age, sex, and comorbidities. There was a direct correlation between the degree of anemia and the risk of mortality when hemoglobin was treated as a continuous variable (HRadj 1.05; [CI]: 1.01-1.09). The hemoglobin level that was maximally predictive of mortality, was 11.5 g/dL in males and 11.8 g/dL in females. These findings identify a routinely measured biomarker that is predictive of disease outcomes and will aid in refining clinical care algorithms and optimize resource allocation. Mechanisms of impacts of anemia on COVID-19 outcome are likely to be multiple in nature and require further investigation.

Thrombopoietin maintains cell numbers of hematopoietic stem and progenitor cells with megakaryopoietic potential

Thrombopoietin has long been known to influence megakaryopoiesis and hematopoietic stem and progenitor cells, although the exact mechanisms through which it acts are unknown. Here we show that MPL expression correlates with megakaryopoietic potential of hematopoietic stem and progenitor cells and identify a population of quiescent hematopoietic stem and progenitor cells that show limited dependence on thrombopoietin signaling. We show that thrombopoietin is primarily responsible for maintenance of hematopoietic cells with megakaryocytic differentiation potential and their subsequent megakaryocyte differentiation and maturation. The loss of megakaryocytes in thrombopoietin knockout mouse models results in a reduction of megakaryocyte-derived chemokine platelet factor 4 (CXCL4/PF4) in the bone marrow and administration of recombinant CXCL4/PF4 rescues the loss of quiescence observed in these mice. CXCL4/PF4 treatment does not rescue reduced hematopoietic stem and progenitor cell numbers, suggesting that thrombopoietin maintains hematopoietic stem and progenitor cell numbers directly.

New insights into hematopoietic differentiation landscapes from single-cell RNA sequencing

Single-cell transcriptomics has recently emerged as a powerful tool to analyze cellular heterogeneity, discover new cell types, and infer putative differentiation routes. The technique has been rapidly embraced by the hematopoiesis research community, and like other technologies before, single-cell molecular profiling is widely expected to make important contributions to our understanding of the hematopoietic hierarchy. Much of this new interpretation relies on inference of the transcriptomic landscape as a representation of existing cellular states and associated transitions among them. Here we review how this model allows, under certain assumptions, charting of time-resolved differentiation trajectories with unparalleled resolution and how the landscape of multipotent cells may be rather devoid of discrete structures, challenging our preconceptions about stem and progenitor cell types and their organization. Finally, we highlight how promising technological advances may convert static differentiation landscapes into a dynamic cell flux model and thus provide a more holistic understanding of normal hematopoiesis and blood disorders.

Population snapshots predict early haematopoietic and erythroid hierarchies

The formation of red blood cells begins with the differentiation of multipotent haematopoietic progenitors. Reconstructing the steps of this differentiation represents a general challenge in stem-cell biology. Here we used single-cell transcriptomics, fate assays and a theory that allows the prediction of cell fates from population snapshots to demonstrate that mouse haematopoietic progenitors differentiate through a continuous, hierarchical structure into seven blood lineages. We uncovered coupling between the erythroid and the basophil or mast cell fates, a global haematopoietic response to erythroid stress and novel growth factor receptors that regulate erythropoiesis. We defined a flow cytometry sorting strategy to purify early stages of erythroid differentiation, completely isolating classically defined burst-forming and colony-forming progenitors. We also found that the cell cycle is progressively remodelled during erythroid development and during a sharp transcriptional switch that ends the colony-forming progenitor stage and activates terminal differentiation. Our work showcases the utility of linking transcriptomic data to predictive fate models, and provides insights into lineage development in vivo.