Biology subjects

Passegue, E.

Publications and source records attributed to Passegue, E..

8 recordsLinked to original sources

bioRxiv2026

NicheScribe: consistent and generalizable annotation of stromal cells in the murine bone marrow niche

Hematopoietic stem and progenitor cells (HSPC) depend on interactions with nearby stromal cells to support their homeostatic functions and mount responses to perturbations. The murine bone marrow (BM) niche can be profiled using single-cell RNA sequencing (scRNA-seq), but there is considerable inconsistency in cell type identification, and uncertainty over how populations can be isolated prospectively by flow cytometry. Here, we produced new scRNA-seq reference datasets using purified populations of murine BM stromal cells, which we used to create a bespoke classifier for stromal cells. Our NicheScribe approach is consistent, accurate, and generalizable to query datasets irrespective of methods used for cell isolation. Moreover, consistent annotation permits comparative analyses of the same stromal cells across different bone types and perturbations like inflammation, neoplasia, and aging. Our work provides new tools for consistent cell type annotation in the murine BM niche and new insights for combined molecular and functional analyses.

cell biology↗

bioRxiv2026

Glutamine addiction is a therapeutic target to block emergency myelopoiesis

Inflammation-driven emergency myelopoiesis (EM) contributes to the progression of many solid cancers and inflammatory diseases, yet therapeutic strategies to selectively suppress EM without compromising hematopoiesis remain lacking. Here, we use functional and single-cell transcriptomic analyses to determine metabolic programs organizing the hematopoietic hierarchy, myeloid lineage commitment, and myeloid differentiation. We identify de novo glutamine biosynthesis as a stem cell-specific survival mechanism allowing independence from exogenous glutamine. We show that myeloid differentiation is characterized by Myc-driven upregulation of mitochondrial respiration, which is hyperactivated during EM and renders myeloid progenitors dependent on glutaminolysis to fuel the TCA cycle. Both genetic and pharmacologic targeting of glutaminase suppresses EM and impairs breast tumor progression by reducing intratumoral neutrophil infiltration. Our study defines a central role for Myc-glutaminolysis in driving EM, identifies glutaminolysis as a therapeutic target to normalize maladaptive EM, and highlights myeloid overproduction as a systemic problem requiring HSPC targeting. HIGHLIGHTSO_LIHSC survival depends on de novo glutamine biosynthesis via glutamine synthetase C_LIO_LIMyc hyperactivation drives mitochondrial biogenesis during emergency myelopoiesis C_LIO_LIMyeloid progenitors become glutamine-addicted to fuel Myc-driven TCA cycle activity C_LIO_LIGlutaminase deficiency in HSPCs blunts tumor-promoting neutrophil production C_LI ETOC BLURBOlson et al. show that emergency myelopoiesis, the inflammatory overproduction of myeloid cells that drives regeneration, depends on Myc-driven mitochondrial respiration and glutamine addiction in hematopoietic progenitors. Targeting glutaminase in hematopoietic stem and progenitor cells suppresses pathological myelopoiesis, reduces tumor-promoting neutrophil production, and slows breast tumor growth.

immunology↗

bioRxiv2025

Quantitative molecular cartography of emergency myelopoiesis reveals conserved modules of hematopoietic activation

Hematopoietic stem and progenitor cells (HSPC) respond to infections, inflammation, and regenerative challenges using a collection of cellular and molecular mechanisms termed emergency myelopoiesis (EM) pathways. However, it remains unclear how various EM inducers regulate HSPCs using shared or distinct molecular mechanisms. Here, we generate a comprehensive and generalizable cell annotation method (HemaScribe) and a refined quantitative model of hematopoietic differentiation (HemaScape) using single cell RNA sequencing (scRNA-seq) of HSPCs, which we apply to a broad range of EM modalities. We uncover multiple strategies to enhance myelopoiesis acting at different levels of the HSPC hierarchy, which are associated with both unique and shared transcriptional response modules. In particular, we identify a myeloid progenitor-based module of EM engagement across diverse inflammatory challenges, which informs outcome in adult and pediatric human acute myeloid leukemia. Collectively, our work illuminates fundamental regulatory mechanisms in hematopoietic regeneration that have direct translational applications in disease contexts. HIGHLIGHTSO_LINew HemaScribe method for hematopoietic progenitor annotation in scRNA-seq datasets C_LIO_LIDifferent emergency myelopoiesis (EM) inducers act at distinct hematopoiesis levels C_LIO_LIUnique and shared transcriptional response modules enacted by different EM inducers C_LIO_LIA myeloid progenitor EM module informs outcome in acute myeloid leukemia C_LI eTOC BLURBSwann et al. conduct comparative analysis of single cell RNA sequencing data from multiple emergency myelopoiesis models, finding that different perturbations act at various levels of the hematopoietic hierarchy and recruit distinct sets of molecular mechanisms to enhance myelopoiesis. In particular, they identify a conserved myeloid progenitor-based activation module across multiple disease conditions, which informs outcome in human acute myeloid leukemia. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC="FIGDIR/small/656712v2_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@ffcd62org.highwire.dtl.DTLVardef@50eaeorg.highwire.dtl.DTLVardef@6df44org.highwire.dtl.DTLVardef@12bfacf_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2024

Inflammation perturbs hematopoiesis by remodeling specific compartments of the bone marrow niche

Hematopoietic stem and progenitor cells (HSPC) are regulated by interactions with stromal cells in the bone marrow (BM) cavity, which can be segregated into two spatially defined central marrow (CM) and endosteal (Endo) compartments. However, the importance of this spatial compartmentalization for BM responses to inflammation and neoplasia remains largely unknown. Here, we extensively validate a combination of scRNA-seq profiling and matching flow cytometry isolation that reproducibly identifies 7 key CM and Endo populations across mouse strains and accurately surveys both niche locations. We demonstrate that different perturbations exert specific effects on different compartments, with type I interferon responses causing CM mesenchymal stromal cells to adopt an inflammatory phenotype associated with overproduction of chemokines modulating local monocyte dynamics in the surrounding microenvironment. Our results provide a comprehensive method for molecular and functional stromal characterization and highlight the importance of altered stomal cell activity in regulating hematopoietic responses to inflammatory challenges.

cell biology↗

bioRxiv2023

Maternal IL-10 restricts fetal emergency myelopoiesis

Neonates, in contrast to adults, are highly susceptible to inflammation and infection. Here we investigate how late fetal liver (FL) mouse hematopoietic stem and progenitor cells (HSPC) respond to inflammation, testing the hypothesis that deficits in engagement of emergency myelopoiesis (EM) pathways limit neutrophil output and contribute to perinatal neutropenia. We show that despite similar molecular wiring as adults, fetal HSPCs have limited production of myeloid cells at steady state and fail to activate a classical EM transcriptional program. Moreover, we find that fetal HSPCs are capable of responding to EM-inducing inflammatory stimuli in vitro, but are restricted by maternal anti-inflammatory factors, primarily interleukin-10 (IL-10), from activating EM pathways in utero. Accordingly, we demonstrate that loss of maternal IL-10 restores EM activation in fetal HSPCs but at the cost of premature parturition. These results reveal the evolutionary trade-off inherent in maternal anti-inflammatory responses that maintain pregnancy but render the fetus unresponsive to EM activation signals and susceptible to infection. HIGHLIGHTSO_LIThe structure of the HSPC compartment is conserved from late fetal to adult life. C_LIO_LIFetal HSPCs have diminished steady-state myeloid cell production compared to adult. C_LIO_LIFetal HSPCs are restricted from engaging in emergency myelopoiesis by maternal IL-10. C_LIO_LIRestriction of emergency myelopoiesis may explain neutropenia in septic neonates. C_LI eTOC BLURBFetal hematopoietic stem and progenitor cells are restricted from activating emergency myelopoiesis pathways by maternal IL-10, resulting in inadequate myeloid cell production in response to inflammatory challenges and contributing to neonatal neutropenia.

developmental biology↗

bioRxiv2023

Autophagy counters inflammation-driven glycolytic impairment in aging hematopoietic stem cells

Aging of the hematopoietic system promotes various blood, immune and systemic disorders and is largely driven by hematopoietic stem cell (HSC) dysfunction (1). Autophagy is central for the benefits associated with activation of longevity signaling programs (2), and for HSC function and response to nutrient stress (3,4). With age, a subset of HSCs increases autophagy flux and preserves some regenerative capacity, while the rest fail to engage autophagy and become metabolically overactivated and dysfunctional (4). However, the signals that promote autophagy in old HSCs and the mechanisms responsible for the increased regenerative potential of autophagy-activated old HSCs remain unknown. Here, we demonstrate that autophagy activation is an adaptive survival response to chronic inflammation in the aging bone marrow (BM) niche (5). We find that inflammation impairs glucose metabolism and suppresses glycolysis in aged HSCs through Socs3-mediated impairment of AKT/FoxO-dependent signaling. In this context, we show that inflammation-mediated autophagy engagement preserves functional quiescence by enabling metabolic adaptation to glycolytic impairment. Moreover, we demonstrate that transient autophagy induction via a short-term fasting/refeeding paradigm normalizes glucose uptake and glycolytic flux and significantly improves old HSC regenerative potential. Our results identify inflammation-driven glucose hypometabolism as a key driver of HSC dysfunction with age and establish autophagy as a targetable node to reset old HSC glycolytic and regenerative capacity. One-Sentence SummaryAutophagy compensates for chronic inflammation-induced metabolic deregulation in old HSCs, and its transient modulation can reset old HSC glycolytic and regenerative capacity.

cell biology↗

bioRxiv2021

Secretory MPP3 reinforce myeloid differentiation trajectory and amplify myeloid cell production

Recent lineage tracing analyses revealed multipotent progenitors (MPP) to be major functional contributors to steady-state hematopoiesis (1-6). However, we are still lacking a precise resolution of myeloid differentiation trajectories and cellular heterogeneity in MPPs. Here, we found that myeloid-biased MPP3 (2, 3) are functionally and molecularly heterogeneous, with a distinct subset of myeloid-primed secretory cells with high endoplasmic reticulum (ER) volume and Fc{gamma}R expression. We show that Fc{gamma}R+/ERhigh MPP3 are a transitional population for rapid production of granulocyte/macrophage progenitors (GMP), which directly amplify myelopoiesis through inflammation-triggered secretion of cytokines in the local bone marrow (BM) microenvironment. Our results identify a novel regulatory function for a subset of secretory MPP3 that controls myeloid differentiation through lineage-priming and cytokine production, and act as a self-reinforcing amplification compartment in stress and disease conditions. One-Sentence SummaryA secretory subset of multipotent hematopoietic progenitors augment myelopoiesis in stress and diseases conditions.

immunology↗

bioRxiv2021

Stromal inflammation is a targetable driver of hematopoietic aging

Hematopoietic aging is marked by a loss of regenerative capacity and skewed differentiation from hematopoietic stem cells (HSC) leading to dysfunctional blood production. Signals from the bone marrow (BM) niche dynamically tailor hematopoiesis, but the effect of aging on the niche microenvironment and the contribution of the aging niche to blood aging still remains unclear. Here, we characterize the inflammatory milieu in the aged marrow cavity that drives both stromal and hematopoietic remodeling. We find decreased numbers and functionality of osteogenic mesenchymal stromal cells (MSC) at the endosteum and expansion of pro-inflammatory perisinusoidal MSCs with deterioration of sinusoidal endothelium in the central marrow, which together create a degraded and inflamed old niche. Molecular mapping at single cell resolution confirms disruption of cell identities and enrichment of inflammatory response genes in niche populations. Niche inflammation, in turn, drives chronic activation of emergency myelopoiesis pathways in old HSCs and multipotent progenitors (MPP), which promotes myeloid differentiation at the expense of lymphoid and erythroid commitment and hinders hematopoietic regeneration. Remarkably, niche deterioration, HSC dysfunction and defective hematopoietic regeneration, can be improved by blocking inflammatory IL-1 signaling. Our results demonstrate that targeting niche inflammation is a tractable strategy to restore blood production during aging.

cell biology↗