Biology subjects

Beaudin, A. E.

Publications and source records attributed to Beaudin, A. E..

8 recordsLinked to original sources

bioRxiv2026

Developmental IL7/IL7R signaling in fetal resident tissue macrophages regulates adaptive responses to liver injury

Resident tissue macrophages (RTMs) originate from multiple fetal hematopoietic waves and seed organs during the prenatal window where they acquire tissue-specific homeostatic functions. Several growth factors within the fetal niche are required for RTM development, but knowledge of how these signals program tissue-specific RTM survival, identity, and function during the prenatal window is limited. Here, we investigated the functional role of developmental IL7/IL7R signaling on fetal RTM survival and function. IL7 deficiency impaired neonatal RTM establishment, similar to IL7R deficiency, and IL7 was broadly expressed in fetal tissues and co-localized with IL7R+ macrophages. IL7/IL7R signaling regulated cell cycle, apoptotic, and inflammatory transcriptional pathways and activated phospho-AKT signaling in fetal liver myeloid cells. IL7R deletion impaired proliferation of fetal liver monocyte precursors and increased fetal liver macrophage apoptosis. Specific Cre-mediated IL7R deletion in fetal definitive HSC-derived, but not EMP- derived, macrophages caused irrecoverable postnatal loss of IL7R-expressing macrophages in specific tissues, including the liver, demonstrating a specific temporal requirement for IL7R expression during fetal myelopoiesis. Prenatal IL7R blockade subsequently impaired adaptive responses to chronic fibrotic liver injury in adulthood, associated with increased monocyte infiltration and upregulation of pro-inflammatory signaling pathways. These findings redefine IL7 as a developmental myeloid niche factor and demonstrate that IL7/IL7R signaling is co-opted during fetal development to imprint durable RTM programs that shape postnatal tissue immunity and adaptive responses to injury.

immunology↗

bioRxiv2026

Maternal Folate Nutrition Programs Adult Hematopoietic Stem Cell Function Through Mitochondrial Remodeling

Folic acid fortification for the prevention of neural tube defects has been a cornerstone of public health policy for nearly three decades, but its broader consequences for other developing organ systems, particularly the hematopoietic system, are poorly studied. Hematopoietic stem cell (HSC) emergence overlaps developmentally with neural tube closure, and folate-dependent one-carbon metabolism is critical for nucleotide synthesis, cellular methylation, and redox balance, positioning folate as a candidate regulator of HSC programming. Using dietary models of maternal folate deficiency or supplementation in mice, we demonstrate that maternal folate acts as a dose-dependent developmental tuner of hematopoiesis, programming adult offspring HSC function through divergent mitochondrial and chromatin states. Maternal folate deficiency impaired adult HSC self-renewal, associated with mitochondrial defects, disrupted cristae, elevated proteotoxic stress and a stress-adapted chromatin landscape. In contrast, maternal folate supplementation enhanced HSC self-renewal accompanied by improved mitochondrial quality control and CDC42-associated organelle remodeling, and established chromatin states permissive for stem cell maintenance. Fetal HSC metabolomics identified shifts in one-carbon intermediates, pyruvate and lipid pools, suggesting that divergent fetal metabolic states provide substrate-level inputs that drive persistent and opposing chromatin programs in offspring HSCs. Our findings establish maternal folate availability as an unappreciated regulator of lifelong hematopoietic output demonstrating that a single maternal micronutrient, folate, is sufficient to program adult HSC function and regenerative capacity through persistent metabolic and mitochondrial programming.

cell biology↗

bioRxiv2023

Prenatal inflammation reprograms hyperactive ILC2s that promote allergic lung inflammation and airway dysfunction

Allergic asthma is a chronic respiratory disease that initiates in early life, but causal mechanisms are poorly understood. Here we examined how prenatal inflammation shapes allergic asthma susceptibility by reprogramming lung immunity from early development. Induction of Type I interferon-mediated inflammation during development provoked expansion and hyperactivation of group 2 innate lymphoid cells (ILC2s) seeding the developing lung. Hyperactivated ILC2s produced increased IL-5 and IL-13, and were associated with acute Th2 bias, eosinophilia, and decreased Tregs in the lung. The hyperactive ILC2 phenotype was recapitulated by adoptive transfer of a fetal liver precursor following exposure to prenatal inflammation, indicative of developmental programming. Programming of ILC2 function and subsequent lung immune remodeling by prenatal inflammation led to airway dysfunction at baseline and in response to papain, indicating increased asthma susceptibility. Our data provide a link by which developmental programming of progenitors by early-life inflammation drives lung immune remodeling and asthma susceptibility through hyperactivation of lung-resident ILC2s. One Sentence SummaryPrenatal inflammation programs asthma susceptibility by inducing the production of hyperactivated ILC2s in the developing lung.

immunology↗

bioRxiv2022

Fetal hematopoietic stem cells are activated during acute prenatal infection with Toxoplasma gondii and IFNγ

Infection directly influences adult hematopoietic stem cell (HSC) function and differentiation, but much less is known about the fetal hematopoietic response to infection during pregnancy. Here, we investigated the fetal hematopoietic response to maternal infection with Toxoplasma gondii (T. gondii), an intracellular parasite that elicits Type II IFN{gamma}-mediated maternal immunity. The effects of maternal IFN{gamma} on developing HSCs and the signals that mediate these interactions have not been investigated. Our investigation reveals that the fetal HSCs respond to T. gondii infection with virulence-dependent changes in proliferation, self-renewal potential, and lineage output. We demonstrate that maternal IFN{gamma} crosses the fetal-maternal interface and is perceived by fetal HSCs. By comparing the effects of maternal IFN{gamma} injection with maternal T. gondii infection, our observations reveal that IFN{gamma} mimics aspects of the fetal HSC response to infection. Moreover, our data disentangle the role of infection-induced inflammatory cytokines in driving the expansion of downstream hematopoietic progenitors. Our findings illuminate that the fetal HSC response to prenatal infection is distinct from the adult HSC response to IFN{gamma}-induced inflammation.

immunology↗

bioRxiv2022

Prenatal inflammation perturbs fetal hematopoietic development and causes persistent changes to postnatal immunity

Adult hematopoietic stem and progenitor cells (HSPCs) respond directly to inflammation and infection, resulting in both acute and persistent changes to quiescence, mobilization, and differentiation. Here we show that fetal HSPCs respond to prenatal inflammation in utero, and that the fetal response shapes postnatal hematopoiesis and immunity. Heterogenous fetal HSPCs showed divergent responses to maternal immune activation (MIA), including changes in quiescence, expansion, and lineage-biased output. Single cell transcriptomic analysis of fetal HSPCs in response to MIA revealed specific upregulation of inflammatory gene profiles in discrete, transient HSC populations, that propagated expansion of lymphoid-biased progenitors. Beyond fetal development, MIA caused the inappropriate expansion and persistence of fetal lymphoid-biased progenitors postnatally, concomitant with increased cellularity and hyperresponsiveness of fetal-derived innate-like lymphocytes. Our investigation demonstrates how inflammation in utero can direct the trajectory of output and function of fetal-derived immune cells by reshaping fetal HSC establishment.

cell biology↗

bioRxiv2021

IL7R is required for hematopoietic stem cell reconstitution of tissue-resident lymphoid cells

Traditional, adult-derived lymphocytes that circulate provide adaptive immunity to infection and pathogens. However, subsets of lymphoid cells are also found in non-lymphoid tissues and are called tissue-resident lymphoid cells (TLCs). TLCs encompass a wide array of cell types that span the spectrum of innate-to-adaptive immune function. Unlike traditional lymphocytes that are continuously generated from hematopoietic stem cells (HSCs), many TLCs are of fetal origin and poorly generated from adult HSCs. Here, we sought to understand the development of murine TLCs across multiple tissues and therefore probed the roles of Flk2 and IL7R, two cytokine receptors with known roles in traditional lymphopoiesis. Using Flk2- and Il7r-Cre lineage tracing models, we found that peritoneal B1a cells, splenic marginal zone B (MZB) cells, lung ILC2s and regulatory T cells (Tregs) were highly labeled in both models. Despite this high labeling, highly quantitative, in vivo functional approaches showed that the loss of Flk2 minimally affected the generation of these cells in situ. In contrast, the loss of IL7R, or combined deletion of Flk2 and IL7R, dramatically reduced the cell numbers of B1a cells, MZBs, ILC2s, and Tregs both in situ and upon transplantation, indicating an intrinsic and more essential role for IL7R. Surprisingly, reciprocal transplants of WT HSCs showed that an IL7R-/- environment selectively impaired reconstitution of TLCs when compared to TLC numbers in situ. Taken together, our data revealed functional roles of Flk2 and IL7R in the establishment of tissue-resident lymphoid cells.

cell biology↗

bioRxiv2017

Tn5Prime, a Tn5 based 5’ Capture Method for Single Cell RNA-seq

RNA-seq is a powerful technique to investigate and quantify entire transcriptomes. Recent advances in the field have made it possible to explore the transcriptomes of single cells. However, most widely used RNA-seq protocols fail to provide crucial information regarding transcription start sites. Here we present a protocol, Tn5Prime, that takes advantage of the Tn5 transposase based Smartseq2 protocol to create RNA-seq libraries that capture the 5 end of transcripts. The Tn5Prime method dramatically streamlines the 5 capture process and is both cost effective and reliable. By applying Tn5Prime to bulk RNA and single cell samples we were able to define transcription start sites as well as quantify transcriptomes at high accuracy and reproducibility. Additionally, similar to 3 end based high-throughput methods like Drop-Seq and 10X Genomics Chromium, the 5 capture Tn5Prime method allows the introduction of cellular identifiers during reverse transcription, simplifying the analysis of large numbers of single cells. In contrast to 3 end based methods, Tn5Prime also enables the assembly of the variable 5 ends of antibody sequences present in single B-cell data. Therefore, Tn5Prime presents a robust tool for both basic and applied research into the adaptive immune system and beyond.

genomics↗

bioRxiv2017

Nanopore Long-Read RNAseq Reveals Widespread Transcriptional Variation Among the Surface Receptors of Individual B cells

Understanding gene regulation and function requires a genome-wide method capable of capturing both gene expression levels and isoform diversity at the single cell level. Short-read RNAseq, while the current standard for gene expression quantification, is limited in its ability to resolve complex isoforms because it fails to sequence full-length cDNA copies of RNA molecules. Here, we investigated whether RNAseq using the long-read single-molecule Oxford Nanopore MinION sequencing technology (ONT RNAseq) would be able to identify and quantify complex isoforms without sacrificing accurate gene expression quantification. After successfully benchmarking our experimental and computational approaches on a mixture of synthetic transcripts, we analyzed individual murine B1a cells using a new cellular indexing strategy. Using the Mandalorion analysis pipeline we developed, we identified thousands of unannotated transcription start and end sites, as well as hundreds of alternative splicing events in these B1a cells. We also identified hundreds of genes expressed across B1a cells that displayed multiple complex isoforms, including several B cell specific surface receptors and the antibody heavy chain (IGH) locus. Our results show that not only can we identify complex isoforms, but also quantify their expression, at the single cell level.

genomics↗