Biology subjects

Bowman, T. V.

Publications and source records attributed to Bowman, T. V..

6 recordsLinked to original sources

bioRxiv2026

Embryonic TGF-β signaling imposes persistent changes to HSPC clonality and inflammatory landscape

Embryonic hematopoiesis is essential for establishing lifelong blood and immune system function. During development, hematopoietic stem and progenitor cells (HSPCs) acquire intrinsic programs that persist into adulthood and can influence disease susceptibility, yet the molecular signals governing these early-life decisions remain poorly understood. Here, we investigated the role of developmental Transforming Growth Factor-{beta} (TGF-{beta}) signaling in regulating HSPC lineage bias and long-term hematopoietic outcomes. Using the zebrafish model, we found that transient embryonic TGF-{beta} signaling inhibition during the HSPC specification window altered their frequency and migration after emergence from the hemogenic endothelium and movement into the key secondary maturation and expansion niche. Single-cell transcriptomic analysis of embryonic HSPCs revealed repression of migration- and cytoskeleton-associated genes alongside dampened expression of myeloid/macrophage-related genes following ALK5 inhibition. Functionally, early ALK5 blockade reduced macrophage numbers and promoted an M2-like immunosuppressive transcriptional profile. These developmental perturbations produced sustained effects on hematopoietic and immune function into adulthood, including diminished inflammatory gene expression, reduced clonal complexity, and impaired regenerative capacity. Together, our findings identify embryonic TGF-{beta} signaling as a key developmental regulator of HSPC fate and immune programming, with potential implications for immune dysfunction and susceptibility to inflammatory-related disease later in life. PAPER HIGHLIGHTS- Transient developmental signaling perturbations reshape hematopoietic trajectories - Embryogenic TGF-{beta} signaling instructs HSPC lineage priming and macrophage specialization - Early HSPC programming establishes persistent inflammatory states, clonal diversity, and modifies regenerative capacity

developmental biology↗

bioRxiv2025

Hematopoietic Single Cell Atlas Reveals a Diverse Repertoire of Lymphoid Cells in Larval Zebrafish

Embryonic development is a critical time window for the establishment of the hematopoietic and immune systems. During embryogenesis, hematopoietic stem and progenitor cells (HSPCs) that possess divergent differentiation preferences arise and sustain lifelong hematopoiesis. How the pace and differentiation repertoire of native hematopoiesis is set in development and how it evolves as the organism grows is incompletely elucidated. Here, we use temporal lineage tracing of the emerging hematopoietic system during zebrafish development coupled with single cell RNA sequencing to define the origins of larval and adult hematopoietic cells. In both larvae and adult tissues, HSPCs arising earlier during embryogenesis show a predilection for lymphoid lineage production while those arising later are skewed towards erythroid. Moreover, early arising HSPCs are the main contributors to adult tissue resident lymphocytes. Mechanistically, early and late arising HSPCs show divergent transcriptional signatures and differential sensitivities to the levels of the transcription factor Runx1. Additionally, we identified that young larvae possess a more heterogeneous set of lymphoid cells than previously recognized including diverse T-lymphocytes and Innate Lymphoid-like Cells (ILCs). We demonstrated that these newly described larval ILC-like cells reside in lymphoid and mucosal organs and are responsive to viral mimic immune stimulation, indicating their relevance in early vertebrate life. The work provides new fundamental knowledge on how the heterogeneous HSPC pool establishes early immune hierarchies during embryogenesis and its persistence in adulthood.

developmental biology↗

bioRxiv2025

Identification and classification of abundant RNA-binding proteins in the mouse lens and interactions of Carhsp1, Igf2bp1/ZBP1, and Ybx1 with crystallin and β-actin mRNAs

RNA-binding proteins (RBPs) are critical regulators of mRNAs controlling all processes such as RNA transcription, transport, localization, translation, mRNA:ncRNA interactions, and decay. Cellular differentiation is driven by tissue-specific and/or tissue-preferred expression of proteins needed for the optimal function of mature cells, tissues and organs. Lens fiber cell differentiation is marked by high levels of expression of crystallin genes encoding critical proteins for lens transparency and light refraction. Herein we performed proteomic and transcriptomic analyses of RBPs in differentiating mouse lenses to identify the most abundant RBPs and establish dynamic changes of their expression in differentiating lens. Expression analyses include highly abundant RBPs, including Carhsp1, Igf2bp1/ZBP1, Ybx1, Pabpc1, Ddx39, and Rbm38. Binding sites of Carhsp1, Ybx1, and Igf2bp1/ZBP1 were predicted in various crystallin and {beta}-actin mRNAs. Immunoprecipitations using antibodies against Carhsp1, Igf2bp1/ZBP1, and Ybx1 confirmed their interactions with A-, B-, and {gamma}A-crystallin mRNAs. A combination of single molecule RNA FISH (smFISH) and immunofluorescence was used to probe in vivo interactions of these RBPs with A-, B-crystallin, and {beta}-actin mRNAs in cytoplasm and nucleoplasm of cultured mouse lens epithelial cells. Together, these results open new avenues to perform comprehensive genetic, cell, and molecular biology studies of individual RBPs in the lens.

developmental biology↗

bioRxiv2024

RNA Binding Protein Khdrbs1 Regulates Hematopoietic Stem and Progenitor Cell Emergence via Splicing

Definitive hematopoietic stem and progenitor cells (HSPCs) arise through an endothelial-to-hematopoietic transition (EHT), whereby endothelial cells (ECs) acquire a hemogenic fate (HE) and convert to HSPCs. EHT regulators remain incompletely understood. Utilizing published RNA-seq data of ECs, HE/HSPCs, and HSPCs, we defined the alternative splicing landscape of zebrafish EHT and potential RNA binding proteins governing the process. Employing an F0 CRISPR-Cas9 mediated mutagenesis screen, we identified zebrafish homologs of KHDRBS1 as critical for embryonic HSPC formation. Mutagenesis of khdrbs1a/b led to diminished HSPCs and a profound lineage shift in differentiated cells, with the greatest decrease observed in rag+ T-cells. Treatment of mutagenized embryos with the splicing modulator E7107 partially restored HSPCs to near wildtype levels indicating Khdrbs1 splicing regulation drives EHT. Consistently, Khdrbs1 binding motifs were the only ones enriched in EHT alternative splicing events. Identification of EHT-specific splicing regulation provides a deeper understanding of cell fate tuning by splicing.

developmental biology↗

bioRxiv2021

Definitive Hematopoietic Stem Cells Minimally Contribute to Embryonic Hematopoiesis

Hematopoietic stem cells (HSCs) are rare cells that arise in the embryo and sustain adult hematopoiesis. Although the functional potential of nascent HSCs is detectable by transplantation, their native contribution during development is unknown, in part due to the overlapping genesis and marker gene expression with other embryonic blood progenitors. Using single cell transcriptomics, we defined gene signatures that distinguish nascent HSCs from embryonic blood progenitors. Applying a new lineage tracing approach, we selectively tracked HSC output in situ and discovered significantly delayed lymphomyeloid contribution. Using a novel inducible HSC injury model, we demonstrated a negligible impact on larval lymphomyelopoiesis following HSC depletion. HSCs are not merely dormant at this developmental stage as they showed robust regeneration after injury. Combined, our findings illuminate that nascent HSCs self-renew but display differentiation latency, while HSC-independent embryonic progenitors sustain developmental hematopoiesis. Understanding the differences among embryonic HSC and progenitor populations will guide improved de novo generation and expansion of functional HSCs.

developmental biology↗

bioRxiv2018

Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome

Pericentromeric satellite repeats are enriched in 5-methylcytosine (5mC). Loss of 5mC at these sequences is common in cancer and is a hallmark of Immunodeficiency, Centromere and Facial abnormalities (ICF) syndrome. While the general importance of 5mC is well-established, the specific functions of 5mC at pericentromeres are less clear. To address this deficiency, we generated a viable animal model of pericentromeric hypomethylation through mutation of the ICF-gene ZBTB24. Deletion of zebrafish zbtb24 caused a progressive loss of 5mC at pericentromeres and ICF-like phenotypes. Hypomethylation of these repeats triggered derepression of pericentromeric transcripts and activation of an interferon-based innate immune response. Injection of pericentromeric RNA is sufficient to elicit this response in wild-type embryos, and mutation of the MDA5-MAVS dsRNA-sensing machinery blocks the response in mutants. These findings identify activation of the innate immune system as an early consequence of pericentromeric hypomethylation, implicating derepression of pericentromeric transcripts as a trigger of autoimmunity.

molecular biology↗