Biology subjects

Handel, A. E.

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

7 recordsLinked to original sources

bioRxiv2026

Spatial remodeling of the thymic stroma with age disrupts niches for T cell selection and tolerance

Age-associated thymic involution is a major driver of immunosenescence, yet the cellular and spatial mechanisms coordinating age-related thymic remodeling remain incompletely understood. Combining single-cell transcriptomics, chromatin accessibility profiling, and spatial transcriptomics, we generated a spatially resolved multi-omic atlas of the aging mouse thymus. We show that thymic aging is not simply a process of epithelial loss, but a spatial reorganization of the stroma into new microenvironments, including age-associated epithelial states, a fibroblast-supported epithelial progenitor niche, and tertiary lymphoid structures. This remodeling displaces niches supporting positive and negative thymocyte selection and coincides with an intrinsic decline in cortical thymic epithelial cell function. Ligand-receptor mapping identifies medullary fibroblasts as a signaling hub sustaining epithelial progenitors and promoting tertiary lymphoid structure neogenesis, linking these hallmarks of thymic aging. Together, our findings reframe thymic involution as spatial stromal reorganization that links stromal remodeling to impaired thymopoiesis, central tolerance, and immune aging.

immunology↗

bioRxiv2026

Sequential narrative binding by hippocampal CA2/3 sustains lifespan episodic detail retrieval

Hippocampal subfield contributions to the structure of episodic memories across the lifespan remain incompletely understood, particularly regarding the mechanisms underlying sustained retrieval of detailed events regardless of age. Here, we show that focal hippocampal damage in 32 individuals with amnesia produces time-invariant loss of episodic content details (event specifics, place, perceptual, and emotional content) across six decades, sparing only early childhood memories and semantic details. Temporal context details showed non-monotonic vulnerability, with maximal deficits in recent memories. Volumetric analyses revealed distinct anterior-posterior functional gradients: anterior hippocampal CA3 predicted retrieval across 11-55+ years, posterior CA3 across 18-55+ years, whereas CA1 predicted only recent memories. Computational linguistic analyses using Sentence-BERT semantic embeddings quantified narrative organisation within remembered events via consecutive-sentence semantic relatedness (local narrative coherence) and overall semantic alignment (global narrative coherence). Hippocampal CA2/3 damage impaired local but not global narrative coherence, with reduced local coherence mediating episodic detail loss. This dissociation demonstrates that CA2/3 mediates sequential narrative binding through mechanisms dissociable from broader narrative operations. Concordant time-invariant deficits across quantitative measures of episodic content and computational-linguistic based measures challenge classical systems consolidation predictions, supporting parallel hippocampal-cortical contributions to lifespan episodic memory.

neuroscience↗

bioRxiv2025

Decoding memory dysfunction in hippocampal amnesia

The hippocampus reconstructs past experiences by integrating sensory, perceptual, and conceptual information across a cortico-hippocampal autobiographical memory network (AMN). Here, in 18 human participants with amnesia, we decoded the effects of bilateral focal hippocampal damage on distinct autobiographical representations using representational dissimilarity matrices (RDMs). Hippocampal pathology resulted in: (1) impaired generalised episodic memory retrieval RDM model fit in the left angular gyrus; and, (2) reduced distinct episodic memory RDM model fit and trial-by-trial voxel-representational stability in the right angular gyrus, right orbitofrontal cortex, and right inferior frontal gyrus. RDM model fits and mnemonic stability were predicted by total CA23 volumes. Trial-by-trial retrieval stability within the right orbitofrontal cortex and right inferior frontal gyrus predicted autobiographical memory performance, providing the first direct neural correlate between hippocampal dysfunction, altered mnemonic representations, and amnesia. The results demonstrate that hippocampal-mediated amnesia results from impaired mnemonic representational distinctiveness and stability within the AMN.

neuroscience↗

bioRxiv2021

Developmental dynamics of the neural crest-mesenchymal axis in creating the thymic microenvironment

The thymic stroma is composed of epithelial and non-epithelial cells that collectively provide separate microenvironments controlling the homing of blood-born precursors to the tissue, and their subsequent differentiation to functionally mature and correctly selected T cells. While thymic epithelial cells are well characterized for their role in thymopoiesis, a comparably comprehensive analysis of the non-epithelial thymic stroma is lacking. Here we explore at single cell resolution the complex composition and dynamic changes that occur over time in the non-epithelial stromal compartment. We detail across different developmental stages in human and mouse thymus, and in an experimental model of Di George syndrome, the most common form of human thymic hypoplasia, the separate transcriptomes of mouse mesothelium, fibroblasts, neural crest cells, endothelial and vascular mural cells. The detected gene expression signatures identify novel stromal subtypes and relate their individual molecular profiles to separate differentiation trajectories and functions. Specifically, we demonstrate an abundance and unprecedented heterogeneity of diverse fibroblast subtypes that emerge at discrete developmental stages and vary in their expression of key regulatory signalling circuits and components of the extracellular matrix. Taken together, these findings highlight the dynamic complexity of the non-epithelial thymus stroma and link the cells specific gene expression profiles to separate instructive roles essential for normal thymus organogenesis and tissue maintenance. TeaserSingle cell profiling of thymic stroma identifies a dynamic contribution from neural crest cells to the thymic mesenchyme.

immunology↗

bioRxiv2021

A FOXN1 mutation competitively displaces wild-type FOXN1 from higher order nuclear condensates to cause immunodeficiency

The transcription factor FOXN1 is a master regulator of thymic epithelial cell development and function. Here we demonstrate that FOXN1 expression is differentially regulated during organogenesis and participates in multi-molecular nuclear condensates essential for the factors transcriptional activity. FOXN1s C-terminal sequence regulates the diffusion velocity within these aggregates and modulates the binding to proximal gene regulatory regions. These dynamics are significantly altered in a patient with a mutant FOXN1 which is modified in its C-terminal sequence. This mutant is transcriptionally inactive and acts as a dominant negative factor displacing wild-type FOXN1 from condensates and causing athymia and severe lymphopenia in heterozygotes. Expression of the mutated mouse ortholog, selectively impairs mouse thymic epithelial cell (TEC) differentiation revealing a gene dose dependency for individual TEC subtypes. We have therefore identified the cause for a primary immunodeficiency disease and determined the mechanism by which this FOXN1 gain-of-function mutant mediates its dominant negative effect.

immunology↗

bioRxiv2020

Ageing compromises mouse thymus function and remodels epithelial cell differentiation

Ageing is characterised by cellular senescence, leading to imbalanced tissue maintenance, cell death and compromised organ function. This is first observed in the thymus, the primary lymphoid organ that generates and selects T cells. However, the molecular and cellular mechanisms underpinning these ageing processes remain unclear. Here, we show that mouse ageing leads to less efficient T cell selection, decreased self-antigen representation and increased T cell receptor repertoire diversity. Using a combination of single-cell RNA-seq and lineage-tracing, we find that progenitor cells are the principal targets of ageing, whereas the function of mature thymic epithelial cells is compromised only modestly. Specifically, an early-life precursor cell population, retained in the mouse cortex postnatally, is virtually extinguished at puberty. Concomitantly, a medullary precursor cell quiesces, thereby impairing maintenance of the medullary epithelium. Thus, ageing disrupts thymic progenitor differentiation and impairs the core immunological functions of the thymus.

immunology↗

bioRxiv2018

The structural basis for forkhead box family specificity revealed by the crystal structure of human FOXN1 in complex with DNA

SignificanceFOXN1 is a transcription factor that is essential for the development of the thymus and the production of T-lymphocytes. It is a member of a large family of transcription factors which recognize DNA sequences through the conserved Forkhead (FH) domain. FOXN1 recognizes a DNA sequence that is different from the common consensus binding sequence of FH domains, although key binding residues are identical. We present crystal structures of the FH domain of FOXN1, free and DNA-bound, which shed light on the different binding specificities; the structure also revelas the basis of the immunocompromised nude mutation, as well as a preferential binding to non-methylated CpG motifs.\n\nAbstractFOXN1 is a member of the forkhead box (FOX) family of transcription factors, and plays an important role in thymic epithelial cell differentiation and function. FOXN1 mutations in humans and mice give rise to the \"nude\" phenotype which is marked by athymia. FOXN1 belongs to a subset of the FOX family that recognize an alternate consensus sequence (GACGC), which is different from the more widely-recognized canonical sequence consensus RYAAAYA. Here, we present the structure of FOXN1 in complex with DNA at 1.6 [A] resolution, in which the DNA sequence is recognised by a mixture of direct and water-mediated contacts provided by residues in an a-helix inserted in the DNA major groove (the recognition helix). Comparisons with other FOX family structures reveal that the canonical and alternate DNA sequences are bound in two distinct modes, with partially different registers for the protein DNA contacts. We identify a single alternate rotamer within the recognition helix itself as an important determinant of DNA specificity, and indicate sequence features in the recognition helix that could be used to predict the specificity of other FOX family members. Finally we demonstrate that FOXN1 has a significantly reduced affinity for DNA containing 5-methylcytosine, which may have implications for the role of FOXN1 in thymic senescence.

biochemistry↗