Biology subjects

Jafree, D. J.

Publications and source records attributed to Jafree, D. J..

11 recordsLinked to original sources

bioRxiv2026

Multi-scale modeling of human tissues from spatial transcriptomics with TERRA

Spatial transcriptomics maps gene expression at cellular resolution, revealing how cells organize into multicellular niches. Yet computational analyses remain dataset-specific, without a transferable representation of tissue organization that generalizes across datasets, tasks and tissues or predicts how tissues behave under perturbation. We present TERRA, a foundation model pretrained on 112 million human cells profiled by spatial transcriptomics. From a single pretrained backbone, TERRA yields embeddings at the scale of cells, the genes they express and the neighborhoods in which they reside, and supports spatial in silico perturbation, all applied zero-shot to unseen tissues. At the cell level, in newly generated spatial data for developing pancreas, TERRA identified an islet-associated capillary state which we posit represents a developmental precursor of the mature islet microvasculature. At the gene level, in untreated kidney sections, in silico knockout of immune-checkpoint targets predicted a gene program of immune-checkpoint-blockade-associated nephrotoxicity, which we validated in treatment-exposed tissue and recovered in blood. At the neighborhood level, TERRA mapped macrophages across tissues to identify recurring cross-organ niches, which we term archetypes, including a tumor-boundary niche associated with poor prognosis in kidney cancer. Together, TERRA captures the spatial and multicellular logic of human tissue and predicts, in silico, its response to perturbation, providing a multi-scale framework for tissue biology, therapeutic development and clinical application.

genomics↗

bioRxiv2026

Self-supervised learning for a gene program-centric view of cell states

Single-cell omics has extended the biological interrogation of cell state from examining the expression of individual genes to unbiased profiling of tens of thousands of genes at once. However, extracting biological insights from such high-dimensional data remains challenging. To enable downstream analyses, many computational approaches compress cell state into a single latent representation. This can obscure the structure of underlying gene programs (GP), defined as coordinated sets of biologically related genes, such as signalling pathway response modules or transcription factor targets. Here, we present Tripso, a self-supervised transformer deep learning model which learns multiple GP-specific embeddings from predefined GPs, while also enabling the discovery of novel, data-driven GPs. Tripso facilitates principled comparisons across development, disease, and experimental systems. Firstly, in a dataset of human hematopoietic cells spanning prenatal development through adulthood and aging and including newly generated data, Tripso resolved age-specific GP patterns, including elevated JAK-STAT activity in pediatric hematopoietic cells and postnatal shifts in IKZF1 GP activity during B cell differentiation. Secondly, leveraging Tripso GP embeddings and comparing in vivo to in vitro data, we hypothesized and experimentally validated that inhibition of the SEC61 translocon improved maintenance of hematopoietic stem cells in culture. Finally, Tripsos capacity for data-driven GP discovery revealed a previously uncharacterized tissue-resident memory T cell GP with increased activity in atopic dermatitis. Its spatial co-localization with sebaceous gland-associated immune niches was demonstrated in spatial transcriptomic and proteomic data. Thus, by moving beyond single embeddings of cellular states, Tripso enables interpretable and actionable discoveries, demonstrating how GP-centric modelling can generate hypotheses with substantial biomedical relevance. By anchoring cellular representations in meaningful GPs, Tripso establishes a principled and biologically grounded framework towards the development of interpretable virtual cell models.

bioinformatics↗

bioRxiv2025

A cross model spatial and single-cell atlas reveals the conserved involvement of osteopontin in polycystic kidney disease

Polycystic kidney disease (PKD) arises from mutations in cilia-associated genes, such as PKD1 and PKD2, expressed in renal epithelial cells, leading to progressive kidney dysfunction and end- stage kidney disease (ESKD). PKD patients exhibit significant heterogeneity in disease progression, largely due to genetic and environmental modifiers. Like patients, mouse models of PKD also exhibit significant heterogeneity with regards to the gene mutated, age of disease onset, and rate of disease progression. To elucidate the cellular and molecular consequences of these variables, we constructed an integrated single-cell and spatial transcriptomics atlas across mouse models of PKD, mapping changes in cell type composition, gene expression, and intercellular signaling networks across the whole atlas and within individual models. Consistently across models, single cell RNA sequencing (scRNAseq) data revealed increased Spp1 (osteopontin) expression and signaling from PKD-enriched clusters to Ly6clo monocytes. Global deletion of Spp1 in Pkd1RC/RC mice resulted in reduced cyst severity, improved kidney function, and reduced Ly6clo monocyte numbers, suggesting that SPP1 signaling to Ly6clo monocytes promotes PKD progression. We also created a freely available, searchable website (https://bmblx.bmi.osumc.edu/scPKD/) that can be used to identify cross- and intra-model specific changes in gene expression, guiding researchers to new therapeutic targets for treating PKD.

bioinformatics↗

bioRxiv2025

Genetic lineage tracing identifies intermediate mesoderm as a novel contributor to mammalian kidney lymphatics

The lymphatic vasculature is essential for fluid homeostasis, immune regulation and possesses diverse organ-specific functions. During development, lymphatic endothelial cells (LEC) arise from multiple progenitor sources that form organ-specific lymphatic networks. While the origins of LECs in the heart, skin, and mesentery have been studied, those in the kidney remain unresolved. Here, we combined genetic lineage tracing in mouse embryos with optical clearing and high-resolution three-dimensional imaging to identify two distinct progenitor sources of kidney lymphatics. The majority of kidney LECs originate from a Tie2 endothelial lineage previously linked to venous or capillary vessels. Approximately 15% derive from Osr1 intermediate mesoderm, a lineage that generates kidney nephrons and stroma. Osr1-derived LECs were absent from the heart, mesentery, and skin, indicating a kidney-specific contribution, and arose independently of nephron and stromal lineages. Both Tie2 and Osr1 lineages contributed to vessel sprouting and de novo formation of lymphatic clusters. Revealing a novel cellular origin of LECs and identifying a dual origin for kidney lymphatics, we demonstrate that de novo lymphatic formation can occur from both shared and organ-specific progenitors. This work advances our understanding of how lymphatics assemble during development and provides a framework for targeting kidney lymphatics in disease.

developmental biology↗

bioRxiv2025

Mapping and reprogramming microenvironment-induced cell states in human disease using generative AI

Tissue microenvironments reprogram local cellular states in disease, yet current computational spatial methods remain descriptive and do not simulate tissue perturbation. We present MintFlow, a generative AI algorithm that learns how the tissue microenvironment influences cell states and predicts how tissue perturbations can reprogram them. Applied to three human diseases, MintFlow uncovered distinct pathogenic spatial reprogramming in inflammatory and tumor microenvironments. In atopic dermatitis, MintFlow identified a novel, spatially-imprinted, type 2 (IL13+ITGAE+) epidermal T resident memory cell population (type 2 TRM), and decoded signaling pathways within the perivascular lymphoid niche. In melanoma, MintFlow identified fibrotic stroma resembling keloid scar tissue. In kidney cancer, MintFlow resolved immunosuppressed CD8+ T cell states within tertiary lymphoid structures. Furthermore, MintFlow enabled in silico perturbations of disease-relevant cell states and tissue environments. Regulatory T cell modulation in atopic dermatitis was predicted to suppress the pro-inflammatory tissue environment, supporting manipulation of these cells as a therapeutic target. In kidney cancer, in silico T cell replacement recapitulated immune checkpoint blockade, while spatially targeted macrophage depletion reverted immunosuppressed T cell states. The corresponding gene programs correlated with survival in large kidney cancer patient cohorts. Together, these findings position MintFlow as a tool for unbiased disease mechanism prediction and in silico perturbation, accelerating translational hypothesis generation and guiding therapeutic strategies.

genomics↗

bioRxiv2024

A unique subset of pericystic endothelium associates with aberrant microvascular remodelling and impaired blood perfusion early in polycystic kidney disease

Hallmarks of autosomal dominant polycystic kidney disease (ADPKD), the most common hereditary kidney anomaly, include expanding fluid-filled epithelial cysts, inflammation, and fibrosis. Despite previous work showing the potential of vascular-based therapies, renal microvascular alterations in ADPKD, and their timing, are poorly understood. Using single-cell transcriptomics of human kidney microvasculature, we identify a population of endothelial cells adjacent to cysts in ADPKD. This pericystic endothelium, distinguishable by its expression of osteopontin (SPP1), has a distinct molecular profile compared to the common endothelial cell injury signature in other kidney diseases. SPP1+ pericystic endothelium was also present in an orthologous mouse model of ADPKD before overt kidney functional decline. By interrogating geometric, topological and fractal properties from three-dimensional imaging of early ADPKD mouse kidneys, we show that pericystic endothelium associates with disorganisation and non-uniformity of the renal cortical microvasculature. Concurrently, we detected region-specific reductions in cortical blood flow within ADPKD murine kidneys using arterial spin labelling. We conclude that ADPKD kidneys contain a unique subset of endothelium manifesting with aberrant remodelling and impaired blood perfusion. Its detection, prior to renal functional decline, advocates the vasculature as a therapeutic target to modulate or preserve renal function in early ADPKD.

pathology↗

bioRxiv2023

Micro to macro scale analysis of the intact human renal arterial tree with Synchrotron Tomography

The architecture of the kidney vasculature is essential for its function. Although structural profiling of the intact rodent kidney vasculature has been performed, it is challenging to map vascular architecture of larger human organs. We hypothesised that hierarchical phase-contrast tomography (HiP-CT) would enable quantitative analysis of the entire human kidney vasculature. Combining label-free HiP-CT imaging of an intact kidney from a 63-year-old male with topology network analysis, we quantitated vasculature architecture in the human kidney down to the scale of arterioles. Although human and rat kidney vascular topologies are comparable, vascular radius decreases at a significantly faster rate in humans as vessels branch from artery towards the cortex. At branching points of large vessels, radii are theoretically optimised to minimise flow resistance, an observation not found for smaller arterioles. Structural differences in the vasculature were found in different spatial zones of the kidney reflecting their unique functional roles. Overall, this represents the first time the entire arterial vasculature of a human kidney has been mapped providing essential inputs for computational models of kidney vascular flow and synthetic vascular architectures, with implications for understanding how the structure of individual blood vessels collectively scales to facilitate organ function.

bioengineering↗

bioRxiv2022

Three-dimensional imaging and single-cell transcriptomics of the human kidney implicate perturbation of lymphatics in alloimmunity

Studies of the structural and molecular features of the lymphatic vasculature, which clears fluid, macromolecules and leukocytes from the tissue microenvironment, have largely relied on animal models, with limited information in human organs beyond traditional immunohistochemical assessment. Here, we use three-dimensional imaging and single-cell RNA-sequencing to study lymphatics in the human kidney. We found a hierarchical arrangement of lymphatic vessels within human kidneys, initiating along specialised nephron epithelium in the renal cortex and displaying a distinct, kidney-specific transcriptional profile. In chronic transplant rejection we found kidney allograft lymphatic expansion alongside a loss of structural hierarchy, with human leukocyte antigen-expressing lymphatic vessels infiltrating the medulla, presenting a putative target for alloreactive antibodies. This occurred concurrently with lymphatic vessels invading and interconnecting tertiary lymphoid structures at early stages of lymphocyte colonisation. Analysis of intercellular signalling revealed upregulation of co-inhibitory molecule-mediated CD4+ T cell-lymphatic crosstalk in rejecting kidneys, potentially acting to limit local alloimmune responses. Overall, we delineate novel structural and molecular features of human kidney lymphatics and reveal perturbations to their phenotype and transcriptome in the context of alloimmunity. SUMMARYLymphatics regulate fluid balance and immune cell accumulation but are under-studied in human organs such as the kidney. Jafree and colleagues profiled human kidney lymphatics using three-dimensional imaging and single-cell RNA-sequencing, revealing structural and transcriptional perturbations in rejecting kidney transplants.

immunology↗

bioRxiv2022

Exploration of single-cell transcriptomic landscape identifies aberrant glomerular crosstalk in a murine model of WT1 kidney disease

The glomerulus mediates kidney ultrafiltration through specialised epithelial cells called podocytes which line a basement membrane shared with blood capillary endothelium. Cell-cell crosstalk is critical for glomerular function, but its investigation in childhood glomerular diseases has received little attention. WT1 encodes a transcription factor expressed in podocytes, whose heterozygous variants cause devastating kidney disease in childhood. We used single-cell RNA sequencing and ligand-receptor interaction analysis to resolve the glomerular transcriptional landscape of mice that carry an orthologous human mutation in WT1 (Wt1R394W/+). Podocytes were the most dysregulated cell type in early disease, with disrupted angiogenic signalling preceding glomerular capillary loss. Comparative analyses with additional murine and human glomerular disease datasets identified unique transcriptional changes in WT1 glomerular disease, reflecting a non-immunological pathology, whilst revealing a common injury signature across multiple glomerular diseases. Collectively, this work advocates vascular-based therapies over immunosuppressive drugs in the treatment of WT1 glomerular disease.

cell biology↗

bioRxiv2021

Systemic gene therapy with thymosin β4 alleviates glomerular injury in mice

Plasma ultrafiltration in the kidney occurs across glomerular capillaries, which are surrounded by epithelial cells called podocytes. Podocytes have a unique shape maintained by a complex cytoskeleton, which becomes disrupted in glomerular disease resulting in defective filtration and albuminuria. Lack of endogenous thymosin {beta}4 (TB4), an actin sequestering peptide, exacerbates glomerular injury and disrupts the organisation of the podocyte actin cytoskeleton, however, the effect of exogenous TB4 therapy on podocytopathy is unknown. Here, through interrogating single-cell RNA-sequencing data of isolated glomeruli we demonstrate that Adriamycin, a toxin which injures podocytes and leads to leakage of albumin in the urine of mice, results in reduced levels of podocyte TB4. Systemic administration of an adeno-associated virus vector encoding TB4 prevented Adriamycin-induced podocyte loss and albuminuria. Adriamycin injury was associated with disorganisation of the actin cytoskeleton in vitro, which was ameliorated by exogenous TB4. Furthermore, Adriamycin administration in mice was associated with increased prevalence of podocyte vesicles, a mechanism by which albumin may leak into the urine, which was also prevented by TB4. Collectively, we propose that TB4 gene therapy prevents podocyte injury and maintains glomerular filtration via modulation of the podocyte cytoskeleton thus presenting a novel treatment strategy for glomerular disease.

physiology↗

bioRxiv2021

Multiscale three-dimensional imaging of intact human organs down to the cellular scale using hierarchical phase-contrast tomography

Human organs are complex, three-dimensional and multiscale systems. Spatially mapping the human body down through its hierarchy, from entire organs to their individual functional units and specialised cells, is a major obstacle to fully understanding health and disease. To meet this challenge, we developed hierarchical phase-contrast tomography (HiP-CT), an X-ray phase propagation technique utilising the European Synchrotron Radiation Facilitys Extremely Brilliant Source: the worlds first high-energy 4th generation X-ray source. HiP-CT enabled three-dimensional and non-destructive imaging at near-micron resolution in soft tissues at one hundred thousand times the voxel size whilst maintaining the organs structure. We applied HiP-CT to image five intact human parenchymal organs: brain, lung, heart, kidney and spleen. These were hierarchically assessed with HiP-CT, providing a structural overview of the whole organ alongside detail of the organs individual functional units and cells. The potential applications of HiP-CT were demonstrated through quantification and morphometry of glomeruli in an intact human kidney, and identification of regional changes to the architecture of the air-tissue interface and alveolar morphology in the lung of a deceased COVID-19 patient. Overall, we show that HiP-CT is a powerful tool which can provide a comprehensive picture of structural information for whole intact human organs, encompassing precise details on functional units and their constituent cells to better understand human health and disease.

physiology↗