Daniyal J. Jafree
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View article: Nanobody Immunolabelling and three-dimensional imaging reveals spatially restricted LYVE1 expression by kidney lymphatic vessels in mice
Nanobody Immunolabelling and three-dimensional imaging reveals spatially restricted LYVE1 expression by kidney lymphatic vessels in mice Open
View article: Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography
Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography Open
The architecture of kidney vasculature is essential the organ's specialised functions, yet is challenging to structurally map in an intact human organ. Here, we combined hierarchical phase-contrast tomography (HiP-CT) with topology network…
View article: Genetic lineage tracing identifies intermediate mesoderm as a novel contributor to mammalian kidney lymphatics
Genetic lineage tracing identifies intermediate mesoderm as a novel contributor to mammalian kidney lymphatics Open
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-sp…
View article: Organ-specific features of human kidney lymphatics are disrupted in chronic transplant rejection
Organ-specific features of human kidney lymphatics are disrupted in chronic transplant rejection Open
Lymphatic vessels maintain tissue fluid homeostasis and modulate inflammation, yet their spatial organization and molecular identity in the healthy human kidney, and how these change during chronic transplant rejection, remain poorly defin…
View article: Mapping and reprogramming human tissue microenvironments with MintFlow
Mapping and reprogramming human tissue microenvironments with MintFlow Open
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 t…
View article: Microvascular aberrations found in human polycystic kidneys are an early feature in a <i>Pkd1</i> mutant mouse model
Microvascular aberrations found in human polycystic kidneys are an early feature in a <i>Pkd1</i> mutant mouse model Open
Therapies targeting blood vessels hold promise for autosomal dominant polycystic kidney disease (ADPKD), the most common inherited disorder causing kidney failure. However, the onset and nature of kidney vascular abnormalities in ADPKD are…
View article: Single‐cell transcriptomics identifies aberrant glomerular angiogenic signalling in the early stages of <scp>WT1</scp> kidney disease
Single‐cell transcriptomics identifies aberrant glomerular angiogenic signalling in the early stages of <span>WT1</span> kidney disease Open
WT1 encodes a podocyte transcription factor whose variants can cause an untreatable glomerular disease in early childhood. Although WT1 regulates many podocyte genes, it is poorly understood which of them are initiators in disease and how …
View article: Nanobody immunolabelling and three-dimensional imaging reveals spatially restricted LYVE1 expression by kidney lymphatic vessels in mice
Nanobody immunolabelling and three-dimensional imaging reveals spatially restricted LYVE1 expression by kidney lymphatic vessels in mice Open
Lymphatic vessels are complex three-dimensional (3D) structures that facilitate tissue fluid clearance and regulate immune responses in health and inflammatory contexts. Recent advances in wholemount immunolabelling and 3D imaging have pro…
View article: SGLT1 contributes to glucose-mediated exacerbation of ischemia–reperfusion injury in ex vivo rat heart
SGLT1 contributes to glucose-mediated exacerbation of ischemia–reperfusion injury in ex vivo rat heart Open
Hyperglycaemia is common during acute coronary syndromes (ACS) irrespective of diabetic status and portends excess infarct size and mortality, but the mechanisms underlying this effect are poorly understood. We hypothesized that sodium/glu…
View article: Cardiotrophin‐1 therapy reduces disease severity in a murine model of glomerular disease
Cardiotrophin‐1 therapy reduces disease severity in a murine model of glomerular disease Open
Cardiotrophin‐1 (CT‐1), a member of the interleukin (IL)‐6 cytokine family, has renoprotective effects in mouse models of acute kidney disease and tubulointerstitial fibrosis, but its role in glomerular disease is unknown. To address this,…
View article: A unique subset of pericystic endothelium associates with aberrant microvascular remodelling and impaired blood perfusion early in polycystic kidney disease
A unique subset of pericystic endothelium associates with aberrant microvascular remodelling and impaired blood perfusion early in polycystic kidney disease Open
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 vascu…
View article: Mapping the blood vasculature in an intact human kidney using hierarchical phase-contrast tomography
Mapping the blood vasculature in an intact human kidney using hierarchical phase-contrast tomography Open
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 h…
View article: Hyperglycemic exacerbation of myocardial infarction through SGLT1 - a glucose paradox
Hyperglycemic exacerbation of myocardial infarction through SGLT1 - a glucose paradox Open
Background Hyperglycemia is common during acute myocardial infarction, irrespective of diabetic status, and portends excess mortality. The mechanisms of this adverse outcome remain unelucidated. Objectives To test the hypothesis that eleva…
View article: Single-cell atlas of human kidneys in health, chronic kidney disease and transplant rejection
Single-cell atlas of human kidneys in health, chronic kidney disease and transplant rejection Open
This single-cell RNA-sequencing (scRNA-seq) dataset comprises two files: an RData file (combined_data.RData), which can be loaded into RStudio to generate a Seurat object, and an h5ad object (annotated_combined_adata_full.h5ad) for downstr…
View article: Single-cell atlas of human kidneys in health, chronic kidney disease and transplant rejection
Single-cell atlas of human kidneys in health, chronic kidney disease and transplant rejection Open
This single-cell RNA-sequencing (scRNA-seq) dataset comprises two files: an RData file (combined_data.RData), which can be loaded into RStudio to generate a Seurat object, and an h5ad object (annotated_combined_adata_full.h5ad) for downstr…
View article: Supplementary processed data for Chandler et al. Single-cell transcriptomics identifies aberrant glomerular angiogenic signalling in the early stages of a murine model of WT1 kidney disease
Supplementary processed data for Chandler et al. Single-cell transcriptomics identifies aberrant glomerular angiogenic signalling in the early stages of a murine model of WT1 kidney disease Open
Summary datafiles for Chandler et al. Processed single-cell RNA sequencing data, derived from murine glomeruli (isolated using the dynabead technique) from n = 2 wild-type Wt1+/+ (Ctrl…
View article: Supplementary processed data for Chandler et al. Single-cell transcriptomics identifies aberrant glomerular angiogenic signalling in the early stages of a murine model of WT1 kidney disease
Supplementary processed data for Chandler et al. Single-cell transcriptomics identifies aberrant glomerular angiogenic signalling in the early stages of a murine model of WT1 kidney disease Open
Summary datafiles for Chandler et al. Processed single-cell RNA sequencing data, derived from murine glomeruli (isolated using the dynabead technique) from n = 2 wild-type Wt1+/+ (Ctrl…
View article: Three-dimensional imaging and single-cell transcriptomics of the human kidney implicate perturbation of lymphatics in alloimmunity
Three-dimensional imaging and single-cell transcriptomics of the human kidney implicate perturbation of lymphatics in alloimmunity Open
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 orga…
View article: Exploration of the single-cell transcriptomic landscape identifies aberrant glomerular cell crosstalk in a murine model of WT1 kidney disease
Exploration of the single-cell transcriptomic landscape identifies aberrant glomerular cell crosstalk in a murine model of WT1 kidney disease Open
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 i…
View article: Systemic gene therapy with thymosin β4 alleviates glomerular injury in mice
Systemic gene therapy with thymosin β4 alleviates glomerular injury in mice Open
View article: The timing of auditory sensory deficits in Norrie disease has implications for therapeutic intervention
The timing of auditory sensory deficits in Norrie disease has implications for therapeutic intervention Open
Norrie disease is caused by mutation of the NDP gene, presenting as congenital blindness followed by later onset of hearing loss. Protecting patients from hearing loss is critical for maintaining their quality of life. This study aimed to …
View article: Imaging intact human organs with local resolution of cellular structures using hierarchical phase-contrast tomography
Imaging intact human organs with local resolution of cellular structures using hierarchical phase-contrast tomography Open
View article: Systemic gene therapy with thymosin β4 alleviates glomerular injury in mice
Systemic gene therapy with thymosin β4 alleviates glomerular injury in mice Open
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…
View article: Mechanisms and cell lineages in lymphatic vascular development
Mechanisms and cell lineages in lymphatic vascular development Open
Lymphatic vessels have critical roles in both health and disease and their study is a rapidly evolving area of vascular biology. The consensus on how the first lymphatic vessels arise in the developing embryo has recently shifted. Original…
View article: The Biological Significance and Implications of Planar Cell Polarity for Nephrology
The Biological Significance and Implications of Planar Cell Polarity for Nephrology Open
The orientation of cells in two-dimensional and three-dimensional space underpins how the kidney develops and responds to disease. The process by which cells orientate themselves within the plane of a tissue is termed planar cell polarity.…
View article: Multiscale three-dimensional imaging of intact human organs down to the cellular scale using hierarchical phase-contrast tomography
Multiscale three-dimensional imaging of intact human organs down to the cellular scale using hierarchical phase-contrast tomography Open
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 un…
View article: Diverse species-specific phenotypic consequences of loss of function sorting nexin 14 mutations
Diverse species-specific phenotypic consequences of loss of function sorting nexin 14 mutations Open
View article: Beyond a Passive Conduit: Implications of Lymphatic Biology for Kidney Diseases
Beyond a Passive Conduit: Implications of Lymphatic Biology for Kidney Diseases Open
The kidney contains a network of lymphatic vessels that clear fluid, small molecules, and cells from the renal interstitium. Through modulating immune responses and via crosstalk with surrounding renal cells, lymphatic vessels have been im…
View article: Spatiotemporal dynamics and heterogeneity of renal lymphatics in mammalian development and cystic kidney disease
Spatiotemporal dynamics and heterogeneity of renal lymphatics in mammalian development and cystic kidney disease Open
Heterogeneity of lymphatic vessels during embryogenesis is critical for organ-specific lymphatic function. Little is known about lymphatics in the developing kidney, despite their established roles in pathology of the mature organ. We perf…
View article: Diverse Species-Specific Phenotypic Consequences of Loss of Function <i>Sorting Nexin 14</i> Mutations
Diverse Species-Specific Phenotypic Consequences of Loss of Function <i>Sorting Nexin 14</i> Mutations Open
Mutations in the SNX14 gene cause spinocerebellar ataxia, autosomal recessive 20 (SCAR20) in both humans and dogs. SCAR20 is understood to involve subcellular disruption to autophagy and lipid metabolism. Previously reported studies on the…