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Biology subjects

Riley, P. R.

Publications and source records attributed to Riley, P. R..

11 recordsLinked to original sources

Organ-specific fibroblast dynamics revealed via an integrated experimental-computational framework

Fibrosis is a progressive pathological process driven by dysregulated fibroblast activity and excessive extracellular matrix deposition, leading to scarring, functional decline and eventually organ failure. Although fibroblasts are key mediators of fibrotic remodelling, it remains unclear whether their behaviours are conserved across tissues or organ specific. Here, we combine experimental and computational approaches to dissect fibroblast dynamics underlying cardiac and pulmonary fibrosis. Using in vitro assays, we demonstrate that cardiac and lung fibroblasts differ in morphology, proliferation, and collagen matrix organisation, likely reflecting tissue-specific mechanical and biochemical demands. Lung fibroblasts display higher proliferative capacity and increased myofibroblast activation, forming condition-dependent collagen architectures, with fibres that are more aligned under proinflammatory and fibrotic conditions, but less so under anti-inflammatory conditions. In contrast, cardiac fibroblasts consistently generate diffuse, isotropic collagen matrices across all cytokine conditions. Integrating these data into a mechanistic computational model of fibroblast-collagen interactions, we show that fibroblast motility, rather than cell-cell interactions, dominates tissue dynamics, and that coupling between motility and local collagen density regulates matrix architecture. Simulations reveal that collagen-dependent motility and density-dependent collagen secretion prevent maladaptive matrix alignment, identifying potential mechanisms restraining fibrotic progression. Our findings uncover organ-specific fibroblast behaviours and highlight how integrating experimental and computational frameworks can illuminate the dynamic rules governing fibrosis and inform targeted antifibrotic strategies.

cell biology↗

Distinct roles of the Lyve1 lineage in heart development

Lyve1Cre is widely used to study lymphatic endothelial cells, but its activity in the embryonic heart has not been comprehensively defined. Here we show that the Lyve1 lineage contributes to multiple cardiovascular cell types, including venous endothelium of the sinus venosus forming coronary vessels, endocardial cells generating complementary coronary territories and valve structures, lymphatic endothelial cells required for cardiac lymphatic development, and tissue-resident macrophages within the embryonic myocardium. Functional perturbations demonstrated that Notch1 gain-of-function in Lyve1+ lineages disrupted vascular development, while Prox1 deletion caused severe edema, blood-filled lymphatics, and perinatal lethality. Mid-gestation mutants exhibited underdeveloped, blood-filled lymphatics despite intact blood vasculature, and by late gestation cardiac lymphatics were depleted. These findings reveal distinct cardiovascular roles of the Lyve1 lineage and establish Lyve1Cre as a versatile but non-specific tool, underscoring the need for careful interpretation when investigating heart development and regenerative processes.

developmental biology↗

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↗

Lymphatic endothelium arises directly from specialized angioblasts

The lymphatic vasculature is essential for tissue fluid homeostasis, immune cell surveillance and dietary lipid absorption, and has emerged as a key regulator of organ growth and repair1. Despite significant advances in our understanding of lymphatic function, the precise developmental origin of lymphatic endothelial cells (LECs) has remained a point of debate for over a century2-5. It is currently widely accepted that most LECs are derived from venous endothelium4,6, although other sources have been described, including mesenchymal cells3, hemogenic endothelium7 and musculoendothelial progenitors8,9. Here we show that the initial expansion of mammalian LECs is driven primarily by the in situ differentiation of specialized angioblasts and not migration from venous endothelium. Single-cell RNA sequencing and genetic lineage tracing experiments in mouse revealed a population of Etv2+Prox1+ lymphangioblasts that arise directly from paraxial mesoderm-derived progenitors. Conditional lineage labelling and morphological analyses showed that these specialized angioblasts emerge within a tight spatiotemporal window, and give rise to LECs in numerous tissues. Analysis of early LEC proliferation and migration supported these findings, suggesting that emergence of LECs from venous endothelium is limited. Collectively, our data reconcile discrepancies between previous studies and indicate that LECs form through both de novo specification from lymphangioblasts and transdifferentiation from venous endothelium.

developmental biology↗

Distinct epicardial gene regulatory programmes drive development and regeneration of the zebrafish heart

Unlike the adult mammalian heart, which has limited regenerative capacity, the zebrafish heart can fully regenerate following injury. Reactivation of cardiac developmental programmes is considered key to successfully regenerating the heart, yet the regulatory elements underlying the response triggered upon injury and during development remain elusive. Organ-wide activation of the epicardium is essential for zebrafish heart regeneration and is considered a potential regenerative source to target in the mammalian heart. Here we compared the transcriptome and epigenome of the developing and regenerating zebrafish epicardium by integrating gene expression profiles with open chromatin ATAC-seq data. By generating gene regulatory networks associated with epicardial development and regeneration, we inferred genetic programmes driving each of these processes, which were largely distinct. We identified wt1a, wt1b, and the AP-1 subunits junbb, fosab and fosb as central regulators of the developing network, whereas hif1ab, zbtb7a, tbx2b and nrf1 featured as putative central regulators of the regenerating epicardial network. By interrogating developmental gene regulatory networks that drive cell-specific transcriptional heterogeneity, we tested novel subpopulation-related epicardial enhancers in vivo. Taken together, our work revealed striking differences between the regulatory blueprint deployed during epicardial development and regeneration. These findings challenge the dogma that heart regeneration is essentially a reactivation of developmental programmes, and provide important insights into epicardial regulation that can assist in developing therapeutic approaches to enable tissue regeneration in the adult mammalian heart.

developmental biology↗

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↗

Maternal iron deficiency impacts the placental arterial network.

Placental vascular gene networks in mammals have been largely unexplored due to a lack of well validated molecular markers to identify them. This is required to study how they form in development, and how they are impacted by embryonic or maternal defects, which in-turn adversely affects the forming heart and vasculature. Such defects are known to be a consequence of maternal iron deficiency (ID), the most common nutrient deficiency world-wide. Here we employed marker analysis to characterise the arterial/arteriole and venous/venule endothelial cells (ECs) during normal placental development, and in the context of maternal ID. We reveal for the first time that placental ECs are unique compared with their embryonic counterparts. In the developing embryo, arterial ECs express Neuropilin1 (Nrp1), Delta-like ligand 4 (Dll4) and Notch1, while developing venous ECs express Neuropilin2 (Nrp2), Apj (Aplnr) and Ephrinb4 (Ephb4). However, in the E15.5 placenta, Nrp1 and Notch1 were restricted to arteries, but not continuing arteriole ECs. The arterial tree exclusively expressed Dll4. Nrp2 showed pan-EC expression at E15.5, while Ephb4 was not present at this stage. However, we found the placental venous vascular tree could be distinguished from the arterial tree by high versus low Endomucin (EMCN) and Apj (Aplnr) expression respectively. Using EMCN, we reveal that the placental arterial, but not venous, vascular tree is adversely impacted by maternal ID, with reduced area, total length and number of junctions of all vessels without affecting the EMCN high vessels. Defects to the embryonic cardiovascular system can therefore have a significant impact on blood flow delivery and expansion of the placental arterial tree.

developmental biology↗

Tissue-resident macrophages regulate lymphatic vessel growth and patterning in the developing heart

Macrophages are components of the innate immune system with key roles in tissue inflammation and repair. It is now evident that macrophages also support organogenesis, but few studies have characterized their identity, ontogeny and function during heart development. Here, we show that resident macrophages in the subepicardial compartment of the developing heart coincide with the emergence of new lymphatics and interact closely with the nascent lymphatic capillaries. Consequently, global macrophage-deficiency led to extensive vessel disruption with mutant hearts exhibiting shortened and mis-patterned lymphatics. The origin of cardiac macrophages was linked to the yolk sac and fetal liver. Moreover, Csf1r+ and Cx3cr1+ myeloid sub-lineages were found to play essential functions in the remodeling of the lymphatic endothelium. Mechanistically, macrophage hyaluronan was found to be required for lymphatic sprouting by mediating direct macrophage-lymphatic endothelial cell interactions. Together, these findings reveal insight into the role of macrophages as indispensable mediators of lymphatic growth during the development of the mammalian cardiac vasculature.Summary statement Tissue-resident macrophages are indispensable mediators of lymphatic vessel formation during heart development and function to remodel the vascular plexus.View Full Text

developmental biology↗

Runx1 promotes scar deposition and inhibits myocardial proliferation and survival during zebrafish heart regeneration

Runx1 is a transcription factor that plays a key role in determining the proliferative and differential state of multiple cell-types, during both development and adulthood. Here, we report how runx1 is specifically upregulated at the injury site during zebrafish heart regeneration, but unexpectedly, absence of runx1 results in enhanced regeneration. Using single cell sequencing, we found that the wild-type injury site consists of Runx1-positive endocardial cells and thrombocytes that induce expression of smooth muscle and collagen genes without differentiating into myofibroblasts. Both these populations are absent in runx1 mutants, resulting in a less collagenous and fibrinous scar. The reduction in fibrin in the mutant is further explained by reduced myofibroblast formation and by upregulation of components of the fibrin degradation pathway, including plasminogen receptor Annexin 2A as well as downregulation of plasminogen activator inhibitor serpine1 in myocardium and endocardium, resulting in increased levels of Plasminogen. In addition, we find enhanced myocardial proliferation as well as increased myocardial survival in the mutant. Our findings suggest that Runx1 controls the regenerative response of multiple cardiac cell-types and that targeting Runx1 is a novel therapeutic strategy to induce endogenous heart repair.

developmental biology↗

Functional heterogeneity within the developing zebrafish epicardium

The epicardium is essential during cardiac development, homeostasis and repair and yet fundamental insights into its underlying cell biology, notably epicardium formation, lineage heterogeneity and functional cross-talk with other cell types in the heart, are currently lacking. In this study, we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single-cell RNA-sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion, migration, and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease.

developmental biology↗

Re-purposing Ac/Ds transgenic system for CRISPR/dCas9 modulation of enhancers and non-coding RNAs in zebrafish

Due to its genetic amenability coupled with recent advances in genome editing, the zebrafish serves as an excellent model to examine the function of both coding and non-coding elements. Recently, the non-coding genome has gained prominence due to its critical role in development and disease. Here, we have re-purposed the Ac/Ds maize transposition system to reliably screen and efficiently characterise zebrafish enhancers, with or without germline propagation. We further utilised the system to stably express guide RNAs in microinjected embryos enabling tissue-specific CRISPR/dCas9-interference (CRISPRi) knockdown of lncRNA and enhancer activity without disrupting the underlying genetic sequence. Our study highlights the utility of Ac/Ds transposition for transient epigenome modulation of non-coding elements in zebrafish.\n\nSummary statementWe adapted the Ac/Ds transposition system, which enables continuous expression of guide RNAs for CRISPR/dCas9 perturbation, to examine the function of non-coding RNAs and enhancer elements in zebrafish.

developmental biology↗