Biology subjects

O'Brien, L. L.

Publications and source records attributed to O'Brien, L. L..

7 recordsLinked to original sources

bioRxiv2025

Feature-Driven Whole-Tissue Imaging with Subcellular Resolution

Understanding how subcellular structures and events shape tissue-wide phenomena remains a central challenge in biology. We present Multiscale Cleared Tissue Axially Swept Light-Sheet Microscopy (MCT-ASLM), a platform combining cm-scale imaging with targeted high-resolution interrogation of intact tissues in human-guided or autonomous modes. Capable of capturing fields of view up to 21 mm at micron-scale resolution, MCT-ASLM can seamlessly transition to submicron (~300 nm) isotropic resolution for targeted imaging. This versatility enables comprehensive studies of hierarchical organization and spatially complex processes, including mapping neuronal circuits in rat brains, visualizing glomerular innervation in mouse kidneys, and examining metastatic tumor microenvironments. By bridging subcellular to tissue-level scales, MCT-ASLM offers a powerful method for unraveling how local events contribute to global biological phenomena.

biophysics↗

bioRxiv2024

The tricellular junctional protein Ildr2 helps maintain glomerular podocyte architecture

Podocytes are highly specialized epithelial cells of the glomerular filtration barrier essential for maintaining proper kidney function. Their intricate cellular projections, called foot processes, wrap around the capillary endothelium, interdigitate, and connect to one another via slit diaphragm intercellular junctions to form a sieve-like barrier. Compromise to this unique podocyte architecture can lead to altered glomerular function and eventual kidney disease. We previously identified Immunoglobulin-like domain containing receptor 2 (Ildr2) as a component of the podocyte foot process through proteomic analyses. Ildr2 is a tricellular tight junction constituent and localizes to distinct puncta in podocytes that likely represent these specialized junctions. However, the significance of tricellular tight junctions and Ildr2 to podocyte integrity is unknown. To this end, we generated a conditional knockout mouse with podocyte-specific deletion of Ildr2 (Podocin-Cretg/+;Ildr2fl/flor Ildr2PodKO). Kidneys from Ildr2PodKO adult animals show disruptions to podocyte foot process architecture including effacement and the unique formation of electron dense strands connecting subsets of processes. Additionally, the glomerular basement membrane was significantly thicker in conditional knockouts and histological analyses revealed glomerular collagen and glycoprotein accumulation. Surprisingly, Ildr2PodKO animals displayed no significant albuminuria. When Ildr2PodKO mice were challenged with a stress to kidney function, immunohistochemistry revealed podocyte loss from a subset of glomeruli with concomitant detection of podocytes in urine, although function was still preserved. Collectively, our data provide novel insights into the function of Ildr2 and suggest tricellular junctions help preserve podocyte architecture but are likely not necessary to maintain proper filtration in no or low stress physiological states.

physiology↗

bioRxiv2023

Comprehensive mapping of sensory and sympathetic innervation of the developing kidney

The kidney functions as a finely tuned sensor to balance body fluid composition and filter out waste through complex coordinated mechanisms. This versatility requires tight neural control, with innervating efferent nerves playing a crucial role in regulating blood flow, glomerular filtration rate, water and sodium reabsorption, and renin release. In turn sensory afferents provide feedback to the central nervous system for the modulation of cardiovascular function. However, the cells targeted by sensory afferents and the physiological sensing mechanisms remain poorly characterized. Moreover, how the kidney is innervated during development to establish these functions remains elusive. Here, we utilized a combination of light-sheet and confocal microscopy to generate anatomical maps of kidney sensory and sympathetic nerves throughout development and resolve the establishment of functional crosstalk. Our analyses revealed that kidney innervation initiates at embryonic day (E)13.5 as the nerves associate with vascular smooth muscle cells and follow arterial differentiation. By E17.5 axonal projections associate with kidney structures such as glomeruli and tubules and the network continues to expand postnatally. These nerves are synapsin I-positive, highlighting ongoing axonogenesis and the potential for functional crosstalk. We show that sensory and sympathetic nerves innervate the kidney concomitantly and classify the sensory fibers as calcitonin gene related peptide (CGRP)+, substance P+, TRPV1+, and PIEZO2+, establishing the presence of PIEZO2 mechanosensory fibers in the kidney. Using retrograde tracing, we identified the primary dorsal root ganglia, T10-L2, from which PIEZO2+ sensory afferents project to the kidney. Taken together our findings elucidate the temporality of kidney innervation and resolve the identity of kidney sympathetic and sensory nerves.

developmental biology↗

bioRxiv2023

Netrin-1 directs vascular patterning and maturity in the developing kidney

Blood filtering by the kidney requires the establishment of an intricate vascular system that works to support body fluid and organ homeostasis. Despite these critical roles, little is known about how vascular architecture is established during kidney development. More specifically, how signals from the kidney influence vessel maturity and patterning remains poorly understood. Netrin-1 (Ntn1) is a secreted ligand critical for vessel and neuronal guidance. Here, we demonstrate that Ntn1 is expressed by stromal progenitors in the developing kidney, and conditional deletion of Ntn1 from Foxd1+ stromal progenitors (Foxd1GC/+;Ntn1fl/fl) results in hypoplastic kidneys that display extended nephrogenesis. Despite expression of the netrin-1 receptor Unc5c in the adjacent nephron progenitor niche, Unc5c knockout kidneys develop normally. The netrin-1 receptor Unc5b is expressed by embryonic kidney endothelium and therefore we interrogated the vascular networks of Foxd1GC/+;Ntn1fl/fl kidneys. Wholemount, 3D analyses revealed the loss of a predictable vascular pattern in mutant kidneys. As vascular patterning has been linked to vessel maturity, we investigated arterialization in these mutants. Quantification of the CD31+ endothelium at E15.5 revealed no differences in metrics such as the number of branches or branch points, whereas the arterial vascular smooth muscle metrics were significantly reduced at both E15.5 and P0. In support of these results, whole kidney RNA-seq showed upregulation of angiogenic programs and downregulation of muscle-related programs which included smooth muscle-associated genes. Together, our findings highlight the significance of netrin-1 to proper vascularization and kidney development.

developmental biology↗

bioRxiv2022

Mapping of the podocin proximity-dependent proteome reveals novels components of the kidney podocyte foot process

The unique architecture of glomerular podocytes is integral to kidney filtration. Interdigitating foot processes extend from the podocyte cell body, wrap around fenestrated capillaries, and form specialized junctional complexes termed slit diaphragms to create a molecular sieve. However, the full complement of proteins which maintain foot process integrity, and how this localized proteome changes with disease, remains to be elucidated. Proximity-dependent biotin identification (BioID) enables the identification of spatially localized proteomes. To this end, we developed a novel in vivo BioID knock-in mouse model. We utilized the slit diaphragm protein podocin (Nphs2) to create a podocin-BioID fusion. Podocin-BioID localizes to the slit diaphragm and biotin injection leads to podocyte-specific protein biotinylation. We isolated the biotinylated proteins and performed mass spectrometry to identify proximal interactors. Gene ontology analysis of 54 proteins specifically enriched in our podocin-BioID sample revealed cell junctions, actin binding, and cytoskeleton organization as top terms. Known foot process components were identified and we further uncovered two novel proteins: the tricellular junctional protein Ildr2 and the CDC42 and N-WASP interactor Fnbp1l. We confirmed Ildr2 and Fnbp1l are expressed by podocytes and partially colocalize with podocin. Finally, we investigated how this proteome changes with age and uncovered a significant increase in Ildr2. This was confirmed by immunofluorescence on human kidney samples and suggests altered junctional composition may preserve podocyte integrity. Together, these assays have led to new insights into podocyte biology and supports the efficacy of utilizing BioID in vivo to interrogate spatially localized proteomes in health, aging, and disease.

developmental biology↗

bioRxiv2022

Podocyte lineage marker expression is preserved across Wilms tumor subtypes and enhanced in tumors harboring the SIX1/2-Q177R mutation

Wilms tumors present as an amalgam of varying proportions of three tissues normally located within the developing kidney, one being the multipotent nephron progenitor population. While incomplete differentiation of the nephron progenitors is widely-considered the underlying cause of tumor formation, where this barrier occurs along the differentiation trajectory and how this might promote therapeutic resistance in high-risk blastemal-predominant tumors is unclear. Comprehensive integrated analysis of genomic datasets from normal human fetal kidney and high-risk Wilms tumors has revealed conserved expression of genes indicative of podocyte lineage differentiation in tumors of all subtypes. Comparatively upregulated expression of several of these markers, including the non-canonical WNT ligand WNT5A, was identified in tumors with the relapse-associated mutation SIX1/2 p.Q177R. These findings highlight the shared progression of cellular differentiation towards the podocyte lineage within Wilms tumors and enhancement of this differentiation program through promotion of non-canonical WNT/planar cell polarity signaling in association with SIX1/2 p.Q177R.

cancer biology↗

bioRxiv2021

Ferroptotic stress promotes the accumulation of pro-inflammatory proximal tubular cells in maladaptive renal repair

Overwhelming lipid peroxidation induces ferroptotic stress and ferroptosis, a non-apoptotic form of regulated cell death that has been implicated in maladaptive renal repair in mice and humans. Using single-cell transcriptomic and mouse genetic approaches, we show that proximal tubular (PT) cells develop a molecularly distinct, pro-inflammatory state following injury. While these inflammatory PT cells transiently appear after mild injury and return to their original state without inducing fibrosis, they accumulate and contribute to persistent inflammation after severe injury. This transient inflammatory PT state significantly downregulates glutathione metabolism genes, making them vulnerable to ferroptotic stress. Genetic induction of high ferroptotic stress in these cells after mild injury leads to the accumulation of the inflammatory PT cells, enhancing inflammation and fibrosis. Our study broadens the roles of ferroptotic stress from being a trigger of regulated cell death to include the promotion and accumulation of proinflammatory cells that underlie maladaptive repair.

cell biology↗