Biology subjects

Chung, E.

Publications and source records attributed to Chung, E..

At least 19 recordsLinked to original sources

bioRxiv2026

Immune determinants of leuprolide-associated cardiovascular risk in prostate cancer

Leuprolide, a widely used androgen-deprivation therapy (ADT) for prostate cancer (PC), has been associated with increased cardiovascular events (CVE), although the underlying mechanisms remain unclear. Through integrated spatial transcriptomic analyses of murine heart and immune-stromal profiling in patient blood, we identified immune programs linked to leuprolide-associated CVE risk. Spatial analyses revealed the distinct organization of lymphoid (T+B cells) aggregates and inflammatory macrophages in the plaque following leuprolide exposure that accompanied by ventricular hypertrophy, relative to normal vasculature. Parallel profiling of circulatory soluble and cellular components in patients demonstrated CD8+T cell enriched pattern in ~44% of patients, including memory and type 1 cytotoxic subsets that linked to treatment-induced CVE, such as ventricular dysfunctions, but no contribution of adipocytokines. These translational findings highlight the stratification of leuprolide-associated CVE risk in PC patients based on circulating T cell profiling and could guide the risk mitigation with alternative ADT agents.

immunology↗

bioRxiv2026

HNF4A maintains proximal tubule identity and limits injury-associated cell states in the adult mouse kidney

Introduction: HNF4A is required for proximal tubule maturation during kidney development, but its role in maintaining proximal tubule identity in the adult kidney has not been defined. Following acute kidney injury, Hnf4a expression is rapidly suppressed in proximal tubule cells, coinciding with loss of mature epithelial features and activation of injury-associated transcriptional programs. It remains unknown whether HNF4A loss is sufficient to drive injury-associated transcriptional changes. Methods: We conditionally deleted Hnf4a in mature proximal tubules using Slc34a1Cre in mice and analyzed the consequences of Hnf4a loss in adult kidneys. To identify genes directly regulated by HNF4A, we performed proximal tubule-specific transcriptional profiling together with genome-wide mapping of HNF4A binding sites using CUT&RUN. Results: In Hnf4a mutant kidneys, HNF4A protein initially persisted in proximal tubules but was progressively lost from convoluted proximal tubule cells. Loss of Hnf4a resulted in downregulation of proximal tubule-specific transport and metabolic genes, accompanied by reactivation of developmental and injury-associated genes. CUT&RUN analysis revealed that HNF4A directly regulates genes predominantly involved in solute transport and metabolic processes. Conclusions: These findings identify HNF4A as a key regulator of proximal tubule identity and homeostasis in the adult mouse kidney. Genetic loss of Hnf4a in mature proximal tubules leads to loss of mature proximal tubule gene expression and activation of injury-associated transcriptional programs, implicating Hnf4a suppression as a potential contributor to maladaptive repair after kidney injury.

developmental biology↗

bioRxiv2026

Loss of Hnf1b in differentiated proximal tubule cells uncovers nephron segment plasticity

HNF1B is a transcription factor required for proximal tubule (PT) specification during kidney development, but whether it is also required to maintain PT identity after differentiation remains unknown. Using PT-specific genetic deletion in mice, we found that loss of Hnf1b in differentiated PT cells causes cyst formation and early postnatal lethality. PT-specific transcriptomic analysis revealed downregulation of PT-specific gene programs, including Hnf4a and PT-enriched transport and metabolic genes. Strikingly, Hnf1b-deficient PT cells ectopically activated podocyte-specific genes, including Wt1 and Nphs1, demonstrating that PT cells retain the capacity to engage alternative nephron segment programs when identity-stabilizing mechanisms are disrupted. In addition, loss of Hnf1b disrupted epithelial integrity, as evidenced by reduced epithelial adhesion gene expression and induction of mesenchymal markers. Wnt/{beta}-catenin signaling was also aberrantly activated, suggesting broader dysregulation of epithelial homeostasis. These findings establish HNF1B as a critical post-specification regulator of PT identity that sustains PT-specific transcriptional programs and actively suppresses alternative segmental identity programs.

developmental biology↗

bioRxiv2026

ToxiVerse: A Public Platform for Chemical Toxicity Data Sharing and Customizable Predictive Modeling

Chemical toxicity assessment is critical for drug development and environmental safety. Computational models have emerged as a promising alternative to animal testing and now play a significant role in efficiently evaluating new chemicals. To address the urgent need for providing user-friendly machine learning tools in computational toxicology, we developed ToxiVerse, a public web-based platform. It provides curated toxicity datasets, automatic chemical bioprofiling, and a predictive modeling interface designed for researchers who lack programming expertise. The platform comprises three integrated modules: (i) the Bioprofiler module, which provides chemical descriptors by combining chemical-bioactivity data from PubChem assay with a machine learning-based data gap-filling procedure; (ii) the Database module, which hosts around 50,000 curated unique chemicals covering diverse toxicity endpoints; and (iii) the Cheminformatics module, which allows users to upload their own datasets, use datasets from ToxiVerse, or retrieve existing data from PubChem; perform chemical curation; and automatically generate Quantitative Structure-Activity Relationship (QSAR) models to predict chemicals of interest. ToxiVerse enables researchers to carry out bioprofiling, access curated toxicity datasets, and evaluate chemical toxicity through machine learning-based modeling and prediction. The platform is supported by sample files and a detailed tutorial, and it is freely accessible at www.toxiverse.com. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/708255v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@d92764org.highwire.dtl.DTLVardef@a92f4aorg.highwire.dtl.DTLVardef@15fa39corg.highwire.dtl.DTLVardef@1ee89bc_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2026

A knock-in Six2Cre line reveals transient interstitial potential in nephron progenitors

The developmental relationship between nephron progenitors and the renal interstitium remains unresolved, in part due to limitations of existing lineage tracing tools. The widely used transgenic Six2TGC line, which is routinely employed to target the nephron lineage, exhibits mosaic recombination and altered progenitor dynamics. To overcome these shortcomings, we generate a knock-in Six2Cre mouse allele that faithfully recapitulates endogenous Six2 expression, preserves nephron endowment, and achieves near-complete, non-mosaic recombination. Side-by-side lineage tracing with Six2Cre and Six2TGC, combined with RNA velocity analysis of single-cell RNA-sequencing datasets, reveals a brief interval around embryonic day 11 during which Six2-expressing mesenchymal nephron progenitors contribute to the renal interstitium. This contribution is transient and stage-restricted. These findings reveal an early dual potential within nephron progenitors and define a precise developmental window for dissecting mechanisms that coordinate nephron-interstitium integration.

developmental biology↗

bioRxiv2025

Postmortem brain MRI reveals differential associations of subcortical and limbic volumes with cortical thinning and neuropathology patterns

Structured AbstractO_ST_ABSIntroductionC_ST_ABSThe impact of different neuropathologies on deep brain structures remains to be understood. We examine subcortical and limbic volumetry in neurodegenerative diseases involving p-tau, -synuclein and TDP-43. MethodsWe acquired neuropathological measures and brain segmentations from postmortem analysis of 132 donors with Alzheimers disease (AD), Lewy body disease (LBD), Frontotemporal Lobar Degeneration with TDP-43 (FTLD-TDP) and FTLD-Tau. ResultsLBD had the least subcortical, limbic and cortical atrophy compared to AD, FTLD-TDP and FTLD-Tau. In donors with both AD and LBD pathologies, primary LBD was associated with less atrophy than primary AD. While AD had cortico-subcortical and cortico-limbic morphometric associations, LBD had more limited parieto-occipital cortico-limbic associations. FTLD-TDP had cortico-subcortical while FTLD-Tau had cortico-subcortical and cortico-limbic associations. In AD and FTLD-Tau, hippocampal volumes correlated with p-tau burden, neuron loss and gliosis. In LBD, thalamic -synuclein severity was associated with subcortical/limbic volumes. DiscussionPostmortem neuroimaging reveals disease- and region-specific structure-pathology relationships.

neuroscience↗

bioRxiv2025

Constitutive Yap activation in distal nephron segments disrupts epithelial identity and nephron patterning

The distal nephron segments play a critical role in maintaining electrolyte balance, yet the mechanisms that preserve epithelial identity and segmental organization within this region remain poorly defined. Yes-associated protein (Yap), a key effector of Hippo signaling, is essential for kidney development, but its function in distal nephron epithelia is unknown. Using a genetic gain-of-function approach to activate Yap selectively in distal nephron segments, we found that sustained Yap activity profoundly disrupts epithelial organization and nephron patterning. Lineage tracing revealed that both distal convoluted tubule and connecting tubule cells originate from Slc12a3-expressing cells, and Yap activation in these segments led to increased proliferation, displacement of lineage-labeled cells beyond expected segment boundaries, and loss of segment-specific gene expression. These changes were accompanied by defects in apicobasal polarity and junctional integrity, consistent with epithelial plasticity. Unexpectedly, Yap activation in distal nephron segments also suppressed proximal tubule gene expression, indicating non-cell-autonomous effects on nephron differentiation. Together, these findings identify Yap as a critical regulator of epithelial identity in the distal nephron segments and reveal a previously unrecognized role for Hippo signaling in coordinating intersegmental organization during kidney development.

developmental biology↗

bioRxiv2025

Characterization of hippocampal subfields using histology-based annotated postmortem MRI: Lessons for in vivo segmentation II

High-resolution in vivo magnetic resonance imaging (MRI) of hippocampal subfields is a rapidly advancing field due to their implication in cognition, disorder, and disease. Hippocampal subfield segmentation on in vivo MRI is generally guided by postmortem reference material, which has been limited by small sample sizes that preclude comprehensive characterization of subfield border locations and their variability. Addressing this, we characterized hippocampal subfield border variability in two ultra-high-resolution postmortem MRI datasets with combined annotated histological sections, including cases with and without dementia. We examined: 1) the order of appearance and disappearance of subfields along the long axis of the hippocampus; 2) the order of appearance and disappearance of subicular subregions; 3) the medial-lateral position of subicular subregional boundaries along the hippocampal body; 4) the location of the CA3 relative to hippocampal head digitations; 5) the subfield borders in the hippocampal body relative to a volume proportion of the dark band; and 6) the association of hippocampal length and subiculum-CA1 border location with diagnosis, demographic factors, and factors related to postmortem imaging. Our findings reaffirmed that there is a consistent order of appearance and disappearance of subfields in the hippocampal head and tail, respectively. The subicular subregions exhibited a first in, last out order of appearance and disappearance, and pre/parasubiculum consistently occupied half of the subicular complex in coronal slices throughout the hippocampal body. Hippocampal head digitations were not a reliable landmark for CA3 appearance, but SRLM proportionality did offer a potentially consistent approach for estimating CA2 and CA3 subfield borders in relation to the hippocampal border. No clear relationship was found between the anatomical features and diagnosis, demographic factors, and factors related to postmortem imaging. These findings have implications for the development and harmonization of hippocampal subfield segmentation protocols and interpretation of high-resolution functional MRI studies of the human hippocampus.

neuroscience↗

bioRxiv2025

Developing an anatomically valid segmentation protocol for anterior regions of the medial temporal lobe for neurodegenerative diseases

BackgroundThe anterior portion of the medial temporal lobe (MTL) is one of the first regions targeted by pathology in sporadic Alzheimers disease (AD) and Limbic-predominant Age-related TDP-43 Encephalopathy (LATE) indicating a potential for metrics from this region to serve as imaging biomarkers. Leveraging a unique post-mortem dataset of histology and magnetic resonance imaging (MRI) scans we aimed to 1) develop an anatomically valid segmentation protocol for anterior entorhinal cortex (ERC), Brodmann Area (BA) 35, and BA36 for in vivo 3 tesla (T) MRI and 2) incorporate this protocol in an automated approach. MethodsWe included 20 cases (61-97 years old, 50% females) with and without neurodegenerative diseases (11 vs. 9 cases) to ensure generalizability of the developed protocol. Digitized MTL Nissl-stained coronal histology sections from these cases were annotated and registered to same-subject post-mortem MRI. The protocol was developed by determining the location of histological borders of the MTL cortices in relation to anatomical landmarks. Subsequently the protocol was applied to 15 cases twice, with a 2-week interval, to assess intra-rater reliability with the Dice Similarity Index (DSI). Thereafter it was implemented in our in- house Automatic Segmentation of Hippocampal Subfields (ASHS)-T1 approach and evaluated with DSIs. ResultsThe anterior histological border distances of ERC, BA35 and BA36 were evaluated with respect to various anatomical landmarks and the distance relative to the beginning of the hippocampus was chosen. To formulate segmentation rules, we examined the histological sections for the location of borders in relationship to anatomical landmarks in the coronal sections. The DSI for the anterior MTL cortices for the intra-rater reliability was 0.85-0.88 and for the ASHS-T1 against the manual segmentation was 0.62-0.65. DiscussionWe developed a reliable segmentation protocol and incorporated it in an automated approach. Given the vulnerability of the anterior MTL cortices to tau deposition in AD and LATE, the updated approach is expected to improve imaging biomarkers for these diseases.

neuroscience↗

bioRxiv2025

The thin descending limb of the loop of Henle originates from proximal tubule cells during mouse kidney development

BackgroundThe thin descending limb of the loop of Henle is crucial for urine concentration, as it facilitates passive water reabsorption. Despite its importance, little is known about how this nephron segment forms during kidney development. MethodsWe assembled a large single-cell RNA sequencing (scRNA-seq) dataset by integrating multiple datasets of non-mutant developing mouse kidneys to identify developing thin descending limb cells. To test whether those cells originate from proximal tubule cells, we generated a proximal tubule-specific Cre line, Slc34a1eGFPCre, and conducted lineage tracing. Additionally, given that the transcription factor Hnf4a directly binds to the Aqp1 gene, we examined whether the loss of Hnf4a affects Aqp1 expression in thin descending limb cells. ResultsFrom our scRNA-seq dataset, we identified a small cluster of cells distinct from both the proximal tubule and the thick ascending limb of the loop of Henle. Those cells exhibited high expression of thin descending limb marker genes, including Aqp1 and Bst1. Notably, a subset of proximal tubule cells also expressed thin descending limb marker genes, suggesting that proximal tubule cells may give rise to thin descending limb cells. Using lineage tracing with the Slc34a1eGFPCre line, we found that, at least, a subset of thin descending limb cells are descendants of proximal tubule cells. Furthermore, the loss of Hnf4a, a transcription factor essential for mature proximal tubule cell formation, disrupted proper Aqp1 expression in thin descending limb cells, providing additional evidence of a developmental link between proximal tubule cells and thin descending limb cells. ConclusionOur findings shed new light on the developmental origin of thin descending limb cells and highlight the importance of Hnf4a in regulating their formation. Key PointsO_LIReference single cell RNA-seq dataset of the developing mouse kidney was assembled and used to identify the thin descending limb of the loop of Henle. C_LIO_LILineage analysis of proximal tubules in the mouse kidney shows that proximal tubule cells give rise to the thin descending limb of the loop of Henle. C_LIO_LIDeletion of Hnf4a disrupts the expression of Aqp1 in the thin descending limb of the loop of Henle, highlighting a developmental link between proximal tubules and the loop of Henle. C_LI

developmental biology↗

bioRxiv2024

A Conserved Mechanism of Cardiac Hypertrophy Regression through FoxO1

The heart is a highly plastic organ that responds to diverse stimuli to modify form and function. The molecular mechanisms of adaptive physiological cardiac hypertrophy are well-established; however, the regulation of hypertrophy regression is poorly understood. To identify molecular features of regression, we studied Burmese pythons which experience reversible cardiac hypertrophy following large, infrequent meals. Using multi-omics screens followed by targeted analyses, we found forkhead box protein O1 (FoxO1) transcription factor signaling, and downstream autophagy activity, were downregulated during hypertrophy, but re-activated with regression. To determine whether these events were mechanistically related to regression, we established an in vitro platform of cardiomyocyte hypertrophy and regression from treatment with fed python plasma. FoxO1 inhibition prevented regression in this system, while FoxO1 activation reversed fed python plasma-induced hypertrophy in an autophagy-dependent manner. We next examined whether FoxO1 was implicated in mammalian models of reversible hypertrophy from exercise and pregnancy and found that in both cases FoxO1 was activated during regression. In these models, as in pythons, activation of FoxO1 was associated with increased expression FoxO1 target genes involved in autophagy. Taken together, our findings suggest FoxO1-dependent autophagy is a conserved mechanism for regression of physiological cardiac hypertrophy across species. HIGHLIGHTSO_LIPost-prandial cardiac remodeling in Burmese pythons is associated with dynamic regulation of FoxO1 and autophagy. C_LIO_LIRegression of fed python plasma-induced hypertrophy in mammalian cardiomyocytes is FoxO1-dependent. C_LIO_LIActivation of FoxO1-dependent autophagy is a conserved feature of physiological hypertrophy regression in mammalian models. C_LI

physiology↗

bioRxiv2023

Hedgehog signaling is required for the maintenance of mesenchymal nephron progenitors

Mesenchymal nephron progenitors (mNPs) give rise to all nephron tubules in the mammalian kidney. Since premature depletion of these cells leads to low nephron numbers, high blood pressure, and various renal diseases, it is critical that we understand how mNPs are maintained. While Fgf, Bmp, and Wnt signaling pathways are known to be required for the maintenance of these cells, it is unclear if any other signaling pathways also play roles. In this report, we explored the role of Hedgehog signaling in mNPs. We found that loss of either Shh in the collecting duct or Smo from the nephron lineage resulted in premature depletion of mNPs. Transcriptional profiling of mNPs with different Smo dosages suggested that Hedgehog signaling inhibited Notch signaling and upregulated the expression of Fox transcription factors such as Foxc1 and Foxp4. Consistent with these observations, we found that ectopic expression of Jag1 caused the premature depletion of mNPs as seen in the Smo mutant kidney. We also found that Foxc1 was capable of binding to mitotic condensed chromatin, a feature of a mitotic bookmarking factor. Our study demonstrates a previously unappreciated role of Hedgehog signaling in preventing premature depletion of mNPs by repressing Notch signaling and likely by activating the expression of Fox factors. TRANSLATIONAL STATEMENTPremature depletion of nephron progenitors results in low nephron endowment, leading to high blood pressure and various renal diseases. Sound understanding of the molecular mechanisms underlying the maintenance of nephron progenitors is required for intervention. Although defective Hedgehog signaling is known to cause Pallister-Hall syndrome, its activity in nephron progenitors has been elusive. Here we report that Hedgehog signaling plays an important role in maintaining nephron progenitors. Our findings suggest that Hedgehog signaling pathway is a potential target for enhancing nephron endowment.

developmental biology↗

bioRxiv2023

Photobiomodulation Therapy for a Novel Olfactory Dysfunction Ischemic Stroke Model

A.BackgroundIschemic stroke typically accompanies numerous disorders ranging from somatosensory dysfunction to cognitive impairments, inflicting its patients with various neurologic symptoms. Among pathologic outcomes, post-stroke olfactory dysfunction is frequently observed. Despite the well-known prevalence, therapy options for such compromised olfaction are limited, likely due to the complexity of the olfactory bulb architecture, which encompasses both the peripheral and central nervous systems. As photobiomodulation (PBM) emerged for treating stroke-associated symptoms, the effectiveness of PBM on the stroke-induced impairment of the olfactory function was explored. PurposeTo address the efficacy of PBM therapy on the olfactory bulb damage caused by ischemic stroke using both behavioral and histologic and inflammatory markers in the newly developed stroke mouse models. MethodsNovel mouse models with olfactory dysfunction were prepared using photothrombosis (PT) in the olfactory bulb on day 0. Moreover, post-PT PBM was performed daily from day 2 to day 7 by irradiating the olfactory bulb using an 808 nm laser with the fluence of 40 J/cm2 (325 mW/cm2 for 2 minutes per day). The buried food test (BFT) was used for scoring behavioral acuity in the food-deprived mice to assess the olfactory function before PT, after PT, and after PBM. Histopathological examinations and cytokine assays were performed on the mouse brains harvested on day 8. ResultsThe results from BFT were specific to the individual, with positive correlations between the baseline latency time measured before PT and alterations at the ensuing stages for both the PT and PT+PBM groups. Also in both groups, the correlation analysis showed a significant positive relationship between the early and late latency time changes independent of PBM, implicating a common recovery mechanism. In particular, the PBM treatment largely accelerated the recovery of impaired olfaction after PT with the suppression of inflammatory cytokines while enhancing both the glial and vascular factors (e.g., GFAP, IBA-1, and CD31). ConclusionsThe PBM therapy during the acute phase of ischemia improves the compromised olfactory function by modulating the microenvuronment and tissue inflammation.

neuroscience↗

bioRxiv2022

Interstitial Notch signaling regulates nephron development via the Gata3-Renin axis in the mouse kidney

Notch signaling in the renal interstitium is known to be required for the formation of mesangial cells and Ren1 (Renin)-expressing cells. However, little is known about how interstitial Notch signaling affects nephron development. We found that blocking Notch signaling in the renal interstitium in mice caused developmental arrest of proximal tubules accompanied by defective formation of mesangial cells. We examined the interstitial Pdgfrb mutant kidney which exhibits a similar mesangial cell defect and found that the Pdgfrb mutant kidney showed normal proximal tubule development, suggesting that the absence of mesangial cells was not the cause of defective proximal tubule development. Our single cell RNA-seq analysis of the interstitial Rbpj mutant kidney showed that a subset of proximal tubule genes were downregulated in the mutant kidney and that Gata3 was downregulated in the mutant interstitium during the development of Ren1-expressing cells. We found that deleting Gata3 in the interstitium caused the loss of Renin and the developmental arrest of proximal tubules, phenocopying the interstitial Notch/Rbpj mutants. Our results suggest that interstitial Notch signaling regulates the development of proximal tubules via the Gata3-Renin axis in the mouse kidney.

developmental biology↗

bioRxiv2021

Fast volumetric imaging with line-scan confocal microscopy by an electro-tunable lens

In microscopic imaging of biological tissues, particularly real-time visualization of neuronal activities, rapid acquisition of volumetric images poses a prominent challenge. Typically, two-dimensional (2D) microscopy can be devised into an imaging system with 3D capability using any varifocal lens. Despite the conceptual simplicity, such an upgrade yet requires additional, complicated device components and suffers a reduced acquisition rate, which is critical to document neuronal dynamics properly. In this study, we implemented an electro-tunable lens (ETL) in the line-scan confocal microscopy, enabling the volumetric acquisition at the rate of 20 frames per second with the maximum volume of interest of 315 x 315 x 80 m3. The axial extent of point-spread-function (PSF) was 17.6 {+/-} 1.6 m and 90.4 {+/-} 2.1 m with the ETL operating in either stationary or resonant mode, respectively, revealing significant depth elongation by the resonant mode ETL microscopy. We further demonstrated the utilities of the ETL system by volume imaging of cleared mouse brain ex vivo samples and in vivo brains. The current study foregrounds the successful application of resonant ETL for constructing a basis for a high-performance 3D line-scan confocal microscopy system, which will enhance our understanding of various dynamic biological processes.

bioengineering↗

bioRxiv2021

Quantitative blood flow estimation in vivo by optical speckle image velocimetry

Speckle based methods are popular non-invasive, label-free full-field optical techniques for imaging blood flow maps at single vessel resolution with a high temporal resolution. However, conventional speckle approach cannot provide an absolute velocity map with magnitude and direction. Here, we report a novel optical speckle image velocimetry (OSIV) technique for measuring the quantitative blood flow vector map by utilizing particle image velocimetry with speckle cross-correlations. We demonstrate that our OSIV instrument has a linearity range up to 7 mm/s, higher than conventional optical methods. Our method can measure the absolute flow vector map at up to 190 Hz without sacrificing the image size, and it eliminates the need for a high-speed camera/detector. We applied OSIV to image the blood flow in a mouse brain, and as a proof of concept, imaged the real-time dynamic changes in the cortical blood flow field during the stroke process in vivo. Our wide-field quantitative flow measurement OSIV method without the need of tracers provides a valuable tool for studying the healthy and diseased brain.

biophysics↗

bioRxiv2020

Open-top axially swept light sheet microscopy

Open-top light sheet microscopy (OT-LSM) is a specialized microscopy for the high throughput cellular imaging of large tissues including optically cleared tissues by having all the optical setup below the sample stage. Current OT-LSM systems had relatively low axial resolutions by using weakly focused light sheets to cover the imaging field of view (FOV). In this report, open-top axially swept LSM (OTAS-LSM) was developed for high-throughput cellular imaging with the improved axial resolution. OTAS-LSM swept the tightly focused excitation light sheet across the imaging FOV by using an electro tunable lens (ETL) and collected emission light at the focus of light sheet with a camera in the rolling shutter mode. OTAS-LSM was developed by using air objective lenses and a water prism for simplicity and it had on-axis optical aberration associated with the mismatch of refractive indices between air and immersion medium. The effects of optical aberration were analyzed by both simulation and experiment. The image resolutions were 1.5-1.6m, and approximately 140% of the aberration-free theoretical values. The newly developed OTAS-LSM was applied to the imaging of optically cleared mouse brain and small intestine and it could visualize neuronal networks in the single cell level. OTAS-LSM might be useful for the high-throughput cellular examination of optically cleared large tissues.

neuroscience↗

bioRxiv2020

Hnf4a-mediated regulation of proximal tubule progenitors in the mouse kidney

BackgroundHnf4a is a major regulator of renal proximal tubule (PT) development. In humans, a mutation in HNF4A is associated with Fanconi renotubular syndrome (FRTS), which is caused by defective PT functions. In mice, mosaic deletion of Hnf4a in the developing kidney causes a paucity of PT cells, leading to FRTS-like symptoms. The molecular mechanisms underlying the role of Hnf4a in PT development remain unclear. MethodsWe generated a new Hnf4a mutant mouse model employing Osr2Cre, which effectively deletes Hnf4a in developing nephrons. We characterized the mutant phenotype by immunofluorescence analysis. We performed lineage analysis to test if Cdh6-expressing cells are PT progenitors. We also performed genome-wide mapping of Hnf4a binding sites and differential gene analysis of Hnf4a mutant kidneys to identify direct target genes of Hnf4a. ResultsDeletion of Hnf4a with Osr2Cre led to the complete loss of mature PT cells, causing lethality in the Hnf4a mutant mice. We found that Cdh6high, LTLlow cells serve as PT progenitors and that they show higher proliferation than Cdh6low, LTLhigh differentiated PT cells. We also found that Hnf4a is required for PT progenitors to develop into differentiated PT cells. Our genomic analyses revealed that Hnf4a directly regulates the expression of genes involved in transmembrane transport and metabolism. ConclusionsOur findings show that Hnf4a promotes the development of PT progenitors into differentiated PT cells by regulating the expression of genes associated with reabsorption, the major function of PT cells. SignificanceProximal tubule cells are the most abundant cell type in the mammalian kidney and they perform the bulk of the renal reabsorption function. Despite their importance in kidney function, the molecular mechanisms of proximal tubule development and maturation are not well understood. Here we find that, in the developing mouse kidney, Cdh6high, LTLlow cells act as proximal tubule progenitors and that Hnf4a is required for these cells to further develop into proximal tubules. Our genomic analyses show that Hnf4a directly regulate the expression of genes required for reabsorption such as transmembrane transport genes and metabolism genes. This study advances our understanding of how kidney proximal tubule cells form during development.

developmental biology↗