Biology subjects

Yoder, B. K.

Publications and source records attributed to Yoder, B. K..

8 recordsLinked to original sources

bioRxiv2026

Unmasking Early Renal Fibrosis in Polycystic Kidney Disease Using Noninvasive Precision Molecular MRI of Collagen

Fibrotic remodeling of extracellular matrix is a central driver of autosomal dominant polycystic kidney disease (ADPKD) progression since early stages of the disease. Unfortunately, it cannot be assessed with currently available methodologies before irreversible structural and functional decline, creating a diagnostic blind spot that hinders accurate early risk stratification and management. Here, we report the development of Gd-hProCA32.Collagen, a collagen -targeted protein MRI contrast agent that enables precision molecular MRI (pMRI) of early fibrosis by directly imaging collagen type I deposition in vivo before conventional laboratory and imaging methods detect changes in kidneys and liver of Pkhd1PCK/PCK (PCK) rats and Pkd2 mutant mice. Gd-hProCA32.Collagen, used at 10-fold lower dose, outperformed the widely clinically used agent gadobutrol (Gadovist), detecting approximately 2.8-fold greater total renal cyst volume ([~]8,500 vs [~]3,000 mm3, p<0.0001) and 1.5-fold higher total cyst count ([~]245 vs [~]160, p<0.0001), with superior T1W and T2W kidney AUC (p<0.01 and p<0.001) and preferential sensitivity to small and medium cysts. Signal enhancement in kidneys and liver correlated strongly with histological collagen burden quantified by Sirius red staining, whereas Gadovist showed no meaningful correlation. Gd-hProCA32.Collagen also enabled in vivo visualization of previously undetectable changes resembling radial striations at sites of microcyst cluster-adjacent microfibrosis and sustained delayed MRI enhancement due to specific collagen binding. These results reveal a previously inaccessible subclinical fibrotic phase of cystic kidney and liver disease and establish collagen-targeted pMRI as a strategy for early noninvasive detection and spatial mapping of multi-organ extracellular matrix remodeling when conventional biomarkers remain non-discriminating. One-sentence summaryWe report a first-in-class collagen-targeted MRI contrast agent with Precision molecular MRI that noninvasively reveals a previously inaccessible subclinical fibrotic phase of polycystic kidney disease across kidney and liver, overcoming limitations of current diagnostic methodology.

molecular biology↗

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

Engineering precision zebrafish alleles of human disease

Animal models of human diseases are an essential component of understanding disease pathogenesis and serve as preclinical models for therapeutic evaluation. Recently human patient genome sequencing has defined unique patient variants that result in disease states with different phenotypes than those observed with null alleles. The UAB Center for Precision Animal Modeling (CPAM) serves to analyze patient variant pathogenicity and disease mechanisms through the generation of animal models. We have optimized a zebrafish gene editing platform to successfully generate 11 patient variants (first round: NF1 R1276Q, NF1 G484R, VMA21 G55V, SPOP D144N, SGO1 K23E, Pex10 H310D, and FKRP C318Y; second round: NF1 R681*, NF1 M992del, P53 R175H, and PKD2 L656W) and 1 research allele (p53 K120R). We used CRISPR/Cas9 guide directed cleavage along with single-stranded oligodeoxynucleotide (ssODNs) repair templates to generate these models. We evaluated multiple oligo orientations and sizes, but did not find a unified consensus orientation or size that significantly impacted efficiency, emphasizing the need to empirically evaluate multiple variations for the best homology directed repair (HDR) rate. We determined PCR amplicon Next Generation Sequencing (NGS) evaluation of HDR efficiency at the F0 embryo level is best for determining the ideal guide and oligo combination. Further NGS evaluation of DNA from progeny from F0s (germline derived), not F0 biopsy DNA, is essential to identify germline transmitting founders. Surprisingly we find that most founders exhibit a jackpot effect in the germ line but not in the somatic tissue. We found NGS superior to using ICE (Inference of CRISPR Edits) for determining HDR frequency. When applicable, allelic-specific PCR or allelic specific restriction digestion can be used to genotype mutation carrying F1 generation animals, however we demonstrated that false positives occur. Further, we successfully used high resolution melting curve analysis (HRMA) to differentiate and identify F1 animals with patient variants.

genetics↗

bioRxiv2023

Rab35 is required for embryonic development and kidney and ureter homeostasis through regulation of epithelial cell junctions

Structured AbstractO_ST_ABSBackgroundC_ST_ABSRab35 is a member of a GTPase family of endocytic trafficking proteins. Studies in cell lines have indicated that Rab35 participates in cell adhesion, polarity, cytokinesis, and primary cilia length and composition. Additionally, sea urchin Rab35 regulates actin organization and is required for gastrulation. In mice, loss of Rab35 in the CNS disrupts hippocampal development and neuronal organization. Outside of the CNS, the functions of mammalian Rab35 in vivo are unknown. MethodsWe generated and analyzed the consequences of both congenital and conditional null Rab35 mutations in mice. Using a LacZ reporter allele, we assessed Rab35 expression during development and postnatally. We assessed Rab35 loss in the kidney and ureter using histology, immunofluorescence microscopy, and western blotting. ResultsCongenital Rab35 loss of function caused embryonic lethality: homozygous mutants arrested at E7.5 with cardiac edema. Conditional loss of Rab35, either during gestation or postnatally, caused hydronephrosis. The kidney and ureter phenotype were associated with disrupted actin cytoskeletal architecture, altered Arf6 epithelial polarity, reduced adherens junctions, loss of tight junction formation, defects in EGFR expression and localization, disrupted cell differentiation, and shortened primary cilia. ConclusionRab35 is essential for mammalian development and the maintenance of kidney and ureter architecture. Loss of Rab35 leads to non-obstructive hydronephrosis, making the Rab35 mutant mouse a novel mammalian model to study mechanisms underlying this disease. Significance StatementHydronephrosis, distention of the renal calyces and pelvis, affects 1 in 100 infants. Most cases of hydronephrosis are associated with obstruction. Non-obstructive hydronephrosis is typically associated with impaired ureter development, and requires surgical intervention. Here, we describe a mouse model of non-obstructive hydronephrosis caused by mutations in Rab35. Hydronephrosis in Rab35 mutants is associated with the inability to maintain epithelial cell junctions, defects in EGFR expression, and altered urothelium and smooth muscle integrity of the ureter. The Rab35 mutant mouse is a novel model to study mechanisms and treatment strategies for non-obstructive hydronephrosis.

cell biology↗

bioRxiv2022

Prioritized polycystic kidney disease drug targets and repurposing candidates from pre-cystic and cystic mouse model gene expression reversion

Autosomal dominant polycystic kidney disease (ADPKD) is one of the most prevalent monogenic human diseases. It is mostly caused by pathogenic variants in PKD1 or PKD2 genes that encode interacting transmembrane proteins polycystin-1 (PC1) and polycystin-2 (PC2). Among many pathogenic processes described in ADPKD, those associated with cAMP signaling, inflammation, and metabolic reprogramming appear to regulate the disease manifestations. Tolvaptan, a vasopressin receptor-2 antagonist that regulates cAMP pathway, is the only FDA-approved ADPKD therapeutic. Tolvaptan reduces renal cyst growth and kidney function loss, but it is not tolerated by many patients and is associated with idiosyncratic liver toxicity. Therefore, additional therapeutic options for ADPKD treatment are needed. As drug repurposing of FDA-approved drug candidates can significantly decrease the time and cost associated with traditional drug discovery, we used the computational approach signature reversion to detect inversely related drug response gene expression signatures from the Library of Integrated Network-Based Cellular Signatures (LINCS) database and identified compounds predicted to reverse disease-associated transcriptomic signatures in three publicly available Pkd2 kidney transcriptomic data sets of mouse ADPKD models. We focused on a pre-cystic model for signature reversion, as it was less impacted by confounding secondary disease mechanisms in ADPKD, and then compared the resulting candidates target differential expression in the two cystic mouse models. We further prioritized these drug candidates based on their known mechanism of action, FDA status, targets, and by functional enrichment analysis. With this in-silico approach, we prioritized 29 unique drug targets differentially expressed in Pkd2 ADPKD cystic models and 16 prioritized drug repurposing candidates that target them, including bromocriptine and mirtazapine, which can be further tested in-vitro and in-vivo. Collectively, these indicate drug targets and repurposing candidates that may effectively treat pre-cystic as well as cystic ADPKD. O_FIG O_LINKSMALLFIG WIDTH=110 HEIGHT=200 SRC="FIGDIR/small/518863v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@18af02org.highwire.dtl.DTLVardef@89d45corg.highwire.dtl.DTLVardef@d4fffdorg.highwire.dtl.DTLVardef@1f244b3_HPS_FORMAT_FIGEXP M_FIG Graphical abstract of the study created with Biorender.com. C_FIG

genomics↗

bioRxiv2021

Evolutionarily conserved genetic interactions between nphp-4 and bbs-5 mutations exacerbate ciliopathy phenotypes

Primary cilia are sensory and signaling hubs with a protein composition that is distinct from the rest of the cell due to the barrier function of the transition zone (TZ) at the base of the cilium. Protein transport across the TZ is mediated in part by the BBSome, and mutations disrupting TZ and BBSome proteins cause human ciliopathy syndromes. Ciliopathies have phenotypic variability even among patients with identical genetic variants, suggesting a role for modifier loci. To identify potential ciliopathy modifiers, we performed a mutagenesis screen on nphp-4 mutant C. elegans and uncovered a novel allele of bbs-5. Nphp-4;bbs-5 double mutant worms have phenotypes not observed in either individual mutant strain. To test whether this genetic interaction is conserved, we also analyzed zebrafish and mice mutants. While Nphp4 mutant zebrafish appeared overtly normal, Bbs5 mutants exhibited scoliosis. When combined, Nphp4;Bbs5 double mutant zebrafish did not exhibit synergistic effects, but the lack of a phenotype in Nphp4 mutants makes interpreting these data difficult. In contrast, viable Nphp4;Bbs5 double mutant mice were not obtained and there were fewer mice than expected carrying three mutant alleles. Additionally, postnatal loss of Bbs5 in mice using a conditional allele compromised survival when combined with a Nphp4 allele. As cilia are formed in the double mutant mice, the exacerbated phenotype is likely a consequence of disrupted ciliary signaling. Collectively, these data support an evolutionarily conserved genetic interaction between Bbs5 and Nphp4 alleles that may contribute to the variability in ciliopathy phenotypes.

genetics↗

bioRxiv2021

ATXN10 is required for embryonic heart development and maintenance of epithelial cell phenotypes in the adult kidney and pancreas

Atxn10 is a gene known for its role in cytokinesis during the cell cycle and is associated with Spinocerebellar Ataxia (SCA10), a slowly progressing cerebellar syndrome caused by an intragenic pentanucleotide repeat expansion. Atxn10 is also implicated in the ciliopathy syndromes Nephronophthisis (NPHP) and Joubert Syndrome (JBTS), which are caused by disruption of cilia function leading to nephron loss, impaired renal function, and cerebellar hypoplasia. How Atxn10 disruption contributes to these disorders remains unknown. Here we generated Atxn10 congenital and conditional mutant mouse models. Our data indicate that while ATXN10 protein can be detected around the base of the cilium as well as in the cytosol, its loss does not cause overt changes in cilia formation or morphology. Congenital loss of Atxn10 results in embryonic lethality around E10.5 associated with pericardial effusion and loss of trabeculation. Similarly, tissue specific loss of ATXN10 in the developing endothelium (Tie2-Cre) and myocardium (cTnT-Cre) also results in embryonic lethality with severe cardiac malformations occurring in the latter. Using an inducible Cagg-CreER to disrupt Atxn10 systemically, we show that ATXN10 is also required for survival in adult mice. Loss of ATXN10 results in severe pancreatic and renal abnormalities leading to lethality within a few weeks post ATXN10 deletion in adult mice. Evaluation of these phenotypes further identified rapid epithelial to mesenchymal transition (EMT) in these tissues. In the pancreas, the phenotype includes signs of both acinar to ductal metaplasia and EMT with aberrant cilia formation and severe defects in glucose homeostasis related to pancreatic insufficiency or defects in feeding or nutrient intake. Collectively this study identifies ATXN10 as an essential protein for survival.

developmental biology↗

bioRxiv2020

A Bbs5 mouse model reveals pituitary cilia contributions to developmental abnormalities.

Primary cilia are critical sensory and signaling compartments present on most mammalian cell types. These specialized structures require a unique signaling protein composition relative to the rest of the cell to carry out their functions. Defects in ciliary structure and signaling result in a broad group of disorders collectively known as ciliopathies. One ciliopathy, Bardet-Biedl Syndrome (BBS; OMIM 209900), presents with diverse clinical features, many of which are attributed to defects in ciliary signaling during both embryonic development and postnatal life. For example, patients exhibit obesity, polydactyly, hypogonadism, developmental delay, and skeletal abnormalities along with sensory and cognitive deficits, but for many of these phenotypes it is uncertain which are developmental in origin. A subset of BBS proteins assembles into the BBSome complex, which is responsible for mediating transport of membrane proteins into and out of the cilium, establishing it as a sensory and signaling hub. Here we describe two new mouse models for BBS resulting from a congenital null and conditional allele of Bbs5. Bbs5 null mice develop a complex phenotype including craniofacial defects, skeletal shortening, ventriculomegaly, infertility, and pituitary anomalies. Utilizing the conditional allele, we show that the male fertility defects, ventriculomegaly, and pituitary abnormalities are only found when Bbs5 is mutated prior to P7 indicating a developmental origin. In contrast, mutation of Bbs5 results in obesity independent of the age of Bbs5 loss. Compared to other animal models of BBS, Bbs5 mutant mice exhibit pathologies that suggest a specialized role for Bbs5 in ciliary function.

developmental biology↗