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Ramarapu, R.

Publications and source records attributed to Ramarapu, R..

8 recordsLinked to original sources

Quantitative imaging of corneal endothelial development reveals dynamic but resilient monolayer

The formation of functional corneal endothelial cells during development requires tight coordination between tissue-scale growth and cell-scale organization, yet how these processes are integrated in three dimensions remains poorly understood. Here, we combine high-resolution confocal imaging with quantitative analysis to reconstruct the morphogenesis of the chick corneal endothelium across embryonic development. Using a pipeline integrating 3D nuclear segmentation, Voronoi-based topological mapping, and spatial statistics, we link macroscopic globe expansion to single-cell geometry and lattice organization. We identify a multiphasic relationship between tissue growth and cell density, driven by temporal decoupling of organ expansion and proliferation. During early development, rapid globe expansion induces cellular stretching and spatial heterogeneity, followed by a phase of density accumulation and geometric refinement. Despite these dynamic conditions, the endothelial sheet maintains a robust monolayer architecture with minimal z-axis stratification. Quantitative topological analysis reveals that hexagonal packing is preserved from early stages and progressively refined through reduction of area variability and spatial clustering. Nearest-neighbor and Clark-Evans analyses demonstrate a transition from localized clustering to a more uniform spatial distribution, consistent with increasing packing regularity. Transient out-of-plane deviations coincide with key mechanical transitions, suggesting a role for 3D remodeling in accommodating mechanical stress. Concomitantly, junctional and cytoskeletal organization undergo progressive maturation. N-cadherin is established early at cell-cell interfaces, while Zonula Occludens-1 (ZO-1) transitions from diffuse localization to apically enriched tight junctions aligned with cortical actin. In parallel, microtubule organization becomes increasingly polarized to the apical domain, coinciding with the emergence of primary cilia. Together, these changes reflect coordinated establishment of epithelial polarity, barrier function, and mechanical stability. Overall, our study provides a multiscale, imaging-driven framework for understanding how epithelial tissues achieve and maintain geometric order under mechanical strain, establishing the corneal endothelium as an exemplar for linking developmental mechanics, 3D architecture, and epithelial topology. Summary StatementUsing 3D imaging and quantitative analysis, this work reveals how corneal endothelial cells stay organized and form a regular pattern during growth, despite ongoing changes in tissue size and shape.

developmental biology↗

A spatial and temporal atlas of tubulin isotype expression during neural crest EMT

Epithelial-to-mesenchymal transitions (EMT) require extensive cytoskeletal remodeling to enable changes in cell polarity, adhesion, and migration. Although transcriptional programs controlling EMT are well characterized, how microtubule composition is developmentally regulated during cell state transitions remains poorly understood. Here we establish a spatially resolved resource delineating the expression of - and {beta}-tubulin isotypes during neural crest (NC) EMT and tissue differentiation in the chick embryo. Integration of publicly available single-cell RNA sequencing datasets reveals diverse patterns of tubulin gene expression, ranging from broadly expressed isotypes (TUBA1A, TUBA1B) to more cell-type-restricted transcripts (TUBAL3, TUBB4B). Several tubulin genes, including TUBB3, TUBA3E, and TUBG1, are enriched within NC and NC-associated cell types. Using fluorescent in situ hybridization chain reaction (HCR) to spatiotemporally characterize transcripts encoding selected tubulin isotypes, we validate these patterns and map their expression across developmental stages. These transcript patterns provide a map of tubulin gene expression, but further studies are needed to determine how they relate to microtubule composition. We further identify expression of the microtubule motor genes KIF11 and DYNC1LI1, revealing overlapping expression patterns between tubulin and motor-associated genes during EMT. Together, these data define a cell state-resolved atlas of tubulin gene expression during vertebrate EMT. SIGNIFICANCE STATEMENTThis study identifies tissue-and cell state-associated expression patterns of genes encoding tubulin isotypes and microtubule motors during NC EMT, providing a resource and spatiotemporal expression map for future work investigating how tubulin expression patterns may be linked to cytoskeletal remodeling and cell migration.

developmental biology↗

A molecular and spatial resource defining tubulin isotype organization during corneal development

Microtubules are essential components of the cytoskeleton that support epithelial organization, polarity, and tissue morphogenesis. They are composed of - and {beta}-tubulin heterodimers, each encoded by distinct genes that generate closely related but functionally distinct isotypes. Although several tubulin isotypes have been implicated in ocular development and disease, how isotype diversity is organized during corneal morphogenesis remains poorly defined. Herein, we use the developing chick embryo as a model system to investigate the conservation and spatiotemporal localization of tubulin isotypes during corneal development. Through comparative amino acid sequence analysis, we show that chick and human - and {beta}-tubulin isotypes are highly conserved at structural and catalytic domains, with divergence concentrated in C-terminal regions associated with post-translational modifications. To relate these molecular features to tissue-level organization, we performed a longitudinal immunohistochemical analysis of five tubulin isotypes across key stages of corneal development. We identify distinct and dynamic patterns of isotype enrichment along apico-basal and central-peripheral axes within the cornea, as well as isotype-specific redistribution during epithelial maturation and corneal endothelial differentiation. Notably, TUBA5/TUBA4A exhibits tightly regulated localization, including enrichment at the leading edge of migratory corneal stromal progenitor cells and within the maturing corneal endothelium. Together, these data establish the chick embryo as a conserved and tractable model for studying tubulin isotype diversity in the cornea, and more broadly across other tissues, and to provide a developmental resource linking tubulin sequence identity to spatially defined microtubule organization during epithelial morphogenesis. SUMMARY STATEMENTThis study defines when and where distinct tubulin proteins are deployed during corneal development, providing a resource for understanding cytoskeletal organization in the developing eye.

developmental biology↗

TAZ (Wwtr1) deficiency leads to ER stress and mitochondrial dysfunction in a mouse model of Fuchs' endothelial corneal dystrophy

Fuchs endothelial corneal dystrophy (FECD) impacts over 300 million individuals worldwide with corneal transplantation as the primary treatment. There is a dire need to establish non-surgical alternatives which are dependent on mouse models. Transcriptional co-activator with PDZ-binding motif (TAZ, encoded by Wwtr1) is a mechanotransducer implicated in maintaining homeostasis of corneal endothelial cells (CEnC). Wwtr1-/- (TAZ KO) mice serve as an animal model for late-onset FECD. We combined single-cell transcriptomics, transmission electron microscopy, and immunofluorescence staining to elucidate the mechanisms driving pathogenesis in young (2-month-old) and geriatric (11-month-old) mice. A progressive stress response was observed in TAZ KOs defined by endoplasmic reticulum (ER) stress, mitochondrial structural and functional abnormalities, and impaired Na+/K+ ATPase localization. These changes were accompanied by an altered expression of genes involved in extracellular matrix (ECM) organization, oxidative phosphorylation, macroautophagy and response to oxidative stress. Additionally, we noted age-related differences in cellular response with young TAZ KO CEnCs upregulating macroautophagy and downregulating ECM organization while geriatric TAZ KO CEnCs downregulated macroautophagy, and ECM organization. Both TAZ KO groups downregulated response to oxidative stress and cell-substrate adhesion. Together, these findings establish a mechanistic link between disrupted mechanotransduction and organelle stress in CEnC degeneration, further elaborating on potential mechanisms driving FECD pathogenesis. This positions TAZ KO mice as a translational platform for evaluating non-surgical therapeutic strategies targeting FECD. Significance statementFuchs endothelial corneal dystrophy (FECD) is a common, age-related cause of vision loss involving a depletion of corneal endothelial cells (CEnC) that necessitates corneal transplantation. Understanding why corneal endothelial cells progressively fail in this disease is essential for developing non-surgical therapies. Using transcriptomics, electron microscopy and immunofluorescence staining, we demonstrate that loss of the mechanotransducer TAZ disrupts cellular homeostasis by inducing endoplasmic reticulum stress, mitochondrial dysfunction and improper extracellular matrix and functional protein organization in CEnCs. By linking altered mechanotransduction to organelle stress and endothelial cell loss, these findings provide insight into fundamental disease mechanisms and identify pathways that may be targeted to preserve corneal endothelial function in FECD.

pathology↗

Characterization of immunosenescent alveolar macrophages in rhesus macaques

As the global population ages, understanding the mechanisms underlying age-related diseases becomes increasingly important. Inflammaging, a state of chronic inflammation and immune dysregulation, is a key feature of aging. Macrophages, as master regulators of inflammation, are critical to this process. However, the effects of natural aging on alveolar macrophages (AMs) in the lungs remain poorly understood. In this study, we evaluated AM biology in older compared with young rhesus macaques. We compared cytokine profiles in plasma and bronchoalveolar lavage (BAL) fluid between young and aged macaques and performed single-cell RNA sequencing (scRNA-seq) to characterize age-related transcriptional and functional changes in AMs. Compared to young animals, AMs from aged animals exhibited similar cytokine inflammaging profile observed in the plasma of elderly humans. However, the general decrease of chemokine levels in BAL fluid relative to plasma suggest BAL may not reflect AM status in the lung tissues of rhesus macaques. scRNA-seq data corroborated plasma inflammaging findings, revealing increased inflammatory cytokine responses in AMs from older macaques. The consistent elevation of macrophage migration inhibitory factor (MIF) across plasma, AMs, and BAL fluid marks it as a promising biomarker and potential therapeutic target for age-associated inflammation. scRNA-seq further identified genes and pathways linked to macrophage senescence and turnover, suggesting potential targets for therapeutic intervention. Overall, our findings highlight the essential role of tissue-resident macrophages in pulmonary aging and underscores the need to further investigate their role in age-associated lung disease.

immunology↗

NSAID-mediated cyclooxygenase inhibition disrupts ectodermal derivative formation in axolotl embryos

Embryonic exposures to non-steroidal anti-inflammatory drugs (NSAIDs) have been linked to preterm birth, neural tube closure defects, abnormal enteric innervation, and craniofacial malformations, potentially due to disrupted neural tube or neural crest (NC) cell development. Naproxen (NPX), a common non-steroidal anti-inflammatory drug (NSAID) used to relieve pain and inflammation, exerts its effects through non-selective cyclooxygenase (COX) inhibition. Our lab has identified that the cyclooxygenase (COX-1 and COX-2) isoenzymes are expressed during the early stages of vertebrate embryonic development, and that global inhibition of COX-1 and COX-2 function disrupts NC cell migration and differentiation in Ambystoma mexicanum (axolotl) embryos. NC cells differentiate into various adult tissues including craniofacial cartilage, bone, and neurons in the peripheral and enteric nervous systems. To investigate the specific phenotypic and molecular effects of NPX exposure on NC development and differentiation, and to identify molecular links between COX inhibition and NC derivative anomalies, we exposed late neurula and early tailbud stage axolotl embryos to various concentrations of NPX and performed immunohistochemistry (IHC) for markers of migratory and differentiating NC cells. Our results reveal that NPX exposure impairs the migration of SOX9+ NC cells, leading to abnormal development of craniofacial cartilage structures, including Meckels cartilage in the jaw. NPX exposure also alters the expression of markers associated with peripheral and central nervous system (PNS and CNS) development, suggesting concurrent neurodevelopmental changes.

developmental biology↗

Spatiotemporal Characterization of Cyclooxygenase Pathway Enzymes During Vertebrate Embryonic Development

Vertebrate development is regulated by several complex well-characterized morphogen signaling pathways, transcription factors, and structural proteins, but less is known about the enzymatic pathways that regulate early development. We have identified that factors from the inflammation-mediating cyclooxygenase (COX) signaling pathway are expressed at early stages of development in avian embryos. Using Gallus gallus (chicken) as a research model, we characterized the spatiotemporal expression of a subset of genes and proteins in the COX pathway during early neural development stages. Specifically, here we show expression patterns of COX1, COX2, and microsomal prostaglandin E synthase-2 (mPGES-2) as well as the genes encoding these enzymes. Unique expression patterns of individual players within the COX pathway suggest that they may play non-canonical/non-traditional roles in the embryo compared to their roles in the adult. Future work should examine the function of the COX pathway in tissue specification and morphogenesis and determine if these expression patterns are conserved across species. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/606390v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@109b55aorg.highwire.dtl.DTLVardef@6160a9org.highwire.dtl.DTLVardef@1112bc2org.highwire.dtl.DTLVardef@4fcf20_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract.C_FLOATNO Spatiotemporal characterization of cyclooxygenase pathway enzymes during vertebrate embryonic development. C_FIG

developmental biology↗

Single cell RNA-sequencing of feline peripheral immune cells with V(D)J repertoire and cross species analysis of T lymphocytes

IntroductionThe domestic cat (Felis catus) is a valued companion animal and a model for virally induced cancers and immunodeficiencies. However, species-specific limitations such as a scarcity of immune cell markers constrain our ability to resolve immune cell subsets at sufficient detail. The goal of this study was to characterize circulating feline T cells and other leukocytes based on their transcriptomic landscape and T-cell receptor repertoire using single cell RNA-sequencing. MethodsPeripheral blood from 4 healthy cats was enriched for T cells by flow cytometry cell sorting using a mouse anti-feline CD5 monoclonal antibody. Libraries for whole transcriptome, alpha/beta T cell receptor transcripts and gamma/delta T cell receptor transcripts were constructed using the 10x Genomics Chromium Next GEM Single Cell 5 reagent kit and the Chromium Single Cell V(D)J Enrichment Kit with custom reverse primers for the feline orthologs. ResultsUnsupervised clustering of whole transcriptome data revealed 7 major cell populations - T cells, neutrophils, monocytic cells, B cells, plasmacytoid dendritic cells, mast cells and platelets. Sub cluster analysis of T cells resolved naive (CD4+ and CD8+), CD4+ effector T cells, CD8+ cytotoxic T cells and gamma/delta T cells. Cross species analysis revealed a high conservation of T cell subsets along an effector gradient with equitable representation of veterinary species (horse, dog, pig) and humans with the cat. Our V(D)J repertoire analysis demonstrated a skewed T-cell receptor alpha gene usage and a restricted T-cell receptor gamma junctional length in CD8+ cytotoxic T cells compared to other alpha/beta T cell subsets. Among myeloid cells, we resolved three clusters of classical monocytes with polarization into pro- and anti-inflammatory phenotypes in addition to a cluster of conventional dendritic cells. Lastly, our neutrophil sub clustering revealed a larger mature neutrophil cluster and a smaller exhausted/activated cluster. DiscussionOur study is the first to characterize subsets of circulating T cells utilizing an integrative approach of single cell RNA-sequencing, V(D)J repertoire analysis and cross species analysis. In addition, we characterize the transcriptome of several myeloid cell subsets and demonstrate immune cell relatedness across different species.

immunology↗