Organization Of Epithelial Cells Research Articles

Canonical ligand-dependent and non-canonical ligand-independent EphA2 signaling in the eye lens of wild-type, knockout, and aging mice.

Disruption of Eph-ephrin bidirectional signaling leads to human congenital and age-related cataracts, but the mechanisms for these opacities in the eye lens remain unclear. Eph receptors bind to ephrin ligands on neighboring cells to induce canonical ligand-mediated signaling. The EphA2 receptor also signals non-canonically without ligand binding in cancerous cells, leading to epithelial-to-mesenchymal transition (EMT). We have previously shown that the receptor EphA2 and the ligand ephrin-A5 have diverse functions in maintaining lens transparency in mice. Loss of ephrin-A5 leads to anterior cataracts due to EMT. Surprisingly, both canonical and non-canonical EphA2 activation are present in normal wild-type lenses and in the ephrin-A5 knockout lenses. Canonical EphA2 signaling is localized exclusively to lens epithelial cells and does not change with age. Non-canonical EphA2 signaling is in both epithelial and fiber cells and increases significantly with age. We hypothesize that canonical ligand-dependent EphA2 signaling is required for the morphogenesis and organization of hexagonal equatorial epithelial cells while non-canonical ligand-independent EphA2 signaling is needed for complex membrane interdigitations that change during fiber cell differentiation and maturation. This is the first demonstration of non-canonical EphA2 activation in a non-cancerous tissue or cell and suggests a possible physiological function for ligand-independent EphA2 signaling.

Exploring the Therapeutic Potential of Omega-3 Fatty Acid Supplementation in Dry Eye Syndrome: An In vitro Investigation

ABSTRACT Background: Dry eye syndrome (DES) is a prevalent ocular condition characterized by insufficient tear production or excessive tear evaporation, leading to discomfort and visual disturbances. Omega-3 fatty acids have been proposed as a potential therapeutic intervention for DES due to their anti-inflammatory and lipid modulation properties. Materials and Methods: Cultured human corneal epithelial cells were exposed to various concentrations of omega-3 fatty acids, including eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), for 72 h. Cell viability was assessed using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay, while inflammatory cytokine levels (interleukin-6 (IL-6), interleukin-8 (IL-8)) and lipid profile (measured by lipid staining) were evaluated using enzyme-linked immunosorbent assay. Untreated cells served as controls for comparison. Results: Omega-3 fatty acid supplementation demonstrated a dose-dependent increase in cell viability compared to untreated cells. At optimal concentrations, EPA and DHA significantly enhanced cell viability by 30% and 35%, respectively (P < 0.05). Moreover, omega-3 fatty acid supplementation led to a significant reduction in inflammatory cytokine levels, with a 50% decrease in IL-6 and IL-8 secretion compared to untreated cells (P < 0.01). Additionally, lipid staining revealed improved lipid profile and organization in corneal epithelial cells following omega-3 fatty acid supplementation, indicative of enhanced tear film stability. Conclusion: In vitro findings suggest that omega-3 fatty acid supplementation exerts beneficial effects on cellular markers associated with DES.

Actin cytoskeleton differently regulates cell surface organization of GPI-anchored proteins in polarized epithelial cells and fibroblasts.

The spatiotemporal compartmentalization of membrane-associated glycosylphosphatidylinositol-anchored proteins (GPI-APs) on the cell surface regulates their biological activities. These GPI-APs occupy distinct cellular functions such as enzymes, receptors, and adhesion molecules, and they are implicated in several vital cellular processes. Thus, unraveling the mechanisms and regulators of their membrane organization is essential. In polarized epithelial cells, GPI-APs are enriched at the apical surface, where they form small cholesterol-independent homoclusters and larger heteroclusters accommodating multiple GPI-AP species, all confined within areas of approximately 65-70nm in diameter. Notably, GPI-AP homoclustering occurs in the Golgi apparatus through a cholesterol- and calcium-dependent mechanism that drives their apical sorting. Despite the critical role of Golgi GPI-AP clustering in their cell surface organization and the importance of cholesterol in heterocluster formation, the regulatory mechanisms governing GPI-AP surface organization, particularly in the context of epithelial polarity, remain elusive. Given that the actin cytoskeleton undergoes substantial remodeling during polarity establishment, this study explores whether the actin cytoskeleton regulates the spatiotemporal apical organization of GPI-APs in MDCK cells. Utilizing various imaging techniques (number and brightness, FRET/FLIM, and dSTORM coupled to pair correlation analysis), we demonstrate that the apical organization of GPI-APs, at different scales, does not rely on the actin cytoskeleton, unlike in fibroblastic cells. Interestingly, calcium chelation disrupts the organization of GPI-APs at the apical surface by impairing Golgi GPI-AP clustering, emphasizing the existence of an interplay among Golgi clustering, apical sorting, and surface organization in epithelial cells. In summary, our findings unveil distinct mechanisms regulating the organization of GPI-APs in cell types of different origins, plausibly allowing them to adapt to different external signals and different cellular environments in order to achieve specialized functions.

Breaking Down Barriers: Epithelial Contributors to Monogenic IBD Pathogenesis.

Monogenic causes of inflammatory bowel diseases (IBD) are increasingly being discovered. To date, much attention has been placed in those resulting from inborn errors of immunity. Therapeutic efforts have been largely focused on offering personalized immune modulation or curative bone marrow transplant for patients with IBD and underlying immune disorders. To date, less emphasis has been placed on monogenic causes of IBD that pertain to impairment of the intestinal epithelial barrier. Here, we provide a comprehensive review of monogenic causes of IBD that result in impaired intestinal epithelial barrier that are categorized into 6 important functions: (1) epithelial cell organization, (2) epithelial cell intrinsic functions, (3) epithelial cell apoptosis and necroptosis, (4) complement activation, (5) epithelial cell signaling, and (6) control of RNA degradation products. We illustrate how impairment of any of these categories can result in IBD. This work reviews the current understanding of the genes involved in maintaining the intestinal barrier, the inheritance patterns that result in dysfunction, features of IBD resulting from these disorders, and pertinent translational work in this field.

Single-cell RNA-seq analysis decodes the kidney microenvironment induced by polystyrene microplastics in mice receiving a high-fat diet

In recent years, the environmental health issue of microplastics has aroused an increasingly significant concern. Some studies suggested that exposure to polystyrene microplastics (PS-MPs) may lead to renal inflammation and oxidative stress in animals. However, little is known about the essential effects of PS-MPs with high-fat diet (HFD) on renal development and microenvironment. In this study, we provided the single-cell transcriptomic landscape of the kidney microenvironment induced by PS-MPs and HFD in mouse models by unbiased single-cell RNA sequencing (scRNA-seq). The kidney injury cell atlases in mice were evaluated after continued PS-MPs exposure, or HFD treated for 35 days. Results showed that PS-MPs plus HFD treatment aggravated the kidney injury and profibrotic microenvironment, reshaping mouse kidney cellular components. First, we found that PS-MPs plus HFD treatment acted on extracellular matrix organization of renal epithelial cells, specifically the proximal and distal convoluted tubule cells, to inhibit renal development and induce ROS-driven carcinogenesis. Second, PS-MPs plus HFD treatment induced activated PI3K-Akt, MAPK, and IL-17 signaling pathways in endothelial cells. Besides, PS-MPs plus HFD treatment markedly increased the proportions of CD8+ effector T cells and proliferating T cells. Notably, mononuclear phagocytes exhibited substantial remodeling and enriched in oxidative phosphorylation and chemical carcinogenesis pathways after PS-MPs plus HFD treatment, typified by alterations tissue-resident M2-like PF4+ macrophages. Multispectral immunofluorescence and immunohistochemistry identified PF4+ macrophages in clear cell renal cell carcinoma (ccRCC) and adjacent normal tissues, indicating that activate PF4+ macrophages might regulate the profibrotic and pro-tumorigenic microenvironment after renal injury. In conclusion, this study first systematically revealed molecular variation of renal cells and immune cells in mice kidney microenvironment induced by PS-MPs and HFD with the scRNA-seq approach, which provided a molecular basis for decoding the effects of PS-MPs on genitourinary injury and understanding their potential profibrotic and carcinogenesis in mammals.Graphical

EGFR signaling controls directionality of epithelial multilayer formation upon loss of cell polarity.

Apical-basal polarity is maintained by distinct protein complexes that reside in membrane junctions, and polarity loss in monolayered epithelial cells can lead to formation of multilayers, cell extrusion, and/or malignant overgrowth. Yet, how polarity loss cooperates with intrinsic signals to control directional invasion toward neighboring epithelial cells remains elusive. Using the Drosophila ovarian follicular epithelium as a model, we found that posterior follicle cells with loss of lethal giant larvae (lgl) or Discs large (Dlg) accumulate apically toward germline cells, whereas cells with loss of Bazooka (Baz) or atypical protein kinase C (aPKC) expand toward the basal side of wildtype neighbors. Further studies revealed that these distinct multilayering patterns in the follicular epithelium were determined by epidermal growth factor receptor (EGFR) signaling and its downstream target Pointed, a zinc-finger transcription factor. Additionally, we identified Rho kinase as a Pointed target that regulates formation of distinct multilayering patterns. These findings provide insight into how cell polarity genes and receptor tyrosine kinase signaling interact to govern epithelial cell organization and directional growth that contribute to epithelial tumor formation.

Inversin (NPHP2) and Vangl2 are required for normal zebrafish cloaca formation

Nephronophthisis (NPH), an autosomal recessive ciliopathy, results from mutations in more than 20 different genes (NPHPs). These gene products form protein complexes that regulate trafficking within the cilium, a microtubular structure that plays a crucial role in developmental processes. Several NPHPs, including NPHP2/Inversin, have been linked to extraciliary functions. In addition to defining a specific segment of primary cilia (Inversin compartment), NPHP2 participates in planar cell polarity (PCP) signaling along with Dishevelled and Vangl family members.We used the mutant zebrafish line invssa36157, containing a stop codon at amino acid 314, to characterize tissue-specific functions of zebrafish Nphp2. The invssa36157 line exhibits mild ciliopathy phenotypes and increased glomerular and cloaca cyst formation. These mutants showed enhanced susceptibility to the simultaneous depletion of the nphp1/nphp2/nphp8 module, known to be involved in the cytoskeletal organization of epithelial cells. Notably, simultaneous depletion of zebrafish nphp1 and vangl2 led to a pronounced increase in cloaca malformations in the invssa36157 mutant embryos. Time-lapse imaging showed that the pronephric cells correctly migrated towards the ectodermal cells in these embryos, but failed to form the cloaca opening. Despite these abnormal developments, cellular fate does not seem to be affected in nphp1 and vangl2 MO-depleted invssa36157 mutants, as shown by in situ hybridizations for markers of pronephros and ectodermal cell development. However, significantly reduced apoptotic activity was observed in this double knockdown model, signifying the role of apoptosis in cloacal morphogenesis. Our findings underscore the critical interplay of nphp1, nphp2/Inversin, and vangl2 in orchestrating normal cloaca formation in zebrafish, shedding light on the complex molecular mechanisms underlying ciliopathy-associated phenotypes.

Abstract A067: Cellular cartography reveals transcriptional specificity and spatial organization of diverse luminal epithelial cells in the murine prostate

Abstract Introduction Prostate cancer (PCa) is the second most frequent malignancy in men. Genetically engineered PCa mouse models (GEMMs) do not faithfully recapitulate human PCa progression. Reasons include architectural differences between the multi-lobulated mouse prostate and the human organ, choice of gene promoter (such as probasin, Pbsn) used to regulate transgene expression in GEMMs and lobular differences in susceptibility to castration. Imaging studies showed that androgen deprivation (first line therapy for metastatic PCa) by castration leads to dramatic regression of ventral prostate (VP) by up to 70%. Hence delineating cell type equivalents between the human and mouse prostates and mapping their distribution across the distinct lobes will provide fundamental knowledge to improve GEMMs, to effectively model human PCa. Methods We performed single-cell RNA sequencing (scRNA-seq) of C57BL6 and FVB mice prostates (n=10) to delineate cell type composition. We also conducted sc multi-omics (10X Multiome gene expression+ ATAC) and spatial transcriptomics (10X Visium) of prostates from mice that were unperturbed or castrated (C57BL6) to study transcriptional module (TM) alterations and spatial gene expression among the luminal epithelial (LE) cell types upon castration. Results Analyses of scRNA-seq data from 9,439 cells identified 22 different cell types from epithelial, stromal, and immune compartments and includes 9 different LE cell types that are under-studied. The lack of a standard nomenclature describing murine prostate LE cells in previous scRNA-seq studies poses a challenge for integrative analysis. We resolved this by integrating 4 independent scRNA-seq studies with our data to arrive at unified nomenclature and simultaneously validate our findings by statistical analysis. Multi-omics data analysis revealed LE cells TM differences, suggesting that LE cell diversity is developmentally triggered. Spatial transcriptomics and matched RNA in situ hybridization captured the lobe specific distribution patterns of LE cell types. For e.g., Pbsn+ LE cells were predominantly found across the AP, dorsal and lateral prostate, while Spink1+LE cells containing stemness associated genes (e.g.Tacstd2) were enriched in the VP. Analysis of the castration model revealed susceptibility differences to androgen deprivation among LE populations. Multi-omics analysis also showed a reduction in both chromatin accessibility and transcription of androgen regulated genes upon castration. Finally, cell type enrichment analysis suggests LE cells of the mouse AP and VP as equivalents of human LE and putative cell lineage signatures were enriched in PCa profiles, possibly stratifying PCa patient population. Conclusion A comprehensive mouse prostate cell atlas was built from two mouse strains. We provide a practical reference for the transcriptional and spatial profiles of each epithelial population. LE cells from AP and VP were most sensitive to castration and best represent human LE and the cell type specific genes identified here can guide future GEMM development. Citation Format: Hanbyul Cho, Yuping Zhang, Jean Tien, Jie Luo, June E. Wilke, Saravana M. Dhanasekaran, Rahul Mannan, Lisha Wang, Fengyun Su, Rui Wang, Evan T. Keller, Xuhong Cao, Sethu Pitchaya, Arul M. Chinnaiyan. Cellular cartography reveals transcriptional specificity and spatial organization of diverse luminal epithelial cells in the murine prostate [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A067.

Paracingulin recruits CAMSAP3 to tight junctions and regulates microtubule and polarized epithelial cell organization.

Paracingulin (CGNL1) is recruited to tight junctions (TJs) by ZO-1 and to adherens junctions (AJs) by PLEKHA7. PLEKHA7 has been reported to bind to the microtubule minus-end-binding protein CAMSAP3, to tether microtubules to the AJs. Here, we show that knockout (KO) of CGNL1, but not of PLEKHA7, results in the loss of junctional CAMSAP3 and its redistribution into a cytoplasmic pool both in cultured epithelial cells in vitro and mouse intestinal epithelium in vivo. In agreement, GST pulldown analyses show that CGNL1, but not PLEKHA7, interacts strongly with CAMSAP3, and the interaction is mediated by their respective coiled-coil regions. Ultrastructure expansion microscopy shows that CAMSAP3-capped microtubules are tethered to junctions by the ZO-1-associated pool of CGNL1. The KO of CGNL1 results in disorganized cytoplasmic microtubules and irregular nuclei alignment in mouse intestinal epithelial cells, altered cyst morphogenesis in cultured kidney epithelial cells, and disrupted planar apical microtubules in mammary epithelial cells. Together, these results uncover new functions of CGNL1 in recruiting CAMSAP3 to junctions and regulating microtubule cytoskeleton organization and epithelial cell architecture.

A quantitative biophysical principle to explain the 3D cellular connectivity in curved epithelia.

Epithelial cell organization and the mechanical stability of tissues are closely related. In this context, it has been recently shown that packing optimization in bended or folded epithelia is achieved by an energy minimization mechanism that leads to a complex cellular shape: the "scutoid". Here, we focus on the relationship between this shape and the connectivity between cells. We use a combination of computational, experimental, and biophysical approaches to examine how energy drivers affect the three-dimensional (3D) packing of tubular epithelia. We propose an energy-based stochastic model that explains the 3D cellular connectivity. Then, we challenge it by experimentally reducing the cell adhesion. As a result, we observed an increment in the appearance of scutoids that correlated with a decrease in the energy barrier necessary to connect with new cells. We conclude that tubular epithelia satisfy a quantitative biophysical principle that links tissue geometry and energetics with the average cellular connectivity.

Rhinovirus C replication is associated with the endoplasmic reticulum and triggers cytopathic effects in an in vitro model of human airway epithelium.

The clinical impact of rhinovirus C (RV-C) is well-documented; yet, the viral life cycle remains poorly defined. Thus, we characterized RV-C15 replication at the single-cell level and its impact on the human airway epithelium (HAE) using a physiologically-relevant in vitro model. RV-C15 replication was restricted to ciliated cells where viral RNA levels peaked at 12 hours post-infection (hpi), correlating with elevated titers in the apical compartment at 24hpi. Notably, infection was associated with a loss of polarized expression of the RV-C receptor, cadherin-related family member 3. Visualization of double-stranded RNA (dsRNA) during RV-C15 replication revealed two distinct replication complex arrangements within the cell, likely corresponding to different time points in infection. To further define RV-C15 replication sites, we analyzed the expression and colocalization of giantin, phosphatidylinositol-4-phosphate, and calnexin with dsRNA. Despite observing Golgi fragmentation by immunofluorescence during RV-C15 infection as previously reported for other RVs, a high ratio of calnexin-dsRNA colocalization implicated the endoplasmic reticulum as the primary site for RV-C15 replication in HAE. RV-C15 infection was also associated with elevated stimulator of interferon genes (STING) expression and the induction of incomplete autophagy, a mechanism used by other RVs to facilitate non-lytic release of progeny virions. Notably, genetic depletion of STING in HAE attenuated RV-C15 and -A16 (but not -B14) replication, corroborating a previously proposed proviral role for STING in some RV infections. Finally, RV-C15 infection resulted in a temporary loss in epithelial barrier integrity and the translocation of tight junction proteins while a reduction in mucociliary clearance indicated cytopathic effects on epithelial function. Together, our findings identify both shared and unique features of RV-C replication compared to related rhinoviruses and define the impact of RV-C on both epithelial cell organization and tissue functionality–aspects of infection that may contribute to pathogenesis in vivo.

Planar organization of airway epithelial cell morphology using hydrogel grooves during ciliogenesis fails to induce ciliary alignment.

Topographical cues are known to influence cell organization both in native tissues and in vitro. In the trachea, the matrix beneath the epithelial lining is composed of collagen fibres that run along the long axis of the airway. Previous studies have shown that grooved topography can induce morphological and cytoskeletal alignment in epithelial cell lines. In the present work we assessed the impact of substrate topography on the organization of primary human tracheal epithelial cells (HTECs) and human induced pluripotent stem cell (hiPSC)-derived airway progenitors and the resulting alignment of cilia after maturation of the airway cells under Air-Liquid-Interface (ALI) culture. Grooves with optimized dimensions were imprinted into collagen vitrigel membranes (CVM) to produce gel inserts for ALI culture. Grooved CVM substrates induced cell alignment in HTECs and hiPSC airway progenitors in submerged culture. Further, both cell types were able to terminally differentiate into a multi-ciliated epithelium on both flat and groove CVM substrates. When exposed to ALI conditions, HTECs lost alignment after 14 days. Meanwhile, hiPSC-derived airway progenitors maintained their alignment throughout 31 days of ALI culture. Interestingly, neither initial alignment on the grooves, nor maintained alignment on the grooves induced alignment of cilia basal bodies, an indication of the direction of ciliary beating direction in the airway cells. Planar organization of airway cells during or prior to ciliogenesis therefore does not appear to be a feasible strategy to control cilia organization and subsequent airway epithelial function and additional cues are likely necessary to produce cilia alignment.

New data on the ultrastructure of the proboscis in females of Bonellia viridis (Annelida: Bonellinae)

Although Bonellia viridis is the best studied echiurid species, many features of its anatomy and ultrastructure are still unclear. Detailed data on the organisation of the proboscis may help us to understand the echiurid biology and some aspects of their feeding behaviour. In this study, a detailed description of the proboscis epithelium of females of B. viridis is provided. According to histological specificities, four zones of proboscis stem can be distinguished: dorsal, ventral, and two lateral. These zones differ from each other in ciliation and abundance of bonellin-producing and gland cells. Each zone provides certain functions: protective for dorsal, transport of food particles for ventral, and agglutination of food particles for lateral. Ciliated cells have been described in the epithelium of the dorsal side of the proboscis stem for the first time. These cells probably supply the slow ciliary movements of the proboscis. For the first time, the organisation of epithelial cells is described: these cells contain many pinocytotic vesicles, multivesicular bodies, and phagosomes, whose presence may provide evidence of the ability of epithelial cells to consume nutrients. The absence of continuous basal lamina under the ventral epithelium is ascertained and may be explained by the activity of bonellin-producing cells, which constantly penetrate between epithelial cells. In bonellin-producing cells, voluminous perinuclear space and the contribution of rough endoplasmic reticulum into the formation of bonellin-containing granules are detected for the first time. For the first time, the neurite bundles extending from lateral nerve cords to gland cells and bonellin-producing cells are discovered.

Recent advances in understanding tight junctions

Tight junctions (TJs) are one type of cell–cell junction in epithelial cell types in vertebrates. They form a paracellular diffusion barrier and create the boundary between the apical and basolateral plasma membrane domains. The molecular constituents of TJs have mostly been identified, and now their cell biology has shifted to understanding of their formation, dynamics, and functional regulation as well as their relationship to the organization of epithelial cells. Accumulating novel findings are supported by new methods, including super-resolution microscopy, quantitative microscopy, biophysical measurements, and genome editing-mediated gene manipulation. As a conceptual breakthrough, liquid-liquid phase separation seems to be involved in the formation of TJs as super-molecular complexes. This short article summarizes seminal studies in the cell biology of TJs from the last three years.

A Quantitative Biophysical Principle to Explain the 3D Cellular Connectivity in Curved Epithelia

Epithelial cell organization and the mechanical stability of tissues are closely related. In this context, it has been recently shown that packing optimization in bended/folded epithelia is achieved by a surface tension energy minimization mechanism that leads to a novel cellular shape: the scutoid. However, further cellular and tissue level implications of this new developmental paradigm remain unknown. Here we focus on the relation of this complex cellular shape and the connectivity between cells. We address this problem using a combination of computational, experimental, and biophysical approaches in tubular epithelia. We dissect the contribution of the energetic drivers inducing the complex three-dimensional packing of these tissues. We conclude that tubular epithelia satisfy a novel principle, the “Flintstones’ law”, that links tissue geometry and energetic profiles with the average cellular connectivity in epithelia. Our study unveils a quantitative morphogenetic law with key physiological consequences.

Use of Porous Polystyrene Scaffolds to Bioengineer Human Epithelial Tissues In Vitro.

In vitro epithelial models are valuable tools for both academic and industrial laboratories to investigate tissue physiology and disease. Epithelial tissues comprise the surface epithelium, basement membrane, and underlying supporting stromal cells. There are various types of epithelial tissue and they have a diverse and intricate architecture in vivo, which cannot be successfully recapitulated using two-dimensional (2D) cell culture. Tissue engineering strategies can be applied to bioengineer the organized, multilayered, and multicellular structure of epithelial tissues in vitro. Alvetex® is a porous, polystyrene scaffold that enables fibroblasts to synthesize a complex network of endogenous, humanized extracellular matrix proteins. This creates a physiologically relevant three-dimensional (3D) subepithelial microenvironment, enriched with mechanical and chemical cues, which supports the organization and differentiation of epithelial cells. Such technology has been used to bioengineer different epithelial architectures in vitro, including the simple, columnar structure of the intestine and the stratified, squamous, and keratinized structure of skin. Epithelial tissue models provide a useful platform for fundamental and translational research, with multifaceted applications including disease modeling, drug discovery, and product development.

RNA Expression Classifiers from a Model of Breast Epithelial Cell Organization to Predict Pathological Complete Response in Triple Negative Breast Cancer

Pathological complete response (pCR) to neoadjuvant chemotherapy (NAC) is correlated with better outcomes for breast cancer, especially for triple negative breast cancer (TNBC). We developed RNA expression classifiers from a model of breast epithelial cell organization to predict which patients will achieve pCR to NAC, and which will have residual disease (RD). An exclusive collection of retrospective formalin-fixed, paraffin-embedded (FFPE) pretreatment biopsies from 222 multi-institutional breast cancer patients treated with NAC, including 90 TNBC patients, were processed using standard procedures. A novel strategy using machine learning algorithms and statistical cross-validation were used to develop predictive classifiers based on AmpliSeq differential gene expression analysis of patient samples. Two RNA expression classifiers of 18 genes and 15 genes applied sequentially to the total cohort, classified patients into three distinct classes which accurately identified 83.75% of pCR and 86.62% of RD patients in the total population, and 92.10% of pCR and 80.77% of RD patients in the TNBC subset. This new approach identified a subset of TNBC patients predicted to have RD showing significantly higher levels of Ki-67 expression and having significantly poorer survival rates than the other TNBC patients. Stratification of patients may allow identification of TNBC patients with the worst prognosis prior to NAC, allowing for personalized treatments with the potential to improve patient outcomes.

Three-dimensional data capture and analysis of intact eye lenses evidences emmetropia-associated changes in epithelial cell organization

Organ and tissue development are highly coordinated processes; lens growth and functional integration into the eye (emmetropia) is a robust example. An epithelial monolayer covers the anterior hemisphere of the lens, and its organization is the key to lens formation and its optical properties throughout all life stages. To better understand how the epithelium supports lens function, we have developed a novel whole tissue imaging system using conventional confocal light microscopy and a specialized analysis software to produce three-dimensional maps for the epithelium of intact mouse lenses. The open source software package geometrically determines the anterior pole position, the equatorial diameter, and three-dimensional coordinates for each detected cell in the epithelium. The user-friendly cell maps, which retain global lens geometry, allow us to document age-dependent changes in the C57/BL6J mouse lens cell distribution characteristics. We evidence changes in epithelial cell density and distribution in C57/BL6J mice during the establishment of emmetropia between postnatal weeks 4–6. These epithelial changes accompany a previously unknown spheroid to lentoid shape transition of the lens as detected by our analyses. When combined with key findings from previous mouse genetic and cell biological studies, we suggest a cytoskeleton-based mechanism likely underpins these observations.

Mechanical Cell-to-Cell Interactions as a Regulator of Topological Defects in Planar Cell Polarity Patterns in Epithelial Tissues

A precise structural organization of epithelial cells is needed for the proper functioning and development of different tissues. The epithelial cell packing mechanism is associated with mechanical interactions between cells that place the tissue in a state of the lowest mechanical energy. In addition, the planar cell polarity has been recognized as another important mechanism for the epithelial organization that ensures the orientational ordering of the cells. Planar cell polarity is a consequence of an asymmetric distribution of certain transmembrane proteins which is driven by specific intracellular signaling pathways. Mutations and other disruptions of these pathways were found to cause an impaired cytoarchitecture of the epithelium layer. Mutant cells with disrupted activities of signaling proteins basically represent topological defects, which can lead to dysfunctions in tissue operation. Motivated by the fact that regional variations of bond tensions were found in the vicinity of mutant cells, we implement a computational model that combines the tissue development processes following the concept of mechanical energy minimization and the intracellular polarization. Our results reveal that a decrease in mechanical interactions between normal and mutant epithelium cells represents a conceivable regulatory mechanism that diminishes the impact of topological defects caused by mutant cells.

Gut microbiota maturation during early human life induces enterocyte proliferation via microbial metabolites

BackgroundThe intestinal tract undergoes a period of cellular maturation during early life, primarily characterized by the organization of epithelial cells into specialized crypt and villus structures. These processes are in part mediated by the acquisition of microbes. Infants delivered at term typically harbor a stable, low diversity microbiota characterized by an overrepresentation of various Bacilli spp., while pre-term infants are colonized by an assortment of bacteria during the first several weeks after delivery. However, the functional effects of these changes on intestinal epithelium homeostasis and maturation remain unclear. To study these effects, human neonate feces were obtained from term and pre-term infants. Fecal 16S rDNA sequencing and global untargeted LC-MS were performed to characterize microbial composition and metabolites from each population. Murine enteral organoids (enteroids) were cultured with 0.22 μm filtered stool supernatant pooled from term or pre-term infants.ResultsTerm and pre-term microbial communities differed significantly from each other by principle components analysis (PCoA, PERMANOVA p < 0.001), with the pre-term microbiome characterized by increased OTU diversity (Wilcox test p < 0.01). Term communities were less diverse and dominated by Bacilli (81.54%). Pre-term stools had an increased abundance of vitamins, amino acid derivatives and unconjugated bile acids. Pathway analysis revealed a significant increase in multiple metabolic pathways in pre-term samples mapped to E. coli using the KEGG database related to the fermentation of various amino acids and vitamin biosynthesis. Enteroids cultured with supernatant from pre-term stools proliferated at a higher rate than those cultured with supernatant from term stools (cell viability: 207% vs. 147.7%, p < 0.01), grew larger (area: 81,189μm2 vs. 41,777μm2, p < 0.001), and bud at a higher rate (6.5 vs. 4, p < 0.01). Additionally, genes involved in stem cell proliferation were upregulated in pre-term stool treated enteroid cultures (Lgr5, Ephb2, Ascl2 Sox9) but not term stool treated enteroids.ConclusionsOur findings indicate that microbial metabolites from the more diverse gut microbiome associated with pre-term infants facilitate stem cell proliferation. Therefore, perturbations of the pre-term microbiota may impair intestinal homeostasis.