Modeling epithelial homeostasis and perturbation in three-dimensional human esophageal organoids.

Background: Esophageal organoids from a variety of pathologies including cancer are grown in Advanced Dulbecco's Modified Eagle Medium-Nutrient Mixture F12 (hereafter ADF). However, the currently available ADF-based formulations are suboptimal for normal human esophageal organoids, limiting the ability to compare normal esophageal organoids with those representing a given disease state. Methods: We have utilized immortalized normal human esophageal epithelial cell (keratinocyte) lines EPC1 and EPC2 and endoscopic normal esophageal biopsies to generate three-dimensional (3D) organoids. To optimize ADF-based medium, we evaluated the requirement of exogenous epidermal growth factor (EGF) and inhibition of transforming growth factor-(TGF)-ß receptor-mediated signaling, both key regulators of proliferation of human esophageal keratinocytes. We have modeled human esophageal epithelial pathology by stimulating esophageal 3D organoids with interleukin (IL)-13, an inflammatory cytokine, or UAB30, a novel pharmacological activator of retinoic acid signaling. Results: The formation of normal human esophageal 3D organoids was limited by excessive EGF and intrinsic TGFß receptor-mediated signaling. In optimized HOME0, normal human esophageal organoid formation was improved, whereas IL-13 and UAB30 induced epithelial changes reminiscent of basal cell hyperplasia, a common histopathologic feature in broad esophageal disease conditions including eosinophilic esophagitis. Conclusions: HOME0 allows modeling of the homeostatic differentiation gradient and perturbation of the human esophageal epithelium while permitting a comparison of organoids from mice and other organs grown in ADF-based media.

Tumor niche network-defined subtypes predict immunotherapy response of esophageal squamous cell cancer.

Despite the promising outcomes of immune checkpoint inhibitors (ICIs), resistance to ICI presents a new challenge. Therefore, selecting patients for specific ICI applications is crucial for maximizing therapeutic efficacy. Herein, we curated 69 human esophageal squamous cell cancer (ESCC) patients' tumor microenvironment (TME) single-cell transcriptomic datasets to subtype ESCC. Integrative analyses of the cellular network and transcriptional signatures of T cells and myeloid cells define distinct ESCC subtypes characterized by T cell exhaustion, and interleukin (IL) and interferon (IFN) signaling. Furthermore, this approach classifies ESCC patients into ICI responders and non-responders, as validated by whole tumor transcriptomes and liquid biopsy-based single-cell transcriptomes of anti-PD-1 ICI responders and non-responders. Our study stratifies ESCC patients based on TME transcriptional network, providing novel insights into tumor niche remodeling and potentially predicting ICI responses in ESCC patients.

Epithelial UNC-23 limits mechanical stress to maintain glia-neuron architecture in C. elegans.

For an organ to maintain correct architecture and function, its diverse cellular components must coordinate their size and shape. Although cell-intrinsic mechanisms driving homotypic cell-cell coordination are known, it is unclear how cell shape is regulated across heterotypic cells. We find that epithelial cells maintain the shape of neighboring sense-organ glia-neuron units in adult Caenorhabditis elegans (C. elegans). Hsp co-chaperone UNC-23/BAG2 prevents epithelial cell shape from deforming, and its loss causes head epithelia to stretch aberrantly during animal movement. In the sense-organ glia, amphid sheath (AMsh), this causes progressive fibroblast growth factor receptor (FGFR)-dependent disruption of the glial apical cytoskeleton. Resultant glial cell shape alteration causes concomitant shape change in glia-associated neuron endings. Epithelial UNC-23 maintenance of glia-neuron shape is specific both spatially, within a defined anatomical zone, and temporally, in a developmentally critical period. As all molecular components uncovered are broadly conserved across central and peripheral nervous systems, we posit that epithelia may similarly regulate glia-neuron architecture cross-species.

Experimental Modeling of Host-Bacterial Interactions in Head and Neck Squamous Cell Carcinoma.

The microscopic species colonizing the human body, collectively referred to as the microbiome, play a crucial role in the maintenance of tissue homeostasis, immunity, and the development of disease. There is evidence to suggest associations between alterations in the microbiome and the development of head and neck squamous cell carcinomas (HNSCC). The use of two-dimensional (2D) modeling systems has made significant strides in uncovering the role of microbes in carcinogenesis; however, direct mechanistic links remain in their infancy. Patient-derived three-dimensional (3D) HNSCC organoid and organotypic models have recently been described. Compared to 2D models, 3D organoid culture systems effectively capture the genetic and epigenetic features of parent tissue in a patient-specific manner and may offer a more nuanced understanding of the role of host-microbe responses in carcinogenesis. This review provides a topical literature review assessing the current state of the field investigating the role of the microbiome in HNSCC; including in vivo and in vitro modeling methods that may be used to characterize microbiome-epithelial interactions.

When microplastics are not plastic: Chemical characterization of environmental microfibers using stimulated Raman microspectroscopy.

The abundance of anthropogenic debris dispersed in the environment is exponentially growing, raising concerns about marine life and human exposure to microplastics. Microfibers are the most abundant microplastic type in the environment. However, recent research suggests that most microfibers dispersed in the environment are not made of synthetic polymers. In this work, we systematically tested this assumption by determining the man-made or natural origin of microfibers found in different environments, including surface waters, sediments at depths >5000 m and highly sensitive habitats like mangroves and seagrass, and treated water using stimulated Raman scattering (SRS) microscopy. Our findings show that ¾th of analyzed microfibers are of natural origin. One plastic fiber is estimated per every 50 L in surface seawater, every 5 L in desalinated drinking water, every 3 g in deep sea sediments and every 27 g in coastal sediments. Synthetic fibers were significantly larger in surface seawaters compared to organic fibers due to higher resistance to solar radiation. These results emphasize the necessity of using spectroscopical methods to assess the origin of environmental microfibers to accurately estimate the abundance of synthetic materials in the environment.

Key Genetic Determinants Driving Esophageal Squamous Cell Carcinoma Initiation and Immune Evasion.

BACKGROUND & AIMS: Despite recent progress in identifying aberrant genetic and epigenetic alterations in esophageal squamous cell carcinoma (ESCC), the mechanism of ESCC initiation remains unknown. METHODS: Using CRISPR/Cas 9-based genetic ablation, we targeted 9 genes (TP53, CDKN2A, NOTCH1, NOTCH3, KMT2D, KMT2C, FAT1, FAT4, and AJUBA) in murine esophageal organoids. Transcriptomic phenotypes of organoids and chemokine released by organoids were analyzed by single-cell RNA sequencing. Tumorigenicity and immune evasion of organoids were monitored by allograft transplantation. Human ESCC single-cell RNA sequencing data sets were analyzed to classify patients and find subsets relevant to organoid models and immune evasion. RESULTS: We established 32 genetically engineered esophageal organoids and identified key genetic determinants that drive ESCC initiation. A single-cell transcriptomic analysis uncovered that Trp53, Cdkn2a, and Notch1 (PCN) triple-knockout induces neoplastic features of ESCC by generating cell lineage heterogeneity and high cell plasticity. PCN knockout also generates an immunosuppressive niche enriched with exhausted T cells and M2 macrophages via the CCL2-CCR2 axis. Mechanistically, CDKN2A inactivation transactivates CCL2 via nuclear factor-κB. Moreover, comparative single-cell transcriptomic analyses stratified patients with ESCC and identified a specific subtype recapitulating the PCN-type ESCC signatures, including the high expression of CCL2 and CD274/PD-L1. CONCLUSIONS: Our study unveils that loss of TP53, CDKN2A, and NOTCH1 induces esophageal neoplasia and immune evasion for ESCC initiation and proposes the CCL2 blockade as a viable option for targeting PCN-type ESCC.

Protocol for tumor dissociation and fluorescence-activated cell sorting of human head and neck cancers.

Tumors originating from the head and neck represent diverse histologies and are comprised of several cell types, including malignant cells, cancer-associated fibroblasts, endothelial cells, and immune cells. In this protocol, we describe a step-by-step approach for the dissociation of fresh human head and neck tumor specimens, followed by isolation of viable single cells using fluorescence-activated cell sorting. Our protocol facilitates the effective downstream use of techniques, including single-cell RNA sequencing and generation of three-dimensional patient-derived organoids. For complete details on the use and execution of this protocol, please refer to Puram et al. (2017)1 and Parikh et al. (2022).2.

Tumor Niche Network-Defined Subtypes Predict Immunotherapy Response of Esophageal Squamous Cell Cancer.

Despite the promising outcomes of immune checkpoint blockade (ICB), resistance to ICB presents a new challenge. Therefore, selecting patients for specific ICB applications is crucial for maximizing therapeutic efficacy. Herein we curated 69 human esophageal squamous cell cancer (ESCC) patients' tumor microenvironment (TME) single-cell transcriptomic datasets to subtype ESCC. Integrative analyses of the cellular network transcriptional signatures of T cells, myeloid cells, and fibroblasts define distinct ESCC subtypes characterized by T cell exhaustion, Interferon (IFN) a/b signaling, TIGIT enrichment, and specific marker genes. Furthermore, this approach classifies ESCC patients into ICB responders and non-responders, as validated by liquid biopsy single-cell transcriptomics. Our study stratifies ESCC patients based on TME transcriptional network, providing novel insights into tumor niche remodeling and predicting ICB responses in ESCC patients.

Fate and Effects of Macro- and Microplastics in Coastal Wetlands.

Coastal wetlands trap plastics from terrestrial and marine sources, but the stocks of plastics and their impacts on coastal wetlands are poorly known. We evaluated the stocks, fate, and biological and biogeochemical effects of plastics in coastal wetlands with plastic abundance data from 112 studies. The representative abundance of plastics that occurs in coastal wetland sediments and is ingested by marine animals reaches 156.7 and 98.3 items kg-1, respectively, 200 times higher than that (0.43 items kg-1) in the water column. Plastics are more abundant in mangrove forests and tidal marshes than in tidal flats and seagrass meadows. The variation in plastic abundance is related to climatic and geographic zones, seasons, and population density or plastic waste management. The abundance of plastics ingested by pelagic and demersal fish increases with fish length and dry weight. The dominant characteristics of plastics ingested by marine animals are correlated with those found in coastal wetland sediments. Microplastics exert negative effects on biota abundance and mangrove survival but positive effects on sediment nutrients, leaf drop, and carbon emission. We highlight that plastic pollution is widespread in coastal wetlands and actions are urged to include microplastics in ecosystem health and degradation assessment.

Projecting coral responses to intensifying marine heatwaves under ocean acidification.

Over this century, coral reefs will run the gauntlet of climate change, as marine heatwaves (MHWs) become more intense and frequent, and ocean acidification (OA) progresses. However, we still lack a quantitative assessment of how, and to what degree, OA will moderate the responses of corals to MHWs as they intensify throughout this century. Here, we first projected future MHW intensities for tropical regions under three future greenhouse gas emissions scenario (representative concentration pathways, RCP2.6, RCP4.5 and RCP8.5) for the near-term (2021-2040), mid-century (2041-2060) and late-century (2081-2100). We then combined these MHW intensity projections with a global data set of 1,788 experiments to assess coral attribute performance and survival under the three emissions scenarios for the near-term, mid-century and late-century in the presence and absence of OA. Although warming and OA had predominately additive impacts on the coral responses, the contribution of OA in affecting most coral attributes was minor relative to the dominant role of intensifying MHWs. However, the addition of OA led to greater decreases in photosynthesis and survival under intermediate and unrestricted emissions scenario for the mid- and late-century than if intensifying MHWs were considered as the only driver. These results show that role of OA in modulating coral responses to intensifying MHWs depended on the focal coral attribute and extremity of the scenario examined. Specifically, intensifying MHWs and OA will cause increasing instances of coral bleaching and substantial declines in coral productivity, calcification and survival within the next two decades under the low and intermediate emissions scenario. These projections suggest that corals must rapidly adapt or acclimatize to projected ocean conditions to persist, which is far more likely under a low emissions scenario and with increasing efforts to manage reefs to enhance resilience.

Modeling Oral-Esophageal Squamous Cell Carcinoma in 3D Organoids.

Esophageal squamous cell carcinoma (ESCC) is prevalent worldwide, accounting for 90% of all esophageal cancer cases each year, and is the deadliest of all human squamous cell carcinomas. Despite recent progress in defining the molecular changes accompanying ESCC initiation and development, patient prognosis remains poor. The functional annotation of these molecular changes is the necessary next step and requires models that both capture the molecular features of ESCC and can be readily and inexpensively manipulated for functional annotation. Mice treated with the tobacco smoke mimetic 4-nitroquinoline 1-oxide (4NQO) predictably form ESCC and esophageal preneoplasia. Of note, 4NQO lesions also arise in the oral cavity, most commonly in the tongue, as well as the forestomach, which all share the stratified squamous epithelium. However, these mice cannot be simply manipulated for functional hypothesis testing, as generating isogenic mouse models is time- and resource-intensive. Herein, we overcome this limitation by generating single cell-derived three-dimensional (3D) organoids from mice treated with 4NQO to characterize murine ESCC or preneoplastic cells ex vivo. These organoids capture the salient features of ESCC and esophageal preneoplasia, can be cheaply and quickly leveraged to form isogenic models, and can be utilized for syngeneic transplantation experiments. We demonstrate how to generate 3D organoids from normal, preneoplastic, and SCC murine esophageal tissue and maintain and cryopreserve these organoids. The applications of these versatile organoids are broad and include the utilization of genetically engineered mice and further characterization by flow cytometry or immunohistochemistry, the generation of isogeneic organoid lines using CRISPR technologies, and drug screening or syngeneic transplantation. We believe that the widespread adoption of the techniques demonstrated in this protocol will accelerate progress in this field to combat the severe burden of ESCC.

Integrating environmental variability to broaden the research on coral responses to future ocean conditions.

Our understanding of the response of reef-building corals to changes in their physical environment is largely based on laboratory experiments, analysis of long-term field data, and model projections. Experimental data provide unique insights into how organisms respond to variation of environmental drivers. However, an assessment of how well experimental conditions cover the breadth of environmental conditions and variability where corals live successfully is missing. Here, we compiled and analyzed a globally distributed dataset of in-situ seasonal and diurnal variability of key environmental drivers (temperature, pCO2 , and O2 ) critical for the growth and livelihood of reef-building corals. Using a meta-analysis approach, we compared the variability of environmental conditions assayed in coral experimental studies to current and projected conditions in their natural habitats. We found that annual temperature profiles projected for the end of the 21st century were characterized by distributional shifts in temperatures with warmer winters and longer warm periods in the summer, not just peak temperatures. Furthermore, short-term hourly fluctuations of temperature and pCO2 may regularly expose corals to conditions beyond the projected average increases for the end of the 21st century. Coral reef sites varied in the degree of coupling between temperature, pCO2 , and dissolved O2 , which warrants site-specific, differentiated experimental approaches depending on the local hydrography and influence of biological processes on the carbonate system and O2 availability. Our analysis highlights that a large portion of the natural environmental variability at short and long timescales is underexplored in experimental designs, which may provide a path to extend our understanding on the response of corals to global climate change.

Human-derived Treg and MSC combination therapy may augment immunosuppressive potency in vitro, but did not improve blood brain barrier integrity in an experimental rat traumatic brain injury model.

Traumatic brain injury (TBI) causes both physical disruption of the blood brain barrier (BBB) and altered immune responses that can lead to significant secondary brain injury and chronic inflammation within the central nervous system (CNS). Cell therapies, including mesenchymal stromal cells (MSC), have been shown to restore BBB integrity and augment endogenous splenic regulatory T cells (Treg), a subset of CD4+ T cells that function to regulate immune responses and prevent autoimmunity. We have recently shown that infusion of human cord blood-derived Treg decreased neuroinflammation after TBI in vivo and in vitro. However, while both cells have demonstrated anti-inflammatory and regenerative potential, they likely utilize differing, although potentially overlapping, mechanisms. Furthermore, studies investigating these two cell types together, as a combination therapy, are lacking. In this study, we compared the ability of Treg+MSC combination therapy, as well as MSC and Treg monotherapies, to improve BBB permeability in vivo and suppress inflammation in vitro. While Treg+MSC combination did not significantly augment potency in vivo, our in vitro data demonstrates that combination therapy may augment therapeutic potency and immunosuppressive potential compared to Treg or MSC monotherapy.

Anthropogenic litter density and composition data acquired flying commercial drones on sandy beaches along the Saudi Arabian Red Sea.

Anthropogenic litter density and composition data were obtained by conducting aerial surveys on 44 beaches along the Saudi Arabian Coast of the Red Sea [1]. The aerial surveys were completed with commercial drones of the DJI Phantom suite flown at a 10 m altitude. The stills have a resolution of less than 0.5 cm pixels-1, hence, litter objects of few centimetres like bottle caps are easily detectable in the drone images. We here provide a subsample of the drone images acquired. To spare the time needed to visually count the litter objects in the thousands of drone images acquired, these were automatically screened using an object detection algorithm, specifically a Faster R-CNN, able to perform a binary classification in litter and non-litter and to categorize the objects in classes. The multi-class classification, however, is a challenging problem and, hence, it was conducted only on the 15 beaches that showed the highest performance after the binary classification. The performance of the algorithm was calculated by visually screening a subsample of images and it was used to correct the output of the Faster R-CNN. The described steps allowed to obtain an estimate of the litter density in 44 beaches and the litter composition in 15 beaches. By multiplying the relative abundance of each litter class and the median weight of objects belonging to each class, we obtained an estimate of the total mass of plastic beached on 15 beaches. Possible predictors of litter density and mass are the population and marine traffic densities at the site, the exposure of the beach to the prevailing wind and the wind speed, the fetch length and the presence of vegetation where litter could get trapped. Making such raw data (i.e. litter density and composition and their predictors) available can help building the base for a robust global estimate of anthropogenic litter in coastal environments and it is particularly important if data regards an understudied region like the Arabian Peninsula. Moreover, we share a subsample of the original drone images to allow usage from stakeholders.

Habitat-forming species trap microplastics into coastal sediment sinks.

Nearshore biogenic habitats are known to trap sediments, and may therefore also accumulate biofouled, non-buoyant microplastics. Using a current-generating field flume (TiDyFLOW), we experimentally assessed the mechanisms of microplastic trapping of two size classes, 0.5 mm and 2.5 mm particle size, by three contrasting types of biogenic habitats: 1) seagrasses, 2) macroalgae, and 3) scleractinian corals. Results showed that benthic organisms with a complex architecture and rough surface - such as hard corals - trap the highest number of microplastics in their aboveground structure. Sediment was however the major microplastic sink, accumulating 1 to 2 orders of magnitude more microplastics than the benthic structure. Microplastic accumulation in the sediment could be explained by near-bed turbulent kinetic energy (TKE), indicating that this is governed by the same hydrodynamic processes leading to sediment trapping. Thus, the most valuable biogenic habitats in terms of nursery and coastal protection services also have the highest capacity of accumulating microplastics in their sediments. A significantly larger fraction of 0.5 mm particles was trapped in the sediment compared to 2.5 mm particles, because especially the smaller microplastics are entrained into the sediment. Present observations contribute to explaining why especially microplastics smaller than 1 mm are missing in surface waters.

Enabling a large-scale assessment of litter along Saudi Arabian red sea shores by combining drones and machine learning.

Beach litter assessments rely on time inefficient and high human cost protocols, mining the attainment of global beach litter estimates. Here we show the application of an emerging technique, the use of drones for acquisition of high-resolution beach images coupled with machine learning for their automatic processing, aimed at achieving the first national-scale beach litter survey completed by only one operator. The aerial survey had a time efficiency of 570 ± 40 m2 min-1 and the machine learning reached a mean (±SE) detection sensitivity of 59 ± 3% with high resolution images. The resulting mean (±SE) litter density on Saudi Arabian shores of the Red Sea is of 0.12 ± 0.02 litter items m-2, distributed independently of the population density in the area around the sampling station. Instead, accumulation of litter depended on the exposure of the beach to the prevailing wind and litter composition differed between islands and the main shore, where recreational activities are the major source of anthropogenic debris.

Combination therapy with Treg and mesenchymal stromal cells enhances potency and attenuation of inflammation after traumatic brain injury compared to monotherapy.

The inflammatory response after traumatic brain injury (TBI) can lead to significant secondary brain injury and chronic inflammation within the central nervous system. Cell therapies, including mesenchymal stromal cells (MSC), have led to improvements in animal models of TBI and are under investigation in human trials. One potential mechanism for the therapeutic potential of MSC is their ability to augment the endogenous response of immune suppressive regulatory T cells (Treg). We have recently shown that infusion of human cord blood Treg decreased chronic microgliosis after TBI and altered the systemic immune response in a rodent model. These cells likely use both overlapping and distinct mechanisms to modulate the immune system; therefore, combining Treg and MSC as a combination therapy may confer therapeutic benefit over either monotherapy. However, investigation of Treg + MSC combination therapy in TBI is lacking. In this study, we compared the ability MSC + Treg combination therapy, as well as MSC and Treg monotherapies, to inhibit the neuroinflammatory response to TBI in vivo and in vitro. Treg + MSC combination therapy demonstrated increased potency to reduce the neuro- and peripheral inflammatory response compared to monotherapy; furthermore, the timing of infusion proved to be a significant variable in the efficacy of both MSC monotherapy and Treg + MSC combination therapy in vivo and in vitro.

Stimulated Raman microspectroscopy as a new method to classify microfibers from environmental samples.

Microfibers are reported as the most abundant microparticle type in the environment. Their small size and light weight allow easy and fast distribution, but also make it challenging to determine their chemical composition. Vibrational microspectroscopy methods as infrared and spontaneous Raman microscopy have been widely used for the identification of environmental microparticles. However, only few studies report on the identification of microfibers, mainly due to difficulties caused by their small diameter. Here we present the use of Stimulated Raman Scattering (SRS) microscopy for fast and reliable classification of microfibers from environmental samples. SRS microscopy features high sensitivity and has the potential to be faster than other vibrational microspectroscopy methods. As a proof of principle, we analyzed fibers extracted from the fish gastrointestinal (GIT) tract, deep-sea and coastal sediments, surface seawater and drinking water. Challenges were faced while measuring fibers from the fish GIT, due to the acidic degradation they undergo. However, the main vibrational peaks were still recognizable and sufficient to determine the natural or synthetic origin of the fibers. Notably, our results are in accordance to other recent studies showing that the majority of the analyzed environmental fibers has a natural origin. Our findings suggest that advanced spectroscopic methods must be used for estimation of the plastic fibers concentration in the environment.

Human cord blood-derived regulatory T-cell therapy modulates the central and peripheral immune response after traumatic brain injury.

Traumatic brain injury (TBI) causes a profound inflammatory response within the central nervous system and peripheral immune system, which contributes to secondary brain injury and further morbidity and mortality. Preclinical investigations have demonstrated that treatments that downregulate microglia activation and polarize them toward a reparative/anti-inflammatory phenotype have improved outcomes in preclinical models. However, no therapy to date has translated into proven benefits in human patients. Regulatory T cells (Treg) have been shown to downregulate pathologic immune responses of the innate and adaptive immune system across a variety of pathologies. Furthermore, cellular therapy has been shown to augment host Treg responses in preclinical models; yet, studies investigating the use of Treg as a therapeutic for TBI are lacking. In a rodent TBI model, we demonstrate that human umbilical cord blood Treg modulate the central and peripheral immune response after injury in vitro and in vivo.