Niche Environment Research Articles

Hematopoietic stem cell metabolism within the bone marrow niche - insights and opportunities.

Hematopoiesis unfolds within the bone marrow niche where hematopoietic stem cells (HSCs) play a central role in continually replenishing blood cells. The hypoxic bone marrow environment imparts peculiar metabolic characteristics to hematopoietic processes. Here, we discuss the internal metabolism of HSCs and describe external influences exerted on HSC metabolism by the bone marrow niche environment. Importantly, we suggest that the metabolic environment and metabolic cues are intertwined with HSC cell fate, and are crucial for hematopoietic processes. Metabolic dysregulation within the bone marrow niche during acute stress, inflammation, and chronic inflammatory conditions can lead to reduced HSC vitality. Additionally, we raise questions regarding metabolic stresses imposed on HSCs during implementation of stem cell protocols such as allo-SCT and gene therapy, and the potential ramifications. Enhancing our comprehension of metabolic influences on HSCs will expand our understanding of pathophysiology in the bone marrow and improve the application of stem cell therapies.

Interaction between subventricular zone microglia and neural stem cells impacts the neurogenic response in a mouse model of cortical ischemic stroke

After a stroke, the neurogenic response from the subventricular zone (SVZ) to repair the brain is limited. Microglia, as an integral part of the distinctive SVZ microenvironment, control neural stem / precursor cell (NSPC) behavior. Here, we show that discrete stroke-associated SVZ microglial clusters negatively impact the innate neurogenic response, and we propose a repository of relevant microglia–NSPC ligand–receptor pairs. After photothrombosis, a mouse model of ischemic stroke, the altered SVZ niche environment leads to immediate activation of microglia in the niche and an abnormal neurogenic response, with cell-cycle arrest of neural stem cells and neuroblast cell death. Pharmacological restoration of the niche environment increases the SVZ-derived neurogenic repair and microglial depletion increases the formation and survival of newborn neuroblasts in the SVZ. Therefore, we propose that altered cross-communication between microglial subclusters and NSPCs regulates the extent of the innate neurogenic repair response in the SVZ after stroke.

"Osteo-Organogenesis Niche" Hyaluronic Acid Engineered Materials Directing Re-Osteo-Organogenesis via Manipulating Macrophage CD44-MAPK/ERK-ETV1/5-MRC1 Axis.

The strategy of re-organogenesis provides an optimal framework for restoring complex organ structures and functions in adult damage. While the focus has often been on restoring organogenesis stem cells, there is limited investigations of reverting the environmental niche to support this approach. The guiding principle of "Nature selects the fittest to survive" drives the intricate dynamic changes in cellular events within the niche environment, especially through immune surveillance. The extracellular matrix (ECM) serves as the "self-associated molecular patterns" of the niche, containing extensive data on cell-niche reaction data and acting as the active tuner of immune surveillance. In this study, hyaluronic acid (HA) is identified as a unique component of the ECM in cranial osteo-organogenesis. Mechanistically, HA activates the Cluster of Differentiation 44 (CD44)-Mitogen-Activated Protein Kinase (MAPK)/Extracellular Signal-Regulated Kinase (ERK)-Ets Variant 1/5 (ETV1/5)- Mannose Receptor C-Type 1 (MRC1) axis in macrophages, establishing a distinct immune surveillance during osteo-organogenesis. Furthermore, HA is utilized as a novel engineered material for an "Osteo-organogenesis niche", restoring immune surveillance and synergistically regulating stem cells to achieve re-osteo-organogenesis in cranial defects of rats. Taken together, the study unveils a previously unknown strategy for leveraging re-organogenesis by utilizing "organogenesis niche" ECM engineered materials to manipulate immune surveillance, thereby comprehensively regulating stem cells and other tissue cells effectively for re-organogenesis.

A combinatorial culture strategy to develop pseudomyxoma peritonei organoid models.

Few preclinical models of pseudomyxoma peritonei (PMP) have been developed, probably due to the tumor's low incidence and its peculiar characteristics of slow growth. Therefore, there is a need to develop more refined PMP models that better reflect its characteristics. The aim of the study is to develop a culture strategy to generate organoid models derived from PMP patient samples. We followed a strategy based on combinatorial culture conditions that include the different factors essential for PMP growth and that mimic the microenvironment present in the patients. We cultured PMP samples in the presence of the various factors produced by the niche environment of PMP. We obtained 12 PMP organoid models, each of which grows under specific culture conditions. PMP-derived organoids show long-term expansion capacity and reproduce the genetic landscape and histological phenotype of the tumor of origin. The organoids we developed faithfully reproduce the key features of PMP disease and will allow us to understand the biology of PMP. With them, we will be able to identify key regulatory networks that support PMP progression, providing a platform for multilevel preclinical testing, identify novel diagnostic biomarkers, and generate novel targets for patient treatments.

Anisakis extracellular vesicles elicit immunomodulatory and potentially tumorigenic outcomes on human intestinal organoids

BackgroundAnisakis spp. are zoonotic nematodes causing mild to severe acute and chronic gastrointestinal infections. Chronic anisakiasis can lead to erosive mucosal ulcers, granulomas and inflammation, potential tumorigenic triggers. How Anisakis exerts its pathogenic potential through extracellular vesicles (EVs) and whether third-stage infective larvae may favor a tumorigenic microenvironment remain unclear.MethodsHere, we investigated the parasite's tumorigenic and immunomodulatory capabilities using comparative transcriptomics, qRT-PCR and protein analysis with multiplex ELISA on human intestinal organoids exposed to Anisakis EVs. Moreover, EVs were characterized in terms of shape, size and concentration using classic TEM, SEM and NTA analyses and advanced interferometric NTA.ResultsAnisakis EVs showed classic shape features and a median average diameter of around 100 nm, according to NTA and iNTA. Moreover, a refractive index of 5–20% of non-water content suggested their effective biological cargo. After treatment of human intestinal organoids with Anisakis EVs, an overall parasitic strategy based on mitigation of the immune and inflammatory response was observed. Anisakis EVs impacted gene expression of main cytokines, cell cycle regulation and protein products. Seven key genes related to cell cycle regulation and apoptosis were differentially expressed in organoids exposed to EVs. In particular, the downregulation of EPHB2 and LEFTY1 and upregulation of NUPR1 genes known to be associated with colorectal cancer were observed, suggesting their involvement in tumorigenic microenvironment. A statistically significant reduction in specific mediators of inflammation and cell-cycle regulation from the polarized epithelium as IL-33R, CD40 and CEACAM1 from the apical chambers and IL-1B, GM-CSF, IL-15 and IL-23 from both chambers were observed.ConclusionsThe results here obtained unravel intestinal epithelium response to Anisakis EVs, impacting host’s anthelminthic strategies and revealing for the first time to our knowledge the host-parasite interactions in the niche environment of an emerging accidental zoonosis. Use of an innovative EV characterization approach may also be useful for study of other helminth EVs, since the knowledge in this field is very limited.Graphical

Intact-cell detection of halohydrin dehalogenase activity and preliminary assessment of marine adaptability

Halohydrin dehalogenase (HHDH) can degrade 1,2,3-trichloropropanol and other halogenated alcohols. These enzymes exhibit stereoselectivity and can be used to produce pure chiral epoxides and β-substituted alcohols of industrial value. The discovery of novel HHDHs from microorganisms in niche environments including the sea requires in-situ analysis of HHDH activity. Owing to its high practical value, HheC was selected as a target enzyme to establish an intact-cell method for detecting HHDH activity based on fluorescence spectroscopy. This approach relied on the principle that HHDH activity can change the pH in a system with weak buffering capacity, and that the fluorescence intensity of certain dyes is influenced by pH. The marine adaptability of the assay was subjected to preliminary investigation. The method is simple, rapid, and highly sensitive, as verified using gas chromatography-mass spectrometry. The detection limit of the method was OD600 (optical density at a 600 nm) of 0.025 for microorganisms containing HHDH which have activity comparable to that of HheC. With some improvements, this method holds potential for in-situ analysis and mining of marine microorganisms containing HHDH.

Influence of mesenchymal and biophysical components on distal lung organoid differentiation

BackgroundChronic lung disease of prematurity, called bronchopulmonary dysplasia (BPD), lacks effective therapies, stressing the need for preclinical testing systems that reflect human pathology for identifying causal pathways and testing novel compounds. Alveolar organoids derived from human pluripotent stem cells (hPSC) are promising test platforms for studying distal airway diseases like BPD, but current protocols do not accurately replicate the distal niche environment of the native lung. Herein, we investigated the contributions of cellular constituents of the alveolus and fetal respiratory movements on hPSC-derived alveolar organoid formation.MethodsHuman PSCs were differentiated in 2D culture into lung progenitor cells (LPC) which were then further differentiated into alveolar organoids before and after removal of co-developing mesodermal cells. LPCs were also differentiated in Transwell® co-cultures with and without human fetal lung fibroblast. Forming organoids were subjected to phasic mechanical strain using a Flexcell® system. Differentiation within organoids and Transwell® cultures was assessed by flow cytometry, immunofluorescence, and qPCR for lung epithelial and alveolar markers of differentiation including GATA binding protein 6 (GATA 6), E-cadherin (CDH1), NK2 Homeobox 1 (NKX2-1), HT2-280, surfactant proteins B (SFTPB) and C (SFTPC).ResultsWe observed that co-developing mesenchymal progenitors promote alveolar epithelial type 2 cell (AEC2) differentiation within hPSC-derived lung organoids. This mesenchymal effect on AEC2 differentiation was corroborated by co-culturing hPSC-NKX2-1+ lung progenitors with human embryonic lung fibroblasts. The stimulatory effect did not require direct contact between fibroblasts and NKX2-1+ lung progenitors. Additionally, we demonstrate that episodic mechanical deformation of hPSC-derived lung organoids, mimicking in situ fetal respiratory movements, increased AEC2 differentiation without affecting proximal epithelial differentiation.ConclusionOur data suggest that biophysical and mesenchymal components promote AEC2 differentiation within hPSC-derived distal organoids in vitro.

A novel membrane-on-chip guides morphogenesis for the reconstruction of the intestinal crypt-villus axis

Reconstructing the microscale villous organisation and functionality of the small intestine is essential for developingin vitroplatforms tailored for absorption studies as well as for investigating intestinal morphogenesis in development and disease. However, the current fabrication techniques able to mimic the villus-crypt axis poses significant challenges in terms of reconstruction of the complex 3D microarchitecture. These challenges extend beyond mere structural intricacies to encompass the incorporation of diverse cell types and the management of intricate fluid dynamics within the system. Here, we introduce a novel microfluidic device calledIn-Crypts, which integrates a cell-instructive membrane aimed at inducing and guiding Caco-2 cells morphogenesis. Patterned topographical cues embossed onto the porous membrane induce the formation of a well-organized intestinal epithelium, characterized by proliferating crypt-like domains and differentiated villus-like regions. Notably, our cell-instructive porous membrane effectively sustains stem cells development, faithfully replicating the niche environment ofin vivointestinal crypts thus mirroring the cell biogeography observedin vivo. Moreover, by introducing dynamic fluid flow, we provide a faithful recapitulation of the native microenvironmental shear stress experienced by the intestinal epithelium. This stress plays a crucial role in influencing cell behaviour, differentiation, and overall functionality, thus offering a highly realistic model for studying intestinal physiology and pathology. The resulting intestinal epithelium exhibits significantly denser regions of mucus and microvilli, characteristic typically absent in static cultures, upregulating more than 1.5 of the amount expressed in the classical flattened configuration, enhanced epithelial cell differentiation and increased adsorptive surface area. Hence, the innovative design ofIn-Cryptsproves the critical role of employing a cell-instructive membrane in argument the physiological relevance of organs-on-chips. This aspect, among others, will contribute to a more comprehensive understanding of organism function, directly impacting drug discovery and development.

Numerical study of cavitation shock wave emission in the thin liquid layer by power ultrasonic vibratory machining

In the field of power ultrasonic vibration processing, the thin liquid layer nestled between the tool head and the material serves as a hotbed for cavitation shock wave emissions that significantly affect the material's surface. The precise manipulation of these emissions presents a formidable challenge, stemming from a historical deficit in the quantitative analysis of both the ultrasonic enhancement effect and the shock wave intensity within this niche environment. Our study addresses this gap by innovatively modifying the Gilmore-Akulichev equation, laying the groundwork for a sophisticated bubble dynamics model and a pioneering shock wave propagation model tailored to the thin liquid layer domain. Firstly, our study investigated the ultrasound enhancement effect under various parameters of thin liquid layers, revealing an amplification of ultrasound pressure in the thin liquid layer area by up to 7.47 times. The mathematical model was solved using the sixth-order Runge–Kutta method to examine shock wave velocity and pressure under different conditions. our study identified that geometric parameters of the tool head, thin liquid layer thickness, ultrasonic frequency, and initial bubble radius all significantly influenced shock wave emission. At an ultrasonic frequency of 60 kHz, the shock wave pressure at the measurement point exhibited a brief decrease from 182.6 to 179.5 MPa during an increase. Furthermore, rapid attenuation of the shock wave was found within the range of R0-3R0 from the bubble wall. This research model aims to enhance power ultrasonic vibration processing technology, and provide theoretical support for applications in related fields.

Light-Sheet Microscopy Enables Three-Dimensional Fluorescence Imaging and Live Imaging of Satellite Cells on Skeletal Muscle Fibers.

The ex vivo myofiber culture system has proven to be a useful methodology to explore the biology and behavior of satellite cells within their niche environment. However, a limitation of this system is that myofibers and their associated satellite cells are commonly examined using conventional fluorescence microscopy, which renders a three-dimensional system into two-dimensional imaging, leading to the loss of precious information or misleading interpretation of observations. Here, we report on the use of light-sheet fluorescence microscopy to generate three-dimensional and live imaging of satellite cells on myofibers. Light-sheet microscopy offers high imaging speed and good spatial resolution with minimal photo-bleaching, allowing live imaging and three-dimensional acquisition of skeletal muscle fiber specimen. The potentials of this technology are wide, ranging from the visualization of satellite cell behavior such as cell division and cell migration to imaging the sub-cellular localization of proteins or organelles.

The Toxic Cost of Cheap Usernames: Re-Applying Friedman and Resnick's Framework in Competitive Video Game Networks

Toxicity in video games, acting in a rude, abusive, bullying, or deliberately losing manner, ruins competitive team-based video game experiences for everyone involved. Companies are experimenting with the detection, regulation, and bans of toxic players. Regulation attempts are foiled by the ease with which players can switch accounts by creating new profiles to evade consequences. This article applies the framework of Friedman and Resnick (2001), “The Social Cost of Cheap Pseudonyms”, to address the reputational and repetition cost of online pseudonyms in the niche environment of video game toxicity. Four potential solutions are discussed in the context of modern video game regulation: resource-intensive account set-up, paid dues, real-world identification, and a once-in-a-lifetime identification system that creates a permanent, traceable record of toxicity. The article covers the strengths, weaknesses, feasibility, implementation challenges, and player impact of the potential implementation of these solutions in video game networks.

The Legionella collagen-like protein employs a distinct binding mechanism for the recognition of host glycosaminoglycans

Bacterial adhesion is a fundamental process which enables colonisation of niche environments and is key for infection. However, in Legionella pneumophila, the causative agent of Legionnaires’ disease, these processes are not well understood. The Legionella collagen-like protein (Lcl) is an extracellular peripheral membrane protein that recognises sulphated glycosaminoglycans on the surface of eukaryotic cells, but also stimulates bacterial aggregation in response to divalent cations. Here we report the crystal structure of the Lcl C-terminal domain (Lcl-CTD) and present a model for intact Lcl. Our data reveal that Lcl-CTD forms an unusual trimer arrangement with a positively charged external surface and negatively charged solvent exposed internal cavity. Through molecular dynamics simulations, we show how the glycosaminoglycan chondroitin-4-sulphate associates with the Lcl-CTD surface via distinct binding modes. Our findings show that Lcl homologs are present across both the Pseudomonadota and Fibrobacterota-Chlorobiota-Bacteroidota phyla and suggest that Lcl may represent a versatile carbohydrate-binding mechanism.

Targeting Tumor Heterogeneity by Breaking a Stem Cell and Epithelial Niche Interaction Loop.

Tumor heterogeneity, the presence of multiple distinct subpopulations of cancer cells between patients or among the same tumors, poses a major challenge to current targeted therapies. The way these different subpopulations interact among themselves and the stromal niche environment, and how such interactions affect cancer stem cell behavior has remained largely unknown. Here, it is shown that an FGF-BMP7-INHBA signaling positive feedback loop integrates interactions among different cell populations, including mammary gland stem cells, luminal epithelial and stromal fibroblast niche components not only in organ regeneration but also, with certain modifications, in cancer progression. The reciprocal dependence of basal stem cells and luminal epithelium is based on basal-derived BMP7 and luminal-derived INHBA, which promote their respective expansion, and is regulated by stromal-epithelial FGF signaling. Targeting this interaction loop, for example, by reducing the function of one or more of its components, inhibits organ regeneration and breast cancer progression. The results have profound implications for overcoming drug resistance because of tumor heterogeneity in future targeted therapies.

Biosurfactants as templates to inspire new environmental and health applications

Life exists at an interface. One of the key characteristics of biological cells is compartmentalization, which is facilitated by lipids that create a water-impenetrable barrier to control transport of materials across the hydrophilic-hydrophobic interface. Microbial systems utilize a rich diversity of surfactants beyond lipids to adapt to an environmental niche, modify the properties of an interface, facilitate solubilization of nutrients for metabolism and as antimicrobials. As such, they are a fascinating class of biomolecules to study in terms of how effectiveness in an application or niche environment depends on sequence, structure and chemical properties. Moreover, there is increasing appreciation of the negative health and environmental impacts petrochemical-based surfactants can have, such as soil erosion and toxicity to plants and aquatic life, as well as the carbon footprint and associated greenhouse gas emissions associated with petrochemical surfactant manufacturing. In this review, we discuss the properties of biosurfactants and applications, and highlight key glycolipid-, protein- and peptide-based surfactants described in literature as examples of biosurfactants with unique potential and applications. As society looks towards the transition to a circular bioeconomy, we are excited by the potential of synthetic biology to develop new materials such as biosurfactants to facilitate this important transition.

Enrichment, Characterization, and Proteomic Profiling of Small Extracellular Vesicles Derived from Human Limbal Mesenchymal Stromal Cells and Melanocytes.

Limbal epithelial progenitor cells (LEPC) rely on their niche environment for proper functionality and self-renewal. While extracellular vesicles (EV), specifically small EVs (sEV), have been proposed to support LEPC homeostasis, data on sEV derived from limbal niche cells like limbal mesenchymal stromal cells (LMSC) remain limited, and there are no studies on sEVs from limbal melanocytes (LM). In this study, we isolated sEV from conditioned media of LMSC and LM using a combination of tangential flow filtration and size exclusion chromatography and characterized them by nanoparticle tracking analysis, transmission electron microscopy, Western blot, multiplex bead arrays, and quantitative mass spectrometry. The internalization of sEV by LEPC was studied using flow cytometry and confocal microscopy. The isolated sEVs exhibited typical EV characteristics, including cell-specific markers such as CD90 for LMSC-sEV and Melan-A for LM-sEV. Bioinformatics analysis of the proteomic data suggested a significant role of sEVs in extracellular matrix deposition, with LMSC-derived sEV containing proteins involved in collagen remodeling and cell matrix adhesion, whereas LM-sEV proteins were implicated in other cellular bioprocesses such as cellular pigmentation and development. Moreover, fluorescently labeled LMSC-sEV and LM-sEV were taken up by LEPC and localized to their perinuclear compartment. These findings provide valuable insights into the complex role of sEV from niche cells in regulating the human limbal stem cell niche.

Helicobacter pylori mediated niche environment aberrations promote the progression of gastric cancer

Helicobacter pylori mediated niche environment aberrations promote the progression of gastric cancer

TENDON HEALTH AND DISEASE: EXPLORING THE INTERFASCICULAR NICHE

Tendon injury is debilitating and recalcitrant. With limited knowledge of disease aitiology we have are lacking in effective treatments for this prevalent musculoskeletal complaint.This presentation will outline our findings over the past few years in which we have demonstrated the importance of the interfascicular matrix (IFM) niche in maintaining healthy tendon function and driving disease progression1,2. It will also continue to describe our progress in developing both in vivo and in vitro models to interrogate disease progression.We have developed and validated a rat Achilles tendon overload model, in order to explore the impact of loading on IFM and fascicle structure, and the resulting cell response. Data highlights that structural disruption and inflammatory response both initiate in the IFM region, and can be seen in the absence of demonstrable changes to animal gait, indicating a sub-injury response in the tendon which we hypothesis may drive increased matrix turnover and repair3.We are now looking to interrogate the pathways driving this inflammatory behaviour in an organ-chip model, exploring the interplay between IFM cells and cells within fascicles. We have demonstrated phenotypic distinction of cells from the two niche environments, localized the progenitor phenotype to the IFM region and demonstrated significant mechanosensitivity in the IFM cell population4. We are currently building appropriate niche environments to maintain cell phenotype in our in vitro models, to explore the metabolic changes associated with disease progression.Acknowledgements: This body of work has received funding from: BBSRC (BB/K008412 /1); Versus Arthritis (project grant 20262); Horserace Betting Levy Board (T5); Dunhill Medical Charity (project grant RPGF1802\23); MRC (MR/T015462/1).

Three-dimensional cell culture using CD9-positive cells isolated from marginal cell layer of intermediate lobe of rats sustains in vivo-like primary niche environment.

The adenohypophysis is composed of the anterior and intermediate lobes (AL and IL, respectively), and secretes hormones that play an important role in reproduction. CD9- and SOX2-double (CD9/SOX2) positive cells located in the marginal cell layer (MCL) facing the Rathke's cleft in the AL and IL form the primary stem cell niche in the adult adenohypophysis of rats. In this study, we successfully obtained 3-dimensional (3D) cell aggregates that closely resembled the primary niche of MCL in vivo. After incubation in a Matrigel containing several growth factors, approximately 20% of the cells in the CD9/SOX2-positive cell aggregates were differentiated into hormone-producing cells. The cell aggregates generated in this study may provide insight into the regulation of the pituitary stem/progenitor cell niche and the turnover of hormone-producing cells.

Comparative genomics of the niche-specific plant pathogen Streptomyces ipomoeae reveal novel genome content and organization.

While most plant-pathogenic Streptomyces species cause scab disease on a variety of plant hosts, Streptomyces ipomoeae is the sole causative agent of soil rot disease of sweet potato and closely related plant species. Here, genome sequencing of virulent and avirulent S. ipomoeae strains coupled with comparative genomic analyses has identified genome content and organization features unique to this streptomycete plant pathogen. The results here will enable future research into the mechanisms used by S. ipomoeae to cause disease and to persist in its niche environment.

Non-deterministic reef fish community assembly in an upwelling-influenced transitional subprovince of the southwestern Atlantic

There are two major theories for setting up ecological communities, the Niche Theory and the Neutral Theory. Both seek to explain the main factors that form a community, which is a great challenge, since each community has its particularities and the environment has different ways to manifest. We devised a process-oriented study that sought to establish the role of environmental niche driven by coastal upwelling in the assembly of reef fish communities from exposed and sheltered environments a few kilometers apart, in the region of Arraial do Cabo (southwestern Atlantic). A multivariate hierarchical generalized linear mixed model fitted with Bayesian inference was applied to abundance and presence-absence data from visual census, together with environmental data from satellite and reanalysis. We found a stronger contribution of random effects to abundance variance with 24% for sites and 20.7% for sheltered vs. exposed locations, and weaker environmental effects with 7.1% for surface chlorophyll-a concentration (SCC) and 5.4% for sea surface temperature (SST). Environmental effects had a stronger contribution in the presence-absence model, with 20.1% for SCC and 14.6% for SST. The overall influence of the upwelling environment across all species was negative, e.g., Gymnothorax moringa and Canthigaster figueiredoi showing negative responses to SCC and Parablennius pilicornis and Malacoctenus delalandii to SST. The joint action of migration-niche mechanisms is inferred from the dominance of spatio-temporal structure, limited influence of life history traits and phylogeny, explaining around 95% of species niches in the abundance model. Our results bring new evidence for the importance of different filters for community assembly other than the environment, such as phylogenetic history and dispersal. We also discuss the balance between niche (environment) and neutral (stochasticity) processes for the assembly of reef fish communities in a tropical-subtropical transition zone.