Discrete Microenvironments Research Articles

A cellular and molecular spatial atlas of dystrophic muscle

Asynchronous skeletal muscle degeneration/regeneration is a hallmark feature of Duchenne muscular dystrophy (DMD); however, traditional -omics technologies that lack spatial context make it difficult to study the biological mechanisms of how asynchronous regeneration contributes to disease progression. Here, using the severely dystrophic D2-mdx mouse model, we generated a high-resolution cellular and molecular spatial atlas of dystrophic muscle by integrating spatial transcriptomics and single-cell RNAseq datasets. Unbiased clustering revealed nonuniform distribution of unique cell populations throughout D2-mdx muscle that were associated with multiple regenerative timepoints, demonstrating that this model faithfully recapitulates the asynchronous regeneration observed in human DMD muscle. By probing spatiotemporal gene expression signatures, we found that propagation of inflammatory and fibrotic signals from locally damaged areas contributes to widespread pathology and that querying expression signatures within discrete microenvironments can identify targetable pathways for DMD therapy. Overall, this spatial atlas of dystrophic muscle provides a valuable resource for studying DMD disease biology and therapeutic target discovery.

PI16+ reticular cells in human palatine tonsils govern T cell activity in distinct subepithelial niches

Fibroblastic reticular cells (FRCs) direct the interaction and activation of immune cells in discrete microenvironments of lymphoid organs. Despite their important role in steering innate and adaptive immunity, the age- and inflammation-associated changes in the molecular identity and functional properties of human FRCs have remained largely unknown. Here, we show that human tonsillar FRCs undergo dynamic reprogramming during life and respond vigorously to inflammatory perturbation in comparison to other stromal cell types. The peptidase inhibitor 16 (PI16)-expressing reticular cell (PI16+ RC) subset of adult tonsils exhibited the strongest inflammation-associated structural remodeling. Interactome analysis combined with ex vivo and in vitro validation revealed that T cell activity within subepithelial niches is controlled by distinct molecular pathways during PI16+ RC–lymphocyte interaction. In sum, the topological and molecular definition of the human tonsillar stromal cell landscape reveals PI16+ RCs as a specialized FRC niche at the core of mucosal immune responses in the oropharynx.

A vasculature niche orchestrates stromal cell phenotype through PDGF signaling: Importance in human fibrotic disease

SignificanceTissue fibrotic diseases, for example of the liver and lung, represent a huge unmet medical need. In this study, using single-cell RNA sequencing, cytometry by time of flight (CyTOF), tissue imaging, and functional assays, we identify a complex vascular niche in Dupuytren's disease (DD), a common localized fibrotic condition of the palm, where early-disease-stage tissue can be accessed readily. We uncover a population of myofibroblast precursors within the pericyte compartment and demonstrate that the endothelium instructs the differentiation of functionally distinct stromal cells, thereby orchestrating discrete microenvironments in the fibrotic milieu. Together, these findings provide a basis for the concept of targeting blood vessel signaling to control the progression of human fibrosis.

Anatomy of Hematopoiesis and Local Microenvironments in the Bone Marrow. Where to?

The shape and spatial organization -the anatomy- of a tissue profoundly influences its function. Knowledge of the anatomical relationships between parent and daughter cells is necessary to understand differentiation and how the crosstalk between the different cells in the tissue leads to physiological maintenance and pathological perturbations. Blood cell production takes place in the bone marrow through the progressive differentiation of stem cells and progenitors. These are maintained and regulated by a heterogeneous microenvironment composed of stromal and hematopoietic cells. While hematopoiesis has been studied in extraordinary detail through functional and multiomics approaches, much less is known about the spatial organization of blood production and how local cues from the microenvironment influence this anatomy. Here, we discuss some of the studies that revealed a complex anatomy of hematopoiesis where discrete local microenvironments spatially organize and regulate specific subsets of hematopoietic stem cells and/or progenitors. We focus on the open questions in the field and discuss how new tools and technological advances are poised to transform our understanding of the anatomy of hematopoiesis.

Macrophage Responses to Environmental Stimuli During Homeostasis and Disease.

Work over the last 40 years has described macrophages as a heterogeneous population that serve as the frontline surveyors of tissue immunity. As a class, macrophages are found in almost every tissue in the body and as distinct populations within discrete microenvironments in any given tissue. During homeostasis, macrophages protect these tissues by clearing invading foreign bodies and/or mounting immune responses. In addition to varying identities regulated by transcriptional programs shaped by their respective environments, macrophage metabolism serves as an additional regulator to temper responses to extracellular stimuli. The area of research known as "immunometabolism" has been established within the last decade, owing to an increase in studies focusing on the crosstalk between altered metabolism and the regulation of cellular immune processes. From this research, macrophages have emerged as a prime focus of immunometabolic studies, although macrophage metabolism and their immune responses have been studied for centuries. During disease, the metabolic profile of the tissue and/or systemic regulators, such as endocrine factors, become increasingly dysregulated. Owing to these changes, macrophage responses can become skewed to promote further pathophysiologic changes. For instance, during diabetes, obesity, and atherosclerosis, macrophages favor a proinflammatory phenotype; whereas in the tumor microenvironment, macrophages elicit an anti-inflammatory response to enhance tumor growth. Herein we have described how macrophages respond to extracellular cues including inflammatory stimuli, nutrient availability, and endocrine factors that occur during and further promote disease progression.

The Intersection of Mechanotransduction and Regenerative Osteogenic Materials.

Mechanical signals play a central role in cell fate determination and differentiation in both physiologic and pathologic circumstances. Such signals may be delivered using materials to generate discrete microenvironments for the purposes of tissue regeneration and have garnered increasing attention in recent years. Unlike the addition of progenitor cells or growth factors, delivery of a microenvironment is particularly attractive in that it may reduce the known untoward consequences of the former two strategies, such as excessive proliferation and potential malignant transformation. Additionally, the ability to spatially modulate the fabrication of materials allows for the creation of multiple microenvironments, particularly attractive for regenerating complex tissues. While many regenerative materials have been developed and tested for augmentation of specific cellular responses, the intersection between cell biology and material interactions have been difficult to dissect due to the complexity of both physical and chemical interactions. Specifically, modulating materials to target individual signaling pathways is an avenue of interdisciplinary research that may lead to a more effective method of optimizing regenerative materials. In this work, the aim is to summarize the major mechanotransduction pathways for osteogenic differentiation and to consolidate the known materials and material properties that activate such pathways.

Subcellular drug targeting illuminates local kinase action.

Deciphering how signaling enzymes operate within discrete microenvironments is fundamental to understanding biological processes. A-kinase anchoring proteins (AKAPs) restrict the range of action of protein kinases within intracellular compartments. We exploited the AKAP targeting concept to create genetically encoded platforms that restrain kinase inhibitor drugs at distinct subcellular locations. Local Kinase Inhibition (LoKI) allows us to ascribe organelle-specific functions to broad specificity kinases. Using chemical genetics, super resolution microscopy, and live-cell imaging we discover that centrosomal delivery of Polo-like kinase 1 (Plk1) and Aurora A (AurA) inhibitors attenuates kinase activity, produces spindle defects, and prolongs mitosis. Targeted inhibition of Plk1 in zebrafish embryos illustrates how centrosomal Plk1 underlies mitotic spindle assembly. Inhibition of kinetochore-associated pools of AurA blocks phosphorylation of microtubule-kinetochore components. This versatile precision pharmacology tool enhances investigation of local kinase biology.

Regional and Microenvironmental Scale Characterization of the Zostera muelleri Seagrass Microbiome.

Seagrasses are globally distributed marine plants that represent an extremely valuable component of coastal ecosystems. Like terrestrial plants, seagrass productivity and health are likely to be strongly governed by the structure and function of the seagrass microbiome, which will be distributed across a number of discrete microenvironments within the plant, including the phyllosphere, the endosphere and the rhizosphere, all different in physical and chemical conditions. Here we examined patterns in the composition of the microbiome of the seagrass Zostera muelleri, within six plant-associated microenvironments sampled across four different coastal locations in New South Wales, Australia. Amplicon sequencing approaches were used to characterize the diversity and composition of bacterial, microalgal, and fungal microbiomes and ultimately identify “core microbiome” members that were conserved across sampling microenvironments. Discrete populations of bacteria, microalgae and fungi were observed within specific seagrass microenvironments, including the leaves and roots and rhizomes, with “core” taxa found to persist within these microenvironments across geographically disparate sampling sites. Bacterial, microalgal and fungal community profiles were most strongly governed by intrinsic features of the different seagrass microenvironments, whereby microscale differences in community composition were greater than the differences observed between sampling regions. However, our results showed differing strengths of microbial preferences at the plant scale, since this microenvironmental variability was more pronounced for bacteria than it was for microalgae and fungi, suggesting more specific interactions between the bacterial consortia and the seagrass host, and potentially implying a highly specialized coupling between seagrass and bacterial metabolism and ecology. Due to their persistence within a given seagrass microenvironment, across geographically discrete sampling locations, we propose that the identified “core” microbiome members likely play key roles in seagrass physiology as well as the ecology and biogeochemistry of seagrass habitats.

The Basic Biology of Redoxosomes in Cytokine-Mediated Signal Transduction and Implications for Disease-Specific Therapies

Redox reactions have been established as major biological players in many cellular signaling pathways. Here we review mechanisms of redox signaling with an emphasis on redox-active signaling endosomes. Signals are transduced by relatively few reactive oxygen species (ROS), through very specific redox modifications of numerous proteins and enzymes. Although ROS signals are typically associated with cellular injury, these signaling pathways are also critical for maintaining cellular health at homeostasis. An important component of ROS signaling pertains to localization and tightly regulated signal transduction events within discrete microenvironments of the cell. One major aspect of this specificity is ROS compartmentalization within membrane-enclosed organelles such as redoxosomes (redox-active endosomes) and the nuclear envelope. Among the cellular proteins that produce superoxide are the NADPH oxidases (NOXes), transmembrane proteins that are implicated in many types of redox signaling. NOXes produce superoxide on only one side of a lipid bilayer; as such, their orientation dictates the compartmentalization of ROS and the local control of signaling events limited by ROS diffusion and/or movement through channels associated with the signaling membrane. NOX-dependent ROS signaling pathways can also be self-regulating, with molecular redox sensors that limit the local production of ROS required for effective signaling. ROS regulation of the Rac-GTPase, a required co-activator of many NOXes, is an example of this type of sensor. A deeper understanding of redox signaling pathways and the mechanisms that control their specificity will provide unique therapeutic opportunities for aging, cancer, ischemia-reperfusion injury, and neurodegenerative diseases.

A family business: stem cell progeny join the niche to regulate homeostasis

Stem cell niches, the discrete microenvironments in which the stem cells reside, play a dominant part in regulating stem cell activity and behaviours. Recent studies suggest that committed stem cell progeny become indispensable components of the niche in a wide range of stem cell systems. These unexpected niche inhabitants provide versatile feedback signals to their stem cell parents. Together with other heterologous cell types that constitute the niche, they contribute to the dynamics of the microenvironment. As progeny are often located in close proximity to stem cell niches, similar feedback regulations may be the underlying principles shared by different stem cell systems.

Probe-Dependent Microenvironments within Biodegradable Films Formed from Poly(L-Lactic Acid) and Pluronic 104

We report on the local microenvironment surrounding three small fluorescent probe molecules (pyrene, [6-propionyl-2-(N,N-dimethylamino) naphthalene] (PRODAN), and [4-(dicyanomethylene)-2-methyl-6-(4-dimethylaminostyryl)-4H-pyran] (DCM)) when they are sequestered at low concentration within thin biodegradable films formed from poly( L-lactic acid) (PLLA) and Pluronic P104 blends. Despite each probe molecule being neutral, they sense and report from much different microenvironments in comparison to each other. Specifically, the non-polar pyrene probe senses a slightly more polar microenvironment as the PLLA content in the polymer blend increases. In contrast, the polar PRODAN and DCM probes sense less polar microenvironments as the PLLA content within the polymer blend increases. Time-resolved fluorescence intensity decay experiments on pure PLLA films reveal that each probe molecule encounters significant heterogeneity. Pyrene emits simultaneously from three discrete microenvironments. This is consistent with pyrene molecules reporting from crystalline, amorphous-crystalline intermediate, and amorphous regions. PRODAN and DCM appear to emit from a continuum of microenvironments. These results have ramifications on the performance of biodegradable drug delivery platforms loaded with small drug molecules.

Comparison of soil nutrient fluxes from tree-fall gap zones of an old-growth northern hardwood forest1

The objective of this study was to assess nutrient losses, via soil solutes, from discrete zones of recent, single-tree gaps in an old-growth, northern hardwood forest. Growing season flux rates of all solutes did not differ between the “undisturbed” zones (areas 5 m away from gap-making trees) and “crownfall” zones (areas associated with fallen tree crowns) of the twelve tree-fallgaps we studied. Under assumptions of partial root gap formation (50% root mortality), total cation and anion fluxes were 2-fold greater, and DON and total N fluxes were 2- to 3-fold greater in the “proximate” zones (areas 0–2 m from stumps of snapped, gap-making trees) compared to the crownfall and undisturbed zones. The “pit” zones (areas of disturbed soil associated with tipped-up trees) exhibited 3- to 6-fold greater NH4 , NO3−, and total dissolved N fluxes, and 2-fold greater total cation and anion fluxes than the undisturbed and crownfall zones. We estimated that proximate and pit zones associated with both recent and old tree-fall gaps accounted for 12% and 0.3%, respectively, of the total stand area in this old-growth forest. At the stand level, root throw pits contributed < 1% of the estimated NO3−, total dissolved N, total cations and total anions leaching from the system. Under assumptions of partial root gap formation proximate zones contributed 24–27% of the flux of these solutes. We conclude that the pit zones were inconsequential for nutrient loss and, while proximate zones contributed substantially more to nutrient losses from this system, the majority of nutrients leached from this system (∼ 75%) were leached from undisturbed forest zones. Our results indicate that efforts to account for mechanisms of nutrient loss from old-growth forests must consider variation in leaching rates associated with discrete microenvironments within gaps, and focus greater attention on nutrient retention capacity of the live, intact forest matrix.

Molecular phenotype of airway side population cells.

Lung epithelial-specific stem cells have been localized to discrete microenvironments throughout the adult conducting airway. Properties of these cells include pollutant resistance, multipotent differentiation, and infrequent proliferation. Goals of the present study were to use Hoechst 33342 efflux, a property of stem cells in other tissues, to purify and further characterize airway stem cells. Hoechst 33342 effluxing lung cells were identified as a verapamil-sensitive side population by flow cytometry. Lung side population cells were further subdivided on the basis of hematopoietic (CD45 positive) or nonhematopoietic (CD45 negative) origin. Nonhematopoietic side population cells were enriched for stem cell antigen-1 reactivity and expressed molecular markers specific to both airway and mesenchymal lineages. Analysis of the molecular phenotype of airway-derived side population cells indicates that they are similar to neuroepithelial body-associated variant Clara cells. Taken together, these data suggest that the nonhematopoietic side population isolated from lung is enriched for previously identified airway stem cells.

Compartmentalized Eph receptor and ephrin expression in the thymus

The maturation of T cells is an intricate process involving the interaction of developing thymocytes with discrete microenvironments within the thymus. Numerous studies have indicated that distinct thymic compartments provide signals required for each stage of thymocyte maturation. In this study we performed a comprehensive analysis of the expression patterns of Eph-A receptors and ephrins-A in the thymus using in situ hybridization and reverse transcription–polymerase chain reaction, and show that expression of these molecules is highly compartmentalized. Based on these expression patterns and the known mechanisms of action of Eph receptor/ephrin interactions in other organs, these data suggest that differential Eph receptor expression on discrete subsets of thymic stromal cells may be important in establishing compartment boundaries and preventing intermingling of stromal cell subtypes. Further, together with chemotactic signals such as those provided by chemokines, regulated Eph receptor/ephrin expression on thymocytes may play a role in thymocyte migration.

Characterization of the Microenvironments of PRODAN Entrapped in Tetraethyl Orthosilicate Derived Glasses

6-Propionyl-2-(dimethylamino)naphthalene (PRODAN) has been widely used to probe the internal environment of sol−gel derived glasses. It is generally assumed that the entrapped probe reports primarily on the internal solvent environment, through changes in emission wavelength, lifetime, or anisotropy. However, we show that other effects, such as aggregation of the probe and adsorption of the probe onto the silica surface, can also alter the emission properties of PRODAN, providing further information on the evolution of sol−gel derived glasses. Both the steady-state and time-resolved fluorescence properties of PRODAN were examined when the probe was entrapped in tetraethyl orthosilicate (TEOS) derived glasses. The glasses were prepared using a two-step method that is commonly used for protein entrapment, and aged either in air without washing (dry-aged), in air after a washing step (washed), or in buffer (wet-aged). For all aging methods, the changes in the emission properties of the probe were consistent with at least three discrete microenvironments, reflecting free monomers, free aggregates, and adsorbed species (monomers and/or aggregates), the proportion of which changed as a function of drying time and conditions. The monomeric form of the probe underwent a polarity-sensitive emission shift that reflected changes in the internal solvent composition. However, the aggregates/adsorbates contributed unique features to both the steady-state and time-resolved emission properties of PRODAN that gave insights into changes in the solubility of the probe, consistent with loss of internal solvent as aging of the glass proceeded. This study clearly shows that significant new information can be obtained from studies of PRODAN emission, and demonstrates that time-resolved fluorescence measurements are critical to properly elucidate the environment(s) present within the sol−gel derived materials.

Differential Involvement of the Transcription Factor Blimp-1 in T Cell-Independent and -Dependent B Cell Differentiation to Plasma Cells

Along humoral immune responses, different stimuli drive the differentiation of B lymphocytes to Ig-secreting plasma cells in discrete microenvironments. The Blimp-1 transcription factor is up-regulated early during the transition of mature B cells to IgM-secreting plasma cells. In the present study, we have examined the requirement of Blimp-1 in plasma cell formation after both T cell-independent (LPS) and -dependent (CD40 + IL-4, Th cell lines) stimulation of spleen B cells. B lymphocyte-induced maturation protein (Blimp-1) was expressed early after in vitro LPS stimulation, mainly in a population of IgM+Syndecan+CD43+ preplasma cells. In contrast, the BSAP transcription factor expressed in mature B cells was down-regulated during the differentiation to plasma cells. Treatment of these cultures with Blimp-1-specific antisense phosphorothioate oligonucleotides suppressed both Blimp-1 protein levels and the emergence of IgM+Syndecan+ cells and plasma cells. However, T-B cell cocultures of spleen B cells from C3H/HeJ (H-2k) mice and syngeneic autoreactive SR.10 Th2 cells submitted to the anti-Blimp-1 therapy did not show any significant reduction in IgM- and IgG1-secreting plasma cell formation. Spleen B cells treated with anti-CD40 mAb + IL-4 differentiated to IgG1-secreting cells without significant transcription of the Blimp-1 gene; anti-Blimp-1 treatment subsequently did not have any effect in the later cultures. Altogether, these results suggest that Blimp-1 transcription factor specifically promotes T cell-independent B cell differentiation to plasma cells, probably at preplasma cell stages. In contrast, T cell-dependent plasma cell formation likely evolves through Blimp-1-independent pathways.

A new device for sampling small volumes of water from marine micro-environments

Recent developments in microelectrode technology provide more sensitive measurement of biologically relevant redox species and require less water than traditional wet chemical techniques. To fully exploit the power of this new technology, water samplers capable of collecting small volumes (1–10 ml) from discrete micro-environments were developed. We have designed a new, low-cost water sampler (SIPPER) to draw small volume water samples from discrete locations at deep-sea hydrothermal vents. The sampler successfully operated with the deep submergence vehicle (DSV) ALVIN at 2600 m depth to extract water samples from the fragile tube dwellings of a small polychaete. These samples were electrochemically analyzed on board ship for the presence of biologically important redox species inside the worm tube. Although designed specifically for this study, the sampler can be readily modified for application in a variety of disciplines requiring discrete samples within aquatic micro-environments.

Development, organization and function of the thymic medulla in normal, immunodeficient or autoimmune mice

Thymopoiesis is initiated by the colonisation of the epithelial rudiment with blood-borne hemopoietic precursors. Their subsequent differentiation to the functionally mature T cell subsets is exquisitely linked to sequential interaction with a diverse array of thymic epithelial cells which form discrete microenvironments. The development and organisation of the epithelium, however, is in turn controlled by thymocyte subsets. In particular the medulla organization depends upon activating signals provided by mature thymocytes to epithelial and dendritic cells. These signals are lacking in RelB-deficient mice leading to the disorganization of the corticomedullary junction and abnormal negative selection despite normal thymocyte maturation. This thymic stromal cell architecture phenotype is found in autoimmune diseases suggesting that abnormalities in the establishment of medullary microenvironments might be linked to the development of autoimmunity.

Physiological and molecular mechanisms of lymphocyte homing.

The lymphoid system is functionally compartmentalized in vivo into discrete primary, secondary, and tertiary lymphoid organs. Primary lymphoid tissues--the bone marrow and thymus--are responsible for the production of mature "virgin" lymphocytes. Secondary lymphoid tissues--lymph nodes, the spleen, and gut-associated lymphoid tissues--are specialized for the accumulation and presentation of antigen to both virgin and memory lymphocyte subsets. The remainder of the body's tissues may be considered "tertiary" lymphoid tissues, in that they normally contain only a few lymphoid elements, but in the setting of inflammation can be induced to recruit unique subsets of primarily memory lymphocytes. Each lymphoid tissue is further subdivided into discrete microenvironments, each characterized by a distinct complement of lymphocyte subsets and stromal cells. Lymphocyte homing comprises the physiologic processes by which lymphocytes seek out and localize to particular tissues and to specific microenvironments therein. Homing mechanisms play a major role in the maintenance of these specialized microenvironments and are critical for the dispersal and targeting of naive and memory lymphocyte populations that are required for effective immune surveillance. Here, we provide a brief overview of mechanisms thought to control the homing of lymphocyte populations in vivo, focusing in particular on the adhesive interactions involved in lymphocyte-endothelial cell recognition and in the selective extravasation of lymphocyte populations into secondary and tertiary lymphoid tissues.

The role of growth factors in self-renewal and differentiation of haemopoietic stem cells

Haemopoietic stem cells in vivo proliferate and develop in association with stromal cells of the bone marrow. Proliferation and differentiation of haemopoietic stem cells also occurs in vitro, either in association with stromal cells or in response to soluble growth factors. Many of the growth factors that promote growth and development of haemopoietic cells in vitro have now been molecularly cloned and purified to homogeneity and various techniques have been described that allow enrichment (to near homogeneity) of multipotential stem cells. This in turn, has facilitated studies at the mechanistic level regarding the role of such growth factors in self-renewal and differentiation of stem cells and their relevance in stromal-cell mediated haemopoiesis. Our studies have shown that at least some multipotential cells express receptors for most, if not all, of the haemopoietic cell growth factors already characterized and that to elicit a response, several growth factors often need to be present at the same time. Furthermore, lineage development reflects the stimuli to which the cells are exposed, that is, some stimuli promote differentiation and development of multipotential cells into multiple cell lineages, whereas others promote development of multipotential cell into only one cell lineage. We suggest that, in the bone marrow environment, the stromal cells produce or sequester different types of growth factors, leading to the formation of microenvironments that direct cells along certain lineages. Furthermore, a model system has been used to show the possibility that the self-renewal probability of multipotential cells can also be modulated by the range and concentrations of growth factors present in the environment. This suggests that discrete microenvironments, preferentially promoting self-renewal rather than differentiation of multipotential cells, may also be provided by marrow stromal cells and sequestered growth factors.