SEARCH · PubMed Health

Results for “microenvironmental niches”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources

PubMed2026

Spatially defined microenvironmental niches are associated with clinical outcome and tumor ecosystem diversity in head and neck cancer.

BACKGROUND: Head and neck squamous cell carcinoma (HNSCC) exhibits substantial biological heterogeneity that is not fully explained by human papillomavirus (HPV) status. The spatial organization of tumor, immune, and stromal cell populations and its relationship to clinical outcome remain incompletely understood. METHODS: We performed single-cell spatial transcriptomic and proteomic profiling of 44 primary HNSCC tumors, generating a spatial atlas of 19,471,501 cells across whole-slide tissue sections. Spatial niches and ecosystem states were identified through integrated computational analyses and evaluated for associations with tumor programs, clinicopathologic features, and patient outcomes. FINDINGS: HPV-negative tumors were enriched for fibroblast-rich, immune-poor niches associated with epithelial-mesenchymal transition and hypometabolic tumor programs, whereas HPV-positive tumors displayed more diverse immune, stromal, and vascular niche combinations and were enriched for immunogenic ecosystem states. Approximately 20% of HPV-positive tumors exhibited fibroblast-rich ecosystem architectures resembling HPV-negative disease and were associated with less favorable outcomes than other HPV-positive tumors of similar stage. In patient-derived co-culture models, extracellular matrix-associated fibroblasts were associated with epithelial-mesenchymal transition (EMT)-like tumor states, CD8+ T cell dysfunction, and chemotherapy resistance-associated phenotypes. CONCLUSIONS: Spatial ecosystem architecture is associated with clinically relevant heterogeneity beyond conventional HPV-based classification. Fibroblast-rich, immune-poor ecosystem states characterize a high-risk subset of HPV-positive tumors and may provide a framework for improved biological classification and risk stratification in HNSCC. FUNDING: This work was supported by the National Institutes of Health (R01CA291607 and R21CA267527-01) and the Feldstein Medical Foundation.

Humans↗

PubMed2005

Adult bone marrow stem/progenitor cells (MSCs) are preconditioned by microenvironmental "niches" in culture: a two-stage hypothesis for regulation of MSC fate.

Mesenchymal stem cells (MSCs) are clonal, plastic adherent cells from bone marrow that can differentiate into various tissue lineages, including osteoblasts, adipocytes, chondrocytes, myoblasts, hepatocytes, and possibly even neural cells. Because MSCs are multipotent and their numbers are easily expanded in culture, there has been much interest in their clinical potential for tissue repair and gene therapy. Consequently, numerous studies have been carried out demonstrating the migration and multiorgan engraftment potential of MSCs in animal models and in human clinical trials. Understanding the mechanisms behind MSC cell fate determination is not easy, because the molecular processes that drive engraftment and differentiation are complex. Even in an in vitro system, the molecular cues necessary to induce differentiation are not easily identified or reproduced. In this Perspective, we emphasize the importance of microenvironmental factors in culture and suggest that MSC differentiation in vitro is regulated by a two-stage mechanism involving preconditioning by factors in the culture microenvironment followed by response to soluble differentiating factors.

Adult↗

PubMed2006

Microenvironmental niches in the bone marrow required for B-cell development.

B-cell development is known to occur in a complex bone-marrow microenvironment but its functional organization remains unclear. It is thought that bone-marrow stromal cells create distinct microenvironments, known as niches, that provide support for haematopoiesis and B-cell development. Although it has been more than 20 years since the development of a culture system that allows the growth of B-cell progenitors on bone-marrow-derived stromal cells in vitro, it is only recently that studies have provided a novel basis for understanding the nature of the niches for B-cell development in vivo. This article summarizes the recent advances in research on the earliest B-cell precursors, their requisite environmental factors and the cellular niches that supply these factors and maintain B cells during their development.

Animals↗

PubMed2006

Erythroblastic islands: specialized microenvironmental niches for erythropoiesis.

PURPOSE OF REVIEW: This review focuses on current understanding of molecular mechanisms operating within erythroblastic islands including cell-cell adhesion, regulatory feedback, and central macrophage function. RECENT FINDINGS: Erythroblasts express a variety of adhesion molecules and recently two interactions have been identified that appear to be critical for island integrity. Erythroblast macrophage protein, expressed on erythroblasts and macrophages, mediates cell-cell attachments via homophilic binding. Erythroblast intercellular adhesion molecule-4 links erythroblasts to macrophages through interaction with macrophage alphav integrin. In intercellular adhesion molecule-4 knockout mice, erythroblastic islands are markedly reduced, whereas the erythroblast macrophage protein null phenotype is severely anemic and embryonic lethal. Retinoblastoma tumor suppressor (Rb) protein stimulates macrophage differentiation by counteracting inhibition of Id2 on PU.1, a transcription factor that is a crucial regulator of macrophage differentiation. Rb-deficient macrophages do not bind Rb null erythroblasts and the Rb null phenotype is anemic and embryonic lethal. Lastly, extruded nuclei rapidly expose phosphatidylserine on their surface, providing a recognition signal similar to apoptotic cells. SUMMARY: Although understanding of molecular mechanisms operating within islands is at an early stage, tantalizing evidence suggests that erythroblastic islands are specialized niches where intercellular interactions in concert with cytokines play critical roles in regulating erythropoiesis.

Animals↗

PubMed2002

Functional demonstration of intrathymic binding sites and microvascular gates for prothymocytes in irradiated mice.

Quantitative intrathymic (i.t.) and i.v. adoptive transfer assays for prothymocytes show strict log dose saturation kinetics, consistent with a finite number of i.t. binding sites (microenvironmental niches). This inference is supported here by demonstration of competitive antagonism obeying one-on-one receptor occupancy kinetics during the establishment of thymic chimerism in irradiated adult mice. The results of primary and secondary transfer experiments suggested that hematogenous precursors (i) enter specific i.t. niches between 4 and 24 h after injection, (ii) compete reversibly with subsequently introduced precursors, (iii) establish insurmountable competition within 5-7 days, (iv) mature through the initial stages of thymocytopoiesis preceding proliferative expansion, and (v) vacate the niches between 7 and 14 days after entry. The results also suggested that, as in non-irradiated mice, prothymocyte importation in irradiated mice is a gated phenomenon. Gate closure was indicated by the inability of i.v.-, but not i.t.-, injected bone marrow (BM) cells to induce thymic chimerism when administered 7--14 days after a primary injection and gate opening by the ability of i.v.-injected BM cells to induce thymic chimerism in competition with circulating host prothymocytes. Gate closing was log dose-responsive and could be induced in individual thymic lobes by unilateral i.t. injection, whereas gate opening, which occurs bilaterally, was not initiated until most of the niches for prothymocytes had been vacated. We therefore posit the existence of a series of associated microvascular gates and microenvironmental niches that act in concert to regulate prothymocyte importation and early thymocyte differentiation.

Adoptive Transfer↗

PubMed2006

Regulation of intrathymic T-cell development by Lunatic Fringe- Notch1 interactions.

Intrathymic Notch1 signaling critically regulates T-lineage specification and commitment as well as T-cell progenitor survival and differentiation. Notch1 activation is continuously required during progression of early CD4/CD8-double-negative thymocytes to the CD4/CD8-double-positive stage. This developmental transition occurs as thymocytes migrate from the corticomedullary junction (CMJ) to the outer subcapsular zone (SCZ) of the thymus. Members of two families of structurally distinct Notch ligands, Delta-like 1 and Jagged-1, are expressed by cortical thymic epithelial cells, but it is not known which ligands are functionally required within the CMJ and SCZ microenvironmental niches. Our laboratory has investigated this question by genetically manipulating thymocyte expression of Lunatic Fringe (L-Fng), a glycosyltransferase that enhances sensitivity of Notch receptors to Delta-like ligands. This approach has revealed that low-threshold intrathymic Notch1 signals instruct multipotent thymus-seeding progenitors to suppress their B-cell potential and choose the T-cell fate. This strategy has also revealed that Delta-like Notch ligands are functionally limiting in both the CMJ and SCZ microenvironmental niches. Finally, we discuss our recent demonstration that L-Fng-mediated competition for Delta-like ligands is an important mechanism for regulating thymus size.

Animals↗

PubMed2005

Stem cell engraftment at the endosteal niche is specified by the calcium-sensing receptor.

During mammalian ontogeny, haematopoietic stem cells (HSCs) translocate from the fetal liver to the bone marrow, where haematopoiesis occurs throughout adulthood. Unique features of bone that contribute to a microenvironmental niche for stem cells might include the known high concentration of calcium ions at the HSC-enriched endosteal surface. Cells respond to extracellular ionic calcium concentrations through the seven-transmembrane-spanning calcium-sensing receptor (CaR), which we identified as being expressed on HSCs. Here we show that, through the CaR, the simple ionic mineral content of the niche may dictate the preferential localization of adult mammalian haematopoiesis in bone. Antenatal mice deficient in CaR had primitive haematopoietic cells in the circulation and spleen, whereas few were found in bone marrow. CaR-/- HSCs from fetal liver were normal in number, in proliferative and differentiative function, and in migration and homing to the bone marrow. Yet they were highly defective in localizing anatomically to the endosteal niche, behaviour that correlated with defective adhesion to the extracellular matrix protein, collagen I. CaR has a function in retaining HSCs in close physical proximity to the endosteal surface and the regulatory niche components associated with it.

Animals↗

PubMed1996

The role of stromal cell heparan sulphate in regulating haemopoiesis.

Intimate contact between haemopoietic progenitor cells and elements of the bone marrow stroma is required for progenitor cell proliferation and differentiation. It is believed that the stroma provides particular niches for the development of haemopoietic cells of different lineages. Cytokines, stromal cell surface molecules and molecules of the stromal extracellular matrix all contribute to defining these microenvironmental niches. Data obtained using an in vitro model of haemopoiesis support the view that progenitor cell adhesion to stroma is mediated by multiple receptor-ligand interactions. The possibility of a tethering step, mediated by the engagement of stromal cell heparan sulphate with its ligands on the progenitor cells, preceding stable cell adhesion is discussed. The role of stromal cell heparan sulphate is likely to include cytokine presentation to progenitors as well as the tethering of progenitors to stroma. It is proposed that intracellular signals induced by progenitor cell adhesion to stroma act in association with cytokine induced signals to regulate progenitor cell proliferation and differentiation.

Adipose Tissue↗

PubMed2006

Molecular characterization of retinal stem cells and their niches in adult zebrafish.

BACKGROUND: The persistence in adult teleost fish of retinal stem cells that exhibit all of the features of true 'adult stem cells'--self-renewal, multipotency, and the capacity to respond to injury by mitotic activation with the ability to regenerate differentiated tissues--has been known for several decades. However, the specialized cellular and molecular characteristics of these adult retinal stem cells and the microenvironmental niches that support their maintenance in the differentiated retina and regulate their activity during growth and regeneration have not yet been elucidated. RESULTS: Our data show that the zebrafish retina has two kinds of specialized niches that sustain retinal stem cells: 1) a neuroepithelial germinal zone at the interface between neural retina and ciliary epithelium, called the ciliary marginal zone (CMZ), a continuous annulus around the retinal circumference, and 2) the microenvironment around some Müller glia in the differentiated retina. In the uninjured retina, scattered Müller glia (more frequently those in peripheral retina) are associated with clusters of proliferating retinal progenitors that are restricted to the rod photoreceptor lineage, but following injury, the Müller-associated retinal progenitors can function as multipotent retinal stem cells to regenerate other types of retinal neurons. The CMZ has several features in common with the neurogenic niches in the adult mammalian brain, including access to the apical epithelial surface and a close association with blood vessels. Müller glia in the teleost retina have a complex response to local injury that includes some features of reactive gliosis (up-regulation of glial fibrillary acidic protein, GFAP, and re-entry into the cell cycle) together with dedifferentiation and re-acquisition of phenotypic and molecular characteristics of multipotent retinal progenitors in the CMZ (diffuse distribution of N-cadherin, activation of Notch-Delta signaling, and expression of rx1, vsx2/Chx10, and pax6a) along with characteristics associated with radial glia (expression of brain lipid binding protein, BLBP). We also describe a novel specific marker for Müller glia, apoE. CONCLUSION: The stem cell niches that support multi-lineage retinal progenitors in the intact, growing and regenerating teleost retina have properties characteristic of neuroepithelia and neurogenic radial glia. The regenerative capacity of the adult zebrafish retina with its ability to replace lost retinal neurons provides an opportunity to discover the molecular regulators that lead to functional repair of damaged neural tissue.

Aging↗

PubMed2005

The kinetics of clonal dominance in myeloproliferative disorders.

To study clonal evolution in myeloproliferative disorders, we used stochastic models of hematopoiesis for mouse and cat, species for which the in vivo kinetics of hematopoietic stem cells (HSCs) have been experimentally defined. We determined the consequence if 1 HSC became able to survive without the support of a microenvironmental niche while the rest of its behavior did not change. Neoplastic cells persisted and dominated hematopoiesis in 14% of mice and 17% of cats, requiring mean times of 2.5 +/- 0.5 and 7.0 +/- 1.2 years, respectively (n=1000 simulations/species). In both species, when the number of neoplastic HSCs exceeded 0.5% of all HSCs, clonal dominance was inevitable. Our results can explain the absence of clonal myeloproliferative disorders in mice (lifetime, 2 years), are consistent with clinical observations in cats, and provide insight into the progression of chronic myelogenous leukemia (CML) in humans. They also demonstrate that competition for microenvironmental support can lead to the suppression of normal hematopoiesis as neoplasia evolves. Toxic or immunologic suppression of normal HSCs is not required.

Animals↗

PubMed2007

Upregulation of Flk-1 by bFGF via the ERK pathway is essential for VEGF-mediated promotion of neural stem cell proliferation.

Neural stem cells (NSCs) constitute the cellular basis for embryonic brain development and neurogenesis. The process is regulated by NSC niche including neighbor cells such as vascular and glial cells. Since both vascular and glial cells secrete vascular endothelial growth factor (VEGF) and basic fibroblast growth factor (bFGF), we assessed the effect of VEGF and bFGF on NSC proliferation using nearly homogeneous NSCs that were differentiated from mouse embryonic stem cells. VEGF alone did not have any significant effect. When bFGF was added, however, VEGF stimulated NSC proliferation in a dose-dependent manner, and this stimulation was inhibited by ZM323881, a VEGF receptor (Flk-1)-specific inhibitor. Interestingly, ZM323881 also inhibited cell proliferation in the absence of exogenous VEGF, suggesting that VEGF autocrine plays a role in the proliferation of NSCs. The stimulatory effect of VEGF on NSC proliferation depends on bFGF, which is likely due to the fact that expression of Flk-1 was upregulated by bFGF via phosphorylation of ERK1/2. Collectively, this study may provide insight into the mechanisms by which microenvironmental niche signals regulate NSCs.

Animals↗

PubMed2026

ARCADIA reveals spatially dependent transcriptional programs through integration of scRNA-seq and spatial proteomics.

MOTIVATION: Cellular states are strongly influenced by spatial context, but single-cell RNA sequencing (scRNA-seq) loses information about local tissue organization, while spatial proteomic assays capture limited marker panels that constrain transcriptomic inference. Integrating these modalities can elucidate how spatial niches shape transcriptional programs, yet existing approaches depend on either feature-level correspondence such as gene-protein linkage or cell-level barcode pairing, which is often unavailable. RESULTS: We present ARCADIA (ARchetype-based Clustering and Alignment with Dual Integrative Autoencoders), a generative framework for cross-modal integration that operates without cell barcode pairing and does not assume direct feature-to-feature correspondence. ARCADIA identifies modality-specific archetypes, that is, convex combinations of cells representing extreme phenotypic states, and aligns these anchors across modalities by minimizing the discrepancy between their cell-type composition profiles. The aligned archetypes define a shared coordinate system that anchors dual variational autoencoders (VAEs) trained with cross-modal geometric regularization, preserving archetype structure and spatial neighborhood information while enabling bidirectional translation between modalities. On semi-synthetic CITE-seq data, ARCADIA outperforms existing weak-linkage methods. Applied to independent human tonsil scRNA-seq and CODEX data, ARCADIA reconstructs known tissue architecture and reveals spatially dependent transcriptional programs linking B-cell maturation and T-cell activation or exhaustion to microenvironmental niches. AVAILABILITY AND IMPLEMENTATION: Source code is accessible at https://github.com/azizilab/ARCADIA_public. Reproducibility scripts and data are available at https://github.com/azizilab/arcadia_reproducibility.

Proteomics↗

PubMed1990

Stromal cells in haemopoiesis.

Stromal cells of the bone marrow can provide the growth-promoting and differentiation-inducing molecules which are necessary for haemopoiesis. While the nature of these stimuli is largely unknown, the development of haemopoietic cells in association with stromal cells requires intimate cell contact. Molecules of the extracellular matrix, such as heparan sulphate, are able to bind growth factors and in this way the stromal cells may form microenvironmental niches which preferentially promote development of multipotent and committed cells along discrete lineages. Cells from some patients with acute and chronic myeloid and lymphoid leukaemias are defective in their ability to interact with stromal cells and consequently cannot survive in stromal cell-mediated long-term marrow cultures. We have exploited this phenomenon to obtain normal haemopoietic cells from patients with leukaemia, and to use these cells for successful autografting in patients with acute and chronic myeloid leukaemias.

Animals↗

PubMed2005

Innate-like B cells.

Numerous studies in several species have shown that certain subsets of T and B lymphocytes express antigen receptors which are either semi-invariant, or germline encoded, and often autoreactive. In the case of B cells they appear to use a distinct immune recognition strategy during developmental selection and functional activation. These B cells respond to foreign antigens, and have the ability to protect against a variety of infections; however, they can also react with self or neoself antigens. They appear to use the latter as positively selecting ligands facilitating their entry into and maintenance in a functional repertoire, as well as providing cues for positioning themselves in strategic microenvironmental niches in the immune system and at interfaces with the environment. These innate-like B cell subsets form a bridge between the rapidly occurring innate immune responses, and the slower acting primary, T cell-dependent, adaptive antibody response by providing a rapid T cell-independent antibody response.

Animals↗

PubMed1991

Stromal cell-dependent terminal maturation of K562 erythroleukaemia cells.

K562 cells were cultured over monolayers of various cell types for four days and the characteristics of those cells which became firmly adherent to such monolayers studied. The monolayers used were composed of stromal cells derived from human bone marrow, two human fibroblast lines, human umbilical cord-derived endothelial cells, bone marrow macrophages, blood-monocyte-derived macrophages, a neuroglial cell line (U-251 MG) or mixtures of some of the above. The data showed that K562 cells adhered much more frequently to fibroblasts than to other cell types. In the case of some marrow-derived stromal cell layers grown in human group AB serum, the firmly adherent K562 cells showed morphological evidence of nuclear and cytoplasmic maturation and, especially in the presence of haemin, sometimes developed into erythrocyte-like cells. The maturing cells were weakly or moderately benzidine-positive. By contrast, K562 cells which adhered to monolayers of fibroblasts, endothelial cells or macrophages showed little or no maturation and were either benzidine-negative or only very weakly positive. In experiments employing monolayers made up by mixing skin fibroblasts and endothelial cells or skin fibroblasts, endothelial cells and macrophages, some adherent K562 cells developed into cells resembling early and late polychromatic normoblasts and erythrocytes. The maturing cells were moderately or strongly benzidine-positive. Maturation was most marked in K562 cells adherent to regions of the monolayer containing all three of the stromal cell types. The results indicate that the optimal microenvironmental niche for the development of K562 cells into erythroblasts and erythrocytes may consist of a cluster of closely associated fibroblasts, macrophages and endothelial cells.

Benzidines↗

PubMed2005

Lineage-restricted neural precursors survive, migrate, and differentiate following transplantation into the injured adult spinal cord.

Fetal spinal cord from embryonic day 14 (E14/FSC) has been used for numerous transplantation studies of injured spinal cord. E14/FSC consists primarily of neuronal (NRP)- and glial (GRP)-restricted precursors. Therefore, we reasoned that comparing the fate of E14/FSC with defined populations of lineage-restricted precursors will test the in vivo properties of these precursors in CNS and allow us to define the sequence of events following their grafting into the injured spinal cord. Using tissue derived from transgenic rats expressing the alkaline phosphatase (AP) marker, we found that E14/FSC exhibited early cell loss at 4 days following acute transplantation into a partial hemisection injury, but the surviving cells expanded to fill the entire injury cavity by 3 weeks. E14/FSC grafts integrated into host tissue, differentiated into neurons, astrocytes, and oligodendrocytes, and demonstrated variability in process extension and migration out of the transplant site. Under similar grafting conditions, defined NRP/GRP cells showed excellent survival, consistent migration out of the injury site and robust differentiation into mature CNS phenotypes, including many neurons. Few immature cells remained at 3 weeks in either grafts. These results suggest that by combining neuronal and glial restricted precursors, it is possible to generate a microenvironmental niche where emerging glial cells, derived from GRPs, support survival and neuronal differentiation of NRPs within the non-neurogenic and non-permissive injured adult spinal cord, even when grafted into acute injury. Furthermore, the NRP/GRP grafts have practical advantages over fetal transplants, making them attractive candidates for neural cell replacement.

Alkaline Phosphatase↗

PubMed2000

The immunobiology of gastrointestinal nematode infections in ruminants.

The major gastrointestinal nematode parasites of ruminants all belong to the Order Strongylida and the family Trichostrongyloidea. Despite this close evolutionary relationship, distinct differences exist in the microenvironmental niches occupied by the developmental stages of the various parasites, which may account for the variable susceptibility of the different parasite species to the immune effector mechanisms generated by the host. In addition, different manifestations of resistance have been observed against the adult and larval stages of the same parasite species, and even against the same parasite stage. In particular, both rapid and delayed rejection of infective larval stages of gastrointestinal nematode parasites has been documented. This review will give an overview of the various manifestations of resistance to gastrointestinal nematode parasites of ruminants, as well as the immune mechanisms and antigens associated with the generation of immunity by the ruminant hosts to these parasites. In addition, a working model is provided aimed at reconciling most of the present knowledge on the different immune responses generated during infection with the various parasite rejection profiles. Extrapolation of these results to field conditions will need to take into account the variability imposed by seasonal changes and management practices, as well as the individual variability in immune responsiveness present in outbred animal populations.

Animals↗

PubMed2003

Anatomical loci of HIV-associated immune activation and association with viraemia.

BACKGROUND: Lymphocyte activation, associated with vaccination or infection, can be measured by positron emission tomography (PET). We investigated the ability of PET to detect and measure magnitude of lymph-node activation among asymptomatic HIV-1-infected individuals. METHODS: Initially we assessed PET response in eight HIV-1-uninfected individuals who had received licensed killed influenza vaccine. In an urban teaching hospital, we recruited 12 patients recently infected with HIV-1 (<18 months since seroconversion) and 11 chronic long-term HIV-1 patients who had stable viraemia by RT-PCR (non-progressors). After injection with fluorine-18-labelled fluorodeoxyglucose, patients underwent PET. We correlated summed PET signal from nodes with viral load by linear regression on log-transformed values. FINDINGS: Node activation was more localised after vaccination than after HIV-1 infection. In early and chronic HIV-1 disease, node activation was greater in cervical and axillary than in inguinal and iliac chains (p<0.0001), and summed PET signal correlated with viraemia across a 4 log range (r2=0.98, p<0.0001). Non-progressors had small numbers of persistently active nodes, most of which were surgically accessible. INTERPRETATION: The anatomical restriction we noted may reflect microenvironmental niche selection, and tight correlation of PET signal with viraemia suggests target-cell activation determines steady-state viral replication.

Adolescent↗