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Profiling the activity of G proteins in patient-derived tissues by rapid affinity-capture of signal transduction proteins (GRASP).

The next phase in molecular medicine will require the ability to identify signal transduction events inside a cell, in the biologic context of the disease-host interface and at a given point in time. New technologies are needed to profile the activity of these signaling pathways in patient tissue rather than cultured cell lines since the tumor-host microenvironment influences the cellular proteome. We introduce such a technology, rapid affinity capture of signaling proteins (GRASP), to investigate the activity of signaling pathways from patient-derived carcinomas and benign epithelial surfaces and apply it to studying important signaling events in ovarian carcinoma. During the progression from benign ovarian epithelium to invasive carcinoma, there is loss of repression of Rho A as evidenced by its dissociation from its inhibitor, Rho Guanine Nucleotide Dissociation Inhibitor (RhoGDI). GRASP is more informative than simply profiling transcript or protein levels. Furthermore, GRASP coupled with mass spectrometry allowed us to identify a protein-binding partner of RhoGDI, demonstrating the power of this technology in the discovery of potentially novel protein-protein interactions. GRASP represents an advance in the field of proteomics as it detects protein interactions present in cells as they exist in their native tissue microenvironment.

Carcinoma↗

Human blood-derived macrophages enhance barrier function of cultured primary bovine and human brain capillary endothelial cells.

The characteristic properties of the blood-brain barrier (BBB) forming brain capillary endothelial cells (BCEC) are modulated by their microenvironment, but the cellular sources of the induction signals are still unclear. Apart from astrocytes, another cell type in close contact with cerebral blood vessels is the perivascular macrophages, which are known to be regularly replaced by blood-derived monocytic precursor cells. It is unknown if, and how, these cells may interact with the cerebral endothelium and modulate its BBB-specific functions. In the present study, a cell culture model of the BBB was used to investigate the effect of blood-derived human macrophages on the permeability of cultured bovine and human BCEC, determined by a transendothelial electrical resistance (TEER) measurement. We found that the TEER of postconfluent BCEC was considerably increased by a non-contact coculture with macrophages. After 24 h, we found a TEER augmentation of over 50% compared with the control without coculture, and this effect was comparable to the response of BCEC to a C6 glioma cells coculture. Stimulation or HIV-1 infection of the macrophages did not alter their effect on BCEC monolayer permeability. Investigation of signal transduction pathways showed that TEER increase of BCEC due to macrophage coculture was cAMP-independent and involves neither phospholipase C, protein kinase C nor calmodulin. Our findings demonstrate that macrophages are able to modulate BBB-specific functions in cultured BCEC. Thus, these cells or cerebral cells of monocytic origin (e.g. perivascular macrophages), may be part of the microenvironment of BCEC that modulates their specific properties in vivo.

Adenylyl Cyclases↗

The development of the Xenopus retinofugal pathway: optic fibers join a pre-existing tract.

The developing optic nerve and tract have received considerable attention in recent years, but the cellular and subcellular microenvironment of the growing axons has not been described. In the belief that such a description is essential (though certainly not sufficient) for an understanding of pathway formation, we have examined the normal development of the retinofugal projection of Xenopus laevis. Optic fibers were labeled anterogradely at the retina with horseradish peroxidase (HRP) or the carbocyanine dye, DiI, at stages 32 to postmetamorphosis. The brains were examined both as whole mounts and in sections, light- and electron-microscopically, with the emphasis on tracts associated with the route of the optic fibers. At stage 32, two ventral commissures were present, the anterior and postoptic. They were immediately subjacent to the pia. All tracts and even isolated axons were in similarly superficial locations. The first deep pathway (separated from the pia by cell nuclei) was seen at stage 46; it was a dorsal commissure, probably the posterior. The first retinal axons passed from the optic stalk into the ventral part of the diencephalon, where they coursed along the rostral edge of the postoptic commissure, and maintained this position, relative to the other fibers in the tract of the commissure, throughout the remainder of their contralateral trajectory. They reached the presumptive thalamic and tectal termination sites and arborized. Subsequent optic axons followed this same route, thus enlarging the optic pathway relative to the more slowly growing nonoptic part of the commissure and its tract. Electron microscopy revealed, as early as stage 35, specialized contacts between cellular processes in the neuropil. These contacts had the form of symmetric membranous thickenings; some were associated with vesicles and were presumed to be synapses. We conclude that the early forebrain and midbrain have only two ventral commissural pathways, and most axons that grow out after these pathways have formed add to them rather than establish new tracts. The optic axons travel a stereotyped pathway alongside a pre-existing tract associated with the postoptic commissure. The possibility that optic fiber outgrowth is normally influenced by pre-existing tracts is discussed in relation to recent experimental investigations of fiber growth from ectopic eyes.

Animals↗

SCMO: a deep learning model integrating the single-cell resolution TME ecosystem and multi-omics for survival prediction in CRC patients.

BACKGROUND: Colorectal cancer (CRC) remains a leading cause of global cancer mortality, highlighting the need for precise survival prediction to guide clinical decisions. Although tissue-level multi-omics is widely utilized for survival prediction, its limited resolution cannot capture tumor heterogeneity. Single-cell RNA sequencing (scRNA-seq) enables dissection of the tumor microenvironment (TME) at cellular resolution, supporting personalized prognostic assessment. METHODS: We collected 213 CRC scRNA-seq samples and established a CRC-specific TME atlas comprising 339,060 cells. Using this atlas as a reference, we deconvolved bulk RNA-seq data from TCGA-CRC cohort with the EcoTyper algorithm to reconstruct TME features. Clinical, genomic, and transcriptomic data were obtained from the Xena platform; microbial data were sourced from the BIC database. We integrated TME and multi-omics features through a self-normalizing neural network to construct a deep learning model (single-cell resolution TME ecosystem with multi-omics data [SCMO]) for survival prediction. To enhance interpretability, we utilized the Integrated Gradients algorithm and spatial transcriptomic data to analyze multi-omics and TME features. We performed anticancer drug screening with tumor necrosis factor receptor-associated protein 1 (TRAP1), a critical feature according to the Integrated Gradients algorithm, as a potential target. RESULTS: We identified 13 survival-related TME features from the CRC-specific atlas: 12 cell states and one multi-cellular ecosystem. SCMO, which combined TME and multi-omics features, improved survival prediction and outperformed existing methods, achieving a concordance index of 0.762. The SCMO demonstrated robust performance for long-term predictions, achieving areas under the curve (AUCs) of 0.752, 0.772, and 0.869 for 1-, 3-, and 5-year predictions in the training set, with corresponding test set AUCs of 0.639, 0.756, and 0.772. TME features from the SCMO model revealed that ecosystem density increased with CRC malignancy. Multi-omics features included TRAP1 as a potential drug target. Drug screening identified saikosaponin A as a novel TRAP1 inhibitor, and its anticancer activity was validated in vitro. We developed SCMO-Lite, a simplified model incorporating 12 high-attribution-weight multi-omics features, which demonstrated robust risk stratification. CONCLUSIONS: SCMO combines analytical precision with biological interpretability, offering novel insights for oncology survival prediction.

Humans↗

Dominance of CCL22 over CCL17 in induction of chemokine receptor CCR4 desensitization and internalization on human Th2 cells.

Chemokines and their receptors play a pivotal role in controlling T cell trafficking in immunity and inflammation. Two chemokines, CCL17 and CCL22, activate the chemokine receptor CCR4, expressed on functionally distinct subsets of T cells: cutaneous leukocyte-associated antigen (CLA)+ skin-homing, T helper (Th) 2, and CD25+ T suppressor cells. Here, we compared the ability of CCL17 and CCL22 to promote CCR4 internalization as a mechanism of regulation of receptor function on human Th2 cells. We report that CCL22 is a potent and rapid inducer of CCR4 internalization, while CCL17 is not. CCR4 internalization does not require G protein coupling, while being dependent on lipid rafts integrity and clathrin-coated pits functionality. Cell surface disappearance of CCR4 is rapidly reversed upon removal of exogenous ligand by virtue of receptor recycling. CCR4 internalization leads to a loss of functional responsiveness, while recovery of surface expression leads to re-acquisition of chemotactic sensitivity of Th2 cells. The differential CCR4 desensitization and internalization reported here and the distinct expression patterns of CCL17 and CCL22 observed in vivo suggest that while CCL17 may act first on CCR4 at the endothelial surface to promote vascular recognition, CCL22 could subsequently engage the receptor within the tissue microenvironment to guide cellular localization.

Chemokine CCL17↗

Extracellular matrix deposition by fibroblasts is necessary to promote capillary-like tube formation in vitro.

The contribution of the cellular and fibrillar microenvironment to angiogenesis still remains unclear. Our purpose was to evaluate the effect of the extracellular matrix deposited by fibroblasts on the capacity of human endothelial cells to form capillaries in vitro. We have drastically decreased the amount of extracellular matrix surrounding fibroblasts in our model of endothelialized-reconstructed connective tissue (ERCT) by culturing it without ascorbate. Under these conditions, the number of capillary-like tubes (CLT) formed by endothelial cells was reduced by up to 10-fold after 31 days of culture compared to controls. This decrease was due neither to a variation of MMP-2 and MMP-9 secretion, nor to a reduction in the number of fibroblasts and/or endothelial cells, or a diminution of fibroblast growth factor 2 (FGF2) synthesis. The secretion of vascular endothelial growth factor (VEGF) by fibroblasts accounted for 25-70% of the capillary-like tube formation when tissues were cultured in the presence or absence of ascorbate, as demonstrated by VEGF-blocking studies. The culture of endothelial cells on a similar extracellular matrix but in the absence of living fibroblasts did not promote the formation of CLT, even when tissues were fed with fibroblast-conditioned medium. Thus, the deposition of a rich extracellular matrix by living fibroblasts appeared necessary, but not sufficient to promote capillary-like formation. Fibroblasts seem to induce endothelial cells to spontaneously form CLT by secreting and organizing an abundant extracellular matrix, which creates a microenvironment around cells that could in turn trap growth factors produced by fibroblasts and promote three-dimensional cell organization.

Ascorbic Acid↗

Microenvironmental regulation of hematopoietic stem cells.

A major challenge in hematopoietic biology is the description and understanding of the molecular mechanisms responsible for the regulation of the primitive stem cell compartment. In one sense there exists a wealth of functional and physical properties which provide insight into the biology of the stem cell and its clonal progeny. However, much of this information is descriptive and available only as a function of complex in vivo assays. In order to move beyond these limitations, in vitro systems which accurately recapitulate the self-renewal, differentiation and proliferative behaviors of stem cells are required. We have approached this issue by focusing on the in vivo stem cell microenvironment. Dissection of this microenvironment into discrete cellular entities has yielded a cell line with in vitro stem cell supportive properties consistent with those which might be expected in a stem cell niche. Studies are summarized which suggest that a single stromal cell line provides a milieu which facilitates the in vitro maintenance of transplantable stem cells as well as the generation of large populations of committed progenitors. It is anticipated that this system will allow a direct analysis of stem cell regulatory pathways.

Animals↗

Chondrocytes are released as viable cells during cartilage resorption associated with the formation of intrachondral canals in the rat tibial epiphysis.

The development of cartilage canals is the first event of the ossification of the epiphyses in mammals. Canal formation differs from vascular invasion during primary ossification, since the former involves resorption of resting cartilage and is uncoupled from bone deposition. To learn more about the fate of resorbed chondrocytes during this process, we have carried out structural, cell proliferation, and in situ hybridization studies during the first stages of ossification of the rat tibial proximal epiphysis. Results concerning the formation of the cartilage canals implied the release of resting chondrocytes from the cartilage matrix to the canal cavity. Released chondrocytes had a well-preserved structure, expressed type-II collagen, and maintained the capacity to divide. All these data suggested that chondrocytes released into the canals remained viable for a specific time. Analysis of the proliferative activity at different regions of the cartilage canals showed that the percentage of proliferative chondrocytes at areas of active cartilage resorption was significantly higher than that in zones of low resorption. These results are consistent with the hypothesis that resting chondrocytes surrounding canals have a role in supplying cells for the development of the secondary ossification center. Since released chondrocytes are at an early stage of differentiation greatly preceding their entry into the apoptotic pathway and are exposed to a specific matrix, cellular, and humoral microenvironment, they might differentiate to other cell types and contribute to the ossification of the epiphysis.

Acid Phosphatase↗

Inducible nitric oxide synthase and apoptosis in human B cell lymphomas.

Nitric oxide synthases are isoenzymes that catalyse the synthesis of nitric oxide (NO). NO plays both pathological and physiological roles depending on its rate of synthesis and concentration in cellular source and microenvironment. Apoptosis is an important biological factor in lymphomas. This study evaluates expression of inducible nitric oxide synthase (iNOS) in human lymphomas and its relation with apoptosis. This study comprised 46 cases of B-cell lymphoma. The lymphomas were classified as 3 mantle cell, 5 marginal zone, 4 follicular, 2 Burkitt, 25 diffuse large cell, 2 anaplastic large cell, 3 lymphoblastic, 2 lymphoplasmacytic according to WHO classification of lymphoid neoplasms. Hematoxylin eosin slides of the cases were reviewed and immunoperoxidase technique was performed iNOS and Caspase monoclonal antibodies to selected sections of each case. Antigen staining was carried out with iNOS and Caspase proteins and Ultravision Polyvalent, HRP-AEC kit (Neomarkers-Biogen USA). For the evaluation of iNOS and Caspase, tumor areas with a high density of expression were chosen. Positive stained cells were counted in 5 different areas at a magnification x 40 by an Olympus B x 51 microscope in each case. The iNOS and Caspase expressions were independently recorded by four pathologists and the results were averaged. All of the cases were positive for the iNOS and Caspase. But there is not a statistically important relation between lymphoma grade and iNOS activity. We could not find a correlation between iNOS and patients age. This study reveals the capacity of B-cell neoplasms to express iNOS in situ. In conclusion, our study revealed that there is a positive relation between iNOS expression and apoptosis (p = 0.032 spearman correlation).

Adolescent↗

Integrin-mediated cell-matrix interactions for prosurvival and antiapoptotic signaling after genotoxic injury.

Interactions of cells with their microenvironment modify the cellular sensitivity of normal and tumor cells for radiation- and drug-induced genotoxic injury. The preexistent or acquired cellular resistance against such agents aggravates anticancer therapies and, therefore, complicates the recovery of patients. Recently, integrin-mediated adhesion was shown to improve cell survival of both normal and cancer cells following DNA damage. Here, I will discuss the role of integrins and integrin-mediated signaling cascades in the survival or death response upon genotoxic stress. Detailed knowledge of the responsible molecular processes might provide implications for putative therapies targeting integrins or integrin-associated molecules to achieve an optimization of anticancer treatments.

Antineoplastic Agents↗

Characterization of connexin 30.3 and 43 in thymocytes.

During maturation, thymocytes interact directly and indirectly with different cell types of the thymic microenvironment. Such a cellular communication has been basically ascribed to soluble factors and surface receptors. However, little attention has been given to cellular communication mediated by gap junctions. The existence of these intercellular channels in the immune system remained a controversial issue since the 1970s until recently, when a growing body of evidence has indicated their presence and physiological roles in the immune system. In this work, we investigated whether thymocytes express gap junction-forming proteins (connexins, Cx) and are capable of forming functional intercellular channels. Using RT-PCR, we demonstrated that thymocytes express the mRNA for two Cx isoforms: Cx30.3 and Cx43, but not for Cx26, Cx30, Cx31, Cx31.1, Cx32, Cx33, Cx36, Cx37, Cx40, Cx45, Cx46, and Cx50. In addition, the presence of Cx30.3 and Cx43 was confirmed using different techniques (RNase protection assay, western blot and immunofluorescence). However, despite the expression of these two Cxs, we did not detect functional homocellular coupling between thymocytes or between EL-4 cells (a Cx43 expressing thymic lymphoma-derived cell line) or heterocellular coupling between thymocytes and thymic epithelial cells (TEC) or between EL-4 and TEC in unstimulated conditions. Concluding, in this study, we described for the first time the expression of connexins in thymocytes, which may constitute a new molecule having a functional role in thymocytes maturation.

Animals↗

B cell memory and the long-lived plasma cell.

The germinal center reaction is pivotal to the induction of B cell memory. The signals that regulate this complex microenvironment, with their cellular and molecular consequences, underpin long-term protective immunity. Recent studies have identified many key regulators of the germinal center cycle and have revealed an array of cellular outcomes that further define the memory B cell compartment.

Animals↗

Cord blood serum affects T cells ability to produce and respond to IL-2.

The current literature suggests that cord blood (CB) cells are functionally immature. We previously reported that CB sera inhibit T cell proliferation and suggested that the microenvironment in which CB T cells reside may be, in part, responsible for their reduced function. In this study we have tried to explain some of the actions of the CB sera on peripheral blood mononuclear cells (PBMC). We showed that, as expected CB sera decreased the anti-CD3 and anti-CD28-induced proliferative response of PBMC (p < 0.01) but unexpectedly, increased the interleukin-2 (IL-2) specific proliferation of both a human T cell line (p < 0.005) and T cells within a mononuclear cell population (p < 0.05). These findings prompted us to analyse the effect of CB sera on the T cell ability to make and respond to IL-2. Stimulation of T cells in the presence of CB sera increased the frequency of IL-2 producing cells (p < 0.005) (but not the amount of IL-2 secreted) and resulted in a higher expression of CD25 (p < 0.05). Furthermore CB sera (in the presence and absence of IL-2) made the cells apoptose less (p < 0.005) than adult sera. Our results go some way to explaining the effect of the CB microenvironment on CB cellular function.

Apoptosis↗

Volumetric DNA microscopy for mapping spatial transcriptomes in three dimensions.

The architecture and function of biological systems are inherently three-dimensional, yet most existing spatial transcriptomic technologies remain restricted to thin tissue sections, limiting their capacity to resolve cellular organization and microenvironments within intact tissue volumes. To address this limitation, we developed volumetric DNA microscopy, a scalable, optics-free approach for spatial transcriptome profiling directly within intact biological specimens. The method encodes spatial information into DNA molecules that form a dense intermolecular network in situ, enabling the reconstruction of three-dimensional spatial relationships through short-read sequencing and computational analysis. Here we detail the complete workflow including in situ cDNA synthesis, spatial encoding through DNA nanoball formation, dual-scale proximity bridging between neighboring nanoballs and spatial reconstruction via geodesic spectral embedding. Sequencing libraries can be generated within 7-8 d by a competent graduate-level molecular biologist, followed by standardized downstream computational analysis. Because the workflow requires only routine molecular biology reagents and a benchtop sequencer, volumetric DNA microscopy provides a versatile platform for exploring genetic and morphological features in intact tissues.

Spatial Transcriptomics↗

Expression of nitric oxide synthase isoforms and nitrotyrosine immunoreactivity by B-cell non-Hodgkin's lymphomas and multiple myeloma.

AIMS: Nitric oxide synthases (NOS) are isoenzymes that catalyse the synthesis of nitric oxide (NO). The three main NOS isoforms are: NOS1 or neuronal, NOS2 or inducible, and NOS3 or endothelial. NO plays both physiological and pathological roles, depending on its rate of synthesis and concentration, cellular source and microenvironment. Apoptosis is an important biological factor in low-grade lymphomas, and NO is able to prevent apoptosis. In-situ expression of NOS and synthesis of NO have been shown in several malignant tumours, but not in lymphoid neoplasms. This study evaluates whether human B-cell neoplasms express NOS isoforms, and nitrotyrosine (NY), which is usually interpreted as a marker of NO. METHODS AND RESULTS: We studied the expression of NOS-IR isoforms and NY-IR in 16 cases of B-cell non-Hodgkin's lymphoma (NHL) (five follicle centre cell lymphoma, four small lymphocytic/CLL, and seven diffuse large cell lymphoma), and 10 cases of multiple myeloma (MM). NOS1 was expressed in 5/10 cases of MM, and 15/16 cases of NHL. NOS2 was detected in all cases of MM, and in 14/16 cases of NHL, whereas NOS3 was positive in 3/10 of MM and in only in 1/16 cases of NHL. The expression of NY-IR was observed in 70% of MM cases, and in all cases of B-cell NHL, in a dot-like pattern in few tumour cells. CONCLUSIONS: B-cell neoplasms express neuronal and inducible NOS, and nitrotyrosine. Taken together, our results suggest that B-cell neoplasms can produce NO. The role of NO in the biology, diagnosis and prognosis of B-cell neoplasms remains to be established.

Adult↗

Hematopoietic activity of a stromal cell transmembrane protein containing epidermal growth factor-like repeat motifs.

Primitive hematopoietic stem cells are closely associated with discrete in vivo microenvironments. These "niches" are thought to provide the molecular signals that mediate stem cell differentiation and self-renewal. We have dissected the fetal liver microenvironment into distinct cellular components by establishing an extensive panel of stromal cell lines. One particular cell line maintains repopulating stem cells for prolonged in vitro culture periods. A subtraction cloning strategy has yielded a cDNA that encodes a cell surface glycoprotein with a restricted pattern of expression among stromal cell lines. This molecule, previously identified as delta-like/preadipocyte factor-1, contains epidermal growth factor-like repeats that are related to those in the notch/delta/serrate family of proteins. We have investigated the potential role of this molecule in hematopoietic stem/progenitor cell regulation. We show that the delta-like protein displays activity on purified stem cells by promoting the formation of "cobblestone areas" of proliferation. These cobblestone areas contain both primitive high-proliferative potential progenitors and in vivo repopulating stem cells.

Animals↗

Endometrial-myometrial interface: relationship to adenomyosis and changes in pregnancy.

The endometrial-myometrial interface (EMI) is an important region of the human uterus, which has attracted little research attention. This mucosal-muscular interface has characteristic features when compared with other similar interfaces in the human body. It lacks an intervening tissue layer and as a result, the endometrium sits directly on the myometrium rendering it vulnerable to invasion by the endometrium. Both endometrium and myometrium are sensitive to sex steroids, and their structure and function depend to a large extent on the sex hormonal milieu. Endometrium, which forms one border of the EMI, is a complex tissue consisting of several polarized microenvironments. At a cellular level, sex steroids interact with local mediators secreted by a variety of cell types and are important in maintaining the complex structure and function of the endometrium. Basal endometrium contains prominent aggregates of leukocytes that may be important in controlling local cell growth and function. Myometrium also has a distinct zonal anatomy. The recently described junctional zone differs structurally and functionally from the outer myometrium, although these functions are not yet clearly understood. Embryologically, it originates from müllerian ducts together with endometrium, whereas the outer myometrium has a non-müllerian origin. During early pregnancy, the EMI is disturbed by invading trophoblast. Alterations of myometrial intercellular matrix proteins together with expression of appropriate receptors by the trophoblast seem to regulate this unique interaction. The EMI also is disrupted in adenomyosis. The sequence of events taking place at the EMI during development of this pathology is still debated.

Endometriosis↗

Stimulated healing of recalcitrant wounds by topical application of enriched cell culture medium: a clinical report.

This study was designed to test the efficacy of enriched cell culture medium as a wound dressing. The rationale was to create within the wound space an optimal microenvironment, conducive to cellular proliferation, vascular granulation tissue formation, and epithelialization. This study was performed on various wounds that failed to respond to previous conventional treatments.A total of 288 wounds were within the inclusion criteria, with only contaminated and neoplastic wounds excluded. Most of the patients (80 percent) were ambulatory, and the wounds were examined by the attending physician once every 7 to 14 days at an outpatient clinic. The remaining 20 percent of patients were admitted to the study while hospitalized. Cell culture medium MCDB, supplemented with insulin, thyroxin, and growth hormone, was gelled. The gel was self-applied once a day to freshly washed wounds, covered with a gauze pad, and anchored with netting. Healing started 7 to 14 days after the initiation of treatment with enriched cell culture medium. However, the criterion for success of the treatment was determined on complete wound closure, which was achieved in 189 of 288 wounds (65.6 percent). Wound closure was correlated with the initial wound volume, stage, and origin. The average time required for closure of wounds caused by systemic pathologies (n = 181) and those based on regional status (n = 107) were 12.0 and 4.4 weeks, respectively, compared with 290 and 10.3 weeks of the previous conventional treatment. In 19 extensive wounds, when vascularized granulation tissue was established, a successful surgical closure was attained. Most wounds of patients who did not continue the enriched cell culture medium treatment (34.4 percent) manifested reduced wound volume, ranging from 11 to 98 percent of initial volume. Discontinuation of treatment was associated with difficulties in reaching the clinic for the weekly examination, rather than for reasons directly related to the treatment itself, and occurred significantly earlier during the treatment period.Thus, enriched cell culture medium was effective in stimulating wound healing in recalcitrant wounds. The healing was rapid with minimum scarring and pain. No side effects or allergic reactions were reported or observed.

Administration, Topical↗