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1.
Curr Biol ; 34(9): R343-R345, 2024 May 06.
Article En | MEDLINE | ID: mdl-38714160

Repeated rounds of fusion between apposing myoblasts allow muscles to become multinucleated. New research finds that myoblasts undergoing fusion in the Drosophila embryo respond to hormone signaling from a nearby tissue, resulting in the activation of a myoblast-specific gene necessary for the fusion process.


Cell Fusion , Myoblasts , Animals , Myoblasts/metabolism , Myoblasts/physiology , Drosophila/genetics , Drosophila Proteins/metabolism , Drosophila Proteins/genetics , Drosophila melanogaster/genetics , Signal Transduction , Cell Communication
2.
Cells ; 13(9)2024 Apr 26.
Article En | MEDLINE | ID: mdl-38727289

Extracellular vesicles (EVs) are membrane-bound particles released by cells to perform multitudes of biological functions. Owing to their significant implications in diseases, the pathophysiological role of EVs continues to be extensively studied, leading research to neglect the need to explore their role in normal physiology. Despite this, many identified physiological functions of EVs, including, but not limited to, tissue repair, early development and aging, are attributed to their modulatory role in various signaling pathways via intercellular communication. EVs are widely perceived as a potential therapeutic strategy for better prognosis, primarily through utilization as a mode of delivery vehicle. Moreover, disease-associated EVs serve as candidates for the targeted inhibition by pharmacological or genetic means. However, these attempts are often accompanied by major challenges, such as off-target effects, which may result in adverse phenotypes. This renders the clinical efficacy of EVs elusive, indicating that further understanding of the specific role of EVs in physiology may enhance their utility. This review highlights the essential role of EVs in maintaining cellular homeostasis under different physiological settings, and also discusses the various aspects that may potentially hinder the robust utility of EV-based therapeutics.


Extracellular Vesicles , Humans , Extracellular Vesicles/metabolism , Animals , Cell Communication , Signal Transduction , Homeostasis
3.
Cells ; 13(9)2024 Apr 30.
Article En | MEDLINE | ID: mdl-38727300

Excessive extracellular matrix (ECM) deposition is a defining feature of cardiac fibrosis. Most notably, it is characterized by a significant change in the concentration and volume fraction of collagen I, a disproportionate deposition of collagen subtypes, and a disturbed ECM network arrangement, which directly affect the systolic and diastolic functions of the heart. Immune cells that reside within or infiltrate the myocardium, including macrophages, play important roles in fibroblast activation and consequent ECM remodeling. Through both direct and indirect connections to fibroblasts, monocyte-derived macrophages and resident cardiac macrophages play complex, bidirectional, regulatory roles in cardiac fibrosis. In this review, we discuss emerging interactions between fibroblasts and macrophages in physiology and pathologic conditions, providing insights for future research aimed at targeting macrophages to combat cardiac fibrosis.


Fibroblasts , Fibrosis , Macrophages , Myocardium , Humans , Macrophages/metabolism , Fibroblasts/metabolism , Fibroblasts/pathology , Animals , Myocardium/pathology , Myocardium/metabolism , Extracellular Matrix/metabolism , Cell Communication
4.
Int J Mol Sci ; 25(9)2024 Apr 24.
Article En | MEDLINE | ID: mdl-38731840

Breast cancer (BC) is a global health risk for women and has a high prevalence rate. The drug resistance, recurrence, and metastasis of BC affect patient prognosis, thus posing a challenge to scientists. Exosomes are extracellular vesicles (EVs) that originate from various cells; they have a double-layered lipid membrane structure and contain rich biological information. They mediate intercellular communication and have pivotal roles in tumor development, progression, and metastasis and drug resistance. Exosomes are important cell communication mediators in the tumor microenvironment (TME). Exosomes are utilized as diagnostic and prognostic biomarkers for estimating the treatment efficacy of BC and have the potential to function as tools to enable the targeted delivery of antitumor drugs. This review introduces recent progress in research on how exosomes influence tumor development and the TME. We also present the research progress on the application of exosomes as prognostic and diagnostic biomarkers and drug delivery tools.


Biomarkers, Tumor , Breast Neoplasms , Exosomes , Tumor Microenvironment , Humans , Exosomes/metabolism , Breast Neoplasms/metabolism , Breast Neoplasms/pathology , Breast Neoplasms/therapy , Breast Neoplasms/diagnosis , Female , Biomarkers, Tumor/metabolism , Prognosis , Cell Communication , Drug Resistance, Neoplasm , Drug Delivery Systems/methods , Animals
5.
Front Immunol ; 15: 1340702, 2024.
Article En | MEDLINE | ID: mdl-38690275

The extracellular matrix (ECM) is a complex three-dimensional structure composed of proteins, glycans, and proteoglycans, constituting a critical component of the tumor microenvironment. Complex interactions among immune cells, extracellular matrix, and tumor cells promote tumor development and metastasis, consequently influencing therapeutic efficacy. Hence, elucidating these interaction mechanisms is pivotal for precision cancer therapy. T lymphocytes are an important component of the immune system, exerting direct anti-tumor effects by attacking tumor cells or releasing lymphokines to enhance immune effects. The ECM significantly influences T cells function and infiltration within the tumor microenvironment, thereby impacting the behavior and biological characteristics of tumor cells. T cells are involved in regulating the synthesis, degradation, and remodeling of the extracellular matrix through the secretion of cytokines and enzymes. As a result, it affects the proliferation and invasive ability of tumor cells as well as the efficacy of immunotherapy. This review discusses the mechanisms underlying T lymphocyte-ECM interactions in the tumor immune microenvironment and their potential application in immunotherapy. It provides novel insights for the development of innovative tumor therapeutic strategies and drug.


Extracellular Matrix , Neoplasms , T-Lymphocytes , Tumor Microenvironment , Tumor Microenvironment/immunology , Humans , Extracellular Matrix/metabolism , Extracellular Matrix/immunology , Neoplasms/immunology , Neoplasms/pathology , Neoplasms/metabolism , Neoplasms/therapy , T-Lymphocytes/immunology , T-Lymphocytes/metabolism , Animals , Cell Communication/immunology , Immunotherapy/methods
6.
BMC Immunol ; 25(1): 31, 2024 May 11.
Article En | MEDLINE | ID: mdl-38734625

BACKGROUND: Thyroid eye disease (TED) is an inflammatory process involving lymphocyte-mediated immune response and orbital tissue damage. The anti-insulin-like growth factor-1 receptor (IGF-1R) antibodies produced by B lymphocytes are involved in the activation of orbital fibroblasts and the inflammatory process of orbital tissue damage in TED. The purpose of this study was to explore the role of IGF-1R in the mechanistic connection between orbital fibroblasts and B lymphocytes in TED. METHODS: Orbital fibroblasts sampled from orbital connective tissues and peripheral B lymphocytes isolated from peripheral blood, which were obtained from 15 patients with TED and 15 control patients, were co-cultured at a ratio of 1:20. The level of IGF-1R expression in orbital fibroblasts was evaluated by flow cytometry and confocal microscopy. Transient B lymphocyte depletion was induced with anti-CD20 monoclonal antibody rituximab, while the IGF-1R pathway was blocked by the IGF-1R binding protein. The expression levels of interleukin-6 (IL-6) and regulated upon activation, normal T cell expressed and secreted (RANTES) in the co-culture model were quantified via ELISA. RESULTS: IGF-1R expression was significantly elevated in TED orbital fibroblasts compared to that of controls. A 24-h co-culture of orbital fibroblasts with peripheral B lymphocytes induced elevated expression levels of IL-6 and RANTES in each group (TED patients and controls), with the highest levels occurring in TED patients (T + T group). Rituximab and IGF-1R binding protein significantly inhibited increased levels of IL-6 and RANTES in the co-culture model of TED patients. CONCLUSIONS: IGF-1R may mediate interaction between orbital fibroblasts and peripheral B lymphocytes; thus, blocking IGF-1R may reduce the local inflammatory response in TED. Rituximab-mediated B lymphocyte depletion played a role in inhibiting inflammatory responses in this in vitro co-culture model, providing a theoretical basis for the clinical application of anti-CD20 monoclonal antibodies in TED.


B-Lymphocytes , Coculture Techniques , Fibroblasts , Graves Ophthalmopathy , Receptor, IGF Type 1 , Humans , Graves Ophthalmopathy/metabolism , Graves Ophthalmopathy/immunology , Fibroblasts/metabolism , Receptor, IGF Type 1/metabolism , B-Lymphocytes/immunology , B-Lymphocytes/metabolism , Female , Male , Middle Aged , Adult , Rituximab/pharmacology , Rituximab/therapeutic use , Orbit/metabolism , Orbit/immunology , Lymphocyte Depletion , Interleukin-6/metabolism , Cells, Cultured , Chemokine CCL5/metabolism , Cell Communication , Aged
7.
Front Immunol ; 15: 1382449, 2024.
Article En | MEDLINE | ID: mdl-38745657

Background: Acute Respiratory Distress Syndrome (ARDS) or its earlier stage Acute lung injury (ALI), is a worldwide health concern that jeopardizes human well-being. Currently, the treatment strategies to mitigate the incidence and mortality of ARDS are severely restricted. This limitation can be attributed, at least in part, to the substantial variations in immunity observed in individuals with this syndrome. Methods: Bulk and single cell RNA sequencing from ALI mice and single cell RNA sequencing from ARDS patients were analyzed. We utilized the Seurat program package in R and cellmarker 2.0 to cluster and annotate the data. The differential, enrichment, protein interaction, and cell-cell communication analysis were conducted. Results: The mice with ALI caused by pulmonary and extrapulmonary factors demonstrated differential expression including Clec4e, Retnlg, S100a9, Coro1a, and Lars2. We have determined that inflammatory factors have a greater significance in extrapulmonary ALI, while multiple pathways collaborate in the development of pulmonary ALI. Clustering analysis revealed significant heterogeneity in the relative abundance of immune cells in different ALI models. The autocrine action of neutrophils plays a crucial role in pulmonary ALI. Additionally, there was a significant increase in signaling intensity between B cells and M1 macrophages, NKT cells and M1 macrophages in extrapulmonary ALI. The CXCL, CSF3 and MIF, TGFß signaling pathways play a vital role in pulmonary and extrapulmonary ALI, respectively. Moreover, the analysis of human single-cell revealed DCs signaling to monocytes and neutrophils in COVID-19-associated ARDS is stronger compared to sepsis-related ARDS. In sepsis-related ARDS, CD8+ T and Th cells exhibit more prominent signaling to B-cell nucleated DCs. Meanwhile, both MIF and CXCL signaling pathways are specific to sepsis-related ARDS. Conclusion: This study has identified specific gene signatures and signaling pathways in animal models and human samples that facilitate the interaction between immune cells, which could be targeted therapeutically in ARDS patients of various etiologies.


Acute Lung Injury , Cell Communication , Gene Expression Profiling , Animals , Acute Lung Injury/genetics , Acute Lung Injury/immunology , Mice , Humans , Cell Communication/immunology , Transcriptome , Respiratory Distress Syndrome/immunology , Respiratory Distress Syndrome/genetics , Disease Models, Animal , Single-Cell Analysis , Mice, Inbred C57BL , Neutrophils/immunology , Neutrophils/metabolism , COVID-19/immunology , COVID-19/genetics , Signal Transduction , Male , Macrophages/immunology , Macrophages/metabolism
8.
J Cell Mol Med ; 28(9): e18372, 2024 May.
Article En | MEDLINE | ID: mdl-38747737

Multicellular organisms have dense affinity with the coordination of cellular activities, which severely depend on communication across diverse cell types. Cell-cell communication (CCC) is often mediated via ligand-receptor interactions (LRIs). Existing CCC inference methods are limited to known LRIs. To address this problem, we developed a comprehensive CCC analysis tool SEnSCA by integrating single cell RNA sequencing and proteome data. SEnSCA mainly contains potential LRI acquisition and CCC strength evaluation. For acquiring potential LRIs, it first extracts LRI features and reduces the feature dimension, subsequently constructs negative LRI samples through K-means clustering, finally acquires potential LRIs based on Stacking ensemble comprising support vector machine, 1D-convolutional neural networks and multi-head attention mechanism. During CCC strength evaluation, SEnSCA conducts LRI filtering and then infers CCC by combining the three-point estimation approach and single cell RNA sequencing data. SEnSCA computed better precision, recall, accuracy, F1 score, AUC and AUPR under most of conditions when predicting possible LRIs. To better illustrate the inferred CCC network, SEnSCA provided three visualization options: heatmap, bubble diagram and network diagram. Its application on human melanoma tissue demonstrated its reliability in CCC detection. In summary, SEnSCA offers a useful CCC inference tool and is freely available at https://github.com/plhhnu/SEnSCA.


Cell Communication , Single-Cell Analysis , Humans , Ligands , Single-Cell Analysis/methods , Software , Computational Biology/methods , Algorithms , Support Vector Machine , Sequence Analysis, RNA/methods , Melanoma/metabolism , Melanoma/pathology , Melanoma/genetics , Proteome/metabolism , Neural Networks, Computer
9.
Nano Lett ; 24(19): 5808-5815, 2024 May 15.
Article En | MEDLINE | ID: mdl-38710049

In multicellular organisms, individual cells are coordinated through complex communication networks to accomplish various physiological tasks. Aiming to establish new biological functions in the multicellular community, we used DNA as the building block to develop a cascade of nongenetic reaction circuits to establish a dynamic cell-cell communication network. Utilizing membrane-anchored amphiphilic DNA tetrahedra (TDN) as the nanoscaffold, reaction circuits were incorporated into three unrelated cells in order to uniquely regulate their sense-and-response behaviors. As a proof-of-concept, this step enabled these cells to simulate significant biological events involved in T cell-mediated anticancer immunity. Such events included cancer-associated antigen recognition and the presentation of antigen-presenting cells (APCs), APC-facilitated T cell activation and dissociation, and T cell-mediated cancer targeting and killing. By combining the excellent programmability and molecular recognition ability of DNA, our cell-surface reaction circuits hold promise for mimicking and manipulating many biological processes.


Antigen-Presenting Cells , Cell Communication , DNA , DNA/chemistry , Humans , Antigen-Presenting Cells/immunology , T-Lymphocytes/cytology , T-Lymphocytes/immunology , Lymphocyte Activation , Neoplasms/pathology , Neoplasms/genetics
10.
Front Endocrinol (Lausanne) ; 15: 1365327, 2024.
Article En | MEDLINE | ID: mdl-38737555

Endometriosis is a chronic inflammatory gynecological disease, which profoundly jeopardizes women's quality of life and places a significant medical burden on society. The pathogenesis of endometriosis remains unclear, posing major clinical challenges in diagnosis and treatment. There is an urgent demand for the development of innovative non-invasive diagnostic techniques and the identification of therapeutic targets. Extracellular vesicles, recognized for transporting a diverse array of signaling molecules, have garnered extensive attention as a novel mode of intercellular communication. A burgeoning body of research indicates that extracellular vesicles play a pivotal role in the pathogenesis of endometriosis, which may provide possibility and prospect for both diagnosis and treatment. In light of this context, this article focuses on the involvement of extracellular vesicles in the pathogenesis of endometriosis, which deliver information among endometrial stromal cells, macrophages, mesenchymal stem cells, and other cells, and explores their potential applications in the diagnosis and treatment, conducing to the emergence of new strategies for clinical diagnosis and treatment.


Endometriosis , Extracellular Vesicles , Endometriosis/pathology , Endometriosis/metabolism , Endometriosis/therapy , Endometriosis/diagnosis , Humans , Extracellular Vesicles/metabolism , Female , Endometrium/pathology , Endometrium/metabolism , Animals , Mesenchymal Stem Cells/metabolism , Cell Communication/physiology
11.
J Extracell Vesicles ; 13(5): e12433, 2024 May.
Article En | MEDLINE | ID: mdl-38738585

Extracellular vesicles (EVs) are released by all cells and contribute to cell-to-cell communication. The capacity of EVs to target specific cells and to efficiently deliver a composite profile of functional molecules have led researchers around the world to hypothesize their potential as therapeutics. While studies of EV treatment in animal models are numerous, their actual clinical benefit in humans has more slowly started to be tested. In this scoping review, we searched PubMed and other databases up to 31 December 2023 and, starting from 13,567 records, we selected 40 pertinent published studies testing EVs as therapeutics in humans. The analysis of those 40 studies shows that they are all small pilot trials with a large heterogeneity in terms of administration route and target disease. Moreover, the absence of a placebo control in most of the studies, the predominant local application of EV formulations and the inconsistent administration dose metric still impede comparison across studies and firm conclusions about EV safety and efficacy. On the other hand, the recording of some promising outcomes strongly calls out for well-designed larger studies to test EVs as an alternative approach to treat human diseases with no or few therapeutic options.


Extracellular Vesicles , Humans , Extracellular Vesicles/metabolism , Animals , Cell Communication
12.
J Immunol Res ; 2024: 6343757, 2024.
Article En | MEDLINE | ID: mdl-38715844

This study aims to explore the influence of coinfection with HCV and HIV on hepatic fibrosis. A coculture system was set up to actively replicate both viruses, incorporating CD4 T lymphocytes (Jurkat), hepatic stellate cells (LX-2), and hepatocytes (Huh7.5). LX-2 cells' susceptibility to HIV infection was assessed through measurements of HIV receptor expression, exposure to cell-free virus, and cell-to-cell contact with HIV-infected Jurkat cells. The study evaluated profibrotic parameters, including programed cell death, ROS imbalance, cytokines (IL-6, TGF-ß, and TNF-α), and extracellular matrix components (collagen, α-SMA, and MMP-9). The impact of HCV infection on LX-2/HIV-Jurkat was examined using soluble factors released from HCV-infected hepatocytes. Despite LX-2 cells being nonsusceptible to direct HIV infection, bystander effects were observed, leading to increased oxidative stress and dysregulated profibrotic cytokine release. Coculture with HIV-infected Jurkat cells intensified hepatic fibrosis, redox imbalance, expression of profibrotic cytokines, and extracellular matrix production. Conversely, HCV-infected Huh7.5 cells exhibited elevated profibrotic gene transcriptions but without measurable effects on the LX-2/HIV-Jurkat coculture. This study highlights how HIV-infected lymphocytes worsen hepatic fibrosis during HCV/HIV coinfection. They increase oxidative stress, profibrotic cytokine levels, and extracellular matrix production in hepatic stellate cells through direct contact and soluble factors. These insights offer valuable potential therapies for coinfected individuals.


Bystander Effect , Coculture Techniques , Coinfection , Cytokines , HIV Infections , Hepacivirus , Hepatic Stellate Cells , Hepatitis C , Liver Cirrhosis , Humans , Hepatic Stellate Cells/metabolism , HIV Infections/complications , HIV Infections/metabolism , HIV Infections/virology , HIV Infections/immunology , Hepacivirus/physiology , Hepatitis C/metabolism , Hepatitis C/virology , Hepatitis C/complications , Hepatitis C/immunology , Jurkat Cells , Liver Cirrhosis/metabolism , Liver Cirrhosis/pathology , Liver Cirrhosis/virology , Liver Cirrhosis/etiology , Cytokines/metabolism , Hepatocytes/metabolism , Hepatocytes/virology , HIV/physiology , Oxidative Stress , Cell Communication , CD4-Positive T-Lymphocytes/immunology , CD4-Positive T-Lymphocytes/metabolism , Extracellular Matrix/metabolism
13.
Proc Natl Acad Sci U S A ; 121(20): e2322688121, 2024 May 14.
Article En | MEDLINE | ID: mdl-38709925

Brain metastatic breast cancer is particularly lethal largely due to therapeutic resistance. Almost half of the patients with metastatic HER2-positive breast cancer develop brain metastases, representing a major clinical challenge. We previously described that cancer-associated fibroblasts are an important source of resistance in primary tumors. Here, we report that breast cancer brain metastasis stromal cell interactions in 3D cocultures induce therapeutic resistance to HER2-targeting agents, particularly to the small molecule inhibitor of HER2/EGFR neratinib. We investigated the underlying mechanisms using a synthetic Notch reporter system enabling the sorting of cancer cells that directly interact with stromal cells. We identified mucins and bulky glycoprotein synthesis as top-up-regulated genes and pathways by comparing the gene expression and chromatin profiles of stroma-contact and no-contact cancer cells before and after neratinib treatment. Glycoprotein gene signatures were also enriched in human brain metastases compared to primary tumors. We confirmed increased glycocalyx surrounding cocultures by immunofluorescence and showed that mucinase treatment increased sensitivity to neratinib by enabling a more efficient inhibition of EGFR/HER2 signaling in cancer cells. Overexpression of truncated MUC1 lacking the intracellular domain as a model of increased glycocalyx-induced resistance to neratinib both in cell culture and in experimental brain metastases in immunodeficient mice. Our results highlight the importance of glycoproteins as a resistance mechanism to HER2-targeting therapies in breast cancer brain metastases.


Brain Neoplasms , Breast Neoplasms , Drug Resistance, Neoplasm , Glycocalyx , Quinolines , Receptor, ErbB-2 , Stromal Cells , Humans , Breast Neoplasms/pathology , Breast Neoplasms/metabolism , Breast Neoplasms/drug therapy , Breast Neoplasms/genetics , Female , Brain Neoplasms/secondary , Brain Neoplasms/metabolism , Brain Neoplasms/drug therapy , Brain Neoplasms/pathology , Brain Neoplasms/genetics , Receptor, ErbB-2/metabolism , Receptor, ErbB-2/genetics , Glycocalyx/metabolism , Animals , Cell Line, Tumor , Stromal Cells/metabolism , Stromal Cells/pathology , Quinolines/pharmacology , Mice , Cell Communication , Coculture Techniques , Mucin-1/metabolism , Mucin-1/genetics , Signal Transduction , ErbB Receptors/metabolism , ErbB Receptors/antagonists & inhibitors
14.
Methods Mol Biol ; 2800: 11-25, 2024.
Article En | MEDLINE | ID: mdl-38709474

Fibroblasts are the major producers of the extracellular matrix and regulate its organization. Aberrant signaling in diseases such as fibrosis and cancer can impact the deposition of the matrix proteins, which can in turn act as an adhesion scaffold and signaling reservoir promoting disease progression. To study the composition and organization of the extracellular matrix as well as its interactions with (tumor) cells, this protocol describes the generation and analysis of 3D fibroblast-derived matrices and the investigation of (tumor) cells seeded onto the 3D scaffolds by immunofluorescent imaging and cell adhesion, colony formation, migration, and invasion/transmigration assays.


Cell Adhesion , Cell Movement , Extracellular Matrix , Fibroblasts , Signal Transduction , Extracellular Matrix/metabolism , Fibroblasts/metabolism , Humans , Cell Line, Tumor , Cell Culture Techniques/methods , Neoplasms/metabolism , Neoplasms/pathology , Cell Communication , Cell Culture Techniques, Three Dimensional/methods , Animals , Tissue Scaffolds/chemistry
15.
Am J Reprod Immunol ; 91(5): e13857, 2024 May.
Article En | MEDLINE | ID: mdl-38716824

Preeclampsia, poses significant risks to both maternal and fetal well-being. Exosomes released by the placenta play a crucial role in intercellular communication and are recognized as potential carriers of essential information for placental development. These exosomes transport a payload of proteins, nucleic acids, and lipids that mirror the placental microenvironment. This review delves into the functional roles of placental exosomes and its contents shedding light on their involvement in vascular regulation and immune modulation in normal pregnancy. Discernible changes are reported in the composition and quantity of placental exosome contents in pregnancies affected by preeclampsia. The exosomes from preeclamptic mothers affect vascularization and fetal kidney development. The discussion also explores the implications of utilizing placental exosomes as biomarkers and the prospects of translating these findings into clinical applications. In conclusion, placental exosomes hold promise as a valuable avenue for deciphering the complexities of preeclampsia, providing crucial diagnostic and prognostic insights. As the field progresses, a more profound comprehension of the distinct molecular signatures carried by placental exosomes may open doors to innovative strategies for managing and offering personalized care to pregnancies affected by preeclampsia.


Exosomes , Placenta , Pre-Eclampsia , Humans , Pregnancy , Pre-Eclampsia/metabolism , Exosomes/metabolism , Female , Placenta/metabolism , Placenta/immunology , Biomarkers/metabolism , Animals , Cell Communication
16.
J Transl Med ; 22(1): 422, 2024 May 03.
Article En | MEDLINE | ID: mdl-38702814

BACKGROUND: Intrahepatic cholangiocarcinoma (ICC) is a highly malignant neoplasm and characterized by desmoplastic matrix. The heterogeneity and crosstalk of tumor microenvironment remain incompletely understood. METHODS: To address this gap, we performed Weighted Gene Co-expression Network Analysis (WGCNA) to identify and construct a cancer associated fibroblasts (CAFs) infiltration biomarker. We also depicted the intercellular communication network and important receptor-ligand complexes using the single-cell transcriptomics analysis of tumor and Adjacent normal tissue. RESULTS: Through the intersection of TCGA DEGs and WGCNA module genes, 784 differential genes related to CAFs infiltration were obtained. After a series of regression analyses, the CAFs score was generated by integrating the expressions of EVA1A, APBA2, LRRTM4, GOLGA8M, BPIFB2, and their corresponding coefficients. In the TCGA-CHOL, GSE89748, and 107,943 cohorts, the high CAFs score group showed unfavorable survival prognosis (p < 0.001, p = 0.0074, p = 0.028, respectively). Additionally, a series of drugs have been predicted to be more sensitive to the high-risk group (p < 0.05). Subsequent to dimension reduction and clustering, thirteen clusters were identified to construct the single-cell atlas. Cell-cell interaction analysis unveiled significant enhancement of signal transduction in tumor tissues, particularly from fibroblasts to malignant cells via diverse pathways. Moreover, SCENIC analysis indicated that HOXA5, WT1, and LHX2 are fibroblast specific motifs. CONCLUSIONS: This study reveals the key role of fibroblasts - oncocytes interaction in the remodeling of the immunosuppressive microenvironment in intrahepatic cholangiocarcinoma. Subsequently, it may trigger cascade activation of downstream signaling pathways such as PI3K-AKT and Notch in tumor, thus initiating tumorigenesis. Targeted drugs aimed at disrupting fibroblasts-tumor cell interaction, along with associated enrichment pathways, show potential in mitigating the immunosuppressive microenvironment that facilitates tumor progression.


Bile Duct Neoplasms , Cancer-Associated Fibroblasts , Cholangiocarcinoma , Gene Expression Regulation, Neoplastic , Single-Cell Analysis , Tumor Microenvironment , Cholangiocarcinoma/genetics , Cholangiocarcinoma/pathology , Humans , Tumor Microenvironment/genetics , Cancer-Associated Fibroblasts/metabolism , Cancer-Associated Fibroblasts/pathology , Prognosis , Bile Duct Neoplasms/genetics , Bile Duct Neoplasms/pathology , Bile Duct Neoplasms/metabolism , Transcriptome/genetics , Gene Expression Profiling , Gene Regulatory Networks , Cell Communication
17.
Brief Bioinform ; 25(3)2024 Mar 27.
Article En | MEDLINE | ID: mdl-38706319

Inference of cell-cell communication (CCC) provides valuable information in understanding the mechanisms of many important life processes. With the rise of spatial transcriptomics in recent years, many methods have emerged to predict CCCs using spatial information of cells. However, most existing methods only describe CCCs based on ligand-receptor interactions, but lack the exploration of their upstream/downstream pathways. In this paper, we proposed a new method to infer CCCs, called Intercellular Gene Association Network (IGAN). Specifically, it is for the first time that we can estimate the gene associations/network between two specific single spatially adjacent cells. By using the IGAN method, we can not only infer CCCs in an accurate manner, but also explore the upstream/downstream pathways of ligands/receptors from the network perspective, which are actually exhibited as a new panoramic cell-interaction-pathway graph, and thus provide extensive information for the regulatory mechanisms behind CCCs. In addition, IGAN can measure the CCC activity at single cell/spot resolution, and help to discover the CCC spatial heterogeneity. Interestingly, we found that CCC patterns from IGAN are highly consistent with the spatial microenvironment patterns for each cell type, which further indicated the accuracy of our method. Analyses on several public datasets validated the advantages of IGAN.


Cell Communication , Gene Regulatory Networks , Cell Communication/genetics , Humans , Computational Biology/methods , Algorithms , Single-Cell Analysis/methods , Signal Transduction
18.
Yakugaku Zasshi ; 144(5): 483-488, 2024.
Article Ja | MEDLINE | ID: mdl-38692921

Allergic diseases (e.g., food allergies) are a growing problem, with increasing numbers of individuals experiencing them worldwide. Congruently, the adverse reactions (e.g., anaphylaxis) associated with the administration of vaccines against emerging infectious diseases such as coronavirus disease 2019 (COVID-19) have become a familiar problem. Allergic diseases, which have a wide variety of symptoms, are difficult to prevent or cure; treatment is currently limited to therapeutic drugs or allergen immunotherapy. Therefore, elucidating new allergic regulatory factors that control the allergic (i.e., mast cell) responses is important. While investigating the regulatory mechanisms of the wide range of allergic responses of mast cells, we found that the affinity of allergens to immunoglobin E (IgE) regulates allergic inflammation through the differences in the secretory responses of mast cells and the types and interactions of the cells infiltrating the tissues. Here, we present our recent findings regarding the affinity of allergens to IgE in regulating allergic inflammation, heterogeneous secretory granules inducing diverse secretory responses, and mast cells interacting with neutrophils, thereby regulating the various allergic responses.


Cell Communication , Hypersensitivity , Immunoglobulin E , Mast Cells , Neutrophils , Mast Cells/immunology , Humans , Hypersensitivity/immunology , Hypersensitivity/etiology , Immunoglobulin E/immunology , Neutrophils/immunology , Allergens/immunology , Animals , Food Hypersensitivity/immunology , Food Hypersensitivity/therapy , COVID-19/immunology , COVID-19/prevention & control
19.
Front Immunol ; 15: 1346587, 2024.
Article En | MEDLINE | ID: mdl-38690261

Extracellular vesicles (EVs) are important cell-to-cell communication mediators. This paper focuses on the regulatory role of tumor-derived EVs on macrophages. It aims to investigate the causes of tumor progression and therapeutic directions. Tumor-derived EVs can cause macrophages to shift to M1 or M2 phenotypes. This indicates they can alter the M1/M2 cell ratio and have pro-tumor and anti-inflammatory effects. This paper discusses several key points: first, the factors that stimulate macrophage polarization and the cytokines released as a result; second, an overview of EVs and the methods used to isolate them; third, how EVs from various cancer cell sources, such as hepatocellular carcinoma, colorectal carcinoma, lung carcinoma, breast carcinoma, and glioblastoma cell sources carcinoma, promote tumor development by inducing M2 polarization in macrophages; and fourth, how EVs from breast carcinoma, pancreatic carcinoma, lungs carcinoma, and glioblastoma cell sources carcinoma also contribute to tumor development by promoting M2 polarization in macrophages. Modified or sourced EVs from breast, pancreatic, and colorectal cancer can repolarize M2 to M1 macrophages. This exhibits anti-tumor activities and offers novel approaches for tumor treatment. Therefore, we discovered that macrophage polarization to either M1 or M2 phenotypes can regulate tumor development. This is based on the description of altering macrophage phenotypes by vesicle contents.


Extracellular Vesicles , Macrophage Activation , Macrophages , Neoplasms , Humans , Extracellular Vesicles/immunology , Extracellular Vesicles/metabolism , Macrophages/immunology , Macrophages/metabolism , Neoplasms/immunology , Neoplasms/therapy , Neoplasms/pathology , Neoplasms/metabolism , Animals , Macrophage Activation/immunology , Tumor Microenvironment/immunology , Cell Communication/immunology , Cytokines/metabolism
20.
J Transl Med ; 22(1): 444, 2024 May 11.
Article En | MEDLINE | ID: mdl-38734658

BACKGROUND: Characterization of shared cancer mechanisms have been proposed to improve therapy strategies and prognosis. Here, we aimed to identify shared cell-cell interactions (CCIs) within the tumor microenvironment across multiple solid cancers and assess their association with cancer mortality. METHODS: CCIs of each cancer were identified by NicheNet analysis of single-cell RNA sequencing data from breast, colon, liver, lung, and ovarian cancers. These CCIs were used to construct a shared multi-cellular tumor model (shared-MCTM) representing common CCIs across cancers. A gene signature was identified from the shared-MCTM and tested on the mRNA and protein level in two large independent cohorts: The Cancer Genome Atlas (TCGA, 9185 tumor samples and 727 controls across 22 cancers) and UK biobank (UKBB, 10,384 cancer patients and 5063 controls with proteomics data across 17 cancers). Cox proportional hazards models were used to evaluate the association of the signature with 10-year all-cause mortality, including sex-specific analysis. RESULTS: A shared-MCTM was derived from five individual cancers. A shared gene signature was extracted from this shared-MCTM and the most prominent regulatory cell type, matrix cancer-associated fibroblast (mCAF). The signature exhibited significant expression changes in multiple cancers compared to controls at both mRNA and protein levels in two independent cohorts. Importantly, it was significantly associated with mortality in cancer patients in both cohorts. The highest hazard ratios were observed for brain cancer in TCGA (HR [95%CI] = 6.90[4.64-10.25]) and ovarian cancer in UKBB (5.53[2.08-8.80]). Sex-specific analysis revealed distinct risks, with a higher mortality risk associated with the protein signature score in males (2.41[1.97-2.96]) compared to females (1.84[1.44-2.37]). CONCLUSION: We identified a gene signature from a comprehensive shared-MCTM representing common CCIs across different cancers and revealed the regulatory role of mCAF in the tumor microenvironment. The pathogenic relevance of the gene signature was supported by differential expression and association with mortality on both mRNA and protein levels in two independent cohorts.


Neoplasms , Humans , Neoplasms/genetics , Neoplasms/mortality , Female , Male , Gene Expression Regulation, Neoplastic , RNA, Messenger/genetics , RNA, Messenger/metabolism , Tumor Microenvironment/genetics , Cohort Studies , Transcriptome/genetics , Middle Aged , Cell Communication
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