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Vasighizaker A, Hora S, Zeng R, Rueda L. SEGCECO: Subgraph Embedding of Gene expression matrix for prediction of CEll-cell COmmunication. Brief Bioinform 2024; 25:bbae160. [PMID: 38605638 PMCID: PMC11009470 DOI: 10.1093/bib/bbae160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/30/2024] [Accepted: 03/13/2024] [Indexed: 04/13/2024] Open
Abstract
Recent advances in single-cell RNA sequencing technology have eased analyses of signaling networks of cells. Recently, cell-cell interaction has been studied based on various link prediction approaches on graph-structured data. These approaches have assumptions about the likelihood of node interaction, thus showing high performance for only some specific networks. Subgraph-based methods have solved this problem and outperformed other approaches by extracting local subgraphs from a given network. In this work, we present a novel method, called Subgraph Embedding of Gene expression matrix for prediction of CEll-cell COmmunication (SEGCECO), which uses an attributed graph convolutional neural network to predict cell-cell communication from single-cell RNA-seq data. SEGCECO captures the latent and explicit attributes of undirected, attributed graphs constructed from the gene expression profile of individual cells. High-dimensional and sparse single-cell RNA-seq data make converting the data into a graphical format a daunting task. We successfully overcome this limitation by applying SoptSC, a similarity-based optimization method in which the cell-cell communication network is built using a cell-cell similarity matrix which is learned from gene expression data. We performed experiments on six datasets extracted from the human and mouse pancreas tissue. Our comparative analysis shows that SEGCECO outperforms latent feature-based approaches, and the state-of-the-art method for link prediction, WLNM, with 0.99 ROC and 99% prediction accuracy. The datasets can be found at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84133 and the code is publicly available at Github https://github.com/sheenahora/SEGCECO and Code Ocean https://codeocean.com/capsule/8244724/tree.
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Affiliation(s)
| | - Sheena Hora
- Software Development Department, Amazon, USA
| | - Raymond Zeng
- School of Computer Science, University of Windsor, Windsor, ON, Canada
| | - Luis Rueda
- School of Computer Science, University of Windsor, Windsor, ON, Canada
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2
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Liu K, Wehling L, Wan S, Weiler SME, Tóth M, Ibberson D, Marhenke S, Ali A, Lam M, Guo T, Pinna F, Pedrini F, Damle-Vartak A, Dropmann A, Rose F, Colucci S, Cheng W, Bissinger M, Schmitt J, Birner P, Poth T, Angel P, Dooley S, Muckenthaler MU, Longerich T, Vogel A, Heikenwälder M, Schirmacher P, Breuhahn K. Dynamic YAP expression in the non-parenchymal liver cell compartment controls heterologous cell communication. Cell Mol Life Sci 2024; 81:115. [PMID: 38436764 PMCID: PMC10912141 DOI: 10.1007/s00018-024-05126-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/11/2023] [Accepted: 12/30/2023] [Indexed: 03/05/2024]
Abstract
INTRODUCTION The Hippo pathway and its transcriptional effectors yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ) are targets for cancer therapy. It is important to determine if the activation of one factor compensates for the inhibition of the other. Moreover, it is unknown if YAP/TAZ-directed perturbation affects cell-cell communication of non-malignant liver cells. MATERIALS AND METHODS To investigate liver-specific phenotypes caused by YAP and TAZ inactivation, we generated mice with hepatocyte (HC) and biliary epithelial cell (BEC)-specific deletions for both factors (YAPKO, TAZKO and double knock-out (DKO)). Immunohistochemistry, single-cell sequencing, and proteomics were used to analyze liver tissues and serum. RESULTS The loss of BECs, liver fibrosis, and necrosis characterized livers from YAPKO and DKO mice. This phenotype was weakened in DKO tissues compared to specimens from YAPKO animals. After depletion of YAP in HCs and BECs, YAP expression was induced in non-parenchymal cells (NPCs) in a cholestasis-independent manner. YAP positivity was detected in subgroups of Kupffer cells (KCs) and endothelial cells (ECs). The secretion of pro-inflammatory chemokines and cytokines such as C-X-C motif chemokine ligand 11 (CXCL11), fms-related receptor tyrosine kinase 3 ligand (FLT3L), and soluble intercellular adhesion molecule-1 (ICAM1) was increased in the serum of YAPKO animals. YAP activation in NPCs could contribute to inflammation via TEA domain transcription factor (TEAD)-dependent transcriptional regulation of secreted factors. CONCLUSION YAP inactivation in HCs and BECs causes liver damage, and concomitant TAZ deletion does not enhance but reduces this phenotype. Additionally, we present a new mechanism by which YAP contributes to cell-cell communication originating from NPCs.
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Affiliation(s)
- Kaijing Liu
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangdong, China
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, China
| | - Lilija Wehling
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- Department of Modeling of Biological Processes, COS Heidelberg/BioQuant, Heidelberg University, Heidelberg, Germany
| | - Shan Wan
- Department of Pathology, School of Biology & Basic Medical Sciences, Soochow University, Suzhou, China
| | - Sofia M E Weiler
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Marcell Tóth
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - David Ibberson
- Deep Sequencing Core Facility, CellNetworks Excellence Cluster, Heidelberg University, Heidelberg, Germany
| | - Silke Marhenke
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School (MHH), Hannover, Germany
| | - Adnan Ali
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Macrina Lam
- Division of Signal Transduction and Growth Control, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Te Guo
- Division of Signal Transduction and Growth Control, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Federico Pinna
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Fabiola Pedrini
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Amruta Damle-Vartak
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Anne Dropmann
- Department of Medicine II, Molecular Hepatology Section, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Fabian Rose
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Silvia Colucci
- Department of Pediatric Oncology, Hematology & Immunology, University Hospital Heidelberg, Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Wenxiang Cheng
- Translational Medicine R&D Center, Institute of Biomedical & Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Michaela Bissinger
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Jennifer Schmitt
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Patrizia Birner
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Tanja Poth
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Peter Angel
- Division of Signal Transduction and Growth Control, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steven Dooley
- Department of Medicine II, Molecular Hepatology Section, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Martina U Muckenthaler
- Department of Pediatric Oncology, Hematology & Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Thomas Longerich
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Arndt Vogel
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School (MHH), Hannover, Germany
| | - Mathias Heikenwälder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Kai Breuhahn
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany.
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Wilk AJ, Shalek AK, Holmes S, Blish CA. Comparative analysis of cell-cell communication at single-cell resolution. Nat Biotechnol 2024; 42:470-483. [PMID: 37169965 PMCID: PMC10638471 DOI: 10.1038/s41587-023-01782-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/05/2023] [Indexed: 05/13/2023]
Abstract
Inference of cell-cell communication from single-cell RNA sequencing data is a powerful technique to uncover intercellular communication pathways, yet existing methods perform this analysis at the level of the cell type or cluster, discarding single-cell-level information. Here we present Scriabin, a flexible and scalable framework for comparative analysis of cell-cell communication at single-cell resolution that is performed without cell aggregation or downsampling. We use multiple published atlas-scale datasets, genetic perturbation screens and direct experimental validation to show that Scriabin accurately recovers expected cell-cell communication edges and identifies communication networks that can be obscured by agglomerative methods. Additionally, we use spatial transcriptomic data to show that Scriabin can uncover spatial features of interaction from dissociated data alone. Finally, we demonstrate applications to longitudinal datasets to follow communication pathways operating between timepoints. Our approach represents a broadly applicable strategy to reveal the full structure of niche-phenotype relationships in health and disease.
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Affiliation(s)
- Aaron J Wilk
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA.
| | - Alex K Shalek
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Catherine A Blish
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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Ma Q, Li Q, Zheng X, Pan J. CellCommuNet: an atlas of cell-cell communication networks from single-cell RNA sequencing of human and mouse tissues in normal and disease states. Nucleic Acids Res 2024; 52:D597-D606. [PMID: 37850657 PMCID: PMC10767892 DOI: 10.1093/nar/gkad906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/16/2023] [Accepted: 10/05/2023] [Indexed: 10/19/2023] Open
Abstract
Cell-cell communication, as a basic feature of multicellular organisms, is crucial for maintaining the biological functions and microenvironmental homeostasis of cells, organs, and whole organisms. Alterations in cell-cell communication contribute to many diseases, including cancers. Single-cell RNA sequencing (scRNA-seq) provides a powerful method for studying cell-cell communication by enabling the analysis of ligand-receptor interactions. Here, we introduce CellCommuNet (http://www.inbirg.com/cellcommunet/), a comprehensive data resource for exploring cell-cell communication networks in scRNA-seq data from human and mouse tissues in normal and disease states. CellCommuNet currently includes 376 single datasets from multiple sources, and 118 comparison datasets between disease and normal samples originating from the same study. CellCommuNet provides information on the strength of communication between cells and related signalling pathways and facilitates the exploration of differences in cell-cell communication between healthy and disease states. Users can also search for specific signalling pathways, ligand-receptor pairs, and cell types of interest. CellCommuNet provides interactive graphics illustrating cell-cell communication in different states, enabling differential analysis of communication strength between disease and control samples. This comprehensive database aims to be a valuable resource for biologists studying cell-cell communication networks.
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Affiliation(s)
- Qinfeng Ma
- Precision Medicine Center, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
- Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention, Ministry of Education, Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Qiang Li
- Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention, Ministry of Education, Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Xiao Zheng
- Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention, Ministry of Education, Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Jianbo Pan
- Precision Medicine Center, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
- Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention, Ministry of Education, Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
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5
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Liu Y, Zhao M, Qu H. Identification of cytokine-induced cell communications by pan-cancer meta-analysis. PeerJ 2023; 11:e16221. [PMID: 38054018 PMCID: PMC10695116 DOI: 10.7717/peerj.16221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 09/11/2023] [Indexed: 12/07/2023] Open
Abstract
Cancer immune responses are complex cellular processes in which cytokine-receptor interactions play central roles in cancer development and response to therapy; dysregulated cytokine-receptor communication may lead to pathological processes, including cancer, autoimmune diseases, and cytokine storm; however, our knowledge regarding cytokine-mediated cell-cell communication (CCI) in different cancers remains limited. The present study presents a single-cell and pan-cancer-level transcriptomics integration of 41,900 cells across 25 cancer types. We developed a single-cell method to actively express 62 cytokine-receptor pairs to reveal stable cytokine-mediated cell communications involving 84 cytokines and receptors. The correlation between the sample-based CCI profile and the interactome analysis indicates multiple cytokine-receptor modules including TGFB1, IL16ST, IL15, and the PDGF family. Some isolated cytokine interactions, such as FN1-IL17RC, displayed diverse functions within over ten single-cell transcriptomics datasets. Further functional enrichment analysis revealed that the constructed cytokine-receptor interaction map is associated with the positive regulation of multiple immune response pathways. Using public TCGA pan-cancer mutational data, co-mutational analysis of the cytokines and receptors provided significant co-occurrence features, implying the existence of cooperative mechanisms. Analysis of 10,967 samples from 32 TCGA cancer types revealed that the 84 cytokine and receptor genes are significantly associated with clinical survival time. Interestingly, the tumor samples with mutations in any of the 84 cytokines and receptors have a substantially higher mutational burden, offering insights into antitumor immune regulation and response. Clinical cancer stage information revealed that tumor samples with mutations in any of the 84 cytokines and receptors stratify into earlier tumor stages, with unique cellular compositions and clinical outcomes. This study provides a comprehensive cytokine-receptor atlas of the cellular architecture in multiple cancers at the single-cell level.
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Affiliation(s)
- Yining Liu
- The School of Public Health, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China
| | - Min Zhao
- School of Science and Engineering, University of the Sunshine Coast, Maroochydore DC, Australia
| | - Hong Qu
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
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6
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Chu J. Exploration of the molecular mechanism of intercellular communication in paediatric neuroblastoma by single-cell sequencing. Sci Rep 2023; 13:20406. [PMID: 37990103 PMCID: PMC10663476 DOI: 10.1038/s41598-023-47796-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 11/18/2023] [Indexed: 11/23/2023] Open
Abstract
Neuroblastoma (NB) is an embryonic tumour that originates in the sympathetic nervous system and occurs most often in infants and children under 2 years of age. Moreover, it is the most common extracranial solid tumour in children. Increasing studies suggest that intercellular communication within the tumour microenvironment is closely related to tumour development. This study aimed to construct a prognosis-related intercellular communication-associated genes model by single-cell sequencing and transcriptome sequencing to predict the prognosis of patients with NB for precise management. Single-cell data from patients with NB were downloaded from the gene expression omnibus database for comprehensive analysis. Furthermore, prognosis-related genes were screened in the TARGET database based on epithelial cell marker genes through a combination of Cox regression and Lasso regression analyses, using GSE62564 and GSE85047 for external validation. The patients' risk scores were calculated, followed by immune infiltration analysis, drug sensitivity analysis, and enrichment analysis of risk scores, which were conducted for the prognostic model. I used the Lasso regression feature selection algorithm to screen characteristic genes in NB and developed a 21-gene prognostic model. The risk scores were highly correlated with multiple immune cells and common anti-tumour drugs. Furthermore, the risk score was identified as an independent prognostic factor for NB. In this study, I constructed and validated a prognostic signature based on epithelial marker genes, which may provide useful information on the development and prognosis of NB.
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Affiliation(s)
- Jing Chu
- Department of Pathology, Anhui Provincial Children's Hospital, 39 Wangjiang East Road, Hefei, 230051, Anhui, China.
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Zhang X, Sun S, Ren G, Liu W, Chen H. Advances in Intercellular Communication Mediated by Exosomal ncRNAs in Cardiovascular Disease. Int J Mol Sci 2023; 24:16197. [PMID: 38003385 PMCID: PMC10671547 DOI: 10.3390/ijms242216197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 11/26/2023] Open
Abstract
Cardiovascular diseases are a leading cause of worldwide mortality, and exosomes have recently gained attention as key mediators of intercellular communication in these diseases. Exosomes are double-layered lipid vesicles that can carry biomolecules such as miRNAs, lncRNAs, and circRNAs, and the content of exosomes is dependent on the cell they originated from. They can be involved in the pathophysiological processes of cardiovascular diseases and hold potential as diagnostic and monitoring tools. Exosomes mediate intercellular communication, stimulate or inhibit the activity of target cells, and affect myocardial hypertrophy, injury and infarction, ventricular remodeling, angiogenesis, and atherosclerosis. Exosomes can be released from various types of cells, including endothelial cells, smooth muscle cells, cardiomyocytes, fibroblasts, platelets, adipocytes, immune cells, and stem cells. In this review, we highlight the communication between different cell-derived exosomes and cardiovascular cells, with a focus on the roles of RNAs. This provides new insights for further exploring targeted therapies in the clinical management of cardiovascular diseases.
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Affiliation(s)
- Xiaoyan Zhang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China;
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (S.S.); (G.R.)
| | - Shengjie Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (S.S.); (G.R.)
| | - Gang Ren
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (S.S.); (G.R.)
| | - Wujun Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China;
| | - Hong Chen
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China;
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Wu W, He J. Unveiling the functional paradigm of exosome-derived long non-coding RNAs (lncRNAs) in cancer: based on a narrative review and systematic review. J Cancer Res Clin Oncol 2023; 149:15219-15247. [PMID: 37578522 DOI: 10.1007/s00432-023-05273-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
BACKGROUND AND PURPOSE The intricate mechanisms underlying intercellular communication within the tumor microenvironment remain largely elusive. Recently, attention has shifted towards exploring the intercellular signaling mediated by exosomal long non-coding RNAs (lncRNAs) within this context. This comprehensive systematic review aims to elucidate the functional paradigm of exosome-derived lncRNAs in cancer. MATERIALS AND METHODS The review provides a comprehensive narrative of lncRNA definition, characteristics, as well as the formation, sorting, and uptake processes of exosome-derived lncRNAs. Additionally, it describes comprehensive technology for exosome research and nucleic acid drug loading. This review further systematically examines the cellular origins, functional roles, and underlying mechanisms of exosome-derived lncRNAs in recipient cells within the cancer setting. RESULTS The functional paradigm of exosome-derived lncRNAs in cancer mainly depends on the source cells and sorting mechanism of exosomal lncRNAs, the recipient cells and uptake mechanisms of exosomal lncRNAs, and the specific molecular mechanisms of lncRNAs in recipient cells. The source cells of exosomal lncRNAs mainly involved in the current review included tumor cells, cancer stem cells, normal cells, macrophages, and cancer-associated fibroblasts. CONCLUSION This synthesis of knowledge offers valuable insights for accurately identifying exosomal lncRNAs with potential as tumor biomarkers. Moreover, it aids in the selection of appropriate targeting strategies and preclinical models, thereby facilitating the clinical translation of exosomal lncRNAs as promising therapeutic targets against cancer. Through a comprehensive understanding of the functional role of exosome-derived lncRNAs in cancer, this review paves the way for advancements in personalized medicine and improved treatment outcomes.
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Affiliation(s)
- Wenhan Wu
- Department of General Surgery (Gastrointestinal Surgery), The Affiliated Hospital of Southwest Medical University, Luzhou, China.
| | - Jia He
- Faculty Affairs and Human Resources Management Department, Southwest Medical University, Luzhou, China
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Vetter L, Bajalan A, Ahamed MT, Scasso C, Shafeeq S, Andersson B, Ribacke U. Starvation induces changes in abundance and small RNA cargo of extracellular vesicles released from Plasmodium falciparum infected red blood cells. Sci Rep 2023; 13:18423. [PMID: 37891207 PMCID: PMC10611735 DOI: 10.1038/s41598-023-45590-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023] Open
Abstract
The lethal malaria parasite Plasmodium falciparum needs to constantly respond and adapt to changes within the human host in order to survive and transmit. One such change is composed of nutritional limitation, which is augmented with increased parasite loads and intimately linked to severe disease development. Extracellular vesicles released from infected red blood cells have been proposed as important mediators of disease pathogenesis and intercellular communication but whether important for the parasite response to nutritional availability is unknown. Therefore, we investigated the abundance and small RNA cargo of extracellular vesicles released upon short-term nutritional starvation of P. falciparum in vitro cultures. We show that primarily ring-stage parasite cultures respond to glucose and amino acid deprivation with an increased release of extracellular vesicles. Small RNA sequencing of these extracellular vesicles further revealed human miRNAs and parasitic tRNA fragments as the main constituent biotypes. Short-term starvations led to alterations in the transcriptomic profile, most notably in terms of the over-represented biotypes. These data suggest a potential role for extracellular vesicles released from P. falciparum infected red blood cells in the response to nutritional perturbations, their potential as prognostic biomarkers and point towards an evolutionary conserved role among protozoan parasites.
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Affiliation(s)
- Leonie Vetter
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-17165, Solna, Sweden
| | - Amanj Bajalan
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-17165, Solna, Sweden
| | - Mohammad Tanvir Ahamed
- Department of Learning, Informatics, Management and Ethics, Karolinska Institutet, Tomtebodavägen 18, SE-17177, Solna, Sweden
| | - Caterina Scasso
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-17165, Solna, Sweden
| | - Sulman Shafeeq
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-17165, Solna, Sweden
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-17165, Solna, Sweden
| | - Ulf Ribacke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-17165, Solna, Sweden.
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, SE-75237, Uppsala, Sweden.
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Wang X, Almet AA, Nie Q. The promising application of cell-cell interaction analysis in cancer from single-cell and spatial transcriptomics. Semin Cancer Biol 2023; 95:42-51. [PMID: 37454878 PMCID: PMC10627116 DOI: 10.1016/j.semcancer.2023.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 03/02/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Cell-cell interactions instruct cell fate and function. These interactions are hijacked to promote cancer development. Single-cell transcriptomics and spatial transcriptomics have become powerful new tools for researchers to profile the transcriptional landscape of cancer at unparalleled genetic depth. In this review, we discuss the rapidly growing array of computational tools to infer cell-cell interactions from non-spatial single-cell RNA-sequencing and the limited but growing number of methods for spatial transcriptomics data. Downstream analyses of these computational tools and applications to cancer studies are highlighted. We finish by suggesting several directions for further extensions that anticipate the increasing availability of multi-omics cancer data.
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Affiliation(s)
- Xinyi Wang
- Department of Mathematics, University of California, Irvine, Irvine, CA, United States
| | - Axel A Almet
- Department of Mathematics, University of California, Irvine, Irvine, CA, United States; The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, United States.
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, Irvine, CA, United States; The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, United States; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, United States.
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Luo J, Deng M, Zhang X, Sun X. ESICCC as a systematic computational framework for evaluation, selection, and integration of cell-cell communication inference methods. Genome Res 2023; 33:1788-1805. [PMID: 37827697 PMCID: PMC10691505 DOI: 10.1101/gr.278001.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 09/21/2023] [Indexed: 10/14/2023]
Abstract
Cell-cell communication (CCC) is critical for determining cell fates and functions in multicellular organisms. With the advent of single-cell RNA-sequencing (scRNA-seq) and spatial transcriptomics (ST), an increasing number of CCC inference methods have been developed. Nevertheless, a thorough comparison of their performances is yet to be conducted. To fill this gap, we developed a systematic benchmark framework called ESICCC to evaluate 18 ligand-receptor (LR) inference methods and five ligand/receptor-target inference methods using a total of 116 data sets, including 15 ST data sets, 15 sets of cell line perturbation data, two sets of cell type-specific expression/proteomics data, and 84 sets of sampled or unsampled scRNA-seq data. We evaluated and compared the agreement, accuracy, robustness, and usability of these methods. Regarding accuracy evaluation, RNAMagnet, CellChat, and scSeqComm emerge as the three best-performing methods for intercellular ligand-receptor inference based on scRNA-seq data, whereas stMLnet and HoloNet are the best methods for predicting ligand/receptor-target regulation using ST data. To facilitate the practical applications, we provide a decision-tree-style guideline for users to easily choose best tools for their specific research concerns in CCC inference, and develop an ensemble pipeline CCCbank that enables versatile combinations of methods and databases. Moreover, our comparative results also uncover several critical influential factors for CCC inference, such as prior interaction information, ligand-receptor scoring algorithm, intracellular signaling complexity, and spatial relationship, which may be considered in the future studies to advance the development of new methodologies.
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Affiliation(s)
- Jiaxin Luo
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
| | - Minghua Deng
- School of Mathematical Sciences, Peking University, Beijing, 100871, China
| | - Xuegong Zhang
- Bioinformatics Division of BNRIST and Department of Automation, MOE Key Lab of Bioinformatics, Tsinghua University, Beijing, 100084, China
| | - Xiaoqiang Sun
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China;
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12
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Jin L, Long Y, Zhang Q, Long J. MiRNAs regulate cell communication in osteogenesis-angiogenesis coupling during bone regeneration. Mol Biol Rep 2023; 50:8715-8728. [PMID: 37642761 DOI: 10.1007/s11033-023-08709-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/25/2023] [Indexed: 08/31/2023]
Abstract
Bone regeneration is a complex process that requires not only the participation of multiple cell types, but also signal communication between cells. The two basic processes of osteogenesis and angiogenesis are closely related to bone regeneration and bone homeostasis. H-type vessels are a subtype of bone vessels characterized by high expression of CD31 and EMCN. These vessels play a key role in the regulation of bone regeneration and are important mediators of coupling between osteogenesis and angiogenesis. Molecular regulation between different cell types is important for coordination of osteogenesis and angiogenesis that promotes bone regeneration. MiRNAs are small non-coding RNAs that predominantly regulate gene expression at the post-transcriptional level and are closely related to cell communication. Specifically, miRNAs transduce external stimuli through various cell signaling pathways and cause a series of physiological and pathological effects. They are also deeply involved in the bone repair process. This review focuses on three signaling pathways related to osteogenesis-angiogenesis coupling, as well as the miRNAs involved in these pathways. Elucidation of the molecular mechanisms governing osteogenesis and angiogenesis is of great significance for bone regeneration.
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Affiliation(s)
- Liangyu Jin
- The State Key Laboratory of Oral Diseases, Sichuan University, Chengdu, 610041, PR China
- Department of Oral and Maxillofacial Surgery, West China College of Stomatology, Sichuan University, Chengdu, 610041, PR China
- National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, 610041, PR China
| | - Yifei Long
- The State Key Laboratory of Oral Diseases, Sichuan University, Chengdu, 610041, PR China
- National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, 610041, PR China
| | - Qiuling Zhang
- The State Key Laboratory of Oral Diseases, Sichuan University, Chengdu, 610041, PR China
- Department of Oral and Maxillofacial Surgery, West China College of Stomatology, Sichuan University, Chengdu, 610041, PR China
- National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, 610041, PR China
| | - Jie Long
- The State Key Laboratory of Oral Diseases, Sichuan University, Chengdu, 610041, PR China.
- Department of Oral and Maxillofacial Surgery, West China College of Stomatology, Sichuan University, Chengdu, 610041, PR China.
- National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, 610041, PR China.
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13
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Samuels M, Jones W, Towler B, Turner C, Robinson S, Giamas G. The role of non-coding RNAs in extracellular vesicles in breast cancer and their diagnostic implications. Oncogene 2023; 42:3017-3034. [PMID: 37670020 PMCID: PMC10555829 DOI: 10.1038/s41388-023-02827-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/07/2023]
Abstract
Breast Cancer (BC) is the most common form of cancer worldwide, responsible for 25% of cancers in women. Whilst treatment is effective and often curative in early BC, metastatic disease is incurable, highlighting the need for early detection. Currently, early detection relies on invasive procedures, however recent studies have shown extracellular vesicles (EVs) obtained from liquid biopsies may have clinical utility. EVs transport diverse bioactive cargos throughout the body, play major roles in intercellular communication and, importantly, mirror their cell of origin. In cancer cells, EVs alter the behaviour of the tumour microenvironment (TME), forming a bridge of communication between cancerous and non-cancerous cells to alter all aspects of cancer progression, including the formation of a pre-metastatic niche. Through gene regulatory frameworks, non-coding RNAs (ncRNAs) modulate vital molecular and cellular processes and can act as both tumour suppressors and oncogenic drivers in various cancer types. EVs transport and protect ncRNAs, facilitating their use clinically as liquid biopsies for early BC detection. This review summarises current research surrounding ncRNAs and EVs within BC, focusing on their roles in cancer progression through bi-directional communication with the microenvironment and their diagnostic implications. The role of EV ncRNAs in breast cancer. A representation of the different EV ncRNAs involved in tumourigenic processes in breast cancer. Pro-tumourigenic ncRNAs displayed in green and ncRNAs which inhibit oncogenic processes are shown in red.
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Affiliation(s)
- Mark Samuels
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, JMS Building, Falmer, Brighton, BN1 9QG, UK.
| | - William Jones
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, JMS Building, Falmer, Brighton, BN1 9QG, UK
| | - Benjamin Towler
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, JMS Building, Falmer, Brighton, BN1 9QG, UK
| | - Charlotte Turner
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, JMS Building, Falmer, Brighton, BN1 9QG, UK
| | - Stephen Robinson
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, JMS Building, Falmer, Brighton, BN1 9QG, UK
| | - Georgios Giamas
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, JMS Building, Falmer, Brighton, BN1 9QG, UK.
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14
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Li H, Ma T, Hao M, Guo W, Gu J, Zhang X, Wei L. Decoding functional cell-cell communication events by multi-view graph learning on spatial transcriptomics. Brief Bioinform 2023; 24:bbad359. [PMID: 37824741 DOI: 10.1093/bib/bbad359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/25/2023] [Accepted: 09/18/2023] [Indexed: 10/14/2023] Open
Abstract
Cell-cell communication events (CEs) are mediated by multiple ligand-receptor (LR) pairs. Usually only a particular subset of CEs directly works for a specific downstream response in a particular microenvironment. We name them as functional communication events (FCEs) of the target responses. Decoding FCE-target gene relations is: important for understanding the mechanisms of many biological processes, but has been intractable due to the mixing of multiple factors and the lack of direct observations. We developed a method HoloNet for decoding FCEs using spatial transcriptomic data by integrating LR pairs, cell-type spatial distribution and downstream gene expression into a deep learning model. We modeled CEs as a multi-view network, developed an attention-based graph learning method to train the model for generating target gene expression with the CE networks, and decoded the FCEs for specific downstream genes by interpreting trained models. We applied HoloNet on three Visium datasets of breast cancer and liver cancer. The results detangled the multiple factors of FCEs by revealing how LR signals and cell types affect specific biological processes, and specified FCE-induced effects in each single cell. We conducted simulation experiments and showed that HoloNet is more reliable on LR prioritization in comparison with existing methods. HoloNet is a powerful tool to illustrate cell-cell communication landscapes and reveal vital FCEs that shape cellular phenotypes. HoloNet is available as a Python package at https://github.com/lhc17/HoloNet.
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Affiliation(s)
- Haochen Li
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Tianxing Ma
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Minsheng Hao
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Wenbo Guo
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Jin Gu
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xuegong Zhang
- School of Medicine, Tsinghua University, Beijing 100084, China
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Lei Wei
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
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15
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Mierzejewski B, Ciemerych MA, Streminska W, Janczyk-Ilach K, Brzoska E. miRNA-126a plays important role in myoblast and endothelial cell interaction. Sci Rep 2023; 13:15046. [PMID: 37699959 PMCID: PMC10497517 DOI: 10.1038/s41598-023-41626-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/29/2023] [Indexed: 09/14/2023] Open
Abstract
Muscle satellite cells (SCs) are stem cells and the main players in skeletal muscle reconstruction. Since satellite cells are located near or in direct contact with blood vessels their niche is formed, inter alia, by endothelial cells. The cross-talk between satellite cells and endothelial cells determines quiescence or proliferation of these cells. However, little is known about the role of miRNA in these interactions. In the present study we identified miRNA that were up-regulated in SC-derived myoblasts treated with stromal derived factor-1 (SDF-1) and/or down-regulated in cells in which the expression of CXCR4 or CXCR7, that is, SDF-1 receptors, was silenced. SDF-1 is one of the important regulators of cell migration, mobilization, skeletal muscle regeneration, and angiogenesis. We hypothesized that selected miRNAs affect SC-derived myoblast fate and interactions with endothelial cells. We showed that miR-126a-3p inhibited both, myoblast migration and fusion. Moreover, the levels of Cxcl12, encoding SDF-1 and Ackr3, encoding CXCR7, were reduced by miR-126a-3p mimic. Interestingly, the miR-126a-3p mimic significantly decreased the level of numerous factors involved in myogenesis and the miR-126a-5p mimic increased the level of Vefga. Importantly, the treatment of endothelial cells with medium conditioned by miR-126-5p mimic transfected SC-derived myoblasts promoted tubulogenesis.
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Affiliation(s)
- Bartosz Mierzejewski
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warszawa, Poland
| | - Maria Anna Ciemerych
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warszawa, Poland
| | - Wladyslawa Streminska
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warszawa, Poland
| | - Katarzyna Janczyk-Ilach
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warszawa, Poland
| | - Edyta Brzoska
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warszawa, Poland.
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16
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Wang L, Zheng Y, Sun Y, Mao S, Li H, Bo X, Li C, Chen H. TimeTalk uses single-cell RNA-seq datasets to decipher cell-cell communication during early embryo development. Commun Biol 2023; 6:901. [PMID: 37660148 PMCID: PMC10475079 DOI: 10.1038/s42003-023-05283-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 08/24/2023] [Indexed: 09/04/2023] Open
Abstract
Early embryonic development is a dynamic process that relies on proper cell-cell communication to form a correctly patterned embryo. Early embryo development-related ligand-receptor pairs (eLRs) have been shown to guide cell fate decisions and morphogenesis. However, the scope of eLRs and their influence on early embryo development remain elusive. Here, we developed a computational framework named TimeTalk from integrated public time-course mouse scRNA-seq datasets to decipher the secret of eLRs. Extensive validations and analyses were performed to ensure the involvement of identified eLRs in early embryo development. Process analysis identified that eLRs could be divided into six temporal windows corresponding to sequential events in the early embryo development process. With the interpolation strategy, TimeTalk is powerful in revealing paracrine settings and studying cell-cell communication during early embryo development. Furthermore, by using TimeTalk in the blastocyst and blastoid models, we found that the blastoid models share the core communication pathways with the epiblast and primitive endoderm lineages in the blastocysts. This result suggests that TimeTalk has transferability to other bio-dynamic processes. We also curated eLRs recognized by TimeTalk, which may provide valuable clues for understanding early embryo development and relevant disorders.
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Affiliation(s)
- Longteng Wang
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Peking University, Beijing, 100871, China
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Yang Zheng
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Yu Sun
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Shulin Mao
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- Yuanpei College, Peking University, Beijing, 100871, China
| | - Hao Li
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Xiaochen Bo
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
| | - Hebing Chen
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China.
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17
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Tan F, Xuan Y, Long L, Yu Y, Zhang C, Liang P, Wang Y, Chen M, Wen J, Chen G. Single-cell analysis of human prepuce reveals dynamic changes in gene regulation and cellular communications. BMC Genomics 2023; 24:514. [PMID: 37658288 PMCID: PMC10474653 DOI: 10.1186/s12864-023-09615-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/22/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND The cellular and molecular dynamics of human prepuce are crucial for understanding its biological and physiological functions, as well as the prevention of related genital diseases. However, the cellular compositions and heterogeneity of human prepuce at single-cell resolution are still largely unknown. Here we systematically dissected the prepuce of children and adults based on the single-cell RNA-seq data of 90,770 qualified cells. RESULTS We identified 15 prepuce cell subtypes, including fibroblast, smooth muscle cells, T/natural killer cells, macrophages, vascular endothelial cells, and dendritic cells. The proportions of these cell types varied among different individuals as well as between children and adults. Moreover, we detected cell-type-specific gene regulatory networks (GRNs), which could contribute to the unique functions of related cell types. The GRNs were also highly dynamic between the prepuce cells of children and adults. Our cell-cell communication network analysis among different cell types revealed a set of child-specific (e.g., CD96, EPO, IFN-1, and WNT signaling pathways) and adult-specific (e.g., BMP10, NEGR, ncWNT, and NPR1 signaling pathways) signaling pathways. The variations of GRNs and cellular communications could be closely associated with prepuce development in children and prepuce maintenance in adults. CONCLUSIONS Collectively, we systematically analyzed the cellular variations and molecular changes of the human prepuce at single-cell resolution. Our results gained insights into the heterogeneity of prepuce cells and shed light on the underlying molecular mechanisms of prepuce development and maintenance.
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Affiliation(s)
- Fei Tan
- School of Medicine, Shanghai Skin Disease Hospital, Tongji University, Shanghai, 200443, China.
- Shanghai Skin Disease Clinical College, The Fifth Clinical Medical College, Anhui Medical University, Shanghai Skin Disease Hospital, Shanghai, 200443, China.
| | - Yuan Xuan
- Shanghai Skin Disease Clinical College, The Fifth Clinical Medical College, Anhui Medical University, Shanghai Skin Disease Hospital, Shanghai, 200443, China
| | - Lan Long
- Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen, 518172, China
| | - Yang Yu
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Chunhua Zhang
- Department of Dermatology, Shanghai Baoshan Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, 201999, China
| | - Pengchen Liang
- School of Microelectronics, Shanghai University, Shanghai, 201800, China
| | - Yaoqun Wang
- Shanghai Skin Disease Clinical College, The Fifth Clinical Medical College, Anhui Medical University, Shanghai Skin Disease Hospital, Shanghai, 200443, China
| | - Meiyu Chen
- Shanghai Skin Disease Clinical College, The Fifth Clinical Medical College, Anhui Medical University, Shanghai Skin Disease Hospital, Shanghai, 200443, China
| | - Jiling Wen
- Department of Urology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China.
| | - Geng Chen
- School of Medicine, Shanghai Skin Disease Hospital, Tongji University, Shanghai, 200443, China.
- Center for Bioinformatics and Computational Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
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18
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Nail HM, Chiu CC, Leung CH, Ahmed MMM, Wang HMD. Exosomal miRNA-mediated intercellular communications and immunomodulatory effects in tumor microenvironments. J Biomed Sci 2023; 30:69. [PMID: 37605155 PMCID: PMC10440907 DOI: 10.1186/s12929-023-00964-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/11/2023] [Indexed: 08/23/2023] Open
Abstract
Extracellular communication, in other words, crosstalk between cells, has a pivotal role in the survival of an organism. This communication occurs by different methods, one of which is extracellular vesicles. Exosomes, which are small lipid extracellular vesicles, have recently been discovered to have a role in signal transduction between cells inside the body. These vesicles contain important bioactive molecules including lipids, proteins, DNA, mRNA, and noncoding RNAs such as microRNAs (miRNAs). Exosomes are secreted by all cells including immune cells (macrophages, lymphocytes, granulocytes, dendritic cells, mast cells) and tumor cells. The tumor microenvironment (TME) represents a complex network that supports the growth of tumor cells. This microenvironment encompasses tumor cells themselves, the extracellular matrix, fibroblasts, endothelial cells, blood vessels, immune cells, and non-cellular components such as exosomes and cytokines. This review aims to provide insights into the latest discoveries concerning how the immune system communicates internally and with other cell types, with a specific focus on research involving exosomal miRNAs in macrophages, dendritic cells, B lymphocytes, and T lymphocytes. Additionally, we will explore the role of exosomal miRNA in the TME and the immunomodulatory effect.
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Affiliation(s)
- Howida M Nail
- Graduate Institute of Biomedical Engineering, National Chung Hsing University, No. 145, Xingda Rd., South Dist., Taichung City, 402, Taiwan
| | - Chien-Chih Chiu
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, 999078, Macao, China
| | - Mahmoud M M Ahmed
- Department of Soil and Environmental Sciences, National Chung Hsing University, 404, Taichung City, Taiwan
| | - Hui-Min David Wang
- Graduate Institute of Biomedical Engineering, National Chung Hsing University, No. 145, Xingda Rd., South Dist., Taichung City, 402, Taiwan.
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung City, 404, Taiwan.
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19
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Xie Z, Li X, Mora A. A Comparison of Cell-Cell Interaction Prediction Tools Based on scRNA-seq Data. Biomolecules 2023; 13:1211. [PMID: 37627276 PMCID: PMC10452151 DOI: 10.3390/biom13081211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
Computational prediction of cell-cell interactions (CCIs) is becoming increasingly important for understanding disease development and progression. We present a benchmark study of available CCI prediction tools based on single-cell RNA sequencing (scRNA-seq) data. By comparing prediction outputs with a manually curated gold standard for idiopathic pulmonary fibrosis (IPF), we evaluated prediction performance and processing time of several CCI prediction tools, including CCInx, CellChat, CellPhoneDB, iTALK, NATMI, scMLnet, SingleCellSignalR, and an ensemble of tools. According to our results, CellPhoneDB and NATMI are the best performer CCI prediction tools, among the ones analyzed, when we define a CCI as a source-target-ligand-receptor tetrad. In addition, we recommend specific tools according to different types of research projects and discuss the possible future paths in the field.
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Affiliation(s)
- Zihong Xie
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, China;
| | - Xuri Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Antonio Mora
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, China;
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20
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Festa J, AlZaim I, Kalucka J. Adipose tissue endothelial cells: insights into their heterogeneity and functional diversity. Curr Opin Genet Dev 2023; 81:102055. [PMID: 37279621 DOI: 10.1016/j.gde.2023.102055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/04/2023] [Accepted: 04/28/2023] [Indexed: 06/08/2023]
Abstract
Cardiovascular disease is the leading cause of death globally. Endothelial cells (ECs), the key units of all vascular segments, have a significant impact on the health and disease of organisms. Adipose tissue is vital to cardiovascular health, therefore, understanding adipose EC (AdEC) biology is important. Recent data have highlighted the presence of distinct AdEC subpopulations that govern adipose tissue homeostasis. In addition to their role in nutrient metabolism and transport, AdECs are involved in bidirectional cellular communication with adipocytes, among other cells. These interactions are mainly mediated by paracrine factors, including noncoding RNAs. In this review, we highlight recent results showcasing the functions of AdECs in adipose tissue biology, metabolic homeostasis, and changes occurring in obesity.
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Affiliation(s)
- Joseph Festa
- Department of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, 8000 Aarhus C, Denmark. https://twitter.com/@Festa_Science
| | - Ibrahim AlZaim
- Department of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, 8000 Aarhus C, Denmark; Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark. https://twitter.com/@IbrahimAlZaim2
| | - Joanna Kalucka
- Department of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, 8000 Aarhus C, Denmark; Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark.
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21
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Cheng C, Chen W, Jin H, Chen X. A Review of Single-Cell RNA-Seq Annotation, Integration, and Cell-Cell Communication. Cells 2023; 12:1970. [PMID: 37566049 PMCID: PMC10417635 DOI: 10.3390/cells12151970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/10/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for investigating cellular biology at an unprecedented resolution, enabling the characterization of cellular heterogeneity, identification of rare but significant cell types, and exploration of cell-cell communications and interactions. Its broad applications span both basic and clinical research domains. In this comprehensive review, we survey the current landscape of scRNA-seq analysis methods and tools, focusing on count modeling, cell-type annotation, data integration, including spatial transcriptomics, and the inference of cell-cell communication. We review the challenges encountered in scRNA-seq analysis, including issues of sparsity or low expression, reliability of cell annotation, and assumptions in data integration, and discuss the potential impact of suboptimal clustering and differential expression analysis tools on downstream analyses, particularly in identifying cell subpopulations. Finally, we discuss recent advancements and future directions for enhancing scRNA-seq analysis. Specifically, we highlight the development of novel tools for annotating single-cell data, integrating and interpreting multimodal datasets covering transcriptomics, epigenomics, and proteomics, and inferring cellular communication networks. By elucidating the latest progress and innovation, we provide a comprehensive overview of the rapidly advancing field of scRNA-seq analysis.
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Affiliation(s)
- Changde Cheng
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
| | - Wenan Chen
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (W.C.); (H.J.)
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (W.C.); (H.J.)
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
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22
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Chai C, Sui K, Tang J, Yu H, Yang C, Zhang H, Li SC, Zhong JF, Wang Z, Zhang X. BCR-ABL1-driven exosome-miR130b-3p-mediated gap-junction Cx43 MSC intercellular communications imply therapies of leukemic subclonal evolution. Theranostics 2023; 13:3943-3963. [PMID: 37554265 PMCID: PMC10405834 DOI: 10.7150/thno.83178] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/12/2023] [Indexed: 08/10/2023] Open
Abstract
Rationale: In the bone marrow microenvironment (BMME), mesenchymal stem/stromal cells (MSCs) control the self-renewal of both healthy and cancerous hematopoietic stem/progenitor cells (HSPCs). We previously showed that in vivo leukemia-derived MSCs change neighbor MSCs into leukemia-permissive states and boost leukemia cell proliferation, survival, and chemotherapy resistance. But the mechanisms behind how the state changes are still not fully understood. Methods: Here, we took a reverse engineering approach to determine BCR-ABL1+ leukemia cells activated transcriptional factor C/EBPβ, resulting in miR130a/b-3p production. Then, we back-tracked from clinical specimen transcriptome sequencing to cell co-culture, molecular and cellular assays, flow cytometry, single-cell transcriptome, and transcriptional regulation to determine the molecular mechanisms of BCR-ABL1-driven exosome-miR130b-3p-mediated gap-junction Cx43 MSC intercellular communications. Results: BCR-ABL1-driven exosome-miR130a/b-3p mediated gap-junction Cx43 (a.k.a., GJA1) BMSC intercellular communications for subclonal evolution in leukemic microenvironment by targeting BMSCs-expressed HLAs, thereby potentially maintaining BMSCs with self-renewal properties and reduced BMSC immunogenicity. The Cx43low and miR-130a/bhigh subclonal MSCs subsets of differentiation state could be reversed to Cx43high and miR-130a/blow subclones of the higher stemness state in Cx43-overexpressed subclonal MSCs. Both miR-130a and miR-130b might only inhibit Cx43 translation or degrade Cx43 proteins and did not affect Cx43 mRNA stability. The subclonal evolution was further confirmed by single-cell transcriptome profiling of MSCs, which suggested that Cx43 regulated their stemness and played normal roles in immunomodulation antigen processing. Thus, upregulated miR-130a/b promoted osteogenesis and adipogenesis from BMSCs, thereby decreasing cancer progression. Our clinical data validated that the expression of many genes in human major histocompatibility was negatively associated with the stemness of MSCs, and several immune checkpoint proteins contributing to immune escape in tumors were overexpressed after either miR-130a or miR-130b overexpression, such as CD274, LAG3, PDCD1, and TNFRSF4. Not only did immune response-related cytokine-cytokine receptor interactions and PI3K-AKT pathways, including EGR3, TNFRSF1B, but also NDRG2 leukemic-associated inflammatory factors, such as IFNB1, CXCL1, CXCL10, and CCL7 manifest upon miR-130a/b overexpression. Either BCR siRNAs or ABL1 siRNAs assay showed significantly decreased miR-130a and miR-130b expression, and chromatin immunoprecipitation sequencing confirmed that the regulation of miR-130a and miR-130b expression is BCR-ABL1-dependent. BCR-ABL1 induces miR-130a/b expression through the upregulation of transcriptional factor C/EBPβ. C/EBPβ could bind directly to the promoter region of miR-130b-3p, not miR-130a-3p. BCR-ABL1-driven exosome-miR130a-3p could interact with Cx43, and further impact GJIC in TME. Conclusion: Our findings shed light on how leukemia BCR-ABL1-driven exosome-miR130b-3p could interact with gap-junction Cx43, and further impact GJIC in TME, implications for leukemic therapies of subclonal evolution.
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Affiliation(s)
- Chengyan Chai
- Medical Center of Hematology, Second Affiliated Hospital, Army Medical University, Chongqing,400037, China
- State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Ke Sui
- Medical Center of Hematology, Second Affiliated Hospital, Army Medical University, Chongqing,400037, China
- State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Jun Tang
- Medical Center of Hematology, Second Affiliated Hospital, Army Medical University, Chongqing,400037, China
| | - Hao Yu
- Medical Center of Hematology, Second Affiliated Hospital, Army Medical University, Chongqing,400037, China
- State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
| | - Chao Yang
- Medical Center of Hematology, Second Affiliated Hospital, Army Medical University, Chongqing,400037, China
- State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
| | - Hongyang Zhang
- Medical Center of Hematology, Second Affiliated Hospital, Army Medical University, Chongqing,400037, China
- State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
| | - Shengwen Calvin Li
- Neuro-Oncology and Stem Cell Research Laboratory, Center for Neuroscience Research, CHOC Children's Research Institute, Children's Hospital of Orange County (CHOC), 1201 La Veta Ave., Orange, CA 92868-3874, United States of America
- Department of Neurology, University of California-Irvine School of Medicine, 200 S. Manchester Ave. Ste. 206, Orange, CA 92868, United States of America
| | - Jiang F. Zhong
- Department of Basic Sciences, Loma Linda University, Loma Linda, California, 92354, United States of America
| | - Zheng Wang
- Medical Center of Hematology, Second Affiliated Hospital, Army Medical University, Chongqing,400037, China
- State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Xi Zhang
- Medical Center of Hematology, Second Affiliated Hospital, Army Medical University, Chongqing,400037, China
- State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
- Jinfeng Laboratory, Chongqing, 401329, China
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23
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Sugita K, Onishi I, Nakayama R, Ishibashi S, Ikeda M, Inoue M, Narita R, Oshima S, Shimizu K, Saito S, Sato S, Moriarity BS, Yamamoto K, Largaespada DA, Kitagawa M, Kurata M. Indirect CRISPR screening with photoconversion revealed key factors of drug resistance with cell-cell interactions. Commun Biol 2023; 6:582. [PMID: 37264057 PMCID: PMC10235018 DOI: 10.1038/s42003-023-04941-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 05/15/2023] [Indexed: 06/03/2023] Open
Abstract
Comprehensive screenings to clarify indirect cell-cell interactions, such as those in the tumor microenvironment, especially comprehensive assessments of supporting cells' effects, are challenging. Therefore, in this study, indirect CRISPR screening for drug resistance with cell-cell interactions was invented. The photoconvertible fluorescent protein Dendra2 was inducted to supporting cells and explored the drug resistance responsible factors of supporting cells with CRISPR screenings. Random mutated supporting cells co-cultured with leukemic cells induced drug resistance with cell-cell interactions. Supporting cells responsible for drug resistance were isolated with green-to-red photoconversion, and 39 candidate genes were identified. Knocking out C9orf89, MAGI2, MLPH, or RHBDD2 in supporting cells reduced the ratio of apoptosis of cancer cells. In addition, the low expression of RHBDD2 in supporting cells, specifically fibroblasts, of clinical pancreatic cancer showed a shortened prognosis, and a negative correlation with CXCL12 was observed. Indirect CRISPR screening was established to isolate the responsible elements of cell-cell interactions. This screening method could reveal unknown mechanisms in all kinds of cell-cell interactions by revealing live phenotype-inducible cells, and it could be a platform for discovering new targets of drugs for conventional chemotherapies.
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Affiliation(s)
- Keisuke Sugita
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Iichiroh Onishi
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Ran Nakayama
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Sachiko Ishibashi
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Masumi Ikeda
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Miori Inoue
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Rina Narita
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Shiori Oshima
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kaho Shimizu
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Shinichiro Saito
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Shingo Sato
- Center for Innovative Cancer Treatment, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | | | - Kouhei Yamamoto
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | | | - Masanobu Kitagawa
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Morito Kurata
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.
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24
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Cang Z, Zhao Y, Almet AA, Stabell A, Ramos R, Plikus MV, Atwood SX, Nie Q. Screening cell-cell communication in spatial transcriptomics via collective optimal transport. Nat Methods 2023; 20:218-228. [PMID: 36690742 PMCID: PMC9911355 DOI: 10.1038/s41592-022-01728-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/21/2022] [Indexed: 01/24/2023]
Abstract
Spatial transcriptomic technologies and spatially annotated single-cell RNA sequencing datasets provide unprecedented opportunities to dissect cell-cell communication (CCC). However, incorporation of the spatial information and complex biochemical processes required in the reconstruction of CCC remains a major challenge. Here, we present COMMOT (COMMunication analysis by Optimal Transport) to infer CCC in spatial transcriptomics, which accounts for the competition between different ligand and receptor species as well as spatial distances between cells. A collective optimal transport method is developed to handle complex molecular interactions and spatial constraints. Furthermore, we introduce downstream analysis tools to infer spatial signaling directionality and genes regulated by signaling using machine learning models. We apply COMMOT to simulation data and eight spatial datasets acquired with five different technologies to show its effectiveness and robustness in identifying spatial CCC in data with varying spatial resolutions and gene coverages. Finally, COMMOT identifies new CCCs during skin morphogenesis in a case study of human epidermal development.
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Affiliation(s)
- Zixuan Cang
- Department of Mathematics and Center for Research in Scientific Computation, North Carolina State University, Raleigh, NC, USA
| | - Yanxiang Zhao
- Department of Mathematics, The George Washington University, Washington, DC, USA
| | - Axel A Almet
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
| | - Adam Stabell
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Raul Ramos
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Maksim V Plikus
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Scott X Atwood
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA.
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA.
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA.
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25
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Moirangthem A, Gondaliya P, Yan IK, Sayyed AA, Driscoll J, Patel T. Extracellular vesicle‑mediated miR‑126‑3p transfer contributes to inter‑cellular communication in the liver tumor microenvironment. Int J Oncol 2023; 62:31. [PMID: 36660950 PMCID: PMC9851126 DOI: 10.3892/ijo.2023.5479] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 10/24/2022] [Indexed: 01/18/2023] Open
Abstract
Extracellular vesicles (EVs) and their contents are gaining recognition as important mediators of intercellular communication through the transfer of bioactive molecules, such as non‑coding RNA. The present study comprehensively assessed the microRNA (miRNA/miR) content within EVs released from HepG2 liver cancer (LC) cells and LX2 hepatic stellate cells (HSCs) and determined the contribution of EV miRNA to intercellular communication. Using both transwell and spheroid co‑cultures of LC cells and HSCs, miR‑126‑3p within EV was established as a mediator of HSC to LC cell communication that influenced tumor cell migration and invasion, as well as the growth of multicellular LC/HSC spheroids. Manipulation of miR‑126‑3p either by enforced expression using pre‑miR‑126‑3p or by inhibition using antimiR‑126‑3p did not alter tumor cell viability, proliferation or sensitivity to either sorafenib or regorafenib. By contrast, enforced expression of miR‑126‑3p decreased tumor‑cell migration. Knockdown of miR‑126‑3p in tumor cells increased disintegrin and metalloproteinase domain‑containing protein 9 (ADAM9) expression and in HSCs increased collagen‑1A1 accumulation with an increase in compactness of multicellular spheroids. Within LC/HSC spheroids, ADAM9 and vascular endothelial growth factor expression was increased by silencing of miR‑126‑3p but diminished with the restoration of miR‑126‑3p. These studies implicate miR‑126‑3p in functional effects on migration, invasion and spheroid growth of tumor cells in the presence of HSCs, and thereby demonstrate functional EV‑RNA‑based intercellular signaling between HSCs and LC cells that is directly relevant to tumor‑cell behavior.
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Affiliation(s)
| | | | - Irene K. Yan
- Departments of Transplantation and Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Adil Ali Sayyed
- Departments of Transplantation and Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Julia Driscoll
- Departments of Transplantation and Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Tushar Patel
- Departments of Transplantation and Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA
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26
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Laura Francés J, Musolino E, Papait R, Pagiatakis C. Non-Coding RNAs in Cell-to-Cell Communication: Exploiting Physiological Mechanisms as Therapeutic Targets in Cardiovascular Pathologies. Int J Mol Sci 2023; 24:ijms24032205. [PMID: 36768528 PMCID: PMC9916956 DOI: 10.3390/ijms24032205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/10/2023] [Accepted: 01/14/2023] [Indexed: 01/24/2023] Open
Abstract
Cardiovascular disease, the leading cause of death worldwide, has been characterized at the molecular level by alterations in gene expression that contribute to the etiology of the disease. Such alterations have been shown to play a critical role in the development of atherosclerosis, cardiac remodeling, and age-related heart failure. Although much is now known about the cellular and molecular mechanisms in this context, the role of epigenetics in the onset of cardiovascular disease remains unclear. Epigenetics, a complex network of mechanisms that regulate gene expression independently of changes to the DNA sequence, has been highly implicated in the loss of homeostasis and the aberrant activation of a myriad of cellular pathways. More specifically, non-coding RNAs have been gaining much attention as epigenetic regulators of various pathologies. In this review, we will provide an overview of the ncRNAs involved in cell-to-cell communication in cardiovascular disease, namely atherosclerosis, cardiac remodeling, and cardiac ageing, and the potential use of epigenetic drugs as novel therapeutic targets.
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Affiliation(s)
| | - Elettra Musolino
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Roberto Papait
- IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
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27
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Rojas V, Larrondo LF. Coupling Cell Communication and Optogenetics: Implementation of a Light-Inducible Intercellular System in Yeast. ACS Synth Biol 2023; 12:71-82. [PMID: 36534043 PMCID: PMC9872819 DOI: 10.1021/acssynbio.2c00338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Indexed: 12/23/2022]
Abstract
Cell communication is a widespread mechanism in biology, allowing the transmission of information about environmental conditions. In order to understand how cell communication modulates relevant biological processes such as survival, division, differentiation, and apoptosis, different synthetic systems based on chemical induction have been successfully developed. In this work, we coupled cell communication and optogenetics in the budding yeast Saccharomyces cerevisiae. Our approach is based on two strains connected by the light-dependent production of α-factor pheromone in one cell type, which induces gene expression in the other type. After the individual characterization of the different variants of both strains, the optogenetic intercellular system was evaluated by combining the cells under contrasting illumination conditions. Using luciferase as a reporter gene, specific co-cultures at a 1:1 ratio displayed activation of the response upon constant blue light, which was not observed for the same cell mixtures grown in darkness. Then, the system was assessed at several dark/blue-light transitions, where the response level varies depending on the moment in which illumination was delivered. Furthermore, we observed that the amplitude of response can be tuned by modifying the initial ratio between both strains. Finally, the two-population system showed higher fold inductions in comparison with autonomous strains. Altogether, these results demonstrated that external light information is propagated through a diffusible signaling molecule to modulate gene expression in a synthetic system involving microbial cells, which will pave the road for studies allowing optogenetic control of population-level dynamics.
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Affiliation(s)
- Vicente Rojas
- Departamento
de Genética Molecular y Microbiología, Facultad de Ciencias
Biológicas, Pontificia Universidad
Católica de Chile, Santiago 8331150, Chile
- Millennium
Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Luis F. Larrondo
- Departamento
de Genética Molecular y Microbiología, Facultad de Ciencias
Biológicas, Pontificia Universidad
Católica de Chile, Santiago 8331150, Chile
- Millennium
Institute for Integrative Biology (iBio), Santiago 8331150, Chile
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28
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Cui L, Sun F, Xu Y, Li M, Chen L, Chen C, Qian J, Li D, Du M, Wang S. Tim-3 Coordinates Macrophage-Trophoblast Crosstalk via Angiogenic Growth Factors to Promote Pregnancy Maintenance. Int J Mol Sci 2023; 24:ijms24021538. [PMID: 36675047 PMCID: PMC9867110 DOI: 10.3390/ijms24021538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
T-cell immunoglobulin mucin-3 (Tim-3) is an important checkpoint that induces maternal-fetal tolerance in pregnancy. Macrophages (Mφs) play essential roles in maintaining maternal-fetal tolerance, remodeling spiral arteries, and regulating trophoblast biological behaviors. In the present study, the formation of the labyrinth zone showed striking defects in pregnant mice treated with Tim-3 neutralizing antibodies. The adoptive transfer of Tim-3+Mφs, rather than Tim-3-Mφs, reversed the murine placental dysplasia resulting from Mφ depletion. With the higher production of angiogenic growth factors (AGFs, including PDGF-AA, TGF-α, and VEGF), Tim-3+dMφs were more beneficial in promoting the invasion and tube formation ability of trophoblasts. The blockade of AGFs in Tim-3+Mφs led to the narrowing of the labyrinthine layer of the placenta, compromising maternal-fetal tolerance, and increasing the risk of fetal loss. Meanwhile, the AGFs-treated Tim-3-Mφs could resolve the placental dysplasia and fetal loss resulting from Mφ depletion. These findings emphasized the vital roles of Tim-3 in coordinating Mφs-extravillous trophoblasts interaction via AGFs to promote pregnancy maintenance and in extending the role of checkpoint signaling in placental development. The results obtained in our study also firmly demonstrated that careful consideration of reproductive safety should be taken when selecting immune checkpoint and AGF blockade therapies in real-world clinical care.
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29
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Abstract
The Cellular Communication Network Factor (CCN) family is composed of six members: CCN1/CYR61, CCN2/CTGF, CCN3/NOV, CCN4/WISP1, CCN5/WISP2, and CCN6/WISP3. The second member, CCN2/CTGF is a matricellular protein that promotes extracellular matrix (ECM) synthesis and controls angiogenesis. On the other hand, moonlighting/matrix metalloproteinase 3 (MMP3) is an ECM-degrading enzyme that also functions as an intracellular transcription factor. Importantly, extracellular MMP3 is uptaken into cells, translocating into nuclei, and transcriptionally activating CCN2/CTGF gene in cancer and chondrocytes. Thus, the MMP3-CTGF axis balances the matrix metabolism and turnover in the tissue and tumor microenvironments. We established an MMP3 knockout cell line using the CRISPR/Cas9 system, demonstrating the sequential regulatory events of the MMP3-CCN2 axis in the microenvironment. Notably, our protocol is useful for generation of CCN knockout cells as well. Here we serve a protocol of the CRISPR/Cas9-based gene targeting in cultured cells for investigating cellular communication network.
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Affiliation(s)
- Yuka Okusha
- Division of Molecular and Cellular Biology, Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Takanori Eguchi
- Department of Dental Pharmacology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.
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30
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Zhao Y, Sun J, Jin L. The N6-Methyladenosine Regulator ALKBH5 Mediated Stromal Cell-Macrophage Interaction via VEGF Signaling to Promote Recurrent Spontaneous Abortion: A Bioinformatic and In Vitro Study. Int J Mol Sci 2022; 23:ijms232415819. [PMID: 36555463 PMCID: PMC9785252 DOI: 10.3390/ijms232415819] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/29/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Successful conception requires the synchrony of multiple systems and organs. Dysregulation of stromal cell-immune cell interactions has been proposed to be associated with recurrent spontaneous abortion. However, the mechanism of this regulation has not been well elucidated. N6-methyladenosine is one of the most common RNA modifications, and is involved in many pathological processes. Our group has demonstrated that abnormal patterns of m6A modification inhibit trophoblast invasion and contribute to adverse pregnancy outcomes. The association between m6A regulators and stromal cell-immune cell interactions is unclear. We obtained RNA-seq profiles from a GEO dataset and identified differentially expressed m6A regulators between healthy controls and patients with a recurrent spontaneous abortion history. ROC curves, functional enrichment and subclassification analysis were applied to elucidate the role of m6A regulators in pregnancy. We verified the expression of m6A regulators and constructed an overexpression cell line in a coculture system to reveal ALKBH5 function in stromal cell-macrophage interactions. We identified 11 differentially expressed m6A regulators between healthy controls and patients with a recurrent spontaneous abortion history. Then, we identified the correlation between "eraser" genes and "writer" genes. We tested the predictive abilities of the 11 m6A regulators based on another dataset and verified their expression in primary human endometrial stromal cells. We then subclassified three distinct patterns using the 11 genes and visualized genes related to immune infiltration and macrophage function in each cluster. ALKBH5 was proven to be correlated with recurrent spontaneous abortion. To verify the role of ALKBH5 in RSA, we constructed an ALKBH5-overexpression cell line. Finally, we cocultured the overexpression cell line with THP-1 cells. A decrease in M2 differentiation was observed, and this bias could be attributed to the hyposecretion of VEGF in stromal cells. N6-methyladenosine regulators play a pivotal role in stromal cell-immune cell interactions at the maternal-fetal interface. Overexpression of the m6A "eraser" gene ALKBH5 in stromal cells resulted in the hyposecretion of VEGF. Dysregulation of VEGF might impair macrophage recruitment and M2 differentiation, which could be the potential cause of recurrent spontaneous abortion.
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Affiliation(s)
- Yongbo Zhao
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Jiani Sun
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Liping Jin
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
- Correspondence:
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31
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Xu C, Ma D, Ding Q, Zhou Y, Zheng H. PlantPhoneDB: A manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication. Plant Biotechnol J 2022; 20:2123-2134. [PMID: 35842742 PMCID: PMC9616517 DOI: 10.1111/pbi.13893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 07/10/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Ligand-receptor pairs play important roles in cell-cell communication for multicellular organisms in response to environmental cues. Recently, the emergence of single-cell RNA-sequencing (scRNA-seq) provides unprecedented opportunities to investigate cellular communication based on ligand-receptor expression. However, so far, no reliable ligand-receptor interaction database is available for plant species. In this study, we developed PlantPhoneDB (https://jasonxu.shinyapps.io/PlantPhoneDB/), a pan-plant database comprising a large number of high-confidence ligand-receptor pairs manually curated from seven resources. Also, we developed a PlantPhoneDB R package, which not only provided optional four scoring approaches that calculate interaction scores of ligand-receptor pairs between cell types but also provided visualization functions to present analysis results. At the PlantPhoneDB web interface, the processed datasets and results can be searched, browsed, and downloaded. To uncover novel cell-cell communication events in plants, we applied the PlantPhoneDB R package on GSE121619 dataset to infer significant cell-cell interactions of heat-shocked root cells in Arabidopsis thaliana. As a result, the PlantPhoneDB predicted the actively communicating AT1G28290-AT2G14890 ligand-receptor pair in atrichoblast-cortex cell pair in Arabidopsis thaliana. Importantly, the downstream target genes of this ligand-receptor pair were significantly enriched in the ribosome pathway, which facilitated plants adapting to environmental changes. In conclusion, PlantPhoneDB provided researchers with integrated resources to infer cell-cell communication from scRNA-seq datasets.
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Affiliation(s)
- Chaoqun Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and EcologyXiamen UniversityXiamenChina
| | - Dongna Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and EcologyXiamen UniversityXiamenChina
| | - Qiansu Ding
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and EcologyXiamen UniversityXiamenChina
| | - Ying Zhou
- National Institute for Data Science in Health and Medicine, School of MedicineXiamen UniversityXiamenChina
| | - Hai‐Lei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and EcologyXiamen UniversityXiamenChina
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Kaur G, Porter CBM, Ashenberg O, Lee J, Riesenfeld SJ, Hofree M, Aggelakopoulou M, Subramanian A, Kuttikkatte SB, Attfield KE, Desel CAE, Davies JL, Evans HG, Avraham-Davidi I, Nguyen LT, Dionne DA, Neumann AE, Jensen LT, Barber TR, Soilleux E, Carrington M, McVean G, Rozenblatt-Rosen O, Regev A, Fugger L. Mouse fetal growth restriction through parental and fetal immune gene variation and intercellular communications cascade. Nat Commun 2022; 13:4398. [PMID: 35906236 PMCID: PMC9338297 DOI: 10.1038/s41467-022-32171-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 07/18/2022] [Indexed: 11/08/2022] Open
Abstract
Fetal growth restriction (FGR) affects 5-10% of pregnancies, and can have serious consequences for both mother and child. Prevention and treatment are limited because FGR pathogenesis is poorly understood. Genetic studies implicate KIR and HLA genes in FGR, however, linkage disequilibrium, genetic influence from both parents, and challenges with investigating human pregnancies make the risk alleles and their functional effects difficult to map. Here, we demonstrate that the interaction between the maternal KIR2DL1, expressed on uterine natural killer (NK) cells, and the paternally inherited HLA-C*0501, expressed on fetal trophoblast cells, leads to FGR in a humanized mouse model. We show that the KIR2DL1 and C*0501 interaction leads to pathogenic uterine arterial remodeling and modulation of uterine NK cell function. This initial effect cascades to altered transcriptional expression and intercellular communication at the maternal-fetal interface. These findings provide mechanistic insight into specific FGR risk alleles, and provide avenues of prevention and treatment.
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Affiliation(s)
- Gurman Kaur
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jack Lee
- Department of Biomedical Engineering, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Samantha J Riesenfeld
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Matan Hofree
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maria Aggelakopoulou
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | | | - Subita Balaram Kuttikkatte
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Kathrine E Attfield
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Christiane A E Desel
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- University Department of Neurology, University Hospital Magdeburg, Magdeburg, Germany
| | - Jessica L Davies
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Hayley G Evans
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Inbal Avraham-Davidi
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lan T Nguyen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Danielle A Dionne
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Lise Torp Jensen
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Thomas R Barber
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Elizabeth Soilleux
- Department of Pathology, Tennis Court Rd, University of Cambridge, Cambridge, England
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Massachusetts Institute of Technology, Department of Biology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Genentech, 1 DNA Way, South San Francisco, CA, USA.
| | - Lars Fugger
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK.
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK.
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark.
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33
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Lukowicz-Bedford RM, Farnsworth DR, Miller AC. Connexinplexity: the spatial and temporal expression of connexin genes during vertebrate organogenesis. G3 (Bethesda) 2022; 12:jkac062. [PMID: 35325106 PMCID: PMC9073686 DOI: 10.1093/g3journal/jkac062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/24/2022] [Indexed: 11/28/2022]
Abstract
Animal development requires coordinated communication between cells. The Connexin family of proteins is a major contributor to intercellular communication in vertebrates by forming gap junction channels that facilitate the movement of ions, small molecules, and metabolites between cells. Additionally, individual hemichannels can provide a conduit to the extracellular space for paracrine and autocrine signaling. Connexin-mediated communication is widely used in epithelial, neural, and vascular development and homeostasis, and most tissues likely use this form of communication. In fact, Connexin disruptions are of major clinical significance contributing to disorders developing from all major germ layers. Despite the fact that Connexins serve as an essential mode of cellular communication, the temporal and cell-type-specific expression patterns of connexin genes remain unknown in vertebrates. A major challenge is the large and complex connexin gene family. To overcome this barrier, we determined the expression of all connexins in zebrafish using single-cell RNA-sequencing of entire animals across several stages of organogenesis. Our analysis of expression patterns has revealed that few connexins are broadly expressed, but rather, most are expressed in tissue- or cell-type-specific patterns. Additionally, most tissues possess a unique combinatorial signature of connexin expression with dynamic temporal changes across the organism, tissue, and cell. Our analysis has identified new patterns for well-known connexins and assigned spatial and temporal expression to genes with no-existing information. We provide a field guide relating zebrafish and human connexin genes as a critical step toward understanding how Connexins contribute to cellular communication and development throughout vertebrate organogenesis.
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Affiliation(s)
| | - Dylan R Farnsworth
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, OR 97403, USA
| | - Adam C Miller
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, OR 97403, USA
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Kiss E, Fischer C, Sauter JM, Sun J, Ullrich ND. The Structural and the Functional Aspects of Intercellular Communication in iPSC-Cardiomyocytes. Int J Mol Sci 2022; 23:ijms23084460. [PMID: 35457277 PMCID: PMC9031673 DOI: 10.3390/ijms23084460] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/14/2022] [Accepted: 04/16/2022] [Indexed: 02/04/2023] Open
Abstract
Recent advances in the technology of producing novel cardiomyocytes from induced pluripotent stem cells (iPSC-cardiomyocytes) fuel new hope for future clinical applications. The use of iPSC-cardiomyocytes is particularly promising for the therapy of cardiac diseases such as myocardial infarction, where these cells could replace scar tissue and restore the functionality of the heart. Despite successful cardiogenic differentiation, medical applications of iPSC-cardiomyocytes are currently limited by their pronounced immature structural and functional phenotype. This review focuses on gap junction function in iPSC-cardiomyocytes and portrays our current understanding around the structural and the functional limitations of intercellular coupling and viable cardiac graft formation involving these novel cardiac muscle cells. We further highlight the role of the gap junction protein connexin 43 as a potential target for improving cell–cell communication and electrical signal propagation across cardiac tissue engineered from iPSC-cardiomyocytes. Better insight into the mechanisms that promote functional intercellular coupling is the foundation that will allow the development of novel strategies to combat the immaturity of iPSC-cardiomyocytes and pave the way toward cardiac tissue regeneration.
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Affiliation(s)
- Eva Kiss
- Institute of Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120 Heidelberg, Germany;
- George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Târgu Mureș, 540139 Târgu Mureș, Romania
| | - Carolin Fischer
- Center of Neurology, Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, Otfried-Müller-Straße 27, 72076 Tübingen, Germany;
| | - Jan-Mischa Sauter
- Division of Cardiovascular Physiology, Institute of Physiology and Pathophysiology, Heidelberg University, Im Neuenheimer Feld 307, 69120 Heidelberg, Germany; (J.-M.S.); (J.S.)
| | - Jinmeng Sun
- Division of Cardiovascular Physiology, Institute of Physiology and Pathophysiology, Heidelberg University, Im Neuenheimer Feld 307, 69120 Heidelberg, Germany; (J.-M.S.); (J.S.)
| | - Nina D. Ullrich
- Division of Cardiovascular Physiology, Institute of Physiology and Pathophysiology, Heidelberg University, Im Neuenheimer Feld 307, 69120 Heidelberg, Germany; (J.-M.S.); (J.S.)
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg-Mannheim, 10785 Berlin, Germany
- Correspondence:
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35
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O'Brien K, Ughetto S, Mahjoum S, Nair AV, Breakefield XO. Uptake, functionality, and re-release of extracellular vesicle-encapsulated cargo. Cell Rep 2022; 39:110651. [PMID: 35417683 PMCID: PMC9074118 DOI: 10.1016/j.celrep.2022.110651] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 08/06/2021] [Accepted: 03/18/2022] [Indexed: 12/19/2022] Open
Abstract
Extracellular vesicles (EVs) are membrane-encapsulated particles that carry genetically active and protein/lipid cargo that can affect the function of the recipient cell. A number of studies have described the effect of these vesicles on recipient cells and demonstrated their promise as therapeutic delivery vectors. Here we demonstrate functional delivery of EV-encapsulated RNA and protein cargo through use of luminescence and fluorescence reporters by combining organelle-targeted nanoluciferase with fluorescent proteins. We highlight a mechanism by which cells retain internalized cargo in the endosomal compartment for days, usually leading to content degradation. We also identify a mode through which recipient cells re-release internalized EVs intact after uptake. Highlighting these different fates of EVs in recipient cells sheds light on critical factors in steering functional cargo delivery and will ultimately allow more efficient use of EVs for therapeutic purposes.
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Affiliation(s)
- Killian O'Brien
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Stefano Ughetto
- Department of Oncology, University of Turin, 10060 Candiolo, TO, Italy
| | - Shadi Mahjoum
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Anil V Nair
- Program in Membrane Biology, Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Xandra O Breakefield
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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36
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Kirchner L, Averhoff B. DNA binding by pilins and their interaction with the inner membrane platform of the DNA transporter in Thermus thermophilus. Biochim Biophys Acta Biomembr 2022; 1864:183818. [PMID: 34774498 DOI: 10.1016/j.bbamem.2021.183818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 10/13/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
The natural transformation system of Thermus thermophilus has become a model system for studies of the structure and function of DNA transporter in thermophilic bacteria. The DNA transporter in T. thermophilus is functionally linked to type IV pili (T4P) and the major pilin PilA4 plays an essential role in both systems. However, T4P are dispensable for natural transformation. In addition to pilA4, T. thermophilus has a gene cluster encoding the three additional pilins PilA1-PilA3; deletion of the cluster abolished natural transformation but retained T4P biogenesis. In this study, we investigated the roles of single pilins PilA1, PilA2 and PilA3 in natural transformation by mutant studies. These studies revealed that each of these pilins is essential for natural transformation. Two of the pilins, PilA1 and PilA2, were found to bind dsDNA. PilA1 and PilA3 were detected in the inner membrane (IM) but not in the outer membrane (OM) whereas PilA2 was present in both membranes. All three pilins where absent in pilus fractions. This suggests that the pilins form a short DNA binding pseudopilus anchored in the IM. PilA1 was found to bind to the IM assembly platform of the DNA transporter via PilM and PilO. These data are in line with the hypothesis that a DNA binding pseudopilus is connected via an IM platform to the cytosolic motor ATPase PilF.
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Affiliation(s)
- Lennart Kirchner
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Beate Averhoff
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany.
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37
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Dixon EE, Wu H, Muto Y, Wilson PC, Humphreys BD. Spatially Resolved Transcriptomic Analysis of Acute Kidney Injury in a Female Murine Model. J Am Soc Nephrol 2022; 33:279-289. [PMID: 34853151 PMCID: PMC8819997 DOI: 10.1681/asn.2021081150] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/12/2021] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Single-cell sequencing technologies have advanced our understanding of kidney biology and disease, but the loss of spatial information in these datasets hinders our interpretation of intercellular communication networks and regional gene expression patterns. New spatial transcriptomic sequencing platforms make it possible to measure the topography of gene expression at genome depth. METHODS We optimized and validated a female bilateral ischemia-reperfusion injury model. Using the 10× Genomics Visium Spatial Gene Expression solution, we generated spatial maps of gene expression across the injury and repair time course, and applied two open-source computational tools, Giotto and SPOTlight, to increase resolution and measure cell-cell interaction dynamics. RESULTS An ischemia time of 34 minutes in a female murine model resulted in comparable injury to 22 minutes for males. We report a total of 16,856 unique genes mapped across our injury and repair time course. Giotto, a computational toolbox for spatial data analysis, enabled increased resolution mapping of genes and cell types. Using a seeded nonnegative matrix regression (SPOTlight) to deconvolute the dynamic landscape of cell-cell interactions, we found that injured proximal tubule cells were characterized by increasing macrophage and lymphocyte interactions even 6 weeks after injury, potentially reflecting the AKI to CKD transition. CONCLUSIONS In this transcriptomic atlas, we defined region-specific and injury-induced loss of differentiation markers and their re-expression during repair, as well as region-specific injury and repair transcriptional responses. Lastly, we created an interactive data visualization application for the scientific community to explore these results (http://humphreyslab.com/SingleCell/).
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Affiliation(s)
- Eryn E. Dixon
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Parker C. Wilson
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, Missouri
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38
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Balneger N, Cornelissen LAM, Wassink M, Moons SJ, Boltje TJ, Bar-Ephraim YE, Das KK, Søndergaard JN, Büll C, Adema GJ. Sialic acid blockade in dendritic cells enhances CD8 + T cell responses by facilitating high-avidity interactions. Cell Mol Life Sci 2022; 79:98. [PMID: 35089436 PMCID: PMC8799591 DOI: 10.1007/s00018-021-04027-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/06/2021] [Accepted: 11/08/2021] [Indexed: 12/11/2022]
Abstract
Sialic acids are negatively charged carbohydrates that cap the glycans of glycoproteins and glycolipids. Sialic acids are involved in various biological processes including cell-cell adhesion and immune recognition. In dendritic cells (DCs), the major antigen-presenting cells of the immune system, sialic acids emerge as important regulators of maturation and interaction with other lymphocytes including T cells. Many aspects of how sialic acids regulate DC functions are not well understood and tools and model systems to address these are limited. Here, we have established cultures of murine bone marrow-derived DCs (BMDCs) that lack sialic acid expression using a sialic acid-blocking mimetic Ac53FaxNeu5Ac. Ac53FaxNeu5Ac treatment potentiated BMDC activation via toll-like receptor (TLR) stimulation without affecting differentiation and viability. Sialic acid blockade further increased the capacity of BMDCs to induce antigen-specific CD8+ T cell proliferation. Transcriptome-wide gene expression analysis revealed that sialic acid mimetic treatment of BMDCs induces differential expression of genes involved in T cell activation, cell-adhesion, and cell-cell interactions. Subsequent cell clustering assays and single cell avidity measurements demonstrated that BMDCs with reduced sialylation form higher avidity interactions with CD8+ T cells. This increased avidity was detectable in the absence of antigens, but was especially pronounced in antigen-dependent interactions. Together, our data show that sialic acid blockade in BMDCs ameliorates maturation and enhances both cognate T cell receptor-MHC-dependent and independent T cell interactions that allow for more robust CD8+ T cell responses.
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Affiliation(s)
- N Balneger
- Radiotherapy and OncoImmunology Laboratory, Department of Radiation Oncology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 32, 6525 GA, Nijmegen, The Netherlands
| | - L A M Cornelissen
- Radiotherapy and OncoImmunology Laboratory, Department of Radiation Oncology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 32, 6525 GA, Nijmegen, The Netherlands
| | - M Wassink
- Radiotherapy and OncoImmunology Laboratory, Department of Radiation Oncology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 32, 6525 GA, Nijmegen, The Netherlands
| | - S J Moons
- Cluster for Molecular Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - T J Boltje
- Cluster for Molecular Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Y E Bar-Ephraim
- LUMICKS, Pilotenstraat 41, 1059 CH, Amsterdam, The Netherlands
| | - K K Das
- LUMICKS, Pilotenstraat 41, 1059 CH, Amsterdam, The Netherlands
| | - J N Søndergaard
- Center for Infectious Disease Education and Research, Osaka University, Osaka, 565-0871, Japan
| | - C Büll
- Radiotherapy and OncoImmunology Laboratory, Department of Radiation Oncology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 32, 6525 GA, Nijmegen, The Netherlands
- Hubrecht Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - G J Adema
- Radiotherapy and OncoImmunology Laboratory, Department of Radiation Oncology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 32, 6525 GA, Nijmegen, The Netherlands.
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39
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Alfandari D, Ben Ami Pilo H, Abou Karam P, Dagan O, Joubran C, Rotkopf R, Regev-Rudzki N, Porat Z. Monitoring Distribution Dynamics of EV RNA Cargo Within Recipient Monocytes and Macrophages. Front Cell Infect Microbiol 2022; 11:739628. [PMID: 35155269 PMCID: PMC8825493 DOI: 10.3389/fcimb.2021.739628] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 12/31/2021] [Indexed: 12/19/2022] Open
Abstract
Extracellular vesicles (EVs) are produced by across almost all the living kingdoms and play a crucial role in cell-cell communication processes. EVs are especially important for pathogens, as Plasmodium falciparum (Pf) parasite, the leading causing species in human malaria. Malaria parasites are able to modulate the host immune response from a distance via delivering diverse cargo components inside the EVs, such as proteins and nucleic acids. We have previously shown that imaging flow cytometry (IFC) can be effectively used to monitor the uptake of different cargo components of malaria derived EVs by host human monocytes. Here, we take this approach one step further and demonstrate that we can directly investigate the dynamics of the cargo distribution pattern over time by monitoring its distribution within two different recipient cells of the immune system, monocytes vs macrophages. By staining the RNA cargo of the vesicles and monitor the signal we were able to evaluate the kinetics of its delivery and measure different parameters of the cargo’s distribution post internalization. Interestingly, we found that while the level of the EV uptake is similar, the pattern of the signal for RNA cargo distribution is significantly different between these two recipient immune cells. Our results demonstrate that this method can be applied to study the distribution dynamics of the vesicle cargo post uptake to different types of cells. This can benefit significantly to our understanding of the fate of cargo components post vesicle internalization in the complex interface between pathogen-derived vesicles and their host recipient cells.
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Affiliation(s)
- Daniel Alfandari
- Department of Biomolecular Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Hila Ben Ami Pilo
- Department of Biomolecular Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Paula Abou Karam
- Department of Biomolecular Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Osnat Dagan
- Department of Biomolecular Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Carine Joubran
- Department of Biomolecular Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Rotkopf
- Bioinformatics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Neta Regev-Rudzki
- Department of Biomolecular Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, Israel
- *Correspondence: Neta Regev-Rudzki, ; Ziv Porat,
| | - Ziv Porat
- Flow Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
- *Correspondence: Neta Regev-Rudzki, ; Ziv Porat,
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40
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Abstract
NK cells play a crucial role in host protection during tumorigenesis. Throughout tumor development, however, NK cells become progressively dysfunctional through a combination of dynamic tissue-specific and systemic factors. While a number of immunosuppressive mechanisms present within the tumor microenvironment have been characterized, few studies have contextualized the spatiotemporal dynamics of these mechanisms during disease progression and across anatomical sites. Understanding how NK cell immunosuppression evolves in these contexts will be necessary to optimize NK cell therapy for solid and metastatic cancers. Here, we outline the spatiotemporal determinants of antitumor NK cell regulation, including heterogeneous tumor architecture, temporal disease states, diverse cellular communities, as well as the complex changes in NK cell states produced by the sum of these higher-order elements. Understanding of the signals encountered by NK cells across time and space may reveal new therapeutic targets to harness the full potential of NK cell therapy for cancer.
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Affiliation(s)
- Joey H. Li
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at the University of California, Los Angeles (UCLA), Los Angeles, CA, United States
- Medical Scientist Training Program, David Geffen School of Medicine at the University of California, Los Angeles (UCLA), Los Angeles, CA, United States
| | - Timothy E. O’Sullivan
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at the University of California, Los Angeles (UCLA), Los Angeles, CA, United States
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41
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Albanese M, Chen YFA, Hüls C, Gärtner K, Tagawa T, Mejias-Perez E, Keppler OT, Göbel C, Zeidler R, Shein M, Schütz AK, Hammerschmidt W. MicroRNAs are minor constituents of extracellular vesicles that are rarely delivered to target cells. PLoS Genet 2021; 17:e1009951. [PMID: 34871319 PMCID: PMC8675925 DOI: 10.1371/journal.pgen.1009951] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 12/16/2021] [Accepted: 11/16/2021] [Indexed: 12/14/2022] Open
Abstract
Mammalian cells release different types of vesicles, collectively termed extracellular vesicles (EVs). EVs contain cellular microRNAs (miRNAs) with an apparent potential to deliver their miRNA cargo to recipient cells to affect the stability of individual mRNAs and the cells’ transcriptome. The extent to which miRNAs are exported via the EV route and whether they contribute to cell-cell communication are controversial. To address these issues, we defined multiple properties of EVs and analyzed their capacity to deliver packaged miRNAs into target cells to exert biological functions. We applied well-defined approaches to produce and characterize purified EVs with or without specific viral miRNAs. We found that only a small fraction of EVs carried miRNAs. EVs readily bound to different target cell types, but EVs did not fuse detectably with cellular membranes to deliver their cargo. We engineered EVs to be fusogenic and document their capacity to deliver functional messenger RNAs. Engineered fusogenic EVs, however, did not detectably alter the functionality of cells exposed to miRNA-carrying EVs. These results suggest that EV-borne miRNAs do not act as effectors of cell-to-cell communication. The majority of metazoan cells release vesicles of different types and origins, such as exosomes and microvesicles, now collectively termed extracellular vesicles (EVs). EVs have gained much attention because they contain microRNAs (miRNAs) and thus could regulate their specific mRNA targets in recipient or acceptor cells that take up EVs. Using a novel fusion assay with superior sensitivity and specificity, we revisited this claim but found no convincing evidence for an efficient functional uptake of EVs in many different cell lines and primary human blood cells. Even EVs engineered to fuse and deliver their miRNA cargo to recipient cells had no measurable effect on target mRNAs in very carefully controlled, quantitative experiments. Our negative results clearly indicate that EVs do not act as vehicles for miRNA-based cell-to-cell communication.
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Affiliation(s)
- Manuel Albanese
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
- * E-mail: (MA); (WH)
| | - Yen-Fu Adam Chen
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
| | - Corinna Hüls
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
| | - Kathrin Gärtner
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
| | - Takanobu Tagawa
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
| | - Ernesto Mejias-Perez
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
| | - Oliver T. Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
| | - Christine Göbel
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
| | - Reinhard Zeidler
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
- Department of Otorhinolaryngology, Klinikum der Universität München, Munich, Germany
| | - Mikhail Shein
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Anne K. Schütz
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Wolfgang Hammerschmidt
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
- * E-mail: (MA); (WH)
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Forder A, Hsing CY, Trejo Vazquez J, Garnis C. Emerging Role of Extracellular Vesicles and Cellular Communication in Metastasis. Cells 2021; 10:cells10123429. [PMID: 34943937 PMCID: PMC8700460 DOI: 10.3390/cells10123429] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 12/15/2022] Open
Abstract
Communication between cancer cells and the surrounding stromal cells of the tumor microenvironment (TME) plays a key role in promoting metastasis, which is the major cause of cancer death. Small membrane-bound particles called extracellular vesicles (EVs) are released from both cancer and stromal cells and have a key role in mediating this communication through transport of cargo such as various RNA species (mRNA, miRNA, lncRNA), proteins, and lipids. Tumor-secreted EVs have been observed to induce a pro-tumorigenic phenotype in non-malignant cells of the stroma, including fibroblasts, endothelial cells, and local immune cells. These cancer-associated cells then drive metastasis by mechanisms such as increasing the invasiveness of cancer cells, facilitating angiogenesis, and promoting the formation of the pre-metastatic niche. This review will cover the role of EV-mediated signaling in the TME during metastasis and highlight the therapeutic potential of targeting these pathways to develop biomarkers and novel treatment strategies.
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Affiliation(s)
- Aisling Forder
- Department of Integrative Oncology, British Cancer Research Center, Vancouver, BC V5Z 1L3, Canada; (A.F.); (C.-Y.H.); (J.T.V.)
| | - Chi-Yun Hsing
- Department of Integrative Oncology, British Cancer Research Center, Vancouver, BC V5Z 1L3, Canada; (A.F.); (C.-Y.H.); (J.T.V.)
| | - Jessica Trejo Vazquez
- Department of Integrative Oncology, British Cancer Research Center, Vancouver, BC V5Z 1L3, Canada; (A.F.); (C.-Y.H.); (J.T.V.)
| | - Cathie Garnis
- Department of Integrative Oncology, British Cancer Research Center, Vancouver, BC V5Z 1L3, Canada; (A.F.); (C.-Y.H.); (J.T.V.)
- Division of Otolaryngology, Department of Surgery, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
- Correspondence:
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Fox CA, Lethcoe K, Ryan RO. Calcium-induced release of cytochrome c from cardiolipin nanodisks: Implications for apoptosis. Biochim Biophys Acta Biomembr 2021; 1863:183722. [PMID: 34400138 PMCID: PMC8464532 DOI: 10.1016/j.bbamem.2021.183722] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/19/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
Miniature bilayer membranes comprised of phospholipid and an apolipoprotein scaffold, termed nanodisks (ND), have been used in binding studies. When ND formulated with cardiolipin (CL), but not phosphatidylcholine, were incubated with cytochrome c, FPLC gel filtration chromatography provided evidence of a stable binding interaction. Incubation of CL ND with CaCl2 resulted in a concentration-dependent increase in sample turbidity caused by ND particle disruption. Prior incubation of CL ND with cytochrome c increased CL ND sensitivity to CaCl2-induced effects. Centrifugation of CaCl2-treated CL ND samples yielded pellet and supernatant fractions. Whereas the ND scaffold protein, apolipophorin III, was recovered in the pellet fraction along with CL, the majority of the cytochrome c pool was in the supernatant fraction. Moreover, when cytochrome c CL ND were incubated with CaCl2 at concentrations below the threshold to induce ND particle disruption, FPLC analysis showed that cytochrome c was released. Pre-incubation of CL ND with CaCl2 under conditions that do not disrupt ND particle integrity prevented cytochrome c binding to CL ND. Thus, competition between Ca2+ and cytochrome c for a common binding site on CL modulates cytochrome c binding and likely plays a role in its dissociation from CL-rich cristae membranes in response to apoptotic stimuli.
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Affiliation(s)
- Colin A Fox
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV 89557, United States of America
| | - Kyle Lethcoe
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV 89557, United States of America
| | - Robert O Ryan
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV 89557, United States of America.
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Lessi F, Aretini P, Rizzo M, Morelli M, Menicagli M, Franceschi S, Mazzanti CM. Analysis of exosome-derived microRNAs reveals insights of intercellular communication during invasion of breast, prostate and glioblastoma cancer cells. Cell Adh Migr 2021; 15:180-201. [PMID: 34157951 PMCID: PMC8224203 DOI: 10.1080/19336918.2021.1935407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 04/08/2021] [Accepted: 05/20/2021] [Indexed: 12/28/2022] Open
Abstract
MiRNAs represent a mechanism that regulates gene expression in many pathological conditions. Exosomes are known to be secreted from all types of cells, and the exosomes-released molecules are crucial messengers that can regulate cellular processes. We investigated the miRNAs content of exosomes released by cancer cells during the invasion . An invasion stimulus has been generated through scratches created on the confluent cells of cancer cell lines: glioblastoma, breast and prostate cancers.Several miRNAs were found to be significantly differentially abundant during the cell invasion , both in common among different cell lines and exclusive. Understanding the language codes among cells involved in invasion can lead to the development of therapies that can inhibit cellular communication, slowing or eventually stopping their activity.
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Affiliation(s)
| | | | - Milena Rizzo
- Institute of Clinical Physiology (IFC), CNR, Pisa, Italy
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Lin H, Yu J, Gu X, Ge S, Fan X. Novel insights into exosomal circular RNAs: Redefining intercellular communication in cancer biology. Clin Transl Med 2021; 11:e636. [PMID: 34898043 PMCID: PMC8666583 DOI: 10.1002/ctm2.636] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 02/06/2023] Open
Abstract
Exosomes, a special type of membrane-bound extracellular vesicle regarded as an ideal carrier for intercellular messages, play an essential role in intercellular communication both locally and systematically. Recent studies have reported that circular RNAs (circRNAs), members of the noncoding RNA family, are abundant and stable in exosomes. As an essential mediator of intercellular communication within cancer cells or between cancer cells and noncancerous cells, exosomal circRNAs participate in multiple aspects of cancer. In this review, we summarize the biogenesis, properties and functions of exosomal circRNAs. In particular, we describe their intercellular transfer in the tumour microenvironment and associate their biological functions with different phenotypes of cancer. Finally, we discuss potential clinical applications in the future.
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Affiliation(s)
- Huimin Lin
- Department of OphthalmologyNinth People's HospitalShanghai JiaoTong University School of MedicineShanghai20025P. R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular OncologyShanghai20025P. R. China
| | - Jie Yu
- Department of OphthalmologyNinth People's HospitalShanghai JiaoTong University School of MedicineShanghai20025P. R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular OncologyShanghai20025P. R. China
| | - Xiang Gu
- Department of OphthalmologyNinth People's HospitalShanghai JiaoTong University School of MedicineShanghai20025P. R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular OncologyShanghai20025P. R. China
| | - Shengfang Ge
- Department of OphthalmologyNinth People's HospitalShanghai JiaoTong University School of MedicineShanghai20025P. R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular OncologyShanghai20025P. R. China
| | - Xianqun Fan
- Department of OphthalmologyNinth People's HospitalShanghai JiaoTong University School of MedicineShanghai20025P. R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular OncologyShanghai20025P. R. China
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Konishi H, Sato H, Takahashi K, Fujiya M. Tumor-Progressive Mechanisms Mediating miRNA-Protein Interaction. Int J Mol Sci 2021; 22:ijms222212303. [PMID: 34830186 PMCID: PMC8622902 DOI: 10.3390/ijms222212303] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 02/05/2023] Open
Abstract
MicroRNAs (miRNAs) are single-stranded short-chain RNAs that are endogenously expressed in vertebrates; they are considered the fine-tuners of cellular protein expression that act by modifying mRNA translation. miRNAs control tissue development and differentiation, cell growth, and apoptosis in cancer and non-cancer cells. Aberrant regulation of miRNAs is involved in the pathogenesis of various diseases including cancer. Numerous investigations have shown that the changes in cellular miRNA expression in cancerous tissues and extracellular miRNAs enclosed in exosomes are correlated with cancer prognosis. Therefore, miRNAs can be used as cancer biomarkers and therapeutic targets for cancer in clinical applications. In the previous decade, miRNAs have been shown to regulate cellular functions by directly binding to proteins and mRNAs, thereby controlling cancer progression. This regulatory system implies that cancer-associated miRNAs can be applied as molecular-targeted therapy. This review discusses the roles of miRNA-protein systems in cancer progression and its future applications in cancer treatment.
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Affiliation(s)
- Hiroaki Konishi
- Department of Gastroenterology and Advanced Medical Sciences, Asahikawa Medical University, Midorigaoka, Asahikawa 078-8510, Japan;
- Correspondence: ; Tel.: +81-166-68-2462
| | - Hiroki Sato
- Gastroenterology and Endoscopy, Division of Metabolism and Biosystemic Science, Gastroenterology, and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Midorigaoka, Asahikawa 078-8510, Japan; (H.S.); (K.T.)
| | - Kenji Takahashi
- Gastroenterology and Endoscopy, Division of Metabolism and Biosystemic Science, Gastroenterology, and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Midorigaoka, Asahikawa 078-8510, Japan; (H.S.); (K.T.)
| | - Mikihiro Fujiya
- Department of Gastroenterology and Advanced Medical Sciences, Asahikawa Medical University, Midorigaoka, Asahikawa 078-8510, Japan;
- Gastroenterology and Endoscopy, Division of Metabolism and Biosystemic Science, Gastroenterology, and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Midorigaoka, Asahikawa 078-8510, Japan; (H.S.); (K.T.)
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Bhatla SC, Gogna M, Jain P, Singh N, Mukherjee S, Kalra G. Signaling mechanisms and biochemical pathways regulating pollen-stigma interaction, seed development and seedling growth in sunflower under salt stress. Plant Signal Behav 2021; 16:1958129. [PMID: 34429013 PMCID: PMC8526035 DOI: 10.1080/15592324.2021.1958129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 05/04/2023]
Abstract
Sunflower (Helianthus annuus L.) is one of the major oilseed crops cultivated world over for its high-quality oil rich in linoleic acid. It also has established applications in pharmaceutical and biotechnological industries, mainly through recombinant production of unique oil body (OB) membrane proteins-oleosins, which are used for producing a wide variety of vaccines, food products, cosmetics and nutraceuticals. The present review provides a critical analysis of the progress made in advancing our knowledge in sunflower biology, ranging from mechanisms of pollen-stigma interaction, seed development, physiology of seed germination and seedling growth under salt stress, and finally understanding the signaling routes associated with various biochemical pathways regulating seedling growth. Role of nitric oxide (NO) triggered post-translational modifications (PTMs), discovered in the recent past, have paved way for future research directions leading to further understanding of sunflower developmental physiology. Novel protocols recently developed to monitor temporal and spatial distributions of various biochemicals involved in above-stated developmental events in sunflower, will go a long way for similar applications in plant biology in future.
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Affiliation(s)
| | - Mansi Gogna
- Department of Botany, University of Delhi, Delhi, India
| | - Prachi Jain
- Department of Botany, University of Delhi, Delhi, India
| | - Neha Singh
- Department of Botany, Gargi College, University of Delhi, New Delhi, India
| | - Soumya Mukherjee
- Department of Botany, Jangipur College, University of Kalyani, Jangipur, West Bengal, India
| | - Geetika Kalra
- Department of Botany , Acharya Narendra Dev College, University of Delhi, Kalkaji, New Delhi, India
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48
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Somiya M, Kuroda S. Reporter gene assay for membrane fusion of extracellular vesicles. J Extracell Vesicles 2021; 10:e12171. [PMID: 34807503 PMCID: PMC8607979 DOI: 10.1002/jev2.12171] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 11/01/2021] [Accepted: 11/08/2021] [Indexed: 01/05/2023] Open
Abstract
Extracellular vesicles (EVs) secreted by living cells are expected to deliver biological cargo molecules, including RNA and proteins, to the cytoplasm of recipient cells. There is an increasing need to understand the mechanism of intercellular cargo delivery by EVs. However, the lack of a feasible bioassay has hampered our understanding of the biological processes of EV uptake, membrane fusion, and cargo delivery to recipient cells. Here, we describe a reporter gene assay that can measure the membrane fusion efficiency of EVs during cargo delivery to recipient cells. When EVs containing tetracycline transactivator (tTA)-fused tetraspanins are internalized by recipient cells and fuse with cell membranes, the tTA domain is exposed to the cytoplasm and cleaved by tobacco etch virus protease to induce tetracycline responsive element (TRE)-mediated reporter gene expression in recipient cells. This assay (designated as EV-mediated tetraspanin-tTA delivery assay, ETTD assay), enabled us to assess the cytoplasmic cargo delivery efficiency of EVs in recipient cells. With the help of a vesicular stomatitis virus-derived membrane fusion protein, the ETTD assay could detect significant enhancement of cargo delivery efficiency of EVs. Furthermore, the ETTD assay could evaluate the effect of potential cargo delivery enhancers/inhibitors. Thus, the ETTD assay may contribute to a better understanding of the underlying mechanism of the cytoplasmic cargo delivery by EVs.
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Affiliation(s)
- Masaharu Somiya
- SANKEN (The Institute of Scientific and Industrial Research)Osaka UniversityOsakaJapan
| | - Shun'ichi Kuroda
- SANKEN (The Institute of Scientific and Industrial Research)Osaka UniversityOsakaJapan
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49
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Wang T, Wang X, Wang H, Li L, Zhang C, Xiang R, Tan X, Li Z, Jiang C, Zheng L, Xiao L, Yue S. High TSPAN8 expression in epithelial cancer cell-derived small extracellular vesicles promote confined diffusion and pronounced uptake. J Extracell Vesicles 2021; 10:e12167. [PMID: 34796683 PMCID: PMC8602930 DOI: 10.1002/jev2.12167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 11/01/2021] [Accepted: 11/05/2021] [Indexed: 01/08/2023] Open
Abstract
Small extracellular vesicles (sEVs) play a key role in intercellular communication. Cargo molecules carried by sEVs may affect the phenotype and function of recipient cells. Epithelial cancer cell-derived sEVs, particularly those enriched in CD151 or tetraspanin8 (TSPAN8) and associated integrins, promote tumour progression. The mechanism of binding and modulation of sEVs to recipient cells remains elusive. Here, we used genetically engineered breast cancer cells to derive TSPAN8-enriched sEVs and evaluated the impact of TSPAN8 on target cell membrane's diffusion and transport properties. The single-particle tracking technique showed that TSPAN8 significantly promoted sEV binding via confined diffusion. Functional assays indicated that the transgenic TSPAN8-sEV cargo increased cancer cell motility and epithelial-mesenchymal transition (EMT). In vivo, transgenic TSPAN8-sEV promoted uptake of sEVs in the liver, lung, and spleen. We concluded that TSPAN8 encourages the sEV-target cell interaction via forced confined diffusion and significantly increases cell motility. Therefore, TSPAN8-sEV may serve as an important direct or indirect therapeutic target.
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Affiliation(s)
- Teng Wang
- School of MedicineState Key Laboratory of Medicinal Chemical BiologyNankai UniversityTianjinChina
| | - Xin Wang
- State Key Laboratory of Medicinal Chemical BiologyTianjin Key Laboratory of Biosensing and Molecular RecognitionCollege of ChemistryNankai UniversityTianjinChina
| | - Haobin Wang
- Department of Breast & Thyroid SurgeryThe Third People's Hospital of ChengduThe Affiliated Hospital of Southwest Jiaotong UniversityThe Second Chengdu Hospital Affiliated to Chongqing Medical UniversityChengduSichuanChina
| | - Luhan Li
- School of MedicineState Key Laboratory of Medicinal Chemical BiologyNankai UniversityTianjinChina
| | - Chenhong Zhang
- School of MedicineState Key Laboratory of Medicinal Chemical BiologyNankai UniversityTianjinChina
| | - Rong Xiang
- School of MedicineState Key Laboratory of Medicinal Chemical BiologyNankai UniversityTianjinChina
| | - Xiaoyue Tan
- School of MedicineState Key Laboratory of Medicinal Chemical BiologyNankai UniversityTianjinChina
| | - Zongjin Li
- School of MedicineState Key Laboratory of Medicinal Chemical BiologyNankai UniversityTianjinChina
| | - Chunyang Jiang
- Department of Thoracic SurgeryTianjin Union Medical CenterTianjinChina
| | - Lei Zheng
- Department of Laboratory MedicineNanfang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Lehui Xiao
- State Key Laboratory of Medicinal Chemical BiologyTianjin Key Laboratory of Biosensing and Molecular RecognitionCollege of ChemistryNankai UniversityTianjinChina
| | - Shijing Yue
- School of MedicineState Key Laboratory of Medicinal Chemical BiologyNankai UniversityTianjinChina
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50
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AL-Abedi R, Tuncay Cagatay S, Mayah A, Brooks SA, Kadhim M. Ionising Radiation Promotes Invasive Potential of Breast Cancer Cells: The Role of Exosomes in the Process. Int J Mol Sci 2021; 22:ijms222111570. [PMID: 34769002 PMCID: PMC8583851 DOI: 10.3390/ijms222111570] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/21/2022] Open
Abstract
Along with the cells that are exposed to radiation, non-irradiated cells can unveil radiation effects as a result of intercellular communication, which are collectively defined as radiation induced bystander effects (RIBE). Exosome-mediated signalling is one of the core mechanisms responsible for multidirectional communication of tumor cells and their associated microenvironment, which may result in enhancement of malignant tumor phenotypes. Recent studies show that exosomes and exosome-mediated signalling also play a dynamic role in RIBE in cancer cell lines, many of which focused on altered exosome cargo or their effects on DNA damage. However, there is a lack of knowledge regarding how these changes in exosome cargo are reflected in other functional characteristics of cancer cells from the aspects of invasiveness and metastasis. Therefore, in the current study, we aimed to investigate exosome-mediated bystander effects of 2 Gy X-ray therapeutic dose of ionizing radiation on the invasive potential of MCF-7 breast cancer cells in vitro via assessing Matrigel invasion potential, epithelial mesenchymal transition (EMT) characteristics and the extent of glycosylation, as well as underlying plausible molecular mechanisms. The findings show that exosomes derived from irradiated MCF-7 cells enhance invasiveness of bystander MCF-7 cells, possibly through altered miRNA and protein content carried in exosomes.
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