Construction And Application Of An Cell-Cell Communication Platform Based On Single Cell Sequencing Technology

Cell-to-cell communication refers to the signal sent by one cell to another cell through the medium and the corresponding response.There are many ways of communication between cells,including:1.Chemical signaling molecules transmit,including endocrine,paracrine,autocrine,and chemical synapse;2.Cells communicate with each other through the binding of adjacent surface molecules,and cells can contact each other directly.Both signal molecules and receptors are transmembrane proteins of cells.3.Adhering cells to extracellular matrix and achieving metabolic coupling or electrical coupling,etc.Cell-cell communication network is the function basis of a multicellular organism growth,differentiation,and a variety of tissues and organs,maintaining and related physiological activity coordination function,is the key for organs and cells to coordinate their work and fulfill their specific biological functions.The building of cell communication network model is of great significance to help people to understand in different tissues of the body physiological mechanism and different disease pathogenesis mechanism.In the past,the traditional RNAseq sequencing technology can only obtain a sample gene expression in general,heterogeneity information of different gene expression in cells could not be obtained,But in recent years along with the emergence and development of the single cell sequencing technology,people can be relatively easy for obtain the gene-specific expression information of different subtypes in tissues,which makes people have the chance to explore the details of communications between different subtypes cells,so as to better understand the biological functions of different organisms implementation mechanism.Therefore,in recent years,how to establish the communication network between cells through single cell sequencing data has become a hot research field in the bioinformatics.However,most of these studies are limited to simple interactions between ligands and receptors,without paying attention to a series of biochemical reactions that may be caused by cells after receptor activation,and without linking cell communication with the realization of biological functions of cells.Therefore,this study starts with the analysis of ligands and receptors significantly expressed in single cell sequencing data,By analyzing the association between the ligand and receptor data significantly expressed and the functional pathways significantly activated in the sequencing data,a simple and easy-to-use Web analysis platform for the analysis of intercellular communication network was constructed.So as to provide a more simple and easy to use,more stable and reliable way for researchers to realize cell communication network analysis and related functional pathway analysis.First,we integrated a total of 3,057 experimentally verified ligand-receptor pairs from cellphoneDB[1]and Fantom[2].Next,a total of 4,838 functional pathways from MsigDB[3]and Go term were collected for subsequent functional pathway activation analysis and signal set recognition analysis.Then,we use the Django(version number 1.11.20)framework to build our analysis platform,we use the Python(version 2.7)program language to develop our platform,we use Mysql(version 14.14)to store a user's data,we analysis platform will automatically select gene expression in the matrix expression of ligand and receptor,and communications links between different cells using Circos and every returned to the user in a visual way,Our analysis platform then analyzes the activation of the gene pathways associated with the ligand receptors,and then feeds back to the user the activation pathways that are highly relevant to cell communication.In addition,our analysis platform also supports the uploading and storage of user's relevant computing data,and user's computing data and results will be permanently stored on the server.Finally,we take the analysis of cell communication during the disease of Experimental Autoimmune Encephlomyelitis(EAE)as an example,and introduce in detail the use of the analysis platform and the detailed process of the analysis of cell communication in the disease,We use Intercellular communication analysis platform are analyzed in detail EAE single-cell transcriptome data of different stages of disease,to extract the nerve inflammation significantly expression in different stages of ligand receptor interaction relationship between cells,and the ligand receptor interaction relationship built during different nerve inflammation cells intercellular communication network in the composition of the cluster,and further reveals the along with the development of the disease,the change of different cell communication mode is how to affect the differentiation and metabolism of cells and how to regulate the activation of related functional pathways,and systematically elucidate the relevant mechanisms of intercellular communication affecting the progression of neuroinflammatory diseases.