CPPLS-MLP: a method for constructing cell–cell communication networks and identifying related highly variable genes based on single-cell sequencing and spatial transcriptomics data

• Published in: Briefings in bioinformatics Vol. 25; no. 3
• Main Authors: Zhang, Tianjiao, Wu, Zhenao, Li, Liangyu, Ren, Jixiang, Zhang, Ziheng, Wang, Guohua
• Format: Journal Article
• Language: English
• Published: England Oxford Publishing Limited (England) 27.03.2024; Oxford University Press
• Subjects: Algorithms; Animals; Cell Communication; Cell interactions; Cellular communication; Communication; Communication networks; Communications networks; Computational Biology - methods; Gene expression; Gene Expression Profiling - methods; Gene Regulatory Networks; Genes; Genetic diversity; Humans; Immune system; Impact analysis; Ligands; Problem Solving Protocol; Receptors; Single-Cell Analysis - methods; Software; Spatial data; Transcriptome; Transcriptomics; scRNA-seq; highly variable genes; ST-seq; cell communication
• ISSN: 1467-5463; 1477-4054; 1477-4054
• DOI: 10.1093/bib/bbae198

In the growth and development of multicellular organisms, the immune processes of the immune system and the maintenance of the organism’s internal environment, cell communication plays a crucial role. It exerts a significant influence on regulating internal cellular states such as gene expression and cell functionality. Currently, the mainstream methods for studying intercellular communication are focused on exploring the ligand–receptor–transcription factor and ligand–receptor–subunit scales. However, there is relatively limited research on the association between intercellular communication and highly variable genes (HVGs). As some HVGs are closely related to cell communication, accurately identifying these HVGs can enhance the accuracy of constructing cell communication networks. The rapid development of single-cell sequencing (scRNA-seq) and spatial transcriptomics technologies provides a data foundation for exploring the relationship between intercellular communication and HVGs. Therefore, we propose CPPLS-MLP, which can identify HVGs closely related to intercellular communication and further analyze the impact of Multiple Input Multiple Output cellular communication on the differential expression of these HVGs. By comparing with the commonly used method CCPLS for constructing intercellular communication networks, we validated the superior performance of our method in identifying cell-type-specific HVGs and effectively analyzing the influence of neighboring cell types on HVG expression regulation. Source codes for the CPPLS_MLP R, python packages and the related scripts are available at ‘CPPLS_MLP Github [https://github.com/wuzhenao/CPPLS-MLP]’.