Construction and analysis of cell-cell interaction networks and pathways in the human lung

Many of the most challenging diseases of our time have roots in the disruption of cell-cell communication or structural interactions in tissues. Thanks to the development of new experimental technologies, such as scRNA-seq, the study of cell-cell interactions, networks, and pathways in health and disease has become a hot topic in recent years. The lung is an interesting model system because is a vital organ that hosts many kinds of cell-cell interactions (CCIs) and is the epicenter of high mortality diseases such as chronic obstructive pulmonary disease (COPD), lung cancer, tuberculosis, or covid-19. In such a context, our goal is to build cell-cell interaction networks and pathways in the human lung, in both health and disease, and analyze them using network and pathway analysis tools, in order to understand them and being able to predict specific cell-cell interactions and drug targets.

Our group has studied different CCI subnetworks or diseases in the human lung, including: Idiopathic pulmonary fibrosis (IPF) [1,3], COPD [3], the lung microbial interaction network [4], and the pulmonary endothelial cell subnetwork [5]. Besides the human lung, we have also found an increase of cell-cell interactions in other systems [6]. Our research methods include: (i) Text mining and curation of cell-cell interactions [1]; (ii) Benchmarking, design, and application of interaction prediction tools [1,2,3]; (iii) CCI network and pathway analysis [3,4]; and (iv) CCI time-course analysis [5]. Our current plans include: (v) Generation of integrative databases and web platforms [3,4]; (vi) Data labeling for databases and machine learning; and (vii) Machine Learning analyses.

References:

[1] XIE Z, LI X, and MORA A (2023), A comparison of cell-cell interaction prediction tools based on scRNA-seq data, Biomolecules, 13(8), 1211, [Website]
[2] XIE B, JIANG Q, MORA A, and LI X (2021), Automatic cell type identification methods for single-cell RNA sequencing, Computational and Structural Biotechnology Journal, 19;5874 [Website]
[3] XIE Z (2023), A map of cell-cell interactions in the human lung, Master Thesis, Supervisor: Antonio Mora, Language: Chinese, Guangzhou Medical University (China)
[4] LU X (2022), Optimization and development of metatranscriptomics bioinformatics tools, Master Thesis, Supervisor: Antonio Mora, Language: Chinese, Guangzhou Medical University (China)
[5] Ongoing work [Website]
[6] ZHANG J, LI W, XIONG Z, ZHU J, et al. (2023), PDGF-D-induced immunoproteasome activation and cell-cell interactions, Computational and Structural Biotechnology Journal, 21;2405 [Website]