Molecular insight into cellular crosstalk during lung development and disease

Tissue development and function arises from interactions between diverse cell types and lineages, as crosstalk between neighboring cells underlines many biological processes, such as cell activation, differentiation and signaling. Using single-cell RNA sequencing (RNA-seq), we first characterized the cellular composition of the lung during development, and identified vast dynamics in cell composition and their molecular signature. Next, in order to focus on direct cell-cell interactions, we developed a technology of physically interacting cell sequencing (PIC-seq), which combines fluorescently activated cell sorting of physically interacting cells along with massively parallel single-cell RNA-seq and computational modeling to systematically map in situ cellular interactions and characterize their molecular crosstalk. Investigation of T – myeloid cell interactions by PIC-seq following exposure to pathogen, and in tumor microenvironment of early lung adenocarcinoma lesions, revealed an interaction-specific transcription, including upregulation of a costimulatory genes, such as Ccl17, Ccl22, Ebi3 and Cd40, in rare interactions. Together, the study demonstrates how investigation of cellular crosstalk during tissue development and pathology can broaden our understanding regarding novel signaling networks in health and disease. Moreover, PIC-seq technology enables to reveal rare molecular crosstalk between communicating cells essential for the priming of specific cell activation states; therefore it has the capacity to highlight novel molecular targets applicable in infectious disease, autoimmunity, tumor-immunology and immunotherapy.