We isolated immune and non-immune single cells and physically interacting cells along different time-points of tissue development, from different murine tissues. We performed a wide holistic comparative analysis which revealed the shared, but also distinct, tissue-specific immune niches among the examined tissues. We applied advanced computational and functional experiments and revealed tissue-immune mechanisms that maintain homeostasis, and others that induce tissue-specific pathologies.
By focusing on liver development, we found that the immune-related intercellular communication driving liver fetal hematopoiesis is unique and different than the definitive bone-marrow hematopoiesis. We then molecularly and functionally defined this immune-hematopoietic crosstalk in the fetal liver. The combination of physically interacting cell sequencing, immuno-fluorescence and functional assays revealed novel immune-related communication controlling fetal hematopoiesis and liver biology.
We dissected the immune-non-immune crosstalk along the process of mammary gland development and breast cancer progression. We identified a unique immune-tumor cell physical crosstalk induced since neoplasia onward. We functionally validated that this crosstalk induced a pro-tumorigenic pathways by activating a unique signaling niche in the breast tumor microenvironment (TME). Notably, we developed a novel computational methodology to depict the secreted and physical communications in a signaling niche. For that purpose, we applied single cell ligand-receptor analysis together with physically interacting cell sequencing (PIC-seq) analysis, among cells residing in a specific spatial niche.
We found that the physical crosstalk between CD4+ T cells and dendritic cells induces a unique gene program of tumor-helper T cells (Tht) in human non-small cell lung carcinoma (NSCLC) TME. Importantly, we showed that these Thts have a functional role in the anti-tumor immune response following anti-PD1 treatment. Next, we isolated singlet immune and non-immune cells, as well as immune-tumor physically interacting cells from human biopsies derived from treatment-free NSCLC patients. By mapping the secreted and physical interactions in the lung adenocarcinoma TME, we identified different spatial signaling niches, associated with pro- and anti-tumor functions.
In all the ERC-related projects mentioned above we apply novel and high-throughput technologies which are single-cell based methods. Specifically, we perform PIC-seq in order to molecularly dissect the molecular signature of the immune-related physical crosstalk. Moreover, we developed a novel computational methodology to map the secreted and direct crosstalk in a specific cellular niche.
