Periodic Reporting for period 1 - IISN-DC (Understanding the functional role of Immune-related Intercellular Signalling Networks during tissue Development and Cancer)
Reporting period: 2022-04-01 to 2024-09-30
Intercellular signaling networks drive tissue fundamental processes. Immune cells present a wide range of versatile functions and distinctive plasticity, which position them as tissue signaling-hubs during tissue development, homeostasis and cancer. Recent genomic advances have greatly improved our understanding of cell composition and states; however, investigation of the molecular signatures of intercellular crosstalk at the single-cell level remains limited. We explore tissue development, homeostasis and cancer from the point of view of immune-controlled signaling networks, in order to reveal novel therapeutic candidates with high biological and medical impact. Revealing the functional consequences of the whole-tissue signaling networks has the potential to revisit key developmental and cancer immunology questions. First objective is to identify the immune-related intercellular crosstalk drives tissue development and cancer. By that, we aim to highlight tissue-exclusive and shared signaling during tissue physiology or cancer. Second, our project aims to reveal tumor-escape mechanisms, based on physiological signaling networks. Third, the proposal strongly integrates immuno-genomics, functional assays and computational biology, leading to the development of advanced computational methodologies to perform development versus cancer large-scale molecular comparisons for the identification of novel immunotherapy targets.
Successful completion of the project will reveal novel cancer and developmental immunotherapy targets. Concomitantly, findings will comprise a valuable resource for tissue-molecular signaling and will generate a platform for investigating biological enigmas by elucidating consequences of cellular-communication.
Successful completion of the project will reveal novel cancer and developmental immunotherapy targets. Concomitantly, findings will comprise a valuable resource for tissue-molecular signaling and will generate a platform for investigating biological enigmas by elucidating consequences of cellular-communication.
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.
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.
Identifying and molecularly dissecting the bidirectional dialogue between immune and resident non-immune cells during tissue development, homeostasis and cancer remains a holy grail of tissue and cancer biology. Recent years have seen methodological and technical advances in the field of cell-cell communication research, but we are just beginning to understand the underlying biology and the resultant therapeutic opportunities associated with communicating cells at the single-cell level. In this project we produce methodological and conceptual breakthroughs in the emerging fields of developmental immunology, tumor immunology and immuno-genomics, by dissecting tissues through their intercellular signaling networks. Our novel “Immune-Signaling Network Maps” will be beneficial for a very large community of physicians and researchers, including those interested in the functional role of specific cell states and molecules in tissue physiology/cancer, and those who seek to understand global genomic-transcriptomic phenomena related to cell-cell crosstalk across multiple cell types, tissues, and conditions. At the conclusion of this project, we will have an improved understanding of 1) signaling networks which are shared and unique among tissues, leading to the specificity of tissue maintenance and its competence to develop diseases; 2) novel molecular targets for immunotherapy directed to cell-cell communications in the TME; 3) developmental imprinting of intercellular signaling which predispose tissue-specific pathologies during adulthood. The results of the study will also provide improved tools to study molecular signatures of cell-cell communications in appropriate cellular contexts in vitro, in vivo and in human specimens. Ultimately, a successful completion of this project will be a major step towards identifying novel targets for broad immune-related and autoimmune pathologies and cancer types.