Project 1: Murine modeling of tumor-mediated immunosuppression.

We hypothesize that lymph node (LN) metastasis constitutes an essential step in the metastatic cascade of melanomas and head and neck tumors in that such metastases act locally upon the adaptive immune system within the nodes to induce tolerance to the tumor and that leukocytes recirculating from these nodes carry the tolerance to distant sites. Our objectives are to establish whether LN metastases induce perturbations in anti-tumor immunity and to identify the mechanisms of these perturbations. We will a) characterize differences in local and systemic immune responses to metastatic tumors; b) identify differential regulators of tolerance induction by metastatic cells through the use of genomic profiling; and c) identify the molecular mediators of metastatic tolerance induction in mice and humans. Through the use of serial in vivo passaging, we have developed a panel of syngeneic melanoma cell lines that exhibit enhanced LN metastatic potential. We will compare the activation states of these immune cells, cytokine profiles, T cell polarization, and cytolytic activity toward tumor cells using single cell proteomic methods (Project 2). Using cytokine profiling and RNA sequencing on the lines, we will apply computational systems biology approaches (Project 3) to identify the molecules relevant for induction of tolerance. If our hypothesis is proven correct that LN metastasis is an obligate step in the generation of systemic disease due to tolerance induction, targeting the molecules responsible for LN metastasis induced tolerance could prevent and treat metastatic disease.

Project 2: Spatial architecture of tumor-mediated immunosuppression.

Beyond the internal genomic and epigenetic events that occur to drive a cell towards outright carcinogenesis and then metastasis, there co-exist the ordered events a cancer imposes on immune cells it encounters on its progression towards advanced disease. Induction of tolerance, avoidance of apoptosis, and even recruitment of the immune system to aid a tumor’s growth are all poorly understood processes. We propose to undertake deep phenotyping of the 2D and 3D architecture of tumour-lymph node micro-environment—wherein it is expected some of the initial phases of the tumor’s avoidance and recruitment mechanisms are implemented. How is the architecture of the immune environment disrupted in the face of tumor metastasis? Are their micro-communities (as defined by particular cell-cell interactions) whose presence or absence defines an outcome in progression of the tumor? To this end we have developed a technology (ABSeq) that enables us to sensitively and quantitatively image tumors with 60 markers per 3 hours (scalable to 480 in a time-dependent manner) with markers selected from a range of intracellular or surface epitopes (recognized by antibodies) or RNAs. The hypothesis is that an orchestrated corruption of immune surveillance is initiated by cancers as they progress, and that the micro-scale architecture of the lymph node (by way of which cells are talking to whom and what broader effects occur across the lymph node and beyond) is disrupted in a defined manner. A major aim of the research is to, with ABSeq, define the 2D and 3D architecture and communities of immune and cancer cells in draining lymph nodes from 2 cancers (melanoma and head and neck cancer) in murine models and with human samples. Databases of 2D and 3D microenvironments will be publicly created and mined for associations that define the architectural changes that occur as tumors progress and initiate tolerance.

Project 3: Integrative computational modeling of tumor-mediated immunosuppression.

We will develop and apply computational tools to integrate the complex datasets generated by our Center in order to identify candidate mediators of tumor-immune interactions that induce immunosuppression for functional validation. To enrich our ability for interpretation, we will explore signatures of the immune system in a pan-cancer analysis using the TCGA datasets annotated with time to distant metastasis, in the context of node-negative and nodepositive patients. We hypothesize that pan-cancer genes whose expression is strongly associated with time to distant metastasis are more likely to be associated with tumor-intrinsic or microenvironmental processes driving metastasis progression, thus we will prioritize these genes in our integrative computational analysis of our melanoma and head and neck squamous cell carcinoma datasets. Using the RNAseq data generated by our study, we will develop and apply novel network-based computational methods for reconstructing the interactions between malignant and immune subpopulations. Moreover, we will develop and apply new approaches to integrate the spatial information from high dimensional single cell in situ images from Project 2 with the gene expression datasets to further refine our inferences of candidate mediators of immunosuppression. The datasets and computational resources developed by our Project, and Center at large, will not only enable use to deeply explore the role of lymph nodes in tumor-mediated immunosuppression, but will also provide the community with powerful resources for understanding systemic influences on the forces governing metastatic dissemination.


For more information, please visit the Cancer Systems Biology Consortium website.