Defining the landscape of bacterial-colonized microniches in tumors and their role in intratumoral heterogeneity.

PROJECT SUMMARY/ABSTRACT Within a patient’s tumor, malignant cells are surround by a complex and dynamic collection of cell types, which includes the intratumoral microbiota. However, there is a fundamental lack of understanding on how microbes within the tumor microenvironment (TME) interact with human components of the tumor, or how they might contribute to disease progression; presenting a significant barrier to progress. Comparative microbiome analysis has revealed an enrichment of distinct invasive bacterial communities in tumor tissue compared to adjacent normal tissue. Large-scale epidemiological studies have demonstrated a significant correlation between high intratumoral load of specific oncomicrobes, such as Fusobacterium nucleatum in colorectal cancer (CRC), with disease relapse and poorer survival. Yet, while pan-cancer tumor-tissue microbiome studies have exposed the pervasive presence of intratumoral bacterial communities within most cancer types, most of these studies to date have centered on bulk tissue molecular analysis, which obscures the spatial distribution and localized impact of the microbiota within tumors. My team recently discovered that viable intratumoral bacteria have a heterogenous distribution within human oral and CRC tumors, where they form bacterial-colonized microniches (BCMs). These BCMs are metabolically active, dominated by the anaerobic bacterium Fusobacterium nucleatum, and characterized by myeloid cell infiltration, upregulation of immune checkpoint proteins PD1, CTLA4 and Lag3, and reduced T-cell infiltration. Intratumoral heterogeneity (ITH) and associated phenotypic diversification of cellular subpopulations within the TME remain major factors for cancer progression and therapy resistance. In order to understand how the TME contributes to cancer progression and treatment resistance it is imperative that we assess interactions of all components of the tumor ecosystem, both mammalian and prokaryotic. The central hypothesis of this proposal is that BCMs within tumors are contributing to ITH by modulating cancer cell functions, as well as the influx and spatial distribution of immune cell types in colonized tumor regions. In Aim 1, to understand the focal tumor distribution of BCMs, their stroma-immune-tumor cell spatial interactions, we propose to functionally map cellular and metabolic features of BCMs within patient tumor tissues in-situ. In Aim 2 we will delineate the human cell types within patient tumors that harbor intracellular bacteria, the identity of those intracellular bacteria, and their impact on host transcriptional programs at the single cell level. In Aim 3, using animal model systems, we seek to examine the role of the oncomicrobe Fusobacterium nucleatum in remodeling cellular components of the TME. My team has the breadth of experience to accomplish this project as it seeks to apply multi-omic approaches to delineate microbial and host interactions within the TME. Our goal is to advance mechanistic understanding of host-microbiota interactions within the TME with the potential to reveal novel approaches for cancer prevent and treatment.