The sarcoma tumor microbiome as a therapeutic target

Background: Sarcoma is a heterogeneous group of malignant tumors that consist of distinct histological and molecular subtypes, each with unique clinical, therapeutic and prognostic features. Despite immunotherapy showing promise in many cancers, immunotherapeutic approaches in the management of sarcoma have had highly variable response and success rates, for unclear reasons. A promising new approach is to evaluate the tumor microbiome to better understand the tumor microenvironment of sarcoma subtypes and lead to improved treatment options and better outcomes. Objectives: 1) To describe the landscape of sarcoma tumor microbiome at the Ohio State University James Comprehensive Cancer Center (OSUCCC) and relate microbe abundances to tumor infiltrating lymphocytes and hypoxia-associated gene signatures 2) To identify intra-tumor microbes that correlate with immune checkpoint inhibitor (ICI) treatment outcomes in the context of patients with sarcoma at OSUCCC. Methods: Aim 1) We will use OSUCCC samples to obtain RNAseq data to identify microbes in dedifferentiated liposarcoma (ddLPS) subtypes. We will utilize ExoTIC, “Exogenous sequences in Tumors and Immune cells,” a tool recently developed by Dr. Daniel Spakowicz and Dr. Xaiokui Mo, that takes raw RNAseq reads and carefully aligns to both human and non-human reference genomes to identify low-abundance microbes. We will use the TMEsig tool to identify hypoxia signatures. Aim 2) We will then use the Cancer Genome Atlas (TCGA) and Oncology Research Information Exchange Network (ORIEN) databases to associate these samples with clinical outcomes. We will also perform Cox Proportional Hazards regression to identify the microbes associated with overall survival. Hypotheses: 1) Exogenous sequences and the taxa found will be significantly correlated within the ddLPS samples 2) The amount of exogenous sequences observed in the tumor will positively correlate with the amount of lymphocyte cells estimated via deconvolution 3) Anaerobic microbes will be enriched in high hypoxia signatures 4) Increased abundance of the genus Clostridium will be positively correlated with overall survival in the context of treatment with ICIs and the phylum Proteobacteria will be negatively correlated. Clinical relevance: Given the rarity of these cancer subtypes and the inability to readily perform randomized controlled trials, assessing individual characteristics of the tumor subtype with its particular microenvironment (e.g., microbes) can lead to personalized treatment insights and improvements in outcomes. It can also lead to understanding of the role of microbes in eliciting or modifying response to cancer and may lead to biomarker assays that will measure microbes in tumor biopsies as standard of care.