The Role of the Tumor Microbiome in Mucosal Melanoma Development and Antitumor Immunity
Abstract
Background: Cutaneous melanoma (CM) is the most common type of melanoma and typically develops on skin exposed to UV radiation from the sun. However, rare subtypes of melanoma can arise from melanocytes located in non-sun-exposed locations. Mucosal melanoma (MM) occurs on mucosa sites such as the mouth, nose and sinuses, vagina and vulva, and rectum. MM tumors are usually not detected until advanced stages, are challenging to surgically remove, and are highly resistant to traditional melanoma treatments, including immune checkpoint blockade (ICB). Significant progress has been made in understanding and treating cutaneous melanoma (CM) over the past decade, but MM remains poorly understood with few effective treatments. We recently compared total gene expression in CM and MM tumors, and we discovered that MM have lower expression of genes involved in the innate immune pathogen-sensing (IIPS) pathway. The IIPS pathway produces an inflammatory response to eradicate foreign pathogens, but it is also important for melanoma anti-tumor immunity and response to ICB treatments. Since the immune system can detect and kill cancer cells, loss of the IIPS pathway helps makes MM “invisible” to the immune system. The IIPS pathway is commonly turned off when genes in the pathway are epigenetically silenced (undergo modification of the DNA or the histones that control DNA structure). We treated MM cell lines with the drug decitabine, which blocks gene-silencing methylation of DNA, and this treatment led to the re-expression of many critical genes in the IIPS pathway. Studies in CM and other cancers have identified an important role for both the gut and tumor microbiomes (the collection of micro-organisms including bacteria, fungus, and viruses), and its cross-talk with the IIPS pathway, in tumor immune evasion, progression, and ICB response. The microbiome has also been shown to alter DNA modifications such as methylation. However, the MM microbiome, its role in MM immune evasion and ICB response, and its potential as a therapeutic target in MM to have yet to be explored. Scientific Objectives: The overall objectives of this proposal are to (1) establish the role of dysbiosis (changes in the microbiome) in MM epigenetic modifications, IIPS gene suppression, and immune evasion, and (2) determine the impact of MM microbiomes on tumor development, anti-tumor immunity, and ICB response. We hypothesize that distinct features of MM gut and tumor microbiomes will correlate with epigenetic suppression of IIPS pathway genes to support tumor development and ICB resistance, and that modifying MM-specific microbiomes or epigenomes using Food and Drug Administration (FDA)-approved anti-infectives or DNMT inhibition, respectively, will restore ICB sensitivity and anti-tumor immunity through IIPS pathway re-activation. Approach: Aim 1: We will analyze MM-specific gut and tumor microbial features and determine if these unique features correlate with tumor epigenetics, IIPS pathway gene expression, tumor immune cell microenvironment, and patient ICB responses. Bacteria and fungi load, species, diversity, and predicted functional content will be analyzed in primary tumors, stool, and tissue swabs (nasal and vaginal) from both CM and MM patients. Tumor epigenomes and transcriptomes will be analyzed by specific next-generation sequencing methods, ATAC-seq and RNA-seq, respectively. Immune cell microenvironments will be characterized by staining patient tumor tissues with specific immune cell markers, and ICB responses will be determined by clinical chart review. Aim 2: Using a mouse melanoma model that is already known to be sensitive to the ICB treatment anti-PD1, we will evaluate the effect of introducing human MM patient gut microbiomes or tumor microbiomes, and the ability of anti-infectives or decitabine to reverse these effects, on tumor epigenetics, IIPS gene expression, immune cell microenvironment, and response to anti-PD1 therapy.
Document Details
- Document Type
- DoD Grant Award
- Publication Date
- Dec 05, 2021
- Source ID
- W81XWH2110660
Entities
People
- Kasey Couts
Organizations
- United States Army
- University of Colorado Denver