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Abstract
Background Emerging evidence supports an important role for the tumor microbiome in relation to oncogenesis, cancer immune phenotype, cancer progression and treatment outcomes in a number of malignancies. In this study, we investigated the metastatic melanoma tumor microbiome and potential roles in association with clinical outcomes, such as survival, in patients with metastatic disease treated with immune checkpoint inhibitors (ICIs).1–3
Methods Baseline tumor samples were collected from 71 patients with metastatic melanoma prior to treatment with ICIs. Bulk RNA-seq was conducted on the FFPE tumor samples. Clinical outcome following ICI treatment was evaluated as overall survival (> 24 versus < 24 months). The RNA-seq reads were processed to carefully identify exogenous sequences using ExoTIC (Exogenous sequences in Tumor and Immune Cells.4,5 Reads that did not align to the human reference genome were filtered of (1) common laboratory contaminants, (2) taxa that inversely correlate with input RNA quantity, and (3) taxa commonly found in the negative controls of microbiome experiments. DESeq2 was used to perform a differential abundance analysis on the comparison groups at every taxonomic level.
Results The 71 patients with metastatic melanoma ranged in age from 24 to 83 years, 59% were male, and 55% survived > 24 months following the initiation of ICI treatment. Exogenous taxa were identified in the tumor RNAseq, including bacteria, fungi, and viruses (figure 1). Within the tumors responsive to immunotherapy (> 24 months survival), we found a significant enrichment of several microbes, including Fusobacterium nucleatum, Porphyromonas asaccharolytica, Nocardia mangyaensis, and Mollivirus sibericum. Comparatively, the cohort of non-responsive tumors (< 24 months survival) was found to have a significant intra-tumoral enrichment of Fungi, as well as the bacteria Delftia lacustris, Enterobacter hormaechei, Pseudomonas fluorescens, and Moraxella osloensis (figure 2).
Conclusions In investigating the melanoma tumoral microbiome utilizing baseline tumors (prior to initiating ICI) we found significant variations in the exogenous taxa associated with patient outcomes following ICI treatment. Our findings warrant further investigations and potentially support therapeutic strategies to modify the tumor microbiome in order to improve treatment outcomes with ICIs. Ongoing research is evaluating whether these correlations are causally associated with outcomes and evaluating their effect on the tumor immune microenvironment and immune cell infiltration.
References
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A stacked bar plot showing the relative abundances of exogenous taxa found in tumor RNAseq. Taxa are shown on the phylum level and are ordered by the relative abundance of < i >Uroviricota</i >
Differential abundance analysis of taxa found within tumor RNAseq data by the exotic pipeline. Colored points represent significantly (p-value < 0.05) enriched taxa with a high (>1.00) fold-difference in abundance between the groups