Background: Despite the substantial advances in the treatment of systemic cancer, brain metastases are still responsible for significant morbidity and mortality. A better understanding of the mechanisms that facilitate brain metastasis formation can provide opportunities for the development of better diagnostics and therapeutics for this disease. Microbiota has emerged as a significant hallmark of cancer. Our group and others have demonstrated a prominent role for intratumoral microbiota in tumorigenesis, tumor immunity, and response to treatment. Moreover, recent prospective exploration of tumor tissues and retrospective analyses of TCGA datasets have revealed microbial signatures in the tumor tissue, distinct from normal tissue, across several cancer types. However, the current understanding of the composition of intratumoral microbiota in metastatic brain tumors, and their role in disease progression is limited.

Methods: To explore the intratumoral microbiome composition in brain metastases, we retrospectively analyzed datasets from whole-exome sequencing of 126 samples from melanoma, breast, lung, and colorectal cancer patients with brain metastasis that were collected at the MD Anderson Cancer Center. These datasets included 38 brain metastases and matched primary tumor, normal tissue adjacent to the primary tumor, and/or blood samples. Datasets were aligned to the human genome and the resulting filtered dataset was mapped against a comprehensive database containing bacterial genomes and partial assemblies using kraken2. Reads classified as bacterial in origin by kraken2 were then further aligned to a database of all known bacterial and primates using blastn, only reads that were verified to be bacterial were used in table construction. Evaluation of these putative hits and determining potential contaminating sequences are the focus of current research.

Results: Rich bacterial signatures were frequently identified in the brain metastasis datasets (38/38 samples), belonging to major bacterial phyla such as Firmicutes, that have been associated with tumorigenesis and response to therapy. Notably, other bacterial phyla such as Actinobacteria and Tenericutes were also identified that have been associated with the gut-brain axis.

Conclusion: Our findings demonstrate, for the first time, that rich microbial signatures can be harvested from sequencing datasets obtained from metastatic brain tumors and can serve to formulate hypotheses on the origin and the role of microbial signatures. Prospective analyses of the intratumoral microbiome in metastatic brain tumors and in vivo mechanistic studies can further elucidate the role of these microbial signatures in brain metastasis growth and are currently ongoing.

Citation Format: Golnaz Morad, Matthew C. Wong, Kazutaka Fukumura, Jason T. Huse, Sherise D. Ferguson, Nadim J. Ajami, Jennifer A. Wargo. Retrospective analyses of sequencing datasets suggest that intratumoral microbes exist in metastatic brain tumorsRetrospective analyses of sequencing datasets suggest that intratumoral microbes exist in metastatic brain tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2906.