When our clients want to characterize the microbiome of a sample, the most common approach is to use sequencing data to identify the bacterial species present and their relative abundance. However, the umbrella of microbiota includes more than just bacteria: it also includes fungi, which are relatively uncommonly studied in the context of human disease but are emerging as important players in the microbiome.
Fungi and Cancer
In a recent Cell paper, Narunsky-Haziza et. al. comprehensively characterized the presence of fungi in over 17,000 patient samples across 35 cancer types. Termed the “mycobiome,” the distinct signatures of different fungi were detected inside cancerous cells, as well as cell-free fungal DNA being found circulating in blood and plasma samples.
Their analysis had three major areas: identifying the presence and species of fungi in the samples, comparing fungal signatures to more commonly-studied bacterial signatures, and analyzing the fungal data with patient data to look for possible biomarkers. To identify the presence of fungi, the authors performed internal transcribed spacer 2 (ITS2) sequencing (a common method in plant genomics) as well as whole genome shotgun sequencing and RNA-seq.
Surprisingly, different cancer types exhibited distinct mycobiome signatures. Perhaps even more interesting was the finding that there appeared to be interactions between the fungal communities and the bacterial communities within the tumors, which also interacted with the immune cells that infiltrated the tumor. Could these cancer subtype-specific signatures then tell us something more meaningful about tumor immunotherapy response?
New Biomarkers from Fungal DNA
The answer turned out to be yes: fungal signatures did stratify with patient responses to immunotherapy, suggesting yet another player in the complex ecosystem that dictates a tumor’s response to treatment.
Additionally, cell-free fungal DNA circulating in the blood appeared to be a potential biomarker for the detection of some early-stage cancers. Taken together, these data cannot explain whether the patterns observed in these fungal signatures are causative or just correlated. However, they do suggest that the mycobiome warrants further investigation as a source of therapeutic targets and diagnostic information.
Outsourcing Bioinformatics Analysis: How We Can Help
This study highlights the power of leveraging big data and large sample sizes to produce robust, clinically meaningful results. For microbiome analyses, we can help you tackle the challenging computational task of interpreting genomic data. Bridge Informatics’ bioinformaticians are trained bench biologists, so they understand the biological questions driving your computational analysis. Click here to schedule a free introductory call with a member of our team.
Jane Cook, Journalist & Content Writer, Bridge Informatics
Jane is a Content Writer at Bridge Informatics, a professional services firm that helps biotech customers implement advanced techniques in the management and analysis of genomic data. Bridge Informatics focuses on data mining, machine learning, and various bioinformatic techniques to discover biomarkers and companion diagnostics. If you’re interested in reaching out, please email [email protected] or [email protected].