The Tumor Microbiome
An emerging characteristic across human cancer types is the presence and composition of the tumor microbiome, a collection of tumor-associated species of bacteria and fungi that add another layer to cancer’s complexity. Studies have shown that the tumor microbiome can influence responses to immunotherapy and metastasis and that it may even be a source of biomarkers for determining cancer prognosis.
Researchers studying the tumor microbiome in the past have mainly had to rely on bulk sequencing methods. However, bulk sequencing loses the nuanced localized effects of specific types of bacteria, and also prevents the creation of a spatial map of where bacteria interact with host tumor cells.
New Single-Cell Sequencing Method for Tumor-Microbiome Interactions
In a recent Nature paper, Niño et. al. leveraged spatial transcriptomics and single-cell RNA-seq to better visualize the inner workings of the tumor-microbiome interaction. Using 10x Visium spatial transcriptomics, they found that bacteria are mostly found in tumor niches with fewer blood vessels and high immunosuppression, demonstrating that the distribution of bacteria through tumors is not random.
To investigate this further, the authors developed a single-cell RNA-seq method called invasion-adhesion-directed expression sequencing (INVADEseq) that can identify which host cells that the cancer-associated bacteria interact with. Using this method, the authors found that these interactions can produce altered transcription in pathways related to inflammation, metastasis, cell dormancy and DNA repair.
Taken together, these results demonstrate the varied effects of tumor microbiota on tumor physiology. The high resolution provided by spatial and single-cell transcriptomics will afford researchers the ability to investigate these effects in much greater detail going forward.
Outsourcing Bioinformatics Analysis: How We Can Help
The applications of single cell approaches are innumerable, and our clients are at the forefront of tackling research questions using these kinds of sophisticated bioinformatics approaches. However, transforming raw sequence data of any kind into actionable biological insights is no small feat.
As experts across data types from cutting-edge sequencing platforms, we can help you tackle the challenging computational tasks of storing, analyzing and 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, Biochemist & Content Writer, Bridge Informatics
Jane Cook, leading Content Writer for Bridge Informatics, has written over 100 articles on the latest topics and trends for the bioinformatics community. Jane’s broad and deep interdisciplinary molecular biology experience spans developing biochemistry assays to genomics. Prior to joining Bridge, Jane held research assistant roles in biochemistry research labs across a variety of therapeutic areas. While obtaining her B.A. in Biochemistry from Trinity College in Dublin, Ireland, Jane also studied journalism at New York University’s Arthur L. Carter Journalism Institute. As a native Texan, she embraces any challenge that comes her way. Jane hails from Dallas but returns to Ireland any and every chance she gets. If you’re interested in reaching out, please email daniel.dacey@old.bridgeinformatics.com or dan.ryder@old.bridgeinformatics.com.
