University of California San Diego researchers have developed a 3D spatial visualization tool for mapping "'omics" data onto whole organs. The details about this tool appear in yesterday's Cell Host & Microbe.
"Our understanding of the spatial variation of the chemical and microbial make-up of a human organ remains limited," said Pieter Dorrestein, Ph.D. "This is in part due to the size and variability of human organs, and the sheer amount of data we get from metabolomics and genomics studies."
To address this issue, Dorrestein's team developed an open-source workflow for mapping metabolomics and microbiome data onto a 3D organ reconstruction built from radiological images.
First, the researchers obtained a lung from a patient that was affected by cystic fibrosis (CF) and sectioned it. They looked at the presence of bacteria, their metabolites, virulence factors, and any medications given to the patient during treatment. Next, they modified an existing Google Chrome extension to visualize the microbiome and metabolome distributions on an entire organ. To visualize the localization of bacteria and molecules, the team used CT scan images of a human lung and generated a 3D model. Using the "omics" data they had from the cystic fibrosis lung, they were able to impose that data onto the 3D lung.
"We could see that one of the antibiotics administered to the patient prior to collecting the tissue did not penetrate the bottom of the lung—a phenomenon that has not been observed before," said Neha Garg, Ph.D. "This correlated with a higher abundance of the cystic fibrosis-associated pathogen Achromobacter. Thus, different drugs may differentially penetrate the lung, limiting exposure to effective dosage. Our tool allows researchers and clinicians to visualize this significant clinical concern within a human organ for the first time. This has implications for treatment of CF and other diseases."
The researchers have created open-source maps of other molecules and microbes as a resource that scientists researching cystic fibrosis and other lung-associated diseases.
"As future studies unravel more about the microbiome and metabolome, their spatial visualization will provide a means to infer their biological significance," said Dorrestein.