Center for Clinical and Translational Science

It is increasingly understood that the microbiome has an important role in human health. Little is known, however, about the mechanisms that human microbiota use to interact with their human host. At Rockefeller University Drs. Sean Brady and Louis Cohen have worked to advance our understanding of how bacteria interact with human physiology through the study of bacterial small molecules. While little is known about small molecules made by human microbiota, in other microbiomes small molecules mediate environmental interactions and are a resource for therapeutic discovery. A major barrier to the isolation of small molecules from bacteria is the inability to culture many bacterial species. One method to circumvent the culture barrier is the use of functional metagenomics, wherein pieces of bacterial DNA are isolated from an environment and expressed in a heterologous host. The Brady Laboratory at Rockefeller University is a pioneer in the field of functional metagenomics and when Dr. Cohen joined the laboratory as a Clinical Scholar they aimed to apply functional metagenomics methods to the study of human microbiota.

 

In their first study published in the Proceedings of the National Academy of Sciences (USA), Drs. Cohen and Brady coupled functional metagenomics and high-content imaging of a human cells to identify bacterial biosynthetic genes and small molecules whose functions activate inflammatory pathways. This study was made possible in part by the Clinical Scholars program at Rockefeller. As a Clinical Scholar Dr. Cohen was guided through the clinical trial design process, applied for pilot funding from the Helmsley Charitable Trust, and was able to access the resources of both Rockefeller Hospital and the Center for Clinical and Translational Science. With the support of the Clinical Scholars program, Dr. Cohen collected stool samples from phenotypically diverse patients, isolated high molecular weight bacterial DNA, and cloned this DNA into a cosmid vector for transduction into E. coli. E. coli clones were then arrayed in microplates and sterile supernatant transferred to a human NF-κB reporter cell line that was imaged by high content microscopy at the High Throughput Screening Core. This study led to the identification of over 20 novel bacterial biosynthetic genes and the isolation of an N-acyl amide small molecule, commendamide.

 

In a follow-up study published recently in Nature, Drs. Cohen and Brady explored in depth the family of N-acyl amide small molecules produced by human microbiota. In humans N-acyl amides such as the endocannabinoids are signaling molecules with diverse functions often mediated by G protein-coupled receptors (GPCRs). Using publically available sequencing datasets from the human microbiome, 43 phylogenetically diverse N-acyl synthase genes were identified, synthesized, cloned into an inducible expression vector, and transformed into E. coli. Using this system 6 N-acyl amide small molecule families were identified. Each family was screened against a panel of 240 human GPCRs and specific molecule/receptor interactions were identified for GPCRs important to inflammation, immunity, metabolism, and wound healing. Interestingly, the bacterial and human GPCR ligands were structurally similar, suggesting a form of mimicry, and in the case of human and bacterial GPR119, ligands were nearly identical. It was then demonstrated in vitro and in vivo that bacterial GPR119 ligands are able to regulate GLP-1 secretion and blood glucose similar to endogenous GPR119 ligands, suggesting the targeted manipulation of commensal bacterial biosynthetic genes as a potential therapeutic strategy (microbiome-biosynthetic-gene-therapy) for modifying blood glucose, with potential implications for the treatment of diabetes.

 

Based on the success of this research program and his time as clinical scholar at Rockefeller University, Dr. Cohen was able to transition to the Icahn School of Medicine in the Division of Gastroenterology as an assistant professor. Drs. Cohen and Brady continue to collaborate to further elucidate mechanisms through which human microbiota affect host physiology as a way to understand disease pathogenesis and identify novel therapeutic strategies.