Recurring or unresolved inflammation is a key component of many disorders ranging from cancer to diabetes. In many cases, the origin of the inflammation is complex and poorly understood because it involves both genetic and environmental factors such as infectious agents. Inflammatory bowel disease (IBD), which includes Crohn’s disease and ulcerative colitis, is a quintessential example of this challenge. Compelling observations made in patients and animal models indicate that the disease is due to an excessive immune response to intestinal microbes, such as the trillions of “friendly” commensal bacteria that are part of the microbiome.

⇐ Interface between commensal bacteria and the rest of our body.
A hundred trillion bacteria representing 1000 different species colonize our intestines and influence our physiology by providing metabolites and cues to our immune system. Certain inflammatory disorders arise when otherwise innocuous infectious agents such as these commensal bacteria evoke a harmful immune response. Our laboratory aims to understand how the normal balanced co-existence between intestinal microbes and the host immune system is disrupted during disease. The above fluorescence in situ hybridization image shows thousands of bacteria (green) juxtaposed to the colonic epithelium of mice (red cells with blue nuclei). The distance between the bacteria and the host is generated by a mucus layer containing antimicrobial molecules. Image taken by Deepshika Ramanan.






Autophagy (Greek for ‘self-eating’) is an evolutionarily conserved process that we and others have shown regulates inflammation. During autophagy, cytosolic material is delivered to the lysosome via a double membrane vesicle termed the autophagosome. This pathway was first linked to intestinal inflammation when large-scale population genetic studies found that a T300A allele of Atg16L1, a gene that is necessary for the formation of the autophagosome, increases the risk of developing Crohn’s disease. Among the autophagy-related gene variants that have been associated with IBD, this T300A allele of Atg16L1 is notable because it leads to a change in protein sequence and can be found in up to 50% of the population. How can such a common gene variant be responsible for IBD?

We found that Atg16L1 mutant mice develop Crohn’s disease-like pathologies, but only upon infection with an otherwise innocuous intestinal virus called murine norovirus (MNV). This observation suggests that mutations in susceptibility genes interact with specific infectious factors to generate disease pathologies, and provides support for a multi-hit disease model. Therefore, it is possible that common gene variants confer a modest increase in disease susceptibility because their role becomes apparent only in the presence of environmental factors.



Virus-plus-susceptibility gene interaction


Artwork by Marcy Hartstein









What’s special about MNV? Remarkably, we found that MNV can provide the same beneficial cues as commensal bacteria, thus demonstrating for the first time that an intestinal virus can behave similarly to the friendly bacteria that colonize the intestine. Our results in mice suggest that a viruses that inhabit our body, collectively referred to as the virome, should be considered part of the microbiome. We are currently investigating how MNV induces beneficial changes in the host including protection from chemical and infectious damage.

How specific is MNV as a trigger? We found that the same Atg16L1 mutant mice that develop intestinal disease in response to a virus are unexpectedly resistant to intestinal bacterial infections due to an enhanced immune response. This striking observation suggests that Atg16L1 mutation may be beneficial under certain situations, which may explain why the T300A allele was evolutionarily maintained. We are currently investigating the mechanism by which Atg16L1 determines the quality and magnitude of the immune response to intestinal viruses and bacteria.

What about other IBD genes? Another important area we are addressing is the role of other IBD genes such as Nod2 in disease development. Again, we are finding other gene-microbe interactions, suggesting that different IBD genes can combine with different environmental factors to generate intestinal pathologies.

What is the relationship between autophagy and inflammation? Autophagy has been shown to promote immunity by delivering internalized pathogens to endosomes and lysosome for degradation or presentation to immune receptors (i.e. TLRs and MHC molecules). Findings from our group and others are also indicating that autophagy has unappreciated anti-inflammatory roles. We are pursuing these further through the use of other disease models including extra-intestinal infectious disease and graft-versus-host disease, an adverse outcome of hematopoietic stem cell transplants used to treat certain types of cancer.

Funding: We are grateful to all the funding sources and individuals that have supported our research and lab members. Past and current funding sources include the NIH, Damon Runyon Cancer Research Foundation, American Heart Association, Crohn's Colitis Foundation of America, Burroughs Wellcome Fund, Stony Wold-Herbert Fund, Howard Hughes Medical Institute, Colton Center for Autoimmunity, Pfizer, Laura and Isaac Perlmutter Cancer Center at NYU, Puretech Health, Kenneth Rainin Foundation, and generous philanthropic donations by Dr. Bernard Levine and Helen S. Kimmel.