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Our Research


The Cobb lab is broadly focused on immune regulation and the role that carbohydrates (microbial and host) play in related mechanisms. As such, we work at the interface of glycobiology and immunology. The lab can be roughly broken into two areas of research: (1) polysaccharide antigens and the impact of these commensal flora-derived molecules on the susceptibility to develop immune-mediate diseases, such as asthma; and (2) the regulation of host glycosylation and the impact these glycans have upon immune regulatory pathways.

Polysaccharide Antigens and Asthma

For the last decade, we have placed our primary efforts on building a research program on the foundation of Dr. Cobb's discovery in Dennis Kasper's laboratory that some bacterial polysaccharide antigens activate CD4+ T cells by presentation on MHC class II molecules [Cobb et al, Cell, 2004]. This fundamental discovery opened a new world of investigation around how polysaccharides activate the adaptive immune response and the nature of the response after that initial recognition. We have shown that polysaccharide A1 (PSA) from the gut commensal bacterium Bacteroides fragilis is not only presented by MHCII, but it does so in a manner nearly indistinguishable from conventional peptide antigens. The similarities include the dependence upon processing for MHCII binding [Cobb et al, Cell, 2004;Kreisman et al, Glycobiology, 2007], competitive binding with CLIP and other bound peptides in an HLA-DM-dependent fashion, and micromolar affinity [Cobb et al, Glycobiology, 2008]. Importantly, we have also shown these antigen attributes are common with other T cell-activating polysaccharides [Velez et al, Immunology, 2009Young et al, Glycobiology, 2011].

One defining difference between conventional protein/peptide antigens and polysaccharide antigens (glycoantigens) is found in the mechanism of processing to low molecular weight fragments - in the case of glycoantigens, this is mediated by nitric oxide oxidation [Cobb et al, Cell, 2004Velez et al, Immunology, 2009], whereas protein antigens rely upon proteolytic cleavage. In this vein, we have found that defects in the oxidation machinery dramatically impact the PSA-mediated immune response. For example, the human condition known as Chronic Granulotamous Disease is characterized by defects in the NADPH Oxidase complex. We found that mouse models of this genetic disease hyper-respond to PSA through an increased (and likely compensatory) nitric oxide production [Lewis et al, Euro JI, 2011].

Another difference between peptide and polysaccharide antigens we found is that PSA can also stimulate the classical pattern-recognition receptor Toll-like receptor 2 (TLR2) [Wang et al, JExMed, 2006]. Importantly, TLR2 stimulation is required for the production of nitric oxide - the key molecule for PSA processing. This finding directly leads to a model in which PSA and likely other polysaccharide antigens power their own antigen presenting cell activation and initiation of processing.

Another more recently discovered difference is that PSA presentation by MHCII relies upon and is regulated by the complex N-linked glycans on MHCII itself [Ryan et al, JExMed, 2011]. At present it remains unclear whether these host glycans directly participate in the binding of PSA through carbohydrate-carbohydrate interactions or whether the role is indirect through glycan-dependent conformational features of MHCII, but it is clear that loss of complex N-glycans also prevent in vivo responses to PSA [Ryan et al, Glycobiology, 2014].

In moving forward, we have more recently begun to investigate the downstream consequences of T cell activation mediated by PSA. The fruits of this work are found in our two most recent publications. First, we have demonstrated that T cells activated by PSA suppress the asthma response in mice [Johnson et al, Glycobiology, 2014]. The amazing potency of this protection by glycoantigen (GlyAg) can be seen in the ovalbumin (OVA) challenged lungs below. Second, we found that the T cell response to PSA is clonal in nature, revealing for the first time that a carbohydrate antigen can be specifically recognized by CD4+ T cells [Johnson et al, JBiolChem, 2014]. These findings are critically important because exposure to commensal flora like B. fragilis (the bacteria which produces PSA) has been linked to prevention of inflammatory diseases through what is now known as the Hygiene Hypothesis. The idea is that exposure to beneficial microflora (like B. fragilis) limits an individual's susceptibility to the development of allergy and autoimmunity.

Research photo showing T Cells being expressed in the lungs.
(green = EpCAM; red = myeloperoxidase)
from Johnson et al, Glycobiology, 2014

We are working hard to understand how and why PSA are particularly potent initiators of the anti-inflammatory arm of the immune response, especially in asthma. Our award from the Hartwell Foundation is funding the translational application of our findings to the prevention and treatment of asthma in children, while our current NIH funding is focused more on the detailed molecular mechanisms of the PSA response.

Host Glycosylation and Immune Regulation

We published our first set of data in this area in the summer of 2016 in the Proceedings of the National Academy of Sciences (Jones et al PNAS 2016). In this study, we report the creation of a B cell-specific knockout of the α2,6-sialyltransferase enzyme ST6Gal1. This enzyme is solely responsible for the sialylation of N-linked glycans on the Fc portion of IgG molecules. Others have discovered that the presence of sialic acid on these glycans acts as a molecular switch, thereby enabling the sialylated IgG molecule to have a net anti-inflammatory impact. Using this mouse, we discovered that B cells appear to lack the ability to sialylate IgG. This runs counter to the dogma that glycans are remodeled only within the Golgi apparatus of the cells secreting the glycoprotein. We also report evidence that the ST6Gal1 enzyme is released by the liver into the circulation, where it is active and responsible for IgG sialylation outside of the B cell. Moreover, we found evidence that platelet granules are one important source of the sialic acid donor molecule CMP-sialic acid. Thus, together, our data suggests a three-way regulatory axis for IgG sialylation: the mature antibody-secreting plasma cell, platelets, and the liver.

The laboratory is continuing work in this area with an emphasis upon understanding the regulation and detailed molecular mechanisms at play in determining IgG function in vivo. Our work in this area was seeded by funding from the Mizutani Foundation for Glycoscience, but is now supported by an NIH R01 grant through the National Institute for General Medical Sciences (NIGMS).

Interested in Joining the Cobb Lab?

Experience in the Cobb lab will provide a solid background in immunology, cell biology, biochemistry, basic carbohydrate chemistry, glycobiology, molecular biology, animal studies, and confocal imaging - depending on the interests of the trainee.  Please contact Dr. Cobb to arrange a meeting if you are interested in training with us.