A topic that attracted great interest in immunology is understanding not only how transcriptional and epigenetic mechanisms are used to turn genes on but, also, how some genes are turned off in specific cells that, as a result, do not mount an immune response, a phenomenon known as immune tolerance. This is particularly important, because even though we are exposed and respond to potentially harmful antigens on a daily basis, we are at the same time surrounded by innocuous antigens.
“One of my interests over the past couple of decades has been to understand immune tolerance, and find out what keeps T cells from producing inflammatory cytokines in response to ‘self’ antigens,” says Andrew D. Wells, Ph.D., associate professor of pathology and laboratory medicine at the University of Pennsylvania School of Medicine.
Results from many labs indicate that once a T cell has become anergic, it does not respond and does not produce cytokines when subsequently provided with a co-stimulatory signal, suggesting the existence of a type of negative memory that tells the cell not to engage in an immune response. “This led to our hypothesis, years ago, that a more stable modification could be involved, and that perhaps the genes have been silenced through epigenetic mechanisms,” explains Dr. Wells.
The IL-2 and IFN-γ genes provide valuable systems to examine changes that the right combination of signals causes in the local chromatin structure. It is known that primed T cells can produce inflammatory cytokines very quickly, while naïve T cells need to go through several hours of gene remodeling before expressing them.
“In T cells receiving the right antigenic and co-stimulatory signals that after a primary proliferative phase subsequently came back to rest, we found that the promoter structure was different from the one in the naïve cells, with less DNA methylation and more acetylation of histone H3, which are modifications telling the cell that these genes should be kept accessible and turned on quickly again in response to the right signals.”
While it is known that the structure of cytokine gene regulatory regions changes in cells that become tolerant, the enzymes that mediate these processes are ubiquitously expressed, and they do not bind DNA by themselves but are instead recruited to the chromatin.
“We became interested in looking at transcription factors involved in epigenetically silenced genes,” explains Dr. Wells. Two of these transcription factors are the focus of on-going research in Dr. Wells’ laboratory. One of them, FOXP3, is expressed only in a subset of cells called regulatory T cells, which were unveiled during the last 10–15 years and are important for immune tolerance. While anergy turns off T cells when they are not supposed to mount an immune response, regulatory T cells orchestrate an additional layer of control, with unique anti-inflammatory properties.
“We found that FOXP3 binds endogenous cytokine genes in regulatory T cells and remodels chromatin to make them more silent.”
The second transcription factor that Dr. Wells’ lab is focusing on, a protein called Ikaros, is expressed in all T cells. This protein was discovered many years ago and functions in the development of leukocytes in the bone marrow and thymus. “But quite a lot of Ikaros is expressed in mature T cells, and nobody looked carefully at what it is doing there.”
While examining the sequence of the IL-2 promoter, which is well characterized, Dr. Wells and colleagues found a few regions that could function as Ikaros binding sites. “We knew that Ikaros can be a powerful transcriptional repressor, and we reasoned that it could perhaps have a role in mature T cells, in keeping IL-2, and perhaps other genes, turned off under circumstances when a T cell should not make these factors.” Indeed, the Wells lab went on to show that T cells with reduced Ikaros activity tend to overproduce cytokines like IFN-γ and TNF-α, and can cause fatal inflammatory colitis when transferred into mice.
Findings from many labs that use various experimental approaches, and different model systems, reveal that epigenetic modifications play fundamental roles not only during development, but also in shaping biological processes in differentiated adult cells and organisms. As a result of recent advances in this field, old paradigms are replaced by new concepts, and well-known phenomena find mechanistic explanations, underscoring the dynamics of scientific inquiry, and promising attractive prophylactic, diagnostic, and therapeutic applications.