Epigenetic mechanisms that maintain immunological memory in CD4 T cells

We are using T cells as a model to investigate how long-term immunity is maintained for many years in the absence of the infection that initiated the response. Infections trigger the immune system to activate naive T cells to mount an immune response. Once a cycle of infection is over, a small population of long-living memory T cells still remain which retain a memory of previous infections and allow a faster response the second time around. Memory cells underpin the basis of vaccination, and provide the immune system with the capacity to rapidly respond when re-challenged with the same infection.
We recently published studies using an in vitro model to demonstrate that the initial activation of naive T cells leads to permanent alterations in the chromatin structure of their chromosomes. We found that ~3000 sites within chromosomes are converted to islands of active chromatin near genes that respond rapidly to activation in memory T cells but not in naive T cells which have never been activated before. This reprogramming leaves hundreds of genes "ready to go" and able to respond immediately when inducible factors are once again turned on by active T cell receptors (TCRs). In the course of these studies we found that an inducible transcription factor that directs the activation inducible genes (AP-1) has to cooperate with two other factors (ETS-1 and RUNX1) for the initial activation, and after the activating agent had gone away ETS-1 and RUNX1 remain stably bound. Based on this data, we established a hit-and-run model of the establishment of immunological memory whereby AP-1 is required to open up new regions of chromatin around inducible genes, but that once formed, continuous binding of AP-1 is not required for the maintenance of primed genes by ETS-1 and RUNX1.
We know very little about how previously activated T cells are able to retain this memory for many years. This proposal will use normal and genetically modified mice as models to address this question. We already have hints of what molecules may be involved. The maintenance of memory does not require continued activation of those proteins that bind antigens (TCRs). However, previous studies in mice and humans showed that other types of receptors (IL-7R) and OX40) are essential to mount a secondary response by memory T cells. Based on our previous findings, we hypothesize that the long-term maintenance of T cell memory is supported via transient activation of AP-1 by IL 7R and OX40 when memory cells passage through lymph nodes as they migrate about the body, which, in turn, ensures that RUNX1 and ETS-1 remain bound. This continuous reinforcement of epigenetic priming may help explain why memory T cells can persist for many years after an infection.
The information gained from this proposal will help to explain how immunological memory is retained. It will also shed light on abnormal instances of immune activation that are detrimental for the organism as in case of autoimmune diseases. This knowledge is essential if we want to influence immunological memory in a diseased cellular environment. Our basic studies will pave the way for further, more focused approaches to address this issue.

Immunological memory underpins adaptive immunity and is the basis for vaccination. WE aim to understand the epigenetic changes that occur during lymphocyte responses to infection which enable immunological memory. We recently revealed that in contrast to naïve T cells, memory T cells possess thousands of epigenetically primed DNase I Hypersensitive sites (pDHSs) in key inducible genes. We propose that pDHSs leave memory cells poised for rapid responses by maintaining key inducible genes in a more accessible and primed state. Because our previous studies were based mostly on in vitro findings, we now need to determine the importance of these epigenetic changes in endogenous antigen-specific memory CD4 T cell populations generated in vivo, and identify the mechanisms that maintain long term immunological memory. We will then determine how key signals known to support memory CD4 T cell responses impact on these regulatory elements. Collectively, these studies will reveal fundamental information on the mechanisms that establish and maintain immunological memory.
This project brings together three local research groups to apply cutting edge epigenetic approaches to robust in vivo models of memory responses. Our specific goals are:
1. Use a transposase-mediated chromatin accessibility assay (ATAC) to demonstrate that pDHSs are maintained within endogenous antigen-specific memory CD4 T cell populations generated in vivo and dissect how the type of response affects these epigenetic changes.
2. Use gene knock-out models to determine the contributions of OX40 and IL-7 in the maintenance of pDHSS within memory populations in vivo.
3. Delete specific pDHSs from a human IL-3 gene BAC construct in a transgenic mouse model to establish that pDHSs are required for the inducible activation of human genes.
4. Use human T cells to study evolutionary conservation of pDHSs and show that they are equally relevant to human health and disease.

Our work will have a tremendous impact not only on our immediate research field but also beyond. This is especially true because our findings are introducing new concepts into the field of gene regulation whereby transient signals can dramatically reprogram gene expression potential via hit-and-run mechanisms.
The immediate impact of the studies proposed here is that they will lead to a better understanding of the transcriptional basis of T cell memory, and therefore have the potential to benefit all future therapeutic approaches utilizing T cells. These include
(1) Approaches used to stimulate the immune system to fight cancer. Cancer is one of the leading causes of death, and immune therapy is at the forefront of approaches used to fight cancer. The results of our work may lead the way to boosting the T cell response to cancer and benefit millions of cancer patients.
(2) Approaches used to suppress the immune system in immune disorders. An over-active memory T cell compartment is one of the leading causes of allergy and other immune disorders. By unlocking the secrets to how memory T cells are maintained our work could benefit millions of allergy and auto-immune patients. This will enhance the quality of life and improve health.
(3) Our work will identify key components of the pathways that create and maintain memory T cells, providing new candidates for drug companies to design drug against in specific diseases where they may not have been considered previously.
(4) Our work on general concepts of gene regulation and the control of developmental processes will also have an impact on other endeavours, such as the manipulation of the status of organisms by researchers in biotech companies. For example, this might impact on agriculture by leading to new ways to influence animal development, crop yields, or disease resistance.

Who will benefit, and How?

(i) We will make our system-wide data sets publicly available. This will benefit anybody who studies normal or aberrant T cell development in academia, industry or the clinic.
(ii) We will make our expertise available to members from industry and academia who wish to further explore the pathways that we are defining. One significant potential outcome of our work is the identification of transcription factor combinations that regulate T cell memory elements and are maintained during cell division. This will benefit anybody who is interested in manipulating memory T cells.
(iii) Promote the advancement of the career of Sarah Bevington as a research scientist. Our work will enhance the skills base in the UK. Future advances in biology and medicine will depend on building a skills base consisting of researchers which will be capable of thinking both in molecular terms as well as in system-wide terms, and Sarah Bevington the post-doc working on this grant will be trained to do precisely that.
(iv) Our published results, and the ongoing results of this study will continue to be part of lectures here at the University of Birmingham where medical and life sciences students will be introduced into learning advanced concepts of gene regulation and molecular immunology, and what it means to work with "big data".
(v) We are constantly developing new ways of processing and analysing high throughput genomics/epigenomics/transcriptomics data and this will have an impact on the whole field of computational biology. This knowledge is also passed on via masterclasses to masters students.