Orchestration of PI3K-dependent transcriptional programmes by the transcription factor BACH2

CD8+ T cells powerfully coordinate immune responses against intracellular infections and cancer. During immune responses, CD8+ T cells proliferate and differentiate into effector cells that promote elimination of target cells. Effector cells are short-lived and this enables restoration of normal immune function upon resolution of infection. However, a fraction of cells escape this fate and persist to form long-lived memory cells. Memory cells provide a durable self-renewing source of target-specific cells and can persist for decades following infection to generate more efficient secondary responses upon reinfection. CD8+ T cells also become terminally differentiated or exhausted in response to chronic infections and cancer and this impairs their function.

Our previous work has identified a key molecular pathway, termed the phosphoinositide 3-kinase (PI3K) pathway, that powerfully regulates CD8+ T cell differentiation. Activation of the PI3K pathway drives widespread changes in gene expression to promote effector differentiation and prevent the formation of memory cells. Mechanisms by which the PI3K pathway causes changes in gene expression are not fully understood. In this study, we will investigate how the PI3K pathway controls the function of a class of proteins called transcription factors (TFs). TFs bind to regulatory regions within DNA and modulate gene expression to control cellular differentiation. We have recently found that the PI3K pathway controls the function of a transcription factor, BACH2, through a process called phosphorylation. We will investigate this new molecular axis, determining how the PI3K pathway regulates the function of BACH2 to control CD8+ T cell responses. Our experimental approach is divided into three components:

1) We will determine the function of BACH2 in regulating CD8+ T cell responses to infection. To do this, we will use a mouse model in which BACH2 is specifically deleted in CD8+ T cells and study immune responses following infection with experimental pathogens.

2) We will determine how the PI3K pathway controls the function of BACH2 to regulate immune responses to infection using a new mouse model in which BACH2 cannot be phosphorylated. We will also determine how BACH2 phosphorylation regulates BACH2 function at a molecular level.

3) We will test the contribution of BACH2 to PI3K-mediated transcriptional programmes in CD8+ T cells. To achieve this, we will utilise mouse genetics to specifically manipulate the PI3K pathway, and regulated transcription factors in CD8+ T cells, measuring consequences of these experimental manipulations on global gene expression and corresponding this data with analyses of transcription factor binding throughout the genome.

This work will extend our understanding of how the PI3K pathway exerts such pervasive control over CD8+ T cell differentiation and provide insights into how external cues control gene expression to shape the outcome of immune responses. This will provide targets for development of new vaccine approaches and immune-based therapies for chronic infections and cancer.

CD8+ T cells powerfully drive immune responses against intracellular infections and cancer. Following antigen recognition, naïve CD8+ T cells proliferate and differentiate to form effector cells. Effector cells promote clearance of target cells and are short-lived enabling restoration of immune homeostasis once infections have been cleared. A fraction of cells do not fully acquire effector cell characteristics and differentiate into long-lived memory cells. Memory cells provide a durable self-renewing source of antigen-specific cells and enable more efficient secondary responses upon reinfection but are depleted in chronic infections and cancer. Our previous work has demonstrated that the phosphoinositide 3-kinase (PI3K) pathway powerfully regulates CD8+ T cell differentiation by directing widespread changes in gene transcription but mechanisms by which this is achieved are incompletely elucidated.

New data indicates that a transcription factor, BACH2, is regulated by the PI3K pathway in CD8+ T cells and restrains effector differentiation by repressing T cell receptor (TCR)-driven gene transcription. We will investigate how the PI3K pathway controls the function of BACH2 to shape the outcome of immune responses, utilising mouse genetic models and experimental approaches in cellular immunology, protein biochemistry and functional genomics.

Our proposed experiments are organised into three aims:

1) To establish the cell-intrinsic function of BACH2 in regulating endogenous CD8+ T cell responses to infection.
2) To determine how the PI3K pathway controls the function of BACH2 to regulate immune responses to infection.
3) To determine the relative contribution of BACH2 to PI3K-dependent transcriptional programmes in CD8+ T cells.

This will extend our understanding of how the PI3K pathway exerts such pervasive control over CD8+ T cell differentiation and provide insights into how external stimuli direct the outcome of immune responses.

A number of parties will directly benefit from this research:

1. The commercial private sector:

A) The biomedical industry: This research will identify new molecular mechanisms that regulate CD8+ T cell differentiation and function. Findings will be of immediate interest to the private commercial sector for development of new vaccine approaches, and therapies for patients with chronic infections and cancer. In addition, discovery of new biomarkers to determine the activity of the newly developed PI3Kd inhibitor idelalisib. In order to disseminate findings from the research, emphasis will be placed on publication in high-profile multidisciplinary journals and presentation of findings at international conferences attended by academic and private sector researchers. We will encourage collaborations with the private sector to expedite translation of the work. KO has regular contact with scientists at GSK, with whom he has a major research collaboration studying Activated PI3K Delta Syndrome (APDS) patients and with Karus Therapeutics (for whom he is a scientific advisory board member). Babraham Institute Enterprise reviews our research programme for commercially exploitable results before publication. Successful exploitation of results will have immediate impact on the commercial private sector and directly foster UK and global economic growth.

B) The life sciences industry: The work will involve development of new experimental reagents for use in research. Mouse strains and molecular biology reagents will be shared with academic and private sector researchers. Through a commercial collaboration with the life sciences company Rockland Inc., we have developed an antibody for immunoprecipitation of BACH2 which is now commercially available. We are developing an antibody for detection of phospho-S520 BACH2 which is in the testing phase of commercialisation and will be characterised as part of the proposed work. It is anticipated that new reagents and techniques will be amenable to commercialisation. Babraham Institute Enterprise reviews our research programme for commercially exploitable results before publication. We will share relevant pre-publication data with life sciences companies to expedite translation of our findings and to foster economic growth within the UK.

C) Affiliates of the Babraham Institute: Should the research lead directly to commercially exploitable outcomes, the Institute's wholly owned trading arm, Babraham Institute Enterprise has arrangements for protection and development of intellectual property and a track record in exploitation of the Institute's science. This will help to foster economic growth in the UK.

2. The general public:

A) Patients and the National Health Service: The work will create new avenues for translational research, clinical trials and commercial drug development for treatment of patients with chronic infections and cancer and for development of new vaccination strategies. Development of new treatments will directly benefit patients and the National Health Service. Such benefits would be realised in the short- to medium-term (5-10 years).

B) The UK skilled workforce: A post-doctoral research assistant will be employed at a world-class UK Institute and gain research skills relevant for a career in academic science or the private sector. This will have immediate impact by enhancing skills within the UK workforce.

C) Dissemination of information: We will rapidly disseminate knowledge gained from this this research in formats accessible to a variety of end-users including the General Public, Academic Beneficiaries (see Academic beneficiaries) and the Private sector (see above). This will be of immediate benefit to society within the UK and globally. The Babraham Institute also hosts open days for sixth-form school students, participates in the Cambridge Science Festival, conducts in-school visits and hosts the Babraham annual schools day.