Immune Regulation in Inflammation and Cancer

T cells drive immune activation and promote clearance of infections and cancer. However, their function can provoke autoimmune and allergic inflammation. The immune system therefore employs a variety of suppressive mechanisms, known as immunoregulatory mechanisms, to restrain excessive T cell activation and prevent autoimmune and allergic inflammation. It is now known that such suppressive mechanisms inhibit anti-tumour immunity to drive deleterious immunosuppression in cancer. Immunoregulatory mechanisms therefore function as ‘brakes’ within the immune system and are important therapeutic targets in infection, inflammation and cancer. This is exemplified by the clinical efficacy of cancer immunotherapies targeting the immune ‘checkpoints’ PD-1 and CTLA-4 in certain cancers.

We believe that fundamental discovery in the fields of immune regulation and cancer immunosuppression will enable development of new and more effective therapies for patients with presently incurable autoimmune and allergic diseases and cancer. Our research falls within three key areas described below.

Regulatory T (Treg) cell development and function

Regulatory T (Treg) cells are rare immune cells with powerful suppressive functions. Loss of CD4+ Foxp3+ Treg cells results in lethal inflammation, while defects in their function are associated with autoimmunity and allergy. Treg cells also suppress immune responses in cancer. There is intense medical interest in exploiting the powerful biological functions of Treg cells to treat patients with inflammatory diseases, transplantation and cancer. However, most efforts have thusfar been disappointing. We aim to better define mechanisms of Treg development and function, to identify new ways of exploiting or blocking the suppressive function of Treg cells in individuals with inflammation and cancer (Fig. 1).

Immunoregulatory function within the T cell lineage.

Figure 1. Regulatory T cell development. CD4+ effector and regulatory T (Treg) cells arise from common precursor cells within the thymus and periphery by exert opposing functions. Treg-mediated restraint of effector cell function is a critical immunoregulatory mechanism required to prevent lethal inflammation. Modified from Igarashi, Kurosaki and Roychoudhuri, Nat Rev Immunol 2017.

The immunoregulatory function of Treg cells is a major focus of the laboratory’s research. We have demonstrated the non-redundant requirement for the transcription factor BACH2 in Treg development (Nature 2013). Our findings provided a model of early Treg lineage commitment and explained why genetic polymorphisms at the human BACH2 locus are associated with autoimmune and allergic diseases. We established a now widely-accepted molecular model of how BACH2 functions in lymphocytes (Nat Immunol 2016; reviewed in Igarashi, Kurosaki and Roychoudhuri, Nat Rev Immunol 2017). Our research contributed to the discovery of a new human disease called BACH2-related Immunodeficiency and Autoimmunity (Afzali et al., Nat Immunol 2017). This has led to identification and improved management of patients with BRIDA. We showed that BACH2 promotes Treg-mediated cancer immunosuppression (J Clin Invest 2015). We have subsequently developed cell-based reporter assays for BACH2 function (Scientific Reports 2020), enabling a drug discovery programme in collaboration with Cancer Research UK Therapeutic Discovery Laboratories.

Our group showed that a distal enhancer at the prominent human autoimmune/allergic disease risk locus at chromosome 11q13.5 restricts gut inflammation by promoting expression of the TGF-b docking receptor GARP on Treg cells, revealing a novel mechanism of immune regulation in the gut (Nature 2020). We showed that quiescent cells marked by high levels of BACH2 expression are required for maintenance of Treg responses over time (Grant et al., J Exp Med 2020). We showed that CCR8 expression marks Treg cells with highly suppressive function in tumours but that it is dispensable for their accumulation and suppressive function (Immunology 2021).

Suppression of T cell immunity in cancer

Cancers adapt to their immune environment to evade attack. According to the cancer immunoediting hypothesis, tumour development is characterized by an initial ‘elimination’ phase, during which a majority of cancer cells are destroyed by components of innate and adaptive immunity (Fig. 2). This is followed by an ‘equilibrium’ phase, during which pressure from the immune system contributes to evolutionary selection of tumour escape variants that give rise to an ‘escape’ phase characterized by evasion from immune control and unrestrained tumour growth.

How is the function of the immune system suppressed during tumour development?

Figure 2. Phases of tumour development according to the cancer immunoediting hypothesis. Tumour development is characterized by an initial ‘elimination’ phase, during which a majority of cancer cells are destroyed by a variety of components of the innate and adaptive immune systems, including CD8+ T cells and NK cells. This process results, referred to as immunoediting, results in an ‘equilibrium’ phase, during which pressure from the immune system contributes to selection of tumour variants that do not express antigens targeted by the adaptive immune system or have developed mechanisms to suppress immune function. This gives rise to the ‘escape’ phase characterized by recruitment and support of the differentiation and proliferation of immunosuppressive cell types including Treg cells, tumour-associated macrophages and myeloid-derived suppressor cells, expression of inhibitory ligands and such as PD-L1 and production of immunosuppressive factors such as TGF-b resulting in evasion from immune control and unrestrained tumour growth.

While selection of antigen-loss variants represents a mechanism of tumour escape, growth of tumours containing immunogenic epitopes is better explained through an understanding of the critical role of immunosuppression in promoting tumour escape. To achieve this, cancer cells subvert the biochemical, metabolic and ionic environment of tumours to drive immune dysfunction. Using directed tumour evolution and high-throughput CRISPR-based functional genetics, this work aims to identify novel immunoregulatory mechanisms operating within the tumour microenvironment.

We have made progress in understanding mechanisms of tumour immunosuppression. We uncovered mechanisms by which Treg cells contribute to cancer immunosuppression (J Clin Invest 2016). Our group showed that maintenance of durable immunosuppressive Treg responses to cancer require the Treg cells with a quiescent phenotype (J Exp Med 2020). We showed that high interstitial potassium concentrations within tumours limits CD8+ T cell function through suppression of the AKT/mTOR pathway (Nature 2016). We have shown that Treg differentiation is sensitive to local oxygen concentration contributing to lung immune homeostasis but creating a permissive environment for pulmonary cancer metastasis (Cell 2016). We showed that CCR8 marks Treg cells with highly suppressive function within tumours, but is dispensable for their accumulation and function (Immunology 2021). Our research findings and tools form the basis for industrial collaborations with GSK, F-Star Biotechnology and CRUK Therapeutic Discovery Laboratories.

T cell maintenance and dysfunction

T cell responses are clonally expanded from small numbers of antigen-specific naive precursor cells which arose during thymic development. Upon priming, antigen-specific T cell responses must be maintained over long periods of time to enable T cell memory and durable responses to chronic antigens. Our laboratory is interested in the mechanisms that underpin long-lived T cell responses.

CD8+ T cell memory has been the focus of our prior research. However, we have recently become interested in understanding how clonal Treg responses are maintained over time. To work properly, Treg responses need to be remarkably long-lived: Treg cells produced during a critical time-window in early life need to be maintained throughout life to prevent lethal inflammation. Treg populations are maintained despite reduced thymic output of T cells as we age, and in the definitive absence of thymic output. The transfer of mature Treg cells into Treg-deficient mice establishes a long-lived population that prevents lethal inflammation over the lifespan of the host. Maintenance of Treg responses is also critical to immunoregulatory memory, limiting harmful immune reactions upon re-exposure to allergens and infection, and to the efficacy of Treg cell therapies. Much is known about how Treg cells develop, but we have lacked a framework for understanding how Treg responses are maintained. Our recent work has begun to reshape our thinking about how long-lived Treg responses are organised. We have found that long-term maintenance of Treg populations is dependent upon the presence of a subset of functionally quiescent cells marked by high levels of Bach2 expression (Fig. 3; Grant, Yang et al., J Exp Med 2020). We are developing new tools to understand how long-lived immunoregulatory and immunosuppressive Treg responses are maintained and establishing clinical collaborations to determine the consequences of this for inflammatory and allergic diseases and cancer.

Functions of Bach2 in Treg development and maintenance.

Figure 3. Long-term maintenance of Treg responses requires quiescent Bach2-expressing cells.

We have a long-standing interest in T cell memory. We conducted one of the earliest multiplexed single-cell gene expression analyses of immune cells revealing unappreciated heterogeneity in memory CD8+ T responses to vaccination (PNAS 2011). We defined transcriptional and epigenetic programmes of vaccine-induced memory T cells (Vaccine 2015, Cell Mol Immunol 2015). We defined molecular mechanisms by which long-lived memory CD8+ T cell responses to viral infection are maintained (Nat Immunol 2016). We showed that long-term maintenance of Treg populations is dependent upon the presence of a subset of functionally quiescent cells marked by high levels of Bach2 expression (J Exp Med 2020). We have contributed to work showing that inhibition of AKT signalling enables expansion of T cells with a long-lived memory phenotype which mediates superior adoptive immunotherapy responses upon transfer into tumour-bearing recipients (Cancer Res, 2015), and that memory T cell–driven differentiation of naive cells impairs adoptive immunotherapy (J Clin Invest, 2015).

Research Highlights

(For a full list of publications see below)

BACH2 restricts NK cell maturation and function limiting immunity to cancer metastasis

Natural killer (NK) cells are critical to immune surveillance against infections and cancer. Here we show that the transcription factor BACH2 functions as a critical negative regulator of NK cell function within tissues, restricting immunity to cancer metastasis. The findings show that the maturation state of NK cells in tissues is a major determinant of anti-metastatic immunity.

Imianowski, et al., J Exp Med (2022)  [PDF]

IL-2 is inactivated by the acidic pH environment of tumours enabling engineering of a pH-selective mutein

Here, we show that IL-2, a cytokine critical to supporting CD8 T cell and NK cell functions within tumours exhibits markedly compromised binding to the IL-2Rα receptor chain in acidic extracellular environments. Directed evolution was used to screen for IL-2 variants with mutations at the receptor interface that enhanced receptor binding at low pH. A mutated “Switch-2” variant of IL-2 with strong receptor binding at pH 6 but minimal interaction at neutral pH exhibited enhanced in vivo antitumor activity with reduced toxicity in normal tissues.

Gaggero, Martinez-Fabregas, et al., Science Immunology (2022)  [PDF]

CCR8 marks highly suppressive Treg cells within tumours but is dispensable for their accumulation and suppressive function

There is interest in selectively targeting the suppressive function of Treg cells within tumours. We show that high levels of CCR8 expression distinguish highly suppressive Treg cells within tumours, but that genetic deletion of CCR8 has minimal impact on Treg suppressive function or tumor immunity. These findings suggest that CCR8 is not required for Treg suppression within tumours and that depletion of CCR8+ Treg cells rather than blockade of CCR8 function will enable selective cancer immunotherapy.

Whiteside, et al., Immunology (2021)  [PDF]

A distal enhancer at risk locus 11q13.5 promotes suppression of colitis by Treg cells

Genetic variations underlying risk of complex immune-mediated diseases are concentrated within the non-coding genome at enhancers. The functions of a vast majority of enhancers are unresolved. Using CRISPR-based mutagenesis of human disease-associated enhancer homologs in mice, we show that a distal enhancer at the human 11q13.5 immune disease risk locus promotes Treg-mediated suppression of colitis by driving expression of the TGF-β docking receptor GARP on Treg cells.

Nasrallah, Imianowski, et al., Nature (2020)  [PDF]

Recommended by F1000; Commentary in Sci Immunol 5,eabe0976

BACH2 drives quiescence and maintenance of resting Treg cells to promote homeostasis and cancer immunosuppression

Treg cells are maintained over long periods of time despite a continuous requirement for their suppressive function. This study established a critical function of quiescent cells in Treg maintenance. The transcription factor BACH2 is critical for Treg cell development. We show that in mature Treg cells, Bach2 is highly expressed in quiescent cells where it binds to enhancers of genes associated with Treg activation and represses their TCR- and AP-1-driven induction. By imposing quiescence in this subset of Treg cells, BACH2 promotes maintenance of Treg responses, and durable immune suppression in cancer.

Grant, Yang et al., J Exp Med (2020)  [PDF]

A human monogenic inflammatory disease caused by loss-of-function mutations in BACH2

This study describes a human monogenic disease resulting from inactivating mutations of BACH2, termed BACH2-related Immunodeficiency and Autoimmunity (BRIDA). Affected patients have lymphocyte-differentiation defects associated with immunodeficiency and inflammation of the intestinal tract and lungs. This work resulted from an international collaboration with clinical and academic researchers in the US and UK.

Afzali et al., Nat Immunol (2017) 18:813-823.  [PDF]

BACH transcription factors in innate and adaptive immunity

Here we review roles of BACH family transcriptional repressors in innate and adaptive immunity. We highlight similarities at a molecular level in the cell-type-specific activities of the BACH factors, proposing that competitive interactions of BACH proteins with transcriptional activators of the bZIP family form a common mechanistic theme underlying their diverse actions.

Igarashi, Kurosaki and Roychoudhuri, Nat Rev Immunol (2017) 17:437-450.  [PDF]

High levels of extracellular potassium in tumours suppress T cell activation

This study revealed that cell death in the tumour microenvironment releases intracellular potassium into the extracellular microenvironment of tumours, causing profound suppression of T cell activation. High extracellular potassium concentrations impair T cell receptor (TCR)-driven Akt-mTOR phosphorylation and effector programmes. Engineering CD8+ T cells to be resistant to high extracellular potassium in tumours improves adoptive immunotherapy.

Eil et al., Nature (2016) 537:539-543.  [PDF]

Oxygen-sensing by T cells promotes cancer metastasis to the lung

The lung is a frequent site of cancer metastasis but whether there is an immunological component to this susceptibility has been unclear. Here, we show that T cell responses to metastasis within the lung are restricted by high oxygen concentrations. The HIF prolyl hydroxylases PHD1, PHD2 and PHD3 mediate sensitivity of T cells to oxygen, which suppresses Th1 responses and promotes iTreg responses within the lung. As a consequence, immunologic permissivity of the lung to cancer metastasis is dependent upon PHD1, PHD2 and PHD3.

Clever et al., Cell (2016) 166:1117-1131  [PDF]

BACH2 functions as an AP-1 repressor in lymphocytes to promote CD8+ T cell memory

This study was the first to define BACH2 key regulator of lymphocyte quiescence. We found that BACH2 restrains effector differentiation to promote differentiation of long-lived memory CD8+ T cells after viral infection. We found that BACH2 binds to enhancers where it engages in steric competition with AP-1 factors, limiting TCR-driven induction of AP-1 target genes to promote memory formation. Subsequent work has shown that BACH2 is expressed in stem-like progenitors within T cell responses to cancer.

Roychoudhuri et al., Nat Immunol (2016) 17:851-860.  [PDF]

Commentary by Sidwell and Kallies (Nat Immunol 17:744-5.

The transcription factor BACH2 promotes tumour immunosuppression through its function in Treg cell development

This study established a role of BACH2 in Treg-mediated tumour immunosuppression. This function is corroborated by results of a large in vivo screen of host restriction factors to tumour metastasis (Van der Weyden et al., Nature 2017) and provides a basis for a CRUK-funded drug development programme with CRUK Therapeutic Discovery Laboratories to identify small molecule inhibitors of the suppressive activity of BACH2.

Roychoudhuri et al., J Clin Invest (2016) 126:599-604.  [PDF]

The transcriptional repressor BACH2 is required for Treg cell development and suppression of lethal inflammation

This study established the critical function of the transcription factor BACH2 in immunological tolerance. We found that BACH2 is required for early Treg cell development and its deletion in mice results in lethal inflammation. The findings contributed to our understanding of why genetic polymorphisms within the BACH2 locus in humans are associated with susceptibility to autoimmune and allergic diseases (reviewed in Igarashi, Kurosaki and Roychoudhuri, Nat Rev Immunol 2017).

Roychoudhuri et al., Nature (2013) 498:506-10.  [PDF]

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