Epigenetic targets for immunomodulatory therapy in infectious disease and cancer

Project Overview

Figure 1. Strategic approach

This project aims to identify and validate potential epigenetic drug targets for use as immunomodulators. Epigenetic mechanisms play a key role in an effective, coordinate immune response with dysregulation resulting in, or contributing to, diverse disease states. There is growing interest in the therapeutic use of epigenetic inhibitors in infectious disease and cancer but further advances are needed to validate targets and understand potential therapeutic indications.

Human genetics provides experiments of nature to understand the role of specific proteins or processes and underlying mechanism. This is allowing us to map genetic variants involving epigenetic regulator genes and their functional consequences, both in terms of disease risk and differences in gene regulation. We found for example that expression of many chromatin regulators in monocytes is modulated by genetic variants including the histone deacetylase SIRT1and the histone methylation reader PHF19, identifying the likely modulated gene in a GWAS signal for lung squamous cell carcinoma (SIRT1) and for rheumatoid arthritis and celiac disease (PHF19) (Science 2014 343, 1246949).

This project will build on this knowledge to identify and validate potential epigenetic drug targets by an integrated approach (Figure 1). This will leverage human genetics, genomics and epigenomics together with diverse informative data types. Critically, you will establish functional mechanism for regulatory alleles involving epigenetic regulators to determine causal relationships for disease associations and you will resolve the consequences of knock-down of specific genes/proteins for disease relevant phenotypes. You will use cutting-edge genome editing techniques to establish causal relationships between modulating specific alleles, genes and pathways, and the observed cellular immune response and other phenotypes. This will be complemented by using high quality chemical probes generated by our collaborators in the Structural Genomics Consortium with excellent selectivity that can be used at relevant concentrations (<1uM) in cell based assays. These chemical probes inhibit specific epigenetic regulators responsible for gain or loss of methyl or acetyl groups (histone writers and erasers) or binding histones with specific post translational modifications (readers). Experimental work will include different primary human immune cells differentiated from induced pluripotent stem cells allowing efficient application of genome editing including pooled screens, as well as recruitment by genotype through Oxford Biobank bioresource. 

Training Opportunities

This project will provide excellent cross-disciplinary training. You will gain experience and expertise in human genetics, genomics and epigenomics, together with immuno-biology and drug development. The project will combine elements of bioinformatics with substantial wet lab experience. You will work under the supervision of experienced investigators in immunogenetics and epigenetic regulation (Prof Julian Knight) together with advanced genome editing and related approaches (Dr Ben Davies).You will be fully supported by an experienced team of investigators and collaborators with established techniques, platforms and required resources to enable this ambitious project to succeed.

You will be based in the Wellcome Centre for Human Genetics (WHG), an internationally recognised genetics research institute with state of the art facilities for genomic research. You will benefit from location within a campus that includes the Target Discovery Institute with capacity for high throughput screens, the Big Data Institute and the Structural Genomics Consortium together with strong clinical links with immunology and oncology. Students will be encouraged to present and publish their work, attend weekly lab meetings and journal clubs together with departmental seminars and training courses within the WHG and the Medical Sciences Doctoral Training Centre.

Theme

Immunology & Infectious Disease and Cancer Biology

Admissions

Project reference number: 825

Funding and admissions information

Supervisors

Name Department Institution Country Email
Professor Julian C Knight Wellcome Trust Centre for Human Genetics Oxford University, Henry Wellcome Building of Genomic Medicine GBR julian.knight@well.ox.ac.uk
Dr Ben Davies Wellcome Trust Centre for Human Genetics Oxford University, Henry Wellcome Building of Genomic Medicine GBR ben.davies@well.ox.ac.uk

Fairfax BP, Humburg P, Makino S, Naranbhai V, Wong D, Lau E, Jostins L, Plant K, Andrews R, McGee C, Knight JC. 2014. Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression. Science, 343 (6175), pp. 1246949. Read abstract | Read more

To systematically investigate the impact of immune stimulation upon regulatory variant activity, we exposed primary monocytes from 432 healthy Europeans to interferon-γ (IFN-γ) or differing durations of lipopolysaccharide and mapped expression quantitative trait loci (eQTLs). More than half of cis-eQTLs identified, involving hundreds of genes and associated pathways, are detected specifically in stimulated monocytes. Induced innate immune activity reveals multiple master regulatory trans-eQTLs including the major histocompatibility complex (MHC), coding variants altering enzyme and receptor function, an IFN-β cytokine network showing temporal specificity, and an interferon regulatory factor 2 (IRF2) transcription factor-modulated network. Induced eQTL are significantly enriched for genome-wide association study loci, identifying context-specific associations to putative causal genes including CARD9, ATM, and IRF8. Thus, applying pathophysiologically relevant immune stimuli assists resolution of functional genetic variants. Hide abstract

Knight JC. 2013. Genomic modulators of the immune response. Trends Genet., 29 (2), pp. 74-83. Read abstract | Read more

Our understanding of immunity has historically been informed by studying heritable mutations in both the adaptive and innate immune responses, including primary immunodeficiency and autoimmune diseases. Recent advances achieved through the application of genomic and epigenomic approaches are reshaping the study of immune dysfunction and opening up new avenues for therapeutic interventions. Moreover, applying genomic techniques to resolve functionally important genetic variation between individuals is providing new insights into immune function in health. This review describes progress in the study of rare variants and primary immunodeficiency diseases arising from whole-exome sequencing (WES), and discusses the application, success, and challenges of applying genome-wide association studies (GWAS) to disorders of immune function and how they may inform more rational use of therapeutics. In addition, the application of expression quantitative-trait mapping to immune phenotypes, progress in understanding MHC disease associations, and insights into epigenetic mechanisms at the interface of immunity and the environment are reviewed. Hide abstract

Heerboth S, Lapinska K, Snyder N, Leary M, Rollinson S, Sarkar S. 2014. Use of epigenetic drugs in disease: an overview. Genet Epigenet, 6 pp. 9-19. Read abstract | Read more

Epigenetic changes such as DNA methylation and histone methylation and acetylation alter gene expression at the level of transcription by upregulating, downregulating, or silencing genes completely. Dysregulation of epigenetic events can be pathological, leading to cardiovascular disease, neurological disorders, metabolic disorders, and cancer development. Therefore, identifying drugs that inhibit these epigenetic changes are of great clinical interest. In this review, we summarize the epigenetic events associated with different disorders and diseases including cardiovascular, neurological, and metabolic disorders, and cancer. Knowledge of the specific epigenetic changes associated with these types of diseases facilitates the development of specific inhibitors, which can be used as epigenetic drugs. In this review, we discuss the major classes of epigenetic drugs currently in use, such as DNA methylation inhibiting drugs, bromodomain inhibitors, histone acetyl transferase inhibitors, histone deacetylase inhibitors, protein methyltransferase inhibitors, and histone methylation inhibitors and their role in reversing epigenetic changes and treating disease. Hide abstract

Brown PJ, Müller S. 2015. Open access chemical probes for epigenetic targets. Future Med Chem, 7 (14), pp. 1901-17. Read abstract | Read more

BACKGROUND: High attrition rates in drug discovery call for new approaches to improve target validation. Academia is filling gaps, but often lacks the experience and resources of the pharmaceutical industry resulting in poorly characterized tool compounds. DISCUSSION: The SGC has established an open access chemical probe consortium, currently encompassing ten pharmaceutical companies. One of its mandates is to create well-characterized inhibitors (chemical probes) for epigenetic targets to enable new biology and target validation for drug development. CONCLUSION: Epigenetic probe compounds have proven to be very valuable and have not only spurred a plethora of novel biological findings, but also provided starting points for clinical trials. These probes have proven to be critical complementation to traditional genetic targeting strategies and provided sometimes surprising results. Hide abstract

Doudna JA, Charpentier E. 2014. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science, 346 (6213), pp. 1258096. Read abstract | Read more

The advent of facile genome engineering using the bacterial RNA-guided CRISPR-Cas9 system in animals and plants is transforming biology. We review the history of CRISPR (clustered regularly interspaced palindromic repeat) biology from its initial discovery through the elucidation of the CRISPR-Cas9 enzyme mechanism, which has set the stage for remarkable developments using this technology to modify, regulate, or mark genomic loci in a wide variety of cells and organisms from all three domains of life. These results highlight a new era in which genomic manipulation is no longer a bottleneck to experiments, paving the way toward fundamental discoveries in biology, with applications in all branches of biotechnology, as well as strategies for human therapeutics. Hide abstract

Fairfax BP, Makino S, Radhakrishnan J, Plant K, Leslie S, Dilthey A, Ellis P, Langford C, Vannberg FO, Knight JC. 2012. Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles. Nat. Genet., 44 (5), pp. 502-10. Read abstract | Read more

Trans-acting genetic variants have a substantial, albeit poorly characterized, role in the heritable determination of gene expression. Using paired purified primary monocytes and B cells, we identify new predominantly cell type-specific cis and trans expression quantitative trait loci (eQTLs), including multi-locus trans associations to LYZ and KLF4 in monocytes and B cells, respectively. Additionally, we observe a B cell-specific trans association of rs11171739 at 12q13.2, a known autoimmune disease locus, with IP6K2 (P = 5.8 × 10(-15)), PRIC285 (P = 3.0 × 10(-10)) and an upstream region of CDKN1A (P = 2 × 10(-52)), suggesting roles for cell cycle regulation and peroxisome proliferator-activated receptor γ (PPARγ) signaling in autoimmune pathogenesis. We also find that specific human leukocyte antigen (HLA) alleles form trans associations with the expression of AOAH and ARHGAP24 in monocytes but not in B cells. In summary, we show that mapping gene expression in defined primary cell populations identifies new cell type-specific trans-regulated networks and provides insights into the genetic basis of disease susceptibility. Hide abstract

Davenport EE, Burnham KL, Radhakrishnan J, Humburg P, Hutton P, Mills TC, Rautanen A, Gordon AC, Garrard C, Hill AV, Hinds CJ, Knight JC. 2016. Genomic landscape of the individual host response and outcomes in sepsis: a prospective cohort study. Lancet Respir Med, 4 (4), pp. 259-71. Read abstract | Read more

BACKGROUND: Effective targeted therapy for sepsis requires an understanding of the heterogeneity in the individual host response to infection. We investigated this heterogeneity by defining interindividual variation in the transcriptome of patients with sepsis and related this to outcome and genetic diversity. METHODS: We assayed peripheral blood leucocyte global gene expression for a prospective discovery cohort of 265 adult patients admitted to UK intensive care units with sepsis due to community-acquired pneumonia and evidence of organ dysfunction. We then validated our findings in a replication cohort consisting of a further 106 patients. We mapped genomic determinants of variation in gene transcription between patients as expression quantitative trait loci (eQTL). FINDINGS: We discovered that following admission to intensive care, transcriptomic analysis of peripheral blood leucocytes defines two distinct sepsis response signatures (SRS1 and SRS2). The presence of SRS1 (detected in 108 [41%] patients in discovery cohort) identifies individuals with an immunosuppressed phenotype that included features of endotoxin tolerance, T-cell exhaustion, and downregulation of human leucocyte antigen (HLA) class II. SRS1 was associated with higher 14 day mortality than was SRS2 (discovery cohort hazard ratio (HR) 2·4, 95% CI 1·3-4·5, p=0·005; validation cohort HR 2·8, 95% CI 1·5-5·1, p=0·0007). We found that a predictive set of seven genes enabled the classification of patients as SRS1 or SRS2. We identified cis-acting and trans-acting eQTL for key immune and metabolic response genes and sepsis response networks. Sepsis eQTL were enriched in endotoxin-induced epigenetic marks and modulated the individual host response to sepsis, including effects specific to SRS group. We identified regulatory genetic variants involving key mediators of gene networks implicated in the hypoxic response and the switch to glycolysis that occurs in sepsis, including HIF1α and mTOR, and mediators of endotoxin tolerance, T-cell activation, and viral defence. INTERPRETATION: Our integrated genomics approach advances understanding of heterogeneity in sepsis by defining subgroups of patients with different immune response states and prognoses, as well as revealing the role of underlying genetic variation. Our findings provide new insights into the pathogenesis of sepsis and create opportunities for a precision medicine approach to enable targeted therapeutic intervention to improve sepsis outcomes. FUNDING: European Commission, Medical Research Council (UK), and the Wellcome Trust. Hide abstract

Fairfax BP, Knight JC. 2014. Genetics of gene expression in immunity to infection. Curr. Opin. Immunol., 30 pp. 63-71. Read abstract | Read more

Mapping gene expression as a quantitative trait (eQTL mapping) can reveal local and distant associations with functionally important genetic variation informative for disease. Recent studies are reviewed which have demonstrated that this approach is particularly informative when applied to diverse immune cell populations and situations relevant to infection and immunity. Context-specific eQTL have now been characterised following endotoxin activation, induction with interferons, mycobacteria, and influenza, together with genetic determinants of response to vaccination. The application of genetical genomic approaches offers new opportunities to advance our understanding of gene-environment interactions and fundamental processes in innate and adaptive immunity. Hide abstract