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
Associate Professor 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

Davies B, Hatton E, Altemose N, Hussin JG, Pratto F, Zhang G, Hinch AG, Moralli D, Biggs D, Diaz R, Preece C, Li R, Bitoun E, Brick K, Green CM, Camerini-Otero RD, Myers SR, Donnelly P. 2016. Re-engineering the zinc fingers of PRDM9 reverses hybrid sterility in mice. Nature, 530 (7589), pp. 171-6. Read abstract | Read more

The DNA-binding protein PRDM9 directs positioning of the double-strand breaks (DSBs) that initiate meiotic recombination in mice and humans. Prdm9 is the only mammalian speciation gene yet identified and is responsible for sterility phenotypes in male hybrids of certain mouse subspecies. To investigate PRDM9 binding and its role in fertility and meiotic recombination, we humanized the DNA-binding domain of PRDM9 in C57BL/6 mice. This change repositions DSB hotspots and completely restores fertility in male hybrids. Here we show that alteration of one Prdm9 allele impacts the behaviour of DSBs controlled by the other allele at chromosome-wide scales. These effects correlate strongly with the degree to which each PRDM9 variant binds both homologues at the DSB sites it controls. Furthermore, higher genome-wide levels of such 'symmetric' PRDM9 binding associate with increasing fertility measures, and comparisons of individual hotspots suggest binding symmetry plays a downstream role in the recombination process. These findings reveal that subspecies-specific degradation of PRDM9 binding sites by meiotic drive, which steadily increases asymmetric PRDM9 binding, has impacts beyond simply changing hotspot positions, and strongly support a direct involvement in hybrid infertility. Because such meiotic drive occurs across mammals, PRDM9 may play a wider, yet transient, role in the early stages of speciation. 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

Knott GJ, Doudna JA. 2018. CRISPR-Cas guides the future of genetic engineering. Science, 361 (6405), pp. 866-869. Read abstract | Read more

The diversity, modularity, and efficacy of CRISPR-Cas systems are driving a biotechnological revolution. RNA-guided Cas enzymes have been adopted as tools to manipulate the genomes of cultured cells, animals, and plants, accelerating the pace of fundamental research and enabling clinical and agricultural breakthroughs. We describe the basic mechanisms that set the CRISPR-Cas toolkit apart from other programmable gene-editing technologies, highlighting the diverse and naturally evolved systems now functionalized as biotechnologies. We discuss the rapidly evolving landscape of CRISPR-Cas applications, from gene editing to transcriptional regulation, imaging, and diagnostics. Continuing functional dissection and an expanding landscape of applications position CRISPR-Cas tools at the cutting edge of nucleic acid manipulation that is rewriting biology. Hide abstract

Samanta S, Rajasingh S, Cao T, Dawn B, Rajasingh J. 2017. Epigenetic dysfunctional diseases and therapy for infection and inflammation. Biochim Biophys Acta Mol Basis Dis, 1863 (2), pp. 518-528. Read abstract | Read more

Even though the discovery of the term 'epigenetics' was in the 1940s, it has recently become one of the most promising and expanding fields to unravel the gene expression pattern in several diseases. The most well studied example is cancer, but other diseases like metabolic disorders, autism, or inflammation-associated diseases such as lung injury, autoimmune disease, asthma, and type-2 diabetes display aberrant gene expression and epigenetic regulation during their occurrence. The change in the epigenetic pattern of a gene may also alter gene function because of a change in the DNA status. Constant environmental pressure, lifestyle, as well as food habits are the other important parameters responsible for transgenerational inheritance of epigenetic traits. Discovery of epigenetic modifiers targeting DNA methylation and histone deacetylation enzymes could be an alternative source to treat or manipulate the pathogenesis of diseases. Particularly, the combination of epigenetic drugs such as 5-aza-2-deoxycytidine (Aza) and trichostatin A (TSA) are well studied to reduce inflammation in an acute lung injury model. It is important to understand the epigenetic machinery and the function of its components in specific diseases to develop targeted epigenetic therapy. Moreover, it is equally critical to know the specific inhibitors other than the widely used pan inhibitors in clinical trials and explore their roles in regulating specific genes in a more defined way during infection. Hide abstract

Yan H, Tian S, Slager SL, Sun Z, Ordog T. 2016. Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies. Am. J. Epidemiol., 183 (2), pp. 96-109. Read abstract | Read more

Epigenetic information encoded in covalent modifications of DNA and histone proteins regulates fundamental biological processes through the action of chromatin regulators, transcription factors, and noncoding RNA species. Epigenetic plasticity enables an organism to respond to developmental and environmental signals without genetic changes. However, aberrant epigenetic control plays a key role in pathogenesis of disease. Normal epigenetic states could be disrupted by detrimental mutations and expression alteration of chromatin regulators or by environmental factors. In this primer, we briefly review the epigenetic basis of human disease and discuss how recent discoveries in this field could be translated into clinical diagnosis, prevention, and treatment. We introduce platforms for mapping genome-wide chromatin accessibility, nucleosome occupancy, DNA-binding proteins, and DNA methylation, primarily focusing on the integration of DNA methylation and chromatin immunoprecipitation-sequencing technologies into disease association studies. We highlight practical considerations in applying high-throughput epigenetic assays and formulating analytical strategies. Finally, we summarize current challenges in sample acquisition, experimental procedures, data analysis, and interpretation and make recommendations on further refinement in these areas. Incorporating epigenomic testing into the clinical research arsenal will greatly facilitate our understanding of the epigenetic basis of disease and help identify novel therapeutic targets. Hide abstract

Ackloo S, Brown PJ, Müller S. 2017. Chemical probes targeting epigenetic proteins: Applications beyond oncology. Epigenetics, 12 (5), pp. 378-400. Read abstract | Read more

Epigenetic chemical probes are potent, cell-active, small molecule inhibitors or antagonists of specific domains in a protein; they have been indispensable for studying bromodomains and protein methyltransferases. The Structural Genomics Consortium (SGC), comprising scientists from academic and pharmaceutical laboratories, has generated most of the current epigenetic chemical probes. Moreover, the SGC has shared about 4 thousand aliquots of these probes, which have been used primarily for phenotypic profiling or to validate targets in cell lines or primary patient samples cultured in vitro. Epigenetic chemical probes have been critical tools in oncology research and have uncovered mechanistic insights into well-established targets, as well as identify new therapeutic starting points. Indeed, the literature primarily links epigenetic proteins to oncology, but applications in inflammation, viral, metabolic and neurodegenerative diseases are now being reported. We summarize the literature of these emerging applications and provide examples where existing probes might be used. Hide abstract