Accelerating progress to personalised medicine in infectious disease using genomics

Project Overview

Sepsis response

Recruiting centres for Genomic Advances in Sepsis study

Gene expression profiling in white blood cells reveals sepsis response (for details see Lancet ...

The dysregulated host response to infection may cause organ dysfunction and death. This is clinically recognised as the sepsis syndrome. Sepsis is common and devastating, accounting for 5% of deaths in England and 27% of intensive care unit (ICU) admissions. There are few effective therapies available and new approaches are urgently needed. Individual variation in the dysfunctional host response to infection that causes sepsis is a major factor in the failure of clinical trials of immunomodulatory therapies. Sepsis pathogenesis remains poorly understood and biomarkers to assess response and guide targeted therapy are not currently available. This DPhil project aims to understand this, with a view to developing personalised therapy that is appropriate to the individual patient at a particular stage in their illness.

You will join an experienced team of clinicians and scientists who have made significant progress in this area, ensuring the work is tractable and state of the art. The Knight and Hill groups have pioneered work into the genetics of immunity and infectious disease susceptibility.

In sepsis, we have established one of the largest cohorts of patients for genomic studies worldwide, the UK Genomic Advances in Sepsis (GAinS) Study. We performed the first substantive genome-wide association study for outcome in sepsis (Lancet Respiratory Medicine 2015 3, 53-60) and complemented this with functional genomic analysis using white blood cells collected from patients over time during their admission to intensive care. Transcriptomic profiling of these samples revealed gene signatures predictive of the underlying immune response state of patients and early mortality (Lancet Respiratory Medicine 4, 259-271) that is robust to the source of infection (Am J Respir Crit Care Med 196, 328-339). This shows that a genomic approach may allow us to define the nature and stage of a patient's illness, such that an appropriate immunomodulatory therapy could be given at that point in time.

Moreover, we found that a patient's genetic background influenced this with specific genetic variance associated with differences in gene expression dependent on their immune response state. This was further emphasised by our findings in healthy volunteers where we defined expression quantitative trait loci for the response to bacterial endotoxin in healthy volunteers (Science 2014 343, 1246949).

This DPhil project will aim to follow up on these findings in order to understand individual variation in the sepsis response and how this could be used to develop and apply therapy. You will define determinants of the individual response to sepsis, resolving the specific modulated genes and pathways that may be important in sepsis pathogenesis and potential drug targets. You will use large genomic, epigenomic and clinical datasets, both publicly available and those generated in house. You will leverage genomic and epigenomic data to identify and prioritise potential novel drug targets. You will use tools including genome editing to knockdown expression of specific genes or investigate the impact of particular genetic variants to establish mechanism; single cell analysis to define the most relevant cell types to pathogenesis; and immune profiling to understand immune correlates of disease response states.

Training Opportunities

This project will offer a comprehensive training programme in genomic science together with molecular biology and immunology in an internationally recognised genetics research institute (Wellcome Centre for Human Genetics, WHG) with state of the art facilities for genomic research and outstanding bioinformatic and statistical genetics support. The project proposal includes both dry (bioinformatics/ statistics/ computational science) and wet lab (molecular biology/functional genomics/ immunology) work, making it an ideal DPhil project for candidates wishing to gain skills in both areas.

The Knight and Hill laboratories have established sample and data collections for the proposed work. The required wet lab and bioinformatic approaches are well established with expertise in complex trait genetics, gene expression profiling, next generation sequencing technologies including RNA-seq and ChIP-seq, expression quantitative trait mapping, epigenomic profiling, genome editing, immunological assays and other approaches.

Specific training will include

Students will 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

Genetics & Genomics and Immunology & Infectious Disease

Admissions

Project reference number: 824

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
Professor Adrian VS Hill Jenner Institute Oxford University, Old Road Campus Research Building GBR adrian.hill@ndm.ox.ac.uk

van der Poll T, van de Veerdonk FL, Scicluna BP, Netea MG. 2017. The immunopathology of sepsis and potential therapeutic targets. Nat. Rev. Immunol., 17 (7), pp. 407-420. Read abstract | Read more

Sepsis is defined as a life-threatening organ dysfunction that is caused by a dysregulated host response to infection. In sepsis, the immune response that is initiated by an invading pathogen fails to return to homeostasis, thus culminating in a pathological syndrome that is characterized by sustained excessive inflammation and immune suppression. Our understanding of the key mechanisms involved in the pathogenesis of sepsis has increased tremendously, yet this still needs to be translated into novel targeted therapeutic strategies. Pivotal for the clinical development of new sepsis therapies is the selection of patients on the basis of biomarkers and/or functional defects that provide specific insights into the expression or activity of the therapeutic target. Hide abstract

Burnham KL, Davenport EE, Radhakrishnan J, Humburg P, Gordon AC, Hutton P, Svoren-Jabalera E, Garrard C, Hill AVS, Hinds CJ, Knight JC. 2017. Shared and Distinct Aspects of the Sepsis Transcriptomic Response to Fecal Peritonitis and Pneumonia. Am. J. Respir. Crit. Care Med., 196 (3), pp. 328-339. Read abstract | Read more

RATIONALE: Heterogeneity in the septic response has hindered efforts to understand pathophysiology and develop targeted therapies. Source of infection, with different causative organisms and temporal changes, might influence this heterogeneity. OBJECTIVES: To investigate individual and temporal variations in the transcriptomic response to sepsis due to fecal peritonitis, and to compare these with the same parameters in community-acquired pneumonia. METHODS: We performed genome-wide gene expression profiling in peripheral blood leukocytes of adult patients admitted to intensive care with sepsis due to fecal peritonitis (n = 117) or community-acquired pneumonia (n = 126), and of control subjects without sepsis (n = 10). MEASUREMENTS AND MAIN RESULTS: A substantial portion of the transcribed genome (18%) was differentially expressed compared with that of control subjects, independent of source of infection, with eukaryotic initiation factor 2 signaling being the most enriched canonical pathway. We identified two sepsis response signature (SRS) subgroups in fecal peritonitis associated with early mortality (P = 0.01; hazard ratio, 4.78). We defined gene sets predictive of SRS group, and serial sampling demonstrated that subgroup membership is dynamic during intensive care unit admission. We found that SRS is the major predictor of transcriptomic variation; a small number of genes (n = 263) were differentially regulated according to the source of infection, enriched for IFN signaling and antigen presentation. We define temporal changes in gene expression from disease onset involving phagosome formation as well as natural killer cell and IL-3 signaling. CONCLUSIONS: The majority of the sepsis transcriptomic response is independent of the source of infection and includes signatures reflecting immune response state and prognosis. A modest number of genes show evidence of specificity. Our findings highlight opportunities for patient stratification and precision medicine in sepsis. 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

Rautanen A, Mills TC, Gordon AC, Hutton P, Steffens M, Nuamah R, Chiche JD, Parks T, Chapman SJ, Davenport EE, Elliott KS, Bion J, Lichtner P, Meitinger T, Wienker TF, Caulfield MJ, Mein C, Bloos F, Bobek I, Cotogni P, Sramek V, Sarapuu S, Kobilay M, Ranieri VM, Rello J, Sirgo G, Weiss YG, Russwurm S, Schneider EM, Reinhart K, Holloway PA, Knight JC, Garrard CS, Russell JA, Walley KR, Stüber F, Hill AV, Hinds CJ, ESICM/ECCRN GenOSept Investigators. 2015. Genome-wide association study of survival from sepsis due to pneumonia: an observational cohort study. Lancet Respir Med, 3 (1), pp. 53-60. Read abstract | Read more

BACKGROUND: Sepsis continues to be a major cause of death, disability, and health-care expenditure worldwide. Despite evidence suggesting that host genetics can influence sepsis outcomes, no specific loci have yet been convincingly replicated. The aim of this study was to identify genetic variants that influence sepsis survival. METHODS: We did a genome-wide association study in three independent cohorts of white adult patients admitted to intensive care units with sepsis, severe sepsis, or septic shock (as defined by the International Consensus Criteria) due to pneumonia or intra-abdominal infection (cohorts 1-3, n=2534 patients). The primary outcome was 28 day survival. Results for the cohort of patients with sepsis due to pneumonia were combined in a meta-analysis of 1553 patients from all three cohorts, of whom 359 died within 28 days of admission to the intensive-care unit. The most significantly associated single nucleotide polymorphisms (SNPs) were genotyped in a further 538 white patients with sepsis due to pneumonia (cohort 4), of whom 106 died. FINDINGS: In the genome-wide meta-analysis of three independent pneumonia cohorts (cohorts 1-3), common variants in the FER gene were strongly associated with survival (p=9·7 × 10(-8)). Further genotyping of the top associated SNP (rs4957796) in the additional cohort (cohort 4) resulted in a combined p value of 5·6 × 10(-8) (odds ratio 0·56, 95% CI 0·45-0·69). In a time-to-event analysis, each allele reduced the mortality over 28 days by 44% (hazard ratio for death 0·56, 95% CI 0·45-0·69; likelihood ratio test p=3·4 × 10(-9), after adjustment for age and stratification by cohort). Mortality was 9·5% in patients carrying the CC genotype, 15·2% in those carrying the TC genotype, and 25·3% in those carrying the TT genotype. No significant genetic associations were identified when patients with sepsis due to pneumonia and intra-abdominal infection were combined. INTERPRETATION: We have identified common variants in the FER gene that associate with a reduced risk of death from sepsis due to pneumonia. The FER gene and associated molecular pathways are potential novel targets for therapy or prevention and candidates for the development of biomarkers for risk stratification. FUNDING: European Commission and the Wellcome Trust. Hide abstract

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

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