Systems biology of host-pathogen interactions

Bob Hancock's Associate Faculty group utilises systems biology methods and differentiated mutant embryonic stem (ES) cells to understand the complex inter-relationship between the host and the pathogen and enable the development of new therapies against infections.

We have proposed that manipulation of natural innate immunity will serve as a new therapeutic strategy against antibiotic-resistant infections. However to understand the assets and potential deficits of such a strategy we need to understand the extremely complex process of innate immunity (involving as many as 5000 biomolecules).

To understand the complexity of host immune responses to pathogens, we will utilise targeted genetic modifications of stem cells, to enable the investigation of mouse and human genes that have important functions in pathogen-host interactions and favourable host immune responses. Cellular responses to pathogens and their immune-stimulatory molecules will involve high-throughput analysis of their phenotypes using our new bioinformatic tools for studying the systems biology of innate immunity.

[CDC/Janice Haney Carr]

Background

The antibiotic era, stemming from the deployment of penicillin, introduced arguably the most successful medicines of all time, impacting dramatically on life expectancy by decreasing childhood and adult deaths from infections, and enabling complex surgeries, transplantations and cancer chemotherapy (Nature Reviews Drug Discovery 6:28, 2007). Despite this more than one third of all deaths worldwide are due to infections.

Moreover the treatment of infectious diseases is now under severe threat. On the one hand antibiotic resistance is rising rapidly; on the other there are relatively few novel compounds under development or entering the clinic. Thus there is an urgent need to develop new strategies for treating infections.

Adjunctive therapies that make antibiotics work better represent a new approach to treating difficult bacterial infections, and of these one of the most promising is immune modulation (Nature Reviews Microbiology 10:243-254, 2012).

Research

We will pursue several avenues to understand innate immune and inflammatory responses to pathogen molecules and specific disease syndromes and to innate defence regulator (IDR) peptides that we are developing as human and animal immune modulator therapeutics.

High-throughput analysis of homozygous knock-out mutant stem cells

This aim is integrated with the 'Cellular phenotyping of host-pathogen interactions in genetically modified stem cells' programme.

We have developed methods for medium-throughput generation of macrophages from mouse ES cells and have phenotyped these using Cellomics, FACS, Luminex and transcriptomic methods. We are collaborating with a number of Sanger faculty members to use targeted genetic modifications of stem cells to identify the functions of host genes in innate immunity, using stem cells differentiated into macrophages as a model system, comparing these cells to the same cell types obtained from homozygous targeted knock-out cells from mutant mice. In particular we will utilise these methods to determine the mechanism of action of our IDR peptides and the role of specific genes in infections, inflammatory diseases and sepsis.

The long-term intention is to translate this technology to enable an understanding of the same responses in human cells differentiated from knock-out pluripotent stem cells.

RNA-Seq based phenotyping of bacterial and host cells

We have substantial experience in transcriptomics-based phenotyping, including high-throughput sequence based RNA-Seq. Transcriptomics involves a global analysis of the genes that are expressed during challenge and disease, and when performed in high throughput, and analyzed using network/systems biology methods, it can generate exciting new hypotheses for lab testing regarding the roles of genes, pathways and processes in determining mechanistic features of infections, inflammatory diseases (e.g. sepsis, IBD, cystic fibrosis, vasculitis) and the action of immune modulators.

Development of these new insights into mechanisms, pathways, networks of interacting genes and biological processes requires the application of systems/network biology analyses. We have developed databases and analysis platforms to enable such analyses including InnateDB and a fledging program Meta-GEX. We will further develop these tools and promote their usage to analyze the data generated by RNA-Seq.

In particular, we will develop bioinformatic methods for correlating such data with patient parameters, to enable the development of biomarkers, as well as for integrating genetic polymorphism and drug target data into network analyses.

Drug development

We have substantial experience in the translation of basic research and particularly in the development of new anti-infective therapies. We will continue to engage in creating initiatives in the antimicrobial space, based on analysis of the principle mechanisms of resistance and host responsiveness and our new concepts in adjunctive treatment of infections using immunomodulatory and anti-biofilm approaches.

Resources

www.innatedb.com

InnateDB is an open-source, publicly-available curated database and systems biology analysis platform of all experimentally validated molecular interactions and pathways in human, mouse. It is becoming an important tool in immunology as evidenced by the 1.5 million hits per year from 12,000 separate visitors and enables the use of high-throughput genomics data to create hypotheses regarding the mechanisms of disease and immunity.

www.pseudomonas.com

This genomics database for the prominent hospital pathogen Pseudomonas aeruginosa, is provided as a service to the research community as a repository for all genetic and genomic information about this bacterium. It receives more than 15,000 hits daily from more than 20 countries.

Collaborations

We are working closely with a number of researchers and faculty at the Sanger Institute.

  • Microbial pathogenesis. We are collaborating with Gordon Dougan's team on high-throughout phenotyping of host and bacterial cells, as well as the development of new therapeutic strategies based on an understanding of antibiotic resistance.
  • Mouse developmental genetics and ES cell mutagenesis. We are using the stem cell knockouts generated by Bill Skarnes' group for phenotyping after differentiation into macrophages.
  • High-Throughput Gene Targeting. The work of the High-Throughput Gene Targeting group is a huge resource for our research, they have produced numerous conditional targeted mutations in C57BL/6 embryonic stem cells, some of which have been grown into homozygous gene targeted mice.
  • Malaria: Billker group. Oliver Billker leads the project 'Cellular phenotyping of host-pathogen interactions in genetically modified stem cells' of which our major studies are a part. We have collaborated extensively on development of phenotyping assays for differentiated mouse ES cells.

Selected Publications

  • Effective adjunctive therapy by an innate defense regulatory peptide in a preclinical model of severe malaria.

    Achtman AH, Pilat S, Law CW, Lynn DJ, Janot L, Mayer ML, Ma S, Kindrachuk J, Finlay BB, Brinkman FS, Smyth GK, Hancock RE and Schofield L

    Science translational medicine 2012;4;135;135ra64

  • The critical role of histone H2A-deubiquitinase Mysm1 in hematopoiesis and lymphocyte differentiation.

    Nijnik A, Clare S, Hale C, Raisen C, McIntyre RE, Yusa K, Everitt AR, Mottram L, Podrini C, Lucas M, Estabel J, Goulding D, Sanger Institute Microarray Facility, Sanger Mouse Genetics Project, Adams N, Ramirez-Solis R, White JK, Adams DJ, Hancock RE and Dougan G

    Blood 2012;119;6;1370-9

  • InnateDB: facilitating systems-level analyses of the mammalian innate immune response.

    Lynn DJ, Winsor GL, Chan C, Richard N, Laird MR, Barsky A, Gardy JL, Roche FM, Chan TH, Shah N, Lo R, Naseer M, Que J, Yau M, Acab M, Tulpan D, Whiteside MD, Chikatamarla A, Mah B, Munzner T, Hokamp K, Hancock RE and Brinkman FS

    Molecular systems biology 2008;4;218

  • An anti-infective peptide that selectively modulates the innate immune response.

    Scott MG, Dullaghan E, Mookherjee N, Glavas N, Waldbrook M, Thompson A, Wang A, Lee K, Doria S, Hamill P, Yu JJ, Li Y, Donini O, Guarna MM, Finlay BB, North JR and Hancock RE

    Nature biotechnology 2007;25;4;465-72

  • High-throughput generation of small antibacterial peptides with improved activity.

    Hilpert K, Volkmer-Engert R, Walter T and Hancock RE

    Nature biotechnology 2005;23;8;1008-12

  • Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen.

    Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, Hickey MJ, Brinkman FS, Hufnagle WO, Kowalik DJ, Lagrou M, Garber RL, Goltry L, Tolentino E, Westbrock-Wadman S, Yuan Y, Brody LL, Coulter SN, Folger KR, Kas A, Larbig K, Lim R, Smith K, Spencer D, Wong GK, Wu Z, Paulsen IT, Reizer J, Saier MH, Hancock RE, Lory S and Olson MV

    Nature 2000;406;6799;959-64

* quick link - http://q.sanger.ac.uk/hostpath