The human body is continually under assault. A multitude of viruses, bacteria, fungi and parasites all have different modes of attack, with an arsenal of weaponry at their disposal. Confronting this onslaught is a remarkably sophisticated series of defences – the human immune system.

While the sophistication of the immune system is essential to maintain our health, it presents considerable challenges to the scientists trying to unpick how the system works. Not only do researchers want to know how we respond to pathogens, so that new vaccines and drugs can be designed to prevent and treat infections, they are also striving to understand why the immune system sometimes works inappropriately – as in allergy and in autoimmune diseases such as rheumatoid arthritis or type 1 diabetes.

The sequence of the human genome will undoubtedly help to answer these questions, as it holds the genes that encode the entire immune defence system. The initial analysis of the human genome sequence (published in February 2001) has already provided some important clues: 765 proteins that resemble antibodies were identified, many of which might be expected to play a role in immunity.

But the task of deciphering the genome is immense: immunologists need to work out which of the 30–40 000 genes in the genome produce molecules involved in immunity. Even more importantly, they need to know how the genes and molecules work together to keep us healthy. The immune system is so dynamic and complex, involving a plethora of interacting cells and different parts of the body, that a true understanding can only come from work on living organisms. For most immunologists, the model of choice is the laboratory mouse.

A new collaboration between immunologists in Oxford and Australia has recently been awarded a Wellcome Trust programme grant of £1.4 million to analyse the immune system of the laboratory mouse, using a systematic genetic approach. The mouse genome closely resembles that of humans and is the subject of the Mouse Genome Sequencing Project (currently underway at the Wellcome Trust Sanger Centre and at two sequencing centres in the USA). At Canberra, Professor Chris Goodnow is screening mice to find ones that have defects in their immune systems. A bevy of immunologists and geneticists – led by Professor Goodnow and by Professor John Bell and Richard Cornall at the University of Oxford – will then find the mutated genes and determine their effects on immunity.

A systematic approach

"A handful of mice with mutations have taught us the most about immunology in the last 20 years," says Dr Cornall, a Wellcome Trust Senior Research Fellow in Clinical Science at Oxford who is examining genetic effects on autoimmune diseases. "They are the cornerstone of modern immunology." Most of these mice have been found by chance, however, and the limited number available has become something of a bottleneck.

To overcome this problem, Professor Chris Goodnow – a B-cell immunologist investigating autoimmune diseases – has set up a mouse facility at the Australian National University in Canberra. Rather than rely on chance, he is taking a systematic approach that aims to find mutations in as many of the genes involved in immunity as possible. The approach is based on producing mutations in the mouse genome using a substance called ethylnitrosurea (ENU). The effectiveness of systematic mutagenesis was highlighted in the 1980s and 90s, when studies of fruit flies uncovered hundreds of genes involved in development.

ENU was first trialled on mice with coat-colour mutations in the 1980s at the Oakridge Laboratories in the USA, ENU mutates about one in a thousand genes in the sperm genome. As the mouse has approximately 30–40 000 genes, 30–40 mutations should be passed onto the next generation. These mutations can then be analysed to find those that affect the immune system.

Systematic mutagenesis of the mouse is a logistically challenging exercise, and only a few laboratories in the world – notably the MRC Mammalian Genetics Centre in Harwell, the CSF Centre in Germany, and some centres in the USA – have the infrastructure required. These laboratories are using ENU-based mutagenesis primarily to find dominant mutations, in particular those involved in neurological diseases; Canberra is the first laboratory to search systematically for recessive mutations in the genes of the immune system. "The Canberra mouse facility is absolutely world class," says Professor Bell, who is leading the Oxford half of the collaboration. "It is probably the only laboratory in the world that is capable of doing this experiment."

Preliminary screens have already identified about 30 mutations that affect the immune system. “The quality of the screens is crucial,” says Professor Bell. "They have got to be thoughtful screens that mean something. We spent about a year thinking about what screens we were going to do – what questions we wanted to ask."

The mutants identified by Professor Goodnow will be analysed both in Australia and in the UK. "The UK has such a breadth of immunology expertise," says Professor Bell. "In Oxford, for example, we can cover every step in the immune response: we have people who are experts on dendritic cells, CD4 and CD8 T cells, B cells, immune signalling, cell adhesion and so on. So if we get an immunological phenotype that we think is interesting, there is someone within half a mile of this office who can provide you with the functional assay to test what is wrong."

Finding the genes affected in the mice will be undertaken at the Wellcome Trust Centre for Human Genetics at Oxford – a task that will rely heavily upon the data from the mouse genome sequencing project. "We use microsatellite markers to navigate around the mouse genome and to find the region affected," says Dr Cornall. “But in the past we'd only know the general region as the markers are quite far apart. Now, with the mouse genome sequence being generated, we'll know the candidate genes in the region and will be able to pinpoint the affected genes at a much faster rate."

Meanwhile, the effects of the mutations on other genes will be examined using microarrays. "If you have a mutation in a single gene in a pathway, how do you find what other genes are affected in that pathway?" asks Dr Cornall. "We're going to use microarrays to look at gene expression. A mutation in one gene might lead to other genes being turned on or off, so we’d hope to find patterns of gene expression that are characteristic of the pathways."

'Multidisciplinary' is a term often applied to postgenomics projects. In this case, the new collaboration brings together expertise in mutagenesis, functional analysis, gene-finding and microarray studies. "There isn’t anyone in the world who’s doing a project like this for immunology," says Professor Bell. "If you want to systematically pick apart a pathway and provide a functional readout of the role of genes there is no more powerful way to do it. This is the ultimate postgenomics experiment for immunology."

External links

• Mouse Genome Sequencing Project at the Wellcome Trust Sanger Centre
• Wellcome Trust Centre for Human Genetics at the University of Oxford
• Nuffield Department of Clinical Medicine: Contact details for Dr Richard Cornall
• MRC Mammalian Genetics Unit at Harwell