In spring 2007, half-a-dozen scientists huddled around a laptop at a pub in Cambridge in the United Kingdom, to see the preliminary results from the largest ever genetic study of multiple sclerosis (MS). Expectations were high. Three decades had passed since the last genes were discovered to have a link to MS, in a large genomic region called the major histocompatibility complex (MHC).

Using the pub's wireless Internet connection, one of the researchers eagerly downloaded the first batch of data. It was disappointing: the analysis found no gene variants outside the MHC that were associated with MS. “We thought, all this work and once again MS eludes us,” recalls David Hafler, one of the leaders of the International Multiple Sclerosis Genetics Consortium (IMSGC).

The next morning, when the researchers convened again at the University of Cambridge, they were in for a pleasant surprise. “The guy who had downloaded the data said: 'Oh, I made a mistake',” recalls Hafler, who is now head of neurology at Yale University. When the analysis was done again, the program identified variants near two genes that play an important role in the workings of immune cells1.

Yale's David Hafler examines arrays used to elucidate for the first time the genes underlying MS risk. Credit: Mansoor Zaidi

The report included data from almost 4,000 people with MS. In August 2011, the consortium published an even bigger association study. After screening the genomes of nearly 10,000 people with MS, the group found dozens of genetic variants significantly associated with the disease2. An intriguing proportion of these variants fall near genes related to the immune system, bolstering the notion that MS is fundamentally an auto-immune disease that leads to brain degeneration, rather than the other way round. “This disease has an astonishingly immunological flavour,” says Alastair Compston, head of clinical neurosciences at the University of Cambridge and another founding member of the IMSGC.

The hope, Compston says, is that studying these variants will point researchers towards shared biological pathways that would make good targets for drugs.

The big screen

The deluge of candidate genes still leaves researchers a long way short of understanding how genes and the environment interact to cause MS, however. The number of people with auto-immune disorders has risen several-fold in the past few decades, suggesting a strong role in MS for non-genetic factors, such as smoking and vitamin D deficiency. “Finding out what the environmental factors are, and where they interact with genes, that's where the money is,” says Oxford University neurology professor George Ebers, “because that's what you can alter”.

In the mid-1970s, Ebers and Compston were on independent teams that linked a particular part of the MHC to MS3,4. The MHC is a large, 140-gene section of the genome that supports the immune system. These early studies tied MS to so-called class II MHC genes, which make molecules found on immune cells. “It all seemed very straightforward: MS genetics equals MHC equals immunology, end of story,” says Compston.

Studies had shown that when one identical twin has MS, the chance that the other one does too is around 30%. But because only a fraction of this heritability could be explained by variants in the MHC, researchers kept searching for genetic clues. Over the next 20 years, however, no one found any genetic links to MS outside the MHC. “We went into a kind of 35-year void,” Compston recalls.

Some investigators thought the problem was sample size, and that the studies were too small to have the statistical power needed to detect variants that only increase risk by a small amount. To find these, they would need to screen many more people. As a result, several collaborations were formed in the United Kingdom and United States, culminating in 2002 in the IMSGC and, five years later, in the completion of the first large association study of MS.

Immune links

For the consortium's most recent report, published in August 2011, researchers screened 9,772 individuals with MS and 17,376 healthy controls; they pinpointed 57 variants that were significantly associated with the disease. Of the genes implicated by these variants, many are shared with other autoimmune diseases, whereas just two show up in other neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease. Many variants fall near genes involved in a biological pathway that controls the activation of T cells (white blood cells that help to fight infection).

But the consortium's work did not stop there. An upcoming meta-analysis focuses on another 5,000 cases and adds 50 disease-linked variants. This meta-analysis, which the consortium plans to publish in 2012, pools data from published studies and identifies about 100 variants in all, according to Hafler.

With the new list of variants, “we can begin to assemble these networks and really understand at the molecular level what predisposes somebody to develop MS”, says neurologist Philip De Jager of the Brigham and Women's Hospital in Boston, Massachusetts, a member of the consortium. “There's this huge web of interactions.”

Several other association studies are more deeply probing the connections between MS and other auto-immune disorders. Hafler's team has published an analysis of the overlap of variants implicated in MS, Crohn's disease, lupus, type 1 diabetes and other conditions. They found many overlapping pathways; for example, many disease-linked genes are related to interleukin 23, a signalling protein that helps trigger inflammation.

The IMSGC is working on a similar project on a much larger scale. Researchers are using the Immunochip — a gene chip made by Illumina of San Diego, California, that screens for nearly 200,000 genetic variants that have been implicated in about a dozen autoimmune diseases. The guiding idea, De Jager says, is that “all these genes will set your thermostat a certain way”, leading to an immune system that's vulnerable to various developmental or environmental factors. “Maybe if you encounter a particular virus and smoke, and you have a certain collection of variants, you develop Crohn's disease, but if you have a slightly different collection, you develop MS,” he explains. “We don't know how this all works yet.”

Environmental factors

A handful of the variants identified in these association studies highlight one of the most talked-about environmental factors for MS: vitamin D deficiency. Some studies have reported that people with MS have abnormally low levels of vitamin D, and, conversely, that high levels of the vitamin in the blood decrease the risk of getting the disease. Most of the evidence of a link comes from indirect studies of sun exposure, which is by far the largest source of vitamin D. For instance, high-latitude regions tend to have higher rates of MS than low-latitude regions.

Other research suggests that a mother's lack of vitamin D can affect her child. For example, a study pooling data from 42,000 people in Canada, Britain, Denmark and Sweden suggests that a mother's lack of sunlight exposure during the second trimester of pregnancy contributes to the baby's risk of getting MS. Significantly more people with MS were born in May (with the second trimester being the low-sunlight months of November to February), and significantly fewer people with MS were born in November, says Ebers, who led the study.

In 2010, Ebers and colleagues screened the entire genome for all the places where vitamin D can bind. They found that vitamin D influences the expression of 229 genes, many of which are linked to auto-immune diseases5, including MS. This result suggests a mechanism for the vitamin D hypothesis: if an individual doesn't get enough vitamin D, these genes are expressed abnormally, causing MS.

Hints of the vitamin D link also appear in the study published in August 2011, Ebers notes. It found that people with MS carry several variants near genes that encode proteins that help the body activate vitamin D. This proximity, he says, could be a sign that even if they get enough vitamin D, these individuals do not activate the vitamin properly, increasing their risk of disease.

Epidemiological studies have also shown that smoking and exposure to the Epstein–Barr virus are important risk factors for MS. “But vitamin D is one of the front-runners,” says geneticist Jacob McCauley of the University of Miami in Florida. Still, McCauley points out, as with any disease, the link between genetic predisposition and environmental exposure is extremely difficult to study. Teasing out meaningful associations would mean asking thousands of people to recall accurately how often they have been exposed to air pollution, for example, or how much time they have spent in the sun. “The key thing we want to begin to do is combine the environmental with the genetic, to look for interactions,” McCauley says. “It's an area that several of us in the IMSGC feel is lacking in our current studies.”

Keep it in the family

Some researchers are exploring the possibility that the gut microbiome — the mixture of microorganisms in the intestine — is an important environmental factor that influences an underlying genetic predisposition toward MS. “The gut plays a central role in the immune response but has been neglected for decades,” says neurologist Sergio Baranzini of the University of California, San Francisco.

To explore this idea, Baranzini's group and others are genetically screening fecal samples from individuals with MS to see whether they harbour abnormal numbers of various bacterial species. They then plan to sequence the entire genomes of some of these species to see how their genes and proteins might be interacting with those of their host.

Another approach to teasing apart nature and nurture is to compare the genes of twins. In 2010, Baranzini and colleagues sequenced the genomes of two identical female twins, only one of whom had MS. The researchers also sequenced part of the epigenome — the chemical changes to DNA that help determine which genes get turned on — from two other pairs of twins.

The study failed to find any genetic or epigenetic differences between any of the twins. This could mean that only those with MS were exposed to a particular environmental factor. Alternatively, the coverage — that is, the number of times the sequencing machines read the DNA, which correlates with accuracy — could have been too low, Baranzini says.

His team is now sequencing the genomes of a multi-generation family in which several members have MS. They hope to find rare variations in the genome that hit some of the same pathways implicated by the studies of common variants. “We're moving to an even higher depth of coverage, but at a fraction of the cost and a fraction of the time it used to take,” Baranzini says. “That's where the field is going now — sequencing and the search for rare variants.”

Unmasking and, eventually, deciphering this complex code has always been the goal of MS gene researchers, especially the handful of scientists who crowded round the laptop in that English pub. But as the list of genetic clues grows, it is becoming clear how long that may take. “What we have now is a fundamental roadmap of the pathways for the next generation of scientists studying the disease,” Hafler says. “If you want results tomorrow, it ain't gonna happen.”