Nature, Nurture, and What’s in Between

Sifting through DNA

While investigators are debating whether multiple sclerosis is caused, in part, by infections, smoking, or a lack of vitamin D, no one is doubting the involvement of genes. MS is clearly heritable, with 15% to 20% of patients having a close relative with the disease. When it comes to the genetics of MS, researchers are asking which genes matter, and how.

Dozens of genes are thought to contribute to the disease. The most certain player is a particular version of a gene in the HLA (human leukocyte antigen) family, members of which encode proteins that play key roles in the immune system. The variant, HLA-DRB1*1501, more than doubles an individual’s chances of getting MS. Geneticists have identified dozens of other gene variants, or alleles, associated with MS in genome-wide association studies (see “Genetic Associations”). A report published last August by the International Multiple Sclerosis Genetics Consortium brought the total number of MS-associated variants up to 57 (IMSGC, 2011). Furthermore, the report pointed to an additional 50 that showed signs of being linked to MS but did not reach statistical significance. Future studies will elucidate whether chance caused these alleles to appear disproportionately in individuals with MS.

To predict how the MS-associated DNA variants might contribute to the disease, researchers look at the genes they reside in or near. The majority of genetic variants identified thus far are well positioned to cause aberrations in immune responses: The HLA proteins, for instance, help display antigens, typically small chunks of self or nonself proteins, to T cells, and the first non-HLA locus confirmed in MS, the interleukin-7 receptor alpha chain (IL7RA), promotes maturation of B and T cells (Gregory et al., 2007).

Immune-related functions for MS-risk genes make sense to researchers because the immune system seems to provoke much of the central nervous system damage that underlies MS. However, Sergio Baranzini, a geneticist at the University of California, San Francisco, cautions against making assumptions. Even when genes are known for their role in immunity, he says, they might also operate in nervous-system pathways or elsewhere (Baranzini et al., 2009).

Crossed paths: Gene-gene and gene-environment interactions

Genes, of course, don’t act in a vacuum. Genetic variations can exert additional influence when one gene’s product teams up with that of another gene—or with a factor from outside the body. If these interactions amount to more than the sum of their parts, they might explain a conundrum in MS genetics research: Having a family member with MS increases a person’s risk by more than 20-fold, but researchers estimate that—at least with simple models—the known variants account for only about 20% of that boost (IMSGC, 2011). “If you add up all of the genetic risk factors we’ve identified in MS, they don’t account for why heritability can be quite high in families,” says Maja Jagodic, a neuroimmunologist at Karolinska University Hospital in Stockholm. “There’s a missing heritability.” Perhaps the elusive chunk derives from the collision of numerous genetic and environmental factors.

Researchers see plenty of indications that these liaisons occur. “A person can have alleles associated with MS and not have the disease, or they can have MS and be EBV [Epstein-Barr virus]-negative and have plenty of vitamin D,” says Amit Bar-Or, a neurologist at the Montreal Neurological Institute and Hospital of McGill University in Canada and an Accelerated Cure Project scientific adviser. “No one risk factor can predict the disease, so whether we like it or not, we have to recognize that there must be multiple factors interacting.”

Investigators are probing for such associations in multiple ways. For instance, they are checking whether particular MS-implicated gene variants magnify or shrink one another’s effects and whether easily manipulable influences, such as vitamin D, alter the activity or behavior of such genetic trouble spots. They are also delving into other potential mechanisms by which risk factors might team up—and uncovering new relationships by looking for provocative patterns in population-based studies. For instance, one study showed that smoking doubles the risk of MS in individuals who carry MS-susceptibility gene variants compared with those who do not (Hedström et al., 2011). Smoking and these particular genetic variants seem to synergize in a way that fosters MS, the authors suggest. Such work—and other studies like it—opens an avenue toward further research and can also point to prevention strategies, even before the detailed mechanism emerges.

In spring 2011, researchers uncovered a crossroads at which multiple MS-associated genes and vitamin D meet (Mkhikian et al., 2011). This intersection exists along a biochemical pathway, called N-glycosylation, that adds sugars to proteins or lipids. Disrupting this process in rodents triggers symptoms characteristic of MS. Multiple genes play a role in N-glycosylation, and the researchers learned that the process falters in mice with the MS-associated variants of IL2RA and IL7RA. However, if the MS-associated variant of a different gene—MGAT1—is present as well, the process runs smoothly. The variant boosts production of an enzyme involved in N-glycosylation whose quantities slump in the presence of the troublesome versions of IL7RA and IL2RA. Additionally, vitamin D counteracts the effect of the IL2RA and IL7RA variants on N-glycosylation; animals given vitamin D₃ supplements did not get sick. The finding illustrates how the interaction between risk factors could be less intuitive than investigators imagine, says immunologist and study author Michael Demetriou of the University of California, Irvine. “It’s an example where two people might have identical genetic risk factors, and depending on whether or not they are vitamin D deficient, they’ll have a different outcome.” Dissecting a crucial biochemical process such as N-glycosylation, he says, might be a good place to start learning about how gene variants function in MS.

Other putative interactions between genes and the environment have yet to accumulate this much experimental evidence. But researchers have some leads that stem from factors, such as low blood levels of vitamin D, that have been linked to an increased risk of MS (see “The Sunshine Suspect”). Vitamin D influences bodily processes including cell proliferation and immune-system regulation when it sets off a chain of events that eventually governs gene expression. To learn whether DNA and vitamin D meet in a way that leads to MS, researchers are checking whether the bioactive form of the vitamin, calcitriol, changes the activity of genes associated with the disease. In 2009, Sreeram Ramagopalan, a geneticist at the Wellcome Trust Centre for Human Genetics in Oxford, U.K., and his colleagues demonstrated that the vitamin selectively activates HLA-DRB1*1501 (Ramagopalan et al., 2009). However, results from other groups are not consistent with that idea, says Pierre-Antoine Gourraud, a neurologist at the University of California, San Francisco (who is an MSDF scientific adviser). In order to understand how vitamin D might influence MS predisposition through HLA-DRB1, researchers must learn how the nutrient changes the activity of the various versions of the gene, and how those variants influence physiological pathways.

Vitamin D and MS also converge at a gene called CYP27B1, which encodes a protein that helps convert the vitamin into its bioactive form. According to one study—but not some others—patients with MS harbor variations in the gene more commonly than do healthy individuals (Ramagopalan et al., 2011). However, it’s not clear that genetic defects in the vitamin D–synthesis pathway lead to MS because patients with CYP27B1 mutations don’t generally face obvious problems caused by vitamin D deficiency, such as the bone disease rickets. Ramagopalan says the paradox might be explained by the fact that the troublesome variants are rather rare and are typically accompanied by a normal copy of the gene; in this situation, the vitamin’s concentrations might be decreased enough to cause immune-related problems but not bone ailments. In support of the idea, he and his colleagues have reported on three individuals with MS and rickets who each harbor a pair of mutated CYP27B1 genes, and on MS patients with a single miscreant copy of the gene who have low levels of calcitriol (Ramagopalan et al., 2010; Ramagopalan et al., 2011).

Epigenetics explorations

Sometimes environmental factors leave their “mark” on DNA—or the proteins that DNA winds around—changing gene activity for a lifetime. These marks consist of chemical groups that render genes more or less accessible to molecules that turn them on or off. Studying this phenomenon, an example of epigenetics, appeals to MS investigators because it could account for why risk factors linked to MS, such as a lack of vitamin D in utero, occur years before disease onset. A chemical adornment doesn’t cause trouble until the gene it’s bound to is expressed.

What’s more, if epigenetic changes can be passed to the next generation, they might help explain why half-siblings of a person with MS might be more likely to develop the disease if the individuals share a mother than if they share a father (Ebers et al., 2004). Gene modifications related to the disease might be distinct in women, perhaps due to a female-specific hormonal profile or other gender-related physiology. If so, the relevant genes—because they’re chemically embellished differently in men and women—might confer a greater risk when they come from mom than when they come from dad, Ramagopalan says.  

Molecular evidence of epigenetics has only begun to appear in the MS scientific literature. So far, researchers have learned that infectious mononucleosis seems to presage addition of methyl groups on MS-susceptibility genes, among others (Burrell et al., 2011). And in other fields, smoking and stress, two risk factors for MS, have been shown to cause disease-related epigenetic changes in animals and people (Siomi et al., 2011; Launay, 2009).

In addition to discovering the factors capable of causing epigenetic modifications to DNA, researchers need to understand the way each chemical decoration perturbs the pathways it modifies. For example, the addition of acetyl groups to particular proteins might contribute to demyelination in MS, says Patrizia Casaccia, a neuroscientist at Mount Sinai School of Medicine in New York City. Acetyl additions relax the winding of DNA around molecular balls that consist largely of proteins called histones, thereby easing access to factors that turn genes on or off, she says. Her team found that the histones in postmortem brains of MS patients harbor unusually large amounts of acetylation near genes that encode myelin-production inhibitors (Casaccia-Bonnefil et al., 2008; Pedre et al., 2011). Acetylation might harm patients by permitting excessive production of proteins that block myelin production, she speculates. If inhibitor quantities swell, normal wear and tear on myelin might not be repaired and could become a permanent problem, Casaccia says. However, because brain tissue derives from cadavers, the timing of events is impossible to pin down and it’s unclear whether acetyl groups were added before or after disease onset. “It’s like trying to guess what a movie was about based on the last scene,” she says.

From genetics to interventions

Although therapies based on genetic data are not around the corner, MS geneticists are attempting to use what they know to identify who is at risk for the disease. Baranzini’s group, for instance, is developing models to calculate the cumulative risk of individuals who inherit one, two, or 50 genes, and Philip De Jager’s group, at Harvard Medical School in Boston, is collecting information about environmental exposures and genetic risk factors from people who have a relative with MS in the hope of devising an algorithm that can predict who is at highest risk of developing MS. Such an algorithm could lead to the design of studies that explore the transition from health to MS and might eventually lead to strategies that identify individuals who would benefit from early preventive intervention.

Likewise, studies in MS epigenetics have a long climb ahead. But eventually, the research could pay off in new treatments. For instance, drugs currently on the market reverse harmful epigenetic effects by inhibiting enzymes involved in histone deacetylation and other epigenetic processes, Jagodic says. “The beauty of epigenetic modifications is that they may be reversible,” she adds. Researchers who pioneer epigenetic studies in MS realize answers might come slowly, but they’re not deterred. “We’re really just at the start of this,” Ramagopalan says. “It took 10 to 15 years to get where we are now in genomic studies. With epigenomics, it will be the same.”

Key open questions

• How do genetic variants associated with MS affect gene function, and how might they predispose a person to MS?
• How might these or other genetic variants promote disease activity once it’s already begun?
• Can we combine the MS-associated genetic variants in a way that predicts who is at highest risk of MS?
• How do different levels of vitamin D alter the expression of genes associated with MS?
• Which environmental risk factors cause epigenetic modifications of MS-associated genes, and what are the effects of these chemical adornments in each case?

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Thumbnail image on landing page. “Ridderkerk interchange," Mawijk, 2006. Released under Creative Commons Attribution-Share Alike 3.0 Unported License CC BY-SA 3.0.