Disease Double Whammy

Crohn’s disease and Parkinson’s disease are now linked by the LRRK2 gene

At the 2016 Summer Olympics in Rio, seven years after being diagnosed with Crohn’s disease (CD), Kathleen Baker set a swimming world record and bagged two medals. It was after she had just set two national swimming records for her age group back in 2010. Diagnosed, but with no effective treatment, she would suffer from stomach cramps, nausea, and whooping cough, dividing her time between doctors’ offices and pool practice. Baker’s story is even more remarkable considering that she will never be cured of CD. She gives herself biweekly injections. Like Baker, the other million or so CD patients worldwide, usually diagnosed in their teenage years, fight similar battles—they try to keep alive their dreams of going to college, getting married, and pursuing careers.

Dr. Judy Cho, Professor of Medicine and Gastroenterology at Mount Sinai, heads a research group that works to identify the genetic bases of CD and related inflammatory diseases. The researchers hope that understanding the complex network of interdependent molecular processes in cells will lead to a cure. CD is extremely challenging to treat and manage, but Cho finds treating CD to be personally rewarding. “CD is my favorite disease to treat, because I wound up treating a lot of young adults with whom I could make a big difference,” Cho said.

One big step towards a better understanding of CD was recently taken in a study led by Cho and Inga Peter, Professor of Genetics and Genomic Sciences at Mount Sinai. This four-year-long study, involving 51 collaborators from 26 institutions, identified mutations in the LRRK2 gene (pronounced “lurk-two”) strongly associated with CD. Since LRRK2 has long been known to be the major genetic cause for the neurodegenerative disorder Parkinson’s disease (PD), this study provides a direct link between seemingly unrelated CD and PD and hints at a common molecular basis for both diseases.

From its inception, this genetic study was unusual—the researchers did not start with a hypothesis. Like any other disease, they knew that certain variants in the genetic code were responsible for CD. As such, they began by screening hundreds of thousands of possible gene variants in order to compare the genes of CD patients with those of healthy subjects. This initial comparison was done on 5,699 Ashkenazi Jewish patients, since CD is more common in this population.

The researchers succeeded in identifying two categories of mutations: risk mutations, which were more likely to be found in CD patients, and protective mutations, which were more common in healthy subjects. The mutations were determined to lie within the LRRK2 gene, which was implicated in cellular processes central to CD. The strong association between LRRK2 and PD raised many questions, and it gave the project a direction.

To establish a proper link between CD and PD, the researchers focused on individual mutations and expanded their screening to include 24,570 CD and PD cases plus healthy controls. Ultimately, the individual variants associated with CD were also strongly linked to PD; furthermore, they correlated in the same direction—risk variants for CD were also risk variants for PD, and vice versa. This suggested a similar genetic architecture underlying the two diseases.

At this point, a problem arose. Mutations in LRRK2 are inherited together with those in its gene neighbors, so association signals were also being detected from its neighboring regions. To prove that it was LRRK2 responsible for CD and not a neighboring gene, the researchers turned to computational biology. They constructed a model of all gene-gene interactions in the intestine, and then stripped it down to the essential CD genes, intentionally excluding the genes known to be involved in PD, including LRRK2. They then ran a simulation of CD, knowing that only the genes required for CD would be pulled back into their system. LRRK2 was the only gene in its neighborhood that came up.

Up to this point, the researchers had been working based on statistical evidence alone. Now came the most challenging part: to determine whether the identified LRRK2 variants indeed led to biological effects. Peter and her coworkers recalled CD carriers registered with Mount Sinai Medical Center, from whom they obtained blood for biological testing. “For a genetic epidemiologist, functional studies are the most frustrating because you have no control over the data,” Peter said. The risk variant worked—in functional studies, cells that carried this variant exhibited traits characteristic of experimental models of CD and PD. Unexpectedly, there was no indication that the most strongly correlated protective variant had any functional significance. The researchers had seemingly wasted a whole year of collecting and testing blood samples.

Peter and her coworkers quickly moved on to the second most promising neighboring protective variant; testing revealed that it was the variant actually responsible for CD. Interestingly, all people who were recalled for additional blood draws had both protective variants, which explained why the statistical evidence alone was misleading. This costly detour lays out an important lesson in genetic studies. “In this type of analysis, statistical significance is not everything,” Peter said. Often, statistics cannot account for the complexity of biological processes.

Having confirmed the effects of the mutations on human cells, the researchers moved on to the clinical scale, where they examined the effects of LRRK2 mutations on the disease course. They found that the risk mutation led to CD onset at a younger age, so Peter wants to include LRRK2 mutations as markers during genetic screening, which would allow clinicians to determine whether a patient is susceptible to CD early on.

For Peter, incorporating LRRK2 in genetic screening is just a first step. The discovery that the risk mutation leads to an overactive LRRK2 protein implies that drugs could be developed to inhibit LRRK2 and, thus, treat CD. Many PD studies have shown encouraging results. In one study, LRRK2 inhibitors were found to rescue brain cell degeneration in mice. In trying to reverse PD, however, the inhibitors also had unforeseen effects on other cells that use LRRK2. More research is needed on this cell type-specific targeting. The protective variant is a promising candidate, as it reflects the natural biochemical pathways that cells evolved to protect themselves against CD.

Regardless of whether a drug can be developed, this study has far-reaching implications for PD treatment. PD is notoriously hard to treat because it does not show symptoms until years after its onset, at which point treatment is no longer effective. As CD has an earlier age of onset, clinicians can use the identified LRRK2 mutations to determine which CD patients are at high risk of PD and administer preventative measures.

Ultimately, the discoveries made use of a multipronged treatment of mountains of data, including computational biology, statistical analysis, as well as clinical and functional studies. “No one sophisticated bioinformatics approach will allow you to get to the bottom of the problem,” Peter said. She believes that this study demonstrates an important research strategy: attack the problem from as many angles as possible, and then confirm, confirm, and reconfirm the findings.

CD is still far from curable. Based on the findings in this study, Peter and her coworkers are examining the effect of LRRK2 inhibitors on reversing colon inflammation in mice. This push is driven by the promise of genetics in answering many biological problems. “I think we’re going to enter a golden age of medicine, where instead of being a descriptive science, medicine is going to be a molecular science,” Cho said.