Genes causing defective gut lining

The BBC reports that research comparing the genes of thousands of people with or without ulcerative colitis has found four genes of interest. They affect the lining of the intestine, and in those with ulcerative colitis the lining may be letting excessive bacteria through.

Researcher Dr Miles Parkes, Consultant Gastroenterologist at Addenbrooke's Hospital, Cambridge, said: "We have long suspected that genetic defects in the epithelial barrier are important in ulcerative colitis.

"This large scale genetic study provides the first robust genetic evidence that this is the case."

More detailed information about this research is available from the Wellcome Trust.

With the ever increasing knowledge of genetic factors influencing inflammatory bowel disorders it's only a matter of time before more effective and better targeted treatments can be found.

Ineffective interleukin-10?

The Atlanta Journal-Constitution reports that a small study of children with severe colitis has found a genetic mutation that reduced the effectiveness of interleukin-10 in their immune systems. Researchers are now considering whether a subset of adult Crohn's cases have a similar cause. If so, then a more direct treatment could be found.

One child in the study was completely cured by a bone marrow transplant. Although such transplants have been used for severe Crohn's cases, they are highly risky. This research should assist in determining the efficacy of such a treatment.

Interleukins have been implicated in Crohn's in the past, but this is the first study to target IL-10 in particular. It has been suggested that Crohn's is a blanket term for a variety of IBD conditions of various causes, and this research is another indication that this may be true.

Gene implicated in faulty immune response

Research from McGill University Health Centre has shown a link between a gene mutation present in 25% of Crohn's patients and a lack of immune response to mycobacteria. When this connection is fully understood it may lead to new therapies for Crohn's targeting the NOD2 gene involved.

As explained by the lead researcher, Dr. Marcel Behr:

"Now that we have a better understanding of the normal role of NOD2, we think that a mutation in this gene prevents mycobacteria from being properly recognized by the immune system," explained Dr. Behr. "If mycobacteria are not recognized, the body cannot effectively fight them off and then becomes persistently infected."

The full article is published in the Journal of Experimental Medicine (full article requires subscription).

More Crohn's genes found

There hasn't been much Crohn's news for the past few months, but I expect it to pick up around conference time. In the meantime The Children’s Hospital of Philadelphia has released information about a new technique for finding genes associated with a given disease. The researchers have tested this in the area of Crohn's and already found new genes related to the disease.

In a complex disorder such as Crohn's disease, many different genes interact to cause the illness. Research over the past few years have identified many of the genes with the strongest effects, but many other genes with important roles may produce weaker or ambiguous signals in the large-scale studies, and go overlooked.

For children and adults with Crohn's disease, who suffer the debilitating effects of chronic gastrointestinal inflammation, the emerging gene data may open the doors to more effective treatments. "Blocking cell receptors at some points on a biological pathway may produce clinical improvements, but with side effects to the immune system," said Baldassano. "If we can block other molecules further downstream on a pathway, we may achieve better treatments that may be more specific to an individual patient, with fewer side effects."

The full research is available in The American Society of Human Genetics (pay to view).

32 genes for Crohn's - so far

New research featured in Nature Genetics [full article via subscription] has found many more genes which increase the likelihood of a person developing Crohn's. Each gene helps scientists understand the mechanism of Crohn's better, and offers the potential for new targets of therapies.

The Boston Globe reports further:

The genome research has helped produce a "fundamentally new concept" of Crohn's, said Dr. R. Balfour Sartor, chief medical adviser of the Crohn's and Colitis Foundation of America.

The idea, he said, is that in Crohn's disease, cells in the intestine have trouble using the weapons of the innate immune system - such as autophagy - to get rid of bacteria, so the immune system's second line of defense, big-gun T-cells, get called in, causing inflammation.

Reuters has more:

Significantly, three of the individual genes that have been implicated in Crohn's have previously been shown to influence risk of type 1 diabetes and asthma, suggesting a possible common genetic mechanism underlying these disorders.

As we come closer to identifying the cause of Crohn's we will have medications that attack the cause, rather than the symptoms, of the disease. The identification of related genes will no doubt play an important role in this.

Gene therapy moves closer

A report from the Royal Society of Chemistry describes a potential new treatment for Crohn's that has shown promise in mice. RNA interference, a recently developed method of gene therapy, was used to suppress a gene that causes inflammation in the intestine, thus reducing the related symptoms.

RNA interference involves introducing into cells a double strand of RNA corresponding to the nucleic acid sequence of the target gene. This causes the destruction of the equivalent messenger RNA so 'silencing' the gene and preventing expression of the relevant protein.

Its discovery in 1998 by Andrew Fire and Craig Mello earned them the 2006 Nobel prize for medicine. But although their discovery has become a vital technique for molecular biology research it has not yet fulfilled its potential as a therapeutic method.
...
When RNA was injected into mouse with colitis there was a dramatic reduction in intestinal tissue damage and suppression of leukocytes cells invading the gut wall. The mice were also able to absorb food through their gut wall again and started to regain weight. The team found that their results were due to a drop in the level of two cell signalling molecules (cytokines), TNF-alpha and IL-12, that normally drive inflammation and are produced as a result of cyclin D1 synthesis. They also found that the mice were making more of a protective cytokine called IL-10.

There is a long way to go until this research leads to a safe treatment in humans. For example, at this time not all of the genes involved in Crohn's have been identified. I'm sure that gene therapy would want to be as specific as possible to reduce unintended side-effects.

Major new genetic discoveries

When the results of research are reported in three separate BBC reports you can tell it's important. Firstly, the BBC reported an overview:

A major advance in understanding the genetics behind several of the world's most common diseases has been reported.

The landmark Wellcome Trust study analysed DNA from the blood of 17,000 people to find genetic differences.

...

One of the most exciting finds was a previously unknown gene common to type 1 diabetes and Crohn's disease, a type of inflammatory bowel disorder, suggesting that they share similar biological pathways.

The team also unexpectedly found a process known as autophagy - a process of clearing bacteria from within cells - is important in the development of Crohn's disease.

The BBC then gave more details for each disease involved, including this promising quote:

Dr Miles Parkes, consultant gastroenterologist at Addenbrooke's Hospital and the University of Cambridge said: "The study has substantially advanced our understanding of what causes Crohn's disease.

"There is a lot of follow-up work required to fully understand the impact of the genetic associations that we have identified. However they have already provided some major leads regarding possible new treatment options."

Finally, the BBC did a great easy to read description of how the research came about, how it was performed, and what it means to afflicted people:

For example in Crohn's disease, the team did not expect to find that autophagy - a process of removing unwanted bacteria from within cells - was an important factor.

They now plan to study this further to find out if it is associated with specific bacteria and there are treatments available which effect autophagy that researchers can investigate for use in Crohn's disease.

You can look at the nitty gritty by going directly to Nature, where they note the interesting finding:

An emerging theme from molecular genetic studies of CD is the importance of defects in autophagy and the processing of phagocytosed bacteria. A number of other specific components within innate and adaptive immune pathways are also highlighted.

Amongst their technical details is that there seems to be some relation to

...IRGM (immunity-related guanosine triphosphatase; the human homologue of the mouse Irgm/Lrg47), the strongest signal being at rs1000113 (P = 5.1 times 10-8). IRGM encodes a GTP-binding protein which induces autophagy and is involved in elimination of intracellular bacteria, including Mycobacterium tuberculosis67. Reduced function and/or activity of this gene would be expected to lead to persistence of intracellular bacteria, consistent with existing models of CD pathogenesis57 and the recent ATG16L1 association64 (see above).

This is extremely interesting when you review my earlier blog entry about a possible Crohn's vaccine, which operated on exactly that bacteria.

All of this news leads me to think that it won't be too long before we get a treatment for the cause, rather than the symptoms, of Crohn's.

Genome discoveries

Hot on the heels of the US and Canadian gene findings is another genome-led research article, this time from Belgium. You can read the very technical article online in full at PLoS Genetics. I present the author summary in full here, because the article itself is too complicated for me to summarise:

Individual susceptibility to many common diseases is determined by a combination of environmental and genetic factors. Identifying these genetic risk factors is one of the most important objectives of modern medical genetics, as it paves the way towards personalized medicine and drug target identification. Recent advances in SNP genotyping technology allows systematic association scanning of the entire genome for the detection of novel susceptibility loci. We herein apply this approach to Crohn disease, which afflicts an estimated 0.15% of the people in the developed world and identify a novel susceptibility locus on Chromosome 5. A unique feature of the novel 5p13.1 locus is that it coincides with a 1.25-Mb gene desert. We present evidence that genetic variants at this locus influence the expression levels of the closest gene, PTGER4, located 270 kb away, in the direction of the centromere. PTGER4 encodes the prostaglandin receptor EP4 and is a strong candidate susceptibility gene for Crohn disease as PTGER4 knock-out mice have increased susceptibility to colitis.

More Crohn's genes found

It has now been conclusively shown that genetics plays a role in the development of Crohn's disease, with the release of a study in Nature Genetics (full article available for purchase for US$30). Data from the Human Genome Project was used to compare the genes of people with and without the disease. The ABC mention:

Scientists previously had some indications of a genetic component to Crohn's disease. It tends to run in families and is more common in certain ethnic groups, especially people of central and eastern European Jewish descent.

Pinpointing the genes that predispose people to Crohn's disease could help lead to new ways to treat it, say the researchers.

Amongst all the other areas of research into Crohn's, we shall now have to keep an eye on developments in gene therapy.

Interleukin receptor mutation found

A variety of media outlets have covered the new research that has found a gene mutation relating to the inflammation protein interleukin-23. (The roles of the different interleukins are summarised in the Wikipedia.) In this study, the DNA of people with Crohn's was compared with that of people without Crohn's. A mutation in the interleukin-23 receptor was one of their findings.

The BBC notes:

The fault is in a gene receptor present in healthy people without inflammatory bowel disease but rare in those with the condition.

Further background is provided by the Baltimore Sun:

In 2001, scientists identified the first major gene underlying Crohn's disease. Called Nod2, the gene regulates the immune system's response to bacteria in the gut. People with one flawed copy have twice the normal risk of developing the disease, researchers found. Two flawed copies and the risk jumps 20- to 40-fold.

Researchers have since uncovered a handful of other suspicious gene mutations thought to play a role in inflammatory bowel disease. But the new finding marks the first time researchers have identified a mutation that may actually help protect against Crohn's.

The potential result of this finding is better drug therapies, eventually.

Where'd my gene go?

The German Cancer Research Center, DKFZ have an article which describes a possible genetic cause of Crohn's disease.

Patients with Crohn’s disease of the colon have one copy less than healthy persons of the beta-defensin 2 gene, a gene coding for an important defense molecule of the body.

[...]

Defensins are part of the arsenal of defense weapons used by the human immune system. [...] Patients with Crohn’s disease of the colon (colonic CD) have a lower level of beta-defensins in the mucous membranes.

Defensin genes are arranged in nests, called clusters, on chromosome 8. The number of clusters varies considerably across the population; this is technically called a polymorphism. The research team has now shown that patients with colonic CD have on average only three copies of the gene encoding beta-defensin 2, whereas healthy control persons as well as patients with small bowel CD or ulcerative colitis, another inflammatory bowel disease, have an average of four copies of this gene per cell.

The researchers showed that a lower number of gene copies is indeed associated with reduced production of the endogenous antibiotic, which explains the known low defensin level. They presume that this causes the defense of the intestinal mucous membrane to become porous so that bacteria can attach to and invade the mucous membrane, which leads to the typical inflammatory hot spots of Crohn’s disease.

The purpose of the defensin is described by MedicineNet as:

A family of potent antibiotics made within the body by neutrophils (a type of white blood cell) and macrophages (cells that can engulf foreign particles). The defensins play important roles against invading microbes. They act against bacteria, fungi and viruses by binding to their membranes and increasing membrane permeability.

The DKFZ work is an extension of earlier research published in PNAS which examined the connection between Crohn's disease and reduced defensin levels.

The pathogenesis of Crohn's disease (CD), an idiopathic inflammatory bowel disease, is attributed, in part, to intestinal bacteria that may initiate and perpetuate mucosal inflammation in genetically susceptible individuals. Paneth cells (PC) are the major source of antimicrobial peptides in the small intestine, including human {alpha}-defensins HD5 and HD6. We tested the hypothesis that reduced expression of PC {alpha}-defensins compromises mucosal host defenses and predisposes patients to CD of the ileum. We report that patients with CD of the ileum have reduced antibacterial activity in their intestinal mucosal extracts. These specimens also showed decreased expression of PC {alpha}-defensins, whereas the expression of eight other PC products either remained unchanged or increased when compared with controls. The specific decrease of {alpha}-defensins was independent of the degree of inflammation in the specimens and was not observed in either CD of the colon, ulcerative colitis, or pouchitis. The functional consequence of {alpha}-defensin expression levels was examined by using a transgenic mouse model, where we found changes in HD5 expression levels, comparable to those observed in CD, had a pronounced impact on the luminal microbiota. Thus, the specific deficiency of PC defensins that characterizes ileal CD may compromise innate immune defenses of the ileal mucosa and initiate and/or perpetuate this disease.