Genetic link to severe childhood obesity

Scientists in Cambridge have discovered that the loss of a key segment of DNA can lead to severe childhood obesity. This is the first study to show that this kind of genetic alteration can cause obesity. The results are published 6 December 2009 in Nature.

The study, led by Dr Sadaf Farooqi from the University of Cambridge and Dr Matt Hurles from the Wellcome Trust Sanger Institute, looked at 300 children with severe obesity.

The team scanned each child’s entire genome looking for types of mutation known as copy number variants (CNVs). CNVs are large chunks of DNA either duplicated or deleted from our genes. Scientists believe this type of mutation may play an important role in genetic diseases.

By looking for CNVs that were unique in children with severe obesity, compared with over 7,000 controls (apparently healthy volunteers from the Wellcome Trust Case Control Consortium 2), they found that certain parts of the genome were missing in some patients with severe obesity.

According to Dr Farooqi: “We found that part of chromosome 16 can be deleted in some families and that people with this deletion have severe obesity from a young age.

“Our results suggest that one particular gene on chromosome 16 called SH2B1 plays a key role in regulating weight and also in handling blood sugar levels. People with deletions involving this gene had a strong drive to eat and gained weight very easily.”

Dr Matt Hurles adds: “This is the first evidence that copy number variants have been linked to a metabolic condition such as obesity. They are already known to cause other disorders such as autism and learning difficulties.”

The findings also have implications for diagnosing severe childhood obesity, which has on occasion been misattributed to abuse by parents who have been assumed to be deliberately overfeeding their children and causing their severe obesity.

“This study shows that severe obesity is a serious medical issue that deserves scientific investigation,” says Dr Farooqi. “It adds to the growing weight of evidence that a wide range of genetic variants can produce a strong drive to eat. We hope that this will alter attitudes and practices amongst those with professional responsibility for the health and well-being of children.”

● Citation: Elena G. Bochukova et al. Large, rare chromosomal deletions associated with severe early-onset obesity. Nature, 6 December 2009



Module of genes affects atherosclerosis development

By measuring the total gene activity in organs relevant for coronary artery disease (CAD), scientists at the Swedish medical university Karolinska Institutet have identified a module of genes that is important for the recruitment of white blood cells into the atherosclerotic plaque.

The findings, which are published in the open-access journal PLoS Genetics, suggest that targeting the migration of white blood cells in the development of atherosclerosis may help to reduce the risk for adverse clinical effects such as ischemia and myocardial infarction.

Atherosclerosis is the major cause of myocardial infarction and stroke, and is responsible for half of all deaths in Western countries. Complications of atherosclerosis are rapidly increasing as a major cause of death also in developing countries; the World Health Organisation has predicted that this will become the number one killer this year.

“It has been an exciting research project, which has gone on for nearly seven years, involving many different disciplines from thoracic surgeons to mathematicians,” says team leader Dr. Johan Björkegren at Karolinska Institutet in Stockholm. “I believe that this kind of clinical study will follow in the aftermath of the large number of ongoing genomewide association studies.”

Rather than individual genes or individual DNA variants, the discovery encompasses a group of 128 functionally related genes in a ‘module’ or ‘network’, which explains their mutual interactions. The involvement of most of these genes in CAD has not previously been known, but it has been known that they are involved in endothelial function and angiogenesis.

Through the collaboration with Dr Eric Schadt’s team at Washington University, Seattle, the researchers were also able to take advantage of previously published genome-wide association studies (GWAS) of CAD to show that the gene module they have discovered is enriched for inherited risk of developing myocardial infarction.

“The GWAS are genetic epidemiology studies often involving tens of thousands of patients and controls, originally designed to link isolated DNA locus to the risk of developing complex common disorders, such as atherosclerosis,” says Dr Björkegren. “These studies now need to be complemented with clinical studies where the patients are also screened for intermediate molecular phenotypes in disease-relevant organs. The computational capacities and expertise required to address simultaneously all molecular activities and their relative risk-enrichment are available, all that remains is to start recruiting this kind of cohorts.”

The findings suggest that the severity of atherosclerosis depends on the rate of the migration of white blood cells from the blood into the atherosclerotic plaques. Although this pathway is already known to play a role in atherosclerosis, the Swedish findings suggest that it is the rate limiting step for disease progression. However, Dr Björkegren admits that the exact roles of all 128 genes in atherogenesis remain unexplained. Future studies will focus on understanding the details of how these genes actually contribute to atherosclerosis in cell cultures and animal model systems.

● Citation: Hägg et al. Multi- Organ Expression Profiling Uncovers a Gene Module in Coronary Artery Disease Involving Transendothelial Migration of Leukocytes and LIM Domain Binding 2: The Stockholm Atherosclerosis Gene Expression (STAGE) Study. PLoS Genetics, 2009; 5 (12): e1000754 DOI: 10.1371/journal.pgen.1000754



Faulty body clock may make kids bipolar

Malfunctioning circadian clock genes may be responsible for bipolar disorder in children. Researchers writing in the open access journal BMC Psychiatry found four versions of the regulatory gene RORB that were associated with paediatric bipolar disorder.

Alexander Niculescu from Indiana University School of Medicine, Indianapolis, US, worked with a team of researchers at Harvard, UC San Diego, Massachusetts General Hospital and SUNY Upstate Medical University to study the RORA and RORB genes of 152 children with the condition and 140 control children. They found four alterations to the RORB gene that were positively associated with being bipolar.

Niculescu commented: “Our findings suggest that clock genes in general, and RORB in particular, may be important candidates for further investigation in the search for the molecular basis of bipolar disorder.”

RORB is mainly expressed in the eye, pineal gland and brain. Its expression is known to change as a function of circadian rhythm in some tissues, and mice without the gene exhibit circadian rhythm abnormalities. According to Niculescu: “Bipolar disorder is often characterised by circadian rhythm abnormalities and this is particularly true among paediatric bipolar patients. Decreased sleep has even been noted as one of the earliest symptoms discriminating children with bipolar disorder from those with attention deficit hyperactivity disorder (ADHD). It will be necessary to verify our association results in other independent samples, and to continue to study the relationship between RORB, other clock genes, and bipolar disorder.”

● Citation: Casey L McGrath et al, Evidence for Genetic Association of RORB with Bipolar Disorder, BMC Psychiatry 2009, 9:70doi:10.1186/1471-244X-9-70 www.biomedcentral.com/1471- 244X/9/70



Researchers speed up deciphering histone code

 A team of Princeton biologists and engineers has improved the speed and accuracy of measuring an enigmatic set of proteins that influences almost every aspect of how cells and tissues function. The new method offers a long-sought tool for studying stem cells, cancer and other problems of fundamental importance to biology and medicine.

The research allows scientists an unprecedented look at a special class of proteins called histones, which are at the core of every chromosome and control the way instructions in DNA are carried out. Despite rapid progress in understanding the information encoded in DNA and genes, scientists have achieved much less insight into the so-called “histone code”, which determines why a gene in one cell functions differently than the same gene in another cell.

“We take a cutting-edge approach to a field that has been using more or less the same techniques for the past 15 years,” said Benjamin Garcia, assistant professor of molecular biology, who supervised the experimental aspects of the study.

The technique reduces by a factor of 100 the time it takes to analyse histones, while requiring far less sample material and achieving much more nuanced results than existing methods.

The researchers published their results in the October 2009 issue of Molecular & Cellular Proteomics.

Despite carrying identical DNA, all cells in a body aren't identical - a cell in the kidney looks and functions very differently from one in the brain. What makes this specialisation possible is a set of instructions stored outside of genes or DNA – “epigenetic” information – that helps each cell adapt to its context. Key players in this process are histones, tiny protein spindles that the 6- foot-long DNA molecule wraps itself around in forming a chromosome.

Scientists have long known that histones acquire a variety of small chemical decorations - small molecules attached here and there along the length of the histone. The type and location of these add-ons can regulate nearby genes. Single modifications are known to turn genes on or off, but what happens when multiple modifications occur in combinations – the “histone code” – remains a mystery.

The researchers have developed the first practical means to distinguish between various modified forms of a histone. Under conventional tests two histones with very different functions could appear identical if they have the same set of modifications but at different locations on the molecule. Before now, efforts to distinguish such subtle differences were extremely difficult and time consuming.



The new shape of DNA

Most of us carry a mental picture of DNA in its iconic form – the famous double helix unveiled by Francis Crick and James Watson. But researchers are beginning to develop a new picture of DNA that shows the molecule’s more dynamic side, which is capable of morphing into a large number of complex shapes. This shape-shifting ability permits proteins to attach and read the right region of DNA so genes can be turned on or off at the proper time.

The findings show that proteins are adept at reading nuances in the shape of the double helix. Those variations in shape transmit information about where proteins need to bind to make sure the right genes are activated or silenced during development.

“The ideal double helix should not be viewed as a rigid entity but rather seen as a first approximation to a large set of more complex shapes that are recognised by proteins so as to bind to DNA in a sequencespecific fashion,” said Barry Honig, Howard Hughes Medical Institute investigator at Columbia University.

Honig and his colleagues have discovered a new mechanism by which proteins recognise specific regions of DNA. Their research is reported in the October 29, 2009, issue of the journal Nature.

Scientists have long known that specialised DNA-binding proteins, such as transcription factors that activate and repress genes, look for their docking sites on DNA by scanning the genome for a specific nucleotide sequence that says “bind here”. When proteins recognise that sequence, they bind to DNA and begin to do their jobs. But over the last 20 years, researchers have accumulated evidence that the physical shape of DNA can also influence where and when proteins attach to DNA.

The new studies published in Nature by Honig and his colleagues extend those results and describe a new recognition strategy that proteins use to identify and bind to DNA. The coiled, complementary strands of DNA form ‘major’ and ‘minor’ grooves, to which proteins can bind.

“The question for us was, why is that important?” Honig says. “What we showed is that the electrostatic potential of the DNA – which is used to attract positive charges – is stronger when a groove is narrow.”

They found that narrow minor grooves tended to attract parts of the protein that contained the amino acid arginine, which is positively charged. They saw that there are many arginine binding sites in DNA that have narrower minor grooves and that these have more negative electrostatic potentials that attract positively charged regions of proteins.

“The proteins are actually reading the shape of the DNA through its effect on electrostatic potential,” Honig says. “Sequence determines shape, which determines the affinity for arginines – a mechanism made possible because DNA does not form a perfect double helix.”



Modified stem cell therapy cures adult sickle cell disease

A modified blood adult stemcell transplant regimen has effectively reversed sickle cell disease in nine of 10 adults who had been severely affected by the disease, according to results of a US National Institutes of Health study in the 10 December issue of the New England Journal of Medicine.

“This trial represents a major milestone in developing a therapy aimed at curing sickle cell disease,” said NIDDK Director Griffin P. Rodgers M.D., a co-author of the paper. “Our modified transplant regimen changes the equation for treating adult patients with severe disease in a safer, more effective way.”

In trials by other investigators, nearly 200 children with severe sickle cell disease were cured with bone marrow transplants after undergoing a regimen in which their own marrow was completely destroyed with chemotherapy. That regimen, however, had proven too toxic for adults, who have years of accumulated organ damage from the disease and are less able to tolerate complete marrow transplantation.

In contrast to the established method in children, this adult trial sought to reduce toxicity by only partially replacing the bone marrow. The much longer lifespan of normal red blood cells, compared to sickle red blood cells, allows the healthy cells to outlast and completely replace the diseasecausing cells.

To achieve this goal, the investigators used a low dose of radiation to the whole body and two drugs, alemtuzumab and sirolimus, to suppress the immune system. Alemtuzumab depletes immune cells, but does not adversely affect blood stem cells. Sirolimus does not block the activation of immune cells, but inhibits their proliferation, creating a balance that potentially helps prevent rejection of the new stem cells.

The radiation favorably conditions the bone marrow, where donor stem cells move in and begin producing new, healthy red blood cells. After a median two and a half years follow-up, all 10 recipients were alive and sickle cell disease was eliminated in nine.

“Remarkably, the treatment did not result in graft-versushost disease (GVHD) for any of the participants,” noted Susan B. Shurin, MD, acting director of the NHLBI. GVHD is a common complication of stem cell transplantation and can lead to serious problems, such as rash, diarrhea and nausea, liver disease, or death. “We are continuing to explore better treatments with fewer side effects to help the millions of sickle cell patients worldwide. This is a very important study because it lessens the toxicity of a therapy known to be highly effective.”



Stem cells used to treat eye disease

Newly published research, by investigators, at the North East England Stem Cell Institute (NESCI) in the journal Stem Cells reported the first successful treatment of eight patients with “Limbal Stem Cell Deficiency” (LSCD) using the patients’ own stem cells without the need of suppressing their immunity.

LSCD is a painful, blinding disease that requires long-term, costly treatment with frequent clinic visits and intensive hospital admissions. The vision loss due to LSCD makes this disease not only costly, but often requires social support due to the enormous impact on a patient’s quality of life. This is further magnified by the fact that LSCD mostly affects young patients.

Dr Francisco Figueiredo, a member of the NESCI team, said: “Corneal cloudiness has been estimated to cause blindness in eight million people (10% of total blindness) worldwide each year. A large number of ocular surface diseases, both acquired and congenital, share features of partial or complete LSCD.”

He added that chemical burns to the eye were the most common cause of LSCD.

Professor Lako, another member of the NESCI team, said: “This study demonstrates that transplantation of cultured corneal stem cells without the use of animal cells or products, is a safe and effective method of reconstructing the corneal surface and restoring useful sight in patients with unilateral LSCD.

He added that this research shows promise to help hundreds of people regain their sight and offers a new treatment for people with LSCD.

Professor Michael Whitaker FMedSci, Co-Director of NESCI, which is a collaboration between Durham and Newcastle Universities, Newcastle NHS Foundation Trust and other partners, said: “Stem cells from bone marrow have been used successfully for many years to treat cancer and immune disease, but this is the first successful stem cell therapy using stem cells from the eye without animal products to treat disease. Because the early results look so promising, we are thinking hard now about how to bring this treatment rapidly into the clinic as we complete the necessary clinical trials.”

A larger study involving 24 new patients is currently underway with funding from the UK’s Medical Research Council.

● Citation: Kolli S, Ahmad S, Lako M, Figueiredo F, “Successful clinical implementation of corneal epithelial stem cell therapy for treatment of unilateral limbal stem cell deficiency”, STEM CELLS, 2009, DOI: 10.1002/stem.276