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“Researchers find new risk regions associated with primary biliary cirrhosis”

“Researchers have newly identified three genetic regions associated with primary biliary cirrhosis (PBC), the most common autoimmune liver disease, increasing the number of known regions associated with the disorder to 25.

The team used a DNA microchip, called Immunochip, to survey more thoroughly regions of the genome known to underlie other autoimmune diseases to discover if they play a role also in PBC susceptibility. By combining the results from this survey with details of gene activity from a database called ENCODE, they were able to identify which cells types are most likely to play a role in PBC.

PBC affects approximately one in every three thousand people in the UK, and one in a thousand women over the age of 40. Inflammation in the bile ducts blocks the flow of bile, damaging the liver cells and causing further inflammation and scarring, and in severe cases will result in the need for a liver transplant.

There is currently no cure for PBC, so treatment is focused on slowing down the progression of the disease and treating any symptoms or complications that may occur. The biological pathways underlying primary biliary cirrhosis are poorly understood, although autoimmunity, where the body attacks its own cells, is known to play a significant role.

“Previous genetic screens have identified 22 regions of the genome underlying PBC risk, and many of these are known to play a role in other autoimmune diseases, such as multiple sclerosis and type I diabetes,” says Dr Carl Anderson, co-senior author from the Wellcome Trust Sanger Institute. “Using the Immunochip we were able to perform a much more thorough screen of the genomic regions previously associated with other autoimmune diseases. This resulted in us identifying a further three regions involved in PBC risk and identifying additional independent signals within some of those we already knew about.”

The advantage of Immunochip over genome-wide technologies is that it focuses only on regions of the genome known to be associated with an autoimmune disease and thus captures more of the genetic variation within these regions. Immunochip can therefore be used to more thoroughly test these key candidate genes for association to a whole-host of immune-related traits, and identify low frequency and rare genetic variants associated with disease that would likely be missed by a microarray that covers a broader range of genetic regions.

The researchers found five genomic regions with multiple independent signals associated with the disorder, with one small region on chromosome 3 harbouring four independent association signals. These findings suggest that densely genotyping or sequencing known disease regions will be a powerful approach for identifying additional genetic risk variants and for further elucidating the role of rare genetic variation in complex disease risk.

“This study has allowed us to better understand the genetic risk profile of PBC and, by comparing our results with similar studies of other autoimmune diseases, we hope to further characterise the genetic relationship between this group of clinically diverse but biologically related disorders” says Dr Richard Sandford, co-senior author from the University of Cambridge “Over the next few years we will be extending our studies to search for genetic variants that affect disease course and treatment response. We hope that our studies will have a clinical impact, either directly through a more personalized approach to treatment or indirectly by furthering our understanding of the biological pathways underlying PBC leading to new treatments.”

The most associated genetic variant within the newly implicated TYK2 gene was a low-frequency variant previously associated with multiple sclerosis (MS) that changes the coding sequence of the gene. Previous studies in MS have shown that individuals that carry a single copy of this variant have significantly reduced TYK2 activity, suggesting that modulation of TYK2 activity might represent a new therapeutic approach for the treatment of PBC.

“This study is an example of how people with rare conditions like primary biliary cirrhosis can work together with scientists and physicians to find a path towards drug targets and treatments for these diseases,” says Collette Thain, MBE, Chief Executive of the PBC Foundation. “Although this is just the beginning of a long road to finding the genetic basis of PBC, with each study we are moving closer and closer to finally understanding and tackling this disease.” – article from The Wellcome Trust Sanger Institute

PacBio RS and 454 DNA sequencing at engencore.sc.edu

“Ecosystems with a high degree of biodiversity can cope with more stress, such as higher temperatures or increasing salt concentrations, than those with less biodiversity. They can also maintain their services for longer, as botanists and ecologists from the universities of Zurich and Göttingen have discovered. Their study provides the first evidence of the relationship between stress intensity and ecosystem functioning.

Higher average temperatures and increasing salt concentrations are stress factors that many ecosystems face today in the wake of climate change. However, do all ecosystems react to stress in the same way and what impact does stress have on ecosystem services, such as biomass production? Botanists and ecologists from the universities of Zurich and Göttingen demonstrate that a high level of biodiversity aids stress resistance.

Higher number of species leads to greater stress resistance

The scientists studied a total of 64 species of single-celled microalgae from the SAG Culture Collection of Algae in Göttingen. These are at the bottom of the food chain and absorb environmentally harmful CO2 via photosynthesis. “The more species of microalgae there are in a system, the more robust the system is under moderate stress compared to those with fewer species,” says first author Bastian Steudel, explaining one of the results. Systems with a higher number of species can thus keep their biomass production stable for longer than those with less biodiversity.

In all, the researchers studied six different intensities of two stress gradients. In the case of very high intensities, the positive effects of biodiversity decreased or ceased altogether. However, increasing stress in systems with few species had a considerably more negative impact than in those with high biodiversity levels. “The study shows that a high degree of biodiversity under stress is especially important to maintain biomass production,” says Steudel’s PhD supervisor Michael Kessler, summing up the significance of the research project.

Literature:

Bastian Steudel, Andy Hector, Thomas Friedl, Christian Löfke, Maike Lorenz, Moritz Wesche, Michael Kessler. Biodiversity effects on ecosystem functioning change along environmental stress gradients. Ecology Letters. 5 September, 2012. doi: 10.1111/j.1461-0248.2012.01863.x” – article from the University of Zurich

PacBio RS and 454 DNA sequencing at engencore.sc.edu

“Study examines the genetic architecture of gene activity in twins to functionally link genes involved in human disease”

“A new study points the way to discover genetic variants that affect human health. It is the first study to use unique sets of samples from twins that mean the team can unpick the relative contributions of genetic variants in the genome and the environment in controlling activity of key genes.

The team’s method enabled them to establish a functional link for more than 350 putative disease-causing genetic variants, including cancer, skin disease, immune system disease and obesity, to a specific gene. Their study also shows the way in which new approaches will be able to uncover the ‘missing’ variants important for human disease.

Genetic researchers have, since the decoding of the human genome, identified thousands of genetic variants associated with human disease. In many cases, these variants are relatively common in human populations (perhaps one in twenty people), but their effects are often rather slight. These statistical associations often involve multiple genes and both the genes and variants that are the direct cause of the disease remain, for the most part, unknown.

In this project, the team looked at the effects that genetic variants had on activity of thousands of genes in three tissue types from more than 850 twins. Twin studies – use both identical twins which are genetically identical and non-identical twins – can help to tease out the role of genes and the role of environment: if two people are genetically identical, differences in disease development is most likely to be due to environmental influences.

They hoped to uncover genetic variants that drove different levels of activity of one or more genes. These variants could be important in development of disease.

“We generated the most precise estimates to date of how heritable gene activity is in humans, and this was made possible by using the twins,” says Elin Grundberg, lead analyst in the study, from the Wellcome Trust Sanger Institute and King’s College London. “We found that variants that lie close to genes, called cis variants, account for 30-36 per cent of the genetic component in gene activity.”

The team measured the activity of thousands of genes in three tissues – skin, adipose and cell lines derived from blood: these tissues are important for disease from eczema to cancer. They then looked to see if different levels of activity were associated with different genetic variants in the human genome. They looked at variants that lay close to each gene, called cis variants, as well as those that lay elsewhere, called trans variants.

They found thousands of regions in the genome where gene activity was different in the tissue samples. For 358 of these, they found a candidate association between the genetic variant, the altered gene activity and a disease, homing in on the causative gene.

The twin samples enabled them to look in more detail at inheritance of variants that affect gene activity. They estimate that about half of the genetic effects remain to be uncovered, residing in variants that are relatively rare in humans.

“This is the first time that anyone has looked at the contribution of genetic and non-genetic factors to gene activity in tissues from twins, a set of samples that allow us to unpick the genetics of human disease,” says Tim Spector, Head of the Department of Twin Research, from King’s College London. “We are grateful to all the volunteers in the TwinsUK study: without them and their altruistic gift, we wouldn’t be able to make these advances in this way. For the first time we are able to quantify the contribution of rare regulatory variants to gene expression levels.” says Emmanouil Dermitzakis, Louis-Jeantet Professor of Genetics, University of Geneva Medical School. “This is a great step in elucidating the identity and contribution of such rare regulatory variants to complex disease risk”

Importantly, the twins sample set and the associated issue studies meant the team could uncover in greater depth the influence of variants at a distance – trans variants – on gene activity. Such variants tend to be master regulators of gene activity, affecting many genes, but also tend to be active in one tissue, suggesting each tissue has a set of such regulators.

The results are from the MuTHER (Multiple Tissue Human Expression Resource) project, and the research was led by Panos Deloukas from the Wellcome Trust Sanger Institute, Tim Spector from the Department of Twin Research and Genetic Epidemiology at King’s College London, Mark McCarthy from the Wellcome Trust Centre for Human Genetics, University of Oxford, and Emmanouil Dermitzakis from the Department of Genetic Medicine and Development at the University of Geneva Medical School, Switzerland.

The team’s experiments provide the foundation and set the requirements for new discovery of trans variants. To tease out these important variants – as well as the rarer cis variants close to genes – will need more samples than used or, indeed, expected.

“Identifying variants which control the activity of many genes is a greater challenge than we anticipated but we are developing appropriate tools to uncover them and understand their contribution to disease,” comments Panos Deloukas, Senior Group Leader, from the Wellcome Trust Sanger Institute. “Modern human genetics combined with samples donated by the participants in studies such as TwinsUK is making great strides towards finding the genetic culprits behind human disease. We are in a period of rich discovery and we must ensure these are made available as widely as we can, to drive the search for new diagnostics and treatments.”

The data are available for the three tissues can be accessed through the browsable Genevar tool at the Sanger Institute website.” – article from the Wellcome Trust Sanger Institute

PacBio RS and 454 DNA sequencing at engencore.sc.edu

“Smoke poisoning can be caused by a number of things, including cyanides, the salts of hydrocyanic acid. Because the quick diagnosis and treatment of victims with cyanide poisoning is critical and often lifesaving, it is very surprising that a cyanide test for emergency situations is not yet available. Now, chemists at the University of Zurich have developed a simple and reliable procedure to detect blood cyanide in less than two minutes.

The main cause of cyanide poisoning is smoke inhalation in closed spaces during fires. Cyanides, the salts of hydrocyanic acid, inhibit cellular respiration and may lead to coma or death. The rapid administration of a cyanide antidote is essential for successful treatment. Previously, detecting cyanide in the blood took up to an hour and could only be performed in the laboratory, a lengthy process that is poorly suited for emergency situations. As a result, emergency doctors and paramedics are forced to administer antidotes based solely on presumptive diagnoses. Now, chemists at the University of Zurich have succeeded in detecting blood cyanide in less than two minutes and without any laboratory equipment: UZH chemists Christine Männel-Croisé and Felix Zelder combined a cyanide color test with an extraction method to produce results quickly and reliably.

The newly developed procedure works with only a tiny drop of blood mixed in a detection vial with a pH buffer, water, and a cobalt-based chemosensor. If the blood contains cyanide, the solid phase of the vial turns purple.

Faster, easier, more versatile

“What I like most about our method is that detection is possible solely with the naked eye, and it needs only a drop of blood,” says Zelder. Quantitative measurements are also possible, thereby enabling emergency responders to determine the grade of cyanide poisoning. The correct dosage of antidote can be chosen, and detoxification can be monitored during treatment. “In principle, our method meets all the requirements for application in emergency situations,” explains Christine Männel-Croisé. Currently, Männel-Croisé and Zelder are in discussion with paramedics to test their method in cases of emergency.

Literature:

Christine Männel-Croisé and Felix Zelder. Anal. Methods, 6 July 2012. doi: 10.1039/c2ay25595b” – article from the University of Zurich

PacBio RS and 454 DNA sequencing at engencore.sc.edu

“Vitamin B12 is vital. In collaboration with colleagues from Canada, Germany and the United States, researchers from Zurich’s University Children’s Hospital and the University of Zurich have succeeded in decoding a novel cause of hereditary vitamin B12 deficiency. They have discovered an important gene that determines how vitamin B12 gets into cells. Their discovery enables the diagnosis and treatment of this rare genetic disease.

Vitamin B₁₂ is vital for cell division, the synthesis of red blood cells and the functioning of the nervous system. Unable to produce the vitamin itself, the human body has to obtain it via animal proteins. So far it has been known that on its way into the cell vitamin B₁₂ is absorbed by little organelles, so-called lysosomes. From there, the vitamin enters the cell interior with the aid of the transport protein CblF, which was discovered by the same research team three years ago. The researchers now show that a second transport protein is actually necessary for this step, thus providing evidence of another cause of hereditary vitamin B₁₂ deficiency.

Gene mutation prevents transport of vitamin B₁₂

The scientists in Switzerland and Canada each examined an individual patient with symptoms of the CblF gene defect, yet without an actual defect in this gene. Using different methods, including sequencing all the coding segments of the genetic information, they were able to identify two mutations in the same gene in both patients.

The gene in question encodes the protein ABCD4, which was previously known as an ABC transporter in other cell organelles, albeit with an insufficiently defined function. It is now clear that it is a vitamin B₁₂ transporter: “We were able to detect ABCD4 in the lysosomes of human skin cells – right next to the already known CblF protein” explains Matthias Baumgartner, a professor of metabolic diseases at Zurich’s University Children’s Hospital. By adding intact ABCD4 protein to the patients’ cells, the researchers were able to rescue the vitamin B₁₂ transport and compensate for the genetic defect. “We also discovered that a targeted change in the ATP binding site of ABCD4 triggered a loss of function,” says Baumgartner. Thus both ABCD4 and CblF proteins are responsible for the transfer of vitamin B₁₂ from the lysosomes into the cell interior, and ATPase activity is involved. Baumgartner concludes: “The results obtained enable the diagnosis and treatment of this hereditary vitamin B₁₂ deficiency.”

Literature:

David Coelho, Jaeseung C. Kim, Isabelle R. Miousse, Stephen Fung, Marcel du Moulin, Insa Buers, Terttu Suormala, Patricie Burda, Michele Frapolli, Martin Stucki, Peter Nürnberg, Holger Thiele, Horst Robenek, Wolfgang Höhne, Nicola Longo, Marzia Pasquali, Eugen Mengel, David Watkins, Eric A. Shoubridge, Jacek Majewski, David S. Rosenblatt, Brian Fowler, Frank Rutsch, Matthias R. Baumgartner. Mutations in ABCD4 cause a new inborn error of vitamin B₁₂ metabolism. Nature Genetics. 26 August, 2012. Doi:10.1038/ng.2386″ – article from the University of Zurich

PacBio RS and 454 DNA sequencing at engencore.sc.edu