The first patient was a mystery.

Arriving at Duke six years ago at the age of three, the youngster had mild developmental delays and physical characteristics that included a large body and large head circumference. A genetic analysis showed mutation of a specific gene, known as ASXL2, which had never been singled out as causing disease.

The youngster’s doctor, Vandana Shashi, a professor of paediatrics for the Division of Medical Genetics at Duke University School of Medicine, told his parents their son likely had a rare and yet-unidentified disease. And she promised to remain vigilant if any other cases popped up in the medical literature that might provide additional clues.

After none turned up, Shashi set out to see if the mystery case might be solved, instead, using the tools of the Undiagnosed Diseases Network (UDN) at the National Institutes of Health, which links Duke and six other medical teaching sites around the country. The participating centres pool information and innovations about diseases that are so rare they often stump the broader medical community.

Within just six weeks — connected to other UDN research labs and an international database of genes and disease characteristics called GeneMatcher — Shashi had a remarkable trove: Five additional children, all with the same physical features and the ASXL2 gene mutation.

“We can now definitively say this is a newly identified disease,” Shashi said. “With just one case, we could not say the gene mutation was the underlying cause. But with six cases, all with the same ASXL2 mutation, it is definitive.”

The new disease, which still has no name, does have similarities to two other rare genetic disorders arising from related genes. A condition called Bohring-Opitz syndrome is the result of a mutation of the ASXL1 gene, while Bainbridge-Ropers syndrome is caused by a flaw in the ASXL3 gene. Both conditions are also rare, and result in similar, but more severe impairments.

It’s unknown how the ASXL2 genetic mutation arises, but Shashi said identifying the root cause of the children’s condition is a first step, and could help drive new therapies and treatment approaches.

The immediate benefit is to the families of the children, who now have an answer to their most basic question.

“It has been wonderful to be connected to other families who share this genetic condition,” said Teresa Locklear, whose son, Issac, was the first patient to present with the mutation at Duke. “When we started, we hoped we would find other families with children who were older than Isaac, to provide a sort of roadmap for what to expect. But it turns out, Isaac is the oldest and we are the ones sharing our experiences with parents of younger children, and that’s been so rewarding.”

Study co-author Loren del Mar Peña, assistant professor in the Department of Pediatrics at Duke, said reducing isolation for families with a rare disease has tremendous impact.

“These families feel truly alone when their child clearly has a disorder, and yet there is no name for it, and no community of people they can relate to with shared experiences,” Peña said. “This will help them be able to connect with others and compare notes. That’s a huge deal – to know you aren’t the only one and there a five other children out there.”

Duke University corporate.dukehealth.org/news-listing/network-and-gene-tools-help-quickly-identify-new-rare-genetic-disease

Penn State biomaterials scientists have developed a new, inexpensive method for detecting salt concentrations in sweat or other bodily fluids. The fluorescent sensor, derived from citric acid molecules, is highly sensitive and highly selective for chloride, the key diagnostic marker in cystic fibrosis.

‘Salt concentrations can be important for many health-related conditions,’ said Jian Yang, professor of biomedical engineering. ‘Our method uses fluorescent molecules based on citrate, a natural molecule that is essential for bone health.’

Compared to other methods used for chloride detection, Yang’s citrate-based fluorescent material is much more sensitive to chloride and is able to detect it over a far wider range of concentrations. Yang’s material is also sensitive to bromide, another salt that can interfere with the results of traditional clinical laboratory tests. Even trace amounts of bromide can throw off test results. With the citrate-based sensor, Yang’s group can distinguish the difference between chloride and bromide. The group is also working to establish a possible new standard for bromide detection in diagnosis of the disease.

Yang is collaborating with Penn State electrical engineer professor Zhiwen Liu to build a handheld device that can measure salt concentrations in sweat using his citrate-based molecules and a cell phone. This could be especially useful in developing countries where people have limited access to expensive analytical equipment.

‘We are developing a platform material for sensing that is low cost, can be automated, requires no titration by trained staff or expensive instrumentation as in hospitals, and provides fast, almost instantaneous, results,’ said Liu.

‘Beyond cystic fibrosis, our platform can also be used for many other diseases, such as metabolic alkalosis, Addison’s disease, and amyotrophic lateral sclerosis. All of those diseases display abnormal concentrations of chloride in the urine, serum or cerebral spinal fluid,’ Yang said.

According to the U.S. National Library of Medicine, cystic fibrosis is a common genetic disease within the white population in the United States. The disease occurs in 1 in 2,500 to 3,500 white newborns. Cystic fibrosis is less common in other ethnic groups, affecting about 1 in 17,000 African Americans and 1 in 31,000 Asian Americans.’

Penn State news.psu.edu/story/426864/2016/09/20/research/low-cost-sensor-cystic-fibrosis-diagnosis-based-citrate

Researchers from ERIBA, Radboud UMC, XJTU, Saarland University, CWI and UMC Utrecht have made a big step towards a better understanding of the human genome. By identifying large DNA variants in 250 Dutch families, the researchers have clarified part of the ‘dark matter’, the great unknown, of the human genome. These new data enable researchers from all over the world to study the DNA variants and use the results to better understand genetic diseases.

Although our knowledge of the human DNA is extensive, it is nowhere near complete. For instance, our knowledge of exactly which changes in our DNA are responsible for a certain disease is often insufficient. This is related to the fact that no two people have exactly the same DNA. Even the DNA molecules of identical twins have differences, which occur during their development and ageing. Some differences ensure that not everybody looks exactly alike, while others determine our susceptibility to particular diseases. Knowledge about the DNA variants can therefore tell us a lot about potential health risks and is a first step towards personalized medicine. Many small variants in the human genome – the whole of genetic information in the cell – have already been documented. Although it is known that larger structural variants play an important role in many hereditary diseases, these variants are also more difficult to detect and are, therefore, much less investigated.

By comparing the DNA of 250 healthy Dutch families with the reference DNA database the researchers were able to identify 1.9 million variants affecting multiple DNA ‘letters’. These variants include large sections of DNA that have disappeared, moved or even appear out of nowhere. When this happens in the middle of a gene that encodes a certain protein, it is likely that the functionality of the gene, and thus the production of the protein, is compromised. However, large structural variants often occur just before or after the coding part of a gene. The effect of this type of variation is hard to predict.

In the paper two occasions are described in which an extra piece of DNA was found just outside the coding region of a gene. In these occasions the variants had a demonstrable effect on the gene regulation. This proves that even structural variants that occur outside the coding regions need to be monitored closely in future DNA screenings. The catalogue of variants provided by this research enables other scientists to predict the occurrence of large structural variants from the known profile of the smaller ones. This technique opens new possibilities for studying the effects of large structural changes in our genomes.

Additionally, the research resulted in the discovery of large parts of DNA that were not included in the genome reference. This ‘extra’ DNA does contain parts that could be involved in the production of proteins. One of the extra pieces of DNA that was described in the paper is a new ‘ZNF’ gene that has previously never been found in humans. Nevertheless it appears to be present in roughly half of the Dutch population. This particular gene is a member of the ZNF gene family that was known from the reference genomes of several species of apes. The new variant will now be added to the human reference database. Authors subsequently showed that this gene is also present in genomes of several other human populations, however its function remains unknown. The fact that these and other pieces of ‘dark matter’ now have been placed on the genetic map enables scientists worldwide to study them and use the results to better understand human genetic diseases.

EurekAlert www.eurekalert.org/pub_releases/2016-10/su-mt100716.php

ETH researchers have discovered a molecule in liver cells that controls the release of fat into the bloodstream. This “lock keeper” is present in large quantities in overweight people and leads indirectly to vascular narrowing.

Anyone attending Munich’s famous Oktoberfest will know it can leave physical traces; fatty foods and plenty of alcohol cause the liver to work overtime. This organ stores a portion of any fat consumed (and also converts alcohol to fat), but releases it again once the revelry is over.

However, should the excesses continue – and if they are not offset by exercise and sport – the person becomes overweight and diabetic, leading to a condition known as fatty liver. If corrective action is taken in time, the liver can usually recover completely from its fatty degeneration. In severe cases the organ becomes inflamed – a condition that is almost impossible to treat.

Fatty liver is also associated with elevated blood fat values. When the liver becomes fatty it seeks relief by releasing fat into the bloodstream, including “good” fat in the form of high density lipoprotein (HDL), but also “bad” fat, such as low density lipoprotein (LDL), and its precursor, very low density lipoprotein (VLDL).
If the concentration of LDL and VLDL in the blood is too high, vascular constriction forms through atherosclerotic plaques. Should a plaque detach itself, there is a real risk of a vascular blockage, which results in a heart attack or stroke.

Markus Stoffel, Professor of Molecular Health Sciences at ETH Zurich, has been working with his team in collaboration with other scientists in Switzerland, Germany and the US to gain a closer understanding of the connection between excess weight, fatty liver and vascular constriction. And this has led to a surprising discovery: the scientists succeeded to identify a protein in liver cells known as vigilin, which acts as a kind of “lock keeper”. It regulates the release of fats, including VLDL, from the liver into the bloodstream.

The researchers found vigilin in large quantities in the liver cells of overweight mice – and humans. “The level of vigilin in the liver cells of people with fatty livers bears a strong correlation with the percentage of fat in the liver,” explains Stoffel. “In other words, the more fat liver cells contain, the higher the quantity of vigilin.”

In a study the ETH professor and his co-workers demonstrate that the primary function of vigilin is to regulate proteins that transport fat out of the liver. However, the molecule does not bind directly to these transport proteins, but rather to certain points of the associated messenger RNA.
The messenger RNA is the transcription of a gene. It represents the construction plan for the associated protein and is transported from the cell nucleus to the ribosomes. These molecular machines use the messenger RNA to build the protein.

The assumption is that vigilin supplies the ribosomes with the messenger RNA to which it is bound. But it is not just a transport vehicle, it also accelerates production of the associated protein.

One of these proteins “promoted” by vigilin is apolipoprotein B (ApoB), which is responsible for exporting triglycerides from the liver. Triglycerides also promote vascular calcification when present in concentrated form in overweight people.

In order to establish the causal relationship between vigilin and vascular calcification, the researchers stemmed formation of this protein in the livers of mice using a new process of RNA interference. As a consequence of this intervention, these animals suffered far less from atherosclerosis than animals who processed vigilin normally. By contrast, increased vigilin formation led to substantial deposits in the vessels.

“Vigilin intervenes at the level of gene regulation, which has barely been investigated to date,” says Stoffel. Our knowledge of how genes are regulated at the level of DNA is improving all the time. And the regulatory processes by which DNA templates are transcribed into messenger RNA are increasingly understood. But regulation of the step from messenger RNA to protein is something we know much less about. This makes the knowledge that vigilin has a regulatory function at this level all the more valuable. And researchers are particularly excited by the fact that vigilin is the first RNA-binding protein found in the context of fatty livers and diabetes.

ETH Zurich www.ethz.ch/en/news-and-events/eth-news/news/2016/09/vigilin-the-lock-keeper.html