A genetic mutation responsible for a debilitating childhood neurological condition known as Aicardi syndrome has been identified by the Translational Genomics Research Institute (TGen).

In a study researchers identified mutations to a gene known as TEAD1, which not only affects formation of the brain but also the retina, the part of the eye responsible for helping turn light into nerve impulses.

In addition, the TGen study found that – contrary to previous studies – Aicardi syndrome may also occur in boys, as well as girls.

Within five months of birth, children with Aicardi syndrome experience: spasms or seizures; ice-cream-scoop-like divots in the retina known as chorioretinal lacunae; and a partial or complete absence of a key brain structure called the corpus callosum, which normally connects the two sides, or hemispheres, of the brain.

‘Discovering the first gene mutation associated with Aicardi syndrome is a revolutionary finding with many implications about how children with this disorder might be best identified and treated in the future,’ said Dr. Matt Huentelman, Co-Director of TGen’s Center for Rare Childhood Disorders and the study’s senior author.

To identify genetic factors in the cellular pathways involved in AIC, TGen researchers sequenced the genomes of 10 children with the disorder, as well as their parents. By screening the billions of pieces of genetic information, they discovered a mutation in TEAD1.

‘Discovery of a specific genetic change associated with AIC will help improve diagnosis, provide a better understanding of the disease biology, and lead to better treatment approaches,’ said Dr. Vinodh Narayanan, Medical Director of TGen’s Center for Rare Childhood Disorders and one of the study’s authors.
TEAD1 has previously been associated with Sveinsson’s syndrome, an inherited progressive weakening of the eye’s retina and choroid, a layer of nerves and blood vessels that connects the retina to the optic nerves. The TGen study suggests that TEAD1 mutations can lead to other chorioretinal complications, such as chorioretinal lacunae.

The TGen study also found that the children in this study also share a potential pathogenic, or disease-causing, mechanism: the altered expression of genes associated with neuronal development; retinal development; cell-cycle control; and synaptic plasticity, the ability of synapses to strengthen or weaken over time in response to increases or decreases in their activity.

Most surprising was the finding that AIC might also be more common among boys than previously thought because the TEAD1 mutation is on an autosome, a chromosome not linked to sex.

AIC had been strongly presumed by geneticists to be an X-linked-dominant disorder occurring almost exclusively in females. However, no gene on the X chromosome has ever been conclusively associated with AIC.

‘Our study strongly challenges this notion by demonstrating a deleterious mutation of TEAD1 on an autosome,’ said Dr. Isabelle Schrauwen, a Research Assistant Professor in Dr. Huentelman’s lab and the lead author of the study. ‘These findings are of clinical importance because they demonstrate AIC linked to autosomal mutations, and therefore for the first time rule-in a likely much higher frequency of AIC in boys.’ Translational Genomics Research Institute (TGen)

An analysis of five families has revealed a previously unknown genetic immunodeficiency, says an international team led by researchers from Boston Children’s Hospital. The condition, linked to mutations in a gene called DOCK2, deactivates many features of the immune system and leaves affected children open to a unique pattern of aggressive, potentially fatal infections early in life.

As the researchers—led by Kerry Dobbs and Luigi Notarangelo, MD, of Boston Children’s Division of Allergy and Immunology—reported today in the New England Journal of Medicine, DOCK2 deficiency may be detectable by newborn screening and is curable with a hematopoietic stem cell transplant (HSCT).

Genetic immunodeficiencies, such as X-linked severed combined immunodeficiency (X-SCID) or Wiskott-Aldrich syndrome (WAS), are a group of devastating conditions where mutations to specific genes cause either functional defects in or interfere with production of T-cells and other components of a patient’s immune system. These defects increase a patient’s susceptibility to a range of severe infections at an early age.

Conditions for which the causative genes are known, such as X-SCID, can be screened for at birth, allowing for early detection and, when appropriate, curative treatment with a hematopoietic stem cell transplant.

‘Until recently, a correct diagnosis for babies born with SCID or other combined immunodeficiencies, such as DOCK2 deficiency, could be made only after these babies had developed serious infections, which could lead to death or compromise the efficacy of an HSCT,’ said Notarangelo, who is a professor of pediatrics at Harvard Medical School. ‘Newborn screening for these diseases is now available for most babies with SCID born in the USA, and this gives increased chances of definitive cure by performing the transplant while the baby is still well.’

In the current study, Notarangelo, Dobbs and their colleagues at the Rockefeller University and the Center for Molecular Medicine in Austria, conducted genetic, genomic and immunological analyses on five patients from Lebanon, Finland, Turkey and Honduras/Nicaragua who early in life demonstrated symptoms indicating a severe but distinctive immunodeficiency, one that left patients susceptible to a broad range of infections but particularly vulnerable to viruses. Three out of the five patients were born of closely related parents, and three were successfully treated by HSCT.

The team discovered through whole exome sequencing that all five patients harboured mutations in DOCK2, mutations that rendered the DOCK2 protein inactive. The mutations had profound effects on multiple aspects of the patients’ immune systems, causing a profound decrease in T-cells and defects in T-, B- and natural killer (NK) cell function.

The study data show that defects in DOCK2, which helps immune cells react to external chemical signals, can have a profound effect on several aspects of immunity, including unforeseen affects on how non-immune cells (such as cells of the skin) respond to viruses.

Notarangelo noted that the data expand the field’s understanding of the basic molecular mechanisms underlying human immunity, while adding a new diagnostic target for newborn screening. Boston Children’s Hospital

Chemists at Caltech have developed a new sensitive technique capable of detecting colorectal cancer in tissue samples—a method that could one day be used in clinical settings for the early diagnosis of colorectal cancer.

Colorectal cancer is the third most prevalent cancer worldwide and is estimated to cause about 700,000 deaths every year. Metastasis due to late detection is one of the major causes of mortality from this disease; therefore, a sensitive and early indicator could be a critical tool for physicians and patients.

A paper describing the new detection technique by Caltech graduate student Ariel Furst (PhD ’15) and her adviser, Jacqueline K. Barton, the Arthur and Marian Hanisch Memorial Professor of Chemistry, are the paper’s authors.

‘Currently, the average biopsy size required for a colorectal biopsy is about 300 milligrams,’ says Furst. ‘With our experimental setup, we require only about 500 micrograms of tissue, which could be taken with a syringe biopsy versus a punch biopsy. So it would be much less invasive.’ One microgram is one thousandth of a milligram.

The researchers zeroed in on the activity of a protein called DNMT1 as a possible indicator of a cancerous transformation. DNMT1 is a methyltransferase, an enzyme responsible for DNA methylation—the addition of a methyl group to one of DNA’s bases. This essential and normal process is a genetic editing technique that primarily turns genes off but that has also recently been identified as an early indicator of cancer, especially the development of tumours, if the process goes awry.

When all is working well, DNMT1 maintains the normal methylation pattern set in the embryonic stages, copying that pattern from the parent DNA strand to the daughter strand. But sometimes DNMT1 goes haywire, and methylation goes into overdrive, causing what is called hypermethylation. Hypermethylation can lead to the repression of genes that typically do beneficial things, like suppress the growth of tumours or express proteins that repair damaged DNA, and that, in turn, can lead to cancer.

Building on previous work in Barton’s group, Furst and Barton devised an electrochemical platform to measure the activity of DNMT1 in crude tissue samples—those that contain all of the material from a tissue, not just DNA or RNA, for example. Fundamentally, the design of this platform is based on the concept of DNA-mediated charge transport—the idea that DNA can behave like a wire, allowing electrons to flow through it and that the conductivity of that DNA wire is extremely sensitive to mistakes in the DNA itself.

In the present study, Furst and Barton started with two arrays of gold electrodes—one atop the other—embedded in Teflon blocks and separated by a thin spacer that formed a well for solution. They attached strands of DNA to the lower electrodes, then added the broken-down contents of a tissue sample to the solution well. After allowing time for any DNMT1 in the tissue sample to methylate the DNA, they added a restriction enzyme that severed the DNA if no methylation had occurred—i.e., if DNMT1 was inactive. When they applied a current to the lower electrodes, the samples with DNMT1 activity passed the current clear through to the upper electrodes, where the activity could be measured.

‘No methylation means cutting, which means the signal turns off,’ explains Furst. ‘If the DNMT1 is active, the signal remains on. So we call this a signal-on assay for methylation activity. But beyond on or off, it also allows us to measure the amount of activity.”

Using the new setup, the researchers measured DNMT1 activity in 10 pairs of human tissue samples, each composed of a colorectal tumour sample and an adjacent healthy tissue from the same patient. When they compared the samples within each pair, they consistently found significantly higher DNMT1 activity, hypermethylation, in the tumorous tissue. Notably, they found little correlation between the amount of DNMT1 in the samples and the presence of cancer—the correlation was with activity.

‘The assay provides a reliable and sensitive measure of hypermethylation,’ says Barton, also the chair of the Division of Chemistry and Chemical Engineering.  ‘It looks like hypermethylation is good indicator of tumourigenesis, so this technique could provide a useful route to early detection of cancer when hypermethylation is involved.’ Caltech

Studies on mice reveal that a special protein in the brain’s tiniest blood vessels may affect the risk of stroke. Peter Carlsson, professor in genetics at the University of Gothenburg, and his research team are publishing new research findings about how the blood-brain barrier develops and what makes the capillaries in the brain different from small blood vessels in other organs.

The brain’s smallest blood vessels differ from those in other organs in that the capillary walls are much more compact. The nerve cells in the brain get the nutrients they need by molecules actively being transported from the blood, instead of passively leaking out from the blood vessels.

This blood-brain barrier is vital, because it enables strict control over the substances with which the brain’s nerve cells come into contact. It has a protective function that if it fails, increases the risk of stroke and other complications.

The smallest blood vessels, the capillaries, have a type of cell called pericytes. These are essential to the development of the blood-brain barrier. Pericytes are also found in other organs, and researchers have previously been unable to find out what gives the brain’s pericytes this unique ability.

The Gothenburg research team has found that the brain’s pericytes contain a protein, FoxF2, which is not present in the pericytes of other organs, and which coordinates the changes that make the blood vessels compact. FoxF2 is needed in order for the blood-brain barrier to form during foetal development.

“Mice that have too little or too much FoxF2 develop various types of defects in the brain’s blood vessels,” explains Peter Carlsson, professor at the University of Gothenburg’s Department of Chemistry and Molecular Biology.

In humans, researchers have noted that major changes in a region of chromosome 6 have been associated with an increased risk of stroke, but it has not been known which of the genes in the area are responsible for this risk.

“The FoxF2 gene is an extremely interesting candidate, as it is located right in the middle of this region, and research is under way now in collaboration with clinical geneticists to investigate the extent to which variations in the FoxF2 gene affect people’s risk of suffering a stroke,” says Peter Carlsson. University of Gothenburg

Infectious diseases such as hepatitis C and some of the world’s deadliest superbugs — C. difficile and MRSA among them — could soon be detected much earlier by a unique diagnostic test, designed to easily and quickly identify dangerous pathogens.

Researchers at McMaster University have developed a new way to detect the smallest traces of metabolites, proteins or fragments of DNA. In essence, the new method can pick up any compound that might signal the presence of infectious disease, be it respiratory or gastrointestinal.

‘The method we have developed allows us to detect targets at levels that are unprecedented,’ says John Brennan, director of McMaster’s Biointerfaces Institute, where the work was done.

‘The test has the best sensitivity ever reported for a detection system of this kind — it is as much as 10,000 times more sensitive than other detection systems,’ he says.

Using sophisticated techniques, researchers developed a molecular device made of DNA that can be switched ‘on’ by a specific molecule of their choice — such as a certain type of disease indicator or DNA molecule representing a genome of a virus — an action that leads to a massive, amplified signal which can be easily spotted.

Another important advantage of the new test, say researchers, is that the method does not require complicated equipment so tests can be run at room temperature under ordinary conditions.

‘This will be the foundation for us to create future diagnostic tests,’ explains Yingfu Li, a professor in the Departments of Biochemistry and Biomedical Sciences, Chemistry and Chemical Biology.

‘This invention will allow us to detect anything we might be interested in, bacterial contamination or perhaps a protein molecule that is a cancer marker. Our method can sensitively detect all of them, and it can do so in a relatively short period of time.’

Researchers are currently working to move the test onto a paper surface to create a portable point-of-care test, which would completely eliminate the need for lab instruments, allowing users — family physicians, for example — to run the test.

The Biointerfaces Institute has developed a series of paper-based screening technologies which enable users to generate clear, simple answers that appear on test paper indicating the presence of infection or contamination in people, food or the environment. McMaster University