Researchers led by the University of Dundee’s Professor Dario Alessi have developed a new method of measuring the activity of disease-causing mutations in the LRRK2 gene, a major cause of inherited Parkinson’s disease.

The team believes this research could help pave the way for future development of a clinical test that could facilitate evaluation of drugs to target this form of the condition.

Mutations in the LRRK2 gene are the most common cause of genetic Parkinson’s disease. The most common disease-causing mutation in this gene increases the activity of the LRRK2 protein three-fold, implying this may contribute towards the symptoms of the disease in patients. It also suggests that drugs that reduce the activity of the protein (LRRK2 inhibitors) may help treat patients with this form of inherited Parkinson’s disease.

“It is important to better understand how disruption in LRRK2 biology causes Parkinson’s disease and whether a drug that targeted the LRRK2 enzyme would offer therapeutic benefit,” said Professor Alessi, lead author on the study.

“Current drug treatments only deal with symptoms of the condition, such as tremors, but do not affect the progression of Parkinson’s disease. An important question is whether an LRRK2 therapy might have potential to slow progression of the condition, which no other current therapy is able to do.”

When the LRRK2 protein is active it stops another cellular protein called Rab10 from fulfilling its function in the body. There are many proteins in the Rab family, and a number of them have been shown to be low in number or deactivated in different forms of Parkinson’s disease.

The new method of measuring these was developed by a collaboration of researchers from Dundee, The Michael J. Fox Foundation for Parkinson’s Research, GSK and the University of Hong Kong. It analyses how much of the Rab10 protein has been deactivated – a process where phosphate groups are added to the Rab10 molecules by the LRRK2 protein – as a measure of heightened LRRK2 protein activity.

This new experimental assay is straightforward, requires only small amounts of sample material and is suitable for adapting to analyse large samples. This contrast with current mass spectrometry technology that is more complex and cumbersome and requires larger sample sizes.

While acknowledging that more work is needed, the researchers believe this breakthrough could help with future drug developments for patients with this form of Parkinson’s disease.

Professor Alessi continued, “The prediction is that elevation of LRRK2 activity leads to Parkinson’s disease, and this is now testable using our assay. The expectation is that if a sub-group of patients can be identified with elevated LRRK2 activity, these individuals might benefit most from LRRK2 inhibitors.

University of Dundee www.dundee.ac.uk/news/2016/lab-method-sheds-light-on-how-genetic-mutations-cause-inherited-parkinsons-disease.php

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Scientists have captured new images of a calcium-shuttling molecule that has been linked to aggressive cancers. The three-dimensional structure could help researchers develop novel therapies and diagnostic tools for diseases that are caused by a malfunction in calcium adsorption.

Alexander Sobolevsky’s lab at Columbia University Medical Center is studying a family of proteins called “Transient receptor potential (TRP)” channels. These proteins line surfaces inside the body, such as the intestine, and form pores that help calcium cross a dense barrier of lipid and protein called the membrane to reach the interior of the cell.

“Scientists have found that a TRP channel variant, called TRPV6, is present in excess amounts in the tumour cells of some cancer patients,” says senior author Alexander Sobolevsky, PhD, who is an assistant professor in the Department of Biochemistry and Molecular Biophysics at Columbia University Medical Center. “And patients who have higher quantities of TRPV6 seem to have a more aggressive form of the disease.”

In order to uncover how these channels guide calcium into the cell, and how disease can occur when this process becomes unregulated, Sobolevsky’s lab used a technique called X-ray crystallography. This process involved growing crystals of TRPV6 and exposing them to an X-ray beam. The scientists then used the diffraction pattern produced by the X-rays to map out a 3D model of the protein.

The structure—which represents a single frozen state of the channel—reveals that the surface of TRPV6 pore is lined with negative charges. This configuration helps attract calcium ions, which are positively charged. The calcium ions are then shuffled from location to location inside of the pore, up to three molecules at a time, as they pass through into the cell.

“In future, we could use this model to design drugs that can target some types of tumour cells by plugging up TRP channels on their surfaces,” says Sobolevsky.

Ordinarily the calcium ingested from our diet is used by the body to regulate a variety of processes including the beating of the heart, muscle contractions, and brain signalling. In addition to various forms of cancer, altered calcium uptake and TRPV6 expression has also been linked to Crohn’s and kidney stone diseases in mouse models. Further research needs to be done to determine the extent that alteration in TRP channel activity leads to disease progression.

Columbia University Medical Center newsroom.cumc.columbia.edu/blog/2016/07/15/new-structure-calcium-shuttling-molecule-help-scientists-target-aggressive-cancers/

Researchers from the National Institutes of Health and their colleagues identified the genetic cause and a possible therapeutic target for a rare form of paediatric progressive neuropathy. Neuropathy, damage or disease affecting the peripheral nervous system, can range from rare conditions linked to a patient’s exome to more common causes like diabetes and viral infections. Neuropathies can affect both motor and sensory neurons, producing muscle weakness, numbness, pain, and a wide range of symptoms.

These types of discoveries underscore the importance of the families who volunteer to participate in clinical research. “This case superbly illustrates how the intensive study of children with very rare neurological disorders can lead quickly to a deep knowledge of a specific genetic condition, as well as uncover mysteries of the nervous system relevant to a wide spectrum of disorders,” said Walter J. Koroshetz, M.D., director of NINDS.

In their report, researchers examined a 10-year-old child with early onset, progressive neuropathy primarily affecting his ability to walk, grasp, and perform fine motor skills. When the patient’s complete genetic makeup, or genome, was analysed, a mutation was found in the gene associated with the protein KCC3. This protein is important for the ability of cells to respond to swelling.

When a neuron swells, KCC3 is involved in the mechanism that drives fluid out, returning the cell to normal. In the absence of this protein (in what is called a loss-of-function mutation), extreme swelling of the neurons can occur, which in turn leads to nerve damage.

In the study, the patient’s mutation affected the ability of KCC3 to turn off once it was no longer needed, leading to the opposite effect—shrunken neurons that also fail to communicate properly. This is referred to as a gain-of-function mutation, causing the affected protein to behave in a new and damaging way.

“This protein, KCC3, has been connected to other forms of neuropathy in the past,” said Carsten G. Bonnemann, M.D., a senior investigator in the Neuromuscular and Neurogenetic Disorders of Childhood Section at NINDS and a senior author of the paper. “What’s unique here is that this is the first time that we have seen a gain-of-function mutation in the KCC3 protein that leads to neuropathy.”

NIH www.nih.gov/news-events/news-releases/novel-genetic-mutation-may-lead-progressive-loss-motor-function

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