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

Coeliac disease is a chronic, immunological disease that is manifested as intolerance to gluten proteins present in wheat, rye and barley. This intolerance leads to an inflammatory reaction in the small intestine that hampers the absorption of nutrients. The only treatment is a strict, life-long, gluten-free diet.

It has been known for some time that coeliac disease develops in people who have a genetic susceptibility, but despite the fact that 40% of the population carry the most decisive risk factor (the HLA-DQ2 and DQ8 polymorphisms), only 1% go on to develop the disease. ‘What we have here is a complex genetic disease in which many polymorphisms play a role, each making a very small contribution to its development,’ explained the UPV/EHU researcher Ainara Castellanos, who has led the work published in Science.

One of the added risk factors is to be found, according to this research, in the so-called ‘junk’ DNA, in other words, in 95% of the DNA. It is the least-known part because, unlike the remaining 5%, it is not involved in synthesising proteins. Nevertheless, light is gradually being shed on its role in the control of the overall functioning of the genome, in other words, it regulates important processes in our organism such as immune response and that is where it might be possible to find the causes of auto-immune diseases such as coeliac disease.

A key gene in the regulating of the inflammatory response observed in coeliac patients has been found in one of the regions of the junk genome: it is the 1nc13. The ribonucleic acid produced by this gene belongs to the family of long, non-coding RNAs or lncRNA and is responsible for maintaining the normal levels of expression of pro-inflammatory genes. In coeliacs, this non-coding RNA is hardly produced at all so the levels of these inflammatory genes are not properly regulated and their expression is increased. But besides being produced in low quantities, the 1nc13 produced by coeliac patients has a variant that alters the way it functions. ‘That way an inflammatory environment is created and the development of the disease is encouraged,’ said Ainara Castellanos.

‘This study confirms the importance of the regions of the genome previously regarded as ‘junk’ in the development of common complaints such as coeliac disease and opens up the door to a new possibility for diagnosis. Right now, we are interested in finding out whether the low levels of this RNA are an early feature of coeliac disease (and of other immune diseases), which could be used as a diagnostic tool before its onset,’ explained the UPV/EHU’s lecturer in Genetics José Ramón Bilbao, another of the authors of the work. University of the Basque Country

The formation of large numbers of polyps in the colon has a high probability of developing into colon cancer, if left untreated. The large-scale appearance of polyps is often due to a hereditary cause; in this case the disease can occur in multiple family members. Under the leadership of human geneticists of the University Hospital Bonn, a team of researchers discovered genetic changes in the MSH3 gene in patients and identified a new rare form of hereditary colon cancer.

Colon polyps form like mushroom-shaped growths from the mucosa and are several millimetres to several centimetres in size. They are benign and generally do not cause any symptoms – however, they can turn into malignant tumours (colon cancer). Physicians refer to the development of a large number of polyps in the colon as ‘polyposis.’ Scientists have already discovered several genes associated with a polyposis. ‘However, about one-third of families affected by the disease do not have any abnormalities in these genes,’ says Prof. Dr. Stefan Aretz, head of the working group at the Institute of Human Genetics at the University of Bonn Hospital. Therefore, there would have to be even more genes involved in the formation of polyps in the colon.

Together with pathologists from the University Hospital Bonn, scientists from the Yale University School of Medicine in New Haven (USA), and the Frankfurt University Hospital, the team working with Prof. Aretz investigated the genetic material (DNA) of more than 100 polyposis patients using blood samples. In each patient, all of the about 20,000 protein-coding genes known were simultaneously examined. In this process, the scientists filtered the rare, possibly relevant genetic changes out of the gigantic quantity of data, like the proverbial needle in a haystack. In two patients, genetic changes (mutations) were discovered in the MSH3 gene on chromosome 5.

Proof of causes is like a trial based on circumstantial evidence

‘The challenge is proving the causal connection between the mutations in this gene and the disease,’ says Prof. Aretz. The process is similar to that of a trial based on circumstantial evidence. Family members also play a role here: The siblings with the disease have to have these same MSH3 mutations as the patient who was first examined, but not the healthy relatives. That was the case. In addition, the scientists investigated the consequences for patients resulting from the loss of function of the MSH3 gene. ‘It involves a gene for the repair of the genetic material,’ reports Dr. Ronja Adam, one of the two lead authors from Prof. Aretz’s team. ‘The mutations cause the MSH3 protein to not be formed.’ Since the protein is missing in the cell nucleus of the patient´s tissues, there is an accumulation of genetic defects. The mutations which are not repaired then predispose to the more frequent occurrence of polyps in the colon.

The newly discovered type of polyposis, in contrast to many other forms of hereditary colon cancer, is not inherited dominantly, but instead recessively. ‘This means that siblings have a 25 percent chance of developing the disease; however, the parents and children of affected persons only have a very low risk of developing the disease,’ explains Dr. Isabel Spier from the Institute of Human Genetics, who was also very involved in the study.

The annual colonoscopy is the most effective cancer screening method for polyposis patients. As a result, the development of colon cancer can be effectively prevented. By investigating the MSH3 gene, a clear diagnosis can be made prospectively in some other, previously unexplained polyposis cases. Afterwards, healthy persons at risk in the family can be tested for the mutations. ‘Only proven carriers would need to take part in the intensive surveillance program,’ says the human geneticist. In addition, science would gain new insights into the development and biological foundations of tumours through the identification of mutations in the MSH3 gene. Prof. Aretz: ‘The knowledge about molecular mechanisms which lead to cancer is also a precondition for the development of new targeted drugs.’

University of Bonn www.uni-bonn.de/Press-releases/discovery-of-a-novel-gene-for-hereditary-colon-cancer