Virginia Tech researchers have identified a biomarker in pre-diabetic individuals that could help prevent them from developing Type II diabetes.

The researchers discovered that pre-diabetic people who were considered to be insulin resistant — unable to respond to the hormone insulin effectively — also had altered mitochondrial DNA.

Researchers made the connection by analysing blood samples taken from 40 participants enrolled in the diaBEAT-it program, a long-term study run by multiple researchers in the Fralin Translational Obesity Research Center and funded by a grant from the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK).

Participants did not have diabetes or cardiovascular disease, but were pre-diabetic and showed signs of insulin resistance.

Blood samples revealed participants had lower amounts of mitochondrial DNA with a higher amount of methylation — a process that can change the expression of genes and mitochondrial copy numbers in cells — than healthy people.

Mitochondrion is responsible for converting chemical energy from food into energy that cells can use.

‘If the body is insulin resistant, or unable to respond properly to insulin, it could affect a person’s mitochondrial function and overall energy levels,’ said Zhiyong Cheng, an assistant professor of human, nutrition, foods, and exercise in the College of Agriculture and Life Sciences and a Fralin Life Science Institute affiliate. ‘Mitochondrial alterations have previously been observed in obese individuals, but this is the first time we’ve made the molecular link between insulin resistance and mitochondrial DNA changes.’

Cheng and collaborator Fabio Almeida, an assistant professor of human nutrition, foods and exercise in the College of Agriculture and Life Sciences and a Fralin Life Science Institute affiliate, think this link could be important for treating pre-diabetic individuals to prevent Type 2 Diabetes.

According to the NIDDK, more than 2 out of 3 adults are considered overweight and more than 1 out of 3 adults are considered obese. The growing epidemic of obesity is largely attributed to energy overconsumption — taking in more food calories than the body burns through physical activity.

‘There is no known cure for Type 2 diabetes, and early diagnosis and intervention is critical to prevent this disease,’ said Almeida. ‘Discovery of the biomarker in obese, pre-diabetic individuals advances our understanding of how diabetes develops and provides evidence important for future diagnosis and intervention.’ EurekAlert

When it comes to needles and drawing blood, most patients agree that bigger is not better. But in the first study of its kind, Rice University bioengineers have found results from a single drop of blood are highly variable, and as many as six to nine drops must be combined to achieve consistent results.

The study examines the variation between blood drops drawn from a single finger-prick. The results suggest that health care professionals must take care to avoid skewed results as they design new protocols and technologies that rely on finger-prick blood.

“We began looking at this after we got some surprising results from our controls in an earlier study,” said lead investigator Rebecca Richards-Kortum, Rice’s Malcolm Gillis University Professor and director of Rice 360°: Institute for Global Health Technologies. “Students in my lab are developing novel, low-cost platforms for anaemia, platelet and white blood cell testing in low-resource settings, and one of my students, Meaghan Bond, noticed there was wide variation in some of the benchmark tests that she was performing on hospital-grade blood analysers.”

The benchmark controls are used to gauge the accuracy of test results from the new technology under study, so the variation among the control data was a sign that something was amiss. What wasn’t immediately clear was whether the readings resulted from a problem with the current experiments or actual variations in the amount of haemoglobin, platelets and white blood cells (WBC) in the different drops of blood.

Richards-Kortum and Bond designed a simple protocol to test whether there was actual variation, and if so, how much. They drew six successive 20-microliter droplets of blood from 11 donors. As an additional test to determine whether minimum droplet size might also affect the results, they drew 10 successive 10-microliter droplets from seven additional donors.

All droplets were drawn from the same finger-prick, and the researchers followed best practices in obtaining the droplets; the first drop was wiped away to remove contamination from disinfectants, and the finger was not squeezed or “milked,” which can lead to inaccurate results. For experimental controls, they use venipuncture, the standard of care in most hospitals, to draw tubes of blood from an arm vein.

Each 20-microliter droplet was analysed with a hospital-grade blood analyser for haemoglobin concentration, total WBC count, platelet count and three-part WBC differential, a test that measures the ratio of different types of white blood cells, including lymphocytes and granulocytes. Each 10-microliter droplet was tested for haemoglobin concentration with a popular point-of-care blood analyser used in many clinics and blood centres.

“A growing number of clinically important tests are performed using finger-prick blood, and this is especially true in low-resource settings,” Bond said. “It is important to understand how variations in finger-prick blood collection protocols can affect point-of-care test accuracy as well as how results might vary between different kinds of point-of-care tests that use finger-prick blood from the same patient.”

Bond and Richards-Kortum found that haemoglobin content, platelet count and WBC count each varied significantly from drop to drop.

“Some of the differences were surprising,” Bond said. “For example, in some donors, the haemoglobin concentration changed by more than two grams per deciliter in the span of two successive drops of blood.”

Bond and Richards-Kortum found that averaging the results of the droplet tests could produce results that were on par with venous blood tests, but tests on six to nine drops blood were needed to achieve consistent results.

“Finger-prick blood tests can be accurate and they are an important tool for health care providers, particularly in point-of-care and low-resource settings,” Bond said. “Our results show that people need to take care to administer finger-prick tests in a way that produces accurate results because accuracy in these tests is increasingly important for diagnosing conditions like anaemia, infections and sickle-cell anemia, malaria, HIV and other diseases.” Rice University

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