Colon cancer is one of the leading causes of cancer-related deaths worldwide, and researchers are hard at work to understand the disease’s complex molecular underpinnings. In a new study researchers from the University of Pennsylvania describe two related genes in the Musashi family that are required for colon cancer to develop, and that may be useful targets for effective treatment.

The work, led by Christopher Lengner, an assistant professor in the Department of Biomedical Sciences in Penn’s School of Veterinary Medicine, challenges a paradigm in the field whereby activation of a molecular signalling cascade known as the Wnt pathway is held responsible for the majority of colon cancer cases in humans. The new findings suggest that the Musashi genes, MSI1 and MSI2, act in a path parallel to the Wnt pathway and may be equally important for driving colon cancer.

The work also indicates that the two genes, which encode RNA-binding proteins, are functionally redundant.

“The data suggest that either MSI protein is sufficient to support cancer,” Lengner said. “If you want to use these proteins as a drug target, you’d have to design a drug that will inhibit both of them.”

While researchers have known for some time that MSI1 was expressed in colon cancer, the mechanism by which it acted and its functional requirement for the disease were not well understood. The related protein MSI2 had not been rigorously examined in the context of colon cancer until earlier this year, when a paper by Lengner and colleagues found that it could trigger activation of cellular metabolic processes that fuel cancerous cells in the intestines.

“Considering the expression patterns of these two proteins during homeostasis, or normal conditions, you would expect their function when they were hijacked by cancer could be similar in supporting tumour growth,” said Ning Li, first author on the study and a postdoctoral fellow in Lengner’s lab.

The current work took both proteins into account. Whereas the prior paper found that MSI2 was consistently overexpressed in intestinal cancer tissue, Lengner and colleagues found that MSI1 was more variable, overexpressed in some samples and under-expressed in others, compared to normal tissue. When they bred mice in which they could induce overexpression of MSI1 in the intestine, the cells of the intestine began to divide rapidly and lost their ability to differentiate, just as mice with inducible overexpression of MSI2 had.

They found that inducing MSI1 turned on a similar set of genes as MSI2 overexpression did, including genes related to RNA processing and translation, necessary processes for manufacturing the required components for cancer’s rapid cell growth. The analysis also revealed that activating MSI1 caused a set of genes to be expressed that match the effect of losing the function of APC, a tumour suppressor gene that is inactivated in more than 80 percent of cases of human colon cancer.

As they had done with MSI2, the researchers also conducted an experiment that reveals the RNA transcripts to which MSI1 binds, and they found high levels of similarity to the set of transcripts bound by MSI2. Notably, both proteins bind tumor suppressors, such as Pten, which activates cellular metabolism through a protein complex called mTORC1. Further experiments confirmed MSI1 promoted mTORC1 activity.

“We concluded that these proteins are functioning in the same pathways and acting redundantly not only because they are binding similar proteins but also because when you overexpress them, the phenotype is identical,” Lengner said. “They appear to have identical oncogenic properties.” Penn News

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