Researchers from the University of Ottawa Heart Institute (UOHI), together with the teams of Dr. Martin Farrell at Oxford University, and Dr. Sekar Kathiresan at the Broad Institute, have found the answer to an ongoing debate in the cardiovascular scientific world. Dr. Ruth McPherson and Dr. Majid Nikpay, researchers at the UOHI’s Ruddy Canadian Cardiovascular Genetics Centre, report that the genetic basis of heart disease is largely derived from the cumulative effect of multiple common genetic variants, rather than from a few rare variants with large effects.

The study used the data from the 1000 Genomes project in order to obtain information on close to 10 million genetic variants (called SNPs). The analysis involved 60,000 heart disease patients, 120,000 healthy individuals, from a total of 48 studies around the world. Not only is the number of genetic variants much greater than the approximately 1 million previously studied, this is the first time that researchers have been able to study the link of rare genetic variants present in as few as 1 in 1000 people at risk of heart disease.
“Our analysis provides a comprehensive survey of the fine genetic architecture of coronary artery disease (CAD), showing that genetic susceptibility to this common disease is largely determined by common SNPs of small effect size rather than just a few rare variants with large effects,” say the authors of this important study.

Dr. Majid Nikpay, post-doctoral fellow at the Ottawa Heart Institute, also used an alternative statistical method of analysis to find two new risk markers that have an effect only if an individual has inherited two copies of the “bad gene”, that is one from each parent. In addition to discovering a total of 10 new risk markers, by using other statistical approaches, this research team has produced a list of 202 genetic variants in 129 gene regions that together explain approximately 23% of the heritability of coronary heart disease as compared to only 11% reported in previous studies.
“Many of these genetic variants are likely to exert their effects on the walls of arteries, making them more susceptible to the common heart disease risk factors such as cigarette smoking, diabetes and cholesterol,” added Dr Ruth McPherson, Director of the Ruddy Canadian Cardiovascular Genetics Centre at the University of Ottawa Heart Institute.

A number of preventative strategies target the vessel wall (control of blood pressure and smoking cessation), but the large majority of existing drug treatments for lowering CAD risk operate through manipulation of circulating lipid levels and few directly target vessel wall processes. Detailed investigation of new aspects of vessel wall biology that are implicated by genetic association but have not previously been explored in atherosclerosis may provide new insights into the complex etiology of disease and, hence, identify new targets. University of Ottawa Heart Institute

Variations in genes involved in normal bone development are associated with an 8- to 15-fold increased risk for osteonecrosis in young patients with acute lymphoblastic leukaemia (ALL), according to research led by St. Jude Children’s Research Hospital and Children’s Oncology Group investigators.

Osteonecrosis is a major side effect of ALL treatment with chemotherapy. About 15 percent of ALL patients develop the complication, which is caused by reduced blood flow to bones in the hips and other joints and leads bone to break down faster than it is replaced. For patients, the results may include stiffness, pain, disability and joint-replacement surgery. ALL patients aged 10 to 20 years old are at particularly high risk for osteonecrosis.

This study is the first to focus on genetic risk factors for osteonecrosis in ALL patients less than 10 years old, an age group that accounts for about 75 percent of newly identified ALL patients and about half of ALL patients who develop osteonecrosis. Researchers used genome-wide association studies to check the DNA of 1,186 ALL patients less than 10 years old for single changes in the 3.2 billion “letters” or chemical bases that make up the human genetic code.

Researchers checked for genetic variations that were more common in 82 young ALL patients who developed osteonecrosis than in 287 who did not. The screening was then repeated with an additional 817 ALL patients younger than 10 years old. The patients were treated in clinical trials of the Children’s Oncology Group, an international clinical trials group focused exclusively on paediatric cancer.

Patients with osteonecrosis were eight to 15 times more likely to have genetic variations located near BMP7, a gene important for normal bone development.

“The goal of this and earlier studies is to identify and understand genetic and other risk factors for osteonecrosis so we can identify patients at high risk for the side effect and develop interventions to prevent the disease,” said first author Seth Karol, M.D., a St. Jude Physician Scientist Training Program fellow. Karol works with the study’s senior author Mary Relling, Pharm.D., chair of the St. Jude Department of Pharmaceutical Sciences.

A variation in the glutamate receptor gene GRID2 was also associated with a greater likelihood of osteonecrosis in ALL patients younger than 10. GRID2 belongs to a family of genes that carries instructions for assembling receptor proteins on the cell membrane that cells rely on to respond to the chemical messenger glutamate. The finding confirms previous research that reported variations in other glutamate receptor genes were associated with an elevated risk of osteonecrosis, with the prior study primarily identifying the risk in patients aged 10 and older.

“The finding that the genetic variations that affect osteonecrosis risk differ by age was unexpected,” Karol said. “The results suggest that as children age, particularly when bone growth is accelerated during adolescence, certain gene variants may become more or less important.”

Additional research is planned to expand the search for osteonecrosis genetic risk factors to include additional ALL treatment regimens and subtypes of the disease. Working in laboratory models, researchers also plan to study how gene variants affect osteonecrosis risk in order to help lay the groundwork for intervention to prevent the disease. St. Jude Children’s Research Hospital

Research has led to a greater understanding of how certain genetic variants can ‘switch’ on or off the regulatory elements which control the expression of genes and ultimately the manifestation of an individual’s characteristics and disease predispositions.

These variants are found in regions of the genome which are not directly responsible for coding genes, but which instead have a regulatory function. Not much is yet known about these regions, however, research into how the variants work could eventually lead to new clues about how human diseases might be understood at a genetic level and, ultimately, controlled.

“We know many genetic variants are associated with different diseases, but since most of them lie in the non-coding part of the genome, we often don’t know what the precise mechanisms underlying these associations are,” explains Judith Zaugg, who led the study at EMBL. “Our results, and the computational approaches we have developed mean it will now be possible to take these variants and link them back to the regulatory network within the DNA to identify the specific gene that is associated with them. This might enable us to unravel the causal mechanisms behind certain inherited diseases.”

‘Switches’ controlling gene expression might be far apart on DNA strand, but close in 3D space.

Key to the process are regions in the non-coding part of the DNA that harbour specific sequences, called enhancers and promoters. These are responsible for activating the expression of a particular gene. Promoters are located close to the gene they regulate. Enhancers, in contrast, can be far away from their target gene in terms of genomic location and might require physical interaction with the promoter of a gene to propagate the activity signal. One of the big challenges in understanding how genes are controlled is to link these enhancers to their target genes.

In this study, the team has generated molecular profiles from 75 human individuals that were sequenced as part of the 1000 Genomes Project – an international collaboration to produce an extensive catalogue of human genetic variation.

They used epigenetic marks to identify enhancers and promoters within the subjects’ genome and, using a second technology (Hi-C) were able to map how enhancers and promoters were interacting in three-dimensional space. As well as charting the specific interactions between promoters and enhancers using genotype information, the team were able to find genetic associations between physically interacting regions of the genome, thus providing evidence for functional interactions between enhancers and promoters.

Map of genetic ‘switches’ will pave the way for understanding the molecular basis of complex genetic diseases.

An unexpected finding was that often it was not only genetic variants in enhancers that were associated with gene expression, but also regulatory elements in promoters of a distal genes that were physically and genetically connected to the gene of interest.

Genes are known to physically interact with multiple enhancers. In addition, the team also discovered that some promoters are genetically controlled by two or more enhancers, meaning that the enhancers either work in combination to affect gene expression or compensate each other. For example, if one individual lacks a particular enhancer there might be a backup enhancer that could compensate for the loss. Such a compensation mechanism could explain why it is so difficult to identify the causal variants of complex genetic diseases.

“The approach we used enables us to map links between genes and their regulatory elements,” says Fabian Grubert, who led the work at Stanford University, in Michael Snyder’s lab. “Further studies in different tissues will add even more detail to the map, and hopefully will allow us to identify all the enhancers and promoters that influence a single gene under different conditions.” EMBL

A simple, ultrasensitive microRNA sensor developed by researchers from the School of Science at Indiana University-Purdue University Indianapolis, the IU School of Medicine and the IU Melvin and Bren Simon Cancer Center holds promise for the design of new diagnostic strategies and, potentially, for the prognosis and treatment of pancreatic and other cancers.

In a study the IUPUI researchers describe their design of the novel, low-cost, nanotechnology-enabled reusable sensor. They also report on the promising results of tests of the sensor’s ability to identify pancreatic cancer or indicate the existence of a benign condition by quantifying changes in levels of microRNA signatures linked to pancreatic cancer.

‘We used the fundamental concepts of nanotechnology to design the sensor to detect and quantify biomolecules at very low concentrations,’ said Rajesh Sardar, Ph.D., who developed the sensor. ‘We have designed an ultrasensitive technique so that we can see minute changes in microRNA concentrations in a patient’s blood and confirm the presence of pancreatic cancer.’ Sardar is an assistant professor of chemistry and chemical biology in the School of Science at IUPUI and leads an interdisciplinary research program focusing on the intersection of analytical chemistry and the nanoscience of metallic nanoparticles.

‘If we can establish that there is cancer in the pancreas because the sensor detects high levels of microRNA-10b or one of the other microRNAs associated with that specific cancer, we may be able to treat it sooner,’ said Murray Korc, M.D., the Myles Brand Professor of Cancer Research at the IU School of Medicine and a researcher at the IU Simon Cancer Center. Korc worked with Sardar to improve the sensor’s capabilities and led the testing of the sensor and its clinical uses as well as advancing the understanding of pancreatic cancer biology.

‘That’s especially significant for pancreatic cancer, because for many patients it is symptom-free for years or even a decade or more, by which time it has spread to other organs, when surgical removal is no longer possible and therapeutic options are limited,’ said Korc. ‘For example, diagnosis of pancreatic cancer at an early stage of the disease followed by surgical removal is associated with a 40 percent five-year survival. Diagnosis of metastatic pancreatic cancer, by contrast, is associated with life expectancy that is often only a year or less.

‘The beauty of the sensor designed by Dr. Sardar is its ability to accurately detect mild increases in microRNA levels, which could allow for early cancer diagnosis,’ Korc added.

Over the past decade, studies have shown that microRNAs play important roles in cancer and other diseases, such as diabetes and cardiovascular disorders. The new IUPUI nanotechnology-based sensor can detect changes in any of these microRNAs.

The sensor is a small glass chip that contains triangular-shaped gold nanoparticles called ‘nanoprisms.’ After dipping it in a sample of blood or another body fluid, the scientist measures the change in the nanoprism’s optical property to determine the levels of specific microRNAs.

‘Using gold nanoprisms may sound expensive, but it isn’t because these particles are so very tiny,’ Sardar said. “It’s a rather cheap technique because it uses nanotechnology and needs very little gold. $250 worth of gold makes 4,000 sensors. Four thousand sensors allow you to do at least 4,000 tests. The low cost makes this technique ideal for use anywhere, including in low-resource environments in this country and around the world.’ IUSM