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

Each year approximately 1 in 1,000 pregnant women will experience peripartum cardiomyopathy, an uncommon form of often severe heart failure that occurs in the final month of pregnancy or up to five months following delivery. But the cause of peripartum cardiomyopathy has been largely unknown – until now. Researchers from the Perelman School of Medicine at the University of Pennsylvania analysed the genetic variants that have been associated with another form of inherited cardiomyopathy, and determined that peripartum cardiomyopathy is often the result of a genetic mutation.

Researchers analysed 43 genes in 172 women who experienced peripartum cardiomyopathy, and found that 15 percent of the group had genetic mutations, usually in their TTN gene, which encodes the instructions for making the Titin protein. This protein—named after the Greek gods, Titans—is the largest protein in the body and directly affects the heart’s ability to contract and relax. Of the women analysed, 26 were identified to have mutations on the TTN gene, an effect that is significantly higher than any other reported finding for the cause of peripartum cardiomyopathy.

“Until now, we had very little insight into the cause of peripartum cardiomyopathy,” said the study’s senior author, Zoltan Arany, MD, PhD, an associate professor of Cardiovascular Medicine. “There had been theories that it was linked to a viral infection, or paternal genes attacking the mother’s circulatory system, or just the stresses of pregnancy. However, this research shows that a mutation in the TTN gene is the cause of a significant number of peripartum cardiomyopathies, even in women without a family history of the disease.”

This sizable percentage indicates that peripartum cardiomyopathy is caused by genetic mutations. The same mutations are also present in many who experienced dilated cardiomyopathy, a condition in which the heart’s ability to pump blood is decreased when the main pumping chamber becomes weak and enlarged. This is similar to peripartum cardiomyopathy but most often occurs in older patients. However, the two diseases are not the same. For example, a woman with the genetic mutation for dilated cardiomyopathy will not always experience peripartum cardiomyopathy, and women with the peripartum cardiomyopathy mutation will not always experience dilated cardiomyopathy later in life. How the same mutations can lead to different conditions in different people remains an unanswered question.

Arany added, “these findings will certainly inform future peripartum cardiomyopathy research, with possible implications on genetic testing and preventive care. Though, more research is unquestionably needed. We’re continuing to follow these women and we’re gathering data for hundreds of others around the world, with the goal of identifying the cause of peripartum cardiomyopathy in the remaining 85 percent of women with this condition, and ultimately using what we learn to improve the care of these women and their newborns.” Penn Medicine News

Many cancers include increased copies of the gene MET. But in which cases is MET driving the cancer and in which do these increased copies happen to ‘ride along’ with other molecular abnormalities that are the true cause of the disease? The answer influences whether a tumour will respond to drugs that inhibit MET, like crizotinib. A University of Colorado Cancer Center study sheds light on the best method to determine the threshold at which MET amplification becomes clinically relevant.

‘Generally, there are two ways that the number of copies of the MET gene can be increased: The tumour can make multiple copies of the entire chromosome on which it sits — chromosome 7 — or it can amplify just the MET region. In the first case, MET is unlikely to be the specific driver of the cancer’s biology, it may just be a ride along. But if the MET region is amplified separate from the rest of the chromosome, this would suggest that the MET gene is indeed the area of specific importance to the cancer,’ says Sinead Noonan, MD, investigator at the CU Cancer Center, senior thoracic oncology fellow at the CU School of Medicine, and the study’s first author.

The goal of the current study was to find evidence supporting the above hypothesis and to identify a group of MET-driven patients in which crizotinib would be effective.

To do so, Noonan worked with Marileila Garcia, PhD, CU Cancer Center investigator and professor of Oncology at the CU School of Medicine, who assessed the genetics of over 1,000 lung cancer patients. Using the low level criteria commonly used for defining an increase in MET copy number, independent of whether it was increased by increasing the overall number of copies of the chromosome or just that region of the chromosome, 14.4 percent of these samples were positive for MET copy number gain. The group then looked at another measure, comparing MET copy number to the number of chromosome 7 centromeres — the center point of the chromosome — which allowed them to see how specifically MET was amplified in comparison with the chromosome as a whole. When the low level criteria for defining an increase in MET copy number using the ratio of MET to centromere 7 was used, only 4.5 percent of these cases were positive.

Now the question was what ratio of MET to centromere 7, exactly, defined patients whose tumours were driven by this gene amplification and so would be most susceptible to MET inhibition via crizotinib.

‘There is almost always only one driver abnormality in any given tumour,’ Noonan says. But in 47 percent of the tumours defined by the minimal MET-to-centromere-7 ratio criteria, the group was able to identify other known genetic drivers, including mutations or gene rearrangements in EGFR, KRAS, BRAF, ALK, ERBB2, RET or ROS1.

‘Strikingly, as we looked at cases with higher and higher MET positivity, the degree of overlap with other known drivers decreased,’ Noonan says. In other words, as the MET-to-centromere-7 ratio increased, the group was less likely to find any other candidates for the cause of the cancer.

A group completely free from overlap with other known cancer drivers was only found in the group in which MET overbalanced centromere 7 by 5 times. Using the other common method of simply counting MET, independent of the ratio, it was impossible to find a group without additional known genetic driver.

‘I think these data really help to solidify MET-to-centromere ratio as the better measure for defining a lung cancer driven by MET copy number,’ says D. Ross Camidge, MD, PhD, Joyce Zeff Chair in Lung Cancer Research at the CU Cancer Center and the senior author of the study. ‘While the highest ratio only occurs in 0.34 percent of cases, it has clearly been associated with responses to crizotinib approaching 70 percent. However, responses have also been seen at lower ratios. Overall, if we look across all levels of MET-ratio positive cases but exclude those with other identifiable drivers we can identify a group representing 2.4 percent of adenocarcinomas which is ripe for further investigation as potential MET-sensitive subtypes of lung cancer.’ ScienceDaily