Researchers from Boston University School of Medicine (BUSM) and George Washington University (GWU) have developed a method to rapidly identify pathogenic species and strains causing illnesses, such as pneumonia, that could help lead to earlier detection of disease outbreaks and pinpoint effective treatments more quickly.
Emerging sequencing technologies have revolutionised the collection of genomic data for bioforensics, biosurveillance and for use in clinical settings. However, new approaches are being developed to analyse these large volumes of genetic data. Principal investigator Evan Johnson, PhD, assistant professor of medicine at BUSM, and Keith Crandall, PhD, director of the Computational Biology Institute at GWU, have created a statistical framework called Pathoscope to identify pathogenic genetic sequences from infected tissue samples.

This unique approach can accurately discriminate between closely related strains of the same species with little coverage of the pathogenic genome. The method also can determine the complete composition of known pathogenic and benign organisms in a biological sample. No other method can accurately identify multiple species or substrains in such a direct and automatic way. Current methods, such as the standard polymerase chain reaction detection or microscope observation, are often imperfect and time-consuming.
‘Pathoscope is like completing a complex jigsaw puzzle. Instead of manually assembling the puzzle, which can take days or weeks of tedious effort, we use a statistical algorithm that can determine how the picture should look without actually putting it together,’ said Johnson. ‘Our method can characterise a biological sample faster, more accurately and in a more automated fashion than any other approach out there.’

This work will be relevant in a broad range of scenarios. For example, in hospitals, this sequencing method will allow for rapid screening of thousands of infectious pathogens simultaneously, while being sensitive enough to monitor disease outbreaks caused by specific pathogenic strains. Veterinarians can even apply the method in their practices. This research is also applicable outside of clinical settings, allowing officials to quickly identify agents of bioterrorism (e.g. in a tainted letter) and harmful pathogens on hard surfaces, soil, water or in food products.
‘This approach has the ability to drastically change the process for identifying and combating pathogens, whether they’re in a hospital, veterinarian’s office or salmon stream,’ Crandall said. Researchers plan to conduct more studies to further verify the efficacy of their approach, and will soon begin to work with the aquaculture industry, helping fishermen with water-quality surveillance.

A little bit of learned fear is a good thing, keeping us from making risky, stupid decisions or falling over and over again into the same trap. But new research from neuroscientists and molecular biologists at USC shows that a missing brain protein may be the culprit in cases of severe over-worry, where the fear perseveres even when there’s nothing of which to be afraid. In a study, researchers examined mice without the enzymes monoamine oxidase A and B (MAO A/B), which sit next to each other in a human’s genetic code as well as on that of mice.
Prior research has found an association between deficiencies of these enzymes in humans and developmental disabilities along the autism spectrum, such as clinical perseverance, the inability to change or modulate actions along with social context. ‘These mice may serve as an interesting model to develop interventions to these neuropsychiatric disorders,’ said University Professor and senior author Jean Shih, Boyd & Elsie Welin Professor of Pharmacology and Pharmaceutical Sciences at the USC School of Pharmacy and the Keck School of Medicine of USC. ‘The severity of the changes in the MAO A/B knockout mice compared to MAO A knockout mice supports the idea that the severity of autistic-like features may be correlated to the amounts of monoamine levels, particularly at early developmental stages.’
Shih is a world leader in understanding the neurobiological and biochemical mechanisms behind such behaviours as aggression and anxiety. In this latest study, Shih and her co-investigators — including lead author Chanpreet Singh, a USC doctoral student at the time of the research who is now at the California Institute of Technology (Caltech), and Richard Thompson, USC University Professor Emeritus and Keck Professor of Psychology and Biological Sciences at the USC Dornsife College of Letters, Arts and Sciences — expanded their past research on MAO A/B, which regulates neurotransmitters known as monoamines, including serotonin, norepinephrine and dopamine. Comparing mice without MAO A/B with their wild-type littermates, the researchers found significant differences in how the mice without MAO A/B processed fear and other types of learning. Mice without MAO A/B and wild mice were put in a new, neutral environment and given a mild electric shock. All mice showed learned fear the next time they were tested in the same environment, with the MAO A/B knockout mice displaying a greater degree of fear. But while wild mice continued to explore other new environments freely after the trauma, mice without the MAO A/B enzymes generalised their phobia to other contexts — their fear spilled over onto places where they should have no reason to be afraid. ‘The neural substrates processing fear in the brain is very different in these mice,’ Singh said. ‘Enhanced learning in the wrong context is a disorder and is exemplified by these mice. Their brain is not letting them forget. In a survival issue, you need to be able to forget things.’
The mice without MAO A and MAO B also learned eye-blink conditioning much more quickly than wild mice, which has also been noted in autistic patients but not in mice missing only one of these enzymes. Importantly, the mice without MAO A/B did not display any differences in learning for spatial skills and object recognition, the researchers found, ‘but in their ability to learn an emotional event, the [MAO A/B knockout mice] are very different than wild types,’ Singh said. He continued: ‘When both enzymes are missing, it significantly increases the levels of neurotransmitters, which causes developmental changes, which leads to differential expression of receptors that are very important for synaptic plasticity — a measure of learning — and to behavior that is quite similar to what we see along the autism spectrum.’ University of Southern California

Scientists at the National Cancer Institute (NCI) have generated a data set of cancer-specific genetic variations and are making these data available to the research community.
This will help cancer researchers better understand drug response and resistance to cancer treatments.
‘To date, this is the largest database worldwide, containing 6 billion data points that connect drugs with genomic variants for the whole human genome across cell lines from nine tissues of origin, including breast, ovary, prostate, colon, lung, kidney, brain, blood, and skin,’ said Yves Pommier, M.D., Ph.D., chief of the Laboratory of Molecular Pharmacology at the NCI in Bethesda, Md., in an interview. ‘We are making this data set public for the greater community to use and analyse.
‘Opening this extensive data set to researchers will expand our knowledge and understanding of tumorigenesis [the process by which normal cells are transformed into cancer], as more and more cancer-related gene aberrations are discovered,’ Pommier added. ‘This comes at a great time, because genomic medicine is becoming a reality, and I am very hopeful this valuable information will change the way we use drugs for precision medicine.’
Pommier and colleagues conducted whole-exome sequencing of the NCI-60 human cancer cell line panel, which is a collection of 60 human cancer cell lines, and generated a comprehensive list of cancer-specific genetic variations. Preliminary studies conducted by the researchers indicate that the extensive data set has the potential to dramatically enhance understanding of the relationships between specific cancer-related genetic variations and drug response, which will accelerate the drug development process.
The NCI-60 human cancer cell line panel is used extensively by cancer researchers to discover novel anti-cancer drugs. To conduct whole-exome sequencing, Pommier and his NCI team extracted DNA from the 60 different cell lines, which represent cancers of the lung, colon, brain, ovary, breast, prostate, and kidney, as well as leukaemia and melanoma, and catalogued the genetic coding variants for the entire human genome. The genetic variations identified were of two types: type I variants corresponding to variants found in the normal population, and type II variants, which are cancer-specific.
The researchers then used the Super Learner algorithm to predict the sensitivity of cells harboring type II variants to 103 anti-cancer drugs approved by the FDA and an additional 207 investigational new drugs. They were able to study the correlations between key cancer-related genes and clinically relevant anti-cancer drugs, and predict the outcome.

The data generated in this study provide means to identify new determinants of response and mechanisms of resistance to drugs, and offer opportunities to target genomic defects and overcome acquired resistance, according to Pommier. To enable this, the researchers are making these data available to all researchers via two database portals, called the CellMiner database and the Ingenuity systems database. American Association for Cancer Research

It turns out the love hormone oxytocin is two-faced. Oxytocin has long been known as the warm, fuzzy hormone that promotes feelings of love, social bonding and well-being. It’s even being tested as an anti-anxiety drug. But new Northwestern Medicine research shows oxytocin also can cause emotional pain, an entirely new, darker identity for the hormone.

Oxytocin appears to be the reason stressful social situations, perhaps being bullied at school or tormented by a boss, reverberate long past the event and can trigger fear and anxiety in the future.

That’s because the hormone actually strengthens social memory in one specific region of the brain, Northwestern scientists discovered.

If a social experience is negative or stressful, the hormone activates a part of the brain that intensifies the memory. Oxytocin also increases the susceptibility to feeling fearful and anxious during stressful events going forward.

(Presumably, oxytocin also intensifies positive social memories and, thereby, increases feelings of well being, but that research is ongoing.)

The findings are important because chronic social stress is one of the leading causes of anxiety and depression, while positive social interactions enhance emotional health. The research, which was done in mice, is particularly relevant because oxytocin currently is being tested as an anti-anxiety drug in several clinical trials.

‘By understanding the oxytocin system’s dual role in triggering or reducing anxiety, depending on the social context, we can optimise oxytocin treatments that improve well-being instead of triggering negative reactions,’ said Jelena Radulovic, the senior author of the study and the Dunbar Professsor of Bipolar Disease at Northwestern University Feinberg School of Medicine.

This is the first study to link oxytocin to social stress and its ability to increase anxiety and fear in response to future stress. Northwestern scientists also discovered the brain region responsible for these effects — the lateral septum – and the pathway or route oxytocin uses in this area to amplify fear and anxiety.

The scientists discovered that oxytocin strengthens negative social memory and future anxiety by triggering an important signalling molecule — ERK (extracellular signal regulated kinases) — that becomes activated for six hours after a negative social experience. ERK causes enhanced fear, Radulovic believes, by stimulating the brain’s fear pathways, many of which pass through the lateral septum. The region is involved in emotional and stress responses. Northwestern University

Massachusetts General Hospital (MGH) researchers and their colleagues have used digital versions of a standard molecular biology tool to detect a common tumour-associated mutation in the cerebrospinal fluid (CSF) of patients with brain tumours. In their report, the investigators describe using advanced forms of the gene-amplification technology polymerase chain reaction (PCR) to analyse bits of RNA carried in membrane-covered sacs called extracellular vesicles for the presence of a tumour-associated mutation in a gene called IDH1.
‘Reliable detection of tumour-associated mutations in cerebrospinal fluid with digital PCR would provide a biomarker for monitoring and tracking tumours without invasive neurosurgery,’ says Xandra Breakefield, PhD, of the MGH Molecular Neurogenetics Unit, corresponding author of the paper. ‘Knowing the IDH1 mutation status of these tumours could help guide treatment decisions, since a number of companies are developing drugs that specifically target that mutant enzyme.’
Both normal and tumour cells regularly release extracellular vesicles, which contain segments of RNA, DNA or proteins and can be found in blood, CSF and other body fluids. A 2008 study from the MGH team was able to identify a relatively large tumour-associated mutation in extracellular vesicles from the blood of brain tumour patients, but most current diagnostic technologies that analyse CSF do not capture molecular or genetic information from central nervous system tumours.
In addition, explains Leonora Balaj, PhD, of MGH Neurology, co-lead author of the current report, ‘Tumour-specific EVs make up only a small percentage of the total number of EVs found in either blood or cerebrospinal fluid, so finding rare, single-nucleotide mutations in a sample of blood or CSF is very challenging. These digital PCR techniques allow the amplification of such hard-to-find molecules, dramatically improving the ability to identify tumour-specific changes without the need for biopsy.’
The current study used two forms of digital PCR – BEAMing and Droplet Digital PCR – to analyse extracellular vesicles in the blood and CSF of brain tumour patients and healthy controls for the presence of a single-nucleotide IDH1 mutation known to be associated with several types of cancer. Both forms of PCR were able to detect both the presence and abundance of mutant IDH1 in the CSF of 5 of the 8 patients known to have IDH1-mutant tumours. Two of the three mutation-positive tumours that had false negative results were low grade and the third was quite small, suggesting a need for future studies of more samples to determine how the grade and size of the tumours affect the ability to detect mutations. The failure to detect tumour-associated mutations in blood samples with this technology may indicate that CSF is a better source for extracellular vesicles from brain tumours.
The ability to non-invasively determine the genetic makeup of brain tumours could have a significant effect on patient care, explains study co-author Fred Hochberg, MD, MGH Neurology. ‘The current approach for patients who may have a brain tumour is first to have a brain scan and then a biopsy to determine whether a growth is malignant. Patients may have a second operation to remove the tumour prior to beginning radiation therapy and chemotherapy, but none of these treatments are targeted to the specific molecular nature of the tumour.
‘Having this sort of molecular diagnostic assay – whether in spinal fluid or blood – would allow us to immediately initiate treatment that is personalised for that patient without the need for surgical biopsy,’ he adds. ‘For some patients, the treatment could shrink a tumour before surgical removal, for others it may control tumour growth to the point that surgery is not necessary, which in addition to keeping patients from undergoing an unnecessary procedure, could save costs. We still have a long way to go to improve survival of these malignancies, so every improvement we can make is valuable.’ Massachusetts General Hospital