Recent advances in large-scale clinical DNA sequencing have led to genetic diagnoses for many rare disease patients, but the diagnosis rate based on these approaches is still far from perfect. On average, clinicians are unable to provide a genetic diagnosis for over half of patients in the clinic. The lack of a clear genetic diagnosis can lead to profound uncertainty about patients’ long-term prognoses, treatment options, and family planning decisions.
In a new Science Translational Medicine study, a team led by researchers from the Broad Institute of MIT and Harvard and the National Institute of Neurological Disorders and Stroke adds RNA sequencing to the diagnostic toolkit to identify disease-causing mutations buried inside the genome.
The researchers sequenced the RNA from muscle samples of 50 patients with undiagnosed genetic muscle disorders — who had undergone extensive genetic testing — and, in conjunction with DNA sequence information and a reference database, successfully located pathogenic mutations that had previously gone undetected in one-third of the patients. The study firmly positions RNA sequencing as a tool that adds additional power to the existing set of technologies deployed to solve genetic disease mysteries.
“For some patients, we know that there is variation in the human genome, with an effect on the transcript, that we just haven’t been capturing with our traditional genetic sequencing methods,” says senior author Daniel MacArthur, co-director of the Medical and Population Genetics Program at the Broad Institute and group leader at Massachusetts General Hospital. “With RNA sequencing, we were able to take a set of patients who had gone through diagnostic odysseys — often lasting many years, where many methods had been used to try to detect the cause of their disease without success — and find the biological answers that previous technologies had missed.”
Having a molecular diagnosis in-hand is a medical milestone for some patients and their families, and opens the door to potential therapies while offering some peace of mind. “For example, one patient’s family had opted to delay having other children until they knew the genetic basis of her condition,” MacArthur adds. “Our clinical collaborators were able to report that they had found the genetic cause, and now the parents have the option of prenatal testing for that mutation.”
The study demonstrates that RNA sequencing, or RNA-seq, applied to relevant tissue samples and coupled with genetic analysis, can detect pathogenic mutations hidden in the noncoding sections of a gene, highlight relevant mutations missed in the noise of whole-genome analysis, and rule out other genetic variants suspected to cause disease. Previously, the technology was rarely applied in a clinical setting, and then only for single patients when specific mutations were already suspected — but the research team saw the potential for RNA-seq to augment other clinical tools earlier in diagnostics.

Broad Institute of MIT and Harvard
www.broadinstitute.org/news/rna-sequencing-applied-tool-solve-patients%E2%80%99-diagnostic-mysteries

Loss of a key protein leads to defects in skeletal development including reduced bone density and a shortening of the fingers and toes — a condition known as brachydactyly. The discovery was made by researchers at Penn State University who knocked out the Speckle-type POZ Protein (Spop) in the mouse and characterized the impact on bone development. The research redefines the role of Spop during bone development and provides a new potential target for the diagnosis and treatment of bone diseases such as osteoporosis.
“The Spop protein is involved in Hedgehog signalling — a well-studied cell-tocell communication pathway that plays multiple roles during development,” said Aimin Liu, associate professor of biology at Penn State and the corresponding author of the study. “Previous studies done in cell culture suggested that Spop negatively regulates or ‘turns down’ Hedgehog signalling. However, in our study, we show that Spop positively regulates the pathway downstream of a member of the Hedgehog family, a protein called Indian Hedgehog, during bone development. This new understanding adds to our knowledge of the genetic basis of bone development and could open new avenues to study bone disease.”
Indian Hedgehog (Ihh) plays an essential role in bone development. It is near the top of a hierarchical cascade of genes that program cells to produce cartilage and bone. Ihh controls gene expression by regulating the activity of the transcription factors — proteins that control the expression of other genes — Gli2 and Gli3. Gli2 acts mainly as an activator of gene expression and Gli3 acts mainly to repress gene expression. The Spop protein tags the Gli proteins to be degraded in the cell. “Previous studies led to a hypothesis that a loss of Spop function would increase Hedgehog signalling because the Gli activators were no longer being degraded,” said Hongchen Cai, a graduate student at Penn State and an author of the paper. “We were surprised to see in our study the repressor of gene expression, Gli3, built up in developing bone, but not the activator of gene expression, Gli2. This imbalance led to an overall decrease in Hedgehog signalling.”
In order to study the role of Spop in bone development more closely, the researchers knocked the gene out specifically in the limb. Limbs that lacked Spop had less dense bone, mimicking osteopenia — a human condition characterized by low bone density, but not as severe as osteoporosis. The limbs also had shorter than normal fingers and toes. The researchers also showed that the effects of losing Spop could be mitigated by simultaneously reducing the amount of Gli3 in the limbs.

Penn State http://tinyurl.com/jx3y6nj

Over a fourth of the eighty samples tested positive for new psychoactive substances.
In the last decade hundreds of new psychoactive substances (NPS) have emerged in the drug market, taking advantage of the delay occurring between their introduction into the market and their legal ban.  According to the Drug Enforcement Agency (DEA) NPS describes a recently emerged drug that may pose a public health threat.  The DEA issues a quarterly Emerging Threat Report, which catalogues the newest identified NPS.
NPS tend to mimic the psychotropic effects of traditional drugs of abuse, but their acute and chronic toxicity, and side-effects are largely unknown.  While seizure data from the DEA is often used to indicate what new drugs are being sold in the US, there is a lack of research examining and confirming who has been using such drugs.
Joseph J. Palamar, PhD, MPH, a New York University researcher, has been researching incidental and intentional use of NPS by young adults.  His current line of inquiry has focused on survey methods, qualitative interviews, and hair sampling to ascertain frequency and type of NPS use by nightclub-goers–a demographic which traditionally has a relaxed view towards recreational drug experimentation and use.
NPS are common adulterants in drugs such as ecstasy (MDMA), which has seen an increase in popularity since it became marketed as “Molly”.  Ironically, “Molly” connotes a product that is pure MDMA. In a related study, Palamar and his team found that four out of ten nightclub/festival attendees who used ecstasy or “Molly” tested positive for “bath salts” despite reporting no use.
In their current study, “Hair Testing for Drugs of Abuse and New Psychoactive Substances in a High-Risk Population,” Dr. Alberto Salomone, an affiliated researcher at the Centro Regionale Antidoping e di Tossicologia “A. Bertinaria”, Orbassano, Turin, Italy and Dr. Palamar, affiliated with NYU’s Center for Drug Use and HIV Research (CDUHR), collected hair samples from 80 young adults outside of New York City nightclubs and dance festivals, from July through September of 2015.  Hair samples from high-risk nightclub and dance music attendees were tested for 82 drugs and metabolites (including NPS) using ultra-high performance liquid chromatography–tandem mass spectrometry.
“Hair analysis represents a reliable and well-established means of clinical and forensic investigations to evaluate drug exposure, said Dr. Salomone.  “Hair is the most helpful specimen when either long-time retrospective information on drug consumption is of interest.” “Most NPS can no longer be detected in urine, blood, or saliva within hours or days after consumption, but hair is particularly beneficial because many drugs can be detected months after use.”
Of the eighty samples, twenty-six tested positive for at least one NPS—the most common being a “bath salt” (synthetic cathinone) called butylone (present in twenty-five samples). The “bath salts” methylone and even alpha-PVP (a.k.a.: “Flakka”) were also detected. The researchers find the presence of Flakka alarming as this drug has been associated with many episodes of erratic behaviour and even death in Florida. Other new drugs detected included new stimulants called 4-FA and 5/6-APB.
“We found that many people in the nightclub and festival scene have been using new drugs and our previous research has found that many of these people have been using unknowingly,” said Dr. Palamar, also an assistant professor of Population Health at NYU Langone Medical Center (NYULMC).
Hair analysis proved a powerful tool to Drs. Salomone and Palamar and their team, allowing them to gain objective biological drug-prevalence information, free from possible biases of unintentional or unknown intake and untruthful reporting of use.

NYU Langone Medical Center
www.nyu.edu/about/news-publications/news/2017/march/hair-testing-shows-high-prevalence-of-new-psychoactive-substance.html

Cancer of the oropharynx has become increasingly common: In the United States alone, the number of newly diagnosed cases has tripled over the past three decades. About 70 percent of these tumours are caused by infection with human papillomavirus (HPV) type 16.

Tim Waterboer and his colleagues at the German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ) in Heidelberg have now revealed that an antibody test that they developed can detect early if a person has a very high risk of developing an HPV-associated cancer of the oropharynx. The DKFZ researchers collaborated in this project with colleagues from the International Agency for Research on Cancer (IARC) and the U.S. National Cancer Institute.

The immune system responds to an infection with HPV by producing antibodies against components of the virus. HPV protein E6 is produced by chronically infected cells and plays an important role in the development of cancer. Therefore, antibodies against E6 are regarded as very valuable indicators.

In the new study, the scientists investigated blood samples from the U.S. PLCO study. For this early cancer detection study, approximately 150 000 healthy participants were recruited between 1993 and 2001 and cancers that they developed in the period under investigation were documented. The DKFZ researchers studied 198 blood samples from patients with tumours of the oropharynx. The samples had been taken when the participants entered the study, i.e., long before the onset of the disease. The control samples were from 924 PLCO participants without cancer diagnosis.

In 42.3 percent of the patients with oropharyngeal cancer, the DKFZ researchers were able to detect antibodies against HPV16 E6 in their blood samples. "This pretty much corresponds to the percentage of HPV-related cases of oropharyngeal cancer that we expected to find for that time in the American population," Tim Waterboer said. By comparison, only 0.5 percent of individuals in the control group tested positive to HPV16 E6.

Tumour tissue of some study patients was also available for study besides the blood samples. Based on the activity of viral genes in the tissue, the researchers were able to identify the tumours that had been caused by HPV. They found that only those patients tested positive to the antibodies whose cancer was in fact associated with HPV16.

If the test result for HPV16 E6 antibodies is positive once, it remains stable over many years, discovered the researchers in study participants from whom blood samples had been obtained repeatedly over a long time. In some cases, the blood samples had been taken up to 13 years prior to cancer diagnosis. "This means that a single blood sample test taken at any point of time might be sufficient for assessing a person’s risk for developing cancer of the oropharynx within the next 10 years," said Waterboer.

Nevertheless, detection of HPV16-E6 antibodies is –at least for now – not a suitable method for early cancer detection in larger population groups. "The occurrence of new cases of oropharyngeal cancer is rather low at about five cases per 100 000 inhabitants," said Waterboer, who is the study head. "That means that although the test is highly specific, very many healthy people would receive false positive results. However, in certain high-risk groups, up to ten times more people can develop the disease. HPV16 E6 antibody detection is the first ever easy-to-analyze biomarker that enables us to narrow down the circle of individuals who are at an extremely high risk of developing the cancer." The DKFZ virologists are currently examining possibilities of making the biomarker applicable in the clinic.

However, the test for antibodies against HPV16 E6 is not suitable for assessing the risk for cervical cancer and other HPV-associated cancers in genital areas. As opposed to cancer of the oropharynx, the revealing antibodies do not occur here before the cancer becomes clinically detectable.

DKFZwww.dkfz.de/en/presse/pressemitteilungen/2017/dkfz-pm-17-19-A-biomarker-for-cancer-of-the-oropharynx.php

Experts at the European Committee on Antimicrobial Susceptibility Testing (EUCAST), who define the optimal drug concentrations to inhibit the growth of pathogens, have found that genetic methods cannot yet be used to test for susceptibility in a number of important bacterial species. Although there have been advances in whole genome sequencing (WGS), which allows to determine the DNA sequence of an organism’s genome at a single time, there are still several hurdles to overcome before this type of genetic testing can be used in clinical laboratories, they concluded.
A EUCAST subcommittee dedicated to reviewing the role of WGS in antimicrobial susceptibility testing (AST) considered the most recent published evidence on the use of whole genome sequencing as a tool for susceptibility testing. The group – comprising of over a dozen leading experts and led by Prof. Neil Woodford, Head of Public Health England’s Antimicrobial Resistance and Healthcare Associated Infections Reference Unit – did not rule out that it will one day be possible for a single assay to predict how a species of bacteria will respond to a specific antimicrobial drug, but there is little evidence to suggest we will reach this point in the near future.
EUCAST’s technical data coordinator, Prof. Gunnar Kahlmeter of the Central Hospital, Växjö, Sweden, said that it is premature to suggest that breakpoints and recommendations for phenotypic susceptibility testing will no longer be required as genetic methods will supersede them any time soon. “To be of use in a clinical situation, WGS will need to predict antimicrobial resistance and also antimicrobial susceptibility, which are two quite different things. It will also be necessary for WGS to quantify the degree of resistance for an organism, something which is currently not possible.”
The group has chosen to compare how WGS can predict whether or not the organism belongs to the wild type (is without resistance mechanisms) with the same prediction performed through the use of the epidemiological cut-off values (ECOFFs) developed by EUCAST. Whether or not and in that case how this can be extended to clinical breakpoints is discussed in the paper.
The EUCAST subcommittee also highlighted that there is currently no way to assess how accurate different WGS laboratories are, and that there is an urgent need to establish a single public database of all known resistance genes within different bacterial species so that data can be shared and compared more easily.
The EUCAST experts also note that WGS technology is currently limited because it cannot be used to analyse specimens directly – bacteria can only be sequenced once they have been cultured. This inevitably leads to significant time delays and additional financial costs, which is usually prohibitive for most laboratories.
EUCAST recommends that whole-genome sequencing should be made a research and funding priority in the future to expand on our current knowledge and to develop more sophisticated prediction tools. As bacteria continue to develop multiple resistance mechanisms, unravelling the genetics of their interaction with antimicrobials will become even more challenging and even more necessary, particularly as we face the spectre of extreme drug resistance and global failure of some antimicrobials.www.escmid.org