Most of us would be lost without Google maps or similar route-guidance technologies. And when those mapping tools include additional data about traffic or weather, we can navigate even more effectively. For scientists who navigate the mammalian genome to better understand genetic causes of disease, combining various types of data sets makes finding their way easier, too.

A team at the Salk Institute has developed a computational algorithm that integrates two different data types to make locating key regions within the genome more precise and accurate than other tools. The method could help researchers conduct vastly more targeted searches for disease-causing genetic variants in the human genome, such as ones that promote cancer or cause metabolic disorders.

“Most of the variation between individuals is in noncoding regions of the genome,” says senior author Joseph Ecker, a Howard Hughes Medical Institute investigator and director of Salk’s Genomic Analysis Laboratory. “These regions don’t code for proteins, but they still contain genetic variants that cause disease. We just haven’t had very effective tools to locate these areas in a variety of tissues and cell types—until now.”

Only about two percent of our DNA is made up of genes, which code for proteins that keep us healthy and functional. For many years, the other 98 percent was thought to be extraneous “junk.” But, as science has developed ever more sophisticated tools to probe the genome, it has become clear that much of that so-called junk has vital regulatory roles. For example, sections of DNA called “enhancers” dictate where and when the gene information is read out.

Increasingly, mutations or disruption in enhancers have been tied to major causes of human disease, but enhancers have been hard to locate within the genome. Clues about them can be found in certain types of experimental data, such as in the binding of proteins that regulate gene activity, chemical modifications of proteins (called histones) that DNA wraps around, or in the presence of chemical compounds called methyl groups in DNA that turn genes on or off (an epigenetic factor called DNA methylation). Typically, computational methods for finding enhancers have relied on histone modification data. But Ecker’s new system, called REPTILE (for “regulatory-element prediction based on tissue-specific local epigenomic signatures”), combines histone modification and methylation data to predict which regions of the genome contain enhancers. In the team’s experiments, REPTILE proved more accurate at finding enhancers than algorithms that rely on histone modification alone.

 “The novelty of this method is that it uses DNA methylation to really narrow down the candidate regulatory sequences suggested by histone modification data,” says Yupeng He, a Salk graduate student and first author of the paper. “We were then able to test REPTILE’S predictions in the lab and validate them with experimental data, which gave us a high degree of confidence in the algorithm’s ability to find enhancers.”

Salk Institute www.salk.edu/news-release/finding-way-around-dna/

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