Posted tagged ‘genetics’

Drug blocks Zika and other deadly viruses in cells cultures, Stanford study finds

December 12, 2017

Photo of Jan Carette by Paul Sakuma

A team of Stanford researchers is developing approaches to thwart a family of deadly viruses, called flaviviruses, by targeting the human cells that host these invading pathogens.

Flaviviruses include the dengue-fever, yellow-fever, West Nile and Zika viruses transmitted to humans by mosquitoes, as well as encephalitis transmitted by ticks. Unfortunately, approved antiviral drugs for these diseases aren’t currently available.

So, instead of the traditional approach of attacking an individual virus directly, the researchers focused on the cellular factors of their human hosts that are essential to many viral infections.

“Generally, when you develop a drug against a specific protein in dengue virus, for instance, it won’t work for yellow fever or Zika, and you have to develop new antivirals for each,” said Stanford virologist Jan Carette, PhD, in a recent Stanford news release. “Here, by targeting the host rather than a specific virus, we’ve been able to take out multiple viruses at once.”

Earlier, the team genetically profiled human cells to identity the host factors necessary for the viruses to replicate inside the cells — revealing new candidate targets for antiviral drug development. Specifically, they demonstrated the importance of the oligosaccharyltransferase (OST) complex that attaches sugar molecules to proteins. They found flaviviruses did not infect their genetically engineered cells without OST.

In the new study, recently published in Cell Reports, the Stanford researchers collaborated with scientists at Yale University to test the effectiveness of a drug called NGI-1, which inhibits the activity of the OST complex.

They showed that low concentrations of NGI-1 could be used to block the viruses from replicating without harming the host cells — successfully reducing the infection by 99 percent when treating cells immediately after they were infected by Zika or dengue virus, and by 80 percent when administered 24 hours after infection.

Their study also indicated that the viruses are unlikely to become resistant to NGI-1. “When you target a host function rather than a viral protein, it’s usually much more difficult for a virus to develop resistance,” Carette said in the release.

The researchers are now busy with follow-up studies to test NGI-1 in small animal models of dengue fever and are also developing similar drugs with improved specificity.

This is a reposing of my Scope blog story, courtesy of Stanford School of Medicine.

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Researchers investigate fruit flies as a step towards understanding the human brain

December 7, 2017

Photo by nuzree

Researchers have been trying to map out the brain’s complex neural circuits to understand how diseases like Parkinson’s disrupt healthy brain communication, in hopes of designing better therapies.

That, obviously, is not easy. So a Stanford research team led by biology professor Liqun Luo, PhD, and bioengineer and physicist Stephen Quake, PhD, are instead studying fruit fly brains — yes, those pesky bugs that fly around your bananas.

Specifically, they have mapped out a blueprint for the fruit fly’s olfactory neurons — identifying how specific gene and protein activity correlates with the biological circuitry of different neuronal cell types. The researchers focused on a fruit fly’s sense of smell because the function, physiology and anatomy of its olfactory system are well known, making it a simple and ideal test bed for their research.

They measured the gene expression profiles using a single-cell sequencing technology developed for mice and human cell types, which they modified to work for the smaller and simpler fruit fly cells.

The team determined different types of neurons express genes differently during development, but gene expression between the neuron types becomes indistinguishable as the flies mature, as recently reported in Cell.

“Once the brain is wired up, the fly doesn’t need to express those genes that help them in choosing the connection partners,” said first author and Stanford biology postdoc Hongjie Li, PhD, in a recent news release. “So there is less gene expression in the adult flies.”

The researchers are a long way from using their technique to map the human brain, but they aren’t daunted by the challeng. “By further developing this approach, we hope to one day reverse-engineer and perhaps even repair defective circuitry in the human brain,” Li said in the release.

This is a reposting of my Scope blog story, courtesy of Stanford School of Medicine.

The skinny on how chickens grow feathers and, perhaps, on how humans grow hair

July 24, 2017

How do skin cells make regularly spaced hairs in mammals and feathers in birds? Scientists had two opposing theories, but new research at the University of California, Berkeley surprisingly links them.

The first theory contends that the timing of specific gene activation dictates a cell’s destiny and predetermines tissue structure — for example, in the skin, gene activation determines whether a skin cell becomes a sweat gland cell or hair cell, or remains a skin cell. The second theory asserts that a cell’s fate is determined instead by interacting with other cells and the material that it grows on.

Now, Berkeley researchers have found that the creation of feather follicles (like hair follicles) is initiated by cells exerting mechanical tension on each other, which then triggers the necessary changes in gene expression to create the follicles. Their results were recently reported in Science.  

“The cells of the skin in the embryo are pulling on each other and eventually pull one another into little piles that each go on to become a follicle,” said first author Amy Shyer, PhD, a post-doctoral fellow in molecular and cell biology at the University of California, Berkeley, in a recent news release. “What is really key is that there isn’t a particular genetic program that sets up this pattern. All of these cells are initially the same and they have the same genetic program, but their mechanical behavior produces a difference in the piled-up cells that flips a switch, forming a pattern of follicles in the skin.”

The research team grew skin taken from week-old chicken eggs on different materials with varying stiffness. They found that the stiffness of the substrate material was critical to forming feather follicles — material that was too stiff or too soft yielded only one follicle, whereas material with intermediate stiffness resulted in an orderly array of follicles.

“The fundamental tension between cells wanting to cluster together and their boundary resisting them is what allows you to create a spaced array of patterns,” said co-author Alan Rodgues, PhD, a biology consultant and former visiting scholar at Berkeley.

The researchers also showed that when the cells cluster together, this activated genes in those cells to generate a follicle and eventually a feather.

Although the study used chicken skin, the researchers suggest that they have discovered a basic mechanism, which may be used in the future to help grow artificial skin grafts that look like normal human skin with hair follicles and sweat pores.

This is a reposting of my Scope blog story, courtesy of Stanford School of Medicine.

Clinical guidance on genetic testing: A Q&A

April 18, 2017

 

Earlier this month, an FDA ruling gave 23andMe permission to market its personal genetic tests for 10 diseases, including Parkinson’s and late-onset Alzheimer’s.

But with the increase in genetic testing at home and in clinical settings comes challenges. What do physicians do with all of these data? And how do they evaluate the validity and clinical utility of genetic tests?

To tackle these questions and others, the National Academy of Medicine formed a committee to provide guidance. I recently spoke with one of the committee members, Sean David, MD, DPhil, an associate professor of medicine at Stanford, about the committee’s new recommendations and report.

What inspired you to participate in the NAM Committee on the Evidence for Genetic Testing?

“The National Academy of Medicine consensus reports have high impact on national health policy and practices, so I jumped at the chance. In our work at Stanford, we struggle with advising patients on which genetic tests to recommend, which ones to order when requested by a patient and how to interpret results from the many direct-to-consumer genetic tests. We need guidance and a framework for making these decisions. The NAM committee addressed this challenge.

Years ago, I had a patient bring in a whole stack of direct-consumer whole genome sequencing results that showed her genetic risks for different illnesses. She asked me to interpret it for her, but there was far too much for me to consume during our brief office visit. And it was unclear what criteria to use when evaluating these tests. There’s been a rapid increase in the development of genetic tests with thousands of commercially available tests, but limited evidence regarding their validity for diagnosing disease and improving patient outcomes.”

What was the committee’s mission?

“Our charge was to examine the relevant medical and scientific literature to determine the evidence base for different types of genetic tests, as well as recommend a framework for decision-making regarding the use of genetic tests in clinical care.

This is the first consensus report on this topic. Although it was designed for the Military Health System, it should still be applicable to both military and civilian populations and may set benchmarks for private insurance companies. The report also encourages different agencies to cooperate and create a clinical data repository of evidence-based genetic testing decisions, which will be available to everyone. I think someone needs to do this to set the standard. Once that’s been done, at least we’ll have something we can all use as a benchmark.”

How can this decision-making framework help guide clinical practice?

“The decision framework can be used by physicians to determine which genetic tests are really ready for prime time in the clinic. For example, we know that if people are tested based on their family history and found to be at high risk for hereditary breast or ovarian cancer, they can have interventions that will improve their survival and outcomes. By using the decision framework, a physician can come up with a quick triage decision that it’s a ‘yes’ test for someone with several family members with breast and/or ovarian cancer, and one that really all providers should know about.

Other genetic tests like tests for Alzheimer’s aren’t as clear. For instance, there could be a genetic test for a particular rare form of early onset Alzheimer’s associated with a particular mutation. If someone has that mutation, he may have a very high risk of early onset Alzheimer’s disease. Do we screen people for that? It will depend on the clinical testing scenario. If someone has family members who developed Alzheimer’s in their 40s, then it might be a good diagnostic test. Whereas, there might be another genetic test for associated risk of dementia where the causal relationship with Alzheimer’s may not be established. That’s an issue of clinical validity. So we might not offer that test routinely — to avoid giving patients information that might be misleading and might even cause some harm.

In addition, ethical, legal and social implications of genetic testing are important. For many patients — including parents of children with undiagnosed rare diseases — genetic testing may help end a diagnostic odyssey. Oftentimes geneticists will order whole genome testing without testing for something specific. There may be thousands or even millions of different genetic markers that are tested with the hope that they’ll find something that leads to a diagnosis. Evidence of clinical utility may be lacking in scenarios like these, but taking into account the value of tests to patients and their families is important — the context matters. There needs to be a certain amount of clinical judgment, and the committee isn’t saying anything against this.”

This is a reposting of my Scope blog story, courtesy of Stanford School of Medicine.

Genomic screening may help predict breast cancer survival

March 21, 2017

Photo by 3dman_eu

Breast cancer patients are often faced with a difficult decision at the end of their primary treatment: Should they get systemic adjuvant therapy, such as the anti-estrogen drug tamoxifen? Such therapies lower the risk that the cancer will come back, but they also carry the risk of potentially serious side effects.

What would be helpful is for physicians to have a way to predict which patients have the best prognosis and might not need adjuvant therapy. Now, researchers from the Lawrence Berkeley National Laboratory may have a solution, according to a study recently published in Oncotarget.

The research team analyzed clinical patient data and large genomic datasets of normal and tumor breast tissues — identifying 381 genes associated with the relapse-free survival of breast cancer patients. With further analysis, they were able to develop a scoring system based on a 12-gene signature that predicts breast cancer survival. Patients with a low score were more likely to live longer.

Senior author Antoine Snijders, PhD, a research scientist at Berkeley Lab, explained in a recent news release:

“Distinguishing patients with good prognosis could potentially spare them the toxic side effects associated with adjuvant therapy. Determining prognosis involves a range of other clinical factors, including tumor size and grade, the degree to which the cancer has spread, and the age and race of the patient. Our scoring system was predictive of survival independent of these other variables.”

The study showed that their 12-gene signature was effective at predicting patient survival for two specific subtypes of breast cancer — luminal-A and HER2 — but it wasn’t effective for other subtypes.

In addition, the researchers identified seven genes as potential tumor suppressors that could be targeted when developing new breast cancer therapies. They hope that their work will help doctors and patients make more informed treatment decisions, as well as help others develop better breast cancer drugs.

This is a reposting of my Scope blog story, courtesy of Stanford School of Medicine.

Head injuries alter genes linked to serious brain disorders, new study shows

March 13, 2017

Photo by geralt

Traumatic brain injuries, like those caused by concussions, are common. But suffering even a mild brain injury boosts the likelihood of developing neurological and psychiatric disorders, such as Alzheimer’s disease and posttraumatic stress disorder, years later. Exactly how and why that happens remains a mystery.

“Very little is known about how people with brain trauma — like football players and soldiers — develop neurological disorders later in life,” said Fernando Gomez-Pinilla, PhD, a University of California, Los Angeles professor of neurosurgery and of integrative biology and physiology, in a recent news release.

Now, Gomez-Pinilla and his colleagues have discovered that a brain injury harms “master” genes that control other genes throughout the body. This triggers the alteration of hundreds of genes, which are linked to disorders like Alzheimer’s disease, Parkinson’s disease, PTSD, attention deficit hyperactivity disorder and depression. Their study was recently published in EBioMedicine.

In the study, the researchers trained 20 rats to navigate through a maze. They then injected a fluid into the brain of half the rats to simulate a concussion-like brain injury. When all the rats were retested in the maze, the rats with a brain injury took about 25 percent longer than the controls to solve the maze — indicating a change in basic cognitive function.

Next, the team investigated how the brain injuries altered the rats’ genes. They analyzed RNA samples from the rats’ white blood cells and hippocampi, the part of the brain that plays a central role in memory processes. In the injured rats, they found almost 300 genes had been altered in the hippocampus and over 1200 genes in the white blood cells.

More than 100 of these altered genes have counterparts in humans that are linked to neurological and psychiatric disorders. The researchers concluded that concussive brain injury reprograms key genes and this reprogramming could make neurological and psychiatric disorders more likely.

In addition, almost two dozen of the altered genes occurred in both the hippocampus and white blood cells. The researchers hope this genetic signature can be used to develop a gene-based blood test that determines whether a brain injury has occurred and whether future neurological disorders are likely.

They also hope their identification of master genes can give scientists new targets to develop better pharmaceuticals for brain disorders. However, more research is needed to fully understand the role of these master genes. Gomez-Pinilla said he now plans to study the phenomenon in people who have suffered a traumatic brain injury.

This is a reposing of my Scope blog story, courtesy of Stanford School of Medicine.

Feeling fatigued? Your genes may be partially responsible, a new study says

March 7, 2017

Photo by geralt

How often, in the last two weeks, have you felt tired or lacked energy?

Daily? Never? For me, and I’m guessing for many of you, the answer is somewhere in between.

Researchers posed that question to tens of thousands of study participants to investigate whether tiredness has a genetic basis. They found that genes play a small but significant role in overall fatigue.

The multi-institutional team of researchers analyzed genetic data from the UK Biobank for 108,976 individuals who reported whether they had felt tired in the last two weeks. The participants selected four possible answers, ranging from “not at all” to “nearly every day”; most answered either “not at all” or “several days.”

The researchers found that genetic factors account for about 8 percent of the participants’ differences in self-reported tiredness, according to a paper recently published in Molecular Psychiatry. This implies that tiredness is largely due to other factors, such as not getting enough sleep.

Some inherent factors such as personality traits or poor health can contribute, however. By averaging tiredness across a large sample and performing a genomic-wide association study, the researchers identified genetic links between tiredness and inherent factors — using the UK Biobank’s data on the participants’ physical health, mental health, personality and cognitive functioning.

They found that an individual’s genetic predisposition to some physical and mental illnesses — not just the presence of these illnesses — was associated with feeling tired. For instance, people who were genetically prone to Type 2 diabetes were also prone to tiredness, even if they did not have diabetes.

The authors summarized that tiredness is a “partly heritable, heterogeneous and complex phenomenon,” which requires further research to fully understand. However, they indicate that most people’s differences in tiredness can be attributed to external factors such as the lack of sleep.

This is a reposting of my Scope blog story, courtesy of Stanford School of Medicine.


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