Posts tagged genetics

Buck Institute study provides insight for new therapeutics that target the interaction between ApoE4 and a Sirtuin protein

The major genetic risk factor for Alzheimer’s disease (AD), present in about two-thirds of people who develop the disease, is ApoE4, the cholesterol-carrying protein that about a quarter of us are born with. But one of the unsolved mysteries of AD is how ApoE4 causes the risk for the incurable, neurodegenerative disease. In research published this week in The Proceedings of the National Academy of Sciences, researchers at the Buck Institute found a link between ApoE4 and SirT1, an “anti-aging protein” that is targeted by resveratrol, present in red wine.

The Buck researchers found that ApoE4 causes a dramatic reduction in SirT1, which is one of seven human Sirtuins. Lead scientists Rammohan Rao, PhD, and Dale Bredesen, MD, founding CEO of the Buck Institute, say the reduction was found both in cultured neural cells and in brain samples from patients with ApoE4 and AD. “The biochemical mechanisms that link ApoE4 to Alzheimer’s disease have been something of a black box. However, recent work from a number of labs, including our own, has begun to open the box,” said Bredesen.

The Buck group also found that the abnormalities associated with ApoE4 and AD, such as the creation of phospho-tau and amyloid-beta, could be prevented by increasing SirT1. They have identified drug candidates that exert the same effect. “This research offers a new type of screen for Alzheimer’s prevention and treatment,” said Rammohan V. Rao, PhD, co-author of the study, and an Associate Research Professor at the Buck. “One of our goals is to identify a safe, non-toxic treatment that could be given to anyone who carries the ApoE4 gene to prevent the development of AD.”

In particular, the researchers discovered that the reduction in SirT1 was associated with a change in the way the amyloid precursor protein (APP) is processed. Rao said that ApoE4 favored the formation of the amyloid-beta peptide that is associated with the sticky plaques that are one of the hallmarks of the disease. He said with ApoE3 (which confers no increased risk of AD), there was a higher ratio of the anti-Alzheimer’s peptide, sAPP alpha, produced, in comparison to the pro-Alzheimer’s amyloid-beta peptide. This finding fits very well with the reduction in SirT1, since overexpressing SirT1 has previously been shown to increase ADAM10, the protease that cleaves APP to produce sAPP alpha and prevent amyloid-beta.

AD affects over 5 million Americans – there are no treatments that are known to cure, or even halt the progression of symptoms that include loss of memory and language. Preventive treatments are particularly needed for the 2.5% of the population that carry two genes for ApoE4, which puts them at an approximate 10-fold higher risk of developing AD, as well as for the 25% of the population with a single copy of the gene. The group hopes that the current work will identify simple, safe therapeutics that can be given to ApoE4 carriers to prevent the development of Alzheimer’s disease.

(Source: buckinstitute.org)

In a biological quirk that promises to provide researchers with a new approach for studying and potentially treating Fragile X syndrome, scientists at the University of Massachusetts Medical School (UMMS) have shown that knocking out a gene important for messenger RNA (mRNA) translation in neurons restores memory deficits and reduces behavioral symptoms in a mouse model of a prevalent human neurological disease. These results, published today in Nature Medicine, suggest that the prime cause of the Fragile X syndrome may be a translational imbalance that results in elevated protein production in the brain. Restoration of this balance may be necessary for normal neurological function.

"Biology works in strange ways," said Joel Richter, PhD, professor of molecular medicine at UMMS and senior author on the study. "We corrected one genetic mutation with another, which in effect showed that two wrongs make a right. Mutations in each gene result in impaired brain function, but in our studies, we found that mutations in both genes result in normal brain function. This sounds counter-intuitive, but in this case that seems to be what has happened."

Fragile X syndrome, the most common form of inherited mental retardation and the most frequent single-gene cause of autism, is a genetic condition resulting from a CGG repeat expansion in the DNA sequence of the Fragile X (Fmr1) gene required for normal neurological development. People with Fragile X suffer from intellectual disability as well as behavioral and learning challenges. Depending on the length of the CGG repeat, intellectual disabilities can range from mild to severe.

While scientists have identified the genetic mutation that causes Fragile X, on a molecular level they still don’t know much about how the disease works or what precisely goes wrong in the brain as a result. What is known is that the Fmr1 gene codes for the Fragile X protein (FMRP). This protein probably has several functions throughout the neuron but its main activity is to repress the translation of as many as 1,000 different mRNAs. By doing this, FMRP controls synaptic plasticity and higher brain function. Mice without the Fragile X gene, for instance, have a 15 to 20 percent overall elevation in neural protein production. It is thought that the inability to repress mRNA translation and the resulting increase in neural proteins may somehow hamper normal synaptic function in patients with Fragile X. But because FMRP binds so many mRNAs, and some proteins become more elevated than others, parsing which mRNA or combination of mRNAs is responsible for Fragile X pathology is a daunting task.

From Frog Egg to Fragile X

For years, Dr. Richter had been studying how translation, the process in which cellular ribosomes create proteins, went from dormant to active in frog eggs. He discovered the key gene controlling this process, the RNA binding protein CPEB. In 1998, Richter found the CPEB protein in the rodent brain where it played an important role in regulating how synapses talk to each other. At this point, his work began to move from exploring the role of CPEB in the developmental biology of the frog to how the CPEB protein impacted learning and memory. A serendipitous research symposium with colleagues at Cold Spring Harbor got him thinking about CPEB and Fragile X syndrome.

"Here I was, an outsider, a molecular biologist who had worked for years with frog eggs, in the same room with neurobiologists and neurologists, when they started talking about Fragile X syndrome and translational activity," said Richter. "It got me thinking that the CPEB protein might be a path to restoring the translational imbalance they were discussing."

Richter knew that CPEB stimulated translation and that FMRP repressed it. He also knew that animal models lacking the CPEB protein had memory deficits and that both proteins bound to many of the same mRNAs – the overlap may be as higher as 33 percent. The thought was that by taking away a protein that stimulated translation might counterbalance the loss of the repressor FMRP protein, thereby restoring translational homeostasis in the brain and normal neurological function.

"It was one of those kind of goofy ‘what if’ sort of things," said Richter.

To test his hypothesis, Richter developed a double knockout mouse model that lacked both the FMRP gene that caused Fragile X and the CPEB gene. When they began measuring for Fragile X pathologies what they found was almost too good to be true.

"We measured a host of factors, biochemical, morphological, electrophysiological and behavioral phenotypes," said Richter. "And we kept finding the same thing. By knocking out both the FMRP and CPEB genes we were able to restore levels of protein synthesis to normal and corrected the disease characteristics of the Fragile X mice, making them almost indistinguishable from wild type mice."

Most importantly, tests to evaluate short-term memory in the double knockout mice also showed normal results with no indications of Fragile X pathology. This suggested an experiment to test whether CPEB might be a potential therapeutic target for Fragile X to benefit patients. Richter and colleagues took adult Fragile X mice and injected a lentivirus that expresses a small RNA to knock down CPEB in the hippocampus, which is a brain region that is important for short-term memory. Subsequent tests showed improved short-term memory in these mice, indicating that at least this one characteristic of Fragile X syndrome, which is generally thought to be a developmental disorder, can be reversed in adults.

"People with Fragile X make too much protein," said Richter. "By using CPEB to recalibrate the cellular machinery that makes protein we’ve shown that tamping down this process has a profoundly good impact on mouse models with Fragile X. It may be that a similar approach could be beneficial for kids with this disease."

The next step for Richter and colleagues is to determine which, of the more than 300 mRNAs that both CPEB and FMRP bind to, contribute to Fragile X syndrome and how. They’ll also begin looking at small molecules and other avenues that, like the ablation of the CPEB protein, might be able to slow down the synthesis of protein. “There are several small molecules that we know affect the translational apparatus,” Richter said. “Some cross the blood/brain barrier, some are toxic, and some are not. We’d like to investigate those.”

"This is another, great example of how basic science translates to human disease," said Richter. "If we had started out looking at the human brain, not knowing about the CPEB protein and its role in translational activity, we wouldn’t have had any idea where to start or what to look for. But because we started out in the frog, where things are much easier to see, and because more often than not these processes are conserved, we’ve learned something new and totally unexpected that may have a profound impact on human disease."

(Source: eurekalert.org)

Many negative effects of drinking, such as transitioning into heavy alcohol use, often take place during adolescence and can contribute to long-term negative health outcomes as well as the development of alcohol use disorders. A new study of adolescent drinking and its genetic and environmental influences has found that different trajectories of adolescent drinking are preceded by discernible gene-parenting interactions, specifically, the mu-opioid receptor (OPRM1) genotype and parental-rule-setting.

Results will be published in the March 2014 issue of Alcoholism: Clinical & Experimental Research and are currently available at Early View.

"Heavy drinking in adolescence can lead to alcohol-related problems and alcohol dependence later in life," said Carmen Van der Zwaluw, an assistant professor at Radboud University Nijmegen as well as corresponding author for the study. "It has been estimated that 40 percent of adult alcoholics were already heavy drinkers during adolescence. Thus, tackling heavy drinking in adolescence may prevent later alcohol-related problems."

Van der Zwaluw said that both the dopamine receptor D2 (DRD2) and OPRM1 genes are known to play a large role in the neuro-reward mechanisms associated with the feelings of pleasure that result from drinking, as well as from eating, having sex, and the use of other drugs.

"Different genotypes may result in different neural responses to alcohol or different motivations to drink," she said. "For example, OPRM1 G-allele carriers have been shown to experience more positive feelings after drinking, and to drink more often to enhance their mood than people with the OPRM1 AA genotype. In addition, we chose to examine the influence of parental alcohol-specific rules because research has shown that, more than general measures of parental monitoring, alcohol-specific rule-setting has a considerable and consistent effect on adolescents’ drinking behavior."

Van der Zwaluw and her colleagues used data from the Dutch Family and Health study that consisted of six yearly waves, beginning in 2002 and including only adolescents born in the Netherlands. The final sample of 596 adolescents (50% boys) were on average 14.3 years old at Time 1 (T1), 15.3 at T2, 16.3 at T3, 17.7 at T4, 18.7 years at T5, and 19.7 years at T6. Saliva samples were collected in the fourth wave to enable genetic testing. Participants were subsequently divided into three distinct groups of adolescent drinkers; light drinkers (n=346), moderate drinkers (n=178), and heavy drinkers (n=72).

"It was found that adolescent drinkers could be discriminated into three groups: light, moderate, and heavy drinkers," said Van der Zwaluw. "Comparisons between these three groups showed that light drinkers were more often carriers of the OPRM1 AA ‘non-risk’ genotype, and reported stricter parental rules than moderate drinkers. In the heavy drinking group, the G-allele carriers, but not those with the AA-genotype, were largely affected by parental rules: more rules resulted in lower levels of alcohol use."

Van der Zwaluw explained that although evidence for the genetic liability of heavy alcohol use has been shown repeatedly, debate continues over which genes are responsible for this liability, what the causal mechanisms are, and whether and how it interacts with environmental factors. “Longitudinal studies examining the development of alcohol use over time, in a stage of life that often precedes serious alcohol-related problems, can shed more light on these issues,” she said. “This paper confirms important findings of others; showing an association of the OPRM1 G-allele with adolescent alcohol use and an effect of parental rule-setting. Additionally, it adds to the literature by demonstrating that, depending on genotype, adolescents are differently affected by parental rules.”

The bottom line is that parents can be a positive influence, Van der Zwaluw noted. “This study shows that strict parental rules prevent youth from drinking more alcohol,” she said. “However, one should keep in mind that every adolescent responds differently to parenting efforts, and that the effects of parenting may depend on the genetic make-up of the adolescent.”

(Source: eurekalert.org)

Project delves deeply in genomics of 599 glioblastoma multiforme cases to better target disease

When The Cancer Genome Atlas launched its massively collaborative approach to organ-by-organ genomic analysis of cancers, the brain had both the benefit, and the challenge, of going first.

TCGA ganged up on glioblastoma multiforme (GBM), the most common and lethal of brain tumors, with more than 100 scientists from 14 institutions tracking down the genomic abnormalities that drive GBM.

Five years later, older and wiser, TCGA revisited glioblastoma, producing a broader, deeper picture of the drivers – and potential therapeutic targets – of the disease published in the Oct. 10 issue of Cell.

“The first paper in 2008 characterized glioblastoma in important new ways and illuminated the path for all TCGA organ studies that have followed,” said senior author Lynda Chin, M.D., professor and chair of Genomic Medicine and scientific director of the Institute for Applied Cancer Science at The University of Texas MD Anderson Cancer Center.

“Our new study reflects major improvements in technology applied to many more tumor samples to more completely characterize the landscape of genomic alterations in glioblastoma,” said Chin, who was also co-senior author of the first paper while she was on the faculty of Dana-Farber Cancer Institute in Boston.

“Information generated by this unbiased, data-driven analysis presents new opportunities to discover genomics-based biomarkers, understand disease mechanisms and generate new hypotheses to develop better, targeted therapies,” Chin said.

About 23,000 new cases of GBM are predicted in the United States during 2013 and more than 14,000 people expected to die of the disease. Most patients die within 15 months of diagnosis.

Well of rich, detailed data will nurture better treatment  

New information about genetic mutations, deletions and amplifications; gene expression and epigenetic regulation; structural changes due to chromosomal alterations, proteomic effects and the molecular networks that drive GBM make for a deep, broad dataset that will underpin research and clinical advances for years to come.

“Our main contribution is this tremendous resource for the GBM research community, which is already heavily relying on the earlier TCGA study,” said co-lead author Roeland Verhaak, Ph.D., assistant professor of Bioinformatics and Computational Biology at MD Anderson. “Whatever new treatments people come up with for GBM, I’m very confident that their discovery and development will in some way have benefited from this rich and detailed data set,” he said.

The Cell paper describes analysis of tumor samples and molecular data from 599 patients at 17 study sites. Detailed clinical information including treatment and survival was available for almost all cases

New targetable mutations

In addition to confirming significantly mutated genes discovered earlier, such as the tumor suppressors TP53, PTEN and RB1 and the oncogene PIK3CA, the analysis identified 61 new mutated genes.  The most frequent mutations occurred in from 1.7 to 9 percent of cases.  

Two of these, BRAF and FGFR, might have more immediate clinical relevance, Verhaak noted. MD Anderson neuro-oncologists are checking to see if patients have these mutations. Drugs are available to address those variations now, Verhaak said. The BRAF point mutation in GBM is the same commonly found in melanoma, which is treated by a new class of drugs.

More twists and turns for EGFR

The larger data set and an improved analytical algorithm allowed major refinement of gene amplification and deletion information. For example, common amplification events were found to occur more frequently than previously known, including amplification of the epidermal growth factor receptor (EGFR) on chromosome 7.

EGFR is both amplified and mutated frequently in GBM; yet therapeutic efforts targeting EGFR so far have failed. “We found EGFR is more frequently altered than we already thought,” Verhaak said.

Overall, the EGFR gene was mutated, rearranged, amplified or otherwise altered in 57 percent of tumors. Increased EGFR protein levels in GBM cells correlated with the many mechanisms of EGFR alteration, Verhaak said.

A treatment based on EGFR still has great potential, he noted. But strategies to target EGFR will need to address the likelihood that different alterations of EGFR might be present in the same tumor and affect the impact of targeted drugs.

Breaking GBM into molecular subtypes

Verhaak and other researchers in recent years have begun to classify GBM tumors by gene expression. Four such subgroups — neural, proneural, mesenchymal and classical — were further characterized by DNA methylation pattern, signaling pathway activity and by clinical measures such as survival and treatment response. Methylation of a gene turns it off.

Understanding the subgroups could establish biomarkers to guide treatment and identify new therapeutic targets.

The team found, for example, that the survival advantage of the proneural subtype depends on a specific DNA methylation pattern known as G-CIMP and that DNA methylation of the MGMT gene may serve as a biomarker of treatment response in the classical subtype.

(Source: mdanderson.org)

Eating disorders like anorexia nervosa and bulimia often run in families, but identifying specific genes that increase a person’s risk for these complex disorders has proved difficult.

Now scientists from the University of Iowa and University of Texas Southwestern Medical Center have discovered—by studying the genetics of two families severely affected by eating disorders—two gene mutations, one in each family, that are associated with increased risk of developing eating disorders.

Moreover, the new study shows that the two genes interact in the same signaling pathway in the brain, and that the two mutations produce the same biological effect. The findings suggest that this pathway might represent a new target for understanding and potentially treating eating disorders.

"If you’re considering two randomly discovered genes, the chance that they will interact is small. But, what really sealed the deal for us that the association was real was that the mutations have the same effect," says Michael Lutter, UI assistant professor of psychiatry and senior author of the study.

Overall, the study, published Oct. 8 in the Journal of Clinical Investigation, suggests that mutations that decrease the activity of a transcription factor—a protein that turns on the expression of other genes—called estrogen-related receptor alpha (ESRRA) increase the risk of eating disorders.

The challenge of finding genes for complex diseases

Anorexia nervosa and bulimia nervosa are fairly common, especially among women. They affect between 1 and 3 percent of women. They also are among the most lethal of all psychiatric diseases; about 1 in 1,000 women will die from anorexia.

Finding genes associated with complex diseases like eating disorders is challenging. Scientists can analyze the genetics of thousands of people and use statistics to find common, low-risk gene variations, the accumulation of which causes complex disorders from psychiatric conditions like eating disorders to conditions like heart disease or obesity.

On the other end of the spectrum are very rare gene variants, which confer an almost 100 percent risk of getting the disease. To track down these variants, researchers turn to large families that are severely affected by an illness.

Lutter and his colleagues were able to work with two such families to identify the two new genes associated with eating disorders.

"It’s basically a matter of finding out what the people with the disorder share in common that people without the disease don’t have," Lutter explains. "From a theoretical perspective, it’s straightforward. But the difficulty comes in having a large enough group to find these rare genes. You have to have large families to get the statistical power."

In the new study, 20 members from three generations of one family (10 affected individuals and 10 unaffected), and eight members of a second family (six affected and two unaffected) were analyzed.

Two genes, one pathway

The gene discovered in the larger family was ESRRA, a transcription factor that turns on the expression of other genes. The mutation associated with eating disorders decreases ESSRA activity.

The gene found in the second family is a transcriptional repressor called histone deacetylase 4 (HDAC4), which turns off transcription factors, including ESRRA. This mutation is unusual in the sense that it increases the gene’s activity—most mutations decrease or destroy a gene’s activity.

Importantly, the team also found that the two affected proteins interacted with one another; HDAC4 binds to ESRRA and inhibits it.

"The fact that the HDAC4 mutation happens to increase the gene activity and happens to increase its ability to repress the ESSRA protein we found in the other family was just beyond coincidence," Lutter says.

The two genes are already known to be involved in metabolic pathways in muscle and fat tissue. They also are both regulated by exercise.

In the brain, HDAC4 is very important for regulating genes that form connections between neurons. However, there’s almost nothing known about ESRRA in the brain, although it is expressed in many brain regions that are disrupted in anorexia.

Lutter and his colleagues plan to study the role of these genes in mice and in cultured neurons to find out exactly what they are doing in the brain. They will also look for ways to modify the genes’ activity, with the long-term goal of finding small molecules that might be developed into therapies for eating disorders.

They also plan to study patients with eating disorders and see if other genes associated with the ESSRA/HDAC4 brain pathway are affected in humans.

(Source: medicine.uiowa.edu)

About 70 percent of a person’s intelligence can be explained by their DNA — and those genetic influences only get stronger with age, according to new research from The University of Texas at Austin.

The study, authored by psychology researchers Elliot Tucker-Drob, Daniel Briley and Paige Harden, shows how genes can be stimulated or suppressed depending on the child’s environment and could help bridge the achievement gap between rich and poor students. The findings are published online in Current Directions in Psychological Science.

To investigate the underlying mechanisms at work, Tucker-Drob and his colleagues analyzed data from several studies tracking the cognitive ability and environmental circumstances of twin and sibling pairs. According to the findings, genetic factors account for 80 percent of cognition for children in economically advantaged households. Yet disadvantaged children – who rank lower in cognitive performance across the board – show almost no progress attributable to their genetic makeup.

This doesn’t mean disadvantaged children are genetically inferior. Instead, they have less high-quality opportunities, such as learning resources and parental involvement, to reach their genetic potential, Tucker-Drob says. 

“Genetic influences on cognitive ability are maximized when people are free to select their own learning experiences,” says Tucker-Drob, who is an assistant professor of psychology. “We were born with blueprints; the question is how are we using our experiences to build upon our genetic makeup?”

In a related study, Daniel Briley, a psychology doctoral student, examined how genetic and environmental influences on cognition change over time. Using meta-analytic procedures — the statistical methods used to analyze and combine results from previous, related literature — Briley examined genetic and environmental influences on cognition in twin and sibling pairs from infancy to adolescence.

According to his findings, published in the July issue of Psychological Science, genes influencing cognition become activated during the first decade of life and accelerate over time. The results emphasize the importance of early literacy and education during the first decade of life.

“As children get older, their parents and teachers give them increasing autonomy to do their homework to the best of their ability, pay attention in class, and choose their peer group,” says Briley. “Each of these behaviors likely influences their academic development. If these types of behaviors are influenced by genes, then it would explain why the heritability of cognitive ability increases as children age.”

Tucker-Drob says this research highlights the possibilities for bridging the achievement gap between the rich and poor.

“The conventional view is that genes place an upper limit on the effects of social intervention on cognitive development,” says Tucker-Drob. “This research suggests the opposite. As social, educational and economic opportunities increase in a society, more children will have access to the resources they need to maximize their genetic potentials.”

(Source: utexas.edu)