Small molecules shed light on cancer therapies

Posted by Biomechanism 

Patients suffering from aggressive brain cancer will benefit from the results of a University of Illinois study that could advance the development of targeted gene therapies and improve prognosis.

“We have advanced the understanding of the role of microRNAs on glioblastoma multiforme, a deadly brain cancer, by studying the networks between the microRNAs and their target genes associated with different stages of cancer development and progression,” said Kristin Delfino, a U of I doctoral candidate in animal science with a focus in genetics and bioinformatics.

What exactly are microRNAs? microRNAs are small, non-coding RNA molecules that regulate the expression of genes such as oncogenes or tumour suppressor genes. U of I researchers used a novel approach to identify the simultaneous association between thousands of microRNAs, target genes, and glioblastoma progression and survival.

Delfino integrated clinical information such as race, gender, therapy, survival, and cancer stage from 253 patients with genome-wide microRNA and gene expression data.

“We looked at the big picture and how microRNAs work together,” Delfino said. “When you look at a single microRNA alone, it can seem significant. But when you evaluate it in the context of all other microRNAs, some turn out to be more significant and others may not be as significant as they appear on their own. The systems biology approach that we implemented is critical for understanding the gene pathways influencing cancer.”

The study evaluated 534 microRNAs together, unlike the typical method of studying one at a time. They confirmed 25 microRNAs previously associated with glioblastoma survival and identified 20 other microRNAs associated with the initiation or growth of other cancer types, such as breast cancer, ovarian cancer and gastric adenocarcinoma.

“These findings suggest common pathways that can be targeted with similar drugs already developed and tested for other cancers,” said Sandra Rodriguez Zas, co-researcher and U of I professor of animal science and bioinformatics.

In addition, researchers found that some of the microRNA biomarkers of survival are personalised, Rodriguez Zas said. This means they are handy for patients of a specific race, gender or therapy. Other microRNAs are equally effective regardless of the clinical conditions of the patient.

“These biomarkers can serve as the basis to dig deeper into cancer studies,” Delfino said. “Cancer affects us all in one way or another. Unfortunately, we still don’t know how it’s caused, what takes place when it is caused and how to cure it. But these biomarkers guide us in developing specific gene therapies to target glioblastoma.”

Today, patients can quickly and cheaply be screened for microRNA and target gene levels, Rodriguez Zas said.

“Based on our research, that information can be used to select the most effective therapy and develop prognosis strategies,” Rodriguez-Zas said.

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This study, “Therapy-, Gender- and Race-specific microRNA Markers, Target Genes and Networks Related to Glioblastoma Recurrence and Survival,” was published in Cancer Genomics & Proteomics. Co-researchers include Kristin Delfino, Nicola Serao, Bruce Southey and Sandra Rodriguez Zas, all of the U of I.

Effects of prenatal smoking on infant neurodevelopment may be worse than feared: study

Posted by Biomechanism 

In one of the largest studies of its kind to date, researchers have found that babies born to mothers who smoke while pregnant face substantial delays in early neurological development, and the effects may be stronger than researchers had previously thought.

According to the study, published in the Journal of Human Capital, smoking may cause as much as a 40 percentage point increase in the probability of being at risk of developmental problems in babies between 3 and 24 months old. The effects were strongest among children from poor families, the research found.

“This study underscores the dangers of prenatal smoking,” said George Wehby, a professor at the University of Iowa’s College of Public Health and the study’s lead author. “We hope it also highlights the need for continued efforts to discourage expectant mothers from smoking.”

Study subjects were recruited from health clinics in Argentina, Brazil, and Chile. In all, nearly 1,600 children were included, making this one of the largest studies of prenatal smoking and neurodevelopment. The researchers surveyed mothers about their smoking habits, and neurological screening, which included cognitive tests and assessments of communication and basic neurological function, were administered to children by trained physicians.

Nearly 11 percent of mothers in the sample had smoked during pregnancy.

Part of the reason smoking affects poor children to a greater degree is that poor mothers who smoke tend to do so in greater quantity, the study found. But the number of cigarettes doesn’t fully explain the difference. “Being of higher socioeconomic status may offset some of the adverse smoking effects through better health behaviors and improved access to prenatal care,” Wehby said.

Previous studies have found similar adverse effects of prenatal smoking, but no previous work has tried to isolate the smoking effect from other potentially confounding factors, the researchers say. For example, mothers who smoke may also be more likely to drink and engage in other activities that could harm their babies. If that’s the case, then studies may overestimate the adverse effects of cigarettes. On the other hand, women who have high risk pregnancies have an extra incentive to avoid smoking, but still have babies with reduced neurodevelopment. If that’s the case, then studies may underestimate the effects of smoking.

Wehby and his team used a statistical technique that helps to account for these biases, which are difficult to observe directly. They took advantage of differences in smoking behaviors across the geographic locations of the mothers. Geographic differences in smoking are expected to be caused by variation in cigarettes prices and smoking policies, but are unlikely to be related to the unobservable individual-level preference for taking risk. This control allows the researchers to pin-point the smoking effect specifically.

With the controls in place, the smoking effect was found to be stronger than without them, suggesting previous studies that didn’t use such controls had actually underestimated the effects of smoking.

Despite increased awareness of the dangers of smoking, rates of prenatal smoking remain surprisingly high. According to the Centers for Disease Control and Prevention, 12 percent of pregnant American women reported that they smoked while pregnant in 2005.

“Given the importance of early child health and neurodevelopment for future wellbeing, targeted interventions to reduce prenatal smoking may result in significant improvements in child development and long-run human capital,” Wehby said.

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George L. Wehby, Kaitlin Prater, Ann Marie McCarthy, Eduardo E. Castilla, Jeffrey C. Murray, “The Impact of Maternal Smoking during Pregnancy on Early Child Neurodevelopment.” Journal of Human Capital 5:2 (Summer 2011).

Chemists discover most naturally variable protein in dental plaque bacterium

by Biomechanics 

Two UC San Diego chemists have discovered the most naturally variable protein known to date in a bacterium that is a key player in the formation of dental plaque. 

The chemists, who announced their discovery in this week's early online edition of the journal Proceedings of the National Academy of Sciences, say they believe the extreme variability of the protein they discovered in the bacterium Treponema denticola evolved to adhere to the hundreds of different kinds of other bacteria that inhabit people's mouths. They call the protein they discovered "Treponema variable protein," or TvpA for short, and estimate that it is a million to a billion times more variable than the proteins that play a primary role in vertebrate immune systems—the only other known natural system for massive protein variation. 

"In Treponema denticola, we found a protein we call TvpA, that varies considerably more than proteins of the immune system and, to our knowledge, this protein is the most variable natural protein described to date," said Partho Ghosh, a professor of chemistry and biochemistry at UC San Diego who headed the research effort. "We don't know what it does in this bacterium, but our hypothesis is that it enables it to adhere to the biofilm, commonly known as dental plaque, that exists in people's mouths." 

Ghosh explained that dental plaque varies from person-to-person in the kinds of bacteria that adhere to the teeth to form this biofilm. Because plaque grows in a sequential way and because T. denticola is one of the last key players in the formation of plaque, Ghosh said the bacterium has no idea what kinds of other bacteria will be present to adhere to.

"We suspect that by varying TvpA, T. denticola is able to find a TvpA variant that is able to adhere to whichever bacterium is already present in the biofilm," Ghosh said.

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Ghosh and Johanne Le Coq, a postdoctoral fellow in his laboratory now working at the Spanish National Cancer Center in Madrid, determined the structure of their newly discovered protein and its extreme variability using a powerful X-ray "microscope" at the Advanced Photon Source at the Argonne National Laboratory near Chicago. Their research project was supported by the U.S. Department of Energy, National Cancer Institute, National Institute of General Medical Science and National Institute of Allergy and Infectious Diseases.

Eco-labeled seafood is not always what it seems

Posted by Biomechanism 

When you buy what looks to be a nice piece of certified sustainable fish at the supermarket, you’d like to think that’s exactly what you’re getting. Unfortunately, things aren’t always what they seem, according to researchers who have analyzed DNA isolated from store-bought, eco-labeled Chilean sea bass and report their findings in the August 23 issue of Current Biology, a Cell Press publication.

Chilean Sea Bass not what it appears to be. Photo: Reuters

“We found that, for fish purchased in US groceries, not all those labeled as MSC-certified Chilean sea bass are actually MSC-certified Chilean sea bass,” said Peter Marko of Clemson University. MSC stands for the Marine Stewardship Council, an international organization dedicated to recognizing and rewarding sustainable fishing.

In the case of Chilean sea bass, MSC certification labels should indicate that a fish was harvested from the only recognized sustainable Chilean sea bass fishery, a population living in waters surrounding the sub-Antarctic island of South Georgia and a nearby plateau called Shag Rocks, Marko explained.

In fact, some of the fish that his team purchased turned out to be other species entirely. Of those that were Chilean sea bass, some 15 percent were genetically distinct from fish collected previously from the certified fishery. One sample carried a haplotype (defined as a combination of genetic variants in cellular components known as mitochondria) that has only been found on the other side of the globe, in the southern Indian Ocean. Other haplotypes that the researchers uncovered amongst fish marked with an MSC-certified label commonly trace to South American waters, and still others had never been recorded before in previous genetic surveys.

“The simplest explanation for this result is that other species plus Chilean sea bass from other, uncertified fisheries are being added to the supply chain for MSC-certified Chilean sea bass,” Marko said. Although unexpected, “the results are not exactly shocking,” given widespread mislabeling in the seafood industry and potential profits to be made.

It isn’t clear who is responsible for the misleading labels, given that fish pass through many hands from the time they are caught to the time they are purchased.

“There is no question that organizations like the Marine Stewardship Council are trying their best to guide consumers to sustainably harvested seafood, but it is currently difficult to guarantee the geographic origins of fish,” Marko said. He added that the MSC has been working on ways to confirm fishes’ origins, and the new study may serve as a model for how to go about that.

The only thing it seems that concerned consumers can really do for now is keep Chilean sea bass off their dinner menus. “At a grocery or on a plate in a restaurant, Chilean sea bass from South Georgia looks the same as Chilean sea bass from other parts of the world,” Marko said.

A New Nuance to Neurons

Posted by Biomechanism 

A fundamental new discovery about how nerve cells in the brain store and release tiny sacs filled with chemicals may radically alter the way scientists think about neurotransmission – the electrical signaling in the brain that enables everything from the way we move, to how we remember and sense the world.

The data in Hua et al. support a model for the recycling of synaptic vesicles proposed by the Edwards lab several years ago. The model predicts that different synaptic vesicle pools derive from different endocytic pathways. Recycling pool vesicles appear to originate from clathrin- and adaptor protein 2 (AP2)-dependent endocytosis, and resting pool vesicles from a pathway involving the adaptor protein AP-3. Image by S. Voglmaier and R. Edwards/UCSF.

According to the scientists at the University of California, San Francisco (UCSF) who conducted the research, the discovery doesn’t change the players involved so much as it reveals that the rules of the game are very different than previously assumed. Better understanding these rules may help researchers find new ways of addressing neurological diseases like Parkinson’s, which may arise in part because these normal brain processes go awry.

The players in question are known as vesicles – tiny sacs filled with neurotransmitters, the chemicals that neurons release to transmit a signal to the next neuron in the circuit.

Scientists have known about these vesicles and the important role they play in brain function for decades, but mystery remained because there appear to be two distinct pools of vesicles, with no understanding of what accounts for the distinction. All the tiny vesicles in an average neuron look the same, even to a trained eye peering through a powerful microscope – the same way a bunch of players wearing the same color on a given field of play would seem to belong to the same team.

In the journal Neuron this month UCSF professor Robert Edwards and his colleagues present the first evidence that, despite their appearance, vesicles in the two pools have distinct identities and fates, which are defined by the particular proteins on their surfaces.

“They look identical, but they contain different proteins,” Edwards said.

How the Brain Transmits Information

Neurons, which make up the white matter in the brain and the nerves that run throughout the body, are basically just specialized cells with very long extensions – sometimes a meter or more in length.

Down these spaghetti-like nerve fibers travel electrical impulses, which will cause the neuron to release some of these tiny vesicle sacs, spilling their chemical contents into the synapse, a gap between the nerve ending and the next neuron. The chemicals then seep over to the adjoining neuron, sometimes triggering it to fire in turn.

This basic game of neurotransmission is played trillions of times over by the 10 billion or so neurons in the human brain. Some neurons are so active that they fire as many as 100 times a second, requiring mechanisms to sustain these high rates.

The vesicles play a crucial role in this process because they allow neurons to fire when ready. Neurons use the vesicles to package the chemicals and transport them in advance so that they can release as soon as an electrical impulse arrives. Since the release sites are far away from the cell center, the vesicles must recycle locally to maintain high rates of release.

For years, scientists have observed that while all vesicles appear identical, they actually exist in two different pools. The smaller pool, found at the extreme land’s end of the neuron, holds the ones that release neurotransmitters when an electrical impulse arrives. After release, the vesicles are quickly recycled for continued use, and for this reason scientists have called this the “recycling” pool of vesicles.

The second pool of vesicles can be much larger, accounting for up to 80 percent of all the vesicles at a synapse. Surprisingly, these vesicles do not respond to electrical impulses. Instead they sit dormant when the signal arrives and, because of this, scientists have dubbed this the “resting” pool.

“It’s not clear what they respond to or what their function is,” Edwards said.

Because the vesicles in the two pools appear to be identical under the microscope, nobody knew if there was actually any difference between them. In the past, many scientists hypothesized that the difference was simply a matter of location – the recycling ones come into play when an electrical impulse arrives simply because they happen to be at the right spot for release.

But some scientists pondered whether the identity of the vesicles determines their behavior and not the other way around – that the recycling ones are in the right spot because they are the ones destined to be released. It’s sort of like asking whether a soccer player is a goalie because he happens to block shots near the goal, or because he’s designated to be the goalie.

The new work essentially shows that goalies block shots because they’re goalies.

Proteins Determine the Fate

In their paper, Edwards and his colleagues show that vesicles in the two different pools contain different proteins and that these differences determine how they behave. Using a technique for labeling proteins with glowing molecules derived from jellyfish, they were able to show that a protein called VAMP7 is present at high levels in the resting pool rather than the recycling pool, which contains more of other synaptic vesicle proteins.

This shows that the body makes and maintains different pools of vesicles containing different proteins for different purposes: release or some other function. According to Edwards, the observation has far-reaching implications for our understanding of how neurotransmitters are packaged, transported and released from neurons.

“What’s happening is not a simple, monolithic process,” he said.

The observation gives new insight into the function of the brain at the most basic, microscopic level. It also may help unravel some of the secrets of neurological diseases, aspects of which may be related to how vesicles are produced and released.

According to Edwards, resting vesicles are involved in a separate not-well-understood process in which neurons spontaneously release vesicles, which may help them adjust the types of connections they make with each other as well as the strength of those connections. This process may play a role in neurological diseases, many of which are characterized by changes in the type and strength of synapses.

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The article, by Zhaolin Hua, Sergio Leal-Ortiz, Sarah M. Foss, Clarissa L. Waites, Craig C. Garner, Susan M. Voglmaier, Robert H. Edwards appears in the August 11, 2011 issue of the journal Neuron.

This work was supported by a fellowship from the American Heart Association and a grant from the National Institute of Mental Health, one of the National Institutes of Health.

UCSF is a leading university dedicated to promoting health worldwide through advanced biomedical research, graduate-level education in the life sciences and health professions, and excellence in patient care.

A new set of building blocks for simple synthesis of complex molecules

Posted by Biomechanism 

CHAMPAIGN, Ill. — Assembling chemicals can be like putting together a puzzle. University of Illinois chemists have developed a way of fitting the pieces together to more efficiently build complex molecules, beginning with a powerful and promising antioxidant.

Graduate student Seiko Fujii and chemistry professor Martin Burke developed a novel class of chemical “building blocks” to more efficiently synthesize complex molecules, such as the antioxidant synechoxanthin.

Led by chemistry professor Martin Burke, the team published its research on the cover of the chemistry journal Angewandte Chemie.

Burke’s group is known for developing a synthesis technique called iterative cross-coupling (ICC) that uses simple, stable chemical “building blocks” sequentially joined in a repetitive reaction. With more than 75 of the building blocks available commercially, pharmaceutical companies and other laboratories use ICC to create complex small molecules that could have medicinal properties.

“There’s pre-installed functionality and stereochemistry, so everything is set in the building blocks, and all you have to do is couple them together,” said graduate student Seiko Fujii, the first author of the paper.

However, ICC has been limited to only molecules with one type of polarity. Now, the group has developed reverse-polarity ICC, which allows a chemist to optimize the ICC process to match the target molecules’ electronic structure. The reversal in polarity enables a whole new class of building blocks, so researchers can synthesize molecules more efficiently and even construct molecules that standard ICC cannot.

For example, in the paper, the group used the new method to make synechoxanthin (pronounced sin-ecko-ZAN-thin), a molecule first isolated from bacteria in 2008 that shows great promise as an antioxidant.  Studies suggest that synechoxanthin allows the bacteria that produce it to live and thrive in highly oxidative environments.

“We as humans experience a lot of oxidative stress, and it can be really deleterious to human health,” said Burke, who also is affiliated with the Howard Hughes Medical Institute. “It can lead to diseases like cancer and atherosclerosis and neurodegenerative disorders. Evidence strongly suggests that synechoxanthin is a major part of the bacteria’s solution to this problem. We’re excited to ask the question, what can we learn from the bug? Can it also protect a human cell?”

Studies on the activity of synechoxanthin have been limited by the difficulty of extracting the molecule from bacterial cultures. Burke’s group successfully synthesized it from a mere three types of readily available, highly stable, non-toxic building blocks. Thanks to the ease of ICC, they can produce relatively large quantities of synechoxanthin for study as well as derivatives to test against the natural product.

“Because this building-block-based design is inherently flexible, once we’ve made the natural product, we can make any derivative we want simply by swapping in one different building block, and then using the reverse-polarity ICC to snap them together,” Burke said. “That’s where synthesis is so powerful. Oftentimes, the cleanest experiment will require a molecule that doesn’t exist, unless you can piece it together.”

Researchers can also use blocks that have been “tagged” with a fluorescent or radioactive dye to make it easier to study the molecule and its activity. For example, Fujii next plans to synthesize both synechoxanthin and its apolar derivative with tags so that NMR imaging can reveal its location and orientation within a cell’s membrane, possibly providing clues to its activity.

“After we have all these molecules in hand, we’re really excited to test the antioxidant activity of them in a model membrane,” Fujii said.