Cancer Causing Gene Protein Found

Dr. Tak Mak and scientists at The Campbell Family Institute for Breast Cancer Research at Princess Margaret Hospital have discovered the role of two "cousins" in the genetic family tree of cancer development.

The findings, published online today in the journal Genes and Development, plant the seed for a critical new branch of scientific inquiry, says Dr. Mak, principal investigator. Dr. Mak, Director of The Campbell Family Institute is also a Professor, University of Toronto, in the Departments of Medical Biophysics and Immunology.

The cousins are proteins related to the gene p53 family – the patriarch known for two decades to be the master gatekeeper that controls all cancer development. When gene p53 is defective, it loses its ability to regulate healthy cells and suppress cancer.

"Until now, we thought these cousins (TAp73 protein isoforms) were not involved in cancer. Our results prove that they are. This is fundamental to understanding every human cancer and furthering the science."

In the lab, Dr. Mak and his team challenged traditional thinking about the role of these proteins. "Before, scientists studied only whether these proteins were present or absent. We decided to study how they interact with each other and discovered that they actually have a split personality. When we turn one 'on' or 'off', the other changes behavior and becomes part of the cancer-causing process. The key is understanding the ratio of the interaction."

"The next step is to understand how the ratio affects cell division that leads to human cancer," says Dr. Mak, whose work was supported by the Canadian Institutes for Health Research.
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Gene variant increases risk of asthma

A tiny variation in a gene known as CHI3L1 increases susceptibility to asthma, bronchial hyperresponsiveness and decline in lung function, researchers report early online in the New England Journal of Medicine. (The printed version will appear in the April 17 issue). The gene variant causes increased blood levels of YKL-40, a biomarker for asthma. A slightly different version of the genetic variation lowers YKL-40 levels and protects against asthma.

Although the original discovery came from a study of a genetically isolated population, the Hutterites of South Dakota, the researchers were able to confirm the same connections between the CHI3L1 variations, YKL-40 levels and asthma susceptibility in three genetically diverse Caucasian populations from Chicago; Madison, Wisconsin; and Freiberg, Germany.

This gene, "may have important implications in the early identification of, susceptibility to, and prevention and treatment of asthma,” said Elizabeth G. Nabel, M.D., director, the National Heart, Lung, and Blood Institute.

"This is exciting because it connects asthma susceptibility to a whole new pathway at the protein and the genetic levels," said study author Carole Ober, professor of human genetics at the University of Chicago Medical Center. "There is a good deal more we need to find out about this connection, but now we know where to look."

"This is also the most significant genetic discovery based on our years of gathering data on asthma in the Hutterites," Ober added. "This is a group with enormous potential to advance our understanding of the genetic underpinnings of disease. We now have a remarkable collection of data, which we expect will lead us to many more insights."

Ober and colleagues at the University of Chicago had long been searching for genetic factors that could influence the risk of common diseases, such as asthma. To simplify this quest, they have focused since 1994 on the Hutterites, a genetically isolated U.S. religious community descended from about 90 people. The Hutterites came to the United States in 1874 and settled in small communal farming colonies in what is now South Dakota. Today Hutterite communities are present in the Dakotas, Minnesota, Montana, Washington and Canada.

They provide an ideal community for genetic studies because they are all members of a large pedigree that is known back to the 1700's and they live communally, sharing resources and maintaining a traditional lifestyle. "They eat the same food, live off the same allowance and have the same education," said Ober, who has been working with them since 1979. They have similar, but not identical genomes. "So the genes that make a difference are easier to detect."

In 1996 and 1997, Ober's team gathered clinical data about asthma from more than 700 members of the Hutterite communities, and stored blood samples that were recently used to measure YKL-40 levels. About 11 percent of Hutterites had asthma and another 12 percent had bronchial hyperresponsiveness.

The genetic studies took on a sharper focus in 2007, when a team led by Geoffrey Chupp of Yale University showed that, on average, patients with asthma had higher levels of the protein YKL-40 in their blood than people without asthma, and that those with more severe asthma had even higher levels.

YKL-40, a natural suspect as a cause of asthma, belongs to a family of enzymes called chitinases. These enzymes are part of the innate immune system's response to chitin, a common biologic polymer found especially in insects – including dust mites and cockroaches, which have been associated with asthma – as well as in certain disease-causing organisms, including fungi and parasitic worms. The chitinases help break down chitin. They also trigger inflammation, which is a central component of asthma.

Working with Chupp's laboratory, Ober found that mean YKL-40 levels were also increased among Hutterites with asthma or hyperresponsive airways. Ober's group also showed that these elevated YKL-40 levels were handed down from generation to generation, indicating that differences between individuals were due nearly entirely to genetic differences.

So they began looking for variations in the CHI3L1 gene on chromosome 1 that codes for YKL-40. They found one very slight genetic difference between those with asthma and those without. Hutterites with asthma were more likely to have a small but consistent variation in one part of the gene, called a promoter, which regulates when the gene is expressed.

That variation changes one DNA base pair, out of the 3 billion in the human genome, at a location in the CHI3L1gene known as -131C/G. Those with asthma were more likely to have a cytosine (C), rather than guanine (G) at this location.

Those inheriting two copies of a C at -131 had higher YKL-40 levels and an asthma prevalence of 0.20. Those with CG had intermediate YKL-40 levels and an asthma prevalence of 0.12. Those with GG had the lowest YKL-40 levels and a prevalence of only 0.08, less than half that of the CC allele.

To see if these results could be generalized from the genetically isolated Hutterite population to a more diverse group, the researchers tested the same variations in the CHI3L1 gene in 178 Caucasian children enrolled in prospective birth cohort, known as COAST, a collaboration led by Robert Lemanske of the University of Wisconsin at Madison.

They also looked for correlations between asthma and SNP -131C/G in two clinical samples, one from the Children's University Hospital in Freiberg, Germany (344 children with asthma and 294 without), and one from the asthma clinics at the University of Chicago Medical Center (99 children and adults with asthma and 197 without).

In the two clinical samples, those with the CC configuration at position 131 were more likely to have asthma, with CG intermediate and GG the lowest risk of the disease. In the COAST cohort, many subject were still too young to have developed asthma, but the genetic patterns was closely associated with YKL-40 levels, and this association was already present at birth.

The authors suspect that the change from C to G at this site reduces expression of the gene, resulting in lower levels of YKL-40 and protection from asthma.

Although variation in CHI3L1 appears to be one of the most significant genetic triggers yet discovered for susceptibility to asthma, it is far from the sole cause of the disease, the researcher caution. In the Hutterites, it explains 9.4 percent of the variance in YKL-40 levels, suggesting that additional genetic variants also influence these levels. Finding those variations "could identify additional genes," they add, "with significant impact on asthma risk and lung function."

"This evolutionarily ancient pathway involving the innate immune system plays a surprisingly important role in asthma pathogenesis," said Ober, "and a single genetic variant in the CHI3L1 gene may account for most of this risk."

This could have a significant impact on drug development, she added. "For some people, if you block YKL-40 you might dramatically reduce the severity of the disease. Knowing the genotype at SNP -131C might identify those who most likely to benefit from such a treatment."

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Genome analysis reveals new protein associated with breast cancer progression

A novel systems-based approach that combines comprehensive gene expression profiling with genome-wide transcription factor analysis and protein-protein interaction has led researchers to an important genetic marker that can help physicians know which breast cancer patients are at highest risk and will require more aggressive treatment, a research team based at the University of Chicago Medical Center reports in the April 15, 2008, issue of the journal Molecular Systems Biology.

The researchers found that high expression of a protein known as H2A.Z, which is associated with the expression of genes within the nucleus, can help physicians predict which patients are most at risk for disease spread and death. It could also serve as a new target for therapy.

“Elevated H2A.Z expression is significantly associated with metastasis and shorter survival, and it could quickly help doctors make better predictions and treatment choices for their patients,” said study director Kevin White, PhD, professor of human genetics and director of the Institute for Genomics and Systems Biology at the University of Chicago and Argonne National Laboratory. “It could also provide clues to new therapies.”

“But, perhaps more important,” he added, “we think we have developed an integrated approach to genomic analysis that can be applied to a wide range of cancers.”

Instead of a standard whole-genome analysis, looking for genetic variations that correlate with disease risk, White and colleagues integrated multiple genetic technologies to measure the effects of estrogens, which play a crucial role in many breast cancers, on multiple cellular pathways, what they refer to as a “transcriptional regulatory cascade.”

The female hormone estrogen acts by binding to the estrogen receptor, which carries the hormone’s signal to a cell’s nucleus, where it activates many other genes. One of those genes is a known cancer-related gene called c-MYC, which in turn regulates its own cascade of gene targets.

White’s team set out to map out the many sequential genetic events that occur in breast cancer cells after estrogen binding, using a series of innovative technologies. They ultimately found that estrogen-stimulated c-MYC enhanced production of H2A.Z, which altered the positioning and activation of various genes in ways that increased the odds that a cancer would spread to the lymph nodes and ultimately to distant sites, often resulting in the patient’s death.

This is not a simple process. In tumor cells from patients with estrogen-dependent breast cancers, the researchers found estrogen affected 1,615 genetic regions. One of those was the promoter for the gene for c-MYC, which, when activated, could bind another set of overlapping 311 genetic regions.

Both estrogen and c-MYC interact with the gene for H2A.Z, leading to increased production of this protein in breast cancer cells. When the researchers looked at tumor tissue samples collected from 500 patients, they found that elevated levels of H2A.Z were highly correlated with the spread of the cancer to lymph nodes and decreased patient survival. Adding H2A.Z expression to other known risk factors provided “significant prognostic information,” the authors note, “beyond what these factors alone provide.”

“Although it has been implicated in genomic stability and gene transcription, H2A.Z has never been reported to be associated with cancer,” said White. “We would not have found this clinically important factor without taking such a large-scale integrated approach.”

“We suspect this integrated systems approach will lead us to a number of previously unsuspected genes that play a role in disease initiation and progression,” he said. “Many of these could become targets for new treatments.”

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Less sleep, more TV leads to fat toddlers

Infants and toddlers who sleep less than 12 hours a day are twice as likely to become overweight by age 3 than children who sleep longer. In addition, high levels of television viewing combined with less sleep elevate the risk, so that children who sleep less than 12 hours and who view two or more hours of television per day have a 16 percent chance of becoming overweight by age 3.

“Mounting research suggests that decreased sleep time may be more hazardous to our health than we imagined,” says Elsie Taveras, assistant professor in Harvard Medical School’s Department of Ambulatory Care and Prevention and lead author on the study. “We are now learning that those hazardous effects are true even for young infants.”

Results are published in the April 2008 issue of Archives of Pediatric & Adolescent Medicine.

The study team identified 915 mother-infant pairs from Project Viva, a long-term study of the effects of diet and other lifestyle factors on maternal and child health over time. Infant weight and measurements were taken at several in-person visits up to 3 years of age. Mothers reported how many hours their child slept per day on average at 6 months, 1 year, and 2 years postpartum.

Parents were also asked to report the average number of hours their children watched television on weekdays and weekends.

The combination of low levels of sleep and high levels of television viewing appeared to be synergistic and was associated with markedly higher body mass index (BMI) scores and increased odds of becoming overweight.

“Although previous studies have shown a similar link between sleep restriction and overweight in older children, adolescents, and adults, this is the first study to examine the connection in very young children,” says Matthew Gillman, Harvard Medical School associate professor and director of the Obesity Prevention Program in the Department of Ambulatory Care and Prevention. Gillman is also the study’s senior author.

Television viewing is also a known risk factor for children becoming overweight.

These study results support efforts to reduce television viewing and to promote adequate sleep to help reduce unhealthy childhood weight gain. Children who are overweight are often at higher risk for obesity and related conditions, such as hyperlipidemia, hypertension, asthma, and type 2 diabetes.

“Getting enough sleep is becoming more and more difficult with TV, Internet, and video games in the rooms where children sleep,” says Taveras. “Our findings suggest that parents may wish to employ proven sleep hygiene techniques, such as removing TV from children’s bedrooms, to improve sleep quality and perhaps sleep duration.”

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Arizona Cancer Center Studying Benefits of Green Tea Extract

The Arizona Cancer Center at The University of Arizona is studying the effects of Polyphenon E, a green tea extract, on prostate cancer prevention. This study will determine whether Polyphenon E affects cancer-related biomarkers in blood and/or prostate tissue in men with prostate cancer.

Tea is one of the world’s most consumed beverages. Polyphenon E is a chemically defined, decaffeinated, catechin-enriched green tea extract. Catechins are plant chemicals that are considered powerful antioxidants and have multiple beneficial biological effects that could lead to cancer prevention.

Prostate cancer is the most common type of cancer found in American men, other than skin cancer. The American Cancer Society estimates that there will be about 186,320 new cases of prostate cancer in the United States in 2008.

Past and ongoing research in numerous experimental studies and in one clinical trial provide evidence that green tea or green tea extracts such as Polyphenon E may have the potential to lower the risk of prostate cancer in the human population. However, rigorous clinical investigations are needed to determine whether green tea extracts such as Polyphenon E are effective at preventing prostate cancer.

The three-year study at the Arizona Cancer Center will recruit men with a recent diagnosis of organ-confined prostate cancer and scheduled to have the prostate removed within three to six weeks from the start of the study.

Eligible participants will take either four Polyphenon E capsules or a matched placebo each morning with food up to the day of their surgery. They will provide blood samples prior to capsule intake and again right before surgery. In addition, they will complete a diary and calendar of the capsules and other medications taken, illnesses and hospitalizations. All qualified participants will be compensated for their role in this study.

Following their surgery, tissue from their prostates will be analyzed to determine whether any of the tea components can be detected.

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Heart Dieases predetermined by oxygen levels in the Womb

The amount of oxygen available to a baby in the womb can affect their susceptibility to developing cardiovascular disease later in life.

Research from scientists at the University of Cambridge indicates that your risk of developing cardiovascular disease can be predetermined before birth, not only by your genes, but also by their interaction with the quality of the environment you experience in the womb. Their research was presented this week at the annual Society for Endocrinology, British Endocrine Society meeting. The Cambridge researchers, led by Dr Dino Giussani, examined the role that oxygen availability in the womb plays in programming your susceptibility to different diseases. His group found that babies that don’t receive enough oxygen in the womb, e.g. due to pre-eclampsia (high-blood pressure during pregnancy) or placental insufficiency, are more likely to suffer from cardiovascular disease when they are adult. A reduction of oxygen levels in the womb can lead to reduced growth rates in the baby and to changes in the way that their cardiovascular, metabolic and endocrine systems develop. Combined, these alterations to the development of key systems in the body can leave the baby more prone to developing cardiovascular disease later in life. Dr Giussani’s research also indicates methods by which we can potentially combat this problem. The detrimental effects of low oxygen levels on the development of the fetus’ cardiovascular system appear to be due to the generation of oxidative stress. Treatment with antioxidants in animal pregnancies complicated by low oxygenation can reverse these effects on the developing cardiovascular system and this could form the basis for new therapeutic techniques to prevent the early origin of heart disease in complicated human pregnancy. Cardiovascular disease is the most common cause of death in the UK, accounting for 4 in every 10 deaths. Almost 2.6 million people are affected by heart and circulatory conditions in the UK, with someone having a heart attack every 2 seconds. Dr Giussani said: “We have known for a while that changes in maternal nutrition can affect fetal development and influence disease susceptibility later in life, but relatively little work has investigated how low oxygen levels in the womb may affect infant development. Our research shows that changes to the amount of oxygen available in the womb can have a profound influence on the development of the fetus in both the short and long term, and trigger an early origin of heart disease. “Interestingly, the adverse effects on the developing heart and circulation of poor fetal oxygenation are due to oxidative stress. This gives us the opportunity to combat prenatal origins of heart disease by fetal exposure to antioxidant therapy. This may halt the development of heart disease at its very origin, bringing preventative medicine back into the womb.”

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Gene's 'selective signature' helps scientists identify instances of natural selection in microbial evolution

Microbes, the oldest and most numerous creatures on Earth, have a rich genomic history that offers clues to changes in the environment that have occurred over hundreds of millions of years.

While scientists are becoming increasingly aware of the many important environmental roles played by microbes living today--they process the food in our intestines, they keep carbon moving through the ocean food web, they can be harnessed to process sewage and build specific proteins--they still know little about these tiny critters, particularly marine microbes, which generally are classified into species based on their ecological niche. For instance, two species of marine microbe might look very similar physically, but one may have adapted to life in a particularly dark part of the ocean, while its sister species may have adapted to feeding off a nutrient that is rare in most parts of the ocean, but exists in abundance in one small area.

Scientists at MIT who are trying to understand existing microbes by studying their genetic history recently created a new approach to the study of microbial genomes that may hasten our collective understanding of microbial evolution.

The researchers have reversed the usual order of inquiry, which is to study an organism, then try to identify which proteins and genes are involved in a particular function. Instead, they have come up with a simple mathematical formula that makes it possible to analyze a gene family (a single type of gene or protein that exists in many creatures) simultaneously in a group of ecologically distinct species.

This means that we can begin to identify occurrences of natural selection in an organism's evolution simply by looking at its genome and comparing it with many others at once. This would allow them to take advantage of the nearly 2,500 microbes whose genomes have already been sequenced.

The new method determines the "selective signature" of a gene, that is, the pattern of fast or slow evolution of that gene across a group of species, and uses that signature to infer gene function or to map changes to shifts in an organism's environment.

"By comparing across species, we looked for changes in genes that reflect natural selection and then asked, 'How does this gene relate to the ecology of the species it occurs in?'" said Eric Alm, the Doherty Assistant Professor of Ocean Utilization in the Departments of Civil and Environmental Engineering and Biological Engineering. Natural selection occurs when a random genetic mutation helps an organism survive and becomes fixed in the population. "The selective signature method also allows us to focus on a single species and better understand the selective pressures on it," said Alm.

"Our hope is that other researchers will take this tool and apply it to sets of related species with fully sequenced genomes to understand the genetic basis of that ecological divergence," said graduate student B. Jesse Shapiro, who coauthored with Alm a paper published in the February issue of PLoS Genetics.

Their work also suggests that evolution occurs on functional modules--genes that may not sit together on the genome, but that encode proteins that perform similar functions.

"When we see similar results across all the genes in a pathway, it suggests the genomic landscape may be organized into functional modules even at the level of natural selection," said Alm. "If that's true, it may be easier than expected to understand the complex evolutionary pressures on a cell."

For example, in Idiomarina loihiensis, a marine bacterium that has adapted to life near sulfurous hydrothermal vents in the ocean floor, the genes involved in metabolizing sugar and the amino acid phenylalanine underwent significant changes (over hundreds of millions of years) that may help the bacterium obtain carbon from amino acids rather than from sugars, a necessity for life in that ecological niche. In one of I. loihiensis' sister species, Colwellia psychrerythraea, some of those same genes have been lost altogether, an indication that sugar metabolism is no longer important for Colwellia.

Shapiro and Alm focused on 744 protein families among 30 species of gamma-proteobacteria that shared a common ancestor roughly one to two billion years ago. These bacteria include the laboratory model organism E. coli, as well as intracellular parasites of aphids, pathogens like the bacteria that cause cholera, and soil and plant bacteria. They mapped the evolutionary distance of each species from the ancestor and incorporated information about the gene family (for instance, important proteins evolve more slowly than less-vital ones) and the normal rate of evolution in a particular species' genome in order to determine a gene's selective signature.

"These are experiments we could never perform in a lab," said Alm. "But Mother Nature has put genes into an environment and run an evolutionary experiment over billions of years. What we're doing is mining that data to see if genes that perform a similar function, say motility, evolve at the same rate in different species. To the extent that they differ, it helps us to understand how change in core genes drives functional divergence between species across the tree of life."

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New research provides insight into menopause

nsight into why females of some species undergo menopause while others do not has proven elusive despite an understanding of the biological mechanisms behind the change.

However, new research by scientists at the Universities of Cambridge and Exeter suggests that menopause is an adaptation to minimize reproductive competition between generations of females in the same family unit.

Even in 'natural fertility' human societies (i.e., those without access to modern medicine or technology) women typically survive for many years after they have ceased to reproduce. Menopause represents an evolutionary puzzle because theory suggests that there should be no selection for genes which promote survival past the end of reproduction. The current explanation was proposed 50 years ago and is known as the 'grandmother hypothesis': Natural selection can favour post-reproductive survival if older non-breeding women can help their children survive and reproduce.

The problem is that data from natural fertility societies suggests that grandmothering benefits are too small to favour switching off reproduction by age fifty in order to help. So while the grandmother hypothesis can explain why women continue to survive after they have stopped breeding, it can't explain why they stop breeding in the first place.

In this paper, published today in the journal PNAS, the researchers propose that the timing of reproductive cessation in humans is best understood as an evolutionary adaptation to reduce reproductive competition between generations of females in the same family unit.

Reproductive competition is ubiquitous in other cooperative vertebrates, but up to now its potential role in human life history evolution has been overlooked. The research demonstrates that humans are unique among primates because there is almost no overlap of reproductive generations. In natural fertility populations, women on average have their first baby at 19 years and their last baby at 38 years; in other words, women stop breeding when the next generation starts to breed.

Moreover, the scientists go on to demonstrate that this pattern is expected given the female-dispersal system thought to characterize ancestral humans. Female dispersal means that reproductive competition in ancestral human families would have involved 'mothers-in-law' competing with 'daughters-in-law'. In these circumstances younger females have a decisive advantage in competition because a mother-in-law is related to her daughter-in-law's offspring (and therefore share's an interest in her reproductive success), but not vice versa.

The researchers developed a simple mathematical model of this competition which predicts that older women should cease breeding when younger women in the same social unit start to breed. This hypothesis and model can thus explain the observed timing of reproductive cessation in humans, and so contributes to a much better understanding of how menopause evolved.

Despite vast differences in wealth, resources, and access to medicine, women in all societies experience menopause. This suggests that the human fertility schedule is hard-wired into our genetic makeup as a consequence of our evolutionary history, prior to more recent cultural and technological advances.

Dr Michael Cant at the University of Exeter explains, “Women everywhere experience a rapid decline in fertility after the age of forty, culminating in menopause around ten years later. Our study helps to explain why this phase of rapid 'senescence' of the reproductive system starts when it does, and why women, on average, stop having children a full ten years before the onset of menopause.”

It also helps to explain why in some societies (particularly in Africa and Asia), women are required by social law to stop having children when their first grandchild is born. A better understanding of the selective forces that have shaped the genetically programmed human fertility schedule may in future provide medical insights into the genetic causes of premature ovarian failure and other diseases of low fertility.

“The grandmother hypothesis was proposed 50 years ago by the American evolutionary biologist George Williams,”says Dr Cant. “However, data on grandmother effects indicate that something key is missing from Williams’ argument. Our study suggests the missing part of the puzzle, and generates a raft of new testable predictions.”

Dr Rufus Johnstone at the University of Cambridge adds, “It should open up new avenues for research on menopause and fertility in humans, and provide new insights into the evolution of menopause in the two other species in which it occurs under natural conditions - killer whales and pilot whales."

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Growth hormone also guides brain wiring

A human hormone known to stimulate the growth of cells throughout the body has a new role - helping to set up the proper nerve connections in the odor center of the brain, according to University of California, Berkeley, scientists.

Airborne scent chemicals (inset) stimulate odor receptors in the nasal cavity, which send signals to the brain's olfactory bulb (yellow) located in the frontal lobe of the brain just above the nasal bone. These connections are set up during early development when sensory nerves in the nose send axons into the brain (blue and gold) that target specific neurons in the bulb to create a map of sensory information that displays a mirror symmetry across the bulb’s midline (dashed line). When IGF signaling is disrupted (right), the blue axons collapse toward the bulb’s midline, resulting in a distortion of this sensory map, demonstrating the critical role played by IGF in wiring the brain. (John Ngai/UC Berkeley; inset courtesy Nobel prize committee)

The hormone, insulin-like growth factor (IGF), is well-known to biomedical researchers and has been tested as a therapy for diabetes and some growth disorders. Until now, decades of research have turned up only one solid role for IGF, however, and that is to makes cells grow and multiply.

Neuroscientist John Ngai, Coates Family Professor of Neuroscience and director of the Functional Genomics Laboratory at UC Berkeley, and his colleagues have now found that IGF plays a critical role in setting up the connections between chemical detectors in the nose and the brain's olfactory centers. These centers, the olfactory bulbs, are a pair of raisin-sized structures in the front part of the brain that analyze signals from the many odor receptors in the nose.

IGF joins a small number of identified molecules known to direct the growth of nerve cells in the brain during its development, making it "another tool in the brain's tool kit for how you wire up the brain," Ngai said.

Aside from what this reveals about how the brain wires itself as it grows, these molecules could become important therapeutically once doctors begin implanting new cells, perhaps stem cells, into the brain to cure neurodegenerative diseases, Ngai said.

"Even if you figure out a way to grow new cells to replace dying cells, those cells still need to make proper connections," Ngai said. "So, anything you know about what drives normal connectivity in the brain will help you figure out how to get those new cells to wire up correctly."

Ngai and colleagues at UC Berkeley, the Shanghai Institutes of Biological Sciences in China and Columbia University Medical Center reported their findings in the March 27 issue of the journal Neuron.

The molecules netrin, ephrin, semaphorin, slit and now IGF are called axon guidance molecules because as nerves stretch their tentacle-like axons out into the brain to connect with other neurons, these molecules act as signposts to steer the axons to the correct brain cells. As the brain grows during early development to some 3 billion nerve cells, each nerve cell makes, on average, 10,000 connections with other nerve cells, so "guidance cues" are critical.

"Cells from the retina of the eye, for example, carry signals into your brain conveying information about the outside world, and these go back into your brain in a very ordered projection such that there is a topographic map of the visual world from the retina at each successive layer of relays in the brain," Ngai said. "Something must order those connections, or otherwise you wouldn't be seeing a coherent image."

So far, these axon guidance cues include chemoattractants that make axons grow toward them, and chemorepellants, which make them turn away. As shown by Ngai's colleagues in China, IGF is an attractant; the growth cones of axons turn toward higher concentrations of the hormone.

Compared to the visual system, the brain's odor system is still poorly understood, but it appears to have its own uniquely ordered connections, Ngai said. The nose contains some 5 million nerve cells, each of which carries only one kind of odor receptor out of about 1,000 different odor receptors, each tuned to detect different chemicals or odorants. Nose nerve cells that detect the same odorant send their axons to the same region of the olfactory bulb, and it appears that neurons that detect similar chemicals, such as different alcohols, send their axons to nearby areas of the bulb.

Scientists previously had discovered that each of our two olfactory bulbs is divided down the middle between two mirror-image representations of the nasal odor receptors. Ngai and his colleagues found that IGF is responsible for setting up these mirror images within the bulb.

"IGF signaling is absolutely required for this mirror symmetry," he said. "In the absence of IGF function, you lose information from the sensory axons of the nose to one half of the bulb."

Axons from the nose appear to express receptors for IGF on their growth cones, which allow the growth cones to essentially sniff out the IGF in the olfactory bulb and follow the trail to the proper target cells. Without the IGF produced in the olfactory bulb, the growing axons do not make the turn-off to the outer half of each bulb, but instead go only to the inner side nearest the midline of the brain.

Both of the IGF protein's forms, dubbed IGF-1 and IGF-2, are expressed by cells in the olfactory bulb, as determined by DNA microarray screens and other techniques.

While IGF appears critical in the early stages of olfactory development, when the basic architecture of the olfactory bulb is being set up in the fetus and perhaps also after birth, other axon guidance cues are no doubt needed to more finely direct the growth of axons, Ngai said. He is continuing to investigate these other cues, and also to map the nose's chemical receptors to specific areas of the bulb. Ngai and his colleagues also are following up on some early leads indicating that IGF may serve as a chemoattractant in other parts of the developing brain.

"We are seeing an emerging picture with IGF," Ngai said. "Over the past three years, there have been studies from others showing a role for IGF signaling in establishing the shape of certain neurons, and other studies showed that IGF is required for how fast axons grow. The present study tells us that IGF is actually being used as a chemoattractant. This is a new role for IGF in development."

Ngai's coauthors are former UC Berkeley graduate students Jonathan A. Scolnick and Cynthia D. Duggan, Kai Cui and Xiao-bing Yuan of the Institute of Neuroscience at the Chinese Academy of Sciences, and Shouhong Xuan and Argiris Efstratiadis of the Department of Genetics and Development at Columbia University Medical Center.

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Study shows indicator for cardiovascular events

Gene panels may someday identify patients needing more intense monitoring, treatment

A study appearing in this week’s (March 19) New England Journal of Medicine (NEJM) confirms that a combination of gene variants previously associated with cholesterol levels does reflect patients’ cholesterol levels and can signify increased risk of heart attack, stroke, or sudden cardiac death. Led by researchers from the Massachusetts General Hospital (MGH) cardiology division, the study’s findings are a first step toward the ability to identify individuals who might benefit from earlier use of cholesterol-lowering medications and other measures to combat elevated risk.

“The prospect of personalized medicine has received much hype, but until recently, there has been little hard evidence to support the promise,” says Sekar Kathiresan, MGH director of preventive cardiology, the paper’s lead author. “We feel that our data provides two insights. First, we provide a foundation for the possibility that a panel of gene variants will eventually be useful in preventive cardiac care. Second, we show that the combinations of multiple variants related to cholesterol importantly contribute to the genetic risk for heart attack.”

It is estimated that about half the variation in high-density lipoprotein (HDL) and low-density lipoprotein (LDL) cholesterol levels is inherited, rather than being caused by lifestyle factors such as diet and exercise. While studies have associated several gene variants with cholesterol levels, exactly how those variants impact the risk of cardiovascular disease is unclear. The current study was designed to explore the influence of those variants on the risk of cardiovascular events — heart attack, stroke, or sudden cardiac death — and whether measuring such variants could help predict risk better than simply measuring HDL and LDL levels.

Because the effects of individual gene variants appear slight, the research team looked at a combination of nine single-nucleotide polymorphisms (SNP) previously associated with cholesterol levels. They analyzed data from 5,414 Swedish adults who participated in a major prospective epidemiological study and correlated data — including standard measurements of HDL and LDL cholesterol and the presence of the nine gene variants — with information on the participants’ subsequent medical histories available from a registry of information collected on all Swedish citizens. After the initial genotyping of participants not receiving lipid-lowering therapy, participants were assigned a genotype score ranging from zero to 18, based on how many copies of the unfavorable SNPs they carried. Of the participants who had no cardiovascular events before enrolling in the study, 238 suffered a heart attack, stroke, or cardiac death during the subsequent 10.6 years.

Higher genotype scores did reflect higher LDL (“bad”) cholesterol and lower HDL (“good”) cholesterol levels. Importantly, those with genotype scores of 11 or higher had a 63 percent greater risk of a cardiovascular event than did those with scores of 9 or lower. Although testing for the panel of nine SNPs was not better than standard risk factors for predicting cardiac events in the overall population, among participants classified at intermediate risk by standard measures, adding the nine-SNP panel significantly improved the ability to distinguish truly elevated or reduced risk levels.

“A current clinical dilemma is how early to start patients on cholesterol-lowering medications, like statins, that can reduce the risk of heart attack. Our data suggest that those individuals classified as higher risk based on a genetic test may deserve more intense pharmacological and lifestyle treatments,” says Kathiresan. “But before we can move from our pilot data to information that can impact the care of patients with or at risk for cardiovascular disease, we need to discover all the risk-related variants — and there will probably be 50 to 100 — and then conduct clinical studies confirming that this information can reliably guide patient care.” Earlier this year Kathiresan, an instructor in medicine at Harvard Medical School, and colleagues from the Broad Institute of MIT and Harvard began this gene-discovery process and identified six new cholesterol-associated gene variants in a separate study published in Nature Genetics.

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Know thyself and you’ll know others better

Using functional MRI (fMRI) scanning, researchers have found that the region of the brain associated with introspective thought “lights up” when people infer the thoughts of others like themselves. However, this is not the case when we’re considering people we think of as different politically, socially, or religiously.

Published in the current issue of the Proceedings of the National Academy of Sciences, the study was led by Adrianna Jenkins, a graduate student in the Department of Psychology in the Faculty of Arts and Sciences at Harvard University, with Jason Mitchell, assistant professor of psychology at Harvard. Jenkins and Mitchell’s co-author was C. Neil Mcrae of the University of Aberdeen.

“Our research helps to explain how and when people draw on their own inner experiences to make inferences about the experiences of others,” says Jenkins. “The findings suggest that the part of the brain that is responsible for introspection also helps us to understand what other people might be thinking or feeling. But this primarily seems to be the case for people who we perceive to be similar to ourselves.”

Psychologists have not fully understood how it is that we make numerous, and often accurate, inferences about others’ thoughts and feelings. Some have guessed that we use aspects of our own experience to model the thoughts of others, while others posit that we acquire a knowledge base from observations and societal rules that guides our understanding of others’ mental states.

This study suggests that both processes may be used in different contexts. We may only use ourselves to understand others when we think our minds and experiences are sufficiently similar to those of the other person.

Previous research has shown that the region of the brain associated with introspection, the ventromedial prefrontal cortex (vMPFC), is also associated with understanding the thoughts and feelings of others.

Jenkins and colleagues tested whether individuals are more likely to access this self-referential region of the brain when considering the thoughts of a similar person or someone who is different. They used fMRI scans to examine brain activity when individuals were asked about their thoughts or feelings about an everyday experience, and what they imagine that another person might think or feel about a similar experience.

The study involved 13 students, both graduate and undergraduate, who, at the end of the study, all identified themselves as politically liberal.

At the beginning of the study, the subjects were shown photographs of two unfamiliar individuals, and then given a brief descriptive paragraph about each. One was described as a student with liberal political and social attitudes who attends a college in the Northeast, and the other as a conservative, fundamentalist Christian at a Midwestern university.

The subjects were asked a series of questions about their own thoughts or feelings, and the thoughts or feelings of the liberal or conservative individual. The questions were about everyday experiences such as “How much do you enjoy doing crossword puzzles?” or “How likely is it that he would get frustrated while sitting in traffic?”

By examining the brain’s activity in the vMPFC, the researchers saw that when the subjects considered the possible responses of the “liberal,” they employed the part of their brain that is active when they think about their own reactions. By contrast, the researchers did not see activity in this region of the brain when the subjects were considering the thoughts and preferences of the “conservative” student.

According to Jenkins, it’s possible that we rely on our own perspective to assess the potential thoughts and feelings of people who we think are similar, while we may make inferences regarding the thoughts of dissimilar others based on a different process.

Further research will examine whether it is possible to manipulate this effect and utilize the more introspective thought process when assessing the feelings of dissimilar others.

A forthcoming study in Psychological Science, led by Daniel Ames with Jenkins, Mitchell, and Mahzarin Banaji, the Richard Clarke Cabot Professor of Social Ethics and Carol K. Pforzheimer Professor at Radcliffe, considers whether or not the application of this self-referential thought process is immutable. In this study, the participants were asked to write a short essay from another person’s perspective. The results suggest that after an individual assumes another’s perspective (in this case by writing the essay), he or she is more likely to use the vMPFC region of the brain when later making inferences regarding that person’s thoughts or feelings.

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Neurologists Engineer First System of Human Nerve-Cell Tissue

Researchers at the University of Pennsylvania School of Medicine have demonstrated that living human nerve cells can be engineered into a network that could one day be used for transplants to repair damaged to the nervous system. They report their findings in the February issue of the Journal of Neurosurgery.

“We have created a three-dimensional neural network, a mini nervous system in culture, which can be transplanted en masse,” explains senior author Douglas H. Smith, MD, Professor, Department of Neurosurgery and Director of the Center for Brain Injury and Repair at Penn.

Although neuron transplantation to repair the nervous system has shown promise in animal models, there are few sources of viable neurons for use in the clinic and insufficient approaches to bridge extensive nerve damage in patients.

The Stretch Test
In previous work, Smith’s group showed that they could induce tracts of nerve fibers called axons to grow in response to mechanical tension. They placed neurons from rat dorsal root ganglia (clusters of nerves just outside the spinal cord) on nutrient-filled plastic plates. Axons sprouted from the neurons on each plate and connected with neurons on the other plate. The plates were then slowly pulled apart over a series of days, aided by a precise computer-controlled motor system, creating long tracts of living axons.

These cultures were then embedded in a collagen matrix, rolled into a form resembling a jelly roll, and then implanted into a rat model of spinal cord injury. After the four-week study period, the researchers found that the geometry of the construct was maintained and that the neurons at both ends and all the axons spanning these neurons survived transplantation. More importantly, the axons at the ends of the construct adjacent to the host tissue extended through the collagen barrier to connect with the host tissue as a sort of nervous tissue bridge.

The Next Step
Now, the researchers have taken the next step and are applying this technique to living human nerve cells. Smith and his team obtained human dorsal root ganglia neurons (due to their robustness in culture) to engineer into transplantable nervous tissue.

The root ganglia neurons were harvested from 16 live patients following elective ganglionectomies, and four thoracic neurons were harvested from organ donors. The neurons were purified and placed in a specially designed growth chamber. Using the stretch growth technique, the axons were slowly pulled in opposite directions over a series of days until they reached a desired length.

The neurons survived at least three months in culture while maintaining the ability to generate action potentials, the electrical signals transmitted along nerve fibers. The axons grew at about 1 millimeter per day to a length of 1 centimeter, creating the first engineered living human nervous tissue constructs.

“This study demonstrates the promise of adult neurons as an alternative transplant material due to their availability, viability, and capacity to be engineered,” says Smith. “We’ve also shown the feasibility of obtaining neurons from living patients as a source of neurons for autologous, or self, transplant as well as from organ donors for allografts.”

Penn co-authors are Jason H. Huang, Eric L. Zager, Jun Zhang, Robert G. Groff IV, Bryan J. Pfister, M. Sean Grady, and Eileen Maloney-Wilensky. Akiva S. Cohen from The Children’s’ Hospital of Philadelphia was also a co-author.
The authors thank the Gift of Life program and the family members of the organ donors for their support and selfless sacrifice. This work was funded by the National Institutes of Health.
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Breast cancer gene carriers’ risk ‘amplified’ by additional genes

Many women with a faulty breast cancer gene could be at greater risk of the disease due to extra ‘risk amplifying’ genes, according to research published in this week in the American Journal of Human Genetics.

Cancer Research UK scientists, including lead author Professor Doug Easton at the University of Cambridge, have found that common versions of two genes – FGFR2 and TNRC9 – known to increase breast cancer risk in the general population - also increase the risk in women carrying damaged versions of the BRCA2 gene.

Around one in eighteen women will develop breast cancer by the age of 65. On average, half of women carrying a faulty BRCA2 gene will develop the disease by the age of 70.

This study found that particular combinations of the FGFR2 and TNRC9 genes modify the breast cancer risk in BRCA2 mutation carriers.

Around twenty percent of the BRCA2 mutation carriers have the lowest risk combination of the FGFR2 and TNRC9 genes. The researchers found that their risk is lowered so four in every 10 women in this category are expected to develop breast cancer.

But one per cent of BRCA2 mutation carriers have the highest risk combination of FGFR2 and TNRC9 genes. Seven in every 10 women in this category are predicted to develop the disease.

These findings are the first step in a series of studies hunting for breast cancer susceptibility genes, which aims to better monitor and treat women with a family history of the disease.

Professor Easton, director of Cancer Research UK’s Genetic Epidemiology Unit at the University of Cambridge, said: “This is the first time we have found evidence that common changes in other genes can amplify the risk of breast cancer in women known to have faulty BRCA genes.

“This is the first step in finding a set of genes that modify the risk in BRCA carriers, and may influe nce how we monitor women with a family history of the disease.”

The study brings together results from international research groups looking at a total of more than 10,000 women carrying a BRCA1 or BRCA2 mutation. Dr Lesley Walker, Cancer Research UK’s director of cancer information, said: “It’s important to remember that the prevalence of this combination of gene faults is rare in the general population. But advances like this will add to our ability to identify those most at risk for clinical monitoring, detecting the disease earlier in those who develop it.”
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Potential Alzheimer’s Disease Drug Target Identified

In findings with the potential to provide a therapy for Alzheimer’s disease patients where none now exist, a researcher at the University of California, San Diego and colleagues have demonstrated in mice a way to reduce the overproduction of a peptide associated with the disease. The study, which showed substantial improvement in memory in an animal model of Alzheimer’s disease, was led by Vivian Y. H. Hook, Ph.D., professor of the Skaggs School of Pharmacy and Pharmaceutical Sciences and professor of neurosciences, pharmacology and medicine at the UCSD School of Medicine, together with American Life Science Pharmaceuticals of San Diego. The study will be published in the March 21 edition of the Journal of Biological Chemistry, online March 14.

A hallmark sign of Alzheimer’s disease, seen during autopsy of a patient’s brain, is the accumulation of amyloid plaque deposits composed primarily of the neurotoxic beta-amyloid (Aβ) peptide which is believed to be a major factor in the cause of the disease. The Aβ peptides are “cut” out from a larger protein called the amyloid precursor protein (APP) and bind together to form plaques in brain regions responsible for memory. One drug strategy to fight Alzheimer’s disease is to reduce production of Aβ.

“We discovered two chemical compounds that inhibit a new enzyme target, leading to reduced production of beta-amyloid and improved memory in a mouse model of Alzheimer’s disease,” said Hook.

Accumulation of Aß and plaque build-up are initiated when the large precursor protein, APP, a long string of amino acids, is “cut” into the smaller, neurotoxic Aβ peptides that generate amyloid plaques. Protease enzymes, a type of protein, are the “scissors” that cut the large APP to generate Aβ peptides. The protease must cut the APP amino acid sequence in two places: at the beta-secretase and the gamma-secretase sites. In this study, by inhibiting and therefore preventing the enzymatic “scissors” from “cutting” the APP chain into smaller peptides, the research team observed improved memory, as well as reduced levels of beta-amyloid protein in the brain, in mice bred to exhibit Alzheimer’s disease symptoms.

In the past, many scientists have focused on a mutant beta-secretase sequence only seen in one extended family of patients in Sweden with Alzheimer’ disease, Hook explained. This mutation, the so-called Swedish mutation, was known to result in an overproduction of Aβ. Past research has shown that this Swedish mutant sequence is cut by a protease called BACE1.

Hook and colleagues found that a different protease, called Cathepsin B (CatB) works to cut the normal beta-secretase site – which is the site present in more than 99 percent of patients with Alzheimer’s disease – but not the Swedish mutant site. They also tested compounds that inhibit CatB – E64d and CA074Me –in a mouse model of Alzheimer’s disease with the normal beta-secretase site.

“After drug treatment, using water maze memory tests, we found that the mice exhibited great improvement in their memory, as well as reduced brain levels of beta amyloid,” said Hook. “These results are consistent with previous research indicating that CatB is elevated in brains of patients with Alzheimer’s disease.”

She added that a drug that duplicates this reduction by targeting CatB in humans could be an effective treatment for Alzheimer’s disease in the more than 99 percent of individuals with the normal beta-secretase site. “By disabling the enzyme’s ability to cut the ‘beta’ end of the amino acid sequence, researchers may discover a way to limit production of neurotoxic Aβ and reduce amyloid plaques in the brain.”

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A Protein that Triggers Aggressive Breast Cancer

SATB1 is a nuclear protein well known for its crucial role in regulating gene expression during the differentiation and activation of T cells, making it a key player in the immune system. But SATB1 has now revealed a darker side: it is an essential contributing factor in the most aggressive forms of breast cancer.

SATB1 forms a three-dimensional cage-like structure within the cell nucleus (left) that binds to DNA specific sites within genes, reorganizes chromatin, and recruits enzymes that promote the expression or suppression of genes (right).

Breast cancer cells need SATB1 to become metastatic; metastasis — the stage when cells break away from the original tumor and spread to other parts of the body — is the final step of solid tumor progression and is the most common cause of death in cancer patients.

"In breast tumors, SATB1 reprograms the genome to change the expression of hundreds of genes, promoting tumor growth and metastasis," says Terumi Kohwi-Shigematsu, a scientist in the Life Sciences Division of the Department of Energy's Lawrence Berkeley National Laboratory who, with her colleagues, discovered SATB1 and has since investigated its many functions. She says, "SATB1's role in breast cancer is a new paradigm for the way tumors progress."

Kohwi-Shigematsu, working with Berkeley Lab's Hye-Jung Han and Yoshinori Kohwi, and with Jose Russo of the Fox Chase Cancer Center in Philadelphia, found that when SATB1 is detected in a breast tumor, the cancer is highly likely to progress or recur.

Moreover, by introducing SATB1 into otherwise nonmetastatic breast cancer cells, invasive tumors can be induced in mice; conversely, removing SATB1 from metastatic cells not only abolishes metastasis and tumor growth in mice but also returns cells to their normal appearance in vitro. The researchers have published these and other findings in the March 13, 2008 issue of Nature.

How SATB1 works

Kohwi-Shigematsu and Kohwi originally identified a class of DNA sequences they called base-unpairing regions (BURs), a finding that led Kohwi-Shigematsu's group to the discovery of "special AT-rich sequence binding protein 1" (SATB1). SATB1 binds to BURs in double-stranded DNA by recognizing the BURs' distinctive phosphate-backbone structure. BURs contain unusual sequence contexts that readily unzip to expose DNA's individual strands.

As a nuclear architectural protein, SATB1 forms what Kohwi-Shigematsu calls a "3‑D chickenwire network" inside the nucleus of the cell. SATB1 anchors chromosomes to its cage-like structure by tethering the BURs in the target genes, thus serving as a kind of "glue" for these genes. SATB1 folds and remodels the chromatin — the intertwined DNA and proteins that form chromosomes — into new shapes, bringing even distant parts of the genome together for coordinated control of gene expression and regulation.

SATB1 also globally regulates histone status in the chromatin by recruiting histone-modifying enzymes to the target-gene loci. Histones are the proteins around which DNA in chromatin is wound like thread on a spool; histone status renders DNA sequences accessible or inaccessible for transcription.

Early on, SATB1's ability to regulate gene expression was identified as critical to T-cell development. Although Kohwi-Shigematsu and her colleagues have found several other cell types that use SATB1 to reshape chromatin and regulate gene expression in a similar way, SATB1 is not expressed in all cells. SATB1 seems particularly important in cells which must change their function — as do many progenitor cells, including the thymocytes that turn into T cells. And as cancerous cells must do to turn into metastatic cells.

"Hye-Jung Han of our group started by looking at two dozen breast-cell lines, including normal human epithelial cells" — epithelial cells are the kind that form the linings of hollow glands in the breast — "and both nonmetastatic and metastatic breast cancer cells," Kohwi-Shigematsu says. "Only the metastatic cells expressed SATB1, with the most aggressive breast cancer cells showing the highest levels of the protein."

The researchers examined over 2,000 human primary breast cancer tissue samples for which clinical follow-up studies were available. The highest levels of SATB1 were in samples from patients whose survival times had been shortest; patients whose tumor samples had no SATB1 expression generally had longer survival times.

The analysis showed that a high level of SATB1 expression by itself is an excellent indicator of poor prognosis — independent of whether breast cancer cells have already metastasized to the lymph nodes at the time of diagnosis.

SATB1 takes command

The reason why SATB1 is a good prognostic marker is because SATB1 drives breast cancer cells to become invasive, as revealed by both in vitro and in vivo studies.

The researchers performed in vitro studies of highly metastatic cell lines, reducing SATB1 expression through the use of shRNAs, "short-hairpin-interfering" RNAs, that dramatically reduced the invasive capacity of these cells and also reduced their capacity for unattached growth — a necessity if metastasizing cancer cells are to travel through the blood and lymph vessels.

With increasing stages of breast cancer, initially nonmalignant cells making up the acini in the breast become increasingly disorganized and finally metastasize (top). Breast cells cultured in a three-dimensional matrix form acinar structures, but the expression of SATB1 in these cells causes increasing disorganization. When SATB1 expression is reduced in these metastatic cells, they return to normal appearance (bottom).

Other in vitro studies used normal breast epithelial cells, the kind that form the hollow oriented structures called acini, the milk-secreting glands of the breast. Normal cells form similar, well-organized acinar structures in vitro, whereas in highly metastatic epithelial cell lines these structures are disorganized and lack polarity. When SATB1 expression is reduced in the metastatic cell lines, they too form the kind of polarized, uniform acinar structures found in normal mammary epithelial cells.

These in vitro results were confirmed in vivo, in mice. Nine weeks after human aggressive breast cancer cells were injected into the tails of test mice, these cells developed into metastatic nodules (tumors) on the lungs. But when SATB1 expression was reduced or removed from the injected cancer cells, the mice developed fewer or even no nodules, depending on the remaining levels of SATB1. Once SATB1 is greatly reduced, these cells no longer form tumors when injected directly into breast fat pads.

In vivo studies also established that cancer cells which do not normally express SATB1, and do not normally metastasize, can become aggressive if they are modified to express SATB1. Once SATB1 is expressed, they form large tumors when injected into breast fat pads; they then invade the blood circulatory system and form metastatic tumors in lungs.

The tests of human breast cancer cell lines in mice allowed the researchers to establish that, for these cells, SATB1 is necessary and sufficient for tumor growth and metastatic activity.

"SATB1 is a key player in the metastasis of breast cancer cells, controlling expression of over a thousand genes," says Kohwi-Shigematsu. "It increases the expression of genes that promote tumor growth and reduces the expression of tumor suppressors. Among the regulated genes are numerous growth-factor genes and genes affecting cell adhesion, cell signaling, cell-cycle regulation, and other functions."

Among the important genes regulated by SATB1, the researcher identified many that are already known to play a role in aggressive breast cancers, including the epidermal growth factor gene ERBB2, otherwise known as HER2.

"What we have found is a new model of altered gene regulation during the progression of tumors, which depends on SATB1's reprogramming of the gene expression profile," Kohwi-Shigematsu says. "What results is a new and aggressive cancer phenotype that promotes both tumor growth and metastasis."

The discovery of SATB1's key part in aggressive breast cancer has profound implications for prognosis and for possible new treatments for cancer's most malignant forms. At the same time, the discovery opens a wide field of fundamental scientific inquiry, beginning with the most basic questions. What determines the particular sets of genes affected by SATB1 in specific tissues? What other factors may work together with SATB1?

"An important question is what turns on SATB1 during breast cancer progression," says Kohwi-Shigematsu. "That's just the beginning of the things we really want to know."

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On a 'roll': MIT researchers devise new cell-sorting system

Capitalizing on a cell's ability to roll along a surface, MIT researchers have developed a simple, inexpensive system to sort different kinds of cells--a process that could result in low-cost tools to test for diseases such as cancer, even in remote locations.

Rohit Karnik, an MIT assistant professor of mechanical engineering and lead author of a paper on the new finding appearing last week in the journal Nano Letters, said the cell-sorting method was minimally invasive and highly innovative.

"It's a new discovery," he said. "Nobody has ever done anything like this before."

The method relies on the way cells sometimes interact with a surface (such as the wall of a blood vessel) by rolling along it. In the new device, a surface is coated with lines of a material that interacts with the cells, making it seem sticky to specific types of cells. The sticky lines are oriented diagonally to the flow of cell-containing fluid passing over the surface, so as certain kinds of cells respond to the coating they are nudged to one side, allowing them to be separated out.

Cancer cells, for example, can be separated from normal cells by this method, which could ultimately lead to a simple device for cancer screening. Stem cells also exhibit the same kind of selective response, so such devices could eventually be used in research labs to concentrate these cells for further study.

Normally, it takes an array of lab equipment and several separate steps to achieve this kind of separation of cells. This can make such methods impractical for widespread screening of blood samples in the field, especially in remote areas. "Our system is tailor-made for analysis of blood," Karnik said. In addition, some kinds of cells, including stem cells, are very sensitive to external conditions, so this system could allow them to be concentrated with much less damage than with conventional multistage lab techniques.

"If you're out in the field and you want to diagnose something, you don't want to have to do several steps," Karnik said. With the new system, "you can sort cells in a very simple way, without processing."

Now that the basic principle has been harnessed in the lab, Karnik estimates it may take up to two years to develop into a standard device that could be used for laboratory research purposes. Because of the need for extensive testing, development of a device for clinical use could take between five and 10 years, he estimated.

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MIT researchers demonstrate protective role of microRNA

Snippets of genetic material that have been linked to cancer also play a critical role in normal embryonic development in mice, according to a new paper from MIT cancer biologists.

The work, reported in the March 7 issue of Cell, shows that a family of microRNAs--short strands of genetic material--protect mouse cells during development and allow them to grow normally. But that protective role could backfire: The researchers theorize that when these microRNAs become overactive, they can help keep alive cancer cells that should otherwise die--providing another reason to target microRNAs as a treatment for cancer.

Discovered only a decade ago, microRNAs bind to messenger RNAs (mRNAs), preventing them from delivering protein assembly instructions, thereby inhibiting gene expression. The details of how microRNAs act are not yet fully understood.

"The scientific community is busy trying to understand what specific biological functions these microRNAs affect," said Andrea Ventura, lead author of the paper and postdoctoral associate in the Koch Institute for Integrative Cancer Research at MIT (formerly known as the Center for Cancer Research).

Ventura--who works in the laboratory of Tyler Jacks, director of the Koch Institute--and her colleagues studied the function of a family of microRNAs known as the miR-17~92 cluster.

Previous research has shown that the miR-17~92 cluster is overactive in some cancers, especially those of the lungs and B cells.

To better understand these microRNAs' role in cancer, the researchers decided to study their normal function. Knocking out microRNA genes and observing the effects can offer clues into how microRNA helps promote cancer when overexpressed.

They found that when miR-17~92 was knocked out in mice, the animals died soon after birth, apparently because their lungs were too small. Also, their B cells, a type of immune cell, died in an early stage of cell development.

This suggests that miR-17~92 is critical to the normal development of lung cells and B cells. In B cells, these microRNAs are likely acting to promote cell survival by suppressing a gene that induces cell death, said Ventura.

"Understanding why these things are happening provides important insight into how microRNAs affect tumorigenesis," he said.

The researchers theorize that when miR-17~92 becomes overactive in cancer cells, it allows cells that should undergo programmed cell death to survive.

Blocking microRNAs that have become overactive holds promise as a potential cancer treatment. Research is now being done on molecules that prevent microRNAs from binding to their target mRNA.

More work needs to be done to make these inhibitors into stable and deliverable drugs, but Ventura said it's possible it could be done in the near future.

The exact genes targeted by miR-17~92 are not known, but one strong suspect is a gene called Bim, which promotes cell death. However, a single microRNA can have many targets, so it's likely there are other genes involved.

The researchers also studied the effects of knocking out two other microRNA clusters that are closely related to miR-17~92 but located elsewhere in the genome.

They found that if the other two microRNA clusters are knocked out but miR-17~92 remains intact, the mice develop normally. However, if miR-17~92 and one of these similar clusters are removed, the mice die before birth, suggesting there is some kind of synergistic effect between these microRNA families.

Other MIT authors of the paper are Amanda Young, graduate student in biology; Monte Winslow, postdoctoral fellow in the Center for Cancer Research (CCR); Laura Lintault, staff affiliate in the CCR; Alex Meissner, faculty member at the Broad Institute of MIT and Harvard; Jamie Newman, graduate student in biology; Denise Crowley, staff affiliate at the CCR; Rudolf Jaenisch, professor of biology and member of the Whitehead Institute for Biomedical Research; Phillip Sharp, MIT Institute Professor; and Jacks, who is also a professor of biology.

The research was funded by the National Institutes of Health and the National Cancer Institute.

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Device allows scientists to control gene activity across generations of cells

Just as cells inherit genes, they also inherit a set of instructions that tell genes when to become active, in which tissues and to what extent. Now, Rockefeller University researchers have built a device that, by allowing scientists to turn genes on and off in actively multiplying budding yeast cells, will help them figure out more precisely than before how genes and proteins interact with one another and how these interactions drive cellular functions.

�A slight disturbance in the abundance of a single protein can affect the functioning of a cell dramatically,�� says Gilles Charvin, a postdoc who works with both Eric Siggia, head of the Laboratory of Theoretical Condensed Matter Physics, and Frederick Cross, headof the Laboratory of Yeast Molecular Genetics. �So, we wanted to devise a way to supply a single cell with a controlled pulse of protein at any time and then see how the cell would respond,�� he says.

Although scientists have had the tools to track single cells and measure the protein levels within them, the new device allows scientists to track them for a longer period of time while not only monitoring but also controlling the activity of genes. The precision with which the device can track single cells also allows scientists to construct pedigrees, making it possible to compare gene activity from one cell to the next.

The device relies on electrovalves to control a flow of media, which travels through a tube and then diffuses across a porous membrane to reach the budding yeast cells. The cells are clamped between this membrane and a soft material, which forces them to bud horizontally without damage.

That was the major design hurdle,�� says Charvin. �To create a device in which cells don�t move, so that you can track hundreds of single cells for a long time � about eight rounds of cell division � which typically lasts 12 hours.��

In order to induce the activity of a gene, the researchers used inducer molecules that diffuse through the cell membrane and control DNA segments called promoters. The molecule�s presence silences the promoter, which silences the expression of the gene; the molecule�s absence, on the other hand, activates the promoter, which activates the gene to crank up the molecule�s production.

By exploiting this principle, the scientists showed that they could successfully turn specific genes on and off by controlling the flow of an inducer molecule called methionine. They observed that pulses as short as 10 minutes led to changes in protein levels that could be measured.

The group used this device to study the cell cycle by putting a gene that must be expressed for cells to divide under the control of the methionine promoter, and showed that budding yeast cells would stop and start dividing in perfect synchrony with alternating pulses of media that did and didn�t contain methionine. �Like slaves, the cells relied on the external pulse we gave them to figure out what to do next,� says Charvin. �We thought this was a pretty striking illustration of the capabilities of this device.�
SOURCE

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Evolving complexity out of 'junk DNA'

Vertebrates - animals such as humans that possess a backbone - are the most anatomically and genetically complex of all organisms, but explaining how they achieved this complexity has vexed scientists since the conception of evolutionary theory.

Alysha Heimberg of Dartmouth College and her colleagues showed that microRNAs, a class of tiny molecules only recently discovered residing within what has usually been considered ‘junk DNA’, are hugely diverse in even the most lowly of vertebrates, but relatively few are found in the genomes of our invertebrate relatives.

She explained: “There was an explosive increase in the number of new microRNAs added to the genome of vertebrates and this is unparalleled in evolutionary history.”

Co-author, Dr Philip Donoghue of Bristol University’s Department of Earth Sciences continued: “Most of these new genes are required for the growth of organs that are unique to vertebrates, such as the liver, pancreas and brain. Therefore, the origin of vertebrates and the origin of these genes is no coincidence.”

Dr Kevin Peterson of Dartmouth College said: “This study not only points the way to understanding the evolutionary origin of our own lineage, but it also helps us to understand how our own genome was assembled in deep time.”

Source

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ARTIFICIAL SWEETENERS LINKED TO WEIGHT GAIN

Want to lose weight? It might help to pour that diet soda down the drain. Researchers have laboratory evidence that the widespread use of no-calorie sweeteners may actually make it harder for people to control their intake and body weight. The findings appear in the February issue of Behavioral Neuroscience, which is published by the American Psychological Association (APA).

Psychologists at Purdue University's Ingestive Behavior Research Center reported that relative to rats that ate yogurt sweetened with glucose (a simple sugar with 15 calories/teaspoon, the same as table sugar), rats given yogurt sweetened with zero-calorie saccharin later consumed more calories, gained more weight, put on more body fat, and didn't make up for it by cutting back later, all at levels of statistical significance.

Authors Susan Swithers, PhD, and Terry Davidson, PhD, surmised that by breaking the connection between a sweet sensation and high-calorie food, the use of saccharin changes the body's ability to regulate intake. That change depends on experience. Problems with self-regulation might explain in part why obesity has risen in parallel with the use of artificial sweeteners. It also might explain why, says Swithers, scientific consensus on human use of artificial sweeteners is inconclusive, with various studies finding evidence of weight loss, weight gain or little effect. Because people may have different experiences with artificial and natural sweeteners, human studies that don't take into account prior consumption may produce a variety of outcomes.

Three different experiments explored whether saccharin changed lab animals' ability to regulate their intake, using different assessments – the most obvious being caloric intake, weight gain, and compensating by cutting back.

The experimenters also measured changes in core body temperature, a physiological assessment. Normally when we prepare to eat, the metabolic engine revs up. However, rats that had been trained to respond using saccharin (which broke the link between sweetness and calories), relative to rats trained on glucose, showed a smaller rise in core body temperate after eating a novel, sweet-tasting, high-calorie meal. The authors think this blunted response both led to overeating and made it harder to burn off sweet-tasting calories.

“The data clearly indicate that consuming a food sweetened with no-calorie saccharin can lead to greater body-weight gain and adiposity than would consuming the same food sweetened with a higher-calorie sugar,” the authors wrote.

The authors acknowledge that this outcome may seem counterintuitive and might not come as welcome news to human clinical researchers and health-care practitioners, who have long recommended low- or no-calorie sweeteners. What's more, the data come from rats, not humans. However, they noted that their findings match emerging evidence that people who drink more diet drinks are at higher risk for obesity and metabolic syndrome, a collection of medical problems such as abdominal fat, high blood pressure and insulin resistance that put people at risk for heart disease and diabetes.

Why would a sugar substitute backfire? Swithers and Davidson wrote that sweet foods provide a “salient orosensory stimulus” that strongly predicts someone is about to take in a lot of calories. Ingestive and digestive reflexes gear up for that intake but when false sweetness isn't followed by lots of calories, the system gets confused. Thus, people may eat more or expend less energy than they otherwise would.

The good news, Swithers says, is that people can still count calories to regulate intake and body weight. However, she sympathizes with the dieter's lament that counting calories requires more conscious effort than consuming low-calorie foods.

Swithers adds that based on the lab's hypothesis, other artificial sweeteners such as aspartame, sucralose and acesulfame K, which also taste sweet but do not predict the delivery of calories, could have similar effects. Finally, although the results are consistent with the idea that humans would show similar effects, human study is required for further demonstration.

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