A new study reveals that the metadherin gene (MTDH) plays a role in both cancer metastasis and resistance to chemotherapy.  The research, published by Cell Press in the January 6th issue of the journal Cancer Cell, identifies MTDH as a promising therapeutic target for high risk breast cancers.

“Most breast cancer patients resist currently available therapeutic regimens and succumb to recurrent tumors that spread to distant vital organs, such as lung, bone, liver and brain,” explains senior study author, Dr. Yibin Kang from the Department of Molecular Biology at Princeton University.  “Resistance to chemotherapy and metastasis remain major challenges to curative therapy.”

Previous research identified several clinically applicable genetic signatures associated with poor clinical outcomes of breast cancer.  However, the signatures differed between independent studies, making it difficult to identify overlapping, functionally relevant genes that might be useful for understanding, and eventually preventing, breast cancer metastasis and chemoresistance.

To further unravel the complex genetic events involved in breast cancer, Dr. Kang and colleagues developed a sophisticated computational algorithm designed to identify genomic changes in an extensive collection of breast tumor samples.  The researchers discovered abnormally high copy numbers of chromosomal region 8q22 in more than 30% of breast cancers examined.  Patients having this type of breast cancer often had a shorter survival time due to recurrent and metastatic cancers.

The researchers went on to find that among a handful of genes in the 8q22 region, MTDH was responsible for both increased metastasis and increased resistance to chemotherapeutics.  MTDH protein increased metastasis of breast cancers to distant organs by enhancing the binding of cancer cells to blood vessels in these organs.  In addition, MTDH protein promoted cell survival, allowing cancer cells to become more resistant to a wide variety of chemotherapeutic agents that are currently used to treat breast cancer.  Further, when the researchers genetically altered the cancer cells to reduce expression of MTDH, the tumor cells became less capable of metastasis and more likely to be eliminated by chemotherapeutic agents.

“These findings establish MTDH as an important therapeutic target for simultaneously enhancing chemotherapy efficacy and reducing metastasis risk,” concludes Dr. Kang.  “Molecular targeting of MTDH may not only prevent the seeding of breast cancer cells to the lung and other vital organs but also sensitize tumor cells to chemotherapy, thereby stopping the deadly spread of breast cancer.”

Researchers at the University of Maryland School of Medicine have identified a common gene variant that appears to influence people’s risk of developing high blood pressure, according to the results of a study being published online Dec. 29, 2008 in the Proceedings of the National Academy of Sciences (PNAS).

The STK39 gene is the first hypertension susceptibility gene to be uncovered through a new technique called a genome-wide association study and confirmed by data from several independent studies.  Located on chromosome 2, the gene produces a protein that helps to regulate how the kidneys process salt, which plays a key role in determining blood pressure.

“This discovery has great potential for enhancing our ability to tailor treatments to the individual – what we call personalized medicine – and to more effectively manage patients with hypertension.  We hope that it will lead to new therapies to combat this serious public health problem worldwide,” says the senior author, Yen-Pei Christy Chang, Ph.D., an assistant professor of medicine and of epidemiology and preventive medicine at the University of Maryland School of Medicine.

But, Dr. Chang says, more research is needed.  “Hypertension is a very complex condition, with numerous other genetic, environmental and lifestyle factors involved.  The STK39 gene is only one important piece of the puzzle,” she says.  “We want to determine how people with different variations of this gene respond to diuretics and other medications, or to lifestyle changes, such as reducing the amount of salt in their diet.  This information might help us discover the most effective way to control an individual patient’s blood pressure.”

One in four Americans has elevated blood pressure, or hypertension, which can lead to death or result in complications, such as cardiovascular disease, stroke and end-stage kidney disease.  Doctors consider the ideal systolic and diastolic blood pressure to be less than 120/80.  (The numbers reflect the pressure of the blood against the arteries when the heart beats and is at rest.)  When blood pressure is elevated, doctors recommend lifestyle changes or prescribe medications, such as diuretics, which force the kidneys to remove water from the body, in order to treat the condition.

However, patients respond differently to treatments and finding the best treatment among all the possible ones for specific patients is still a “try and see” process, according to Dr. Chang.

Scientists believe multiple genes are involved in the most common form of high blood pressure called essential hypertension.  But, because so many factors affect blood pressure, including diet, exercise and stress levels, it has been difficult to pinpoint a specific gene or group of genes, says the lead author, Ying Wang, Ph.D., a researcher at the University of Maryland School of Medicine.

The University of Maryland researchers identified the link between the STK39 gene and blood pressure by analyzing the DNA of 542 members of the Old Order Amish community in Lancaster County, Pa., scanning approximately 100,000 genetic markers across the entire genome for variants known as single nucleotide polymorphisms, or SNPs, associated with systolic and diastolic blood pressure.  The researchers found strong association “signals” with common variants of the serine/threonine kinase gene, or STK39, and confirmed their findings in another group of Amish people and in four other groups of Caucasians in the United States and Europe.

People with one particular variant showed slight increases in blood pressure compared to those with a more common form of the gene and were more likely to develop hypertension, researchers found.  The researchers estimate that about 20 percent of Caucasians in the general population have this variant of the STK39 gene.

“With this new ’scanning’ approach – the genome-wide association study – we are able to uncover genes that have previously eluded us.  The field of complex disease genetics has undergone a revolution in terms of discovering new genes and understanding the genetic basis of common adult-onset diseases,” says co-author Alan R. Shuldiner, M.D., professor of medicine; head of the Division of Endocrinology, Diabetes and Nutrition; and director of the Program in Genetics and Genomic Medicine at the University of Maryland School of Medicine.

The study being published online in PNAS is titled, “Whole-genome association study identifies STK39 as a novel hypertension susceptibility gene.”  It will appear in the print edition of PNAS early next month.

The Amish are ideal for such studies because they are a genetically homogeneous people whose forefathers came to Pennsylvania from Europe in the mid-1700s and share a similar diet and rural lifestyle.  Because many in the Amish community don’t have regular medical check-ups, they often don’t know they have high blood pressure or take medications for it, according to Dr. Chang.  The Amish appear to have as much hypertension as other Caucasians.  As a result of the study, some of the participants learned that they had hypertension and were able to start treatment.

The research, which was funded by the National Institutes of Health, is a spin-off project of another University of Maryland study – the Amish Family Diabetes study – looking for genes that may cause type 2 diabetes.  Researchers at the School of Medicine already have identified a number of genes that may play a role in the development of this type of diabetes.

Researchers from Uppsala University have discovered a mechanism that silences several genes in a chromosome domain.  The findings, published in today’s on-line issue of Molecular Cell, have implications in understanding the human disorder Beckwith-Wiedemann syndrome.

In mammals the cells contain two copies of each chromosome, one inherited from the mother and one from the father.  The genes on the chromosomes can either be active or inactive.  If a gene is active on the maternal chromosome, the corresponding gene is usually active also on paternal chromosome.  However, in some domains of the chromosome the activity is shut down on one of the chromosomes but not on the other.  The genes in these domains cannot be activated the normal way but are completely silenced.  The present study shows for the first time how this silencing of several genes on a chromosome is accomplished.

The research group, led by Chandrasekhar Kanduri, has studied a domain with several silenced genes on chromosome 7 in the mouse.  The corresponding domain with silenced genes is located on the human chromosome 11.  When part of this domain is transcribed a long RNA molecule, Kcnq1ot1-RNA, is formed.  This RNA does not give rise to any protein, instead it mediates the silencing of eight to ten genes in a much larger area on the chromosome.  Based on their findings the researchers have suggested a model for how this is accomplished.  The Kcnq1ot1-RNA binds to the DNA in the domain and recruits specific enzymes that chemically modify DNA-binding proteins.  This modification makes the DNA inaccessible for transcription and thereby the genes cannot be activated.  In addition, the Kcnq1ot1-RNA targets the silenced domain to a specific area in the cell nucleus.  There it is protected during cell division and the genes will stay silenced also in the daughter cells.

– We show for the first time how a long RNA molecule can establish and maintain silencing of multiple genes in a large domain on the chromosome, says Chandrasekhar Kanduri.  The popular belief is that it is only a gene located in the same area as where the long RNA molecule is transcribed from that can be silenced.

This mechanism is important for understanding the genetic disorder Beckwith-Wiedemann Syndrome.  In this condition silencing of the chromosome 11 domain does not function properly and both copies of the genes in the domain become inactive, instead of just one.  Less protein is produced from the genes, leading to the excess growth characteristics associated with the syndrome: enlargement of organs in the foetus and an increased risk for tumours in the affected organs.

Clubfoot, one of the most common birth defects, has long been thought to have a genetic component.  Now, researchers at Washington University School of Medicine in St. Louis report they have found the first gene linked to clubfoot in humans.

Their research will be published in the Nov. 7 issue of the American Journal of Human Genetics.

By studying a multi-generation family with clubfoot, the scientists traced the condition to a mutation in a gene critical for early development of lower limbs called PITX1.  While other genes are also likely to be linked to clubfoot, the new finding is a first step toward improved genetic counseling and the development of novel therapies.

“To our knowledge this report is the first evidence for PITX1 mutation in human disease,” said Christina Gurnett, M.D., Ph.D., assistant professor of neurology, of pediatrics and of orthopedic surgery at the School of Medicine.  “Once we identified the mutation, we proved that all of the individuals in this family with lower extremity malformations also have the mutation.  Having large families to work with is very helpful in genetic research.”

Gurnett and her colleagues analyzed the DNA of 35 extended family members of an infant male patient of Matthew Dobbs, M.D., associate professor of orthopedic surgery at the School of Medicine and a clubfoot specialist at St. Louis Children’s Hospital and St. Louis Shriners Hospital.  The patient, the most severely affected in the family, had clubfoot in both feet, duplicated first toes and was missing the tibia in the right leg.

Gurnett and Dobbs visited the family members in their community to examine their lower limbs and to take DNA samples.  They found that 13 family members were affected: Five additional family members had clubfoot, which was more severe in the right foot in three of them.  Five others had lower limb abnormalities including flatfoot, an underdeveloped patella and hip dysplasia.

Through the genome-wide study, Gurnett and her colleagues found a region on chromosome 5 that was common to all family members affected.  From there, they identified a mutation in a gene critical for early development of lower limbs called PITX1.  The PITX1 mutation was found in all affected family members and in three carriers who showed no clinical symptoms.

Dobbs, senior author of the study, said the finding is an exciting step in developing a better understanding of the genetic basis of clubfoot, which affects about 1 in 1,000 new births.

“Clubfoot is a complex disorder meaning that more than one gene as well as environmental factors will be discovered to play a role in its etiology,” Dobbs said.  “Identifying the genes for clubfoot will allow for improved genetic counseling and may potentially lead to new and improved treatment and preventive strategies for this disorder.”

Dobbs treats children with clubfoot and other orthopedic abnormalities using the Ponseti method, a treatment that involves weekly casting and the manipulation of clubfoot soon after birth.  In 2007, Dobbs developed a new dynamic brace called the Dobbs brace for clubfoot that allows active movement, preservation of muscle strength in the foot and ankle and fewer restrictions on the child than the traditional brace.

About 80 percent of clubfoot cases are idiopathic, meaning the cause is unknown and the patient has no other birth defects.  A familial link plays a role in about 25 percent of cases.  The condition occurs in males twice as often as in females and occurs more often in the right foot.  About half of the cases affect both feet, including the bones, muscles, tendons and blood vessels.  If untreated, those affected walk on the outside of their feet, which can lead to long-term pain and disability.

Gurnett said some clinical characteristics of the family members with the PITX1 mutation suggest that the genetic defect may be linked to idiopathic clubfoot.  First, the majority of the affected family members had clubfoot, but no other abnormalities.  Second, there were five females who carried the gene but did not have clubfoot, which supports the lower incidence of clubfoot in females.  Third, clubfoot affects the right foot more frequently, a hallmark of mutations in PITX1.

Previous studies had shown a relation between PITX1 and the development of hindlimbs in other vertebrates.  In mice, a loss of PITX1 leads to shorter femur length and fewer digits on the right foot than on the left.  An alteration of the gene in a developing chick wing changes it so that it looks more like a leg.  In vertebrates such as the manatee and stickleback fish, an alteration has resulted in evolutionary changes in the development of the pelvis.

“It’s our job to prove that this is going to be important for many kids with clubfoot,” Gurnett said.  “Until now, we didn’t know whether clubfoot was a muscle, nerve, spinal cord or brain problem.  Now, we have an idea that clubfoot may result from mutations of genes that are involved in early limb development.”

Gurnett said she and her colleagues will take the finding back to the lab to look for other factors involved in the pathway or how environmental effects may influence the gene.  She and Dobbs, who have been studying the genetics of clubfoot for a decade, plan to investigate the frequency of PITX1 gene mutations in other families with clubfoot.

Scientific research shows that certain genes can influence a person’s likelihood to contract particular diseases, cancer for example. New research at the Masonic Cancer Center, University of Minnesota demonstrates that genetic markers may also show a person’s likelihood to survive the disease.

A research study led by Brian Van Ness, Ph.D., has successfully identified combinations of genes associated with early clinical relapse of multiple myeloma, a cancer of the white blood cells that produce antibodies. These results raise the possibility that a patient’s genetic background exerts an important influence on the patient’s prognosis and response to treatment.

“Ultimately, the goal of this research is to predict drug efficacy and toxicity based on a patient’s genetic profile, and develop individualized assessments and predictions for the right drug, at the right dose, for the right patient,” Van Ness said. This approach offers the dual benefits of avoiding unnecessary treatment for patients less likely to respond to a particular drug, and targeting treatments to those who will benefit most.

The findings are reported in the current issue of the research journal BMC Medicine. Van Ness heads the University’s Department of Genetics, Cell Biology, and Development, and conducts research through the Masonic Cancer Center.

In this study, Van Ness and his colleagues used genetic information that the International Myeloma Foundation has gathered from myeloma patients worldwide through its program, Bank On A Cure®. This first-of-its-kind program involves several of the major treatment and research centers for myeloma worldwide and thousands of myeloma patients who donate DNA samples to the bank. The University of Minnesota houses one of the program’s two DNA banks (the other is in London), and Van Ness is co-director of the program.

“Although myeloma is considered a fatal disease, individual patients have widely varied rates of disease progression and response to treatment because of attributes encoded in their DNA,” Van Ness said.

According to Van Ness, the research study findings demonstrate that cancer outcomes differ because patients vary in the ways they absorb, distribute, metabolize, and transport drugs across cell membranes. Individual variations in genes that regulate these biologic processes may not only affect the effectiveness of the drug, but also can result in adverse side effects.

The findings from this study pave the way for similar investigations into other cancers, neurological and cardiovascular conditions, organ transplants, and other diseases.

Scientists already knew that flowering plants, unlike animals require not one, but two sperm cells for successful fertilisation.

The mystery of this ‘double fertilization’ process was how each single pollen grain could produce ‘twin’ sperm cells. One to join with the egg cell to produce the embryo, and the other to join with a second cell in the ovary to produce the endosperm, a nutrient-rich tissue, inside the seed.

Double fertilisation is essential for fertility and seed production in flowering plants so increased understanding of the process is important.

Now Professor David Twell, of the Department of Biology at the University of Leicester and Professor Hong Gil Nam of POSTECH, South Korea report the discovery of a gene that has a critical role in allowing precursor reproductive cells to divide to form twin sperm cells.

Professor Twell said: “This collaborative project has produced results that unlock a key element in a botanical puzzle.

The key discovery is that this gene, known as FBL17, is required to trigger the destruction of another protein that inhibits cell division. The FBL17 gene therefore acts as a switch within the young pollen grain to trigger precursor cells to divide into twin sperm cells.

“Plants with a mutated version of this gene produce pollen grains with a single sperm cell instead of the pair of sperm that are required for successful double fertilization.

“Interestingly, the process employed by plants to control sperm cell reproduction was found to make use of an ancient mechanism found in yeast and in animals involving the selective destruction of inhibitor proteins that otherwise block the path to cell division.

“Removal of these blocks promotes the production of a twin sperm cell cargo in each pollen grain and thus ensures successful reproduction in flowering plants.

“This discovery is a significant step forward in uncovering the mysteries of flowering plant reproduction. This new knowledge will be useful in understanding the evolutionary origins of flowering plant reproduction and may be used by plant breeders to control crossing behaviour in crop plants.

“In the future such information may become increasingly important as we strive to breed superior crops that maintain yield in a changing climate. Given that flowering plants dominate the vegetation of our planet and that we are bound to them for our survival, it is heartening that we are one step closer to understanding their reproductive secrets.”

Researchers at the University of Leicester are continuing their investigation into plant reproduction. Further research underway in Professor Twell’s laboratory is already beginning to reveal the answers to secrets about how the pair of sperm cells produced within each pollen grain aquires the ability to fertilize.

Working as part of a multi-institutional collaboration, scientists at Washington University School of Medicine in St. Louis have assembled the most complete catalog to date of the genetic changes underlying the most common form of lung cancer.  The research, published Oct. 23 in Nature, helps lay the foundation for more personalized diagnosis and treatment of a disease that is the leading cause of U.S. cancer deaths.

The research team identified 26 genes that are frequently mutated in a type of cancer called lung adenocarcinoma, a finding that more than doubles the number of genes already known to be linked to the deadly disease.  What’s more, by casting a wide net in their search for genetic alterations, the scientists are now beginning to see intriguing relationships.  They found that some of the same genes associated with lung tumors are also defective in other cancers, that smokers and non-smokers with lung cancer have distinct genetic defects and that several molecular pathways underlie most of the mutations.

“This genomic approach has given us a completely different view of lung cancer,” says Richard K. Wilson, Ph.D., director of Washington University’s Genome Sequencing Center and one of the study’s lead authors.  “This broad view will allow scientists to more accurately categorize tumors, which should speed efforts to develop more targeted therapies to fight the disease.”

More than 1 million people worldwide die of lung cancer each year, including more than 160,000 in the United States.  About 40 percent of them are adenocarcinoma, a type of non-small cell lung cancer and one that is exceedingly difficult to treat.  Only about 15 percent of patients are still alive five years after diagnosis.

“By harnessing the power of genomic research, this pioneering work has painted the clearest and most complete portrait yet of lung cancer’s molecular complexities,” says Alan E. Guttmacher, M.D., acting director of the National Human Genome Research Institute, the agency that funded the research.

The Nature study was conducted as part of the Tumor Sequencing Project, a collaborative effort to assemble a genome-wide catalog of the genetic mutations in lung adenocarcinoma.  Like most cancers, lung adenocarcinoma arises from changes that accumulate in people’s DNA over the course of their lives.  However, little is known about the precise nature of these genetic alterations, how they occur and how they disrupt biological pathways to cause cancer’s unfettered cell growth.

Working with lung cancer samples donated by 188 patients from across the United States, the group sequenced 623 suspect genes and compared them to the same genes in healthy tissues from the same patients.  Initially, they found more than 1,000 mutations across the samples.  Looking more closely, the researchers identified 26 genes mutated in a significant number of samples.  Most of the genes had not previously been associated with lung cancer but are found in other tumors.

The new genes fingered in lung adenocarcinoma include:

* Neurofibromastosis 1: Mutations in this gene cause a rare inherited neurological disorder that increases the risk of tumors that form on nerve tissues, including the brain, spinal cord and individual nerves;

* Ataxia telangiectasia mutated (ATM): Mutations of this gene have been found in a rare inherited neurological disorder and in various types of leukemia and lymphoma;

* Retinoblastoma 1: Mutations in this gene have linked to a rare childhood cancer that begins in the retina;

* Adenomatosis polyposis coli (APC): Mutations of this gene are common in colon cancer.

The team also examined the effects of the genetic mutations on biological pathways and determined which of the pathways is most crucial to lung adenocarcinoma.  This line of discovery is essential to efforts to develop new and better treatments for cancer.

For example, the researchers discovered that more than 70 percent of the 188 tumors had at least one mutation affecting the mitogen-activated protein kinase (MAPK) pathway, indicating it plays a pivotal role in lung cancer.  Based on those findings, the researchers suggested new treatment strategies for some subtypes of lung adenocarcinoma might include compounds that affect this pathway.  One such group of compounds, the MEK inhibitors, has produced promising results in mouse models of lung cancer.

“Looking at the pathways helps simplify the picture,” Wilson explains.  “Generally, we found that each mutation only occurs in a small percentage of the tumor samples, but when we looked at all the mutations that intersect a particular signaling pathway, we were surprised to find a lot of overlap in only a handful of pathways.  This gives us a much better idea of what goes wrong in cells when they become cancerous.”

Additionally, the finding that more than 30 percent of tumors had mutations affecting the rapamycin (mTOR) pathway raises the possibility that the drug rapamycin might be tested in lung adenocarcinoma.  The drug, which inhibits mTOR, is approved for use in organ transplants and renal cancer.

The researchers also analyzed the patterns of genetic changes in both smokers and non-smokers with lung cancer.  About 90 percent of lung cancer is linked to smoking, but 10 percent of patients diagnosed with the disease have never smoked.  They found that the number of mutations detected in tumor samples from smokers was significantly higher than in tumors from never-smokers.  Smokers’ tumors contained as many as 49 mutations, while none of the never-smokers’ tumors had more than five.

More work is needed to determine the clinical significance of these differences.  However, doctors do know that in some other types of cancer, high mutation levels may cause a tumor to spread rapidly or be resistant to treatment.

The study also confirmed previous observations that indicated lung cancer in never-smokers may be triggered by different genetic mutations than those in smokers.  For example, mutations in the epidermal growth factor (EGFR) gene were prevalent in tumors from non-smokers, while mutations in the KRAS and Src tyrosine kinase 11 genes were common in tumors from smokers.

“Our findings underscore the value of systematic, large-scale genome studies for exploring cancer.  We now must move forward to apply this approach to even larger groups of samples and a wider range of cancers,” Wilson says.

In infancy, genes are the key influence on a child’s ability to deal with stress. But as early as 6 months of age, parenting plays an important role in changing the impact of genes that may put infants at risk for responding poorly to stress.That’s the message from a new study by researchers at the University of North Carolina-Chapel Hill, Pennsylvania State University, the University of North Carolina-Greensboro, and North Carolina State University. It appears in the September/October 2008 issue of the journal Child Development.

The researchers looked at 142 infants who had been placed in a stressful situation—being separated from their mothers—when they were 3, 6, and 12 months old. They measured infants’ heart rates while they were exposed to the stressor, isolating a cardiac response called vagal tone. Vagal tone acts like a brake on the heart when the body is in a calm state, but during a challenging situation, this brake is withdrawn, allowing heart rate to increase so the body can actively deal with the challenge.

They also collected DNA to determine which form of a dopamine receptor gene the infants carried; specific forms of this gene are related to problems in adolescence and adulthood including aggression, substance abuse, and other risky behaviors. To assess the mothers’ behavior as high or low in sensitivity, they also videotaped the mothers and their infants playing together for 10 minutes when the babies were 6 months old.

Both genes and parenting were found to be important to the infants’ development of the way in which the brain helps regulate cardiac responses to stress. At 3 and 6 months old, those infants with the form of the dopamine gene associated with later risky behaviors did not display an effective cardiac response to the stressor (a decrease in vagal tone which takes the brake off the heart so it can respond appropriately), while those infants with the non-risk version of the gene did. At these early ages, the researchers found, it didn’t appear to matter whether mothers were sensitive or not.

However, by the time the infants were 12 months old, the pattern changed. Infants with the risk form of the gene who also had mothers who were highly sensitive now showed the expected cardiac response while they were exposed to the stressful situation. Those infants with the risk form of the gene who had insensitive mothers continued to show the ineffective cardiac response to the stressor. These findings suggest that although genes play a role in the development of physiological responses to stress, environmental experience (such as mothers’ sensitive care-giving behavior) can have a strong influence, enough to change the effect that genes have on physiology very early in life. The researchers suggest this may be because of the cumulative effect on infants of exposure to their mothers’ behavior.

“Our findings provide further support for the notion that the development of complex behavioral and physiological responses is not the result of nature or nurture, but rather a combination of the two,” says Cathi Propper, research scientist at the University of North Carolina-Chapel Hill and the study’s lead author. “They also illustrate the importance of parenting not just for the development of children’s behavior, but for the underlying physiological mechanisms that support this behavior.

“Lastly, infancy is an important time for developing behavioral and biological processes. Although these processes will continue to change over time, parenting can have important positive effects even when children have inherited a genetic vulnerability to problematic behaviors.”

Although every cell of our bodies contains the same genetic instructions, specific genes typically act only in specific cells at particular times. Other genes are “silenced” in a variety of ways. One mode of gene silencing depends upon the way DNA, the genetic material, is packed in the nucleus of cells.

When packed very tightly around complexes of proteins called histones, the DNA double helix is rendered physically inaccessible to molecules that mediate gene expression. Now, a research team that includes Michael Q. Zhang, Ph.D., a professor at Cold Spring Harbor Laboratory (CSHL), has published a comprehensive analysis of modification patterns in histones.

Using a new technology called ChIP-Seq, the team identified 39 histone modifications, including a “core set” of 17 modifications that tended to occur together and were associated with genes observed to be active.

Modification Patterns With Different “Personalities”

Scientists have long known that chemical changes at particular locations in histone complexes influence how tightly the DNA is wrapped around the histones. “But it is important to know whether particular modifications occur together in characteristic patterns, or if these patterns can predict gene activities,” Dr. Zhang explained.

At the heart of the team’s efforts to determine this, Keji Zhao, Ph.D., of the National Heart, Blood, and Lung Institute of the National Institutes of Health, and his colleagues developed a method to map modifications in human white blood cells known as CD4+ T cells. First they used an enzyme to cut the DNA into short segments, which remained attached to histone “spools.” For each of 39 distinct histone modifications, the scientists used an antibody to extract matching histone-DNA combinations. Finally, they used the ChIP-Seq DNA-sequencing technology to determine which parts of the genome were bound to each type of modified histone.

The team’s most recent research, published in the July 2008 issue of Nature Genetics, maps the DNA locations that bind to histones containing molecular configurations called acetyl groups at 18 different positions in the “tails” of the histone proteins. The scientists combined this information with earlier maps for 19 different changes called methylation modifications, and for replacement of one of the histone proteins with a well-known variant.

The various modifications showed distinctive “personalities,” each preferentially associating with particular regulatory regions of genes.

Looking for Patterns

Mapping many modifications enabled the researchers to explore whether different types tend to appear together in the same type of DNA regulatory regions. They found that some recurring combinations did occur frequently at “promoter” and “enhancer” regions in DNA, which are known to increase the activity of nearby genes. In particular, the team identified one combination of 17 modifications that was present in more than a quarter of the more than 12,000 promoter regions they examined.

On average, the genes corresponding to this “backbone” set were expressed more actively. That is to say, they were activated, setting the cellular machinery in motion to produce specific proteins, the workhorses of most life processes.

The rich relationships detected by the researchers among the various histone modifications suggests that specific combinations might carry specific meanings. Previous researchers have proposed a “histone code” hypothesis, which posits that a particular combination of modifications may be recognized by a particular protein module. Some scientists believe such histone code may determine the activity of a given gene.

But, cautions Dr. Zhang, while there are patterns, like the backbone, that are highly correlated, “none of them has exact predictive value.” He maintains “there must be something else” that also affects gene activity.

Since genes with higher or lower expression levels may have the same patterns of modification, and not all active genes share a common pattern, the reality is likely more complex than a universal histone code that predicts exact gene expression level. Nonetheless, the new research provides a rich data source for understanding how specific combinations of histone modifications modulate the effects of many genes, in turn helping to modify activity within and among cells. “Critical future research should focus on finding proteins that target histone modifications to genetic regions with particular sequences,” Dr. Zhang emphasized.

Keeping the genome stable is a “sister act” of matched chromatids – the pairs of the double helix DNA molecule that exist during the chromosome duplication in the S phase of the cell cycle.

Maintaining the chromatids in their sister pairs rests with Eco1, a kind of enzyme known as an acetyltransferase.  Now researchers at Baylor College of Medicine, in a collaboration of two laboratories, have shown that Eco1 and its human homologue maintain sister chromatid cohesion and thus genome stability through a chemical process called acetylation that affects Smc3, one of the key components of the cohesion protein complex.  A report on their work appears in the current online issue of the journal Molecular Cell.

This activity is critical to maintaining the stability of the cell’s genome and its survival, said Dr. Jun Qin, associate professor of biochemistry and molecular biology and molecular and cellular biology at BCM and a senior author of the report.

“If a cell lacks this acetyltransferase activity, it’s dead,” said Dr. Xuewen Pan, assistant professor of biochemistry and molecular biology and molecular and human genetics at BCM and also a senior author.

“This is critical for genome stability, cell growth and organism survival,” said Qin.

“The collaboration in this work was important,” he said.  His laboratory carried out the work in human cells, and Pan’s did the work in yeast.

“We pooled the resources of our two laboratories and took advantage of the power of the genetics in yeast and the power of proteomics and cell biology in the human.  If a single labor had worked on this project, we would not have as complete a story,” Qin said.

The identification of five genes involve in the metastasis of breast tumours to the lung is the principal finding of a scientific team made up of two bodies from the University of Navarra, the Applied Medical Research Centre (CIMA) and the University Hospital of the University of Navarra.

Doctor Alfonso Calvo, researcher in the area of Oncology at the CIMA, led the work with the special collaboration of Doctor Ignacio Gil Bazo, cancer specialist from the University Hospital.  The study made up a significant part of Mr Raúl Catena’s PhD thesis.

For this research, recently published in the scientific journal Oncogene, a transgenic mouse model which presented a greater tendency for developing metastasis was employed.  The increase in what is known as the Vascular Endothelial Growth Factor (VEGF) in its mammary glands triggered profound changes in the tumoural structure, which enabled the malignant cells to leave the tumour and invade the lungs.

Finally, the pattern of genes responsible for this tumoural migration to the lungs was analysed and this was compared to that shown by women with breast tumours with pulmonary metastatic affectation.  It was shown that five of these genes were common to the animal model and patients with breast cancer.  Most effective ways of treatment

According to the results of this study, of the five genes identified, the Tenascina-C gene seems to be a good therapeutic target for the treatment of metastatic breast cancer.  In fact, the blocking of the expression of this gene in the animal model enabled a significant reduction, both in tumour growth and in the incidence of pulmonary metastasis.

This new discovery in the complex network that is the metastasis process of tumours provides key data on the knowledge of cancer and its spreading, at the same time identifying new targets for which new pharmaceutical medicines that contribute to more efficacious treatment of this disease can be designed.

Researchers at the University of Cincinnati (UC) are looking for ways to reduce or prevent heart damage by starting where the problem often begins: in the genes.

Following a heart attack, cells die, causing lasting damage to the heart.

Keith Jones, PhD, a researcher in the department of pharmacology and cell biophysics, and colleagues are trying to reduce post-heart attack damage by studying the way cells die in the heart—a process controlled by transcription factors.

Transcription factors are proteins that bind to specific parts of DNA and are part of a system that controls the transfer of genetic information from DNA to RNA and then to protein.  Transfer of genetic information also plays a role in controlling the cycle of cells—from cell growth to cell death.

“We call it ‘gene regulatory therapy,’” says Jones.

So far, studies have identified the role for an important group of interacting transcription factors and the genes they regulate to determine whether cells in the heart survive or die after blood flow restriction occurs.

Often, scientists use virus-like mechanisms to transfer DNA and other nucleic acids inside the body.

The “virus” takes over other healthy cells by injecting them with its DNA.  The cells, then transformed, begin reproducing the virus’ DNA.  Eventually they swell and burst, sending multiple replicas of the virus out to conquer other cells and repeat the process.

Now, UC researchers are further investigating new, non-viral delivery mechanisms for this transfer of DNA.

“We can use non-viral delivery vehicles to transfer nucleic acids, including transcription factor decoys, to repress activation of specific transcription factors in the heart,” Jones says, adding that the researchers have made this successfully work within live animal models.  “This means we can block the activity of most transcription factors in the heart without having to make genetically engineered mice.”

Jones will be presenting these results at the International Society for Heart Research in Cincinnati, June 17-20.

He says this delivery mechanism involves flooding the cells with “decoys” which trick the transcription factors into binding to the decoys rather than to target genes, preventing them from activating those genes.

“We can use this technology to identify the target genes and then investigate the action of these genes in the biological process,” Jones says.

He says that this delivery has limitations and advantages.

“It can be used to block a factor at any point in time and is reversible,” he says.  “However, right now, a specific delivery route must be used to target the tissue or cell.”

Jones and other researchers are hoping that this new technology will allow them to directly address the effects of gene regulation in disease, as opposed to using classical drugs that treat symptoms or have significant adverse outcomes.

“So far, this seems to cause no adverse effects in animals,” he says.  “We are hopeful and are working toward pre-clinical studies.”

Viruses are true experts at importing genetic material into the cells of an infected organism. This trait is now being exploited for gene therapy, in which genes are brought into the cells of a patient to treat genetic diseases or genetic defects. Korean researchers have now made an artificial virus. As described in the journal Angewandte Chemie, they have been able to use it to transport both genes and drugs into the interior of cancer cells.

Natural viruses are extremely effective at transporting genes into cells for gene therapy; their disadvantage is that they can initiate an immune response or cause cancer. Artificial viruses do not have these side effects, but are not especially effective because their size and shape are very difficult to control—but crucial to their effectiveness. A research team headed by Myongsoo Lee has now developed a new strategy that allows the artificial viruses to maintain a defined form and size.

The researchers started with a ribbonlike protein structure (β-sheet) as their template. The protein ribbons organized themselves into a defined threadlike double layer that sets the shape and size. Coupled to the outside are “protein arms” that bind short RNA helices and embed them. If this RNA is made complementary to a specific gene sequence, it can very specifically block the reading of this gene. Known as small interfering RNAs (siRNA), these sequences represent a promising approach to gene therapy.

Glucose building blocks on the surfaces of the artificial viruses should improve binding of the artificial virus to the glucose transporters on the surfaces of the target cells. These transporters are present in nearly all mammalian cells. Tumor cells have an especially large number of these transporters.

Trials with a line of human cancer cells demonstrated that the artificial viruses very effectively transport an siRNA and block the target gene.

In addition, the researchers were able to attach hydrophobic (water repellant) molecules—for demonstration purposes a dye—to the artificial viruses. The dye was transported into the nuclei of tumor cells. This result is particularly interesting because the nucleus is the target for many important antitumor agents.

Scans of the genome of patients with schizophrenia have revealed rare spontaneous copy number mutations that account for at least 10 percent of the non-familial cases of the disease. Researchers describe specific genetic mutations present in individuals who have schizophrenia, but not present in their biological parents who do not have the disease. These individuals were eight times more likely to have these mutations than unaffected individuals. This new data, reported in the May 30 on-line issue of Nature Genetics, will help researchers account for the persistence of schizophrenia in the population despite low birth rates among people with the disease.Researchers at Columbia University Medical Center scanned the genome of 1,077 people which included 152 individuals with schizophrenia, 159 individuals without schizophrenia, and both of their biological parents for copy number mutations. They found mutations, either a gain or loss of genes, in 15 individuals diagnosed with schizophrenia that were not present in the chromosomes of either biological unaffected parent. Only two of such mutations were found in those without schizophrenia. Study subjects were from the European-origin Afrikaner population in South Africa, a genetically homogenous population that is ideal for genetic evaluation.

“We now know the cause of around 10 percent of the cases of sporadic schizophrenia,” said Maria Karayiorgou, M.D., professor of psychiatry, Columbia University Medical Center, the senior author on the study. “Schizophrenia is not as much of a ‘big black box’ as it used to be. The identification of these genes lets us know what brain development pathways are involved in disease onset, so that in the future we can look at better ways of treating this devastating disease.”

Schizophrenia affects approximately 1 percent of the population worldwide. About 40 percent of the disease is thought to be inherited, with the other 60 percent sporadically showing up in people whose family history does not include the disease.

One of the new or de novo mutations researchers found in more than one affected individual in this study was a deletion of a region of chromosome 22. Dr. Karayiorgou had previously provided evidence that loss of genes in this region, 22q11.2, was responsible for introducing “new” or sporadic cases of schizophrenia in the population. This confirms 22q11.2 as the only known recurrent such mutation linked to schizophrenia.

“We have already demonstrated 22q11.2 to be involved in sporadic schizophrenia and we have made considerable progress in understanding the underlying biological mechanisms,” said Dr. Gogos. “Now, we have a new set of mutations that we can investigate. The more information we have about the biological basis for this disease, the more information we can provide to those who suffer from it and their families.”

“Such abnormal deletions or duplications of genetic material are increasingly being implicated in schizophrenia and autism,” explains National Institute of Mental Health Director Thomas R. Insel, M.D. “Now we have a dramatic demonstration that genetic vulnerabilities for these illnesses may stem from both hereditary and non-hereditary processes. This line of research holds promise for improved treatments – and perhaps someday even prevention – of developmental brain disorders.”

Karayiorgou and co-senior author Joseph A. Gogos, M.D., Ph.D., associate professor of physiology and neuroscience at Columbia University Medical Center, agree that the goal is for psychiatrists to be able to inform patients that they have a mutation that is causing their disease and ultimately to be able to tailor treatments to individual patients based on their specific mutation. This tailored treatment is a ways off, according to Dr. Karayiorgou, but she says patients and their families are relieved to know that there is a biological cause of their illness.

The researchers plan to extend their screen for additional de novo mutations by using increased resolution scans to study additional families. They also plan to scrutinize further genes affected by the identified mutations through human genetics and animal model approaches.

The two studies in the May 30th issue of Cell, a Cell Press publication, uncover the crystal structure and biochemical activity of an enzyme known as XPD helicase taken from Sulfolobus archaea, microbes distinct from bacteria that share many fundamental genes with humans. For reasons that had remained rather mysterious until now, point mutations in human XPD sometimes at neighboring sites can spell the difference between cancer-prone xeroderma pigmentosa, the aging disorder known as Cockayne syndrome and another aging disorder called trichothiodystrophy.

If you consider the linear sequence of XPD and map the [disease-linked] point mutations onto it, there is nothing clear about why they would be causative for one of the three diseases or another, said Jill Fuss of The Scripps Research Institute. By having these structures for XPD, we suddenly see how it is working.

The protein from archaea is a simplified model, but that doesn’t stop us learning a lot about the biology of the human enzyme, said Malcolm White of University of St Andrews, who led the other study. Archaeal protein structures are often very close matches to the equivalent proteins from humans, even though they diverged from one another three billion years ago. We can learn a lot about human health by looking deep into evolutionary time.

Archaea have particular similarities with humans and other eukaryotes in the way in which they process information, including DNA replication, transcription and repair, White explained. One of those common elements is XPD helicase, a component of a fundamental complex (known as TFIIH) with roles in initiating the transcription of genes into the templates for protein and in the repair of damaged DNA. In both instances, the helicase parts the two DNA strands at either the transcription start site or the site of DNA damage.

Defects in XPD are known to underlie xeroderma pigmentosa (XP), Cockayne syndrome (CS) and trichothiodystrophy (TTD). Although people with all three diseases share a sensitivity to the sun, they differ greatly in their predispositions to cancer or accelerated aging, explained John Tainer, who led the Scripps study. XP patients show several 1000-fold increase in skin cancer, whereas neither CS nor TTD patients show an increase in the cancer incidence despite their sun sensitivity. Furthermore, both CS and TTD are premature aging diseases plus developmental disorders, with CS patients being more severely affected and exhibiting severe mental retardation from birth.

Both teams now have evidence to explain what separates the diseases despite their similar molecular causes. They find that XP-causing mutations in XPD all fall in sites where the helicase binds ATP (the energy currency of the cell) or DNA. Those alterations leave the enzyme unable to function in DNA repair. However, the overall effect on the structure of the enzyme is minimal. As such, the enzyme still fills its position in the TFIIH complex, allowing transcription to proceed. That inability to repair defects, leaves those with XP prone to developing cancer as mutations arise and go uncorrected.

In the case of TTD, the defect is quite different, White said. TTD-linked mutations are found all over the protein at points important to its interactions with other proteins. Therefore, those mutations leave the protein floppy, destabilizing the entire TFIIH complex and causing defects in both transcription and repair.

It is thought that the transcription defects protect against cancer, but lead to an increase in cell death and therefore the rapid aging symptoms seen in TTD patients, White said.

As for CS, Tainer’s group suggests it results when defects in XPD lock the protein into a rigid position. As a result, they said, the protein may stick in repair mode and cut out DNA at sites where it should be transcribing.

White agrees that CS seems to result from mutations that influence the XPD protein’s flexibility. However, he’s not yet sure exactly how that leads to the symptoms of CS.The new insights into XPD point to the importance of whole proteins, not just their active sites.

“We’ve been able to characterize three activities together with the structure”, Tainer said. “We’ve shown how mutations in the binding site alone can cause cancer. Scientists often thought it was just the active sites that were important that other changes wouldn’t matter. But we see that other changes can lead to very severe defects.”

The results also hold an important general lesson for the value of protein structure for understanding gene function. The results of the Human Genome Project have revealed associations between sequence mutations and particular diseases or disease risks, but in many cases we don’t know why, Tainer said. As in the case of XPD, the protein structures may hold the key.