University Times

NSF funds comp sci research

The National Science Foundation has awarded grants to the following primary investigators in the Department of Computer Science:

• Alexandros Labrinidis, Panos K. Chrysanthis and Liz Marai have been awarded $1.6 million for “Understanding the Universe Through Scalable Navigation of a Galaxy of Annotations.”

• Chrysanthis and Labrinidis also have received a $200,000 Early-Concept Grant for Exploratory Research (EAGER) for “Energy-Efficient Transaction Processing.”

• Chrysanthis was awarded $50,000 for a workshop on sustainable energy-efficient data management.

• Sangyeun Cho received a $100,000 EAGER award for “Foundations for Predictive Resource Management in Next-Generation Multicore Processor Systems.”

• Adam Lee was awarded $150,000 for “Collaborative Research: Improved Privacy Through Exposure Control.”

Education research grants awarded

The School of Education recently announced the following grants to faculty members:

• John Jakicic of the Department of Health and Physical Activity received a five-year $2.5 million National Institutes of Health grant to use advanced MRI technology to examine the influence of exercise within the context of weight management on cardiac structure. This will be one of the first studies to quantify the structural changes of the heart structure and function in response to weight loss and exercise in overweight and obese adults.

This research is expected to impact exercise recommendations for overweight and obese adults.

• Chris Lemons of the Department of Instruction and Learning received a three-year $1.45 million grant from the Institute of Education Sciences to create interventions for teaching reading to children with Down syndrome.

Asthma research published

School of Medicine researchers have identified a molecular pathway that helps explain how an enzyme that is elevated in asthma patients can lead to the increased mucus production and inflammation that is characteristic of the lung condition.

Their findings, reported online in Proceedings of the National Academy of Sciences, reveal a unique molecule that could be targeted to develop new asthma treatments.

An enzyme called epithelial 15-lipoxygenase 1 (15LO1) metabolizes fatty acids to produce an eicosanoid known as 15 hydroxyeicosaetetranoic acid (15 HETE) and is elevated in the cells that line the lungs of asthma patients, explained Sally E. Wenzel, professor of medicine and director of the UPMC Asthma Institute at the School of Medicine. Her team showed in 2009 that the enzyme plays a role in mucus production.

“In this project, we found out 15 HETE is conjugated to a common phospholipid,” she said. “That complex, called 15HETE-PE, and 15LO1 behave as signaling molecules that appear to have a powerful influence on airway inflammation.”

By examining lung cells from 65 people with asthma, the researchers found that both 15LO1 and 15HETE-PE displace an inhibitory protein called PEBP1 from its bond with another protein called Raf-1, which when freed can lead to activation of extracellular signal-regulated kinase (ERK). Activated ERK commonly is observed in the epithelial, or lung lining, cells in asthma, but until now the reason for that was not understood.

Mark T. Gladwin, chief of the medical school’s Division of Pulmonary, Allergy and Critical Care Medicine, said, “This is an important study as it directly explores the important role of 15-lipoxygenase 1 in the airway epithelial cells of patients with asthma, which immediately establishes the relevance to human disease.”

Other experiments showed that knocking down 15LO1 decreased the dissociation of Raf-1 from PEBP1, which in turn reduced ERK activation. The pathway ultimately influences the production of factors involved in inflammation and mucus production.

Wenzel said, “These results show us on both a molecular and mechanistic level and as mirrored by fresh cells from the patients themselves that the epithelial cells of people with asthma are very different from those that don’t have it. It also gives us a potential treatment strategy: If we can prevent Raf-1 displacement, we might have a way of stopping the downstream consequences that lead to asthma.”

Pitt co-authors included Jinming Zhao and John B. Trudeau of medicine and Claudette M. St. Croix of environmental and occupational health.

The study was funded by the National Institutes of Health (NIH) and the American Heart Association.

Researchers grow new blood vessels

Bioengineering faculty member Yadong Wang has developed a minimally invasive method of delivering growth factor to regrow blood vessels using a unique delivery platform.

His research, which could lead to new treatments for heart disease, appeared in the Aug. 1 issue of the journal Proceedings of the National Academy of Sciences.

Wang also is a faculty member in the medical school’s Department of Surgery and is affiliated with the McGowan Institute for Regenerative Medicine (MIRM).

Typically, the body quickly destroys free-floating growth factor. But the addition of heparin, which bonds growth factor to its receptor on the cell surface, increases the activity of growth factor and stabilizes it.

In this first-ever report of using a coacervate (an aggregate of tiny oil droplets) for the controlled delivery of a heparin/growth factor complex, using fibroblast growth factor-2, the team grew new blood vessels in mice. Wang said, “We had structures that resembled arterioles — small arteries that lead to a network of capillaries.” The new blood vessels remained a month after the injection.

The trick, they discovered, was to use a polycation — a molecule with multiple positive charges — to neutralize heparin’s many negative charges and bring it out of solution into a coacervate.

Heparin-growth factor complexes typically are water-soluble and dissolve within seconds after being injected. However, the coacervate prevents that, allowing the growth factor to do its work of regenerating blood vessels.

Because the coacervate is not very viscous, it could be injected through a catheter to treat heart disease — a huge advantage over open-heart surgery.

The growth factor complex could be injected soon after a heart attack to change how the heart repairs itself. “Our hope would be to reduce scarring, keep as much of the muscle alive as possible and induce quick blood vessel formation to bring as many nutrients as possible in order to re-establish an environment for muscle growth,” Wang said.

Wang has gone on to use his unique delivery platform to study the controlled release of other growth factors that bind heparin: nerve growth factor; vascular endothelial growth factor; epidermal growth factor; bone morphogenetic proteins, and many others. “In all cases, the controlled delivery using coacervate was much more effective,” said Wang.

“This treatment is very promising in bench-to-bedside translation,” he said. His research plans include eventual human clinical trials. His team also will use a disease model to investigate the efficiency of the treatment in heart attacks.

Pitt co-authors were Johnny Huard of bioengineering and the departments of orthopaedic surgery, molecular genetics and pathology as well as MIRM; and Hunghao Chu, Jin Gao and Chien-Wen Chen, all of bioengineering and surgery.

Formation of enamel studied

Dental researchers are piecing together how tooth enamel forms, which could lead to new nanoscale approaches to developing biomaterials. Their findings were reported online in the Proceedings of the National Academy of Sciences.

Dental enamel is the most mineralized tissue in the body and combines high hardness with resilience, said Elia Beniash, an oral biology faculty member in the School of Dental Medicine. Those properties are the result of its unique structure, which resembles a complex ceramic microfabric.

“Enamel starts out as an organic gel that has tiny mineral crystals suspended in it,” he said. “In our project, we recreated the early steps of enamel formation so that we could better understand the role of a key regulatory protein called amelogenin in this process.”

Beniash and his team found that amelogenin molecules self-assemble in stepwise fashion. Just like connecting a series of dots, amelogenin assemblies stabilize tiny particles of calcium phosphate, which is the main mineral phase in enamel and bone, and organize them into parallel arrays. Once arranged, the nanoparticles fuse and crystallize to build the highly mineralized enamel structure.

“The relationship isn’t clear to us yet, but it seems that amelogenin’s ability to self-assemble is critical to its role in guiding the dots, called prenucleation clusters, into this complex, highly organized structure,” Beniash said. “This gives us insight into ways that we might use biologic molecules to help us build nanoscale minerals into novel materials, which is important for restorative dentistry and many other technologies.”

Co-authors include Ping-An Fang of oral biology and James F. Conway of the Department of Structural Biology.

The research was funded by NIH and the Commonwealth of Pennsylvania.

Pharmacy, dental research funded

The Schools of the Health Sciences recently announced the following awards:

• Heiko Spallek, a faculty member in the School of Dental Medicine, received $190,000 from the National Institute of Dental and Craniofacial Research to explore how to share clinical research with practicing dentists quickly and effectively.

• Xiang Qun Xie of the School of Pharmacy received a $412,711 grant from NIH to study a promising approach to design new drugs for hematopoietic stem cell therapies that may have a significant impact on future stem cell drug research and development.

MCC cancer trigger found

Researchers at the University of Pittsburgh Cancer Institute (UPCI) have identified the oncoprotein that allows a common and usually harmless virus to transform healthy cells into a rare but deadly skin cancer called Merkel cell carcinoma (MCC). Their findings, published recently in the Journal of Clinical Investigation, could improve diagnosis for MCC and may help in understanding how other cancers arise.

Three years ago, Yuan Chang and Patrick S. Moore of the UPCI cancer virology program discovered a new human cancer virus called Merkel cell polyomavirus (MCV), which causes most cases of MCC. But it was not clear how the virus triggered cancer development.

To figure that out, a team led by UPCI research associate Masahiro Shuda examined the viral proteins that might trigger cancer cell growth.

After establishing human MCC cell lines, the scientists learned that knocking out a viral protein called “small tumor protein,” or sT, stopped the cancer cells from replicating. When they introduced sT into healthy cells in the lab, the cells took on the characteristics of cancer cells.

“This was a surprise because the viral sT proteins from other similar viruses that cause cancers in laboratory animals do not directly increase cancer activity in cells,” Shuda said. “Once we found this, we had to next understand the biological mechanisms that make MCV sT a cancer-causing protein, or oncoprotein.”

The MCV sT triggers a cellular process called “cap-dependent translation” that allows certain cellular oncoproteins to be made, Moore explained.

Although the cancers caused by MCV are rare, the virus is important because it helps scientists pinpoint cell pathways that are key to more common cancers. These cancers also might activate cap-dependent translation through a DNA mutation rather than through a virus infection.

In related studies recently published in Emerging Infectious Diseases, the team showed MCV infects four out of five healthy adults, where it remains a silent resident in skin cells without causing any symptoms. Only when specific mutations occur in the DNA of the virus — for example, by ultraviolet light exposure — does it have potential to cause cancer. The researchers now are working to identify new agents to target MCC cancer cells that may be more active and less toxic.

MCV is the first virus in the family of polyomaviruses shown to cause human cancer, but six other polyomaviruses that infect humans recently have been discovered and scientists actively are seeking to find out if they are cancer-causing viruses as well. MCV is the second human cancer virus found by the Chang-Moore laboratory, which previously discovered the virus causing Kaposi’s sarcoma — the most common cancer among AIDS patients.

Other co-authors were Hyun Jin Kwun and Huichen Fung, both of the cancer virology program.

The research was funded by NIH, the American Cancer Society and UPCI.

GSPH investigates blood disease cluster

An investigation led by researchers from the Graduate School of Public Health is seeking to determine whether there is a continuing cluster of a rare blood disorder in a tri-county area of eastern Pennsylvania.

Investigators traveled to Carbon, Luzerne and Schuylkill counties in August to provide information about polycythemia vera (PV) and related blood disorders known as myeloproliferative neoplasms (MPNs) and to interview residents who have been diagnosed with, or suspect they have, PV or MPNs. Researchers  plan to return to the area this month.

MPNs include essential thrombocythemia, primary myelofibrosis and chronic myeloid leukemia.

PV is a rare illness that causes the body to make too many red blood cells, according to the Agency for Toxic Substances and Disease Registry (ATSDR). It can lead to blood clots, heart attacks and strokes. Its cause is not known, but the ATSDR reports that some studies published more than 25 years ago indicated that PV possibly could be caused by exposure to chemicals such as benzene, embalming fluid and petroleum products, or radiation.

This investigation, funded by the Pennsylvania Department of Health and ATSDR, will run through fall 2012. It is a followup to a 2008 study and is designed to get a better idea of the true rate of PV and MPNs in the area.

The team includes Jeanine Buchanich of biostatistics and Kristen Mertz of epidemiology.

For more information on PV and the earlier study, visit www.atsdr.cdc.gov/sites/polycythemia_vera/index.html.

Squamous cell cancer mutations ID’d

Pitt researchers are among teams of scientists who have not only confirmed some genetic abnormalities previously suspected in head and neck squamous cell cancer but also found unexpected ones.

In papers published online in Science, researchers from Pitt, the Broad Institute, Dana-Farber Cancer Institute, Johns Hopkins Kimmel Cancer Center and the University of Texas MD Anderson Cancer Center have confirmed the involvement of defects in the tumor suppressor gene p53 and found that mutations in the NOTCH family of genes also may play a role in these cancers.

Jennifer R. Grandis, a faculty member in the School of Medicine’s otolaryngology and pharmacology and chemical biology departments, director of the head and neck program at the University of Pittsburgh Cancer Institute and a senior author of one of the Science papers, said, “There was a really big gap in knowledge that was an obstacle to doing the right kind of research” about head and neck cancer.

“If we didn’t know the spectrum of the mutations that were in our patients’ tumors, we couldn’t begin to develop more appropriate therapies.”

She and co-author Levi A. Garraway, a senior associate member of the Broad Institute and faculty member at Dana-Farber Cancer Institute and Harvard Medical School, decided to study a Pitt collection of 74 pairs of tumor and normal tissue samples using the Broad Institute’s capacity to perform whole-exome sequencing.

The exome represents the tiny fraction of the genome that encodes proteins. Focusing on just these protein-producing genes allows scientists to zero in on mutations that alter key proteins involved in cancer growth.

Another collaboration was unfolding among cancer geneticists, sequencing experts, clinical researchers and surgical oncologists at Johns Hopkins, MD Anderson and Baylor College of Medicine to study 32 pairs of head and neck tumor and normal tissue samples by whole-exome sequencing and validate the findings in an additional 88 samples.

Both teams found mutations in the p53 gene in a little more than half of the tumors they studied.

The next most common mutation occurred in NOTCH1, which showed up in about 15 percent of tumors. NOTCH1 controls how cells differentiate into other kinds of cells, mature, stop dividing and ultimately die. In head and neck cancer, mutations turned NOTCH1 off, blocking differentiation and trapping cells in a proliferative, pro-cancer state.

Garraway said, “Head and neck cancer is complex and there are many mutations, but we can infer there is a convergence on a cellular process for which we previously did not have genetic evidence. It shows that if you do a genome sequencing project of this size you can gain major new biological insights.”

Co-author Kenneth W. Kinzler, a Johns Hopkins faculty member, said, “The mutational analysis of NOTCH clearly indicated the power of genetic changes determining the function of these genes. It gives us an important clue to start studying their function.”

NOTCH1’s inactivation in head and neck cancer was surprising because in other cancers, such as leukemia, too much NOTCH signaling leads to cancer.

Kinzler said, “Our study suggests that a gene’s role can depend on the tumor type.  In some cases, a gene can act as a growth promoter in cancer, and in other cases, such as head and neck cancer, the same gene behaves as a growth suppressor.”

Efforts to combat the mutated p53 tumor suppressor gene with targeted drugs, for example, so far have been unsuccessful.

The next step, the scientists agree, is to tease out how the genes function in normal cells, whether they form the lining of the larynx, pharynx or another anatomical site affected by head and neck cancer.

Grandis said, “The race will be on to figure out the function and particularly the therapeutically relevant function of these mutations.”

Translating these discoveries into therapies for patients will take more studies and more time, but the revelations set a course for the future, the scientists said.

Nishant Agrawal, a head and neck surgical oncologist at Johns Hopkins and a lead author of one of the Science papers, said the studies offer few clues about the significance of NOTCH mutations, adding that further studies will be needed to define its role in prognosis, diagnosis and/or treatment. “The idea is to use these genetic alterations to predict a patient’s prognosis and define personalized treatment strategies tailored to their cancer’s genome,”Agrawal said.

Jeffrey N. Myers, professor of head and neck surgery at MD Anderson, said both groups’ work highlights the complexity of the disease and its multiple gene abnormalities. “It has told us new things that will give us both clinical and scientific opportunities to study in the near and long term,” Myers said. “I think that we’re also in a position to design very specific clinical studies to further understand the significance of these mutations, as well as to begin to think about potentially targeting some of the abnormalities.”

Those studies could include looking at patients with different mutations in addition to p53 and the NOTCH family to see how well they fare.

The research reported by the Pitt, Broad and Dana-Farber group was supported by funding from the Carlos Slim Health Institute, the National Human Genome Research Institute, the National Cancer Institute, the Starr Cancer Consortium, the Novartis Institutes for BioMedical Research and the American Cancer Society.

Bioengineering research funded

The National Institute of Neurological Disorders and Stroke has awarded funding through May 2016 for bioengineering faculty member Aaron Batista’s project, “Differential Contributions of Frontal Lobe Areas to Eye/Hand Coordination.”

The institute’s funding for the project in 2011 totaled nearly $325,000.

Antibiotics quell COPD

A multicenter team that includes researchers from the School of Medicine has found that patients with chronic obstructive pulmonary disease (COPD) had fewer episodes of acute worsening of their lung disease and a better quality of life if they took a daily dose of a commonly used antibiotic. The findings were reported in the New England Journal of Medicine.

Even patients who are treated with standard bronchodilator and steroid inhalers to control COPD symptoms commonly have one or more flare ups of the disease, explained Frank Sciurba, a faculty member in medicine and leader of the local arm of the study.

“Several small studies suggested that antibiotics called macrolides can have immune-modulating and anti-inflammatory effects that led to fewer exacerbations of COPD,” he said. “Our large trial shows it is true, and provides a way to improve the quality of life for patients whose breathing has been terribly impaired by this progressive and deadly disease.”

For the study, which was conducted by the COPD Clinical Research Network led by the University of Colorado Denver Health Sciences Center, more than 1,100 COPD patients from 17 sites in 12 academic centers participated in the trial. About half of them were assigned randomly to take the macrolide antibiotic azithromycin every day for a year, while the rest took a placebo daily for the same time period. The Pitt arm enrolled 91 participants.

The median time to first COPD exacerbation was 266 days in the azithromycin group and 174 days in the placebo group. Also, exacerbations occurred 27 percent less frequently in the azithromycin group. There was a slightly greater likelihood of hearing problems in the azithromycin group, which is a known risk of prolonged use of the antibiotic, and the presence of antibiotic-resistant organisms was detected in some patients, although the infection rate was not higher.

More research needs to be done to assess the safety of using azithromycin in COPD patients for longer than a year, and it’s not clear what impact that might have on antibiotic resistance, said co-investigator John Reilly, a Pitt faculty member in the Department of Medicine.

According to the National Heart, Lung and Blood Institute, COPD affects over 12 million people in the United States and is the third leading cause of death in the United States.

For more information about projects at the Emphysema/COPD Research Center, visit www.dept-med.pitt.edu/paccm/ebli.html.

Schizophrenia’s roots probed

In the Journal of Neuroscience, Pitt researchers report progress in understanding how drugs act on dopamine-producing neurons that could enable them to create more targeted treatments.

Schizophrenia’s symptoms of — paranoia, hallucinations and the inability to function socially — can be managed with antipsychotic drugs. But exactly how these drugs work has long been a mystery.

Now, Pitt researchers at Pitt have discovered that antipsychotic drugs work akin to a Rube Goldberg machine — that is, they suppress something that in turn suppresses the bad effects of schizophrenia, but not the exact cause itself.

In a paper published in the Journal of Neuroscience, they say that pinpointing what’s actually causing the problem could lead to better avenues of schizophrenia treatment that more directly and efficiently target the disease.

Senior author Anthony Grace said, “In the past five years or so, we’ve really started to understand what may be going wrong with the schizophrenic brain.” Grace is a Distinguished Professor of Neuroscience and professor of psychology in the School of Arts and Sciences and professor of psychiatry in the School of Medicine.

Schizophrenia is made up of three different types of symptoms. Antipsychotic medications work best on so-called positive symptoms, which are added onto a “normal” personality. They include hallucinations and delusions, such as hearing voices, thinking people are after you or thinking you’re being targeted by aliens. These are the symptoms most likely related to a neurotransmitter called dopamine, said Grace, who since 1978 has studied the role dopamine plays in the schizophrenic brain.

The other two categories of symptoms are negative (what’s missing from the normal personality — the ability to interact socially or hold down a job; or emotional flattening) and cognitive (the ability to think linearly or concentrate on one thing at a time).

These two really aren’t addressed well by antipsychotic drugs, he said. “Blocking the dopamine system seems to fix classic hallucinations and delusions a whole lot better than it fixes the other problems.”

It’s long been known that after several weeks of treatment with antipsychotic drugs, dopamine-producing neurons are inactivated. “It would suggest to us that in schizophrenia there is not too much dopamine, but rather the dopamine system is too responsive,” said Grace. Therefore, by inactivating the neurons, this over-responsivity should be able to be treated. “If there were just too much dopamine in the brain, one would expect the biggest treatment effect would be at the beginning and then it would diminish,” Grace said. But the actual effect is different — it builds over a couple days and then is constant, without the tolerance seen with other drug treatments.

This didn’t fit with clinical observation. “Patients respond in the first few days, but we took weeks to see results in our normal animals,” Grace said.

Grace’s team developed a rat model that approximates some of the key features of schizophrenia. Using these antipsychotic drugs, they found that what takes weeks to occur in a normal rat happened in a couple days in the schizophrenia-model rats. “It fits very well with the time course we see in human patients,” said Grace.

He hypothesizes that the difference is due to the schizophrenic brain’s dopamine system working overtime. Current antipsychotic drugs work by blocking dopamine receptors and stopping dopamine neurons from firing. “Using these drugs, we’re fixing the overreactivity by causing the neurons to be inactive,” said Grace. “It would be better to fix overreactivity by correcting what causes it. It’s like fixing a car that’s going too fast by taking out the engine instead of lifting your foot off the gas.”

The next step, he said, is to try to fix the problem at its source. In the schizophrenic brain, it’s not just the dopamine system that’s hyperresponsive. The hippocampus also is hyperactive. Grace’s research shows that this hippocampal hyperactivity probably causes the dopamine system to go into overdrive.

Grace recently published a paper in the Neuropsychopharmacology in which he looked at a novel compound that works on another neurotransmitter, called GABA. “What we found in animal models, and others have found postmortem in schizophrenic patients, is that the hippocampus is lacking a certain type of GABA-ergic (GABA-producing) neuron that puts the brakes on the system,” said Grace. “What we’re trying to do is fix the GABA system that’s broken and, by doing that, stabilize the system so the dopamine system responses are back to normal, so that we can actually fix what’s wrong rather than trying to patch it several steps downstream. The dopaminergic system is easier because we have a good handle on what’s going on,” he said. “Cognitive symptoms are more complex. We’re trying to get a handle on how to approach those. Hopefully we can use some of this novel compound that we think is going to fix more of the symptoms and test in these domains.”

Co-authors were Kathryn Gill, a postdoctoral fellow in neuroscience; and Pierangelo Cifelli and Ornella Valenti, researchers who have returned to positions in Italy.

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The University Times Research Notes column reports on funding awarded to Pitt researchers as well as findings arising from University research.

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