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CRI Scientists Discover Vitamin C Regulates Stem Cell Function and Suppresses Leukemia Development

Not much is known about stem cell metabolism, but a new study from the Children’s Medical Center Research Institute at UT Southwestern (CRI) has found that stem cells take up unusually high levels of vitamin C, which then regulates their function and suppresses the development of leukemia.

“We have known for a while that people with lower levels of ascorbate (vitamin C) are at increased cancer risk, but we haven’t fully understood why. Our research provides part of the explanation, at least for the blood-forming system,” said Dr. Sean Morrison, the Director of CRI.

The metabolism of stem cells has historically been difficult to study because a large number of cells are required for metabolic analysis, while stem cells in each tissue of the body are rare. Techniques developed during the study, which was published in Nature, have allowed researchers to routinely measure metabolite levels in rare cell populations such as stem cells.

The techniques led researchers to discover that every type of blood-forming cell in the bone marrow had distinct metabolic signatures – taking up and using nutrients in their own individual way. One of the main metabolic features of stem cells is that they soak up unusually high levels of ascorbate. To determine if ascorbate is important for stem cell function, researchers used mice that lacked gulonolactone oxidase (Gulo) – a key enzyme that most mammals, including mice but not humans, use to synthesize their own ascorbate.

Loss of the enzyme requires Gulo-deficient mice to obtain ascorbate exclusively through their diet like humans do. This gave CRI scientists strict control over ascorbate intake by the mice and allowed them to mimic ascorbate levels seen in approximately 5 percent of healthy humans. At these levels, researchers expected depletion of ascorbate might lead to loss of stem cell function but were surprised to find the opposite was true – stem cells actually gained function. However, this gain came at the cost of increased instances of leukemia.

“Stem cells use ascorbate to regulate the abundance of certain chemical modifications on DNA, which are part of the epigenome,” said Dr. Michalis Agathocleous, lead author of the study, an Assistant Instructor at CRI, and a Royal Commission for the Exhibition of 1851 Research Fellow. “The epigenome is a set of mechanisms inside a cell that regulates which genes turn on and turn off.  So when stem cells don’t receive enough vitamin C, the epigenome can become damaged in a way that increases stem cell function but also increases the risk of leukemia.”

This increased risk is partly tied to how ascorbate affects an enzyme known as Tet2, the study showed. Mutations that inactivate Tet2 are an early step in the formation of leukemia. CRI scientists showed that ascorbate depletion can limit Tet2 function in tissues in a way that increases the risk of leukemia.

These findings have implications for older patients with a common precancerous condition known as clonal hematopoiesis. This condition puts patients at a higher risk of developing leukemia and other diseases, but it is not well understood why certain patients with the condition develop leukemia and others do not. The findings in this study might offer an explanation.

“One of the most common mutations in patients with clonal hematopoiesis is a loss of one copy of Tet2. Our results suggest patients with clonal hematopoiesis and a Tet2 mutation should be particularly careful to get 100 percent of their daily vitamin C requirement,” Dr. Morrison said. “Because these patients only have one good copy of Tet2 left, they need to maximize the residual Tet2 tumor-suppressor activity to protect themselves from cancer.”

Researchers in the Hamon Laboratory for Stem Cell and Cancer Biology, in which Dr. Morrison is also appointed, intend to use the techniques developed as part of this study to find other metabolic pathways that control stem cell function and cancer development. They also plan to further explore the role of vitamin C in stem cell function and tissue regeneration.

Dr. Morrison is a Professor of Pediatrics at UT Southwestern, a Cancer Prevention and Research Institute of Texas (CPRIT) Scholar in Cancer Research, and a Howard Hughes Medical Institute (HHMI) Investigator. He also holds the Mary McDermott Cook Chair in Pediatric Genetics at UT Southwestern and the Kathryne and Gene Bishop Distinguished Chair in Pediatric Research at Children’s Research Institute at UT Southwestern.

CRI and UTSW co-authors include Dr. Zhiyu Zhao, Assistant Professor at CRI and of Pediatrics at UT Southwestern; Dr. Weina Chen, Associate Professor of Pathology at UT Southwestern; Dr. Corbin Meacham, Dr. Rebecca Burgess, and Dr. Malea Murphy, postdoctoral researchers; and Dr. Ralph DeBerardinis, Associate Professor at CRI, of Pediatrics, and in the Eugene McDermott Center for Human Growth & Development. Dr. DeBerardinis, who holds the Joel B. Steinberg, M.D. Chair in Pediatrics and is a Sowell Family Scholar in Medical Research at UTSW, also is the Director of CRI’s Genetic and Metabolic Disease Program and Chief of the Division of Pediatric Genetics and Metabolism at UTSW.

The National Institutes of Health, HHMI, CPRIT, and donors to the Children’s Medical Center Foundation supported this work.

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Combination of Traditional Chemotherapy, New Drug Kills Rare Cancer Cells in Mice

An experimental drug combined with the traditional chemotherapy drug cisplatin, when used in mice, destroyed a rare form of salivary gland tumor and prevented a recurrence within 300 days, a University of Michigan study found.

Called adenoid cystic carcinoma, or ACC, this rare cancer affects 3,000-4,000 people annually, and typically arises in the salivary glands. It’s usually diagnosed at an advanced stage, is very resistant to therapy, and there’s no cure. People may have read about ACC in the news lately, because elite professional runner Gabe Grunewald is currently undergoing her fourth round of treatment since her 2009 ACC diagnosis.

Typically, oncologists treat ACC tumors with surgery and radiation. They rarely use chemotherapy because ACC is extremely slow-growing, and chemotherapy works best on cancers where cells divide rapidly and tumors grow quickly, said Jacques Nör, a U-M professor of dentistry, otolaryngology and biomedical engineering, and principal investigator on the study.

The Nör lab treated ACC tumors with a novel drug called MI-773, and then combined MI-773 with traditional chemotherapy cisplatin. MI-773 prevents a molecular interaction that causes tumor cells to thrive by disarming the critical cancer fighting protein, p53.

Study co-author Shaomeng Wang, U-M professor of medicine, pharmacology and medicinal chemistry, discovered MI-773, which is currently licensed to Sanofi.

Researchers believe that blocking that interaction sensitized ACC cancer cells to cisplatin––a drug that under normal conditions, wouldn’t work. When administered to the mice with ACC tumors, the cisplatin targeted and killed the bulk cells that form the tumor mass, while MI-773 killed the more resistant cancer stem cells that cause tumor recurrence and metastasis.

“This drug MI-773 prevents that interaction, so p53 can induce cell death,” Nör said.  “In this study, when researchers activated p53 in mice with salivary gland cancer, the cancer stem cells died.”

The key is that in many other types of cancer, p53 is mutated so it can’t kill cancer cells, and this mutation renders the MI-773 largely ineffective. However, in most ACC tumors p53 is normal, and Nör said researchers believe this makes these tumors good candidates for this combined therapy.

Researchers performed two different types of experiments to test ACC tumor reduction and recurrence. First, they treated tumors in mice with a combination of MI-773 and cisplatin, and tumors shrank from about the size of an acorn to nearly zero.

In the second experiment, the acorn-sized tumors were surgically removed, and for one month the mice were treated with MI-773 only, with the hope of eliminating the cancer stem cells that fuel recurrence and metastasis.

“We did not observe any recurrence in the mice that were treated with this drug after 300 days (about half of mouse life expectancy), and we observed about 62 percent recurrence in the control group that had only the surgery,” Nör said. “It’s our belief that by combining conventional chemotherapy with MI-773, a drug that kills more cancer stem cells, we can have a more effective surgery or ablation.”

One limitation of the study is that it’s known that about half of all ACC tumors recur only after about 10 years, and this observational period was only 300 days.

In a typical metastasis, the cancer cells spread through the blood to other parts of the body. But ACC cancer cells like to move by “crawling” along nerves, and it’s common for ACC tumor cells to follow the prominent facial nerves to the brain––picture a mountain climber ascending a rope––where it’s often fatal.

Research is still too early-stage to know how humans will respond, and the drug will work primarily in tumors where p53 is normal. If p53 is mutated, which is fairly common in other tumor types, this drug won’t work as well, Nör said.

The work was funded by the Adenoid Cystic Carcinoma Research Foundation, U-M and the National Institutes of Health.

The study, “Therapeutic Inhibition of the MDM2-p53 interaction prevents recurrence of adenoid cystic carcinomas,” appeared earlier this year in the journal Clinical Cancer Research.

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Prostate Cancer Cells Become ‘Shapeshifters’ to Spread to Distant Organs

Johns Hopkins Kimmel Cancer Center scientists report they have discovered a biochemical process that gives prostate cancer cells the almost unnatural ability to change their shape, squeeze into other organs and take root in other parts of the body. The scientists say their cell culture and mouse studies of the process, which involves a cancer-related protein called AIM1, suggest potential ways to intercept or reverse the ability of cancers to metastasize, or spread.

Results of the research are described in the July 26 issue of Nature Communications.

For the study, the Johns Hopkins scientists mined publically available research data on the genetics and chemistry of hundreds of primary and metastatic cancers included in five studies of men with prostate cancer. They found that a gene called AIM1 (aka “absent in melanoma 1”), which makes proteins also called AIM1, is deleted in approximately 20 – 30 percent of prostate cancers confined to the gland and about 40 percent of metastatic prostate cancers. In addition, the scientists found, on average, two- to fourfold less amounts of AIM1 expression in metastatic prostate cancers compared with normal prostate cells or those from men with prostate cancers confined to the prostate, suggesting that reduction of AIM1 proteins is somehow linked to tumor spread.

Aside from its link to the development of melanoma, a deadly skin cancer, scientists knew little about the function of AIM1.

“Our experiments show that loss of AIM1 proteins gives prostate cancer cells the ability to change shape, migrate and invade. These abilities could allow prostate cancer cells to spread to different tissues in an animal and presumably a person,” says Michael Haffner, M.D., Ph.D., a pathology resident and former postdoctoral fellow at the Johns Hopkins Kimmel Cancer Center who is involved in the research. “It’s not the whole story of what is going on in the spread of prostate cancer, but it appears to be a significant part of it in some cases.”

Looking more closely at the AIM1 gene and its protein levels in prostate cancer tissues, the Johns Hopkins scientists found that many times, even when the gene isn’t completely deleted and its protein production is reduced, its location in the prostate cancer cell is highly abnormal compared with normal prostate cells. This occurs even in primary prostate cancer cells, which have invaded the local structures to form invasive cancer within the prostate gland, say the scientists.

The research team used dyes to track the location of AIM1 proteins in human cells grown in the lab and followed where they appear in normal and cancerous prostate tissues. In normal prostate cells, AIM1 was located along the outside border of each cell and paired up with a protein called beta-actin that helps form the cell’s cytoskeleton, or scaffolding. However, in prostate cancer cells, the protein spread away from the outer border of the cells and no longer paired up with beta-actin.

The scientists found this pattern among a set of human prostate tissue samples including 81 normal prostates, 87 localized prostate cancers and 52 prostate cancers that had spread to the lymph nodes.

“It appears that when AIM1 protein levels drop, or when it’s abnormally spread throughout the cell instead of confined to the outer border, the prostate cancer cells’ scaffolding becomes more malleable and capable of invading other tissues,” says Vasan Yegnasubramanian, M.D., Ph.D., associate professor at the Kimmel Cancer Center and a member of the research team. With AIM1, the scaffold, Yegnasubramanian says, keeps normal cells in a rigid, orderly structure. Without AIM1, cells become more malleable, shapeshifting nomads that can migrate to other parts of the body, he says.

To track how these shapeshifting cancer cells move, the Johns Hopkins scientists, with Steven An, Ph.D., an expert in cellular mechanics and an associate professor at the Johns Hopkins Bloomberg School of Public Health, took a close-up look at AIM1-lacking prostate cancer cells, using sophisticated and quantitative single-cell analyses designed to probe the material and physical properties of the living cell and its cytoskeleton.

They found that cells lacking AIM1 remodeled their scaffolding more than twice as much as cells that had normal levels of AIM1, and that they exert three- to fourfold more force on their surroundings than cells with normal levels of the protein. Such cellular properties are reminiscent of cells with high potential to invade and migrate, An notes.

In addition, the scientists found that AIM1-lacking prostate cells were capable of migrating to unoccupied spaces on a culture dish or invading through connective tissue-like materials at rates fourfold higher than cells with normal levels of AIM1.

Next, the scientific team implanted human prostate cancer cells engineered without AIM1 in five mice and found that the cells spread to other tissues at levels 10 to 100 times more than cells with normal levels of AIM1 that were implanted in five similar mice. However, the AIM1-lacking cells were not able to establish full colonies and tumors at those other tissues, suggesting that AIM1 depletion is not the whole story in the spread and growth of metastatic prostate cancer.

“AIM1 may help prostate cancer cells disseminate throughout the body, but something else may be helping them form full-blown metastatic tumors when they get there,” says Yegnasubramanian.

The Johns Hopkins scientists plan to further study what happens to the AIM1 protein to cause its abnormal location in prostate cancers and identify other proteins and genes that work with AIM1 to cause metastasis. Such studies could help scientists find new drug targets aimed at preventing or reversing prostate metastasis.

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New Therapeutic Approach for Difficult-to-Treat Subtype of Ovarian Cancer Identified

Scientists from The Wistar Institute demonstrate how a mutation in ovarian clear cell carcinoma can be exploited to design a targeted treatment.

A potential new therapeutic strategy for a difficult-to-treat form of ovarian cancer has been discovered by Wistar scientists. The findings were published online in Nature Cell Biology.

Ovarian clear cell carcinoma accounts for approximately 5 to 10 percent of American ovarian cancer cases and about 20 percent of cases in Asia, ranking second as the cause of death from ovarian cancer. People with the clear cell subtype typically do not respond well to platinum-based chemotherapy, leaving limited therapeutic options for these patients.

Previous studies, including those conducted at The Wistar Institute, have revealed the role of ARID1A, a chromatin remodeling protein, in this ovarian cancer subtype. When functioning normally, ARID1A regulates expression of certain genes by altering the structure of chromatin – the complex of DNA and proteins in which DNA is packaged in our cells. This process dictates some of our cells’ behaviors and prevents them from becoming cancerous.

“Conventional chemotherapy treatments have proven an ineffective means of treating this group of ovarian cancer patients, meaning that alternative strategies based on a person’s genetic makeup must be explored,” said Rugang Zhang, Ph.D., professor and co-program leader in Wistar’s Gene Expression and Regulation Program and corresponding author of the study. “Therapeutic approaches based on the ARID1A mutation have the potential to revolutionize the way we treat these patients.”

Recent studies have shown that ARID1A is mutated in more than 50 percent of cases of ovarian clear cell carcinoma. Mutations of ARID1A and the tumor suppressor gene TP53 are mutually exclusive, meaning that patients with a mutation of ARID1A do not also carry a mutation of TP53. Despite this, the function of TP53, which protects the integrity of our genome and promotes programmed cell death, is clearly impaired as patients with the disease still have a poor prognosis.

In this study, Zhang and colleagues studied the connection between ARID1A and histone deacetylases (HDACs), a group of enzymes involved in key biological functions. They found that HDAC6 activity is essential in ARID1A-mutated ovarian cancers. They were able to show that HDAC6 is typically inhibited by ARID1A, whereas in the presence of mutated ARID1A, HDAC6 levels increase. Because HDAC6 suppresses the activity of TP53, therefore inhibiting its tumor suppressive functions, higher level of HDAC6 allow the tumor to grow and spread.

Using a small molecule drug called rocilinostat that selectively inhibits HDAC6, the Zhang lab found that by blocking the activity of the enzyme in ARID1A-mutated cancers, they were able to increase apoptosis, or programmed cell death, in only those tumor cells containing the ARID1A mutation. This correlated with a significant reduction in tumor growth, suppression of peritoneal dissemination and extension of survival of animal models carrying ARID1A-mutated ovarian tumors.

“We demonstrated that targeting HDAC6 activity using a selective inhibitor like rocilinostat represents a possible therapeutic strategy for treating ovarian clear cell carcinoma and other tumors impacted by mutated ARID1A,” said Shuai Wu, Ph.D., a postdoctoral fellow in the Zhang lab and co-first author of the study. “Inhibitors like the one we used in this study have been well-tolerated in clinical trials, so our findings may have far-reaching applications.”

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Childhood obesity major link to hip diseases

New research from the University of Liverpool, published in the Archives of Disease in Childhood journal, shows a strong link between childhood obesity and hip diseases in childhood.

Significant hip deformities affect around 1 in 500 children. Slipped Capital Femoral Epiphysis (SCFE) is the most common hip disease of adolescence. The condition always requires surgery, can cause significant pain, and often leads to a hip replacement in adolescence or early adulthood.

Children with a SCFE experience a decrease in their range of motion, and are often unable to complete hip flexion or fully rotate the hip inward. Unfortunately many cases of SCFE are misdiagnosed or overlooked, because the first symptom is knee pain, referred from the hip. The knee is often investigated and found to be normal. Early recognition of SCFE is important as the deformity may worsen if the slip remains untreated.

Factors explored

In an effort to identify children at higher risk of this condition researchers from the University’s Institute of Translational Medicine, led by National Institute of Health Research (NIHR) Clinician Scientist and Senior Lecturer in Orthopaedic Surgery Daniel Perry, examined hospital and community based records to explore factors associated with SCFE, and explanations for diagnostic delays.

All of the records examined were of individuals under 16-years-of-age with a diagnosis of SCFE and whose electronic medical record was held by one of 650 primary care practices in the UK between 1990 and 2013.

Using the height and weight of children recorded in the notes at some point before the disease was diagnosed the researchers were able to identify that obese children appear at highest risk of this condition.

The study was funded by the Academy of Medical Sciences.

Best evidence

Daniel Perry, who is also an Honorary Consultant Orthopaedic Surgeon at Alder Hey Children’s Hospital, said: “This is the best evidence available linking this disease to childhood obesity – which makes this condition to be one of the only obesity-related disease that can cause life-long morbidity starting in childhood.

“A significant proportion of patients with SCFE are initially misdiagnosed and those presenting with knee pain are particularly at risk.

“Ultimately this study helps us to better understand one of the main diseases affecting the hip in childhood. Whilst we confirm a strong association with obesity, we are still unable to say that obesity causes this disease.”

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Researchers Studying Debilitating Lung Disease that Targets Puerto Ricans

Loyola Medicine is enrolling patients in the first major study of a rare, debilitating lung disease that disproportionately affects people from Puerto Rico.

The hereditary disease is called Hermansky-Pudlak syndrome (HPS). It can cause bleeding problems, low vision, albinism and in some patients, a debilitating and often fatal lung disease called pulmonary fibrosis, said Loyola Medicine pulmonologist Daniel Dilling, MD.

HPS affects fewer than 1 in 500,000 people worldwide. But it is more common in certain geographic pockets, especially Puerto Rico, where it affects 1 in 1,800 people.

Loyola is the only center in Illinois participating in a multicenter study of how HPS develops in patients over time. The first Loyola HPS patient to enroll is Jonathan Colon, 44, of Chicago, whose parents are from Puerto Rico. Puerto Ricans who have HPS are believed to have descended from a single founding patient.

Mr. Colon has pulmonary fibrosis, characterized by a buildup of scar tissue in the lungs. Pulmonary fibrosis makes breathing increasingly difficult, and in later stages patients need supplemental oxygen around the clock. Small exertions such as walking across a room can leave a patient gasping for breath. Without a lung transplant, the condition can be fatal.

The course of the disease varies among patients. Mr. Colon was diagnosed relatively early in the disease, and is taking a new drug that has slowed the progression of his pulmonary fibrosis. Dr. Dilling said Mr. Colon eventually may need a lung transplant. The operation would be challenging, because in HPS patients, blood does not coagulate normally, increasing the risk of bleeding.

Dr. Dilling said people of Puerto Rican descent who have albinism (abnormally light coloring) should be screened for HPS to ensure early treatment. Many Puerto Ricans with albinism do not know they are at risk for HPS, Dr. Dilling said.

The study is called “A Longitudinal Study of Hermansky-Pudlak Syndrome Pulmonary Fibrosis.” Its purpose is to identify the earliest evidence of pulmonary disease in individuals who are at risk for HPS pulmonary fibrosis. Researchers also hope to identify biomarkers that will help them understand the cause of HPS pulmonary fibrosis and facilitate future clinical trials. (A  biomarker is a substance in the body that predicts the incidence or outcome of a disease.)

The study is funded by the National Heart, Lung and Blood Institute of the National Institutes of Health. Principal investigator of the overall study is Lisa Young, MD, of Vanderbilt University.

For 29 years, Loyola has operated the largest and most successful lung transplant program in Illinois. More than 900 lung transplants—by far the most of any center in Illinois—have been performed and Loyola’s 40 lung transplants in 2016 were more than all other programs in Illinois combined.

Loyola’s lung transplant program regularly evaluates and successfully performs transplants in patients who have been turned down by other centers in Chicago and surrounding states and consistently records outstanding outcomes.

Loyola also is the only center in Illinois to join the recently launched Rare Lung Diseases Consortium, which is spearheading cutting-edge research on HPS and other rare lung diseases.The consortium is a unique collaboration among patient groups, researchers and the National Institutes of Health. Its mission is to conduct research into new diagnostic tests and treatments, provide clinical research training and focused clinical care and educate patients, physicians, researchers and the public about rare lung diseases.

The study will enroll about 150 patients aged 12 and older who have been diagnosed with HPS. For more information about enrolling at the Loyola site, contact Josie Corral, RN, at 708-216-5744 or at  jcorral@luc.edu.

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First Large-Scale Genomic Analysis of Key Acute Leukemia Will Likely Yield New Therapies

A consortium including St. Jude Children’s Research Hospital and the Children’s Oncology Group has performed an unprecedented genomic sequencing analysis of hundreds of patients with T-lineage acute lymphoblastic leukemia (T-ALL). The results provide a detailed genomic landscape that will inform treatment strategies and aid efforts to develop drugs to target newly discovered mutations.

The data will also enable researchers to engineer better mouse models to probe the leukemia’s aberrant biological machinery.

The project’s 39 researchers were led by Charles Mullighan, M.D., MBBS, a member of the St. Jude Department of Pathology, with co-corresponding authors Jinghui Zhang, Ph.D., chair of the St. Jude Department of Computational Biology and Stephen Hunger, M.D., of the Children’s Hospital of Philadelphia. The research was selected for advance online publication today in the journal Nature Genetics.

“This first comprehensive and systematic analysis in a large group of patients revealed many new mutations that are biologically significant as well as new drug targets that could be clinically important,” Mullighan said. “Leukemias typically arise from multiple genetic changes that work together. Most previous studies have not had the breadth of genomic data in enough patients to identify the constellations of mutations and recognize their associations.”

T-ALL is a form of leukemia in which the immune system’s T cells acquire multiple mutations that freeze the cells in an immature stage, causing them to accumulate in the body. ALL is the most common type of childhood cancer, affecting about 3,000 children nationwide each year. T-ALL constitutes about 15 percent of those cases. While about 90 percent of children with ALL can be cured, many still relapse and require additional treatment.

The multi-institutional effort involved sequencing the genomes of 264 children and young adults with T-ALL—the largest such group ever analyzed. The study involved sophisticated analysis of multiple types of genomic data, led by Yu Liu, Ph.D., a postdoctoral fellow in Zhang’s Computational Biology laboratory and first author of the study. Their analyses identified 106 driver genes—those whose mutations trigger the malfunctions that block normal T cell development and give rise to cancer. Half of those mutated genes had not been previously identified in childhood T-ALL.

The study enabled the researchers to compare the frequencies of mutations among patients whose cancerous cells were sequenced at the same detailed level, Mullighan said. Also important, he said, was that all the patients had uniform treatment, which enabled the researchers to draw meaningful associations between the genetics of their cancer and the response to different treatments. Such associations will enable better diagnosis and treatment of T-ALL with existing drugs.

Researchers analyzed the cancerous T cells as well as those that treatments had rendered non-cancerous. Comparing the two populations of cells could reveal valuable clues about why specific treatments were successful in thwarting particular cancer-causing mutations.

The findings revealed significant unexpected findings. “We went into this study knowing that we didn’t know the full genomic landscape of T-ALL,” Hunger said. “But we were surprised that over half of the new targets and mutations were previously unrecognized. It was particularly unexpected and very striking that some mutations were exclusively found in some subtypes of T-ALL, but not others.”

Cancers are driven by mutations in genes that are the blueprint for protein enzymes in signaling pathways in cells—the biological equivalent of circuits in a computer. While a cancer may arise from an initial founding mutation, that mutation triggers a cascade of other mutations that help drive the cancer.

The new genomic analysis confirmed that T-ALL was driven by mutations in known signaling pathways, including JAK–STAT, Ras and PTEN–PI3K.

However, the new analysis identified many more genetic mutations in those known pathways. The findings offered more targets for drugs to shut down the aberrant cells. “So the frequency of the patients that are potentially amenable to these targeted approaches is higher than we appreciated before,” Mullighan said.

The researchers also found cases in which the same T-ALL subtype had mutations in different pathways triggered by the same cancer-causing founding mutation. “We believe this finding suggests we can target such subtypes with an inhibitor drug for one of the pathways, and it’s likely to be effective,” Mullighan said.

The multitude of new mutations uncovered in the new study will also enable researchers to use genetic engineering to create mouse models that more accurately reflect human cancer, he said. Such models are invaluable for understanding the biological machinery of T-ALL, as well as testing new drug strategies. “We now have a launching pad, if you will, to design mouse models that include multiple genetic mutations to more faithfully reflect the leukemias we see in humans,” Mullighan said.

The research also offers a broader lesson for genomic studies of cancers, Zhang said. “Our study is further evidence that if you systematically study a large enough population with careful, detailed genomic analysis, you will discover new mutational patterns of collaboration or exclusion across multiple genes unique to each T-ALL subtype,” she said.

The study was a collaboration between the St. Jude Children’s Research Hospital – Washington University Pediatric Cancer Genome Project, the Children’s Oncology Group (COG) and the National Cancer Institute’s Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative. COG is a federally supported clinical trials group focused exclusively on childhood cancer. TARGET uses genomic analysis of COG samples to identify therapeutic targets and spur development of more effective treatment for childhood cancer.

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Research could give insight into genetic basis of of the human muscle disease, myopathy

Pioneering research using the tropical zebrafish could provide new insights into the genetic basis of myopathy, a type of human muscle disease.

An international research team, led by Professor Philip Ingham FRS, inaugural Director of the University of Exeter’s Living Systems Institute — has taken the first steps in determining the central role a specific gene mutation in a poorly characterised human myopathy.

Myopathies are diseases that prevent muscle fibres from functioning properly, causing muscular weakness. At present, there is no single treatment for the disease, as it can develop via a number of different pathways.

One particular type is nemaline myopathy, which primarily affects skeletal muscles and can lead to sufferers experiencing severe feeding and swallowing difficulties as well as limited locomotor activity.

Mutations in a specific gene, called MY018B, have recently been found to be present in people exhibiting symptoms of this disease, but the role these mutations play in muscle fibre integrity has until now been unclear.

In this new research, the Ingham team, based in Singapore and Exeter, has used high-resolution genetic analysis to create a zebrafish model of MYO18B malfunction; this research takes advantage of the remarkable similarity between the genomes of zebrafish and humans, — which have more than 70 per cent of their genes in common.

The Singapore/Exeter team found that the MYO18B gene is active specifically in the ‘fast-twitch’ skeletal muscles of the zebrafish, typically used for powerful bursts of movement. Crucially, by studying fish in which the MYO18B gene is disrupted, they were able to show that it plays an essential role in the assembly of the bundles of actin and myosin filaments that give muscle fibres their contractile properties.

The team believe this new research offers a vital new step towards understanding the cause of myopathy in humans, which in turn could give rise to new, tailored treatments in the future.

The leading research is published in the scientific journal, Genetics.

Professor Ingham, said: “The identification of a MYO18B mutation in zebrafish provides the first direct evidence for its role in human myopathy and gives us a model in which to study the molecular basis of MYO18B function in muscle fibre integrity.”

A pioneer in the genetic analysis of development using fruit flies and zebrafish as model systems, Prof Ingham is internationally renowned for his contributions to several influential discoveries in the field of developmental biology over the last century.

This is the latest research by Professor Ingham that has revealed important links between the processes that underpin normal embryonic development and disease.

His co-discovery of the ‘Sonic Hedgehog’ gene, recognised as one of 24 centennial milestones in the field of developmental biology by Nature, in 2004, led directly to the establishment of a biotechnology company that helped develop the first drug to target non-melanoma skin cancer.

The research comes at the University of Exeter holds the official opening of the Living Systems Institute with an Opening Symposium event, from July 5-6 2017.

Two Nobel Laureates, Sir Paul Nurse FRS and Christiane Nüsslein-Volhard ForMemRS, who separately won the Nobel Prize for Physiology or Medicine, will deliver keynote speeches as part of the opening event.

The high-profile event, held at the University’s Streatham Campus marks the official opening of the LSI — a £52 million inter-disciplinary research facility designed to bring new, crucial insights into the causes and preventions of some of the most serious diseases facing humanity.

A Zebrafish Model for a Human Myopathy Associated with Mutation of the Unconventional Myosin MYO18B is published in Genetics.

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HPV Testing Leads to Earlier Detection and Treatment of Cervical Precancer

Women who receive human papillomavirus (HPV) testing, in addition to a pap smear, receive a faster, more complete diagnosis of possible cervical precancer, according to a study of over 450,000 women by Queen Mary University of London (QMUL) and the University of New Mexico (UNM) Comprehensive Cancer Center.

HPV is a virus that can cause cervical, vaginal, penile and anal cancers. More than 520,000 cases of cervical cancer are diagnosed worldwide each year, causing around 266,000 deaths. A common screening procedure for cervical cancer is the Pap smear, which tests for the presence of precancerous or cancerous cells on the cervix.

The study, published in JAMA Oncology, used data from the New Mexico HPV Pap Registry in the United States. It is the first comprehensive evaluation of HPV testing on the long-term outcomes of women who had received a borderline abnormal Pap test result.

A total of 457,317 women were included in the study. Of these, 20,677 women (4.5 percent) received a borderline abnormal result through a Pap smear and were followed in the study for five years. Some of the women with borderline abnormal Pap smear results had an HPV test.

HPV testing led to a 15.8 percent overall increase in the detection of cervical precancers and time to detection was much shorter (a median of 103 days versus 393 days).

Virtually all cervical pre-cancers were detected in women who tested positive for HPV, suggesting HPV testing to be a good additional screening method after the Pap smear. Colposcopy, which is a medical examination of the cervix, could then be focused on women who would need it most: those with a positive HPV test.

At the same time, however, HPV testing of women resulted in 56 percent more biopsies and a 20 percent increase in surgical treatment procedures performed. Most of the additional biopsies were for low grade lesions which could have regressed, indicating some overtreatment due to HPV testing.

Professor Jack Cuzick from QMUL said: “This study shows that knowing a woman’s HPV status can help determine her likelihood of needing additional procedures, and prioritise immediate treatment and medical resources to the women who need them most.”

Professor Cosette Wheeler from the UNM Comprehensive Cancer Center said: “The benefits of HPV testing outweigh the harms observed but it’s important to understand and quantify the harms as well.”

The authors warn that, as this was an observational study, the use of HPV testing was not randomised. So, it is also possible that there could be socioeconomic or other relevant differences among health care facilities that have not been measured.

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New inhibitor drug shows promise in relapsed leukemia

A new drug shows promise in its ability to target one of the most common and sinister mutations of acute myeloid leukemia (AML), according to researchers at the Perelman School of Medicine at the University of Pennsylvania and Penn’s Abramson Cancer Center. The Fms-like tyrosine kinase 3 (FLT3) gene mutation is a known predictor of AML relapse and is associated with short survival. In a first-in-human study, researchers treated relapsed patients with gilteritinib, an FLT3 inhibitor, and found it was a well-tolerated drug that led to frequent and more-sustained-than-expected clinical responses, almost exclusively in patients with this mutation. They published their findings today in The Lancet Oncology.

FLT3 is one of the most commonly mutated genes in AML patients. FLT3 mutations are found in about 30 percent of patients’ leukemia cells. Clinically, these mutations are associated with aggressive disease that often leads to rapid relapse, after which the overall survival is an average of about four months with current therapies. To avoid relapse, oncologists often recommend the most aggressive chemotherapy approaches for patients with FLT3 internal tandem duplication (FLT3-ITD), including marrow transplantation. But even that cannot always stave off the disease.

The FLT3 gene is present in normal bone marrow cells and regulates the orderly growth of blood cells in response to daily demands. When the gene is mutated in a leukemia cell, however, the mutated cells grow in an uncontrolled manner unless the function of FLT3 is turned off.

“Other drugs have tried to target these mutations, and while the approach works very well in the laboratory, it has proven very challenging to develop FLT3 inhibitors in the clinic for several reasons,” said Alexander Perl, MD, MS, an assistant professor of Hematology Oncology in Penn’s Abramson Cancer Center and the study’s lead author. “First, we’ve learned it takes unusually potent inhibition of the FLT3 target to generate clinical responses. Second, many of these drugs are not selective in their activity against FLT3. When they target multiple kinases, it can lead to more side-effects. That limits whether you can treat a patient with enough drug to inhibit FLT3 at all. Finally, with some FLT3 inhibitors, the leukemia adapts quickly after response and cells can develop new mutations in FLT3 that don’t respond to the drugs at all. So ideally, you want a very potent, very selective, and very smartly designed drug. That’s hard to do.”

For this phase 1/2 clinical trial, Perl and his team evaluated the drug gilteritinib – also known as ASP2215 – at increasing doses in patients whose AML had relapsed or was no longer responding to chemotherapy. The team focused on dose levels at 80mg and above, which were associated with more potent inhibition of the FLT3 mutation and higher response rates. They found these doses were also associated with longer survival. Of the 252 patients on this study, 67 were on a 120mg dose and 100 were on a 200mg dose. Seventy-six percent (191) of the patients on the trial had a FLT3 mutation. Overall, 49 percent of patients with FLT3 mutations showed a response. Just 12 percent of patients who didn’t have the mutation responded to the drug.

“The fact that the response rate tracked with the degree of FLT3 inhibition and was so much lower among patients who did not have an FLT3 mutation gives us confidence that this drug is hitting its target,” Perl said.

In leukemia cells, FLT3 itself can mutate again to a form called a D835 mutation that is resistant to several FLT3 inhibitors treatments. Gilteritinib, however, remains active against D835 mutations in laboratory models of leukemia. Clinical response rates from the trial appeared to be the same, whether patients had a FLT3-ITD alone or both a FLT3-ITD and a D835 mutation. The response rates also were similar in patients in whom gilteritinib was their first FLT3 inhibitor and those who previously were treated with other FLT3 inhibitors.

The drug was also generally well-tolerated. The three most common side effects attributed to the drug were diarrhea in 41 patients (16 percent), fatigue in 37 (15 percent), and abnormal liver enzyme tests in 33 (13 percent). These generally were mild in severity and discontinuation of gilteritinib for side effects was uncommon (25 patients, 10 percent).

“These look like data you want to see for a drug to eventually become a standard therapy,” Perl said, though he noted more research will be necessary.

A new multicenter trial, which compares gilteritinib to standard chemotherapy in patients with FLT3 mutations who relapsed or did not respond to initial therapy, is now underway, and Penn’s Abramson Cancer Center is one of the sites.

There are also studies underway that give the drug in combination with frontline chemotherapy and as an adjunct to bone marrow transplantation in hopes of preventing relapse altogether.

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Penn study details impact of antibiotics, antiseptics on skin microbiomes

The use of topical antibiotics can dramatically alter communities of bacteria that live on the skin, while the use of antiseptics has a much smaller, less durable impact. The study, conducted in mice in the laboratory of Elizabeth Grice, PhD, an assistant professor of Dermatology in the Perelman School of Medicine at the University of Pennsylvania, is the first to show the long-term effects of antimicrobial drugs on the skin microbiome. Researchers published their findings today in the journal Antimicrobial Agents and Chemotherapy.

The skin, much like the gut, is colonized by a diverse multitude of microorganisms which generally coexist as a stable ecosystem — many of which are harmless or even beneficial to the host. However, when that ecosystem is disturbed or destabilized, colonization and/or infection by more dangerous microbes can occur. Antiseptics, such as ethanol or iodine, are commonly used to disinfect the skin prior to surgical procedures or following exposure to contaminated surfaces or objects. Topical antibiotics may be used to decolonize skin of specific types of bacteria or for rashes, wounds, or other common conditions.

In the gut, research shows medication that alters microbial communities can lead to complications like Clostridium difficile, or C. diff — which causes diarrhea and is the most common hospital-acquired infection. But when it comes to the skin, the impact of these medications on bacteria strains like Staphylococcus aureus, or S. aureus — the most common cause of skin infections — is still largely unstudied.

“We know antibiotics and antiseptics can be effective in stopping the growth of certain bacteria, but we wanted to know about the larger impact these treatments can have on the resident microbial communities on the skin,” said the study’s lead author, Adam J. SanMiguel, PhD, a researcher in the Grice Laboratory at Penn.

Researchers treated the skin of hairless mice with a variety of antibiotics, including a narrowly targeted mupirocin ointment and a broadly applicable triple-antibiotic ointment (TAO) containing bacitracin, neomycin, and polymyxin B. All of the antibiotics changed the makeup of the microbial communities, and, in a key finding of the study, the impact of that change lasted for days after treatment stopped.

“The problem in this case isn’t antibiotic resistance, but instead, how long the disruption of the skin microbiomes continues,” SanMiguel said. “That disruption opens the door for colonization by an unwanted strain.”

The researchers similarly evaluated antiseptics, using alcohol or povidone-iodine and comparing those treatments with two control groups – mice treated with water and mice entirely untreated. They found neither antiseptic caused responses similar enough to cluster the mice together into groups based on their microbiomes. They also found no clear difference between the treatment groups and the control groups when comparing the relative number of individual bacteria strains.

“We thought antiseptics would be even more disruptive to microbial communities than antibiotics since they are less targeted, but it turns out the opposite is true,” SanMiguel said. “It shows how stable the skin microbiome can be in the face of stress.”

However, both antibiotic and antiseptic treatments removed skin resident bacteria that compete against the pathogenic S. aureus to colonize the skin. Colonization with S. aureus is a risk factor for developing a skin infection.

“This gives us a better understanding of how topical antimicrobials affect the skin microbiome and what kind of impact their disturbance can have in the context of pathogenic colonization,” said Grice, the study’s senior author. “This helps us anticipate their potential effects.”

The researchers say this work can provide the foundation for greater understanding of how the skin defends against infection. They have already begun similar testing in humans.

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Cardiac stem cells from heart disease patients may be harmful

Patients with severe and end-stage heart failure have few treatment options available to them apart from transplants and “miraculous” stem cell therapy. But a new Tel Aviv University study finds that stem cell therapy may, in fact, harm heart disease patients.

The research, led by Prof. Jonathan Leor of TAU’s Sackler Faculty of Medicine and Sheba Medical Center and conducted by TAU’s Dr. Nili Naftali-Shani, explores the current practice of using cells from the host patient to repair tissue — and contends that this can prove deleterious or toxic for patients. The study was recently published in the journal Circulation.

“We found that, contrary to popular belief, tissue stem cells derived from sick hearts do not contribute to heart healing after injury,” said Prof. Leor. “Furthermore, we found that these cells are affected by the inflammatory environment and develop inflammatory properties. The affected stem cells may even exacerbate damage to the already diseased heart muscle.”

Tissue or adult stem cells — “blank” cells that can act as a repair kit for the body by replacing damaged tissue — encourage the regeneration of blood vessel cells and new heart muscle tissue. Faced with a worse survival rate than many cancers, many heart failure patients have turned to stem cell therapy as a last resort.

“But our findings suggest that stem cells, like any drug, can have adverse effects,” said Prof. Leor. “We concluded that stem cells used in cardiac therapy should be drawn from healthy donors or be better genetically engineered for the patient.”

Hope for improved cardiac stem cell therapy

In addition, the researchers also discovered the molecular pathway involved in the negative interaction between stem cells and the immune system as they isolated stem cells in mouse models of heart disease. After exploring the molecular pathway in mice, the researchers focused on cardiac stem cells in patients with heart disease.

The results could help improve the use of autologous stem cells — those drawn from the patients themselves — in cardiac therapy, Prof. Leor said.

“We showed that the deletion of the gene responsible for this pathway can restore the original therapeutic function of the cells,” said Prof. Leor. “Our findings determine the potential negative effects of inflammation on stem cell function as they’re currently used. The use of autologous stem cells from patients with heart disease should be modified. Only stem cells from healthy donors or genetically engineered cells should be used in treating cardiac conditions.”

The researchers are currently testing a gene editing technique (CRISPER) to inhibit the gene responsible for the negative inflammatory properties of the cardiac stem cells of heart disease patients. “We hope our engineered stem cells will be resistant to the negative effects of the immune system,” said Prof. Leor.

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Gut bacteria could protect cancer patients and pregnant women from Listeria, study suggests

Researchers at Memorial Sloan Kettering Cancer Center in New York have discovered that bacteria living in the gut provide a first line of defense against severe Listeria infections. The study, which will be published June 6 in The Journal of Experimental Medicine, suggests that providing these bacteria in the form of probiotics could protect individuals who are particularly susceptible to Listeria, including pregnant women and cancer patients undergoing chemotherapy.

Listeria monocytogenes is a major pathogen acquired by eating contaminated food, but healthy adults can generally fend off an infection after suffering, at worst, a few days of gastroenteritis. However, some individuals, including infants, pregnant women, and immunocompromised cancer patients, are susceptible to more severe forms of listeriosis, in which the bacterium escapes the gastrointestinal tract and disseminates throughout the body, causing septicemia, meningitis, and, in many cases, death.

Patients with some forms of cancer are as much as 1,000 times more likely to develop listeriosis, possibly because chemotherapy drugs can suppress a patient’s immune system. But a team of researchers led by Simone Becattini and Eric G. Pamer wondered whether the gut microbiome–the community of bacteria that naturally lives in the gastrointestinal tract–might also play a role in limiting L. monocytogenes infection. Chemotherapy disrupts the microbiome, and gut bacteria are known to prevent other food-borne pathogens from colonizing the gastrointestinal tract by, for example, secreting antibacterial toxins.

The researchers found that disrupting the microbiome with antibiotics made laboratory mice more susceptible to L. monocytogenes infection, increasing the pathogen’s ability to colonize the gastrointestinal tract and spread into the circulatory system to cause the animals’ death. The effect of antibiotics was even more noticeable in immunocompromised mice lacking key immune cells; these animals succumbed to even small doses of L. monocytogenes if their microbiomes were disrupted by antibiotic treatment.

Mice treated with the common chemotherapy drugs doxorubicin and cyclophosphamide were vulnerable to Listeria infection, and they became even more susceptible when they were also treated with antibiotics.

The researchers identified four species of gut bacteria–all members of the Clostridiales order–that together were able to limit L. monocytogenes growth in laboratory cultures. Transferring these probiotic bacteria into germ-free mice protected the rodents from Listeria infection by limiting the pathogen’s ability to colonize the gastrointestinal tract and disseminate into other tissues. “Thus, augmenting colonization resistance functions in immunocompromised patients by introducing these protective bacterial species might represent a novel clinical approach to prevent L. monocytogenes infection,” says Becattini.

“Our results also raise the possibility that in other at-risk categories for listeriosis, such as infants or pregnant women, disruptions to the gut microbiome could be a contributing factor to susceptibility,” Becattini continues. “Pregnant women in their third trimester, the phase in which susceptibility to Listeria is known to be highest, show an altered microbiome, with a marked reduction in Clostridiales species.”

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Cancer therapy shows promise for psoriasis treatment

HDAC inhibitors, already widely used to treat cancer, may be an effective therapy for psoriasis as well, scientists report.

They have shown that HDAC3 inhibitors are particularly adept at increasing expression of aquaporin-3, or AQP3, a channel that transports glycerin, a natural alcohol and water attractor, which helps skin look better and aids healthy production and maturation of high-turnover skin cells.

“We’ve found that HDAC3 normally inhibits expression of AQP3 and we think we can use this knowledge to treat patients with psoriasis,” said Dr. Vivek Choudhary, molecular biologist and physiologist in the Department of Physiology at the Medical College of Georgia at Augusta University.

MCG scientists knew that AQP3 levels were lower in psoriasis than in healthy skin, said Choudhary, corresponding author of the study in the Journal of Investigative Dermatology. The protein helps skin cells proliferate, differentiate into the right kind of cells and get to the right location in the body. It also aids the skin’s hydration, wound recovery and elasticity. Histone deacetylase, which they found suppresses AQP3, helps regulate gene expression and protein function.

Since the immune system is believed to play a key role in psoriasis, many current treatments generally suppress the immune response, which increases the risk of infections, even cancer. MCG scientists hope they can one day instead directly enhance the presence of AQP3 or maybe its key cargo glycerin.

Psoriasis is one of the most common skin disorders, with red, flaky patches most often erupting on the elbows, knees, scalp and back, said Dr. Wendy B. Bollag, cell physiologist in the MCG Department of Physiology and the study’s senior author.

Like cancer, inflammation and excessive proliferation of cells are a psoriasis hallmark. That common ground and other emerging clues got the scientists thinking about the treatment potential of HDAC inhibitors. But first they had to establish a relationship.

When they introduced a broad-acting HDAC inhibitor to normal skin cells, or keratinocytes, – both mouse and human – they found expression of AQP3 went up within 24 hours, the first time the relationship had been noted.

They reiterated that AQP3 was critical because when it was missing, there was no commensurate increase in glycerin. AQP3 knockout mice also further clarified AQP3’s role in skin hydration, elasticity and wound healing and that it is glycerin – rather than water – that is most key to these healthy functions.

They also found that p53, a known, natural tumor suppressor that also supports cell differentiation, helps the HDAC inhibitors enable more AQP3 and ultimately more glycerin, Choudhary said. HDACs also are known to inhibit p53 activity. However overexpressing p53 by itself did not result in increased functional levels of AQP3, the scientists found.

The MCG scientists first used the HDAC inhibitor, suberoylanilide hydroxamic acid, or SAHA, which was approved by the Food and Drug Administration more than a decade ago to treat cutaneous T cell lymphoma, which has symptoms that can include dry, itchy skin as well as enlarged lymph nodes.

“We think this is one of the ways it works,” Bollag said of SAHA and their new findings. They also used several other HDAC inhibitors and found the ones that suppressed HDAC3 were also most effective at increasing AQP3.

AQP3 is adept at hauling glycerin, the backbone of many lipids and typically a key ingredient in skin lotion. Bollag’s lab reported in the Journal of Investigative Dermatology in 2003 that glycerin helps skin cells mature properly. Inside skin cells, phospholipase D – an enzyme that converts fats or lipids in the external protective cell membrane into cell signals – and AQP3 interact. AQP3 hands off glycerin, which produces phosphatidylglycerol, which, in turn, aids skin cell differentiation.

“We think phosphatidylglycerol is the key,” Bollag said of the positive results. “If you don’t have enough, you may have psoriasis.”

The Bollag lab and others also had found that AQP3, which is present in psoriasis, appears rather immature and out of place, largely inside the cell cytoplasm instead of on the protective, outer cell membrane. The inner location puts quite a damper on its normal mature function of transporting glycerin, water and other substances through the membrane.

“If you use antibodies to visualize where AQP3 is in the keratinocytes, you will see it nicely outlining the cells because it’s right there on the plasma membrane,” Bollag said. “So clearly it’s normally expressed in keratinocytes but the fact that we can upregulate it even more with an HDAC3 inhibitor suggests that normally HDAC3 keeps it in check.”

Cambridge, Massachusetts-based biotech company Shape Pharmaceuticals Inc., currently has a topical version of an HDAC inhibitor in clinical trials for cutaneous T cell lymphoma. If psoriasis patients end up taking HDAC inhibitors, low doses or a topical application likely would help avoid some side effects, including nausea, Bollag said.

One way HDAC inhibitors help fight cancer is by temporarily loosening DNA, increasing the expression of tumor-suppressing genes and making the tumor more vulnerable. HDAC inhibitors also are being explored for their potential in treating neurological diseases such as Huntington’s.

Others have provided evidence that dysregulation of AQP3 contributes to psoriasis and AQP3 is linked to other skin diseases as well like atopic dermatitis – the most common type of eczema and vitiligo, which results in white patches on the skin.

Interestingly, even though psoriatic cells are known for their propensity to replicate, it’s hard to grow an adequate number of cells for scientific study: they increase a certain amount then go quiet. There also is no real animal model of psoriasis. Moving forward, the MCG scientists may try developing a model using a topical drug for genital warts since some patients who take it develop psoriasis.

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Researchers Uncover Key Role for MicroRNA in Inflammatory Bowel Disease

An international team of researchers has discovered that a microRNA produced by certain white blood cells can prevent excessive inflammation in the intestine. The study, “Myeloid-derived miR-223 regulates intestinal inflammation via repression of the NLRP3 inflammasome,” which will be published May 9 in The Journal of Experimental Medicine, shows that synthetic versions of this microRNA can reduce intestinal inflammation in mice and suggests a new therapeutic approach to treating patients with Crohn’s disease or ulcerative colitis.

Inflammatory bowel disease (IBD), including Crohn’s disease and ulcerative colitis, affects almost 2 million people in the US. Although IBD is caused by a complex mix of genetic and environmental factors, it is thought to be initiated by an excessive immune response against bacteria in the gut. This immune response involves the recruitment of various white blood cells, such as neutrophils and monocytes, into the intestine and the activation of a protein complex in these cells known as the inflammasome. The inflammasome, in turn, activates the proinflammatory signaling molecules IL-1β and IL-18, which stimulate the further influx of white blood cells.

MicroRNAs are small RNA molecules that can bind and repress protein-coding messenger RNAs. An international team of researchers led by Eóin McNamee at the University of Colorado-Anschutz Medical Campus found that IBD patients showed increased levels of a microRNA called miR-223 during active bouts of inflammation. This microRNA was also elevated in laboratory mice with colitis.

miR-223 is produced by neutrophils and monocytes and has previously been shown to repress the messenger RNA encoding NLRP3, a key component of the inflammasome. McNamee and colleagues found that mice lacking miR-223 expressed higher levels of NLRP3, causing increased IL-1β production and enhanced susceptibility to intestinal inflammation.

In contrast, mice treated with lipid nanoparticles containing synthetic RNA molecules that mimic miR-223 showed lower levels of NLRP3 and IL-1β and were accordingly protected from experimentally induced colitis.

“Our study highlights the miR-223–NLRP3–IL-1β regulatory circuit as a critical component of intestinal inflammation,” McNamee says. “miR-223 serves to constrain the level of NLRP3 inflammasome activation and provides an early brake that limits excessive inflammation. Genetic or pharmacologic stabilization of miR-223 may hold promise as a future novel therapy for active flares in IBD.”

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Stalking the ‘Unknown Enemy’: Doctors Turn Scope On Rare Diseases

By Anna Gorman, Kaiser Health News
Photos by Heidi de Marco

WHITTIER, Calif. — Lynn Whittaker stood in the hallway of her home looking at the framed photos on the wall. In one, her son, Andrew, is playing high school water polo. In another, he’s holding a trombone.

The images show no hint of his life today: the seizures that leave him temporarily paralyzed, the weakness that makes him fall over, his labored speech, his scrambled thoughts.

Andrew, 28, can no longer feed himself or walk on his own. The past nine years have been a blur of doctor appointments, hospital visits and medical tests that have failed to produce answers.

“You name it, he doesn’t have it,” his mother said.

Andrew has never had a clear diagnosis. He and his family are in a torturous state of suspense, hanging their hopes on every new exam and evaluation.

Recently, they have sought help from the Undiagnosed Diseases Network, a federally funded coalition of universities, clinicians, hospitals and researchers dedicated to solving the nation’s toughest medical mysteries. The doctors and scientists in the network harness advances in genetic science to identify rare, sometimes unknown, illnesses.

At UCLA, one of the network’s sites, Andrew’s medical team would later map his genetic makeup, then bring him in for a week of exams and consultations with specialists.

Writing A New Disease Encyclopedia

The Undiagnosed Diseases Network was founded in 2015 with a $43 million grant from the National Institutes of Health (NIH). Building on work already being done at NIH, the initiative expanded to include universities across the country: Duke, Columbia and Stanford are among the other sites. The goals are to provide answers for patients with mysterious diseases and to learn more about the disorders.

A proposal last month by President Donald Trump to cut the NIH budget by $5.8 billion could put the program in jeopardy.

Even with the best technology and the finest brains at work, progress is slow. Since its launch, the network has received nearly 1,400 applications on behalf of patients. It has accepted 545 for review so far. Just 74 of the cases have been diagnosed, including 11 at UCLA. Andrew Whittaker’s case is among many in progress.

It’s like battling “an unknown enemy,” said Euan Ashley, one of the principal investigators of the network’s Stanford University site. “That is a particular form of torment that other patients don’t have.”

A diagnosis can end families’ painful odyssey while helping physicians and scientists better understand rare diseases and human physiology, said Rachel Ramoni, former executive director of the network, which is based at Harvard University.

Researchers throughout the network use advanced medical technology. For example, to study patients’ gene expression and disease progression, they can make models using nearly transparent zebrafish, whose genetic structure is similar to that of humans. And scientists can conduct whole genome sequencing, which allows the medical team to read a patient’s DNA and identify changes that can reveal what may be causing a disease.

“We have powerful techniques to look at every gene that is being expressed as well as every gene that is inherited,” said Stanley Nelson, one of UCLA’s principal investigators and the lead doctor on Andrew’s case. “This is an example of true precision medicine.”

Nelson said the network can examine all known genes — not just the ones believed to have mutations that cause diseases. Doing that can lead to the discovery of new illnesses.

“Part of what we have to do is keep building that library, that encyclopedia of what gene and what gene mutations cause what symptoms,” Nelson said. “It’s just incomplete at this moment.”

Already the work is helping patients and their families come to terms with their illnesses. In one case, at Stanford, a toddler was diagnosed with two rare diseases, including a connective tissue disorder called Marfan Syndrome, after doctors conducted a form of sequencing that looks for changes in coded genetic segments known as exons.

Sometimes answers come from something decidedly lower-tech: collaboration among clinicians and researchers who share experiences, data and expertise.

“A lot of times your ability to be diagnosed depends on who is in the room,” Ramoni said. “And what we are doing with the network is we are expanding exponentially the number of people in the room.”

Doctors at one institution might think their patient is a unique case, only to learn that colleagues elsewhere have a patient with a similar illness. But even when diseases are diagnosed or gene mutations are discovered, treatments may still not be available.

A Life-Changing Mystery

Andrew Whittaker’s odyssey began one afternoon at age 19, when he started trembling and couldn’t speak. Doctors suspected he was suffering from anxiety and prescribed medication to control it. But Andrew said he continued to have “episodes,” during which everything just went blank.

“It’s like there’s not enough blood going to your brain,” he said. “You can’t think.”

Andrew also started losing his balance and falling off his bicycle. The family visited several hospitals. Doctors discovered that the receptors in his brain were malfunctioning and that he lacked sufficient dopamine, a chemical compound in the body responsible for transmitting signals between nerve cells. As a result, Andrew has some symptoms similar to those of Parkinson’s disease. Doctors also confirmed he was having seizures.

Still, Andrew’s symptoms didn’t add up to any known disease.

One afternoon last fall at precisely noon, as Andrew sat propped up on the living room couch, Lynn’s phone alarm sounded, signaling it was time for his medication. Lynn pried open Andrew’s hand, which was clenched into a fist, and dropped in the pills.

To keep Andrew from falling, the family has lowered his bed and removed carpet from the house. They also bought him a wheelchair. Their precautions don’t always work. One morning, Lynn was in the kitchen when she heard a crash. “I ran in there and he’s laid flat on his back,” she said.

Lynn gives Andrew his medicine. (Heidi de Marco/KHN)

Lynn says not knowing what is causing her son’s disease is devastating. “We don’t know what we are dealing with,” she says. “We just know it’s worsening … and it’s like somebody ripping your insides out.” (Heidi de Marco/KHN)

Andrew is close to his mom. But he also gets frustrated. He can’t shower or dress without her help. He’s had to give up the things he loved to do: printing T-shirts. Skateboarding. Shooting short films. He’s lost friends and can’t imagine dating anymore.

“Girlfriends? Forget about it,” he said, his face twitching as he talks. “They want a guy who can do stuff for them, not the other way around.”

Running The Medical Gauntlet

On a Monday morning in late January, Andrew and his parents were in an exam room at UCLA. Lynn teased her son, saying she was going to put him in a freezer until doctors figured out what was wrong.

“Then we’ll pull you back out again,” she said, smiling.

“I’ll never get pulled out,” Andrew responded.

“Yes, you will,” she said. “You will.”

Lynn and Dave Whittaker describe the progression of Andrew’s disease to Nelson. (Heidi de Marco/KHN)

Nelson performs various tests on Andrew Whittaker during his appointment at UCLA. (Heidi de Marco/KHN)

The Whittakers undergo genetic testing during Andrew’s examination. Nelson suspects Andrew’s illness could be genetic, so he may find answers by comparing his genome with his parents’. (Heidi de Marco/KHN)
 

Nelson, Andrew’s main doctor, walked into the room. He told Andrew he’d read through the medical records. “We’re going to try to figure you out.”

The work Nelson does is personal. His teenage son, Dylan, has Duchenne muscular dystrophy, a genetic disorder that causes muscle degeneration and weakness. Nelson knows his son’s disease will eventually take his life, but he said having a diagnosis makes all the difference.

“My heart very much goes out to the families that don’t even get an adequate diagnosis,” he said.

Nelson suspects that Andrew’s disease is genetic as well.

He asked the Whittakers to describe their son’s journey, then he conducted a short physical exam, asking Andrew to push against his hand and touch his own nose. Andrew trembled and his shoulders tensed, but he did it.

The rest of the week, Andrew underwent several other diagnostic tests, including a muscle biopsy, an EEG, MRI and a lumbar puncture. He remained upbeat, though running the medical gauntlet clearly wore him out. He also met with UCLA specialists in brain degeneration and muscle and nerve disorders.

At week’s end, Nelson sat down with the family to explain what he’d found. He had reviewed Andrew’s genome and compared it with that of both parents. Andrew had one copy of a defective gene that leads to Parkinson’s but the genome sequencing didn’t show a second copy, without which it could not be Parkinson’s.

He explained that Andrew’s illness was clearly progressive and that his brain was shrinking, making it harder for him to process language and information. Nelson said he still didn’t have a diagnosis — he believed it was a brand-new disease.

Nelson planned to continue poring over the test results, conducting additional exams and communicating with others in the network. He also is analyzing Andrew’s muscle tissue, skin and blood to see whether any mutated gene is expressed abnormally.

Even in the absence of a clear diagnosis, Nelson said, rare diseases like Andrew’s help educate scientists and may help other patients. “These are the people we as a society will owe a great debt of gratitude,” he said. “They are effectively donating their lives to this process.”

Lynn Whittaker was disappointed. “We are still left with just hope that they will come up with something,” she lamented. “What else do we have?”

Andrew said his relatives have asked if he’s scared the doctors will find something. “I’m more scared if they don’t,” he replied.

KHN’s coverage in California is funded in part by Blue Shield of California Foundation.

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The “Geneva Signature” Measures the Safety and Efficiency of a Vaccine Against Ebola Virus Disease

An international team based at Geneva University Hospitals (HUG) and at the University of Geneva (UNIGE), Switzerland, has succeeded in defining a “signature” composed of a small number of inflammatory markers that can be monitored in order to understand how a promising anti-Ebola virus vaccine stimulates the immune system. The researchers inoculated 115 volunteers with either a high dose or a low dose of the rVSV-ZEBOV anti-Ebola vaccine, or with placebo. By analyzing the differences between the three groups, they found that it is sufficient to monitor only 5 substances that are naturally present in the blood in order to define immune responses to the vaccine. The “Geneva rVSV-ZEBOV signature” is published in a scientific paper, in Science Translational Medicine. It’s an easy-to-use equation adding up the concentrations of these 5 substances or markers, most of which are mediated by monocytes, a class of white blood cells known to be active in combatting Ebolavirus in infected individuals. The signature is also expected to inform investigations of safety and immunogenicity of other emerging vaccines.

The 2014–2015 Ebola epidemic affected several countries in West Africa, leading to the death of more than 11’000 people. Although this epidemic of Ebolavirus disease is over, there is no knowing if, when or where another may strike. It is therefore more important than ever to find a reliable vaccine against this deadly disease. Research on vaccines, which was ongoing during the epidemic in West Africa, is now yielding promising results.

Important progress in understanding the vaccine

In an article published on April 12, 2017, in Science Translational Medicine[1], a team from the HUG and the UNIGE, working in collaboration with researchers and clinicians in several other countries in Europe and Africa, has defined a formula that measures the reliability and efficiency of vaccines that might help prevent or limit future outbreaks.

The rVSV-ZEBOV vaccine (recombinant vesicular stomatitis virus–vectored Zaire Ebola vaccine) had already been shown to stimulate the immune system in human volunteers; and in a field trial in 2015 it successfully protected people who had been exposed to Ebola patients from contracting the disease themselves. Yet concerns had been raised during the Geneva trial regarding side effects. What the Geneva team has now published is a detailed examination of the blood plasma of 115 healthy volunteers from Geneva, some of whom received either a low-dose or a high dose of vaccine, while others received a placebo vaccine.

When a vaccine enters the bloodstream, dozens of inflammatory markers that are naturally present see their concentrations change over the next few days. The researchers investigated 15 of them (different varieties of chemokines or cytokines). They found that 1-3 days after the vaccine was administered, the concentration of 6 of these 15 markers had measurably increased. Using a statistical procedure known as principal components analysis, the Geneva team succeeded in producing a simple score that makes the activity of the vaccine much easier to monitor. This “signature” contains only 5 of the 6 markers most likely to change in the presence of the rVSV-ZEBOV vaccine: together, they account for over two-thirds (68%) of the variation in blood cytokine/chemokine activity.

The Geneva Signature found in Gabon

The signature was found to be stronger in volunteers who received the higher dose than in those who got the lower dose.

Importantly, the “Geneva signature” was applied to blood samples from a similar trial that took place in Lambaréné, Gabon, where healthy volunteers had also received the rVSV-ZEBOV vaccine. The same markers were elevated and correlated with side effects and later immunity in the same way.

The 5 markers in the signature are: monocyte attractant protein 1 (MCP-1), the interleukin-1 receptor antagonist (IL-1Ra), tumor necrosis factor (TNF-alpha), interleukin-10 and interleukin-6. Several of these are produced by monocytes or are known to interact with them, so the results imply that monocytes play a critical role in the efficacy and safety of the rVSV-ZEBOV vaccine.

In the case of many other vaccines, such as one recently developed against H1N1 influenza, the chemical markers mostly belong to another category of white blood cells: lymphocytes. Taken together, these signatures help understand how vaccines stimulate the immune system in very different ways to tackle various types of virus. This latest discovery therefore opens up encouraging perspectives for investigating the safety, efficacy and mechanisms of other emerging vaccines.

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Nova Southeastern University Researchers Studying How to Disrupt Bacteria to Treat Infections

Bacteria are everywhere. And despite widespread belief, not all bacteria are “bad.” However, to combat those that can cause health issues for humans, there has been an over-reliance on the use of antibiotics – so much so, that many of them are now proving ineffective due to bacteria developing increased resistance to them.

“More and more antibiotics are essentially becoming useless,” says Robert Smith, Ph.D., assistant professor in the Department of Biological Sciences at NSU’s Halmos College of Natural Sciences and Oceanography. “Even the most routine infections, such as ear infections that are often seen in children, are becoming more challenging and expensive to treat.”

This notion isn’t new – just prior to winning his Nobel Prize in 1945, Alexander Fleming, the scientist who discovered antibiotics, warned that overusing them would lead to bacteria that were no longer killed by these drugs.  Since then, scientists and bacteria have been locked in a deadly arms race. While scientists rush to discover new antibiotics, bacteria fight back by developing new tools to resist antibiotics. In recent years, the bacteria have been winning.

So this paradigm led researchers at NSU to take another look at how bacteria do what they do to see if there was another way to approach this issue. Researchers are now focusing on developing new ways to treat infections that reduce the use of antibiotics. And what the NSU researchers found, working with colleagues from Duke University and the University of Minnesota, was interesting.

Their findings are detailed in the March 27th edition of Scientific Reports (http://www.nature.com/articles/s41598-017-00588-9).

One way that bacteria infect people is by working together. First, they build a home called a biofilm, and then use chemicals to “talk with each other.” This allows the bacteria to coordinate an attack on the infected person. Led by NSU graduate Cortney Wilson, Smith’s lab recently discovered that by shaking the house that the bacteria have built, the ability of the bacteria to talk to one another is affected. Wilson earned her Master’s from NSU and is now at the University of Colorado, Boulder.

“We found that shaking the bacteria forced them to face a decision; do they want to grow, or do they want to cooperate,” Smith said. “And if we shook them at just the right frequency, we created enough confusion that the bacteria could do neither effectively.”

Smith notes that this strategy to prevent bacteria from talking to one another has promise in reducing the need for antibiotics. The team of scientists hope to begin testing their theory in more species of bacteria, and eventually in mice.

“It is a very exciting time for our research team. We are looking forward to building upon our very promising results and to moving our strategy into the clinic.”

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‘Neuron-Reading’ Nanowires Could Accelerate Development of Drugs to Treat Neurological Diseases

A team led by engineers at the University of California San Diego has developed nanowires that can record the electrical activity of neurons in fine detail. The new nanowire technology could one day serve as a platform to screen drugs for neurological diseases and could enable researchers to better understand how single cells communicate in large neuronal networks.

“We’re developing tools that will allow us to dig deeper into the science of how the brain works,” said Shadi Dayeh, an electrical engineering professor at the UC San Diego Jacobs School of Engineering and the team’s lead investigator.

“We envision that this nanowire technology could be used on stem-cell-derived brain models to identify the most effective drugs for neurological diseases,” said Anne Bang, director of cell biology at the Conrad Prebys Center for Chemical Genomics at the Sanford Burnham Medical Research Institute.

The project was a collaborative effort between the Dayeh and Bang labs, neurobiologists at UC San Diego, and researchers at Nanyang Technological University in Singapore and Sandia National Laboratories. The researchers published their work Apr. 10 in Nano Letters.

Researchers can uncover details about a neuron’s health, activity and response to drugs by measuring ion channel currents and changes in its intracellular potential, which is due to the difference in ion concentration between the inside and outside of the cell. The state-of-the-art measurement technique is sensitive to small potential changes and provides readings with high signal-to-noise ratios. However, this method is destructive — it can break the cell membrane and eventually kill the cell. It is also limited to analyzing only one cell at a time, making it impractical for studying large networks of neurons, which are how they are naturally arranged in the body.

“Existing high sensitivity measurement techniques are not scalable to 2D and 3D tissue-like structures cultured in vitro,” Dayeh said. “The development of a nanoscale technology that can measure rapid and minute potential changes in neuronal cellular networks could accelerate drug development for diseases of the central and peripheral nervous systems.”

The nanowire technology developed in Dayeh’s laboratory is nondestructive and can simultaneously measure potential changes in multiple neurons — with the high sensitivity and resolution achieved by the current state of the art.

The device consists of an array of silicon nanowires densely packed on a small chip patterned with nickel electrode leads that are coated with silica. The nanowires poke inside cells without damaging them and are sensitive enough to measure small potential changes that are a fraction of or a few millivolts in magnitude. Researchers used the nanowires to record the electrical activity of neurons that were isolated from mice and derived from human induced pluripotent stem cells. These neurons survived and continued functioning for at least six weeks while interfaced with the nanowire array in vitro.

Silicidation is usually used to make contacts to transistors, but this is the first time it is being used to do patterned wafer bonding, Dayeh said. “And since this process is used in semiconductor device fabrication, we can integrate versions of these nanowires with CMOS electronics.” Dayeh’s laboratory holds several pending patent applications for this technology.
To overcome this hurdle, researchers invented a new wafer bonding approach to fuse the silicon nanowires to the nickel electrodes. Their approach involved a process called silicidation, which is a reaction that binds two solids (silicon and another metal) together without melting either material. This process prevents the nickel electrodes from liquidizing, spreading out and shorting adjacent electrode leads.

Dayeh noted that the technology needs further optimization for brain-on-chip drug screening. His team is working to extend the application of the technology to heart-on-chip drug screening for cardiac diseases and in vivo brain mapping, which is still several years away due to significant technological and biological challenges that the researchers need to overcome. “Our ultimate goal is to translate this technology to a device that can be implanted in the brain.”

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Researchers Develop Mouse That Could Provide Advance Warning of Next Flu Pandemic

Researchers in Germany have developed a transgenic mouse that could help scientists identify new influenza virus strains with the potential to cause a global pandemic. The mouse is described in a study, “In vivo evasion of MxA by avian influenza viruses requires human signature in the viral nucleoprotein,” that will be published April 10 in The Journal of Experimental Medicine.

Influenza A viruses can cause devastating pandemics when they are transmitted to humans from pigs, birds, or other animal species. To cross the species barrier and establish themselves in the human population, influenza strains must acquire mutations that allow them to evade components of the human immune system, including, perhaps, the innate immune protein MxA. This protein can protect cultured human cells from avian influenza viruses but is ineffective against strains that have acquired the ability to infect humans.

To investigate whether MxA provides a similar barrier to cross-species infection in vivo, Peter Staeheli and colleagues at the Institute of Virology, Medical Center University of Freiburg, created transgenic mice that express human, rather than mouse, MxA. Similar to the results obtained with cultured human cells, the transgenic mice were resistant to avian influenza viruses but susceptible to flu viruses of human origin.

MxA is thought to target influenza A by binding to the nucleoprotein that encapsulates the virus’ genome, and mutations in this nucleoprotein have been linked to the virus’ ability to infect human cells. Staeheli and colleagues found that an avian influenza virus engineered to contain these mutations was able to infect and cause disease in the transgenic mice expressing human MxA.

MxA is therefore a barrier against cross-species influenza A infection, but one that the virus can evade through a few mutations in its nucleoprotein. Staeheli and colleagues think that their transgenic mice could help monitor the potential dangers of emerging viral strains. “Our MxA-transgenic mouse can readily distinguish between MxA-sensitive influenza virus strains and virus strains that can evade MxA restriction and, consequently, possess a high pandemic potential in humans,” Staeheli says. “Such analyses could complement current risk assessment strategies of emerging influenza viruses, including viral genome sequencing and screening for alterations in known viral virulence genes.”