Forty-Six Gene Sequencing Test for Cancer Patients in UK

The first multi-gene DNA sequencing test that can help predict cancer patients' responses to treatment has been launched in the National Health Service (NHS), thanks to a partnership between scientists at the University of Oxford and Oxford University Hospitals NHS Trust.

The test uses the latest DNA sequencing techniques to detect mutations across 46 genes that may be driving cancer growth in patients with solid tumours. The presence of a mutation in a gene can potentially determine which treatment a patient should receive.

The researchers say the number of genes tested marks a step change in introducing next-generation DNA sequencing technology into the NHS, and heralds the arrival of genomic medicine with whole genome sequencing of patients just around the corner.

The many-gene sequencing test has been launched through the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC), a collaboration between Oxford University Hospitals NHS Trust and Oxford University to accelerate healthcare innovation, and which has part-funded this initiative.

The BRC Molecular Diagnostics Centre carries out the test. The lab, based at Oxford University Hospitals, covers all cancer patients in the Thames Valley area. But the scientists are looking to scale this up into a truly national NHS service through the course of this year.

The new £300 test could save significantly more in drug costs by getting patients on to the right treatments straightaway, reducing harm from side effects as well as the time lost before arriving at an effective treatment.

'We are the first to introduce a multi-gene diagnostic test for tumour profiling on the NHS using the latest DNA sequencing technology,' says Dr Jenny Taylor of the Wellcome Trust Centre for Human Genetics at Oxford University, who is programme director for Genomic Medicine at the NIHR Oxford BRC and was involved in the work. 'It's a significant step change in the way we do things. This new 46 gene test moves us away from conventional methods for sequencing of single genes, and marks a huge step towards more comprehensive genome sequencing in both infrastructure and in handling the data produced.'

Dr Anna Schuh, who heads the BRC Molecular Diagnostics Centre and is a consultant haematologist at Oxford University Hospitals, adds: 'Patients like the idea of a test that can predict and say up front whether they will respond to an otherwise toxic treatment. What the patient sees is no different from present. A biopsy is taken from the patient's tumour for genetic testing with a consultant talking through the results a few days later. It is part of the normal diagnostic process.'

Cancer is often described as a genetic disease, since the transition a cell goes through in becoming cancerous tends to be driven by changes to the cell's DNA. And increasingly, new cancer drugs depend on knowing whether a mutation in a single gene is present in a patient's cancer cells.

For example, a lung cancer patient may have a biopsy taken to check for changes in the EGFR gene. If there is a mutation, the patient may then be treated with a drug that works as an EGFR inhibitor. If there is no mutation, such drugs won't work and the patient would get a different drug that would be more effective for them. Knowing the presence or absence of mutations in a certain gene can choose the treatment path for that patient.

The NHS can currently test for mutations in 2 or 3 genes -- genes called BRAF, EGFR or KRAS -- using older sequencing technology that has been around for decades. Efforts are being made to look at increasing the number of cancer genes sequenced to nine as standard.

The Oxford scientists are the first to make such multi-gene tests possible in the NHS using the latest DNA sequencing techniques. The NHS service they have launched looks for mutations in 46 genes, and they are now working towards verifying the use of a test involving 150 genes.

Having a diagnostic test or 'panel' that can screen for mutations in multiple genes at once will be important for access to all the new cancer drugs that are coming along.

'It will be very difficult to manage in NHS diagnostic labs without gene panels,' explains Dr Schuh. 'Currently, new cancer drugs tend to get approved alongside a diagnostic test specific to that drug which can determine which patients will benefit. But as more and more drugs like this come along, we can't possibly run all the many different separate tests this could mean. We need one test for a range of drugs.'

Dr Taylor adds: 'We wanted a test that would use the latest DNA sequencing techniques to detect a wide range of mutations in a wide range of genes. A test that would be able to cover more cancers and more treatments, all for a similar cost to conventional methods.'

The test is run on a next generation sequencing platform from Life Technologies Corporation, called the Ion Personal Genome Machine (PGM(TM)). The test and accompanying software have been substantially modified as requested by the Oxford team to fulfil diagnostic standards in their lab.

This work was co-funded by the Technology Strategy Board, the UK's innovation agency, through a grant to the NIHR Oxford BRC, Life Technologies Corporation, AstraZeneca, and Janssen Research & Development, LLC, one of the Janssen Pharmaceutical Companies.

As part of the test development, the Oxford team looked to improve the initial sample preparation in the lab, and to provide the software and infrastructure support to handle and analyse the amount of information involved. Most importantly, the Oxford group has carried out tests and comparisons to verify the robustness of the technique with cancer biopsies direct from patients.

The team compared the new 46 gene test against conventional techniques for 80 consecutive cancer biopsies in the hospital lab's workflow.

The next-generation DNA sequencing method detected all the mutations the conventional method did; it detected new mutations the conventional method didn't; and detected mutations present at much lower levels in the samples. The time taken for the 46 gene test also fitted into the standard turnaround time for samples at the lab.

There is definite benefit in screening some of the 46 genes included in the test; there is probable or likely clinical benefit in screening some of the others; mutations in further genes might be important in some cancers but not others; and the other genes, we don't know as yet. But having this information means researchers can investigate whether a mutation has biological significance.

'We can keep data, bank it and link it with anonymised clinical data on patients' cancers for future research,' explains Dr Schuh.

The test looks for mutations in 'hotspot' regions of each gene -- areas where mutations are more likely to occur. This does mean the test may miss up to 5% of mutations, as they can occur elsewhere, but this is still significantly better than the 'false negative' rate using current methods.

It can also detect mutations present in only 5% of the tumour cells present in a sample. This is much lower than is possible currently, and is important in being able to capture information from cells present in only small numbers in a tumour, but which are still important in driving cancer growth.

Having shown that it is possible to introduce the 46 gene test as an NHS service, the researchers are now moving on to investigate the potential of a test that will sequence 150 genes. The team will use the test first of all with 500 existing samples from patients taking part in cancer clinical trials to be able to compare the results retrospectively with information from the trials. They will then use the test with 1000 new cancer biopsies to better understand how the extra information could be used in guiding treatments for patients and their outcomes.

Dr Schuh says: '"Panel" tests have significant potential while we wait for the cost of sequencing whole patient genomes to come down. Even then, panel tests may be with us for some time. After whole genome sequencing does come into use, it may be that panel tests are used first with patients' biopsies, with only those whose panel test shows no result having their entire DNA sequenced to look for rarer genetic changes.'

Lord Howe, Health Minister, said: 'We want to be among the best countries in the world at treating cancer and know that better tailored care for patients could potentially save lives.

'Health research like this is incredibly important and I'm delighted we could support the work of researchers in Oxford through the National Institute for Health Research Biomedical Research Centre.

'By rapidly translating findings from genetics research into real benefits for patients, their work will make sure that patients get the right treatments straight away, reduce potential side effects and also help us use NHS funds more effectively.'

The 46-gene panel is based on Ion AmpliSeq(TM) chemistry from Life Technologies Corporation. The test requires a very small amount of DNA (5 nanograms), an advantage when working with clinical samples that are typically limited in quantity.

The Ion Personal Genome Machine (PGM(TM) and Ion AmpliSeq(TM) are for Research Use Only, not intended for use in diagnostic procedures. Life Technologies intends to pursue CE-IVD designation for the PGM.

Story Source:

The above story is reprinted from materials provided by University of Oxford.

Courtesy: ScienceDaily 

Scientists Confirm First Two-Headed Bull Shark

Scientists have confirmed the discovery of the first-ever, two-headed bull shark.The study, led by Michigan State University and appearing in the Journal of Fish Biology, confirmed the specimen, found in the Gulf of Mexico April 7, 2011, was a single shark with two heads, rather than conjoined twins.

There have been other species of sharks, such as blue sharks and tope sharks, born with two heads. This is the first record of dicephalia in a bull shark, said Michael Wagner, MSU assistant professor of fisheries and wildlife, who confirmed the discovery with colleagues at the Florida Keys Community College.

"This is certainly one of those interesting and rarely detected phenomena," Wagner said. "It's good that we have this documented as part of the world's natural history, but we'd certainly have to find many more before we could draw any conclusions about what caused this."

The difficulty of finding such oddities is due, in part, to creatures with abnormalities dying shortly after birth. In this instance, a fisherman found the two-headed shark when he opened the uterus of an adult shark. The two-headed shark died shortly thereafter and had little, if any, chance to survive in the wild, Wagner added.

"You'll see many more cases of two-headed lizards and snakes," he said. "That's because those organisms are often bred in captivity, and the breeders are more likely to observe the anomalies."

The shark was brought to the marine science department at Florida Keys Community College. From there, it was transported to Michigan State's campus for further examination.

Wagner and his team were able to detail the discovery with magnetic resonance imaging. Without damaging the unique specimen, the MRIs revealed two distinct heads, hearts and stomachs with the remainder of the body joining together in back half of the animal to form a single tail.

As part of the published brief, Wagner noted that some may want to attribute the deformed shark to exposure to pollutants.

"Given the timing of the shark's discovery with the Deepwater Horizon oil spill, I could see how some people may want to jump to conclusions," Wagner said. "Making that leap is unwarranted. We simply have no evidence to support that cause or any other."

Journal Reference:

1. C. M. Wagner, P. H. Rice, A. P. Pease. First record of dicephalia in a bull sharkCarcharhinus leucas(Chondrichthyes: Carcharhinidae) foetus from the Gulf of Mexico, U.S.A.. Journal of Fish Biology, 2013; DOI: 10.1111/jfb.12064

Courtesy: ScienceDaily

Old Mice, Young Blood: Rejuvenating Blood of Mice by Reprogramming Stem Cells That Produce Blood

The blood of young and old people differs. In an article published recently in the scientific journal Blood, a research group at Lund University in Sweden explain how they have succeeded in rejuvenating the blood of mice by reversing, or re-programming, the stem cells that produce blood.

Stem cells form the origin of all the cells in the body and can divide an unlimited number of times. When stem cells divide, one cell remains a stem cell and the other matures into the type of cell needed by the body, for example a blood cell.*

"Our ageing process is a consequence of changes in our stem cells over time," explained Martin Wahlestedt, a doctoral student in stem cell biology at the Faculty of Medicine at Lund University, and principal author of the article.

"Some of the changes are irreversible, for example damage to the stem cells' DNA, and some could be gradual changes, known as epigenetic changes, that are not necessarily irreversible, even if they are maintained through multiple cell divisions. When the stem cells are re-programmed, as we have done, the epigenetic changes are cancelled."**

The discovery that forms the basis for the research group's method was awarded the Nobel Prize in Medicine last year.

The composition of blood is one example of how it ages; blood from a young person contains a certain mix of B- and T-lymphocytes and myeloid cells.***

"In older people, the number of B- and T-lymphocytes falls, while the number of myeloid cells increases," said Martin Wahlestedt.

When an elderly person is affected by leukemia, the cancer often has its origin in the myeloid cells, of which the elderly have more. Being able to 're-start' the blood, as Martin and his colleagues have done in their studies on mice, therefore presents interesting possibilities for future treatment.

"There is a lot of focus on how stem cells could be used in different treatments, but all that they are routinely used for in clinical work today is bone marrow transplants for diseases where the blood and immune systems have to be regenerated," said Martin Wahlestedt, continuing:

"A critical factor that gives an indication of whether the procedure is going to work or not is the age of the bone marrow donor. By reversing the development of the stem cells in the bone marrow, it may be possible to avoid negative age-related changes."

Even if the composition of the blood in old and young mice is remarkably like that in young and elderly people, Martin Wahlestedt stressed that the science is still only at the stage of basic research, far from a functioning treatment. The research group is pleased with the results, because they indicate that it may not primarily be damage to DNA that causes blood to age, but rather the reversible epigenetic changes.

*About stem cells:

There are different types of stem cells. Embryonic stem cells, which can be extracted from an embryo at an early stage, have the capacity to develop into all types of cell. Stem cells are also found in adults, where they have more limited development potential, but can divide in principle an unlimited number of times. For example, blood cell-forming stem cells in bone marrow create all types of blood cell and stem cells in the brain create many different types of brain cell.

**About epigenetics:

Epigenetics is a term that has historically been used to describe the aspects of genetics that cannot be explained by the composition of an individual's DNA alone. For tissue and organs to form, a number of different types of cell must be developed. This happens through the activation and de-activation of different genes. When a cell formed in this manner then divides again, the gene expression can be maintained in the daughter cells. This is referred to as 'epigenetic inheritance'. The epigenetic mechanisms, or which genes are activated or de-activated, can be affected by factors such as age, chemicals, drugs and diet.

*** About the composition of blood:

B- and T-lymphocytes and myeloid cells are all white blood cells. Lymphocytes, as the name suggests, are particularly common in the lymphatic system. T-lymphocytes patrol the body and recognise a specific bacteria or virus. B-lymphocytes 'remember' old infections and can quickly be activated again if required. This memory capacity is the mechanism behind immunity. The myeloid cells belong to the blood system's 'big eaters' -- they neutralise damaged tissue, dead cells, and to a certain extent also bacteria.

Journal Reference:

1. M. Wahlestedt, G. L. Norddahl, G. Sten, A. Ugale, M.-A. Micha Frisk, R. Mattsson, T. Deierborg, M. Sigvardsson, D. Bryder. An epigenetic component of hematopoietic stem cell aging amenable to reprogramming into a young state. Blood, 2013; DOI: 10.1182/blood-2012-11-469080

Courtesy: ScienceDaily

Physical Activity Does Not Protect Against in Situ Breast Cancer, Epidemiological Study Finds

Non-invasive or in situ breast cancer is characterised by the fact that it does not invade or does not multiply in other cells and unlike invasive breast cancer, it is not benefited by physical exercise. The experts suggest that exercise would only have protective effects once the tumour starts to invade the breast tissue.

A European study published in the 'Cancer Epidemiology, Biomarkers & Prevention' journal has analysed the association between physical activities and in situ or non-invasive breast cancer, or, in other words, cancer that has not yet invaded cells within or outside of the breast.

Headed by researchers from ten European countries including Spain, the work carried out under the framework of the European Prospective Investigation into Cancer and Nutrition (EPIC) concludes that physical activity has no relation with the risk of developing this type of non-invasive cancer.

After more than eleven years following a European cohort of 283,927 women, 1,059 of whom had in situ cancer, the authors also found no association depending on exercise type.

In addition, the results did not vary between women of pre- and post-menopausal age or between obese and non-obese women. The same does not occur in the case of invasive cancer, where epidemiological studies have demonstrated that this factor is associated with a lesser risk.

"The aetiology (cause) of in situ breast cancer could be different to that of invasive breast cancer, or rather physical activity has a protective effect only in later stages of the carcinogenesis process. This would explain why no association has been found in non-invasive breast cancer," upholds María José Sánchez Pérez, Director of the Granada Cancer Registry and one of the authors of the study.

An in situ ductal carcinoma of the breast is the most frequent form of non-invasive breast cancer in women and is a risk factor or precursor for the development of invasive breast cancer. Therefore, the association between physical activity and this cancer would indicate that exercise could act as a protective factor in the early stages of the carcinogenesis process. However, it has been found that this is not the case.

Different results for invasive cancer

A previous study carried out on the same cohort investigated the association between physical activity and the risk of developing invasive breast cancer. It was discovered that physically active menopausal women have a 14% less chance of developing this cancer compared to their sedimentary menopausal counterparts.

The results revealed that moderate to intense physical activity in general decreases the risk of developing breast cancer by 8% and 14% respectively. This effect was similar for recreational physical activity and domestic chores.

In fact, in the expert report published by the World Cancer Research Fund (WCRF) in 2007, as well as in its updated version in 2010, it was confirmed that there is enough evidence on the protective effects of physical activity but this evidence is somewhat more convincing in the case of menopausal women.

One of the most frequent of tumours

Breast cancer continues to be the most frequent of cancers amongst women living in developed countries. Despite experiencing a decrease over the last decade, its incidence still remains high due to the lifestyle of the population: reproduction patterns, diet, sedentary lifestyle, etc.

At present primary prevention constitutes the main approach in the attempt to reduce the incidence of this cancer. "Thanks to sufficient evidence, the risk factors associated with breast cancer are obesity in menopausal women and alcohol consumption, whereas physical activity and breastfeeding provide protection against the development of this cancer," concludes Sánchez.

Journal References:

1. K. Steindorf, R. Ritte, A. Tjonneland, N. F. Johnsen, K. Overvad, J. N. Ostergaard, F. Clavel-Chapelon, A. Fournier, L. Dossus, A. Lukanova, J. Chang-Claude, H. Boeing, A. Wientzek, A. Trichopoulou, T. Karapetyan, D. Trichopoulos, G. Masala, V. Krogh, A. Mattiello, R. Tumino, S. Polidoro, J. R. Quiros, N. Travier, M.-J. Sanchez, C. Navarro, E. Ardanaz, P. Amiano, H. B. Bueno-de-Mesquita, F. J. B. van Duijnhoven, E. Monninkhof, A. M. May, K.-T. Khaw, N. Wareham, T. J. Key, R. C. Travis, K. B. Borch, V. Fedirko, S. Rinaldi, I. Romieu, P. A. Wark, T. Norat, E. Riboli, R. Kaaks. Prospective Study on Physical Activity and Risk of In Situ Breast Cancer. Cancer Epidemiology Biomarkers & Prevention, 2012; 21 (12): 2209 DOI: 10.1158/1055-9965.EPI-12-0961
2. Karen Steindorf, Rebecca Ritte, Piia-Piret Eomois, Annekatrin Lukanova, Anne Tjonneland, Nina Føns Johnsen, Kim Overvad, Jane Nautrup Østergaard, Françoise Clavel-Chapelon, Agnès Fournier, Laure Dossus, Birgit Teucher, Sabine Rohrmann, Heiner Boeing, Angelika Wientzek, Antonia Trichopoulou, Tina Karapetyan, Dimitrios Trichopoulos, Giovanna Masala, Franco Berrino, Amalia Mattiello, Rosario Tumino, Fulvio Ricceri, J.Ramón Quirós, Noémie Travier, María-José Sánchez, Carmen Navarro, Eva Ardanaz, Pilar Amiano, H.Bas. Bueno-de-Mesquita, Franzel van Duijnhoven, Evelyn Monninkhof, Anne M. May, Kay-Tee Khaw, Nick Wareham, Tim J. Key, Ruth C. Travis, Kristin Benjaminsen Borch, Malin Sund, Anne Andersson, Veronika Fedirko, Sabina Rinaldi, Isabelle Romieu, Jürgen Wahrendorf, Elio Riboli, Rudolf Kaaks. Physical activity and risk of breast cancer overall and by hormone receptor status: The European prospective investigation into cancer and nutrition. International Journal of Cancer, 2013; 132 (7): 1667 DOI: 10.1002/ijc.27778

Courtesy: ScienceDaily

Contaminated Diet Contributes to Exposure to Endocrine-Disrupting Chemicals: Phthalates and BPA

While water bottles may tout BPA-free labels and personal care products declare phthalates not among their ingredients, these assurances may not be enough.

According to a study published February 27 in the Nature Journal of Exposure Science and Environmental Epidemiology, we may be exposed to these chemicals in our diet, even if our diet is organic and we prepare, cook, and store foods in non-plastic containers. Children may be most vulnerable.

"Current information we give families may not be enough to reduce exposures," said Dr. Sheela Sathyanarayana, lead author on the study and an environmental health pediatrician in the UW School of Public Health and at Seattle Children's Research Institute. She is a physician at Harborview Medical Center's Pediatric Environmental Health Specialty Unit, and a UW assistant professor of pediatrics.

Phthalates and bisphenol A, better known as BPA, are synthetic endocrine-disrupting chemicals. Previous studies have linked prenatal exposure to phthalates to abnormalities in the male reproductive system. Associations have also been shown between fetal exposure to BPA and hyperactivity, anxiety, and depression in girls.

The researchers compared the chemical exposures of 10 families, half of whom were given written instructions on how to reduce phthalate and BPA exposures. They received handouts prepared by the national Pediatric Environmental Health Specialty Units, a network of experts on environmentally related health effects in children. The other families received a five-day catered diet of local, fresh, organic food that was not prepared, cooked or stored in plastic containers.

When the researchers tested the participants' urinary concentrations of metabolites for phthalates and BPA, they got surprising results. The researchers expected the levels of the metabolities to decrease in those adults and children eating the catered diet.

Instead, the opposite happened. The urinary concentration for phthalates were 100-fold higher than the those levels found in the majority of the general population. The comparison comes from a study conducted by the National Health and Nutrition Examination Survey. This is a program of studies managed by the Centers for Disease Control and Prevention and designed to assess the health and nutritional status of adults and children in the United States.

The concentrations were also much higher for children as compared to the adults. The researchers then tested the phthalate concentrations in the food ingredients used in the dietary intervention. Dairy products -- butter, cream, milk, and cheese -- had concentrations above 440 nanograms/gram. Ground cinnamon and cayenne pepper had concentrations above 700 ng/g, and ground coriander had concentrations of 21,400 ng/g.

"We were extremely surprised to see these results. We expected the concentrations to decrease significantly for the kids and parents in the catered diet group. Chemical contamination of foods can lead to concentrations higher than deemed safe by the US EPA," said Dr. Sheela Sathyanarayana.

Using the study results, the researchers estimated that the average child aged three to six years old was exposed to 183 milligrams per kilogram of their body weight per day. The U.S. Environmental Protection Agency's recommended limit is 20 mg/kg/day.

"It's difficult to control your exposure to these chemicals, even when you try," said Sathyanarayana. "We have very little control over what's in our food, including contaminants. Families can focus on buying fresh fruits and vegetables, foods that are not canned and are low in fat, but it may take new federal regulations to reduce exposures to these chemicals."

The other researchers in the study included Garry Alcedo (Seattle Children's Research Institute), Brian E. Saelens and Chuan Zhou (UW Department of Pediatrics, Seattle Children's Research Institute), Russell L. Dills and Jianbo Yu (UW Department of Environmental and Occupational Health Sciences) and Bruce Lanphear (BC Children's Hospital and Simon Fraser University).

Their paper is titled, "Unexpected results in a randomized dietary trial to reduce phthalate and bisphenol A exposure."

The study was supported through by the Center for Ecogenetics and Environmental Health in the Department of Environmental and Occupational Health Sciences in the UW School of Public Health. A grant from the National Institute of Environmental Health provides major support for the center.

Journal Reference:

1. Sheela Sathyanarayana, Garry Alcedo, Brian E Saelens, Chuan Zhou, Russell L Dills, Jianbo Yu, Bruce Lanphear. Unexpected results in a randomized dietary trial to reduce phthalate and bisphenol A exposures. Journal of Exposure Science and Environmental Epidemiology, 2013; DOI: 10.1038/jes.2013.9

Courtesy: ScienceDaily

Viruses Can Have Immune Systems: A Pirate Phage Commandeers the Immune System of Bacteria

A study published today in the journal Nature reports that a viral predator of the cholera bacteria has stolen the functional immune system of bacteria and is using it against its bacterial host. The study provides the first evidence that this type of virus, the bacteriophage ("phage" for short), can acquire a wholly functional and adaptive immune system.

The phage used the stolen immune system to disable -- and thus overcome -- the cholera bacteria's defense system against phages. Therefore, the phage can kill the cholera bacteria and multiply to produce more phage offspring, which can then kill more cholera bacteria. The study has dramatic implications for phage therapy, which is the use of phages to treat bacterial diseases. Developing phage therapy is particularly important because some bacteria, called superbugs, are resistant to most or all current antibiotics.

Until now, scientists thought phages existed only as primitive particles of DNA or RNA and therefore lacked the sophistication of an adaptive immune system, which is a system that can respond rapidly to a nearly infinite variety of new challenges. Phages are viruses that prey exclusively on bacteria and each phage is parasitically mated to a specific type of bacteria. This study focused on a phage that attacks Vibrio cholerae, the bacterium responsible for cholera epidemics in humans.

Howard Hughes Medical Institute investigator Andrew Camilli, Ph.D., of Tufts University School of Medicine led the research team responsible for the surprising discovery.

First author Kimberley D. Seed, Ph.D., a postdoctoral fellow in Camilli's lab, was analyzing DNA sequences of phages taken from stool samples from patients with cholera in Bangladesh when she identified genes for a functional immune system previously found only in some bacteria (and most Archaea, a separate domain of single-celled microorganisms).

To verify the findings, the researchers used phage lacking the adaptive immune system to infect a new strain of cholera bacteria that is naturally resistant to the phage. The phage were unable to adapt to and kill the cholera strain. They next infected the same strain of cholera bacteria with phage harboring the immune system, and observed that the phage rapidly adapted and thus gained the ability to kill the cholera bacteria. This work demonstrates that the immune system harbored by the phage is fully functional and adaptive.

"Virtually all bacteria can be infected by phages. About half of the world's known bacteria have this adaptive immune system, called CRISPR/Cas, which is used primarily to provide immunity against phages. Although this immune system was commandeered by the phage, its origin remains unknown because the cholera bacterium itself currently lacks this system. What is really remarkable is that the immune system is being used by the phage to adapt to and overcome the defense systems of the cholera bacteria. Finding a CRISPR/Cas system in a phage shows that there is gene flow between the phage and bacteria even for something as large and complex as the genes for an adaptive immune system," said Seed.

"The study lends credence to the controversial idea that viruses are living creatures, and bolsters the possibility of using phage therapy to treat bacterial infections, especially those that are resistant to antibiotic treatment," said Camilli, professor of Molecular Biology & Microbiology at Tufts University School of Medicine and member of the Molecular Microbiology program faculty at the Sackler School of Graduate Biomedical Sciences at Tufts University.

Camilli's previous research established that phages are highly prevalent in stool samples from patients with cholera, implying that phage therapy is happening naturally and could be made more effective. In addition, a study published by Camilli in 2008 determined that phage therapy works in a mouse model of cholera intestinal infection.

The team is currently working on a study to understand precisely how the phage immune system disables the defense systems of the cholera bacteria. This new knowledge will be important for understanding whether the phage's immune system could overcome newly acquired or evolved phage defense systems of the cholera bacteria, and thus has implications for designing an effective and stable phage therapy to combat cholera.

Additional authors are David W. Lazinski, Ph.D., senior research associate in the Camilli lab at Tufts University School of Medicine, and Stephen B. Calderwood, M.D., Morton N. Swartz, M.D. academy professor of medicine at Harvard Medical School, and chief, division of infectious disease and vice-chair, department of medicine at Massachusetts General Hospital.

Research reported in this publication was supported by the National Institute of Allergies and Infectious Diseases of the National Institutes of Health under award numbers R01AI55058, R01AI045746, and R01AI058935.

Journal Reference:

1. Kimberley D. Seed, David W. Lazinski, Stephen B. Calderwood, Andrew Camilli. A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity. Nature, 2013; 494 (7438): 489 DOI: 10.1038/nature11927

Courtesy: ScienceDaily

Reprogramming Cells to Fight Diabetes

For years researchers have been searching for a way to treat diabetics by reactivating their insulin-producing beta cells, with limited success. The "reprogramming" of related alpha cells into beta cells may one day offer a novel and complementary approach for treating type 2 diabetes. Treating human and mouse cells with compounds that modify cell nuclear material called chromatin induced the expression of beta cell genes in alpha cells, according to a new study that appears online in the Journal of Clinical Investigation.

"This would be a win-win situation for diabetics -- they would have more insulin-producing beta cells and there would be fewer glucagon-producing alpha cells," says lead author Klaus H. Kaestner, Ph.D., professor of Genetics and member of the Institute of Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania. Type 2 diabetics not only lack insulin, but they also produce too much glucagon.

Both type 1 and type 2 diabetes are caused by insufficient numbers of insulin-producing beta cells. In theory, transplantation of healthy beta cells -- for type 1 diabetics in combination with immunosuppression to control autoimmunity -- should halt the disease, yet researchers have not yet been able to generate these cells in the lab at high efficiency, whether from embryonic stem cells or by reprogramming mature cell types.

Alpha cells are another type of endocrine cell in the pancreas. They are responsible for synthesizing and secreting the peptide hormone glucagon, which elevates glucose levels in the blood.

"We treated human islet cells with a chemical that inhibits a protein that puts methyl chemical groups on histones, which -- among many other effects -- leads to removal of some histone modifications that affect gene expression," says Kaestner. "We then found a high frequency of alpha cells that expressed beta-cell markers, and even produced some insulin, after drug treatment.

Histones are protein complexes around which DNA strands are wrapped in a cell's nucleus.

The team discovered that many genes in alpha cells are marked by both activating- and repressing-histone modifications. This included many genes important in beta-cell function. In one state, when a certain gene is turned off, the gene can be readily activated by removing a modification that represses the histone.

"To some extent human alpha cells appear to be in a 'plastic' epigenetic state," explains Kaestner. "We reasoned we might use that to reprogram alpha cells towards the beta-cell phenotype to produce these much-needed insulin-producing cells."

Co-authors are Nuria C. Bramswig, Logan Everett, Jonathan Schug, Chengyang Liu, Yanping Luo, and Ali Naji, all from Penn, and Markus Grompe, Craig Dorrell, and Philip R. Streeter from the Oregon Health & Science University. The Oregon group developed a panel of human endocrine cell type-specific antibodies for cell sorting.

The research was supported by the National Institute of Diabetes and Digestive and Kidney Diseases (U01 DK070430, U42 RR006042, U01DK089529, R01DK088383, U01DK089569) and by the Beckman Research Center/NIDDK/Integrated Islet Distribution Program (10028044).

Journal Reference:

1. Nuria C. Bramswig, Logan J. Everett, Jonathan Schug, Craig Dorrell, Chengyang Liu, Yanping Luo, Philip R. Streeter, Ali Naji, Markus Grompe, Klaus H. Kaestner. Epigenomic plasticity enables human pancreatic α to β cell reprogramming. Journal of Clinical Investigation, 2013; DOI: 10.1172/JCI66514

Courtesy: ScienceDaily