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Pumpkin Genomes Sequenced, Revealing Uncommon Evolutionary History

For some, pumpkins conjure carved Halloween decorations, but for many people around the world, these gourds provide nutrition. Scientists at Boyce Thompson Institute (BTI) in New York and the National Engineering Research Center for Vegetables in Beijing have sequenced the genomes of two important pumpkin species, Cucurbita maxima and Cucurbita moschata. The finished genomes appear in the October 9, 2017 issue of Molecular Plant, which highlights the work on its cover. The open-access article is titled “Karyotype Stability and Unbiased Fractionation in the Paleo-Allotetraploid Cucurbita Genomes.” "Pumpkins are used as a staple food in many developing countries and are cultivated all over the world for their culinary and ornamental uses," said Dt. Zhangjun Fei, Associate Professor at BTI, Cornell Adjunct Associate Professor of Plant Pathology and a senior author of the paper. Over two-thirds of the world's pumpkins, squash, and gourds are produced in Asia alone. The researchers sequenced the two different pumpkin species to better understand their contrasting desirable traits: Cucurbita moschata is known for its resistance to disease and other stresses, such as extreme temperatures, while C. maxima is better known for its fruit quality and nutrition. Additionally, the hybrid of these two species, called “Shintosa” has even greater stress tolerance than C. moschata, and is often used as a rootstock for other cucurbit crops, such as watermelon, cucumber, and melon. Growers will cut the pumpkin seedling from its roots, and fuse the stems of other cucurbits onto it, giving them strong, resistant roots to grow from. Once deciphered, the genome sequences are an important resource for further scientific research and breeding of Cucurbita crops.

Interest in Bipolar Disorder Drug Lithium Exposes Possible Link with Splicing Factors and May Lead to Better Understanding of Leukemia Progression

A research project that began 20 years ago with an interest in how lithium treats mood disorders has yielded insights into the progression of blood cancers such as leukemia. The open-access article, which centers on a protein called GSK-3, was published online on September 15, 2017, and will be published in the November 3, 2017 issue of the Journal of Biological Chemistry. The article is titled “Phosphoproteomics Reveals That Glycogen Synthase Kinase-3 Phosphorylates Multiple Splicing Factors and Is Associated with Alternative Splicing.” Lithium is considered a highly effective treatment for bipolar disorder and other mood disorders, but it still works in only a fraction of patients and has a number of side effects. Furthermore, its mechanism of action is poorly understood, hampering efforts to improve on it. In 1996, Dr. Peter Klein of the University of Pennsylvania discovered that one of lithium's biological activities was inhibiting GSK-3, an enzyme that modifies other proteins by attaching phosphate molecules, a process called phosphorylation. Lithium's effect on GSK-3 affected the development of animal cells, but it is still unknown what connection, if any, this has to psychiatric disease. Since then, Dr. Klein, now a professor of medicine at the University of Pennsylvania, has been investigating many different aspects of GSK-3 activity. "In this paper, we were trying to find out what proteins in the cell are affected by GSK-3 inhibition," Dr. Klein said. "We compared cells with GSK-3 to cells completely lacking GSK-3 to ask how other proteins changed." "Mood disorders are so multifaceted in terms of the pathways and pathologies involved; it's really difficult to pin down a specific pathway," said Dr. Mansi Shinde, a former graduate student in Dr. Klein's research group who led the new study.

Scientists Unveil Sequence of Water Buffalo Genome

An international team of researchers led by the University of Adelaide in Australia has published the full genome of the water buffalo - opening the way for improved breeding and conservation of this economically important animal. The consortium of partners in Australia, Italy, China, Brazil, and the USA, with additional contributors in other countries, say they have now created the tools needed to apply modern molecular breeding systems to water buffalo. "Water buffaloes were domesticated about 5,000 years ago, and since then have been of economic importance for milk, meat, and as a work animal around the world," says consortium leader Professor John Williams, Director of the University of Adelaide's Davies Research Centre at the Roseworthy campus. "They are particularly important in developing countries and, in specialized markets, they provide milk for products such as mozzarella cheese in Italy. The water buffalo is a key agricultural animal because it is able to adapt to diverse environments, and is particularly tolerant of disease. "In Australia, they were brought to Northern Territory in the early 19th century and today there are milking herds of buffalo in Northern Territory and in South Australia." There are two subspecies of water buffalo. The researchers sequenced the genome of the River buffalo, which have been selected for milk production through organized breeding programs in Italy, India, the Philippines, and Brazil. Professor Williams says such advances in genomics have revolutionized dairy cattle breeding and now the same molecular tools will be available for water buffalo breeding. This project is another great example of the University of Adelaide's depth and expertise in research areas related to food innovation.

Exosome-Associated MicroRNAs May Be Powerful Biomarkers for Multiple Sclerosis, New Study Shows

A breakthrough study led by the University of Sydney's Brain and Mind Centre and Royal Prince Alfred Hospital has revealed unique molecules in the blood of people with multiple sclerosis (MS) that could become definitive diagnostic biomarkers of the world's most common neurologic disability in young adults. Published online today (October 30, 2017) in Scientific Reports, the discovery identifies tiny “dysregulated” micro-RNA molecules that correctly diagnose MS and discriminate between patients at different disease stages - all in a simple blood test. The open-access article is titled “Exosomal MicroRNA Signatures in Multiple Sclerosis Reflect Disease Status.” Currently, there is no definitive test for MS. Diagnosis and disease monitoring rely on several parameters, including clinical examination, MRI, cerebrospinal fluid assessment, and electrophysiology. MS is a chronic disease, so current diagnostic and monitoring tests are costly and still have limited utility to discriminate between different stages of the disease. In addition to identifying biomarkers that distinguish healthy people from those with MS, the researchers identified nine unique micro-RNA molecules that differentiate between two MS sub-types: relapsing-remitting MS (RRMS) and progressive MS. Relapsing-remitting MS (RRMS) affects 70 percent of MS patients and often evolves into a secondary progressive form of MS. 10-15 percent of people with MS are diagnosed with a progressive form of the disease from the outset known as primary progressive MS. The team also validated eight out of nine micro-RNA molecules in an independent group of progressive MS cases, confirming the reproducibility of the findings.

Virus-Based Treatment Delivers Chemotherapy Specifically to Glioma Brain Tumor Cells--Phase 1 Cancer Trial Led by University of Minnesota Medical School's Dr. Clark Chen Shows Promise

New data from a Phase I clinical trial led by Clark Chen, M.D., Ph.D., Lyle French Chair in Neurosurgery and Head of the University of Minnesota Medical School Department of Neurosurgery shows more than a quarter of patients with recurrent high-grade glioma, a form of brain cancer, were alive more than three years after treatment. "Given the deadly nature of this disease, three-year survival is rarely reported in the recurrent setting. It is notable that the survival benefit was seen across a range of patients and not just limited to patients with specific genetic mutations," said Dr. Chen. "This finding indicates that many patients could benefit from this treatment." As Dr. Chen explained in an October 27, 2017 presentation (http://www.abstractsonline.com/pp8/#!/4557/presentation/619) at the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics in Philadelphia, two steps were involved in the treatment of the 56 patients who participated in this clinical trial. First, patients were injected with Toca 511, which is a replicating virus that only infects actively dividing tumor cells. Once inside the cancer cell, the virus delivered a gene for an enzyme, cytosine deaminase (CD). As the virus began to replicate and spread to other cancer cells, it programmed them to make CD. Next, patients received a pill, Toca FC, which is an inert compound. Once inside the cancer cell, CD converted Toca FC into the anticancer drug 5-fluorouracil, which killed the cancer cell. In addition to destroying the cancer cells, 5-fluorouracil killed certain immune suppressive myeloid cells, thus boosting the patient's immune system to recognize and attack the cancer cells. "The treatment we tested in this trial delivers local chemotherapy specifically to the brain tumor.

Blocking Fibroblast Activation Protein (FAP) in Normal Cells May Impede Pancreatic Cancer, Penn Vet Team Shows

Cancer of the pancreas is a deadly disease, with a median survival time of less than six months. Only one in 20 people with pancreatic cancer survives five years past the diagnosis. The reason is the cancer's insidiousness; tumor cells hide deep inside the body, betraying no symptoms until late in the disease, when the cancer has almost invariably spread to other organs. New findings from a University of Pennsylvania-led team offer a promising target for future therapies that could potentially root out even well-hidden metastatic cancer lesions. When they deleted the gene encoding this protein in mice with the disease, the animals lived longer, and the cancer's spread to other organs was reduced. "We thought that by targeting this protein we would see a big change in the primary tumor, and, while we do see a delay, the big change was in the metastasis," said Dr. Ellen Puré, the study's senior author and Chair of the Department of Biomedical Science in Penn's School of Veterinary Medicine. "It looks like this protein might be a druggable target, so we're hoping that with some additional follow-up work, it's something that we'll see go into patients." Dr. Puré collaborated on the work with Penn Vet's Drs. Albert Lo, Elizabeth L. Buza, Rachel Blomberg, Priya Govindaraju, Diana Avery, and James Monslow; Dr. Chung-Pin Li of Taipei Veterans General Hospital and National Yang-Ming University School of Medicine; and Dr. Michael Hsiao of the Academia Sinica Genomics Research Center in Taipei. Their paper was published online on October 5, 2017 in the Journal of Clinical Investigation Insight.

ReNeuron Wins New Grant to Advance Its Exosome Therapy Platform

ReNeuron Group plc (the "Company") (AIM: RENE), a UK-based global leader in the development of cell-based therapeutics, was pleased to announce, on October 27, 2017, that it is the lead industry participant in a new grant award from the Welsh Government to advance its emerging exosome therapy platform. The grant has been awarded under the Welsh Government’s SMARTExpertise scheme and will help fund a £1.2 million (~$1.6 million) collaborative program of work to be undertaken by ReNeuron, Ig Innovations, and Swansea University Medical School. The work program will establish methods to refine and optimize the manufacturing process for generating ReNeuron’s CTX cell-derived exosomes with the highest biological efficacy, methods to enhance the characterization of the CTX-derived exosomes against solid tumors to identify new cancer targets, and methods to characterize exosomes with potential therapeutic benefit derived from ReNeuron’s broader proprietary cell line library. ReNeuron is exploiting its exosome therapy platform as a potential new nanomedicine targeting cancer and as a potential delivery system for drugs that would otherwise be unable to reach their site of action. The SMARTExpertise grant follows the award of a grant to ReNeuron last year from Innovate UK to develop manufacturing systems and to conduct pre-clinical testing relating to the Company’s exosome therapy platform. Commenting on the grant award, Dr. Randolph Corteling, Head of Research at ReNeuron, said: “We are delighted to have won this new grant under the Welsh Government’s SMARTExpertise scheme. As a Wales-based business, we are very pleased to be able to work with leading Welsh academic and industry collaborators in order to further progress development of our high-potential exosome therapy platform towards clinical application.”

Survey Results: Genetics Specialists’ Views on Genome Editing; Findings Reported at ASHG 2017 Annual Meeting

Genetics professionals around the globe hold varying views on genome editing in humans, agreeing with the general public on some aspects and differing on others, according to survey results presented on October 19, 2017 at the American Society of Human Genetics (ASHG) 2017 Annual Meeting in Orlando, Floroida. The results were presented by Professor Kelly Ormond, MS, Certified Genetic Counselor, of the Stanford Center for Biomedical Ethics. Led by Alyssa Armsby (photo), MS, of the Stanford University School of Medicine, researchers surveyed members of ten international genetics organizations on their attitudes toward research and potential clinical applications of genome editing, as well as how this relatively new technology fits in with their world view. The CRISPR/Cas9 system, a genome editing tool introduced in 2013, has quickly become widely used in genetics research due to the ease with which it can be customized and its effectiveness across cell types and species. Its quick adoption has sparked social and ethical questions, within both the scientific community and society more broadly, about how it should be studied and used. “There is a need for an ongoing international conversation about genome editing, but very little data on how people trained in genetics view the technology,” said Ms. Armsby. “As the ones who do the research and work with patients and families, they’re an important group of stakeholders,” she said. Among the 500 genetics professionals included in the analysis, the researchers found high support (>85%) for research into somatic uses of gene editing, which mirrors surveys of the American public.

American Society of Human Genetics (ASHG) Honors Kári Stefánsson with William Allan Award

The American Society of Human Genetics (ASHG) has named Kári Stefánsson, MD, founder of deCODE Genetics, the 2017 recipient of the annual William Allan Award. The Allan Award, which recognizes a scientist for substantial and far-reaching scientific contributions to human genetics, was established in 1961 in memory of William Allan, MD (1881-1943), one of the first American physicians to conduct extensive research on human genetics and hereditary diseases. Dr. Stefánsson was to receive his award, which will include an engraved medal and $25,000 prize, on October 18, 2017 during ASHG’s 67th Annual Meeting in Orlando, Florida. He was to present his William Allan Award address immediately thereafter. In 1996, Dr. Stefánsson founded deCODE Genetics with the vision of a large-scale population study in Iceland, a country with a relatively small, isolated, and homogenous population; a high-quality healthcare system; and extensive genealogical records. Through active engagement with the Icelandic population, deCODE has now collected DNA samples from more than 160,000 individuals and contributed greatly to public education about genetics in the country. Their work has inspired similar large-scale studies in other countries, including the UK Biobank and the United States’ All of Us initiative. Central to Dr. Stefánsson’s approach is the use of a single unique identifier for each individual, which allows researchers to measure hundreds of different genotypes and phenotypes in the context of each other and has led to important insights. His group published an influential genetic map in 2002, and has identified variants associated with varied phenotypes, such as type 2 diabetes, prostate cancer, heart attack, and schizophrenia.

American Society of Human Genetics (ASHG) Honors Arthur Beaudet with Victor A. McKusick Leadership Award

The American Society of Human Genetics (ASHG) named Arthur L. Beaudet (photo), MD, Henry and Emma Mayer Professor in the Department of Molecular and Human Genetics and the Department of Pediatrics at Baylor College of Medicine, as the 2017 recipient of the annual Victor A. McKusick Leadership Award. This award, named in honor of the late Victor A. McKusick, MD, recognizes individuals whose professional achievements have fostered and enriched the development of human genetics as well as its assimilation into the broader context of science, medicine, and health. The ASHG presented the McKusick Award, which included a plaque and $10,000 prize, to Dr. Beaudet on October 17, 2017 during the organization’s 67th Annual Meeting in Orlando, Florida. In the 1980s, Dr. Beaudet and colleagues were the first to document uniparental disomy, a phenomenon in which a person receives two copies of a chromosome from one parent and zero from the other, in humans. In the following years, the researchers drew an important distinction between genetic and epigenetic diseases that both lead to altered expression of the same genes, and identified ways to study these and better understand the conditions they caused. Currently, Dr. Beaudet’s research focuses on neuronal carnitine deficiency as a risk factor for autism; the role of genomic imprinting in diseases such as Prader-Willi syndrome, Angelman syndrome, and autism; and prenatal genetic diagnosis based on fetal cells isolated from maternal blood. In addition to his scientific leadership, ASHG also recognizes Dr. Beaudet’s contributions to the Society and the broader research community. A longtime member of ASHG, he belonged to its Program Committee from 1984-86, its Board of Directors from 1987-90, and its Awards Committee from 2010-12, and served as President in 1998.

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