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News Article | May 10, 2017
Site: www.eurekalert.org

Reported in Nature today, one of the largest sets of high quality human induced pluripotent stem cell lines from healthy individuals has been produced by a consortium involving the Wellcome Trust Sanger Institute. Comprehensively annotated and available for independent research*, the hundreds of stem cell lines are a powerful resource for scientists studying human development and disease. With collaborative partners from King's College London, the European Bioinformatics Institute, the University of Dundee and the University of Cambridge, the study also investigates in unprecedented detail the extensive variation between stem cells from different healthy people. Technological advancements have made it possible to take an adult cell and use specific growth conditions to turn back the clock - returning it to an early embryonic state. This results in an induced pluripotent stem cell (iPSC), which can develop into any type of cell in the body. These iPSCs have huge scientific potential for studying the development and the impact of diseases including cancer, Alzheimer's, and heart disease. However, the process of creating an iPSC is long and complicated and few laboratories have the facilities to characterise their cells in a way that makes them useful for other scientists to use. The Human Induced Pluripotent Stem Cell Initiative (HipSci) project used standardised methods to generate iPSCs on a large scale to study the differences between healthy people. Reference sets of stem cells were generated from skin biopsies donated by 301 healthy volunteers, creating multiple stem cell lines from each person. The researchers created 711 cell lines and generated detailed information about their genome, the proteins expressed in them, and the cell biology of each cell line. Lines and data generated by this initiative are available to academic researchers and industry. Dr Daniel Gaffney, a lead author on the paper, from the Wellcome Trust Sanger Institute, said: "We have created a comprehensive, high quality reference set of human induced pluripotent stem cell lines from healthy volunteers. Each of these stem cell lines has been extensively characterised and made available to the wider research community along with the annotation data. This resource is a stepping stone for researchers to make better cell models of many diseases, because they can study disease risk in many cell types, including those that are normally inaccessible." By creating more than one stem cell line from each healthy individual, the researchers were able to determine the similarity of stem cell lines from the same person. Prof Fiona Watt, a lead author on the paper and co-principal investigator of HipSci, from King's College London, said: "Many other efforts to create stem cells focus on rare diseases. In our study, stem cells have been produced from hundreds of healthy volunteers to study common genetic variation. We were able to show similar characteristics of iPS cells from the same person, and revealed that up to 46 per cent of the differences we saw in iPS cells were due to differences between individuals. These data will allow researchers to put disease variations in context with healthy people." The project, which has taken 4 years to complete, required a multidisciplinary approach with many different collaborators, who specialised in different aspects of creating the cell lines and characterising the data. Dr Oliver Stegle, a lead author on the paper, from the European Bioinformatics Institute, said: "This study was only possible due to the large scale, systematic production and characterisation of the stem cell lines. To help us to understand the different properties of the cells, we collected extensive data on multiple molecular layers, from the genome of the lines to their cell biology. This type of phenotyping required a whole facility rather than just a single lab, and will provide a huge resource to other scientists. Already, the data being generated have helped to gain a clearer picture of what a typical human iPSC cell looks like." Dr Michael Dunn, Head of Genetics and Molecular Sciences at Wellcome, said: "This is the fantastic result of many years of work to create a national resource of high quality, well-characterised human induced pluripotent stem cells. This has been a significant achievement made possible by the collaboration of researchers across the country with joint funding provided by Wellcome and the MRC. It will help to provide the knowledge base to underpin a huge amount of future research into the effects of our genes on health and disease. By ensuring this resource is openly available to all, we hope that it will pave the way for many more fascinating discoveries." *Data and cell lines from this study are being made available through http://www. , the European Collection of Authenticated Cell Cultures (ECACC) and the European Bank for Induced Pluripotent Stem Cells (EBiSC). Hipsci brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a global induced pluripotent stem cell resource for the research community. http://www. King's College London is one of the top 25 universities in the world (2016/17 QS World University Rankings) and among the oldest in England. King's has more than 29,600 students (of whom nearly 11,700 are graduate students) from some 150 countries worldwide, and some 8,000 staff. King's has an outstanding reputation for world-class teaching and cutting-edge research. In the 2014 Research Excellence Framework (REF), eighty-four per cent of research at King's was deemed 'world-leading' or 'internationally excellent' (3* and 4*). Since our foundation, King's students and staff have dedicated themselves in the service of society. King's will continue to focus on world-leading education, research and service, and will have an increasingly proactive role to play in a more interconnected, complex world. Visit our website to find out more about Vision 2029, King's strategic vision for the next 12 years to 2029, which will be the 200th anniversary of the founding of the university. http://www. The European Bioinformatics Institute (EMBL-EBI) is a global leader in the storage, analysis and dissemination of large biological datasets. EMBL-EBI helps scientists realise the potential of 'big data' by enhancing their ability to exploit complex information to make discoveries that benefit humankind. EMBL-EBI is at the forefront of computational biology research, with work spanning sequence analysis methods, multi-dimensional statistical analysis and data-driven biological discovery, from plant biology to mammalian development and disease. We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 22 member states and two associate member states, and are located on the Wellcome Genome Campus, one of the world's largest concentrations of scientific and technical expertise in genomics. http://www. The Wellcome Trust Sanger Institute is one of the world's leading genome centres. Through its ability to conduct research at scale, it is able to engage in bold and long-term exploratory projects that are designed to influence and empower medical science globally. Institute research findings, generated through its own research programmes and through its leading role in international consortia, are being used to develop new diagnostics and treatments for human disease. http://www. Wellcome exists to improve health for everyone by helping great ideas to thrive. We're a global charitable foundation, both politically and financially independent. We support scientists and researchers, take on big problems, fuel imaginations and spark debate. http://www.


Researchers have discovered that protection from the most severe form of malaria is linked with natural variation in human red blood cell genes. A study from the Wellcome Trust Sanger Institute, the Wellcome Trust Centre for Human Genetics and their collaborators has identified a genetic rearrangement of red blood cell glycophorin receptors that confers a 40 per cent reduced risk from severe malaria. Published in Science, this is the first study to show that large structural variants in human glycophorin genes, which are unusually common in Africa, are protective against malarial disease. It opens a new avenue for research on vaccines to prevent malaria parasites invading red blood cells. More than 200 million people a year are infected with malaria and the disease caused the deaths of nearly half a million people worldwide in 2015. Transmitted by mosquitos, the most widespread malarial parasite in Africa is Plasmodium falciparum; it is also the most dangerous. Plasmodium parasites infect human red blood cells and gain entry via receptors on the cell surface. Previous studies on natural resistance to malaria had implicated a section of human genome near to a cluster of receptor genes. These receptors - glycophorins - are located on the surface of red blood cells and are amongst many receptors that bind Plasmodium falciparum. However, it is only now that they have been shown to be involved in protection against malaria. Researchers investigated the glycophorin area of the genome in more detail than before using new whole-genome sequence data from 765 volunteers in the Gambia, Burkina Faso, Cameroon and Tanzania. Using this new information they then undertook a study across the Gambia, Kenya and Malawi that included 5310 individuals from the normal population and 4579 people who were hospitalised from severe malaria. They discovered that people who have a particular rearrangement of the glycophorin genes had a 40 per cent reduced risk of severe malaria. Dr Ellen Leffler from the University of Oxford, first author on the paper, said. "In this new study we found strong evidence that variation in the glycophorin gene cluster influences malaria susceptibility. We found some people have a complex rearrangement of GYPA and GYPB genes, forming a hybrid glycophorin, and these people are less likely to develop severe complications of the disease." The hybrid GYPB-A gene is found in a particular rare blood group - part of the MNS* blood group system - where it is known as Dantu. The study found that the GYPB-A Dantu hybrid was present in some people from East Africa, in Kenya, Tanzania and Malawi, but that it was not present in volunteers from West African populations. Dr Kirk Rockett from the University of Oxford, said: "Analysing the DNA sequences allowed us to identify the location of the join between glycophorins A and B in the hybrid gene. It showed us that the sequence is characteristic of the Dantu antigen in the MNS blood group system." Studying the glycophorin gene cluster to determine differences between the sequences of the three genes with confidence is extremely challenging. This study gives insights into unpicking the region and how it connects to the MNS blood group system and impacts malaria susceptibility. Professor Dominic Kwiatkowski, a lead author from the Wellcome Trust Sanger Institute and University of Oxford, said: "We are starting to find that the glycophorin region of the genome has an important role in protecting people against malaria. Our discovery that a specific variant of glycophorin invasion receptors can give substantial protection against severe malaria will hopefully inspire further research on exactly how Plasmodium falciparum invade red blood cells. This could also help us discover novel parasite weaknesses that could be exploited in future interventions against this deadly disease." Ellen M Leffler et al. (2017). Resistance to malaria through structural variation of red blood cell invasion receptors. Science. DOI: 10.1126/science.aam6393 *The MNS system is a human blood group system based on two genes - glycophorin A and glycophorin B - on chromosome 4. There are 46 antigens in the system; the most common are called M, N, S, s and U. For more information about malaria please see http://www. The Malaria Genomic Epidemiology Network (MalariaGEN) is an international community of researchers working to understand how genetic variation in humans, Plasmodium parasites, and Anopheles mosquitoes affects the biology and epidemiology of malaria - and using this knowledge to develop new tools to inform malaria control. The network currently involves researchers in more than 40 malaria-endemic countries with a coordinating centre at Oxford University and the Wellcome Trust Sanger Institute. https:/ The Division is one of the largest biomedical research centres in Europe, with over 2,500 people involved in research and more than 2,800 students. The University is rated the best in the world for medicine, and it is home to the UK's top-ranked medical school. From the genetic and molecular basis of disease to the latest advances in neuroscience, Oxford is at the forefront of medical research. It has one of the largest clinical trial portfolios in the UK and great expertise in taking discoveries from the lab into the clinic. Partnerships with the local NHS Trusts enable patients to benefit from close links between medical research and healthcare delivery. A great strength of Oxford medicine is its long-standing network of clinical research units in Asia and Africa, enabling world-leading research on the most pressing global health challenges such as malaria, TB, HIV/AIDS and flu. Oxford is also renowned for its large-scale studies which examine the role of factors such as smoking, alcohol and diet on cancer, heart disease and other conditions. https:/ The Wellcome Trust Sanger Institute is one of the world's leading genome centres. Through its ability to conduct research at scale, it is able to engage in bold and long-term exploratory projects that are designed to influence and empower medical science globally. Institute research findings, generated through its own research programmes and through its leading role in international consortia, are being used to develop new diagnostics and treatments for human disease. http://www. Wellcome exists to improve health for everyone by helping great ideas to thrive. We're a global charitable foundation, both politically and financially independent. We support scientists and researchers, take on big problems, fuel imaginations and spark debate. http://www.


When the first busloads of migrants from Syria and Iraq rolled into Germany 2 years ago, some small towns were overwhelmed. The village of Sumte, population 102, had to take in 750 asylum seekers. Most villagers swung into action, in keeping with Germany’s strong Willkommenskultur, or “welcome culture.” But one self-described neo-Nazi on the district council told The New York Times that by allowing the influx, the German people faced “the destruction of our genetic heritage” and risked becoming “a gray mishmash.” In fact, the German people have no unique genetic heritage to protect. They—and all other Europeans—are already a mishmash, the children of repeated ancient migrations, according to scientists who study ancient human origins. New studies show that almost all indigenous Europeans descend from at least three major migrations in the past 15,000 years, including two from the Middle East. Those migrants swept across Europe, mingled with previous immigrants, and then remixed to create the peoples of today. Using revolutionary new methods to analyze DNA and the isotopes found in bones and teeth, scientists are exposing the tangled roots of peoples around the world, as varied as Germans, ancient Philistines, and Kashmiris. Few of us are actually the direct descendants of the ancient skeletons found in our backyards or historic homelands. Only a handful of groups today, such as Australian Aborigines, have deep bloodlines untainted by mixing with immigrants. “We can falsify this notion that anyone is pure,” says population geneticist Lynn Jorde of the University of Utah in Salt Lake City. Instead, almost all modern humans “have this incredibly complex history of mixing and mating and migration.” Wind back the clock more than a thousand years—a trivial slice of time compared with the 200,000 years or so since our species emerged—and stories of exclusive heritage or territory crumble. “Basically, everybody’s myth is wrong, even the indigenous groups’,” says population geneticist David Reich of Harvard University. Tacitus, the Roman historian, reports that in 9 C.E. a member of the Germanic Cherusci tribe called Arminius led a rebellion against the Romans near the village of Kalkriese in northern Germany. Against all odds, the tribes slaughtered three Roman legions in what became known as the Battle of the Teutoburg Forest. After Tacitus’s account resurfaced in the 15th century, German nationalists resurrected the myth of Arminius, who is often depicted as a blond, muscular young chieftain and known as Hermann. Hailed as the first “German” hero, he was said to have united the Germanic tribes and driven the Romans from their territory. That was considered the start of a period when fearsome Germanic tribes such as the Vandals swept around Europe, wresting territory from Romans and others. In the 20th century, the Nazis added their own dark spin to that origin story, citing Arminius as part of an ancient pedigree of a “master race” from Germany and northern Europe that they called Aryans. They used their view of prehistory and archaeology to justify claims to the tribes’ ancient homelands in Poland and Austria. Scholars agree that there was indeed a real battle that sent shock waves through the Roman Empire, which then stretched from the island of Britain to Egypt. But much of the rest of Arminius’s story is myth: The Romans persisted deep in Germania until at least the third century C.E., as shown by the recent discovery of a third-century Roman battlefield in Harzhorn, Germany. And Arminius by no means united the more than 50 Germanic tribes of the time. He persuaded five tribes to join him in battle, but members of his own tribe soon killed him. Moreover, Arminius and his kin were not pure “Aryan,” if that term means a person whose ancestors lived solely in what is now Germany or Scandinavia. The Cherusci tribe, like all Europeans of their day and later, were themselves composites, built from serial migrations into the heart of Europe and then repeatedly remixed. “The whole concept of an ethnic German … it’s ludicrous when you look at the longue durée [long time] scale,” says archaeologist Aren Maeir of Bar-Ilan University in Ramat Gan, Israel. After World War II, many scholars recoiled from studying migrations, in reaction to the Nazi misuse of history and archaeology. The Nazis had invoked migrations of “foreign” groups to German territory to justify genocide. “The whole field of migration studies was ideologically tainted,” says archaeologist Kristian Kristiansen of the University of Gothenburg in Sweden. Some researchers also resisted the idea that migration helped spread key innovations such as farming, partly because that might imply that certain groups were superior. Nor did researchers have a reliable method to trace prehistoric migrations. “Most of the archaeological evidence for movement is based on artifacts, but artifacts can be stolen or copied, so they are not a real good proxy for actual human movement,” says archaeologist Doug Price of the University of Wisconsin in Madison, who tracks ancient migration by analyzing isotopes. “When I started doing this in 1990, I thought people were very sedentary and didn’t move around much.” Today, however, new methods yield more definitive evidence of migration, sparking an explosion of studies. The isotopes Price and others study are specific to local water and food and thus can reveal where people grew up and whether they later migrated. DNA from ancient skeletons and living people offers the “gold standard” in proving who was related to whom. The new data confirm that humans have always had wanderlust, plus a yen to mix with all manner of strangers. After the first Homo sapiens arose in Africa, several bands walked out of the continent about 60,000 years ago and into the arms of Neandertals and other archaic humans. Today, almost all humans outside Africa carry traces of archaic DNA. That was just one of many episodes of migration and mixing. The first Europeans came from Africa via the Middle East and settled there about 43,000 years ago. But some of those pioneers, such as a 40,000-year-old individual from Romania, have little connection to today’s Europeans, Reich says. His team studied DNA from 51 Europeans and Asians who lived 7000 to 45,000 years ago. They found that most of the DNA in living Europeans originated in three major migrations, starting with hunter-gatherers who came from the Middle East as the glaciers retreated 19,000 to 14,000 years ago. In a second migration about 9000 years ago, farmers from northwestern Anatolia, in what is now Greece and Turkey, moved in. That massive wave of farmers washed across the continent. Ancient DNA records their arrival in Germany, where they are linked with the Linear Pottery culture, 6900 to 7500 years ago. A 7000-year-old woman from Stuttgart, Germany, for example, has the farmers’ genetic signatures, setting her apart from eight hunter-gatherers who lived just 1000 years earlier in Luxembourg and Sweden. Among people living today, Sardinians retain the most DNA from those early farmers, whose genes suggest that they had brown eyes and dark hair. The farmers moved in family groups and stuck to themselves awhile before mixing with local hunter-gatherers, according to a study in 2015 that used ancient DNA to calculate the ratio of men to women in the farming groups. That’s a stark contrast to the third major migration, which began about 5000 years ago when herders swept in from the steppe north of the Black Sea in what is now Russia. Those Yamnaya pastoralists herded cattle and sheep, and some rode newly domesticated horses, says archaeologist David Anthony of Hartwick College in Oneonta, New York. In the journal Antiquity last month, Kristiansen and paleogeneticist Eske Willerslev at the University of Copenhagen reported that the sex ratios of the earliest Yamnaya burials in central Europe suggest that the new arrivals were mostly men. Arriving with few women, those tall strangers were apparently eager to woo or abduct the local farmers’ daughters. Not long after the Yamnaya invasion, their skeletons were buried with those of women who had lived on farms as children, according to the strontium and nitrogen isotopes in their bones, says Price, who analyzed them. The unions between the Yamnaya and the descendants of Anatolian farmers catalyzed the creation of the famous Corded Ware culture, known for its distinctive pottery impressed with cordlike patterns, Kristiansen says. According to DNA analysis, those people may have inherited Yamnaya genes that made them taller; they may also have had a then-rare mutation that enabled them to digest lactose in milk, which quickly spread. It was a winning combination. The Corded Ware people had many offspring who spread rapidly across Europe. They were among the ancestors of the Bell Beaker culture of central Europe, known by the vessels they used to drink wine, according to a study by Kristiansen and Reich published this month. “This big wave of Yamnaya migration washed all the way to the shores of Ireland,” says population geneticist Dan Bradley of Trinity College in Dublin. Bell Beaker pots and DNA appeared about 4000 years ago in burials on Rathlin Island, off the coast of Northern Ireland, his group reported this year. This new picture means that the Hermann of lore was himself a composite of post–ice age hunter-gatherers, Anatolian farmers, and Yamnaya herders. So are most other Europeans—including the ancient Romans whose empire Arminius fought. The three-part European mixture varies across the continent, with different ratios of each migration and trace amounts of other lineages. But those quirks rarely match the tales people tell about their ancestry. For example, the Basques of northern Spain, who have a distinct language, have long thought themselves a people apart. But last year, population geneticist Mattias Jakobsson of Uppsala University in Sweden reported that the DNA of modern Basques is most like that of the ancient farmers who populated northern Spain before the Yamnaya migration. In other words, Basques are part of the usual European mix, although they carry less Yamnaya DNA than other Europeans. Farther north, the Irish Book of Invasions, written by an anonymous author in the 11th century, recounts that the “Sons of Míl Espáine … after many wanderings in Scythia and Egypt” eventually reached Spain and Ireland, creating a modern Irish people distinct from the British—and linked to the Spanish. That telling resonates with a later yarn about ships from the Spanish Armada, wrecked on the shores of Ireland and the Scottish Orkney Islands in 1588, Bradley says: “Good-looking, dark-haired Spaniards washed ashore” and had children with Gaelic and Orkney Islands women, creating a strain of Black Irish with dark hair, eyes, and skin. Although it’s a great story, Bradley says, it “just didn’t happen.” In two studies, researchers have found only “a very small ancient Spanish contribution” to British and Irish DNA, says human geneticist Walter Bodmer of the University of Oxford in the United Kingdom, co-leader of a landmark 2015 study of British genetics. The Irish also cherish another origin story, of the Celtic roots they are said to share with the Scots and Welsh. In the Celtic Revival of the 19th and 20th centuries, writers such as William Butler Yeats drew from stories in the Book of Invasions and medieval texts. Those writings described a migration of Gaels, or groups of Celts from the mainland who clung to their identity in the face of later waves of Roman, Germanic, and Nordic peoples. But try as they might, researchers so far haven’t found anyone, living or dead, with a distinct Celtic genome. The ancient Celts got their name from Greeks who used “Celt” as a label for barbarian outsiders—the diverse Celtic-speaking tribes who, starting in the late Bronze Age, occupied territory from Portugal to Turkey. “It’s a hard question who the Celts are,” says population geneticist Stephan Schiffels of the Max Planck Institute for the Science of Human History in Jena, Germany. Bodmer’s team traced the ancestry of 2039 people whose families have lived in the same parts of Scotland, Northern Ireland, and Wales since the 19th century. These people form at least nine genetic and geographic clusters, showing that after their ancestors arrived in those regions, they put down roots and married their neighbors. But the clusters themselves are of diverse origin, with close ties to people now in Germany, Belgium, and France. “‘Celtic’ is a cultural definition,” Bodmer says. “It has nothing to do with hordes of people coming from somewhere else and replacing people.” English myths fare no better. The Anglo-Saxon Chronicle recounts that in 449 C.E., two Germanic tribespeople, Hengist and Horsa, sailed from what is now the Netherlands to southeast England, starting a fierce conflict. As more Angles, Saxons, and Jutes arrived, violence broke out with the local Britons and ended in “rivers of blood,” according to accounts by medieval monks. Scholars have debated just how bloody that invasion was, and whether it was a mass migration or a small delegation of elite kings and their warriors. An answer came in 2016 from a study of the ancient DNA of Anglo-Saxons and indigenous Britons, who were buried side by side in the fifth and sixth centuries in a cemetery near Cambridge, U.K. They lived and died together and even interbred, as shown by one person who had a mix of DNA from both Britons and Anglo-Saxons, and a genetic Briton who was buried with a large cruciform Anglo-Saxon brooch. Although the stories stress violence, the groups “were mixing very quickly,” says Duncan Sayer, an archaeologist at the University of Central Lancashire in Preston, U.K., who co-wrote the study. The team went on to show that 25% to 40% of the ancestry of modern Britons is Anglo-Saxon. Even people in Wales and Scotland—thought to be Celtic strongholds—get about 30% of their DNA from Anglo-Saxons, says co-author Chris Tyler-Smith of the Wellcome Trust’s Sanger Institute in Hinxton, U.K. The boom in studies of migration is centered on Europe, where access to ancient remains is relatively easy and cold climates can help preserve DNA. But geneticists are beginning to probe the makeup of ancient people elsewhere. For example, findings from recent excavations in Israel are close to solving a long-standing mystery from the Bible: the identity of the ancient Philistines. In biblical texts, those “uncircumcised” people are known as the bitter enemies of the Israelites; the name “Philistine” is still a slur in English. They’re said to have lived in Canaan, between present-day Tel Aviv and Gaza in Israel. They ate pork, battled Samson’s armies, and stole the Ark of the Covenant. Goliath, whom David slew with a sling, was a Philistine. But after Old Testament times, the group disappears from both scripture and historical accounts. To find the Philistines’ origins, researchers have studied artifacts and remains from ancient Philistine cities in Israel. The evidence, including isotopic analysis, shows that the Philistines were a motley crew of immigrants, possibly pirates, who hailed from many ports, bringing pigs from Europe and donkeys in caravans from Egypt. “The Philistines are an entangled culture from western Anatolia, Cyprus, Greece, the Balkans, you name it,” says Maeir, who has directed excavations at the Philistine city of Gath for 2 decades. Maeir says he thinks that the Philistines soon intermarried with people already living in Canaan instead of going extinct. If so, the loathsome Philistines are part of the ancestral stock for both Palestinian Muslims and Israeli Jews. Those groups, so full of enmity today, are genetically closely related, according to a study in 2000 of the paternally inherited Y chromosomes of 119 Ashkenazi and Sephardic Jews and 143 Israeli and Palestinian Arabs. Seventy percent of the Jewish men and half of the Arab men inherited their Y chromosomes from the same set of paternal ancestors who lived in the Middle East within the last few thousand years. As techniques for probing ethnic origins spread, nearly every week brings a new paper testing and often falsifying lore about one ancient culture or another. The Kashmiri of northern India do not seem to be related to Alexander the Great or the lost tribes of Israel. Parsis in Iran and India are not solely of ancient Iranian heritage, having mixed with local Indian women, although Parsi priests do descend chiefly from just two men. “Ethnic groups in the past and present create an ‘imagined past’ of the longtime and ‘pure’ origins of their group,” Maeir says. But that created past often has “little true relation to the historical processes” that actually created the group, he says. So far, the origin stories that appear to hew most closely to reality belong to indigenous peoples around the world. For example, the Tlingit and Tsimshian tribes of British Columbia in Canada and Alaska claim to have lived along the west coast of North America from “time immemorial.” Living tribespeople do descend in part from three ancient Native Americans who lived in the region 2500 to 6000 years ago, according to DNA analyses published last month. Even so, most modern Native Americans are not directly related to the ancient people who lived in the same areas because their offspring moved, were displaced, or went extinct over the millennia, Reich says. In Australia, aboriginal stories recall even longer connections to their lands, even seeming to refer to times when sea levels rose and fell more than 15,000 years ago. Those claims are among the few that genome studies support. DNA evidence puts aboriginal ancestors on the continent 40,000 to 60,000 years ago. Once the first Australians arrived, they settled in three regions and remained in those discrete homelands for tens of thousands of years, a DNA study published in March suggests. But the Aborigines are rare among the peoples of Earth, where migrations have been the norm. Almost always, Reich says, “the idea that the ancestors of any one population have lived in the same place for tens of thousands of years with no substantial immigration is wrong.” Back in Sumte in the fall of 2015, the 750 refugees from Syria arrived on schedule. The adults mostly kept to themselves, learning German and taking occasional construction jobs. But their children sang “O Tannenbaum” in a local church at Christmas and their teens ventured out often, seeking cellphone signals in the quiet town. In the following months, almost all the refugees dispersed to larger towns throughout Germany. In time, some of the young immigrants will contribute their DNA to the next generation of Germans, re-enacting on a small scale the process of migration and assimilation that once played out repeatedly on this same land—and far beyond.


News Article | May 15, 2017
Site: www.sciencemag.org

When the first busloads of migrants from Syria and Iraq rolled into Germany 2 years ago, some small towns were overwhelmed. The village of Sumte, population 102, had to take in 750 asylum seekers. Most villagers swung into action, in keeping with Germany’s strong Willkommenskultur, or “welcome culture.” But one self-described neo-Nazi on the district council told The New York Times that by allowing the influx, the German people faced “the destruction of our genetic heritage” and risked becoming “a gray mishmash.” In fact, the German people have no unique genetic heritage to protect. They—and all other Europeans—are already a mishmash, the children of repeated ancient migrations, according to scientists who study ancient human origins. New studies show that almost all indigenous Europeans descend from at least three major migrations in the past 15,000 years, including two from the Middle East. Those migrants swept across Europe, mingled with previous immigrants, and then remixed to create the peoples of today. Using revolutionary new methods to analyze DNA and the isotopes found in bones and teeth, scientists are exposing the tangled roots of peoples around the world, as varied as Germans, ancient Philistines, and Kashmiris. Few of us are actually the direct descendants of the ancient skeletons found in our backyards or historic homelands. Only a handful of groups today, such as Australian Aborigines, have deep bloodlines untainted by mixing with immigrants. “We can falsify this notion that anyone is pure,” says population geneticist Lynn Jorde of the University of Utah in Salt Lake City. Instead, almost all modern humans “have this incredibly complex history of mixing and mating and migration.” Wind back the clock more than a thousand years—a trivial slice of time compared with the 200,000 years or so since our species emerged—and stories of exclusive heritage or territory crumble. “Basically, everybody’s myth is wrong, even the indigenous groups’,” says population geneticist David Reich of Harvard University. Tacitus, the Roman historian, reports that in 9 C.E. a member of the Germanic Cherusci tribe called Arminius led a rebellion against the Romans near the village of Kalkriese in northern Germany. Against all odds, the tribes slaughtered three Roman legions in what became known as the Battle of the Teutoburg Forest. After Tacitus’s account resurfaced in the 15th century, German nationalists resurrected the myth of Arminius, who is often depicted as a blond, muscular young chieftain and known as Hermann. Hailed as the first “German” hero, he was said to have united the Germanic tribes and driven the Romans from their territory. That was considered the start of a period when fearsome Germanic tribes such as the Vandals swept around Europe, wresting territory from Romans and others. In the 20th century, the Nazis added their own dark spin to that origin story, citing Arminius as part of an ancient pedigree of a “master race” from Germany and northern Europe that they called Aryans. They used their view of prehistory and archaeology to justify claims to the tribes’ ancient homelands in Poland and Austria. Scholars agree that there was indeed a real battle that sent shock waves through the Roman Empire, which then stretched from the island of Britain to Egypt. But much of the rest of Arminius’s story is myth: The Romans persisted deep in Germania until at least the third century C.E., as shown by the recent discovery of a third-century Roman battlefield in Harzhorn, Germany. And Arminius by no means united the more than 50 Germanic tribes of the time. He persuaded five tribes to join him in battle, but members of his own tribe soon killed him. Moreover, Arminius and his kin were not pure “Aryan,” if that term means a person whose ancestors lived solely in what is now Germany or Scandinavia. The Cherusci tribe, like all Europeans of their day and later, were themselves composites, built from serial migrations into the heart of Europe and then repeatedly remixed. “The whole concept of an ethnic German … it’s ludicrous when you look at the longue durée [long time] scale,” says archaeologist Aren Maeir of Bar-Ilan University in Ramat Gan, Israel. After World War II, many scholars recoiled from studying migrations, in reaction to the Nazi misuse of history and archaeology. The Nazis had invoked migrations of “foreign” groups to German territory to justify genocide. “The whole field of migration studies was ideologically tainted,” says archaeologist Kristian Kristiansen of the University of Gothenburg in Sweden. Some researchers also resisted the idea that migration helped spread key innovations such as farming, partly because that might imply that certain groups were superior. Nor did researchers have a reliable method to trace prehistoric migrations. “Most of the archaeological evidence for movement is based on artifacts, but artifacts can be stolen or copied, so they are not a real good proxy for actual human movement,” says archaeologist Doug Price of the University of Wisconsin in Madison, who tracks ancient migration by analyzing isotopes. “When I started doing this in 1990, I thought people were very sedentary and didn’t move around much.” Today, however, new methods yield more definitive evidence of migration, sparking an explosion of studies. The isotopes Price and others study are specific to local water and food and thus can reveal where people grew up and whether they later migrated. DNA from ancient skeletons and living people offers the “gold standard” in proving who was related to whom. The new data confirm that humans have always had wanderlust, plus a yen to mix with all manner of strangers. After the first Homo sapiens arose in Africa, several bands walked out of the continent about 60,000 years ago and into the arms of Neandertals and other archaic humans. Today, almost all humans outside Africa carry traces of archaic DNA. That was just one of many episodes of migration and mixing. The first Europeans came from Africa via the Middle East and settled there about 43,000 years ago. But some of those pioneers, such as a 40,000-year-old individual from Romania, have little connection to today’s Europeans, Reich says. His team studied DNA from 51 Europeans and Asians who lived 7000 to 45,000 years ago. They found that most of the DNA in living Europeans originated in three major migrations, starting with hunter-gatherers who came from the Middle East as the glaciers retreated 19,000 to 14,000 years ago. In a second migration about 9000 years ago, farmers from northwestern Anatolia, in what is now Greece and Turkey, moved in. That massive wave of farmers washed across the continent. Ancient DNA records their arrival in Germany, where they are linked with the Linear Pottery culture, 6900 to 7500 years ago. A 7000-year-old woman from Stuttgart, Germany, for example, has the farmers’ genetic signatures, setting her apart from eight hunter-gatherers who lived just 1000 years earlier in Luxembourg and Sweden. Among people living today, Sardinians retain the most DNA from those early farmers, whose genes suggest that they had brown eyes and dark hair. The farmers moved in family groups and stuck to themselves awhile before mixing with local hunter-gatherers, according to a study in 2015 that used ancient DNA to calculate the ratio of men to women in the farming groups. That’s a stark contrast to the third major migration, which began about 5000 years ago when herders swept in from the steppe north of the Black Sea in what is now Russia. Those Yamnaya pastoralists herded cattle and sheep, and some rode newly domesticated horses, says archaeologist David Anthony of Hartwick College in Oneonta, New York. In the journal Antiquity last month, Kristiansen and paleogeneticist Eske Willerslev at the University of Copenhagen reported that the sex ratios of the earliest Yamnaya burials in central Europe suggest that the new arrivals were mostly men. Arriving with few women, those tall strangers were apparently eager to woo or abduct the local farmers’ daughters. Not long after the Yamnaya invasion, their skeletons were buried with those of women who had lived on farms as children, according to the strontium and nitrogen isotopes in their bones, says Price, who analyzed them. The unions between the Yamnaya and the descendants of Anatolian farmers catalyzed the creation of the famous Corded Ware culture, known for its distinctive pottery impressed with cordlike patterns, Kristiansen says. According to DNA analysis, those people may have inherited Yamnaya genes that made them taller; they may also have had a then-rare mutation that enabled them to digest lactose in milk, which quickly spread. It was a winning combination. The Corded Ware people had many offspring who spread rapidly across Europe. They were among the ancestors of the Bell Beaker culture of central Europe, known by the vessels they used to drink wine, according to a study by Kristiansen and Reich published this month. “This big wave of Yamnaya migration washed all the way to the shores of Ireland,” says population geneticist Dan Bradley of Trinity College in Dublin. Bell Beaker pots and DNA appeared about 4000 years ago in burials on Rathlin Island, off the coast of Northern Ireland, his group reported this year. This new picture means that the Hermann of lore was himself a composite of post–ice age hunter-gatherers, Anatolian farmers, and Yamnaya herders. So are most other Europeans—including the ancient Romans whose empire Arminius fought. The three-part European mixture varies across the continent, with different ratios of each migration and trace amounts of other lineages. But those quirks rarely match the tales people tell about their ancestry. For example, the Basques of northern Spain, who have a distinct language, have long thought themselves a people apart. But last year, population geneticist Mattias Jakobsson of Uppsala University in Sweden reported that the DNA of modern Basques is most like that of the ancient farmers who populated northern Spain before the Yamnaya migration. In other words, Basques are part of the usual European mix, although they carry less Yamnaya DNA than other Europeans. Farther north, the Irish Book of Invasions, written by an anonymous author in the 11th century, recounts that the “Sons of Míl Espáine … after many wanderings in Scythia and Egypt” eventually reached Spain and Ireland, creating a modern Irish people distinct from the British—and linked to the Spanish. That telling resonates with a later yarn about ships from the Spanish Armada, wrecked on the shores of Ireland and the Scottish Orkney Islands in 1588, Bradley says: “Good-looking, dark-haired Spaniards washed ashore” and had children with Gaelic and Orkney Islands women, creating a strain of Black Irish with dark hair, eyes, and skin. Although it’s a great story, Bradley says, it “just didn’t happen.” In two studies, researchers have found only “a very small ancient Spanish contribution” to British and Irish DNA, says human geneticist Walter Bodmer of the University of Oxford in the United Kingdom, co-leader of a landmark 2015 study of British genetics. The Irish also cherish another origin story, of the Celtic roots they are said to share with the Scots and Welsh. In the Celtic Revival of the 19th and 20th centuries, writers such as William Butler Yeats drew from stories in the Book of Invasions and medieval texts. Those writings described a migration of Gaels, or groups of Celts from the mainland who clung to their identity in the face of later waves of Roman, Germanic, and Nordic peoples. But try as they might, researchers so far haven’t found anyone, living or dead, with a distinct Celtic genome. The ancient Celts got their name from Greeks who used “Celt” as a label for barbarian outsiders—the diverse Celtic-speaking tribes who, starting in the late Bronze Age, occupied territory from Portugal to Turkey. “It’s a hard question who the Celts are,” says population geneticist Stephan Schiffels of the Max Planck Institute for the Science of Human History in Jena, Germany. Bodmer’s team traced the ancestry of 2039 people whose families have lived in the same parts of Scotland, Northern Ireland, and Wales since the 19th century. These people form at least nine genetic and geographic clusters, showing that after their ancestors arrived in those regions, they put down roots and married their neighbors. But the clusters themselves are of diverse origin, with close ties to people now in Germany, Belgium, and France. “‘Celtic’ is a cultural definition,” Bodmer says. “It has nothing to do with hordes of people coming from somewhere else and replacing people.” English myths fare no better. The Anglo-Saxon Chronicle recounts that in 449 C.E., two Germanic tribespeople, Hengist and Horsa, sailed from what is now the Netherlands to southeast England, starting a fierce conflict. As more Angles, Saxons, and Jutes arrived, violence broke out with the local Britons and ended in “rivers of blood,” according to accounts by medieval monks. Scholars have debated just how bloody that invasion was, and whether it was a mass migration or a small delegation of elite kings and their warriors. An answer came in 2016 from a study of the ancient DNA of Anglo-Saxons and indigenous Britons, who were buried side by side in the fifth and sixth centuries in a cemetery near Cambridge, U.K. They lived and died together and even interbred, as shown by one person who had a mix of DNA from both Britons and Anglo-Saxons, and a genetic Briton who was buried with a large cruciform Anglo-Saxon brooch. Although the stories stress violence, the groups “were mixing very quickly,” says Duncan Sayer, an archaeologist at the University of Central Lancashire in Preston, U.K., who co-wrote the study. The team went on to show that 25% to 40% of the ancestry of modern Britons is Anglo-Saxon. Even people in Wales and Scotland—thought to be Celtic strongholds—get about 30% of their DNA from Anglo-Saxons, says co-author Chris Tyler-Smith of the Wellcome Trust’s Sanger Institute in Hinxton, U.K. The boom in studies of migration is centered on Europe, where access to ancient remains is relatively easy and cold climates can help preserve DNA. But geneticists are beginning to probe the makeup of ancient people elsewhere. For example, findings from recent excavations in Israel are close to solving a long-standing mystery from the Bible: the identity of the ancient Philistines. In biblical texts, those “uncircumcised” people are known as the bitter enemies of the Israelites; the name “Philistine” is still a slur in English. They’re said to have lived in Canaan, between present-day Tel Aviv and Gaza in Israel. They ate pork, battled Samson’s armies, and stole the Ark of the Covenant. Goliath, whom David slew with a sling, was a Philistine. But after Old Testament times, the group disappears from both scripture and historical accounts. To find the Philistines’ origins, researchers have studied artifacts and remains from ancient Philistine cities in Israel. The evidence, including isotopic analysis, shows that the Philistines were a motley crew of immigrants, possibly pirates, who hailed from many ports, bringing pigs from Europe and donkeys in caravans from Egypt. “The Philistines are an entangled culture from western Anatolia, Cyprus, Greece, the Balkans, you name it,” says Maeir, who has directed excavations at the Philistine city of Gath for 2 decades. Maeir says he thinks that the Philistines soon intermarried with people already living in Canaan instead of going extinct. If so, the loathsome Philistines are part of the ancestral stock for both Palestinian Muslims and Israeli Jews. Those groups, so full of enmity today, are genetically closely related, according to a study in 2000 of the paternally inherited Y chromosomes of 119 Ashkenazi and Sephardic Jews and 143 Israeli and Palestinian Arabs. Seventy percent of the Jewish men and half of the Arab men inherited their Y chromosomes from the same set of paternal ancestors who lived in the Middle East within the last few thousand years. As techniques for probing ethnic origins spread, nearly every week brings a new paper testing and often falsifying lore about one ancient culture or another. The Kashmiri of northern India do not seem to be related to Alexander the Great or the lost tribes of Israel. Parsis in Iran and India are not solely of ancient Iranian heritage, having mixed with local Indian women, although Parsi priests do descend chiefly from just two men. “Ethnic groups in the past and present create an ‘imagined past’ of the longtime and ‘pure’ origins of their group,” Maeir says. But that created past often has “little true relation to the historical processes” that actually created the group, he says. So far, the origin stories that appear to hew most closely to reality belong to indigenous peoples around the world. For example, the Tlingit and Tsimshian tribes of British Columbia in Canada and Alaska claim to have lived along the west coast of North America from “time immemorial.” Living tribespeople do descend in part from three ancient Native Americans who lived in the region 2500 to 6000 years ago, according to DNA analyses published last month. Even so, most modern Native Americans are not directly related to the ancient people who lived in the same areas because their offspring moved, were displaced, or went extinct over the millennia, Reich says. In Australia, aboriginal stories recall even longer connections to their lands, even seeming to refer to times when sea levels rose and fell more than 15,000 years ago. Those claims are among the few that genome studies support. DNA evidence puts aboriginal ancestors on the continent 40,000 to 60,000 years ago. Once the first Australians arrived, they settled in three regions and remained in those discrete homelands for tens of thousands of years, a DNA study published in March suggests. But the Aborigines are rare among the peoples of Earth, where migrations have been the norm. Almost always, Reich says, “the idea that the ancestors of any one population have lived in the same place for tens of thousands of years with no substantial immigration is wrong.” Back in Sumte in the fall of 2015, the 750 refugees from Syria arrived on schedule. The adults mostly kept to themselves, learning German and taking occasional construction jobs. But their children sang “O Tannenbaum” in a local church at Christmas and their teens ventured out often, seeking cellphone signals in the quiet town. In the following months, almost all the refugees dispersed to larger towns throughout Germany. In time, some of the young immigrants will contribute their DNA to the next generation of Germans, re-enacting on a small scale the process of migration and assimilation that once played out repeatedly on this same land—and far beyond.


News Article | May 26, 2017
Site: www.eurekalert.org

Scientists have discovered a genetic variant that enables an isolated Greek population to live long and healthy lives despite having an animal fatty diet A genetic variant that protects the heart against cardiovascular disease has been discovered by researchers at the Wellcome Trust Sanger Institute and their collaborators. Reported today (26th May 2017) in Nature Communications, the cardioprotective variant was found in an isolated Greek population, who are known to live long and healthy lives despite having a diet rich in animal fat. In Mylopotamos, northern Crete the population are unusual as they have a diet that is rich in animal fat and should cause health complications, yet they have good health and live to an old age. In an attempt to solve the puzzle, scientists made a genetic portrait of the population by sequencing the entire genome of 250 individuals to get an in-depth view. This was the first time Mylopotamos villagers had their whole genome sequenced. The team then used the results to give a more detailed view of approximately 3,200 people for whom previous genetic information was known. Scientists discovered a new genetic variant that was not previously known to have cardioprotective qualities. The variant, rs145556679*, was associated with lower levels of both 'bad' natural fats - triglycerides - and 'bad' cholesterol - very low density lipoprotein cholesterol (VLDL). These factors lower the risk of cardiovascular disease. The cardioprotective variant may be almost unique to the Mylopotamos population. The genome sequencing results of a few thousand Europeans has only revealed one copy of this variant in a single individual in Tuscany, Italy. A separate variant in the same gene has also been found to be associated with lower levels of triglycerides in the Amish founder population in the United States. Lorraine Southam, joint first author from the Wellcome Trust Sanger Institute, said: "By studying isolated populations, we are able to identify those genetic variants that are at a higher frequency compared to cosmopolitan populations and this in turn increases our power to detect if these variants are disease causing. With isolated populations, we can get a unique view into rare genetic variants that play important roles in complex human diseases." The combination of genetic data from isolated populations presented statistical complications due to the relatedness of individuals. In this study, scientists designed new software called METACARPA to address these statistical challenges. Arthur Gilly, joint first author from the Wellcome Trust Sanger Institute, said: "METACARPA was specifically designed to work well on shared data. This new software is able to utilise summary data to detect relatedness of individuals or even overlap of data sets and account for it, therefore making the study more robust." The team also studied an isolated population from mountainous villages in the Pomak region of northern Greece. Scientists studied the genetics of 1700 people in the population. They discovered four separate genetic variants that affect diastolic blood pressure, fasting glucose levels, white blood cell count and haemoglobin levels. Lead author, Professor Eleftheria Zeggini from the Wellcome Trust Sanger Institute said: "This study shows the importance of looking at the entire genome to better understand the genetic architecture of a population. We are finding new genetic variants we haven't seen before. We have discovered a medically relevant genetic variant for traits related to cardiovascular disease, the most common cause of death worldwide." *Genetic variant, rs145556679 rs145556679 resides within an intron of the Down syndrome cell adhesion molecule like 1 (DSCAML1) gene, which is involved in cell adhesion in neuronal processes and is expressed in heart, liver, pancreas, skeletal muscle, kidney and brain. This new genetic variant adds to the growing list of cardioprotective variants found in this isolated population. http://www. METACARPA METACARPA is a tool that performs scalable meta-analysis between genetic association studies, both effect-size based and p-value based, while correcting for unknown sample overlap. http://www. Funding: This work was supported by Wellcome and the European Research Council. The Wellcome Trust Sanger Institute is one of the world's leading genome centres. Through its ability to conduct research at scale, it is able to engage in bold and long-term exploratory projects that are designed to influence and empower medical science globally. Institute research findings, generated through its own research programmes and through its leading role in international consortia, are being used to develop new diagnostics and treatments for human disease. http://www. Wellcome exists to improve health for everyone by helping great ideas to thrive. We're a global charitable foundation, both politically and financially independent. We support scientists and researchers, take on big problems, fuel imaginations and spark debate. http://www.


News Article | April 17, 2017
Site: www.newscientist.com

Up to a fifth of women with breast cancer may benefit from drugs that are currently reserved for less common cases of the disease, caused by faulty genes. A study by Serena Nik-Zainal, at the Sanger Institute in Cambridgeshire, UK, and her team found that thousands of breast cancers share biochemical similarities to cases caused by BRCA1 and BRCA2 mutations. Faulty BRCA genes are thought to account for between 1 and 5 per cent of the 55,000 cases of breast cancer diagnosed in the UK each year. A type of drug called PARP inhibitors can be used to treat these cancers, and were specifically designed to target tumours with defects in these genes. But Nik-Zainal’s findings suggest 8,000 more people with breast cancer may also respond to these drugs. “Our study shows that there are many more people who have cancers that look like they have the same weaknesses as patients with faulty BRCA1 and BRCA2 genes,” says Nik-Zainal. The team made this discovery by analysing the biochemical pathways in breast cancer tissue samples from 560 people. Of these, 22 had been diagnosed with BRCA mutations and 55 had previously undiagnosed BRCA mutations. A further 47 people had BRCA genes with no recognised mutations, but the repair mechanisms usually controlled by these genes were still faulty. “It’s possible there are other ways of turning off BRCA1 and 2 that we don’t understand, perhaps involving other genes,” says Nik-Zainal. PARP inhibitors block the action of an enzyme that helps cancer cells with faulty BRCA genes to survive. Because they specifically target cancer cells, they have relatively few side effects. “A lot of people who could be getting these treatments are not being offered them,” says Nik-Zainal. “Further investigation is needed to fully understand the clinical implications of these findings for future patients,” said Delyth Morgan, of the charity Breast Cancer Now. “But this study firmly opens the door for trials to assess whether up to one in five patients might benefit from PARP inhibitors.” Read more: Counting genetic mutations predicts how soon you’ll get cancer


News Article | March 23, 2016
Site: www.nature.com

The data on TP53 mutations (including allele frequency) and CNVs in pan-tumours and AML are derived from The Cancer Genome Atlas (TCGA) data in the cBioPortal for Cancer Genomics (http://www.cbioportal.org/; accessed on 29 October 2014). Only sequenced samples with allele frequency information provided were included in our analysis. Considering potential normal tissue contamination, samples with TP53 mutation allele frequency above 0.6 were considered as a homozygous mutation. The SNP data were visualized in IGV and statistics for AML outcome were analysed in Prism 6. Since cBioPortal only has a few non-Hodgkin lymphoma cases available, we used published data to extract TP53 mutation and deletion information18, 30, 31, 32, 33, 34. Clinical outcomes were annotated from follow-up data available within the Gene Expression Omnibus GSE34171 series. CNV analysis was performed using published AML and DLBCL tumour copy number data in Affymetrix SNP Array 6.0 .cel format (http://cancergenome.nih.gov/)18, 35, 36, 37 according to GISTIC2.0 (ref. 14). Specifically, the following GISTIC parameters and values were used following the latest TCGA Copy Number Portal analysis version (3 November 2014 stddata__2014_10_17; http://www.broadinstitute.org/tcga/gistic/browseGisticByTissue): core GISTIC version 2.0.22; reference genome build hg19; amplification threshold 0.1; deletion threshold 0.1; high-level amplification threshold 1.0; high-level deletion threshold 1.0; broad length cut-off 0.50; peak confidence level 0.95; cap 1.5; gene-GISTIC, true; arm-level peel-off, true; significance threshold 0.25; join segment size 8; X chromosome removed, false; maximum segments per sample 2,000; minimum samples per disease 40. To create a conditional 11B3 chromosome deletion, the MICER strategy was used15. Briefly, MICER clones MHPN91j22 (centromeric to Sco1) and MHPP248j19 (telomeric to Alox12) (Sanger Institute) were introduced into AB2.2 ES cells (129S5 strain, Sanger Institute) by sequential electroporation, followed by G418 (neomycin; 180 μg ml−1) and puromycin (1 μg ml−1) selection, respectively. Successful recombination events were confirmed by Southern blotting using the hybridized probes designated in Supplementary Table 2 as described38. The cis- and trans-localizations of two loxP sites in doubly targeted ES cells were further distinguished by PCR with df-F and df-R, or dp-F and dp-R (Supplementary Table 2), respectively, after Adeno-cre infection and HAT (Gibco) selection. Correct cis-ES clones in which two loxP sites were integrated into the same allele were used to generate chimaera mice by blastocyst injection. The F1 pups were genotyped with 11B3-F and 11B3-R primers (Supplementary Table 2) and those positive backcrossed to C57BL/6 mouse strains for more than 10 generations. All of the mouse experiments were approved by the Institutional Animal Care and Use Committee at the Memorial Sloan Kettering Cancer Center. Eμ-Myc, Vav1-cre, Ella-cre, Trp53LSL-R270H/+, Trp53LSL-R72H/+, Trp53+/−, Trp53fl/+ and Rag1−/− mice were ordered from Jackson Laboratories21, 39, 40, 41, 42, 43, 44 and the Arf+/− mouse strain is a gift from C. Sherr45. Eμ-Myc mice with different Trp53 alterations were monitored weekly with disease state being defined by palpable enlarged solid lymph nodes and/or paralysis. Tumour monitoring was done as blinded experiments. For lymphoma generated by transplantation, 1 million Eμ-Myc HPSCs from embryonic day (E)13.5 fetal liver or autoMACS-purified B220+ B progenitor cells isolated from 6–8-week mouse bone marrow were transduced with retroviruses, followed by tail-vein injection into sublethally irradiated (6 Gy, Cs137) C57BL/6 mice (Taconic; 6–8-week old, female, 5–10 mice per cohort)11, 46. All recipient mice were randomly divided into subgroups before transplantation and monitored as described earlier. The generation of AML proceeded as previously reported29. Briefly, retrovirally infected c-Kit+ haematopoietic stem and progenitor cells were transplanted into sublethally irradiated (6 Gy, Cs137) C57BL/6 mice, followed by routine monitoring of peripheral blood cell counts and Giemsa–Wright blood smear staining. For secondary transplantation experiments, 1 million leukaemia cells were transplanted into sublethally irradiated (4.5 Gy) mice. The immunophenotypes of resulting lymphomas and leukaemias were determined by flow cytometry as previously reported using antibodies purchased from eBioscience11, 29. Statistical analysis of all survival data was carried out using the log-rank test from Prism 6. No statistical methods were used to predetermine sample size. MSCV-Myc-IRES-GFP and MLS-based retroviral constructs harbouring a GFP or mCherry fluorescent reporter and targeting Ren, Trp53, Eif5a, Nf1 or Mll3 have all been reported before11, 29, 47. For the tandem shRNA experiments performed in Fig. 3, mirE-based shRNAs targeting two different genes were cloned into an MLS-based vector in an analogous fashion to what has been previously described48, 49. Retrovirus packaging and infection of HSPCs was done as previously reported11, 29. B220+ cells were isolated from the bone marrow of 6-week-old Eμ-Myc mice by autoMACS positive selection with anti-B220 microbeads (Militeny Biotech). After overnight culture, cells were infected with retroviruses carrying the indicated shRNAs. Two days after infection, 0.5 × 106 cells were washed with PBS followed by annexin V buffer (10 mM HEPES, 140 mM NaCl, 25 mM CaCl , pH 7.4), and incubated at room temperature with Pacific Blue annexin V (BD Biosciences) and propridium iodide (PI; 1 μg ml−1; Sigma-Aldrich) for 15 min and analysed on a LSR II flow cytometer (BD Biosciences). For arachidonic acid treatment, pre-B cells were cultured out from bone marrow cells in pre-B cell medium (RPMI1640, 10% FBS, 1% penicillin/streptomycin, 50 μM β-mercaptoethanol, 3 ng ml−1 IL-7). After 3 days culture, pre-B cells were treated with a series concentration of arachidonic acid (Cayman Chemical) for 20 h, followed by annexin V staining as described earlier. Lymphoma cells isolated from lymph nodes of diseased animals were treated with vehicle (PBS) or 1 μg ml−1 adriamycin for 4 h. Whole cell lysates were extracted in cell lysis buffer (Cell Signaling Technology) supplemented with protease inhibitors (Roche), followed by SDS–PAGE gel electrophoresis and blotting onto PVDF membranes (Millipore). Eμ-Myc;Arf−/− lymphoma cell lines were used as a positive control for p53 induction. The p53 antibody used was obtained from Novocastra (NCL-p53-505) and horseradish peroxidase (HRP)-conjugated β-actin antibody from Sigma (AC-15). Alox15b expressions were examined in NIH3T3 cells, which were infected by shRNAs targeting Ren or Alox15b and then selected by G418. Anti-Alox15b antibody is from Sigma (SAB2100110), and HRP-conjugated GAPDH antibody is from ThermoFisher Scientific (MA5-15738-HRP). RNA-seq and data analysis were performed by the Integrated Genomic and Bioinformatics core at the Memorial Sloan Kettering Cancer Center. Briefly, total RNA from 11B3fl/Trp53fl;shNf1;shMll3;Vav1-cre or Trp53fl/fl;shNf1;shMll3;Vav1-cre leukaemia cells (four lines per cohort), isolated from the bone marrow of moribund mice, was isolated by Trizol extraction (Life Technologies). After ribogreen quantification (Life Technologies) and quality control on an Agilent BioAnalyzer, 500 ng of total RNA (RNA integrity number > 8) underwent polyA selection and Truseq library preparation according to instructions provided by Illumina (TruSeq RNA Sample Prep Kit v.2) with 6 cycles of PCR. Samples were barcoded and run on a Hiseq 2500 in a 50 bp/50 bp paired-end run, using the TruSeq SBS Kit v.3 (Illumina). An average of 45 million paired reads were generated per sample. At the most the ribosomal reads represented 0.1% and the percentage of mRNA bases was close to 65% on average. The output from the sequencers (FASTQ files) was mapped to the mouse genome (mm9) using the rnaStar (https://code.google.com/p/rna-star/) aligner, with the two-pass mapping methods. After mapping, the expression counts of each individual gene were computed using HTSeq (http://www-huber.embl.de/users/anders/HTSeq), followed by normalization and differential expression analysis among samples using the R/Bioconductor package DESeq (http://www-huber.embl.de/users/anders/DESeq). Gene set enrichment analysis (GSEA) was performed with Broad’s GSEA algorithm. A list of all primers used for PCR analysis is given in Supplementary Table 2. For detection and quantification of 11B3 recombination/deletion two methods were employed. In both cases genomic DNA (gDNA) was extracted from lymphoma or leukaemia cells using Puregene DNA purification kit (Qiagen). Initially, semi-quantitative PCR was used to detect the recombined 11B3 allele using primers df-F and df-R, generating a 2.2 kb product (Fig. 2d). The estimated frequency of recombination was determined by dropping gDNA from 11B3+/− into 11B3fl/+ at various ratios. For qPCR of the 11B3 deletion (Fig. 2e), SYBR Green PCR Master Mix (Applied Biosystems) was used and cycling and analysis was carried out on a ViiA 7 (Applied Biosystems). Primers 11B3-Q-F and 11B3-Q-R were used to detect the floxed allele, and to estimate the frequency of 11B3 deletion. Allelic frequency in UPD analysis (Extended Data Fig. 5a) was determined similarly, in this case with serial dilution of wild-type gDNA into DNase-free water to construct a standard curve. Two-tailed t-test is used for statistics analysis by Prism 6. For p21 gene expression examination by RT–qPCR, RNA was isolated with Trizol, cDNA was synthesized with SuperScript III First-Strand Synthesis System (Life Technologies) and qPCR was performed as described earlier with primers p21-Q-F and p21-Q-R. Trp53 exons (2–10) were amplified from genomic DNAs of 11B3-deleted lymphomas by PCR (see Supplementary Table 2 for primer sequences) and subjected to Sanger sequencing. Mutations were called only if detected in sequencing reads carried out in the forward and reverse direction. SNP analysis of isolated lymphoma (tumour) or tail (normal) genomic DNAs from the same tumour-bearing mouse were carried out by Charles River laboratory. Briefly, a SNP Taqman assay with competing FAM- or VIC-labelled probes was used to detect the relevant C57BL/6 and 129S SNPs (D11Mit4 and D11NDS16) as described previously50. Genomic DNA was extracted from freshly isolated lymphoma cells from one Eμ-Myc;11B3fl/+;Vav-cre mice. One microgram of DNA was sonicated (17 W, 75 s) on an E220 sonicator (Covaris). Samples were subsequently prepared using standard Illumina library preparation (end repair, poly A addition, and adaptor ligation). Libraries were purified using AMPure XP magnetic beads (Beckman Coulter), PCR enriched, and sequenced on an Illumina HiSeq instrument in a multiplexed format. Sequencing reads per sample were mapped using Bowtie with PCR duplicates removed. Approximately 2.5 million uniquely mappable reads were further processed for copy number determination using the ‘varbin’ algorithm51, 52 with 5,000 bins, allowing for a median resolution of ~600 kb. GC content normalization, segmentation and copy number estimation was calculated as described53. A custom shRNA library was designed to target mouse homologues (six shRNAs for one gene) to all human protein-coding genes on chromosome 17p13.1 from ALOX12 to SCO1, except TP53 and EIF5A. shRNAs were cloned into a retrovirus-based vector MLS by pool-specific PCR as previously described11. Eμ-Myc HSPCs infected with pooled shRNAs were transplanted into sublethally irradiated recipient mice. Resulting tumours were harvested, and used to extract contained shRNAs, followed by HiSeq in HiSeq 2500 (Illumina). Twenty-two oligonucleotides of shRNAs used in this study are listed in Supplementary Table 3. Total lipids were extracted using Folch’s method54 and analysed by LC-MS as previously described55. Briefly, freshly harvested cells were homogenized by chloroform/methanol (2:1, v-v). After being washed by water, the lipid-containing chloroform phase is evaporated. Dried lipids were dissolved in 100 μl 95% acetonitrile (in H O), sonicated for 3–5 min, and spiked with 10 μl of 500 ng ml−1 deuterated internal standard solution (IS; arachidonic acid-d8; Cayman Chemical, 390010). Then, 5 μl samples were injected into Acquity ultra performance liquid chromatography (UPLC) system (Waters), equipped with Acquity UPLC BEH C18 column (100 mm × 2.1 mm I.D., 1.7 μm; Waters). Samples were washed through the column with a gradient 0.1% formic acid: acetonitrile mobile elution from 35:65 (v:v) to 5:95 for 10 min. Flow rate was 0.25 ml min−1. Right after HPLC, samples were analysed in a Quattro Premier EX triple quadrupole mass spectrometer (Waters), which has electrospray negative mode and MasslynxV4.1 software. For each run, a standard curve was generated with different concentration of arachidonic acid lipid maps MS standard (Cayman Chemical, 10007268) mixed with IS (50 ng ml−1 final concentration). Arachidonic acid standard m/z is 303.2, and IS is 311.3. Three Eμ-Myc lymphoma cell lines generated from Trp53fl/+;Vav1-cre or 11B3fl/+;Vav1-cre tumour-bearing mice were cultured in BCM medium (45% DMEM, 45% IMDM, 10% FBS, 2 mM glutamine, 50 μM β- mercaptoethanol, 1× penicillin/streptomycin) in 96-well plates. Cells were treated with the indicated concentrations of 4-hydroxycyclophosphamide (Toronto Research Chemicals) or vincristine (Bedford Laboratories) for 3 days. The number of living cells was determined by PI staining and cell counting on a Guava EasyCyte (EMD Millipore). Leukaemia cell lines from Trp53∆/∆ or 11B3∆/Trp53∆;shNf1;shMll3 mice were treated with cytarabine (araC; Bedford Laboratories) or JQ1 (a gift from J. Bradner) in stem cell medium (BCM medium supplemented with 1 ng ml−1 IL-3, 4 ng ml−1 IL-6 and 10 ng ml−1 SCF) and cell viability after 3 days was determined similarly. All cytokines are from Invitrogen.


News Article | February 15, 2017
Site: www.eurekalert.org

A team at the Wellcome Trust Sanger Institute has discovered how a promising malarial vaccine target - the protein RH5 - helps parasites to invade human red blood cells. Published today in Nature Communications, the study reveals that a previously mysterious protein on the surface of the parasite called P113 anchors the RH5 protein, and provides a molecular bridge between the parasite and a red blood cell. The discovery could be used to make a more effective malaria vaccine. More than 200 million people a year are infected with malaria and the disease caused the deaths of nearly half a million people worldwide in 2015. Children under the age of five made up 70 percent of these deaths. Malaria is caused by Plasmodium parasites which are spread by infected mosquitos and an effective vaccine would vastly improve the lives of millions of people. Previous research by teams at the Sanger Institute discovered that to invade human red blood cells, Plasmodium parasites need RH5 to bind to a receptor called basigin on the surface of the blood cells. However, it was not known how RH5 was attached to the surface of the parasite. In this latest study the researchers discovered that when the Plasmodium RH5 protein is released, it is immediately caught by another parasite protein called P113. Thousands of P113 molecules on the surface of each parasite act like a Velcro chain, capturing RH5 at the surface of the parasite. The tethered RH5 then binds to the basigin receptor on the human red blood cell, bridging the gap just long enough to let the parasite invade the blood cell. Dr Julian Rayner, an author on the study from the Sanger Institute, said: "We knew both proteins were essential for invasion but this is the first time anyone has seen the interaction between RH5 and P113 and showed that they work together. In theory, an antibody that blocked P113 could stop RH5 binding and so prevent the parasite from gaining entry to red blood cells. This makes the P113 protein another good vaccine target." Two more proteins - CyRPA and RIPR - were already known to be essential to the parasite and to form a complex with RH5. The researchers uncovered the details of how these three proteins bound to each other* and that only one small part of the RH5 protein was needed to bind P113. This small region could become an easy-to-produce and cost-effective part of a multi-component malaria vaccine. Dr Francis Galway, first author on the study from the Sanger Institute, added: "RH5 is an excellent vaccine target because it is essential for invasion by all strains of Plasmodium falciparum - the species of parasite that causes the most severe disease in humans. This study shows us the binding partners for the RH5 protein and how these work together to allow the parasite to enter red blood cells. This gives us important information about this vaccine target." Dr Gavin Wright, lead author from the Sanger Institute, said: "There is a great need for an effective malaria vaccine, and the RH5 complex is the most important link between parasite and host that we yet know of. This study shows us how this works, and reveals other essential malarial proteins to target. As RH5 is only exposed from the parasite briefly, a combination vaccine based on P113, RH5 and other proteins in the complex could be more effective than RH5 alone." For more information about malaria please see: http://www. For more information about developing malaria vaccines please see: http://www. * A pair of proteins, CyRPA and RIPR, were already known to be essential to the parasite and form a complex with RH5. This study found that CyPRA bound to the RH5 C-terminal region, and that RIPR bound to CyPRA. The Wellcome Trust Sanger Institute is one of the world's leading genome centres. Through its ability to conduct research at scale, it is able to engage in bold and long-term exploratory projects that are designed to influence and empower medical science globally. Institute research findings, generated through its own research programmes and through its leading role in international consortia, are being used to develop new diagnostics and treatments for human disease. http://www. Wellcome exists to improve health for everyone by helping great ideas to thrive. We're a global charitable foundation, both politically and financially independent. We support scientists and researchers, take on big problems, fuel imaginations and spark debate. http://www.


News Article | October 27, 2016
Site: www.eurekalert.org

For the first time, scientists have revealed ancient gene mixing between chimpanzees and bonobos, mankind's closest relatives, showing parallels with Neanderthal mixing in human ancestry. Published today in the journal Science, the study from scientists at the Wellcome Trust Sanger Institute and their international collaborators showed that 1% of chimpanzee genomes are derived from bonobos. The study also showed that genomics could help reveal the country of origin of individual chimpanzees, which has strong implications for chimpanzee conservation. Chimpanzees and bonobos are great apes found only in tropical Africa. They are endangered species and are supposedly fully protected by law, yet many chimpanzees and bonobos are captured and held illegally. To aid the conservation effort, researchers analysed the whole genome sequences of 75 chimpanzees and bonobos, from 10 African countries, and crucially included 40 new wild-born chimpanzees from known geographic locations. They discovered that there was a strong link between the genetic sequence of a chimpanzee, and their geographic origin. Dr Chris Tyler Smith, from the Wellcome Trust Sanger Institute, said: "This is the largest analysis of chimpanzee genomes to date and shows that genetics can be used to locate quite precisely where in the wild a chimpanzee comes from. This can aid the release of illegally captured chimpanzees back into the right place in the wild and provide key evidence for action against the captors." Chimpanzees and bonobos are the closest living relatives of human beings. They diverged from a common ancestor between 1.5 and 2 million years ago and live in different areas of tropical Africa. Until now, it was thought that gene flow between the species would have been impossible, as they were physically separated by the Congo River. The study confirmed a main separation between chimpanzees and bonobos approximately 1.5 million years ago, and the presence of four chimpanzee subspecies in different regions. However, the researchers also found there were two additional gene flow events between the chimpanzee and bonobo populations, indicating that at least some individuals found their way across the river. Dr Yali Xue, from the Sanger Institute, said: "We found that central and eastern chimpanzees share significantly more genetic material with bonobos than the other chimpanzee subspecies. These chimpanzees have at least 1% of their genomes derived from bonobos. This shows that there wasn't a clean separation, but that the initial divergence was followed by occasional episodes of mixing between the species. The study also included researchers from Spain, Copenhagen Zoo and the University of Cambridge and showed that there have been at least two phases of secondary contact, 200-550 thousand years ago and around 150 thousand years ago, mirroring what is believed to have happened during the last 100 thousand years of the evolution of humans. Dr Tomàs Marquès-Bonet, leader of the study from the Institute of Biological Evolution (University Pompeu Fabra and CSIC), Barcelona, said: "This is the first study to reveal that ancient gene flow events happened amongst the living species closest to humans - the bonobos and chimpanzees. It implies that successful breeding between close species might have been actually widespread in the ancestors of humans and living apes." The Institute of Evolutionary Biology (IBE) is a joint center between Pompeu Fabra University (UPF) and the Spanish National Research Council (CSIC), and was created in 2008 in Barcelona. IBE researchers study the processes and mechanisms that generate biodiversity, including fields like genetics and molecular evolution, population biology, biology of complex systems and the recovery of ancient DNA. https:/ The Wellcome Trust Sanger Institute is one of the world's leading genome centres. Through its ability to conduct research at scale, it is able to engage in bold and long-term exploratory projects that are designed to influence and empower medical science globally. Institute research findings, generated through its own research programmes and through its leading role in international consortia, are being used to develop new diagnostics and treatments for human disease. http://www. Wellcome exists to improve health for everyone by helping great ideas to thrive. We're a global charitable foundation, both politically and financially independent. We support scientists and researchers, take on big problems, fuel imaginations and spark debate. http://www.


News Article | November 10, 2016
Site: news.yahoo.com

LONDON (Reuters) - A multidrug-resistant superbug infection that can cause life-threatening illness in people with cystic fibrosis (CF) has spread globally and is becoming increasingly virulent, British researchers said on Thursday. In a study published in the journal Science, the researchers said the bug, a species of multidrug-resistant bacteria called Mycobacterium abscessus (M. abscessus), can cause severe pneumonia and is particularly dangerous for patients with CF and other lung diseases. "The bug initially seems to have entered the patient population from the environment, but we think it has recently evolved to become capable of jumping from patient to patient, getting more virulent as it does so," said Andres Floto, a Cambridge University professor who co-led the study. Cystic fibrosis is a relatively rare genetic disorder that affects the respiratory, digestive and reproductive systems. It causes patients' lungs to become clogged up with thick, sticky mucus and makes them vulnerable to respiratory infections. In this study, researchers from Cambridge and the Wellcome Trust Sanger Institute sequenced the genomes of more than 1,000 samples of mycobacteria from 517 CF patients at specialist clinics in Europe, the United States and Australia. They found that the majority of patients had picked up transmissible forms of M. abscessus that had spread globally. Further analysis suggested the infection may be transmitted within hospitals via contaminated surfaces and through the air, the researchers said - presenting a serious challenge to infection control practices in hospitals. Because the superbug has already become resistant to many antibiotics, it is also extremely difficult to treat successfully, Floto said. Patients infected with it need 18 months or more of treatment with a combination of powerful antibiotics, and fewer than one in three cases is cured. Julian Parkhill of the Sanger Institute, who worked on this study, said that while its findings were alarming for CF patients, they did also provide a degree of hope. "Now that we know the extent of the problem and are beginning to understand how the infection spreads, we can start to respond," he said. The sequencing data has thrown up potential new drug targets, he explained, and the researchers now plan to focus on seeking to develop new medicines to beat the bug.

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