No Escape

Biological safety lock for genetically modified organisms 

The creation of genetically modified and entirely synthetic organisms continues to generate excitement as well as worry.

Such organisms are already churning out insulin and other drug ingredients, helping produce biofuels, teaching scientists about human disease and improving fishing and agriculture. While the risks can be exaggerated to frightening effect, modified organisms do have the potential to upset natural ecosystems if they were to escape.

Physical containment isn’t enough. Lab dishes and industrial vats can break; workers can go home with inadvertently contaminated clothes. And some organisms are meant for use in open environments, such as mosquitoes that can’t spread malaria.

So attention turns to biocontainment: building in biological safeguards to prevent modified organisms from surviving where they’re not meant to. To do so, geneticists and synthetic biologists find themselves taking a cue from safety engineers.

“If you make a chemical that’s potentially explosive, you put stabilizers in it. If you build a car, you put in seat belts and airbags,” said George Church, Robert Winthrop Professor of Genetics at Harvard Medical School and core faculty member at the Wyss Institute.

And if you’ve created the world’s first genomically recoded organism, a strain of Escherichia coli with a radically changed genome, as Church’s group announced in 2013, you make its life dependent on something only you can supply.

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Church and colleagues report Jan. 21 in Nature that they further modified their 2013 E. coli to incorporate a synthetic amino acid in many places throughout their genomes. Without this amino acid, the bacteria can’t perform the vital job of translating their RNA into properly folded proteins.

The E. coli can’t make this unnatural amino acid themselves or find it anywhere in the wild; they have to eat it in specially cooked-up lab cultures.

A separate team reports in Nature that it was able to engineer the same strain of E. coli to become dependent on a synthetic amino acid using different methods. That group was led by a longtime collaborator of Church’s, Farren Isaacs of Yale University.

The two studies are the first to use synthetic nutrient dependency as a biocontainment strategy, and suggest that it might be useful for making genetically modified organisms safer in an open environment.

In addition, “We now have the first example of genome-scale engineering rather than gene editing or genome copying,” said Church. “This is the most radically altered genome to date in terms of genome function. We have not only a new code, but also a new amino acid, and the organism is totally dependent on it.”

Church’s team, led by first authors Dan Mandell and Marc Lajoie, HMS research fellows in genetics, also made the E. coli resistant to two viruses, with plans to expand that list.

The modifications offer theoretically safer E. coli strains that could be used in biotechnology applications with less fear that they will be contaminated by viruses, which can be financially disastrous, or cause ecological trouble if they spill. (E. coli is one of the main organisms used in industry.)

Hooked on amino acids

Scientists have been exploring two main biocontainment methods, but each has weaknesses. Church was determined to fix them.

One method involves turning normally self-sufficient organisms like E. coli into auxotrophs, which can’t make certain nutrients they need for growth. Humans are auxotrophs, which is why we need to include vitamins and other “essential” nutrients in our diets.

Altering the genetics of E. coli so they can’t make a naturally occurring nutrient doesn’t always work, said Church, because some of them manage to scavenge the nutrient from their surroundings. He lowered that risk by making the E. coli dependent on a nutrient not found in nature.

Another pitfall of making auxotrophs is that some E. coli could evolve a way to synthesize the nutrient they need. Or they could acquire the ability while exchanging bits of DNA with other E. coli in a process called horizontal gene transfer.

Church believes his team protected against those possibilities because it had to make 49 genetic changes to the E. coli to make them dependent on the artificial nutrient. The chance one of the bacteria could randomly undo all of those changes without also acquiring a harmful mutation, he said, is incredibly slim.

Church’s solution also took care of concerns he had with another biocontainment technique, in which genetic “kill switches” make bacteria vulnerable to a toxin so spills can be quickly neutralized. “All you have to do to kill a kill switch is turn it off,” which can be done in any number of ways, Church said. Routing around the dependency on the artificial amino acid is much harder.

Church determined that another key to making a successful “synthetic auxotroph” was to ensure that the E. coli’s lives depended on the artificial amino acid. Otherwise, escaped E. coli could keep rolling along even if they couldn’t make or scavenge it. So his group targeted proteins that drive the essential functions of the cell.

“If you put it off on the periphery, like on the paint job of your car, the car will still run,” he explained. “You have to embed the dependency smack in the middle of the engine, like the crank shaft, so it now has a particular part you can only get from, say, one manufacturer in Europe.”

Building a safer bacterium

The need to choose a process essential to E. coli survival and a nutrient not found in nature “limited us to a small number of genes,” Church said. His team used computational tools to design proteins that might cause the desired “irreversible, inescapable dependency.” They took the best candidates, synthesized them and tested them in actual E. coli.

They ended up with three successful redesigned essential proteins and two dependent E. coli strains. “Using three proteins together is more powerful than using them separately,” Church said. He envisions future E. coli modified to require even more synthetic amino acids to make escape virtually impossible.

As it was, the escape rate—the number of E. coli able to survive without being fed the synthetic amino acid—was “so low we couldn’t detect it,” Church said.

The group grew a total of 1 trillion E. coli cells from various experiments, and after two weeks none had escaped. “That’s 10,000 times better than the National Institutes of Health’s recommendation for escape rate for genetically modified organisms,” said Church.

The weaknesses in Church’s methods remain to be seen. For now, he is satisfied with the results his group has obtained by pushing the limits of available testing.

“As part of our dedication to safety engineering in biology, we’re trying to get better at creating physically contained test systems to develop something that eventually will be so biologically contained that we won’t need physical containment anymore,” said Church.

In the meantime, he said, “we can use the physical containment to debug it and make sure it actually works.”

This work was funded by the U.S. Department of Energy (grant DE-FG02-02ER63445).


Gene-Editing Guide

New method identifies genome-wide off-target effects of CRISPR-Cas

Harvard Medical School investigators at Massachusetts General Hospital have developed a method for detecting unwanted DNA breaks—across the entire genome of human cells—induced by the popular gene-editing tools called CRISPR-Cas RNA-guided nucleases (RGNs). 

Members of the same team that first described these off-target effects in human cells describe their new platform, called GUIDE-seq (Genome-wide Unbiased Identification of Double-stranded breaks Evaluated by Sequencing) in a report published in Nature Biotechnology.

“GUIDE-seq is the first genome-wide method of sensitively detecting off-target DNA breaks induced by CRISPR-Cas nucleases that does not start with the assumption that these off-target sites resemble the targeted sites,” said J. Keith Joung, HMS associate professor of pathology at Mass General and senior author of the paper. “This capability, which did not exist before, is critically important for the evaluation of any clinical use of CRISPR-Cas RNA-guided nucleases.”

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Used to cut through a double strand of DNA in order to introduce genetic changes, CRISPR-Cas RNA-guided nucleases combine a bacterial gene-cutting enzyme called Cas9 with a short RNA segment that matches and binds to the target DNA sequence. In a 2013 Nature Biotechnology paper, Joung and his colleagues reported finding that CRISPR-Cas RNA-guided nucleases could also induce double-strand breaks at sites with significant differences from the target site, including mismatches of as many as five nucleotides. 

Because such off-target mutations could potentially lead to adverse effects, including cancer, the ability to identify and eventually minimize unwanted double-strand breaks would be essential to the safe clinical use of these RNA-guided nucleases, the authors noted.

The method they developed involves using short, double-stranded oligonucleotides that are taken up by double-strand breaks in a cell’s DNA, acting as markers of off-target breaks caused by the use of CRISPR-Cas. Those tags allow the identification and subsequent sequencing of those genomic regions, pinpointing the location of off-target mutations. 

Experiments with GUIDE-seq showed it was sensitive enough to detect off-target sites at which CRISPR RNA-guided nucleases induced unwanted mutations of a gene that occur with a frequency of as little as 0.1 percent in a population of cells. These experiments also revealed that no easy rules would predict the number or location of off-target double-strand breaks, since many such mutations took place at sites quite dissimilar from the targeted site. 

Two existing tools, designed to predict off-target mutations by analysis of the target sequence, were much less effective than GUIDE-seq in predicting confirmed off-target sites and also misidentified sites that did not prove to have been cut by the enzyme. Comparing GUIDE-seq with a tool called ChIP-seq, which identifies sites where proteins bind to a DNA strand, confirmed that ChIP-seq does not provide a robust method for identifying CRISPR-Cas-induced double-strand breaks.

GUIDE-seq was also able to identify breakpoint hotspots in control cell lines that were not induced to express the CRISPR RNA-guided nucleases. 

“Various papers have described fragile genomic sites in human cells before,” Joung noted, “but this method may be the first to identify these sites without the addition of drugs that enhance the occurrence of such breaks. We also were surprised to find those breaks occurred largely at different sites in the two cell lines used in this study. The ability to capture these RNA-guided nuclease-independent breaks suggests that GUIDE-seq could be a useful tool for studying and monitoring DNA repair in living cells.”

In addition, GUIDE-seq was able to verify that their approach for improving the accuracy of CRISPR-Cas by shortening the guiding RNA segment reduced the number of double-strand breaks throughout the genome. Joung also expects that GUIDE-seq will be useful in identifying off-target breaks induced by other gene-editing tools. 

Along with pursuing that possibility, Joung noted the importance of investigating the incidence and detection of off-target mutations in human cells not altered to create cell lines—a process that transforms them into immortalized cancer cells. Understanding the range and number of off-target mutations in untransformed cells will give a better picture of how CRISPR-Cas RNA-guided nucleases and other tools would function in clinical applications.

“The GUIDE-seq method is very straightforward to perform, and we intend to make the software for analyzing sequencing data available online to noncommercial researchers at in the near future,” adds Joung. 

A patent application covering the GUIDE-seq technology has been filed.

Support for the study includes National Institutes of Health (NIH) Director’s Pioneer Award DP1 GM105378; NIH grants R01 GM088040, R01 AR063070 and F32 GM105189; the Jim and Ann Orr Massachusetts General Hospital Research Scholar Award; and Defense Advanced Research Project Agency grant W911NF-11-2-0056.

Adapted from a Mass General news release.


Warning Signs

Two studies identify pre-cancerous state in the blood 

Image: bubaone/iStock

Researchers from the Broad Institute of MIT and Harvard, Harvard Medical School and Harvard-affiliated hospitals have uncovered an easily detectable, “pre-malignant” state in the blood that significantly increases the likelihood that a person will go on to develop blood cancers such as leukemia, lymphoma or myelodysplastic syndrome.

The discovery, which was made independently by two research teams affiliated with the Broad and partner institutions, opens new avenues for research into early detection and prevention of blood cancer. Findings from both teams appear this week in the New England Journal of Medicine.

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Most genetic research on cancer to date has focused on studying the genomes of advanced cancers, to identify the genes that are mutated in various cancer types. These two new studies instead looked at somatic mutations—mutations that cells acquire over time as they replicate and regenerate within the body—in DNA samples collected from the blood of people not known to have cancer or blood disorders. 

Taking two very different approaches, the teams found that a surprising percentage of those sampled had acquired a subset—some but not all—of the somatic mutations that are present in blood cancers. These people were more than ten times more likely to go on to develop blood cancer in subsequent years than those in whom such mutations were not detected.

The “pre-malignant” state identified by the studies becomes more common with age; it is rare in those under the age of 40, but appears with increasing frequency with each decade of life that passes, ultimately appearing in more than 10 percent of those over the age of 70.

Carriers of the mutations are at an overall 5 percent risk of developing some form of blood cancer within five years.

This “pre-malignant” stage can be detected simply by sequencing DNA from blood.

“People often think about disease in black and white—that there’s ‘healthy’ and there’s ‘disease’—but in reality most disease develops gradually over months or years. These findings give us a window on these early stages in the development of blood cancer,” said Steven McCarroll, senior author of one of the papers.

McCarroll is assistant professor of genetics at HMS and director of genetics at the Broad’s Stanley Center for Psychiatric Research.

Benjamin Ebert, HMS associate professor of medicine at Brigham and Women’s Hospital and an associate member of the Broad, is the senior author of the other paper.

The mutations identified by both studies are thought to originate in blood stem cells, and confer a growth-promoting advantage to the mutated cell and all of its “clones”—cells that derive from that original stem cell during the normal course of cell division. These cells then reproduce at an accelerated rate until they account for a large fraction of the cells in a person’s blood.

The researchers believe these early mutations lie in wait for follow-on, “cooperating” mutations that, when they occur in the same cells as the earlier mutations, drive the cells toward cancer. The majority of mutations occurred in just three genes; DNMT3A, TET2, and ASXL1.

“Cancer is the end stage of the process,” said Siddhartha Jaiswal, a Broad associated scientist and HMS clinical fellow at Massachusetts General Hospital who was first author of Ebert’s paper. “By the time a cancer has become clinically detectable it has accumulated several mutations that have evolved over many years. What we are primarily detecting here is an early, pre-malignant stage in which the cells have acquired just one initiating mutation.”

The teams converged on these findings through very different approaches.

Ebert’s team had hypothesized that, since blood cancers increase with age, it might be possible to detect early somatic mutations that could be initiating the disease process, and that these mutations also might increase with age. They looked specifically at 160 genes known to be recurrently mutated in blood malignancies, using genetic data derived from approximately 17,000 blood samples originally obtained for studies on the genetics of type 2 diabetes.

They found that somatic mutations in these genes did indeed increase the likelihood of developing cancer, and they saw a clear association between age and the frequency of these mutations. They also found that men were slightly more likely to have mutations than women, and Hispanics were slightly less likely to have mutations than other groups.

Ebert’s team also found an association between the presence of this “pre-malignant” state and the risk of overall mortality independent of cancer. People with these mutations had a higher risk of type 2 diabetes, coronary heart disease and ischemic stroke as well. Additional research will be needed to determine the nature of these associations.

McCarroll’s team discovered the phenomenon while studying a different disease. They, too, were looking at somatic mutations, but they were initially interested in determining whether such mutations contributed to risk for schizophrenia. The team studied roughly 12,000 DNA samples drawn from the blood of patients with schizophrenia and bipolar disorder, as well as healthy controls, searching across the whole genome at all of the protein-coding genes for patterns in somatic mutations.

They found that the somatic mutations were concentrated in a handful of genes. The scientists quickly realized they were cancer genes. The team then used electronic medical records to follow the patients’ subsequent medical histories, finding that the subjects with these acquired mutations had a 13-times elevated risk of blood cancer.

McCarroll’s team conducted follow-up analyses on tumor samples from two patients who had progressed from this pre-malignant state to cancer. These genomic analyses revealed that the cancer had indeed developed from the same cells that had harbored the “initiating” mutations years earlier.

“The fact that both teams converged on strikingly similar findings, using very different approaches and looking at DNA from very different sets of patients, has given us great confidence in the results,” said Giulio Genovese, a computational biologist at the Broad and first author of McCarroll’s paper. “It has been gratifying to have this corroboration of each other’s findings.”

Jaiswal will present the findings on Dec. 9 at the American Society of Hematology Annual Meeting in San Francisco.

All of the researchers involved emphasized that there is no clinical benefit today for testing for this pre-malignant state; there are no treatments currently available that would address this condition in otherwise healthy people. However, they say the results open the door to entirely new directions for blood cancer research, toward early detection and even prevention.

“The results demonstrate a way to identify high-risk cohorts—people who are at much higher than average risk of progressing to cancer—which could be a population for clinical trials of future prevention strategies,” McCarroll said. “The abundance of these mutated cells could also serve as a biomarker—like LDL cholesterol is for cardiovascular disease—to test the effects of potential prevention therapies in clinical trials.” 

Ebert agrees:

“A new focus of investigation will now be to develop interventions that might decrease the likelihood that individuals with these mutations will go on to develop overt malignancies, or therapeutic strategies to decrease mortality from other conditions that may be instigated by these mutations,” he said.

The researchers also say that the findings show just how important it is to collect and share large datasets of genetic information: Both studies relied on DNA samples collected for studies completely unrelated to cancer.

“These two papers are a great example of how unexpected and important discoveries can be made when creative scientists work together and with access to genomic and clinical data,” said Broad deputy director David Altshuler, HMS professor of genetics at Massachusetts General Hospital and one of Ebert’s co-authors.

“For example,” Altshuler said, “Steve’s team found stronger genetic relationships to cancer than they have yet found for the schizophrenia endpoint that motivated their original study. The pace of discovery can only accelerate if researchers have the ability to apply innovative methods to large datasets.”

McCarroll’s team was supported by the Stanley Center for Psychiatric Research, the National Human Genome Research Institute (NHGRI) and the National Institute of Mental Health (NIMH). Ebert’s team was funded by the National Institutes of Health (NIH), the Gabrielle’s Angel Foundation and the Leukemia and Lymphoma Society.

Genetic data for Ebert’s paper was collected with support from the NIH (T2D-GENES, Longevity Genes Project); the Medical Research Council and Wellcome Trust (Go-T2D); the Slim Initiative for Genomic Medicine in the Americas; and NHGRI and the National Heart, Lung, and Blood Institute and the National Institute on Minority Health and Health Disparities (Jackson Heart Study).

Adapted from a Broad Institute of MIT and Harvard news release.


Marching to Our Own Sequences

Study finds DNA replication timing varies among people

Steven McCarroll and Amnon Koren describe their surprising findings and how they made their discovery by tapping into an existing online database of genome sequencing data. Video: Rick Groleau and Stephanie Dutchen

Imagine being asked to copy a library of books. Doing it yourself would take forever. You’d probably call some friends and come up with a plan to divide and conquer.

That’s what a human cell does when faced with the task of replicating six billion letters of DNA each time it divides. Instead of reading each chromosome in one slow pass, DNA replication machinery dives in at many origin points. Some segments get copied earlier or later than others.

A new study from geneticists at Harvard Medical School and the Broad Institute of Harvard and MIT has found that this replication plan—including where the origin points are and in what order DNA segments get copied—varies from person to person.

The study, published online Nov. 13 in Cell, also identifies the first genetic variants that orchestrate replication timing.

“Everyone’s cells have a plan for copying the genome. The idea that we don’t all have the same plan is surprising and interesting,” said Steven McCarroll, assistant professor of genetics at HMS, director of genetics for the Stanley Center for Psychiatric Research at the Broad and senior author of the paper.

“It’s a new form of variation in people no one had expected,” said first author Amnon Koren, postdoctoral fellow at HMS and the Broad. “That’s very exciting.”

Hidden orchestrator

DNA replication is one of the most fundamental cellular processes, and any variation among people is likely to affect genetic inheritance, including individual disease risk as well as human evolution, the authors said.

It’s been known that replication timing affects mutation rates; DNA segments that are copied late or too early tend to have more errors. The new study indicates that people with different timing programs therefore have different patterns of mutation risk across their genomes.

For example, McCarroll’s team found that differences in replication timing could explain why some people are more prone than others to certain blood cancers.

Researchers had previously known that acquired mutations in the gene Janus kinase 2, or JAK2, lead to these cancers. They had also noticed that people with such JAK2 mutations tend to have a distinctive set of inherited genetic variants nearby, but they weren’t sure how the inherited variants and the new mutations were connected. McCarroll’s team found that the inherited variants are associated with an “unusually early” replication origin point and proposed that JAK2 is more likely to develop mutations in people with that very early origin point.

“Replication timing may be a way that inherited variation contributes to the risk of later mutations and diseases that we usually think of as arising by chance,” said McCarroll.

Untapped riches

McCarroll, Koren and colleagues were able to make these discoveries in large part because they invented a new way to obtain DNA replication timing data. Turned out, it was hiding in plain sight.

Until now, to study replication timing, scientists needed to painstakingly “grow cells for a couple of weeks and sort them with a special machine and do a big, complicated, expensive, time-consuming experiment”—all to obtain material from just a few people at a time, said Koren.

The team suspected there was an easier way. They turned to the 1000 Genomes Project, which maintains an online database of sequencing data collected from hundreds of people around the world.

Because much of the DNA in the 1000 Genomes Project had been extracted from actively dividing cells, the team hypothesized that information about replication timing lurked within.

They were right. They counted the number of copies of individual genes in each genome. Because early replication origins had created more segment copies at the time the sample was taken than late replication origins had, they were able to create a personalized replication timing map for each person.

“People had seen these patterns before, but just dismissed them as artifacts of sequencing technology,” said McCarroll. After conducting numerous tests to rule out that possibility, “we found that they reflect real biology.”

The researchers then compared each person’s copy number information with his or her genetic sequence data to see if they could match specific genetic variants to replication timing differences. From 161 samples, they identified 16 variants. The variants were short, and most were common.

“I think this is the first time we can pinpoint genetic influences on replication timing in any organism,” said Koren.

The variants were located near replication origin points, leading the team to wonder if they affect replication timing by altering where a person’s origin points are. They also suspect that the variants work by altering chromatin structure, exposing local sequences to replication machinery. The team intends to find out. They also want to search for additional variants that control replication timing.

“These 16 variants are almost certainly just the tip of the iceberg,” said Koren.

The door is open

As more variants come to light in future studies, researchers will be better able to manipulate replication timing in the lab and learn more about how it works and what its biological significance is.

Such studies should flourish now that the team has shown that “all you need to do to study replication timing is grow cells and sequence their DNA, which everyone is doing these days,” said Koren. The new method “is much easier, faster and cheaper, and I think it will transform the field because we can now do experiments in large scale.”

“We found that there is biological information in genome sequence data,” added McCarroll. “But this was still an accidental biological experiment. Now imagine the results when we and others actually design experiments to study this phenomenon.”

This research was funded by the National Human Genome Research Institute (R01 HG 006855), the Integra-Life Seventh Framework Programme (grant #315997), the Stanley Center for Psychiatric Research, the Howard Hughes Medical Institute and the Harvard Stem Cell Institute.


New Branch Added to European Family Tree

Genetic analysis reveals Europeans descended from at least three ancient groups

This skull of a 7,000-year-old German farmer was among the ancient human bones that revealed more about the genetic heritage of present-day Europeans. Image: Joanna Drath/University of Tübingen

The setting: Europe, about 7,500 years ago.

Agriculture was sweeping in from the Near East, bringing early farmers into contact with hunter-gatherers who had already been living in Europe for tens of thousands of years.

Genetic and archaeological research in the last 10 years has revealed that almost all present-day Europeans descend from the mixing of these two ancient populations. But it turns out that’s not the full story.

Researchers at Harvard Medical School and the University of Tübingen in Germany have now documented a genetic contribution from a third ancestor: Ancient North Eurasians. This group appears to have contributed DNA to present-day Europeans as well as to the people who travelled across the Bering Strait into the Americas more than 15,000 years ago.

“Prior to this paper, the models we had for European ancestry were two-way mixtures. We show that there are three groups,” said David Reich, professor of genetics at HMS and co-senior author of the study.

“This also explains the recently discovered genetic connection between Europeans and Native Americans,” Reich added. “The same Ancient North Eurasian group contributed to both of them.”

The research team also discovered that ancient Near Eastern farmers and their European descendants can trace much of their ancestry to a previously unknown, even older lineage called the Basal Eurasians.

The study was published online Sept. 17 in Nature.

Peering into the past

To probe the ongoing mystery of Europeans’ heritage and their relationships to the rest of the world, the international research team—including co-senior author Johannes Krause, professor of archaeo- and paleogenetics at the University of Tübingen and co-director of the new Max Planck Institute for History and the Sciences in Jena, Germany—collected and sequenced the DNA of more than 2,300 present-day people from around the world and of nine ancient humans from Sweden, Luxembourg and Germany.

The ancient bones came from eight hunter-gatherers who lived about 8,000 years ago, before the arrival of farming, and one farmer from about 7,000 years ago.

The researchers also incorporated into their study genetic sequences previously gathered from ancient humans of the same time period, including early farmers such as Ötzi “the Iceman.”

“There was a sharp genetic transition between the hunter-gatherers and the farmers, reflecting a major movement of new people into Europe from the Near East,” said Reich.

Ancient North Eurasian DNA wasn’t found in either the hunter-gatherers or the early farmers, suggesting the Ancient North Eurasians arrived in the area later, he said.

“Nearly all Europeans have ancestry from all three ancestral groups,” said Iosif Lazaridis, a research fellow in genetics in Reich’s lab and first author of the paper. “Differences between them are due to the relative proportions of ancestry. Northern Europeans have more hunter-gatherer ancestry—up to about 50 percent in Lithuanians—and Southern Europeans have more farmer ancestry.”

Lazaridis added, “The Ancient North Eurasian ancestry is proportionally the smallest component everywhere in Europe, never more than 20 percent, but we find it in nearly every European group we’ve studied and also in populations from the Caucasus and Near East. A profound transformation must have taken place in West Eurasia” after farming arrived.

When this research was conducted, Ancient North Eurasians were a “ghost population”—an ancient group known only through the traces it left in the DNA of present-day people. Then, in January, a separate group of archaeologists found the physical remains of two Ancient North Eurasians in Siberia. Now, said Reich, “We can study how they’re related to other populations.”

Room for more

The team was able to go only so far in its analysis because of the limited number of ancient DNA samples. Reich thinks there could easily be more than three ancient groups who contributed to today’s European genetic profile.

He and his colleagues found that the three-way model doesn’t tell the whole story for certain regions of Europe. Mediterranean groups such as the Maltese, as well as Ashkenazi Jews, had more Near East ancestry than anticipated, while far northeastern Europeans such as Finns and the Saami, as well as some northern Russians, had more East Asian ancestry in the mix.

The most surprising part of the project for Reich, however, was the discovery of the Basal Eurasians.

“This deep lineage of non-African ancestry branched off before all the other non-Africans branched off from one another,” he said. “Before Australian Aborigines and New Guineans and South Indians and Native Americans and other indigenous hunter-gatherers split, they split from Basal Eurasians. This reconciled some contradictory pieces of information for us.”

Revised flow chart of European ancestry incorporating the new data about Ancient North Eurasians (ANE), West European hunter-gatherers (WHG), early European farmers (EEF) and Basal Eurasians. Image courtesy David Reich

Next, the team wants to figure out when the Ancient North Eurasians arrived in Europe and to find ancient DNA from the Basal Eurasians.

“We are only starting to understand the complex genetic relationship of our ancestors,” said co-author Krause. “Only more genetic data from ancient human remains will allow us to disentangle our prehistoric past.”

“There are important open questions about how the present-day people of the world got to where they are,” said Reich, who is a Howard Hughes Medical Investigator. “The traditional way geneticists study this is by analyzing present-day people, but this is very hard because present-day people reflect many layers of mixture and migration.

“Ancient DNA sequencing is a powerful technology that allows you to go back to the places and periods where important demographic events occurred,” he said. “It’s a great new opportunity to learn about human history.”

This project was supported in part by the National Cancer Institute (HHSN26120080001E and NIH/NCI Intramural Research Program), National Institute of General Medical Sciences (GM100233 and GM40282), National Human Genome Research Institute (HG004120 and HG002385), an NIH Pioneer Award (8DP1ES022577-04), National Science Foundation (HOMINID awards BCS-1032255 and BCS-0827436 and grant OCI-1053575), Howard Hughes Medical Institute, German Research Foundation (DFG) (KR 4015/1-1), Carl-Zeiss Foundation, Baden Württemberg Foundation and the Max Planck Society.


Genes and Immunity

T lymphocyte activation integrates immunologic and genetic history

Image: National Human Genome Research Institute

Researchers from Harvard Medical School and the Broad Institute of MIT and Harvard have uncovered unexpectedly complex patterns in the T lymphocyte responses that individual people mount, reflecting environmental influences as well as a genetic component. The study lays the groundwork for further explorations into the relative contributions of genes and their environment on immunological processes, the scientists said, which could illuminate autoimmune disease and its genetic underpinnings.

The findings are reported in Science and stem from the ImmVar Project, a wide-ranging analysis of variation in gene expression in the immune system. Christophe Benoist, Morton Grove-Rasmussen Professor of Immunohematology at HMS, and Aviv Regev, a Broad Institute core member, an associate professor at MIT, and  Howard Hughes Medical Institute investigator, led the third and final phase, which focused on CD4+ T cells, immune cells that are major players in autoimmune disease.

In this study, after the scientists accounted to the best possible extent for environmental influences and immunological history, they still found that the ancestry of the donor significantly affected T cell responses. “There is a signature of variation in adaptive immune response,” Benoist said. “In general, there is stronger activation of some genes in people of African ancestry, in particular for a type of response in T helper 17 (Th17) cells that tend to protect us from microbes that enter airways or the intestinal tract.  Those responses are also highly involved in autoimmune disease.” 

"The combination of careful immunological work, high-throughout assays, and sophisticated analytics essential to dissect such a complex system could only have happened within the partnership of the ImmVar consortium, bringing together the expertise of immunologists and clinicians in the Harvard-affiliated hospitals with genomics and computational experts at the Broad and MIT," Regev said.

In autoimmune diseases such as rheumatoid arthritis, inflammatory bowel disease and multiple sclerosis, immune cells mistakenly attack the body’s own tissues as if they were invaders. In healthy people, the immune system achieves a state of tolerance, quelling defensive measures after a threat has abated.

Scientists have previously identified genes that are important in controlling the autoimmune response, but this is the first time that differences in T cell activation between population groups have been revealed.

In the current study, the scientists analyzed blood samples collected from 348 healthy volunteers representing African, Asian or European ancestry. After the researchers genotyped the samples and isolated CD4+ T cells, the T cells were activated in cell culture to model their response to antigens. A computational analysis measured which genes were turned on or off in the cells from each person.

Activation of autoimmune-associated genes can vary between individuals in a complicated interplay of genes and environment. Each person’s immunological history is written in a constellation of events, from being vaccinated against the measles in childhood to having the flu last winter. Benoist compares it to learning and personality: All the memories you accumulate make you who you are.

In one’s immunological history, “environment” also encompasses the microbial world people inhabit. The hygiene hypothesis holds that people who have encountered more challenges to their immune system—harmful microbes—are less likely to have the runaway response that is the hallmark of autoimmune disease. People who grow up exposed to fewer microbes may have difficulty stopping the immune response when it is no longer needed.

There is a strong inherited component to autoimmune disease, but changing one’s environments is also important, Benoist noted. People who relocate to a new region tend to acquire the frequency of autoimmune disease of where they are going, observational research has reported. For example, he said, there is little autoimmune disease in India, but people of Indian origin who have lived in the US, from an early age have about the same frequency of autoimmune disease as people of European origin who also live in the US.

One possibility is that at least some of this variation may reflect evolutionary adaptations to the pathogens people encountered during human migrations out of Africa 50,000 years ago. A more robust immune response would have been advantageous in sub-Saharan Africa but deleterious at higher latitudes, with fewer microbial pathogens.

“It’s a tantalizing idea, but it’s highly speculative,” Benoist said.

This work was supported by National Institute of General Medical Sciences grant RC2 GM093080, NIH F32 Fellowship (F32 AG043267), HHMI, and a Harry Weaver Neuroscience Scholar Award from the National Multiple Sclerosis Society (JF2138A1).


Sweet Feat

How hummingbirds evolved a novel mechanism of sweet taste detection

Everything about hummingbirds is rapid. An iridescent blur to the human eye, their movements can be captured with clarity only by high-speed video.

Anna’s hummingbird (Calypte anna) in the Santa  Monica Mountains, Calif. Image: Maude Baldwin

Slowed down on replay, their wings thrum like helicopter blades as they hover near food. Their hearts beat 20 times a second and their tongues dart 17 times a second to slurp from a feeding station.

It takes only three licks of their forked, tube-like tongues to reject water when they expect nectar. They pull their beaks back, shake their heads and spit out the tasteless liquid. They also are not fooled by the sugar substitute that sweetens most diet cola.

These hummingbirds look mad.

The birds’ preference for sweetness is plain, but only now can scientists explain the complex biology behind their taste for sugar. Their discovery required an international team of scientists, fieldwork in the California mountains and at Harvard University’s Concord Field Station, plus collaborations from Harvard labs on both sides of the Charles River. 

Now, in a paper published in Science, the scientists show how hummingbirds’ ability to detect sweetness evolved from an ancestral savory taste receptor that is mostly tuned to flavors in amino acids. Feasting on nectar and the occasional insect, the tiny birds expanded throughout North and South America, numbering more than 300 species over the 40 to 72 million years since they branched off from their closest relative, the swift.

“It’s a really nice example of how a species evolved at a molecular level to adopt a very complex phenotype,” said Stephen Liberles, HMS associate professor of cell biology. “A change in a single receptor can actually drive a change in behavior and, we propose, can contribute to species diversification.”

Anna's hummingbirds (Calypte anna) reject most artificial sweeteners. In this video, slowed to 10 percent of regular speed, the birds drink from sucrose-containing feeders (feeders 3 and 6) but reject aspartame (feeder 1).  Video: Maude Baldwin.

This sweet discovery all started with the chicken genome. Before scientists sequenced its genes, people assumed that chickens and all birds taste things the same way that mammals do: with sensory receptors for salty, sour, bitter, sweet and the more recently recognized umami taste, which comes from the Japanese word for savory.

The canonical view stated there was a sweet receptor present in animals, much smaller than the large families of receptors involved in smell and bitter taste perception—vital for sensing safe food or dangerous predators.

Some animals have lost certain taste abilities. The panda, for example, feeds exclusively on bamboo and lacks savory taste receptors. Carnivores, notably cats, are indifferent to sweet tastes. The gene for tasting sweetness is present in their genomes, but it’s nonfunctional. Scientists suspect that an interplay between taste receptors and diet may effectively relegate the sweet taste receptor into a pseudogene that does not get turned on and eventually disappears.

The chicken genome is another story: It has no trace of a sweet-taste receptor gene. Faced with this all-or-nothing scenario, Maude Baldwin, co-first author of the paper, had one reaction.

“The immediate question to ornithologists or to anybody who has a birdfeeder in the backyard was: What about hummingbirds?” she recalled. “If they are missing the single sweet receptor, how are they detecting sugar?”

More bird genomes were sequenced, and still no sweet receptor.

So began Baldwin’s quest to understand how hummingbirds detected sugar and became highly specialized nectar feeders. A doctoral student in organismic and evolutionary biology and the Museum of Comparative Zoology, she is a member of the lab of Scott Edwards, Professor of Organismic and Evolutionary Biology and Curator of Ornithology in the Museum of Comparative Zoology. She sought out Liberles at a meeting of the International Symposium on Smell and Taste in San Francisco. They agreed to work together on experiments that would eventually reveal how hummingbirds evolved and diversified, based on a change in their taste receptor.

After cloning the genes for taste receptors from chickens, swifts and hummingbirds—a three-year process—Baldwin needed to test what the proteins expressed by these genes were responding to. She joined forces with another scientist at another International Taste and Smell meeting. Yasuka Toda, a graduate student of the University of Tokyo and co-first author of the paper, had devised a method for testing taste receptors in cell culture.

Together they showed that in chickens and swifts the receptor responds strongly to amino acids—the umami flavors—but in hummingbirds only weakly. But the receptor in hummingbirds responds strongly to carbohydrates—the sweet flavors.

“This is the first time that this umami receptor has ever been shown to respond to carbohydrates,” Baldwin said.

Toda mixed and matched different subunits of the chicken and hummingbird taste receptors into hybrid chimeras to understand which parts of the gene were involved in this change in function. All told, she found 19 mutations, but there are likely more contributing to this sweet switch, Baldwin and Liberles suspect.

“If you look at the structure of the receptor, it involved really dramatic changes over its entire surface to accomplish this complex feat,” Liberles said. “Amino acids and sugars look very different structurally so in order to recognize them and sense them in the environment, you need a completely different lock and key. The key looks very different, so you have to change the lock almost entirely.”

Once the mutations were discovered, the next question was, do they matter? Does this different taste receptor subunit drive behavior in the hummingbirds?

Back at the feeding stations, the birds answered yes. They spat out the water, but they siphoned up both the sweet nectar and one artificial sweetener that evoked a response in the cell-culture assay, unlike aspartame and its ilk. It’s not nectar, with its nutritional value, but it’s still sweet.

“That gave us the link between the receptor and behavior,” Liberles said. “This dramatic change in the evolution of a new behavior is a really powerful example of how you can explain evolution on a molecular level.”

This work underscores how much remains to be learned about taste and our other senses, Liberles said.

“Sensory systems give us a window into the brain to define what we understand about the world around us,” he said. “The taste system is arguably a really direct line to pleasure and aversion, reward and punishment, sweet and bitter. Understanding how neural circuits can encode these differentially gives us a window into other aspects of perception.”

The work was supported by National Science Foundation grants DDIG 1110487, SICB, Sigma Xi; the Fulbright Commission and Science Foundation Ireland Research Frontiers Program EOB2673; National Institutes of Health RO1DC013289; and JSPS, LS037.


What Grandma Ate

A new study looks at how epigenetic effects are passed down 

iStock image/ParkerDeen

When a pregnant mother is undernourished, her child is at a greater than average risk of developing obesity and type 2 diabetes, in part due to so-called ‘epigenetic’ effects.

A new study led by an HMS researcher at Joslin Diabetes Center and a scientist at the University of Cambridge demonstrates that this ‘memory’ of nutrition during pregnancy can be passed through sperm of male offspring to the next generation, increasing risk of disease for grandchildren as well. In other words, to adapt an old maxim, ‘you are what your grandmother ate.’

The study also raised questions over how epigenetic effects are passed down from one generation to the next—and for how long they will continue to have an impact.

The mechanism by which we inherit characteristics from our parents is well understood: We inherit half of our genes from our mother and half from our father. However, epigenetic effects, whereby a ‘memory’ of the parent’s environment is passed down through the generations, are less well understood.

The best understood epigenetic effects are caused by a mechanism known as ‘methylation’ in which the molecule methyl attaches itself to our DNA and acts to switch genes on or off.

In the study, published in the journal Science and funded mainly by the Medical Research Council and the Wellcome Trust, the international team of researchers showed that environmentally-induced methylation changes occur only in certain regions of our genome (our entire genetic material)—but, unexpectedly, that these methylation patterns are not passed on indefinitely.

Researchers examined the impact that under-nutrition during pregnancy had on offspring in mouse models and looked for the mechanisms by which this effect was passed down through the generations. The male offspring of an undernourished mother were, as expected, smaller than average and, if fed a normal diet, went on to develop diabetes.  Strikingly, the offspring of these were also born small and developed diabetes as adults, despite their own mothers never being undernourished.

 “When food is scarce, children may be born ‘pre-programmed’ to cope with undernourishment. In the event of a sudden abundance in food, their bodies cannot cope and they can develop metabolic diseases such as diabetes. We need to understand how these adaptations between generations occur since these may help us understand the record levels of obesity and type 2 diabetes in our society today,” said Anne Ferguson-Smith, from the department of genetics at the University of Cambridge.

To see how the effect might be passed on, the researchers analyzed the sperm of offspring before the onset of diabetes to look at the methylation patterns. They found that the mouse’s DNA was less methylated in 111 regions relative to a control sperm.

These regions tended to be clustered in the non-coding regions of DNA—areas of DNA responsible for regulating the mouse’s genes. They also showed that in the grandchildren, the genes next to these methylated regions were not functioning correctly. The offspring had inherited a ‘memory’ of its grandmother’s under-nutrition.

Unexpectedly, however, when the researchers looked at the grandchild’s DNA, they found that the methylation changes had disappeared: the memory of the grandmother’s under-nutrition had been erased from the DNA, or at least, was no longer being transmitted via methylation.

“This was a big surprise: dogma suggested that these methylation patterns might persist down the generations,” added co-author and HMS assistant professor of medicine Mary-Elizabeth Patti, director of the Joslin Genomics Core and director of the Hypoglycemia and Severe Insulin Resistance Clinic at Joslin. 

“From an evolutionary point of view, however, it makes sense. Our environment changes and we can move from famine to feast, so our bodies need to be able to adapt. Epigenetic changes may in fact wear off. This could give us some optimism that any epigenetic influence on our society’s obesity and diabetes problem might also be limited and/or reversible,” Patti said. 

The researchers are now looking at whether epigenetic effects no longer have an impact on great-grandchildren and their subsequent offspring. 

Adapted from a Joslin Diabetes Center news release


Aspirin’s Two Sides

Common genetic variant influences whether aspirin prevents cardiovascular disease—or raises risk

Aspirin is the gold standard for antiplatelet therapy and a daily low-dose aspirin is widely prescribed for the prevention of cardiovascular disease.Image: Shutterstock

Now, a new study suggests that common genetic variation in the gene for catechol-O-methyltransferase (COMT) may modify the cardiovascular benefit of aspirin and, in some people, may confer slight harm. The findings, from Harvard Medical School investigators at Beth Israel Deaconess Medical Center and Brigham and Women’s Hospital, are published in the American Heart Association journal Arteriosclerosis, Thrombosis, and Vascular Biology.

“This is one of the few cases where you can identify a single genetic polymorphism which has a significant interaction with aspirin such that it affects whether or not it protects against cardiovascular disease,” said first author Kathryn Hall, an HMS research fellow and investigator in the Division of General Medicine and Primary Care at Beth Israel Deaconess.

COMT is a key enzyme in the metabolism of catecholamines, a group of hormones that include epinephrine, norepinephrine and dopamine. These hormones are implicated in a broad spectrum of disorders, including hypertension.

“We were initially interested in finding out if the COMT gene affected people’s susceptibility to cardiovascular disease, such as myocardial infarction or ischemic stroke,” Hall said.

Knowing that aspirin is commonly prescribed for the prevention of cardiovascular disease, the investigators also wanted to learn if genetic variation in COMT would influence aspirin’s potential benefit.        

To answer these questions, the researchers used data from the Women’s Genome Health Study, a cohort of more than 23,000 women who were followed for 10 years in a randomized double-blind, placebo-controlled trial of low-dose aspirin or vitamin E for the primary prevention of cardiovascular disease. Their analysis focused on val158met, a common variant in the COMT gene. Individuals who have two copies of the gene for the enzyme’s high-activity valine form, the “val/vals,” have been shown to have lower levels of catecholamines compared to individuals who have two copies of the gene for the enzyme’s low-activity methionine form, the “met/mets.” The val/met people are in between.

“When we examined women in the placebo arm of the trial, we found that the 23 percent of the women who were ‘val/vals’ were naturally protected against cardiovascular disease,” said senior author Daniel Chasman, HMS associate professor of medicine at Brigham and Women’s. He is also a genetic epidemiologist in the Division of Preventive Medicine at the hospital. “This finding, which was replicated in two other population-based studies, was in itself of significant interest.”

The investigation further revealed the surprising discovery that when the women with the val/val polymorphism were allocated to aspirin, this natural protection was eliminated.

“As we continued to look at the effects of drug allocation, we found that val/val women who were randomly assigned to aspirin had more cardiovascular events than the val/vals who were assigned to placebo,” says Chasman. Among the 28 percent of women who were met/met, the opposite was true, and these women had fewer cardiovascular events when assigned to aspirin compared to placebo. The benefit of aspirin compared to placebo allocation for met/mets amounted to reduction of one case of incident cardiovascular disease for 91 treated women over 10 years of study follow-up. By contrast, the harm of aspirin compared to placebo allocation for the val/val women was an increase of one case per 91 treated.

The researchers further found that rates of cardiovascular disease were also reduced in met/met women assigned to vitamin E compared to those assigned to placebo.

The authors stressed that the findings will require further research and replication to understand their potential for clinical impact. Nonetheless, they note that because aspirin is preventively prescribed to millions of individuals and the COMT genetic variant is extremely common, this study underscores the potential importance of individualizing therapies based on genetic profiles.

“What this study suggests is that we can be smarter about the groups of patients that would most likely benefit from aspirin,” said study coauthor Joseph Loscalzo, chairman of the Department of Medicine and physician-in-chief at Brigham and Women’s. He is also the Hersey Professor of the Theory and Practice of Physic at HMS. “Rather than give aspirin to all patients with risk factors for heart disease, we need to use modern genomics and genetics to identify those individuals for whom aspirin has the greatest benefit and the lowest risk of adverse effects.”    

One possible reason for the val/val protection could lie in COMT’s role in the breakdown of epinephrine, the “fight or flight” hormone, which is tightly linked to regulation of the cardiovascular system.

“When epinephrine levels rise in response to stress, blood pressure goes up and high blood pressure is a precursor to heart disease,” said Hall. “One possibility is that val/val individuals have less epinephrine than met/met individuals because their COMT is more efficient at breaking it down. This might help to naturally protect them against cardiovascular disease—that’s our working hypothesis. It’s harder to explain why the effect is modified by aspirin and that’s what we’re in the lab aggressively trying to figure out.”

The Women’s Genome Health Study is supported by HL043851 and HL080467 from the National Heart, Lung, and Blood Institute and CA 047988 from the National Cancer Institute. This study was also supported by NIH grants T32A5000051; R01AT004662; K24AT004095; R21AT002860; 3R01AT004662-02S1from the National Center for Complementary and Alternative Medicine.

Adapted from a Beth Israel Deaconess news release.


A Crisper Version of CRISPR

New genome-editing tool reduces risk of off-target mutations

A next-generation genome-editing system developed by Harvard Medical School investigators at Massachusetts General Hospital substantially decreases the risk of producing unwanted, off-target gene mutations. In a paper published in Nature Biotechnology, the researchers report a new CRISPR-based RNA-guided nuclease technology that uses two guide RNAs, significantly reducing the chance of cutting through DNA strands at mismatched sites.

“This system combines the ease of use of the widely adopted CRISPR/Cas system with a dimerization-dependent nuclease activity that confers higher specificity of action,” said J. Keith Joung, HMS associate professor of pathology at Mass General and senior author of the report. “Higher specificity will be essential for any future clinical use of these nucleases, and the new class of proteins we describe could provide an important option for therapeutic genome editing.”

Engineered CRISPR-Cas nucleases are genome-editing tools that combine a short RNA segment matching its DNA target with a DNA-cutting enzyme called Cas9. The tools have been the subject of much investigation since their initial development in 2012. Easier to use than the earlier zinc finger nuclease (ZFN) and transcription activator-like effector nuclease (TALEN) systems, they have successfully induced genomic changes in several animal model systems and in human cells. But in a previous Nature Biotechnology paper published in June 2013, Joung’s team reported that CRISPR-Cas nucleases could produce additional mutations in human cells, even at sites that differed from the DNA target by as much as five nucleotides (the subunits of DNA).  

To address this situation, the investigators developed a new platform in which the targeting function of Cas9 was fused to a nuclease derived from a well-characterized enzyme called Fokl, which functions only when two copies of the molecule are paired, in a relationship called dimerization. This change essentially doubled the length of DNA that must be recognized for cleavage by these new CRISPR RNA-guided Fokl nucleases, significantly increasing the precision of genome editing in human cells. Joung and his colleagues also demonstrated that these new RNA-guided Fokl nucleases are as effective at on-target modification as existing Cas9 nucleases that target a shorter DNA sequence.

“By doubling the length of the recognized DNA sequence, we have developed a new class of genome-editing tools with substantially improved fidelity compared with existing wild-type Cas9 nucleases and nickases,” the enzymes that cleave a single DNA strand, said Joung, who is associate chief for research in the Mass General Department of Pathology. 

The research team also has developed software that enables users to identify potential target sites for these new RNA-guided Fokl nucleases. The freely available software package is ZiFiT Targeter.

The study was supported by National Institutes of Health Director’s Pioneer Award DP1 GM105378; NIH grants R01 GM088040, P50 HG005550 and R01 AR063070; and the Jim and Ann Orr Massachusetts General Hospital Research Scholar Award. Joung is a co-founder of Editas Medicine Inc., which has an exclusive option to license the new CRISPR RNA-guided Fokl nuclease technology for therapeutic applications.

Adapted from a Mass General news release.