Publisher Health

One-letter difference in our DNA determines whether BCG vaccine provides good protection against tuberculosis or not. Researchers at Radboudumc have elucidated how that one letter difference affects the activation and deactivation of the immune system. The discovery, published in Nature Genetics, not only provides more insight into interleukin-driven inflammatory responses, but also opens up new possibilities for (re)guiding the immune system.
People can react very differently to the same pathogen or vaccination. One person gets sick from an invading bacterium, for instance, while another doesn’t. And some vaccines work much better on some people than on others. The main reason for these individual differences lies in our genetic material, our genome. A genome differs from person to person. It is this diversity that largely determines how we react to pathogens and vaccinations.
Our complete genome consists of more than 3 billion DNA molecules. In these biological DNA letters our heredity is stored. Only a small portion of these letters, about 2 percent, contain information for the proteins at work in our bodies. Those proteins are the work forces in our cells; they build us up, repair us, keep us alive. The 2 percent of the genome that codes for proteins is called the exome. It was long thought the other 98 percent of our DNA was actually redundant. It was genetic waste — ‘junk DNA’ without a function.
Vaccine against tuberculosis
We now know that this ‘junk DNA’, hereafter referred to as the non-coding genome, is indeed very important. That 98 percent may not make proteins, but it can help to shape them, coordinate their production and so on. The genome does so by making pieces of RNA. Such a piece of non-coding RNA interferes with all kinds of processes in the body. Including the chance that you will (not) get sick from a pathogen. Or whether or not a vaccine will protect you properly.
Let’s take the BCG vaccine that protects against tuberculosis (TB) as an example. This vaccine appears to protect not only against TB, but against more infections by (epigenetic) changes that the vaccine evokes in blood-forming stem cells in the bone marrow.
Different DNA letter, different immune response
Among other things, those stem cells produce the white blood cells that are important in the immune system. But the BCG vaccine does not work equally well in everyone! It turns out just one letter difference in the hereditary material drives this distinction. Such a ‘one letter difference’ is called a single-nucleotide polymorphism, in short SNP and pronounced as ‘snip’. In people with the letter G (for guanine) at this place in the genome, vaccination works very well. For people with an A (for adenine) the vaccine works only moderately. Therefore the question is: how can one letter difference have such an impact on the functioning of a person’s immune system?

Musa Mhlanga and Ezio Fok of Radboudumc and their colleagues tried to answer this question. Fok: “We know that a BCG vaccine activates interleukin-1β. This triggers an inflammatory process through which the immune system builds up protection against tuberculosis and other pathogens. But why does it work really well in people with a G-SNP and is it less efficient in those with an A-SNP? What exactly happens there in that molecular incubator, why do those G and A cause such a big difference in the way our immune system functions?”
Director of the inflammatory process
The researchers discovered that the SNP is part of a long stretch of non-coding RNA (lncRNA) they named AMANZI. AMANZI appears to be the director of interleukin-1β (IL-1β) which is at the core of the inflammatory process. After the BCG vaccine is administered, AMANZI activates IL-37 and triggers the anti-inflammatory response that regulates the activity of IL-1β. This process of regulating IL-1β is important to achieving a long-term memory of vaccination through a process called trained immunity. Prof Mihai Netea at RUMC first observed trained immunity in 2013 to be important in how vaccines like BCG are protective.
“This process takes place in people with the G-SNP,” says Mhlanga, “but it’s less effective in people with an A-SNP. In them [A-SNP], AMANZI stably maintains the IL-37 ‘brake’. As a result, neither the immune responses to the vaccine and the pathogen proceed properly because IL-1β is dampened. So people with the G-SNP build up a functional defense, where in people with the A-SNP this is not the case. To check, we removed the A-SNP AMANZI variant in white blood cells. As a result we saw pro-inflammatory protection building up again, showing the effect of the one-letter difference in AMANZI once again.”
Epigenetics
AMANZI exerts its influence by turning genes on and off, the research field of epigenetics. In the journal Nature Genetics, the researchers show in detail how long stretches of noncoding RNA (lncRNA) execute this and how small variations of just one letter affect such an epigenetic process, with profound consequences. This applies not only to AMANZI but undoubtedly to many more lncRNAs, they argue. Those variations can be neutral, but can also affect processes in the immune system negatively or positively.
In this particular case, it involves an interleukin-driven inflammatory process. Mhlanga: “Several lncRNAs play a role in this process, and single-letter differences — SNP’s in other words — may also enhance or attenuate the effect of this inflammatory process. Further research is needed to understand the combined effect of multiple polymorphisms on these IL-1β-driven immune responses. Ultimately, we want to map all components of IL-1β signaling and trained immunity in order to find out their clinical usability. Importantly, nine out of ten SNPs are in noncoding regions of the genome.”

Enamel, the hardest and most mineral-rich substance in the human body, covers and protects our teeth. But in one of every 10 people — and in one third of children with celiac disease — this layer appears defective, failing to protect the teeth properly. As a result, teeth become more sensitive to heat, cold and sour food, and they may decay faster. In most cases, the cause of the faulty enamel production is unknown.
Now, a study by Prof. Jakub Abramson and his team at the Weizmann Institute of Science, published recently in Nature, may shed light on this problem by revealing a new children’s autoimmune disorder that hinders proper tooth enamel development. The disorder is common in people with a rare genetic syndrome and in children with celiac disease. These findings could help develop strategies for early detection and prevention of the disorder.
Tooth enamel is made up primarily of mineral crystals that are gradually deposited on protein scaffolds during enamel development. Once the crystals are in place, the protein scaffold is dismantled, leaving behind a thin but exceptionally hard layer that covers and protects our teeth. A strange phenomenon was identified in people with a rare genetic disorder known as APS-1: Although the enamel layer of their milk teeth forms perfectly normally, something causes its faulty development in their permanent teeth. Since people with APS-1 suffer from a variety of autoimmune diseases, Abramson and his team hypothesized that the observed enamel defects may also be of an autoimmune nature — in other words, that their immune system could be attacking their own proteins or cells that are necessary for enamel formation.
In general, autoimmune diseases occur when the immune system’s T cells or its antibodies mistakenly trigger an immune response against the body’s own cells or tissues. To prevent these incidents of “friendly fire,” T cells developing in the thymus gland need to first be educated to discriminate between the body’s own proteins and those of foreign origin. To this end, T cells are presented with short segments of self-proteins that make up various tissues and organs in the body. When a “poorly educated” T cell erroneously identifies a self-protein in the thymus as a target for attack, that T cell is labeled as dangerous and destroyed, so that it could not cause any damage after being released from the thymus.
This critical education step is impaired in APS-1 patients as a result of a mutation in a gene known as the autoimmune regulator (Aire). This gene is essential for the T cell education process: It produces a protein that is responsible for the collection of self-proteins presented to the T cells in the thymus. In their new study, scientists from Abramson’s lab in Weizmann’s Immunology and Regenerative Biology Department, led by research student Yael Gruper, sought to work out how mutations in the Aire gene lead to deficient tooth enamel production. The researchers discovered that, in the absence of Aire, proteins that play a key role in the development of enamel are not presented to the T cells in the thymus gland. As a result, T cells that are liable to identify these proteins as targets are released from the thymus, and they encourage the production of antibodies to the enamel proteins. But why do these autoantibodies damage permanent teeth and not baby teeth?
The answer to this question lies in the fact that milk teeth develop in the embryonic stage, when the immune system is not yet fully formed and cannot create autoantibodies. In contrast, the development of enamel on permanent teeth starts at birth and continues until around the age of six, when the immune system is sufficiently mature to thwart enamel development. Furthermore, the researchers found a correlation between high levels of antibodies to enamel proteins and the severity of the harm to enamel development in children with APS-1. This strengthens the assumption that the presence of enamel-specific autoantibodies in childhood can potentially lead to dental problems.
When the researchers looked into deficiencies in enamel development in people with other autoimmune diseases, they found a very similar phenomenon in children with celiac disease, a relatively common autoimmune disorder that affects around 1 percent of people in the West. When people with this disease are exposed to gluten, their immune system attacks and destroys the cellular layer lining the small intestine, leading to attacks on other self-proteins in the intestine.

In an attempt to understand how celiac disease, known to cause intestinal damage, may also cause damage to tooth enamel, the researchers first examined whether people with this disease have autoantibodies that attack enamel. They found that a large proportion of celiac patients have these autoantibodies, just as do people with APS-1. But the “education” that takes place in the thymus gland of these patients seems normal, so why do they develop these antibodies? The researchers hypothesized that some proteins are found in both the intestine and the dental tissue and that these proteins play an important role in the development of tooth enamel. In this case, the antibodies that identify proteins in the intestine might move through the bloodstream to the dental tissue, where they could start to disrupt the enamel production process.
Since many celiac patients had previously been found to develop sensitivity to cow’s milk, the researchers decided to focus on the k-casein protein, a major component of dairy products. Strikingly, they found that the human equivalent of k-casein is one of the main components of the scaffold necessary for enamel formation. This led them to hypothesize that antibodies produced in the intestines of celiac patients in response to certain food antigens, such k-casein, may subsequently cause collateral damage to the development of enamel in the teeth, similarly to the way in which antibodies against gluten can eventually trigger autoimmunity against the intestine.
Indeed, they discovered that most of the children diagnosed with celiac had high levels of antibodies against k-casein from cows’ milk, which in many cases can also react against k-casein’s human equivalent expressed in the enamel matrix. This means that in theory, the same antibodies that are produced in the intestine against the milk protein could act against the human k-casein in the teeth.
These findings could have implications for the food industry. “Similarly to the lessons learned from gluten, we can assume that the consumption of large quantities of dairy products could lead to the production of antibodies against k-casein,” Abramson explains. “This protein increases the amount of cheese that can be produced from milk, so the dairy industry deliberately raises its concentration in cow’s milk. Our study, however, found that the milk k-casein is a potent immunogen, which may potentially trigger an immune response that can harm the body itself.”
Tooth enamel flaws are common, not just among people with celiac disease or APS-1. “Many people suffer from impaired tooth enamel development for unknown reasons,” Abramson says. “It is possible that the new disorder we discovered, along with the possibility of diagnosing it in a blood or saliva test, will give their condition a name. Most important, early diagnosis in children may enable preventive treatment in the future.”

Hard-to-detect colorectal pre-cancerous lesions known as serrated polyps, and the aggressive tumors that develop from them, depend heavily on the ramped-up production of cholesterol, according to a preclinical study from researchers at Weill Cornell Medicine. The finding points to the possibility of using cholesterol-lowering drugs to prevent or treat such tumors.
In the study, published Oct. 13 in Nature Communications, the researchers analyzed mice that develop serrated polyps and tumors, detailing the chain of molecular events in these tissues that leads to increased cholesterol production.
They confirmed their findings in analyses of human serrated polyps and tumors, and showed in mouse models that replicate the human cancer that blocking cholesterol production prevented the progression of these types of intestinal tumors.
“Serrated-type polyps and tumors currently are not treated differently from other colorectal neoplasias, but as our work shows, they have this specific metabolic vulnerability that can be targeted,” said study co-senior author Dr. Jorge Moscat, a Homer T. Hirst III Professor of Oncology in Pathology, Vice-Chair for Cell and Cancer Pathobiology in the Department of Pathology and Laboratory Medicine and a member of the Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine.
The other co-senior author is Dr. Maria Diaz-Meco, also a Homer T. Hirst III Professor of Oncology in Pathology and a member of the Meyer Cancer Center at Weill Cornell Medicine. The study’s first author is Dr. Yu Muta, a postdoctoral associate in the Moscat/Diaz-Meco laboratories.
Cholesterol is generally considered a pro-growth molecule, being a building block for cell membranes and having other growth-supporting functions. Prior studies have linked high blood cholesterol levels to various cancers, including colorectal cancers. However, it hasn’t been clear that lowering cholesterol, for example with common statin drugs, can prevent colorectal cancers.
“Trials of statins to prevent colorectal cancer have had conflicting results,” Dr. Diaz-Meco said. “Our findings suggest that this is because targeting cholesterol has a preventive but selective effect only against polyps and tumors of this serrated type.”
Serrated polyps are so-called because of their sawtooth appearance under a microscope. They are flatter than ordinary colorectal polyps and can often be missed during colonoscopies. Yet the tumors into which they develop, which account for roughly 15 to 30 percent of colorectal cancers, contain many “metaplastic” cells that are particularly invasive and resistant to treatments.

Several years ago, the Moscat/Diaz-Meco team linked serrated polyps and tumors to low levels of two enzymes known as aPKCs. They showed that mice engineered to lack these aPKC enzymes in their gut linings reliably form serrated polyps and then aggressive tumors.
In the new study, the scientists found that in serrated-type tumors in these mice, and even in intestinal tissue poised to develop these types of cancerous lesions, cholesterol synthesis was strikingly upregulated, suggesting that cholesterol may be an early driver of tumor development.
The researchers revealed how the absence of aPKC enzymes, especially in metaplastic tumor cells, unleashes the activation of a transcription factor called SREBP2, which switches on cholesterol production. Tests on colorectal polyp and tumor samples from human patients dovetailed with the mouse findings. They found, for example, that only serrated-type tumors had low aPKC levels concomitant with the accumulation of SREBP2, a driver and a marker of upregulated cholesterol biosynthesis in the serrated cancer cells.
Lastly, the researchers tested a combination of two cholesterol synthesis-blocking drugs, including the widely used atorvastatin. The treatment, delivered when the low-aPKC mice were still quite young, significantly lowered the rate at which both serrated polyps and tumors later formed — and the serrated-type tumors that did form were less aggressive than those normally arising in the untreated mice.
The results indicate that targeting cholesterol could be a viable strategy for treating and preventing serrated-type colorectal tumors. The Moscat and Diaz-Meco labs are now hoping to set up an initial clinical trial of a cholesterol-lowering intervention in patients from whom serrated colorectal polyps have been removed.
“Currently when these polyps are detected early with colonoscopy, they are removed and patients have to hope that they don’t come back,” Dr. Moscat said. “In the future, we hope to have a more active method to prevent this very aggressive form of cancer before it is fully developed and more difficult to treat.”

The images of Israeli child hostages being freed from Hamas captivity are heartwarming, but for most of these children, the release is just the start of a long rehabilitation process. Countless studies have shown that exposure to warfare, abuse and other traumatic events at a young age significantly raises the risk of ill health, social problems and mental health issues later in life. Now, a new study by researchers at the Weizmann Institute of Science provides a reason for optimism. In research conducted on mice, published Friday in Science Advances, a team headed by Prof. Alon Chen discovered brain mechanisms that go awry as a result of exposure to trauma in infancy and showed that these changes may be reversible if treated early.
Our brains have a wonderful quality known as plasticity, the ability to change throughout our lives. As may be expected, in our early years, when the brain is still developing, it is at peak plasticity. This manifests in, for example, the aptitude for learning languages, but this also entails a heightened sensitivity to traumatic events, which are liable to leave a scar that only intensifies with age. Many studies provide evidence for the latter effect, but very little is known about the way that exposure to trauma at a young age affects the different kinds of brain cells and the communication between them in adulthood.
Chen’s laboratory in Weizmann’s Brain Sciences Department focuses on the molecular and behavioral aspects of the response to stress. In previous studies, Chen’s team examined how stress during pregnancy affects mouse offspring when they reach maturity. In the current research, the scientists, led by Dr. Aron Kos, studied how trauma experienced shortly after birth affects mouse pups later in life. To advance the understanding of this topic, the researchers pulled together the strengths of Chen’s lab: its expertise in exploring the brain’s molecular processes at the highest possible resolution, using genetic sequencing on the level of individual cells; the ability to use cameras to track dozens of behavioral variables in a rich social environment intended to recreate natural living conditions; and the ability to process the massive quantities of data generated in this environment, using machine learning and artificial intelligence tools.
This comprehensive behavioral mapping revealed that mice exposed after birth to a traumatic event — in the case of this study, being neglected by their mothers — displayed a variety of behaviors indicating that they found themselves at the bottom of the dominance hierarchy. “Equivalent behaviors in humans might include high levels of introversion, social anxiety and having an avoidant personality, all known to be characteristic of posttrauma,” says Dr. Juan Pablo Lopez, a former postdoctoral fellow in Chen’s joint laboratory at Weizmann and the Max Planck Institute of Psychiatry in Munich, and today head of a research group in the Department of Neuroscience at the Karolinska Institute in Stockholm.
In the next stage of the study, the researchers exposed some of the adult mice that had experienced trauma in infancy to a stressful social situation: bullying by other mice. Ultimately, they created four groups of adult mice: those that had not been exposed to any trauma; those that had not been exposed to trauma in infancy but were subjected to bullying as adults; mice that were exposed to trauma only in infancy; and mice that were exposed to both trauma in infancy and bullying as adults. To find out how exposure to early trauma disrupts the brain and what happens as a result of this in adulthood, the researchers carried out a meticulous comparison of the four groups, using RNA sequencing at the single-cell level in the hippocampus, a brain area known to play an important role in social functioning. The comparison revealed that early trauma left a mark on different types of cells, primarily affecting gene expression in two subpopulations of neurons, those belonging to the glutamatergic excitatory system and those belonging to the GABA inhibitory system. This effect was especially strong in mice that had been exposed to both trauma in infancy and bullying as adults.
Cells in the brain communicate with one another by means of electrical signals, which can be excitatory, that is, stimulating, or inhibitory. An excitatory signal encourages communication between brain cells, whereas an inhibitory signal represses it, like the gas and brake pedals in a car. Normal brain functioning requires a balance between the excitatory and inhibitory signals, which is lacking in many psychiatric disorders. One of the ways of assessing the brain’s electrical activity and the balance between excitatory and inhibitory signals is through electrophysiological measurements. Such measurements, performed in the hippocampus of the mice by Dr. Julien Dine, a former staff scientist at the Weizmann Institute and currently a pharmaceutical electrophysiologist, supported the molecular findings: Exposure to trauma in early childhood disrupted the balance between excitatory and inhibitory signals in adulthood.
Having discovered a brain mechanism that is disrupted in adulthood as a result of early trauma — and having identified this disruption as an imbalance between the excitatory and inhibitory signals — the researchers tried to find a way to fix it. During a brief treatment window shortly after the early trauma, they gave the mice a well-known antianxiety drug — diazepam, known commercially as Valium — which affects the GABA inhibitory system. This short course of treatment led to results that were nothing less than stunning: The treated mice were able to fully or almost fully avoid the behavioral future that awaited them and were no longer at the foot of the social ladder. “Understanding the molecular and functional mechanisms allowed us to neutralize the negative behavioral impact of trauma with a drug given shortly after exposure to traumatic incidents,” Kos explains. “This certainly should not be seen as a recommendation to treat young trauma patients with drugs, but our findings do highlight the importance of early treatment for successful rehabilitation.”
Intense, ongoing stress can, at any age, contribute to disease, from psychiatric disorders to obesity and diabetes. But in the first years of life — and also in the womb — such stress can have dramatic ramifications. “The wars in Israel, Ukraine, Sudan and elsewhere, and the unprecedented global refugee crisis that is caused, in part, by climate change, alongside an increased understanding of the long-term harm caused by exposure to war and violence at a young age — all these highlight the need for better rehabilitation capabilities,” says Chen. “Our new study identifies a key brain mechanism that is especially sensitive to childhood trauma. But the most exciting part is the prospect of using the plasticity of the young brain to help it recover, avoiding the toll this trauma can exact in adulthood.”
Also participating in the study were Dr. Joeri Bordes, Carlo de Donno, Dr. Elena Brivio, Stoyo Karamihalev, Dr. Alec Dick, Lucas Miranda, Rainer Stoffel, Cornelia Flachskamm and Dr. Mathias V. Schmidt from the Max Planck Institute of Psychiatry; Dr. Malte D. Luecken, Dr. Maren Büttner and Prof. Fabian J. Theis from the Helmholtz Zentrum München; Dr. Suellen Almeida-Correa from Weizmann’s Brain Sciences Department; and Serena Gasperoni from the Karolinska Institute.
Prof. Alon Chen holds the Vera and John Schwartz Professorial Chair in Neurobiology. His research is supported by the Ruhman Family Laboratory for Research on the Neurobiology of Stress; and by the Licht Family.

Researchers at the National Institutes of Health have mapped the 3D organization of genetic material of key developmental stages of human retinal formation, using intricate models of a retina grown in the lab. The findings lay a foundation for understanding clinical traits in many eye diseases, and reveal a highly dynamic process by which the architecture of chromatin, the DNA and proteins that form chromosomes, regulates gene expression. The findings were published in Cell Reports.
“These results provide insights into the heritable genetic landscape of the developing human retina, especially for the most abundant cell types that are commonly associated with vision impairment in retinal diseases,” said the study’s lead investigator, Anand Swaroop, Ph.D., chief of the Neurobiology, Neurodegeneration, and Repair Laboratory at the National Eye Institute (NEI), part of NIH.
Using deep Hi-C sequencing, a tool used for studying 3D genome organization, the researchers created a high-resolution map of chromatin in a human retinal organoid at five key points in development. Organoids are tissue models grown in a lab and engineered to replicate the function and biology of a specific type of tissue in a living body.
Genes, the sequences that code for RNA and proteins, are interspersed throughout long strands of DNA. Those DNA strands get packaged into chromatin fibers, which are spooled around histone proteins and then repeatedly looped to form highly compact structures that fit into the cell nucleus.
All those loops create millions of contact points where genes encounter non-coding DNA sequences, such as super enhancers, promoters, and silencers that regulate gene expression. Long considered “junk DNA,” these non-coding sequences are now recognized to play a crucial role in controlling which genes get expressed in a cell and when. Studies of chromatin’s 3D architecture shed light on how these non-coding regulatory elements exert control even when their location on a DNA strand is remote from the genes they regulate.
At each of the five key retinal organoid developmental stages, billions of chromatin contact point pairs were sequenced and analyzed.
The findings reveal a dynamic picture: Spatial organization of the genome within the nucleus is transformed during retinal development, facilitating expression of specific genes at key time periods. For example, at a stage when immature cells start developing retinal cell characteristics, chromatin contact points shift from a mostly proximal-enriched state to add more distal interactions.
There also appears to be a hierarchy of compartments that organize the contact point interactions. Some of these compartments, called “A” and “B,” are stable, but others swap during development, which further serves to enhance or inhibit gene expression.
“The datasets resulting from this research serve as a foundation for future investigations into how non-coding sections of the genome are relevant for understanding divergent phenotypes in single gene mutation (Mendelian) disorders, as well as complex retinal diseases,” Swaroop said.
The study was funded by the NEI Intramural Research Program (ZIAEY000450 and ZIAEY000546). NEI is part of the National Institutes of Health.

Infection with the stomach bacterium Helicobacter pylori could increase the risk of developing Alzheimer’s disease: In people over the age of 50, the risk following a symptomatic infection can be an average of 11 percent higher, and even more about ten years after the infection, at 24 percent greater risk. These are the findings of a study by Charité — Universitätsmedizin Berlin and McGill University (Canada), now published in the journal Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association.* The researchers analyzed three decades’ worth of patient data.
As today’s populations age, dementia is set to become more common, tripling in prevalence in the next 40 years. With no cure in sight so far, researchers are trying to pinpoint the risk factors involved in dementia, in hopes of specifically targeting those factors.
Helicobacter pylori enters the central nervous system
Researchers have long suspected Helicobacter pylori, a common gut microbe, of being a potential risk factor. Nearly one-third of all people in Germany are infected with this type of bacteria. An infection can be asymptomatic, but the bacteria can also cause inflammation of the stomach lining or even stomach cancer. Numerous lab studies have also found a link between H. pylori infection and the central nervous system. “We know that the bacterium can reach the brain via various routes, potentially causing inflammation, damage, and the destruction of neurons there,” explains Prof. Antonios Douros, a pharmacoepidemiologist at Charité and the first author of the study. When the stomach has been damaged by these microbes, it is also no longer able to absorb Vitamin B12 or iron effectively, which also increases the risk of dementia.
However, many of the studies performed to date on the association between H. pylori infection and Alzheimer’s disease suffered from methodological limitations — for example because the number of people studied was simply too low. One outcome of this was that before now, it was also not possible to say just how strong a link there is between this type of bacterial infection and Alzheimer’s disease.
Representative study of over four million people
Douros, Prof. Paul Brassard of McGill University in Montreal, and their colleagues have now compensated for those limitations. Not only did their study have a very large sample size, at over four million people, but it also considered the time interval between infection and a possible increase in the risk of Alzheimer’s disease. The researchers used data gleaned from electronic patient records in the UK to quantify the link between H. pylori and Alzheimer’s disease over the course of a person’s lifetime.
“Our study shows that symptomatic infections with H. pylori after the age of 50 can be associated with an eleven percent increase in the risk of Alzheimer’s disease. The risk increase peaks at 24 percent about a decade after the initial infection,” Douros says, summarizing the team’s findings. But that doesn’t mean everyone who has experienced a symptomatic infection will necessarily go on to develop Alzheimer’s disease. The calculations show an increase in the relative risk compared to people who did not experience a symptomatic H. pylori infection after the age of 50.
Are H. pylori infections a modifiable risk factor?
“To us, this finding reinforces the assumption that an H. pylori infection could be a modifiable risk factor for Alzheimer’s disease,” Douros concludes. However, the researchers caution that whether efforts to eradicate this gut microbe might actually affect the development of Alzheimer’s disease, and if so to what extent, would need to be tested in large-scale randomized studies first.

A Cambridge-led study has shown why many women experience nausea and vomiting during pregnancy — and why some women, including the Duchess of Cambridge, become so sick they need to be admitted to hospital.
The culprit is a hormone produced by the fetus — a protein known as GDF15. But how sick the mother feels depends on a combination of how much of the hormone is produced by the fetus and how much exposure the mother had to this hormone before becoming pregnant.
The discovery, published today in Nature, points to a potential way to prevent pregnancy sickness by exposing mothers to GDF15 ahead of pregnancy to build up their resilience.
As many as seven in ten pregnancies are affected by nausea and vomiting. In some women — thought to be between one and three in 100 pregnancies — it can be severe, even threatening the life of the fetus and the mother and requiring intravenous fluid replacement to prevent dangerous levels of dehydration. So-called hyperemesis gravidarum is the commonest cause of admission to hospital of women in the first three months of pregnancy.
Although some therapies exist to treat pregnancy sickness and are at least partially effective, widespread ignorance of the disorder compounded by fear of using medication in pregnancy mean that many women with this condition are inadequately treated.
Until recently, the cause of pregnancy sickness was entirely unknown. Recently, some evidence, from biochemical and genetic studies has suggested that it might relate to the production by the placenta of the hormone GDF15, which acts on the mother’s brain to cause her to feel nauseous and vomit.
Now, an international study, involving scientists at the University of Cambridge and researchers in Scotland, the USA and Sri Lanka, has made a major advance in understanding the role of GDF15 in pregnancy sickness, including hyperemesis gravidarum.

The team studied data from women recruited to a number of studies, including at the Rosie Maternity Hospital, part of Cambridge University Hospitals NHS Foundation Trust and Peterborough City Hospital, North West Anglia NHS Foundation Trust. They used a combination of approaches including human genetics, new ways of measuring hormones in pregnant women’s blood, and studies in cells and mice.
The researchers showed that the degree of nausea and vomiting that a woman experiences in pregnancy is directly related to both the amount of GDF15 made by the fetal part of placenta and sent into her bloodstream, and how sensitive she is to the nauseating effect of this hormone.
GDF15 is made at low levels in all tissues outside of pregnancy. How sensitive the mother is to the hormone during pregnancy is influenced by how much of it she was exposed to prior to pregnancy — women with normally low levels of GDF15 in blood have a higher risk of developing severe nausea and vomiting in pregnancy.
The team found that a rare genetic variant that puts women at a much greater risk of hyperemesis gravidarum was associated with lower levels of the hormone in the blood and tissues outside of pregnancy. Similarly, women with the inherited blood disorder beta thalassemia, which causes them to have naturally very high levels of GDF15 prior to pregnancy, experience little or no nausea or vomiting.
Professor Sir Stephen O’Rahilly, Co-Director of the Wellcome-Medical Research Council Institute of Metabolic Science at the University of Cambridge, who led the collaboration, said: “Most women who become pregnant will experience nausea and sickness at some point, and while this is not pleasant, for some women it can be much worse — they’ll become so sick they require treatment and even hospitalisation.
“We now know why: the baby growing in the womb is producing a hormone at levels the mother is not used to. The more sensitive she is to this hormone, the sicker she will become. Knowing this gives us a clue as to how we might prevent this from happening. It also makes us more confident that preventing GDF15 from accessing its highly specific receptor in the mother’s brain will ultimately form the basis for an effective and safe way of treating this disorder.”
Mice exposed to acute, high levels of GDF15 showed signs of loss of appetite, suggesting that they were experiencing nausea, but mice treated with a long-acting form of GDF15 did not show similar behaviour when exposed to acute levels of the hormone. The researchers believe that building up woman’s tolerance to the hormone prior to pregnancy could hold the key to preventing sickness.

Co-author Dr Marlena Fejzo from the Department of Population and Public Health Sciences at the University of Southern California whose team had previously identified the genetic association between GDF15 and hyperemesis gravidarum, has first-hand experience with the condition. “When I was pregnant, I became so ill that I could barely move without being sick. When I tried to find out why, I realized how little was known about my condition, despite pregnancy nausea being very common.
“Hopefully, now that we understand the cause of hyperemesis gravidarum, we’re a step closer to developing effective treatments to stop other mothers going through what I and many other women have experienced.”
The work involved collaboration between scientists at the University of Cambridge, University of Southern California, University of Edinburgh, University of Glasgow and Kelaniya University, Colombo, Sri Lanka. The principal UK funders of the study were the Medical Research Council and Wellcome, with support from the National Institute for Health and Care Research Cambridge Biomedical Research Centre.

A previously mysterious small RNA molecule in mice is found to play a crucial role in gene expression, and may be the first identified member of a new class of regulatory RNAs.
RNA (ribonucleic acid) is best known as the messenger RNA (mRNA) that carries a copy of a gene’s information out from the cell nucleus to where it can be decoded to make protein molecules. But RNA also performs other key functions, including the regulation of gene activity by a variety of small non-coding RNAs — those whose genetic sequence is not used to generate proteins.
One such non-coding RNA is the small RNA called 4.5SH, found only in small rodents including mice and rats. It is produced from multiple copies of its gene, leading to the accumulation of up to 10,000 copies of the RNA molecule per cell.
A team of researchers led by Professor Shinichi Nakagawa at Hokkaido University has discovered a new role for 4.5 SH RNA — circumventing mutations in mouse DNA during the maturation of mRNA. Their findings were published in the journal Molecular Cell.
“4.5SH RNA was discovered in the 1970s, yet despite its abundance and presence in many types of tissues, its function had remained a mystery for over 40 years,” says Nakagawa.
To understand its role, the researchers created mutations in mouse embryos that abolished 4.5SH production, discovering that this caused early death at the embryo stage.
“It was known that the mouse genome has many lethal mutations in genes that code essential proteins,” explains Nakagawa. “4.5 SH RNA has the ability to detoxify these mutations in bulk — essentially, it is a natural gene therapy to protect against mutations.”
Analysis of the structure of 4.5SH RNA showed that it is composed of two modules. One serves as a sensor to find abnormal sequences, and the other brings in a tool that prevents the incorporation of the abnormal sequences into mRNA by a process called alternative splicing.

“To our knowledge, this is the first example of a naturally produced RNA that can regulate alternative splicing in a definitive on/off manner,” says Nakagawa. “Our research also suggests that a substantial portion of such non-coding RNAs may be involved in controlling alternative splicing.”
The researchers were also able to use 4.5SH to design a programmable molecular system that could manipulate splicing in cells in selected ways. This might become a new and useful tool for genetic engineering.
“Our discovery suggests the possibility of developing new gene therapy drugs that recognize only specific genetic mutations by modifying the sensor module of 4.5 SH RNA, so we may be able to prevent toxic regions associated with disease from being expressed,” Nakagawa explains.

Karthik Shekhar and his colleagues raised a few eyebrows as they collected cow and pig eyes from Boston butchers, but those eyes — eventually from 17 separate species, including humans — are providing insights into the evolution of the vertebrate retina and could lead to better animal models for human eye diseases.
The retina is a miniature computer containing diverse types of cells that collectively process visual information before transmitting it to the rest of the brain. In a comparative analysis across animals of the many cell types in the retina — mice alone have 130 types of cells in the retina, as Shekhar’s previous studies have shown — the researchers concluded that most cell types have an ancient evolutionary history. These cell types, distinguished by their differences at the molecular level, give clues to their functions and how they participate in building our visual world.
Their remarkable conservation across species suggests that the retina of the last common ancestor of all mammals, which roamed the earth some 200 million year ago, must have had a complexity rivaling the retina of modern mammals. In fact, there are clear hints that some of these cell types can be traced back more than 400 million years ago to the common ancestors of all vertebrates — that is, mammals, reptiles, birds and jawed fish.
The results will be published Dec. 13 in the journal Nature as part of a 10-paper package reporting the latest results of the BRAIN Initiative Cell Census Network’s efforts to create a cell-type atlas of the adult mouse brain. The first author is Joshua Hahn, a chemical and biomolecular engineering graduate student in Shekhar’s group at the University of California, Berkeley. The work was an equal collaboration with the group of Joshua Sanes at Harvard University.
The findings were a surprise, since vertebrate vision varies so widely from species to species. Fish need to see underwater, mice and cats require good night vision, monkeys and humans evolved very sharp daytime eyesight for hunting and foraging. Some animals see vivid colors, while others are content with seeing the world in black and white.
Yet, numerous cell types are shared across a range of vertebrate species, suggesting that the gene expression programs that define these types likely trace back to the common ancestor of jawed vertebrates, the researchers concluded.
The team found, for example, that one cell type — the “midget” retinal ganglion cell — that is responsible for our ability to see fine detail, is not unique to primates, as it was thought to be. By analyzing large-scale gene expression data using statistical inference approaches, the researchers discovered evolutionary counterparts of midget cells in all other mammals, though these counterparts occurred in much smaller proportions.

“What we are seeing is that something thought to be unique to primates is clearly not unique. It’s a remodeled version of a cell type that is probably very ancient,” said Shekhar, a UC Berkeley assistant professor of chemical and biomolecular engineering. “The early vertebrate retina was probably extremely sophisticated, but the parts list has been used, expanded, repurposed or refurbished in all the species that have descended since then.”
Coincidentally, one of Shekhar’s UC Berkeley colleagues, Teresa Puthussery of the School of Optometry, reported last month in Nature that another cell type thought to have been lost in the human eye — a type of retinal ganglion cell responsible for gaze stabilization — is still there. Puthussery and her colleagues used information from a previous paper co-authored by Shekhar to select molecular markers that helped identify this cell type in primate retinal tissue samples.
The discoveries are, in a sense, not a total surprise, since the eyes of vertebrates have a similar plan: Light is detected by photoreceptors, which relay the signal to bipolar, horizontal and amacrine cells, which in turn connect with retinal ganglion cells, which then relay the results to the brain’s visual cortex. Shekhar uses new technologies, in particular single-cell genomics, to assay the molecular composition of thousands to tens of thousands of neurons at once within the visual system, from the retina to the visual cortex.
Because the number of identified retinal cell types varies widely in vertebrates — about 70 in humans, but 130 in mice, based on previous studies by Shekhar and his colleagues — the origins of these diverse cell types were a mystery.
One possibility that emerged from the new research, Shekhar said, is that as the primate brain became more complex, primates began to rely less on signal processing within the eye — which is key to reflexive actions, such as reacting to an approaching predator — and more on analysis within the visual cortex. Hence the apparent decrease in molecularly distinct cell types in the human eye.
“Our study is saying that the human retina may have evolved to trade cell types that perform sophisticated visual computations for cell types that basically just transmit a relatively unprocessed image of the visual world with the brain so that we can do a lot more sophisticated things with that,” Shekhar said. “We are giving up speed for finesse.”
The team’s new detailed map of cell types in a variety of vertebrate retinas could aid research on human eye disease. Shekhar’s group is also studying molecular hallmarks of glaucoma, the leading cause of irreversible blindness in the world and, in the U.S., the second most common cause of blindness after macular degeneration.

Yet, while mice are a favorite model animal for studying glaucoma, they have very few of the midget retinal ganglion cell counterparts. These cell types make up only 2% to 4% of all ganglion cells in mice, whereas 90% of retinal ganglion cells are midget cells in humans.
“This work is clinically important because, ultimately, the midget cells are probably what we should care about the most in human glaucoma,” Shekhar said. “Knowing their counterparts in the mouse will hopefully help us design and interpret these glaucoma mouse models a little better.”
Single-cell transcriptomics
Shekhar and Sanes have, for the past eight years, been applying single-cell genomic approaches to profile the mRNA molecules in cells to categorize them according to their gene expression fingerprints. That technique has gradually helped identify more and more distinct cell types within the retina, many of them through studies that Shekhar initiated while a postdoctoral fellow with Aviv Regev, one of the pioneers of single-cell genomics, at the Broad Institute. It was in her lab that Shekhar began working with Sanes, a  retinal neurobiologist who became Shekhar’s co-advisor and collaborator.
In the current study, they wanted to expand their single-cell transcriptomic approach to other species to understand how retinal cell types have changed through evolution. They gathered, in all, eyes from 17 species: human, two monkeys (macaque and marmoset), four rodents (three species of mice and one ground squirrel), three ungulates (cow, sheep and pig), tree shrew, opossum, ferret, chicken, lizard, zebrafish and lamprey.
With Sanes’ team at Harvard conducting the transcriptomic experiments and Shekhar’s team at UC Berkeley conducting the computational analysis, many new cell types were identified in each of the species. They then mapped this variety to a smaller set of “orthotypes” — cell types that have likely descended from the same ancestral cell type in early vertebrates.
For bipolar cells, which are a class of neurons that lie between the photoreceptors and retinal ganglion cells, they found 14 distinct orthotypes. Most extant species contain 13 to 16 bipolar types, suggesting that these types have evolved little. In contrast, they found 21 orthotypes of retinal ganglion cells, which exhibit greater variation among species. Studies thus far have identified more than 40 distinct types in mice and about 20 different types in humans.
Interestingly, the pronounced evolutionary divergence among types of retinal ganglion cells, as compared to other retinal classes, suggests that natural selection acts more strongly on diversifying neuron types that transmit information from the retina to the rest of the brain.
They also found that numerous transcription factors, which have been implicated in retinal cell type specification in mice, are highly conserved, suggesting that the molecular steps leading to the development of the retina might be evolutionarily conserved, as well.
Based on the new work, Shekhar is refocusing his glaucoma research on the analogs of midget cells, called alpha cells, in mice.
The work was supported primarily by the National Institutes of Health (K99EY033457, R00EY028625, R21EY028633, U01MH105960, T32GM007103), the Chan-Zuckerberg Initiative (CZF-2019-002459) and the Glaucoma Research Foundation (CFC4). Shekhar also acknowledges support from the Hellman Fellows Program. Sanes was funded in part by NIH’s Brain Research Through Advancing Innovative Neurotechnologies Initiative, or the BRAIN Initiative.

University of Pittsburgh researchers have developed a new embryo-like model derived from adult cells that replicates key features of early human development, including the generation of blood cells.
Described today in Nature, the new heX-Embryoid model provides a unique window into early human development, which has been shrouded in mystery because of ethical and technical challenges of studying this period of life. HeX-Embryoids, which do not use fetal tissue and cannot develop into an embryo, could enhance research on genetic diseases and infertility and make cells to replace or repair tissues for regenerative medicine applications.
“Human embryos — unlike those in other species, including some of our closest primate relatives — embed themselves into the uterine wall to proceed with development. Because the embryo is smaller than the tip of a sewing needle and hidden from view, these early stages are difficult to study,” said senior author Mo Ebrahimkhani, M.D., associate professor in the Department of Pathology, the Pittsburgh Liver Institute and the Department of Bioengineering at Pitt. “Our embryo-like model will unlock this ‘black box’ of human development, which could help solve the mystery of why about 60% of pregnancies fail in the first two weeks — before the mother even misses a menstrual period — and pave the way for new therapies.”
Remarkably, the heX-Embryoid models formed structures similar to the first sites to produce blood cells that support the developing embryo called blood islands. The researchers also detected progenitors of red blood cells, platelets and different types of white blood cells. According to Ebrahimkhani, the generation of blood cells is a key advance of this embryo model that pushes the field forward.
“We were able to model something extremely similar to the earliest stages of blood production in humans,” said Ebrahimkhani, who is also a member of the Pittsburgh Liver Research Center and the McGowan Institute of Regenerative Medicine of Pitt and UPMC. “This is exciting because there are extensive possibilities to apply this model to better understand how blood is formed and develop better methods for growing cells for blood transfusions, novel cell therapies and hematopoietic stem cell transplants.”
To develop heX-Embryoids, the researchers started with induced pluripotent stem cells (iPSCs), which are generated from adult cells that have been reverted to a state where they can develop into any other cell. Then they programmed the iPSCs with a genetic circuit that directs early tissue development, which is only switched on by a chemical called doxycycline. When these engineered iPSCs are mixed in a lab dish with standard iPSCs and induced by adding doxycycline, the engineered cells grow and trigger the standard iPSCs to organize into three-dimensional structures that resemble certain features of an embryo.
In normal embryonic development, cells repeatedly sort and divide to eventually form distinct sections: the trophoblast, which will become the placenta, an extra-embryonic cell layer that produces the nutrient-providing yolk sac and the embryonic layer that will give rise to the embryo itself and the amniotic sac that protects the developing embryo.

Like an embryo, heX-Embryoids have embryonic tissue and a yolk sac structure. The tissue remains anchored to the lab dish as it grows, forming a large sheet of yolk sac with dozens of embryoids sitting side by side.
“The yolk sac doesn’t contribute directly to making cells that form the embryo, but it’s a really important tissue because it’s responsible for nourishment and influencing where the head and tail of the embryo will be positioned,” said lead author Joshua Hislop, a graduate student in Ebrahimkhani’s lab at Pitt. “Other embryo-like models have had very limited differentiation of yolk sac tissue, so our model offers a unique opportunity to robustly follow this structure and study events like blood development.”
HeX-Embryoids do not contain the placenta-forming trophoblast layer, and the yolk sac is open, not a closed cavity. The lack of these features prevents embryoids becoming a true embryo or having the potential to be implanted to develop completely.
Because heX-Embryoids are derived from reprogrammed adult skin cells, they could theoretically be made from any individual, allowing researchers to study diverse genetic backgrounds.
An important advantage of the heX-Embryoid system over other embryo-like models is that it self-organizes as it grows from the two-dimensional lab dish, uses standard growth media and is switched on by a single chemical, rather than relying on a complicated cocktail of growth factors that can be difficult to replicate. According to Ebrahimkhani, this unique approach means that heX-Embryoids can be easily stored, shipped and grown in different labs with a high level of efficiency.
“For a model to be adopted by the scientific community and do its job of contributing to new discoveries, it must be efficient,” said Ebrahimkhani. “For example, it will be very difficult to make progress in researching miscarriage if the model itself fails most of the time. Our heX-Embryoid model overcomes this problem.”
Other authors on the study were Kamyar Keshavarz F., Rayna Schoenberger, Ryan LeGraw, Jeremy Velazquez, Ph.D., Tahere Mokhtari, Mohammad Naser Taheri, Matthew Rytel, Simon Watkins, Ph.D., Donna Stolz, Ph.D., and Samira Kiani, M.D., all of Pitt; Qi Song, Ph.D., Amir Alavi, Ph.D., and Ziv Bar-Joseph, Ph.D., all of Carnegie Mellon University; Susana Chuva de Sousa Lopes, Ph.D., of Leiden University Medical Center; and Berna Sozen, Ph.D., of Yale University.
This research was supported by the National Heart, Lung, and Blood Institute (R01 HL141805), the National Science Foundation (#2134999), the National Institutes of Health (1R01GM122096, OT2OD026682, 1U54AG075931, 1U24CA268108, T32 EB001026 and 1S10OD019973-01), the National Institute of Biomedical Imaging and Bioengineering (EB028532), the Pittsburgh Liver Research Center (NIHNIDDK P30DK120531), the Pitt Department of Pathology startup fund, the Pitt Center for Biological Imaging and the Pitt Flow Cytometry Core facilities.