ndrew Bergantz, a junior at WashU, speaks about his experience living on the autism spectrum. Andrew Bergantz is a junior at WashU majoring in mechanical engineering and minoring in aerospace engineering. This talk was given at a TEDx event using the TED conference format but independently organized by a local community.
According to some estimates, hundreds of genes may be associated with autism ), but it has been difficult to determine which mutations are truly involved in the disease and which are incidental. New work published in the journal Science Translational Medicine led by researchers at Baylor College of Medicine shows that a novel computational approach can effectively identify genes most likely linked to the condition, as well as predict the severity of intellectual disability in patients with autism using only rare mutations in genes beyond those already associated with the syndrome.
Knowing which genes contribute to autism , researchers can then study them to better understand how the condition happens and use them to improve predicting the risk of the syndrome and more effectively advise parents of potential outcomes and treatments.
“Autism is a very complex condition and many cases do not have a clear genetic explanation based on current knowledge,” said first author Dr. Amanda Koire, a graduate student in the Dr. Olivier Lichtarge lab during the development of this project. She is currently a psychiatry research resident at Brigham and Women’s Hospital, Harvard Medical School.
There is not one gene that causes the majority of autism cases, the researchers explained. “The most commonly mutated genes linked to the syndrome only account for approximately 2% of the cases,” said Lichtarge, Cullen Chair and professor of molecular and human genetics, biochemistry and molecular biology and pharmacology and chemical biology at Baylor. “The current thought is that the syndrome results from a very large number of gene mutations, each mutation having a mild effect.”
The challenge is to identify which gene mutations are indeed involved in the condition, but because the variants that contribute to the development of autism are individually rare, a patient by patient approach to identify them would likely not succeed. Even current studies that compare whole populations of affected individuals and unaffected parents and siblings find genes that only explain a fraction of the cases.
The Baylor group decided to take a completely different perspective. First, they added a vast amount of evolutionary data to their analyses. These data provided an extensive and open, but rarely fully accessed, record of the role of mutations on protein evolution, and, by extension, on the impact of human variants on protein function. With this in hand, the researchers could focus on the mutations most likely to be harmful. Two other steps then further narrowed the resolution of the study. A focus on personal mutations, that are unique to each individual, and also on how these mutations add up in each molecular pathway.
Exploring the contribution of de novo missense mutations in autism
The researchers looked into a group of mutations known as missense variants. While some mutations disrupt the structure of proteins so severely as to render them inactive, missense mutations are much more common but are harder to assess than loss-of-function mutations because they can just tweak the protein’s function a little or severely impair it.
“Some loss-of-function mutations have been associated with the severity of autism , measured by diminished motor skills and IQ, but missense mutations had not been linked to the same autismpatient characteristics on a large-scale due to the difficulty in interpreting their impact,” said co-author Dr. Panagiotis Katsonis, assistant professor of molecular and human genetics at Baylor. “However, people with autism are more likely to carry a de novo missense mutation than a de novo loss-of-function mutation and the tools previously developed in our lab can help with the interpretation of this majority of coding variants. De novo or new mutations are those that appear for the first time in a family member, they are not inherited from either parent.”
The researchers took on the challenge to identify, among all the de novo missense mutations in a cohort of patients with autiusm and their siblings as a whole, those mutations that would distinguish between the patients and the unaffected siblings.
A multilayered approach
The team applied a multilayered strategy to identify a group of genes and mutations that most likely was involved in causing autism .
They first identified a group of de novo mutations by examining the sequences of all the protein coding genes of 2,392 families with members with autism that are in the Simons Simplex Collection. Then, they evaluated the effect of each missense mutation on the fitness or functionality of the corresponding protein using the Evolutionary Action (EA) equation, a computational tool previously developed in the Lichtarge lab. The EA equation provides a score, from 0 to 100, that reflects the effect of the mutation on the fitness of the protein. The higher the score, the lower the fitness of the mutated protein.
The results suggested that among the 1,418 de novo missense mutations affecting 1,269 genes in the patient group, most genes were mutated only once.
“Knowing that autism is a multigenic condition that presents on a spectrum, we reasoned that the mutations that were contributing to autism could dispersed amongst the genes of a metabolic pathway when examined at a cohort level, rather than being clustered on a single gene,” Koire said. “If any single component of a pathway becomes affected by a rare mutation, it could produce a clinical manifestation of autism , with slightly different results depending on the specific mutation and the gene.”
Without making any a priori assumptions regarding which genes or pathways drive ASD, the researchers looked at the cohort as a whole and asked, in which pathways are there more de novo missense mutations with higher EA scores than expected?
The team found that significantly higher EA scores of grouped de novo missense mutations implicated 398 genes from 23 pathways. For example, they found that axonogenesis, a pathway for the development of new axons in neurons in the brain, stood out among other pathways because it clearly had many missense mutations that together demonstrated a significant bias toward high EA scores indicating impactful mutations. Synaptic transmission and other neurodevelopmental pathways were also among those affected by mutations with high EA scores.
“As a result of layering together all these different complementary views of potential functional impact of the mutations on the biology, we could identify a set of genes that clearly related to autism ,” Lichtarge said. “These genes fell in pathways that were not necessarily surprising, but reassuringly related to neurological function. Some of these genes had been linked to autism before, but others had not been previously associated with the syndrome.”
“We also were very excited to see a relationship between the EA score of the mutations in those genes linked to ASD and the patient’s IQ,” Koire said. “For the new genes we found linked to ASD, the mutations with higher EA scores were related to a 7 point lower IQ in the patients, which suggests that they have a genuine biological effect.”
“This opens doors on many fronts,” said co-author Young Won Kim, graduate student in Baylor’s Integrative Molecular and Biomedical Sciences Graduate Program working in the Lichtarge lab. “It suggests new genes we can study in autism , and that there is a path forward to advise parents of children with these mutations of the potential outcomes in their child and how to best involve external support in early development intervention, which has shown to make a huge difference in outcome as well.”
“Our findings may go beyond autism ,” Lichtarge said. “This approach, we hope, could be tested in a wide set of complex diseases. As many genome sequence data become increasingly accessible for research, it should then be possible to interpret the rare mutations which they yield as we showed here. This may then resolve better than now the polygenic basis of various adult diseases and also improve estimates of individual risk and morbidity.”
By mapping its genetic underpinnings, researchers at University of California San Diego School of Medicine have identified a predictive causal role for specific cell types in type 1 diabetes, a condition that affects more than 1.6 million Americans.
The findings are published in the May 19, 2021 online issue of Nature.
Type 1 diabetes is a complex autoimmune disease characterized by the impairment and loss of insulin-producing pancreatic beta cells and subsequent hyperglycemia (high blood sugar), which is damaging to the body and can cause other serious health problems, such as heart disease and vision loss. Type 1 is less common than type 2 diabetes, but its prevalence is growing. The U.S. Centers for Disease Control and Prevention projects 5 million Americans will have type 1 diabetes by 2050. Currently, there is no cure, only disease management.
The mechanisms of type 1 diabetes, including how autoimmunity is triggered, are poorly understood. Because it has a strong genetic component, numerous genome-wide association studies (GWAS) have been conducted in recent years in which researchers compare whole genomes of persons with the same disease or condition, searching for differences in the genetic code that may be associated with that disease or condition.
In the case of type 1 diabetes, identified at-risk variants have largely been found in the non-coding regions of the genome. In the Nature study, senior author Kyle Gaulton, PhD, an assistant professor in the Department of Pediatrics at UC San Diego School of Medicine, and colleagues integrated GWAS data with epigenomic maps of cell types in peripheral blood and the pancreas. Epigenomic mapping details how and when genes are turned on and off in cells, thus determining the production of proteins vital to specific cellular functions.
Specifically, researchers performed the largest-to-date GWAS of type 1 diabetes, analyzing 520,580 genome samples to identify 69 novel association signals. They then mapped 448,142 cis-regulatory elements (non-coding DNA sequences in or near a gene) in pancreas and peripheral blood cell types.
“By combining these two methodologies, we were able to identify cell type-specific functions of disease variants and discover a predictive causal role for pancreatic exocrine cells in type 1 diabetes, which we were able to validate experimentally,” said Gaulton.
Pancreatic exocrine cells produce enzymes secreted into the small intestine, where they help digest food.
Co-author Maike Sander, MD, professor in the departments of Pediatrics and Cellular and Molecular Medicine at UC San Diego School of Medicine and director of the Pediatric Diabetes Research Center, said the findings represent a major leap in understanding the causes of type 1 diabetes. She described the work as “a landmark study.”
“The implication is that exocrine cell dysfunction might be a major contributor to disease. This study provides a genetic roadmap from which we can determine which exocrine genes may have a role in disease pathogenesis.”
A tiny, 3D model of the intestines formed from anti-inflammatory cells known as Paneth cells (green and red) and other intestinal cells (blue) is seen in the image above. Researchers at Washington University School of Medicine in St. Louis and the Cleveland Clinic used such models, called organoids, to understand why a Western-style diet rich in fat and sugar damages Paneth cells and disrupts the gut immune system. Ta-Chiang Liu
Eating a Western diet impairs the immune system in the gut in ways that could increase risk of infection and inflammatory bowel disease, according to a study from researchers at Washington University School of Medicine in St. Louis and Cleveland Clinic.
The study, in mice and people, showed that a diet high in sugar and fat causes damage to Paneth cells, immune cells in the gut that help keep inflammation in check. When Paneth cells aren’t functioning properly, the gut immune system is excessively prone to inflammation, putting people at risk of inflammatory bowel disease and undermining effective control of disease-causing microbes. The findings, published May 18 in Cell Host & Microbe, open up new approaches to regulating gut immunity by restoring normal Paneth cell function.
“Inflammatory bowel disease has historically been a problem primarily in Western countries such as the U.S., but it’s becoming more common globally as more and more people adopt Western lifestyles,” said lead author Ta-Chiang Liu, MD, PhD, an associate professor of pathology & immunology at Washington University. “Our research showed that long-term consumption of a Western-style diet high in fat and sugar impairs the function of immune cells in the gut in ways that could promote inflammatory bowel disease or increase the risk of intestinal infections.”
Paneth cell impairment is a key feature of inflammatory bowel disease. For example, people with Crohn’s disease, a kind of inflammatory bowel disease characterized by abdominal pain, diarrhea, anemia and fatigue, often have Paneth cells that have stopped working.
Liu and senior author Thaddeus Stappenbeck, MD, PhD, chair of the Department of Inflammation and Immunity at Cleveland Clinic, set out to find the cause of Paneth cell dysfunction in people. They analyzed a database containing demographic and clinical data on 400 people, including an assessment of each person’s Paneth cells. The researchers found that high body mass index (BMI) was associated with Paneth cells that looked abnormal and unhealthy under a microscope. The higher a person’s BMI, the worse his or her Paneth cells looked. The association held for healthy adults and people with Crohn’s disease.
To better understand this connection, the researchers studied two strains of mice that are genetically predisposed to obesity. Such mice chronically overeat because they carry mutations that prevent them from feeling full even when fed a regular diet. To the researchers’ surprise, the obese mice had Paneth cells that looked normal.
In people, obesity is frequently the result of eating a diet rich in fat and sugar. So the scientists fed normal mice a diet in which 40% of the calories came from fat or sugar, similar to the typical Western diet. After two months on this chow, the mice had become obese and their Paneth cells looked decidedly abnormal.
“Obesity wasn’t the problem per se,” Liu said. “Eating too much of a healthy diet didn’t affect the Paneth cells. It was the high-fat, high-sugar diet that was the problem.”
The Paneth cells returned to normal when the mice were put back on a healthy mouse diet for four weeks. Whether people who habitually eat a Western diet can improve their gut immunity by changing their diet remains to be seen, Liu said.
“This was a short-term experiment, just eight weeks,” Liu said. “In people, obesity doesn’t occur overnight or even in eight weeks. People have a suboptimal lifestyle for 20, 30 years before they become obese. It’s possible that if you have Western diet for so long, you cross a point of no return and your Paneth cells don’t recover even if you change your diet. We’d need to do more research before we can say whether this process is reversible in people.”
Further experiments showed that a molecule known as deoxycholic acid, a secondary bile acid formed as a byproduct of the metabolism of gut bacteria, forms the link between a Western diet and Paneth cell dysfunction. The bile acid increases the activity of two immune molecules — farnesoid X receptor and type 1 interferon — that inhibit Paneth cell function.
Liu and colleagues now are investigating whether fat or sugar plays the primary role in impairing Paneth cells. They also have begun studying ways to restore normal Paneth cell function and improve gut immunity by targeting the bile acid or the two immune molecules.
Mutations associated with autism can inhibit the release of the bonding hormone oxytocin and cause abnormal social behavior in mice
Researchers understand the neurobiology of autism and develop effective treatments for it. CREDIT Tokyo University of Science
Autism r is a neurodevelopmental condition involving impaired social abilities, and this makes it a fascinating subject for neuroscientists like Prof. Teiichi Furuichi of the Tokyo University of Science who study the neuroscience of social behavior. Prof. Furuichi and his colleagues have previously worked on developing mouse models of autism to unravel the condition’s neurochemical mechanisms, and in a paper recently published in the prestigious Journal of Neuroscience, they provide evidence that a genetic mutation associated with autism can impair the release of a peptide called oxytocin that plays an important role in regulating social behavior. This finding promises to broaden our understanding of the neurobiology of social behavior.
The gene that Prof. Furuichi’s team chose to study is Caps2, which encodes a protein called Ca2+-dependent activator protein for secretion 2 (CAPS2) that regulates the release of brain chemicals (or “neurotransmitters”). Previous studies have shown that CAPS2 deficiencies in mice cause behavioral impairments such as reduced sociality, increased anxiety, and disrupted circadian rhythms. Furthermore, a study of Japanese patients with autism spectrum disorder revealed that some of them had Caps2 mutations that adversely affect the CAPS2 protein’s functions. Prof. Furuichi and his colleagues had previously discovered that the CAPS2 protein is expressed in neurons in the hypothalamus and pituitary gland that release the neuropeptide oxytocin. This information formed the basis of their recent study. As Prof. Furuichi explains, “We hypothesized that CAPS2 deficiencies in mice should alter oxytocin release, which should in turn result in impaired social behavior.”
To test this hypothesis, researchers Shuhei Fujima, Graduate Student at Tokyo University of Science; Yoshitake Sano, Junior Associate Professor at Tokyo University of Science; Yo Shinoda, Associate Professor at Tokyo University of Pharmacy and Life Sciences; Tetsushi Sadakata, Associate Professor in Gunma University; Manabu Abe, Associate Professor at Niigata University; and Kenji Sakimura, a Fellow of Niigata University, among others, led by Prof. Furuichi conducted a series of experiments involving mice that carried genetic alterations that prevented them from expressing the CAPS2 protein. These mice had lower-than-normal oxytocin levels in their blood but higher-than-normal oxytocin levels in the hypothalamus and pituitary gland. The researchers interpreted this finding as evidence that CAPS2 deficiencies impede the normal release of oxytocin from these brain regions into the bloodstream.
Unsurprisingly, the reduced bloodstream levels of oxytocin had clear behavioral effects. When placed inside a rectangular box, the oxytocin neuron-specific CAPS2-deficient mice were unwilling to spend much time in the center of the box, and the researchers interpreted this as evidence of increased anxiety about the risk of a predator attacking them. The CAPS2-deficient mice also exhibited diminished willingness to engage in social interactions when introduced to unfamiliar mice. Interestingly, spraying an oxytocin solution into the noses of the CAPS2-deficient mice acted to restore their willingness to socially interact with unfamiliar mice.
Based on these findings, Prof. Furuichi and his colleagues conclude that the CAPS2 protein plays a critical role in facilitating the release of peripheral oxytocin into the bloodstream. They similarly suggest that CAPS2 is also involved in the release of central oxytocin into the brain regions relating to the control of sociality. Given the key role that oxytocin plays in regulating social behaviors, this could help to explain how mutations in the Caps2 gene could lead to atypical patterns of social behavior in persons with autism spectrum disorder. When asked about the social significance of his team’s work, Prof. Furuichi remarks, “We believe that this research, although basic, is an important achievement that will contribute to the development of tools for the early molecular diagnosis and effective treatment of autism spectrum disorder.”
Given the relatively high prevalence of autism and how extremely disabling severe cases can be, the development of effective treatments would have major benefits for people with autism and the society as a whole.