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In the latest of ongoing efforts to expand technologies for modifying genes and their expression, researchers in the lab of Neville Sanjana, PhD, at the New York Genome Center (NYGC) and New York University (NYU) have developed chemically modified guide RNAs for a CRISPR system that targets RNA instead of DNA. These chemically-modified guide RNAs significantly enhance the ability to target — trace, edit, and/or knockdown — RNA in human cells.
In a study published today in Cell Chemical Biology, the team explores a range of different RNA modifications and details how the modified guides increase efficiencies of CRISPR activity from 2- to 5-fold over unmodified guides. They also show that the optimized chemical modifications extend CRISPR targeting activity from 48 hours to four days. The researchers worked in collaboration with scientists at Synthego Corporation and New England BioLabs, bringing together a diverse team with expertise in enzyme purification and RNA chemistry. To apply these optimized chemical modifications, the research team targeted cell surface receptors in human T cells from healthy donors and a “universal” segment of the genetic sequence shared by all known variants of the RNA virus SARS-COV-2, which is responsible for the COVID-19 pandemic.
Increasing the efficiencies and “life” of CRISPR-Cas13 guides is of critical value to researchers and drug developers, allowing for better gene knockdown and more time to study how the gene influences other genes in related pathways.
“CRISPR RNA guide delivery can be challenging, with knockdown time limited due to rapid guide degradation. We were inspired by the guide modifications developed for other DNA-targeting CRISPRs and wanted to test if chemically modified guides could improve knockdown time for RNA-targeting CRISPR-Cas13 in human cells,” says Alejandro Méndez-Mancilla, PhD, a postdoctoral scientist in the lab and co-first author of the study.
Drawing on the lab’s previous study that outlined principles for optimal Cas13 guide design, published in Nature Biotechnology in March 2020, the researchers systematically applied and tested a variety of chemical modifications. For example, they found that adding 3 bases with a different type of chemical bond linking them to each other (phosphorothioate modification) extended RNA target knockdown ability by several days in a human cell line. In primary T cells, the phosphorothioate modification resulted in 60 — 65% knockdown of expression of CD46, a receptor involved in immune system regulation, as compared to achieving 40 — 45% knockdown when using an unmodified guide.
The team also found that certain methylation and inverted terminator modifications also improved Cas13 activity. For all modifications, the placement of these modified RNA bases was also crucial. When placed incorrectly, the modifications resulted in guide RNAs that did not function. “We hope the improved effectiveness and stability from these modified CRISPR Cas13 guides will help pave the way for use of RNA-targeting CRISPRs in primary cells,” says Hans-Hermann Wessels, PhD, a postdoctoral scientist in the lab who is a co-first author of the study.
“These modified guides further expand the toolbox for genome and transcriptome engineering. For non-coding elements in the human genome, targeting DNA may not be effective, and other organisms, such as RNA viruses like coronavirus or flu, cannot be targeted at all,” said Dr. Sanjana, Core Faculty Member, NYGC, Assistant Professor of Biology, NYU, and Assistant Professor of Neuroscience and Physiology, NYU Grossman School of Medicine, the study’s senior author.
The team’s test to knockdown the universal leader sequence segment of the RNA virus SARS-CoV-2 in human cells, for example, is only possible using an RNA-targeting CRISPR like Cas13. SARS-CoV-2 enters the cells and releases its RNA genome, which is then transcribed into smaller RNAs, referred to as subgenomic RNAs. These subgenomic RNAs are responsible for making the different proteins required for the virus to replicate and then infect other cells. The universal leader sequence is found at the beginning of each subgenomic RNA. Thus, an effective approach for targeting the universal leader sequence may protect cells against further viral replication and infection.
Also of key import is CRISPR-Cas13’s ability to modulate genetic expression without permanently altering the underlying DNA genome sequence, as do DNA-targeting CRISPRs like Cas9 or Cas12a. “Transient modulation to spur genetic expression outcomes is often preferred in biomedical research and drug development. For example, the messenger RNA vaccines for SARS-CoV-2 express transiently but create an immune memory that lasts beyond their expression lifetime,” notes Dr. Sanjana.
Co-authors of the Cell Chemical Biology study include Mateusz Legut, PhD, a postdoctoral scientist in the lab; Anastasia Kadina, PhD, Senior Scientist, Chemistry Research, Synthego Corporation; Megumu Mabuchi, Associate Scientist,, RNA Biology & Genome Editing, New England BioLabs; John Walker, PhD, Director of Chemistry Research, Synthego Corporation; G. Brett Robb, PhD, Scientific Director, RNA & Genome Editing, and Kevin Holden, PhD, Head of Science, Synthego Corporation.

Celiac disease is a complex, autoimmune disorder that affects genetically susceptible individuals. It is estimated that 1% of the population suffer from this disease. To be able to diagnose celiac disease it is necessary at present to carry out an endoscopy, a test that is not only highly unpleasant, but also costly and in some cases unnecessary. Patients with symptoms of celiac disease undergo an endoscopy, but the symptoms, such as stomach pain, weight loss or anaemia, are very common, and are similar to those of other disorders of the digestive system. In turn, the genetic variant conferring an increased risk of developing celiac disease is present in a high percentage of the healthy population. So many non-celiac patients with symptoms and who are at a genetic risk are needlessly subjected to an endoscopy.
In collaboration with the Biodonostia and Biocruces Institutes and the Txagorritxu and Galdakao Hospitals, researchers from Ikerbasque and the UPV/EHU have now developed a non-invasive method to help diagnose celiac disease and which uses saliva. This research has shown that it is possible to considerably reduce the number of endoscopies, which are currently carried out via a non-invasive method of diagnosis.
This was the procedure they followed: firstly, they confirmed that the same inflammation seen in the intestine of celiac patients could be detected in saliva. The inflammation was then quantified in saliva samples from celiac and control patients. These saliva samples were also tested for the genetic risk of developing celiac disease. With these data on inflammation and genetic risk, a predictive formula was developed. The predictive capacity of this model was subjected to a blind test involving 100 saliva samples, and that resulted in a 73% success rate. In addition, the predictive model displayed a sensitivity of 91%, signifying a 91% success rate among people with celiac disease.
Ainara Castellanos, the lead researcher of the study, and Maialen Sebastian, a pre-doctoral student, consider that the method they have developed “is very useful for screening patients with suspected celiac disease before endoscopy is carried out.” They also recognised that, despite the good results obtained with their prediction model, it is not 100% accurate, which means that the current traditional diagnostic method cannot be totally ruled out. So the authors of this study propose that only those individuals predicted by this model to have celiac disease should undergo an endoscopy, which would considerably reduce the number of endoscopies currently performed.
They also showed that the same saliva sample can also be used to test for the genetic risk of the disease, so it could also offer a non-invasive alternative to genetic testing using blood samples, given that the collecting of saliva samples is more convenient than blood collection.
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Researchers from the University of Turku have discovered a new method of X-ray imaging based on the colouring abilities of the natural mineral hackmanite. The international group of researchers also found out how and why hackmanite changes colour upon exposure to X-rays.
Hackmanite is a natural mineral which glows in the dark. It is also known for its ability to change colour from off-white to pink or violet upon UV exposure. In the recently-published study, the mineral’s colouring abilities were studied under exposure to X-rays.
“Previous studies had published initial results about the way hackmanite changes colour upon exposure to X-rays, but it was unclear why and how this colouring came to be and whether this feature could be useful somehow. We were the first to attempt X-ray imaging using a surface made of hackmanite as the image plate, and the results were very exciting,” says Docent Mika Lastusaari from the University of Turku.
The research group for intelligent photonic materials led by Lastusaari conducts pioneering research of materials with light and colour-related properties at the Department of Chemistry of the University of Turku. The group creates the hackmanites synthetically, which enables them to control the properties of the material and adapt it for different uses by adding or replacing atoms in the basic structure of the material.
“In this research, we studied the behaviour of four types of synthetic hackmanites upon exposure to X-rays in the Karlsruhe synchrotron radiation facility in Germany using a particle accelerator which generates X-rays with tunable energy. All of the samples were positive surprises, and we were able to receive valuable information about how adding different atoms in the basic structure impacts the colouring abilities,” explains Doctoral Candidate Sami Vuori.
“We also noticed that the mechanism of colour changing occurs by X-rays exciting the inner shell electrons, unlike with UV radiation, which causes only the loosest electrons of the outer shells to participate in the colouration,” adds Vuori.
Measuring Radiation Doses and Imaging with the Help of Hackmanite
According to the researchers, hackmanite can be considered to be somewhat of a miracle material due to its many usage possibilities. Now, the usage repertoire of the mineral will also include X-ray imaging as proven by an X-ray image of a dead ant’s body.
“Using hackmanite for imaging has the advantage that it does not require expensive analysis tools for the image to be seen: you can see the image with your own eyes and record it with a camera. As an example, this photo has been taken with a regular DLSR camera after exposure to X-rays. However, its best feature is that the hackmanite film in the photo is not a single-use film: the image can be cleared with the help of light or heat, and a new object can be imaged with the same film,” explains Doctor Isabella Norrbo, who has written her doctoral thesis on hackmanites.
The research was conducted in collaboration with the French University of Lyon, Karlsruhe Institute of Technology, and the Brazilian University of São Paulo.
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Linked to serious health problems including cancer, diabetes and cardiovascular disease, obesity affects more than a third of adults in the United States. Presently, there are few safe and effective nonsurgical therapeutic interventions available to patients with obesity.
Now, a multi-disciplinary team of researchers has demonstrated that a metabolic regulatory molecule called Them1 prevents fat burning in cells by blocking access to their fuel source. Led by microscopy experts at Beth Israel Deaconess Medical Center (BIDMC) and metabolism experts at Weill Cornell Medicine and NewYork-Presbyterian, the study may contribute to the development of a new type of obesity treatment. The team’s findings were published June 9 in Nature Communications.
To help explain how the protein Them1 turns off heat production, BIDMC’s cell biology and microscopy expert, Susan Hagen, PhD, associate vice-chair for research in the Department of Surgery at BIDMC, and Yue Li, PhD, a postdoctoral researcher in her laboratory, used light and electron microscopy to observe Them1 in action in mouse brown fat cells grown in the laboratory.
“Them1 is an interesting molecule,” said Hagen. “If you inhibit or block its expression, metabolism increases and that reduces body weight.”
The experiments showed that when the cells are stimulated to burn fat, a chemical modification causes Them1 molecules to spread out, or diffuse, throughout the cell. This frees the cellular powerhouses called mitochondria to efficiently turn the cell’s fat stores into energy. But when the stimulation stops, Them1 molecules quickly reorganize into a structure called a biomolecular condensate. Situated between the mitochondria and the fats they use as fuel, the condensed Them1 molecules limit energy production.
“It turned out to be so incredibly interesting,” said Hagen, who is also director of Microscopy and Histology Core Facilities at BIDMC and associate professor of surgery at Harvard Medical School. “We asked other microscopy experts whether they had ever seen anything like the unusual images we found in resting cells. Using very sophisticated electron microscopy techniques, we were able to show — for the first time, as far as we know — what the bimolecular condensate looks like in electron microscopy.”
“The study explains a new mechanism that regulates metabolism,” said David Cohen, chief of the Division of Gastroenterology and Hepatology at Weill Cornell Medicine and NewYork-Presbyterian/Weill Cornell Medical Center and the Vincent Astor Distinguished Professor of Medicine at Weill Cornell Medicine. “Them1 hacks the energy pipeline and cuts off the fuel supply to the energy-burning mitochondria. Humans also have brown fat and produce more Them1 in cold conditions, so the findings may have exciting implications for the treatment of obesity.”
Cohen and Hagen, both members of the Harvard Digestive Diseases Center, have been collaborators since 1983. The current study — supported in part by a five-year, multi-PI grant from the National Institutes of Health — also included collaborators with expertise in structural biology from Emory University.
“This was the most fun I have ever had in science in my life,” Hagen added. “Including multiple primary investigators with different expertise gives you the power of doing things that you could never do on your own.”
Co-authors included Yue Li, Samaksh Goyal, Lay-Hong Ang, and Mahnoor Baqai of BIDMC; Norihiro Imai, Hayley T. Nichols, Tibor I. Krisko of Weill Cornell; Blaine R. Roberts, Matthew C. Tillman, Anne M. Roberts, and Eric A. Ortlund of Emory University.
This work was supported by the National Institutes of Health (R01 DK 103046, R01 DK0488730 and NIHT32DK007533), the Harvard Digestive Disease Center (P30 DK034854) and the National Institutes of Health shared-instrumentation grant program for the High Pressure Freezer (S10 OD019988-01), the Pinnacle Research Award from the AAASLD Foundation, Weill Cornell Department of Medicine Pre-Career Award, and an American Heart Association Postdoctoral Fellowship, and a Research Science Institute/Center for Excellence in Education Summer Research Fellowship.

Cutting just 250 calories a day with moderate exercise reaped bigger rewards than exercise alone for older, obese adults. Among older adults with obesity, combining aerobic exercise with a moderate reduction in daily calories resulted in greater improvements in aortic stiffness (a measure of vascular health, which impacts cardiovascular disease), compared to exercise only or to exercise plus a more restrictive diet, according to new research published today in the American Heart Association’s flagship journal Circulation.
Modifiable lifestyle factors such as a healthy diet and regular physical activity may help offset age-related increases in aortic stiffness. Although aerobic exercise generally has favorable effects on aortic structure and function, previous studies have shown that exercise alone may not be sufficient to improve aortic stiffness in older adults with obesity.
“This is the first study to assess the effects of aerobic exercise training with and without reducing calories on aortic stiffness, which was measured via cardiovascular magnetic resonance imaging (CMR) to obtain detailed images of the aorta,” said Tina E. Brinkley, Ph.D., lead author of the study and associate professor of gerontology and geriatric medicine at the Sticht Center for Healthy Aging and Alzheimer’s Prevention at Wake Forest School of Medicine in Winston-Salem, North Carolina. “We sought to determine whether adding caloric restriction for weight loss would lead to greater improvements in vascular health compared to aerobic exercise alone in older adults with obesity.”
This randomized controlled trial included 160 sedentary adults, ages 65-79 years with obesity (BMI=30-45 kg/m2). The average age of the participants was 69 years; 74% were female; and 73% were white. Participants were randomly assigned to one of three intervention groups for 20 weeks: 1) exercise only with their regular diet; 2) exercise plus moderate calorie restriction (reduction of approximately 250 calories/day); or 3) exercise plus more intensive calorie restriction (reduction of approximately 600 calories/day).
The two calorie-restricted groups received pre-made lunches and dinners with less than 30% of calories from fat and at least 0.8 grams of protein per kg of their ideal body weight, prepared under the direction of a registered dietitian for the study; they made their own breakfasts according to the dietitian-approved menu. Everyone in the study received supervised aerobic exercise training four days per week for the duration of the 20-week study at the Geriatric Research Center at Wake Forest School of Medicine.
The structure and function of the aorta were assessed with cardiovascular magnetic resonance imaging to measure aortic arch pulse wave velocity (PWV) (the speed at which blood travels through the aorta) and distensibility, or the ability of the aorta to expand and contract. Higher PWV values and lower distensibility values indicate a stiffer aorta.
The results found that weight loss of nearly 10% of total body weight or about 20 pounds over the five-month study period was associated with significant improvements in aortic stiffness — only in the participants assigned to the exercise plus moderate calorie restriction group. Additional findings include: The exercise plus moderate calorie restriction group had a 21% increase in distensibility and an 8% decrease in PWV. None of the aortic stiffness measures changed significantly in either the exercise-only group or the exercise plus more intensive calorie restriction group. Changes in BMI, total fat mass, percent body fat, abdominal fat and waist circumference were greater in both of the calorie-restricted groups compared to the exercise-only group. Weight loss was similar between the calorie-restricted groups despite nearly two times fewer calories (26.7% reduction in calories vs. a 14.2% reduction in calories) in the intensive calorie restriction group.”Our findings indicate that lifestyle changes designed to increase aerobic activity and moderately decrease daily calorie intake may help to reduce aortic stiffness and improve overall vascular health,” said Brinkley. “However, we were surprised to find that the group that reduced their calorie intake the most did not have any improvements in aortic stiffness, even though they had similar decreases in body weight and blood pressure as the participants with moderate calorie restriction.”
Brinkley added, “These results suggest that combining exercise with modest calorie restriction — as opposed to more intensive calorie restriction or no-calorie restriction — likely maximizes the benefits on vascular health, while also optimizing weight loss and improvements in body composition and body fat distribution. The finding that higher-intensity calorie restriction may not be necessary or advised has important implications for weight loss recommendations to improve cardiovascular disease risk in older adults with obesity.”
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One type of the salmonella bacteria is much more likely to cause disease and fend off frontline antibiotics when acquired in Europe, Asia, and parts of Africa rather than domestically in the United States.
Washington State University researchers aren’t sure yet why salmonella Kentucky isolates from certain parts of the globe are antibiotic resistant while others aren’t, but their findings are a key step toward better understanding and treatment.
“Quite frankly, I think we’ve just gotten lucky this drug-resistant type hasn’t popped up in the U.S. yet,” said Rachel Soltys, a graduate student and first author of a paper on the research in the Journal of Frontiers and Sustainable Food Systems.
The study was conducted in the laboratory of Devendra Shah, an associate professor and the Caroline Engle Distinguished Professor in Research on Infectious Diseases. Shah is part of the university’s large disease research effort and is housed in WSU’s Department of Veterinary Microbiology and Pathology.
Researchers in the Shah lab looked specifically at salmonella Kentucky. Just like other salmonella types, the bacteria thrive in the gastrointestinal tracts of food animals such as chickens and cattle, and are known to cause diarrhea, abdominal pain, and fever in humans.
The researchers found that more than 60% of Washingtonians with a confirmed salmonella Kentucky infection while abroad from 2004 to 2014 were resistant to fluoroquinolones, a group of frontline antibiotics used to treat salmonella infection.

Patients undergoing surgery and other medical procedures are routinely pre-screened for urinary tract infections (UTIs), but the vast majority of these tests are not needed, according to a new investigation by researchers at Massachusetts General Hospital (MGH). The authors of this research letter, published in JAMA Internal Medicine, argue that these unneeded tests not only waste money and resources but also expose patients to potential harms and may worsen the persistent problem of antibiotic resistance.
A urinalysis is a medical test that screens urine for a variety of abnormalities, including the presence of bacteria. Clinicians commonly order a urinalysis if a patient has signs and symptoms of a UTI, such as fever and pain with urination. However, unless a UTI is suspected, urinalysis screening is not recommended except in limited circumstances, such as in pregnant women and patients undergoing urological surgery. That’s because bacteria in urine in the absence of symptoms of infection, known as asymptomatic bacteriuria (ASB), is common and does not require treatment.
Patients scheduled for surgery and certain other medical procedures are often instructed to undergo preoperative urinalyses; those with abnormal results may be treated with antibiotics. Many physicians likely order a urinalysis in asymptomatic patients before operating due to concerns that an unidentified urinary infection could result in complications after surgery, explains infectious diseases specialist and health care epidemiologist Erica S. Shenoy, MD, PhD, associate chief of MGH’s Infection Control Unit. “But the evidence to date does not support screening for and treating ASB for almost all asymptomatic pre-operative patients,” says Shenoy, who is also an associate professor of Medicine at HMS. Guidelines established by the Infectious Disease Society of America (IDSA) and the United States Protective Services Task Force (USPSTF) discourage routine preoperative screening for and treatment of ASB, with the limited exceptions described above.
Shenoy became interested in identifying the prevalence of preoperative urinalyses from her clinical experience: She is often asked by other physicians to advise on cases of abnormal urinalysis results and urine cultures in patients who lacked signs or symptoms of infection but were screened prior to surgery. Shenoy and MGH primary care physician Zirui Song, MD, PhD, along with research assistant Mia Giuriato, BBA, MA, analyzed one of the largest available databases of commercial insurance and Medicare claims. Included in the study were 13,169,656 inpatient and outpatient procedures in which urinalysis is not recommended that were performed between 2007 and 2017. These procedures fell into 14 broad categories, such as breast surgery, spine surgery and joint replacement procedures.
The team found that 25 percent of patients who had these procedures had undergone urinalyses in the 30 days preceding their operations. Within this group, the researchers found that only a small portion (11 percent) had documented indications consistent with a UTI prior to their procedures, suggesting that a urinalysis was appropriate. In the remaining 89 percent of procedures, urinalyses were performed unnecessarily. Perhaps more concerning, the analysis found that between 5.8 percent and 28.0 percent of patients who had urinalyses without plausible indications of a UTI received prescriptions for antibiotics, depending on which procedure they had.
“These antibiotic prescriptions are unnecessary and expose our patients to potential harm,” says Shenoy, noting that the costs to patients and to the system are substantial. Total spending on the inappropriate urinalyses identified in this study was $48,675,408. But Shenoy stresses that the costs of the test are just the beginning. At minimum, a patient may need to take time out of work to visit a lab and pay a portion of the cost of a urinalysis. If an antibiotic is prescribed, it could require additional copayment, interact with another medication the patient takes, or lead to a complication such as Clostridium difficile (“C. diff”) infection. “And there can be downstream societal consequences,” adds Shenoy, since overuse of antibiotics has led to a growing problem of resistance to these important medicines.
Song, an assistant professor of Health Care Policy and Medicine at HMS, says that overuse of urinalyses is just one example of low-value care, or medical treatment that offers little or no benefit to the patient. Insurers and self-insured employers could play a role in curbing the problem, he suggests. “Opportunities to reduce low-value care exist, especially on the provider side,” says Song, through strategies such as reducing reimbursement for unnecessary urinalyses and other services in situations that don’t benefit patients. “Policymakers and purchasers can do more to align providers’ financial incentives with clinical appropriateness.”
This work was supported by the National Institutes of Health and the Laura and John Arnold Foundation.
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Internet-based cognitive behavioral therapy (CBT) for depression is often just as effective as traditional CBT. This is clear from an international study involving scientists at the University of Gothenburg. However, some online treatments have components that can be harmful.
Internet CBT (iCBT) as a method of delivering treatment is on the increase. Nevertheless, it has been unclear to date which parts of the treatment are most helpful against depression, which are less efficacious and which are potentially detrimental to patients.
In an international study, researchers at the University of Gothenburg participated in a systematic literature review and meta-analysis. The study was based on 76 randomized controlled trials (RCTs) in Sweden and elsewhere. In total, the RCTs included 17,521 patients, 71% of whom were women.
The study, under the aegis of Kyoto University in Japan, is now published in The Lancet Psychiatry. One coauthor is Cecilia Björkelund, Senior Professor of Family Medicine at the University of Gothenburg’s Sahlgrenska Academy.
“In mild or moderate depression, the effect of iCBT is as good as that of conventional CBT. For many, it’s a superb way of getting access to therapy without having to go to a therapist. We also saw that it was especially good for the elderly — a finding we didn’t entirely expect,” she says.
Just as in traditional CBT, its online counterpart involves modifying patients’ thoughts, feelings and behaviors that are obstacles in their lives and impair their mood. During the treatment, which often lasts about ten weeks, they are given tasks and exercises to perform on their own.
The factor that proved most significant for the prognosis was the depth of depression at the start of treatment. In milder depression, better results were obtained. Therapist support and text-message reminders increased the proportion of patients who completed the therapy.
“If you’re going to use iCBT in health care, the programs have to be regulated just as well as drugs are, but that’s not the case today. With this study, we’re taking a real step forward. First, the study surveys what’s most effective. Second, it provides knowledge of how to design a program and adapt its composition to patients’ problems,” Björkelund says.
However, iCBT requires continuous therapeutic contact. One reason is the importance of the therapist being able to see an improvement within three to four weeks, ensuring that the trend is not in the wrong direction. Björkelund stresses the great potential danger of depression. In severe depression, internet-mediated therapy is inappropriate.
The study shows the danger of using iCBT with programs that include relaxation therapy. Rather than being beneficial, this may have negative effects, exacerbating depressive symptoms and causing “relaxation-induced anxiety.”
“For a depressed person, it isn’t advisable. Relaxation programs shouldn’t be used as part of depression treatment in health care,” Björkelund says.
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Researchers have analyzed the three-dimensional structure of a protein that suppresses the development of colorectal polyposis, MUTYH, at the atomic level and clarified the repair mechanism for DNA mispairings by MUTYH. Since mutations in the MUTYH gene cause heritable colorectal polyposis, which leads to colorectal cancer, the researchers expect that this work will be useful for future research on heritable colorectal polyposis associated with MUTYH.
Reactive oxygen species produced inside cells oxidize DNA, and when the guanine base in DNA undergoes oxidation, 8-oxoguanine base is produced. Normally, guanine pairs with cytosine, but 8-oxoguanine also pairs with adenine, causing mutations that can lead to cancer and other aging-related diseases.
MUTYH is a protein that finds and removes adenine that has been mispaired with 8-oxoguanine. Mutations in its gene are known to cause heritable colorectal polyposis which can lead to colorectal cancer. Furthermore, the repair efficiency of MUTYH increases when it interacts with PCNA, a protein involved in DNA replication, but the repair mechanisms at the atomic level have not been clarified.
To accurately understand the function of a protein, it is important to know its structure at the atomic level. X-ray crystallography is a method that allows us to observe the molecules of living organisms at a scale of 1 x 10-10 m. Using this method, a research group led by Kumamoto University (Japan) has determined the X-ray crystal structure of MUTYH bound to a mispairing in DNA and the X-ray crystal structure of MUTYH bound to PCNA. Their analysis showed how MUTYH binds to the DNA double helix and searches for adenine:8-oxoguanine mispairings in DNA. Based on the three-dimensional structures of PCNA and MUTYH, the researchers proposed that PCNA serves as a clamp on the DNA double helix and recruits MUTYH to the mispair site, which would clarify the mechanism by which MUTYH and PCNA cooperate to repair DNA. Furthermore, analysis of the 3D structure of MUTYH and DNA showed that mutations in the MUTYH gene reduce the binding affinity of MUTYH to DNA and destabilize the 3D structure of MUTYH, which leads to a decrease of its DNA repair activity.
“Since MUTYH and PCNA are known to work with various proteins involved in DNA repair, the three-dimensional structures that we clarified in this study should serve as a basis for further understanding the DNA repair mechanisms centered around MUTYH and PCNA,” said Associate Professor Teruya Nakamura, who led the study. “We expect that the clarification of their atomic-level structures will be useful for future studies of heritable colorectal polyposis associated with MUTYH.”
This research was posted online in Nucleic Acids Research on 18 June 2021.
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While it is widely known that regular physical exercise decreases the risk of virtually all chronic illnesses, the mechanisms at play are not fully known. Now scientists at the University of Copenhagen have discovered that the beneficial effects of physical exercise may in part result from changes to the structure of our DNA. These changes are referred as ‘epigenetic’.
DNA is the molecular instruction manual found in all our cells. Some sections of our DNA are genes, which are instructions for building proteins — the body’s building blocks — while other sections are called enhancers that regulate which genes are switched on or off, when, and in which tissue. The scientists found, for the first time, that exercise rewires the enhancers in regions of our DNA that are known to be associated with the risk to develop disease.
“Our findings provide a mechanism for the known beneficial effects of exercise. By connecting each enhancer with a gene, we further provide a list of direct targets that could mediate this effect,” says Professor Romain Barrès from the Novo Nordisk Foundation Center for Basic Metabolic Research, the senior author of the research, which was published in Molecular Metabolism.
Exercise improves health of organs including the brain
The team of scientists hypothesized that endurance exercise training remodels the activity of gene enhancers in skeletal muscle. They recruited healthy young men and put them through a six-week endurance exercise program. The scientists collected a biopsy of their thigh muscle before and after the exercise intervention and examined if changes in the epigenetic signature of their DNA occurred after training.
The scientists discovered that after completing the endurance training program, the structure of many enhancers in the skeletal muscle of the young men had been altered. By connecting the enhancers to genetic databases, they discovered that many of the regulated enhancers have already been identified as hotspots of genetic variation between individuals — hotspots that have been associated with human disease.
The scientists speculate that the beneficial effects of exercise on organs distant from muscle, like the brain, may largely be mediated by regulating the secretion of muscle factors. In particular, they found that exercise remodels enhancer activity in skeletal muscle that are linked to cognitive abilities, which opens for the identification of exercise training-induced secreted muscle factors targeting the brain.
“Our data provides evidence of a functional link between epigenetic rewiring of enhancers to control their activity after exercise training and the modulation of disease risk in humans,” says Assistant Professor Kristine Williams, the lead author of this study.
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