Tag Archives: #mutations

A New Technique For Correcting Disease-causing Mutations (Medicine)

Novel method, developed by McGovern Institute researchers, may lead to safer, more efficient gene therapies.

Gene editing, or purposefully changing a gene’s DNA sequence, is a powerful tool for studying how mutations cause disease, and for making changes in an individual’s DNA for therapeutic purposes. A novel method of gene editing that can be used for both purposes has now been developed by a team led by Guoping Feng, the James W. (1963) and Patricia T. Poitras Professor in Brain and Cognitive Sciences at MIT.

“This technical advance can accelerate the production of disease models in animals and, critically, opens up a brand-new methodology for correcting disease-causing mutations,” says Feng, who is also a member of the Broad Institute of Harvard and MIT and the associate director of the McGovern Institute for Brain Research at MIT. The new findings were published online May 26 in the journal Cell.

Genetic models of disease

A major goal of the Feng lab is to precisely define what goes wrong in neurodevelopmental and neuropsychiatric disorders by engineering animal models that carry the gene mutations that cause these disorders in humans. New models can be generated by injecting embryos with gene editing tools, along with a piece of DNA carrying the desired mutation.

In one such method, the gene editing tool CRISPR is programmed to cut a targeted gene, thereby activating natural DNA mechanisms that “repair” the broken gene with the injected template DNA. The engineered cells are then used to generate offspring capable of passing the genetic change on to further generations, creating a stable genetic line in which the disease, and therapies, are tested.

Although CRISPR has accelerated the process of generating such disease models, the process can still take months or years. Reasons for the inefficiency are that many treated cells do not undergo the desired DNA sequence change at all, and the change only occurs on one of the two gene copies (for most genes, each cell contains two versions, one from the father and one from the mother).

In an effort to increase the efficiency of the gene editing process, the Feng lab team initially hypothesized that adding a DNA repair protein called RAD51 to a standard mixture of CRISPR gene editing tools would increase the chances that a cell (in this case a fertilized mouse egg, or one-cell embryo) would undergo the desired genetic change.

As a test case, they measured the rate at which they were able to insert (“knock-in”) a mutation in the gene Chd2 that is associated with autism. The overall proportion of embryos that were correctly edited remained unchanged, but to their surprise, a significantly higher percentage carried the desired gene edit on both chromosomes. Tests with a different gene yielded the same unexpected outcome.

“Editing of both chromosomes simultaneously is normally very uncommon,” explains postdoc Jonathan Wilde. “The high rate of editing seen with RAD51 was really striking, and what started as a simple attempt to make mutant Chd2 mice quickly turned into a much bigger project focused on RAD51 and its applications in genome editing,” says Wilde, who co-authored the Cell paper with research scientist Tomomi Aida.

A molecular copy machine

The Feng lab team next set out to understand the mechanism by which RAD51 enhances gene editing. They hypothesized that RAD51 engages a process called interhomolog repair (IHR), whereby a DNA break on one chromosome is repaired using the second copy of the chromosome (from the other parent) as the template.

To test this, they injected mouse embryos with RAD51 and CRISPR but left out the template DNA. They programmed CRISPR to cut only the gene sequence on one of the chromosomes, and then tested whether it was repaired to match the sequence on the uncut chromosome. For this experiment, they had to use mice in which the sequences on the maternal and paternal chromosomes were different.

They found that control embryos injected with CRISPR alone rarely showed IHR repair. However, addition of RAD51 significantly increased the number of embryos in which the CRISPR-targeted gene was edited to match the uncut chromosome.

“Previous studies of IHR found that it is incredibly inefficient in most cells,” says Wilde. “Our finding that it occurs much more readily in embryonic cells and can be enhanced by RAD51 suggest that a deeper understanding of what makes the embryo permissive to this type of DNA repair could help us design safer and more efficient gene therapies.”

A new way to correct disease-causing mutations          

Standard gene therapy strategies that rely on injecting a corrective piece of DNA to serve as a template for repairing the mutation engage a process called homology-directed repair (HDR).

“HDR-based strategies still suffer from low efficiency and carry the risk of unwanted integration of donor DNA throughout the genome,” explains Feng. “IHR has the potential to overcome these problems because it relies upon natural cellular pathways and the patient’s own normal chromosome for correction of the deleterious mutation.”

Feng’s team went on to identify additional DNA repair-associated proteins that can stimulate IHR, including several that not only promote high levels of IHR, but also repress errors in the DNA repair process. Additional experiments that allowed the team to examine the genomic features of IHR events gave deeper insight into the mechanism of IHR and suggested ways that the technique can be used to make gene therapies safer.

“While there is still a great deal to learn about this new application of IHR, our findings are the foundation for a new gene therapy approach that could help solve some of the big problems with current approaches,” says Aida.

This study was supported by the Hock E. Tan and K. Lisa Yang Center for Autism Research at MIT, the Poitras Center for Psychiatric Disorders Research at MIT, an NIH/NIMH Conte Center Grant, and the NIH Office of the Director.

Featured image: Staining for RAD51 (bright cyan-colored dot) in a fertilized one-cell mouse embryo shows repair of a CRISPR-induced DNA break. Credits: Image courtesy of the researchers.


Paper: “Efficient Homozygous Gene Conversion in Embryos via RAD51-Enhanced Interhomolog Repair”


Provided by MIT

‘Rescue Mutations’ that Suppress Harmful DNA Changes Could Shed Light On Origins of Genetic Disorders (Biology)

The biological phenomenon may play an important role in genetic diseases such as cancer or rare developmental disorders, and explain why certain patients suffer from more severe disease than others

New insights into the ability of DNA to overcome harmful genetic changes have been discovered by scientists at the Wellcome Sanger Institute, the University of Lausanne and their collaborators. The team found that 26 per cent of harmful mutations were suppressed by naturally occurring variants in at least one wild yeast strain. In each instance examined in detail, a single ‘rescue mutation’ was responsible for cancelling out another mutation that would have threatened the organism’s survival.

The study, published today (27 May 2021) in Molecular Systems Biology, provides important information about how DNA variants can suppress undesirable genetic changes. If confirmed in humans, this biological phenomenon could have an important role in genetic diseases such as cancer or rare developmental disorders, and explain why certain patients suffer from more severe disease than others.

Mutations are changes to the letters of DNA that form the genetic code of multi-cellular organisms. They can be a result of errors when DNA replicates during cell division, or the influence of environmental exposures such as ultraviolet light. While most mutations will have no significant effect on how the cell functions, some can be harmful and lead to genetic diseases such as cancer. Other mutations can be beneficial and contribute to genetic diversity in a species through the natural process of evolution1.

With six billion letters of DNA in the human genome, the implications of natural genetic variation are vast. As a result, the precise effect of mutations on the function of genes and cells is not fully understood. Mutations that are harmful in one individual may have no negative effect on another. In some cases, this is because the healthy or resilient individuals carry additional mutations, called suppressors, which counteract harmful DNA changes.

In this study, researchers at the University of Toronto screened 1,106 temperature-sensitive alleles2 from 580 essential genes3 in 10 wild yeast strains to see if natural genetic variation would allow the yeast to grow when exposed to an unfavourably high temperature.

They found that 26 per cent of the 580 essential genes could be circumvented by natural variants in at least one wild yeast strain. Yeast colonies that continued to grow were then sequenced at the Wellcome Sanger Institute, in order to search for specific mutations that could be suppressing the temperature-sensitive allele.

“The proportion of harmful mutations in essential genes that could be supressed was unexpected, and because we only sampled a small fraction of wild yeast strains the percentage of mutations that can be suppressed by natural variants is likely to be much higher. The frequency of suppression suggests it could make an important contribution in other contexts as well – including, potentially, for human disease.”

Professor Jolanda van Leeuwen,a senior author of the paper from the University of Lausanne

Researchers at the University of Lausanne examined 10 instances of suppression in detail to better understand the suppression effect and how it protected cells. To their surprise, in each case a single mutation was responsible for suppressing the temperature-sensitive allele and enabling cells to live and reproduce.

“In biology, explanations tend to be complex, so it’s unusual to find a single ‘smoking gun’. We might have expected a number of genes to combine to overcome a serious genetic defect like the temperature-sensitive allele, so for this to be the result of a single mutation is very surprising.”

Dr Leopold Parts,a senior author of the paper from the Wellcome Sanger Institute

Work is already underway at the Sanger Institute to conduct a similar study in human cells to see how relevant these findings are to the human genome, using commercially available human cell lines from healthy donors. If the same biological phenomenon is at play, it could provide valuable information about how genetic diseases arise and whether ‘rescue mutations’ might one day help clinicians to treat these diseases.

More information

1 For an overview of genetic mutations, see yourgenome.org

2 An allele is a variant form of the same gene. The combination of alleles influences an individual’s physical traits, such as eye colour. For more information, see yourgenome.org

3 Essential genes are those that are absolutely required for the cell to live and reproduce.

Publication:

Leopold Parts, Amandine Batté and Maykel Lopes et al. (2021). Natural variants suppress mutations in hundreds of essential genes. Molecular Systems Biology. DOI: https://doi.org/10.15252/msb.202010138

Funding:

This work was supported by Wellcome, the Swiss National Science Foundation and the Foundation for Medical Research.

Featured image credit: Jolanda van Leeuwen


Provided by Wellcome Sanger Institute

Scientists Discover A New Feature That Distinguishes Modern Humans From Neanderthals (Biology)

Skoltech scientists and their colleagues from Germany and the United States have analyzed the metabolomes of humans, chimpanzees, and macaques in muscle, kidney, and three different brain regions. The team discovered that the modern human genome undergoes mutation which makes the adenylosuccinate lyase enzyme less stable, leading to a decrease in purine synthesis. This mutation did not occur in Neanderthals, so the scientists believe that it affected metabolism in brain tissues and thereby strongly contributed to modern humans evolving into a separate species. The research was published in the journal eLife.

The predecessors of modern humans split from their closest evolutionary relatives, Neanderthals and Denisovans, about 600,000 years ago, while the evolutionary divergence between our ancestors and those of modern chimpanzees dates as far back as 65 million years ago. Evolutionary biologists are after the particular genetic features that distinguish modern humans from their ancestors and may give a clue as to why humans are what they are.

Researchers from the Skoltech Center for Neurobiology and Brain Restoration (CNBR) led by Professor Philipp Khaitovich and their colleagues from the Max Planck Institutes in Leipzig, Dresden and Cologne and the University of Denver studied metabolic differences in the brain, kidney and muscle of humans, chimpanzees, and macaques.

The research supervisor was a renowned evolutionary biologist, Professor Svante Pääbo, who earlier on had discovered the Denisovan and led the Neanderthal Genome Project.

The team looked at an interesting human mutation that leads to amino acid substitution in adenylosuccinate lyase, an enzyme involved in the synthesis of purine inside DNA. This substitution reduces the enzyme’s activity and stability, which results in a lower concentration of purines in the human brain. The team showed that the new mutation is typical for humans only and does not appear in other primates or Neanderthals. The researchers proved that this mutation is indeed the reason for the metabolic peculiarities in humans by introducing it into the mouse genome. The mice subjected to mutation produced fewer purines, whereas an ancestral gene, when introduced into human cells, led to apparent metabolic changes.

“Although a powerful tool for scientists, the decoded human genome, unfortunately, cannot account for all the phenotypic differences between humans. The study of the metabolic composition of tissues can give clues about why functional changes occur in humans. I am delighted that we have succeeded in predicting the metabolic characteristics of modern humans and validated our hypotheses on mouse and cell models, even though we did not have ‘live Neanderthals’ to work on,” says lead author and Skoltech PhD student Vita Stepanova.

Featured image credit: Pavel Odinev/Skoltech


Provided by Skoltech

Scientists Uncover Mutations That Make Cancer Resistant To Therapies Targeting KRAS (Medicine)

Key Takeaways

  • Cancer drugs that inhibit the protein expressed by a mutated form of the KRAS gene might be approved later this year, but cancer cells often develop additional mutations that make them resistant to such targeted drugs.
  • Investigators have identified some of these mutations in a patient and identified strategies to overcome them.

The treatment landscape for KRAS-mutant cancers is rapidly evolving.

— Jessica J. Lin, MD, Center for Thoracic Cancers, Massachusetts General Hospital

A gene called KRAS is one of the most commonly mutated genes in all human cancers, and targeted drugs that inhibit the protein expressed by mutated KRAS have shown promising results in clinical trials, with potential approvals by the U.S. Food and Drug Administration anticipated later this year. Unfortunately, cancer cells often develop additional mutations that make them resistant to such targeted drugs, resulting in disease relapse. Now researchers led by a team at Massachusetts General Hospital (MGH) have identified the first resistance mechanisms that may occur to these drugs and identified strategies to overcome them. The findings are published in Cancer Discovery.

One mutated version of KRAS that commonly arises in cancer cells is called KRAS(G12C), and it produces a mutated KRAS protein that allows the cells to grow and spread in the body. “Now, with the development of KRAS(G12C) inhibitors, the treatment landscape for KRAS-mutant cancers is rapidly evolving,” says co–lead author Jessica J. Lin, MD, an attending physician in the Center for Thoracic Cancers and the Termeer Center for Targeted Therapies at MGH. “KRAS(G12C) inhibitors adagrasib and sotorasib have recently demonstrated promising efficacy and safety in advanced KRAS(G12C)-mutant cancers.”

Although these may be life-saving therapies for many patients, resistance to the drugs is anticipated. Such was the case for a woman in an early clinical trial of adagrasib for lung cancer. After an initial reduction in tumor size, her tumor started growing again.

Analyses by Lin and her colleagues revealed various new tumor mutations in addition to KRAS(G12C). Interestingly, many of these mutations ultimately reactivated the signaling pathway driven by KRAS in cells (called the RAS-MAPK pathway), which is involved in cell growth and division. In addition, the team found a novel KRAS(Y96D) mutation, which further alters the structure of the KRAS(G12C) protein so that it is no longer effectively blocked by adagrasib, sotorasib or other inhibitors. However, experiments revealed that one KRAS(G12C) inhibitor, which binds in a different way to the active state of KRAS, could still overcome this multi-mutant KRAS protein.

“Our results suggest a role for the rational design of distinct KRAS inhibitors to overcome resistance to KRAS(G12C) inhibitors in patients,” says Lin. “Additionally, the convergence of different mutations towards RAS-MAPK reactivation suggests that the greater impact for KRAS(G12C) inhibitors may be in combination with other drugs such as downstream RAS-MAPK pathway inhibitors. These are all areas that need to be further explored.”

Lin emphasizes that this study represents only the tip of the iceberg. “We need to extend our findings and better understand the scope of resistance mechanisms that occur in patients treated with KRAS(G12C) inhibitors and other mutant-specific KRAS inhibitors,” she says. “Ongoing efforts to comprehensively understand the mechanisms of resistance to mutant-specific KRAS inhibitors will be pivotal in developing novel therapeutic approaches and improving care for patients with KRAS-mutant cancers.”

Along with Lin, Noritaka Tanaka, PhD, and Chendi Li, PhD, served as co–lead authors of the study. Co–senior authors were Aaron Hata, MD, PhD, an investigator in the Mass General Center for Cancer Research, Rebecca Heist, MD, MPH, an attending physician in the Center for Thoracic Cancers and the Termeer Center for Targeted Therapy, and Ryan Corcoran, MD, PhD, director of the Gastrointestinal Cancer Center Program and scientific director of the Termeer Center. Additional co-authors included Meagan Ryan, PhD, Junbing Zhang, PhD, Leslie Kiedrowski, MS, MPH, Alexa Michel, Mohammed Syed, Katerina Fella, Mustafa Sakhi, MS, Islam Baiev, Dejan Juric, MD, Justin Gainor, MD, Samuel Klempner, MD, Jochen Lennerz, MD, PhD, Giulia Siravegna, PhD, and Liron Bar-Peled, PhD.

This research was supported by the Mark Foundation for Cancer Research, Stand Up To Cancer and the American Cancer Society.


Reference: Noritaka Tanaka, Jessica J. Lin, Chendi Li, Meagan B. Ryan, Junbing Zhang, Lesli A Kiedrowski, Alexa G. Michel, Mohammed U. Syed, Katerina A. Fella, Mustafa Sakhi, Islam Baiev, Dejan Juric, Justin F. Gainor, Samuel J. Klempner, Jochen K. Lennerz, Giulia Siravegna, Liron Bar-Peled, Aaron N. Hata, Rebecca S. Heist and Ryan B. Corcoran, “Clinical acquired resistance to KRASG12C inhibition through a novel KRAS switch-II pocket mutation and polyclonal alterations converging on RAS-MAPK reactivation”, Cancer Discovery, 2021. DOI: 10.1158/2159-8290.CD-21-0365


Provided by Massachusetts General Hospital

Study Reveals Mutations That Drive Therapy-related Myeloid Neoplasms In Children (Medicine)

Research from scientists at St. Jude Children’s Research Hospital found mutations up to two years before cancer developed, showing an opportunity for early interventions

Children treated for cancer with approaches such as chemotherapy can develop therapy-related myeloid neoplasms (a second type of cancer) with a dismal prognosis. Scientists at St. Jude Children’s Research Hospital have characterized the genomic abnormalities of 84 such myeloid neoplasms, with potential implications for early interventions to stop the disease. A paper detailing the work was published today in Nature Communications.

The somatic (cancer) and germline (inherited) genomic alterations that drive therapy-related myeloid neoplasms in children have not been comprehensively described, until now. The researchers used a variety of sequencing techniques (whole exome, whole genome and RNA) to characterize the genomic profile of 84 pediatric therapy-related myeloid neoplasms. The data came from patients with leukemia, solid tumors or brain tumors who were treated with different types of chemotherapy and who all later developed myeloid neoplasms.

“One thing that we’ve known for a long time is once kids develop this secondary tumor, the outcome is really poor,” said co-corresponding author Jeffery Klco, M.D., Ph.D., St. Jude Pathology. “The alterations that drive these tumors are different in children than they are in adults, underscoring the need to study these tumors specifically in pediatrics.”

Collaboration yields new understanding

Results of the study revealed several notable mutations in the somatic setting, including changes in the Ras/MAPK pathway, alterations in RUNX1 or TP53, and rearrangements of KMT2A. Additionally, the results showed increased expression of a transcription factor called MECOM, which was associated with MECOM’s abnormal proximity to an enhancer as a result of genetic rearrangements.

The research benefited from computational tools developed at St. Jude that are aimed at reducing error rates, including CleanDeepSeq and SequencErr. These approaches help to discriminate between true mutations and sequencing errors.

With these tools, the researchers could trace the mutations back as far as two years before a therapy-related myeloid neoplasm developed, when early interventions could potentially benefit patients.

“This work indicates that we can detect this type of malignancy early, to study if preventative therapies could benefit patients,” said co-senior author Xiaotu Ma, Ph.D., St. Jude Computational Biology.

The study’s other co-corresponding author is Tanja Gruber, Stanford University School of Medicine. Co-first authors are Jason Schwartz, Vanderbilt University Medical Center; Jing Ma, St. Jude; and Jennifer Kamens, Stanford University School of Medicine. Other St. Jude authors of the study are Tamara Westover, Michael Walsh, Samuel Brady, J. Robert Michael, Xiaolong Chen, Lindsey Montefiori, Guangchun Song, Gang Wu, Huiyn Wu, Ryan Hiltenbrand, Kim Nichols, Jamie Maciaszek, Yanling Liu, Priyadarshini Kumar, John Easton, Scott Newman, Jeffrey Rubnitz, Charles Mullighan, Stanley Pounds and Jinghui Zhang. Additional paper authors include Cristyn Branstetter, Arkansas Children’s Northwest Hospital; and Michael Walsh, Memorial Sloan Kettering Cancer Center.

The research was funded in part by grants from the National Institutes of Health (1K08HL150282-01, P30CA021765, R01HL144653), Alex’s Lemonade Stand Foundation, Burroughs Wellcome Fund, EvansMDS Foundation and ALSAC, the fundraising and awareness organization of St. Jude.

Featured image: Xiaotu Ma, Ph.D., St. Jude Computational Biology, and Jeffery Klco, M.D., Ph.D., St. Jude Pathology © St. Jude Children’s Research Hospital


Reference: Schwartz, J.R., Ma, J., Kamens, J. et al. The acquisition of molecular drivers in pediatric therapy-related myeloid neoplasms. Nat Commun 12, 985 (2021). https://doi.org/10.1038/s41467-021-21255-8


Provided by St. Jude Children’s Research Hospital


About St. Jude Children’s Research Hospital

St. Jude Children’s Research Hospital is leading the way the world understands, treats and cures childhood cancer and other life-threatening diseases. It is the only National Cancer Institute-designated Comprehensive Cancer Center devoted solely to children. Treatments developed at St. Jude have helped push the overall childhood cancer survival rate from 20% to 80% since the hospital opened more than 50 years ago. St. Jude freely shares the breakthroughs it makes, and every child saved at St. Jude means doctors and scientists worldwide can use that knowledge to save thousands more children. Families never receive a bill from St. Jude for treatment, travel, housing and food — because all a family should worry about is helping their child live. To learn more, visit stjude.org or follow St. Jude on social media at @stjuderesearch.

Unusual DNA Folding Increases the Rates of Mutations (Biology)

DNA sequences that can fold into shapes other than the classic double helix tend to have higher mutation rates than other regions in the human genome. New research shows that the elevated mutation rate in these sequences plays a major role in determining regional variation in mutation rates across the genome.  Deciphering the patterns and causes of regional variation in mutation rates is important both for understanding evolution and for predicting sites of new mutations that could lead to disease.

A paper describing the research by a team of Penn State scientists is available online in the journal Nucleic Acids Research.

“Most of the time we think about DNA as the classic double helix; this basic form is referred to as ‘B-DNA,’” said Wilfried Guiblet, co-first author of the paper, a graduate student at Penn State at the time of research and now a postdoctoral scholar at the National Cancer Institute. “But, as much as 13% of the human genome can fold into different conformations called ‘non-B DNA.’ We wanted to explore what role, if any, this non-B DNA played in variation that we see in mutation rates among different regions of the genome.”

Non-B DNA can fold into a number of different conformations depending on the underlying DNA sequence. Examples include G-quadruplexes, Z-DNA, H-DNA, slipped strands, and various other conformations. Recent research has revealed that non-B DNA plays critical roles in cellular processes, including the replication of the genome and the transcription of DNA into RNA, and that mutations in non-B sequences are associated with genetic diseases.
 
“In a previous study, we showed that in the artificial system of a DNA sequencing instrument, which uses similar DNA copying processes as in the cell, error rates were higher in non-B DNA during polymerization,” said Kateryna Makova, Verne M. Willaman Chair of Life Sciences at Penn State and one of the leaders of the research team. “We think that this is because the enzyme that copies DNA during sequencing has a harder time reading through non-B DNA. Here we wanted to see if a similar phenomenon exists in living cells.”

The team compared mutation rates between B- and non-B DNA at two different timescales. To look at relatively recent changes, they used an existing database of human DNA sequences to identify individual nucleotides—letters in the DNA alphabet—that varied among humans. These ‘single nucleotide polymorphisms’ (SNPs) represent places in the human genome where at some point in the past a mutation occurred in at least one individual. To look at more ancient changes, the team also compared the human genome sequence to the genome of the orangutan.

They also investigated multiple spatial scales along the human genome, to test whether non-B DNA influenced mutation rates at nucleotides adjacent to it and further away.

“To identify differences in mutation rates between B- and non-B DNA we used statistical tools from ‘functional data analysis’ in which we compare the data as curves rather than looking at individual data points,” said Marzia A. Cremona, co-first author of the paper, a postdoctoral researcher at Penn State at the time of the research and now an assistant professor at Université Laval in Quebec, Canada. “These methods give us the statistical power to contrast mutation rates for the various types of non-B DNA against B-DNA controls.”

For most types of non-B DNA, the team found increased mutation rates. The differences were enough that non-B DNA mutation rates impacted regional variation in their immediate surroundings. These differences also helped explain a large portion of the variation that can be seen along the genome at the scale of millions of nucleotides.

“When we look at all the known factors that influence regional variation in mutation rates across the genome, non-B DNA is the largest contributor,” said Francesca Chiaromonte, Huck Chair in Statistics for the Life Sciences at Penn State and one of the leaders of the research team. “We’ve been studying regional variation in mutation rates for a long time from a lot of different angles. The fact that non-B DNA is such a major contributor to this variation is an important discovery.”

“Our results have critical medical implications,” said Kristin Eckert, professor of pathology and biochemistry and molecular biology at Penn State College of Medicine, Penn State Cancer Institute Researcher, an author on the paper, and the team’s long-time collaborator. “For example, human geneticists should consider the potential of a locus to form non-B DNA when evaluating candidate genetic variants for human genetic diseases. Our current and future research is focused on unraveling the mechanistic basis behind the elevated mutation rates at non-B DNA.”

The results also have evolutionary implications.

“We know that natural selection can impact variation in the genome, so for this study we only looked at regions of the genome that we think are not under the influence of selection,” said Yi-Fei Huang, assistant professor of biology at Penn State and one of the leaders of the research team. “This allows us to establish a baseline mutation rate for each type of non-B DNA that in the future we could potentially use to help identify signatures of natural selection in these sequences.”

Because of their increased mutation rates, non-B DNA sequences could be an important source of genetic variation, which is the ultimate source of evolutionary change.

“Mutations are usually thought to be so rare, that when we see the same mutation in different individuals, the assumption is that those individuals shared an ancestor who passed the mutation to them both,” said Makova, a Penn State Cancer Institute researcher. “But it’s possible that the mutation rate is so high in some of these non-B DNA regions that the same mutation could occur independently in several different individuals. If this is true, it would change how we think about evolution.”

In addition to Guiblet, Makova, Cremona, Eckert, Huang, and Chiaromonte, the research team at Penn State includes Robert S. Harris and Di Chen. The research was funded by the U.S. National Institutes of Health, Penn State Clinical and Translational Sciences Institute, the Penn State Institute of Computational and Data Sciences, the Huck Institutes of the Life Sciences at Penn State, the Penn State Eberly College of Science, the Pennsylvania Department of Health, and the CBIOS Predoctoral Training Program.

Featured image: New research shows that DNA that folds into conformations other than the classic double helix (non-B DNA), which includes as much as 13% of the human genome, leads to elevated nucleotide substitution rates in both the non-B motifs themselves and their flanking regions. These elevated mutation rates are a major contributor to the regional variation in mutation rates across the genome. Credit: Wilfried Guiblet and Dani Zemba, Penn State


Reference: Wilfried M. Guiblet, Marzia A Cremona, Robert S Harris, Di Chen, Kristin A Eckert, Francesca Chiaromonte, Yi-Fei Huang, Kateryna D Makova, Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome, Nucleic Acids Research, 2021;, gkaa1269, https://doi.org/10.1093/nar/gkaa1269 https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa1269/6101603


Provided by Penn State

Rare Genetic Syndrome Identified, Caused by Mutations in Gene SATB1 (Neuroscience)

Advances in DNA sequencing have uncovered a rare syndrome which is caused by variations in the gene SATB1. Discovery of this genetic syndrome is hoped to provide information to families and individuals affected by SATB1-syndrome

The study, co-authored by academics from Oxford Brookes University (UK), University of Lausanne (Switzerland), Radboud University (The Netherlands), University of Oxford (UK), University of Manchester (UK) and led by Max Planck Institute for Psycholinguistics (The Netherlands), discovered three classes of mutations within the gene SATB1, resulting in three variations of a neurodevelopmental disorder with varying symptoms ranging from epilepsy to muscle tone abnormalities.

Recognition of disorder will increase understanding and diagnosis 

An international team of geneticists and clinicians from 12 countries identified 42 patients with mutations in the gene SATB1 who were all displaying a range of similar symptoms, albeit of varying severity.

Variations, or mutations, of SATB1 were found to have different effects in the cell. For example, some variations led to increased activity of the protein which causes a more severe type of disorder, while other variations cause loss of function of the gene and lead to less severe difficulties. 

The SATB1-syndrome is characterised by neurodevelopmental delay, intellectual disability, muscle tone abnormalities, epilepsy, behavioural problems, facial dysmorphism and dental abnormalities.

We hope that the recognition of this new disorder, and the information about the molecular pathways contributing to it, will help the families and individuals affected understand more about the condition and achieve a diagnosis they would not have had previously.

— Dr Dianne Newbury, Senior Lecturer in Medical Genetics and Genomics

Dr Dianne Newbury, Senior Lecturer in Medical Genetics and Genomics at Oxford Brookes University said: “Previously, just one or two cases of patients with SATB1 variations had been described but it was not recognised as a specific syndrome. Patients displaying these characteristics and their families, will have known that they had an undefined neurological condition, but they wouldn’t have known any specific detail about the condition, or why they had it. 

“We hope that the recognition of this new disorder, and the information about the molecular pathways contributing to it, will help the families and individuals affected understand more about the condition and achieve a diagnosis they would not have had previously.”

Three classes of mutation have different effects in the cell

The mutations found in the genome of the patients were found to belong to three different classes. The first mutation class, identified in eight patients, caused a loss of function of the SATB1 gene and halved the production of the encoded protein. This leads to a less severe syndrome characterised by diminished cognitive function, visual problems and facial dysmorphism.

The second class contains four mutations, which encode shorter proteins that are less efficient as they are not positioned correctly in the cell. This second mutation shows as an intermediary syndrome, characterised as more severe than the first, but less severe than the third. 

The third class of variation encompasses the mutations found in the last thirty patients. These modify the encoded protein, making it more active. This altered protein is ‘sticky’ and binds better to DNA, diminishing the expression of genes it regulates and causing a more severe type of disorder, characterised by severe intellectual disability, epilepsy, a motor speech disorder (dysarthria) and specific facial features.

Understanding mutations is key to discovering the origin of genetic diseases

Dr Alexandre Reymond, Director of the Center for Integrative Genomics at the University of Lausanne in Switzerland said: “These results demonstrate that each mutation is different and that is essential to understand their mode of action in order to explain the origin of genetic diseases.

“We must go beyond sequencing, which is only a first step.”

The paper, Mutation-specific pathophysiological mechanisms define different neurodevelopmental disorders associated with SATB1 dysfunction, has been published in The American Journal of Human Genetics.

Featured image: 3D model of the SATB1 protein (in red) linked to the DNA double helix (white-red-blue). The positions of mutations found in patients are highlighted in emerald green. © Nicolas Guex, UNIL


Provided by Oxford Brookes University

New Nature Plants Study Introduces SpRY to Enable the Mutation of Nearly Any Genomic Sequence in Plants (Botany / Agriculture)

UMD Associate Professor Named a Web of Science Highly Cited Researcher for 2020, Expands Plant Genome Editing Potential with a Newly Engineered Variant of CRISPR-Cas9.

Alongside Dennis vanEngelsdorp, associate professor at the University of Maryland (UMD) in Entomology named for the fifth year in a row for his work in honey bee and pollinator health, Yiping Qi, associate professor in Plant Science, represented the College of Agriculture & Natural Resources on the Web of Science 2020 list of Highly Cited Researchers for the first time. This list includes influential scientists based on the impact of their academic publications over the course of the year. In addition to this honor, Qi is already making waves in 2021 with a new high-profile publication in Nature Plants introducing SpRY, a newly engineered variant of the famed gene editing tool CRISPR-Cas9. SpRY essentially removes the barriers of what can and can’t be targeted for gene editing, making it possible for the first time to target nearly any genomic sequence in plants for potential mutation. As the preeminent innovator in the field, this discovery is the latest of Qi’s in a long string of influential tools for genome editing in plants.

Gene editing illustration Image Credit: Shutterstock

“It is an honor, an encouragement, and a recognition of my contribution to the science community,” says Qi of his distinction as a 2020 Web of Science Highly Cited Researcher. “But we are not just making contributions to the academic literature. In my lab, we are constantly pushing new tools for improved gene editing out to scientists to make an impact.”

With SpRY, Qi is especially excited for the limitless possibilities it opens up for genome editing in plants and crops. “We have largely overcome the major bottleneck in plant genome editing, which is the targeting scope restrictions associated with CRISPR-Cas9. With this new toolbox, we pretty much removed this restriction, and we can target almost anywhere in the plant genome.”

The original CRISPR-Cas9 tool that kicked off the gene editing craze was tied to targeting a specific short sequence of DNA known as a PAM sequence. The short sequence is what the CRISPR systems typically use to identify where to make their molecular cuts in DNA. However, the new SpRY variant introduced by Qi can move beyond these traditional PAM sequences in ways that was never possible before.

“This unleashes the full potential of CRISPR-Cas9 genome editing for plant genetics and crop improvement,” says an excited Qi. “Researchers will now be able to edit anywhere within their favorable genes, without questioning whether the sites are editable or not. The new tools make genome editing more powerful, more accessible, and more versatile so that many of the editing outcomes which were previously hard to achieve can now be all realized.”

According to Qi, this will have a major impact on translational research in the gene editing field, as well as on crop breeding as a whole. “This new CRISPR-Cas9 technology will play an important role in food security, nutrition, and safety. CRISPR tools are already widely used for introducing tailored mutations into crops for enhanced yield, nutrition, biotic and abiotic stress resistance, and more. With this new tool in the toolbox, we can speed up evolution and the agricultural revolution. I expect many plant biologists and breeders will use the toolbox in different crops. The list of potential applications of this new toolbox is endless.”

The paper, PAM-less plant genome editing using a CRISPR–SpRY toolbox, is published in Nature Plants, DOI: 10.1038/s41477-020-00827-4. https://www.nature.com/articles/s41477-020-00827-4

Provided by College of Agriculture & Natural Resources – University of Maryland

Even Skin Shielded From the Sun Accumulates Genomic DNA Changes From UV Light (Medicine)

Study of skin cell mutations shows Black people have less damage from UV light than white people.

For the first time, scientists have measured the different types of genomic DNA changes that occur in skin cells, finding that mutations from ultraviolet (UV) light is especially common, but Black individuals have lower levels of UV damage compared to white people. Dmitry Gordenin and colleagues at the National Institute of Environmental Health Sciences, report these findings January 14 in PLOS Genetics.

Fig 1. Schematics of the study design. From each donor, we obtained blood for whole-genome sequencing. In addition, we obtained skin biopsies from the hips of the donors from which fibroblasts and melanocyte clonal lineages were obtained. Fibroblasts were grown up to a million cells and their DNA was directly used for whole-genome sequencing, while melanocytes grew up to 10,000 cells and the DNA was whole-genome amplified and thereafter sequenced. © Saini N et al., 2021, PLOS Genetics

The DNA in our skin cells suffer damage from sources inside and outside the body, leading to genomic changes such as mutations that may lead to cancer. UV light is the major source of these mutations, but byproducts of cellular metabolism, like free radicals, and DNA copying errors that occur during cell division also cause genomic changes. These mutation-causing mechanisms are well known, but previously, no one had been able to accurately measure the relative contributions from each source.

In their new paper, Gordenin and his colleagues quantified the amounts of each type of genomic changes by sequencing the genomes of skin cells donated from 21 Black and white individuals, ranging in age from 25 to 79. The researchers discovered that the total amount of genomic changes from metabolic byproducts accumulates as a person gets older, while the amount of genomic changes caused by UV damage is unrelated to a person’s age. Additionally, they showed that genomic changes from UV light is common, even in skin cells typically shielded from the sun, but it was less prevalent in Black donors compared to white donors.

The researchers suspect that Black individuals may be better protected from UV light due to having higher levels of the skin pigment melanin. Supporting this idea, is the fact that Black people have much lower rates of skin cancer compared to white people. Overall, the new study provides an accurate estimate of the genomic changes that occur in skin cells due to different types of DNA damage, and establishes the normal range of somatic genomic changes across a wide range of ages and of different races, providing a baseline for future research.

The authors add, “The new study provides an accurate estimate of the genomic changes that occur in skin cells due to different types of DNA damage, and establishes the normal range of somatic genomic changes across a wide range of ages and of different races, providing a baseline for future research.”

Funding: This work was supported by the US National Institute of Health Intramural Research Program Project Z1AES103266 to D.A.G. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Reference: Saini N, Giacobone CK, Klimczak LJ, Papas BN, Burkholder AB, Li J-L, et al. (2021) UV-exposure, endogenous DNA damage, and DNA replication errors shape the spectra of genome changes in human skin. PLoS Genet 17(1): e1009302. https://doi.org/10.1371/journal.pgen.1009302 https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1009302

Provided by PLoS Journal