Tag: genetic mutation

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DNA Damage can Stay Unrepaired for Years

On By ModernMedia

The findings are set to change our understanding of genetic mutation

Photo by Sangharsh Lohakare on Unsplash

In a paradigm shift in how we view mutations, researchers uncover forms of DNA damage in healthy cells – most particularly in blood stem cells – that can persist unrepaired for years.

While most known types of DNA damage are fixed by our cells’ in-house repair mechanisms, some forms of DNA damage evade repair and can persist for many years, new research shows. This means that the damage has multiple chances to generate harmful mutations, which can lead to cancer.

Scientists from the Wellcome Sanger Institute and their collaborators analysed family trees of hundreds of single cells from several individuals. The team pieced together these family trees from patterns of shared mutations between the cells, indicating common ancestors.

Researchers uncovered unexpected patterns of mutation inheritance in the trees, revealing that some DNA damage persists unrepaired. In the case of blood stem cells, this can be for two to three years.

The research, published in Nature, changes the way we think about mutations, and has implications for understanding the development of various cancers.

Throughout our life, all of the cells in our body accumulate genetic errors in the genome, known as somatic mutations. These can be caused by damaging environmental exposures, such as smoking, as well as the everyday chemistry occurring in our cells.

DNA damage is distinct from a mutation. While a mutation is one of the standard four DNA bases (A, G, T or C) in the wrong place, similar to a spelling mistake, DNA damage is chemical alteration of the DNA, like a smudged unrecognisable letter. DNA damage can result in the genetic sequence being misread and copied incorrectly during cell division, in a process known as DNA replication. This introduces permanent mutations that can contribute to the development of cancers. However, the DNA damage itself is usually recognised and mended quickly by repair mechanisms in our cells.

If researchers can better understand the causes and mechanisms of mutations, they may be able to intervene and slow or remove them.

In a new study, Sanger Institute scientists and their collaborators analysed data in the form of family trees of hundreds of single cells from individuals. The family trees are constructed from patterns of mutations across the genome that are shared between cells – for example, cells with many shared mutations have a recent common ancestor cell and are closely related.

The researchers collated seven published sets of these family trees, known as somatic phylogenies. The data set included 103 phylogenies from 89 individuals,1 spanning blood stem cells, bronchial epithelial cells and liver cells

The team found unexpected patterns of mutation inheritance in the family trees, revealing that some DNA damage can persist unrepaired through multiple rounds of cell division. This was particularly evident in blood stem cells, where between 15 to 20 per cent of the mutations resulted from a specific type of DNA damage that persists for two to three years on average, and in some cases longer.

This means that during cell division, each time the cell attempts to copy the damaged DNA it can make a different mistake, leading to multiple different mutations from a single source of DNA damage. Importantly, this creates multiple chances of harmful mutations that could contribute to cancer. Researchers suggest that although these types of DNA damage occur rarely, their persistence over years means they can cause as many mutations as more common DNA damage.

Overall, these findings change the way researchers think about mutations, and have implications for understanding the development of cancer.

Source: Wellcome Trust Sanger Institute

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Genomic ‘Butterfly Effect’ Explains Risk for Autism spectrum Disorder

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Photo by Sangharsh Lohakare on Unsplash

Researchers in Japan discovered that a special kind of genetic mutation works differently from typical mutations in how it contributes to autism spectrum disorder (ASD). In essence, because of the three-dimensional structure of the genome, mutations are able to affect neighbouring genes that are linked to ASD, thus explaining why ASD can occur even without direct mutations to ASD-related genes. This study appeared in the scientific journal Cell Genomics.

ASD is a group of conditions characterised in part by repetitive behaviours and difficulties in social interaction. Although it runs in families, the genetics of its heritability are complex and remain only partially understood. Studies have shown that the high degree of heritability cannot be explained simply by looking at the part of the genome that codes for proteins. Rather, the answer could lie in the non-coding regions of the genome, particularly in promoters, the parts of the genome that ultimately control whether or not the proteins are actually produced. The team led by Atsushi Takata at in the RIKEN Center for Brain Science (CBS) examined de novo gene variants (new, non-inherited mutations) in these parts of the genome.

The researchers analysed an extensive dataset of over 5000 families, making this one of the world’s largest genome-wide studies of ASD to date. They focused on TADs – three-dimensional structures in the genome that allow interactions between different nearby genes and their regulatory elements. They found that de novo mutations in promoters heightened the risk of ASD only when the promoters were located in TADs that contained ASD-related genes. Because they are nearby and in the same TAD, these de novo mutations can affect the expression of ASD-related genes. In this way, the new study explains why mutations can increase the risk of ASD even when they aren’t located in protein-coding regions or in the promotors that directly control the expression of ASD-related genes.

“Our most important discovery was that de novo mutations in promoter regions of TADs containing known ASD genes are associated with ASD risk, and this is likely mediated through interactions in the three-dimensional structure of the genome,” says Takata.

To confirm this, the researchers edited the DNA of stem cells using the CRISPR/Cas9 system, making mutations in specific promoters. As expected, they observed that a single genetic change in a promotor caused alterations in an ASD-associated gene within the same TAD. Because numerous genes linked to ASD and neurodevelopment were also affected in the mutant stem cells, Takata likens the process to a genomic “butterfly effect” in which a single mutation dysregulates disease-associated genes that are scattered in distant regions of the genome.

Takata believes that this finding has implications for the development of new diagnostic and therapeutic strategies. “At the very least, when assessing an individual’s risk for ASD, we now know that we need to look beyond ASD-related genes when doing genetic risk assessment, and focus on whole TADs that contain ASD-related genes,” explains Takata. “Further, an intervention that corrects aberrant promoter-enhancer interactions caused by a promotor mutation may also have therapeutic effects on ASD.”

Further research involving more families and patients is crucial for better understanding ASD’s genetic roots. “By expanding our research, we will gain a better understanding of the genetic architecture and biology of ASD, leading to clinical management that enhances the well-being of affected individuals, their families, and society,” says Takata.

Source: RIKEN

Categories : Genetics PaediatricsTags :

Gene Identified for Rare Disorder Involving Extra Fingers and Toes

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Photo by Jonathan Borba on Unsplash

A rare disorder which causes babies to be born with extra fingers and toes and a range of birth defects has been identified in new research published in the American Journal of Human Genetics. The disorder, which has not yet been named, is caused by a genetic mutation in a gene called MAX.

As well as extra digits – polydactyly — it leads to a range of symptoms relating to ongoing brain growth, such as autism. The research marks the first time this genetic link has been identified. It has also found a molecule that could potentially be used to treat some of the neurological symptoms and prevent any worsening of their condition. However, more research is needed to test this molecule before it can be used as a treatment.

Co-led by the University of Leeds, the study focuses on three individuals with a rare combination of physical traits, namely polydactyly, and a much larger than average head circumference – known as macrocephaly.

The individuals share some other characteristics, including delayed development of their eyes which results in problems with their vision early in life.

The researchers compared the DNA of these individuals and found they all carried the shared genetic mutation causing their birth defects.

The latest research was co-led by Dr James Poulter from the University of Leeds; Dr Pierre Lavigne at Université de Sherbrooke in Québec and Professor Helen Firth at Cambridge University.

As with many rare disorders, the disorder currently has no treatments – but in this case, the researchers identified one already undergoing clinical trials which might reverse some of the mutation’s effects.

The study team has highlighted the importance of interdisciplinary research into rare diseases in giving understanding and hope of a treatment to families who often face many years of uncertainty about their child’s condition and prognosis.

The researchers now plan to look for additional patients with mutations in MAX to better understand the disorder and investigate whether the potential treatment improves the symptoms caused by the mutation.

Source: University of Leeds