̽��ֱ�� of Cambridge - mitochondrial DNA

Study in mice shows potential for gene-editing to tackle mitochondrial disorders

cjb250 — Tue, 08 Feb 2022 10:00:16 +0000

Our cells contain mitochondria, which provide the energy for our cells to function. Each of these mitochondria contains a tiny amount of mitochondrial DNA. Mitochondrial DNA makes up only 0.1% of the overall human genome and is passed down exclusively from mother to child.

Faults in our mitochondrial DNA can affect how well the mitochondria operate, leading to mitochondrial diseases, serious and often fatal conditions that affect around 1 in 5,000 people. ̽��ֱ��diseases are incurable and largely untreatable.

There are typically around 1,000 copies of mitochondrial DNA in each cell, and the percentage of these that are damaged, or mutated, will determine whether a person will suffer from mitochondrial disease or not. Usually, more than 60% of the mitochondria in a cell need to be faulty for the disease to emerge, and the more defective mitochondria a person has, the more severe their disease will be. If the percentage of defective DNA could be reduced, the disease could potentially be treated.

A cell that contains a mixture of healthy and faulty mitochondrial DNA is described as ‘heteroplasmic’. If a cell contains no healthy mitochondrial DNA, it is ‘homoplasmic’.

In 2018, a team from the MRC Mitochondrial Biology Unit at the ̽��ֱ�� of Cambridge applied an experimental gene therapy treatment in mice and were able to successfully target and eliminate the damaged mitochondrial DNA in heteroplasmic cells, allowing mitochondria with healthy DNA to take their place.

“Our earlier approach is very promising and was the first time that anyone had been able to alter mitochondrial DNA in a live animal,” explained Dr Michal Minczuk. “But it would only work in cells with enough healthy mitochondrial DNA to copy themselves and replace the faulty ones that had been removed. It would not work in cells whose entire mitochondria had faulty DNA.”

In their latest advance, published today in Nature Communications, Dr Minczuk and colleagues used a biological tool known as a mitochondrial base editor to edit the mitochondrial DNA of live mice. ̽��ֱ��treatment is delivered into the bloodstream of the mouse using a modified virus, which is then taken up by its cells. ̽��ֱ��tool looks for a unique sequence of base pairs – combinations of the A, C, G and T molecules that make up DNA. It then changes the DNA base – in this case, changing a C to a T. This would, in principle, enable the tool to correct certain ‘spelling mistakes’ that cause the mitochondria to malfunction.

There are currently no suitable mouse models of mitochondrial DNA diseases, so the researchers used healthy mice to test the mitochondrial base editors. However, it shows that it is possible to edit mitochondrial DNA genes in a live animal.

Pedro Silva-Pinheiro, a postdoctoral researcher in Dr Minczuk’s lab and first author of the study, said: “This is the first time that anyone has been able to change DNA base pairs in mitochondria in a live animal. It shows that, in principle, we can go in and correct spelling mistakes in defective mitochondrial DNA, producing healthy mitochondria that allow the cells to function properly.”

An approach pioneered in the UK known as mitochondrial replacement therapy – sometimes referred to as ‘three-person IVF’ – allows a mother’s defective mitochondria to be replaced with those from a healthy donor. However, this technique is complex, and even standard IVF is successful in fewer than one in three cycles.

Dr Minczuk added: “There’s clearly a long way to go before our work could lead to a treatment for mitochondrial diseases. But it shows that there is the potential for a future treatment that removes the complexity of mitochondrial replacement therapy and would allow for defective mitochondria to be repaired in children and adults.”

̽��ֱ��research was funded by the Medical Research Council UK, the Champ Foundation and the Lily Foundation.

Reference
Silva-Pinheiro, S et al. In vivo mitochondrial base editing via adenoassociated viral delivery to mouse post-mitotic tissue. Nature Comms; 8 Feb 2022; DOI: 10.1038/s41467-022-28358-w

Defective mitochondria – the ‘batteries’ that power the cells of our bodies – could in future be repaired using gene-editing techniques. Scientists at the ̽��ֱ�� of Cambridge have shown that it is possible to modify the mitochondrial genome in live mice, paving the way for new treatments for incurable mitochondrial disorders.

[This] shows that, in principle, we can go in and correct spelling mistakes in defective mitochondrial DNA, producing healthy mitochondria that allow the cells to function properly

Pedro Silva-Pinheiro

wir0man/Getty Images

Mitochondria - 3D illustration

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Whole genome sequencing increases diagnosis of rare disorders by nearly a third

ta385 — Thu, 04 Nov 2021 06:00:00 +0000

Mitochondrial disorders affect around 1 in 4,300 people and cause progressive, incurable diseases. They are amongst the most common inherited diseases but are difficult for clinicians to diagnose, not least because they can affect many different organs and resemble many other conditions.

Current genetic testing regimes fail to diagnose around 40% of patients, with major implications for patients, their families and the health services they use.

A new study, published in the BMJ, offers hope to families with no diagnosis, and endorses plans for the UK to establish a national diagnostic programme based on whole genome sequencing (WGS) to make more diagnoses faster.

While previous studies based on small, highly selected cohorts have suggested that WGS can identify mitochondrial disorders, this is the first to examine its effectiveness in a national healthcare system – the NHS.

̽��ֱ��study, led by researchers from the MRC Mitochondrial Biology Unit and Departments of Clinical Neuroscience and Medical Genetics at the ̽��ֱ�� of Cambridge, involved 319 families with suspected mitochondrial disease recruited through the 100,000 Genomes Project which was set up to embed genomic testing in the NHS, discover new disease genes and make genetic diagnosis available for more patients.

In total, 345 participants – aged 0 to 92 with a median age of 25 years – had their whole genome sequenced. Through different analyses, the researchers found that they could make a definite or probable genetic diagnosis for 98 families (31%). Standard tests, which are often more invasive, failed to reach these diagnoses. Six possible diagnoses (2% of the 98 families) were made. A total of 95 different genes were implicated.

Surprisingly, 62.5% of the diagnoses were actually non-mitochondrial disorders, with some having specific treatments. This happened because so many different diseases resemble mitochondrial disorders, making it very difficult to know which are which.

Professor Patrick Chinnery from the MRC Mitochondrial Biology Unit and the Department of Clinical Neurosciences at the ̽��ֱ�� of Cambridge, said:

“We recommend that whole genome sequencing should be offered early and before invasive tests such as a muscle biopsy. All that patients would need to do is have a blood test, meaning that this could be offered across the whole country in an equitable way. People wouldn’t need to travel long distances to multiple appointments, and they would get their diagnosis much faster.”

Dr Katherine Schon from the MRC Mitochondrial Biology Unit and the Departments of Clinical Neuroscience and Medical Genetics, said:

“A definitive genetic diagnosis can really help patients and their families, giving them access to tailored information about prognosis and treatment, genetic counselling and reproductive options including preimplantation genetic diagnosis or prenatal diagnosis.”

̽��ֱ��researchers made 37.5% of their diagnoses in genes known to cause mitochondrial disease. These diagnoses were nearly all unique to a particular participant family, reflecting the genetic diversity found in these disorders. ̽��ֱ��impairment of mitochondrial function tends to affect tissues with high energy demand such as the brain, the peripheral nerves, the eye, the heart and the peripheral muscles. ̽��ֱ��study offers a valuable new resource for the discovery of future mitochondrial disease genes.

̽��ֱ��majority of the team’s diagnoses (62.5%) were, however, of non-mitochondrial disorders which had features resembling mitochondrial diseases. These disorders would have been missed if the participants had only been investigated for mitochondrial disorders through muscle biopsy and/or a specific mitochondrial gene panel. These participants were living with a range of conditions including developmental disorders with intellectual disability, severe epileptic conditions and metabolic disorders, as well as heart and neurological diseases.

Chinnery said: “These patients were referred because of a suspected mitochondrial disease and the conventional diagnostic tests are specifically for mitochondrial diseases. Unless you consider these other possibilities, you won't diagnose them. Whole genome sequencing isn’t restricted by that bias.”

A small number of newly diagnosed participants are already receiving treatments as a result. ̽��ֱ��team identified potentially treatable disorders in six participants with a mitochondrial disorder and nine with a non-mitochondrial disorder, but the impact of the treatments has yet to be determined.

Chinnery said: “Diagnostic services are fragmented and unevenly distributed across the UK, and that creates major challenges for people with rare diseases and their families. By delivering a national programme based on this genome-wide approach, you can offer the same level of service to everyone."

Schon said: “If we can create a national platform of families with rare diseases, we can give them the opportunity to engage in clinical trials so we can get definitive evidence that new treatments work.”

̽��ֱ��study points out that the relatively high number of patients with probable or possible diagnoses reflects the need for greater investment into the analysis of functional effects of new genetic variants which could be the cause of disease, but it is not certain at present.

It also argues that rapid trio whole genome sequencing should be offered to all acutely unwell individuals with suspected mitochondrial disorders, so that results can help guide clinical management. Currently in the UK, this is only available for acutely unwell children.

Dr Ellen Thomas, Clinical Director and Director of Quality at Genomics England, said:

“We are very pleased to see significant research like this being enabled by data generously donated by participants of the 100,000 Genomes Project. It is clear from these results how their contributions to a rich and, importantly, secure dataset is critical in facilitating the genomic research that leads to insights like these that then have the potential to return value to the NHS and their patients. We look forward to seeing how these findings could support future care for patients with suspected mitochondrial disorders.”

Reference

KR Schon et al., ‘Use of whole genome sequencing to determine the genetic basis of suspected mitochondrial disorders: a cohort study’, BMJ (2021). DOI: 10.1136/ bmj-2021-066288

Funding

National Institute for Health Research, NHS England, Wellcome, Cancer Research UK and the Medical Research Council within UK Research and Innovation

Whole genome sequencing from a single blood test picks up 31% more cases of rare genetic disorders than standard tests, shortening the ‘diagnostic odyssey’ that affected families experience, and providing huge opportunities for future research.

A definitive genetic diagnosis can really help patients and their families

Patrick Chinnery

Belova59 via Pixabay

Gloved hand holding two blood samples

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Mitochondrial diseases could be treated with gene therapy, study suggests

sc604 — Mon, 24 Sep 2018 15:00:00 +0000

̽��ֱ��researchers, led by the ̽��ֱ�� of Cambridge, applied an experimental gene therapy treatment in mice and were able to successfully target and eliminate the damaged DNA in mitochondria which causes the devastating conditions.

Their results, published in the journal Nature Medicine, could provide a practical route to treating patients with these diseases and may provide a future alternative to mitochondrial replacement therapy, or ‘three-parent IVF’. This is the first time programmable genome engineering tools have been used inside a living animal, resulting in such significant modification of mitochondrial DNA.

Mitochondria are the powerhouses inside our cells, producing energy and carrying their own DNA. They are inherited from a person’s mother via the egg, but if they are damaged, it can result in a serious mitochondrial disease. For example, MELAS Syndrome is a severe multi-system disorder causing progressive loss of mental and movement abilities, which usually becomes apparent in early childhood.

There are typically about 1000 copies of mitochondrial DNA per cell, and the percentage of these that are damaged, or mutated, will determine whether a person will suffer from mitochondrial disease or not. Usually, more than 60% of the mitochondrial DNA molecules in a cell need to be mutated for the disease to emerge, and the more mutated mitochondrial DNA a person has, the more severe their disease will be. Conversely, if the percentage of mutated DNA can be reduced, the disease could potentially be treated.

Mitochondrial diseases are currently incurable, although a new IVF technique of mitochondrial transfer gives families affected by mitochondrial disease the chance of having healthy children – removing affected mitochondria from an egg or embryo and replacing them with healthy ones from a donor.

“Mitochondrial replacement therapy is a promising approach to prevent transmission of mitochondrial diseases, however, as the vast majority of mitochondrial diseases have no family history, this approach might not actually reduce the proportion of mitochondrial disease in the population,” said Dr Payam Gammage, a postdoctoral researcher in the MRC Mitochondrial Biology Unit, and the paper’s first author.

“One idea for treating these devastating diseases is to reduce the amount of mutated mitochondrial DNA by selectively destroying the mutated DNA, and allowing healthy DNA to take its place,” said Dr Michal Minczuk, also from the Medical Research Council (MRC) Mitochondrial Biology Unit, and the study’s senior author.

To test an experimental gene therapy treatment, which has so far only been tested in human cells grown in petri dishes in a lab, the researchers used a mouse model of mitochondrial disease that has the same mutation as some human patients.

̽��ֱ��gene therapy treatment, known as the mitochondrially targeted zinc finger-nuclease, or mtZFN, recognises and then eliminates the mutant mitochondrial DNA, based on the DNA sequence differences between healthy and mutant mitochondrial DNA. As cells generally maintain a stable number of mitochondrial DNA copies, the mutated copies that are eliminated are replaced with healthy copies, leading to a decrease in the mitochondrial mutation burden that results in improved mitochondrial function.

̽��ֱ��treatment was delivered into the bloodstream of the mouse using a modified virus, which is then mostly taken up by heart cells. ̽��ֱ��researchers found that the treatment specifically eliminates the mutated mitochondrial DNA, and resulted in measures of heart metabolism improving.

Following on from these results, the researchers hope to take this gene therapy approach through clinical trials, in the hope of producing an effective treatment for mitochondrial diseases.

This work was supported by the Medical Research Council and was performed in collaboration with Sangamo Therapeutics and the Max Planck Institute for Biology of Ageing in Cologne.

Reference:
Payam A. Gammage et al. ‘Genome editing in mitochondria corrects a pathogenic mtDNA mutation in vivo.’ Nature Medicine (2018). DOI: 10.1038/s41591-018-0165-9.

Researchers have developed a genome-editing tool for the potential treatment of mitochondrial diseases: serious and often fatal conditions which affect 1 in 5,000 people.

One idea for treating these devastating diseases is to reduce the amount of mutated mitochondrial DNA by selectively destroying the mutated DNA, and allowing healthy DNA to take its place.

Michal Minczuk

NICHD/U

Mitochondria

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A shaggy dog story: ̽��ֱ��contagious cancer that conquered the world

cjb250 — Mon, 16 May 2016 23:01:16 +0000

‘Canine transmissible venereal tumour’ (CTVT) is a cancer that spreads between dogs through the transfer of living cancer cells, primarily during mating. ̽��ֱ��disease usually manifests as genital tumours in both male and female domestic dogs. ̽��ֱ��cancer first arose approximately 11,000 years ago from the cells of one individual dog; remarkably, it survived beyond the death of this original dog by spreading to new dogs. ̽��ֱ��cancer is now found in dog populations worldwide, and is the oldest and most prolific cancer lineage known in nature.

In a study published today in the journal eLife, an international team led by researchers at the ̽��ֱ�� of Cambridge studied the DNA of mitochondria – the ‘batteries’ that provide cells with their energy – in 449 CTVT tumours from dogs in 39 countries across six continents. Previous research has shown that at occasional points in history, mitochondrial DNA has transferred from infected dogs to their tumours – and hence to tumour cells in subsequently-infected dogs.

In the new study, the researchers show that this process of swapping mitochondrial DNA has occurred at least five times since the original cancer arose. This discovery has allowed them to create an evolutionary ‘family tree’, showing how the tumours are related to each other. In addition, the unusual juxtaposition of different types of mitochondrial DNA within the same cell unexpectedly revealed that cancer cells can shuffle or ‘recombine’ DNA from different mitochondria.

“At five distinct time-points in its history, the cancer has ‘stolen’ mitochondrial DNA from its host, perhaps to help the tumour survive,” explains Andrea Strakova, from the Department of Veterinary Medicine at the ̽��ֱ�� of Cambridge, co-first author of the study. “This provides us with a set of unique genetic tags to trace how dogs have travelled the globe over the last few hundred years.”

In the evolutionary ‘family tree’, the five main branches are known as ‘clades’, each representing a point in history when mitochondria transferred between dog and tumour. By mapping tumours within these clades to the geographical location where they were found, the researchers were able to see how the cancers have spread across the globe. ̽��ֱ��distance and speed with which the clades have spread suggests that the dogs commonly travelled with human companions, often by sea.

One branch of the CTVT evolutionary tree appears to have spread from Russia or China around 1,000 years ago, but probably only came to the Americas within the last 500 years, suggesting that it was taken there by European colonialists. Conquistadors are known to have travelled with dogs – contemporary artworks have portrayed them both as attack dogs and as a source of food.

Image: 1598 fictional engraving by Theodor de Bry supposedly depicting a Spaniard feeding Indian children to his dogs. Wikipedia

̽��ֱ��disease probably arrived in Australia around the turn of the twentieth century, most likely imported inadvertently by dogs accompanying European settlers.

One of the most surprising findings from the study related to how mitochondrial DNA transfers – and mixes – between the tumour and the host. ̽��ֱ��researchers found that mitochondrial DNA molecules from host cells that have migrated into tumour cells occasionally fuse with the tumour’s own mitochondrial DNA, sharing host and tumour DNA in a process known as ‘recombination’. This is the first time this process has been observed in cancers.

Máire Ní Leathlobhair, the study’s co-first author, explains: “Mitochondrial DNA recombination could be happening on a much wider scale, including in human cancers, but it may usually be very difficult to detect. When recombination occurs in transmissible cancers, two potentially very different mitochondrial DNAs – one from the tumour, one from the host – are merging and so the result is more obvious. In human cancer, the tumour’s mitochondrial DNA is likely to be very similar to the mitochondrial DNA in the patient’s normal cells, so the result of recombination would be almost impossible to recognise.”

Although the significance of mitochondrial DNA recombination in cancer is not yet known, its discovery is now leading scientists to explore how this process may help cancer cells to survive – and if blocking it may stop cancer cells from growing.

Dr Elizabeth Murchison, senior author of the study, said: “ ̽��ֱ��genetic changes in CTVT have allowed us to reconstruct the global journeys taken by this cancer over two thousand years. It is remarkable that this unusual and long-lived cancer can teach us so much about the history of dogs, and also about the genetic and evolutionary processes that underlie cancer more generally.”

̽��ֱ��research was funded by the Wellcome Trust, the Leverhulme Trust and the Royal Society.

Reference
Strakova, A et al. Mitochondrial genetic diversity, selection and recombination in a canine transmissible cancer. eLife; 17 May 2016; DOI: 10.7554/eLife.14552

A contagious form of cancer that can spread between dogs during mating has highlighted the extent to which dogs accompanied human travellers throughout our seafaring history. But the tumours also provide surprising insights into how cancers evolve by ‘stealing’ DNA from their host.

It is remarkable that this unusual and long-lived cancer can teach us so much about the history of dogs, and also about the genetic and evolutionary processes that underlie cancer more generally

Elizabeth Murchison

Mitochondrial genetic diversity, selection and recombination in a canine transmissible cancer

̽��ֱ�� of Cambridge

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. For image use please see separate credits above.

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Richard III – case closed after 529 years

fpjl2 — Tue, 02 Dec 2014 17:46:44 +0000

An international research team has provided overwhelming evidence that the skeleton discovered under a car park in Leicester indeed represents the remains of King Richard III - closing what is probably the oldest forensic case solved to date.

Analysis of all the available evidence confirms identity of King Richard III to the point of 99.999% (at its most conservative).

̽��ֱ��team of researchers, including geneticist Dr Peter Forster from Murray Edwards College and the McDonald Institute for Archaeological Research, and led by Cambridge graduate Dr Turi King have published their findings online today in the journal Nature Communications.

̽��ֱ��researchers collected DNA from living relatives of Richard III and analysed several genetic markers, including the complete mitochondrial genomes, inherited through the maternal line, and Y-chromosomal markers, inherited through the paternal line, from both the skeletal remains and the living relatives.

While the Y-chromosomal markers differ, the mitochondrial genome shows a genetic match between the skeleton and the maternal line relatives. ̽��ֱ��former result is not unsurprising as the chances for a false-paternity event is fairly high after so many generations.

Forster said: “Although the false paternity means we cannot look forward in time, we can trace King Richard’s Y lineage back into prehistory. Historically, the male line of the Plantagenets is recorded back until AD1028 in N France. Using King Richard’s genetic profile, we can go back much further: Richard’s G2a type traces back to the first farmers who migrated from the Near East and Anatolia (modern Turkey) to Europe about 8000 years ago, quickly spreading along the Mediterranean and into Central Europe and France by 5500BC.

"These pioneer farmers carried predominantly G2a types, which today are quite rare, around 1 percent in Europe (see map). And one of these Anatolian farmers was King Richard’s immigrant male ancestor. Incidentally, the descendants of the Plantagenets not only became Kings of England but also of Jerusalem, bringing the migration of this Y chromosome type full circle.”

Map shows locations of 14 living men who are close genetic matches to King Richard – their G2a type is quite rare, around 1 percent in Europe today.

Analysis of the mitochondrial DNA shows a match between Richard III and modern female-line relatives Michael Ibsen and Wendy Duldig. ̽��ֱ��male line of descent is broken at one or more points in the line between Richard III and living male-line relatives descended from Henry Somerset, 5th Duke of Beaufort.

This paper is also the first to carry out a statistical analysis of all the evidence together to prove beyond reasonable doubt that Skeleton 1 from the Greyfriars site in Leicester is indeed the remains of King Richard III.

̽��ֱ��researchers also used genetic markers to determine hair and eye colour of Richard III and found that with probably blond hair - at least during childhood - and almost certainly blue eyes, Richard III looked most similar to his depiction in one of the earliest portraits of him that survived, that in the Society of Antiquaries in London.

“Our paper covers all the genetic and genealogical analysis involved in the identification of the remains of Skeleton 1 from the Greyfriars site in Leicester and is the first to draw together all the strands of evidence to come to a conclusion about the identity of those remains,” said Dr Turi King from the ̽��ֱ�� of Leicester, who lead the research.

“Even with our highly conservative analysis, the evidence is overwhelming that these are indeed the remains of King Richard III, thereby closing an over 500 year old missing person’s case.”

Historically, the male line of the Plantagenets is recorded until Hugues, Count of Perche (documented AD1028 in N France).
Prehistorically, Richard’s male ancestor, carrying a G2a-type, arrived with the first farmers from the Near East and Anatolia (modern Turkey) to Europe about 8000 years ago, quickly spreading along the Mediterranean and into Central Europe and France by 5500BC.

̽��ֱ��research team now plans to sequence the complete genome of Richard III to learn more about the last English king to die in battle.

Adapted from a ̽��ֱ�� of Leicester press release.

DNA and genealogical study confirms identity of remains found in Leicester and uncovers new truths about his appearance and Plantagenet lineage.

Although the false paternity means we cannot look forward in time, we can trace King Richard’s Y lineage back into prehistory

Peter Forster

̽��ֱ�� of Leicester/Carl Vivian

Skull and bones of Richard III

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