Category: Genetics

Categories : Diseases, Syndromes and Conditions GeneticsTags :

Baby with Rare, Incurable Disease is First to Receive Personalised Gene Therapy

On By ModernMedia

NIH-supported gene-editing platform lays groundwork to rapidly develop treatments for other rare genetic diseases.

Photo by Sangharsh Lohakare on Unsplash

A research team supported by the National Institutes of Health (NIH) has developed and safely delivered a personalised gene editing therapy to treat an infant with a life-threatening, incurable genetic disease. The infant, who was diagnosed with the rare condition carbamoyl phosphate synthetase 1 (CPS1) deficiency shortly after birth, has responded positively to the treatment.

The process, from diagnosis to treatment, took only six months and marks the first time the technology has been successfully deployed to treat a human patient. The technology used in this study was developed using a platform that could be tweaked to treat a wide range of genetic disorders and opens the possibility of creating personalised treatments in other parts of the body.

A team of researchers at the Children’s Hospital of Philadelphia (CHOP) and the Perelman School of Medicine at the University of Pennsylvania (Penn) developed the customised therapy using the gene-editing platform CRISPR. They corrected a specific gene mutation in the baby’s liver cells that led to the disorder. CRISPR is an advanced gene editing technology that enables precise changes to DNA inside living cells. This is the first known case of a personalised CRISPR-based medicine administered to a single patient and was carefully designed to target non-reproductive cells so changes would only affect the patient.

“As a platform, gene editing – built on reusable components and rapid customisation – promises a new era of precision medicine for hundreds of rare diseases, bringing life-changing therapies to patients when timing matters most: Early, fast, and tailored to the individual,” said Joni L. Rutter, Ph.D., director of NIH’s National Center for Advancing Translational Sciences (NCATS).

CPS1 deficiency is characterized by an inability to fully break down byproducts from protein metabolism in the liver, causing ammonia to build up to toxic levels in the body. It can cause severe damage to the brain and liver. Treatment includes a low protein diet until the child is old enough for a liver transplant. However, in this waiting period there is a risk of rapid organ failure due to stressors such as infection, trauma, or dehydration. High levels of ammonia can cause coma, brain swelling, and may be fatal or cause permanent brain damage.

The child initially received a very low dose of the therapy at six months of age, then a higher dose later. The research team saw signs that the therapy was effective almost from the start. The six-month old began taking in more protein in the diet, and the care team could reduce the medicine needed to keep ammonia levels low in the body. Another telling sign of the child’s improvement to date came after the child caught a cold, and later, had to deal with a gastrointestinal illness. Normally, such infections for a child in this condition could be extremely dangerous, especially with the possibility of ammonia reaching dangerous levels in the brain.

“We knew the method used to deliver the gene-editing machinery to the baby’s liver cells allowed us to give the treatment repeatedly. That meant we could start with a low dose that we were sure was safe,” said CHOP pediatrician Rebecca Ahrens-Nicklas, MD, PhD.

“We were very concerned when the baby got sick, but the baby just shrugged the illness off,” said Penn geneticist and first author Kiran Musunuru, MD, PhD. For now, much work remains, but the researchers are cautiously optimistic about the baby’s progress.

The scientists announced their work at the American Society of Gene & Cell Therapy Meeting on May 15th and described the study in The New England Journal of Medicine.

Source: NIH/Office of the Director

Categories : Genetics HIVTags :

Researchers Map 7000-year-old Genetic Mutation that Protects Against HIV

On By ModernMedia

Modern HIV medicine is based on a common genetic mutation. Now, researchers have traced where and when the mutation arose – and how it protected our ancestors from ancient diseases.

Photo by Sangharsh Lohakare on Unsplash

What do a millennia-old human from the Black Sea region and modern HIV medicine have in common? Quite a lot, it turns out, according to new research from the University of Copenhagen.

18–25% of the Danish population carries a genetic mutation that can make them resistant or even immune to HIV. This knowledge is used to develop modern treatments for the virus.

Until now, it was unknown where, when, or why the mutation occurred. But by using advanced DNA technology, researchers have now solved this genetic mystery.

“It turns out that the variant arose in one individual who lived in an area near the Black Sea between 6700 and 9000 years ago,” says Professor Simon Rasmussen from the Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR) at the University of Copenhagen, corresponding author of a new study mapping the mutation. He adds:

“HIV is a relatively new disease – less than 100 years old – so it’s almost coincidental and very fascinating that a genetic variation that arose thousands of years ago also protects against a modern virus like HIV.”

Analyzed 900 skeletons

To determine where and when the mutation arose, researchers first mapped it by analysing the genetic material of 2000 living people worldwide. They then developed a new AI-based method to identify the mutation in ancient DNA from old bones.

The researchers examined data from over 900 skeletons dating from the early Stone Age to the Viking Age.

“By looking at this large dataset, we can determine where and when the mutation arose. For a period, the mutation is completely absent, but then it suddenly appears and spreads incredibly quickly. When we combine this with our knowledge of human migration at the time, we can also pinpoint the region where the mutation originated,” explains first author Kirstine Ravn, senior researcher at CBMR.

Thus, the researchers were able to locate the mutation in a person from the Black Sea region up to 9000 years ago – an individual from whom all carriers of the mutation descend.

Immune weakening was beneficial back then

But why do so many Danes carry a millennia-old genetic mutation that protects against a disease that didn’t exist back then?

The researchers believe the mutation arose and spread rapidly because it gave our ancestors an advantage:

“People with this mutation were better at surviving, likely because it dampened the immune system during a time when humans were exposed to new pathogens,” explains Leonardo Cobuccio, co-first author and postdoc at CBMR. He and Kirstine Ravn elaborate:

“What’s fascinating is that the variation disrupts an immune gene. It sounds negative, but it was likely beneficial. An overly aggressive immune system can be deadly – think of allergic reactions or severe cases of viral infections like COVID-19, where the immune system often causes the damage that kills patients. As humans transitioned from hunter-gatherers to living closely together in agricultural societies, the pressure from infectious diseases increased, and a more balanced immune system may have been advantageous.”

Source: University of Copenhagen – The Faculty of Health and Medical Sciences

Categories : Cancer GeneticsTags :

Research Challenges the Understanding of Cancer Predisposition Gene NF-1

On By ModernMedia
Photo by National Cancer Institute on Unsplash

Despite what was previously thought, new research has shown that genetic changes alone cannot explain why and where tumours grow in those with genetic condition neurofibromatosis type 1 (NF-1). Understanding more about the factors involved could, in the future, facilitate early cancer detection in NF-1 patients and even point towards new treatments.

Researchers from the Wellcome Sanger Institute and collaborating institutions, focused on NF-1, a genetic condition that causes specific types of tumours, and investigated how and why these developed.

The study, published in Nature Genetics, reports that the genetic changes thought to cause tumours can be found in normal tissues throughout the body, suggesting that other factors are also necessary for tumour development.

They also uncovered a pattern of changes in the affected gene, NF1, that may explain why the nervous system in particular is a common site for these tumours to develop.

Understanding what other factors are involved in developing these tumours could help inform monitoring programmes for patients with NF-1, who require regular screening to detect tumours early on and could potentially require multiple surgeries and chemotherapy.

In the future, refining our knowledge of why tumours grow in some places and not others may help us identify the patients most likely to need early medical intervention.

This model of tumour development is not unique to NF-1, raising the possibility that similar events occur in related genetic conditions, meaning many more could benefit from tailored management.

NF-1 is a genetic condition that causes brown skin patches, similar to birthmarks, and tumours1. While the tumours are often benign, they can become cancerous over time and may cause a range of symptoms depending on where they are1. For example, NF-1 can cause soft tissue and brain tumours that may restrict movement and vision.

The symptoms and impact of NF-1 can vary greatly from person to person. It is one of the most common inherited genetic conditions, impacting around one in 2500 people. Those with NF-1 have a genetic change that means one copy of the gene encoding the neurofibromin protein, NF1, does not work. It was previously thought that tumours and brown skin patches occurred when the second copy of the gene was lost.

In a new study, researchers from the Sanger Institute, UCL Great Ormond Street Institute of Child Health, Great Ormond Street Hospital, Cambridge University Hospitals NHS Foundation Trust, and their collaborators, studied nearly 500 tissue samples from a child with NF-1 and compared them to tissues from children without the condition.

They found that changes causing a loss of NF1 gene function were not limited to tumours and skin changes but instead can be found throughout other tissues of the child with NF-1 as well. This suggests, whilst advantageous to the affected cells, the mutation is insufficient to cause tumour formation.

For this research, the team applied a new sequencing technology that allowed them to look at genetic changes at a higher resolution than was previously possible and studied additional tissue samples from nine adults with NF-1, showing similar findings.

The team found a pattern of mutations across all patients that showed these were particularly common in tissues of the nervous system. This is a common place for tumours to form in those with NF-1, which can help explain why these tissues are specifically impacted.

“We were astonished to see such extensive genetic changes in the normal tissues of patients with NF-1, seemingly without consequence. This is contrary to our understanding of tumour development in the condition and other related conditions. Additional factors must clearly play a role, perhaps including the cell type and anatomical location affected. Whilst further investigation is needed, I hope this work represents the first step towards developing more personalised care for these patients, such as better identifying who is at greater risk of developing tumours, and adjusting screening to intervene early on and minimise complications.”

Dr Thomas Oliver,co-first author from the Wellcome Sanger Institute and Cambridge University Hospitals NHS Foundation Trust

“NF-1 can have many different impacts on a person’s life. In order to better treat and support those with NF-1, we have to understand more about what is going on at a biological and genetic level, especially in the parts of the body that are most affected, such as the brain and nervous system. Our study showed that these areas of the body have a different pattern of DNA changes, suggesting that if we look further, there could be a potential target for new therapies to help treat or stop tumour development.”

Professor Thomas Jacques,co-senior author from UCL Great Ormond Street Institute of Child Health and Great Ormond Street Hospital

“Loss of the second NF1 gene had always been thought to cause tumours in individuals with NF-1. Our findings fundamentally question this decade-old paradigm and force us to rethink how tumours arise, to pave the way for better screening, prevention, and treatment of cancers.”

Professor Sam Behjati,co-senior author from the Wellcome Sanger Institute and Cambridge University Hospitals NHS Foundation Trust

Source: Wellcome Trust Sanger Institute

Categories : GeneticsTags :

Genes Associated with Plague Survival Linked to Alopecia Risk

On By ModernMedia
Source: Pixabay CC0

In a new JAMA Dermatology study, scientists at King’s found that changes in two parts of the genome work together to influence alopecia risk.

Frontal fibrosing alopecia (FFA) is a highly distressing dermatological disorder which is associated with inflammation, scarring and irreversible hair loss. The disease affects an increasing number of patients worldwide and is caused by genetic and environmental factors.

The study authors conducted a meta-analysis of four cohorts of women with FFA across the UK and Europe. When looking into a cluster of immune genes known as the major histocompatibility complex, which help immune systems recognise foreign substances, they identified specific genetic differences that interact with ERAP1 and increase the risk of developing FFA.

This gene-gene interaction is a rare phenomenon in human genetics, known as “epistasis”. This means that the risk associated with one gene is modified by another gene. Different versions of the two genes involved in this interaction have been observed in some other autoimmune diseases, including psoriasis and ankylosing spondylitis.

Previous research has identified that genetic variants in the ERAP1 and ERAP2 genes were associated with survival of the Black Death, a bubonic plague which swept through Europe in the mid-1300s. Such genetic variants, which are associated with protection from infection, may also make people more prone to certain immune conditions. This new study demonstrates that this is the case for FFA.

“Our study is the largest ever genome-wide association study into frontal fibrosing alopecia (FFA), an inflammatory and scarring condition affecting almost exclusively women,” said Dr Christos Tziotzios, Senior Lecturer of the St John’s Institute of Dermatology at King’s and Consultant Dermatologist at Guy’s and St Thomas’ NHS Foundation Trust

He added: “Since the disease was described in 1994, the number of people affected has increased dramatically. Our newest finding sheds more light into the autoimmune basis of the condition and provides direction for further research into drug development.”

As well as improving our understanding of the genetic factors that drive FFA, the authors hope that these findings can be applied to predict risk of its development while paving the way for new treatments.

The team of scientists are now investigating the prospect of predictive genetic test for FFA risk, while exploring the potential of targeting ERAP1 with highly specific drugs as a new way of treating this condition.

Source: King’s College London

Categories : GeneticsTags :

Review of Research Finds No Link between Sickle Cell Trait and Sudden Death

On By ModernMedia

Expert panel’s findings refute attribution of sudden death to sickle cell trait

Photo by National Cancer Institute on Unsplash

A systematic literature review found no evidence to support that physical exertion without rhabdomyolysis (muscle breakdown) or heat injury can cause sudden death for individuals with sickle cell trait (SCT), nor is there any high-level evidence that SCT causes acute pain crises. These results were published in the American Society of Hematology’s flagship journal, Blood, and informed the Society’s updated position statement on SCT.

“SCT has long been misunderstood, fuelling widespread misinformation and medically inaccurate claims that it can lead to sudden death. This misconception has been especially prominent in cases of Black men with SCT,” said Belinda Avalos, MD, ASH president. “In light of the pervasive, widely publicized, and harmful nature of this myth, the Society aims to further promote accurate information to protect and empower affected communities.”

Individuals with SCT have one copy of the gene associated with sickle cell disease (SCD). SCD is a blood disorder characterised by misshapen blood cells that can cause blockages, leading to infections and episodes of severe pain, often referred to as acute pain crises. Unlike SCD, SCT – which affects over 100 million people worldwide, including 8 to 10% of Black Americans – is not a disease. Individuals with SCT do not go on to develop SCD and generally do not experience any related health complications.  

“To date, this is the most authoritative and definitive systematic review on this subject,” said study author Michael R. DeBaun, MD, MPH, professor of pediatrics and medicine at Vanderbilt University School of Medicine and founder and director of the Vanderbilt-Meharry Sickle Cell Disease Center of Excellence. “This review shows that any primary, secondary, or tertiary cause of death attributable to SCT is not a diagnosis substantiated by the medical evidence.”

ASH convened an expert panel of hematologists and forensic pathologists to systematically review all existing available research to answer two primary questions: 1) Do uncomplicated acute pain crises occur in people with SCT? and 2) Can physical activity above baseline result in sudden death among those individuals?

The experts conducted a multi-database search for English-language studies on SCT and pain crises or mortality, identifying 1474 such citations. Only seven of those studies reported original data, included laboratory testing for SCT in individuals, and addressed the two primary research questions.

Of these studies, none assessed acute pain crises in individuals with SCT compared to those with SCD and only one described death in individuals reported to have SCT. This study of active-duty U.S. soldiers found only that SCT was associated with a higher risk of heat-related-exertional rhabdomyolysis, or muscle breakdown, but not a higher risk of death from any cause. After the implementation of precautions to prevent heat and environmental-related injury in military personnel, the race-adjusted risk of death was no different in individuals with SCT compared to individuals without SCT.

“In the absence of two medical conditions that we are all at risk for, exertional rhabdomyolysis or crush injuries leading to rhabdomyolysis, individuals with SCT are not susceptible to sudden death. Even under these extreme environmental conditions, unexplained sudden death cannot be attributed to SCT,” said Dr. DeBaun. Taken together, these findings demonstrate that “in individuals with SCT, the likelihood of SCT alone or pain crises being the root cause of sudden death is medically impossible,” he added.

While conducting this systematic review, the experts found several studies in which the presence of sickled blood cells at autopsy was cited as evidence of death by acute pain crisis in individuals with SCT. However, the experts did not find any studies that had human data to support this hypothesis, nor any clinical descriptions sufficient to make a diagnosis of an acute pain crisis immediately preceding death.

“Medicine, even in the post-mortem setting, is science,” said corresponding study author Lachelle D. Weeks, MD, PhD, assistant professor of medicine at Harvard Medical School and physician-scientist in the division of population sciences at Dana-Farber Cancer Institute. “Our diagnoses have to make sense and be backed by medical evidence. Given the findings of this study, we owe it to individuals with SCT to ensure that post-mortem examinations check for evidence of rhabdomyolysis and other medical or traumatic causes of death.”

The review had some limitations, most notably a lack of high quality, peer-reviewed direct evidence. To help mitigate this challenge, panel members were encouraged to consider indirect evidence when reviewing abstracts and judged evidence certainty following the GRADE (Grading of Recommendations, Assessment, Development and Evaluation) framework. However, given this paucity of data, the experts hope this review prompts additional SCT research.

Following the results of this study, ASH revised its position statement on SCT, which states that listing “sickle cell crisis” or “sickle cell trait” as a cause of death on an autopsy report for an individual with sickle cell trait is medically inaccurate and without medical evidence of causation. To read the updated statement and learn more about ASH’s advocacy efforts in this area, visit https://hematology.org/advocacy.

Source: American Society of Hematology

Categories : GeneticsTags :

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

Categories : Genetics Neurodegenerative DiseasesTags :

Brain Changes in Huntington’s Disease Seen Decades ahead of Symptoms

On By ModernMedia
Photo by Robina Weermeijer on Unsplash

Subtle changes in the brain, detectable through advanced imaging, blood and spinal fluid analysis, happen approximately twenty years before a clinical motor diagnosis in people with Huntington’s disease, finds a new study led by UCL researchers which appears in Nature Medicine.

The team found that although functions such as movement, thinking or behaviour remained normal for a long time before the onset of symptoms in Huntington’s disease, subtle changes to the brain were taking place up to two decades earlier. These findings pave the way for future preventative clinical trials, offer hope for earlier interventions that could preserve brain function and improve outcomes for individuals at risk of Huntington’s disease.

Huntington’s disease is a devastating neurodegenerative condition affecting movement, thinking and behaviour. It is a genetic disease and people with an affected parent have a 50% chance of inheriting the Huntington’s disease mutation, meaning they will develop disease symptoms – typically in mid-adulthood.

The disease is caused by repetitive expansions of three DNA blocks (C, A and G) in the huntingtin gene. This sequence tends to continually expand in certain cells over a person’s life, in a process known as somatic CAG expansion. This ongoing expansion accelerates neurodegeneration, making brain cells more vulnerable over time.

For the new study, the researchers studied 57 people with the Huntington’s disease gene expansion, who were calculated as being on average 23.2 years from a predicted clinical motor diagnosis.  

They were examined at two time points over approximately five years to see how their bodies and brains changed over time. Their results were compared to 46 control participants, matched closely for age, sex and educational level.

As part of the study, all participants volunteered to undergo comprehensive assessments of their thinking, movement and behaviour, alongside brain scans and blood and spinal fluid sampling.

Importantly, the group with Huntington’s disease gene expansion showed no decline in any clinical function (thinking, movement or behaviour) during the study period, compared to the closely matched control group.

However, compared to the control group, subtle changes were detected in brain scans and spinal fluid biomarkers of those with Huntington’s disease gene expansion. This indicates that the neurodegenerative process begins long before symptoms are evident and before a clinical motor diagnosis.

Specifically, the researchers identified elevated levels of neurofilament light chain (NfL), a protein released into the spinal fluid when neurons are injured, and reduced levels of proenkephalin (PENK), a neuropeptide marker of healthy neuron state that could reflect changes in the brain’s response to neurodegeneration.

Lead author, Professor Sarah Tabrizi (UCL Huntington’s Disease Research Centre, UCL Queen Square Institute of Neurology, and UK Dementia Research Institute at UCL), said: “Our study underpins the importance of somatic CAG repeat expansion driving the earliest neuropathological changes of the disease in living humans with the Huntington’s disease gene expansion. I want to thank the participants in our young adult study as their dedication and commitment over the last five years mean we hope that clinical trials aimed at preventing Huntington’s disease will become a reality in the next few years.”

The findings suggest that there is a treatment window, potentially decades before symptoms are present, where those at risk of developing Huntington’s disease are functioning normally despite having detectable measures of subtle, early neurodegeneration. Identifying these early markers of disease is essential for future clinical trials in order to determine whether a treatment is having any effect.

Co-first author of the study, Dr Rachael Scahill (UCL Huntington’s Disease Research Centre and UCL Queen Square Institute of Neurology) said: “This unique cohort of individuals with the Huntington’s disease gene expansion and control participants provides us with unprecedented insights into the very earliest disease processes prior to the appearance of clinical symptoms, which has implications not only for Huntington’s disease but for other neurodegenerative conditions such as Alzheimer’s disease.”

This study is the first to establish a direct link between somatic CAG repeat expansion, measured in blood, and early brain changes in humans, decades before clinical motor diagnosis in Huntington’s disease.

While somatic CAG expansion was already known to accelerate neurodegeneration, this research demonstrates how it actively drives the earliest detectable changes in the brain: specifically in the caudate and putamen, regions critical to movement and thinking.

By showing that somatic CAG repeat expansion changes measured in blood predicts brain volume changes and other markers of neurodegeneration, the findings provide crucial evidence to support the hypothesis that somatic CAG expansion is a key driver of neurodegeneration.

With treatments aimed at suppressing somatic CAG repeat expansion currently in development, this work validates this mechanistic process as a promising therapeutic target and represents a critical advance towards future prevention trials in Huntington’s disease.

Co-first author of the study, Dr Mena Farag (UCL Huntington’s Disease Research Centre and UCL Queen Square Institute of Neurology) added: “These findings are particularly timely as the Huntington’s disease therapeutic landscape expands and progresses toward preventive clinical trials.”

The research was done in collaboration with experts at the Universities of Glasgow, Gothenburg, Iowa, and Cambridge.

Source: University College London

Categories : Ethics and Law GeneticsTags :

South Africa Amended its Research Guidelines to Allow for Heritable Human Genome Editing

On By ModernMedia
Source: Pixabay CC0

Françoise Baylis, Dalhousie University

A little-noticed change to South Africa’s national health research guidelines, published in May of this year, has put the country on an ethical precipice. The newly added language appears to position the country as the first to explicitly permit the use of genome editing to create genetically modified children.

Heritable human genome editing has long been hotly contested, in large part because of its societal and eugenic implications. As experts on the global policy landscape who have observed the high stakes and ongoing controversies over this technology — one from an academic standpoint (Françoise Baylis) and one from public interest advocacy (Katie Hasson) — we find it surprising that South Africa plans to facilitate this type of research.

In November 2018, the media reported on a Chinese scientist who had created the world’s first gene-edited babies using CRISPR technology. He said his goal was to provide children with resistance to HIV, the virus that causes AIDS. When his experiment became public knowledge, twin girls had already been born and a third child was born the following year.

The fate of these three children, and whether they have experienced any negative long-term consequences from the embryonic genome editing, remains a closely guarded secret.

Controversial research

Considerable criticism followed the original birth announcement. Some argued that genetically modifying embryos to alter the traits of future children and generations should never be done.

Many pointed out that the rationale in this case was medically unconvincing – and indeed that safe reproductive procedures to avoid transmitting genetic diseases are already in widespread use, belying the justification typically given for heritable human genome editing. Others condemned his secretive approach, as well as the absence of any robust public consultation, considered a prerequisite for embarking on such a socially consequential path.

In the immediate aftermath of the 2018 revelation, the organizing committee of the Second International Summit on Human Genome Editing joined the global uproar with a statement condemning this research.

At the same time, however, the committee called for a “responsible translational pathway” toward clinical research. Safety thresholds and “additional criteria” would have to be met, including: “independent oversight, a compelling medical need, an absence of reasonable alternatives, a plan for long-term follow-up, and attention to societal effects.”

Notably, the additional criteria no longer included the earlier standard of “broad societal consensus.” https://www.youtube.com/embed/XAhFoaT6Kik?wmode=transparent&start=0 Nobel laureate David Baltimore, chair of the organizing committee for the Second International Summit on Human Genome Editing, talks about the importance of public global dialogue on gene editing.

New criteria

Now, it appears that South Africa has amended its Ethics in Health Research Guidelines to explicitly envisage research that would result in the birth of gene-edited babies.

Section 4.3.2 of the guidelines on “Heritable Human Genome Editing” includes a few brief and rather vague paragraphs enumerating the following criteria: (a) scientific and medical justification; (b) transparency and informed consent; (c) stringent ethical oversight; (d) ongoing ethical evaluation and adaptation; (e) safety and efficacy; (f) long-term monitoring; and (g) legal compliance.

While these criteria seem to be in line with those laid out in the 2018 summit statement, they are far less stringent than the frameworks put forth in subsequent reports. This includes, for example, the World Health Organization’s report Human Genome Editing: Framework for Governance (co-authored by Françoise Baylis).

Alignment with the law

Further, there is a significant problem with the seemingly permissive stance on heritable human genome editing entrenched in these research guidelines. The guidelines clearly require the research to comply with all laws governing heritable human genome research. Yet, the law and the research guidelines in South Africa are not aligned, which entails a significant inhibition on any possible research.

This is because of a stipulation in section 57(1) of the South African National Health Act 2004 on the “Prohibition of reproductive cloning of human beings.” This stipulates that a “person may not manipulate any genetic material, including genetic material of human gametes, zygotes, or embryos… for the purpose of the reproductive cloning of a human being.”

When this act came into force in 2004, it was not yet possible to genetically modify human embryos and so it’s not surprising there’s no specific reference to this technology. Yet the statutory language is clearly wide enough to encompass it. The objection to the manipulation of human genetic material is therefore clear, and imports a prohibition on heritable human genome editing.

Ethical concerns

Photo by Tingey Injury Law Firm on Unsplash

The question that concerns us is: why are South Africa’s ethical guidelines on research apparently pushing the envelope with heritable human genome editing?

In 2020, we published alongside our colleagues a global review of policies on research involving heritable human genome editing. At the time, we identified policy documents — legislation, regulations, guidelines, codes and international treaties — prohibiting heritable genome editing in more than 70 countries. We found no policy documents that explicitly permitted heritable human genome editing.

It’s easy to understand why some of South Africa’s ethicists might be disposed to clear the way for somatic human genome editing research. Recently, an effective treatment for sickle cell disease has been developed using genome editing technology. Many children die of this disease before the age of five and somatic genome editing — which does not involve the genetic modification of embryos — promises a cure.

Implications on future research

But that’s not what this is about. So, what is the interest in forging a path for research on heritable human genome editing, which involves the genetic modification of embryos and has implications for subsequent generations? And why the seemingly quiet modification of the guidelines?

How many people in South Africa are aware that they’ve just become the only country in the world with research guidelines that envisage accommodating a highly contested technology? Has careful attention been given to the myriad potential harms associated with this use of CRISPR technology, including harms to women, prospective parents, children, society and the gene pool?

Is it plausible that scientists from other countries, who are interested in this area of research, are patiently waiting in the wings to see whether the law in South Africa prohibiting the manipulation of human genetic material will be an insufficient impediment to creating genetically modified children? Should the research guidelines be amended to accord with the 2004 statutory prohibition?

Or if, instead, the law is brought into line with the guidelines, would the result be a wave of scientific tourism with labs moving to South Africa to take advantage of permissive research guidelines and laws?

We hope the questions we ask are alarmist, as now is the time to ask and answer these questions.

Katie Hasson, Associate Director at the Center for Genetics and Society, co-authored this article.

Françoise Baylis, Distinguished Research Professor, Emerita, Dalhousie University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Categories : GeneticsTags :

CRISPR ‘Molecular Scissors’ can Leave Gaping Holes in the Chromosome

On By ModernMedia
CRISPR-Cas9 is a customisable tool that lets scientists cut and insert small pieces of DNA at precise areas along a DNA strand. This lets scientists study our genes in a specific, targeted way. Credit: Ernesto del Aguila III, National Human Genome Research Institute, NIH

The CRISPR molecular scissors have the potential to revolutionise the treatment of genetic diseases. This is because they can be used to correct specific defective sections of the genome. Unfortunately, there is a catch: under certain conditions, the repair can lead to new genetic defects – as in the case of chronic granulomatous disease. This was reported in the journal Communications Biology by a team from the University of Zurich (UZH).

Chronic granulomatous disease is a rare hereditary disease that affects about one in 120 000 people. The disease impairs the immune system, making patients susceptible to serious and even life-threatening infections. It is caused by the absence of two letters, called bases, in the DNA sequence of the NCF1 gene. This error results in the inability to produce an enzyme complex that plays an important role in the immune defence against bacteria and moulds.

The CRISPR tool works…

The research team has now succeeded in using the CRISPR system to insert the missing letters in the right place. They performed the experiments in cell cultures of immune cells that had the same genetic defect as people with chronic granulomatous disease. “This is a promising result for the use of CRISPR technology to correct the mutation underlying this disease,” says team leader Janine Reichenbach, professor of somatic gene therapy at the University Children’s Hospital Zurich and the Institute for Regenerative Medicine at UZH.

… but unfortunately, it’s not perfect

Interestingly however, some of the repaired cells now showed new defects. Entire sections of the chromosome where the repair had taken place were missing. The reason for this is the special genetic constellation of the NCF1 gene: it is present three times on the same chromosome, once as an active gene and twice in the form of pseudogenes. These have the same sequence as the defective NCF1 and are not normally used to form the enzyme complex.

CRISPR’s molecular scissors cannot distinguish between the different versions of the gene and therefore occasionally cut the DNA strand at multiple locations on the chromosome – at the active NCF1 gene as well as at the pseudogenes. When the sections are subsequently rejoined, entire gene segments may be misaligned or missing. The medical consequences are unpredictable and, in the worst case, contribute to the development of leukaemia. “This calls for caution when using CRISPR technology in a clinical setting,” says Reichenbach.

Safer method sought

To minimise the risk, the team tested a number of alternative approaches, including modified versions of CRISPR components. They also looked at using protective elements that reduce the likelihood of the genetic scissors cutting the chromosome at multiple sites simultaneously. Unfortunately, none of these measures were able to completely prevent the unwanted side effects.

“This study highlights both the promising and challenging aspects of CRISPR-based therapies,” says co-author Martin Jinek, a professor at the UZH Department of Biochemistry. He says the study provides valuable insights for the development of gene-editing therapies for chronic granulomatous disease and other inherited disorders. “However, further technological advances are needed to make the method safer and more effective in the future.”

Source: University of Zurich

Categories : Genetics IT in HealthcareTags :

Researchers Find Persistent Problems with AI-assisted Genomic Studies

On By ModernMedia
Photo by Sangharsh Lohakare on Unsplash

In a paper published in Nature Genetics, researchers are warning that artificial intelligence tools gaining popularity in the fields of genetics and medicine can lead to flawed conclusions about the connection between genes and physical characteristics, including risk factors for diseases like diabetes.

The faulty predictions are linked to researchers’ use of AI to assist genome-wide association studies, according to the University of Wisconsin–Madison researchers. Such studies scan through hundreds of thousands of genetic variations across many people to hunt for links between genes and physical traits. Of particular interest are possible connections between genetic variations and certain diseases.

Genetics’ link to disease not always straightforward

Genetics play a role in the development of many health conditions. While changes in some individual genes are directly connected to an increased risk for diseases like cystic fibrosis, the relationship between genetics and physical traits is often more complicated.

Genome-wide association studies have helped to untangle some of these complexities, often using large databases of individuals’ genetic profiles and health characteristics, such as the National Institutes of Health’s All of Us project and the UK Biobank. However, these databases are often missing data about health conditions that researchers are trying to study.

“Some characteristics are either very expensive or labour-intensive to measure, so you simply don’t have enough samples to make meaningful statistical conclusions about their association with genetics,” says Qiongshi Lu, an associate professor in the UW–Madison Department of Biostatistics and Medical Informatics and an expert on genome-wide association studies.

The risks of bridging data gaps with AI

Researchers are increasingly attempting to work around this problem by bridging data gaps with ever more sophisticated AI tools.

“It has become very popular in recent years to leverage advances in machine learning, so we now have these advanced machine-learning AI models that researchers use to predict complex traits and disease risks with even limited data,” Lu says.

Now, Lu and his colleagues have demonstrated the peril of relying on these models without also guarding against biases they may introduce. In their paper, they show that a common type of machine learning algorithm employed in genome-wide association studies can mistakenly link several genetic variations with an individual’s risk for developing Type 2 diabetes.

“The problem is if you trust the machine learning-predicted diabetes risk as the actual risk, you would think all those genetic variations are correlated with actual diabetes even though they aren’t,” says Lu.

These “false positives” are not limited to these specific variations and diabetes risk, Lu adds, but are a pervasive bias in AI-assisted studies.

New statistical method can reduce false positives

In addition to identifying the problem with overreliance on AI tools, Lu and his colleagues propose a statistical method that researchers can use to guarantee the reliability of their AI-assisted genome-wide association studies. The method helps remove bias that machine learning algorithms can introduce when they’re making inferences based on incomplete information.

“This new strategy is statistically optimal,” Lu says, noting that the team used it to better pinpoint genetic associations with individuals’ bone mineral density.

AI not the only problem with some genome-wide association studies

While the group’s proposed statistical method could help improve the accuracy of AI-assisted studies, Lu and his colleagues also recently identified problems with similar studies that fill data gaps with proxy information rather than algorithms.

In another recently published paper appearing in Nature Genetics, the researchers sound the alarm about studies that over-rely on proxy information in an attempt to establish connections between genetics and certain diseases.

For instance, large health databases like the UK Biobank have a ton of genetic information about large populations, but they don’t have very much data regarding the incidence of diseases that tend to crop up later in life, like most neurodegenerative diseases.

For Alzheimer’s disease specifically, some researchers have attempted to bridge that gap with proxy data gathered through family health history surveys, where individuals can report a parent’s Alzheimer’s diagnosis.

The UW–Madison team found that such proxy-information studies can produce “highly misleading genetic correlation” between Alzheimer’s risk and higher cognitive abilities.

“These days, genomic scientists routinely work with biobank datasets that have hundreds of thousands of individuals; however, as statistical power goes up, biases and the probability of errors are also amplified in these massive datasets,” says Lu. “Our group’s recent studies provide humbling examples and highlight the importance of statistical rigor in biobank-scale research studies.”

Source: University of Wisconsin-Madison